texts: What is the best way to calculate the biological diversity of samples from bacterial/viral OTU tables?

texts:
I have a few large OTU tables of bacterial and viral datasets. The samples are across different sites and times.

I would like to visualise the community 'diversity' across the times for which I have data. For example it would be interesting to see if community diversity peaks in the summer months and falls in the winter months- in a repeating pattern.

I have not come across much advice or literature which looks at looking at diversity for large OTU datasets. Considering the OTUs are essentially arbitrary and that there are thousands of them, what is the best way to calculate and visualise the each samples diversity?

With the vegan package on R it is quite easy to calculate the Shannon/Simpsons diversity index for an OTU table. Can you simply use this on a 'raw' table of OTUs?


texts: Why Lungs can't work in water and gills can't work in air?

texts:
Animals with lungs (such as most terrestrial mammals) cannot breathe if submerged in water, and soon suffocate.
Whereas, fish can variously breathe air (at least for few-hours, as some fish frequently need to get air periodically), including those that are bigger than a human (say sharks).
But why? Do fish require less oxygen than lunged terrestrial-animals, despite being active and variously engaging in activities like predation? (so that uptaking only dissolved oxygen, and probably less surface area of gill than lung-alveoli is enough for them?)


texts: Why have ground beetles never evolved the ability to get back up?

texts: This may seem like a funny question, but I've seen so many ground beetles upside down on the floor and wondered why they've never evolved the ability to get back up. Wouldn't something like this drastically increase their survivability?


texts: If the top epidermal layer is burned away, what is it replaced with?

texts:
If the squamous (top) layer of epidermis, or skin, is burned or damaged in another way, will it then be replaced by the next layer of below?

Also, from where does the basal membrane originate? Does it regenerate from a different layer of cells?


texts: Measuring optical density with/without re-suspending cells

texts:
When measuring absorbance using a plate reader, is it necessary (or better) to resuspend the culture if the plate has been sitting still for 1-2 days?

While this could be a good physics question, I am more interested in the correct biological assay technique.

--

The two options are:

1) growing microbes in a plate inside a static incubator and then put the plate in a plate reader without agitating the liquid

2) growing microbes in a plate inside a static incubator and then put the plate in a plate reader after agitating the liquid

In option 2, the agitation could be achieved by gently pipeting the liquid up and down a few times...


texts: what happens when you put enhancer and caat box in prokaryotes


texts: Proof of the equivalence between two ways of defining ESS

texts:
Background

Two common ways of defining what an Evolutionary Stable Strategy (ESS) are:

First definition:
Consider a population composed of populations playing two strategies, $\mathbf{p}$ and $\mathbf{q}$.
Let us denote $W(\mathbf{p})$ the average fitness of the
strategy $\mathbf{p}$. A population consisting of individuals playing $\mathbf{p}$ will be an ESS if, whenever a small amount of deviant individuals playing $\mathbf{q}$, the old type $\mathbf{p}$ fares batter than the newcomers $\mathbf{q}$. This means that for all
$\mathbf{p}\neq \mathbf{q}$,
\begin{equation}
  W(\mathbf{p}) > W (\mathbf{q})
\end{equation}

Second definition: $E(\mathbf{p},\mathbf{q})$ is the payoff for $\mathbf{p}$-strategist against a $\mathbf{q}$-strategist. The strategy $\mathbf{p}$ is an ESS if and only if the following conditions are satisfied:

$E(\mathbf{p},\mathbf{p})\geq E(\mathbf{q},\mathbf{p}) \quad \forall
  \mathbf{q}$
If $\mathbf{q}\neq \mathbf{p}$ and $E(\mathbf{p},\mathbf{p}) = E(\mathbf{q},\mathbf{p})$, then
$E(\mathbf{p},\mathbf{q})> E(\mathbf{q},\mathbf{q})$

Question (shorter version)

The above two ways of defining what an ESS should be equivalent. How can I prove such an equivalence? Alternatively, do you know of a book (or a paper) that has this proof?

Question (longer version)

I understand that the first definition implies the second. According to the first definition:
\begin{align*}
   W(\mathbf{p}) - W (\mathbf{q}) &>0\\
   (1-\epsilon) [E(\mathbf{p},\mathbf{p}) - E(\mathbf{q},\mathbf{p})]
   + \epsilon [E(\mathbf{p},\mathbf{q}) - E(\mathbf{q},\mathbf{q})] &>0
 \end{align*}
where $\epsilon$ is frequency of individuals playing $\mathbf{q}$. Since $0<\epsilon<1$, if the above inequality is true, the conditions 1 and 2 in the second definition must be true. The part that I find less clear is how the second definition implies the first definition. More specifically, that if $\mathbf{p}$ is a strict Nash equilibrium (i.e., $E(\mathbf{p},\mathbf{p})> E(\mathbf{q},\mathbf{p})$), then $W(\mathbf{p}) > W (\mathbf{q})$.


texts: RNeasy Mini Kit low 260/230 ratio -- can I purify this RNA for further use?

texts:
I used Qiagen's RNeasy Mini Kit to isolate RNA from 5*10^5 C28/I2 (immortalized human chondrocytes). However, my yield is low (~25 ng/ul), but my 260/280 ratio is great (~2.3), and my 260/230 ratio is tragic (~0.06). I have already thrown the spin column away, but I would like to know 1) if I could raise my 260/230 ratio for the 40 ul of RNA I extracted, and 2) if I could precipitate the RNA out of solution so as to make a more concentrated solution.

Please let me know if further details are necessary.

Thanks!


texts: How many recombination events are there per generation in humans?

texts:
I'm looking for a reference that tells me how many recombenation events occur in humans from one generation to the next.
Assuming that the human genome is a 3.3 GigaBases long DNA sequence, how many recombination events do you find, and what is he amount of DNA exchanged?
Is it in the order of 0.1%, 1% oder 10%?


texts:
I am learning about (introductory level) biological psychology and the synapse structure came into mind. I do understand that neurotransmitters are transmitted between two neurons via the synapse structure.
What I found about neurotransmitters was that there are several types of them, including amino acid, and other stuff (I don't really know chemistry..). The problem is that, according to the following picture, neurotransmitters are transmitted across the gap. What are the chemicals in the gap at a synapse? There must be some medium that transmits neurotransmitters right?

My guess is that there is a special solution in which neurotransmitters are soluble. Any help will be appreciated. Thanks in advance!


texts: How can I fit the A595 of my unknown samples to the data?

texts:
While I was conducting the Bradford Assay experiment to determine the concentration of my unknowns, I ended up by having an A595 for my unknown samples that is higher than the A595 of the standards. How can I resolve this issue?
wishes.. Micheal.


texts: Why spin live fruit flies in centrifuge?

texts:
I was reading this article about the evolution of monarch butterflies’ resistance to cardiac glycosides: These Butterflies Evolved to Eat Poison. How Could That Have Happened?
And this passage made me curious:

The researchers put the mutant flies in a centrifuge and spun them for ten seconds. Afterward, the flies were overwhelmed by seizures for several minutes.
Ordinary flies, by contrast, immediately walked away from the laboratory carnival ride. Flies with the other two resistance mutations were also unharmed by the procedure.

Given that normal fruit flies are usually unharmed by the centrifuge, what made the researchers decide to spin the flies? I’m not a biologist, I’m a software engineer. So I’m just guessing that it might be a standard lab procedure when studying fruit flies. Assuming the researchers didn’t know the flies with mutation 122 alone would experience seizures, what do researchers usually expect to gain from spinning live flies in a centrifuge?


texts: How do the bacteria producing bacteriocins protect themselves from it?

texts: Whenever there is Col plasmid in a bacteria it will produce bacteriocins which will kill other bacteria around it. Why will the bacteriocin not kill the bacteria which has produced it? How does the Col plasmid also help protect the bacteria from its own bacteriocin?


texts: What is the diameter of the measles virus?

texts: I have searched countless studies. None have given this number. In fact there seems to be no details of any kind about the measles virus.


texts:
I am considering the evolution of plants, specifically considering the chloroplast. I am getting slightly confused and cannot seem to find the information I need to build a coherent picture in my head. Specifically, I have the following questions:

Is the defining feature of a plant cell that it has, or once had, chloroplasts? Is the group of plants all of the species which came from the single common ancestor eukaryotic cell which first acquired a photosynthesising bacterium as an endosymbiont?
In that case, the plants Alectoria sarmentosa (witch's hair lichen) and Monotropa uniflora (Indian Pipe), which are non-photosynthesising plants and do not have chlorophyll, must have some remanant of a chloroplast inside of them (unless they are not actually plants and are just plant-like fungi). My question here is, are these really plants? If so and it is true that plants are defined as all being descendant from this first photosynthesising eukaryote ancestor, then what is their 'remnant chloroplast'? I.e. what organelle do they have that used to be a chloroplast.
If it is true that there are plants which have organelles that used to be chloroplasts but not longer have chlorophyll and photosynthesise, then it is almost certainly the case that the chloroplasts carry out some function other than photosynthesis that is beneficial to the plant's survival (e.g. I know that remnant mitochondria- hydrogenosomes and mitosomes- are useful for fixing iron although they do not carry out respiration). What are the other functions of chloroplast-like organelles?


texts:
What are the differences between white and brown adipose tissue? Here are some that I have come across:

Brown Adipose Tissue                        White Adipose Tissue

Thermogenic                                 Non-thermogenic
Multilocular                                Unilocular
Relatively many mitochondria                Relatively few mitochondria
Vascularised                                Relatively few capillaries
characterized by the presence of leptin     characterized by the presence of UCP-1


texts: Are there U-rich transcriptional pause sites?

texts:
I've heard a statement in a talk that U-rich sequences cause transcriptional pausing. The intuitive explanation for this was that the UTP concentration is lower in the cell than the ATP concentration. Reducing the concentration of an educt obviously reduces the reaction rate, leading to pausing of the RNA polymerase.

After reading up on transcriptional pausing, I haven't found any literature that shares this view. The recent papers I found don't show U-rich sequences and have completely different explanations on how pausing works. Those explanations mainly concern interactions at the edges of the transcription bubble.

