texts: I'm trying to understand the difference between epigenetic and environmental factors. For example, if gene A increases the risk of lung cancer by 50% and smoking increases the risk by another 75% when combined with gene A (just throwing out numbers) person X now has a higher chance of developing lung cancer. However, if for example, certain epigenetic factors are inhibiting the expression of gene A than that 50% higher genetic risk has now decreased because those high-risk genes aren't being fully expressed. The environmental risk factor of smoking still plays a role but it too could be decreased because that 75% increased risk was associated with gene A being fully expressed and not inhibited by epigenetic factors. Am I thinking about this correctly?


texts: In vivo, does it take energy to move double bonds from cis to trans in long chain unsaturated fatty acids

texts:
In vivo, I understood that because all polyunsaturated fatty acids bonds are -cis they are crowded, kinking the molecule, and because of that, the oxidative enzymes cannot initially access them. They first have to be moved to the -trans side to allow the enzymes to act on the double bonds. So my first question: is ATP needed to move double bonds from -cis to -trans? And also, when the long-chain FA like EPA & DHA are oxidized, because of this energy expenditure to move them, wouldn't they yield less total bond energy when oxidized than if they were just oxidized in vitro, e.g. by heating?

If this is true, then how much ATP is used to first get those double bond groups into the -trans position so the oxidation enzymes can reach them? And … thus could I state that in vivo breaking of long chain polyunsaturated fatty acids would not yield as much energy as would in vitro breaking of these bonds?


texts:
I'm working with data downloaded from STRING database (string-db.org) for protein-protein interactions.
My idea is to compare the topology of connections of the same protein on different organisms.

However, I noticed that the same protein can receive different ID on each organism.

So I would like to know if there is any way to convert all ID's into just one pattern.

Thanks.


texts: Why do farts stink, but perfume does not?

texts:
Why is it that natural things like farts, poop, halitosis etc., from which we are always surrounded smell "bad"; whereas manufactured products, such as perfume or glue smell "good" to most of us?

In my understanding, things smell "bad", because they are not good for us. But how are farts not good? And shouldn't artificial things like perfume or glue, which are relatively new to us, smell "bad"?


texts:
I've just seen this animation:

I always thought the firefly glow is ongoing slow chemical reaction, like in glowsticks though through different chemicals. As such it seems impossible to control quickly, like on this image.

Is this image real or edited? Can firefly control it's glow? If it can, how much?


texts: Which sources can I use to study botany and horticulture?

texts:
I refer with this question to those among you who have a strong background and work in fields like: botanics, horticulture, dendrology, etc.

I would like to start building a solid preparation, both practical and theoretical, in horticulture, with a strong scientific background.

I am a physicist at the moment, but I am trying to lay the basis for a career switch. In September I will attend the RHS courses, but in the meanwhile I would like to start studying something on my own.

Is there any introductory, basic, read that you would suggest? Also, if any of you have in mind a sort of "curriculum" (in terms of subjects, books, etc.) or would like to play with it, this would be of great help! Thanks a lot :)


texts: Effect of extracellular molecules on membrane potential

texts:
I am reading about the effect of extracellular potassium and chloride on the membrane potential, and now a question has come to my mind about what would happen if we added some molecules that have no charge to the extracellular? (consider that only K+ and Cl− can cross the membrane.)

I think that membrane potential and volume does not change, but I'm not sure about that.


texts:
I have recently found articles and various claims that turtles (Blanding's turtles as an exact example) could possibly live indefinitely. http://discovermagazine.com/2002/jun/featturtle

This is said to be due to the fact that they

  don't senesce— deteriorate physically— as they grow old

I am highly skeptical of that claim, and on the other side are links such as this http://www.nature.org/ourinitiatives/regions/northamerica/unitedstates/indiana/journeywithnature/blandings-turtles.xml which say they can live up to 70 years (though in the actual article it says 70+)

I realize in the wild that predation, disease, and other causes other than old age could kill turtles, but my question is:

Can blandings turtles die of old age? If so, around what age would this be?


texts: How much of the human body is processed sunlight?

texts: So I believe (and correct me if I'm wrong--it's logic, not research) that the human body is pretty much all just processed sunlight based on the food chain.  How much, if any, of the human body is made up of materials that did not originate from the sun (e.g., various minerals or other trace elements)?


texts: Is there a lower temperature limit, below which we cannot sense a difference in temperature?

texts: At work I have to handle samples stored at -20 and -70 degrees Celsius, and they don't feel that different to me.


texts: Do ants within a colony ever fight or come to conflict?

texts:
I'm investigating how hierarchical groups of a larger organization with a common goal tend to come to conflict with one another over time.  As you decompose a large group (for example a corporation), peer groups may compete in an effort to accomplish short-term goals in an effort to further the corporation as a whole.  For example, two groups of software developers might fight for time on the corporations computer system to finish their immediate deadlines.  Though this typically can be resolved through mediation and compromise, there is a human element where one group might inflate the real need to use such a resource.

I was then wondering if the same situation could ever arise in an ant colony.  Are ants truly purely social and never come to conflict within a colony?  Or can they end up fighting internally if food or space is ever scarce?


texts: Why are different mesenchymal stem cells used for articular, auricular, septal nasal and costal chondrocytes?

texts: Why do stem cell researchers use the mesenchymal stem cells shown in the table above for these specific types of chrondrocytes? Can you only use bone marrow to make articular cartilage, or are there other types of cartilage that can be made using bone marrow, if so which other types of cartilage?


texts: Population size and genetic drift - What are the evidences?

texts:
Wright-Fisher model

From the Wright-Fisher model of genetic drift, the random sampling of allele from one generation to the next is taken from a binomial distribution with parameters $2N$ and $p$, where $N$ is the population size and $p$ the frequency of an allele of interest.

Strength of Genetic drift

The strength of genetic drift can be measured in terms of two different statistics:

variance in allele frequency from one generation to the next
loss of heterozygosity per generation

Variance in allele frequency from one generation to the next

From the above, it is relatelively straight forward to show that the variance in allele frequency in the successive generation is

$$\text{var}\left(p'\right) = \frac{p(1-p)}{2N}$$

, where $N$ is the population size.

Loss of heterozygosity

Heterozygosity decays by $1-\frac{1}{2N}$ every generation

$$H_t = H_{t-1}\left(1-\frac{1}{2N}\right)$$

, where $H_t$, is the expected heterozygosity at time $t$.

Source

See Gillespie: Population Genetics - A concise guide chapter 2 for more info on these predictions.

Question

Do we have empirical evidence that the decay rate in heterozygosity and/or the variance in allele frequency due to genetic drift follows these predictions?


texts: I want to understand a mechanism how at the first times when the life began on earth evolution helped the new species to arise through selection while the same organism also continued to live as not evolved. If natural selection favors survival of the fittest, than why after a living evolves to a new fittest form, the older form still exists while it should be counted as unfit for survival and extinct, I am not sure but bacteria may be an example perhaps and I am not asking about the situations where the unfit form has extinct but both organisms continued to live.


texts: differentially expressed genes of the treated with estradiol samples

texts:
I did differential analysis on samples treated (G1E-ER4) with estradiol (differentiation induced by estradiol) and control (G1E).
The genes that I gor as differentially expressed in G1E-ER4 showed following pathways.

I can explain the first five: estradiol causes stress and more hemoglobin is synthesized during cell differentiation, also tetrypyrrole is involved in hemoglobin synthesis. Cell death might also be caused by stress induced by estradiol.

However, I am not sure why I have cell division or starvation etc pathways.What is considered to be a starvation actually?

response to stress (GO:0006950)
heme metabolic process (GO:0042168)
tetrapyrrole metabolic process (GO:0033013)
regulation of apoptotic process (GO:0042981)
cell death (GO:0008219), death (GO:0016265),programmed cell death (GO:0012501)

mitotic cell cycle (GO:0000278), cell cycle (GO:0007049)
cell division (GO:0051301),nuclear division (GO:0000280)
cellular response to starvation (GO:0009267)
positive regulation of GTPase activity (GO:0043547)
regulation of localization (GO:0032879)


texts:
My question is simple:

Given that evolution is described by random genetic mutations allowing certain members of a species to gain a reproductive advantage over others that coexist in the particular environment- I am curious- single genetic mutations do not seem to really explain complex morphic changes such as the length of a giraffes neck. Instead it appears it must be a compilation of many such mutations. So what are the statistics for mutations? How long does it really take for so many to favorably compile? How does this compare with the reproductive time of the species?


texts:
What I want to do

I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known structure) is enough to figure out whether I want to exclude an entry for subsequent use of the resulting cleaned-up list of entries.

Now, looking up these entries one by one on the website is easy to do, but is very slow and error-prone. I need to be careful copy/pasting accession codes, and it takes a lot of time to go to my list, copy an accession code, go to the website, paste, search, and have my answer once the result page has loaded fully.

In other words, I'm lazy and I think my time would be better spent doing something more interesting than copy/pasting 200 times.

Attempt at a solution

I figured it shouldn't be too difficult to use PyMOL with a bit of scripting to automatically fetch each entry and generate a small image (faster than ray-tracing, which I don't need for this quick inspection). Here is my attempt:

pdb_entries = ['1m18', '1eqz'] # The real list has almost 200 entries, but 2 are enough to test the script

for entry in pdb_entries:
    cmd.fetch(entry, async = 0, path = "./pdb-files")
    filename = "./pdb-imgs/" + entry
    cmd.png(filename, width = 600, dpi = 100, ray = 0, quiet = 0)
    cmd.delete(entry)

Problem

When I save this script as fetch-all.py and run it from within PyMOL with the command run fetch-all.py, the structure files are correctly downloaded in the ./pdb-files directory and images with names matching the PDB accession codes are generated in the ./pdb-imgs directory. So, it seems everything works. Except these images are just black, not showing anything of the structure.

I tried to add cmd.center(entry) and cmd.show("cartoon", entry) before saving the PNG files, but it did not change anything. I also looked up the help page for cmd.png(), thinking I was missing something, but I couldn't find anything I would be obviously missing there.

