texts: Energy use by muscles, actual work done by muscles and more

texts:
Lately, I've started exercising in the gym and outside. I've also started to look at the details of food I eat.

Food usually has a label saying the amount of energy is inside it. For example, some chocolate says it has 400 kilocalorie for 100 grams.

I have some questions about that:

Does the label say the amount of total chemical energy exists inside the food, which will be released if burned, or the energy available to the human body after digested, and because digesting requires energy, the food contains actually MORE energy then written?
When I'm riding on a static bike, it has a screen which counts the kcal I burn. It has a thing connected to my arm, measuring my heart beat. After about an hour of riding, it said I used about 700 kcal. Is it the amount of work I did, i.e if there was a battery connected to the bicycle, I'd generate 700 kcal of electricity, OR, the amount of energy my body LOST, because muscle efficiency is far from 100% (so, I lost 700 kcal, but generated only 150 kcal of electricity, for example)
When doing a physical activity, the heart beat and breathing rate increases. Lets say I'm riding a bicycle or running. Whats the ratio between energy consumed by the muscle to energy consumed by the lungs or heart?


texts: What does 'per capita births and deaths' mean?

texts:
My book says,

  If in a pond there are 20 lotus plants last year and through reproduction 8 new plants are added, taking the current population to 28, we calculate the birth rate as 8/20 = 0.4 offspring per lotus per year.

..

  If 4 individuals in a laboratory population of 40 fruitflies died during a specified time interval, say a week, the death rate in the population during that period is 4/40 = 0.1 individuals per fruitfly per week.

What does per lotus per year, and, per fruitfly per week imply?


texts: How do (commensal and mutualist) microorganisms colonize the seminal vesicles?

texts:
Human's seminal fluid has it's own microbiome (Javurek et al. 2016). How do species of this microbiome (bacteria and eukaryotes) colonize the seminal vesicles?

It is possible that different species would colonize the seminal fluid through different means. What are the possible ways by which such colonization could happen?


texts: Trick fruit trees into flowering later in the spring

texts:
There is a common problem with fruit trees in temperate climates where the trees flower before the last frost. Generally speaking, if the tree has flowered, and the temperature drops below freezing, the flowers die and do not produce fruit.

This is certainly not a new problem. It's my understanding that the problem affects almost the entire fruit farming industry in temperate climates.

I've heard that fruit farmers have large-scale commercial techniques that they use to mitigate the issue, such as:

Covering
Fog or smoke
Wind Machines
Sprinkling
Heating

While these methods might be practical for commercial farmers, not all of them are practical for small-scale urban farmers like me.

Instead of actively protecting the open flowers, would it be possible to trick fruit trees into not flowering as early?

I'm dealing specifically with plants in the prunus genus:

Examples:

Prunus tomentosa
Prunus besseyi x prunus salicina hybrids
Prunus avium x prunus salicina hybrids

Note: I have a related question here: What triggers plants in the prunus genus to flower?


texts: Is this a bed bug? I found it crawling on me in hotel bed

texts: Is this a bed bag? It doesn't have the stripes that I saw in other pictures. I'm traveling and for 5 days I was sleeping in different hotel rooms. What should I do if it is. I searched the bed and found no more.


texts: Why can DNA tests with mixed DNA of several people not be used to detect a criminal in a database?

texts:
Scenario: Two males attack another pair of two males with a weapon. The attackers are fought off and the weapon remains. Why does the police require DNA samples of the two who have been attacked to be able to find out if the two attackers are in the national criminal database?
Or without the specific scenario: Can a DNA profile be created from a sample where several individuals have been involved and it is not possible to separate the cells and assign them clearly so that this profile can then be searched for in a database?
Disclaimer: This happened to me and several years later, I'm simply curious why I had to give a sample to help police find the perpetrators.


texts: Relationship between food decay and electric current

texts:
I am planning to do a little experiment on investigating the relationship between food (organic) decay and the electric current.

I am going to place the food (ex.banana) on top of an aluminum foil, then hook the foil to a battery.

However, this doesn't seem convincing that it's going to work.

Is there any better way to experiment this?

I'm not sure if this falls under "biology" category

Also, it doesn't have to be banana, it could be avocado, lettuce, apple etc.

Thank you


texts: I'm unclear as to the molecular mechanism whereby mRNA is translated into proteins, but non-coding RNA is not similarly translated. How do ribosomes know not to translate non-coding RNA?


texts: Species Identification: Waterborne larvae, Texas USA

texts:
Can you help identify this worm?

It was found in a cup of water at a restaurant (unpleasant, yes), likely came through the water system. (Location: Texas)
Found these images of it online (in which they were also found in water systems - dog bowl, sink), but none of the sites identified it.

Significant features: black head, black pointed tail, clear body with grayish intestines visible, tiny (2-3 mm)

Similar larvae that don't match:
-Mosquito larvae
-Midge larvae

Any insight is appreciated, including if you are familiar with similar looking larvae. Thank you.


texts: To understand synthesis of e-NOS and n-NOS with respect to Ca and calmodulin

texts:
I found this sentence in my notes interesting

  E-NOS and n-NOS are Ca-calmodulin dependent ferments.
  They are synthesized in small concentration as a response to physiological signals which increases the level of Ca2+ in cell.

Does it mean that e-NOS and n-NOS are synthesized by mediation of Ca and calmodulin?

I remember how RNS can be derived from nitric oxide and superoxide.
Are e-NOS and n-NOS expressed on macrophages after induction by cytokines and microbial products, notably interferon-gamma and lipopolysaccharide?


texts: What is the lipid membrane of SARS-CoV-2 made of?

texts:
SARS-CoV-2 is an enveloped virus: in structural diagrams it is drawn with membrane glycoprotein (M), envelope protein (E) and spike protein (S) embedded in a lipid membrane.
What specifically is the lipid membrane made of?
I assume it is derived (somehow) from the host cell membrane, and would have a similar composition.  It doesn't necessarily have the same composition.  If it just host membrane from a typical mammalian cell, it may be mostly phosphatidylcholine (PC) and cholesterol on the outside, and phosphatidylethanolamine (PE), PC and cholesterol on the inside.  It should equilibrate over time, since the virus does not contain a flippase to keep an asymmetrical distribution.
Related questions: Does the composition depend on the cell that the virus was assembled in?  Does it have any selectivity, or does it simply pick a random piece of the host membrane?  How exactly is the viral membrane detached from the host?
Probably most important question: Does the infectivity of the virus depend on the composition of the membrane?


texts:
Plants are autotrophs, meaning that they grow by building organic matter out of inorganic compounds (and energy).
Is it then also true that plants are generally not capable of absorbing organic compounds? There are certainly some plants that can do it, e.g. carnivorous plants absorbing amino acids of their (dissolved) prey. But what about, say, the common sunflower on my balcony?


texts: Do animals exist (for example ostriches, chimps, etc.) that develop the need to mate with humans if they are soley raised and socialized by humans?

texts:
I just watched a German talk show "Nachtstudio" with the title "Die Graugans und der Mensch" (Gosling and People) about the legacy of the famous ethologist and Nobel Prize winner Konrad Lorenz (https://youtu.be/hLkWhGieZvQ). All the participating guests were former students of Lorenz. One statement in the show made by Bernd Lötsch amused me.

At the point where the conversation was about the famous experiment of Lorenz with geese,  Lötsch said that Lorenz was lucky that he had selected goslings for his experiment. He continued by saying that if he had chosen ostriches, it would be likely that the ostrich would have tried to mate with him once it had reached maturity (Lötsch 1988).

Amused by his statement and without any deeper understanding of biological theories (I'm a physicist by training), I would like to ask for critical reflections on Lötsch's statement. I would also appreciate hearing about any studies which examine hypotheses such as this.


texts:
I would like to know what are the mechanisms and overall effects of Zinc on fungi.
I know that Candida albicans is susceptible to Zinc deprivation and Zinc-infused paint is also used to repel mold.


texts: How to calculate biological half life of a drug that is dose dependent?

texts:
I would like to calculate the half-life of a biological drug.

This biological drug is said to have a biological half-life of:

3.33 days when a patient is receiving a dose of 0.04 mg/kg of body weight,
13.4 days when the dose is 0.2 mg/kg
and 14.9 when the dose is 1 mg/kg

How could I extrapolate this information to get biological half-life estimate for 2 mg/kg of body weight?

Could I also graph this? for example in R?


texts: How to measure Na/K channel activation at the membrane level?

texts:
Assume that there are two different signals occurring on the ECG - during depolarization and repolarization in the standard ECG.
I was advised not to use the standard ECG in measuring the exact electrical events during:

stages 0-2
3-4

We can get data about the electric activity of neurons in vivo in Fig. 1 where some data about the electric activity of neurons is present.
So my thought is that a similar technique could probably work with cardiomyocytes.

Fig. 1 Example of measurement for electric activity of neurons in vivo

I estimate that there is about 18% uncertainty when using the standard ECG because of the peak in the stage 1 (Gibbs phenomenon) and those two complete different phases.


texts: Why is HPV vaccines targeted for preteens?

texts:
Why is human papillomavirus products targeted to children before sexual activeness? Could all ages benefit from this vaccine even if they may have or have not contracted a form of HPV to prevent other forms of HPV?

https://okinawa.stripes.com/community-news/preteens-teens-target-audience-hpv-vaccine

I could not find anything where it says it is more effective on younger people vs older people.


texts: Sub-saharan africans (Andamanese, Semang) have the ancestral hair-type, do they also have pediculus humanus capitis lice?

texts:
Do humans with the ancestral hair-type also have pediculus humanus capitis lice? Pubic hair lice, Pthirus pubis, are adapted morphologically to cling onto
coarse body hair, and originates from Pthirus gorillae via a host switch 3.3 Ma1. Pthirus pubis is also, at times, found at the eyelashes of infants.

The ancestral hair type is coarser than the derived, longer and thinner hair type. Is it parasitised by pediculus humanus capitis, or, by a lice that is adapted to cling onto the coarser hair, possibly related to Pthirus pubis?

