texts: Molecular simulations without capping n- and c-terminus of polypeptide

texts:
When running molecular simulations, what is the consequence of not capping the n- and c-terminus?

I have been following gromacs tutorials and haven't come across any that deal with capping the termini, so is it important?


texts:
I may have access to huge quantities of freshly picked bananas. Searching the web, I have found that the sugar content of the average banana is 14g of fructose (could stand to be corrected on this) which should in principle allow for fermentation. The bananas are in no way processed. My questions now are:

(1) How suitable are bananas for ethanol or methanol fermentation?

(2) How exactly is the fermentation workflow? I presume the bananas would be chopped?

(3) considering point (2) what effect would the banana skin have on the fermentation process? Would it be better to ferment the whole fruit including skins or remove the skin before fermentation?

Hope someone can help


texts: Were any 6 armed "tetrapod" fossils ever found? I've seen some lobe finned fish with two sets of shoulders in an evolutionary bio book... I'm curious because I'd like 4 limbed and 2 winged dragons to have existed :)


texts:
In trying to understand evolution better, I have been looking at examples of speciation, and have thus come across the topic of ring species.  I have tried to find concrete examples of how these work, but have been unable to.  This paper deals with one of the frequently quoted examples of ring species, but concludes:

  In conclusion, although ring speciation is theoretically
  possible, the few well-studied examples suggest that it
  occurs infrequently, because the dynamics of species’
  ranges are more likely to result in fragmentation, i.e. periods of allopatry, before the slow process of isolation by
  distance leads to sufficient divergence to allow for circular overlap.

The paper does, however, cite an article on a bird that appears to be a strong example of a ring species, but buying access to it is more expensive than a year´s supply of toilet paper.

Is there hard evidence that ring species exist?  And if so, what is the evidence and what does it teach us about the nature of speciation?


texts: Genetic Imprinting and Cell differentiation

texts:
It does not seem possible that these two processes can coexist:

1) Genetic imprinting is the phenomenon where genes are expressed differently depending on the parent of origin:

1a. Methylated stretches of DNA are not transcribed.

1b. If the gene copy originating with mom is methylated but dad's copy is not, then only dad's copy will be expressed (e.g. Prader Willi syndrome).

1c. Methylation is preserved during cell divisions.

1d. Methylation is wiped at gametogenesis, when females will erase dad's imprints and re-imprint according to maternal imprint before meiosis.

But now I'm reading about the role of epigenetics in cell differentiation, and I discover:

2) Cell differentiation occurs with lineage-specific patterns of methylation.

2a. Immediately after fertilization (prior to the first cell division), the paternal genome undergoes demethylation.

2b. The maternal genome undergoes demethylation during the first few cell divisions.

2c. Cell differentiation is accompanied and perhaps even accomplished by progressive re-methylation following these "wipes."

Source for 2): http://labs.genetics.ucla.edu/fan/papers/HuangK_RM2010.pdf
"DNA methylation in cell differentiation and reprogramming: an emerging systematic view" Huang & Fan (2010). Regen Med. 5(4):531-44.

I suspect that there is no conflict and I merely misunderstand one, the other, or both. Otherwise, how can a pattern of methylation be wiped both during gametogenesis and early embryonic stages and still be inherited?


texts: How to find out the when we had a common ancestor with a particular animal

texts:
For example, Jordan Peterson claims that human and lobsters have a common ancestor X million year ago. I wonder, how does he know it?

I'd be so delighted to visit a website, where I could select two currently existing species and it'd show me how many years ago they had had a common ancestor. Does anything like this exist? Do we at least have a database, so I, as a web programmer, could create this kind of website?


texts: Can some human groups evolve into new species?

texts:
The Sentinelese people are an indigenous people of the Andaman Islands, in the Bay of Bengal, an essentially hunter-gatherer society subsisting through hunting, fishing. There is no evidence of either agricultural practices or methods of producing fire.

Does such uncontacted people have potential to undergo peripatric speciation?
This link says

.......to the fact that the Sentinelese have lived in isolation for 60,000 years: genetically, therefore, there is a direct line between them and their pre-Neolithic ancestors.

Factors:
Geographical and Reproductive Isolation

They live in a  highly isolated and heavily forested Island in the Andaman sea.Any contacts with any other nearby Island has never been reported.

Differences with Mordern Humans
Wikipedia says that:

Behavioral modernity — a suite of changes in Homo sapiens behavior and cognition including abstract thinking, deep planning, symbolic behavior (e.g. art, ornamentation, music), exploitation of large game, and blade technology — is evident from around 40,000–50,000 years ago, and may have emerged abruptly then or may have arisen through gradual steps.

While Sentinels have been isolated for more than 60,000 years.

The Late Upper Paleolithic Model,  refers to the idea that, though anatomically modern humans first appear around 150,000 years ago, they were not cognitively or behaviorally "modern" until around 50,000 years ago. These authors note that traits used as a metric for behavioral modernity do not appear as a package until around 40–50,000 years ago. Klein (1995) specifically describes evidence of fishing, bone shaped as a tool, hearths, significant artifact diversity, and elaborate graves are all absent before this point.

Hints of Mutation:
This tribe miraculously survived 2004 Tsunami despite having small population.
This link says

Close to 150,000 people have been confirmed dead (due to Tsunami)... Sentinalese who live in the archipelago escaped unscathed because they took to the forests and higher ground well in time.
Scientists believe that because of the extreme isolation of the Sentinalese, this tribe has become biomedically valuable...... could be targeted by bio-prospectors for valuable genetic traits that may have long ago vanished in other ethnic or racial groups.

Strange courtship ritual

......this moment, a strange thing happened — a woman paired off with a warrior and sat on the sand in a passionate embrace. This act was being repeated by other women, each claiming a warrior for herself, a sort of community mating, as it were. Thus did the militant group diminish. This continued for quite some time and when the tempo of this frenzied dance of desire abated, the couples retired into the shade of the jungle....


texts: What is the difference between intrinsic and extrinsic apoptosis?

texts: Hello my Professor has been teaching about apoptosis and sometimes makes the distinction between extrinsic and intrinsic. I am not sure if I know for sure what this means. Does this just refer to intrinsic is a cell doing itself while extrinsic refers to Fas ligand? Thanks.


texts:
It has transparent wings which covers the body like an armor. It has shining red orange colour.

I found it in the western ghats of kerala.


texts:
I am wondering if aquatic plants have stomata or not. I know that non-aquatic plants have stomata to release water(transpiration) and oxygen, and to take in carbon dioxide. Do aquatic plants also have stomata, and if so do they take in water through their stomata? If water is taken in through their stomata, wouldn't other substances such as dissolved salts get in the plants vascular system too? Does the aquatic plant use this salt or remove it, and how would they remove it?

Note: I am talking about fully submerged aquatic plants such as kelp.


texts:
The following claim

  Mutations are random

or just the use of the expression

  Random mutations

are very common among lay people.

The claim is very common among lay people. The claim is often made by OPs (such as here, here for example) but also in answers (such as here for example).

What does it mean exactly?
Are mutations really random?


texts: Relationship between inbreeding and sterility in humans

texts:
In general, inbred individuals tend to be at increased risk of sterility as shown in cows (Gonzales-Recio, 2007) or in leghorns (Nordskog and Cheng, 1988) for examples. I only have very quickly looked at a few abstract but it seems that this effect is a bit controversial in humans with two studies showing a negative relationship between consanguinity and sterility (Rao and Inbaraj, 1979; Bittles et al., 2009) and one showing a positive relationship (Ober et al., 1999).

What is the relationship between the inbreeding coefficient $F$ and the (relative or absolute) risk of sterility in humans?

For a definition of the inbreeding coefficient, please see here, here and there or just google inbreeding coefficient.

I am looking for some function, linear or not, that describes the probability of being sterile ($P_s$) as a function of the inbreeding coefficient $F$ in humans. I am aware such measure might differ among human populations but I'll be interested in whatever we can find.


texts:
I am conducting an investigation into the effect of two different grass management techniques (grazing vs. machine-mowing) upon floral biodiversity.

I have collected my data and now need to process it in a way that will yield meaningful and valid results. My data is in the form of 25 samples per area with %-abundance measured for each species in a 0.25m2 quadrat.

I am currently using a non-standard diversity quantification technique, called Disney's index (which I have been led to believe is named eponymously after R.H.L Disney, however I am unable to find any references describing this), in which we assign each species a weight based on percentage abundance, as follows:

We then use these weights to calculate the index as follows (i.e. by computing the sum of the weights of the species, over the number of species):

I want to know if this is the best possible diversity index I could use for this type of analysis, or whether there are others which I should be considering.

Thanks in advance!


texts:
My book says that the excitability of the nerve is increased when increasing the the potassium ion (K+) concentration in the extracellular fluid and vice versa.

I don't understand this mechanism could someone explain it for me!

Thanks in advance!


texts: What plant is this? (Found in Southwest Germany in June)

texts: The picture was taken in Southwest Germany in June, and they covered the ground of a garden we were at...


texts: What is the correct model for enzyme-substrate complementarity?

texts:
This Wikibook shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is  the proper one. However, my biochemistry professor mentioned that often times, enzymes behave as lock and key. I also noticed that the Wikibook doesn't mention which model is in fact true.

The Lock and Key Model

The Induced Fit Model

Is there currently one accepted model? Which is it, and why?


texts: Vomit comes from gastric acid, right? And in gastric acid there is HCl and HCl is corrosive (strong), how come when I vomit, it doesn't destroy things that it (as the vomit) hits (such as floor, table)?


texts: What is the name of this tree with compound leaves?

texts:
Can anyone tell me what is the name of this tree?

It was found in Northern US.

(click on image to enlarge it)


texts: What is coffee effect on muscles ? On sport performances?

texts:
Since coffee is a vaso-restrictor does it have any impact on sport performances ?

