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Allergy

To my understanding, an allergy is a hypersensitivity of the immune system causing a substance in the environment to be identified as pathogenic by the immune system while it is not pathogenic. During an allergic reaction, the immune system triggers histamine, which triggers an inflammatory response just as if the allergen was a pathogen. The resulting symptoms of an allergic response is similar to the symptoms of a cold but without fever.

Fever

To my understanding a fever is an increase in body temperature driven by the body through production of pyrogens, most often in response to a pathogen. This response might be adaptive for various reasons that I am not too interested in discussing here.

Question

According to NIH, an allergic response never causes a fever. Given that the fever is not directly caused by the pathogen but rather is caused by the body, why do allergies not cause fever?

The fact that allergies don't cause fever give me the weird impression that the immune system somewhat "understand" the allergen is not pathogenic otherwise the immune response would be the same in the case of an allergen or a pathogen.

Un-educated guess

Allergic responses implies the firing of IgE. IgE are typically involved in response to parasites such as helminths. Could it be that pathogens leading to an immune responses mediated via IgE never yield to fever. Why would it be the case?

Plasmodium falciparum (which causes malaria) is a pathogen who causes an immune response involving IgE (according to the wikipedia). Malaria's symptoms include high fever (according to Mayo Clinic). Now it would be possible that the pyrogen would be of external origin (not produced by the body but by the pathogen) or it is possible that several immunoglobulin are involved in response to P. falciparum. The same logic hold for Fasciola hepatica (an helminth; common liver fluke) who also causes fever and is who's infection lead to the firing of IgE.


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Can someone help me find be it an article or journal that has the conventional PCR method for the detection of antibiotic resistant genes?

Thanks in advance.


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Dermatophytes are cutaneous keratophilic fungi. They cause concentric skin lesions. As a sample, usually skin scrapings are collected.

When viewed under the KOH mount, they appear transparent but when cultured, they show varied pigmentation. In fact, there is different pigmentation both on the obverse and reverse of the culture media (SDA), which makes pigmentation a differentiating and identification feature. These colors vary from species to species from red to violet.

So here are my questions

Is the pigment secreted out in the medium or retained in the hyphae?
How are the fungi transparent on a KOH mount.
Why is there a different pigmentation on the obverse and reverse?
Why is there no colour in the skin lesions? There is just erythema
if I'm not mistaken.


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I have scoured Google and a number of my anatomy textbooks for a picture of lymph. However, I cannot find any such photo (or video) showing its actual appearance.
Can someone provide a reputable image or source where a photograph of lymph can be seen?
What I do know:

Tortora & Derrickson (14th) A&P textbook mentions it consists of a "clear liquid extracellular matrix that is similar to blood plasma but with much less protein."

A photo purporting to be lymph does exist on Wikipedia, but lacking any further corroboration leads me to remain uncertain of the photo's authenticity.

Context:
I'm preparing a lecture for my 100 level college A&P course, and I was hoping to include a photo for my students to see and compare.
NOTE: I am hoping for a photo of lymph that is not classified as lipid-containing Chyle, for which I can find photos. However, a comparison photo would be ok :)


texts:
Should we centrifuge clear urines first and then cytocentrifuge or just directly cytocentrifuge?
This is done in CYTOLOGY.Should we centrifuge clear uruines first and then cytocentrifuge or just directly cytocentrifuge


texts: Difference between prions and amyloid proteins?

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Amyloid and prions are misfolded proteins, but what, if any, is the difference between them?

Is amyloid a type of prion with a fibrillar structure?


texts: Why don't amino acids get linked in the functional groups of acidic and basic amino acids?

texts:
There are 'acidic' and 'basic' amino acids like aspartate and histidine.

When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the amine groups or acidic groups in the functional groups of the amino acids in the polypeptide?


texts:
Found in the Dolomites, Italy

in a wooden fence:


texts: Why does constant current in electrophoresis mean that the molecule moves at the same rate?

texts:
Two part question:

Part 1:

I have always learned that when running a SDS-PAGE current is what decideds how fast the macro molecules migrate.

However, if the force excerted on a molecule is equal to charge times electric field.

Then wouldn't the speed at which the protein migrates depend more on voltage then current? As the the electric field is a measure of Voltage across an area.

Also, does this change based on the type of electrophoresis? (specifically, Agarose/DNA, and native page)

Part 2:

How do you calculate the time it would take for a molecule to reach the end of a gel based on the length of the gel and either the voltage or current?


texts: Getting PCR amplification at annealing higher than Tm!

texts: I am amplifying a gene where in a gradient pcr i am getting amplification at an annealing temperature about 5 degrees (67) higher than Tm (62.5)? What is wrong here? Also, I am getting a very strong intense band at wrong size for all the temperatures tried below Tm. Pls help


texts: Which kind of electrical brain activity is associated with consciousness and why?

texts:
According to this article The ethical brain

At the end of the week 5 into the 6 (42-43 days) the first electrical brain activity occurs in a pre-born developing human.

And according to the same article

  This activity, however, is not coherent activity of the kind that
  underlies human consciousness, or even the coherent activity seen in a
  shrimp's nervous system

My question is, which kind of electrical brain activity is associated with consciouness and why?


texts: What marine animals exhibit deep hibernation/aestivation?

texts:
Do marine animals exhibit deep hibernation/aestivation as land-based creatures do?

If not, Why?


texts: Which species of centipede is this and is it dangerous to cats?

texts:
My cat was "playing" (aka torturing) with this centipede:

I tried to measure its length with a measurement tape:

Since I know some species of centipede can be poisonous, I tried to find if centipedes can be dangerous to a cat, but the links said it depends of the species.

When the cat tried to catch it, the centipede ran fast to below the carpet or my slipper. Now, when I lift the carpet, it pretends to be dead, although in one occasion the arthropod moved its legs without changing position.

If it matters, I'm in Southern Brazil in a subtropical region and it's 01:30 AM. I don't think it bite my cat, since I'm not seeing any signals of health problems on the cat (also the anxiety of being forced out of my room so they can't interact until I solve the situation).

I think this animal is a Scolopendra, known here as "Lacraia".


texts: Do the antlers re-grow in the same pattern every year?

texts:
I am a software engineer and I am trying to develop a system to identify a deer by its photograph.

Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern next year and if yes, then what are the measurements that are of interest here?

Any pointers for me? Any software that can help me in recognizing a deer?


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I recognize some interesting patterns when analysing DNA methylation of BEAS-2B cells. Does anybody know, if the cell culture is female or male? I already asked the customer support of Sigma Aldrich without success.

Information on the official website just mention "non-cancerous individuals" as source organisms.

http://www.sigmaaldrich.com/catalog/product/sigma/95102433?lang=de&region=DE


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In bacteria, an enzyme called dam methylase (Deoxyadenosine methylase)  methylates adenines (A) in the sequence GATC in the new strand formed after replication.
What role does this methylation play?
I read that it has something to do with proofreading. If this is so, then how?


texts: How long does a signal from the brain take to reach the limbs?

texts:
If the brain sends a signal to move what's the time it takes the signal to travel via neurons to motor neurons in hands, arms and legs?

How fast do those signals travel?


texts: Calibration curve for single radial immunodiffusion

texts: When we draw a calibration curve for single radial immunodiffusion, the curve does not pass through origin. Instead, there is a y intercept. Why does that happen ? Shouldn't zero antigen give zero ring diameter ?


texts: Constitutive Dark Skin vs Facultative Tanned Skin

texts: Most can easily spot the difference between a tanned and dark person. But from my research, the only difference is in the size and concentration of melanin (Jablonski). But this continues to increase with sun exposure, so I was wondering what specific differences are there between people who tan or are naturally dark. Surely they are not the same color, so what is different?


texts: Strategy for tree and shrub identification

texts:
I often find it difficult to identify trees and shrubs even though I have many handbooks and manuals on trees and shrubs in my area (New England). The typical problem is that the species is not in the handbook, or that it is very similar to many other species. For example, hawthorns have many different species which are very similar to each other and most books do not exhaustively list the different hawthorns and their distinguishing characteristics, instead just listing one or two of them.

Web sites are even more fragmented than books and are usually a lot less detailed than the books so even if I search around, the results are often useless.

Am I going about this wrong? What improvements can I make to my strategy for identify trees and shrubs?


texts: Deducing amino acid sequence from a DNA sequence

texts:
The suggested answer to the question is the following: "M L S C D K S D Stop". I do not understand how they get that result.

The question is as follows:

An RNA polymerase transcribes the following DNA sequence, in the direction of the arrow. Which amino acid sequence will be generated?

Thanks in advance!


texts: My father died in 1987.  I have an old cowboy hat of his.  Can I use a FamilyTreeDNA test kit to recover any DNA?


texts: What species is this orange mushroom in Romania?

texts: So I've found these mushrooms near a ditch on a field a few days ago in Romania. Can anyone help me with identifying what species of mushroom is this? The size of a mushroom is about 3-6 cm in diameter. Thanks and a happy new year.


texts: Help with jellyfish species identification

texts:
Our research group (Evolutionary Genetics Group, University of Zurich) has received a letter from a special needs child who has kindly asked us to identify three jellyfish species.

Unfortunately, the letter does not include anything else except three rather low quality cutouts from what I assume is a childrens book. Nobody in our lab has any knowledge about jellyfish taxonomy so any help is greatly appreciated.


texts: I am a poor mathematician looking into the Sars-Cov-2 genome. Is there a proper definition of the word homoplasy? Is it just mutations that happened independently or does there have to be indications that the mutations give an improvement in fitness?


texts:
This thing ran out of the wall of my dorm hallway. It had a lot of what look like antennae, and it's very fast.

(click to enlarge)


texts: Where does our ancestor learn to walk from? How do we control our legs whenever we take a step?  I confuse every time whenever I take one step.


texts: How many kangaroos would you have to add to a northern climate before they could start adapting to it?

texts:
If some enterprising billionaire wanted to introduce Kangaroos to a northern climate such as the northern boreal forest by Fort McMurray in Alberta, would it be possible for the Kangaroo's to survive and adapt to that climate creating a new super kangaroo (which will henceforth be known as the polar-roo)?

How many kangaroos would have to be dumped into the boreal forest before we would have enough to reach the critical mass that some of the kangaroos would be able to adapt and mutate to this new climate and conquer the north?