Now, I guess that there might be multiple mechanisms of transcriptional pausing. But I couldn't find any references in the literature to U-rich pause sites and how they could work. Is there any literature on this? Either on the fact that U-rich sequences tend to be pause sites, or that the concentration difference in NTPs leads to pausing at certain sites.


texts: How can I find the mRNA sequence for a specific prokaryotic gene?

texts:
What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts.

I've looked at various databases like NCBI Gene, Refseq or a specialized one like PRODORIC. But none of them actually contain the mRNA sequence or any information about the untranslated parts of the mRNA. Just the coding sequence itself.

Is that kind of information simply not annotated for many bacteria? I'm not looking at model organisms like E. Coli or B. subtilis, but I would have expected some information to be available.

Is there a database where I can find the actual transcript sequences for prokaryotic genes?


texts: How to transform snail shells into a fertilizer?

texts:
I heard that the chemical structure of the snail shell has elements that help in waste water treatment and in some cases as a fertilizer?

What is the process used to render snail shells into fertilizer and how effective is the derived fertilizer compared his regular peers on the market ?


texts:
Lyonization is the process in which there is inactivation of an X chromosome in females. This process is implicated in mosaic forms of turner's syndrome (in this case the altered X chromosome is Lyonised, thus allowing the normal X Chromosome to express itself).

Is Lyonization considered as a form of genetic imprinting? What is the difference between the two (if no)?
Lyonization is a random process (according to the extent of my knowledge which X chromosome is inactivated is not predicatable). Is genetic imprinting also random?
Is there any known aberration of Lyonization in males? (meaning the single X Chromosome or Y Chromosome gets silenced)


texts: Is every protein encoded by just one gene?

texts:
Beadle and Tatum proposed the “one gene, one enzyme” hypothesis in the 1940s, and this was later modified to “one gene, one protein”, i.e. that one gene codes for one protein.

Have any exceptions to this emerged subsequently? Are there single proteins, parts of which are encoded by separate genes?


texts: With humans, is being transgender innate, or caused by social factors?

texts: In humans, is being transgender something that is innate, or is it caused (or made more likely) by social factors such as their political beliefs, their religious views or their social environment?


texts: Thyroid hormone metabolism and excretion

texts:
My understanding is that hormones generated by the thyroid gland, including, for example, T4, are excreted and recirculated in the body through the digestive tract. The reason for thinking this is that bile acid sequestrants such as cholestyramine cause a lowering of serum T4. In fact, patients who have hypothyroidism are explicitly warned not to use sequestrants for this exact reason. Here is a statement from a clinical trial discussing the effect:

  The enterohepatic circulation of thyroid hormones is increased in
  thyrotoxicosis.Bile-salt sequestrants (ionic exchange resins) bind
  thyroid hormones in the intestine and thereby increase their fecal
  excretion. Based on these observations, the use of cholestyramine has
  been tried. The present study evaluates the effect of low doses of
  cholestyramine as an adjunctive therapy in the management of
  hyperthyroidism. -- clinical trial NCT00677469

Therefore, there would appear to be a metabolic pathway in which T4 is being excreted into the digestive tract and then is later re-absorbed in the lower intestine somehow.

What is this metabolic pathway? How exactly does this mechanism work? Does it have a name?

For more information on thyroid hormone sequestration see:

https://clinicaltrials.gov/ct2/show/NCT00677469

http://www.ncbi.nlm.nih.gov/pubmed/8435884


texts: Possibility and feasibility of producing designed antibodies with bacteria

texts:
As stated here it is possible to produce fragments of antibodies in bacteria and harvest them (from the medium, I guess, but I don't have access to the full article).
As it is possible to design antibodies, would it be possible and feasible to produce important antibodies large scale through bacteria like it is done for example with insulin?


texts: Why are female clones more often produced

texts: As a student of biology when ever I come by artificial cloning, I always find examples of females being cloned - Dolly the sheep, CopyCat, Daisy, etc. The only male I could see was Fibro mouse and a few more. What is the reason behind this? Is the male genome more difficult to be cloned? I am specifically looking for genetic reasons or other complications.


texts: Are there any cases of observed extreme speciation

texts: Is there an observed (direct not indirect) speciation on record showing a species shift within the span of history of recorded science?


texts:
What is the physical mechanism that causes temperature to rise during a fever? I know that somehow the hypothalamus "orders" to increase the standard body temperature regulation, and this should stimulate mitochondria to produce more ATP. Is that right?

Is this the only heating physical mechanism (through increasing production of ATP) that acts during a fever?


texts: Interaction of charged triphosphates with the ATP binding region in proteins

texts:
DNA-histone interactions involve positively charged amino acid side chains groups neutralizing the negatively charged phosphate of the sugar-phosphate backbone. Is the same true for ATP binding sites on proteins?
In most models I’ve seen, it looks like the base, adenine, is involved in the binding. But the triphosphate seems like it would bind specifically to positively charged side-chains. I Googled a bit, but I couldn’t really find any models depicting this. Does anyone know whether this is so?


texts: What are the advantages of blood's redness?

texts:
Although this page (http://evolution.berkeley.edu/evosite/evo101/IIIE5aNotadaptation.shtml) denounces the idea that blood's redness is not an adaptation, I remain inquisitive on the matter since no scientific research has been performed in studying its possible advantages.

Does anyone have any ideas on the advantages of having red blood?

Thank you for your time and effort


texts: Virus titre and copy number of integration

texts: If I need to preform a genome-wide high throughput screen using pooled shRNA library infection followed by deconvolution by deep sequencing, how would I determine the optimal infection rate at which the majority of cells only be infected with single copy of shRNA? Thanks!


texts: Does the fossil record disprove Evolution?

texts:
It is said by people opposed to Evolution, that the fossil record contradicts and disproves it. They say all the animals suddenly appeared, exploded everywhere, were fully formed, had no transitions, no gradualism, no change, and no sign of an evolutionary trend by which they could have emerged from an earlier type.

They then use these quotes to back this up from Evolutionists themselves:

"All the larger groups of animals, e.g. fishes, amphibians, reptiles, mammals seem to have appeared suddenly on the earth, spreading themselves, so to speak, in an explosive manner in their various shapes and forms. Nowhere is one able to observe or prove the transition of one species into another, variation only being possible within the species themselves" Evolutionist, Max Westenhofer as quoted in Dewar's More Difficulties, p. 94

"The evidence of Geology today is that species seem to come into existence suddenly and in full perfection, remain substantially unchanged during the terms of their existence, and pass away in full perfection. Other species take their place, apparently by substitution, not by transmutation" Geologist, Joseph Le Conte

"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology (study of fossils). In any local area, a species does not arise gradually by the steady transformation of its ancestors, it appears all at once and fully formed." -- Dr. Stephen J. Gould, Prof of Geology and Paleontology, Harvard University. Mentioned in one of his regular columns in Natural History Magazine (1977) and also in The Panda's Thumb, 1980, p. 181-182

"different species usually appear and disappear from the record without showing the transitions that Darwin postulated -- we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn't changed much -- We have fewer examples of evolutionary transitions than we had in Darwins' time" Dr. David Raup, a paleontologist at the Field Museum of Natural History in Chicago. Field Museum Natural History Bulletin 50:22- 29

"Evolution requires intermediate forms between species and paleontology does not provide them" Dr. David B. Kitts, Paleontologist

"The known fossil record fails to document a single example of phyletic evolution accomplishing a major morphologic transition" Evolutionist, Dr. Steven M. Stanley

"The record certainly did not reveal gradual transformations of structure in the course of time. On the contrary, it showed that species generally remained constant throughout their history. New types or classes seemed to appear fully formed, with no sign of an evolutionary trend by which they could have emerged from an earlier type." Bowler, 'Evolution: The History of an Idea', 1984, p. 187

"We are still in the dark about the origin of most major groups of organisms. They appear in the fossil record as Athena did from the head of Zeus -- full-blown and raring to go, in contradiction to Darwin's depiction of evolution as resulting from the gradual accumulation of countless infinitesimally minute variations, which, in turn, demands that the fossil record preserve an unbroken chain of transitional forms." Jeffrey H. Schwartz, Sudden Origins: Fossils, Genes, and the Emergence of Species (New York: John Wiley & Sons, 1999)

Is this true? If not, why not? Does the fossil record prove or disprove Evolution?


texts: simple explanation of a crispr screen vs pooled crispr screen?

texts:
I'm familiar with how CRISPR works to make either knockdown or amplification effects for a single gene because you can make precision cuts.

What exactly does a pooled crispr screen do & how does it work?


texts: Is the covid-19 vaccine-induced copy of the protein spike also damaging cells?

texts:
In recent scientific articles, it has been discovered how the spike protein not only is a respiratory disease but also damages blood vessels cells directly, and is connected with higher risk of trombosis.
So, does the Spike Protein produced by the covid-19 vaccine also bring the same risks and damage?
How many spike proteins the immune systems produces after being instructed by the vaccine, and how do they behave afterwards ?
Thank you
EDIT: adding some references
-1) https://www.salk.edu/news-release/the-novel-coronavirus-spike-protein-plays-additional-key-role-in-illness/
-2) https://scitechdaily.com/covid-19-is-a-vascular-disease-coronavirus-spike-protein-attacks-vascular-system-on-a-cellular-level/
-3) here it says how the "creation" of the spike protein happens-> Can spike protein induced cell fusion be triggered by the mRNA vaccine?
EDIT2: Someone in the comments pointed out how articles 1 and 2 reference the same paper, and one paper doesn't constitute discovery.
But how the spike protein which are "created" after the vaccine, behave? Are they the same as the one from Covid-19?
Are they harmful? if not, why ?


texts: Good resource for penguin behavior for non-specialists

texts:
I just returned from Antarctica where we made many shore excursions and spent a great deal of time among penguins -  mainly Gentoo, and some Chinstrap species.

They were fascinating and there were several distinct behavioral patterns that I observed but did not understand.   I'm not really asking for explanations here, but just a good introductory source of penguin behaviours.  When I've searched online everything I've seen is either too general and basic to be helpful, or too technical and specialised for me. I have a strong general science background and I'm an AAAS member and I have one ethology course from decades ago, but reading peer-reviewed research papers on this would be over my head.   We were there in March (late summer) so the juveniles were adult-sized but still had juvenile plumage.