I mean does it go against natural way the body works (sending more blood to muscles due to the increasing needs) or does the body easily bypass this effect ?

Edit : I leanred that coffee has a great impact on sport performances but what realy interests me is to learn more about its vaso-restrictive effect , how doesn't it reduces performances ?


texts: Why can a gene lack of a binding site be expressed in skin cells?

texts:
In order for a specific gene to be expressed in the mammal’s cells, all of the gene’s binding sites must be bound by transcriptional activators. The mammal’s skin cells contain activators that bind to sites B, D, and E, while the mammal’s liver cells contain activators that bind to sites A, C, and E. (From Khan academy)

Why can both Gene 2 and Gene 4 be expressed in skin cells? I think Gene 4 can't since it doesn't have site E.


texts: What if a Point Mutation is seen in only half the coverage for its location?

texts:
I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact.

I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20.

My primary question is: how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?

I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.


texts: Is the bipolar neuron of the retina considered a sensory neuron?

texts:
Any neuron that participates in sending impulses from receptors to CNS are referred as sensory neurons. But I often see bipolar neurons of eye(which according to the above definition should be sensory neurons) being called interneurons. Same is the case with the amacrine cells and the horizontal cells.

So what are sensory neurons? Are all the following retinal neurons sensory?

Rods/Cones,
bipolar neurons,
amacrine cells,
horizontal cells &
neurons of the optic nerve (ganglionic neurons)

And, as soon as the neurons of optic nerve terminate in optic lobe, then are all the neurons in the optic lobe connected to the neurons of optic nerve called interneurons?

Are all the neurons of brain interneurons? Obviously, there are neurosecretory cells in the hypothalamus that  I wouldn't consider interneurons.

Still, wikipedia tells us that only 20% of neurons in the cortex are interneurons.

  Unlike the peripheral nervous system (PNS), the central nervous system, including the brain, contains many interneurons. In the neocortex (making up about 80% of the human brain), approximately 20-30% of neurons are interneurons.

Shouldn't that be about 80%?


texts: Ipsilateral vs contralateral side of body

texts:
I know that the dorsal columns carry ipsilateral information. Is this fact relative to the dorsal column in question?
If I want to talk about the right dorsal column, then the right side of the body would be considered ispilateral. But, if i then go on to talk about the left dorsal column, does this mean that the left side of the body is now considered ipsilateral?


texts: Where does craniocaudal closure of anterior neuropore start?

texts:
Closure of the cranial neuropore is bidirectional, and final closure occurs in the area of the future forebrain. Closure of the caudal neuropore is strictly craniocaudal and finishes at the level of the second sacral segment.

This is what Larsen's Embryology says. I understand that neurulation starts somewhere in the area of the first five somites and then proceeds in both directions - cranial and caudal. The caudal neuropore is closed on day 26 by neurulation in this direction.

But, the cranial neuropore is closed not only by this cranial wave of neurulation but also by another one incoming craniocaudally and the point where they both meet is of final closure. (hence bidirectional)

My doubts - pls correct if any of my interpretations are wrong. Where is this second craniocaudal wave originating? Where is the final point of meeting (I suspect linea terminalis or anterior commissure) ? Could anyone post a picture or a reference to understand this visually (both waves of neurulation)?

PS. I am not talking of primary and secondary neurulation. Which is different and concerns the caudal eminence.


texts:
The word natural here is meant in contrast to it being a sociological construct.

  Is kissing in all its forms something natural for humans? Is it instinctively erotic? Or is it just a conventional form to show trust and intimicy, i.e. the association besically just comes via a social means?

Because the only other advantage of this mouth to mouth contact I could see is maybe for the immune system.


texts:
What is the evolutionary advantage with two lungs (kidneys)? Most living beings only have one heart, one stomach. Most internal organs are not doubled and if one lung fails it is not exactly quite transparent due to having an extra lung. Before modern health care one failed lung would kill the individual.
The same can probably be said for kidneys.


texts: What are the characteristics of a living organism?

texts:
It seemed fairly basic at first, and yet I have to ask because even a quick Google search reveals that it doesn't seem to be quite so straight-forward anymore. After more research, I found multiple lists, some with six points, others seven or eight. Some lists shared six points and only differed on one, but others had five different points and divided and named the points differently such as Respiration vs Metabolism, Adapt vs Evolve, Homeostasis vs simply consisting of cells, etc.

Maybe it never really was simple, but when I learned basic middle school life science in the 1990s I seem to remember a clear and concise list of 7-8 distinct terms. I know they were just the summary given by the author of whatever textbook we used, but I remember several sources having similar lists (cannot say for sure if they were exactly the same), including a textbook, an educational video game, and a poster.

I'm also told that this has become a bit of a debate in the biology community, whether such a black and white distinction of "living" or "not living" is prudent. Questions such as this one on viruses are an example of how it is difficult to categorize life. However, I noted in my research that there was still clearly overlap in meaning of definitions, it was just in description and division of points that they differed. This suggests to me there is still a generally agreed upon core definition that is simply described by different people, specifically authors, with a few areas of possible debate.

What are the current generally agreed upon characteristics, the common denominators? (They all reproduce?)
What characteristics are commonly debated and therefore would unwarranted to claim? (Specifying cell structure?)

With the understanding that an answer will require an objective synthesis of a range of content and opinions, debate on what should or should not be characteristics is discouraged. Rather, an impassioned summary of the current  scientific consensus on this question is what I am looking for.

It seems to me that even if this is a topic of opinionated debate, it is certainly at the core of Biology and would be worthwhile to be addressed in an academic manner, be accessible, and available to reference on this site.

(PS - Not in any way a homework question, never was, just a curious 30-year father. Unless you are counting questions I have to answer from a curious little boy.)


texts: Are the ribosomes specific for each organism

texts: If we removed one ribosome from human and we put it inside horse, would the ribosome perform the as it would in humans or it will not work or somewhere inbetween?


texts: What are parental antagonism & parental conflict?

texts:
I've been reading the chapter by Haig et al in The Genetics and Biology of Sexual Conflict. I think this chapter has them quite unclearly defined. Could anyone describe these two phenomenon more clearly than the chapter does? Real or hypothetical examples would be good to give clarification, and clarification of how they are distinct from sexual conflict and antagonism.

  "Parental Conflict will refer to phenotypic interactions in which
  matrigenes and patrigenes prefer different outcomes"

  "Parental Antagonism occurs when an allele has a relative advantage
  when inherited from one sex but a relative disadvantage when inherited
  from the other."


texts: Why are transcripts translated from 5' to 3' direction?

texts:
What is the mechanism?
In other words, how does the tRNA know whether the codon is in 5' to 3' direction? I also heard that anything that is translated from 3' to 5' direction is degraded. Is it true?


texts: Difference between clonal and subclonal mutations

texts:
I'm a physicist writing a proposal that has to do with cancer as a disease driven by evolutionary selection. As far as I understand, all tumors start with a single precursor (single cell or group of cells), and the other cells derive from this precursor by cycles of alterations and selection processes.

Reading recent articles, such as this, I learned that the derived cells include both clones and subclones. Since I'm not sure I understood things correctly, I have a few questions on the difference between the two words:

Is it OK to call clones the cells derived from the precursors?
When should I use subclones?
In the case of heterogeneity, is it fine to call clonal population a group of clones with the same characteristics?


texts: What kind of beetle is this (2cm long, brown, "V-shaped" body)?

texts:
I've seen this brown beetle, which was about 2cm-3cm long (I guess) near Loch Lomond (Scottland) a few days ago.

What kind of beetle is it?


texts: Do animals have greater tendency to care for their opposite sex siblings due to mate competition among same sex siblings?

texts:
According to the gene-centered view of evolution, siblings have p=1/2 relatedness, thus having greater altruism between them than cousins or unrelated animals.

For species with a conventional sex binary, how does sibling sex relate to altruism? My idea is that siblings of opposite sex show greater altruism than siblings of same sex, since siblings of same sex have more to compete over. Namely, same sex siblings compete for the same pool of mates. Is this something known to be true in studies of species altruism?


texts: C. elegans are either male or hermaphrodites, but why aren't there any females?

texts: From my understanding C. elegans are mainly hermaphrodites but are occasionally males to increase genetic variation. Why is it that random females aren't born instead to achieve he same goal (genetic diversity)?


texts: What are senescent cells doing in our bodies?

texts:
I'm reading a paper that mentioned the elimination of senescent cells delays aging. I'd like to receive more information about it.

The Baker study published in Nature demonstrates that targeted elimination of senescent cells in mice results in remarkable protection from several age-related pathologies, cancer, and makes cancer cells resistant to chemotherapy. I know that senescent cells drive aging, and induce cancer. Can we grow them in cell culture as a kind of stem cells ? How might they contribute to the aging process ?


texts: Is the reason why lipid-soluble molecules can pass through membrane because

texts:
I have been studying about cell membranes and how water molecules are able to pass through it. (https://www.wiley.com/college/boyer/0470003790/animations/membrane_transport/membrane_transport.htm)

It is clear that the water molecules can squeeze through openings in the bilayer. My questions are:

1) Do small, non-polar molecules also enter through these gaps?

2) It states that the whole structure moves when vibrating. Does that mean the hydrophobic tails also move? If so, how do the non-polar molecules dissolve?

3) The top of the membrane is hydrophilic. How do non-polar molecules get past these hydrophilic heads into the hydrophobic interior core where they can be dissolved?

Thanks a lot!


texts: Why are haploid cancer cells not killed by immune system?

texts:
I have seen haploid cancer cells (I think it was leukemia cells) in a lab.

Sperms and eggs are haploid but are not destroyed by the body because they are protected by other cells surrounding them.