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How are natural venoms and toxins (e.g. spider and snake venoms) used to make antidotes? In other words, what is in that venom that is part of a harmful substance but, when used correctly, can actually help us, and why can these molecules help or harm in different situations?
Also, why are we looking to natural toxins to produce new medicines instead of synthetic chemicals we could make or already have?


texts: How to specify a promoter in de novo gene synthesis service?

texts:
I am trying to use a de novo gene synthesis service (Genscript) and one part confuses me:

Where do I pick the choice of promoter? Or is the promoter choice automatic based on my plasmid choice?

e.g. Say I want a regulable promoter (say lac induced by IPTG) how do I specify it? https://www.genscript.com/account/gene_services_gene_synthesis.html

I was given to understand in a related question that with a commercial gene you essentially just "pick the promoter you want"? Or must I somehow manually edit the gene sequence I have to incorporate the promoter I want?

How to put a gene under the control of a regulable promoter?

I can definitely email Genscript in case it is not a part of their default interface but I just wanted to verify my understanding of the matter before I do so.

PS. I even checked out Fischer's GeneArt service & even that interface has nowhere for me to select a specific promoter. Makes me wonder if I am getting the workflow wrong?


texts:
I'm struggling to get a hang on this. I'm getting confused by this sentence from one of my tests:

Each human diploid cell has two sex chromosomes and _____ autosomes.

I'm guessing they're meaning 46, but can someone tell me this in another way? Like in a really easy way, so that I can understand it?


texts: What is the benefit of near-emptying the bloodstream in the mammalian kidney?

texts:
In the normal function of the kidney, the bloodstream is near emptied of fluids as it moves through the glomerulus, in which glomerular filtrate is formed.

As it proceeds through the Nephron, a significant amount of this material is returned to the bloodstream, and only a comparatively timy amount goes into the urine.

Why, in evoultionary terms, is it not more favourable energetically to remove only the small number of molecules, perhaph using specialised channels made of protein and activated only by a certain molecules which need removing, at a potentially huge energy saving?


texts: Tiny white very hard cell bug! Please help to identify!

texts:
I found these bugs walking on the floor/ wall and on my laptop.  And unfortunately I think they could be in my bed, too, since I bring my laptop to bed sometimes.

I live in a big city in the Netherlands without pets. My house has humidity issues.

I have noticed that the bugs are very tough to exterminate; meaning that when trying to squeeze them it really needs a lot of effort for their size. Their size is about 1 - 2 mm and their color is whitish.

Please note that my lightbulb is having a yellow color.so it makes it look darker than normal. It's more white than looks in the picture

This is a pic of it walking on my screen...


texts: Identifying this winged ant with big hind legs

texts:
I found this walking across my floor not too long ago. I am not sure if it is actually an ant, I just chose the best words I could find for the title. It has wings, but does not seem to ever fly. It has antennae and the hind legs looks much larger than I've ever seen on an ant. Moreover, they seem to have a red tint. Any ideas?

Area: U.S. East Coast


texts: I am looking for a good mouse colony census program that tracks the mice we have in the lab, breeding success of breeders, lineages, multiple user access, etc. Jackson labs has a program that does this but is is cumbersome and a bit pricey (softmouse is also an option, though a pricey one). I figured that since colony management is so pervasive there must be a good piece of software to deal with this, but have mostly been out of luck. It would also be great if it is currently supported software that isn't outdated and free or sold at a relatively cheap price. Thanks.


texts: As far as I know the glucose gets processed from carbs and fats and as a result carbon dioxide, water and "energy" are released. The carbon dioxide and water are expelled by the body, and then energy is used by the muscles. But how exactly is it used? What happens to this "energy" and what is it exactly?


texts: Where does the term "cos site" come from?

texts:
The word cosmid is derived from cos sites of lambda phages.

Why are cos sites called cos sites? What does this "cos" refer to?


texts: biological difference between 9 month and 7 month pregnanted humans

texts:
it possible baby born when 7 month of pregnancy, and possible when 9 month pregnancy.
what happen in additional 2 month?
what their difference. do they have different something.


texts: Do pyrosomes reproduce by ways other than cloning?

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I know that Pyrosomes are large colonies of floating tube-like animals that live in the sea, particularly in the tropics. They are just like any type of free floaters

I know  that pyrosomes can reproduce by cloning, but are there any other ways that they can reproduce?


texts: Skeletal muscle has got many many peripheral nuclei. What does "peripheral" mean here?

texts:
Cardiac muscle has got a central nucleus similar to smooth muscle, but skeletal muscle you may recall has got many many peripheral nuclei.

What does "peripheral" mean here?


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Does anyone know anything about the connectivity of the superior colliculus? Or know of any straightforward published literature?

I've got that the superficial layers receive input from the visual system and the deep layers have multi-sensory inputs, but I'm finding conflicting information about the specifics.

I've read one source that suggests inputs are from magno and konio cellular retinal ganglion cells. But as I understand it, these are cell types in the lateral geniculate nucleus, so it's not clear if the inputs are from the LGN, or the retina.

Edit: Figure 2  here, shows "koniocellular" ganglion cells. Which I can't tell if they're meant to come from the LGN, or retina.

This article discusses some of the connectivity, but only with regards to eye fixation, rather than a general overview.


texts: What are the reactions in the body that triggers dizziness after cigar(nicotine) smoking in non-smokers?

texts: Suppose there is a person that has never used nicotine in any form in his/her life. Why does the person get dizzy after a few "shots" from a cigar(nicotine)? What's the difference between using other plants(e.g. marijuana)?


texts: How are the wings of birds, pterosaurs and bats related to each other?

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Homologous organs are organs which have same arrangements of bones, blood vessels and muscles with different functions, and analogous organs are those which have different arrangements of bones but serve same function.

I want to know whether the wings of birds, pterosaurs and bats are analogous or homologous organs. My book says that their wings serve same function and have similar structure but they evolved independently. It confuses me because this seems like a blend of both homologous and analogous organs to me. So which is it?


texts: Why does ionizing radiation cause only DNA double strand breaks?

texts: It's known that ionizing radiation such as X-ray and $\gamma$-ray, cause DNA damage, specifically double strand break. Why is it so? I mean, why not single strand break, why not pyrimidine dimer?


texts: Ray wu DNA sequencing methodology understanding

texts:
I'm trying to understand the method which Ray Wu, developed to sequence the DNA 5' cohesive ends of a lamda phage. I'm reading these two papers written by him, but i stuck at the point where he uses the 32P nucleotides.

Structure and base sequence in the cohesive ends of bacteriophage lambda DNA

Nucleotide sequence analysis of DNA: II. Complete nucleotide sequence of the cohesive ends of bacteriophage λ DNA

It's not clear to me, by reading the papers, the step in which he runs the polymerization of the DNA. Did he use all the 32P nucleotides at once or each one at a time. As i understood he made the DNA pol to use the tritiated nucleotides to fill in the gaps of the 5' cohesive ends and then he cleaves with a DNAase in many  oligonucleotides which later fractionize with electrophoresis. If he added all tritiated nucleotides at once how did he recognize which one is at a specific place ?

Can someone describe the process in more detail using step by step aproach?

Thank you,


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In my VCF file from GATK, I have the following definitions for AD and DP.

AD - Allelic depths for the ref and alt alleles in the order listed
DP - Approximate read depth (reads with MQ=255 or with bad mates are filtered

I don't understand the definitions, can anybody explain in a less technical way?

From what I can read, AD gives the number of reads spanning the reference and variant allele. But what does DP mean? This doesn't look like the total number of reads spanning a variant, so what is this? How does this different to AD?


texts: Any volumetric data for areas of the brain?

texts:
I was trying to write an overview of AI and wanted to quantify some numerical data about the brain.  It is easy to find many sources quoting 100 billion neurons.  However, I would like to get the number of neurons (obviously approximate) in each area.  Also, while I can find the average number of synapses to neuron, it would be nice to know if there are higher numbers is certain areas of the brain.

This is not my field, it would simply be instructive to generate a table of data.
Is there any source, even approximate volume for different areas of the brain?


texts: plausible science for why an enzyme breaks down a substrate better at 4 degrees rather than 20 degrees

texts: An enzyme was found to have an optimal temperature of 20 degrees. The same enzyme in sheep liver extract was found to have an optimal temperature of 4 degrees. What are some of the factors that can contribute to the differences observed?


texts: Help identify this small spiney praying mantis?

texts: Trying to identify this praying mantis for a short film. It's found on the wild cosmos flower. It's found when the flower is in bloom at this time of year (February) in Harare, Zimbabwe.


texts: What types of species can produce genetically identical offspring?

texts: Talking about identical twins, triplets, etc.  I'm curious which types of species are able produce genetically identical offspring.  Let's limit the scope to species that reproduce sexually and instances where the offspring differ genetically from the parents but are identical to that of at least one of their siblings. Are there phyla, classes, et cetera that do not ever produce identical twins?  Kingdoms?  Are there cases of plants producing genetically identical offspring?


texts: How can ingesting a prion "infect" someone?

texts:
That's something that's been bugging me for a while...

Our gastrointestinal tract produces proteases that degrade proteins. Prions are proteins. Shouldn't they be broken by proteases?

Also, how can a prion pass the gastrointestinal barrier? Shouldn't the intestine be able to absorb aminoacids only (instead of full proteins)?


texts: Is it possible to Breed an Animal to have more Females than Males?

texts:
Minute Earth talked about environmental factors that cause animals and humans to have more male or female children: https://www.youtube.com/watch?v=3IaYhG11ckA

Presuming that is accurate, I was wondering if you could artificially select for people or animals who have more children of a certain gender?

As far as I know, there are no animals that do produce notably more males than females, or vice versa, except maybe some insects.


texts: Is there an evolutionary reason why so many white matter tracts decussate in the brainstem and spinal chord?

texts: From a developmental perspective, I would tend to assume that it would be much simpler for the fibers descending from (for instance) the pyramidal tracts, superior cerebellar peduncles, or ascending from the dorsal columns to remain ipsilateral. Can anybody think of a reason why some white matter tracts developed contralaterally?


texts: What do the Clustal Alignment Symbols Mean?

texts: Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?


texts:
Tendons' widths vary widely across humans. E.g.:

{1}: "the mean patellar tendon width was 26.10mm (SD = 3.31; range 18.33mm-33.33mm)"
{2}: "Size of the patellar tendon width, measured at the same location in each patient, ranged from 24 to 35 mm"

Is the tendon width determined by genetic predisposition, and if so, is genetics the sole factor?

