texts: Do animals suffer in agony or pain the same way like homo sapiens suffer?

texts:
When an animal suffer in agony or pain, do they feel it the same way as homo sapiens or human beings?

I saw a documentary where it showed that while the child cattle were being slaughtered mother cattle were crying. Is that really crying or is it just secretion of tears from tear glands like it always happens?

Do they have the sense to feel suffering like we suffer? If it is true then is the sense of suffering prevalent among all the animals equivalently?


texts: How can cabbage worms (Pieris brassicae) smell/see cabbages from a distance?

texts:
Recently I did post a question on gardening stackexchange asking if cabbage worms could smell their way back into my cabbages after I moved them away outside my fence. Answers says yes they do, but it seemed to me opinion-based and I cant find anything to support this answers.

Can this type of worm smell/see or have any other type of sensorial navigation thing that can lead them towards cabbages?


texts: Why MHC class I antigen presentation exist in normal cells?

texts:
The book "Kuby Immunology" states that normal infected cells might present antigenic peptides on their surface via MHC class I, but these can't activate naive CD8 cells. Only infected professional antigen presenting cells have the necessary co=stimulatory signals to do so. This is why cross presentation happens.
But then why does the process of antigen presentation on normal infected cells happen then, if it is of no use?


texts: Are ion channels/resistancies in Rall's model voltage-independent or not?

texts:
In the description of the electrical circuit that models a piece of membrane

in Rall's Scholarpedia article on Ralls model, I read:

  "[...] this conductance [$G_e$] is zero under resting conditions, but
  is turned on by an excitatory synaptic input. [...] this conductance
  is [$G_i$] zero under resting conditions, but is turned on by
  inhibitory synaptic input."

Does this mean, Rall is assuming voltage-dependent ion channels? Or why does he stress, that the conductances can (or even must) be turned on and off?

From an electrical point of you, I would guess, that the three resistancy-battery pairs can be replaced by one such pair that would not be voltage-dependent, and maybe even the battery is not needed, as in cable theory:

Or would Rall's model not work anymore, then? This doesn't get clear to me, and would not have been stressed by the author. (Later in his article, Rall doesn't mention $G_r$, $G_e$, $G_i$ anymore, but talks only about membrane resistance $r_m$.)


texts:
I have a couple of questions regarding the nuclei in the pons, thus I figured it would be best to frame the main question in the way that I did.
My main question, however, is whether the basal pontine nuclei is part of the "cranial nerve nuclei" in the pons or is a separate pontine entity.
Quoting Kandel's Principles of Neural Science (2013),

The ventral portion of the pons contains the pontine nuclei, groups of neurons that relay information about movement and sensation from the cerebral cortex to the cerebellum.

Quoting Carlson's Physiology of Behavior (2013),

The pons contains, in its core, a portion of the reticular formation, including some nuclei that appear to be important in sleep and arousal. It also contains a large nucleus that relays information from the cerebral cortex to the cerebellum.

And while Wikipedia might not be the best source of information all the time, I must quote a few relevant portions which is causing me confusion,

A number of cranial nerve nuclei are present in the pons:
mid-pons: the 'chief' or 'pontine' nucleus of the trigeminal nerve sensory nucleus (V)
mid-pons: the motor nucleus for the trigeminal nerve (V)
lower down in the pons: abducens nucleus (VI)
lower down in the pons: facial nerve nucleus (VII)
lower down in the pons: vestibulocochlear nuclei (vestibular nuclei and cochlear nuclei) (VIII)

I now have broken information about these different kinds of nuclei but I do not know whether the basal pontine nuclei is a part of the cranial nerve nuclei or not.


texts: Mechanics of Peregrine Falcon Dive Pull Up

texts:
There are loads of information on how fast the Peregrine Falcon dives, but aside from having specialized lungs, eyes, etc... to survive the dive.

What mechanics does it use to pull out of such a dive, specifically after it has hit it's prey.

My take is that it uses its momentum to loop back in a U-shape, understand that by changing the angle of attack, this generates the necessary drag & lift to pull out of the dive saftely.

My question is how effective is this & can a larger bird pull this off assuming it has all of said mechanics?


texts:
If we assume that the Brachiosaurus and the modern Giraffe with their long necks both came to be by the need to reach higher-situated vegetable nutrition (which is a somewhat controversial assumption to make, I understand Evolution of long necks in giraffes), what biological reason is there we don't see any kind of modern day equivalent to the Elasmosauri?

Put differently, what environmental factor promoted the evolution of water reptiles with extremely long necks that ceased to exist in a post-cretaceous world? What benefits did Elasmosauri have that later water creatures would not?

Assuming that evolution is shaped by environmental factors, of course.

(And assuming the "water giraffes" weren't simply called "hydras" and extirpated by the ancient greeks. :P )


texts:
According to this article, a small amount of Neanderthal DNA was introduced into the modern human gene pool. How do biologists even know what the Neanderthals' DNA look like?

The article doesn't mention how the science recognize what the Neanderthals' DNA actually is at the first place. So how do we know what the Neanderthals' DNA is if I'm guessing we never tested Neanderthals body cell samples?

If you say "From their bones/skull" but how do you know they are actually Neanderthals and not modern humans with some rare gene mutation or something else?


texts:
It seems that young females (comparing age 15 vs age 24) are 20x more likely to get chlamydia
from a single unprotected sexual encounter with an infected male.  What are the reasons for
this?  Are there other diseases with such extreme age-dependence?

Reference:

Estimating age-dependent per-encounter chlamydia trachomatis acquisition
risk via a Markov-based state-transition model.


texts: Why do some ant workers still wander at night?

texts:
As far as I have seen, the vast majority of workers in colonies of diurnal, non-nomadic species return to their nests and remain there at night. The colonies seem to forage largely during the day. However, a few individuals of said colonies would still wander far from the nest at night. I don’t believe they are lost because they still seem to be following pheromone tracks.

Why do they do that? What drives them to still come out at night and not remain in the nest like most other workers do? Are they any different in terms of caste? Are they always the same individuals? Is there a selection process to decide who will wander off at night? Are they somehow invalid and can't tell day from night? Is that somehow evolutionarily advantageous (e.g. having a few workers take some risk at night, maintaining the pheromone tracks throughout the night so that the other workers don't have to start all over the next morning)?

Someone (jokingly) told me those ants must still be hungry, but I don't immediately buy that explanation because my understanding is that most species will store food in the nest in one form or another anyway, or they just share food by trophollaxis.


texts: Why do some enzymes have giant structures around the active site?

texts:
As a part of my inorganic chem. course (it's a required course at my college), we have a module called Introduction to Bioinorganic Chemistry. There, the prof. showed examples of enzymes like Cytochrome P450 and the drug erythromycin, and circled the active portions.
From what I can see, the active portions are a tiny portion of the actual drug/enzyme, so my question is: why do enzymes (and drugs, for that matter) have huge structures surrounding them?
I tried Googling my question but couldn't find anything relevant to what I was looking for. I suspect that I wasn't using the correct terminology, so the search engine had no idea what I wanted to know.
Simple explanations are preferred, preferably from the high-school level biochemistry side. I've never taken a biology course in school or college. I am a math major and this inorganic chemistry course is a required one. However, I still want to know why the amino acid chains are required, as they don't seem to be doing anything (that's what the active site is for.)
Picture for reference:


texts: Is there a detectable amount of bacterial DNA in the blood of infected persons?

texts:
With which bacterial infection in humans has it been shown that bacterial DNA can be found in the blood?

If any is found it is likely not to be very much, and even difficult to distinguish from human DNA, but presumably recent advances in sequencing should have made it possible.


texts: Transcription of two different factors from the same transcription factor - seeking a relation between concentrations

texts:
Let's assume that:
Factor $X$ enters nucleus and results in the transcription of two different factors, $A$, and  $B$.
$X$ $\to$ $A$
$X$ $\to$ $B$
Can it be expressed as
$[A]=\alpha [X]$ or  $[A]=\frac{\theta (\alpha [X])^n}{1+(\alpha [X])^n}$ and
$[B]=\beta [X]$ or  $[B]=\frac{\theta (\beta [X])^n}{1+(\beta [X])^n}$
where $\theta$ is the Hill coefficient, such that concentrations of A and B have a relation between?
Note: I don't have an education on molecular biology, or biology - terminology might be wrong.


texts: Does photosynthesis occur on cloudy days or does it require direct sunlight?

texts:
In my basic science classes in high school, I have learned that during photosynthesis, plants absorb sunlight and produce food by converting carbon dioxide and water into sugar and starch.

To me, this seems similar to the analogy of solar cells that convert sunlight into electricity. When sunlight falls directly on the solar cell, it produces electricity, but even when it is cloudy with no direct sunlight available, electricity is produced, but with less efficiency.

So can photosynthesis occur in plants only when they are in direct sunlight or does photosynthesis also occur during cloudy weather when the light is diffuse or indirect?


texts: How do I calulcate the amount of concentrated stock solution to add to get the correct dilution?

texts: For example, how much loading buffer (6X) do I need for my PCR reaction with a volume of 25 μl?  What is the general way to calculate it?


texts: Why do some mammals not have testes in a scrotum?

texts:
Coming from an evolutionary approach, Is the only purpose of a scrotum to regulate the temperature of the testes?

Knowing all mammals are warm blooded, shouldn't all mammals have testes in a scrotum?


texts: How does one apply Bayesian inference to quantify a read the deeper you sequence?

texts:
For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule.

What is the normal approach in the field to quantify one's level of certainty in NGS sequencing with Bayesian methods? There is also a statistical question here in terms of how one aligns reads, etc.


texts: Do organs or any structure in the human body shrink/shorten if it's function is no longer useful?

texts:
Charles Darwin was one of the first scientists to theorize on the function of the appendix, which in his day had been identified only in humans and other great apes. He hypothesized that the distant ancestors of these animals survived on a diet of leaves, and so they required a large cecum, a portion of the gut that houses bacteria that can break down stubborn plant tissue. Later, he speculated, these ancestors shifted to a largely fruit-based diet that was easier to digest. A large cecum was no longer necessary, and it began to shrink...Darwin thought the appendix, which juts off of the cecum, is one of its former folds that shriveled up as the cecum shrank. Consequently, he thought it carried no function.