Examples:

(Gentoo) being on beach or snowfield where there was a dense, mainly uniform distribution of adult and juveniles standing or laying around, when in the midst of this a line (typically 4-8) of adults would walk briskly, single file, through the groups of standing individuals, and even through the groups of standing humans, all looking straight ahead and apparently with a sense of purpose.  They would walk out of sight.   Why, and are they connected or related somehow?

(Gentoo) coming up to us and grabbing anything loose like backpack straps, number tags on lifevests, or pantlegs flapping in the wind and pulling.  This was not pecking like they would trying to get an adult to feed them, but I mostly saw this with juveniles.  We were under instructions to not make any noise or motion that would alter their behavior but when one started tugging on my lifevest inflation tab I had to yell to stop him.  (IAATO guidelines are to stay 5m away from wildlife but the penguins didn't attend our orientation seminar and anytime we stood still they came up to us)  Juveniles frequently nestled between our legs if we stood still (all of us were wearing thick, insulated, multi-layers of pants), but this is easy to explain regarding chicks nestling in the adult's brood pouch, since we frequently saw adult-sized juveniles exhibiting other chick behaviours, eg, food-seeking from adults.

(Chinstrap) large groups (30-50) of individuals standing tightly together when many (but not all) would suddenly point their heads up and start to vocalise, sometimes flapping their wings.  This would go on for a minute or so and then stop suddenly. I made videos of this.  I never saw any sign of a threat, say from a skua or seal, nor did they seem to be looking at anything, and nothing obviously changed that made them stop.


texts: How accurate is facial reconstruction in forensics?

texts: I’ve seen on tv where they reconstruct heads and faces from the remains of ancient people and I was wondering if anyone had a source that has pictures of maybe side by side of a facial reconstruction Vs. a picture of the actual person being reconstructed. I know it takes a long time to fully decompose but surely there’s been a reconstruction done of a recent person who’s been photographed


texts: Can anyone identify this plant from Bangladesh?

texts: I have taken the picture from an agriculture university in Bangladesh.


texts: Which organisms have the neuroanatomy Roger Penrose supposes play a role in consciousness?

texts:
In The Road to Reality, Roger Penrose suggests that certain brain structures might play a role in consciousness

  Most particularly, lattice neuronal microtubules, as originally
  suggested by Stuart Hameroff but perhaps also other structures, like
  synaptic clathrins, whose structure closely resembles the c60
  molecules.

He supposes this would have to do with some sort of quantum coherence:

  ...the scheme would require some kind of large scale quantum coherence,
  acting broadly across considerable regions of the brain having
  features in common with high temperature superconductivity.

In general, which organisms have these structures? Are they common?


texts: How does having spare receptors change ED50 in an irreversible agonist

texts:
Competitive antagonists increase the ED50 while the Emax remains the same. Irreversible antagonists do not change the ED50 while decreases the Emax.

Katzung pharmacology, says that the irreversible antagonist may change the ED50 when spare receptors are present. How is that? What difference would it make? Could anyone explain the change graphically?

Spare receptors are said to be present when the Kd (dissociation constant, from the drug-receptor binding curve) is more than the ED50 (from the dose-response curve). This may happen due to

prolonged effect of a drug-receptor interaction or
when the receptors are actually in excess of the drug

ED50 = effective dose at 50% of maximum effect, Kd = Dissociation constant.


texts: Why is an excess number of eosinophils consistent with a violent allergic reaction?

texts: What roles do eosinophils play in allergic reaction?


texts:
Previous Research

I stumbled across a trending reddit post "Lapidaria margaretae looks like stones" (as of 3rd Februrary 2015); but I could not find discussions as to reasons behind why.

Question/s

Why do Lapidaria margaretae look like stones? I am interested in both the morphological/physiological reasons, as well as possible evolutionary mechanisms.
Or perhaps I am asking the wrong question, then what should it be?


texts: Why are mammals not very often (never?) toxic?

texts: Often reptiles or insects have poison to defend themselves or to offend their prey. But I don't know any mammals which are toxic. So are there any mammals using poison and why aren't there so less/any?


texts: How does the Lgr5 receptor contribute to maintaining stemness in the intestine?

texts:
I don't understand the connection between Lgr5 receptor and Wnt between Paneth cells and stem cells. And how does this link to the EphB-EprinB inhibition between transit amplifying cells and differentiated cells?

My book "The molecular biology of the cell" 6th edition (Garland Science) only states that the Lgr5 receptor in the stem cells makes them able to create a mini-gut (organoid), but I am asked to present factors that makes the gut able to totally renew itself and maintain its structure.

I have already answered the Delta-Notch lateral inhibition pathway and its connection to Wnt signaling from the paneth cells in determinating differentiation and maintaining in ability to divide.


texts: Is there a comprehensive life science techniques/methods database?

texts:
There are so many techniques/methodologies in the life sciences that we can use to interrogate interesting questions. The thing is, most of us are completely unaware of the available methods we can employ. Rather, we go with the techniques we are familiar with or that are popular in our subdomains at the time. But that's pretty limiting.

So I'm wondering... we have databases for everything else... is there one for life sciences techniques/methods? Something like this could be immensely helpful in experimental planning. In particular, I think a comprehensive database would help scientists break outside of their spheres of familiarity and to employ less known (but potentially illuminating) methods to their questions.

I know there are journals that publish protocols and methods, but they are fragmented and don't encompass everything.

Does what I'm looking for exist? If not, how might one go about creating such a tool?


texts: Why would the Camargue horses have a white coat while the foal have a dark coat?

texts:
The current issue of the magazine Lonely Planet India(Oct 2013) presents a photo of Camargue Horses which are white coated and mentions that they are born with dark hair. A search shows that the foal are either black, grey or brown coated and gradually turn white around the Third/fourth year.
What could be the possible advantage of that kind of difference between the young and the adult?


texts: Comparative cost of RNA-seq vs sequencing full length cDNAs

texts:
I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data (high coverage for reasonable cost, error rates notwithstanding), but another benefit of RNA-seq data in particular is that they can be used in multiple ways. For example, I am mapping the RNA-seq reads to the genome to estimate transcript abundances and do some differential expression analysis, but I have also assembled the RNA-seq reads de novo to use as evidence for genome annotation.

There are, however, limitations to using RNA-seq-derived transcripts for annotation. Full-length cDNAs would facilitate much more reliable annotation. However, I have no intuition for the relative cost, time commitment, or complexity of extracting and sequencing full-length cDNAs vs next-gen sequencing. Can anyone here comment on this?


texts: What is the name of the baboons that live in Saudi Arabia

texts: In Saudi Arabia there are a lot of baboons in the mountain area. I would like to know what's the name of this specific baboons so I can read about them more:


texts: A compound was proposed by error but then showed very good inhibitory properties. How to argue this in a manuscript?

texts:
In a project, we performed some virtual screening calculations in order to predict inhibitors, and then purchased the compounds and tested them in the lab. One of them was a very good TK inhibitor (IC50 nM).

However, when we processed the results we realized that the presence of this particular compound in the original list of virtual screening hits was due to errors in the original calculations (it was added to the list by random factors, not by docking score).

So now we are writing the paper and we wonder how to argue this. We can not just tell the story like in this post (it was discovered by randomness or by our error). How would you argue this?


texts:
Glucagon stimulates glycogenolysis and gluconeogenesis, thus increasing the plasma glucose concentration — so that tissues get enough glucose in the fasting state.
However glucagon also inhibits glycolysis. In this case, what is the point of having high blood glucose if it cannot be catabolized?


texts: Calculation of Malthusian fertility and mortality from birth and death rates

texts:
In a simple Malthusian model, the population $p$ grows according to $p = p_0e^{rt}$, where $r = \beta - \mu$, $\beta$ is the "fertility" parameter and $\mu$ the "mortality" parameter. In the case of $\beta$, the closest thing to this parameter is the Total Fertility Rate. Is there a meaningful way to convert from one to the other? An easy formula might be something along the lines of
$$
\beta \approx \frac{1}{2T}\text{TFR},
$$
where $T$ is the reproductive lifetime, but this doesn't account for gender imbalances or a more nuanced way of treating the instantaneous nature of the parameter.


texts: Why does decreasing intake of protein prolongs the lifespan of a fly?

texts: A book I read about aging suggests that it is established that a fly lives much longer when it is fed less protein. What does protein intake has to do with the lifespan of an organism? Why not carbohydrates?


texts: Why don't acacia trees prefer increasing tannin levels in their leaves rather than leaving them high?

texts:
According to this article, the Acacia tree has a chemical defence system which leads to the release of ethylene in the surroundings when a herbivore grazes on it. This leads to an increase in tannin concentration in the leaves not only in the plant where the herbivore is grazing but also in the acacias surrounding 45m.

The question is, what prevents acacias to store tannins beforehand? Wouldn't the giraffes totally avoid them then?  Tannins aren't poisonous by themselves (correct me if wrong).


texts: What is the highest pressure at which plants can survive?

texts:
Inspired by this awesome question, I'm looking for the corresponding maximum: what is the highest air pressure at which plant life can survive?

For example, Venus's atmosphere is about 90x as dense as Earth's.  Aside from the other obvious factors, like sulphuric air and boiling temperatures and otherwise resembling hell in every possible way, can plant life survive in such a condition?

Additionally, are some types of plant life more adaptable to high pressure environments than others?  (I'm assuming an air environment, and excluding deep-sea life, etc.)


texts:
From my (limited) understanding, animals get energy from food by breaking chemical bonds between molecules.

There's a lot of water here [citation needed], so it seems like natural selection would favor any organism that could live off it. Why, in the history of life on earth, hasn't an organism appeared that eats water?

Same applies to dirt, rocks -- (although maybe lichen eat rocks? I'm fuzzy on lichen.)

Or air?

Why are humans and other animals like us only equipped to eat certain types of molecules, when others are so much more plentiful?


texts:
I recently found out that certain plants produce needle-shaped crystals called raphides. I am a physicist and I have an experiment in mind that could use these needles, but I would need to extract them from the plant and keep them in a liquid solution somehow.