I read on {3}:

  Tendon length is determined by genetic predisposition, and has not been shown to either increase or decrease in response to environment, unlike muscles, which can be shortened by trauma, use imbalances and a lack of recovery and stretching.{4}

But it didn't mention the tendon width.

References:

{1} Dundon, J. M., R. J. Markert, and M. W. Lawless. "Correlation between patella and patellar tendon width: an anatomic study." Clinical Anatomy 25, no. 3 (2012): 398-400. https://www.ncbi.nlm.nih.gov/pubmed/21853464; https://doi.org/10.1002/ca.21241
{2} Shelbourne, K. Donald, Richard A. Rubinstein JR, Charles D. VanMeter, John R. McCarroll, and Arthur C. Rettig. "Correlation of remaining patellar tendon width with quadriceps strength after autogenous bone-patellar tendon-bone anterior cruciate ligament reconstruction." The American journal of sports medicine 22, no. 6 (1994): 774-778. https://www.ncbi.nlm.nih.gov/pubmed/7856801; https://doi.org/10.1177/036354659402200608
{3} https://en.wikipedia.org/w/index.php?title=Tendon&oldid=885716020
{4} Young, Michael. "A Review on Postural Realignment and its Muscular and Neural Components" http://www.elitetrack.com/article_files/posture.pdf  (mirror)


texts: Can epiphyte share nutrient to host plant?

texts:
Sometimes plant share their nutrient with underground root network

But if there are plant that grow on other tree. Is it possible that it would merge into another tree and sharing resource. I mean opposite to parasite that it not steal resource but give the leftover to the host? Any plant do that?

I heard some plant like Coast Redwood or Banyan could grow their child on their branch as epiphyte. Can them sharing resource between each other?


texts: "Gold standard" for CNV detection methods?

texts:
Is there a generally accepted "gold standard" for testing the performance of CNV detection methods?  I'm interested both in learning about existing datasets that may serve as gold standards for CNV detection, as well in methods for producing such datasets in the first place.

(In case it matters, I'm primarily interested in the evaluation of CNV detection methods in laboratory mice.)

Thanks!


texts:
I was recently asked the following question:

  Compare the following pairs of receptors in the same
  sensory system. Include in your discussion:

  The distribution in the
  sensory epithelium;
  What kind of stimulus is effective in activating
  them;
  Their physiological response properties, function and central
  connections.

  Rods and cones
  Pacinian corpuscles and free nerve endings

In particular, I was not sure what the sensory epithelium is. Is it getting at the fact that Pacinian corpsucles are subcutaneous, while free nerve endings are cutaneous and that cones are centralized at the fovea?

Alos, I am not sure what their "physiological response properties" refers to. Since they are receptors, would their responses just be the output (i.e. peripheral/foveal vision and vibration/pain sense)?


texts: Stem cells and if they can correct a lack of apoptosis

texts: If a cell ,call it C1 has no functioning apoptosis mechanism could a stem cell somehow be 'induced' to be like C1 , at least have the same genome as C1. Then use this stem cell 'duplicate' to 'restart' the apoptosis mechanisms in C1 or even replace C1? ( forgive any broadness or vagueness, I'm trying to be specific)


texts: Where happens MHCII coordination to a self-peptide, and what happens if the bond would be irreversible?

texts:
MHC-II proteins are presenting antigens on the surface of cells with lysosomal activities where they eventually might get transported off by some T-cell receptor-anti-gens, as far as I understand (pls apologise and correct me if I am wrong). I would be interested in two questions regarding this specific immuno-cascade reaction.

It appears that in cases self-pepties are bound to the MHC-II proteins (say HLA-DP2) when they are at the surface already. Where do such self-peptides come from? Do they come from inside the endosomal active cell or could they also come from "outside" from where the T-cell comes?
What would happen if (for some reason)
a) the self-peptide binds "irreversibly" to the MHC-II?
b) the self peptide binds irreversibly to the MHC-II and at the same time is structurally significantly distorted (e.g. if there is something, like a heavy metal bound in-between the MHC-II and the self-peptide)?

(I apologise for the case I got some terminology wrong or some basic concepts, I am no specialist in bio-chemistry.)


texts:
After i had been studing for histology examp i tried to solved one nominclature dilema.Its about fibrocytes and fibroblast.

In my histology book is statment, that fibrocytes is special type of cell which can be differentiated to different cell types by specific occasion ( for example exposure to transcript factors).

Then fibroblast is cell of connective tissue. Its differentiated.

Why is differentiated cell named with blast (usually active type) istead fibrocyte (usually the differentiated one)?


texts:
I want to purify crude alpha-amylase with column chromatography. I am using a spehadex 75, But for some reason I can't find any information on how to make the slurry.

I can quickly find tons of information on how to pack and store a column, but what i really want to know is how much powder and buffer do I mix together?


texts: Do all commercial ionizers produce harmful ozone?

texts:
I'm not a scientist. I have read that negative ions have health benefits. I am interested in increasing the ratio of negative to positive ions in the air in my home.

I see that ionizer machines exist (e.g. https://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3Daps&field-keywords=ionizer).

I have also read that such ionizers produce ozone and that ozone can damage the lungs. Also sorry for not knowing what tags to use.

Do all ionizer machines produce ozone and are the levels produced harmful?

Please forgive me for my ignorance. If this is the wrong place to ask this question then please help me to find the right place.


texts: Weird gelatinous substance in highland bog

texts:
I recently went walking in the highlands in Snowdonia, Wales and we came across this:

Can anyone explain what it is? My guess was some kind of fungus but I'm not positive. The ground was very water logged and boggy.

It looked a lot like frog spawn, but it's autumn here and we wouldn't see frog spawn until Spring. There appeared to be no animals living inside or around it.

It's often called star jelly and there's a whole wikipedia article on Star Jelly talking about it:

  “Star jelly” (also called astromyxin, astral jelly, pwdr sêr, star
  rot, or star shot) is a gelatinous substance sometimes found on grass
  or even on branches of trees.1 According to folklore, it is
  deposited on the earth during meteor showers. Star jelly is described
  as a translucent or grayish-white gelatin that tends to evaporate
  shortly after having “fallen.” Explanations have ranged from the
  material's being the remains of frogs, toads, or worms, to the
  byproducts of cyanobacteria, to the paranormal.[2][3][4][5] Reports of
  the substance date back to the 14th century and have continued to the
  present day.


texts: Do floating plants on a quiet body of water significantly affect the evaporation?

texts: A situation such as a pond where a plant like duck weed covers essentially all visible surface water  : Is evaporation slowed or stopped ?


texts: All neuromodulators (dopamine, serotonin, acetylcholine, histamine, and norepinephrine) act only on metabotropic receptors?

texts: All neuromodulators like dopamine, serotonin, acetylcholine, histamine, and norepinephrine act only on metabotropic receptors?


texts: What's the minimum distance of focus for the lens of a human eye to reach maximum flatness?

texts:
According to the Wikipedia article on eye accomodation, the range in which a human eye can focus is from 7 centimetres away up to essentially an infinite distance. Of course, people can't see things an infinite distance away, but at a certain point the light reflected off an object will come at the eye in effectively parallel paths.

As an eye focuses on objects progressively farther away, it seems to me there would be a point when the lens hits maximum flatness, after which it everything will be equally sharp in focus. Looking at an object 500 metres away or 1000 metres away probably doesn't require any change in the lens. However, going from one metre away to seven requires the ciliary muscles adjust to just the right amount.

My question is, what is a normal minimum distance from the eye at which the lens will reach maximum flatness? Everything else in this question is just for context, so an answer to this, stated in metres from the eye, is all I am seeking.

The article I linked to above mentioned the human eye seeing "13 dioptres", and I have tried to understand dioptres, but it's a little confusing for me. If I understand correctly, the higher the dioptre, the closer you focus, so the 13 dioptres refers to how close the human eye can see. If I have this backwards, please let me know.

In any case, my purpose in asking is to determine the range in which ciliary muscles would be required to do more nuanced work in order to hold the lens at in the right shape. Focusing on something 7 centimetres away, the ciliary muscles are at maximum exertion, and at a certain point and beyond the ciliary muscles are completely relaxed. To hold somewhere in between would require more subtly nuanced, and, I suspect, more difficult work on the part of the ciliary muscles.

At least, I assume that to be the case because I am hypothesizing that the act of contraction for the ciliary muscles would be similar to other muscles. For example, it is easier to do a bicep curl with weight when going from full resting position to maximum contraction, as opposed to stopping at a particular spot somewhere in the middle of the motion. To stop mid-motion requires more muscle control, and, depending on how fast you wanted to do it, can be difficult to be exact.


texts: Given an EC50 value, how do I reproduce the sigmoidal curve from which this was calculated?

texts:
All-trans retinoic acid (atRA) is a potent ligand for a nuclear receptor called retinoic acid receptor alpha (RARa). The concentration of atRA at which RARa is half maximal is 19nM. The dose-response curve is sigmoidal, with concentration (log scale) on the x-axis and percentage of maximal activity on the y.

How would I use this information to reproduce the dose-response curve?

Thanks


texts: Can a hinge joint technically allow rotatory motion?

texts:
Let's use a hinge joint and pivot joint as examples.
When talking about the difference between them in terms of movements permitted, I see that on any websites and textbooks, the term 'rotation' is applied to pivot joint only rather than hinge joint.
For example, according to Moore Clinically Oriented Anatomy 10th edition.

Hinge joints permit flexion and extension only, movements that occur in one plane
(sagittal) around a single axis that runs transversely; thus, hinge
joints are uniaxial joints.
Pivot joints permit rotation around a central axis; thus, they are
uniaxial. In these joints, a rounded process of bone rotates within a
sleeve or ring.