I recently read a source which states the above. It made me wonder that if there is some other organ/part in our body which may shrink as further evolution progresses and it's use diminishes, just like our appendix. I'd like to know if this 'theory of shrinking' applies to any organ that may become useless.


texts:
I have recently peformed an ELISA (Enzyme-linked immunosorbent assay), but I still have some questions, let me first outline what I did:

We had a number (20) of tubes containing fake 'bodily fluids' , namely saliva. One of these tubes contained the Epstein-Barr virus, which on its turn causes Pfeiffer's disease, aka the 'kissing disease' (so we basically conducted an experiment to see how fast the virus would spread within a class if everybody started kissing each other, if you don't mind the crudity).
Everybody mixed their saliva with the saliva of 3 other people, so at the end everybody had a tube with the saliva of 4 different people in it.
Since we worked in pairs of 2, every duo got a microtiter plate with 12 wells in it: 3 wells for a positive control, 3 wells for a negative control, 3 wells for the fluids of 1 of the duo and 3 wells for the fluids of the other one. You pippete in (is that correct?) the fluids accordingly.
After a while you rinse and clean the wells with wash buffer.
Then you pippete in the primary antibody in each well.
After a while you rinse and clean the wells with wash buffer.
Following this you pippete in the secondary antibody (conjugated with the enzyme HRP).
After a while you rinse and clean the wells with wash buffer.
Finally, you add the enzyme substrate (TMB) to each well. This causes a blue color if when in contact with HRP. The positive controls must come out blue, the negative must come out colorless, and the other wells can go either way, depending if you have the virus.

I hope this is not to crudely explained, again. These are my questions concerning the experiment:

What do the components of the acronym 'ELISA' actually stand for? Does immunosorbent refer to the binding of the antigens to the wells? My English isn't too good, and these acronyms and abbreviations often seem foreign to me (nevermind that they are foreign since I'm not English, you get the point I hope).
When you pippete in the saliva in the wells, what actually sticks to the wells? All of the antigens in your saliva? Because it's hard to believe that they make special microtiter plates for every single antigen seperately. I assume it is only the antigens, since the primary antibodies attach to the antigens only, so there is no need for the microtiter plate itself to bind to antibodies.
How would we get the primary and secondary antibody? This is my assumption: The primary antibody we get is by injecting some antigens of the Epstein-Barr Virus into a human and then taking a serum. The secondary antibody could be gotten by injecting a random human primary antibody into ANY animal, irrelevant which anyimal, and then taking a serum. After that you conjugate an enzyme to the secondary antibody. Is this correct?


texts: Can animals like squirrels leave "gifts" or tribute for humans?

texts:
I've heard anecdotal reports of squirrels bringing up gifts to a person's house after that person left out food for them. Sounds bizzare and unbelievable, until I actually saw some kind of a nut right on the welcome mat in front of the door. I moved it and saw that it was eaten (shell fragments) a couple days later, telling me that it was actually a good nut.

This makes me ask - is this just a coincidence, or do some animals, like squirrels indeed offer gifts or tribute to humans?

I'm aware that cats frequently bring killed animals to human doorstep:

  By leaving a dead animal on the back porch, your cat is acting out its
  natural role as mother and teacher. You, her loving owner, represent
  her surrogate family. And frankly, she knows you would never have been
  able to catch that delicious mouse on your own.

However, for squirrels there's no domesticated relationship, humans are not a part of their family. Why would this behavior take place?


texts: Where does vasoconstriction occur in limbs?

texts: When cold or in shock a person's blood vessels constrict in order to preserve heat or to move blood flow to protect vital organs.  I am interested in the mechanism by which this is achieved.  Does this occur along the entire length of the limb or are there 'pinch points' (for example is it possible to simply have a point of vasoconstriction just below the shoulder which would reduce blood flow to the entire arm)?  Am I correct in thinking that the response is neurological rather than endocrinological ?


texts: I found this fruit fly in Pune/India. It was about 1 cm in size. I explored info on several species in same region, but they were different in appearance, especially that black spot in middle of body.


texts: Is it possible to remove the baby from the womb of a mother to cure the baby of a tumor and putting it back in the womb to be delivered naturally (the baby is 6 months)


texts: Can our body adapt to periodic fluctuations in sleep?

texts:
Suppose that if I've to attend a morning class then I must wake at 5 AM in morning. Next, if I don't (attend the class) then I wake up at 7-8 AM.

I've experienced that, since I do attend those classes almost regularly, my body has adjusted itself (sleep cycle) to wake at 5 AM almost precisely without a alarm set and has also decided when to sleep (it seems to demand 7-8 hour of sleep). This, I think, is common to most of us.

Now suppose that I attend classes only on alternate days. Put simply, I wake up at 5 on first and at 8 on the next day and so on. This implies that I am constantly switching my sleep cycle every day. Would my body, now, be able to adapt to this continuously varying cycle (which is but periodic).

I suppose no, and that is just a guess based on my experience. But provided I give my body enough time, I think that it may really adjust to this scenario.

On a side note, assume that (in case it matters) I take a sleep of 7 hours during class days and a sleep of 8.5 hours during holidays to make this data realistic. .


texts: How does Acetaldehyde accelerate mitosis?

texts: I read that one of the ways alcohol is carcinogenic is via accelerated mitosis due to acetaldehyde, I was wondering what pathway caused this acceleration?


texts: Question regarding Rate of Photosynthesis AP Biology Lab

texts:
We are doing a lab on the effects of light intensity/wavelength on the rate of photosynthesis in AP bio and we were asked to visit this website here: http://mhhe.com/biosci/genbio/biolink/j_explorations/ch09expl.htm

The link takes you to a shockwave applet in which you can change the wavelength/intensity and record the ATP production (%). We were supposed to try out as many different combinations of intensity/wavelength and record the respective intensity, wavelength and ATP production (%) in a chart. Now the problem I'm having is that we are to graph this data. How should I go about graphing this? One problem is that for some values in the data, the intensity might be the same with different wavelengths or the wavelength maybe the same with different intensities. Can I do two graphs? One graph? Which one would be best and how should I go about doing so? And here is the chart just in case you want to see the data:

https://drive.google.com/file/d/0B4A27kix-0naMk4wNmNQejd3cGc/edit?usp=sharing


texts: Measuring fitness / lifetime reproductive success (LRS) in Drosophila

texts:
I am planning a fitness assay of Drosophila melanogaster. I'd like to get a good measure of lifetime reproductive success (lrs) but I don't want to count all the offspring produced over a lifetime by 100's of focal flies. The solution I am toying with is to count offspring production over the first few days or weeks. But before I commit to this I need to know if there is existing research material on the following:

Does early reproductive output correlate well with lrs? (this could be a low correlation if a fly trades early-life offspring production for late-life offspring production)

How much of a fly's reproductive output does one need to count before they have a good estimator of lrs? (does counting the offspring produced in the first day of life correlate well to overall lrs or do I need to count more - 5 days, 10 days, 50 days...)


texts: Why is there a size limit on inserts that a plasmid can accept?

texts: Throughout my undergraduate education I have been taught that plasmids can't carry very large inserts, but I have never been told why. Any insight would be greatly appreciated.


texts: Where can I find the common names for the zoology taxonomy?

texts:
Forgive me if my question does not belong here or if I'm using incorrect terms, but I'm not educated in biology at all. I'm investigating the workings of the biological classification system.

I was wondering if there is a list somewhere of all kingdoms, orders, classes, etc., both in Latin and common names?


texts: Why does histamine cause bronchoconstriction?

texts: What purpose does histamine-caused constriction serve in lungs during allergies and such, since it's vasodilator in other parts of body. Wouldn't it be more practical to vasodilate lungs so that white blood cells can arrive and toxins can be flushed more quickly.  Thanks in advance


texts: How can a YAC be screened against a cDNA library and a cosmid library of genomic DNA to find a gene?

texts:
I am reading fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size (doi: 10.1126/science.289.5476.85).

The authors are trying to find the gene that makes tomatoes bigger. As far as I understand, previous research had narrowed it down to "something" in the region of the genome called fw2.2. They are trying to determine the actual genetic elements responsible (which turns out to be a gene similar to human HRAS).

Supposedly, the big-fruit allele is recessive and the small-fruit allele is dominant.

They say (in section Genetic complementation with fw2.2) that:

They got a YAC containing the fw2.2.
They "screened a cDNA library" with the YAC to find transcripts that were potentially relevant. (How?)
They "screened a cosmid library" of genomic fragments to find the stretch of genome that the cosmid came from. (How?)

It is unclear to me how steps 2 and 3 work. Can someone explain how you can take a YAC, cDNA library and cosmid library to find the gene inside the region responsible for your trait, as these researchers describe?


texts: Is it possible to insert DNA without cutting the recognition site with CRISPR/Cas9?

texts:
We are looking for a way to insert DNA into a genome, but we would like to do it in a way that the recognition site stay intact to be able to add again DNA at the same location. Do you know if it is possible or if it is already the way CRISPR/Cas9 does it? Apparently multiple systems were already engineered but the few papers we read weren't about our problem.

Sincerely,

Emilie


texts: Method to estimate age of a variant from genotype data

texts:
I will obtain array genotype data from approximately 60 related individuals who all share a rare pathogenic variant, which is at such a high frequency in the enlarged family due to a founder effect.
Is there any software that I can use to estimate the "age" of this founder effect i.e. how long ago there was a "most recent common ancestor", basing on the haplotypes observed from genotype data?


texts:
Visiting the Maine and California coasts, I've noticed that it is much more common to see marine mammals from the coast in California, including seals, dolphins, and whales. I've been hypothesizing about reasons that this might be the case, and have come up with several ideas.

I'm a tourist, not performing a formal population study. Maybe the numbers are similar, but my measurement method is flawed. I've looked up some better numbers in the NOAA Stock Report:

Seals:

Harbor seals, Maine (75,000) vs. California (27,000),
California Sea Lions, California (257,000).