My questions :

How are haploid and diploid cells differentiated by our immune system ?
Why are the haploid cancer cells not killed ? I know I could as well ask why any cancer cells are not killed but I want to know if there is anything specific about these cells ?
How are these cells generated ? (By meiosis ?!)


texts: Is there a biological neuron that spikes in response to hyperpolarizing currents?

texts:
As some background I've been building Electrophysiological models of neurons, and in the process stumbled upon a model, that in all respects is biologically plausible, but has a bizarre property I didn't think happened in nature. It spikes in response to hyper polarized currents.

My particular model has only one ion channel which is has similar properties to Hodgkin-Huxley's transient sodium channel. It has one activation gate and one inactivation gate.  The reason I only use a single Ion Channel was I was exploring If I could create a minimal spiking neuron with just a single channel. The answer is yes, but has different properties then I expected.

Basically when I inject a hyper-polarizing current it spikes and depolarizing current causes it to stop spiking.

I know that Depolarization block can occur, my current isn't that High, in fact its no current produces no spikes. It has a normal rest potential around -55 mV and Fires upward to about +40 mV.

Also note that If I change the parameters around I get a more normal neuron that spikes in response to depolarizing currents. So the property must be somehow related to the ion channel kinetics.

The question is: Are there biological neurons that spike when hyper-polarizing currents are injected?


texts:
I get conflicting answers.  One would think if it was true, it would be rather seminal and widely known.

There are papers from Khorana[1], Holland[2], and Bretscher[3] (late 60s) that suggest that it is quite easy in the presence of antibiotics like neomycin.

But more recent papers like this one[4] still openly ask the question, and that the only thing we know is that the initial ribosome binding step is similar between RNA and DNA.

I can't reconcile these papers.

Morgan AR, Wells RD, Khorana HG. 1967. Studies on polynucleotides. LXXIV. Direct translation in vitro of single-stranded DNA-like polymers with repeating nucleotide sequences in the presence of neomycin B. Journal of Molecular Biology, 26(3):477-497, doi:1016.10/0022-2836(67)90316-6.
McCarthy BJ, Holland JJ. 1965. Denatured DNA as a direct template for in vitro protein synthesis. Proceedings of the National Academy of Sciences USA, 54(3):880-886.
Bretscher MS. 1969. Ribosome Initiation and the Mode of Action of Neomycin in the Direct Translation of Single-Stranded fd DNA. Cold Spring Harbor Symposia on Quantitative Biology, 34:653-651, doi:10.1101/SQB.1969.034.01.075.
Damiana L, Marty-Detravesa C, Winterhalterc M, Fourniera D, Paquereaua L. 2009. Single-strand DNA translation initiation step analyzed by Isothermal Titration Calorimetry. Biochemical and Biophysical Research Communications, 385(3): 296-301, doi:10.1016/j.bbrc.2009.05.044.


texts: It is correct to construct tree species-based rarefaction curves for birds?

texts:
If I register all the species of birds that uses sp1 tree, then, all the species of birds that use sp2 tree, and so on. With this dataset, I can made a rarefaction curve using "number of tree species" on X axis of the rarefaction graph, instead of using "number of samples"

Is this incorrect? Does anyone knows a paper that made something similar?


texts: Between Cholera and Polio, which disease cannot be controlled by killing the vectors

texts: Since Cholera affects only humans, and also doesn't have an insect vector or animal reservoir host. And Polio is a disease of the central nervous system, spread from person to person through infected fecal matter entering the mouth. Then which one of them can be controlled by killing the vector, I'm not completely sure if cholera doesn't have a vector, but if they don't, then I'll like to know if and how polio can be controlled by killing the vector.


texts: What is the difference (if any) between an Intrinsically Disordered Protein and an Intrinsically Disordered Region

texts:
The wikipedia definition of an Intrinsically Disordered Protein is a protein that lacks a specific 3D structure.  An Intrinsically Disordered Region is similarly defined.  Why are they often listed separately?  Isn't an Intrinsically Disordered Protein just a protein that has at least one Intrinsically Disordered Region?
Just a couple examples:
https://doi.org/10.1002/pro.3680

In contrast to structured proteins, intrinsically disordered
proteins and regions (IDPs and IDRs)

https://doi.org/10.1146/annurev.biophys.37.032807.125924

There are a number of significant differences between the amino acid sequences of IDPs/IDRs and those of structured globular proteins and domains.


texts: What is the meaning of deep winter mixing?

texts: I was reading a paper about eutrophication and there was a term "deep winter mixing" in which an abundant supply of phosphorus is released to the surface waters. I searched a lot but nowhere I could find a definition for that.


texts: What is the native structure of amyloid-beta protein under physiological conditions?

texts: The amyloid-beta protein forms cross-beta structured fibrils. But under normal physiological conditions what is their predominant secondary structure. Is it alpha-helix, random coil or beta-sheet?


texts: Is the structure of human brain white matter fixed at/near birth?

texts:
I have been reading that, with exceptions for a few parts of the human brain, no neurogenesis occurs, so no new neurons are created.  I have also heard that no new axons are formed through the white matter of the brain after birth as well.  I also know that the axons are myelinated, minimizing crosstalk and other interesting structural effects that might occur.

Between those, does that imply that the structure of the white-matter of the brain is fixed at a very young age, and never changes through our life?  It seems like a natural conclusion from the data, but it feels counterintuitive when contrasted with the continuous creation and destruction of synapses which happens so close nearby.


texts: When can a virus modify DNA in every cell of a living organism?

texts:
I've recently heard about experiments with brain tissue, where a virus is introduced in a rats brain, causing a "glow when electric charge is present" protein to be created. This protein then helps to study the brain using optical techniques to detect this glow. As far as I understand, not all cells in the brain were affected by this virus.

It seems like this kind of "virus operation" on DNA is pretty powerful, so my question is : at which point in an organism's life can a virus operation be done in such a way as to affect the entire organism for the rest of its life?

In other words, will a virus is introduced into a young embryo(or sperm), affect all cells and stay with an organism until death? Can it be introduced later and still have "complete effect"?


texts: Are eukaroytic promoters located in the 5' UTR region?

texts: I was wondering if promoter sequences are located on 5'UTR region in eukaryotic organisms?


texts: Theranos blood test's Specificity and Accuracy?

texts:
I am studying the limitations of Theranos device.
They have 238 documents in Google Patents Search (Inassignee as Theranos), here.
Which patents are relevant for their device?
They have 70 tests which are not necessary to consider now.
Just the basics of the device.

My intuition says that it uses PCR to multiply the microliter of blood for the analysis.
What are limiations of multiplying so little blood?
I think this is where their engineering work applies.
What components do you need to multiply?
I think all is not necessary.
Otherwise, the specificity and accuracy can be difficult to hold.

How can Theranos blood test's be specific and accurate compared to conventional full blood test?
I suspect if you can do the conventional full blood test with Theranos device with the same accuracy and specificity as the conventional one.


texts: Is there such thing as "biological cycles" of activity/performance/etc in mammals?

texts:
I'm looking for some information about the cycles of increased/decreased activity, mental performance or endurance that are related to a mammal's age and the time of a season.

First of all, I'm not sure what such cycles would be called. I know of circadian rhythm, which is an ~24 hour cycle. The other cycle I've heard about was circa-septan (7 days?). What keywords should I use to search for cycles that may have period of a month to several months?

The second question is - are there are episodes of increased activity/performance over a mammal's lifetime? I can think of two example - mating rituals may involve fighting and hibernation involves almost no movement at all.  Are there additional events that may last more than a month?

The final question is if the age comes into equation of increased/decreased activity. Lets say a younger rat an and older rat are put into the same maze, would their ability to "solve" the maze be related to age?

This question is rather broad. Maybe there are some keywords or a science branch that deals with these questions and I can refine my search?

I appreciate your input!


texts: Two sets of chromosome and the sequencing output

texts:
Humans have two sets of chromosomes that are not connected in each cell. Am I correct?

I assume while sequencing DNA both of these sets have to be sequenced and the output have to be provided in some order - i.e., paternal set followed by maternal or vice versa, though it may not be possible to know which is paternal and which is maternal.

(I know there are different types of sequencing techniques and output may differ depending on the technique. Here I am speaking of the general case). I tried clarify this question myself. But may be this is such a basic thing that no one seems to touch upon this aspect.


texts: Is there a purpose for nucleated red blood cells in reptile, avian and fish blood?

texts:
I have read, and read, and read documents on this subject but still have no conclusions.

Everything I have read explains why mammals don't have a nucleus (to make more room for the haemoglobin and allow for more oxygen to bind as well as making it easier for the RBC to fit through capillaries) but the reports don't explain why birds, reptiles and fish may still have nucleus in a red blood cell.

Is there really any other function a nucleus has within a red blood cell apart from being the 'brain of the cell?

It's doing my head in, all I've gained from this research is the understanding that birds have a far more advanced respiratory system and their capillaries are bigger than mammals, this still doesn't explain the need for a nucleus, it's actually suggesting they don't need one!

Any enlightenment will be great,

Thanks.

http://onlinelibrary.wiley.com/doi/10.1002/iub.490/pdf


texts: Rationale behind washing off unbound protein antigen in indirect ELISA

texts:
My question is with regards to the usability of the indirect ELISA in measuring protein concentration. Suppose we want to quantify the concentration of a protein. The indirect ELISA method would require one to coat the bottom of the well with protein antigen and wash off unbound antigens.

My question is that wouldn't washing off unbound proteins mean you are 'diluting' the actual protein concentration? Your resulting colour intensity will not reflect the actu protein concentration. Thanks!


texts: Which scientific names designate eyespots?

texts:
I've found that names containing ocellata and ocellatus designate species that feature eyespots. Are there other words in the scientific names that designate eyespots?