Any idea? Thank you all in advance.

Edit: I forgot to mention that this problem of black images happens with the latest PyMOL (2.2.0) and also with an older version (1.7.4).

Edit: when I run the commands inside the loop one by one at the PyMOL prompt, everything works fine, I get images correctly saved. It seems it doesn't work in the context of the loop only. I double checked the loop syntax and it looks fine to me (but I might be missing something; I don't know python very well).

Edit: I also tried cmd.save() instead of cmd.png(), but it did not solve the problem.


texts: Found in a field near Braga, Portugal in October 2018.


texts: What is this long cylindrical white fruit called?

texts:
Location: West Bengal, India
Temperature: 27 °C
Weather: Survive all seasons, although it was raining today
Length: 35 cm (although it can be small or big typically 10 to 40 cm length), girth:10 cm
Weight: 1 kg (estimate)
Appearance: Cylindrical in shape, the outer shell is very hard, color  of shell is typically white to pale yellow(the dark patches is due to mud and dirt). It is really tough to crack the shell but the inside (I believe) is pulpy and fibrous but dry.
Extra information: Not edible (never tried to eat), no smell emitted, colloquially called "monkey's club"(in native language), typically hangs on branches of trees in groups (typically 4 to 6 together)


texts: How would you effect bulk DNA gene therapy for a human?

texts:
Let's imagine  that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to make our genome do what we want, but it's a major refactor.  We're going to have adjust 10-15% of our DNA. (Note this is just a contrived example to suggest why we would want to make such a drastic change - our ability to actually know what changes to make is unimportant for the question.)

How would we replace/or modify this much of our DNA?  It seems the problem is very similar to gene therapy, but on a larger scale.

A few possibilities come to mind.  We could make a virus that would modify our DNA.  Or perhaps we could generate the new genome and inject it into some cells which would then just outlive the others (eg because these cells won't have a Hayflick limit) or will be able to generate lots of new adult stems cells with the "refactored" DNA?


texts: Is there a difference between "cell line" and "cell strain"?

texts:
I'm translating one Russian text where a cell line is transfected to produce a drug. I wonder if I can sometimes use "cell strain" or simply "strain" instead of "cell line" or instead of "producer" (продуцент, meaning "the producer of the drug", i.e. the cells that produce the drug).
I googled and found this answer on Yahoo answers:

Cells in culture can be passaged a finite number of times before reaching a crisis which can be compared with aging. The number of passages, before reaching crisis, has been termed the Hayflick limit and is related to the longevity of the species from which the tissue was originally derived.
Within the Hayflick limit, the cells are referred to as a cell strain.
Cells that survive the crisis and continue to grow are referred to as a cell line. Cell lines can also be derived directly from cancer cells. There are many properties that distinguish cell lines from cell strains, including altered chromosome number, changes at the cell membrane, and reduced requirement for certain growth factors.
Therefore:
A cell strain is defined as an euploid population of cells subcultivated once or twice in vitro, lacking the property of indefinite serial passage. Cell strains ultimately undergo degeration or death (senescence).
A cell line is an aneuploid population of cells that can be grown in cultures indefinitely.

Is this true? Is a cell line always aneuploid and capable of indefinite growth, as opposed to being euploid and incapable of indefinite growth?


texts:
I have recently experienced getting double vision out of one eye. When I cover my dominant right eye the double vision corrects and become a solid image? I am not asking if it is possible to get double (because I have "seen" this) vision from one eye. What can cause this and how does covering the eye that is normal correct the double vision in the eye that getting a double vision?

So to iterate with both eyes open I see 3 images. 2 from the left eye and 1 from the right and the second image from the left eye goes away from covering the right eye for a few minutes.


texts: Are 'homeothermic' and 'endothermic' synonymous?

texts:
I got this question from the comments below this answer. So, do homeothermic and poikilothermic have the same meaning as endothermic and ectothermic, respectively?
 A user also suggested that the terms such as poikilothermic and homeothermic have become obsolete. What is the reason for them being obsolete?


texts: gene expression fold change threshold limit

texts: When interpreting qRT-PCR results, which results are acceptable as fold changes, which are acceptable for housekeeping genes? e.j. a values of 0.8 raw fold changes for a "housekeeping" gene is acceptable as such? and conversely which is the threshold to say that there was "fold change"?


texts: Deviation from Hardy Weinberg equilibrium (HWE)

texts: I have a set of 10 genes, each gene contains around 15 SNPs. I have tested the deviation from Hardy Weinberg equilibrium (HWE) for all SNPs. All of the SNPs didn't deviate from HWE, except 5 SNPs in ABCG8, they had p<0.05. I have found different factors that can affect the HWE. My question: Why for the rest of the SNPs met the HWE, why only 5 SNPs in ABCG8 deviate largely from HWE?


texts: Is there any way the food industry can benefit from biofilms?

texts: I realize all of the disadvantages, but I am wondering if the food industry can actually benefit from the formation of biofilms.


texts: How does sex differentiation work in Paracerceis sculpta, the sexually tetramorphic isopod?

texts:
Paracerceis sculpta is a marine isopod species known for its unusual reproductive strategy:

female: medium-sized; lives in harems run by an α male
α male: large; keeps a harem of females
β male: medium; mimics a female in order to enter a harem and mate
γ male: small; mimics a juvenile in order to slip into a harem and mate

.

How does this 4-way sex differentiation occur? That is, what determines which of the morphs an individual develops into?


texts: Do all prokaryotes have ATP synthases and an electron transport chain?

texts:
I was looking this up and I'm wondering if so far I'm correct about the following:

For the most part eukaryotes do aerobic respiration, which involves glycolysis, the Krebs cycle and oxidative phosphorylation involving ATP synthase and an ETC
Prokaryotes can either do aerobic respiration, anaerobic respiration or fermentation, the first two of which require an ETC and ATP synthases, which would be located in the plasma membrane of the prokaryote

If that is the case, I was wondering if there are prokaryotes that only do fermentation, and if so do they have ATP synthases and an ETC? In other words, are there any organisms without ATP synthases and an ETC (which would force them to survive on fermentation alone, unless there is some other method of energy production in prokaryotes that doesn't use ATP synthases and an ETC that I'm missing)?

Thanks


texts: Can Pfx polymerase add only one 3' A overhang?

texts:
I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ligation reaction was successful, however when I got the sequences, there is an extra T between the 3'end-T of pGem and the start codon of my product. It only happens in the 3' end of pGemT (or 5' end of my product). Can Pfx polymerase generates PCR products with just one 3'end overhang? or Can Taq polymerase add two consecutive dATP during the A-tailing?

Please write me your thoughts ASAP, it has happened twice and it's a pain already :(

GGC CGC GGG A-T-T-T-G ATG GGA AGC ATG AAG

The two Ts in Bold belong to pGemT, the T Italic is the extra T I've got from the sequencing reaction. After the T in Italic you may find the 5'end of my insert. The second T (in bold) from pGemT is the one that ligates with the overhang A added through the A-tailing protocol.


texts: What are the differences between carnitine forms?

texts:
I've heard of L-carnitine, acetyl L-carnitine and L-carnitine L-tartrate. What form(s) occur in meat? What form does the human body manufacture?

Is L-carnitine just a shortened name for L-carnitine L-tartrate?


texts: Why are the Galápagos islands so special?

texts: Why did Darwin formulate his theory of evolution just after his visit to the Galápagos islands? Why were they so special from an evolutionary point of view?


texts: What species is this rabbit-like animal?

texts:
This image was included in something I was browsing through.
It reminds me of my lion head rabbit, but the head shape doesn't match.
Is this some kind of Siberian wild rabbit?


texts: Can a cancerous cell from outside cause cancer in a healthy person?

texts: If a cancerous cell enters the body of a healthy person from someone else's blood or something, will that healthy person get cancer? In human beings.


texts: What is the replacement period of gastrolithes in doves?

texts: Gastrolithes are common in doves and pigeons. Do they keep ingested stones for ever? If not, how often are they to be replaced?


texts: Epilepsy explained by computational neuroscience

texts:
A few years ago, on my maths masters, I did a module in theoretical neuroscience. I was shown that the mathematical framework the course developed for neurons, with a small adjustment in the parameters, would produce spike trains similar to those observed during epileptic kindling. These parametric tweaks could be attributed to mutations in ion channel/receptor structures. This was one of the highlights of the course, and when I came to apply for a math/bio interdisciplinary doctoral program, I cited it as such in my personal statement.

Now the interview is fast approaching, and I'm pretty sure it's going to come up, but for the life of me I can't track down a reference. After four years out of the game, my memory is hazy at best.

As I recall, this had something to do with short term plasticity. Normal neurons' response to unrelentingly high frequency spike trains decayes over time, while pathological neurons' does not. This may however be entirely wrong.

What is a reference for the model I describe above? An introductory/educational treatement is prefered, but the original paper is fine.


texts:
Why can't a type II restriction enzyme cut a nucleic acid with the following base composition:

  A: 28% C: 15% G: 35% T: 22%


texts:
I was asked by my biology teacher to find out it’s name but it seems like a pretty common plant to me so I have no idea how to start. Any idea what type of plant it is?

It was found in Malaysia in my school compound


texts:
The easiest carcinogenic thing for me to grasp is radiation, as it directly messes with DNA. Then it seems there are other compounds that simply mimic hormones, but these shouldn't necessarily cause cancer, right? Then there are things that can accelerate mitosis or mess with other processes, which can inadvertently mess with DNA. So my question is, in general, how many different flavors of carcinogens are there? I know there are a lot, but can someone list a good few? Maybe some examples? I'm most interested in how plastics and things like smoke cause cancer. I think a few examples would be best in aiding my understanding. Thank you!