Whales:

Gray Whales, California (27,000)
Humpback Whale, Maine (900) vs California (15,000)

Dolphins:

Common Short-Beaked Dolphin, Maine (170,000) vs California (839,325)

There are many other species, but these numbers seem to confirm that California has a larger population. Of course, the coast of California is also much larger than the coast of Maine. I'm not sure how to correct for that.

Maybe the fishery in the North Atlantic is more overfished. Wikipedia says that 71% of fish capture comes from the Pacific vs 20% from the Atlantic, but that the Pacific has only twice the volume of the Atlantic[1]. This is much more general than California vs Maine coast, but it suggests that the Pacific has a larger fish population than the Atlantic per volume which could support a larger mammal population.

Maybe there are more protected habitats in California. 15% of the south coast region is protected from fishing. Whereas in Maine, I was able to find information about proposed Marine Protected Areas, but no information about currently protected areas.

Does the coast of California support a larger population of marine mammals than Maine? If so, what factors support the larger population?


texts: Is nucleoside-triphosphate delivery to RNA or DNA polymerase active or passive?

texts:
Are nucleoside triphosphates (NTPs) actively delivered to RNA polymerase (similarly dNTPs to DNA polymerase) through some active chaperoned process, or are they so abundant in the nucleus that they rely simply on stochastic diffusion?

Are there any relevant papers on this process?


texts: Where can one find completed and processed Hi-C datasets?

texts:
I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand with itself within the nucleus).  I am not a bioinformatician, so I am looking for someone that already has some complete data, or a website that may have these available for download.  The more datasets, the better.

Can anyone help me?  If you provide the data yourself, I will be sure to mention you in the foreword to my dissertation.

Thanks!

P.S.  If someone can find data generated specifically by the program "Hi-C Pro" with "allele specific analysis," I would be doubly grateful.


texts:
What is the function of the auricles (conical appendages through the atria) present in the heart?

Do they have any other function than increasing the volume of blood the heart can hold?


texts: What are the evolutionary niches differentiating an apple from a pear?

texts:
So, as far as I understand (basic) evolutionary theories, diversity is generated by "niching." That is, if there is an environmental factor that hasn't been fully used by any species to "profit" off, there will be a tendency to fill up that "niche" and thus speciation occurs (not in one day of course).

I was standing in the kitchen earlier and was wondering: what is the niche that an apple fills in respect to a pear end vice versa? If I'm not mistaken they are form the same family and thus share a common ancestor (albeit I don't know if it is a "recent" ancestor).

Is it a geographical thing or do they genuinely vie for the same thing in a different way? (e.g. a pear aims to be eaten by animals that have small teeth and thus want a softer fruit, while an apple aims to be eaten by the bigger animals, that like a heartier bite).

note: I know that this question might be too speculative and too localised to be any good, but hey, some of you might just know this!


texts:
I have found the following definitions of different types of gametes:

isogametes: gametes looking and behaving the same;
heterogametes: gametes different in size or in behaviour;
oogametes: gametes different in size and behaviour.

I have some doubts about the exact meaning of behaviour in such definitions. I know that there exist species where gametes of the same mating type can originate a zygote, for ex. in some fungi.
Do differing heterogametes and oogametes always belong to different mating types?
Thank you very much for any clarification!


texts: Is there a resource for comparing categories of life along quantifiable dimensions such as species diversity, geographic range, total mass, etc?

texts:
Ideally what I would like is some sort of interactive, sliceable tabular data along the lines of my examples below. The curious individual specifies the level of taxonomic rank, e.g. Kingdom or Class etc., and then can choose to populate several rows from within that category with data on that category's "successfulness" as measured in various ways (of course all the data fields would be estimates)

CLASS        # OF SPECIES  TOT MASS   TOT RANGE    # INDIV.  # CELLS PER INDIV.
Insecta      ???           ???        ???          ???       ???
Mammalia     ???           ???        ???          ???       ???
<click to add a row>

But the user could select a different granularity, so e.g.

FAMILY       # OF SPECIES  TOT MASS   TOT RANGE    # INDIV.  # CELLS PER INDIV.
Formicidae   ???           ???        ???          ???       ???
Felidae      ???           ???        ???          ???       ???

The goal would be to be able to put "superlative" claims about various categories of life into context. I often read claims of a ____'s (species', genus', etc.) success based on one of these or other estimates, but have no intuitive way of attributing an absolute context to the number reported.

Furthermore, such a table / database would just help me form a clearer picture in my own head of "all the life out there" (that we know about). For example, if I wanted to learn all there is to know about every species of "cat" (I am on the internet, after all), how many species are we talking about? Probably on the order of dozens, versus thousands or tens of thousands for ants.

So far I've found "top 10"-style lists and the like, but no single unified searchable tabular database.


texts: I don't know if this is a real claim, I live in Mexico City and most of the people I know are more similar to their father than to their mother? Why is that? Are the x and y cromosomes somehow related to the strength of a particular gen?


texts: On the premise of crop rotation, is there similarly a plant or organism able to provide nutrients into its environment that exists in water biomes?

texts:
I know of the simple concept of crop rotation, and being able to use certain plants to replenish soil, and was wondering if there is a plant or organism that can or does function similarly but in water. I also know there are some plants that are more resilient (and even function or thrive) in soils high in certain compounds and metals (or, conversely lacking in certain nutrients or conditions), that are otherwise detrimental for other plants or organisms. I am therefore also wondering which plants or organisms function similarly, but again--in water, rather than on land.

I have a particular interest in saltwater environments, but also would like to know if there is something in freshwater environments that provides this function.


texts: Do hedonic chemicals in humans work as anhedonic in other organisms?

texts:
We have various neurotransmitters that cause pleasure or feelings of love in humans. Do they work in this way for all other animals and organisms ?
What about reptiles, insects, crustaceans ?

I don't know how far science is assuming the state of subjective experience in other organisms, but how far can we say that other organisms would feel the effects of neurotransmitters in ways that we would recognise from our own experience ?
For instance, we could assume that another primate experiences dopamine in a similar thing to humans, but what about non-mammals, animals of other classes ?


texts: Genetic coding question, amino acid to base relationship

texts:
I'm studying for a test and I am confused by these problems/statements.

How many amino acids will 18  bases code for? Answer: 6. I got this right.
If a certain complete protein has 33 amino acids that compose it, then exactly how many bases will it take to code the entire thing?

The answer to 2. is 105, but I'm confused on how we arrived at this answer. If possible or if necessary, please explain the related concepts to me!


texts: While calculating photosynthetic efficiency, do we take into account the Gross Primary Production or the Net Primary Production ?


texts: What percent of e coli genes are necessary for survival?

texts: I would like to know, in a typical e coli genome what percent of genes the organism could not survive without. That is, if all the other genes evolved except that one, the organism would not be viable.


texts: Variations in action potential threshold and temporal coding

texts:
I would like to ask a few questions about things I'm not sure I understand in a paper Action potential threshold of hippocampal pyramidal cells (...).

(1) At the start the paper considers the possibility of irregular firing patterns of action potentials may be an argument to hold that the information processed by the CA1 neurons is a temporal code. I think it is hard to see the relation of final results (see the abstract) with these initial considerations. Do the results support the temporal coding hypothesis of CA1 neurons? How?

(2) At the end of the first page it says the following: "significant variations in action potential threshold would have implications for the precise timing of action potentials since the probability of initiating an action potential could not be predicted by only fluctuations in the membrane potential".

Does this mean that they aim to explain the irregular patterns by means of the fluctuations in the threshold?

I also don't see how from "the probability of initiating an action potential could not be predicted by only fluctuations in the membrane potential" follows that "significant variations in action potential threshold would have implications for the precise timing of action potentials".


texts:
I haven't really paid attention to the raw food diet and the claims of its supporters until now. A passage from this website says:

  The basic premise behind preparing raw food is not to cook food above 118ºF. Cooking food denatures both the protein and the fats. So instead of your body using the food it simply stores it.”
  When food is cooked above 118ºF, 85% of the food's natural enzymes are destroyed. This forces your body to generate the enzymes necessary to digest the food. This results in partially digested foods that can clog the body's intestinal tract and arteries.

It's possible this passage, which is from a chef describing the main benefit of raw food diets, misquotes the chef or wasn't phrased properly. I am assuming that the chef is talking about plant-based foods, like vegetables and legumes, when she says food. But given what's here, I read this as:

'-When cooked food (food prepared above 118ºF) is eaten, denatured proteins and fats are not 'useful', other than fat (storage).

-Food has natural enzymes (and the speaker may be equating proteins and fats with enzymes?); they get destroyed by cooking.

-Digestion that occurs via the enzymes an eater creates are ... bad? Not as efficient as the enzymes that are 'naturally' in the food?

-Digestion via the enzymes that an eater produces lead to partial digestion.'

My shoddy recollection of biology class is that we produce saliva and related enzymes to break down food items we ingest, like a tomato cut from the vine. Those items will not produce enzymes within themselves that will aid digestion inside other animals that consume said tomato. Why would it?

My question is: do I have the wrong understanding of digestion? Should humans rely on the "natural enzymes" that are in uncooked plant food for digestion and good nutritional benefits?


texts: What causes the characteristic 'gleam' in the eye of a living being?

texts:
The title is pretty much what I seek to know.
Unless the other person is play-acting, one can often make out the eye of a living person has a shine-of-life to it; a cadaver does not. Similarly the gleam appears brighter when a person is feverish, or excited otherwise ... or has some infection in the eye itself.

What causes this gleam? Is it merely nervous electricity at work that disappears when the system is shutdown/crashed?


texts: Could we tell that cancerous cells behave that way because-of their genetic machinery is work in a "primitive" way like Amoeba?

texts:
Amoeba sp. is unicellular, so can't form a tissue. It need not go through any apoptosis. It just continuously get doubled.

Could we compare them with cancer-cells?

or in-reverse,

could we tell that cancer-cells are a sort of mutated cell, that is behaving like Amoeba, or behaving in a primitive manner, and lost its later-upgrades?