The problem I need to solve is: I want to fill the category Eye shapes in nature, therefore any method for finding such species is welcomed.


texts:
So some people are better at doing stuff than others of the same age..in other words, they have talent.

So I am asking, what is the science behind talent? What is different in their brains than others which give them an advantage?

By talent I mean excelling in physical performances like sports and mental abilities like IQ


texts: Does contracting Rubella give one some kind of immunity to Measles and vice versa?

texts:
Both these diseases- Measles and Rubella, have very similar symptoms, have similar complications and are often confused for one another. And both the diseases have a common MMR vaccine. So, are the culprit viruses also related, so that contracting one can give one at least partial immunity to the other as well?

The similarity in symptoms is striking. Both the diseases may start with cold and fever. Both give one rashes, that start from face, and spread to rest of the body. Both have similar complications associated with them like brain infection. In the end, both can cause miscarriage, preterm birth, or stillbirth, as well as a variety of birth defects in pregnant women.

I know from this source that lab tests exist which can tell whether a person has immunity to one of the MMR diseases (Measles, mumps and rubella) and not the other, implying that there is a possibility of immunity to one and not the other. But since the vaccines like MMR only ensure immunity for 99% people who get the shot, my question is- does there exist partial immunity (in some people and not others, or in less severe attack and not otherwise) to Rubella if one has contracted Measles before and vice versa?


texts: Why is there a distinction between an *allergic* and an *immune* response?

texts: Our immune system has evolved to protect us against potentially dangerous non-self particles. I have difficulty in understanding why there is a distinction called an allergic response: what’s wrong with using the term immune response full stop? Surely a person’s immune system should react to a particle of grass pollen in EXACTLY the same way as it does to a non-self protein expressed on cells of some transfused blood. The mystery that I absolutely don’t understand is why our body can then differentiate the scale of the response.


texts: Are enzyme inhibitors only a possibility?

texts:
I take 3 medications that metabolize by the same liver enzyme cyp2d6. A drug interaction checker told me that on or two of the medications i take may slow metabolism of another by altering drug metabolism. Ive had no side effects or interactions from this combination of drugs. Ive also read of people being on the same combination of drugs with no problems. If a drug is considered an enzyme inhibitor, is it a definite that it will slow metabolism and raise blood levels of another drug, or is this just a possibility?
Thanks for any feedback


texts: Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a parallel structure. I learned that these beta strands are a zigzag sequence of amino acids, but what traits of beta strands differentiate it from the primary structure? Or are the beta strands just primary structures that link together to make beta sheets?


texts: I have recently learned that one of the best ways to isolate a protein in industry is via Chromatography. What are other ways enzymes are isolated in industry? Are there other ways?


texts:
How rapidly do human mitochondrial ribosomes turn over?
The inside of the mitochondrion is a highly oxidizing environment that can damage RNA and DNA. How long do mitochondrial ribosomes last before needing to be replaced?


texts: Can an epidemic span multiple countries?

texts:
Can an epidemic centralised in one area be still considered an epidemic if it spans multiple countries? If so what is the limit to the number of countries a disease can infect in one region before it is considered a pandemic?
take for example this image

Say the circle was the area where the outbreak has occurred
Would it be considered an epidemic or a pandemic?
Thanks


texts: Are there parts of DNA that do not have genes?

texts:
A question in my genetics class is "Are the number of genes proportional to the genome size?"
The answer is "no," and is it because the genome is the entirety of all the DNA in an organism, but that there are some segments of DNA that don't have genes on them?  Can someone explain this?  Thank you!


texts: How does anadromous fish physiology "know" to switch from salt to freshwater and back?

texts: What mechanism allows anadromous fish (like salmon) to switch from salt to fresh water and back?  How does the fish "know" to switch its physiology and do other fish possess the biochemical machinery for this?  How difficult would it be to genetically engineer salt tolerance into a freshwater fish?


texts:
http://en.wikipedia.org/wiki/Temporal_lobe

Does this have something to do with tempo (time?)

Temporal lobe is behind (posterior) to frontal lobe, inferior to parietal lobe and is in front of occipital lobe.

Why it's called temporal?


texts: How can the Ames test detect a human carcinogen?

texts:
Using the Ames test, we add a mutagen to auxotrophic salmonella with mutations in the histidine pathway and rat liver extract to simulate metabolism.  How would we know if the carcinogen is a human carcinogen or not?

I'm guessing that if a mutagen showed no growth without the rat liver extract, but then growth with the rat liver extract this would mean that it is a human carcinogen. Is this true?


texts: How are we able to find the specific sites at which DNA binding proteins bind?

texts: We know that some DNA binding proteins are site specific, that is they recognise and bind to a specific nucleotide sequence. My question is how can we precisely tell at which sites they bind? Is it the amino acid sequence of the protein? Or is it the repetitiveness factor in case they bind to multiple locations on the chromosome?


texts: How long is one generation for a mosquito?

texts: For instance, humans are said to have an average generation time of 20 years. I've heard that mosquitos go through 10 generations in a year. Is that information correct?


texts: What are the programming languages important to learn for a geneticist or bioinformatician?

texts:
I am interested in learning more about both genomics and bioinformatics, with emphasis on genomics. I was told after taking an introductory course of genomics that the programming language "R" and "python" are widely used. However having asked about learning genomics before on this fourm, I was suggested alot of books for learning genomics with "Perl". I was also told anecdotally that "perl" is falling "out of favor" and "Python" and "R" are desired.

To give background on my coding skills, I flunked out of computer science due to poor coding skills and poor math skills. I still had an interest in the field and therefore started studying genomics and biology instead.
I would categorize my self as a beginner in java and python in terms of skills.

I was also told anecdotally that the best way to learn coding is by having a project. But I feel incompetent in my coding skills to even attempt anything.
I tried to learn Python via "Codecademy" and their 13 hour course for python. Having completed it I felt lost enough to make this post, looking for further guidance. I tried to read a bioinformatics book based in Python, but I missed the handholding and directed exercises that Codecademy gave me.

Should one interested in genomics learn the coding language, R or Perl? Also what would be the best ways to learn these for one who does "not excel" in coding?

If this post seems opinion based mods feel free to delete it or move it, I just was not sure how to phrase my concerns adequately.


texts: Inexperienced divers damage coral, but parrot fish eating coral doesn't do damage?

texts:
I've been learning about life on coral reefs. Recently I've become aware of the damage to coral reefs caused by tourism and inexperienced divers:
1) Corals have a thin membrane which keeps them healthy. Touching them could break this membrane, causing infection which can lead to death.
2) Stepping on, leaning on, and sitting on coral could smash their polyps.

I am not against being responsible as a diver, respecting nature, arriving and leaving without a trace. I'm just curious what the difference is between human and animal contact. Parrot fish eat coral, taking bites out of it, leaving exposed areas and this damages the coral. I've seen footage of sharks having feeding frenzies on reefs, where they smash into the reef during the commotion and while trying to catch their prey. Fish rub up against coral and peck at them to get algae, and crustaceans walk on the coral with legs that seems like it would break the thin protective membrane on the coral.

Obviously, as humans we technically do not belong in their world, so I'm sure there are reasons for damage with that alone; but why does marine life causing damage not cause actual damage? Or does it, and it just repairs differently or faster somehow?


texts: Forgot to vortex antibody before staining

texts:
Ugh. Did an immunofluorescence experiment last weekend, forgot to vortex both my primary and my secondary antibody solutions.

And my final result looks dimmer than it should be. Is it possible that not vortexing contributed to this?

I guess the question is, is vortexing really necessary? It would come down to the fluid dynamics. How long does it take for a drop of antibody to reach equilibrium in a 1000µL Eppendorf tube? Is it really more than just a few seconds? Is vortexing really necessary?


texts: Is there redundancy in the auditory system like there is in the visual system?

texts:
In the early visual system, there is a great deal of overlap between retinal ganglion cells, which results in redundancy of the signals that neurons carry to higher visual processing areas in the brain.

Is there a similar type of redundancy in the early auditory system?


texts: Why and how is DNA synthesis so much faster then RNA synthesis in bacteria?

texts:
DNA synthesis in E. coli is 20x faster than RNA synthesis at 1000nt/s vs 50nt/s. (Mirkin'05)

I find that perplexing since DNA polymerization has better proofreading than the RNA variety, which requires extra time as you need to backtrack, excise, and replace. Also, in bacteria there's almost no splicing, so that doesn't slow you down. And the 1000nt/s is a single replication fork. We are not talking about several replisomes together clocking 1knt per second.

Is there an explanation of this or, in the absence of evidence, hypotheses?


texts: Does inorganic particles have pattern recognition receptor?

texts: Does silica or carbon particles (inorganic substances causing silicosis and anthracosis) have Pattern Recognition Receptor (PRR) on macrophages/dendritic cells? Because phagocytic activity depends on PRR. If it doesn't have how it engulfs it?


texts:
In high school we studied the inheritance of eye color, as it was explained to us in the most simple way: blue eye color is a recessive, monogenic, autosomal trait. Now I know that it is a bit more complicated than that; there are several genes which determine the inheritance of eye color. That's as far as I my knowledge goes.

Which are these genes and what do they encode for? How is the eye color trait inherited? Provided that a man with blue eyes and a woman with brown eyes have a child, can the probability of their child to have blue eyes be calculated?


texts: How can I improve efficiency of Ecoli transformation?

texts:
I am an intern in biology institute. I have a 17.3kbp plasmid need to transform to Ecoli. But I have tried many time but have no or very few colony on LB plate.

I know large plasmid have less frequency in transformation, How can I improve chance of successful transformation?