How can I do this? Is this possible/hard to do? Does anybody know how to do this or have any experience?


texts: Congenital blindness due to retinitis pigmentosa - does it exist?

texts:
Retinitis pigmentosa (RP) patients typically become blind after a period of years in which their eye sight slowly deteriorates due to photoreceptor degeneration. Generally RP patients develop night-blindness first, then tunnel vision, after which finally the central eye sight diminishes leaving them with basically no eye sight, barred some crude residual light perception. The wiki page on RP has more information when needed. Typically, the process from diagnosis of RP to (near) complete loss of eye sight takes years to decades.

However, Chebat et al. (2007) make mention that their study group, consisting of congenitally blind subjects, includes one person with RP (see table 1 in the linked article). Hence, this implicates that this particular subject was blind from birth due to effects of RP.

Is anyone familiar with newborns blinded by the effects of RP?

Reference
Chebat et al. Neuroreport 2007;18:1901-4


texts:
I would like to know what is this plant ? Does anybody have an idea ? Somebody offered it to me but there is no explanation about how to care about it...
Some purple flowers appeared, during 2-3 days. And now it seems it lacks something, but I don't really know what to do :(

Any idea ?
Thank you very much !


texts: How does de-myelination occur in multiple sclerosis?

texts:
From what I understand, only the oligodendrocytes are affected in multiple sclerosis, and they are attacked by T cells which cross the blood-brain barrier. This leads me to two questions:

How is the blood-brain barrier affected in MS that allows T lymphocytes to cross the barrier?
Why do the T lymphocytes attack the oligodendroccytes? And when they do, what is the mechanism for de-myelination?

Thank you in advance!


texts:
I have read a journal that describes sequential passaging with the purpose of measuring resistance development in bacteria. I would like to know more about how the method works ie. what does "passage" mean?

https://www.nature.com/nature/journal/v517/n7535/pdf/nature14098.pdf, Methods part, under resistance studies


texts: How is SARS-CoV-2 'deactivated' for some Covid vaccines (for example Covaxin)?

texts:
Some Covid vaccines like Covaxin employ a 'Whole-Virion Inactivated Vero Cell'.
How is the virion 'deactivated' for the vaccine?


texts: Under what conditions does the body burn fats, proteins and carbohydrates?

texts:
Searching the internet, I have found lots of conflicting information from various fitness sites concerning when the human body burns fats, proteins and carbohydrates.

My basic understanding was that the body will first utilize glucose and glycogen stores, followed by fats and finally proteins once the fat and glycogen stores become depleted.  Also I believe there is some overlap in this process.

However many fitness websites claim that during high intensity physical activity, the body will prefer to burn protein over fat.

Scientifically speaking, when does the body ordinarily burn the following food groups (proteins, fats and carbohydrates) and how does exercise influence this process?

If you are able to provide graphs or data to back up your answer this will be extra helpful because I am bored of all the speculation I see on other sites.


texts: I have heard that offspring can't grow taller than either of their parents but I've also heard that sometimes some gene activation can skip generations. Is it possible for a child to grow taller than their tallest parent?


texts: Do vitamin enriched foods preserve their value when exposed to higher temperatures?

texts:
At what temperatures do different kinds of vitamins are destroyed or lose their nutritional value?

Imagine you went to the store and bought vitamin enriched cacao powder. Then you made yourself a hot drink by pouring boiling water. How much in general(approximately) vitamins were destroyed by that heat.

"How to prepare/cook" usually doesn't have this kind of information. Thus any benefits of vitamins are lost(?).


texts: Has it been confirmed yet that the DNA found in dinosaurs was really DNA?

texts: I hear different sources claiming different things, bbc said they did, wikipedia says it hasn't which is it?


texts: How does a cell create/gain its initial ribosomes for protein synthesis?

texts: I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes to pass on to the created organism?


texts: What signals histone methyl transferases to function?

texts:
I wanted to find out if anyone knows what stimulates histone methyltransferases to function?  I know that it is a process still trying to be understood, but I can't find anything that seems to direct the activity of the enzymes.  Additionally, where do the methyl groups come from that the enzymes transfer onto the histones?

Thanks!


texts: Why are there relatively more predators on the land than in the oceans?

texts:
Our biology teacher told us that among worse conditions one of the reason that intelligent life had actually evolved on land is that there is a more important selective pressure due to the bigger number of predators.

Is there really relatively fewer predators (in numbers) on the land? What is the cause of this phenomenon?


texts: Is it possible to have life that feeds on thermal energy

texts:
On earth, as far a we know, there are two main ways that bacteria gain energy.

First, there is Photosynthesis, the transition of light into chemical based energies such as ATP.

Second, there are chemical processes in which the cell breaks down a variety of molecules down to gain energy from the reactions. A example of this is Chemosynthesis.

Is it possible for their to be a bacteria or type of organism that gains energy from thermal energy?

For example, there could be a bacteria that lives in a volcanic area, somewhere hot enough that there is a excess of thermal energy. Would there be a way for such a cell to use this thermal energy in much the same way that some cells use Sunlight in Photosynthesis?


texts: Is tactile perception two-dimensional or three-dimensional? Can tactile sense be mapped on 2-dimensional map of the surface of the human body or does human receive tactile signal as a 3D position (owing that internal organs can also feel pain)?


texts: Snake with red eyes and black skin found in a plant pot

texts:
It was found dead/stiff in an empty plant pot in a kitchen.

Could it be a young Höllenotter (a melanistic vipera berus, photo in Wikimedia Commons)?

Is the reddish/brownish part an injury? And what are the greyish parts (especially at the snout)?

Size (only estimated)

Diameter: 2.2 cm
Length (in this rolled-up state): 10–12 cm

Location

Western Germany.

In the kitchen were three plants pots in a row that were used for culinary herbs, one still had basil, the other two were empty for some time. It’s unknown if the snake was already there when the pot was emptied.


texts: Are Schwann cells the sole source of myelination in PNS?

texts: Are Schwann cells the only source of myelin for axons in the peripheral nervous system, or are there other neuroglia or other processes that result in myelination of PNS axons?


texts: What happens to blood after a person dies?

texts:
After a human dies, what happens to their blood?  I know that it tends to accumulate in the lower areas of the body, whichever parts are closest to the ground, but I am wondering about coagulation.  Does the blood always coagulate?  How long does this take?  Does it ever "de-coagulate"?  If so, how long does that take?  If it coagulates, then "de-coagulates", does it "re-coagulate"?  How long does that take?

Note:  I'm asking this question because I am a fan of The Walking Dead, but I have always been a bit puzzled by the fact that on that show, the blood of zombies (who are dead) is consistently depicted as being fluid, dark red, and not coagulated at all.  I'm obviously not asking about the particulars of zombie blood, because zombies don't exist (yet).  I'm just curious as to whether it is possible for blood to remain liquid, and similar in appearance to the blood of living people, after death has occurred.  You can see my related question, on SF&F.SE, by clicking here.


texts: May two reactions, that share the same reactant, fire at the same moment?

texts:
I'm studying metabolic networks from a bioinformatics point of view, but I guess my question is pretty biological so I thought that maybe here I could get the best answers.

So, as the title says I was wondering, if I have one metabolite that is involved in two different reactions as reactant, is it possible that they both start at the same time at a certain point? I'm assuming that, in order to fire, the reactions need a certain amount of that metabolite, so if there is enough concentration to make both start, can the two reactions actually start in the same exact moment? What if the concentration of the metabolite is not enough to "satisfy" both?
Between the lines, are reactions mutually exclusive with respect to the shared metabolite or not?
In my mind, the quickest of the two gets the amount that it needs from the metabolite and the other one will just wait for the latter to have again enough concentration, is this intuition correct?

If you think this question is not appropriate, I will delete it and ask somewhere else. Any suggestion, also books or similar about the topic, is welcome!
I'm a computer scientist and I know just the basics of molecular biology, but I think that my job is mainly speaking to biologists in order to find solutions to different problems, so this is the reason why I chose to write here basically.


texts: Why do the brains of cocaine-users shrink faster than the brains of non-cocaine users?

texts:
http://news.sciencemag.org/sciencenow/2012/04/cocaine-may-age-the-brain.html?rss=1

  Cocaine-dependent individuals showed a significantly greater-than-normal age-related decline in gray matter in prefrontal and temporal regions compared with healthy controls. By contrast, parts of the striatum appeared resistant to age-related volume decline in the cocaine-using group. Enlarged striatal volume has frequently been reported in stimulant-dependent individuals,5, 6 possibly reflecting a marker of reduced dopamine neurotransmission in this dopamine-rich brain region where drugs like cocaine work. Decline in striatal dopamine receptor density has been associated with normal age-related cognitive decline.7 The relative absence of age-related changes in the striatum of cocaine-dependent people may thus reflect another feature of an abnormal brain ageing process.

Could it be related to possible neurotoxicity, or to the long-term effects of dopamine receptor downregulation? Could the effects also be generalizable to those who take dopamine-based ADD medications?

A link to the Letter to the Editor appeared in Molecular Psychiatry to which the ScienceNow article refers:
Cocaine dependence: a fast-track for brain ageing?


texts: I read that nucleoli are made of DNA, RNA, and nucleolus organizer regions. I don't quite understand how that happens with NORs. Isn't there an envelope delimiting the nucleolus from the rest of the nucleus content? Do NORs from different chromosomes come together? I mean, they are not detaching from the rest of the chromosome and aggregating freely...


texts: Why is the mosquito a definitive host in malaria?

texts:
I thought that the definition of a definitive host was that the parasite had to sexually reproduce in that particular host.

I've been told that mosquitoes are the definitive host for the plasmodium parasite, but I thought that the fertilization (and thus the sexual reproduction) takes place in the human?


texts: How does rho-dependent termination occur?

texts:
Rho-dependent termination is not fully understood but there’s a brief description in almost every concerned book about it.
In Snustard and Instant notes-Molecular Biology it is written that, the rho protein binds a stretch of 72 nucleotides at the 3' end of the nascent RNA, which could be a recognition site and then moves along 5' -> 3' direction separating the DNA-RNA hybrid.
But how's it possible, rho binding to 3' end (which is not free) and moving in 5'-> 3' (if so it is sure to fall off!)?
Diagram from Berg showing something opposite, i.e. it has attached to the 5' end and is moving in 5' -> 3' direction.

