texts: Pattern in parental care behaviour from lower to higher animals?

texts:
I was studying about parental care behavior. There seems a pattern present in this behavior in case of vertebrates. The more evolutionary advanced class the animal belongs to, the greater effort an animal gives to care its off spring?

Is it a real pattern?

My current thinking is that if the pattern is indeed real, it is because the more complex an animal is, it takes more time to get fit with the environment, so it takes more effort for parents to get them ready for the environment. Am I close?


texts: Why are some protein sequences known but their 3D structure isn't?

texts: Why are there some proteins that have a known amino acid sequence, but their 3D structure is not known? Wouldn't finding the former in a lab lead to the discovery of the latter? Please correct me if I have misunderstood something.


texts: When does the first "random mutation" of DNA (have to) occur?

texts:
When reading about how evolution happens, "random mutations" are often spoken of.

As far as I understand, "random mutation" refers to the unsuccessful self-replication of DNA (the new version of which is then passed on correctly). But when does this change happen? During fertilization? Shortly before (in the sperm or egg itself) or shortly thereafter? And what is the last possible time for that to happen so that it gets passed onto every cell in the body and eventually brings forth a new physical trait?

I hope the questions make sense, I don't have a lot of background in biology.

Edit for completeness: When is the earliest possible moment for a mutation to take place? (A mutation that will ultimately make it to the offspring and eventually cause a new trait.) Is it in the ovaries/testicles or even before that?


texts: Are there adaptations in tropical fish to compensate for less oxygen in water?

texts:
Warmer water means that the amount of gases- especially oxygen- dissolved in it reduces, since solubility of gases in a solution in most cases decrease with an increase in temperature.
I'm interested in knowing if tropical fish have any adaptations to account for this reduced oxygen compared to fish in colder waters. Any modification of the gills maybe?
Referencing the below articles, I have come to the conclusion that tropical fish end up migrating to shallower waters or cooler habitats due to the oxygen depletion, showing that this decrease in oxygen is serious enough to affect them. However, this may be due to excessive heating of oceans due to global warming. I'm curious about whether fish in tropical regions have any adaptations for living in ocean water that is heated purely by natural means, not anthropogenic ones.

References:
https://www.usgs.gov/media/images/temperature-affects-dissolved-oxygen-concentrations
https://www.pca.state.mn.us/sites/default/files/wq-iw3-24.pdf
https://www.sciencedaily.com/releases/2015/06/150604162455.htm
https://www.nationalgeographic.com/science/article/150313-oceans-marine-life-climate-change-acidification-oxygen-fish


texts: Can the extinct Chinese Paddlefish be revived?

texts:
I learned that a rare and unique giant Chinese Paddlefish recently became extinct. I'm wondering if samples of DNA were collected by scientists to allow reviving of the specie in the future.
My quick Google check only revealed one paper that studied DNA of the fish 15 years ago - so there is a possibility that some DNA information exist out there. But is it enough to restore the species?
I'm interested in learning about any organisations or projects that would systematically collect genetic material of all endangered species. Is there a way to ask them about this specific fish?


texts: is it possible to visualize coronavirus infection and what type of assays are routinely used?

texts:
There has been some electron micrograph of SARS-COV-2 published; but are there any fluorescent/ confocal-fluorescent image of them? or is it possible to do them?  I know that viruses are usually much smaller than capacity of light microscope but I think by using any immunofluorescent probe or FISH technique it is possible to visualise the locations occurance of the virus in cell or tissue. At least one website says it is possible to visualise viral infections using fluorescence techniques.

Now is there any such image for SARS-COV-2, and is it possible to take?


texts:
Human beings have evolved from their ancestors to their modern forms adapting many changes in structure and I would assume that every change has a significance.

So, what is the cause of our hair turning white at old age? Was it meant for frightening away predators at old age when our body is weak? Or what is it actually?


texts: Can any one help id this bug or at least tell me if it could be biting my kids

texts: We live on the gold coast in australia. We started looking into what these bugs were after my son became covered in severe bites. Hes always reacted a little bit to bites but this was intense.  The initial bite looked somewhat like a raised welt which he has scratched at but now over a week later hes saying they are still itchy and even with bandaging and covering the areas hes still getting more bites.  I have attached a photo of the bugs that are around at the moment but also some of the bites. we get alot of mosquitos and midgies (sand flies) but hes never reacted to those bites like this. We have recently had a flood in the area so everything is still wet. Its change of season so its cooling down.  Any help would be amazing in helping treat our son but also hopefully prevent further issues


texts: What is the reasoning behind naming proteins first found in Drosophila as paired box? All I could find on internet is that it was first found in Drosophila as a protein with paired domain, but I couldn't find anything about the term box along with it. Could anyone please signify the terms paired and box in the name of that protein?


texts: Use of progesterone in preventing ovulation?

texts:
I have heard that progesterone in contraceptive pills or interuterine devices have been known to prevent ovulation. How is this possible since the LH and FSH are only affected by oestrogen not progesterone (am i wrong?)  Also,  my textbook says hormonal intrauterine devices contain progesterone to lessen uterine lining but doesnt the uterine get maintained by progesterone ?