Edit: I also just realized this is not the Chemistry Stack Exchange, I think I am more interested in the chemistry side of this question, but it might need to be migrated.


texts: "Blood circulation". Why blood bleeds in atmosphere ?

texts: If our body's blood pressure is 120 mm-Hg then why blood goes out of our body in 760 mm -Hg pressure if we have cuts?


texts: Cereal Alpha and Beta Amylase temperature range and reaction rate

texts:
This question is motivated by a practical application in bread making.
While it is well known which are the optimal (highest reaction rate) temperatures for both alpha and beta amylase, I am not able to find any precise information concerning reaction rate as a function of temperature.

How does alpha and beta amylase activity change when temperature decreases?
At which temperatures does their activity stop?


texts: how does a dna probe work in DNA fingerprinting?

texts:
It says in my textbook ' after hybridisation with VNTR probe,  the autoradiogram gives many bands of different sizes '.  I tried looking on the net and it said there that probe is ' a radioactively labeled ssdna which binds to complementary dna '
My question is,  how do we know that if the DNA we are testing does contain complementary sequences?


texts:
You are heterozygous at locus A. Both of your alleles, A1 and A2, have a 10% allele frequency in the population. If you are one of 22 people in a room, how many people do you expect to share a locus A allele with?

I come up with 6.8, working like so:

22 people = 44 locus A alleles in the room = 4.4 A1 alleles and 4.4 A2 alleles at 10% frequency.

I have one of each, leaving 3.4 of each allele to the rest of the room. So, looking at both alleles, there are 6.8 shared alleles out there.

My answer assumes that these alleles are all in different people - I don't know how to account for the probability of someone else having two of them. So I know I am wrong already. Is that last step all I'm missing, or have I gone wrong in a more fundamental way?

(Context: This was a question on a grad-level immunology exam. None of us students could agree on the answer afterwards, and the confused wording (I rephrased it above) made us strongly suspect the professor doesn't have the right answer either, so we wanted to see what the answer actually is for when the exams are graded.)


texts:
I am wondering what really powers the myosin head to undergo the power stroke to push the actin filaments towards the M-line. I have 2 thoughts:

when ATP in the myosin head gets hydrolyzed, the energy released is stored in the head. This energy powers for the power stroke.

when ATP is hydrolyzed, inorganic phosphate and ADP leave accordingly (90deg--> 50deg --> 45deg), the conformational changes of myosin head proteins cause the power stroke.

I think (2) is more plausible as the order of actions (moving actin filaments by 6.7nm + 1.3nm in order) is more 'conventional'(wiki), rather than a single action (using energy by ATP hydrolysis, a 1-step boost of energy).
However, if (2) is really correct, then may I ask what is the energy released in (1) used for in the myosin head, does it just simply fade away as heat energy?
thank you very much.


texts: I have been introduced to the term "phytomass" and I was wondering if phytomass can be both photosynthetic and non-photosynthetic?


texts: How does sodium ion increase blood pressure?

texts: So I have been reading about the RAAS system and I was wondering how  natrium (sodium ) ions increase blood pressure.I have been looking up on the internet and have yet to find an answer.Help


texts: Do antimuscarinic drugs increase cAMP or cGMP

texts:
Activation of muscarinic receptors M2 and M4 inhibits adenylate cyclase which reduces cAMP levels. It would be expected that antimuscarinics such as ipratropium would increase cAMP levels. However, the pharmacological action of ipratropium is said to be mediated through increased cGMP levels [1]. Why is this the case?

[1] https://www.ncbi.nlm.nih.gov/pubmed/138578


texts: Explanation for hyenas asymmetric legs length

texts: Hyenas seem to have disproportionately short hind legs. It may be the opposite, maybe the front ones lengthened to raise their heads even higher than their already long necks do. In any case, this trait is not seen in any other cursorial animal (that I know), asymmetry is not a good Ally in the long run. So why?


texts: What fraction of biomass is cultivated by humans? Have we increased the number of large animals?

texts:
What fraction of "large animals" are domesticated by humans, compared to those who are wild? I mean cows, pigs, sheep, horses, dogs, cats in relation to comparable wild animals. Different measurements to a similar effect would also be of interest. Possibly including even chicken and fisheries.

I wonder if there are more "large animals" alive on Earth today than thousands of years ago when human agriculture was much smaller?

I'd also be interested in some measurement of how large a fraction of vegetable life on Earth consists of our agricultural cereals et cetera.


texts: Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by condensation in cytoplasm in the presence of water ?


texts:
Where can i find already analyzed ChIP-Seq Data? Is there any database or any web tool that takes ChIP-seq raw data and automatically analyzes them? Or is there any database that provides some API to analyze the raw data it provides. I am new to ChIP-seq data analysis and i really need these to create a web-based platform for mapping ChIP-seq data. Thanks in advance.
I found some interesting data in genome.edu. Is there another database?


texts: IPTG and lac operator with e coli for foreign gene question

texts: We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to the lac operator, which from what I've found just deals with lactose. Is there some other function that has? How can this be related to or effect the thing we put in and what we're doing? I'm missing the connection here.


texts: What exactly causes SSRIs, SNRIs, and tricyclics to induce akathisia?

texts:
Such as too high neurotransmitter levels (serotonin/dopamine/other) or the method of drug delivery or some other reason?

Please keep in mind I know very little about this subject, I apologize for the vagueness


texts: How do parasitic fungi sense optimal fruiting conditions from inside the host?

texts: Question is pretty straight forward. Are there generally any chemical cues?


texts: Example of species that went extinct because of excessive hunting by non-humanoid predators?

texts: I was wondering if there were any species that went extinct for being excessively hunted/eaten by predators? I don't mean human hunting. For example, I wish to know if there's a species of frog that are now extinct, because they were driven to extinction by predation by snakes. In fact I'm also OK with examples where a species/class of plant or grass went extinct due to overgrazing? I want to know because I've always heard people say "Nature corrects itself" or "hunting is under control in the natural environment" etc. Is this argument valid?


texts: I have one sequence that composed of sequences of three genes. I should determine the direction of each gene, but two of these genes are disrupted, and I can't determine the initial codon. Does anyone knows how I can determine the direction of genes?


texts: What controls specific gene silencing during cell differentiation?

texts:
I am intrigued by the fact that all cells of our body use the same DNA. How do the cells differentiate during the post fertilisation divisions?

I read about gene silencing, which can be an answer to this. But still I do not understand how the cells decide which gene it is supposed to silence, by making the micro RNA.

Consider a zygote that is beginning to divide. I would assume that the chemical and physical context of each daughter cells would be more or less similar in beginning. Then how can there be a differentiation? Is there some supervising authority present in the zygote that decides what to make out of each daughter cell?


texts: Cellular Respiration in Boiling Conditions

texts:
Here's the question:

  Imagine that you are given 25 germinating pea seeds that have been placed in boiling water for 5 minutes. You place these seeds in a respirometer and collect data. Predict the rate of oxygen consumption (i.e. cellular respiration) for these seeds and explain your reasons.

I'm thinking that there will be no cellular respiration and thus no oxygen consumption because the boiling probably messes it up, but I'm not sure why that is...


texts:
I know that keystone species are those that play a crucial role in an ecosystem, but since all species are interdependent upon each other and each occupy their own niche, aren't they all important?

How do you know which organisms are keystone species?


texts: Why is nitrogen isotopic labelling required for protein NMR?

texts: Why is labelling required for Nitrogen (by 15N) for studying structure of a protein using NMR?


texts:
I am looking for a system with which I can deliver (large quantities of) ssDNA in vivo (say in mice). I do not know whether it is of importance but the 5' end of the ssDNA fragments are assumed to be phosphorylated.

If you could suggest some efficient delivery systems to me I would be very delighted.

Many thanks for your help in advance!


texts: What causes plants in the prunus genus to reach anthesis?

texts:
In a related question, I ask how to trick fruit trees into flowering later in the spring by prolonging frozen ground conditions.

However, I'm starting to realize that I don't actually understand what triggers plants to flower in the spring in the first place. Possibilities include:

Photoperiodism
Air temperature
Soil/root temperature

It seems to me that this is a simple enough question. I'm guessing that plants in a certain genus would have a fairly specific genetic program that would stipulate when they should flower.
For example:

If root temperature is greater than X (for greater than Y duration), and daylength is greater than Z, then initiate flowering.

I'm not looking for the specific values (example x = 10 degrees C); the values would likely vary by species or even by plant. I'm just wondering what the primary variables are.


texts: James Allison's T-cell discovery technique

texts:
The excerpt on Wired magazine of The Breakthrough by Charles Graeber has the following description of how James Allison found the T-cell receptor.

  Suddenly it seemed so obvious: If Allision could rig up a way to
  compare B cells and T cells, devise a lab experiment that put one
  against the other and let their redundant surface proteins cancel each
  other out, the receptor should be the molecule that didn’t cancel out.
  Essentially, he was looking for a needle in a haystack, and his idea
  was to set fire to the haystack and sift the ashes—or as Allison puts
  it, “pick it out of the weeds.” Whatever was left would be the needle
  he was looking for.

It is a vivid metaphor. But the author does describe in more specific detail how the cancellation actually works. Can someone give such a description?


texts:
Why eggs of some helminths( Diphyllobothrium latum, Trichuris trichiura, Ascaris lumbricoides etc)  are stained with bile while eggs of other helminths( Hymenolepis nana, Enterobius vermicularis etc.) are not?

Some sites say that its because, more the lipid content better is the staining with bile of egg, then how eggs of ascaris are bile stained whose outer shell is made of proteins?


texts: Can bacteria only thrive in agar solution?

texts: In petri dish, agar is most commonly used for culturing bacteria. So is there any other easily obtainable food sources for culturing bacteria.


texts:
How old does one (male and female human) have to be in order to reproduce
Im thinking that it's 13 for a boy and 3 for a girl, is that right?


texts:
According to this article, Here is why we're not cloning humans
there are species who are easy to clone and other who are hard to clone. Cats and mices would be in the easy to clone set , and dogs and humans would be in the hard/very hard to clone set. Why is this so? Why is easy to clone cats but it's hard to clone dogs?


texts: Most well studied termite species or a species that I could use to compare termite genes for functional annotation

texts:
I am working with termites and I have a set of genes that I would like to compare with a species similar to termites so that I could elucidate its function. I am looking for a species that is similar to what Drosophila Melanogaster is to bees where to elucidate the functions of bee genes, it is compared to genes in D. melanogaster. Or how most worm genes is compared to genes in C. elegans. Similarly, if there is a well studied termite species, I could work with that.