  The ancestral hair form is frizzier and much shorter. It survives in sub-Saharan Africans and in other groups whose ancestors never left the tropics, notably the Andamanese, the Semang, the Aeta, and the natives of Australia and Papua New Guinea. The latter groups are descended from humans who spread out of Africa along the southern route into South and Southeast Asia.2

References

Reed, D. L., Light, J. E., Allen, J. M., & Kirchman, J. J. (2007). Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biology, 5(1), 7. doi:10.1186/1741-7007-5-7
Frost, P. (2015) Evolution of Long Head Hair in Humans. Advances in Anthropology, 5, 274-281. doi: 10.4236/aa.2015.54021


texts: How to design the primer when you don't have GC?

texts:
I have treated my RNA with sodium bisulfite so all my cytosine is converted into thymine. Then I used that RNA for my RT reaction. I have a cDNA template without Cs. Now I am trying to amplify that region with PCR.

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

Is there any other way to fix the problem?

My primer concentration is 200nm.


texts: What are the environmental conditions for larval Haemonchus contortus to survive?

texts:
What is known about the environmental limits for Haemonchus contortus to survive outside of a host organism in its larval stages?
I'm interested in knowing:

temperature tolerance levels
preferred humidity levels
pH tolerance
how long can it survive outside of the tolerated ranges?


texts:
TLDR: Can anyone state a extraction and isolation method(s) for genomic DNA for hair that will be used for PCR, in detail is preferable since I am a novice.

I tried googling for DNA extraction methods for hair(follicles and/or root) and found various sources, the one that had the most detail involved the use or organic compounds we do not have access to. Is their preferred method of extracting DNA from hair, given that the genomic DNA would be in low amounts, I figure that might have something to do with the extraction process.


texts: I find these in forests in Oregon, western half, though they're probably on the eastern half as well. They live under pieces of wood and bark, and have a small web across the ground. Mine will eat crickets, but I think they eat carpenter ants, termites, and maybe pillbugs/sowbugs. It seems about an inch long, red on the thorax and legs, and dark grey and slightly hairy on the abdomen. The closest to this spider I've found is sowbug killers -- they're in my backyard, but they're smaller then this spider and also are a light tan on a hairless abdomen, with lighter colored legs. The fangs also seem different shapes but I'm not sure about that.


texts:
Karl von Frisch discovered waggle dance [1] as communication system when bees talk about feed resources;
Long story short, using a polar coordinate system, bees dance to reveal flowers to sisters.
My question is simple: how can this be possible since bees are in hives, which are dark?
That is, how can a bee sees its sister dancing in a dark hive?

[1] https://en.wikipedia.org/wiki/Waggle_dance


texts: I have sequences of the Cytochrome c oxidase I (COI) from several populations of Peringia ulvae (Mollusca; Gastropoda; Littorinimorpha; Hydrobiidae). I need additional COI sequences from a specific population. When using the same primers and PCR protocol as for the other populations, I do not get any PCR product for the specific population. My PI suggested me to design internal COI primers for Peringia ulvae. How can I do that? Should I use the COI sequences from the other populations?


texts: Why does protein kinase C activated by different means have different effects?

texts: I could be way off base but I think I remember learning that Protein Kinase C has some effects when activated by one pathway and other effects when activated by another. How does this happen? Is it just phosphorylated differently or what?


texts: What is the maximal insert length for PCR based homologous recombination in S. cerevisae

texts:
I would like to insert a 6 kbp construct, which I have on a plasmid into the genome of S. cerevisiae. This plasmid was originally constructed to integrate at the HIS locus via homologous recombination after transformation with the plasmid. The problem is that the strain I would like to use is HIS-Δ0, so the complete HIS-ORF has been deleted so that the plasmid will not insert via homologous recombination.

My question is now whether I can still insert my construct into the genome via PCR based homologous recombination, by amplifying the region of interest on the plasmid with primers which have a homology to the genomic sequence where I would like to insert my construct. I am afraid that 6 kbp are too much to transform yeast cells efficiently. Does anyone have experience with such long inserts?

thanks for your help,
Jannis


texts: Can plants survive indefinitely without external supply of gases at compensation point?

texts: During photosynthesis, there is a point at which the light intensity is such that the rate of photosynthesis exactly matches the rate of respiration called the compensation point. What this means is that the plant can essentially utilize the $\ce{CO_2}$ produced during respiration for photosynthesis and the $\ce{O_2}$ produced during photosynthesis for respiration. But, does this mean, that a plant which has been given an initial supply of $\ce{CO_2}$ and $\ce{O_2}$ and then subsequently put into another gas (still in compensation point light intensity), say nitrogen, can survive indefinitely? (or as long as it's life span).


texts:
I am reading an article on developmental biology and cannot understand (even after searching the internet) what is meant by "out-titration".
For example, in this phrase:

  We have previously shown that Drf1, together with Cut5, Treslin and Recq4, are out-titrated on chromatin by increasing N/C ratios in vitro.

From this article: Chk1 Inhibition of the Replication Factor Drf1 Guarantees Cell-Cycle Elongation at the Xenopus laevis Mid-blastula Transition

Thank you!!


texts:
I have been reading about Pavlovian brain conditioning and it seems that documented cases are mostly limited to motor reflexes (like conditioning an eyelid to close when hearing a tone) or taste aversion . Basically information flowing through Cerebellum and Hippocampus. Are there proofs or scientific studies about the limitations of such conditioning? Or studies about what can be associated and what not?

Let's imagine for example that a subject looks at a black neutral screen and whenever some tone is played, the screen turns bright red. After an intense conditioning would it be possible that this subject, when blindfolded would see some red when hearing that same tone?


texts:
This is an mRNA strand of mouse meta-globin:

  5'-ccccagauacggaauucgaau-3'

  A) Which small RNA (below) is most likely to regulate expression of
  meta-globin?

  5'-auucgaauuuucuaucugggg-3'
  5'-ggggucuaucuuuuaagcuua-3'
  5'-ccccagauacggaauucgaau-3'
  5'-uaagcuuaaggcauagacccc-3'

  B) This RNA most likely?

  acts as an siRNA
  inhibit meta-globin translation
  increase meta-globin translation
  help transport meta-globin mRNA back into the nucleus

My attempt:

I think A is 2 because the strand is complementary and will bind nicely to the mRNA strand.  For B, I'm between 2 and 3, but cant decide.


texts: Is this a valid definition of independent assortment?

texts: "Allelic combinations separate randomly. I.e. a parent might be Aa and Bb for two traits but that doesn't necessarily mean the gametes will strictly be AB or ab but any of a number of combinations. I.e. blue eyes does not imply short height or something."


texts: Are hormone secretion variations the same for a pair of monozygotic twins?

texts: I have recently read a paper about how stress affects morning salivary cortisol levels in an individual. I am conducting a study on monozygotic twins and was wondering if cortisol levels would fluctuate similarly in a pair of twins, or whether cortisol and other hormones are unrelated to the genetic makeup of the twins.


texts:
Since deaf people can't hear, is relaxing and falling asleep easier for them? In general, do they sleep better than hearing people?

Of course some hearing people have no trouble getting to sleep, but others awaken whenever they hear a sound.


texts: Genes, chromosomes, base pairs and the 23 pairs

texts: OK so I'm a bit confused. Does a chromosome consist of genes and do genes consist of DNA? What about the 23 pairs in sexual reproduction? I can't remember what the pairs consist of


texts: Light and Dark Reaction of photosynthesis?

texts:
I'm having a hard time understanding light and dark reactions because all the sites I've gone through provide different equations. Some say photolysis is H20 = H+ + O2 while some present it as H20 = H+ + OH-. Moreover some have given that NADP+ + H+ = NADPH and some have stated that NADPH+H+ = NADPH2
Could someone provide me with a better, more detailed explanation of both the light and dark phases with the equation of all the reactions that occur during the process, as well as the site of occurrence.


texts: I reconstitute my primers in nuclease free water ( no sterilised) this morning and I forgot them at 4 degrees, acording to the instructions, they should be storage at -20 after the reconstitution. I am wondering if it will affect to have them overnight at 4 degrees, just for one day.


texts: What is the biological basis for the perception of time?

texts: How is the "time axis" of memories encoded in the brain? I guess the time of the event could be "stored" with each event, but how is this translated into neurons etc.?


texts: What is the biding site code recognized by the parts of the spliceosome

texts:
Another question about another Youtube video. At 0:50, the splicing process begins to remove the non-coding section of the DNA (intron), so the different parts of the spliceosome attach to the borders on the intron.

My question is, what is the code found in the borders of the intron which is recognized by the parts of the spliceosome, so they attach to it ?

For example, in the transcription of the DNA, the process begins after the transcription factor "TBP" recognizes the code "TATA" in the DNA string, then attaches to it. This triggers a whole process described by this video.


texts:
I am trying to find some reliable gene kit by which you can rapidly test Toxoplasma gondii.
I am not sure if it exists.
I have an intuition that some tests done during 90s-00s on this species had high false negatives.

Which genes should you detect to find Toxoplasma gondii in a gene kit?


texts: Taking care of Birds: Unwanted species scaring away a less common one from a birdhouse

texts:
Near my house, I have set up a birdhouse, which has become home to a pair of Oriental Magpie Robins. They are not a common species in Delhi, India, and are generally shy of human interaction and avian conflict (territory disputes with other species):

However, the birdhouse is constantly visited by a pair of Common Myna. This bird is notorious for being an invasive species and had chased away a pair of Oriental Magpie Robins in the past.

Is there some way for me to get rid of the Mynas without scaring away the Oriental Magpie Robins? The bird is a real menace and I'm afraid it'll push away the Oriental Magpie Robin and other species of smaller birds that visit my locality. It is already considered an invasive species in Australia and South Africa. I don't want to kill the Myna, and trapping is out of the question as well. I just want to scare it off or restrict access to the birdhouse. Is there some way to make the birdhouse and surrounding area more appealing to the Oriental Magpie Robins?

^Oriental Magpie Robin. The darker one is male, the lighter one is female.

^Myna.