I never see the word 'rotation' being used to describe hinge joints' motion, however, doesn't hinge joint technically allow rotation, just that the rotation for hinge and for pivot joints are over a different axis? For example, at the anatomical position, flexion in the elbow's hinge joint involves rotating the joint along the tranverse axis.
So my question is, can a hinge joint technically allow rotatory motion? If not, am I misunderstanding what is meant by 'rotation'/'rotatory motion'?


texts: What is the difference between different brain regions

texts:
The brain is separated into different regions, and different regions perform different tasks. Well, what are the differences between these regions on the cellular/systemic level. The brain is made up of neurons and other cells, but how come one part is used to process sound and another is used to process, say, smell? Are they like different computer circuit boards - using the same components but are wired differently?

And anyways, why did evolution not come up with a brain that uses the entire brain to process something, would that not be more efficient?


texts:
Does DNA polymerase I in bacteria use forward or reverse exonuclease activity to remove RNA primers? One of my books says it uses 5' to 3', but another says it uses 3' to 5' exonuclease activity.

Update: I know RNase H can remove the primers, but the exonuclease activity of pol I can also remove them.


texts:
I'm wondering what kind of snake is the one in the attached photo. It looks like Vipera aspis but It seemed a bit too big (lenght of about 1 meter).

This photo was taken near Como, in the north of Italy, in the woods of Parco Spina Verde.


texts: Purpose of intensive protein synthesis in G1 phase of mitosis

texts: What is the purpose of intensive protein synthesis in G1 phase of mitosis, and what purposes do these synthesized proteins serve? Why are lipids and carbohydrates not synthesized intensively as well?


texts: Is a flower having 12 petals trimerous or tetramerous?

texts: Suppose if a flower has 12 petals. Then 12 is a multiple of both 3 and 4. So which category of flower is it? Is it trimerous or tetramerous?


texts:
What is the coefficient of relatedness between a queen bee and her daughter if the male that mated with the queen was the queen’s own son?

The answer should be 0.75, but I keep getting 1 because 0.5(queen-daughter) + 0.5(queen-male) * 1(male-daughter) = 1.

1 also makes sense because all of the daughter's genes come from the queen. However, I do understand that there is a chance that the genes inherited from the daughter's mother and father may overlap. How is that calculated?


texts: Why is sex hurtful for some animals but pleasurable for others?

texts: Sex seems to be pretty hurtful for feline for example. On the other hand sex is pleasurable for humans. Why is sex pleasurable for some and not for others? How do these things evolve?


texts: Are the proteolytic enzymes in syconiums and nettles identical to those in rennet?

texts:
I would like to compare rennet capability under various conditions. The issue is, I don't want to use calf rennet, but I can't figure out if nettle and syconium, which also coagulate milk, contain regular rennet or other enzyme? If so, what is its name? It's quite important.
Thank you.


texts: What is the pathogenuc mechanism of brown pigment lipofuscin in muscle atrophy?

texts:
I think it is autophagy. Lysosomal degradation. Autophagocytosis.

Example of the brown pigment (lipofuscin) here:

I am not sure if autophagy is the right answer to the "pathogenic" mechanism of atrophy.

Is autophagy the pathogenic mechanism of atrophy?
Or what pathogenic mechanism is involved if you see lipofuscin in the histologic slide?


texts: What does NaOH do for the plating of Bacillus subtilis?

texts:
A book called Molecular Biological Methods for Bacillus called for plating Bacillus subtilis cells on LB-agar plates with the following components:

  A general-purpose medium containing per litre:

  Bacto-tryptone 10 g

  Bacto-yeast extract 5 g

  NaCl 10 g

  1 M NaOH 1.0 ml

  Autoclave (151b/in^2, 30 min). For LB agar plates solidify with 1.5% (w/v)
  agar; for LB overlay use 0.7% agar.

The first three components and their corresponding amounts are the same as what I normally work with, but I usually add distilled water for plating E. coli instead of NaOH. According to Wikipedia's entry on lysogeny broth, NaOH can be added to adjust LB's pH. But the protocol here mentions nothing of that sort. In other protocols of the book, at least it would say "adjust to pH -- with 10 M NaOH" or 1 M NaOH, etc. So if it is not to adjust the pH for the growth of Bacillus subtilis, what other purpose does NaOH do for the bacteria?

Also, I usually autoclave my LB or LB-agar for 2 hours instead of 30 minutes. Would autoclaving at 2 hours instead of 30 minutes affect NaOH?


texts: Neural coupling between Pinsky-Rinzel (reduced Traub) neuron with a Wang-Buzsaki neuron?

texts:
I have read two papers related to modeling neurons. The first one is the paper by Pinsky and Rinzel and the second one by Wang and Buzsaki. The first mentioned neuron model is a excitatory neuron based on NMDA and AMPA neurotransmitters. The second one is inhibitory neuron model based on GABA. So I modeled them individually. Now trying to couple such that pre synaptic PR neuron will connect to post synaptic WB neuron which also connects to PR neuron. That is in effect an excitatory-inhibitory coupling with feedback.

Now how would the action potentials of both neuron look like?
Will both oscillate, or only WB neuron alone oscillate?
Is there any specific conditions for the oscillations to occur?

Any speculations, ideas, references (like books, related papers) would be helpful.

NOTE : By action potentials, I mean the neuronal membrane voltage signal which varies with time.


texts: Will Fst (inbreeding coefficient) always be a value close or at 0 in asexual populations?

texts:
FST is the average inbreeding coefficient of a total population. The equation is:
$F_{ST} = \frac{Var(S)}{Var(T)} $
$Var(S)$ = variance in the frequency of the allele between different subpopulations, weighted by the sizes of subpopulations
$Var(T)$ = variance of the allelic state in the total population
If $F_{ST}$ equals 0 that means there is no population differentiation and there is no heterozygosity in the population. The ceiling for $F_{ST}$ is one so there is population differentiation and the population is all heterozygotes.
If the population is asexual, meaning they are parthenogenetic, would $F_{ST}$ be at or close to 0? Can this not be assumed?
In the context of this question I am considering the whole genome or just one allele.


texts: What is the origin of viruses? How could they get both living and non-living characteristics?

texts: I read that viruses are called intermediate between living and non-living particles. Well, if so, then where did they originate from?  From living or non-living? If they originated from either living or non-living then how could they have both the characteristics of living and non-living?


texts: Where can I obtain Sputnik virophage samples?

texts: I'm working on a project where I'm trying to use virophages as viral vectors in introducing CRISPR-Cas proteins into other viruses. I was wondering where I might be able to find replication-defective Sputnik virophages or other virophages for this kind of experiment?


texts: Is it possible to make bones ossify much slower in adults?

texts:
According to Can we artificially increase human growth using HGH,

  But during normal human development bones ossify in the process, and in human adults the bones are completely ossified and can't grow in length anymore.

Is it possible to make the ossification process much longer?


texts: Are prions an important driver in evolution?

texts:
I understand that prions have been implicated in the passing on of epigentic information[1]. Are prions thought to play a significant role in the evolution of organisms?

 Alberti S, Halfmann R, King O, Kapila A, Lindquist S. 2009. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137: 146–58.


texts: Do men and women have the same number of genes?

texts: As far as I know, humans have 23 pairs of chromosomes, each one which contains a particular amount of genes. But in the "last" pair, men have a XY pair chromosome, and women have a XX pair chromosome. Does the missing "leg" of the XY pair make men to have fewer genes than women, and if so, how many genes do each sex have?


texts:
I'd like to know the name of a gene with the following description of effects:

Humans having two copies of this gene with a certain mutation aren't able to acquire human language, but otherwise their intelligence is not depressed
The human version of the gene differs significantly from the one found in the great apes
The human version of the gene was transferred to mice, and it was reported that the "voice" and the communication of the so-manipulated mice differs from the one of "wild" mice
If I remember correctly, the gene has the letter "x" in it like hox or pox or pax but alas, memory can be faulty

What is the name of this gene?

Bonus question: What are relevant publications concerning the gene described?


texts: what is linkage disequilibrium supposed to measure?

texts: During reading about genetics I came across with the term of linkage disequilibrium, and I do not really understand what it supposed to mean. What is linkage disequilibrium? My current understanding that it is "deviation from independent assortment",


texts: After RNA isolation and before following experiments, I know that RNA quality so called RNA integrity is so important. So why there is a RNA fragmentation kit? Do we need RNA intact or fragmented? (RNA will be used for biotinylation and RT-qPCR afterwards)


texts: What medical and commercial proteins are made using genetically modified animals?

texts:
Recombinant technologies in micro-organisms being used to produce commercial and medically useful proteins like insulin are fairly common.

However some proteins are still produced commercially in genetically modified animals. Why are animals a better choice than microorganisms, and which are the most common proteins produced this way?


texts: Is there a known or quantifiable correlation between capsaicin and its effect on the body's metabolism?

texts: I've often heard that spicy foods can speed up your metabolism, I presume, due to the capsaicin.  Though I'm sure this is a minor effect - I doubt eating a pound of jalapenos a day will help me lose weight - has the medical/nutrition community quantified how various levels of capcaicin affect the body's metabolism?


texts: Practical Question about Evolution, Population Genetics and Speciation

texts:
North American cicada male of the genus Magicicada sing depending on the species at different times of the day and attract the females of the corresponding species. The species are very similar, but when crossing they have sterile (infertile) offspring.

In the species M. tredecim the time of the song is determined by the gene locus EARLYBIRD in an intermediate inheritance: The allele EARLYBIRD leads in the homozygous state to morning singing, the allele earlybird leads in the homozygous state to evening singing, heterozygotes sing at noon.

How does the frequency of the earlybird allele in the species M. tredecim change when the number of females of M. tredecassini increases? Does it increase, decrease, or does it remain the same?

I think it would not change the frequency of the earlybird allele, because they don't have a evolutionary advantage. But maybe it could also decrease the frequency, because infertile descendants sounds like a disadvantage? But I'm totally not sure and can't provide a real 'biological' reason since my thoughts are more like intuition.


texts: To what exten do children produce antibodies against covid-19?

texts:
Here in Sweden all kindergartens and schools up to the month of June the year people turn 16 remain open. In almost all other European country schools are closed.

I do not really know why our schools are open, the official policy is unclear. One idea though is to get the children to catch the disease while the elders remain in hiding in order to acquire more immunity in the society.