The ultimate goal is to create a gene network with termite genes, hopefully on STRING.


texts: Ramifications and possibility of a diet consuming exclusively of human semen

texts:
Semen is a thick, nutritious liquid, rich in vitamins (such as C, B12), amino acids, lipids, monosaccharides (fructose), et cetera. Can semen's ability to fulfill the needs of human organism provide enough essential nutrients to keep the body alive and functional? And if so, would it be a healthy life?

Can a glass of ejaculate a day keep The Reaper/doctor away? If not, how long could a person survive on a "diet" like this?


texts: What percentage of Americans have Native Indian ancestry?

texts:
What percentage of americans have native indian ancestry?

I tried to find the answer online and it's difficult to search for.


texts:
I recently read an article on how DNA barcoding was used to identify species present in health products.

I also read an article about how Real-Time PCR was used to identify meat species in meat products.

I'm curious as to why one method is used over another. I know that DNA barcoding uses mitochondrial DNA to detect species, and Real-Time PCR uses species-specific primers to detect species.

Am I correct in thinking that real-time PCR cannot identify unknown species, but can tell you if the DNA matches a specific species you're looking for? For example, if I test for E. zebra but find something else, I cannot identify that unknown species and more testing is required?

Whereas in DNA barcoding, all I do is match the results against a huge list of known species in a database, which means I can identify unknown species without providing any prior knowledge?


texts: Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?

texts:
The pET plasmid is used for protein expression with T7 promotor in expression strains, such as E.coli BL21(DE3)

It contains a lacI gene which codes for the lac repressor protein, a protein of interest under the control of a T7 promoter for T7 RNA polymerase and a lac operator which can block transcription, directly behind the promotor. The lac operon is another control of transcription of the protein of interest.

Furthermore, T7 polymerase is located in the genome as well under the control of the lac operon.

When IPTG is added, the lac repressor is inactivated -> T7 polymerase and therefore the protein of interest will be expressed.

The Lac I gene is already present in the genome of the expression strain used, why is it also cloned into the pET vectors?


texts: For someone who is interested in learning about the discovery of epigenetics, which are the foundational defining papers in the area?


texts: How does sexual reproduction generate more genetic variation?

texts:
I'm curious as to why sexual reproduction generates genetic variation. For me, the term genetic variation is a little ambiguous. The way I understand it, it's the number of alleles at a locus in a population or "group" of organisms.

But sexual reproduction only "reshuffles" alleles, and doesn't generate new ones (most of the time, at least). So why does it create genetic variation?

Thank you for reading.


texts: How to predict cancer-related proteins in Protein-Protein Interaction networks

texts:
Protein-Protein Interaction networks are known. It's an undirected graph. Each row of the networks is like this (Protein 2 - Protein 6), and It represents the interaction between Protein 2 and Protein 6.

networks:
Protein 2 - Protein 6
Protein 4 - Protein 5
Protein 6 - Protein 5
Protein 5 - Protein 7
...

In this networks, It is known that some of proteins are cancer-related proteins, some are nonCancer-related proteins,

The known proteins:
Protein 4,Cancer
Protein 6,nonCancer
Protein 7,nonCancer
Protein 10,Cancer
...

But the vast majority of proteins is unknown whether is cancer-related protein or noncancer-related protein. How to use these known cancer-related proteins and nonCancer-related proteins to predict the protein whether is or not a cancer-related protein.

I do not know how to solve this problem. I need your help. Thank you very much.


texts: Can a non-response to a vaccine be tested?

texts:
The BioNTech/Pfizer vaccine against SARS-CoV-2 is said to be 90% effective.
Is there a test to establish the (degree of) success in individuals of a vaccine at provoking the desired immune response? Or will we all have to hope for the best?


texts:
I want to know what's the approximate percentage of understood human DNA, as in, which part does what. I'm not asking for details, just the amount.

Thank you.


texts: Requirements for soil sample transportation over long distance

texts:
I need to collected soil sample from agricultural area far away from my lab. It would required about a week for the sample to arrive to lab. I need the soil sample for genomic DNA isolation (metagenomics) as well for isolation of certain species and culture them.

Therefore, the cells in the soil sample needs to be viable. What are the possible ways to long distance transportation of soils sample with intact viable cells?


texts: In peacocks and peahens, the peahens prefer mating with peacocks having a large and bright tail. But how is having a large tail an indicator of genetic "fitness" (in survival terms) ? If having a large and bright tail is not related with genetic superiority, then what is the point of having the mating ritual?


texts: Is the dehydration process used twice in the preparation of permanent slides?

texts:
I am taught "preparation of permanent slides" by one of my teachers in the course of Biological Techniques. He gave me the following steps to prepare a permanent slide:

Totally, there are seven steps in that, however the confusion lies in the fact that the step involved in dehydration is used twice. I didn't understand that if the specimens are dehydrated once, then why is there need of dehydrating them again? Isn't it that after the dehydrating step, the specimen is rehydrated in the staining process, then there will again be the need of dehydration process?


texts: Why is DNA replication so much faster in prokaryotes than eukaryotes?

texts:
There are many statements to be found on the internet of the sort:

“DNA replication occurs at elongation rates of about 500 nucleotides
per second in bacteria and about 50 nucleotides per second in
vertebrates.”

However none that I have read attempt to explain this order-of-magnitude difference. Is it known why?


texts: About acetyl-coA in the Krebs Cycle of respiration

texts:
In respiration, Krebs cycle starts with acetyl coenzyme A which is made from pyruvate.

However, it is said that the cycle keeps repeat it self with oxaloacetate turning back to citrate and cycle starts again, so why is acetyl coenzyme A constantly supplied to the cycle?

According to that logic, shouldn't there be no need for acetyl-coA after the first round?


texts: Difference between Diffuse Optical Tomography and Optical Tomography

texts:
What are there the differences between these two modalities?

Diffuse Optical Tomography (DOT)
Optical Tomography (OT)

Are there forms of OT that are not DOT?


texts: Vitamins located closely under the peel?

texts:
I came across an old saying (I would even call it a myth) that vitamins are concentrated under (or close under) the peel of apples or potatoes and
other fruit. This implies that they are more healthier when not pealed. My question is: Is this true? And does it make sense to concentrate important
substances there, where they might get lost when the peel is damaged?


texts: I have noticed that many of the freeze-sensitive vaccines are antigen only vaccines, for example Hib, pneumococcus, and tetanus vaccines. Why are these vaccines damaged by freezing? Are inactivated or killed vaccines like IPV damaged by freezing? How about live vaccines?


texts:
In Estonia, the product bought from the shop lasts about 2-3 days, in Finland 3-5 days and In Oslo Norway 7 days.

The better infrastructure of transportation explains some for Finland and Norway.
But how on earth so big difference between Norway and Finland?

I heard today that some countries are fluoridating milk.
Ii is not in Finland and Norway.
However, it may be the case that some minerals are existing naturally more in Norway than in Finland. Also, more rain dissolves more minerals in Norway than in Finland.

How can pasteurized milk last 7 days?


texts:
During the dinosaurs time 100-200 million years ago there were giant insects like 1 meter long. An example is here. One of the theories why they could grow this big is that oxygen level was much higher than now. Now we have like 20% oxygen in the air and that time it was 30 or 40.
The question:
If I make a tank/aquarium with 40% oxygen and all the equipment to make this oxygen concentration constant. I put there modern insects, dragon fly, worms, slugs, etc. Will they grow to much bigger size than normal from the 1-2 generations, or I will need to have 100 or 1000 generations before they will be bigger?


texts: Bilirubin metabolism pathway in non-human primates (NHP)?

texts: In human UGT1A1 seems to be the only relevant enzyme to glucuronidate unconjugated bilirubin into excreted forms. Is the pathway the same for e.g. the Cynomolgus monkey (Macaca fascicularis) in vivo? In case UGT1A1 is potently inhibited are there any other potential enzyme to glucuronidate/metabolise unconjugated bilirubin in NHP? Any reference would be highly appreciated.


texts: Pandas are going extinct, mostly due to habitat destruction. This leads me to the question:  How fast can an average adult panda run? (more specifically Giant Panda)


texts: Effects of Polyphasic vs Monophasic sleep in humans

texts:
Why do humans practice monophasic sleep cycles?

When altering one's circadian rhythm to a Polyphasic sleep schedule, how much would that affect development?

Is Monophasic sleep (once per day) chosen because of biological evolution or is it due to cultural influence?


texts: Question about alternative polyadenylation

texts:
I know that alternative polyadenylation creates different transcript isoforms. My question is whether alternative polyadenylation ever results in differences in the terminal/last exon? The only case I can think where it might be is if the terminal exon is alternatively spliced?

EDIT:
I think what I was trying to ask was for a given gene, what factors could cause the transcripts to end in different locations. I drew a picture and it helped me figure it out a little
Here are 4 transcripts for a given gene, each of which end at a different location. Exon's C and D end in different locations because D is completely different exon than C that is being spliced to exon B. Exon on C and E start at the same location, but exon E is shorter, due to a UTR-Alternative polyA event. Exon B and F start at the same location, but F is shorter due to a Coding APA change. So alternative polyadenylation drives the formation of transcripts 1,3,4 while alternative splicing drives the formation of transcript 2. So I guess to rephrase my question, are there any other biological process that can affect where a transcript ends


texts: What is the simplest biological organism from which a DNA sample has been or could be obtained?  Could the resulting DNA be processed and examined in such a way that the resulting information would give biologists a rudimentary understanding of life's minimal requirements?


texts: Is Fluoride really that good for tooth enamel?

texts:
Recently, I started to pay more attention to my teeth because of the high number of tooth decays, and I'm trying to understand different concepts and biological functions of the teeth and bone. By searching around, I have found that enamel is the strongest bio-material in our body and that it is the main player in tooth decay. So I started searching for methods to restore the enamel, and I can see that most of the dentists recommend using Fluoride-based toothpaste. At the same time, the literature tells us that Fluoride is quite toxic. So I looked for healthy options available for end-users, and the organic toothpaste that I found are all without Flouride.