Update: The Mynas seem to be guarding the bird house from a distance, since I have been shooing them away. The Oriental Magpie Robin hasn't showed up since.


texts: Does vaccination make the immune system "lazy"?

texts:
I was having this discussion with a friend over vaccination against the flu. Although he agrees that vaccination against almost all diseases is necessary, he said that flu shots are not. He argued that the immune system is like the muscular system. It constantly goes through training. Flu shots deprive the body from "natural exercise" since, he believes, we need to train our immune system by getting "the right amount" of the real viruses from the environment. In other words, if we do too much vaccination (and flu shots are "too much") we make our immune system lazy.
Is this true? I know that there is a difference between natural immunization and vaccination, is it correct though to say that the latter makes your immune system lazy? I was under the impression that vaccination's function resembles more the way we learn and memory and less the musclar system which can get lazy.


texts: what are the ethical considerations when preparing a bacterial culture for testing antibiotic resistance?

texts:
I cannot think of any ethical issues associated with preparing a bacterial culture to test antibiotic resistance. The bacteria I am using is Bacillus Megaterium so its not pathogenic.
Thanks in advance for your help!


texts: Does a mutation in the sense strand of a particular gene affect the polypeptide formed?

texts:
Recently, I came across this picture which represents the DNA sense strand of a gene.

The ‘Altered’ picture shows a (frameshift) mutation in the nucleotide sequence in which a T base is deleted.

The sense strand is not transcribed — the anti-sense strand is transcribed. So why is there a change in the amino acids of the translation product when a mutation occurs in the sense strand, if the sense strand does not produce amino acids? Does a mutation in the sense strand change the nucleotide sequence of the transcribed sense strand?


texts: Is emergence connected to nature's transition between fractal regimes at different size scales?

texts:
A fractal algorithm like Mandelbrot is self-similar in all size scales. This is not the case in nature. A tree is fractal in the sense that each branch is similar to the tree as a whole. But that is only true at a certain range of scales, about 0.1 - 10 meter. The forest does not look like one tree, nor does the texture at millimeter scale or the cellular structure at microscopic scale. At those scales the tree may or not be fractal, but at least it is not fractal in the same way as on the 1 meter size. Nature breaks the fractal regime after only a couple or so self-similar scales.

Are these transitions between fractal regimes studied by biology?

Are there any ideas around about how different fractal regimes might be connected with emergent phenomena? At very small scales there exists no tree, but only elementary quantum particles/waves. Macromolecules and cells and the tree and the forest each emerge as a phenomena on different size scales. I wonder if this emergence is matched by the different fractal regimes at those scales?


texts: Why do nerve cells convert electric signals to chemical signals?

texts:
One would assume that a faster response time in the nervous system would be beneficial. However, nerve cells have to convert electrical impulses to chemical signals and cross a synapse. Why didn't nerve cells evolve in such a way as to transmit signals purely electronically, and what was the evolutionary need for the current, more complicated structure of the nerve cell?

I've seen answers on how synapses ALLOW for more complicated structures, but never how the synapse came to be. Is it even possible to have a brain structure without converting between electrical and chemical signals? If not, why not? If so, why synapses?


texts:
A farmer purchases f1 hybrid seeds. These seeds contain four heterozygous loci that give a significant increase in crop yield when compared to either homozygote. Two of these loci are on the same chromosome and show partial linkage. If the farmer allows the f1 plants to self-fertilize, what is the probability that a seed from the resulting f2 generation has all four heterozygous loci?

a) at least 1/2

b) between 1/2 and 1/4

c) between 1/4 and 1/8

d) between 1/8 and 1/16

e) less than 1/16

I think it's either d or e. For the first two genes (unlinked), there is 1/2 chance to get heterozygote. So, 1/2 * 1/2 = 1/4. For the next two linked genes, if they were unlinked, it would be 1/2*1/2 = 1/4 for a total of 1/16. But since they are linked, I'm thinking that the chance for heterozygote might be reduced, so maybe the answer is e) less than 1/16?? Not sure where to end, though...


texts:
What is the trigger for DNA to produce proteins or RNA?

I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses to react to its inner state or external events and in turn initiate transcription.


texts:
In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and what defines a genetic marker?

There are many different KINDS of genetic markers as defined by wikipedia, RFLP, SNP and many more. But when you click these, you get a technique not a sequence. So I'm confused as to whether markers are techniques to find DNA sequences or if they are literally DNA sequences?
If they are literally DNA sequences, are they sequences that everyone has?
Example of RFLP:

  In molecular biology, restriction fragment length polymorphism, or
  RFLP (commonly pronounced “rif-lip”), is a technique that exploits
  variations in homologous DNA sequences.


texts: Why doesn't the Tsetse fly wipe out all animal life in its range?

texts: The Tsetse fly, which is native to interior West Africa, carries the protozoan that causes sleeping sickness, a disease which was apparently invariably fatal before the advent of modern medications. Since there is no way to prevent being bitten by this insect, why did it not kill off all animal life in its range?


texts: Estimating RPM to RCF in Methods from Older Papers

texts:
I'm attempting to replicate a cell biology method from a 1958 Laboratory Investigation paper. The protocol is for the isolation of an extracellular matrix protein, and a key step is a centrifugation carried out for 2 hours at 2300 rpm. Apparently it was not common practice to list make, model, and rotor size of centrifuges, so I am a little lost as to what settings to use on my own centrifuge to get the same rcf.

Are there any good starting points for estimating the proper settings? e.g. who the major centrifuge suppliers were at the time or what models would be seen as 'standard' for a cell biology lab?


texts: How are animal patterns encoded in the dna?

texts:
After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this information in?

On the bird below, there is a pattern of gradient in a circle, wavy stripes, spots, a very soft caustic or honey combed pattern, among others.

I am interested in both the process of producing this pattern in a particular bird (which proteins do what), and also what coordinates this process (what in the dna controls these proteins).

For instance, some guesses: maybe some random seed is encoded in each organism, and that determines the initial conditions of some proteins, which through a cellular automata type mechanism the patterns are randomly but reproducible produced in each feather (I think this is similar to the reaction diffusion idea). Another possibility is that the information in the pattern is encoded somehow, pixel-wise (crazy!), in the JPEG style DCT basis, in the JPEG-2000 style wavelet basis, in the gabor basis, from some deep representation of some neural network, or something else.

Any insights and links would be appreciated.


texts: Why is there complementary base pairing for DNA? Why can't A pair with C given that they can all form hydrogen bond?


texts: If a receptor is inhibited throughout embryogenesis, could there be observable phenotypic differences in the adult?

texts:
So I read a journal article entitled "Maternal hypoxia and caffeine exposure depress fetal CV function during primary organogenesis" (Momoi, et al., 2012) and in essence the article speaks of the period of time in embryological development when the cardiovascular system is developing as being the time when the fetus is most susceptible to epigenetic events, and how adenosine and its A2 receptor have a role in dilating coronary arteries in hypoxic conditions. It later goes on to say that since caffeine is an adenosine A2 receptor antagonist, mothers who consume caffeine regularly create a suboptimal environment for the fetus - this is referred to in the article as IUGR (intrauterine growth restriction).

My question is: Are there any effects (or do you believe there could be effects) of this inhibition occurring during development that affect the fetus later in life? As in, do you think there would be adult phenotypic changes of any kind due to the regular inhibition of a receptor during development?

I thought about this for a while and all that was apparent to me is that if the mother was both consuming caffeine and hypoxic, then the fetus could experience myocardial damage because its coronary arteries wouldn't be receiving the signal to dilate and the heart might be "starved" of the proper oxygenation. But even so, the receptor would still be present in the adult. Do you think there could be a decrease in transcription of a receptor that is continuously blocked (you don't need to address this in your answer -- notice that I'm asking for an opinion, which you can choose to give or withhold)?

FYI: I'm writing a review on how maternal prenatal health contributes to the epigenetic profile of offspring and I'm actually focusing more on the epigenetic contributions to the adult hypertensive phenotype. I stumbled upon the CV/adenosine article and was curious about whether there could be any long-term changes, so I asked all you wise folk. It has been observed that mothers fed a low-protein diet give birth to children with reduced nephron count and glomerular hypertrophy -- my goal is to understand what the current state of knowledge of this mechanism is. So if you have any ideas about anything here, or you've got an awesome resource related to this material, I'd really appreciate hearing about it.


texts: What was the evolutionary reason for cross lateralization of the brain?

texts: In the human brain the right hemisphere controls the left side of the body and the left hemisphere controls the right side of the body. What led to this development? Why doesn't the left side of the brain control the left side and vice-versa?


texts: How much do arteries expand during pulse?

texts: Arteries expand during a pulse. The amount of expansion may differ from artery to artery. How much do arteries expand? I understand it might be a range. Inform the same. Even values specific to some arteries will be fine.


texts:
16% of people in a population can not roll their tongue .what is the frequency of people which are heterozygous of this character? Please ,any one help and guide me to solve these kind of problems.
 I tried to solve it using punnet square but i failed .

So i tried my best please help me to solve this.


texts:
This snake is in our yard, south of Deming NM, in Luna County.
Approximate length is about 3 1/2 feet.
It moved slowly at the time, but was being picked on by a couple of medium-sized birds.
It is basically black with a black, narrow head.
The body and snout have pale yellowish markings.  On the body, the yellow is individual scales, so almost spotted.  And on the snout, more like lines or stripes.
I have some good photos, and even videos, but it says the files are too big - need to be under 2 giggleburps or something and I don't know how to do that.


texts: Ways to distinguish between purifying selection and selective sweep

texts:
When looking a population genomic data, regions of low diversity (lower than expected; such as in a region of high recombination) can indicate either purifying selection of deleterious mutations or a selective sweep of an adaptive mutation. What are some ways one can tell which one occurred?

One way I've heard of is to use an outgroup that did not live through the same events as the main group. If the outgroup also has low diversity, it means nonsynonymous mutations in that region are deleterious regardless of events, and so those homogeneous regions likely underwent purifying selection. If the outgroup has high diversity in those regions, the main group likely went through a selective sweep.

What are other ways to distinguish between the two?


texts: How to validate the regulatory interactions inferred from gene expression data?

texts: My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate that the interactions are correct? I have used Lung Cancer dataset from NCBI GEO with ID: GDS2771. Also, how to get the set of genes responsible for a disease (in this case lung cancer) , and how to quantify their expression levels as over or under expressed?


texts: Is phosphofrucrokinase1 PFK1 found in the liver?

texts:
I am trying to understand glycolysis control. One thing I am stuck on is whether there is PFK1 in the liver, or only PFK2.