It seemed to me when I came to know that,  mutation in many possible, separate genes, can cause mutation (probably that's why all environmental articles about different mutagens lead to the same disease... cancer). So I was wondering about there could be a common-cause behind all these cancers ... which maybe a loss in all latter-upgrades.


texts: PBS or TBS, where cannot use each buffers?

texts:
As you know, Tris buffered saline and Phosphate buffered saline is multipurpose. For finding each buffer's use, there's so many use experiment for PBS and TBS. TBS uses for western blotting, and PBS uses for cell culture.

but some experiment never use PBS and some experiment never use TBS, I want to ask this situation which when you use TBE but never use PBS, and the opposite situation(use TBS but never use PBS), For example, When you western-blotting with alkaline phosphatase never use PBS and PBS-T. this case, phosphate inhibits AP, and amine-coupling with NHS-EDC, never use Tris buffer because it have primary amine.


texts: Mechanism for earthworms to get into a roof gutter

texts:
While cleaning accumulated muck from a roof gutter on my house, I found a few earthworms living in the muck. I am intrigued about what mechanism may have allowed the earthworms to reach that location. Some hypotheses:

Live worm crawls up a downpipe
Live worm dropped by an overflying bird
Cocoon is stuck to the outside of a bird (feet), falls off while the bird is overflying the roof
Cocoon passing through bird digestive system and deposited on the roof

What is the likely mechanism for earthworms to reach that location?


texts: If an organism is supported only by cartilage, does it have an endoskeleton?

texts: Lamprey and sharks lack bones, but does this mean they are not classified as having an endoskelton? Does an organism need bone to be considered as having an endoskeleton?


texts: What goes into a vaccine placebo, typically and in the specific case of Pfizer's SARS-CoV-2 vaccine trials?

texts:
I am curious about what actually goes into a vaccine placebo formulation, given that there were apparently some reactions reported by trial subjects who received the Pfizer SARS-CoV-2 placebo.
From what I've been able to find out online, the actual vaccine contains as principle ingredients (simplified):

mRNA (active ingredient) to make the target antigen (spike protein)
lipids (to protect the mRNA and facilitate its delivery into cells)
salt(s) to adjust pH and match the salinity of blood
sugar to address issues which occur when the vaccine is frozen

An injectable placebo could be as simple as a saline solution... if so, how could reactions be explained? Is it entirely psychosomatic?  Is the Pfizer SARS-CoV-2 trial placebo the complete formulation (or some subset of vaccine components) minus the active (mRNA) ingredient?
The lipids have been implicated in allergic reactions to the actual vaccine; would they have been present in the placebo and account for the placebo reactions?


texts: What's the rationale behind freezing one's eggs if cells can be cloned?

texts:
It seems to me there's a lot of discussions around the topic of somebody freezing her eggs.

What I don't understand though are the following:

Why would you freeze your eggs when you know that the technology for transforming a somatic cell into an egg today exists, or doesn't it see here?
Is it proven that freezing doesn't alter biological activity and hence not diminish the chance of giving birth to a malformed child?

To me it seems way easier and safer (and less expensive) to artificially produce female gametes than freezing them and, 10 years later, unfreeze and hope for them to be still biologically active.


texts: Is there a difference between ISH and ISHH? (In Situ Hybridization, In Situ Hybridization Histochemistry)

texts:
I came across the term ISHH in my document and discovered that it stands for In Situ Hybridization Histochemistry. I's translating to Russian a document that uses this abbreviation.
Example from the PubMed:

We then validated these findings by using a combination of tools, including the analysis of an additional brain region in an independent subject cohort, cross-validation with an alternate custom microarray platform, and follow-up with in situ hybridization histochemistry (ISHH).

Is there any difference between ISH and ISHH, or are these just synonyms for the same method, in situ hybridization?


texts: What's the smallest size a human eye can see?

texts:
During a biology experiment at school, where we would look at waterweeds under a microscope, my teacher said something about that it's impossible for the human eye to see the cells without a magnifying glass of some sort. So, I saw that as a challenge, and decided to check if I could see the cells. And after holding the leaves really close to my face, I was indeed able to see tiny rectangles.

Since I was curious about it now, I decided to look some more things up. First, I tried to find out the actual size of waterweed cells. Based on this 640x enlarged image, which features cells of 5mm wide and 10 - 15mm long in the picture (which corresponds with of roughly 8µm wide and 15µm long).

I left this in the back of my head for a long time then, but I just looked at my cotton sleeve, and noticed tiny fibers. Not the ones that are woven together, but ones that are standing out from it. So, after looking it up, it turns out that cotton fibers are 10 µm wide.

So, I wondered, what is the smallest size a human eye can actually see? According to a whole bunch of sources all across the internet, it's either 200-400µm, 100µm, or 58-75µm. I also hear 'the width of a human hair' very often, but those can range from 17 to 181µm.


texts: Is induction and derepression the same thing?

texts:
Induction

This is a definition that our professor mentioned in class $-$the process of turning on the expression of gene in the response to a substance in the enviornment is called induction.

Derepression

From wikipedia $-$ in genetics and biochemistry the removal of repression, such as of an operon so that gene transcription occurs or is enhanced, with the net result frequently being elevation of the level of a specific enzyme. This effect is called derepression.

In lac operon when Allolactose molecule is present in the medium (in the bacterial cell) it binds to the monomer of repressor and reduces the binding affinity of repressor to the operator site and the RNA polymerase is free to synthesis a polycistronic mRNA. Thus the allolactose molecule turns on the expression of lac operon by removing repression.

So I conclude that in lac operon induction is same as derepression. But does it hold true for all operons or there are operons in which induction is achieved without repressing the repressor?


texts: Why is Ibuprofen contraindicated in asthma patients?

texts: So yesterday a patient showed up at the clinic with a massive swelling in his left face region. Upon examination it was found to be due to infected first premolar. Dentist recommended him to get the tooth extracted as the patient also had generalized attrition and abrasion. The patient was an asthmatic and diabetic on Ecosprin. The dentist while prescribing him medicines said that he won't prescribe him Ibuprofen as the patient was asthmatic. I have been looking for an explanation since then and Rang and DaLe have something to say about the isomers of COX enzyme. I am looking for a simple explanation.


texts: What is the identity of this flower found in Mavericks Beach in Half Moon Bay, California, USA?

texts:
Please help identify this flower I saw in Mavericks Beach in Half Moon Bay, California. It was smelling soooo good, you can feel from distance. I want to buy and plant in my garden.

Thank you,


texts: Do animals exist which have good vision, but see only grayscale?

texts:
In computer vision the color information is often discarded, as most object recognition tasks seem to work just as well on the greyscale image (even better, because there is less unnecessary information).

Do animals exist which have good vision (e.g. see sharp, many details), but only see greyscale / very limited colors?


texts:
This question was posed to me by my Biology teacher:

Consider a hypothetical emergency situation of a person shot by a bullet in the heart. The bullet goes into the body and comes out from it, causing a total of two "holes" in the heart, one each in the "dorsal" as well as "ventral" side of the heart. Blood starts coming out.

Now in an ordinary situation, if the blood continues to flow out, the person will die. But there is a twist, the person has been given an infinite supply of blood from some sort of medical equipment. (Nothing like this actually exists in real life, but you might consider this a "conceptual Biology textbook problem".) The person's heart beats at a normal rate of ~72/second.

Now here is the question :

  Considering, the "infinite" supply of blood available, will the person survive?

Will the heart develop some sort of clot or something similar to prevent further leakage of blood, as it forms due the cuts on arms or legs? Is some medical assistance required besides the "infinite" supply of blood?

NOTE : You might make the following assumptions ---

There is no doctor/surgeon to help. Just you and your faithful "machine".
The blood provided by the "machine" is 100% compatible with the blood group of the person.
The "machine" is connected in such a way that after the complete loss of the "original" blood of the person, now the blood provided by "machine" runs in the arteries of the person.
The veins and arteries of the person are 100% OK. The only part affected is the heart "perforated" by the bullet.


texts: How to model missing residues on a protein from multiple PDB files?

texts:
I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as possible. Is there a tool (web-server, software) available to do this?

In a particular application, I have one additional requirement. One of the PDB files is special (call it the template), in the sense that I only want to add missing residues to it. That is, the resulting model should contain the special pdb file, and align perfectly to it, the only difference being that the resulting model has some additional residues that were completed from the information in the other pdb files. Okay, the resulting model should not align "perfectly" to the template. I'll allow some relaxation in the connecting points. But still, the idea is that the template PDB should carry a "larger weight".

So, those are the two problems: 1) How to reconstruct a more complete model from a bunch of PDB files of the same protein? 2) How to complete missing residues in one PDB file using information from other PDB files of the same protein?


texts:
I need to get HapMap 3 phased haplotype data. Where can I find it?

Actually I need these data for specific populations and a specific gene. What is the easiest way to find data?

I hope I can find an answer. Thank you!


texts: Does every gland type have stem cells for regeneration?

texts:
Is there any gland in which there are no stem cells?

I know that:

sebaceous gland is maintained by unipotent stem cells
thyroid gland - some stem cells, apparently unipotent

Glands about which potency I am not sure

pancreas gland - contains probably many types stem cells, at least unipotent
pituitary gland - not sure if any exist

I cannot find any such gland that does not have stem cells.


texts: Why does a caloric reflex test induce sideways movement of the eyes?

texts:
By my understanding the semi-circle canals in the inner ear are oriented in each of the 3 dimensional planes to sense rotation of the head. When the head moves, the fluid inside of the canals does not move with it causing relative motion (like the objects inside of a suddenly breaking car), moving hairs on the walls of the canal.
In the caloric test we inject cold water into the ear which causes a convection current in the canals hence moving the hairs and mimicking head movement. However, I can't understand why the horizontal canal is disrupted, since convection currents move in the direction of gravity. It seems logical that the canal oriented up/down would be most affected. The cold causing water to move downwards, mimicking rotation about the anterior/posterior axis.


texts: Could there be some safe, hypothetical way of turning on and of thermoregulation?

texts: This is something I thought of with the whole artificial gill concept.  Could a modification to the brain/nervous system allow a human to turn off their thermoregulation in air/water of the right temperature range, so they wouldn't have to expend as much oxygen?


texts: From 46 human chromosomes, is each one from a single parent?

texts:
Humans have 23 pairs of chromosomes. Each chromosome in pair is homologous to another one in pair.