Now my questions are:

Should I go for an organic Toothpaste without Flouride or a non-organic with Flouride for restoring the enamel?
Is Flouride really the only enamel restorer?
Can it be replaced with something else for the restoration?

I'm a mechanical engineer and I can understand technical language, therefore any type of technical explanation would be great (even with chemical reactions)


texts: How to categorize non-coding sequences in the genome?

texts:
I'm trying to wrap my head around the diversity of functions in a genome. Obviously, you've got coding and non-coding regions. But within "non-coding" regions, it seems to be a "wild west" to me. Transposable elements, SINEs, LINEs, transposons, retrotransposons, introns, promotors, etc. Have we annotated genomes enough to have a comprehensive list of the types of non-coding sequences?

It'd be really helpful for me to have a list of the types of non-coding sequences and sub-categories (where relevant). Wikipedia seems to break out a list but the figure on the same page for the human genome doesn't match. Can anyone provide a good reference for how to categorize non-coding sequences?


texts: Why is the spinal cord shortened in some vertebrates (cauda equina) but not in others?

texts:
Hodos, 2009, mentions that the "spinal cord tail" that humans have is not present in most vertebrates. This page mentions cauda equina is not present early on in human embryonic development, but forms later on because vertebral column gets longer. Hodos mentions anglerfish (Lophius piscatorius) also have a "spinal cord tail". What does it look like across other species, like, wolves, gorillas, tigers, crocodiles, dolphins, elephants? Mainly, instead of going species specific, is there any pattern to why some species develop a cauda equina while others do not?
Edit: I can add that according to Uehara, teleosts in general have a spinal cord that extends along the entire vertebral canal, while tetraodontiform fishes have a shortened spinal cord with a cauda equina. This corroborates Hodos claim that most vertebrates have a spinal cord runs the entire length of the vertebral column (teleosts account for 50% of all vertebrates, so... ) Have looked up that dogs have a cauda equina. But, have not been able to understand exactly why some species develop a cauda equina while others do not.
Edit: more context, from Uehara, 2015, "the spinal cord in the majority of the teleosts, the urodelan amphibians, and the reptilian sauropsids and birds extends through the entire vertebral canal, but in the anuran amphibians and mammals is significantly shorter than the vertebral canal."
Edit: more references giving good overview of phylogeny and shortening of spinal cord, but, not really a definitive cause. Nieuwenhuys, 1964 and 1998, and Kuhlenbeck, 1975.
References
Hodos W. (2009) Evolution of the Spinal Cord. In: Binder M.D., Hirokawa N., Windhorst U. (eds) Encyclopedia of Neuroscience. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-29678-2_3171
Uehara, M., Hosaka, Y. Z., Doi, H., & Sakai, H. (2015). The shortened spinal cord in tetraodontiform fishes. Journal of morphology, 276(3), 290–300. https://doi.org/10.1002/jmor.20338
Nieuwenhuys, R. (1964). [Progress in Brain Research] Organization of the Spinal Cord Volume 11 || Comparative Anatomy of the Spinal Cord. , (), 1–57. doi:10.1016/s0079-6123(08)64043-1
Nieuwenhuys, R., ten Donkelaar, H. J., & Nicholson, C. (1998). The Meaning of It All. In The Central Nervous System of Vertebrates (pp. 2135–2195). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-18262-4_24
Kuhlenbeck, H. (1975). The Central Nervous System of Vertebrates, Vol. 4 (Spinal Cord and Deuterencephalon) || VIII. The Spinal Cord. , (), 1–287. doi:10.1159/000395633


texts: Enzyme inhibitors against common cold viruses

texts:
Would some inhibitors of viral enzymes work against common cold viruses? Are there any studies? What could a treatment look like?

A lot of common cold viruses are rhino viruses which are picorna viruses. All picorna viruses contain two cysteine proteases, designated 3C and 2A according to Handbook of Proteolytic Enzymes
Volume 2, 2013, Pages 2402-2406
David S.Wishart Would it suffice to inhibit either of them?


texts: Burning fat transferred from one part of the body to another

texts:
While doing some research on cosmetic surgery, I discovered that there are several ways of doing breast enhancements, one of which was using body fat. While I haven't researched this method, I assume they transfer the patients body fat from one part of the body to another.

Would the body use this transferred fat for as energy, or would it ignore it as it wasn't stored there in the first place? Does the body differentiate fat cells stored in different parts of the body?


texts: How and where do nerves share pathways to the brain?

texts:
I am interested in understanding how pain receptors send signals to the somatosensory cortex (the part of the brain that registers various nerve signals such as pain, presure, temperatures, etc).

Specifically, I'm interested in whether or not two distinct nerves/receptors share, or don't share, "channels of communication" to the cortex.

For example, say I touch the very tip of my finger to a hot stove, and, say, only 10 "temperature-sensing nerves" are triggered to transmit pain signals to my brain:

Do each of these 10 nerves send 10 distinct signals to my brain, traveling down 10 completely 10 channels?; or
Do each of these 10 nerves send 10 distinct signals to, say, my spinal cord, where they are then combined into 1 large pain signal and forwarded on to the brain?; or
Something else entirely?

Here's an awful illustration of the question I'm asking:

In Scenario #1, both nerves send 2 distinct signals to the brain, and those signals are kept distinct/isolated throughout the course of their entire journey to the brain.

In Scenario #2, both nerves send 2 distinct signals to the spinal cord, but the spine then combines them and only forwards 1 signal on to the brain.

I''m sure in reality it's neither of these scenarios, and is something much more complex. But I'm curious and want to know!


texts: white and brown mushrooms. same species but...?

texts:
On Cooking SE and Wikipedia we wonder if someone can claify:

Are white vs brown immature fruiting bodies of Agaricus bisporus different stages of development like many kinds of fruit change color as they ripen? Or are they different cultivars or are they due to different environmental conditions when forming?

Bonus: what isnthe brown pigmentation? Is the difference in taste due to that or meerly correlated with it but due to some other difference?


texts: Highest Pressure Human Body Can Survive In?

texts:
One design for underwater human inhabited environments is to have equal pressure between the surrounding water and the submerged habitat, thus allowing a section of the floor to be open to the water and removing the necessity for strong plating to protect it.  This requires the air pressure within the environment to be greater than atmospheric pressure so that it can withstand the pressure of both the atmosphere and the pressure from the overlying water.

So how much pressure can the human body survive in without need for special suits and breathing apparatuses (as this would place a limit on how deep you could build such an environment without special accommodation)?

Edit: So far i've found an article about a man trapped in a sunken boat who survived for days in an air pocket trapped in the bathroom 100 feet down.  He couldn't resurface without the use of a diving bell and gradual decompression; but this case provides a lower bound for how high the highest pressure can be.

Calculations:  14.7 psi (atm pressure) + 1200 inches*0.037 psi/in^3 = 60 psi for the underwater pocket (roughly 4 times atmospheric pressure).
http://news.nationalgeographic.com/news/2013/12/131204-nigerian-air-bubble-survival-shipwreck-viral-video-science/


texts: How does the availability of a reference genome aid in microsatellite analysis?

texts:
I'm planning to use microsatellites to examine fine-scale population structure between several breeding colonies of birds. Most of my DNA will be extracted from feathers and the yield isn't sufficient for RAD-seq.
Originally I had planned to send DNA samples from several individuals at two of my colonies to a company. I will be using DNA from blood for this process. They are able to provide me with 20-30 polymorphic microsatellites and their primers.
It now seems that a reference genome will be available soon and so that brings me to my questions. First, does the availability of a reference genome make the microsatellite identification process that much easier that I should identify them myself? Second, does the availability of a reference genome increase the ease of genotyping individuals or help minimize genotyping error? Finally, is there a utility for the reference genome in my context that I'm not considering?


texts:
I don't have a strong biological background but, in studying statistics, I met the idea of regression to the mean. e.g. children of tall parents tend to be shorter than their parents, and so on.

Does this interact with evolution ?


texts: Why didn't these scientists restore electrical activity in this pig's brain?

texts:
This experiment was published in Nature Magazine: Pig brains kept alive outside body for hours after death. The researchers used a system called BrainEx to revive certain metabolic and physiological functions to a disembodied pig's brain, but they never attempted to restart electrical activity.

Why did they stop short of restarting electrical activity in this pig's brain?


texts:
How do plants get carbon? From air or soil? How is it different for aquatic plants and algae?

According to https://en.wikipedia.org/wiki/Soil_organic_matter soil has 3.3 times the size of the atmospheric pool of carbon.


texts: By what mechanism does Risperidone swell breast tissue?

texts:
There has been much talk of the anti-psychotic drug Rispeirdone causing un-natural breast tissue growth as well as galactorhea (milk production). Especially in young men and boys.

What is the mechanism of this drug that is causing this? Is it actually introducing some amount of female hormones into the male's body or is just causing increased production of them?


texts: Fish "coming back to life" after being frozen

texts:
I've encountered a clip on Youtube showing a goldfish thrown in liquid nitrogen and immediately after to normal water and swimming normally. In the explanation to the clip it says:

  For everyone that is worried about the goldfish, it survived and was perfectly fine until we fed him and a few of his friends to our turtles. (Which is what they were bought for in the first place!)

I am wondering now as to several issues.

If the goldfish wasn't fed to the turtles and was allowed to live out its life, would it suffer any long term damages from the act?

Is time an issue here, if the fish was kept frozen for a longer time, would it suffer more damage and would it be able to be revived?

Is the size and nature of the fish's body a factor? Would a larger animal or an animal with better resistance to frost that would take more time to completely freeze have damage due to gradual freezing of body and systems?