Edit : I have yet to receive a satisfactory answer... Help anyone?


texts:
I had came across an insect  near my backyard in India(Kerala). I haven't seen this one before and I searched web to find out what insect is this and found its image which saying its a "Giraffe Weevil" (Trachelophorus giraffa). The link below says that this insect is endemic to Madagascar.

http://en.wikipedia.org/wiki/Giraffe_weevil and

They are herbivore insects, with adults feeding on a tree that is commonly known as the "giraffe beetle tree"
(Dichaetanthera arborea)

This states that these insects need the "giraffe beetle tree"(Dichaetanthera arborea) which is also native to Madagascar.

So how come this insect could be found in India(Kerala), and further more all the above links state that the long neck of these dimorphic insects are evolved for fighting and nest making but they do tell that after mating the females will make the nest and lay one egg inside, So did the male insect make any nest in reality, if so then why the male have to perform both nest making and fighting.[Sorry for the errors,also there are more links to this]


texts: Is there a bacterium that became a virus?

texts:
Is it possible for a virus to be a descendant of a bacterium that was not through horizontal gene transfer?

How I think this could happen:

Suppose a species of bacteria lives in an environment where it gets all the resources it needs to reproduce (and let's assume that there will be no major changes in the environment).  That is, if it loses a gene that synthesizes some substance (or regulates some process), it will not be at an evolutionary disadvantage.  Because it can achieve this from the environment.  Even depending on the gene, it can even be an evolutionary advantage, as it can become more efficient when it comes to reproducing.  And I have seen that an experiment was carried out related to this question, it was shown that viruses can lose some genes in an environment where it can naturally find the protein that is associated with those genes.  Thus, there is a chance that this species will become so simple, that it will end up becoming a virus.


texts: Does dairy negatively affect the voice for singing?

texts:
Singers and actors are warned not to consume dairy, primarily milk, before a performance. From personal experience, I know that this is a very valid warning. It is commonly assumed that this is due to milk causing either more or thicker phlegm.

Has the mechanism behind this been studied and verified?


texts: Protein purification: Linear elutions or stepwise elution, using imidazole or pH gradient?

texts:
I now work in a lab with a protein and a pre-made purification protocol, were they purify a His-tagged protein using linear elution which then gives a steady increase in the imidazole concentration. However, I am curious to as if you plainly have to test which elution scheme you want to use, or if there are some "rule-of thumb" on what is a more standard way to elute protein, and what in general is more common?

Also, say for instance (just as an example) that I use a protocol which in the end loses about 80% of the protein before it's pure, is one of the first things you could do is to change the elution schemes to increase the yield? Are there other very basic things one can do to optimize a purification protocol which has not been so thoroughly optimized?

So basically:

Is linear "usually" better/more common than stepwise?
Is imidazole gradient "usually" better/more common than pH gradient?


texts:
Location : Lyon, France

I think it's one of the laziest trees I've ever seen XD


texts: Is there any difference between fascia and skin ?Are both the different names of the same thing?

texts: Skin is the outermost layer of the body ,and it consists of two layers; epidermis and the second layer the dermis .There is another layer the (third layer) beneath the dermis called superficial fascia or subcutaneous tissue. I want to know that is superficial facia  a part of skin.?Can we say that fascia is another name of skin?


texts: Do Tumor-Infiltrating T Cells Experience Any Prolonged Effects Due To Hypoxia After They Return To Normoxia?

texts:
Adoptive cell transfer (ACT) therapy using tumor-inflitrating lymphocytes (TIL) is at the cutting edge of immuno-oncology treatments involving metastatic melanoma and other indications (1). The idea is that at some point during the growth of a tumor, some T cells attempted to mount an immune response, extravasated and got into the tumor, but they became overwhelmed and exhausted. The therapy itself involves taking these cells out from some excised tumor, reversing their condition and since they're already neo-antigen specific from having attempted an attack on that cancer: Expand them, put them back in the patient, let them hit the tumor much harder than before.