Does this imply, that the entire chromosome in any cell is obtained from only one parent? I mean entire single chromosome from one parent, and entire homologous one -- from another parent?

This is obviously true for sex chromosomes, especially in boys. They get Y from father and X from mother.

Is similar true for any other pair of chromosomes?

Or they are exchanging genes during mitosis too?

I.e. parents data is distributed grouped by chromosome or by gene?


texts: How do cone cells underneath capillaries receive light?

texts:
Came across this image of retina's cross section:
1) How do the cone cells directly underneath the blood vessel ('demarcated in the picture') receive a spectrally correct representation of the incident light? Wouldn't the blood absorb most of the spectrum, leaving only red behind. Is it because the blood vessel is too thin?

2) The fovea region seems to be void of any such capillaries, how do the cells then receive nutrition and oxygen?


texts:
I have used a standard protocol (I will give the bibliography below) to extract RNA from an algae (Posidonia) but I have get literally nothing, since I could not even see traces of the two rRNA. I think that I have failed because the huge quantity of salt and/or carbohydrates in algae in comparison with terrestrial plants. My final objective is to get mRNA and then sequence it, so I need a very good extraction.
Any ideas of paper I could read to go above this problem?
Gambino, G., Perrone, I., & Gribaudo, I. (2008). A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants.Phytochemical Analysis, 19(6), 520-525.


texts:
I am currently working on antibiotic resistance and I would be very interested to know which bacteria has no plasmid, in a similar way than M. tuberculosis.
This would help me a lot for my work and I did not succeed to get that much information online.

Thank you very much for your answer !


texts: Why is the quality range of fastq format so broad?

texts:
Referring to fastq format, it is clear that in fastq format, there are 94 quality value for a sequenced Nucleic Acid of a DNA sequence read and they are:

!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

So, I have two questions:

Why is the quality value range so broad (94 levels)?
In a particular case of analyzing data, we saw, the frequency of I is so high, which is not a good quality. So, why would we accept such a poor quality in research?


texts:
Consider the below phylogeny. taxon1 and 2 are sister taxa but:
- share a brown color coat
- differ from their closest common ancestor (light color coat)

Is this a case of homoplasy (Analogous trait)?


texts: Do "virgin" ant queens ever shed their wings?

texts: In species that reproduce sexually, if an ant queen goes on a nuptial flight and does not successfully mate, will she still shed her wings and try to found a colony (although she probably won't succeed because unfertilized eggs will result in drones only)?


texts: How is excess semen removed if ejaculation does not occur?

texts:
There are some attempts to answer the question that I found via cursory Google search, but none of them were appropriately sourced.

This site claims that they are "recycled like blood cells", but the blood cells are recycled using the spleen, and I don't think spermatozoa normally enter the blood stream at any point in time.

This other site contradicts the first site, and claims that they are removed from the body by "dripping" them, therefore expelling them in the normal urine stream.

What is the actual process through which semen is removed if ejaculation does not occur?


texts: What type of nutrients can be applied foliarly?

texts:
I am interested in what type of nutrients can you spray on plants? Which ones do get used by a plant and which ones make no difference.

By nutrients I mean general fertilisers N,P,K and also micro elements.


texts:
DNA sequence of a gene can be altered in a number of ways. Gene mutations have varying effects on health, depending on where they occur and whether they alter the function of essential proteins.

I know that there different types of mutations.

Missense, Nonsense, Insertion, Deletion, Duplication, Silent, Frameshift indel, Repeat expansion, Inframe indel, stoploss, splicing.

Can anyone please tell me which mutations are Point mutations and which come under Indels?

Thank you


texts:
I understand that land-snail-slime and slug-slime are made of mucus.

Externally, one kind of mucus is produced by the foot of the gastropod
and is usually used for crawling on.
https://en.wikipedia.org/wiki/Snail_slime

Travelling on a trail of mucus seems very expensive. How do snails manage to replace it so abundantly without ever running out? Do they ever run out - if so, what happens to them?


texts: Is this a grackle with an unusually long decurved bill (Phoenix AZ, USA)

texts:
Can someone help me identify this bird (sorry only had the iphone)? It looks like a grackle, but the bill is much longer than any I have seen. The bill looks like a Le Conte's thrasher, but it was all black. It looked pretty ratty because he was molting. It was definitely black, and in an area with lots of grackles.

The pictures don't do it justice, it was a really long bill. The pictures were taken in Phoenix, Arizona, US on Greenway bike path near Thomas Rd on 7 Sept 2014.

The picture is not that clear, but it definitely was not something that the bird was holding in his beak. That was my first thought when I saw him, but I watched him awhile, it was very clearly his beak that was long and decurved. Sure wish I had my real camera at the time.


texts: What percentage of the human genome hasn't been sequenced yet? If percentage estimates aren't precise, why is it difficult to estimate?

texts:
What percentage of the human genome hasn't been sequenced yet? I have read different estimates, e.g.:

https://www.genome.gov/human-genome-project/Completion-FAQ (mirror): "In the April 2003 version, there are less than 400 gaps and 99 percent of the genome is finished with an accuracy rate of less than one error every 10,000 base pairs"
https://www.statnews.com/2017/06/20/human-genome-not-fully-sequenced/ (mirror):  "Church estimates 4 percent to 9 percent of the human genome hasn’t been sequenced. Miga thinks it’s 8 percent."

If there isn't a consensus on the percentage of the human genome that hasn't been sequenced yet, why is it difficult to estimate?


texts:
So the last class of antibiotics were made in 1984 (I think), which makes it appear as though they are hard to find(/design maybe). How is it then they were discovered? Was it by chance? I know some where accidents, but how are the majority found, testing lots of chemicals on your target?

I imagine now we would have the capability to quickly identify structures and molecules unique to pathogens and be able to model them on a computer, and generate suitable proteins or other compounds that can interfere with their bonding/properties to damage the pathogen?

For something like a 70s ribosome in a pathogen, what is the process of being able to understand its structure, its shape, etc? How much effort does it take to model onto a computer? Or instead a single protein (as a 70s ribosome will be more complex), how long does it take to model a new protein?

Thanks for any help :)


texts: Is new idea equivalent to forming new synaptic connection?

texts:
We get new ideas quite frequently hence I am curious that is getting new idea equvant to formation of new synaptic connections? I am aware of neural plasticity but somehow doubt that it happens quite rapid.
Since that idea was missing before one creates it makes me believe that the structure of synaptic connection was not present earlier and once the new idea was formed then the structure to simulate/produce that idea was created.
If that's the case that that's lots of neurons being connected/disconnected in few seconds which don't seem physically possible.


texts: Why not use non-visual self-recognition to test for consciousness in an organism?

texts:
Background

A well-known test for consciousness in an organism is to observe its ability to recognise itself in a mirror (see wikipedia article: "Mirror test").

Question

Why haven't I come across a "non-visual" mirror test? I.e. one that involves one of the other senses?

For example, how about testing for consciousness in bats by using an "audio mirror", the premise being that perhaps bats may recognise themselves through echolocation?

(image adapted from here)


texts: Is it hydrogen atoms or electrons that are passed along an electron transport chain?

texts: I am so confused because my book says it is electrons which are passed along the electron transport chain but all we are considering is hydrogen ions (H+) and hydride ions (H-). Can someone clear that up for me ?


texts: My bio book refers to HEMOZOIN that is responsible for the shiver during malaria. How does hemozoin work to raise the body heat?


texts: How do I find a protein from this DNA sequence?

texts:
I have a DNA sequence from a sequencer. How can I determine what protein is it? I tried some translator but it didn't help. What protein is this and how can I determine it?

The sequence: CGTTCTATAGATACGCGATGACGGTATACCATCCGCAAAGT

Thank you very much!


texts:
We found this tiny snake in the finished part of our basement today. We live in the St. Louis, Missouri area.

The snake is dark greenish-grayish and has very faint lines running the length of its body.  Any idea if it is dangerous/what we should do with it?


texts: Are domesticated animals really "more intelligent," or is that a myth/misunderstanding?

texts:
Often do I hear people speaking of how the domestic house cats are more friendly, less ferocious, less savage-like, and smarter and/or than their distinct but equivalent feline-species friends, like lions, tigers, jaguars, panthers, leopards, cheetahs, etc. Is this provably true in any form or way?

Are domesticated animals really "smarter" or less ferocious, or are some simply, but assumption of lessened threat potential, more so inclined to deem the house cat/dog as less ferocious simply because it's not such a big threat? Look at it this way:

This little beast here is "very cute" because he/she is small and barely 9 lbs. When playing, he/she isn't directly threatening to many human's safety, and many people are not afraid of cats; however, is he/she really smarter because he/she is safer and less dangerous to us humans only?

This beast, however, is hundreds of pounds heavier and many feet longer. Is it considered more savage-like because it can seriously harm and possibly kill humans by playing a little rough, which is like how a 9 lb. house cat would play equivalently, but would give you some light scratches at worst.

I've also heard arguments about "friendliness" of felines, usually claiming that house cats are friendlier due to evolution and nurturing/upbringing; lions/tigers, on the other hand, are claimed to be naturally unfriendly and have "more wild" in the, and incapable of being as "friendly" or "trustworthy" as a house cat. Point is, I'm probably not the only person who's heard this. Also, consider other animals, like dogs.

Dogs come from the grey wolf, to put it simply. Compare both a typical house dog and a wild grey wolf, and it's pretty obvious that many would assume the house dog is safer, friendlier, and less harmful, despite the fact that some domesticated dog breeds can pack a greater bite than the wild grey wolf.