Does the fact that fish have cold blood affect the result of the experiment?


texts: Photo taken April 27 in Savannah Georgia


texts: Why are sarcomas rare compared to carcinomas?

texts:
A sarcoma (from the Greek σάρξ sarx meaning "flesh") is a cancer that
  arises from transformed cells of mesenchymal origin. Thus, malignant
  tumors made of cancellous bone, cartilage, fat, muscle, vascular, or
  hematopoietic tissues are, by definition, considered sarcomas. This is
  in contrast to a malignant tumor originating from epithelial cells,
  which are termed carcinoma. Human sarcomas are quite rare. Common
  malignancies, such as breast, colon, and lung cancer, are almost
  always carcinoma.

ref: https://en.wikipedia.org/wiki/Sarcoma

I was wondering why most of the tumors come from epithelial cells?


texts: It seems to be an important issue the parasitic control and even some pursue the eradication of some species. Most of the researchers in parasitology are focused on the host damage and population regulation. How do we perceive and value the function of parasites? Is it really needed a change in paradigms and views of dependent species? How important is to conserve them?


texts: What is the difference among biochemistry, molecular biology, molecular genetics and structural biology?

texts:
I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this what I understand of the following areas.

Biochemistry:  The study of metabolic pathways, enzyme kinetics, bioenergetics and the chemical mechanisms of the reactions. It does study molecular structure, but only of small molecules such as monomers, metabolites and coenzymes.
Molecular biology: The study of information pathways, such as transcription, splicing and replication. It applies as well to techniques such as PCR.
Molecular genetics: The study of how a genotype creates a particular phenotype. For example, it would be the study of why an allele produces smooth peas while another one produces wrinkled ones.
Structural biology:  Elucidating the structure of macromolecules (proteins, nucleic acids) and their complexes. It uses X-ray crystallography, NMR and cryo-electron microscopy to study them.

So, are my definitions accurate? If not, why?


texts:
Place: Bangalore, India

Month: September, 2015

Current weather: Cloudy and rainy

Google images search was just giving me dragonfly photos. That organism is on grass blade.

Image is captured by me.


texts: Which eukaryotic species had evolved the most after losing ability of sexual reproduction?

texts:
It seems sexual reproduction is ubiquitous in eukaryotes, so it is important despite needing excessive resources spent. It is an evolutionary adaptation for better evolution.
Still, there are species that had lost their ability to reproduce sexually. I wonder how far a species can evolve after losing the ability. Are there any species that really innovated after they lost sexual reproduction?


texts:
I am coding a DNA translater, based on the homosapiens genome, & i knowing that the data provided from NCBI is surely not 100% precise (there may be some base changes / removes etc...)

, & i want to prevent/bypass those mistakes to get a 'close' list of the REAL chain of proteins produced, so i was wondering how the frameshift do not change an entire species, taking into consideration that if 1 or 2 bases are removed , => then all the dna/rna translation will be modified therefore => ALL proteins will change & even the start/stop codons will change its location

(am not a biologist, am asking why the frameshift doesnt do that & create a new species from 1 or 2 base changes??)


texts: Determining the Value of Inhibition constant

texts:
I am trying to understand how the inhibition constant is calculated for competitive inhibition.

$\frac{K^{app}}{V^{app}} = \frac{1+I/K_i}{V/K_m}$.

But often in secondary plots, $\frac{K^{app}}{V^{app}} $ vs Inhibitor concentration is plotted and the inhibition constant , $K_i$ is obtained from slope $1/K_i$. How is the slope equal to  $1/K_i$ from the above equation?
Could someone explain?


texts: I am wondering if each cell in human body starts consuming ten percent more energy, how much food one has to consume compared to normal intake?


texts: Why does a light object appear lighter in your peripheral vision when it's dark?

texts:
So, I am not sure I can reproduce it via images, but the steps are:

1) At night, open a window and have a look at the surface of the earth

2) Suppose there's an object that reflects a tiny amount of light

3) When you actually try to focus your eyes at this object, you either don't see anything (depends on the amount of light it reflects) or you can hardly see it

4) When you focus your eyes on something that is 3-10 metres away, you can easily see this object with your ambient vision. Not the details, but it seems that it reflects more light.

Why does it happen?


texts: How is HIV evolutionarily viable despite its extreme virulence?

texts: How does HIV survive natural selection? And how has it managed to kill far more than any non-airborne virus in recorded history?


texts: How far can a mosquito fly over the sea?

texts: My question is: how far can a mosquito fly over the sea? I am interested to know, because from this, I could possibly deduce on which islands there either might not be mosquitoes or on which it would be achievable to eradicate all mosquitoes until somebody brings another larva.


texts: I extracted RNA from skin and quantified it in an Nanodrop machine. The 260/230 ratio was very low and two peaks appeared in the absorbance curve, but the RNA is ressuspended in RNAse free water. How can I clean it?


texts: What is a regulable promoter? And how does one regulate it?

texts:
I'm reading a patent where they (in S. cerevisae YNP5 strain):

  downregulate the ERG9 gene by replacing the native ERG9 promoter with
  the regulable MET3 promoter

What's a regulable promoter and how does one regulate it? Must one add something to the broth to down-regulate the expression?

I don't see anything special in the culture medium.


texts: Differing Flow Cytometry Genome Sizes and Sexual Mating Implies Differing Chromosome Counts

texts:
Do the fundamental principles of genetics strongly suggest the following is a derived conjecture?

If 2 flowering plant species A and B have widely differing genome size (at a minimum a 50% difference) based on flow cytometry and normal successful sexual mating of A and B is indicated based on the flow cytometry measured genome sizes of the embryo and endosperm of the seeds produced by crossing A and B, then A and B differ in number of chromosomes to a degree indicative of ploidy level differences.

Corn, Cotton, and Rice are three genus where large genome size differences do not mean differences in chromosome counts.

The Vireya in the genus Rhododendron are a group that have large genome size differences between species where multi-generational hybrids between such species appears to be possible at least in some cases. Documentation suggests that all Vireya have the same chromosome counts indicating diploids.


texts:
I'd appreciate some help identifying these three corvids I photographed in Austria during the Summer:

I know identifying corvids can be difficult and I'm not an ornithologist -- just an amateur bird watcher. After looking through many images of various crow species and their hybrids, I've tentatively identified these as:

Carrion crow (Corvus corone)
Carrion crow × Hooded crow (Corvus corone × Corvus cornix)
Carrion crow × Hooded crow (Corvus corone × Corvus cornix)
I initially believed this to be a Hooded crow (Corvus cornix), but the broken coloration on the wings made me think it might actually be a hybrid as well.

Can someone here either confirm my identification or provide a more informed identification?


texts: Low-tech or low-cost technique for quantitative estimation in enzymology

texts:
If an accurate measurement of enzymologic quantities is needed, then following established methods in the field is necessary.
However, it is sometime of great usefulness to ballpark a value before committing to taking the necessary time for protein purification, or buying the necessary equipment/reagents.
For such purpose a little "hack" can go a long way. This often involve using an available equipment
to substitute for another (e.g. maybe I have a FACS readily availably, however no HPLC).
I am seeking examples of "unconventional" use of lab technique that
can be used to determine enzymologic quantities ($K_d$, $V_{max}$, $K_i$ ...) as a first estimate -- whether you have partaked in such heresies, or have merely seen them used, possibly even in a non-formal/DIY environment.


texts:
I am reading a journal paper about the relationship between the protein NCAM2 and autism, and I have come across the following statement:

We report three patients affected with neurodevelopmental disorders
and harbouring 21q21 deletions involving NCAM2 gene.

I am not sure what a 21q21 deletion is. I have read that 21q refers to long arm of chromosome 21, and that 21q21 refers to position 21 on the long arm of chromosome 21.
However would a 21q21 deletion, refer to this whole section of the chromosome being missing, with this section including the NCAM2 gene? Any insights are appreciated.


texts: Does Rough ER (RER) produce phospholipids?

texts:
I have found out that rough endoplasmic reticulum (RER) produces membranes. Therefore it has to produce phospholipids, but I thought that the smooth ER was where the synthesis of lipids occurs.

What specific part of the ER produce phospholipids?


texts:
Endemism on islands is quite a common phenomenon, at least at the level of species or genera. Old continental fragments like Madagascar or New Caledonia may even harbour endemic families which went extinct on the continents. I also know of the odd example of Lactoridaceae that comprise only one species which is endemic to the Juan Fernandez Islands.

Do you know other instances of endemic families on islands? What about Hawai'i, the Canaries or Galapagos?


texts: What spider is this? Is this invasive or dangerous?

texts:
Hi the picture below has been taken here,
I've never seen such a spider, is it an invasive specie or a dangerous one?

thank you


texts: Veins collapse when empty. That's because they have thin and almost inelastic walls. What has inelasticity and thinness of the walls to do with the collapsing of the veins?


texts: Usually only microbes, specifically bacteria are used to express genes of other species for various functions. But, it is possible to try and express an animal gene into a plant. Bacteria like Bacillus thuringiensis is used in many plants like cotton, to modify them to BT cotton with insecticidal properties. Can one use an animal gene to get those characteristics in the plant?


texts:
I had a filling which involved drilling the tooth, but the drilling did not touch the nerve. According to the x-ray taken at the same time, the nerve is in fact some distance from where the filling was taking place (lower right molar).

Now the local anesthetic has worn off, my tooth is aching. The gums do not hurt (so it is not caused by the dentist applying pressure to the area) and as far as I am aware there are no other nerves within the enamel of the tooth.

So, why does my tooth ache? Is it something to do with the nerve 'waking up' after being anesthetized?