Edit: As far as I am aware, there is no pfk2 in muscle cells, only pfk1. This is entirely under allosteric control of ATP/AMP ratio to control the rate of glycolysis compared with gluconeogenesis. In the liver there is pfk2 which ensures that there is hormonal control of the rate of glycolysis. However is there also pfk1 so that there is a rate of glycolysis sufficient for liver cells to survive, irrespective of the hormone signals?


texts: Chills down the spine with certain music?

texts:
I am sure many of us know the feeling of that tingling chill down our spines when listening to certain music.

I experienced this most when my younger brother played an emotional piano piece for a talent show (brought me to tears).

What causes that?
Is music the only stimulus to elicit that spine-tingling?
And in terms of evolution, why?


texts:
I live in Massachusetts and I notice that there are a lot fewer bugs than when I was a child. 40 years ago if you drove around for 4 or 5 hours in the summer the grill of your car would collect a noticeable amount of bugs. Nowadays, I can drive for the whole summer and there is not a single bug on my car. I rarely see a butterfly of any kind. I have not seen a monarch butterfly in years. When I was kid butterflies were omnipresent in any meadow or field. Even 20 years ago I remember cursing all those annoying Japanese beetles flying around. Haven't seen one in years. There used to be huge gypsy moth infestations. Even in off years, you would see the caterpillars plastered all over the sidewalks. Nowadays, sidewalks are all clean, not a single squashed bug.

I thought maybe this was because of mosquito spraying. In Massachusetts for many years we have had these huge mosquito spraying programs that cover every square inch of the state. The method used is what they called ultra low volume spraying or something like that. Even so, I can't see how it would be possible. For example, I saw a schedule for spraying in my county on an each day they would have 5 different towns listed. I don't see how a few trucks could possibly spray anywhere enough insecticide to depopulate 5 towns worth of bugs. I mean in my town alone there are probably a couple hundred roads and many areas that have no road access. How many roads can they possibly drive in one night? It doesn't seem possible, yet there no bugs.

Is there some kind of cumulative effect, or are these poisons so incredibly powerful that they just wipe everything out with even tiny amounts being released? How plausible is it that pesticides and mosquito spraying is affecting insect populations?


texts: Why should phospholipid non-polar tails be "protected" in the membrane bilayer?

texts:
lipids are arranged within the membrane with polar head towards the outer side and non polar tails towards inner side, this ensures that the non polar tail is protected from aqueous environment.

My question is why should we protect non polar part ,will it destroy in contact with polar part?
 What should be the correct reason for bilayer arrangement?


texts:
This question pertains to the KRAS wikipedia page, and I just want to double check and clarify my own understanding of how this mutation works in cancer.
It states:

K-Ras protein acts like a switch that is turned on and off by the GTP and GDP molecules.

So if K-Ras is a switch, does that mean that when there is K-Ras mutation, it functions defectively so that it does not shut off? So for example when it binds to GTP and converts it to GDP, KRAS does not shut off regardless of GTP is converted to GDP and this would lead to / cause cancer.
So I guess I have several questions to my reasoning above..

Why does excess conversion of GTP to GDP lead to cancer? Is it because this is specifically pertaining to the the RAS pathway?

When I referenced above "it" is the K-Ras binding event the K-Ras protein binding to GTP then converting to GDP caused by the K-RAS gene not being able to function correctly? I'm just confused if its the K-Ras gene causing the problem or the K-Ras protein being the problem, or is it both?

If K-Ras acts as a molecular switch, how to GEFs/GAPs effect K-Ras mutations? Because I know GEFS activate the conversion of of GTP to GDP, but what is its relationship to KRAS/K-Ras?

In the next line it states:

When the protein is bound to GDP, it does not relay signals to the cell's nucleus.

Is this saying when K-Ras is bound to GDP, that the conversion of GTP to GDP won't ever stop? I kind of just don't understand why this was written or what its relevance is. Or is it simply stating K-Ras can only turn on GTP to convert it in to GDP but not the other way around?


texts: What is the name of cell structures that have an adaptation to increase their surface area?

texts: Epithelial cells that line the small intestine have an adaptation to increase their surface area - what is the name of these structures? And why would the small intestine require a large surface area?


texts: Why was it so hard to decode the corn genome?

texts:
My teachers growing up told me it was impossible to decode the maize genome. But yet its been done.

Why was decoding the genome so significant, and what made it so difficult?


texts: Relative microRNA comparison from from TCGA data?

texts:
I have a conceptual question that I was hoping someone could answer.

Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data?  Can I do this after normalizing the data?  Does it matter if I use RSEM or RPKM values.  It seems to me that it should be legitimate in any case since microRNAs are approximately the same length, but maybe I am overlooking something.

For example, I am following a paper published in Nature Communications entitled "Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif".  The authors download the data and collapse isoform reads to a single read count using the reads.  They say they used the reads per million microRNAs mapped, which establishes each microRNA read count as a fraction of the total microRNA population.  The authors then do upper quartile normalization which they say is important because a subset of microRNAs (miR-143 in particular) contributes so significantly to the total read count.  In the text, the authors appear to use the resulting values to do a direct comparison between microRNAs.

I definitely want the collapsed isoforms, and I think it makes sense to do the normalization.  However, I would like to say that a particular microRNA is expressed x-fold higher than another.  Can I do this from the collapsed and normalized data?

If this has already been answered, I apologize.  I could not find it.  Thanks.


texts: How does the body switch between aerobic and anaerobic respiration?

texts: Lets take the case of a person doing heavy exercise. Aerobic respiration is taking place, but oxygen is about to be finished up. Glycolysis occurs, Krebs cycle finishes. Now NADH and FADH2  enter electron transport system (ETS) to form ATP, but at the last step, cytochrome c oxidase cannot get oxygen as it just finished up. Now, what happens to the ongoing ETS? Does it go in reverse order and then arnon cycle to get back Acetyl co-A and respire anaerobically, or does this process get paused and respiration switches over to anaerobic mode till oxygen supply is replenished?


texts: If silver nanoparticles kill bacteria by penetrating the cell membrane, why don't they also kill human cells on contact?

texts: Apparently, the silver from the nanoparticles can penetrate the cell wall of bacteria and kill them from the inside. Why, then, doesn't the same happen to human cells, e.g. the skin on my foot when I wear nanosilver-coated antibacterial socks, or the stomach lining when people drink nanosilver-treated water? Is it because the cell wall is different in bacteria than in multicellular organisms?


texts: Where does the initial action potential come from?

texts:
When talking about action potentials we say that previous neurons caused an action potential in this neuron and that this neuron's action potential caused the same in further neurons.

But what is the origin of the first-ever action potential?
Maybe in a living organism, there are no action potentials initially because the brain is always "on" and some part of the brain can always initiate processes in an other. If that is the case then how is the brain turned "on" initially? If not, then how does the first action potential get triggered from the "resting state"?


texts: What are the frequency ranges of most marine mammal vocalizations?

texts:
I am trying to determine a list of frequency ranges into which marine mammal vocalizations fall.
Ideally, I would like a list showing where the most popular marine mammal vocalizations fall, followed by the species name. That being said, I only really care about frequencies above 20 kHz, should they exist.

Example: (Numbers fabricated)

Orcas       : 30-40 kHz
Dolphins    : 100 kHz
Blue Whales : 60-88 kHz

etc.

Even if the list is 'quick and dirty', thats ok. The list will essentially point me to which species' songs/sounds I need to study.

Some additional context, this wikipedia link as well as this one have some nice sound files of many marine mammals' songs/sounds. I am trying to avoid having to download each one and analyze their spectral content. (I could, but would rather not).


texts: What is the name of this injured species?

texts:
Location: South India

Size: 2-3cm

looks like injured species, unable to stand.


texts: How do Neurotransmitters get into the neurons?

texts:
This may be a dumb question. I'm not a Neuroscientist. I'm just trying to learn more about the brain to improve my AI learning algorithms…

I understand that there are different kinds of neurotransmitters that either increase or decrease the possibility of firing an electrical impulse through the axon. I also understand that these Neurotransmitters do not actually pass through the whole cell (Correct me if I'm wrong…), so they only travel from the Cell's terminal to the next cell's body.

So my question is: How do these Neurotransmitters get into the cell's terminal? Blood? And the more important question: How are these Neurotransmitters distributed among the different neurons? It cannot be at random, or equally distributed, because we have different "reactions" to different Neurotransmitters. For example if Dopamine is produced it gets sent to these different cells in our brain which makes the activation of its cell more likely (if I understood correctly). Dopamine is also known to increase our feelings of lust and makes us more focussed (and more). But if Dopamine got sent to ALL of the Neurons in our brain, thus make the activation of EVERY cell more likely, it would bring total chaos to our brain. (Eg. Make our fear-part of the brain activate more easily, but this is not the case.). So how are these Neurotransmitters distributed?

Thanks in advance


texts: Does the human hand have 27 degrees of freedom?

texts:
I have counted the degrees of freedom in my hand over and over and I keep getting the number 19.

Suppose each finger has 3 degrees of freedom. Then 5 * 3 = 15. The wrist can rotate around or back and forth so that contributes to 4 degrees of freedom. In total the hand has 19 degrees of freedom.

From a cursory google search, I can notice that it is commonly agreed upon that human hand has 27 degrees of freedom. Can someone provide a good reference and explanation for this?


texts: What causes the range of severity of neurological deficits in Down's syndrome?

texts:
It's known that the severity of symptoms caused by a trisomy 21 varies from individual to individual. Part of the explanation for this range of severity is the finding that 94% of Down's syndrome sufferers have a full trisomy, ie., all of the cells in their body have an extra copy of chromosome 21, while others have an underlying translocation (mostly a chunck of chromosome 21 being attached to 14). The last group has mosaic Down syndrome, where just a portion of cells is affected due to errors later in development.

However, this cannot be the only cause of the variation, as it would basically mean that 94% of all Down's syndrome patients should have similar complaints. Indeed, symptom variability is greater, as far as I am aware. I am specifically interested in the range of mental deficits caused by Down's syndrome:

  The majority of children with Down syndrome function in the mild to moderate range of mental retardation. However, some children are not mentally retarded at all; they may function in the borderline to low average range; others may be severely mentally retarded.