Comparing the house dog's behavior to the wild grey wolf is also not a good measure of "friendliness", as compare a savage Homo sapiens from an uncivilized territory to a common city person, and you'd think the same thing: that the savage human is "less intelligent" and the city person is more so.


texts: Why will tissue from identical twin be rejected in some cases?

texts:
Also, transplants from one identical twin to another are almost never rejected.
[ Source: Medline Plus ]

Why can a tissue from an identical twin be rejected ?


texts: Why doesn't Fenoxaprop-P-ethyl damage cool season lawns?

texts:
For controlling bermudagrass, Cynodon dactylon, a serious perennial grassy lawn weed in my area, I use the herbicide Fenoxaprop-P-ethyl. It kills the bermudagrass rather well, without damaging the cool season lawn grass in the least.

I believe Fenoxaprop-P-ethyl acts by inhibiting the synthesis of fatty acids in the meristematic tissues of the weedy grasses (designed especially for bermudagrass).

How does this mode of action not affect the 'good' grasses (the fescues, bluegrasses, and ryegrasses popular in my area)?


texts: What is this insect? And does it eat aphids on plants?

texts:
I found this insect that looks like a praying mantis on my plant which was infested with aphids. I sprayed neem oil and most aphids died, even one of these praying mantises did. But here in this picture is one and I want to know if it is going to eat the aphids so I can stop spraying neem and killing every bug in the process.

The insect is around 2 centimeters long.

This is in a hot and humid area in the middle east. The plant, I guess, is from the jasmime family. It produces small scented roses (hasn't flowered yet due to the aphids problem).


texts: What are these tiny creatures swimming around my aquarium?

texts:
I was checking out my aquarium today, and decided to scoop out a water sample and take a look at it more closely. What I discovered were numerous, very, very tiny white worms (?) swimming around in the water.

The worms hover around 1 mm or smaller, almost invisible to the naked eye, with some exceptional specimens reaching nearly 2 mm in length. They swim very fluently, not by wiggling or waving their bodies around, but simply, effortlessly gliding through the water.

I checked them out under a microscope, and recorded some videos. I apologize in advance for the lackluster quality, as I'm not working with expensive equipment here. It took me hours to locate the worms under the microscope, made no easier by how surprisingly fast they are.

Here's a picture:

When I first saw this, I wasn't sure I was looking at the right thing. As you can see in this video, it appears to stay rooted at the tail, while wiggling its head (?) around in various directions. Its most notable characteristic is the two ball-like structures on the front of its body. I have a feeling that those structures will be key here.

This next part was very poorly recorded, but boy did it surprise me when I saw it. Eventually, the worm stretched forward, its head seemingly morphing into three parts (video):

Finally, here's one more clip showing off how fast they can be when they want to (I swear it's not even sped up!). I wasn't able to get it back under the microscope at this point.

Does anyone know what these are, or at least what kinds of worms they might be related to (with respect to the ball-like structures on its head)?

For a little extra background, I found these in my native tank sourced with creatures caught in southern Alberta. The tank contains some longnose dace, which have been a source of concern due to heavy flashing (scratching) ever since I caught them. It makes me wonder if these worms are related, such as some kind of parasite. I'm happy to have them if they're some harmless detritus worm-- any members of the cleanup crew are welcome-- but if they're something to be worried about, I'd prefer to know.


texts: Relationship between mN and mg in vessel contraction studies?

texts:
What is the relationship between mN and mg as the units involved to measure the changes in contraction?  A tool most widely used is an instrument called myograph. In these exoeriments, either units of mg or mN is used without any mention of why. Note that the first two examples use an experimental tool called a myograph - used to measure the force produced by a muscle (in this case muscular blood vessels) when under contraction. Both examples mention tension. Wether these myograph experiments are completely different i'm unsure.

This example shows force as 'mN' from this paper Fig 1A a.
Those who are interested the caption is as follows
"Effects of Li+-PSS and NMDG-PSS in PGF2α-preconstricted pulmonary arteries. Intrapulmonary arteries (IPA) were first exposed to 80 mM K+, and endothelial function was assessed by relaxation of PGF2α contractions (10 μM) to acetylcholine (10 μM). Following a period of recovery, IPA were preconstricted to 10–15% 80K using PGF2α, and then physiological saline solution (PSS) was replaced by Li+-PSS in the continuing presence of the same concentration of PGF2α in endothelium-intact IPA"

This example shows units as 'g'. note that some examples from other papers also use units of mg essentiall x1000 similar to other unit conversions from
this paper Fig 1a.
The caption is pretty much the same as 1. Particularly thromboxane A2 (TXA2) is a pharmacological agent affecting a set of ion channels:
"Requirement of thromboxane A2 (TXA2) for hypoxic pulmonary vasoconstriction (HPV) in rat pulmonary arteries (PAs). A: hypoxia alone (3% PO2) did not induce contraction of PA (left). In the presence of 10 nM U46619, hypoxia induced a strong contraction equivalent with the response to high K+ (80K, right)"

For a third example click here. It does interestingly state "The PA rings were stretched to a predetermined optimal passive tension of 750 mg". As such mg (or g) is an alternative representation of a unit of force as presumed. Figure 1 in this link again demonstrates mg as an y-axis unit of measurement under myograph experiment


texts: What keeps a virus from spreading from one species to the other, when it can infect both?

texts:
I have read that there have been cases where animals (some tigers, also a dog) have been infected by Covid-19 through a human host. At the same time, I read that currently it is deemed unlikely that the virus can spread back from those animals to humans (in the same source). Regarding the infection of other animals like tigers there is also this question which has some sources.

That makes no sense for me, I would think outside of the body, a virus is the same independent of the source and so any species that can catch it should be able to spread it to any other species that can also catch it. Are there any reasons why this would not be the case, in general?


texts: Effects of tobacco smoke on plant health

texts:
We know that tobacco smoking is associated with a wide range of negative health effects in humans, which holds for active smoking, second hand smoking and probably even third hand smoking.

What are the effects of second hand smoke exposure on plants?

For example the german wikipedia page on nitrogen dioxide claims that exposure to nitrogen dioxide leads to reduced yield in apple and pear trees, white birch, barley and salad. It is also stated that first physical signs of alterations can be detected with one time exposure at levels as low as 3 ppb for less than one hour. However I cannot access the source because it is a book.

Bonus: How does cannabis smoke differ from tobacco smoke with respect to plant health?


texts: Do mRNA vaccines cause transfected cells to be killed by cytotoxic T cells?

texts:
Based on my research on how mRNA vaccines (specifically for COVID-19) work:
An mRNA sequence, that contains the sequence of the coronavirus spike protein, is absorbed by some cells. These cells now produce foreign coronavirus spike protein. These cells then present some of the produced foreign spike protein on their surface via MHC I complexes so that they can activate a cytotoxic T cell and cause it to produce lots of copies of itself (cell-mediated immune response). Some of the foreign spike proteins are also released from the transfected cells which allow for B cells to activate a humoral immune response and for professional antigen-presenting cells to present the foreign spike protein on MHC II complexes to activate helper T cells.
My Question:
As far as I understand it, once a cytotoxic T cell encounters a cell that has a foreign protein presented on an MHC I complex, the T cell kills the cell that has presented the foreign protein before it leaves. This means the cells transfected with mRNA through the COVID-19 vaccine (even though a coronavirus hasn't actually hijacked them) will eventually be killed by cytotoxic T cells that encounter them since they are presenting foreign spike proteins on their surface. Is this not toxic for the body since it is killing your own cells? Or does the fact that the mRNA sequences are not self-replicating contain these cell deaths to only the transfected cells and only a few cells die in this process so that the vaccine is not toxic overall?


texts: What is a good biochemistry reference for reading papers about metabolic pathways associated with human disease?

texts:
I studied first and second year biology at university about 15 years ago, taking courses in cell biology, comparative physiology, microbiology, and human cell biology. I also took the supporting courses in organic chemistry, but I have never taken a formal biochemistry class.

Recently, a family member developed a rare cancer and we have been reading through journal papers in nutrition and medicine while trying to understand how diet plays a role. These make extensive reference to specific metabolic pathways in human cells -- some I am familiar with, but many which I am not. In all cases though, my cursory education in the pathways of metabolism and cell function feels inadequate.

So, what are some comprehensive biochemistry texts that can be used as a reference for reading papers in the nutritional and medical sciences?

I would prefer not to use a "concepts" book as one might find in a light version of a course. I am not a shy reader and am not daunted by the prospect of using a more comprehensive book as a learning vehicle, nor of having to do further backtracking to the world of organic chemistry when I encounter a class of molecules that deserves attention.

Lastly, I'm on a bit of a budget too. If you know of a book with a long lineage that is likely to be offered cheaply in previous editions, it would be of tremendous value.


texts: Do serotonergic (5-HT2A-mediated) psychedelics elicit stimulant effects?

texts:
I know that 5-HT2A partial agonism is the key mechanism of action of serotonergic psychedelics but I also know that some research (e.g. the selective (no activity on any other known receptor sites) 5-HT2A inverse agonist/antagonist eplivanserin was being investigated as a sedative) says that central blockade of the 5-HT2A receptors induces sedation which is in opposition to the effect of 5-HT2A partial agonists.

I have a partial answer to my question. I heard from LSD users that they find it regularly causes sleeplessness for the duration of its effects, which is likely due to stimulant/wakefulness-promoting (eurogenic) effects. Albeit just because it is true for one serotonergic psychedelic doesn't necessarily mean it is true for all serotonergic psychedelics. Especially since LSD affects a wide range of serotonin and other receptor subtypes.


texts: How can parentage test be accurately done even though crossing over occurs?

texts: As crossing over occurs when gametes are secreted, so when a zygote is formed after fertilization, the base pairs of DNA in the child should be different from that of the parents. So when gel electrophoresis occurs, the position of DNA fragments of the child shouldn't be the same as half of their father and mother. But why is this statement wrong? sorry for bad English.


texts: Is Batesian mimicry more important for females?

texts:
Myrmarachne plataleoides  is a jumping spider that mimics the Kerengga or weaver ant (Oecophylla smaragdina) in both morphology and behaviour. However, the two sexes appear different:

Myrmarachne plataleoides (Female)

Myrmarachne plataleoides (Male)

Some links suggest that in dimorphic arthropods the females more exactly mimic the model. Is this true? If so, why would this sex difference exist?