Thanks everyone.


texts: Identify this roadside plant in Montserrat, Spain

texts: Photographed in April; growing abundantly on the side of a rocky path in Montserrat, Spain.  Up to maybe 1 foot (30 cm) in height.


texts: What will CD spectroscopy show when L- and D- forms of proteins are mixed?

texts: What will happen if equimolar concentration of L- and D- forms of proteins are mixed and we take the circular dichroism reading? Will the positive and negative ellipticity cancel each other out or will there be positive and negative ellipticity of identical magnitude?


texts: What is the difference between a predator and a parasite?

texts:
A human encountering a tiger or a malaria plasmodium is likely to suffer, and the tiger/plasmodium is likely to gain from the transaction. Not necessarily a good example, and I am aware that a successful parasite avoids prematurely killing its host, but I can't see any fundamental difference.

Of course it's like pornography: "we know it when we see it". But is there a formal, generally-accepted distinction?


texts: High protein turnover rate and protease inhibitors?

texts:
I work with mice, and I want to see what happens to some specific proteins in the mouse brain after IL-1b injection (intracerebroventricular).

I have a problem: when I measure the mRNA and protein levels, I see that there are some differences between them.

It can be like:  mRNA (upregulated)  Protein (no difference)

Is it possible that these proteins have a high turnover rate? If so, how can I prevent that?

Can I (if it is possible) inject (intracerebroventricular) IL-1b mixed with protease inhibitors?


texts: How many mutated genes from a complementation test?

texts: With 1, 3, and 5 being defective together, that means they are on the same gene. 3 and 5 are defective together too, meaning they are on the same gene as 1. Why does this slide say that there are 3 mutated genes? I must be missing something, I don't think I understand something.


texts:
This guy was found in central Virginia, under a flower pot. He's about 3 inches long, because part of his tail is either missing or it's just short. He looked dried out, so of course I wet my hand, scooped him into a small container, and moved him to our birdbath (which is on the ground and had been recently rinsed so the ground was plenty moist). I ran my hand (still wet) over his back and he seemed happier and started moving around.
However, I can't seem to find on Google just what kind of salamander he is. The VA Herpetological Society has an entry for a Jefferson Salamander, but those are only found in North/West VA. Attached is a picture of him (blurry, sorry) when I found him. I have a video of him coming out of the container and going under the leaves next to the birdbath, but it's too big of a file to put on here. Instead, here is a link to the file in my Google Drive: Salamander
Edit: I checked some pictures I had of him, and he has five toes on his hind legs. He is a dark gray-brown with faint mottling and a semi-light underbelly. Sorry that I didn't say this earlier. Hope this helps!
Can anyone identify him?


texts: Can all animals of the same species crossbreed?

texts:
For example, take Canis lupus, the species of dog and wolf. Within their species, can all dog and wolf types crossbreed? We can forget the logistics and assume this is all done through artificial insemination or in vitro methods (let's assume that the in vitro methods would be feasible).

If yes to the main question, does cross-breeding stop at the species class, or does cross-breeding extend across other taxonomic classes? From what I gathered, the taxonomic classes seem somewhat loose in their definitions. Perhaps I should ask, is there a rule "in general" to cross-breeding?

Let me know if this question ought to be refined in any way.


texts: Is it possible for an anti-cancer monoclonal antibody to target the two repressor domains in the N and C terminal of the TBX3 protein ?


texts: What are the effects of buffer on genomic DNA shearing by sonication?

texts:
Expt: I have isolated genomic DNA from LNCaP cells and would like to crosslink a small molecule (Chem-seq) to the DNA.  The small molecule is an alkylator so it will crosslink DNA on its own.  The buffer I am using for the crosslinking is TKMC (10 mM Tris-HCl [pH 7], 10 mM KCl, 10 mM MgCl2, 5 mM CaCl2).  After crosslinking I want to fragment the genome to 100 - 600 bp (300-400 bp average).  I am using a Bioruptor 300.

Question:  Should the TKMC buffer be sufficient for sonication?  Most references I have found use TE buffer (pH 7.5 - 8), and I can't find a reference using TKMC.

More info:  I tried a direct comparison between the two buffers (TKMC v TE pH8) and the TE buffer seems to fragment to smaller sizes compared to the TKMC buffer.

For example: Biorupter 300, Low setting, 1 cycle = 30/30 ON/OFF @ 3 C, 5 ng/uL DNA in 300 uL

average frag size @ 30 cycles: TE = 350bp, TKMC = 500bp

Any suggestions?  Using TE buffer for my alkylation crosslinking would not work due to presence of EDTA.  Should I play around with the cycle ON/OFF times?

Any help would be awesome!  Thanks.

UPDATE:

After running a comparison between TKMC, TKMC + 1mM EDTA, TKMC + 10 mM EDTA there was a slight tightening up of the fragment range as I added EDTA.  In addition, the fragment range (sizes) was smaller when EDTA was added (compared to TKMC w/o EDTA, after the same number of cycles).  The results were not drastic but there was indeed a noticeable effect on fragment size and range.  I will proceed with adding EDTA before sonication.  Thank you for your suggestions!


texts:
Following my answer to this question, a debate ensued on whether the loss in population of one species (namely red squirrels) due to its lesser resistance to a pathogen brought by a competing species (namely squirrel parapoxvirus and grey squirrel) should be labelled as a result of interspecies competition or not. Here I will try to state it as a question with in a more general setting. I'll give my own answer to it, and would welcome other views on the issue.

Assume the following: Species $A$ lives in a closed ecosytem and has reached carrying capacity $A=M_A$. At time $0$, a new species $B$ is introduced which is in competition with $A$, and additionally bears a pathogen to which it is resistant but which causes a high lethality rate in $A$.

It is observed that $A$ dimishes while $B$ thrives. Can we necessarily ascribe it to interspecific competition?


texts: What's the explanation for those shivers/shudders that happen at random times?

texts:
They happen at any time, presenting as a sudden urge to shiver/shudder all at once. It originates in the neck and shoulders, feels like instant gooosebumps then out of total reflex shoulders roll back and neck cringes. Happens every couple of months and comes out of nowhere, then gone without a trace.

I have read about myoclonic jerks but this doesn't sound the same.

Where do these impulses come from and what's the physiological explanation?


texts: How long can a plant generate oxygen from its own carbon dioxide, produced during nighttime?

texts:
I recently bought one of these miracle fruit plants (Synsepalum dulcificum).  Since they are of tropic origin, they need higher humidity and temperature as we have it here in Austria. So I decided to cover it in a transparent plastic bag, together with a small water basin, in order to maintain better conditions.

Assuming the bag is absolutely gas-tight, allowing no diffusion, my question is:

For how long could the plant generate $\ce{O2}$ from its own $\ce{CO2}$, produced during night? And as a little subquestion: Will the plant eventually run out of oxygen at night?

I know there are no exact answers to this, so an rough approximation is more than enough for me.

Just to give you better notion of my experimental conditions:

enclosed gas volume: ~ 3 L
(onesided) leaf surface area: ~ 0.5 dm$^2$
temperature: ~ 15$-$25 °C


texts: Can people with paralyzed eye muscles see?

texts:
As far as I am aware, the saccades of the eye are central to visual perception. If the eye is held still, the human stops seeing, even if light is reaching the retina and the visual pathway is intact.

But we recently had a question on UX.stackexchange about possible improvements to a visual+EEG interface used for communication with locked-in patients. The designer asking it mentioned that eye tracking devices are unlikely to work, because the patients' eyes can't move. This surprised me, as I would have thought that the patients must be able to move their eyes if they are able to read the device's screen. But I have never had contact with a locked-in person, and assume that the asker knew more about them than I do.

So, are there situations in which a human's eye muscles are paralyzed, so the eyeballs cannot be moved in their orbits, but this human still has visual perception and can mentally process information in his/her field of view?


texts: what will be the effect of cockroach bite?

texts:
I know the cockroaches are creepy for humans. But I want to know why humans are afraid of cockroaches and what will be the effect of there bite on my body. Can I touch them or if they walk over my foot is safe for me!

Are they toxic like snake or scorpion?
How they bite us?
What will be the effect if more than one cockroaches bite me?
Do I still get any disease if they don't bite me but present in my house?

There is already a question related to cockroaches bite on this form but it's about cockroaches lay eggs or not while biting and it doesn't explain the possible effects of the bite.


texts:
So I'm sitting in my office and all of a sudden a small spider is gliding down on a web string from the ceiling, right in front of my eyes, and down onto my desk. It proceeds to make a few awkward movements which looked like it was having problems correctly coordinating its legs. Then it flipped on the back and had its legs curled up (like it was dying).

A few seconds later it suddenly started moving with the awkward movements (like it was trying to walk) for a few seconds before collapsing again. It's been doing this on and off about 3 to 4 times. As far as I can tell, the unconscious periods are becoming longer and the waking periods shorter.

What's happening here? Is it dying (of stress / bitten by a female spider / old age) ?

Edit: The whole process has now been going on for over 30 minutes. During the times it moves, it looks like it cannot use the foremost pair of legs. Here are two pictures of the (really tiny) spider with a shopping cart token coin for scale:


texts: Why does the open tree of life have 2600 species of rose?

texts:
The open tree of life has 2754 species and subspecies with the prefix Rosa.

Wiki says:

  There is significant disagreement over the number of true rose
  species. Some species are so similar that they could easily be
  considered variations of a single species. Lists of rose species
  usually show between 100 and 150.

The thing is that a subspecies in the open tree taxonomy (OTT) should be written with a different latin name, and I can find at least 400 OTT rosa that are listed as individual species and not subspecies.

Is the OTT not very coherent in terms of accepted species?


texts: What if we blend hydras to form a soup. will they still regenerate to form new individuals?

texts: Hydras can regenerate if cut into pieces. But if we take a pound of alive hydras in a blender/grinder and blend/grind them to form a jelly like liquid made of hydras where we have finely blended them, then will this soup turn into millions of hydras or they will die and rot


texts: Is it possible to isolate cells harboring a specific DNA sequence?

texts:
Suppose on cell subpopulation harbours within its genome a specific DNA sequence that do not exist in other cell subpopulations. Is it technically possible to isolate such subpopulation ? and if yes, how ?