Not only do you need to reverse exhaustion in the TIL, but you also need to have the right population of T cells to get the best response. The factors involved are beyond this question, and so I'll get to the point.

In the tumor environment, the T cells become exhausted and their expression profile changes (2). It makes them more prone to apoptosis and they lose effector functions like GranzymeB production. You can tell how this is problematic. My suspicion is that in the tumor the T cells may become hypoxic, and what we know is that in the oxygen-sensing pathway, hypoxia inducible factors exert their effect. Normally, these should be kept in check by inhibiting proteins if they get produced under normoxia:

And so to my question:

After prolonged exposure to hypoxia, are there any regulatory or transcriptional changes that after prolonged return to normoxia render either of HIF1α or HIF2α active where they would normally be repressed?

Whether I just need a fresh set of eyes or the data just doesn't exist, I haven't necessarily found it obviously. I'd like to know if there's a remnant hypoxia-like regulation framework that remains after O2 gets back to normal that affect pathways like mTORC1/2. Thanks if advance for any insights!


texts: How are the physiological properties of mitochondria measured?

texts:
this is my first question on BiologySE. I am a Physics and Mathematics student currently doing a project on cell growth simulation. I am doing literature survey and I have a question about cellular biology experimental methods.

I understand that the membrane potential is a measure of mitochondrial functionality (higher potential means more efficient electron transport chain). Additionally, the mitochondrial volume is also an indicator of mitochondrial efficiency (higher volume, higher area, more places to do electron transport).

I would like to have some points elucidated.

In particular, can these mitochondrial membrane potential and volume...

be measured for a single cell, or only in a population?
be measured non-destructively, leaving the cell alive?
be measured simultaneously, or experiments measuring one necessarily make the other unavailable?

I am thinking mostly of in vitro experiments of course.


texts: Did my wildlife camera take a picture of a lynx?

texts:
A wildlife camera took a photograph of an animal. Unfortunately this is the only picture my camera collected. This picture was taken in the central interior of British Columbia, Canada. The distance from the camera to the subject is a few meters, and the height of the camera off the ground was probably about 40 - 50 cm.

Is this animal a lynx? It looks like it might have those fine tufts on its ears and a reduced tail.


texts: Names for effects of sleep deprivation on the brain & body

texts:
When staying awake for a long period (3 or 4 days), some weird phenomena can occur. In my experience, it was always triggered by thinking too deeply and has in other occasions too.

Do these things have names at all?


texts: Why do I need a flu shot every year, while many other vaccinations last years or even a lifetime?

texts:
Is it a viral vs. bacterial thing?
Is there just more variety among types of flu than other diseases, so that this year's vaccines don't cover next year's flu?


texts: Electrical transmission vs Chemical transmission

texts:
"The advantage of electrical transmission, apart from speed, is it can favour synchrony in firing. For example, in the brain stem a nucleus called the inferior olive can generate oscillations due to gap junctions."

Can somebody explain this idea? I do not understand the meaning of oscillations in this context. Do they mean that the neuron can send impulses and receive them at the same rate ? Is that what they're trying to put across ?

Source:Lecture Handouts


texts: Comparing SIFT and PolyPhen to other methods

texts:
I'm looking for a database of nsSNP (non synonymous single nucleotide polymorphisms) and their effects. As I understand, the common methods to predict this are SIFT and PolyPhen, and I want to compare them to other methods.

The database needs to list the old sequence and the new one (or that I'd be able to infer that somehow), and their effect (whether harmful or not).

What are my options?


texts: Human somatic cells have 22 pairs of homologous chromosomes?

texts: I am studying for my Bio class and I am stuck with questions that I came up with during this chapter of Meiosis. I understand that human somatic cell is made up of 22 pairs of autosomes and 1 pair of sex chromosome. I am confused about what made up each pair of autosomes? is that 1 chromosome from the father and 1 chromosome from mother made up 1 pair of autosomes in somatic cells? and therefore, since each pair of autosomes consisted of 1 chromosome from dad and 1 from mom, we can say human somatic cells consisted of 22 pairs of homologous chromosomes (not to mention the sex of the human), right?


texts:
This year, Oxford Nanopore MinION has been shipped to some researchers for testing.

The advantage of a table-top sequencer for diagnostics and personalized medicine is obvious. Similarly, research "in the field" and forensic science could be aided greatly by this device. My question is about the applications in the research lab.

What does MinION do that a well-equipped lab with access to Sanger and next-gen sequencing cannot already do?

How well does the MinION work? How powerful is it?

What important scientific discoveries are being made using the MinION?