Reference
Phyologenetics of mimicry


texts:
I am using gemini to query databases made from vcf files, which contain data from multiple samples. However, I need to query data only from one sample, (for which I currently use grep to filter the results and > it into a txt file).
I tried experimenting with the --sample-filter option in gemini, the documentation I found however says only:

  gemini query --sample-filter "phenotype=2" -q "YOUR_QUERY"

db_info says the table samples contains name, but when I try doing

  gemini query --sample-filter "name='S2'" -q "YOUR_QUERY"

I'll get error, that I have an syntax error in my query. I tried putting there "sample_name=='S2'" even tried other criteria, like sample_id, but couldn't get this work.

So please, do you know how should I get this work, or have any other advice?

Thank you very much.


texts:
I'm curious to find out what kind of beetle this is. Google lens search suggested a type of longhorn beetle, but I am not convinced.

The photo is taken in Karnataka, in India

Thanks!!


texts: Do any terrestrial herbivores use auditory crypsis for predator avoidance?

texts:
Some terrestrial predators "stalk" their prey: they sneak up on it slowly, maintaining a low profile, while keeping as close to silent as possible.  This makes sense from an evolutionary perspective: silent predators catch more prey.

However, the prey near where I live are hopelessly noisy.  Deer will freeze if they suspect the presence of a predator, then bolt when they see one for sure.  Squirrels and other small mammals run around at top speed all the time - you can hear them dozens of feet away, rustling the dead leaves around.  Hedgehogs just wander, making a similar noise.  It seems like the only "stealth" option they have, as far as sound is concerned, is to remain still.

Are there any examples of terrestrial herbivores evolving to move more quietly in order to avoid predation? I'm not looking for a comprehensive list, but rather simply individual examples.


texts: Survivorship Curves: Type II curve mortality rate is not constant?

texts:
In graphs of survivorship curves, I'm seeing that the Type II curves are straight lines, and the supplementary text says that the mortality rate is constant (i.e. the slope of the line is constant). However, it's also clearly stated that the y-axis is a logarithmic scale, which means that the original Type II curve is exponential:
$$\ln y=-rx+b$$
$$y=Ae^{-rx}$$

This implies that the real mortality rate is not constant, but changes as $$y'=-Ar(e^{-rx})$$
How are we defining the word rate, anyway?


texts: How does Golgi's neural histological stain work?

texts:
What is known about the targets of Golgi staining of neurons? Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?

The current wikipedia article says the mechanism is still not fully understood. What is preventing us from using the advanced molecular biology techniques to understand the process?


texts: Database of predicted protein-ligand binding/docking score

texts:
Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB?

My phrase "binding score" is deliberately generic, since any such score would be fine. In particular, some docking energy, i.e. scoring function, would be great. (Don't worry, I am aware that these docking energies are not perfect :) ).

I am looking for comprehensive coverage and the same score across bound pairs, meaning that experimental measures are obviously impossible; however, I am hoping there are people who ran some docking scoring function across all the protein-ligand pairs in the PDB, or at least some large number of them.

I am aware of the many database which hold experimentally determined binding data of protein-ligand structural complexes.
For instance, Binding Moad, Binding DB, PDB-Bind, and SC_PDB are all good for what they are meant to do.
However, they have (1) poor coverage (i.e. not all the complexes have affinity data or they don't include some complexes) and (2) use heterogeneous scores/measures (e.g. IC50, KD, etc...).

This is not the same as this question, since I am looking for comprehensive coverage and computationally determined scores, not experimentally determined ones.


texts: Difference between Fragmentation and Budding

texts: I have heard about two terms stating similar things - Fission and Fragmentation . I know Amoeba undergoes fission and Fragmentation is done by spirogyra. So what's the main difference between them?


texts: Is it possible for two brown-eyed parents to have blue-eyed child?

texts:
Here's the (real) story: A young man has stunning blue eyes. On his mother's side are lots of instances of blue eyes, but on his father's side is no history of blue eyes. Both parents have brown eyes.

When he was born, with these bright blue eyes, it was considered a "miracle". As an adult, he still has these potent blue eyes.

How is this possible?

I obviously understand the popular science behind dominant and recessive genes. The mother could be Bb, but if the father was BB, it doesn't seem possible that he could have blue eyes... but I've read more on eye colour recently, and it appears to be a lot more complicated than I initially thought.

For example, this article goes into some detail explaining How Blue Eyed Parents Can Have Brown Eyed Children, but I've not seen anything that talks about it being the other way around: Could a BB parent have a bb child?

If so, how? And what is the rough probability of such a thing?


texts: Question about equilibrium potential formula

texts:
My biology book says, that the equilibrium potential for an ion with a charge of +1 is: $$E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)$$

Where does the 62 mV come from? How was this value derived? I understand that it's the equilibrium voltage of $\ce{Na+}$.


texts: Determining potential protease sites within a recombinant protein

texts: My expressed proteins are frequently truncated and I'm trying to figure out which bands are which. The first thing to come to mind is using PeptideCutter from ExPASy but there is just a data deluge of potential sites. I was curious what other strategies exists for determining the potential breaks asides using LC-MS.


texts: Relationship between our microbiome and personalized nutrition

texts:
Recently, it has been asked whether there are 'metabolic types' between humans that can benefit from a sort of personalized nutrition. One answer suggested that one discerning factor could be the human microbiome. It is known that host–microbial symbiotic states might respond differently to diet and drug intake, but whether this can be useful for personalized nutrition is less clear to me. I wonder:

does the microbiome affect food metabolism? (useful for personalized nutrition)

OR

is the food that we eat affecting the microbiome? (less useful for personalized nutrition)

I know the answer is probably both, but there are examples causally demonstrating one branch and excluding the other?


texts: How could 45 milligrams of a substance equal 4,500 micrograms?

texts: In this book, the author repeatedly states that 45 milligrams of vitamin K2 equals 4,500 micrograms.  I thought 1 mg = 1000 mcg.  How could this be?


texts: Determining if a Protein Model Contains a Backbone Clash

texts:
I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be accepted for publication.

What is the best (reproducible) method to determine if a particular protein model contains a backbone clash?


texts: Were there any vertebrates with 6 or more limbs?

texts:
My question is actually a bit more broad than what's in the title, but I don't know how to put it succinctly.  When I was trying to find the answer to that question, I found that all known terrestrial vertebrates are ultimately descended from a species of lobe-finned fish that had 2 sets of bilaterally symmetric fins (which excludes the dorsal and ventral fins), which were the basis for the limbs of its tetrapodal descendants.

The best way I can think of to phrase the question is: Does paleontology has any evidence of a vertebrate that had 3 (or more) sets of bilaterally symmetric limbs or lobe-based fins?  I'd like the focus to stay away from ray-finned fish, even though they're vertebrates and related.

This is not the common question, which is whether there is or can be a mammal/reptile species with more than four limbs.  The essence of that question's answer is that mammals and reptiles both evolved from a common ancestor species that were tetrapods, and that it's extremely difficult to change the genetic floor plan in the necessary way without causing fatal problems (along with other evolutionary issues).  By and large, this common question is so common that it chokes out the type of question that I have, making my amateur attempts at further research difficult to impossible.


texts:
I know that lipids are carried around the body in the blood either as micelles or by lipid-binding proteins which allow them to be solved.

Lipids can't always be integrated in a membrane though, the phospholipids used in membranes have to be synthesised somewhere from a precursor which will also by hydrophobic.

Consequently, at some point there will have to be transport of lipids within the cell where the lipids will need to be in solution. How is this facilitated?


texts: Plasmid addiction system in high-copy number plasmids

texts: Are there high-copy number plasmids that utilize a plasmid-addiction system?


texts: Golden Brown Flying beetle identification

texts:
Bug (probably a beetle) flew into my house tonight with golden body and black stripes. I live in pacific asia.

.


texts:
Is there an estimate for when the ability of sneezing evolved? A little bit of research, and some critical review of my memories tell me that:

Many, if not maybe all mammals sneeze.
Some reptiles sneeze, like turtles and iguanas.
According to this answer, I see some consider also some fish and even sponges to be capable of sneezing. However, I'd be curious to know if this is the actual same concept of sneezing, and not a stretch of definition, given that fish and sponges don't have lungs!

If it's common among mammals, I infer that it is very likely that this ability exists since at least 200 million years. I'd in fact suspect to be very unlikely that all mammals developed it independently after branching out from common ancestors. I am confident the sneezing of turtles is really comparable to ours  and that although more explosive, also iguanas'. These reptiles (according to my superficial and inexperience Google research) are known to exist since more than 215 and 190 million years respectively.

However, I don't know how old a common ancestors of turtles, iguanas, and mammals can be dated. Or how likely it is that they independently developed this skill.

I'd be very curious to know if any expert ever dated this ability.


texts:
Found indoors in Florianopolis, Brazil.

Is able to hang from a web like something inside the jar.


texts: Calculating fraction of protein unfolded from spectroscopy data

texts:
This is a question from a homework pset of previous year. We are given the absorbance at 222nm of both a wild type and mutant protein at different temperatures. We are then asked to calculate various thermodynamic quantities from these data. The first thing it asked for is the Tm of both wt and mutant. To get the Tm, I need the fraction of protein unfolded, since Tm is defined as the temperature at which fraction unfolded is 0.5. However, I am confused as to how to calculate fraction unfolded. In the answer key, the professor used a equation, f=2*(A222-0.5), without any explanation. Can anyone explain to me where does this equation come from?

Edit: Sorry, I forgot to tell you that f stands for fraction unfolded.

Thank you very much
Zeyuan


texts: LB, TB media, and yeast extract are also yellow but at the heart of the question. What chemical(s) make E. coli yellow?


texts:
Could someone explain to me the role played by the Fc region of an antibody as well as the purpose of isotype switching? According to Wikipedia, it's to allow the antibody to be usable by different Fc receptors, but I don't get what Fc receptors are for.