However, according to some Chinese study younger people seem to be able to fight the disease without antibodies. In the age group 15-39 the number of antibodies found were less then a third of the number of antibodies found in the age group 60-85.

https://www.scmp.com/news/china/science/article/3078840/coronavirus-low-antibody-levels-raise-questions-about

Question: To what extent does infected people in the age group 0-16 develop antibodies against covid-19?

I know that presence of antibodies do not necessarily guarantee immunity against reinfection but if children do not produce enough antibodies they will obviously not be immune.


texts: Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

texts: A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a transporter to remove cadmium? My other thought is that the interaction only appears as a result of the methods the scientists used to determine the structure of the protein.


texts: Exclusion and inclusion criteria for healthy controls in colorectal cancer study

texts:
I'm working on colorectal cancer, and I'm facing a problem in the sampling step, I can't figure out how to choose healthy subjects. In the literature, I've found many criteria that are different and sometimes not clear or the author don't mention how he chooses his control samples.
PS: I'll collect stool samples, not tissues.


texts: Can the restless leg syndrome may have been caused due to natural selection?

texts:
Disclaimer: I don't know how much restless the leg has to be, in order to be considered a syndrome.

RLS runs not only in my family but also several people in the locality. My hypothesis is that RLS is a genetic/epigenetic adaptation to prevent mosquitoes or other insects from sucking blood. I, indeed, live in a malaria zone. I don't know enough biology to device a scientific experiment to prove my hypothesis.

Is there any scientific research done in this field? Someone who is well versed in this field should try it.


texts: Are your finger muscles and tendons interconnected?

texts:
Are finger muscles and tendons interconnected? If they are interconnected, then if i exercise one finger will it train the other fingers since they are interconnected and share the same muscles in the forearm? (correct me if im wrong)

I have done some research but i cant find the answer for example(if your thumb joint is injured you should avoid using stress balls to exercise the other fingers, why?)


texts:
I'm using a 300l/h trickling filter consisting of 4 round chambers in vertical alignment with 11cm diameter, 5cm height and 5cm distance for the trickling (100 to 500 holes per level) in a 15cm pipe. The top is open in order to allow air exchange. 2 chambers are filled with 2 to 4mm gravel, one with filter cotton and one with clay pipes. It is used for nitrification of aquarium water.

The filter is loud and I want to muffle it. I already figured out that laying 2 levels of microfiber towel on top of it helps. I also have the option to build a wooden enclosure.

What measures should I take in order to reduce the available oxygen for the nitrifying bacteria as few as possible? Could the exchange through the towels be sufficient? Should I use a special membrane in the enclosure? Does it make sense to connect an aquarium air pump to the inside of the filter?


texts: Difference between sequential and conformational epitope

texts: Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


texts: How long does it take for a genetic trait to dissipate if its no longer selected for?

texts:
Have their been any studies or experiments done that provide insight into the persistence of genetic traits if an environmental shift suddenly causes that trait to be neutrally selected for? Does it take 100s of generations to reach equilibrium or only a few?

For example, how long can we expect the effects of birth control to take in decoupling human behavior related to sex from human behavior related to having children?


texts: Terminology question about the correct term for areas of biological research

texts:
I am writing a paper about DNA sequence prediction. DNA sequence prediction is done across various areas of biology, including, for example, RSS sequence prediction (in immunology) and prediction of promoter regions in vertebrate DNA sequences.

I was just wondering how one would describe such specific areas as "RSS sequence prediction" and "promoter region prediction". To be concrete, I wanted to write something like:

  This paper describes a method of DNA sequence prediction using
  standard Bayesian modelling techniques. While there is much existing
  work on DNA sequence prediction, most of this work is in the context
  of biological research. Typically the techniques used are very
  specific to the biological subdomain under consideration. Also, these
  techniques often use use additional biological information about the
  biological sequences under consideration, besides the sequence data
  itself.

Is the term subspeciality the correct term to use here? Would biological area or biological domain/subdomain be better, or some other term?

Incidentally, if anyone knows other areas where DNA sequence prediction is used, please mention it/them. Thanks.


texts: qPCR : Cross-contamination while sealing plate

texts:
I'm trying to do realtime PCR on a plasmid and I have my positive and negative controls close to each other along with a no-template control. I add 1 ul of my template last into the 96 well plates (on the side wall of the well, to be precise) and I seal the plate with optical adhesive seal (applying pressure with hand) and centrifuge afterwards.

While sealing I have noticed that the template drop I add on the side of the wells is being wicked up and is likely spreading into the neighboring wells. I notice amplification even in wells where I added water instead of the template

Has anybody notice the same or has any suggestions for how to avoid this? Do you add template into the liquid in the well or onto the side wall?


texts:
A vague question, but let me try to explain. My friend explained to me that in females, some cells use one X chromosome, while all others use the other X chromosome. This can result in some differences of appearance of certain individuals. The Wikipedia page on X-inactivation shows an example. There is a picture there that shows a cat with fur of two colors, each showing in seemingly random groups. My friend had explained that when one cell "deactivates" its X chromosome, all of its descendants have the same deactivated X chromosome, so it makes sense that the similar colors appear in groups on the cat's coat.

But it seems tigers' coats are much more complicated than that. The pattern on a tiger's coat is not completely random. They make very discernible shapes. There are clear borders inside which only black fur grows, and outside of which only orange fur grows. How is this possible?

I'm not suggesting that the patters on tigers' fur is in any way related to X-inactivation, since I know that only applies to female mammals. But X-inactivation seems like a "natural" phenomenon, while the stripes on a tiger (or other animals with complex patters) seem a bit more bizarre. How do the cells on a tiger's body know which color to show and still follow the pattern?


texts: Do mutant alleles result from mutation of the wild type?

texts: The allele that encodes for the most common form of a phenotype in natural population is called a wild type allele and all the rest of the alleles encoding forms other than the wild type are called mutant alleles. Do they result from mutations of the wild type allele?


texts: Where does an organism store reserves of amino acids?

texts:
Where does an organism store reserves of the amino acids it needs to build various proteins it needs:

in the liver?
in the blood?
in every cell?


texts: A Chinese man has been drinking gasoline to relieve his pain for 25 years. How does the human body metabolize gasoline? Also, what are the side-affects to gasoline?


texts: What does it mean for a protein to be dominant-negative?

texts:
I am reading this journal paper, which investigates the interaction of the NCAM protein and the Pak1 protein. In this paper I have come across the term "dominant-negative Pak1" and "constitutively active Pak1". I am not sure what exactly is meant by a protein being dominant-negative. I have searched online and found that dominant negative refers to a mutation whose gene product adversely affects the normal wild-type gene product within the same cell (with this occurring if the product can still interact with the same elements as the wild-type product, but block some aspect of its function).
Would I be correct in inferring that dominant-negative Pak1 is a mutated version of the wild-type Pak1 and interferes with the normal activity of wild-type Pak1 in cells? Any insights are appreciated.


texts:
If an alpha helix is discontinued for a short while and then continues in a different direction, I prefer to call in "kinked". If the helix is simply uniformly following one direction, I prefer to call it "straight", but I have been corrected, and been told that it is called "linear". Which is right?

Thank you!


texts: How are cells of the cornea transparent?

texts: We know that cells have mitochondria, chromosomes and other organelles so that's why they are opaque but can you say how the cells present in the eye cornea are transparent and allow light to pass through?


texts: Do ectotherms think slower when they are cold?

texts:
Animals near the ectotherm side of the endotherm-ectotherm spectrum rely on external heat sources to regulate their body temperature. When they are cold, overal enzyme activity and metabolic rate is lower.

My question is if these animal tend to 'think' slower when cold?

To be honest, my knowledge of brain physiology is very sketchy, I'm not sure biochemical activity plays a large role vs. electrical and diffusion processes and the latter would be less temperature dependant. So I'm not sure we would expect ectotherms to 'think' slower.

OTOH, wikipedia on endotherms states ...

  Some ectotherms, including several species of fish and reptiles, have been shown to make use of regional endothermy, where muscle activity causes certain parts of the body to remain at higher temperatures than the rest of the body. This allows for better locomotion and use of the senses in cold environments.

The source for this claim is on google books, just not the relevant pages (Willmer, Pat; Stone, Graham; Johnston, Ian (2009). Environmental Physiology of Animals)

I'm also not sure how to define 'thinking' within this wide range of animals, I'll take any metric for  speed at cognitive tasks or reacting to external stimuli.


texts: What does orbital mean in orbital frontal cortex?

texts:
Orbital frontal cortex is where decisions are made.

What does the word orbital there mean?

I looked around in wikipedia and never find it.


texts: How can rooted and unrooted (phylogenetic) trees be distinguished from one another

texts:
I understand that rooted and unrooted phylogenetic trees are similar in structure

But how can they be easily identified as one or the other?

Is it simply based on the presence or lack of a named root (the root is identified as a particular ancestor) or outgroup?


texts: Key points of Wagner's theory of innovation

texts:
What are the key points of Andreas Wagner's "theory of innovation" from his book The Origins of Evolutionary Innovations?

Specifically:

What is new in his theory?
What problems in evolutionary theory does it address*?


texts: Visualising a subset of the tree of life

texts:
I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess at their evolutionary relationships?

The best site I managed to find so far is http://itol.embl.de/itol.cgi, which allows you to select specific species from the main tree to plot into a sub-tree, but the tree itself is rather small, so more detailed comparisons cannot be made.


texts: Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

texts:
DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length?

A related question can be found here: why-are-there-exactly-four-nucleobases-in-dna


texts: Help me identify these creatures found in sink

texts:
The conical flask was kept in a sink for about 3 or 4 week, was waterfilled, and I have no idea if they grown after the flask was waterfilled or before the flask was waterfilled. We do not work with animals so these arenot any experimental material, but maybe they are soil borne if the conical flask contained soil sample (I do not have any idea what was kept in that flask before it was left in that sink)

They were not moving and they were sticked firmly on the glass wall. They had some constriction marks. Length apporox 0.2 to 0.5 cm, Width approx 0.1 to 0.3 cm. colour pale white to brown.


texts: Is intelligence correlated with neural calorie usage?

texts: The human brain uses a lot of calories in comparison to other species, that is usually explained by referencing the intelligence disparity between Humans and other Animals. My question is how far does that go? Do individuals with radically improved intelligence also use radically more calories? And peripherally, does that caloric need place an upper limit on human intelligence?


texts:
Scientists made a new image of brain.