What is the right thing?


texts:
I've been doing a bit of armchair biology lately, and have been interested in the metabolic flexibility of neurons. My understanding is that, besides glucose, many neurons can metabolize lactic acid or ketones. However, some reports point out that some neurons can only metabolize glucose, without ever indicating which, or in what regions of the brain. (It may be that the following exert is suggesting that each individual neuron is using a mix of fuel sources. I have not been able to find much via the Google.)

From the linked book:

  When changing slowly from a carbohydrate diet to an almost completely
  fat diet, a person's body adapts to use far more acetoacetic acid than
  usual, and in this instance, ketosis normally does not occur. For
  instance, the Inuit (Eskimos), who sometimes live almost entirely on a
  fat diet, do not develop ketosis. Undoubtdly, several factors, none of
  which is clear, enhance the rate of acetoacetic acid metabolism by the
  cells. After a few weeks, even the brain cells, which normally derive
  almost all of their energy from glucose, can derive 50 to 75 percent
  of their energy from fats.

Which neurons and regions of the brain can only burn glucose?


texts: Type of Tree With Somewhat Squarish Fruit

texts:
I live in the SF Bay Area and am trying to identify a tree on my street. It's the fruit that is confusing me -- does anyone know what this fruit is?
It's not a rare tree -- there are at least several more on the surrounding streets.

Mature leaves are about 6" long and greater.


texts: Why do restriction enzymes tend to have an even number of bases in their recognition site?

texts:
When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases.

I wondered if this was just a co-incidence, so I took the data from this site for over a thousand known recognition sites and put it into a spreadsheet (XLS uploaded here).  The results are probably best summarised graphically:

Stats Test: Chi Squared Goodness of Fit.

Null Hypothesis:
There is no significant difference between the number of restriction sequences
that are an odd or even length.

|---------|----------|----------|-----|-------|----------|
|  Trait  | Observed | Expected | O-E |(O-E)^2|(O-E)^2 /E|
|---------|----------|----------|-----|-------|----------|
|  Odd    |    172   |  231.5   |-59.5|3540.25|  15.293  |
|  Even   |    291   |  231.5   | 59.5|3540.25|  15.293  |
|---------|----------|----------|-----|-------|----------|

Chi Squared Value = 30.586

P=0.05, 1 Degree of Freedom: Critical Value of 3.841

H0 rejected with 95% confidence (indeed with 99.9%+ confidence)

Can anyone explain or suggest why it is more common that restriction enzymes recognition sites have an even number of bases?

Updates

Expanded dataset to include new recognition sites from the resource that 96well linked to.
Removed all duplicate recognition sites leaving 465 distinct recognition sequences (my fault for not removing them in the first instance)
Ran stats test on the data
See Previous Version


texts: What types of light can't a plant photosynthesize in?

texts:
I have a plant on my desk, and it got me to wondering: Can my plant use the light from my monitors to photosynthesize? If so, what light (apart from green light, to a degree) can't plants use to perform photosynthesis?

I know that plants have the photosynthetic pigments to absorb many different wavelengths of light (primarily red and blue) but would there be certain types of light it can't use?

(The specific plant by the way is Schlumbergera truncata)


texts: Can mutation take place in G1 and G2 phases during the cell cycle?

texts: We know that the DNA replicates during the S phase in Interphase. There it might undergo a number of mutations. We also know that the forward half strands are more susceptible to undergoing a mutation since they live most of their lives single-stranded. But can mutation take place anytime before or after the replication? It is weird that the strands "wait" to open up in the S phase and only then undergo a mutation.


texts: Scientific name for the union point of a plant stem and root

texts:
Is there a word that describes the meeting point of a plants growing stem and its root?
Is this the same term for aerial roots above soil level?


texts: If action potential is "all or nothing" then how are finely tuned signals sent from one neuron to another?

texts: If the action potential is an "all or nothing" phenomenon, then how is one type of neurotransmitter secreted rather than another? Let's say, for example, if a neuron received an excitatory post synaptic potential that initiated a graded potential that initiated an action potential, what specific signaling cascade or mechanism would denote the release of one excitatory neurotransmitter (say nor-epinephrine) over another (say dopamine) ?


texts: Is mate choice in non-human primates MHC-dependent?

texts: Whether the major histocompatibility complex (MHC) affects or not mate choice in humans seems mired in controversy at the moment. Without implying that looking at non-human primates would solve this controversy, I'm still curious if some sort of scientific consensus could be reached in non-human primates regarding MHC and mate selection.


texts: With the 5$ covid19 test - an antigen test - , would trials (most likely) be independent?

texts:
Actual question
What would typically cause antigen tests to give a false positive or false negative and would these causes be typically independent (if we run the test twice it won't automatically fail twice) or would such tests typically fail in the same manner and thus consistently give the same result for the same person? Or is this completely different from antigen test to antigen test and nothing can be said in general?
I hope this question is narrow enough, and I totally accept an answer of 'nothing can be said in general'.
Background
Abbott’s BinaxNOW was recently approved by the FDA. These are the false positives and false negatives rates given by Abbott:

Abbott says that the test correctly diagnoses a coronavirus infection 97.1 percent of the time, and correctly returns a negative result 98.5 percent of the time.

Therefore, the probability that one has the disease given that they test positive is - if I didn't make a naive mistake in my application of Bayes theorem and assuming 1% of the population currently has it - only 39%. This obviously is... pretty bad.
The useful thing about Bayes theorem though is that we can also calculate the chance of actually having Covid19 if we take the test twice assuming that both trials are independent (97%).


texts: Do adjacent axons in a nerve influence each other?

texts:
Suppose I have a nerve fiber consisting of several axons all running in parallel to each other.  When an action potential is generated in a certain axon, this will alter the concentration of sodium and potassium ions inside the axon, and in the extracellular fluid around that axon.

The question is, will this change in ion concentration in the extracellular fluid, alter the threshold potential of an adjacent axon, which shares the same extracellular fluid?


texts: How does the Cuttlefish camouflage itself accurately despite being color-blind?

texts: I have seen/read that the Cuttlefish is able to camouflage itself extremely accurately. I have also seen/read that they are completely color-blind, though see with very high contrast. How does the Cuttlefish manage to blend itself so well to its changing surroundings if it is not able to perceive the colors it is changing itself to?


texts: Forum on synthetic biology and hypothetical biology?

texts:
I am interested in synthetic biology, but not a scientist, and would like some advice on where to look for an online forum on synthetic biology and creating fictional species and animals or if someone could suggest the best website to set such a forum up on.

The current research into synthetic biology with biobricks and all the complicated discussion of biochemistry and genetics is too advanced for myself and not what I am interested in. I have fictional ideas of how to create new organisms and symbiotic organisms that are designed and grown for humans to wear and utilise and would like to bounce ideas off other people who may be in to the same area - the potential application of synthetic biology in the far future.
Thank you for any suggestions.


texts: How can one identify an organism from its dissymmetry ratio?

texts: If I am given the dissymmetry ratio of an organism ((A+T)/(G+C) is a constant), how can I identify the source of the DNA and classify the organism?


texts: Is there any documented case in which floating substances led to the introduction of a new species?

texts:
Floating substances in the marine or freshwater environment often carry hitch hiking organisms. It is argued that many species may use this dispersal vector to reach new habitats, however to my knowledge there is no hard evidence / no documented case. This may be because of the difficulty to associate an established species with a certain vector of introduction.

By floating substances I refer to natural floating substances such as detached algae, trees or pumice and those of anthropogenic origin such as litter items, detached buoys, etc. (in whatever aquatic environment: sea, lakes, rivers)

Any help to find a reference / documented case study is very welcome!


texts: Does the NMDA antagonist, Memantine that's used to prevent Excitotoxicity cause brain damage?

texts:
Does the NMDA antagonist, Memantine that's used to prevent excitotoxicity in Alzheimer's disease (AD) and Dementia with Lewy Bodies (DLB) cause brain damage? I know that in rodents NMDA antagonists like ketamine and phencyclidine (PCP) cause a form of brain damage known as Olney's lesions. Despite Olney's lesions never being directly observed in primates like humans, permanent brain damage from chronic ketamine exposure has been observed in adolescent cynomolgus monkeys.1

Reference List

Sun, Lin; Qi Li, Qing Li, Yuzhe Zhang, Dexiang Liu, Hong Jiang, Fang Pan, David T. Yew (2012). "Chronic ketamine exposure induces permanent impairment of brain functions in adolescent cynomolgus monkeys". Addiction Biology. doi:10.1111/adb.12004. PMID 23145560.


texts: Mendelian dominant trait involved with Hypodontia

texts: If the absence of teeth is a dominant trait, then why is it not seen in generations? My teacher taught that absence of teeth is a mendelian dominant trait, but why don't we see this trait if it is dominant?


texts: Would muscle fatigue still occur if aerobic conditions for a working muscle is maintained?

texts:
Put another way if the muscle is given everything it needs to contract and do work will it ever get tired or have a reduction in energy efficiency?

As far as I understand muscles depend upon a blood supply delivering oxygen and nutrients (e.g. glucose and calcium) to effectively contract at its best level of performance. With the ability to work under anaerobic conditions if need be but producing lactic acid as a by-product which reduces the muscles ability to contract and therefore producing fatigue.

I also know that muscles are dependent upon temperature to work efficiently like the rest of the body. So, if the muscles temperature was able to be regulated well enough to maintain efficiency and aerobic conditions are met could fatigue be negated?


texts: What is the impact of selection on orthologous and paralogous genes? How would this impact differ in different regions of protein coding genes?

texts: Since paralogs increase the size of the genome and provide more opportunity for the evolution of novel characteristics, would they be more prone to selection?


texts: I'm never going to run these type of experiments but I do need to have a good idea of their timescale. After I fix my cells, if I stained my cells with histology stains like DAPI, Fluorescein, and various labeled antibodies, how long do I have to wait before I can examine my cells with microscopy?


texts: What is the function of nodes of Ranvier in axons?

texts:
In a neuroscience class I'm taking, it was explained that myelin covers axons in sections, the uncovered sections are called nodes of Ranvier, and signals propagate much faster in the covered sections.