What is the source of the variability in the neurological deficits? For the sake of answerability it may be best to narrow the scope down to the larger chunk of Down's syndrome sufferers with a full trisomy. Does any, or all of the variability in neurological deficits has to do with the stochastic process of X-inactivation?


texts: I am working on gene networks and I currently have the honey bee gene network to work with. What I am missing is a gene network that I could compare it with. Could you please guide me to a database/website that I could use to download a gene network and use for my study. I am looking for gene networks from closely related species (hopefully another honey bee gene species (other than Apis mellifera or a hymenopteron. I am open to all flying insect species really. Kindly advice.


texts: Can difference in the expression potential of alleles lead to dominance?

texts:
Several hour ago I was in thoughts what allele dominance really means on molecular level. As we know from basic genetics, if the organism had Aa type of some gene so trait is controlled by this gene would be equal to AA case. And we see it only when our organism is growing up. I'd like to know, how it works on molecular level, why Aa = AA in phenotype? I suggest, that expression level of A locus is greater than a locus and if so, why? Is that because of chemical structure of dominance allele that RNA polymerase interact with it more frequent?

Please, help me to understand. Thanks.

P.S. I don't consider different gene interactions as epistasis etc. just give you simplest example to describe what I want to know, but any useful considerations are appreciated.


texts: What is the difference between a cytokine, a hormone and a protein hormone?

texts:
I'm trying to figure out the difference between hormone, cytokine and protein hormone. It's clear to me that all three are biological messengers, but there seems to some ambiguity and overlap between terms and I'm trying to understand the nuances.

In brief:

What do each of these three terms mean and how are they different?
Do any of the three terms represent a superset of the others? e.g are all cytokines, hormones? Are protein hormones just a subset of hormones?
Are the terms context specific at all? For example, cytokines are referenced in the context of immunology below, but are they actually fundamentally different from hormones?

If there is context-dependence, under which contexts should each word be used?
Are there any canonical examples of each? e.g Prolactin is given as an example of a protein hormone below, how about for cytokines and ordinary hormones?

  In June 1905, Ernest Starling, a professor of physiology at University College London, UK, first used the word 'hormone' in one of four Croonian Lectures—'On the chemical correlation of the functions of the body'—delivered at the Royal College of Physicians in London. Starling defined the word, derived from the Greek meaning 'to arouse or excite', as “the chemical messengers which speeding from cell to cell along the blood stream, may coordinate the activities and growth of different parts of the body” [1]

  Cytokines and chemoattractant cytokines known as chemokines are highly localized soluble signaling proteins produced by many cells of the immune system (neutrophils, monocytes, macrophages, B-cells, and T-cells) to regulate immune responses [2]

  A great deal of evidence has accumulated and confirmed that hormones secreted by the neuroendocrine system play an important role in communication and regulation of the cells of the immune system. Among protein hormones, this has been most clearly documented for prolactin (PRL), growth hormone (GH), and insulin-like growth factor-1 (IGF-I), but significant influences on immunity by thyroid stimulating hormone (TSH) have also been demonstrated. [3]

References

[1]: Tata JR. One hundred years of hormones. EMBO Reports. 2005;6(6):490-496. doi:10.1038/sj.embor.7400444.

[2]: Stenken JA, Poschenrieder AJ. Bioanalytical Chemistry of Cytokines-A Review. Analytica chimica acta. 2015;853:95-115. doi:10.1016/j.aca.2014.10.009.

[3]: Kelley KW, Weigent DA, Kooijman R. Protein Hormones and Immunity. Brain, behavior, and immunity. 2007;21(4):384-392. doi:10.1016/j.bbi.2006.11.010.


texts: Are there any proteins assembled from non-adjacent parts of the genome?

texts:
Many proteins are assembled from multiple exons with the introns between adjacent exons being spliced out. But are there any proteins that have unrelated to them exons in the middle of their sequence?

I think the equivalent question would be: are there any protein-coding genes (in any species) that are broken in two or more parts by another protein-coding gene(s)?


texts:
I have been analyzing TCGA Ovary Cancer data. In Somatic Mutation data, there is data of mutations in all the chromosomes (1-22 and X), but amazingly, I have found one (just one) row of Y Chromosome mutation as well. What can it mean?

For Reference, I have pasted that row below:

icgc_mutation_id icgc_donor_id project_code chromosome chromosome_start
MU42454          DO28056       OV-US        Y          13500742

chromosome_end chromosome_strand mutation_type
13500742       1                 single base substitution

reference_genome_allele mutated_from_allele mutated_to_allele
G                       G                   A

consequence_type aa_mutation cds_mutation gene_affected   transcript_affected
stop_gained      R194*       580C>T       ENSG00000183704 ENST00000331172


texts: Why pouring salt in the wounds is painful?

texts: Pouring salt in the wounds is so painful. I am sure you all experienced this. whats happend there?


texts: Microsatellites and Minisatellites: Which of these form the basis of DNA fingerprinting?

texts:
I'm in a fix.

 Prepare yourself for a long read

We've just learned about minisatellites and microsatellites at class (okay, by "learned", I mean we were told their definitions and essentially nothing else... hardly surprising, since we aren't expected to know more than that at school).

Shortly afterwards, we touched on the topic of DNA profiling, and my textbook went on to state:

  Minisatellites are hypervariable and are specific to each individual. This uniqueness is employed in DNA profiling.

Which would imply that the repetitive DNA fragments used in DNA profiling (VNTRs - Variable Number Tandem Repeats) are (only?) minisatellites.

Fine.

However, the Wikipedia pages on minisatellites and microsatellites (I linked both of them earlier on in this post) mention:

  (Minisatellites and microsatellites)... together are classified as VNTR (variable number of tandem repeats) DNA. Confusingly, minisatellites are often referred to as VNTRs, and microsatellites are often referred to as short tandem repeats (STRs) or simple sequence repeats (SSRs).

If I interpreted this correctly, it's saying;

"Both minisatellites and microsatellites are classified as VNTRs. But when one normally talks about "VNTRs" he/she is referring to minisatellites. Microsatellites are, instead, commonly referred to as STRs/SSRs."

Okay, so far so good.

The Wikipedia page on microsatellites explicitly states that they (the microsatellites) are the ones you deal with in DNA profiling. However, the Wikipedia page on minisatellites carries no clear indication of their (minisatellites) use in DNA profiling.

Ugh.

And to compound my confusion, the Wikipedia page on DNA profiling states:

  DNA profiling uses repetitive ("repeat") sequences that are highly variable,called variable number tandem repeats (VNTRs), in particular short tandem repeats (STRs), also known as microsatellites, and minisatellites.

Which suggests that both minisatellites and microsatellites are used in DNA profiling (as they're both VNTRs), but microsatellites are more relevant in this regard.

Summing up what I said:

My textbook  says that DNA profiling makes use of VNTRs.
My textbook (and teacher) says DNA profiling makes use of only minisatellites.
Wikipedia says that VNTRs refer to both minisatellites and microsatellites.
Wikipedia says that VNTRs are typically mentioned in reference to minisatellites. Whereas microsatellites (which are strictly "VNTRs") are better known as STRs/SSRs.
Wikipedia says (explicitly) that microsatellites are used in DNA profiling. It doesn't mention minisatellites in this regard.
Wikipedia says that both minisatellites and microsatellites are used in DNA profiling, but minisatellites are use more often.

 This inconsistency over the three Wikipedia articles I've linked is seriously annoying

My question(s),

1) I'm told that VNTRs are used in DNA profiling. Does this refer to both minisatellites and microsatellites...or just minisatellites?

2) If only one of them is used, why disregard the other? They're both (technically) VNTRs aren't they? So shouldn't either of them work just fine?


texts: When DNA is at its uncondensed form, what can it do?

texts:
I think it can do two things:

The cell may be duplicating the genome during S phase.
The cell may be transcribing the DNA into mRNA.

Question: Can the two activities occur at the same time or one at a time? In other words, are cells efficient multi-taskers?


texts: Humans have Cannabinoid receptors. Does that mean we're meant to consume cannabis?

texts: I know the answer is no. But what then explains the name of these receptors being specific to Cannabinoid found in cannabis? Aren't Cannabinoid receptors exclusive to Cannabinoid? Why are they named like that, if not?


texts:
Apologies in advance for asking bit naive question. I have looked up for this concept a lot but didn't find anything.
The wikipedia (I know its not authentic all the time, but I think works well for definitions atleast) page on Complementarity says:

  The degree of complementarity between two nucleic acid strands may vary, from complete complementarity (each nucleotide is across from its opposite) to no complementary (each nucleotide is not across from its opposite) and determines the stability of the sequences to be together

This is quite new concept for me and how come we can have basepairing between opposite nucleotides if there isn't 100% complementarity? Any evidences behind it?


texts: What are the dangers related to keeping a human brain alive outside of a human body?

texts:
I am interested in learning about the feasibility of keeping a human brain alive outside of a human body.

The question: What obstacles do we need to overcome to be able to keep a human brain alive outside of a human body?

The problems I am taking into consideration are:

connecting nerves with an artificial skeleton, (no need to connect spinal cord?)
delivering signals to the brain to avoid sensory deprivation?,
keeping brain in a "healthy state" as long as possible,
augmenting and stimulating brain,
connecting the brain to external devices without hurting it,
maintaining blood supply,blood transfusion problems (allergic reactions and hives, fever, hemolytic reactions, iron overload etc.)
can a brain be in a sleep mode? keeping brain in a "work" mode,
can a brain function without hormones?,
can we copy a brain?,
can we grow a brain? part of a brain?,
regenerating brain, slowing down the process of brain degeneration,
does the brain need bone marrow to properly function,
maintaining cerebrospinal fluid supply.

I asked this question on Quora, https://www.quora.com/What-must-be-the-conditions-to-keep-a-brain-alive-outside-of-a-body


texts: Movement of stem cells from mother to fetus

texts:
Recent results from J Lee Nelson and colleagues (Sci Am. 2008 Feb;298(2):64-71; available as full text through Google) show that cells from the mother were found in a person aged 46. Logically, these cells should be stem cells, as any other cells would die in such a long period of time.
So, what stem cells could be transferred from mother to fetus?
Why doesn't the immune system reject those cells?


texts: Why is Aorta sometimes called Compression chamber?

texts:
I find this statement that Aorta is called Compression Chamber in my study materials.