I wonder, what is this arc (denoted by blue)?

Is it the caudate nucleus?


texts: Is it possible to use PCR to test for Machado-Joseph disease?

texts:
Machado–Joseph disease (MJD) is a rare inherited neuromuscular disease that is caused by a mutation in the gene ATXN3. The protein encoded by this gene contains "CAG" repeats in the coding region, and the expansion of these repeats from the normal 12-44 to 52-86 is the most common cause of the disease.
It is well known that amplification of repetitive DNA by PCR is prone to errors, mainly caused by misalignment/slippage of the polymerase during the elongation phase.
Does anyone know if there exists a specialized PCR protocol or polymerase that could accurately amplify the repetitive region of ATXN3 such that one could then use gel electrophoresis or Sanger sequencing to approximate the number of CAG repeats?


texts: What are potential side effects of myostatin inhibitors?

texts:
Myostatin inhibitors, which are being developed to treat muscle wasting diseases like muscular dystrophy, are likely to be abused by athletes. What are the potential long-term side-effects of taking a myostatin inhibitor? Will it have different side-effects for patients compared to healthy athletes (especially young athletes that are still developing)?  Could there be adverse drug interactions with other common performance enhancing drugs like EPO, hGH, and anabolic steroids?

Sources I've explored (StackExchange is only allowing me to insert two hyperlinks):

New Muscle Drugs Could Be The Next Big Thing In Sports Doping - NPR story by Jon Hamilton
Wikipedia entry on myostatin
Wyeth found one of its drugs to be safe in a clinical trial, but it stopped development because the drug was ineffective at increasing muscle mass.
An internet search mainly brings up dieting and body building forums, which I do not trust.
According to a review by Breitbart et al. 2011, myostatin inhibition does not have negative effects on cardiac tissue.
According to a review by Allen et al. 2012, the increase in muscle mass caused by myostatin inhibition leads to be metabolic health (e.g. lower glucose levels and higher insulin sensitivity).


texts: What is the evolutionary advantage to a lifespan limit?

texts:
How/Why

Do Koi have a lifespan of hundreds of years?
Do humans have a lifespan of decades?
Do dogs have such a short lifespan?

Within these questions I pose further questions.  How does size relate to lifespan. Elephants?

If dogs were to evolve independent of humans (at this point) would they rule the world?


texts: I know that sodium deficiency can be deadly. But why is it deadly? Is it because of your muscles getting so rigid that you can't get something with salt in it? Is it because of your brain not able to send signals? Is it because of excess urination to try to get the sodium levels right? Is it because of anemia leaving red blood cell ghosts(the membranes of rbcs) in your bloodstream? Is it a combination of all these factors?


texts: Has anyone modelled calcium oscillations using Matlab software?

texts:
I have been trying to model calcium oscillations using MatLab, but I cannot obtain the oscillation.

I created a function where I put all the equations and used ode15s to call the function.  I have listed the equations and the code.

Can anyone tell me why I am not obtaining the oscillations?

These are the equations along with the codes:

r(:,3) = ( (((.029*0.13*1.049 + .21.*.5.*.144).*initi(:,1)) ./  (.144.*1.049.*(.5+ .13)) ) .*( 1- initi(:,3)) ) - (( (.21 *.5 + .029 *.9434) ./ (.5 +.9434) ).*initi(:,3));

  The values of the upper case Ks are obtained as follows:

  and the value of p is 0.5

a(:,1) = power (( (.5 .* initi(:,1) .*(1 - initi(:,3))) ./ ((.5 + .13 ).*(initi(:,1) + .0823)) ),3); % p_o

  Jserca is directly substituted in the equation shown below

r(:,1) = (( 1.11.*  a(:,1) + .02 ) .* (  initi(:,2) - initi(:,1) ) ) -( .9 .*  power(initi(:,1),2)) ./ ( power(.1,2) + power(initi(:,1),2) );

 r(:,2) = - r(:,1) .*5.5; % Ce

  The constants are shown here:

  And this is the desired result:

  But I obtain this!

  And this is my code:

function[t, initi, r,a]= deyoung()
clear all;
clc;
close all;

%--------------------------------------------------------------------------
% Initial conditions
%--------------------------------------------------------------------------
initi(:,1) = 0;  %  C
initi(:,2) = .9; %  y
initi(:,3) = .5; %  Ce

%--------------------------------------------------------------------------
% ODEs
%--------------------------------------------------------------------------
icon=initi;

tspan=[0 100];

options = odeset('RelTol', 1e-08, 'AbsTol', 1e-08);

[t,initi] = ode15s(@(t,initi) oper(t,initi),tspan,icon, options );

[r,a] = oper(t,initi);

figure();
plot(t,initi(:,1),t,initi(:,3));

end

function [r,a]=oper(t,initi)

    initiSize = size(initi);

    initiColumnCount = initiSize(2);

    if ( initiColumnCount == 1)
        initi = initi';
        a = zeros(1,1);
    else
        initiRowCount = initiSize(1);
        a = zeros(initiRowCount, 1);
        r = zeros(initiRowCount, initiColumnCount);
    end

    % y
    r(:,3) = ( (((.029*0.13*1.049 + .21.*.5.*.144).*initi(:,1)) ./  (.144.*1.049.*(.5+ .13)) ) .*( 1- initi(:,3)) ) - (( (.21 *.5 + .029 *.9434) ./ (.5 +.9434) ).*initi(:,3));

    %Po
    a(:,1) = power (( (.5 .* initi(:,1) .*(1 - initi(:,3))) ./ ((.5 + .13 ).*(initi(:,1) + .0823)) ),3); % p_o

    %C
    r(:,1) = (( 1.11.*  a(:,1) + .02 ) .* (  initi(:,2) - initi(:,1) ) ) - ( .9 .*  power(initi(:,1),2)) ./ ( power(.1,2) + power(initi(:,1),2) );

    %Ce
    r(:,2) = - r(:,1) .*5.5; % Ce

    r = r';

end


texts: Evolution question on speciation? Really confusing!

texts:
Okay, my teacher assigned this homework question, but nothing like this was ever given in our textbook.
Suppose that a type of tree tends to speciate over 10 million years and a species of fly tends to speciate over 1 million years. In the event of a mass extinction, which of the following predictions would LIKELY be true?

A) It is impossible to determine how many niches or species the trees and flies would lead to over time.
B) The trees would fill more niches and create more species than the flies.
C) The flies would fill more niches and create more species than the trees.
D) They would both lead to the same number of species.

I am stuck between A, B, and D because A would have merit, as speciation period may not always correlate to have many changes occur, B may have merit because it could be showing a Gradual model of speciation, and D may have merit because they might both just end up as the one species described? Any help, not even an answer but guidance would be really great.


texts: I was carrying a can of very cold liquid, had something heavy in my other hand so couldn't switch hands. After a few minutes, I started to feel very intense pain. I was very surprised. cold is just atoms moving slower. This makes more sense if you think about how heat, or burns can cause pain. But heat can cook tissue and disable it, it makes sense it would hurt.


texts:
Wondering if there is a comprehensive list/database of cell types, similar to this wiki list of cell types in the human body. It lists probably 100+ different types, but this is just for a human. If we include all animals, and plants, and bacteria, and single celled organisms, etc. then the list would probably get larger.

Wondering if any such aggregation exists, either just as a collection of lists or as a database of cell types. Doing a search returns CELLPEDIA, but the last results are from 2011, so it looks like it never came to be. I also saw MorphoBase, but it didn't look like it was there either. But something like that would be good, otherwise just a list. Basically like a cell taxonomy.


texts: I found it in the forest but I've never seen anything like it so I took it home to see what it is. Does anyone know?


texts: Are there eukaryotes with fully working mitochondria but without mitochondrial genes?

texts:
Are there eukaryotic organisms with fully working mitochondria that do not have genes in the mitochondria?  By fully working, I mean ones which can carry out oxidative phosphorylation, unlike reduced mitochondria like organelles such as mitosomes in Giardia lamblia.

Is it possible to transfer all mitochondrial genes to the nuclear DNA and still have fully-functioning mitochondria?


texts: How does discontinuous distribution provide evidence for evolution?

texts:
One of the evidences for evolution is bio-geographical evidence.

In it,'discontinuous distribution' is mostly cited as an evidence.

For example,

Alligators are found only in south-eastern US & eastern  China; elephants are found only in Africa & in & around India; lung fishes are found only in South America, Australia, Africa.

Their distribution is discontinuous due to possible changes like continental drift etcetera.

But, I am not understanding how these discontinuous distributions prove evolution.

Can anyone help me explain how they provide evidence for evolution?


texts:
Can there be medium height(neither tall nor short) pea plants in Mendel's experiment?

All textbooks I have read seem to imply that pea plants have to be either tall or short, nothing in between.


texts: Why pellet and resuspend E. coli for plasmid prep

texts: For maxipreps, cant you just add all the stuff that would be in P1 (RNase A, EDTA) then just add P2? Because if we pellet cells then resuspend theres got to be a reason, right? Is it slats and other stuff in the media that mess with lysis?


texts: Can HIV be automatically cured by waiting until CD4 T cells count drop to 0?

texts: As I know, HIV needs host cell, CD4 T cell to repicate itself, and at late stage of AIDS, count of this cell in patient will drop to 0, my question is, if we can provide a sterilised environment for AIDS patients at late stage, will HIV be cured because CD4 T cells drop to 0 and hence no host cell for HIV to replicate itself?


texts:
A patient diagnosed with cancer takes antiproliferative drugs. Suppose the intake of drug(dose) is 250mg and excreted amount 125 mg. Amount of excreted drug as metabolites 1 and 2 are 75mg and 50mg. T1/2 is 4 hours. Calculate its elimination rate constant (K).