Some additional information about the cells. All different subpopulations are B-cells. But only one of these subpopulation harbors a specific DNA sequence. We do not think that this sequence is transcribed, and if so in a very lowly expressed manner. We also know that this sequence is only present in one of the two alleles. The main idea of this experiment is to follow this subpopulation at different time points. As the relative abundance of this subpopulation compared to the whole B-cell population is low, we wanted to isolate them in order to study them (DNA mutation, RNA expresion, etc...)

Thanks


texts: qPCR: Huge variation in fold change of genes between biological replicates

texts:
I am trying to validate my RNAseq data by doing qpcr for which I am looking at the fold change of few genes across various timepoints of treatment conditions. I am getting huge amount of variation (in thousand folds ) in my biological replicates. I thought may be it is due to genomic DNA contamination so thats why I repeated all my experiment and did DNase treatment twice but still I am having such variations. I am using two reference genes EF and GAPDH and I also have variations in the Ct values of reference genes across various timepoints. I will really appreciate it if you could suggest me with possible problems and solutions.

Thank you, Ambika


texts: Why have parasites not evolved to be harmless?

texts:
I have yet to understand why so many viruses or bacteria haven't evolved to be harmless (specifically, I don't know of any harmless virus). I think it would be greatly beneficial for a virus to control his population and use natural transfer channels that dont cause discomfort(like feces), since it would be allowed to stay in an organism indefinitely and would have a lifetime channel for transmission, hopefully getting to be the most common strain.

So, why have viruses not evolved to be harmless to their hosts?


texts: What is the physiological function of the CoV-2 targeted ACE2-Mas receptor pathway on lung/nasal epithelial cells?

texts:
CoV-2 targets ACE2 receptor on epithelial cells, pneumocytes, as well as nasal cells which seem to be cells of the nervous system (loss of smell is a symptom of Covid).
ACE2-Receptor is rather well known for its role in blood pressure regulation.
Much less seems to be known about the role of ACE2 as a receptor of cells of pneumocytes of the lung, alternatively of nasal nerve cells (expressing neuropilin as "marker"; very new reports).
Considering that CoV-2's destruction of ACE2-cells leads to a loss of angiotensin 1-7 and its action  on  Mas-receptor, what is the function of MAS-receptor signaling not primarily in blood pressure regulation but within the context of epithelia of lung, airways and nerve cell's of the nose? What physiological function gets lost if CoV-2 destroys ACE2-cells of the lung and nose epithelia?
Refering to blood pressure:
AC Simões e Silva et al
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682698/
"Most available evidence supports a counter-regulatory role for Ang-(1-7) by opposing many actions of Ang II on AT1 receptors, especially vasoconstriction and proliferation. Many studies have now shown that Ang-(1-7) by acting via Mas receptor exerts inhibitory effects on inflammation and on vascular and cellular growth mechanisms."
Refering to asthma as related to Covid because of dry cough as a sypmtom
El-Hashim at al.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402818/
"Angiotensin-(1–7) [Ang-(1–7)] has anti-inflammatory effects in models of cardiovascular disease and arthritis, but its effects in asthma are unknown."


texts:
Currently playing with some ideas for a project and needed some guidance. I am wondering, both in Drosophila melanogaster and in general, is the amount of heterochromatin a cell/nucleus can produce limited/consistent or variable?

Does one cell in a D. melanogaster produce a similar amount of heterochromatin as another cell in the same fly or another fly (assuming same conditions - environment etc.) or is the heterochromatin production quite variable? How is heterochromatin production regulated?


texts:
I am not a biologist - my background is in quantitative sciences, and I am trying to answer a rather quantitative question:
How much oxygen does a brain consume?
This however raises many sub-questions of purely biological nature:

How is the brain supplied by oxygen? (My naive understanding is that lungs tie oxygen to hamoglobin, which is then carried by blood to cells, which then ingest the oxygen, converting it to ATF. Is this correct? Does this apply to neurons as well?)
How much energy a neuron or the whole brain consumes per unit time? (e.g., per hour, in energy units or oxygen content)

I will appreciate explanations in laymen terms or references to accessible literature.


texts: Is the complement system a part of innate or adaptive immunity

texts:
I've been reading about the complement system, as part of the human immune system. The complement system is introduced as part of the article on innate immunity on Wikipedia. This classification makes obvious sense in the case of the alternative pathway, which is obviously not dependent on any specific pathogen.

However, I'm confused about whether this is an appropriate classification for the classical pathway (and, therefore, the system writ large) since the classical pathway is activated by antigen:antibody complexes and only by certain antibody isotypes (IgG and IgM). It is, therefore, to some extent pathogen specific and it is also, clearly, activated by and dependent upon the humoral immune response (generally classed as part of adaptive immunity).

So, in short, is it best to classify the complement system as part of the innate immunity (and, if so, why is that?), or would it be better to restrict ourselves to the observation that it is, to a greater or lesser extent, part of both types of immunity?


texts: Why do most negatively charged phospholipids concentrate in the inner leaftlet?

texts:
Due to the asymmetry of the lipid membrane, negatively charged phospholipids such as phosphatidylserine, phosphatidylinositol are concentrated in the inner leaflet, creating a different charge distribution between the two leaflets.
Why do most of the negatively charged phospholipids concentrate in the inner leaflet?


texts:
How much time is needed for the fermentation to acetic acid production cycle, and the conversion of apple vinegar in a sealed container incubated at 37 °C?
Should be in the fully closed?
What is right yeast?
I do it with powder, grated apple in a plastic soda bottle and I add a few peas and a slice of bread. I am waiting for make that.
If you have a better idea on what to do to get a good apple cider vinegar produce in my own house.


texts: What is the relationship between DNA molecules and the chromosomes?

texts:
Regarding the human genome, if the DNA molecule is two continuous strands, with each gene occupying a segment in it, and there are 46 chromosomes each with some genes, where is the physical boundary of each gene?

My understanding of a molecule is a collection of atoms bound together by covalent bonds thus giving the substance its properties.

My reading so far gives me the understanding that the nucleus of a cell contains DNA, whose molecule is that famous double helix. At the same time, I read that the genes are packed into 46 chromosomes. This got me confused. How is the DNA molecule split into 46 parts?


texts: Which frequency of UV light damages DNA?

texts: I have read that UV light can damage pure DNA (DNA that has been extracted and purified). Is there a particular frequency threshold where this damage occurs or is it more of a gradient where the high frequency, the more damage. I want to understand how much damage light can do at what frequencies.


texts: How do muscle cells synthesize glycogen?

texts: Hexokinase enzyme is present in all cells (including muscle cells) and can be suppressed by excessive G-6-P product. So that's why in the liver, glucokinase can act on glucose without inhibition of it despite excessive G-6-P product; that's why it can generate glycogen and not let excessive glucose flow back in bloodstream. My question is then: why muscle cells can generate glycogen despite having HK instead of GK? Because as i said above, HK activity is dependent on intracellular glucose level, and cannot phosphorylate glucose to hold it inside the cell. So glucose enters back to bloodstream and prevents the synthesis of glycogen?


texts: Method for preparation of LB agar plates with Ag+?

texts:
I need a method for preparing LB agar plates with 1 mM concentration of AgNO3.
I can not seem to find a method online, does anyone know of one that I could use?

Here are my main questions regarding the method:

a. Do I add the silver before or after I autoclave?

b. do I add the silver in a liquid form for powder?

Thanks.


texts: What does the 4DTv (four-fold synonymous) mean?

texts:
I saw this sentence "4DTv is the transversion rate at fourfold synonymous codon positions, and ranged from zero (for recently duplicated paralogs) to ~0.5 (for paralogs derived from an ancient evolutionary past)." at this paper and another paper.

I have searched 4DTv or four-fold synonymous on google, but I did not find the answers showed at the following lines.

And my questions:

(1) Does the value of 4DTv range from 0 to 0.5?

(2) Why 4DTv closed to 0.5 indicate that an ancient evolutionary was happended?


texts:
In India, there is a recent outbreak of this disease after many consumed lychees.
Many people link this to lychee's "toxins".
I'm not a biology major hence can't elaborate further on this, but here are some links.

Link 1

Link 2

Here is another that claims that lychees must not be consumed empty stomach .

Link 3


texts: Is solving cancer required in order to avoid aging?

texts:
When the telomerase enzyme is not active the telomere shortens every time the cell duplicates leading to a reproductive limit (Hayflicks limit).
On one hand this is a believed reason for aging. On the other hand this makes a mutated cell more difficult to acquire cancer, since in order to become cancerous, it would need to mutate such that the telomere enzyme becomes active.

The telomere enzyme is not active in most human cells.
Therefore activating the telomerase enzyme in somatic (body) cells could theoretically decrease aging but would also increase the risk of cancer.

Am I right to assume that in order to avoid aging of humans one would first need to "solve cancer"?


texts: I want to know more about positive feedback in gene regulation and to know the similarity and differences between positive and negative feedbacks.


texts: Why digest proteins into peptides for Liquid Chromatography - Mass Spectrometry?

texts:
Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides  so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is the problem of infering the original protein from its constituent peptides.
Why is this digestion step needed when you have to go back to protein level ? Is it just technological limitation?


texts:
The title of this question is Google suggestion verbatim, when I tried to write it. Yet, I found no answer specifically for Turkish hazelnuts.

Turkish hazelnut is a tree and it's fruit looks different from normal hazelnuts growing on hazelnut shrubs.