Aorta can

it keeps blood flowing
it can accumulate potential energy for bumping and compression

However, why aorta is called chamber and particularly compression chamber?
I heard this term today first time.


texts: How is the renal osmotic gradient maintained even though the blood osmolarity changes?

texts:
I am a high school student and I am a little confused in 2 things related to our urinary system:

We know in our kidneys a countercurrent mechanism exists due to which there is a steep gradient of osmolarity is observed as we go deep inside the medulla and due to which water gets reabsorbed from the descending limb of Henle's loop into the ascending limb of vasa recta but due to the countercurrent of vasa recta osmolarity of blood doesn't changes but as collecting duct descends deep into the medulla it also loses water. Where does this water get drained? Does it get absorbed into a blood vessel? I don't think so because if the blood  is also moving down with the collecting duct then it should also lose water as osmolarity increases as we go down.

We know that ADH increases the water reabsorption from the distal parts of nephron via aquaporins but if more aquaporins are there the collecting duct should pass urine of 1200mosml osmolarity, shouldn't it? and in that case will the concentration gradient in the medulla be maintained? if yes then how?  I am not able to imagine how our kidney would behave if blood of increased osmolarity get into it.


texts: NCBI-geo differences between platforms,series and samples

texts:
This is the first time that I use NCBI-GEO and I've faced with 3 different categories inside it. They are platform, sample and series.

NCBI-GEO have GEO-Overview section to explain these terms to ones who are new to this website, however; although I read it a couple of times, I could not understand it totally.GEO-Overview page The terms are a bit complex for the ones who are not familiar with the concepts. Therefore, is there anyone who could explain them with simpler words ?

In my situation, I use NCBI-GEO to get RNA-seq data for the C. Elegans organism. I've downloaded the following SRA file : NCBI-geo C. Elegans sample

As far as I understood, a sample contains an individual organism's information.(In my case its a single C.elegans organism)

Series are somehow the collection of multiple samples I guess. I wonder what is the criteria to put different samples into same series?

And lastly, what is the differences between platforms and series ? I thought that each organism have a single platform, in other words, I thought I could find all the things about lets say C.elegans in its platform but I saw that a single organism type may have a lot of different platforms.

So, I'm seeking to learn these concepts and I think this website is the correct place to ask it. If my question is off topic, sorry about that I was not aware of it.


texts: Has a new functional structure ever been observed arising spontaneously?

texts:
Have we ever observed a new functional biological structure arising spontaneously such as a new functional organ (sensory or otherwise. such as tracing some creature in the past few hundred years which had no electroreception organ and now has evolved this organ)

Or has what we observed been limited to changes in existing structures.

(Lenski's E. coli bacteria is not what i am looking for since it is a change in an existing metabolic system (not a new functional structure) and furthermore e-coli already had some ability to use citrate as an energy source )

Looking for a completely new functional organ (such as a new sensory organ) that we have actually observed - not deduced from fossil record.

Also not looking for something trivial such as a new/modified enzyme or protein molecule but rather a new organ in a species at least the size of an insect.


texts: Can we call a sorbent-filled pipette tip "microcolumn"?

texts:
I came across the use of the word "microcolumn" in a Russian text. This word was used to describe a ZipTip® C18 Pipette Tip. It took me some time and some e-mailing to the author to realize that the pipette tip was the "microcolumn".

Is it okay to use the word "microcolumn" when describing such a pipette tip in English? Would the English reader understand?

  The samples were applied to the MALDI plate using the dried-droplet method.
  To apply the samples, we used ZipTip C18 (microcolumns for desalting and concentration of proteins and peptides). We washed the microcolumn with 80% acetonitrile, then with 0.1% TFA in water. We next performed the binding of the sample by aspirating and dispensing it through the media multiple times (10 cycles), then washed it with 0.1% TFA in water. We eluted the sample using a 20 mg/ml solution of the matrix (2,5-dihydroxybenzoic acid) in 50% acetonitrile with 2 mM sodium acetate.


texts: Where can I find values, or estimates, of the density of cells in human tissues? Maybe an overall estimate, or distinct values for distinct tissues? Or maybe not human, but mammal tissues (which should be similar)?


texts: How and where, in the human brain, are memories stored?

texts:
Background
I am a computer programmer who is fascinated by artificial intelligence and artificial neural networks, and I am becoming more curious about how biological neural networks work.
Context & what I think I understand
In digesting all I have been reading, I am beginning to understand that there are layers to neural networks.  A front-line layer of neurons may receive, for example, a visual stimulus such as a bright light.  That stimulus is taken in by the front-line neurons, each of which produce a weighted electro-chemical response that results in a binary decision to pass an electrical charge through its axon to the dendrites of the tens of thousands of neurons to which it is connected.
This process repeats through layers channeling the electrical signals and focusing them based on their permutations until ultimately a charge is passed to a focused response mechanism such as the nerves that control shrinking of the pupils.
Hopefully I got that correct.
Preamble to the question ;)
Assuming that I am not completely off-base with my basic understanding of how a biological neural network operates, I am beginning to grasp how an input (stimulus) results in an output (response) such as motor movement or reflexes.  That would just seem to be basic electricity of open and closed circuits.
HOWEVER, what confuzzles me still is how a memory is stored.  The analogy to an electrical circuit breaks down here, for in a circuit I can't really stop the flow of electrons unless I dam up said electrons in a capacitor.  If I do that, once the electrons are released (accessed), they are gone forever whereas a memory endures.
So. . .
How the heck are memories constructed and stored in the human brain?  Are they stored in a specific region?  If so, where?


texts: Does any animal species have two sexes and more genders?

texts:
Are there any animal species that have two sexes and a kind of different internal diversification in two genders or more? I don't mean something like different-task-based diversity, but something biological?
For example let's imagine a species with:

2 sexes (male and female)
2 gender (A and B)

and individuals can match iff they are not only of different sex but also of different gender.
So you can only have Ma-Fb, Mb-Fa.


texts: Can my eyes adjust instantly to my friend's glasses?

texts: My eyesight is pretty much perfect, but I noticed that whenever I try any of my friends glasses, from really thin to extremely thick, my eyes seem to adjust to them within seconds and let me see perfectly fine. Is this weird or abnormal, I was just really curious.


texts: Does drinking water affect oral thermometer accuracy?

texts:
According to various sources (including Mayo and Cleveland Clinics), one must wait a certain number of minutes before an accurate oral temperature reading may be taken. However, these two sources (and others) seem to disagree on the duration of this wait. In this case, the different is three fold.

When attempting to get an accurate reading of an oral temperature, what external forces play a part in the actual temperature of the tissue in the mouth, how long would it actually take for any small amount of residual tap water to assimilate its temperature to that of the mouth and body temperature, and how long does it actually take for the tissue in the mouth to fully return to normal after drinking room temperature water?


texts: Validity of Acoustic Weapon Effects on Biological Organisms?

texts:
There is alot of rather contradictory information present on the biological effects of acoustic weapons with a bevy of scientific articles claiming that they cause harm to biological organisms with effects such as nausia, gagging, and disorientation. These articles are mostly from older scientific articles and modern government scientific reports on the issue, and statements by military leaders overseeing the development of the weapons (including defence contractors). Contradictory claims are also being made by a multitude of scientific sources from a variety of different countries and backgrounds.

I am not sure which one is correct after reading about a dozen articles from both sides. Does anyone have any insight on this issue?

Of note, there are a multitude of crackpots and conspiracy theorists that believe that the acoustic weapons are real and can do outworldly things- the media seems to have bought into these speculations thouroughly and should probably not be trusted.

Here are two articles (one claiming they work and the other denying it especially pertaining to infrasound):

Bioeffects of Selected Nonlethal Weapons

Acoustic Weapons - A Prospective Assessment


texts:
Squirrels have the ability to eat toxic mushrooms as described below. Are there any mushrooms that they can't eat without dying?

  According to Dr. John Rippon, an IMA member and world expert on fungal diseases, squirrels have an interesting adaptation that allows them to eat mushrooms containing deadly amanita-toxins without being affected. There are three important chemicals in the amanitas. Two will knock you right off, but are destroyed in cooking. The third one is the interesting one: it consists of the second amanitin, bound tightly to a glycoprotein molecule. When we digest the mushroom, the enzymes in our gut break the bond between the toxin and the glycoprotein, leaving the toxin free to enter our bloodstream, while the glycoprotein is excreted (a glycoprotein is a [protein containing sugar molecules and accounts for the viscous properties of mucus], in case you don't know). What the squirrels have done is line their gut with a toxin-compatible glycoprotein, so that as soon as it gets split from its original glycoprotein molecule, it gets rebound to the squirrel glycoprotein, and excreted along with it. Obviously, the squirrels don't cook their food to destroy the first two molecules, but presumably those get bound in exactly the same way. Thus, squirrels and a few other animals (guinea pigs also, I believe) can eat mushrooms that are highly toxic to other animals with no ill effects.  Source


texts: What about 23andMe's SNP test gives it such bad efficacy as a diagnostic tool?

texts: The recent news about the FDA stopping the google backed 23andMe service selling any more kits got me thinking. I understand the company may have been selling it as a medical tool prematurely, but what is it about SNP analysis that makes it so poor as at predicting disposition? Even other SNP companies have similar problems with accuracy and can't agree on disease disposition (Tonellato et al., 2011). Why might they differ from 23andMe's predictions?


texts: Is Pars intermedia functional in humans?

texts:
My textbook says, "Pars intermedia secretes only one hormone called melanocyte stimulating hormone (MSH)."
My teacher says that in humans MSH is secreted by the anterior lobe because the Pars intermedia is poorly developed and almost merged with the Pars distalis. I am confused as to what is correct. I find nothing wrong in both the arguments. So, is the Pars intermedia in humans functional or not?


texts:
I'm looking find a cheat sheet for protein biology to stick on my desk to remind of some of the key principles of protein biology. I seem to remember the specific and complex principles in protein biology but at the expense of the basics.