My idea is : amount actually used from the body is 250(dose) - 125mg amount excreted= 125mg. Which means that we are at steady state. Steady state is reached after 4 half lives (t1/2). Taking this into consideration we calculate 4 k respectively: K=0.693/4 ; K=0.693/8 ; K=0.693/12 ; K=0.693/16


texts: Why a continuous supply of energy is needed to support a weight?

texts:
What motivates this question is the apparent discrepancy between the concept of Work in physics and in physiology.
Work in physics is defined as the dot product of the force applied to move a certain object by its displacement:
$W = \vec{F} \cdot \vec{d}$
$\text{ Work  =  (Force) $\cdot$ (Displacement)}$
Where $\vec{F}$ is the force vector, and $\vec{d}$ is the displacement vector.
Now if there is some weight lying on a table, it takes no Work at all to maintain its present configuration, since both $\vec{F}$ and $\vec{d}=0$, As a result $W=0$. In other words, this weight-table system does not need to be provided with energy at all, for the table to be able to support the weight, because it takes no energy to support it.
What about an identical case but with a human hand supporting a weight(at a constant height) at this time? Although according to the above reasoning one should expect that it does not need any energy to support the weight, this is not what we observe in everyday life, because when I hold the weight, it takes a tremendous amount of effort to support and maintain its position.
When I looked up the reason behind this, I found out that it has to do with the fact that the muscles of the arm are skeletal muscles not a smooth one.
If the arm were made out of smooth muscles, then it would take no effort or energy at all to support any weight at a fixed height.On the other hand, the muscle fibers that contract to support the weight in Skeletal muscles has to be continuously provided with energy to be able to support it, and hence although no mechanical work is applied on the weight so $W=0$, nevertheless energy is wasted in the form of heat in this process, and hence we get tired after holding an object for some time.
So what is the mechanism by which Skeletal muscles support certain weight? Why it needs continuous supply of energy while holding an object? How is this energy supplied( my guess is:some component of a cell breaking down molecules so as to transfer chemical energy to mechanical contraction of muscle fibers)?And how it differs from smooth muscles?


texts: What is the difference between sinew and tendon?

texts:
I wonder what the difference between sinew and tendon is. I searched for it but didn't get any clear answer:

https://www.quora.com/Whats-the-difference-between-sinew-and-tendon:

  They are often used interchangably but to be technical, a tendon
  connects a muscle to a bone. The term sinew also seems to include
  ligaments which connect bones to bones. It is however, not a medical
  term.

https://answers.yahoo.com/question/index?qid=20070410182936AA2Kcnk

  Sinew is another word for muscle which is the functional unit of
  movement.

  Tendons connect bone to muscle to make movement possible: The muscle
  contracts and pulls the bone that it's connected to Source(s)

http://the-difference-between.com/tendon/sinew :

  Sinew is a synonym of tendon. As nouns the difference between sinew
  and tendon is that sinew is (anatomy) a cord or tendon of the body
  while tendon is (anatomy) a tough band of inelastic fibrous tissue
  that connects a muscle with its bony attachment.

http://www.thefreedictionary.com/sinew

  sinew = tendon

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

  A tendon (or sinew) is a [...]

Is sinew a synonym for tendon, and if not what is the difference?


texts: Does sample buffer require EDTA for protein separation on SDS PAGE?

texts: In sample buffer preparation we add EDTA, but if SDS-PAGE is for protein then is it necessary to add EDTA in sample buffer? What is role of EDTA in sample buffer for protein separation for SDS-PAGE.


texts: Why do some insects constantly move their abdomens?

texts: Why do some insects, such as wasps, constantly move their abdomens?


texts: What global habitat classification systems are there?

texts:
I am an IT guy, not a biologist or ecologist, but have ended up with (roughly) the task "given this Latitude/Longitude pair, return the 'habitat' at that location". The points of interest in practice are likely to come from Europe or North America, but could come from anywhere. All data points will be terrestrial, not marine. What habitat means isn't fully defined, and I'm looking for a best-practice answer.
At this point I thus have a question: "what are the well-regarded global habitat classification systems?". A basic search leads me to the IUCN Red List Habitat classification 3.1. From there, I find some nice recent research work by Jung et al that attempts to map the world onto an IUCN habitat type by combining data from a Koppen-Geiger climate classification system, from Copernicus land-cover data and from an ecoregion+biome classification coming from the WWF. This classification has had a number of iterations, but currently seems to have 867 ecoregions in 14 biomes. The resulting map is at approx. 100m resolution and maps on to 47 of the IUCN habitats.
To my amateur, all of this seems great, but is it the state-of-the-art? Or are there other habitat classification schemes out there? Where should I be reading?
Many thanks indeed for any help and apologies in advance if I have broken any rules of the site - this is my first post.


texts: Role of isopropanol in plasmid isolation

texts: In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? How does it not renature every other macromolecule?


texts:
I read once that we have two sources for proteins:

Protein that is made in cells
Protein that is made in labs

However, based on Miller–Urey experiment, it's argued that amino acids can be made from initial Earth's condition, and from this link, it seems that protein-first world is a hypothesis.
Yet if we accept that proteins could be made before cells, then the process that made proteins in the first place is still out there. This means that we should be able to find proteins outside cells or labs in nature.
Do we find protein not of cellular origin in nature?


texts: How do bull semen companies get the semen out of the bulls?

texts:
Prompted by this article, which discusses the low number of bulls who sire US dairy cows.

How do semen companies extract semen from bulls?

The procedure to extract semen from humans is simple enough, but I'm struggling to picture a lab operator masturbating a fully grown bull until it ejaculates to collect semen. Is there some kind of specialized equipment involved? What does the operating procedure look like?


texts: I recently found at least 50 of these little bugs roaming around my window  sills indoors in my bedroom right behind the head of my bed. I can’t seem to find what they are. I’d love tips on what they are or how to get rid of them. They’re extremely small probably no larger than 1 mm. I tried vacuuming them away but I still see plenty of them.


texts: Is the mesenterium a synonym for the mesocolon?

texts: On biodigital anatomy browser I found a structure called the mesocolon. I didn't find the term in Uberon and I'm unclear whether it's simply a synonym for mesenterium or whether it's a separate concept.


texts: Do ant colonies prioritize survival of particular members above others?

texts:
In some (perhaps small) human communities people may starve because they have no income. This could be interpreted as a consequence of them not participating in the community, hence they don't get any income and are left to their fate of starvation. Also, we can imagine that important members of the community are less likely to starve, as they are given priority treatment (e.g. a royal family will less likely starve to death during a given famine).

Do ants in a given colony allow members to starve when they don't serve the colony, even if there is no scarcity of food?
Secondly, do ants follow a chain of importance and are members of least importance allowed to starve first in times of shortage?


texts: Can the colour of skin change with age? Can a dark skinned person become fair or vice versa?  Can Melanocyte production vary?


texts: How do opportunistic infections affect an immunocompromised or AIDS patient?

texts:
I mean, everyone knows that AIDS patients don't die of the HIV infection, rather the opportunistic infections. But if HIV only affects T lymphocytes, and destroys them, then that means only cell mediated immunity and humoral immunities are affected (since B cells need helper T cells to be activated).

The body should still be producing other types of leukocytes like neutrophils and macrophages, which should eliminate most bacteria. So does HIV infection render the mononucleaf phagocytic system useless as well? If yes, how so?


texts: If an axon is completely myelinated (doesn't even have Nodes of Ranvier), is it faster than an un-myelinated axon when conducting action potentials?


texts: What kind of snake is this? Seen in Peru along the Inca Trail

texts: I have been searching so much to find out what kind of snake this is. It looked black with white stripes. We found it on the Inca Trail to Machu Picchu in Peru. It was about 2500 m above sea level.


texts: How do you derive steady-state conditions from the open-state differential equation of ion channels?

texts:
My books describes this differential equation for the open state of an ion channel:

Where $k$ are the rate constants,

$k_1$ denotes a forward reaction

$k_{-1}$ denotes a reverse reaction in the Markov model

$O$ is the open state, $C$ is the closed state.

According the principle of mass conservation
 $ C + O = 1 $
where $ C $ denotes the closed state

"From here, it can simply shown that under steady-state conditions that $O_{\inf} = \frac{k_1}{k_1 + k_{-1}}$

and the relaxation time constant of the reaction $\tau = \frac{1}{k_1 + k_{-1}} $ "

My question is, how are $O_{\inf}$ and $\tau$ derived?


texts: Mammal Statistics about Natural Death Versus Being Killed?

texts:
Is there data determining what percentage of mammals die a natural death (disease, old age) and what percentage die due to being killed and/or eaten by other mammals?

In watching wildlife documentaries over the years I'm accustomed to footage of mammals killing each other. So it makes me curious if wildlife mammals are more or less likely to be "murdered" by other mammals than humans are to be murdered by humans.


texts: Is it possible to mathematically model the growth of plants?

texts:
Are there mathematical equations that represent/model the growth of plants?
For example, if I have a Bellis perennis and I want to know how it develops in a given environment (Sun is shining, defined amount of water etc).
How can one say if it grows a certain height and leafs and all other organs?
I don't want a generic solution for this like using L-System and stuff, I just want to have a source where I can research growth rules for a given plant, flower or tree.

Background:
I'm making a kind of mini-game for a computer-graphics course at university.
Think of it like a 1st-person shooter where you take a seed and plant it into the earth.
The plant starts to grow and you will see it grow like in real life.
Of course there are some environmental constraints that should be taken into account:
A. Time
B. (Sun)Light
C. Water
D. Other nutrition stuff like fertilizer

Don't bother about the technical aspects, i just want to know about the biological aspects of plant-growth.
Let's assume we have a sunflower plant. As it starts to grow I get a couple of questions:
1. How fast does the plant stem grow according to a well defined amount of luminosity and water?
2. When do the first leaves develop?
3. How much thickness the stem gains per day/hour/minute?
4. What happens when suddenly there is less amount of luminosity and/or water? How the growth-rate will be affected?

These are only a few questions that arise when i think about this topic. Therefore i want to have a mathematical description of plant-growth under the environmental constraints mentioned above. I don't need a generic approach, but it would be nice to see such a formalism for e.g. a sunflower or Bellis Perennis. I also don't care about things that won't be able to see in the scene, like micro-biological-level - i just care about the whole architecture of the plant (stem, branches, leafes, fruits, (root)).

I did a lot of search on this topic including the computer modeling side:
http://algorithmicbotany.org/papers/
https://www.informatik.uni-konstanz.de/en/deussen/publications/
But these sources focus more on techniques on how to generate images instead of the biological aspects.
Another book I've searched too solve my questions is "On Growth and Form" by Darcy Wentworth Thompson, but thats too general for my needs.