But if it is faster for signals to propagate along myelinated regions of the axon, why doesn't the entire axon get covered by myelin? Wouldn't that make it faster?


texts: I'm curious what plant this is! I found it at 37°52'23.2"N 122°16'55.3"W (north of Oakland, California, USA).


texts: UCP1-3826 A>G rs1800592 different effects in moderately obese vs obese

texts:
UCP1 gene encodes an uncoupling protein which promotes the transformation of fatty acids into heat (thermogenesis) redirecting from oxidation to ATP. By merit of the fatty oxidation redirection, UCP1 reduces oxidative stress. Elevated glucose can activate UCP1. UCP1 is expressed in brown adipose tissue and in endothelial cells.
The rs1800592 G polymorphism is in the promoter region of UCP1 and reduces the amount of gene expression. With less UCP1 less thermogenesis takes place and more fatty acid oxidation, which produces ATP. A high ATP flux activates lipogenesis. It follows that the UCP1-reducing G allele would be obesogenic, and this is in agreement with studies in the overweight and moderately obese.
But in obese individuals, the GG genotype decreases type 2 diabetes risk.
Why would this be?


texts:
I know that some plants die for old age like a
lettuce. But there are trees like Baobabs or larger Ficus in the tropics of whom we don't know their age. And trees like spruce reaching 9950 years old, which die for environmental factors and not by age.

However, E.g. when we multiply vegetatively an olive or cacao tree, we use a fragment or clone from a unique individual passing the same genetic information, again and again.

Then, can these plants live forever?


texts: When is it better for a gene to cause a biased sex ratio?

texts:
Because genes are selfish and want to maximise their transmission from generation to generation, if they can distort a population's sex ratio, isn't it always in their interest to cause a biased sex ratio? Or are there cases when distorting the sex ratio isn't in their interest because they decrease the overall fitness at the higher level, i.e., incur too much damage in the individual/population? Their main priority is still to subsist in a population before spreading, right?
Thanks in advance :)


texts: How is atrophied muscle different than normal muscle in a chemical or biological way?

texts: I am a writer with a question for a story I'm working on. In it, the character suffers from muscle atrophy due to spinal damage. So that I can portray this accurately, what would cause this type of wasting? I'm hoping there is a chemical or biological difference between atrophied and regular muscle.


texts: Search engine for biological/medical/epidemiological science literature

texts:
I hope this question is appropriate for this exchange (I think it is too specific for meta?).

We are looking for a search engine that is capable of performing a search of all available biological/medical/epidemiological scientific literature (So more on the scope of Google than Elsevier or similar subscription services) and providing as many as possible of the following features:

Keyword search
Range of dates
Boolean terms (AND NOT etc.)
Option to download and sort
Email alerts.

Does anyone know of a search engine or service that has these capabilities? (A paid subscription is fine).

Thank you in advance for your patience.


texts: What does it exactly mean to sequence the genome of a species?

texts:
Since all organisms are different from each other - that is, we all have different alleles, some SNP, microsatellites, etc. -, what does it exactly mean, for the genome of a species, to be sequenced? I understand what it means for an organism's genome to be sequenced, but I don't really get what it means for a species.

I'm quite confused about this. Thanks in advance for the help!


texts: Does evolution produce organisms perfectly adapted to their environment?

texts: I have this biology assignment with this chosen topic. I have no idea where to start researching. I have studied the mechanisms and theories of evolution. I just don't know which relates to the topic. The task is to persuade an audience of one side, either yes evolution produces perfectly adapted organisms or no evolution does not produce perfectly adapted organisms. I have started research on the blind spot of the vertebrate eye and that might be case scenario for the topic. If you have anything to add at all that would help me complete this project. It is much appreciated. Thank you in advance!


texts: What is the definition of a stringent/relaxed plasmid?

texts:
I have found a publication which proposes some definitions, including a definition for strict and relaxed replication. The definitions are:

Relaxed control of plasmid replication. Relaxed control should be used in reference to plasmid replication that is not obligatorily coupled to chromosome-replication.
Stringent control of plasmid replication. Stringent control should be used in reference to plasmid replication that is obligatorily coupled to chromosome replication.

However, the publication is from 1976. Are these definitions current? If no, what is the current definition?


texts: Why is a membrane polar on the outside and non-polar in the inside?

texts: Why would the phospholipid bilayer want to be polar on the outside and non-polar in the inside? why would it not want to be the opposite?


texts: what is the natural way of rose to propagate by its vegetative cells?

texts: I have read that rose reproduces sexually. But I have also heard that it can propagate by its vegetative cells (vegetative cells in its root). Is this correct? If yes, can I know how does it propagate by its roots?


texts:
I've noticed different functions in different R libraries have different ways of assessing significance for Blomberg's K. For instance, picante's phylosignal looks at a distribution of PIC variance values from shuffled trait values to assess significance; when phytool's phylosig calculates a null distribution of Blomberg K values for shuffled traits.

What is the interpretative difference between the two and when should one approach be used over another? And what does it mean if the observed Blomberg's K is greater than 1 (traits less similar than expected under Brownian Motion model of evolution), but significantly greater (or less) than the null distribution of Blomberg's K-values?


texts: What leads to the different types of navels?

texts:
Obviously, there are "innies" and "outies" in the human belly button world.  Both are the result of a knot tied in the umbilical cord just after birth.

But why do some belly buttons become outies while others become innies?  Is it related to how the doctor ties the knot, or is it related to how the knot heals?


texts: Why does uncompetitive inhibition decrease the Michaelis constant?

texts:
I can't seem to find a good resource online that clearly outlines the difference between an uncompetitive, noncompetitive, and mixed inhibitor (I understand competitive inhibitor though).

More specifically, why does uncompetitive inhibition decrease the Michaelis constant?

From wikipedia:

  This reduction in the effective concentration of the E-S complex increases the enzyme's apparent affinity for the substrate through Le Chatelier's principle (Km is lowered) and decreases the maximum enzyme activity (Vmax), as it takes longer for the substrate or product to leave the active site. Uncompetitive inhibition works best when substrate concentration is high. An uncompetitive inhibitor need not resemble the substrate of the reaction it is inhibiting.

The Lineweaver-Burk Plot:

  By TimVickers - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=4549560

The uncompetetive inhibitor essentially "locks" the substrate in the enzyme thereby preventing the enzyme from catalyzing the substrate which would then decrease the amount of free enzyme. That should not, however, alter the value of $K_m$ because any copies of the enzyme that are still active ("not locked") maintain the same affinity for the substrate. I applied that same logic to noncompetitive inhibition (no change in $K_m$), hence the confusion.


texts: Is every evolutionary change an improvement?

texts:
In evolution, an species mutates and evolves over large genetic time spans. But every big change (say, swimming to walking, or walking to flying) is made up of countless micro-changes over the course of many many years and many many generations.

My question, does each "micro-change" have to be an improvement over the prior iteration? Or can evolution initiate micro-changes, knowing the current generation won't see the final result for an arbitrary number of years?


texts: When transmembrane proteins destined for the plasma membrane are in the ER membrane are they in their final folded form?

texts:
I am studying how transmembrane proteins are made and I have read that proteins that are destined for the plasma membrane are initially in the ER membrane and do not get translocated into the ER lumen unlike other proteins.
I was wondering when a transmembrane protein destined for the cell membrane is in the ER membrane, is in its native form (e.g. final, folded form?). I am asking this because I read that the ribosomes are on the ER membrane, and that protein translocation through the ER membrane occurs co-translationally, meaning that it's occurring as the mRNA is being translated. Would the protein get folded as it's moving through the ER membrane?
Any insights are appreciated.


texts: How much Open Access Data is there in genetics?

texts:
Type of data of interest

I would like to consider

Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...)
Genetic - phenotype data (disease-related data, QTL, etc...)
Sequence annotation and function
Transcriptomic data

I would like to include data on any living thing (including data from fossils) and not only human data. To avoid issues of semantic I would leave out epigenetic data.

Question

How much (in bytes) of such data is available in Open Access online?

Difficulties

I realize getting to such estimate might be hard and the estimate may be very inaccurate. Also, the format used for storing these data will definitely affect the relationship between information content and storage usage. But if someone can give just a rough order of magnitude, a vague intuition, it would already help. Is it a few terabytes or a few petabyte or even more?

I would welcome as well a detail of how you got to this estimate. I am particularly interested in what fraction of it is human data (if you happen to get to such fine detail).


texts: Which magnoliophyta groups are NOT pollinated by bees and why?

texts:
Considering the bees as the family Apidae which families of flowering plants are definitely not pollinated by them and what could be the reasons?

-Could you say that the relationship is preserved at the family level?

(Please suppose that both groups live in the same geographic context)


texts: The berries of the fruit are sweet. The tree is growing in Israel.


texts: How does a protein reach its substrate within the cell?

texts:
After a protein has been synthesized and its the final tertiary/quartenary adopted, how does it reach its substrate within the cell and what causes it to interact with it?

The transcription factors for a particular gene are proteins which are translated from genes on some other portion of the DNA. (That happens in the cytoplasm) But how do the transcription factors know that it has to diffuse into DNA region of the nucleus.


texts: Could a 3D Printed Plant Seed be Possible with Existing Technology?

texts:
The first genetically cloned animal was Dolly the sheep. As I understand it, this was possible because all that was needed was an embryo containing the cloned genetic material and a womb for that embryo to grow in. Would the same process also work to clone a plant?

I assume that the problem with embryonic cloning techniques and plants stems (forgive the pun) from the need to implant it into a host seed without destroying its ability to germinate. I haven't found a reference that claims this has been attempted... If anyone knows of a study related to this, I would love to read it.

Given my assumption I tried to imagine another way to achieve this goal which lead me here, to pose my question to the brilliant minds of this community:

  Is it possible to implant a cloned plant embryo into a synthetic 3d printed seed that would germinate with existing technology.