Just to be clear it is not a severe ache or of any concern, only in the background, and I am curious as to the cause. The dentist did say it would ache, so it's obviously a normal thing, but I didn't think to ask why!


texts: What do the initial cell divisions look like in bird embryogenesis?

texts: The germ disc in a bird (a disc because its a chordate) is a mystery to me. The ovum (yolk) is a huge mass of nutrients. It then gets impregnated. Then, what? What does the initial cell divisions look like (they can't be symmetrical since yolk is clearly pushed to one end of the whole thing. )


texts: In my garden, I'm growing broccoli. I was spraying it with water the other day, and I noticed that water bounced off the leaves. When I just misted it instead of a full-on spray, the water beads collected, but stayed as beads instead of spreading out. Some of them bounced off, but some accumulated. So what makes that happen? I know the leaf is hydrophobic, but I haven't found by searching Google if there's a coating of some type on the leaf or if it's something else that's making it hydrophobic.


texts: ADCs: by what mechanism are antibodies internalised

texts:
I read that ADCs (Antibody-Drug Conjugates) act by a -mab for a particular target being bonded to a cytotoxic compound. From my high-school-with-crayons knowledge of antibodies, however, one part of the mechanism stands out as being strange: the internalisaiton of the complex into the cell.

In my head, antibodies are either free in plasma or expressed bound to the surface of cells. How and why (mechanistically/evolutionarily/functionally) does this antibody internalisation take place? Is it a natural process in most organisms, or a backdoor which must be engineered into the ADC?

The usual sources for neophytes are quiet in this area, and the advanced material is bewildering.


texts: Aerobe or facultative anaerobe organism that metabolizes acetate?

texts: I'm assuming bacteria, but will take any suggestions.  Organism must survive primarily on the acetate (plus trace elements), but I can give/take electrons, if necessary.  Not interested in strict anaerobes.  I've tried Shewanella oneidensis, but have not succeeded in getting it to eat any acetate (just lactate).  Feel free to give journal refs.  Self-promotion won't be frowned upon if it's helpful.  :-)  Opportunity for joint pub, if successful.


texts: Has the concept of allostasis been adopted in biology, in place of homeostasis?

texts:
Peter Sterling, among others, has been a prominent critic of the concept of homeostasis.  He instead proposes a process called allostasis.

Homeostasis involves having fixed set points for physiological parameters, and when we deviate from those set points, there are mechanisms that restore them.

However, Sterling argues that this process of homeostasis is inefficient and inflexible.  Instead, he posits that the brain is constantly predicting physiological needs based on environmental and bodily demands, such that the "set point" changes depending on the context.  So your mean blood pressure might be X in one context, but Y in another.  And rather than responding after a deviation from the mean, the brain predicts those deviations and adjusts the body accordingly.  This is allostasis.

Allostasis is much more in line with what we know about the brain (e.g., Clark, 2013), but has this idea been adopted much in biology?  Based on my memory from biology class not long ago, it seems like homeostasis is still considered a central feature of living things.

Thanks!


texts: Surface Power Density of Fluorescing Reaction

texts: I am looking to find out what is the ballpark power density of a fluorescing PCR reaction using a SYBR Green or Taq Man dye might be. Is it on the order of $E_e=1mW/cm^2$, less or more? Any help of data would be useful.


texts: When comparing oral infection v IV infection in mice, why would the CFU given be different volumes?

texts: In the paper, orally infected mice are given 1x10^9 CFU of C. Rodentium and IV infected mice are given 5x10^7 CFU of the pathogen. Does anyone know if there is a generic reason for this? Thanks in advance.,


texts: What are some examples of genes that code for multiple proteins?

texts: The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come across any specific examples of this. Are any such systems known? Or is this more theoretical?


texts: Which monkey species features two distinct male phenotypes?

texts:
I remember coming across a popular science article years ago about a monkey species which featured two male genotypes: the first were good looking males who acquired social status (as alphas or betas) within the group and could thus achieve reproductive succes. The alternative (less frequent) phenotype achieved similar fitness by adopting an outgroup (omega) lurking rapist kind of reproductive strategy.

Does anybody know which species and whose observervations I could be referring to? I'm curious to find out if this was a valid observation and if any further research has been done on this phenomenon.


texts: Does every mitochondrion in a cell contain the same DNA?

texts:
I know that mitochondria of eukaryotes have their own DNA, more similar to that of bacteria than to the rest of the cell's DNA. I also know that a cell can have plenty of mitochondria, and I understand each of them has it's own DNA. Is it the same DNA?

I know that when a human is conceived, the mitochondria of the sperm are destroyed and don't contribute to the new cell. If there were no mutations and the process started with a cell with homogenous mDNA, that would mean that the mDNA not only within one cell but among all of the descendants was the same. But there are mutations because we have different mDNAs. Then shouldn't the mutations cause variety within single cells? It's hard for me to believe that there can even be a single human cell in the world that has homogenous mDNA because, if I understand correctly, an ovum retains many mitochondria during conception, not just one, so at least some of the variety within the ovum should be passed over to the conceived human. But perhaps it's extremely difficult for a cell with variously DNAed mitochondria to survive? Can it be estimated what the percentage of human cells with homogenous or nearly homogenous mDNA is across the world?

I'm asking this because I've heard that the mDNA can be considered another chromosome. I wonder if then every single piece of mitochondrial DNA should be considered another chromosome.

Please note that all I know about biology is what I learned in high school several years ago and the bits I know from Wikipedia and other internet sources. I would like to ask for possibly accessible answers.

EDIT: Reading up on this, I came across the term heteroplasmy. So it does happen that mitochondria of an organism can store different genetic information. But the article seems to suggest that it is an anomaly rather than the normal course of things. That seems strange to me. I understand of course that some mutations have to be harmful, but shouldn't some mutations and some kinds of in-cell variety turn out to be neutral or even advantageous?

I've also just read that a mitochondrion stores more than one copy of its DNA. That seems to allow for variation even within a single mitochondrion.

EDIT 2: I think it's possible that my question is unclear. There seem to be four levels on which mDNA variety can be considered: a species, an organism, a cell, a mitochondrion. I ask the answerers to focus on the third one. I will be happy to learn about the other levels too and I will consider such information on-topic, but my main question is about what happens in a cell.


texts: Are porins on the inner or on the outer membrane of mitochondria?

texts: I've looked at multiple resources and they are saying different things.


texts: How many possible human genotypes are there that produce distinct phenotypes?

texts:
This and this Quora question ask how many unique human genotypes are possible. The answers take the combinatorial approach of raising the 4 possible base pairs to a power which is some appreciable fraction of the 3 billion base pairs in the human genome, to get absurdly large numbers like $10^\text{many millions}$. But as many of the answers point out, this is a gigantic overestimate, because the vast majority of those gene sequences wouldn't produce anything remotely resembling a human, and even among the tiny fraction that do, there are enormous numbers of sequences that produce phenotypically identical humans (after all, most mutations don't produce any detectable effect). (When I say that two genomes "produce indistinguishable phenotypes," I am holding the environment fixed and only considering the genome's contribution to the phenotype.)

It seems to me that in order to avoid counting non-human genomes or double-counting phenotypically equivalent genomes, the better approach is use genes rather than base pairs as the combinatorial building blocks. The human genome has at most 20,000 protein-coding genes, and apparently most genes have two alleles, although some have only one and others have more than two. (I'm defining an allele as an equivalence class of phenotypically indistinguishable DNA sequences that form a single viable gene. For the purpose of this calculation, we can mentally group together the two chromosomes' versions of the same gene, and increase our allele count to include any interactions between the two chromosomes' sequences.) [Edit: according to the answer below (which I find much more trustworthy than this Quora link), this is a huge underestimate for the typical number of alleles per gene, with a better estimate being ~300. Needless to say, this dramatically changes the final answer.] This would produce a maximum of $2^{20000} \approx 10^{6020}$ possible phenotypically distinguishable genomes. While this is obviously still an astronomically high number, it's an infinitesimally tiny fraction of the estimates produced in the Quora answers.

Is my reasoning correct?


texts: Electrodes in the brain and 'repetitive orgasms'

texts:
The advent of chlorpromazine in 1955 put an end to one of the more bizarre chapters in American psychiatry.$^1$ Dr. Robert Heath implanted wires or delivered injections of acetylcholine (a neurotransmitter) deep into the 'septal regions' of the brains of men and women with various physical and mental disorders. His discovery of the brain's 'pleasure center' actually preceded the discovery of the same center in rats by about 20 years [Baumeister, below, at 272].

In one of his papers$^2$ Heath describes intense orgasmic experiences on the part of his patients in response to his treatments, which he dutifully records on EEGs.

His description of Patient b-5 is especially interesting. He relates: "The patient became more attuned to her environment, answered questions more rapidly and accurately, and solved simple mathematical problems with more ease...and in most instances, within another 5 to 10 minutes, this [heightened attunement] culminated in repetitive orgasms." [Heath, below, at 12].

In addition to refreshing my interest in solving simple mathematical problems, this article made me wonder whether this area of research had been resumed in some form. Many of the ethical and technical problems discussed in Maumeister's article seem surmountable, especially in light of computer-aided visualization of brain structures. Not to mention that a kindred treatment, ECT (electroshock), which can still actually be done involuntarily, has seen something of a comeback in the U.S. since the 1940s. ECT is basically controlled destruction of brain tissue, which seems to cast Heath's work in a kinder light.

So my question is whether this thread has been taken up or whether, as one VIP put it, the absence of evidence is evidence of absence. I was unable to turn anything up.

Thanks for any enlightenment.

$^1$ Baumeister, The Tulane Electrical Brain Stimulation Program: A Historical Case Study in Medical Ethics (2000), J. of the History of the Neurosciences 9 (3): 262-78. See page 270.

$^2$Heath, Pleasure and Brain Activity in Man, (1972) Journal of Nervous and Mental Disease 154 (1): 3-17.


texts:
How can botox cure wrinkels?

Do wrinkles caused by tension of some muscles in the skin?

Can these muscles be relaxed by hypnosis or training?


texts: I understand that mass spec is widely used to study PTMs like glycosylation of proteins, but how can mass spec determine correct PTM structure of say glycosylation if two glycan structures have the same mass but different arrangement (i.e. isobaric)? Also, how can mass spec determine the difference between structural isomers?


texts: Why do people remove excess solution after they put on a coverslip?

texts:
Today, my classmate and I stained a slide of cheek cells. After we put on a coverslip, our teacher said that we are supposed to remove excess solution using a tissue.