Can anyone point me to a protein biology cheat sheet or formulate some suggestions to go on one?

EDIT

What I am looking for:

Amount of amino acids in a helix turn
Amino acids typically found in Beta sheets and Helices
The types of protein interactions (i.e. ionic, hydrophobic) and the  amino acids usually involved.
Definition of Globular and fibrous form
Types of post-translational modifications
Any other useful characteristics


texts:
I have acorns from an oak tree. They look like:

but I would like to speed up their maturation so they split and I can separate the caps:

How can I speed up this maturation process?


texts: Is there a photobleaching-resistant, cell-permeant viability stain in the far red part of the spectrum?

texts:
I am looking for a live-cell–impermeable dye for viability. (The cells cannot be permeabilized and fixed in this experiment.)  I would prefer with excitation and emission spectra similar to Cy5, but I can be flexible here as long as the spectra are far away from Hoechst.

I have tried TOPRO3, but it seems to lose its brightness after a few exposures, so I would like something more resistant to photobleaching.


texts: What would be “Sternum-Intermediate” distance?

texts:
I've asked this question on the English Language & Usage board, not being entirely sure whether this question is strictly medical, or just English knowledge suffices to answer.

Do note I am no native speaker, hence I am afraid to misinterpret the possibly obvious thing.

In an article written by Wheat et al Engineernig for Life - Kinect Report the authors use the scanning device to calcuate distances on the human body.

The measured distances are: Sternum-Intermediate, Inter-nipple and Sternum-nipple (see Table 3.). The latter two are obvious. The first one, however, not so much. Unfortunately, the authors do not provide a definition, probably assuming it is clear to the reader.

What would be the Sternum-Intermediate? Is this the sternum's length or is "Intermediate" some specific body part?


texts: How do I "reinoculate" a petri dish with new bacteria?

texts:
Hypothetical question, intended to find a general procedure rather than case-specific recommendations:

I have a petri dish full of growth medium with a large population of gram-negative, anaerobic bacteria of numerous types growing in it. How would I go about replacing the existing population with lactobacillus and streptococcus strains?

Rules:

The growth medium cannot be washed out of the petri dish
The petri dish cannot be treated with anything a human body can't handle, i.e. no blasting with bleach
After the procedure is complete, the original bacteria should have little to no chance of returning, even given months or years in the petri dish


texts:
On the wiki page for proto-cadherins, they write, "The cytoplasmic domain also mediates intracellular retention, a property which distinguishes the clustered protocadherins from the related classical cadherins." citing the following source.
Unfortunately, I was unable to find much anything to go off. Anyone know off-hand what this terminology is referencing?


texts: Can bacterial RNA be degraded at -80⁰C in a SDS solution?

texts:
I would like to know if bacterial RNA in a 1.5 mL 2%SDS solution can be degraded.

Comes from a pellet of pure liquid culture.


texts: What is the role of various immune cells in demylinating neuropathy?

texts:
Is there a simple description or article of the life cycle of tcells and other immune cells and how they become programmed to attack the myelin of the nerves?

When I try to read through an article like this: http://m.neurology.org/content/56/1/74.full its pretty frustrating. I consider myself fairly technical but not versed in biological systems.


texts: How to interpret the simple sequence repeat (SSR) on the coding sequence, but not the related protein sequence?

texts:
I have predicted some SSR repeat on the gene of interest using SSRLocator program, which the result creates a question for me. Please consider the below sequence, which is part of gene sequence of interest (coding sequence):

GGTGATGAGGTAGAGGAAGAGGCTGAGGAACCCTACGAAGAAGCCACAGA
GAGAACCACCAGCATTGCCACCACCACCACCACCACCACAGAGTCTGTGG
AAGAGGTGGTTCGAGAGGTGTGCTCTGAACAAGCCGAGACGGGGCCGTGC

The program reported CCA motif as a repeat; since this repeat located on CDS, I expected to find the related amino acid track (prolin), but I observed the Threonine track in the corresponding protein sequence.Threonine is coded by ACC. Now I would like to know which motif is really a repeat, CCA or ACC. Is it possible to consider CCA as a repeat, but just on the transcript level not protein sequence or the real repeat is ACC and the software didn't work well here? Please share me any your opinion in this regard.

Thanks so much for your help and participation.


texts:
I saw a documentary awhile back and they were profiling a certain species of monkey which regularly swims underwater. I can't recall which species it was but they said it was rare for primates to do this - diving under the surface, holding ones breath, and swimming completely submerged.

I'm wondering which type of monkey this was and what other primates, besides humans, are known to engage in underwater swimming? Is there a reason this behavior evolved? My guess is that it has to do with foraging for food in mangrove type environments and possibly for avoidance of predators.


texts: Are there dog breeds that are so far apart genetically that they can't produce viable offspring?

texts:
Obviously, a very large dog would have difficulties mating with a very small dog and vice versa.

But putting that problem aside (using, say, insemination), considering the large variation of dog breeds, are there any two breeds that are so different genetically that they can't produce viable offspring together?


texts: This insect was seen in Nairobi, Kenya. Underside is striped black and white. What is it?


texts: Resilience to the neurotoxins of Indian King Cobra

texts:
I read on Wikipedia about this:

King Cobra - Wikipedia

In Thailand, a concoction of alcohol and the ground root of turmeric is ingested, which has been clinically shown to create a strong resilience against the venom of the king cobra, and other snakes with neurotoxic venom.

Though, I have been in the village parts of India where King Cobra is frequently encountered, I have never heard of this knowledge.

Can somebody please explain the scientific basis of this statement and possible reasons for this?

[PS]: Can somebody also please create a tag for "Snakes"?


texts: Chance of child inheriting at least one copy of an allele - heterozygote mother, unknown father

texts:
Our genetics professor has posted up working for previous examination answers, but I am not convinced that his answer is correct. My answer is close but may just be due to co-incidence.

Question: There is a dominant "risk" allele with a frequency of 5%; what is the chance that a woman with one copy of this allele, and her husband will have a child with at least one copy of the allele.

Heterozygote frequency: 0.095
Non-risk allele homozygote frequency: 0.9025
Risk allele homozygote frequencyy: 0.0025

Professor's answer:  0.50 (woman's chance of passing allele) + 0.095/2 (heterozygote frequency in population divided by chance of passing allele) = 0.5475

My answer:  There are three possible situations, that the husband is homozygous recessive, homozygous dominant and heterozygous. The probability that any child will have the allele in each situation is 50%, 75% and 100% respectively.
Hence my answer = (50% x 0.9025) + (75% x 0.095) + (100% x 0.0025) = 0.525


texts: Probably a moth larvae but better to confirm

texts:
What I know,
It reacts to light
the red seems to be blood but can't say for sure
1 to 10 mm
it has a casing of something soft fabric possibly
it grabs to walls


texts: Why do our epiphyseal plates close up in our late teens or early twenties?

texts:
What causes our epiphyseal plates close up in our late teens or early twenties?

I realize that one's genetics plays the main role in this. I assume there is a gene that controls the epiphyseal plates in our long bones. I guess there would be genes dedicated to every single epiphyseal plate found in our body too. So to rephrase the question:

Why does the gene for our epiphyseal plates turn off in our lates teens or early twenties?


texts: Will wiping a phone down with isopropyl alcohol daily breed bacteria resistant to disinfectants?

texts: The title says it all. If you disinfect something more regularly, aren't you just selecting for bacteria which are most robust to that method of disinfection? I've heard it said about some medications that they "can't cause antibacterial resistance". In particular I've read that this is claimed about topical benzoyl peroxide in the context of skincare. Do these claims have any weight to them?


texts:
How could I compare what a normal eye can see to a camera lens?
I just went through a very comprehensive article @ CambridgeInColor, but I'm still not really clear.

When I take a picture with a SLR camera from an object about 30m from me: what focal length do I need to use, how should I present this picture to truly capture what the eye can see (because of the 40-60° that we see 100% everything)? And how should I print it to scale?
Are there any options so I can put a ruler, or a human being at a certain point to be able to show the differences?

I hope I'm clear here, but if not, please comment and I'll try to explain better!
What I'm aiming for is that I need a picture, but not a picture in itself, but more like what the eye will see at that position. Not what the camera registers.

Thanks


texts: "Prime" structure of DNA Double Helix: Confusion

texts:
In this video on DNA replication, the diagram shows the unwound DNA as still being anti-parallel, but the first diagram in this post on Biology SE shows that the individual strands are 5'____5' and 3'_____3'. So my question is the following:

Does a single, unwound strand of DNA run as either 5'______3' or 3'_______5', or does it run either 5'______5' or 3'________3'?


texts: Is it possible for a human to get rabies from a rabies vaccine meant for dogs?

texts: What would happen if a human was injected with a rabies vaccine meant for dogs? I know vaccines can contain weak or dead strains of the virus, but is it possible that the human could become infected with rabies from a vaccine meant for dogs? My thinking is that maybe a dogs' immune system is more suited to deal with a weak strain of rabies that would otherwise infect a human.


texts: why selecting cells after gene editing with CRISPR Cas9?

texts:
I am new to the CRISPR Cas9 genome editing system and I have the above basic question.

Another way to think about this: what would happen if after cells are transfected, the cultures are left to grow without any selection. Thus, if a mutation disrupts a cell cycle gene (e.g. p53), such cells will proliferate more and the culutre will be populated by those cells rather than healthy cells.

Is this a valid reasoning?


texts: combustion vs biological oxidation of glucose

texts:
I am a high school student and I am a little confused in cellular respiration,
To represent respiration many biology text books just writes, C6H12O6 + 6 O2 --> 6 CO2 + 6 H2O But in actual biological oxidation of glucose 10 molecules of water are release and not 6, so where does the 4 molecule go?
please explain this in simple language, because I am at the high school level .I, don't know much about this, so please keep your answer on to the point.


texts: NADH vs. NADPH: Where is each one used and why that instead of the other?

texts: I know NADH is used in cellular respiration and NADPH is used in photosynthesis. What difference does the phosphate group make that the same one isn't or can't be used for both? Is there a greater reason for this separation or is it just coincidental? Why can't the two be interchanged?


texts:
It sounds like some kind of crow but not really. Here is my recording: https://www.youtube.com/watch?v=4TsKFUugot8&feature=youtu.be#t=06s

This bird always wakes me up at 04:00 and this started in late June. I live in a village in Hungary.