While the website of Oxford Nanopore has a list of publications, the most recent one is from 2013. This is before the early access program began - I am particularly interested in developments since February 2014.


texts:
PlantNET describes the inflorescences of Daviesia acicularis as:

  Racemes reduced to 1 flower

How is a 1-flowered raceme different from a single flower?


texts: Variance in Fst in the infinite island model

texts:
The most famous result in the study of structured populations come from Sewall Wright. He showed that in an island model, where each subpopulation is of size $N$ and the migration rate is $m$, then the pairwise $F_{ST}$ is

$$F_{ST} = \frac{1}{4Nm+1}$$

This equation gives the expected $F_{ST}$. Because populations are finite in size ($N$), genetic drift yield this value to vary.

What is the variance in $F_{ST}$ in the infinite island model?

References

evolution in mendelian population is the original paper who derived this result from Sewall Wright.

Indirect measures of gene flow and migration: FST≠$\frac{1}{4Nm+1}$ is an influential paper in the field.

GENE FLOW IN NATURAL POPULATIONS is a famous review as well.


texts: The Hawk-Dove game: why is the average payoff half of the difference between reward and cost?

texts:
My question is about the well known Hawk-Dove model used in game theory. It concerns two strategies: the Hawk, which always fights the opponent, and the Dove, which does not fight and will either retreat or share. The payoffs for each of the possible encounters are presented in a matrix. Now, say that the reward (R) is 10 units and the cost of fighting (C) is 5 units. When a Dove meets a Hawk, it will retreat: Dove gets 0 and Hawk gets R=10. Vice versa, when a Hawk meets a Dove, Hawk gets R=10 and Dove gets 0 because it retreats. When two Doves meet, they will share the benefits; both Doves get R/2, in this case 5. These three, I have no problem understanding.

My issue is with the payoff when two Hawks meet. I understand that, under the assumptions of the model, both Hawks have a 50% probability of winning. I also understand that the winner gets R and loser pays C. But I'm completely stuck at why the average payoff is given as (R-C)/2. When you input the numbers above, it gives you a value of 2.5. How is the average payoff in an encounter between two Hawks 2.5 if one receives 10 and the other loses 5?


texts: Deletion errors with Phusion Polymerase?

texts:
I was wondering if anyone has ever seen large deletions (~40-50 bp) occur when using phusion polymerase to clone a gene.  I have recently tried using Circular Polymerase Extension cloning to clone a 200 bp insert into a 6.5kb plasmid and obtained two separate clones with 40bp+ deletions in the center of the insert.

Phusion has a 5'->3' exonuclease activity, but I didn't think it could cut in the center of a sequence.  While our inserts were created with oligo synthesis, it is my understanding that such large deletions are rare with oligo synthesis. If you have heard of this happening please let me know.


texts: What biological systems are affected by Vitamin B6 (or B vitamins in general)?

texts:
B vitamins and particularly the B6 vitamin appears to the one of the main ingredients in energy drinks.

There has been anecdotal evidence from people interested in dreaming that ingestion of vitamin B6 at night time changes the pattern of dreaming and is likely to produce "lucid" dreams.

From a biological standpoint, what is the effect of the B6 vitamin on the human body and brain? Do other animals require the same vitamin?

Are B vitamins in any way related to the circadian rhythm regulation within some organ systems? Does it speed up metabolism?

I would be grateful for any scholarly papers on the subject or keywords that I may look up myself.

Thank you!


texts: What does "radiographic progression" mean in cancer?

texts:
I tried looking up the definition of the term "radiographic progression" using Google and medical dictionary, etc., but I couldn't find its meaning anywhere. All research articles that I found just use it, so I assume it is something common.

Please explain to me what "radiographic progression" means. I really appreciate it.


texts: What part of the body holds the most pain receptors?

texts:
What part of the body holds the most pain receptors or is likely to cause someone to feel the most intense pain?

I thought it was the eyes but I can't find that source anymore.


texts: I'm trying to save these baby birds' lives, and I need to know their species so that I can know how/what to feed them. Please help me ASAP .


texts: Inbreeding of selfing and outcrossing plant

texts:
I am reading John H. Gillespie's Population Genetics A Concise Guide Section 4.3 Inbreeding. I do not understand these two paragraphs quoted below concerning selfing and outcrossing.

The first paragraph states that an outcrosser individual leaves behind on average two gametes one in an ovule and the other in a pollen.

The second paragraph states that a mutant selfer will leave behind three gametes for every two of the outcrossing plants, with two in its selfed offspring and one in its outcrossed offspring.