One such tree is planted close to my house, so I was wondering if I could eat all the nuts on the ground.


texts: Why are the genomes of Humans 99.5% the same?

texts:
Human's DNA sequence is said to be roughly 99.5% equal. As far as I understand, this means that if I walked up to you and compared our DNA, the sequence of base pairs would be 99.5% the same.

My question is: Why is there only 0.5% variation in our DNA? I can think of two reasons:

For some reason, the other 99.5% (roughly) is locked in place. These sections, if changed, either result in us not being 'human', or simply get some sort of genetic disease and so aren't very good mutations.
There hasn't been enough time. I remember hearing that all humans have a common ancestor some long time ago. If that's the case, perhaps over time only about 0.5% of our DNA has had time to randomly mutate, and if we wait a really really really long time, more and more of our DNA will mutate, and we will become 'less like each other'.

Or am I completely misunderstanding the situation? I didn't take biology in high school so answers should be simple please.


texts: How many cells are in prophase on this onion root tip slide?

texts:
In the following image, I have to identify the cells in the different phases (not counting the cells that are too faded to see), and it's fairly easy to identify metaphase, anaphase, and telophase, but I'm not sure I'm doing it right for prophase vs. interphase.

I try to see if there's a nucleolus or not, but sometimes it's difficult. When I counted, I got 7 cells in prophase. Is this close to what you guys see or am I way off?

Thanks!


texts: What is the correct classification of population groups of homo sapiens?

texts: The classification system of the United States census into various races of humans is a bad way to classify population groups of humans, because both East Asians and South Asians are classified the same, yet they look different and are genetically distinct. So, has anyone proposed a more scientifically accurate classification of population groups of homo sapiens?


texts: If hermaphrodite C. elegans can reproduce with females?

texts: C. elegans can self fertilize, or they can mate with males. But are they able to mate with females? Or is there some kind of morphological barrier that prevents that?


texts: Help identify this insect with a fan tail

texts: I am trying to identify this creature... I took the shot in Medellín, Colombia. It is about 1cm in size.


texts: Book recommendations: biological data analysis/error

texts:
I'm working as an undergrad in a tissue culture lab, and I have the most experience with statistics out of everyone in the lab. However, most of the knowledge I have in statistics is from my math courses which are mainly theoretical.

Does anyone have good recommendations for books on biological experimental design, data analysis, and statistical error? I'd prefer that they be specific to biology, but if there are some good general books with applications that works for me as well. I just want to get a feel for any specific knowledge I will need.


texts: Purpose of K+ channels in action potential

texts:
I understand that they serve to repolarize the neuron after the Na+  influx. What I don't understand is why this is important.

Meaning, let's say all the K+  channels disappeared. So now the potential is up near +50 mV about. It doesn't go back down quickly, because the K+  channels aren't there. Instead, we have to wait until the Na+/K+  pump can restore the proper intra-/extra- cellular balance between them. And then the neuron can fire again.

I can see that it will take longer for the potential to be restored. But don't we have to wait until the Na+  concentration is restored before we can fire again anyway? If we don't wait, wouldn't that interfere with maintaining sufficient/proper extracellular Na+ concentrations (which I would assume would have other effects)? And the same amount of time will be needed for the Na+ balance to be restored.

So what do we really gain by having a way to restore the charge differential?


texts: Besides X. morgani praedicta, are there any species whose existence was predicted before they were discovered?

texts:
The orchid A. sesquipedale has a spur so long that at the time of its discovery, no insect was known that could pollinate it.

This led Charles Darwin to predict the existence of an undiscovered moth based on the idea that the moth and the orchid had co-evolved. That moth, X. morgani praedicta, was subsequently discovered in 1903 – a triumph for early evolutionary biology.

Has it ever happened again that a species was predicted to exist before being discovered?


texts: What is the result of modifying the reagents in the Sanger method?

texts: If one of the dideoxynucleotides is omitted while using the Sanger method how would that affect the chain termination method of DNA sequencing?


texts: Bird Identification: New Delhi, April 2018

texts:
I've looked in Birds of the Indian Subcontinent (BNHS version, not Inskipp) and two phone apps and still can't find this, although I am a newbie tourist so am probably making a basic mistake. Seen today, 2018-04-07, 9:00 local time, in a New Delhi urban garden.

Maybe 25cm long. Uniform grey above, mottled grey below, grey legs with slight orange tinge. Orange-yellow bill, very slim light eye ring. I wondered about a large grey babbler, but all the pictures I can find seem less grey.

Thanks!


texts: Why does the ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process?

texts: Why does the human  ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process??Please help me with it.


texts: How does the counter-current multiplier work in the nephrons?

texts:
Why is the counter-current multiplier called like that? What is flowing in the opposite direction to the glomerular filtrate for it to be called "counter-current"?

Can you please explain the counter-current multiplier mechanism in the loop of Henle in the nephron, including details about the ascending limb, descending limb and the collecting duct?

I have searched it everywhere and I cannot find a satisfactory explanation that I can fully understand.


texts: Why might food spoil faster in Ireland than the US?

texts: An American is staying in my house for the summer and claims that food (specifically, bread and milk) spoils a lot faster here than at home in California. Is there a significant difference in chemical content (preservatives etc.), or other factors, that might explain this?


texts: Understanding the concept of a "Place Field" and the difference between place cells and grid cells

texts:
I have 3 questions that are interrelated:

After reading the proper literature on the subject, my understanding of the place field is that it's a place in space to which an animal's place cell reacts by firing. Then there might also be another place in field to which the same place cell reacts by firing. Is this understanding correct?

1.1 Why is it called place "field," what does the "field" actually imply, etymologically speaking?

1.2. The Wikipedia Grid Cell Page says that:

  By contrast, if a place cell from the rat hippocampus is examined in the same way (i.e., by placing a dot at the location of the rat's head whenever the cell emits an action potential), then the dots build up to form small clusters, but frequently there is only one cluster (one "place field") in a given environment, and even when multiple clusters are seen, there is no perceptible regularity in their arrangement.

So then what are those "clusters", i.e. I guess the place fields, are they the ones I highlighted in red on this picture (sorry, I am a very visual learner!) and also, why do they fire in clusters?

The Wikipedia Page has the following description of this picture but I am still not sure I am understanding it correctly:

  Spatial firing patterns of 8 place cells recorded from the CA1 layer of a rat. The rat ran back and forth along an elevated track, stopping at each end to eat a small food reward. Dots indicate positions where action potentials were recorded, with color indicating which neuron emitted that action potential.

The first question stems from the second and the main one I am confused about: what is actually the difference between the place cells and the grid cells, in a layman terms (beyond the obvious structural differences, i.e. that the place cells are pyramidal neurons and the grid cells fire in a hexagonal pattern)?
In terms of their functional differences, is the difference mainly in the fact that the grid cells are theoretically responsible for path integration, whereas "The place cells are thought, collectively, to act as a cognitive representation of a specific location in space, known as a cognitive map" ( O’Keefe John, 1978 ).

What is the physiological or anatomical difference between.... Available from: https://www.researchgate.net/post/What_is_the_physiological_or_anatomical_difference_between_place_cells_and_grid_cells_in_the_hippocampus [accessed Aug 16, 2017].

O'Keefe, John (1978). The Hippocampus as a Cognitive Map. ISBN 978-0198572060.


texts: Macromolecule levels in daughter cells after fission

texts:
When a prokaryote undergoes binary fission, how are the non-DNA macromolecules distributed between the two daughter cells? This is motivated by comments on a previous question and a G+ discussion. I am primarily interested in explicit mathematical models.

Naive model
For DNA, each copy is attached to a different part of the cell membrane, to ensure each of the daughters receives a copy. As far as I understand, there isn't such specific mechanism in place for other macromolecules. If we are allowed to assume that non-DNA macromolecules are distributed uniformly through the parent cell than this would mean the two daughter cells would receive half the proteins within statistical fluctuation. This has a specific meaning: if there are $N$ molecules of type A in the parent, then the difference in number of type A molecules in the two daughters after fission will be on the order of $\sqrt{N}$.
However, this model might be wrong. For instance, as the new cell-wall is being formed it could have in it specific pumps that either balance the protein levels below chance (producing an average difference lower than $\sqrt{N}$) or to create asymmetries higher than chance. Altenrnatively, the initial distribution of macromolecules in the parent could be far from symmetric for some other reasons. Which is the case?
If the naive model is correct, is there experimental evidence explicitly showing this?


texts: Does the Rayleigh formula apply to electron microscopes or only light microscopes?

texts:
I am asked to determine the resolving power of both a TEM (transmission electron microscope) and a SEM (scanning electron microscope) and given the Rayleigh formula below.

$$Resolution=\frac{0.61\lambda}{N.A.}$$
Where $\lambda=0.0039$nm since the wavelength of an electron is $0.039$ angstroms and $1Å=0.1$nm.

I am also told that the N.A. the numerical aperture for the TEM is $0.01$

So, $$Resolution=\frac{0.61(0.0039nm)}{0.01}=0.24nm$$

For the SEM I am not given the N.A. but I am told that the resolution is $10$nm

My problem is if I use the Rayleigh formula  $$Resolution=\frac{0.61\lambda}{N.A.}=10nm$$ I get $$N.A.=0.0002379$$ Which would imply that the aperture for the SEM is greater than that of TEM since N.A for TEM is $0.01$ and SEM is $0.00023$ $$0.01>0.00023$$.

My problem is that I'm told the greater the aperture (smaller value of aperture) the greater the resolution but as you can see from the equations above this doesn't seem to make sense, The only explanation I can think of is that the Rayleigh formula does not apply to electron microscopes. Any advice would be greatly appreciated thank you.


texts:
I was recently fascinated when I learned about polysaccharides (I am a biology newbie) and was wondering about some of their properties. After doing some googling I was unable to find any information regarding this scenario.
This is purely theoretical, I am not insane enough to actually try this.