For context,

I'm reading about affinity maturation and learning about how ecological and evolutionary processes --- division, selection, and mutation --- drive the maturation of B cells leading to high-affinity plasmocytes that can better target a foreign antigen. Because all this happens on the Fab fragment, it makes sense to me why the Fab region is important in the antibody.
I'm not trained in cell biology.
My goal is to understand the general purpose of the Fc region and how isotype switching may be a major determinant for specific immunological or physiological outcomes, although I'd love to hear anything interesting!

Thanks in advance!


texts:
Background:

From Genomes:

The temperature of a PCR mixture is first set at 94 °C so that denaturation of DNA can happen. Then it is reduced to 50–60 °C, which results in some rejoining of the single strands of the target DNA, but also allows the primers to attach to their annealing positions. After this DNA synthesis begins as the temperature is raised to 72 °C, the optimum for Taq polymerase.

  In this first stage of the PCR, a set of ‘long products’ is synthesized from each strand of the target DNA. These polynucleotides have identical 5′ ends but random 3′ ends, the latter representing positions where DNA synthesis terminates by chance.
  [Subsequent cycles give] rise to ‘short products’ whose 5′ and 3′ ends are both set by the primer annealing positions.

Now Wikipedia says:

  [...] Final elongation: This single step is optional, but is performed at a temperature of 70–74 °C (158–165 °F) (the temperature range required for optimal activity of most polymerases used in PCR) for 5–15 minutes after the last PCR cycle to ensure that any remaining single-stranded DNA is fully elongated.

Questions:

I’m wondering that if the shortening of the length of new DNA is purely by chance. From Wikipedia it appears that the length of the DNA synthesised can be controlled by the temperature of the mixture?

  To carry out a PCR experiment, the target DNA is mixed with Taq DNA polymerase, a pair of oligonucleotide primers, and [...]

A pair of primer cannot support the increasing number of PCR cycles, are primers added later/ throughout the process?

Besides it seems to me that the temperature of the mixture has to be changed according to the phases of the cycle. Is it changed? How is it determined that which phase of the cycle the DNAs are in?

P.S. I'm not sure if this post should be broken down into two posts or more. Suggest if you feel that's necessary.


texts: What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry.  What is the significance of using 8M urea? and how does it affect the proteins?


texts: Why the position of facial organs is the same for almost all animals on Earth?

texts: I was questioning myself on why the position of facial organs (eyes, nose, mouth) is the same for almost all animals on Earth ? Is it because of a common ancestor in evolutionary history ? We don't see animals with a mouth on the forehead and eyes on the chin. This face pattern looks universal, is there some biological cause behind, natural selection?


texts: How hard is it to build a promotor in a DNA that initiates DNA transcription when specific hormones are around

texts:
I have an idea that you could find out which substances are within a sample in vitro that you are investigating by creating DNA that has a bunch of different promotors for different substances you are interested in.

After inserting those DNA strains you could do nucleotide sequencing and as nucleotide sequencing allows you to to read a lot of data you could read the sequencing behind the promotors.

How complicated would it be to build DNA with promotors for dozens of medically relevant substances?


texts: Is epilepsy more heritable from maternal side?

texts:
I am thinking if paternal or maternal genetic line is the risk factor.
Mitochondrial DNA is coming from maternal line.
I do not know the pathogenesis of epilepsy so well that I could answer my question.

Is epilepsy more heritable from the maternal side?


texts: As bacteria are involved in the production of ethanol through fermentation and ethanol is also used as antiseptic that kills bacteria, so how and why bacteria are involved in the synthesis of such alcohol which is lethal for itself(bacteria)?


texts: How to pipette accurate volumes from BSA solution without air bubbles?

texts:
I'm new to immunohistochemistry and there's one step I'm having problems with. Generally I can pipet volumes pretty accurately and avoid air bubbles, but:

1) The BSA solution that I made (with PBS and BSA crystals - then vortexing) had a lot of air bubbles that wouldn't settle over time

2) I couldn't avoid air bubbles in my pipet even though I placed the tip under the layer of bubbles

How should I improve my technique? (Also, will having slightly different concentrations of the blocking and primary antibody serums greatly affect the result?)

Thanks,
L


texts: Concentration calculation of Factor VIII for Elisa

texts:
I have the following problem. I'm trying to get the concentration calculation for an Excel sheet that will calculate values from an Elisa plate.

The basis is a standard curve with the following values:

Std: PreDil factor 1: 40
PreDil factor 2: 55
---> Total Predilution = 2200
Concentration: 2123  µg/ml

Dilution  1:20      1:40    1:80

Std 1     1,3910    0,6360  0,2850

Std 2     1,4020    0,6360  0,3140

Std 3     1,3500    0,6250  0,2880

Std 4     1,4470    0,6810  0,2900

The sample values are the following:

Predilution: 15

Dilution 1:20   1:40   1:80

Sample   0,4060 0,1940 0,0760

According to the program that has been in use earlier, the concentration shall become 4,786 µg/ml. How do I calculate this in the best way? Unfortunately, I can't seem to get the right answer.

To add more context to the question. I work on a project to move an old program that calculated the concentrations to a new excel sheet. Unfortunately, I do not perform these analyses myself as I work on another part of the lab.

However, the question is based on how to get the concentration value of the undiluted sample. The standard used have an undiluted concentration of 2123 µg/ml. It is pre-diluted in two steps, first 1/40 and then 1/50 giving a total dilution of 1/2200.

The Standard is then analysed for three different doses 1/20, 1/40 and 1/80. Two times at the beginning of the run, and two times in the end.

The Sample is pre-diluted 1/15 to then be analysed for the same three doses as the standard.

What I have done now is that I used the Parallel Line model to try to calculate the concentration. Unfortunately, I don´t get the same answer as the earlier calculation program (Which is 4,786), and I have been able to figure out is that the problem is that I get a slight shift in the relative potency. Unfortunately, I can´t find where the problem lies.

Hopefully, this clears it up a small bit.


texts:
For the heart muscles, it is the extracellular Ca2+ that is necessary for the contraction, but for the skeletal muscles, it is intracellular Ca2+.

One of my answers on a test was the following: "In cardiac muscles, an augmentation of the intracellular Ca2+ concentration is necessary for muscle contraction".

Therefore, I'm confused. For the heart, is it extracellular or intracellular Ca2+ that determines contraction?


texts: Why is it that only humans are ashamed of certain critical biological activities

texts:
Humans are ashamed of certain activities that are critical to our survival.
Examples: mating, defecation, exposing certain parts of our bodies
This restricts some activities from being performed while others are around (usually only if others are also humans).
Perhaps it is because we are the only species who is capable of feeling ashamed?
What are the advantages of this mechanism in terms of survival as a species?


texts: Name of scientist who discovered lifesaving drug and chose not to patent it?

texts:
I recall reading about a 20th century scientist who made a life-saving drug that could have patented it and made millions. He chose not to and saved the lives of millions around the globe.

I thought it was Frederick Banting - but it doesn't sound quite right.

None of the others in this list seem quite right.

My question is: What is the name of scientist who discovered lifesaving drug and chose not to patent it?


texts: Text or source (preferably free) for learning developmental biology

texts:
I might have to take a graduate level course in developmental biology, of which I have never taken a course in before. The course website lists no recommended texts. Therefore, I assume we will be doing a more independent study, and I would want to have a book or source to better facilitate that study.

Any recommendation, free or not free, is welcome.


texts: Protein structures given in PDB and SNP's

texts: There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB incorporate the SNP's into their structure? If not, is there a way to visualize protein structure using any tool after a SNP on the protein? I know that tools like SIFT exist but they only say whether or not a SNP is harmful or not. They don't comment on the structure of the protein in anyway.


texts: Why does a human's field of view narrow when moving faster?

texts:
A relative of mine is a driving instructor and he regularly likes to bring up that the field of view narrows noticeably when driving at higher speeds.
Is this true, why is this so and does this apply for other species as well (for example, leopards, who are widely known for their fast speed)?


texts:
I read that opsonins are a type of antibody that play a vital role in chemotaxis and phagocytosis in general. The fact of them being antibodies though, got me confused. Antibodies are, to my knowledge (however inadequate it may be) , released by plasma cells after macrophages present antigens. Yet my book says that pathogens are covered in antibodies (opsonin) which help the macrophage initiate phagocytosis. How can antibodies (opsonin) be present before the APC Present the antigens to activate the production of antibodies?

P.S.: I'm a college student so there's probably a lot of things I'm missing out on. Please do fill me in :)


texts: What is the role of the pyrrolidine/piperidine moieties in fagopyrins?

texts: Fagopyrins are phototoxic compounds that cause fagopyrism. They are chemical compounds related to hypericin and pseudohypericin. Some variations lack one or both methyl groups, which I think is to streamline the molecule so it better fits in membranes and so increase damage. The main difference from (pseudo)hypericin though is the presence of pyrrolidine or piperidine (or both) moieties, which may come from L-proline and L-piperidine-1-carboxylate (in turn from L-lysine) respectively. So, what is the function of those moieties in the fagopyrin molecules? Does it render fagopyrins more toxic than (pseudo)hypericin?


texts: Why is uracil, rather than thymine, used in RNA?

texts:
This question was posed on SE Biology some time ago, but all the answers, including the accepted one, answered a different question instead: “Why is thymine, rather than uracil, used in DNA?”. I therefore changed the title to match the answers, giving notice that, if the change were approved, I’d post the original separately question myself (and answer it, if necessary). Here it is:

  It is believed that thymine replaced uracil (the RNA base) in DNA because of the deleterious effects of slow spontaneous deamination of cytosine to uracil: by employing thymine instead of uracil, any uracil in DNA would clearly be aberrant, allowing a specific mechanism of repair (involving uracil DNA glycosylase) to evolve with impunity. As this was clearly advantageous, why didn’t RNA also evolve to use thymine instead of uracil?

N.B. By “why?” I mean “how can one rationalize the fact that?”. Obviously, the answer to this type of question is not, and probably cannot be, known with certainty.