Why should we do this? I am so confused


texts: What software is there available for quantitative structure–activity relationship (QSAR) pharmacological studies?

texts: QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what software is available to assist me in doing these studies.


texts: What is the use of male plants in nature?

texts: If pollination is done by insects like bees and through the air, then what is the use of male plants in nature?


texts: Can we disambiguate competing molecular mechanisms of learning and plasticity by measuring electrical activity of neurons?

texts:
I have been reading with fascination about the several molecular- and cellular-scale mechanisms and structural changes that underlie what we refer to as long-term plasticity. For instance, [1], [2], [3].

In particular, there seem to be at least: synaptic scaling, synaptic pruning, synaptogenesis, spinogenesis, neurogenesis.

My questions:

How do each of the above mechanisms/ events affect the classical extracellular single/ multi-unit spikes, postsynaptic potentials (LFPs), and local electric fields? Does a mechanistic forward model exist, which specifies the biophysical transformation from synapse-level changes to spikes and LFPs? Are there spike simulators out there that model these properties?
Using such a forward model, can we solve a statistical inverse problem to infer anything at all about these LTP/LTD-induced small-scale structural and functional changes?
For instance, one metric of analysis could be: post-spike-time filters (self-terms and cross-terms) inferred using statistical point-process models. Another could be the shape of the action potential itself, which is typically used only for spike sorting, and then discarded.
Has something along these lines been done? Or is it infeasible? If so, why?
Finally, If anyone could give a brief overview of the gamut of synapse-scale physiological/ imaging techniques used to characterize these mechanisms, I would be very grateful!


texts: How many generations does it take for one species to become a new one?

texts:
First lets consider that a species is a group of individuals that can reproduce by breeding fertile offsprings.

It's usually said that evolution takes a very long time. Lets say that 1000 generations are required for species A to evolve into species B.

Which species would generation 999 belong to, A or B ?
If A then it means that there was no evolution in 999 generations and that the entire evolution is going to happen in a single generation from 999 to 1000.
If B then which specie does generation 998 belong to ?
etc etc

In the end it seems to me that if there is evolution it can only be instantaneous, but that requires many improbable things, one of them being that the spermatozoids and ovules of species A contain DNA of species B !

How does that work ?

EDIT this is not a duplicate I'm not asking what a species is I'm asking what is the genetic process of evolution, how do we move up in the evolution tree.


texts: Where can I find SARS-CoV-2 genome sequences for the UK?

texts: I have downloaded and analysed the sequences of 832 complete samples from the European Nucleotide Archive but I cannot find a single one that was from the UK. I have also tried Genbank and they do not seem to have any UK ones either. I'm still waiting for my logon for Gisaid - looks like they may have some. Is there anywhere else I can try?


texts: Why is the Hill muscle model only applicable to isometric contractions?

texts:
From what I've read, Hill's muscle model provides a reasonable model of isometric contraction.
However, there are other forms of contraction, such as concentric, eccentric, or isotonic contractions.
Is Hill's model inadequate for describing those other types of contractions? If so, why?


texts: Are the hyphae in mushrooms unicellular or multi-cellular?:

texts:
The mycelium is just a collection of hyphae.

Are these hyphae unicellular or multicellular?

If there's any problem in my question please inform me. Thanks!


texts: Do ants really find the shortest path to a food source?

texts:
There exist many computational intelligence algorithms based on the observation that ants deposit pheromones in such a way that they find the shortest path to food sources. This logic is used to optimize computer networks.

I cant really relate to that. I have seen ants take an extremely long path to food. This is not always for safety reasons either. What do biologists have to say about this?


texts: Can we produce synthetic red blood cells lacking antigens?

texts:
I had an idea come to me during Biology class and I immediately asked my teacher, but she couldn't really answer the question, so I'll ask it here.

What are the limiting factors in the production of synthetic red blood cells with no antigens? I mean, we do have the human genome mapped, but am I naive to think that we have genetic technology capable of doing this?

If red blood cells are too complex to manufacture, is it feasible to manufacture much smaller particles of just hemoglobin inside small spheres of cell membrane and use that as a temporary replacement for red blood cells?

(I was at a medical research talk a while ago and one professor was explaining that there are many other proteins bound onto a red blood cell that aren't of the ABO or RH system. Normally this isn't a problem for recipients who only occasionally received transfusions but for people who need a long-term supply of blood, their bodies do get sensitized to the foreign proteins and will eventually start attacking the foreign red blood cells).


texts: A question on exclusion of study participants for an Exome genotyping array

texts:
I'm reading a paper that used whole exome sequencing on an African
 American and European populations to discover novel low frequency and
rare variants associated with lipid levels & the risk of coronary
heart disease.

They used the Illumina Human exome genotyping array that was designed
based on coding variants discovered from sequencing the exomes of
12,000 individuals. Therefore, they selected their participants from a
study who were not among the 12,000 individuals utilized to design the
array .

My question is: Why would they select individuals who were not among
the 12,000 used to design the array? (I'm thinking because maybe it
could produce false positives associations? bias?)


texts: How do memory cells(B-cells) encounter pathogens?

texts:
From what I understand, once the infection is handled, some of the B cells capable of producing the correct antigens are stored for the long-term in the lymph nodes.

They will start multiplying again upon encountering the pathogen again.

What I don't understand is how can these cells, that should be in relatively small numbers, can effectively encounter the pathogen ? Do all pathogens travel to the lymph nodes? Do the memory B cells travel out and encounter pathogens?


texts: What is the function of spongin in sea sponges?

texts:
Sea sponges (Porifera) use different types of skeletons to support their structures. Some skeletons are built from minerals, some are built from proteins like spongin, and some use both.

My question is about spongin. What is the benefit of having a skeleton made exclusively of spongin? (What advantages does it have compared to other types of skeletons?)


texts: Should heart-to-body energy consumption ratio equal oxygen consumption ratio?

texts:
The human heart pumps oxygen to the body, and the heart itself requires oxygen.

Both the body and the heart use energy, usually expressed in calories or ergs.

If we look at the energy consumption (in Watts) of the heart as a fraction $F$ of the energy consumption of the body as a whole it is about

$F \approx \frac{1.3}{91.3}=0.014.$

Humans consume about 550L of oxygen per day per this website and the heart itself consumes about 8 ml of $O_2$ per 100g per minute at rest according to this site. Assuming an average global human heart mass of about 310g (Google) the daily total heart oxygen consumption is about  (8ml x 3.1 x 1440 min) = 35712 ml or 35.7L of oxygen. The ratio $R$ of heart to body oxygen consumption is thus about

$R \approx \frac{36}{550-36} = \frac{36}{514} =0.07$

These figures are rough at best but not rough enough to account for a discrepancy of a factor of 5 in the ratios. Can someone suggest what might account for the difference?

The calculation seems to show that the heart's proportional consumption of oxygen is a lot higher than its proportional consumption of energy. My understanding is that the respective oxygen consumption of the heart and body are a good reflections of their respective energy consumption. Is that a sound assumption?

Thanks for any insights.


texts: How prevalent is Taq polymerase in adding 3' A overhangs to the PCR product?

texts:
I am conducting a mutagenesis on a gene in vivo of which I need to ligate into an expression vector.  The primers I have designed overlap restriction sites of which I plan to use to ligate into the expression vector.  The parts between the primers I will try to create mutants with error prone PCR.

My concern is the 3' A overhangs that are created from Taq polymerase.  How prevalent is this?  If it is highly common, what is the best way to account for these additions when trying to ligate my PCR product into the vector?


texts: Fossil record of previously thought extinct animals

texts:
I was watching this video from the Youtubers SciShow titled "7 Animals We Used to Think Were Extinct (But Aren't!)." Some of the extinct animals, were suspected to have gone extinct close to half a billion years ago, which leads me to believe that their fossils were obviously found in layers corresponding to those time periods and not in newer layers; however, since these animals are known to be still present today, I was wondering how it is possible that they do not have fossils in newer layers of the earth. Similarly, What caused the sudden stoppage of fossils?

I know very little about evolution, biology, and fossil records except from what is taught in high-school, and haven't taken a biology course in a few years, so if it is possible to get a simple answer that a biology ignorant person could understand I would greatly appreciate it! Thank you!

https://www.youtube.com/watch?v=e_TjrqWTV5s&t=187s


texts: Where can I find DNA Sequence data for colon cancer

texts:
I am a computer scientist studying pattern recognition, and I am hoping to do some supervised learning on colon cancer.  Unfortunately, I'm having a heck of a time finding DNA data in the following format.

Benign DNA (Adenoma?)     Malignant DNA (Carcinoma?)
A                         A
A                         A
T                         G
G                         G
C                         C

So I just need two columns (don't care if it goes down for 3 billion records/ amino acids): one with the good DNA and one with the bad.

Is there anywhere I can find data in that specific format?


texts:
What drives evolution forward? I heard that climate change drives species to evolve and adapt. Is there any other mechanism that is encoded in our DNA by which species can over abrupt changes, evolve and adapt?

Say for example Jupiter's moon Europa. If I find species of fishes here in Earth that could theoretically, barely survive on those oceans. If I come back in 5 million years will they look the same they did when I placed them there? or is the process of natural selection universal, and I would expect to see changes in the fishes due to their new environment which is not Earth. basically would foreign species also evolve and adapt.


texts: What is the most primitive organism that can die of aging?

texts:
I know that simple organisms containing of just few cells have no mechanism of dying because of aging. I guess, they typically die due to being out of food or due to becoming someone else's food.

Leaving aside the numerous theories of what can be the origin of such phenomenon as aging, I'm asking a simple question: what is the most primitive organism known so far which has the feature of aging and (as a consequence) dying, even if the environment is perfect?


texts: Do all chromosomes in one human body contains same genome?

texts:
As I understand it, each nucleus of a cell contains multiple chromosomes. Each chromosome has multiple DNAs. Each DNA contains some specific gene sequences. That sequence is called Genome.

My question, do all chromosomes in cells in a human body contain same types of genomes (i.e. gene sequences)?