What are the effect of the ovules and pollen here? How are these two statistical conclusions drawn? I would like to have a very detailed explanation.

Some interesting evolutionary questions arise with species that are capable
of both selfing and outcrossing. For example, in many plant species there is
an intrinsic advantage to selfing, which leads to the evolutionary conundrum:
Why don't all plant species self? The situation is illustrated in Figure 4.4. The
outcrossing pedigree on the right represents a typical individual in an outcrossing population of constant size. This individual leaves behind, on average, two gametes, one carried in an ovule and the other in a pollen grain. These gametes appear as filled circles in the figure.

Figure 4.4: The gametes produced by a selfer and an outcrosser. The p to the right of
an arrow indicates that the parent’s contribution came from pollen; an o indicates it
came from an ovule. The filled circles represent gametes from the illustrated parents;
the open circles represent gametes chosen at random from the gamete pool.
Suppose a mutant appears that self-fertilizes all of its ovules, M illustrated
on the left side of the figure. Suppose also that there is enough pollen in each
individual of this species that the few grains needed for self-pollination by the
mutant represent a small fraction of the total pollen. As a consequence, the
selfing mutant has essentially the same quantity of pollen available for outcrossing as does a nonselfing individual. All else being equal, the selfing mutant will leave behind three gametes for every two of the outcrossing plants, as indicated by the three filled circles in the figure. Two of the gametes are in its selfed offspring; one is in its outcrossed offspring. Thus, the mutant should increase in frequency, perhaps leading to the establishment of selfing as the usual mode of reproduction.


texts: How a vegan can consume all the needed varied proteins / amino acids?

texts:
I would like to ask if there are some proteins that the human body needs and can being endowed only from meat?

According this:

  Other protein sources, such as fruits, vegetables, grains, nuts and
  seeds, lack one or more essential amino acids. Vegetarians need to be
  aware of this. People who don’t eat meat, fish, poultry, eggs, or
  dairy products need to eat a variety of protein-containing foods each
  day in order to get all the amino acids needed to make new protein.

How a vegan can complete these missing proteins?


texts: Is there any way to make protein pass through cell membrane?

texts: Protein cannot pass cell membrane because it's a large molecule. Until now, is there any technique that can make protein pass through the cell membrane in vivo? I want to create a protein-drug that must be accessible DNA to reach it's site of reaction. How possible can i do it?


texts: Is evolution the reason why water is colourless for our eyes?

texts:
Liquid water is transparent to most of the visible spectra, whereas it absorbs infrared.
Similarly, the air is almost transparent to the visible spectra too.
Could these be the reasons why our eyes evolved to "see" the visible spectra, and not IR or UV?
(Also, are there other animal species for whom water is not colourless?)


texts: Why does beta-2-Thienylalanine inhibit bacterial growth?

texts:
I'm trying to obtain a better understanding of the Guthrie Test, which checks whether people have a disease called PKU.
The Guthrie test uses bacteria to check for Phenylalanine (the amino acid) in blood samples. If both Phe and B-2-thienylalanine are available on the medium, the bacteria will grow. However, if only B-2-thienylalanine is available the bacteria will not grow.

In all of the articles I can find, I have seen no explanation, just a link to a paper that I can't find on the internet.:
" A standard culture of Bacillus subtilis was incubated on agar in the presence of an antagonist of phenylalanine (B-2-thienylalanine), which prevents the bacteria from growing.3 " Link
The reference they mention here is:
"The inhibition assay: Its use in screening urinary specimens for metabolic differences associated with mental retardation" by R. Guthrie from 1960.

Do we know what mechanism this protein is inhibiting?

Any help would be greatly appreciated.


texts: Is the colour of a chrysalis predetermined?

texts:
Usually, chrysalis of butterflies camouflages with the surface it is attached to, for protection, as I understand it. There are exceptions, though; For example, the golden chrysalis of Euploea core is reflective and literally pops out of its background. My point is, what is the evolutionary advantage of that?

Edit: user -personjerry pointed out that shiny colours indicate poison.
So the main question now is,  if the aim was to scare off predators, why aren't they red/black in colour (as red means impending danger in the animal world)? Also, wouldn't developing a red pigment be much easier?  In these cases, is the colour predetermined?


texts: Relation between biomass and radius of roots system

texts:
Is there a known relation between the mass of a plant to the size of its roots?