I know we have successfully 3D printed living tissue using state of the are equipment like the 3d Bioplotter. If you guys don't think it is currently possible then what technological advances would need to be made to achieve this goal.

Note: The answer to my question is relevant to a number of possible applications. A hypothetical "Seed Printer" could be used in a future manned mission to Mars. Due to the logistics of shipping supplies to mars, it could be more practical (cost effective) to ship the raw material needed for printing seeds than it would to send actual seeds.

Edit*: Thanks for the comments, I feel a little foolish for not knowing about artificial seed coats prior to posting this question. In light of new information, I would like to additionally ask:

  What are the current limitations of creating artificial seed coats that could possibly be enhanced with the application of 3d printing technology.


texts: What is the name of this type of inflorescence?

texts:
I was having a look at a rhizophora plant (from the mangrove family), and I got curious about its inflorescence. I can't make out what kind of inflorescence it is.

Here is a photo of the inflorescence.

Does anyone know which kind of inflorescence it is?


texts: Bats observed hunting insect prey - any evidence of "handedness" (laterality) in circular flight pattern?

texts:
Whilst watching a bat hunting on the wing at dusk (most likely was a species common to my urban UK location, e.g. pipistrelle) its flight pattern around the garden comprised circles, several metres in diameter, but I'm reasonably sure going in the same direction - in this case it seemed always to be turning to its left. (The circular flight pattern is something I've observed many times.) Is there any evidence in bats of a preferred direction of circular "sweep" whilst hunting? More generally, are bats known to exhibit left/right- handedness (or laterality in technical-speak) and does/could this manifest itself in flight patterns?
What I've already tried to answer my question:
Searched this site for related questions/answers + tried Internet searches with variations on circular flight for bats- results included a 2013 Nature paper, Bandyopadhyay, P., Leinhos, H. & Hellum, A. Handedness helps homing in swimming and flying animals. Sci Rep 3, 1128 (2013). https://doi.org/10.1038/srep01128 - fascinating stuff re. handedness and advantages for homing, but the brown bat featured was trained and observed under controlled lab conditions. Hoped that someone here with knowledge of the subject could provide a research paper/book ref., etc. I posted this question out of simple curiosity - I'm not a biologist and so don't have institutional access to many papers (just the Abstracts).


texts: Effect of interruption of photoperiod in a short day plant

texts:
When a short day plant is exposed to its critical period of darkness it flowers. But when it is exposed to a small period of red light which exceeds the critical period it doesn't flower.

But when it is exposed to small and equal amounts of red light and far red light it flowers even though it exceeds the critical period of light.

How is this possible?


texts: Is this is a parasitic wasp, which I found in Blackpool Lancashire?

texts:
A wasp I photographed on my van window in Blackpool just before it attacked me.
Is it true that it’s rare to see them in the UK?


texts: What happened to the gypsy moth epidemics in the Northeast US?

texts:
I remember that back in the 1980s, 1980-1984, gypsy moths were a veritable plague in the Northeast United States. They were literally everywhere. Sidewalks were covered with their squashed bodies (of the caterpillar). You would drive through areas and every single tree would have dozens of nests. Every summer would be gypsy-moth-a-geddon.

By the late 1980s this completely ended for some reason. I sometimes see a gypsy moth caterpillar here or there, but it is a rarity.

What happened? Did a predator proliferate? Was there a pathogen or disease that wiped them out?


texts:
The fact that exercise is healthy is a bit counter intuitive to me. If we have any machine, a car for example, the less we use it the longer it lasts. Then how is it that using our body to do sports, to a reasonable amount, lead to longer or healthier life?

My guess is that lack of activity might resemble starvation no matter how much food we consume. Then the body instead of repairing itself tries to save energy as much as it can. Are there any other ideas to explain why exercise is good?


texts: Would you guys know any kind of differential equations that would dictate population growth without relying on Lotka Volterra ? Thanks ^^


texts: Can Leptospirosis be spread through human urine

texts:
I am wondering if Leptospirosis can be spread via the urine of an infected human individual. All of the sources I have been able to find on the web have stated that the disease is primarily spread through infected animal urine, however, none of them mention human urine.

However, Wikipedia states:

  After 7 to 10 days the microorganism can be found in fresh urine

Which would imply that it could be spread via the urine of an infected individual?


texts:
I read that cytoplasmic incompatibility in Wolbachia occurs when wolbachia-infected male insects mate with wolbachia-free female insects and produce non-viable offspring. By contrast, wolbachia-infected female hosts produce successful offspring irrespective of the infection status of their mate.

I was wondering - what are the long-term effects of this on the size/structure of a insect population? How will this be different from a non-infected population?


texts: Why don’t humans have eyes at the back of their heads?

texts: How does evolution rule out the possibility of humans or others fragile herbivores from having 2 pairs of eyes, one at the front and the other at the back of their heads? Why didn’t that ever happen?


texts: Must I HPLC-purify my PCR Primers for amplicon sequencing with PacBio SMRT?

texts: I would like to order some primers for amplicon sequencing. I am using universal tag primers (unusually long 30-mers recommended by PacBio for SMRT, both F&R) + barcodes (16-mers).   The resulting order of 192x46bp oligos is prohibitively expensive, because of the recommended HPLC purification. The increased expense is related to purification and to the increase in minimum scale (amount) required for ordering.   My question is this: what are the worst-case scenarios (and likelihood thereof) if I do not HPLC-purify primers for PacBio SMRT sequencing?  I am generally looking to make the process of sequencing heterozygous RT-PCR products less expensive, so additional advice in that vein would be terrific, especially from experienced users.  Additional, minor and clarifying side-questions. The PacBio recommended primer, the Universal Tag 30-mer primer seems a bit long to me, and possibly unnecessarily so. Does anyone know why they would insist on a 30-mer? It's a bit irritating that there is no specific reason given, and combined with the unnecessarily long symmetric 16-mer barcodes, and 5’-block (5’ NH4-C6), they are pushing up the cost for little transparently good reason. Perhaps I am wrong. Any offered reasoning on these points would be appreciated.


texts:
The light reactions, if seen as a whole, are basically the oxidation of water to provide energy (ATP) to fuel the Calvin Cycle. The photons provide the activation energy for the same.

How then can we say that during chemo-synthesis bacteria get ATP in the first step by oxidizing inorganic substances like $H_2S$ or $CH_4$ because ultimately, it is similar to the light reactions and will require some activation energy?

Where does this energy come from?


texts: What do cells do when they aren't creating proteins?

texts:
I've always thought that the majority of the "work" in a cell is protein production, until I read the following.

The Wikipedia article on the central dogma of molecular biology states this:

  80% of the human genome is transcribed even though only 1% codes for
  proteins.

and this:

  Current research focuses on investigating the function of non-coding
  RNA, that is, RNA that does not follow the dogma trend and does not
  code for polypeptides.

If 99% of what's transcribed isn't used for creating proteins, what is it used for?  If it's not known - are there any hypotheses?


texts: Preserving/disinfecting meat with alcohol?

texts:
I'm considering safer ways to handle raw meat and it occurred to me that alcohol might be useful.

I'm considering, say, sealing pieces of meat in a container with 40% alcohol or higher in fridge or possibly freezer.

My question is what effects will this have on potential bacteria/parasites in and on the surface of the meat, and what will happen over time.

Different results as per higher concentrations/volume of alcohol and various temperatures are a plus.


texts: How many neurons do we have in our forearm?

texts: I am developing a neural interface, getting signals from the forearm and mapping them to hand gestures. The question we have at the moment is what is the upper bound of information bandwidth that we could tap into, meaning if we were to engineer an electrode so small that we could listen to every single neuron in the forearm, how many neurons could we listen to?


texts: Can improper/inadequate exhalation in humans trigger migraines?

texts: Is there any relation between  one's breathing pattern and occurrence of headaches? How does inadequate exhalation affect humans?


texts: Selection Pressure on Orca Whale Coloration

texts: What is the proposed selection pressure that leads to the distinctive coloration of Orca whales? I can find nothing in the literature.


texts: Genomic instability of cancer cells in h&e image

texts:
Is there are any books or papers on the topic of visual differences(analyzing H&E microscopy) of high grade cancer cells vs low grade cancer cells vs non-cancer cells?

In particular, I am trying to measure how much of genome was altered by analyzing images.


texts: Open Reading Frames vs Coding Sequences (CDS), are they different?

texts: The two terms confuse me for a long time. What is the difference between ORF and CDS. Some people say ORF could contain intron and CDS does not. The wikipedia definition of ORF does not contains intron. Could someone define the two terms and point out their differences? Thanks!


texts: Since RNA viruses and retroviruses all have high mutation rates, why do only a few viruses have the virtue of variability?

texts: We have been taught that it's difficult to make vaccines to influenza, HIV and HCV because they lack the proofreading mechanism, hence have high mutation rates. But most RNA viruses and retroviruses are still antigenically stable, such as measles, rabies, polio, yellow fever, HBV etc. So why do only a few viruses successfully become variable? Is it because their receptors allow flexibility, or their glycoproteins have sophisticated conformations that allow more mutations?


texts: How do mutations of viruses lead to drug resistance?

texts:
For instance, after starting zidovudine monotherapy against HIV, resistance develops against the drug because of a point mutation in the RNA transcriptase enzyme to which the drug binds.

So how does the virus ‘know’ to mutate this particular enzyme?


texts: How to manufacture different sized micelles in nano -scale?

texts:
I am trying to answer q5:

  "How can you manufacture micelles in A) nanometerer -scale B) and in ten nanometer -scale?"

  My Thinking

    Observations and some thinking

    Oil in water forms a micelle here, not making it soluble.
    Whey protein in Water forms a micelle or is this due to other reason? Protein folding with hydrophopic-tailed-and-hydrophilic-headed-particels? Is this micelle or not?

    Required Vocabulary about one answer

    what is IVC?
    PLoS?
    "[E]xtrusion step" = some sort of burst?
    PCR=Polymerase chain reaction here.
    monodisperse = A collection of objects that "have the same size, shape, or mass." (source
    here).


texts: Is there a publically available database of microbes that details what their wastes and food sources are

texts:
Is there a publically available database of microbes that contains what their wastes and chemical food sources are in addition to other traits.