So are there any formal descriptions of plant-growth that take luminosity, water etc into account?


texts: Biochemical coupling between two enzymatic reactions - Enzymes physically associated?

texts:
I am wondering what the exact definition of biochemical coupling between two enzymatic reactions is. I know that these two enzymatic reactions have to

share the same intermediate(s)
one is thermodynamically favorable and the other is not.

So  the thermodynamically unfavorable reaction can happen when it coupled with the  thermodynamically favorable reaction. I just want to confirm that : Do these two enzymes have to be physically associated with each other? Since I do not have any evidence to support the physically interactions between these two enzymes, can I still use the term "biochemical coupling"?

Many thanks.


texts: What is the difference between vegetable and fruit?

texts: Is there any exact definition of vegetable and fruit? How can new plant be classified?


texts: Why do some trees flower year round, others only once

texts:
Depending on latitude, rains, and pollinator behavior, etc. some trees flower only once a year such as oak trees, others twice (such as pipe organ cati as a response to pollinating bats) and yet others continously such as figs (I believe, not sure).

However I noticed that arbutus unedo (straberry tree) has both immature flowers, mature flowers young fruit and ripe fruit on the tree at the same time. To mky knowlesge, fig tress in amazonia behave differently: the whole tree is roughly in the same state at once, either "flowering" developing fruit, bearing ripe fruit.

My question is what ecological role does Arbutus U. fill that it has this feature?


texts:
I just found these small insects on a Saponaria.

After search, it could be Halyomorpha halys, but I am really not sure.

Can anyone confirm? If so, should I kill them as they are considered as agricultural pest?

They are about 3-5mm. I am living in the south of Paris (48.814766, 2.334659)


texts: Is there a standard formula/calculation for sexual dimorphism?

texts:
Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use

$$\frac{\text{Female value}}{\text{Male value}} -1$$

This would give negative values when the female value is smaller than the males, and positive when male is smaller. My issue with this though is that when a female is twice the size of a male its value is -0.5, while when a male is twice the size of a female its value is 1.0, so they do not spread symmetrically around 0.

Edit:

Just playing around with some dummy data in R I came up with a possible solution

$$0.5 - \frac{\text{Female}}{\text{Female + Male}}$$

This gives a zero centred value with equal distribution around the mean. For example, when Females are twice the size of males the value is -0.166, and when males are twice the size of females the value is 0.166, when they are the same size it is 0.


texts: Organisms with the most extreme sensory capabilities? (sight, smell, sound)

texts:
Background

It is quite mind boggling to imagine what it would be like to be missing sight, sound, touch, smell, taste etc.

Question

  Which organism holds the record for most extreme sensory limits for: sight, smell and sound? (one for each)

This would help give an idea of the "biological limits" of sense.


texts: Is there a database of pollen-seed distances across plant species?

texts:
I was enjoying Richard Smith's excellent answer to this question, and wondered:

If you consider the pollen/seed distribution range to be plant locomotion, is there a database that compares these distances across plant taxa, or perhaps a paper that treats these distances as a trait (in a phylogenetic context, for example)? One might assume that in the transition from wind-pollination to animal pollination (or from wind seed dispersal to animal seed dispersal) there is a sacrifice of decreased distance for increased "accuracy", but maybe this isn't the case.

It seems like this information should be around somewhere – it has relevance to evolution, speciation, climate change adaptation, etc.


texts: Western Cascade forest, in a small clearing in the grasses. Possibly related to leafhoppers? Looks a little bit similar, and it was able to jump quite well. The last pair of legs are arranged the same exact way as leafhoppers. Assuming it's within Hemiptera. I've never seen one before.


texts: Is anaerobic activity during ketosis possible?

texts:
When a person's glucose and glycogen stores are depleted, which can occur due to fasting or due to a diet consisting largely of fat (like eskimo diets), the body produces its energy by breaking down triglycerides into fatty acids.  Fatty acids can be then converted to Acetyl-CoA, which can consequently enter the citric acid cycle, generating ATP.*

Now normally when a cell does not receive sufficient oxygen to undergo its natural processes, it usually breaks down glucose anaerobically to generate ATP and lactic acid.  However, in the case where the body is running off fatty acids (e.g. fast, or fat/protein only diet), how does the body respond to such anaerobic situations?

*(Note:  In this situation many fatty acids are first taken up into the liver and converted to ketone bodies, which are subsequently converted to Acetyl-CoA after being taken up in the required tissues, hence causing "ketosis" as in the title)


texts: What is intercalary mitosis in bacteria?

texts:
According to Wikipedia, in vegetative reproduction fragmentation takes place, and Spirogyra simply undergoes intercalary mitosis to form new filaments.

How is 'intercalary' defined in a bacterial context, does have to do anything blank or dead cells of Spirogyra?


texts: What should be used to protect coconut wood from water?


texts: Why are chromatophore in phaeyophycae chloroplasts integrated within the endoplasmic reticulum?

texts: Why are chromatophore in phaeyophycae chloroplast integrated within the endoplasmic reticulum? While reading about phaeyophycae I came across this point, but couldn't figure out why and what could be the evolutionary basis for this?


texts: How to start learning disease profiling?

texts:
I am student of Biological Sciences and interested to learn profiling in order to characterize the state of organisms (especially diseases). You know that there are different types of profiling like, Genome, Proteome, Metabolic and many more.
I am confused from where should I learn in order to understand principles of profiling.
Kindly, guide me.

Thank you!


texts: What do the letters 'p' and 'c' mean in mutation descriptions?

texts:
Example:

  NM_000525.3(KCNJ11):c. 67A>G ( p. Lys23Glu) AND Permanent neonatal diabetes mellitus

Does "p" stand for "polymorphism"?

What does the letter "c" stand for?


texts: If a mother had a child with her own son, could a paternity test yield positive result for the son's father?

texts:
Let's imagine a family composed of Mr A and Mrs B, who have a son named John.

Now, if for whatever twisted reason, John had a child with Mrs B, could a paternity test yield positive result for Mr A ?

Since John's genes all come from Mr A and Mrs B, the child's genes would all come originally from Mr A and Mrs B as well. Thus it seems to me like the test could suggest Mr A is the father of the child.

Or would there definetly be some "red flags" that suggest something wrong happened ?
Like, for example, if the child is a girl, that would mean both of her X chromosomes originally came from Mrs A (since John's X chromosome comes from his mother, as for all males), possibly even the same chromosome twice.

Let's consider that only Mr. A is tested, and not John. Would the child be considered genetically close enough to Mr. A that a test could attest that he is probably the child's father, granting there is no other test showing someone else as a much more likely candidate ?


texts: iodine: how did they manage without it in old ages? (People who were living far from the sea)

texts:
Knowing that today iodine comes either from fish products or (artificially) enriched table salt, how did people who lived far from the sea survive before (especially during the the Middle Ages)?

Edit 1: nowadays we could find some iodine in cow milk, cheese and eggs but those sources are artificial

  (Increased iodine content in food due to greater use in: food
  processing, animal rations, antimicrobial agents...)

source

Edit 2

  A small amount of iodine enters the atmosphere and, through rain,
  enters ground water and soil near the sea

source

Summarized of the comments: thanks to  ddiez this question has been partially answered. But as vsz pointed out the the mystery remains:

  areas with iodine deficiency didn't get completely depopulated during the Middle Ages
  seems to suggest that it does not affect all people that severely.

So the question remains: could humans survive and reproduce without any iodine source?

Edit 3:

  “If all women in the UK took iodine supplements while pregnant, IQ
  would rise by 1.2 points per child” but some says "Some observational studies suggest supplements could even lower IQ, perhaps because excess iodine might harm the thyroid gland." (Newscientist, August 2015)


texts: Species Identification: Liberian "kiss-meat" snail

texts:
Before my wife immigrated to the US from Liberia as a kid, she loved eating "kiss meat". It's a freshwater snail they collect from the swamp during the rainy season and eat as a delicacy, so called because you suck the meat out with a kiss.
Here's a YouTube video of this process, so you can get a good look at the snail and see its habitat (mangroves).
This is the best image from the video that I could find. They've been washed and the rear of their shell has been broken off. I can't get Stack Exchange to let me add a second picture );

I have not been able to find any other references to these snails, except under the name "kiss meat". Would anyone be able to identify these?
(Note: There seems to be a similar looking brackish snail commonly called "African Periwinkle". I don't think this is the same thing.)


texts: Can a protein falling below a threshold trigger another response?

texts: Is it possible that the falling of the concentration of a protein below a threshold triggers the release or production of another protein?


texts:
Is it possible to experimentally determine $k_1$ and $k_{-1}$ of the Michaelis Menten model:

$\ce{E + S <-->[k_1][k_{-1}] ES ->[k_{cat}] E + P}$,

or their ratio?


texts: Identifying internal structures of dissected fish

texts:
Note : Images displayed below might be disturbing to some people.

I have dissected a fish for the first time ! I have some idea of what some of the structures might be but I am not sure and so would like your help.

1.Here is the fish I dissected. Are the white structures (towards the dorsal surface) muscles ? They are beautifully arranged.

2.I want to know what the yellow coloured structure (towards the ventral side) is. I guess it's the intestine. It looks "noodly". Here is a close up.

3.I have pointed at two different parts in the following images. I want to know whether they are part of the same structure - ie swim bladder or whether they are two different structures altogether. When I poked one of the parts the other part increased in size ,so I guess it's one structure but I just wanna make sure.


texts: what happens to rna length if we have a termination site in additional to the original one

texts: if we have an RNA transcription and we add an additonal temination site in  the middle , will i have two RNA molecules or just a short one ?


texts: Can you grow a plant from a seed to flower stage with only Aeroponics system

texts:
I have recently started studying indoor farming with the help of aeroponics system. But from what I know have read (I may have misunderstood or misread something, so please excuse me for that). The growth of plant via an aeroponic system began when the seedling has developed enough roots for transplanting from soil to the cup (or whatever is the technical term for the holder used in the system) like in the photo below.

Is this true? Or they use aeroponics system for the growth of the seed too? And if not, what if we put the seed in a bag of fabric, that allows the excess water to drain while storing enough to keep the seed in a moist environment, and keeping the light intensity to a minimum. For argument sake, how about we discuss a simple bean plant.