For example, can I take the root size to be proportional to the biomass of the plant like in this relation: $$R = R_0 (1+EB) $$, where $R_0$ is the minimal size of the root (i.e. the diameter of the seedling), $B$ is the biomass of the plant, $E$ is some parameter, and $R$ is the length of a typical root?


texts:
I would like to view the chromatogram traces from a few ABI (.ab1) files. I would prefer to use python for this, or a function with python bindings, or at least some open source package such as EMBOSS.

If after viewing a plot I could also extract the plotted data in the form of an array, that would be a huge plus.

I have tried the relevant Biopython parser, but it only returns a list of nucleotides (not th actual chromatogram). I have also tried abiview, but I get plots such as this, which makes absolutely no sense:

Could you help me out?


texts:
Why is it necessary to have a DMSO alone control when DMSO has been used as the solvent (vehicle) in the treated conditions?

And, in this case, why is the viability of the untreated condition lower than the vehicle (DMSO alone)?


texts: E. coli bioreactor or E. coli fermenter?

texts:
I have a Requirements Specification in Russian for a "Fermenter" that would be used for "E. coli cultivation". This E. coli strain would be used to make a generically-engineered drug. The "fermenter" would consist of two "reactors" of 200 and 2000 liters, linked by a "pipeline system for transferring the half-finished product between them".

Would the whole thing be called a "Bioreactor" or "Fermenter", or are the two terms interchangeable here?


texts:
Origin of the word "cancer"

  The disease was first called cancer by Greek physician Hippocrates (460-370 BC). He is considered the “Father of Medicine”. Hippocrates used the terms carcinos and carcinoma to describe non-ulcer forming and ulcer-forming tumors. In Greek this means a crab. The description was names after the crab because the finger-like spreading projections from a cancer called to mind the shape of a crab. – source

So the cancer cells spread in a way that tumor looks like a crab. Why? Why doesn't it, for example, have a potato-like spread in which cancer cells form a sphere?


texts: Where do class 2 preservatives end up after digestion?

texts: Do anybody know what happens to class 2 preservatives in general after they are digested - i.e details like weather they are absorbed into blood as simplest elements or excreted out or assimilated to a part of the body. If the question is oversimplified, please tell where sodium propionate or any other convenient ones eventually end up at.


texts: As we know that coils and loops are evolutionary variable regions where mutations,deletions, and insertions frequently occur. So does it mean that they don't have much role in the structure of protein? If it so then what are the factors for the protein core structure formation?


texts: How did genome replication first synchronise with cell division?

texts:
It is obvious that cell division in living organisms is now synchronised almost perfectly with DNA replication and, furthermore, the line of division has to intersect exactly the space between the two copies of all the DNA molecules in the cell.  I know that as otherwise, most cells would be either empty or have a lot of excess DNA strands, which would lead to an eventual termination of replication due to scarcity of resources and energy required to trigger it.

Some theories (https://www.ncbi.nlm.nih.gov/books/NBK26876/) suggest the first protocell might have formed by a liposome simply gobbling up a self-replicating molecule. However, how would the molecule then 'know':

when exactly it should replicate so that the replication coincides with the liposome diving and
where in the molecule it should be located at the time of division, so that its copy ends up in a different daughter cell to itself

?


texts: Is there a biological or technical reason for a 40 Ct cutoff in nucleic acid detection assay?

texts:
I have developed and validated a modified a nucleic acid test (NAT) for SARS-COV-2 detection using real-time RT-PCR (aka rRT-PCR, aka RT-qPCR). My assay is not for diagnostic use, but for donor screening (which are similar, but different enough to require independent validations). The PCR step is sensitive enough to detect a roughly a single gene copy per reaction, but not always with a sub 40 Ct (which may or may not be an issue).
You see, the protocol is built around the primer/probe sets first published by the US CDC, so I initially adopted the criteria in the CDC EUA protocol, which stipulate a Ct value < 40.00 to classify a target as positive. This means is that amplification with a Ct value of 39.99 is classified as positive, while a nearly identical amplification curve with a Ct of 40.01 is classified as negative. Looking at similar NATs for in vitro diagnostics, most use this same cutoff. It seems fairly common with tests for other pathogens too.
For a little background, using a cutoff like this reduces the potential for subjective classification errors between users by providing a qualitative, binary interpretation for an ostensibly quantitative data readout. The trade-off is that an improperly assigned cutoff can result in systematic classification errors that are universal among all users. Anyone who has used one of the protocols based on the CDC probes has noticed that the two primer/probes sets targeting the SARS-CoV-2 viral genome do not perform equally well. It's common for test results to be classified as "inconclusive" when one viral target is positive, but the other is "negative" because of a Ct value just above the 40Ct cutoff. (I've already tweaked my protocol to reduce this kind of error, but could not eliminate it completely).
As I am writing this up for publication, I'm wondering if it would be better (more honest) to recommend a Ct cutoff that reflects the empirical range of Ct values in my validation studies, as opposed to keeping it at some seemingly arbitrary round number (even if it is almost universal among similar tests). Doing so would not change any of the major findings I report (sensitivity, specificity, etc.), but would change some of the numeric values. More importantly, I think it could help prevent misclassification of late-amplifying samples as negative.
Does anyone know of a biological or technical reason why this cutoff should not exceed a Ct of 40? Maybe this is just some convention that is blindly carried forward; or maybe there's some quirk of TaqMan chemistry to justify this value that I'm just not aware of.