So that I could do like a sorted search for microbes that eat Ammonia or excrete sulfuric acid?

Cant seem to Google this one.


texts: Do lobsters possess a nervous system to feel pain?

texts:
I was reading an article, which it mentions that lobsters do not have a nervous system:

  Lobsters have very poor eyesight and no nervous system. They walk slowly
  on the sea floor but are capable of swimming backwards by the curling
  and uncurling movement of their abdomen.

But in Wikipedia, I read that only 3 types of multi cellular animals do not posses a nervous system:

  The only multicellular animals that have no nervous system at all are
  sponges, placozoans, and mesozoans, which have very simple body plans.

Which none of them seemed like a lobster to me. In this answer, it is claimed that every living organism feels pain somehow.

Now I would like to know the answers of these questions:

Is the article about the lobsters true? They have no nervous system which means they feel no pain even if killed?
Is the claim in the answer true? Literally one of the claims must be wrong, since they conflict with each other somehow.


texts: Could someone help me identify this insect?

texts:
Does anyone know what this insect is? I put a rubber ball on my lawn, and within seconds a bunch of these insects (maybe 15 or 20) landed on it. I took a look around and saw that there were lots of them flying low near the grass or sitting on the grass (they were not as obvious on the lawn as on an orange ball :).
Location: Massachusetts (USA).


texts: Biology experiment with algae method help

texts: I'm planning a biology experiment I need to complete. I was planning on measuring the affect of pH on algae growth. I chose chlorella to be the test algae I use (are there any algae that would be easier to test?) and I have no idea how to measure the growth. My school does not have a spectophotometer, just basic biology and chemistry stuff. Also how can I change the pH of the water for my different samples? I'm a beginner and don't really have much experience so any help is appreciated!


texts: PCR a plasmid with self-complimentary regions?

texts:
I am trying to do a PCR using a plasmid as the template, pretty basic stuff. But the problem is that my forward primer just happens to bind to another location on the plasmid in the reverse orientation, in between the proper forward binding site and the reverse binding site. This isn't an example of non-specific binding, the sequences are perfect because the plasmid contains self-complimentary regions and my forward primer just happens to land right on it.

Here is a diagram:

Simply optimizing the melting point or magnesium concentrations probably won't help, because the sequences are the same. I'm doing this cloning to insert a reporter gene into the vector, and I need to place it very precisely, so I don't know if I can order a new set of primers, the insert needs to fit there.

The bad PCR product is about 500 bases shorter than the good product, but I only see the bad band on gel when I run a normal PCR. If I reduce the amount of forward primer and increase the reverse oligo, I can see the good band, but the bad band is still there and the total yield is much lower.

So my idea right now is to do an asymmetric PCR using the reverse primer only, then add forward primer to create the double-stranded DNA, then separate the good and bad bands using gel electrophoresis. But I don't have a clue how many cycles I should run each step, or how much forward primer to add, etc. Additionally, asymmetric PCR has low yield due to arithmetic amplification, but once I add the forward primers it can begin symmetric PCR and geometrically amplify both bands, but I think the shorter bad band wins out.

Does anyone here have experience with this sort of complex PCR, or suggestions to improve my yield?


texts: Why does the amount of adipose tissue contribute the most to the total body water amount in humans?

texts:
I don't quite get this concept. An obese individual will have a greater fat content in their body, and thus will have 45% water in their bodies (for example), versus a slim person that will have 75% of body water and a much lower fat level.
Is this because fat is made up of about 10% water, so the more fat you have in your body, the more water it "takes up" from the entire body water supply of your body?


texts: How the brain is affected by Alzheimer's disease

texts:
What exactly happens to the neurones in the brain?
why can't they be repaired/restored?
Why is it that there are so called 'good days'? What happens to the brain on such days?


texts: What photoreceptors are necessary to permit infrared vision?

texts:
Humans have red green and blue photoreceptors allowing them to sense colours in the spectrum of about 400-700nm. Certain proteins allow for the extending of wavelength range in the RGB receptors, this however is only perceived as more shades of the colour in question. Additional photoreceptors are necessary to sense a new colour, explicitly separate from RGB.

Organisms such as mantis shrimp can sense infrared light as they have 12-16 cones, allowing them to see into the infrared spectrum.

The issue is that there seems to be no information detailing the the structure of mantis shrimp eyes, specifically regarding the the aspects of which are responsible for vision into the near infrared spectrum (roughly 700-1000nm).

What would the cones of an organism that saw exclusively in infrared look like? (assuming the organism had eyes like a human)

Would they be differently coloured or structurally different to our own?


texts: What structures (i.e. organs) are suspended by tensile forces?

texts:
In several areas of biomechanical literature I have read, the concept of "tensegrity" has arisen. Definitions are as follows:

  “The integrity of a stable structure balanced by continuous structural
  members (cables) in tension and discontinuous structural members
  (struts) in compression.” (Zhang, 1)

and then

  “A tensegrity structure is recognized by its distinct set of
  compression elements (struts) that appear to float within a network of
  tensioned cables.” (Scarr)

I am highly skeptical about its applicability. Some authors (e.g. Evan Osar) suggest that tensegrity can be applied to the spine. However, the spine fundamentally does not fit the definitions provided above because its non-tensile components are connected / touching. Tensegrity involves floating

My Question:

Are there any areas of the body that would potentially qualify under this definition of tensegrity?

One example I can think of is the suspension of organs in the body, but I am unsure about this.

Sources:

Osar, Evan. Corrective Exercise Solutions to Common Shoulder and Hip Dysfunction. BookBaby, 2012.

Scarr, Graham. Biotensegrity: The Structural Basis of Life. Handspring Publishing, United Kingdom, 2014.

Zhang, Jing Yao, and Makoto Ohsaki. Tensegrity structures: form, stability, and symmetry. Vol. 6. Springer, 2015.


texts: What is the purpose of requiring two separate binding systems for the antibody response?

texts:
I've read that in most cases, B-cell activation requires helper T-cells.  This requires antigen binding by both antibodies and T-cell receptors, using two different antigen-binding proteins, recognizing two different epitopes.

Why is this so complex?  Would the overall antibody system still work if B-cells required only antibody/B-cell receptor binding?


texts:
On the Wikipedia I found this photo of a red fox, labeled as being taken at Quesnel Lake, British Columbia:

Why would the fox have blue legs? Is that normal for a Red Fox?


texts: Can a tree survive if someone cuts all buds?

texts:
My thought was to cut all buds of a deciduous tree at spring and see if it can survive a year and develop new buds and leaves next spring. Assuming the tree is already grown and not a sapling.

If the loss of all buds would be to fatal, how many would a tree need to recover?


texts: Why is the strength of genetic drift inversely proportional to the population size?

texts: I saw a concept on the Internet that says "the strength of genetic drift is inversely proportional to the population size". I don't know why they are inversely proportional? Can somebody explain? Thank you all!


texts: What percentage of fish are herbivorous vs. carnivorous?

texts: It appears that the majority of fish we eat are carnivorous, such as salmon and tuna. This got me wondering how common herbivores and carnivores are among fish species. I couldn't find an answer to this question through a cursory search of the internet.


texts:
We know that flies can perceive changes in the world around them up to seven times faster than a human - we appear slow to them.

I'm wondering how this is possible. Is it just that information travelling is limited by the speed of light, and it has a shorter distance to travel across a flies brain? Or is there some metabolic or other biological reason for this?

(It would be great to speed up a human's brain - but I'm sure there are a million reasons why that is not possible).

My question is: Is the reason that flies can perceive things faster because their brains are smaller?


texts: Can you identify this (possibly waterstoring) plant?

texts:
My son brought home a sapling, and after 4 years in a pot it is now about 30 cm or a foot high (from the "ground" to the top of the "stem"). It doesn't need a lot of water and can go weeks without being watered, in fact it seems to me as if it is storing water in the thicker upper part of its stem. When I water it "too much", new leaves start to grow. There are tiny "blossoms" along the stem, and every now and then small, dark brown, spherical seeds about 2 mm in diameter pop out from the "blossom" and are thrown across the room as far as a meter (about a yard) or two.

What plant is this?

I believe that it is not native to my European home but some kind of decorative plant imported and sold through a florist or imported privately, but I'm not sure.


texts:
I'm working with some orchid species, and i encounter a specific issue. Some of those species deposits upon their seed coat a wax layer. This layer makes seeds behave in a very hydrophobic way. You cannot dispense them in a pour water.

That behavior has many impacts. One of the most significant is that it does not let water come in touch with the actual seed and then with embryo to make it sprout.

So i tried many ways to remove that layer but nothing actually seemed to work out.

I treated seeds with the following chemicals:

a) 1% NaOCl with some dish soap water solution for 10min. After throwing seeds into this solution you could see that they can be evenly dispensed in it and come in touch with the solution. But if you wash them up with pure water for example 3 times they are getting back their hydrophobic behavior.

b) 1% H2SO4 water solution for 10min. I thought that with this treatment waxes will be removed from the seeds but nothing like that happened. Maybe they had been better dispensed in the pure water comparing to the previous treatment but nothing significantly changed.

c) 93% ethanol solution for 1, 2, 3, ... 30min. results here were also very disappointed. While the seeds are immersed into ethanol, they were very well dispensed into the liquid without any hydrophobic behavior. After three washes with pure water, hydrophobic properties came back.

Treatment time seems not to play any significant role on the results.

My conclusion is that there is no destruction of the waxes with the above chemicals. The only thing that happened probably, is the creation of a Micelle around the seed, which make it for a while (the time that it was in the solutions with soap and ethanol) non hydrophobic.

Finally my question is, if there is any way to destruct chemically, to some grade the waxes. So even when you put the seeds in a pour water not be so much hydrophobic.

Thank you.


texts: Is it correct that Afterload=Preload+Active tension?

texts: Preload causes development of equal amount of passive tension which leads to distension of heart muscle. Further, afterload causes development of active tension or cross bridge formation which initiates contraction. Passive tension+ active tension counter balance the afterload to cause contraction of cardiac muscle at a particular velocity. (I used NLM concepts here)