If my only source of carbohydrates was ingestion of pure glycogen,
could I live healthily? (assuming I obtain all other necessities for
life)
Approximately how many grams of glycogen would I need to live for a
week (assuming I weigh 150 lbs)? Is this even possible to calculate?
What does pure glycogen taste like?


texts:
Non-allelic or non-alletic

I stumbled across the term in my Human Genetics textbook. It didn't explain it there, and a quick google search only showed scientific papers that refer to 'recombinations with non-allelic genes' without explaining what they are.


texts: Excluding the Exon, What Does the Rest of the Genome Do?

texts:
The exon is the portion of the genome that encodes protein synthesis, if I understand correctly.

But, this exon is apparently less than 5% of the genome.

So, what does the rest of the genome do?


texts:
In relation to microbiology and the naming of the various areas of the plant as it relates to microbial inhabitance, I am confused as to the difference between the terms endorhiza and rhizosphere.

In this case I see rhizosphere referred simply to as the 'roots', but in this case I also see endorhiza explained simply as 'roots' also.

However in this case, I see a further explanation for endorhiza (which does make sense etymologically): 'internal root tissues'.

Does this mean endorhiza is be a sub-term for the area inside the roots, and the larger area of the rhizome in general represented by rhizosphere, and that is the difference?


texts: SARS-CoV-2 proteome: is the SPIKE protein not an issue for a hospitalized patient?

texts:
I am performing molecular docking of ligands using the modeled proteome of SARS-Cov-2. My question is, after a patient is hospitalized, is the SPIKE protein not really an issue anymore, since its role for binding with ACE2 has already been carried out?  Or, is SPIKE an ongoing issue that is not only an early event in the causal pathway?

Rationale is that SPIKE is quite large, and takes more than a minute of run-time per ligand -- thinking about excluding it to speed up runs.  NSP15 is also another "larger" protein, but I know NSPs are translated inside infected cells - so should be included in docking.


texts:
Here is a typical EEG reading:

(source: frontalcortex.com)
I understand that each row corresponds to the signal read between two sensors on a standard 10-20 (or 10-5) distribution setup (e.g. C3-P3).
What I'm missing here is: what waves are we actually seeing here - alpha, beta, etc.? Or do EEGs not really contain wave types, and instead just show voltage differentials between sensors?


texts:
How to differentiate between 2 toads one of them result of artificial parthenogenesis and the other from renucleation?

I answered that the toad resulting from artificial parthenogensis is identical to the mother

While the other toad which result from renucleation is identical to that which the nucleus was taken from

My answer is so unrealistic and I can't find any other answer so I though I could use some help.


texts:
I don't know if the felines got originated on America or on Africa, but I do know there are species of cat in America and Africa that belong to the same family and genus (Felidae & Panthera).

How did the evolution of these animals beat the vastness of the ocean? The same way as Homo sapiens? Or did they coexisted before Pangea split?


texts: Do all signalling pathways have something that can inhibit them? If the signal pathway is benefitial  and it is inhibited would the inhibitor be caused by a biological problem?  Are all inhibitors controlled by some subcellular  mechanism?


texts: Why do we have two sets of teeth? Why do earlier shed and new teeth replace them? In humans, kids do not have any need for replacement of the teeth. Why don't the milk teeth grow themselves? Or why don't we have a set of small permanent teeth as our first teeth?


texts: given that micro tubules are involved in so many processes in cells, it seems that such a complex "highway" would require some advanced underlying mechanism to orchestrate its assembly in a direction needed for the cell, such as towards a kinetochore. multiple search results on google and textbooks simply just state polymerization as is without explaining how these events happen. so how are microtubules polymerized and how is this polymerization oriented directionally ?


texts: Is the increased/decreased enzyme activity (tyrosinase) caused by an environmental factor (UV radiation) considered to be gene expression?

texts: My AP Bio assignment asks that I research the effects of UV radiation on melanin production, but the directions and questions suggest that UV radiation influences gene expression. From what I could find, such as on this university site or this abstract on NCBI, it seems that UV-B radiation directly affects the enzyme tyrosinase, which is responsible for producing melanin from tyrosine. So here is what I'm wondering: is our lesson wrong in stating that UV radiation affects gene expression, since it seems that it actually affects enzyme activity?


texts:
So this question is part math, part biology, but I'm asking about the biology part here (or maybe the chemistry part).
Basically I'm asking about my attempt to calculate the possible brightness per unit mass of GFP, and I'm asking if it makes sense.  Here's what I've done:
(I'm ignoring the quantum yield which should be 0.8):

GFP molar mass=27,000 amus (27 kDa)

1 mole weighs 27 kilograms

therefore 1 gram=(6.02*10^23)/27000=2*10^19 molecules of GFP

Assumption that I'm asking about; I'm assuming in this calculation that GFP releases light from one excited electron (roughly 2.5 electron volts).  How many electrons are excited in GFP fluorescence?

(2*10^19)/(6*10^18), (the number of electrons in a Coulomb/amp)=3.3 amps

Brightness=2.5*3.3
=8.25 joules per gram

From Researchgate:
" The time constant of the fast, pH-dependent chemical process decreases with pH from 300 microseconds at pH 7 to 45 microseconds at pH 5..."
Given that's the case, that's roughly 3000 emissions (or 3333) per second (at 7 Ph), so
1 gram of GFP would have a maximum brightness of 24,750 watts, if there was enough UV light, or 25 watts for a milligram.
That sounds plausible, although high.  Does that make sense, or what part of this calculation was wrong?


texts: Can the liver prioritize it's metabolizing potential?

texts:
Let's assume we have two toxins - one of which is routinely metabolized by the liver, and the other is new to the organism (consider for example alcohol in a heavy drinker and any other drug that is taken for the first time) and they are administered at once.
Does the liver have any way to prioritize metabolizing either of these substances or does it happen simultaneously for both?


texts: What is this microscopic image from Peter Gabriel's New Blood album cover?

texts: This image appears on the cover of Peter Gabriel's album New Blood.  It appears to be a photograph of some microscopic biological cell.  But it doesn't look like a blood cell to me.   What kind of cell is it?


texts:
E. coli lives in lower intestine. But exactly where can we find E. coli, and where is there none (or a really small amount) of it?
I need the exact names of parts of the lower intestine where we can find E. coli.


texts:
Many eukaryotic organisms like yeasts, hydras , planarias, plants etc reproduce asexually.

Replication of End of linear DNA pose a limit to the number of cell divisions.

My question : Do asexually reproducing organisms have telomerase in all their cells ? Is the telomerase activated at specific times at specific places ?

If they don't, how can they reproduce infinitely ?


texts: Does the corpus callosum have a significant relationship with motor memories/ muscle memories?

texts: With the corpus callosum located in the cerebrum, and motor memories having a closer relationship to the cerebellum (which I'm not quite sure about), is there a significant relationship between the corpus callosum and motor memories? Do motor memories process in one hemisphere and are then shared with the other- if so, how? Thank you so much for your time and patience!


texts: How can some residues in the active site of enzymes be protonated with a pKa < 7?

texts:
It is reported in many papers, that some residues in the active site of enzymes need to be protonated to get functional enzyme, where these residues have a low pKa (for let us say 5).

How can that happen in the physiological conditions (with pH=~7.4)?

It is mentioned that a raise in the pKa value is happening during the catalytic activity to get that protonation state. But how is that happening?

Here is a publication where this protonation and pKa raising is described.

https://www.ncbi.nlm.nih.gov/pubmed/7306491

  This conclusion is confirmed by the result that a group with a pK value of 6.7 must be protonated for the binding of methotrexate. It is proposed that the binding involves the formation with N-5 of dihydrofolate or N-1 of methotrexate of a hydrogen bond which has considerable ionic character and which lies within a hydrophobic environment. Further, it is suggested that the same hydrogen acts as an auxiliary catalyst which facilitates hydride transfer from NADPH to dihydrofolate for its conversion to tetrahydrofolate. Evidence to support this suggestion comes from the finding that the V profile is similar to the V/K profile except that the pK of the group which must be protonated for maximum enzyme activity is shifted upward by about 2 pH units. Such an increase in a pK value is consistent with the formation of a hydrogen ionic bond in the ternary enzyme-NADPH-dihydrofolate complex. The results of inactivation experiments with trinitrobenzenesulfonate appear to indicate that a lysine residue is necessary to maintain the enzyme in its active conformation.


texts: The fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%?

texts:
I would appreciate help in understanding the meaning, logic, and, in particular, how to interpret the phrase:

The fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%

I could ask numerous question regarding the biology (including what happens to the rest of the genome, and positive selection) and formal logic of this statement, but maybe I could impose, and just leave it to whomever kindly replies.
This remark comes from the abstract of Grauer & al. "On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE"
And the Abstract itself:
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
Thanks


texts: Why is the ability to drink salt water so rare in land-animals?

texts:
Apparently, some species are capable of drinking salt water, like the sea lion and otter.

But given how rare fresh water is, and how abundant salt water is, why have more land animals not evolved to drink it? Why are kidneys capable of handling such a thing so uncommon?

I understand that evolution doesn't necessarily always do what's most efficient on a macro scale, but this drives me nuts.

So many animals live less than a five minute walk from the shores of an ocean, and such water is so abundant that they'd never be thirsty.


texts: Does size correlate with sensory abilities?

texts:
On average, do smaller animals have senses inferior to those of bigger animals?  I ask because it seems like a somewhat logical assumption: smaller eyes would in theory collect less light, and smaller ears would in theory collect less sound.

Or is size just irrelevant?


texts: Identification of beetle: black with orange stripe and 2 orange dots

texts: I found the following beetle in a wooded area in Essen, Belgium. Does anybody know what species it is? Thanks in advance.