texts: Can disease resistance from vaccination be inherited?

texts: If a person has taken a vaccine against a particular disease and is resistant to that disease, will his/her children will be resistant to that disease??


texts: How do platelets produce proteins (if they do)?

texts: I'm aware that platelets don't contain a nucleus, but do contain mitochondria (so have mtDNA) and rough endoplasmic reticulum / Golgi. Since platelets require many important cell surface proteins (such as aIIb b3 for ECM binding), are these proteins (1) synthesized de novo in the mitochondria using mtDNA, and then somehow shuttled to the ER / Golgi for secretion, (2) remnants from proteins that were synthesized in their megakaryocyte precursors and not actually created anew, or (3) synthesized via some other mechanism I'm not aware of? Online sources weren't clear on this question. Thanks!


texts: Does the deletion of Chromosome 20 cause immunity against prion disease?

texts: I was reading recently about prion disease and it caught my attention that a normal prion protein is coded n chromosome 20, therefore, in order for an infectious prion protein to attack, there must be already normal unsedimented prion proteins, does that mean the deletion of chromosome 20 in meiosis lead to immunity against prion disease, since the protein is not coded, that is if the human survives without chromosome 20


texts: Is there such thing as Animal non-verbal body language?

texts:
Have there been any studies done on the animal use of their bodies to signal, communicate or express their emotions, particularly to members of other species (ex: humans)?

I've been observing a very intelligent indoor-outdoor cat who has been doing the same sideways stretching posture every day he met me. There has been a number of other postures that the cat has been using - tearing at a carpet with claws, or dragging himself against the carpet by using claws that I've repeatedly observed.

Another cat was thumping her head against a door to "knock" and indicate that the cat is outside.

To me, these gestures appeared as clear expressions of intent or emotional state.

Other experiment involved "trained" geese at a local pond who would indirectly approach humans to ask for food. Their body, neck and head position appear to indicate intent (is the animal grazing towards the human or away from the human).

Yet another experiment involves nesting birds who start to clearly express their displeasure at me located near their nesting area. They repeatedly produce high pitched screech until I move away.

For example I repeatedly see geese assume this gesture to intimidate other geese.

As a human, I'm very conditioned to vocal and eye related coordination, and this "non-verbal" language is fascinating to me.

Have there been any studies in how indoor/outdoor - partially domesticated animals communicate with humans?

Is it true that this communication uses their entire body and not just the vocal cords?

Is there some "foundation" language that would be similar among members of the same species, or is it entirely a learned skill that has nothing to do with evolutionary adaptation?

Finally, is there some sort of a brain complexity cut off at which level the animals can no longer understand if they are being communicated with?


texts:
Why would this be "L-cysteine"? This is taken from the answer key for my biochem final.

From what I understand if the -NH3(+) is on the left then the alpha-amino acid is in the L-configuration.

Am I wrong, or is my prof wrong?


texts: Bergmann's rule and Allen's rule: endotherms and ectotherms

texts: Surface area to volume ratio (in terms of heat conservation) is not the only mechanism, but it is still an important mechanism for explaining Bergmann's rule and Allen's rule. Given that, I want to know why these rules are primarily applied to endotherms. I know there are some ectotherms that follow the rules, but here I am not asking for examples.


texts: Why does skin sometimes suddenly itch when you stretch it?

texts:
Sometimes, when I bend over, areas of my skin like my back can suddenly itch quite intensely. Sometimes it may be another part of my body and the pattern seems to be a part of the skin organ that is not used to stretching quite that much in that spot, perhaps the skin not being so flexible there.