I really need to know and don't know where to ask.


texts: Is DNA replication a serial or parallel process?

texts:
This video entertainingly supplements this 3d animation of DNA strand replication. Does this process happen serially from the beginning to the end of a DNA strand (like having to unzip a six foot long zipper - example A below) or does the strand get chopped up into chunks, unzipped individually, replicated then brought back together (example B)?

I suspect the answer is case A. If so, is any phase of replication done in a parallel fashion? I would think something has to be (since it happens so fast and serial anything is typically very slow in comparison).


texts: downloading a reference genome for alignment

texts:
I am currently working through the code example on the MATLAB website. It requires me to download the reference genome of Arabidopsis thaliana (thale cress) so I can use BowTie2 to align the Chip-Seq experiment data. I need it in a .fa file.

Since I am very very new to this, what is the database where I can use to download this reference genome? How do I search for something like this? Thanks

EDIT: spoke too soon. I think the NCBI website did it for me. Under the Representitive -> Reference genome section. Is this correct?

EDIT2: The answer was in the MATLAB page also. The bioinformatics toolbox provides a function:

% getgenbank('NC_003070','FileFormat','fasta','tofile','ach1.fasta');
% getgenbank('NC_003071','FileFormat','fasta','tofile','ach2.fasta');
% getgenbank('NC_003074','FileFormat','fasta','tofile','ach3.fasta');
% getgenbank('NC_003075','FileFormat','fasta','tofile','ach4.fasta');
% getgenbank('NC_003076','FileFormat','fasta','tofile','ach5.fasta');


texts: Name two reasons why it is impossible to determine a gene's nucleotide sequence from the amino acid sequence of the polypeptide

texts: I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason.


texts: Reflex muscular activity in three months old fetus

texts:
At the end of the third month, reflex activity can be evoked in
  aborted fetuses, indicating muscular activity

This quote is from Langman's Medical Embriology.
Have I misunderstood it or it is really talking about muscular reflexes in aborted fetuses?

Do we have any video proof or something like that?

How does it happen and why?

Why do we need a muscular reflex during prenatal life?


texts: I found it hanging on the wall at night. It was approximately an inch long. Near my dormitory there is a lot of birch trees. The photo was taken in Prague, Czech Republic.


texts:
I watching some TV program some time ago and a guy in it mentioned that when-ever museums display real dinosaur bones (as opposed to a replica) the bones are painted over with a lead paint, because they are radioactive.

The sentence was not qualified (so he did not e.g. say that just some bones found somewhere are radioactive).

So is this true of most or all dinosaur bones, or just some of them? If I ever find a huge dino fossil somewhere, should I be concerned?


texts:
The leaves of the chestnut tree in our back yard have, for a while, developed these stains on them:

..which don't appear to be a normal feature of this tree's leaves, at least according to the pictures on Wikipedia (I'm no botanist).

Also, the grass at the bottom of & around the tree does not (no longer?) grows around its root:

Its fruit, on the other hand, appear to me to be healthy:

We've only moved here for a few months, so am not sure whether it has always been like this or whether the tree only got infested in the last period.

Does the leaves' degradation + non-fertile ground around its root, signal that the tree is sick? If so, is there some "medicine" I can get for it myself, or would I have to speak to the administrators of the garden? Thanks in advance for any thoughts!


texts: Is protein folding symmetric with respect to reversing the sequence order?

texts:
Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A.

For example (these are made-up proteins):

protein A = [G,A,L,G,M,F,R]
protein B = [R,F,M,G,L,A,G]

Will the 3D structure of protein B be somehow identical, or perhaps the mirror image, of the 3D structure of protein A?


texts: What's the correct name for the war of sexes in evolution?

texts: I'm searching for the correct term for the part of the selfish gene evolution regarding sexes. In nature, this means the evolution of the traits such as the ducks' adaptation to "trap" the drakes' penises in order to restrict the male from attending to other females.


texts: Is there any species (subespecies?) whose DNA or RNA contains only in stem-loop structures?

texts:
I am a computer-scientist working in nucleic acids from the perspective of Formal Language Theory. I am dealing with several papers that analyze the Stem-Loop structure of DNA.

I would like some solid reference that confirms (or negates):

1) The existence of these structures

2) The existence of a (species, subespecies, ...) whose DNA or RNA has been confirmed to have strings which are a pure stem-loop structure.


texts: Why are prions in animal diets not destroyed by the digestive system?

texts:
According to CBC:

  Mad cow disease is the common name for a condition known technically as bovine spongiform encephalopathy, or BSE. [...] The only known source of mad cow disease is from animal-based feed contaminated with tissue from a diseased animal. The original source of BSE is believed to have been feed containing tainted meat from sheep with a related disease called scrapie.

As prions are proteins, I would expect any that were contaminating food to be broken down to amino acids by the proteases in the digestive system. Why does this not occur?


texts: What is the actual speed of nerve impulses in humans?

texts:
For an undergrad assignment I read a biology paper that mentioned the speed of nerve imuplses to be 440 km/h in myelinated fibers. However, our biology teacher told us that this reported conduction speed is not true. So my question is:

What is the actual speed of myelinated fibers?


texts: What (open) software there are for simulating behaviour of human (cortical) neurons?

texts:
Is there any reliable open-source software for simulating the behaviour of human cortical neurons? I am looking for serious software, so let's assume I have access to a computer with more than 10,000 computing cores.

What I would like to do is to scan a subject's brain with MRI, record EEG during a simple task (e.g. listening to tone pips), project the EEG data to the cortical surface calculated from the MRI (solve the so-called electromagnetic inverse problem), and once that is done try to simulate the behavior of the cortical neurons at the "active" regions.

This simulation part is new to me, the rest I know quite well. All hints and ideas are welcome!


texts: What determines the efficiency of electron production in photosynthetic bacteria?

texts:
Is there a specific gene involved, perhaps? Would one be able to genetically engineer a bacterium to oxidize water and generate electrons quicker? I am speaking about this biological problem in terms of an application to solar cells.

Edit: I am not inquiring to the existence of a gene responsible for photosynthesis, I am inquiring as to why some exoelectrogenic bacteria can produce electrons in electron transport more efficiently than others. Is there a reason for this that can be traced to a certain gene that makes certain exoelectrogens superior to others?


texts: Why are some chemical dangerous to aquatic environment only?

texts:
Recently I was changing the thermal grease on my PC. I have noticed on the back of box, that the grease is not dangerous when ingested or when touched. But there was specifically stated, that is dangerous to aquatic organisms.

What is so special about aquatic chemistry, that the grease is dangerous to them? I would guess that the chemistry of mammals, reptiles, and birds would be quite similar to that of fish.


texts: about lipid oxidation, does acid fatty transforms in glucose?

texts:
Lipid oxidation generates fatty acid and glycerol going into the bloodstream.

Can they be converted into glucose by gluconeogenesis or are they turnd into ketone bodies?


texts: How does nitrogen gas partial pressure change when ascending during scuba dive?

texts:
Scuba divers suffer decompression illness in which during sudden ascension, gas bubbles form in blood vessels and do not get reabsorbed quickly, leading to various problems including a stroke.
The mechanism is as follows. At high pressure, more nitrogen gas in the air can be dissolved in the blood. This is due to Henry's law, which states that with greater partial gas pressure exerted onto the liquid, more gas is dissolved. When the partial pressure of nitrogen gas returns to normal, solubility of the blood decreases, leading to the formation of gas.

From above, it seems that the air that blood is exposed to (the lung's alveoli in most cases) changes in the partial pressure of nitrogen gas. Another study isolated the effect of partial pressure by conducting an experiment in which the subject's breathed air was changed from heliox (combination of helium and oxygen) to nitrox (combination of nitrogen and oxygen) without change in total pressure and this led to bubble formation.

However, it is hard to imagine that the pressure of the air breathed in by a scuba diver would change, due to the fact that air is brought from an oxygen tank that seems to be independent of outside pressure. Thus I ask the question: if the air breathed in by the diver does not change with depth, how does nitrogen partial pressure exerted on the blood change?


texts: I heard people use silicone sheet for reducing raised scars (i.e., keloids). I was wondering what is the rational behind it, and whether it actually works.


texts: Is an axillary bud a type of intercalary meristem?

texts:
I have read that some cells that are left behind from the shoot apical meristem constitute axillary buds and that these are capable of forming a branch or a flower.
So will the axillary bud also be called a meristem? And if so, will they be called the intercalary meristem?


texts: What kind of bird did I hear at three AM in Germany

texts:
I woke up at three AM from some sort of industrial noise outside. In addition to the noise I heard some creaking like from a stuck door. After the initial noise had ended, something that sounded like birds calling continued for at least 30 minutes.

The most common call sounded like staccato tweeting that lasted for about a second and increased in tone height. This call I heard many times. There were also some slower, non staccato beeps but no continuous singing like you'd hear from a blackbird.

I'm in southern Germany, in a city near a park. The area is brightly lit. It could conceivably be bats, but in my experience they don't tweet loudly and they dont make a staccato noise.


texts: How important is the antigen presented by cTECs during TCR beta-selection?

texts:
During beta selection, a candidate T cell tries to use its pre-TCR to bind to cTECs in the thymus. If tonic signaling occurs between the pre-TCR and the cTEC MHC, then it will progress through later stages of T-cell development.
If the pre-TCR needs to be antigen-specific, then the only cells passing through beta-selection will be those with affinity for thymic proteins, which seems like a problem. Is beta-selection actually antigen-dependent?


texts: Intermediate of Krebs cycle that can form Chlorophyll?

texts:
This was a question in a test in my school today.

Q) Which intermediate of Krebs cycle further can form chlorophyll?

A) Oxaloacetic acid
B) Citric acid
C) Succinyl CoA
D) Fumarate

Given answer was (C).

How can Succinyl CoA form chlorophyll? All I could find was related to porphyrine ring. Can anyone explain it or recommend a good source?


texts: Difference between feral and domesticated honey?

texts: Is there any significant differences in composition (and/or taste) between the honey of wild ("feral") honeybees versus that of domesticated ones used in beekeeping?