I realise that temperature, dryness, and a whole lot of other external and internal factors can come into play, but if my scenario is not too broad, and I'm pretty sure it's a universal trait in skin physiology, (and I don't have any skin allergies either), what is the basic science behind this phenomenon of skin stretching when it's not used to it, and you do it very suddenly?


texts: Could plasmids and conjugation mechanisms be used against antibiotic-resistant bacteria?

texts:
I'm surprised no one has mentioned something like this.
Plasmids are often exchanged between bacteria, sometimes through conjugation. In particular, conjugation could be considered an "open-port" vulnerability.
Intuitively, there are several schemes that exploit plasmids and bacterial conjugation that could form alternatives to antibiotics:
1: Pwnage by Conjugation
A specially engineered nanoscale capsule or specially rigged bacterial cell is programmed to call out to target bacteria for conjugation. When the conjugation tunnel is opened, the capsule or rigged bacterial cell floods the target bacterium with toxins or malicious RNA designed to sabotage it.
2: Fake Conjugation
A specially designed novel antibiotic contains a conjugation-signaling structure. When a bacterium docks with the antibiotic molecule, the antibiotic irreversibly latches on and tears a massive hole in the bacterium from the inside.
3: Backdoor Plasmids
Plasmids that confer significant advantages are isolated from naturally-occuring bacteria and a special "crash gene" is added to the plasmids. The modified plasmids are implanted back into bacteria that are known to spread them around.
The crash gene's promoter listens for a small set of chemical cues. If it detects a certain threshold of 1 of these cues, it becomes active and sabotages the bacterium. The gene could code for a toxin that specifically damages bacteria. Alternately the promoter could be specifically designed so it never releases the chemical cue, forcing the bacterium to repeatedly produce a garbage produce and waste its resources.
4: Bad Neighbor Plasmid
This might be more difficult to build. A synthetic plasmid encodes 2 products: The first confers a significant benefit to prevent bacteria from discontinuing it through natural selection. The other product is periodically ("randomly") transcribed and vandalizes other plasmids, causing large numbers of nonsense mutations. A set of special markers on the synthetic plasmid protects it from vandalism by its own product. This could silently remove antibiotic resistance from bacterial populations and the bacteria have no way of "knowing" they've been sabotaged until it's too late.


texts: Why can humans tolerate eating onions but other mammals like dogs and cats cannot?

texts: Onions are one of the many foods we shouldn't feed our pets. Looking it up, I learned that onions cause hemolytic anemia in MANY species: cattle, sheep, horses, dogs, cats, and even some primates. If anything, WE'RE the odd ones out. A few sulfur-containing organic compounds found in onions were fingered as the causative agents, and oxidative damage to red blood cells following decreased activity of glucose-6-phosphate dehydrogenase was the most mentioned mechanism. How do humans avoid this?


texts: What is meant by "opposing plasma membrane" with respect to cell adhesion molecules?

texts:
I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about cell adhesion molecules (CAMs) and I have come across the following:

CAMs are involved in homo‐ or heterophilic interactions with molecules
positioned on opposing plasma membranes, and such interactions are
referred to as trans‐interactions. In addition, CAMs are often
involved in homo‐ or heterophilic interactions with other
membrane‐associated molecules positioned in the same plasma membrane.
Such membrane‐lateral interactions are referred to as
cis‐interactions.

I know that cell adhesion molecules are proteins mediation cell-cell or cell-extracellular matrix interactions. However, in the above excerpt from the book in the following statement: CAMs are involved in homo‐ or heterophilic interactions with molecules positioned on opposing plasma membranes, I am not sure what exactly is meant by "opposing plasma membranes". I think that this refers to the plasma membrane of a neighbouring cell the CAM is interacting with, however I am not fully certain.
Any insights are appreciated.


texts: The probability of indirect human fertilization (follow-up)

texts:
This question is a follow-up to
this one.

I've been wondering how small that probability is. As we all know, "safe" sex, that is (correctly) using a condom and all that, isn't perfectly safe. So, in order to put this question into perspective, I'd like to know which one (safe sex or indirect insemination) has the greater chance to lead to impregnation. In other words, can you explain the probability of this scenario in terms a layman like me can understand?

Thanks in advance!


texts:
Around August I started discovering these small critters throughout my apartment. They're around 0.5-1mm long, black with six legs and two stubby antennae. I keep my glasses on the floor by my bed when I sleep and every morning, they're are 5-8 of them crawling over my glasses. The same thing happens with my hat. A number of them have died on the window sill. What are they and what are the best ways of getting rid of them? (More pictures here: https://imgur.com/a/31Thi)

Thanks!


texts: What is an effective method for putting on blue rubber butyl stoppers?

texts:
They look like this.

We have to do a lot of gas sampling and these are really difficult to assemble. I've been scouring the internet for advice but there are none. Do you have experience with these? Have you found a good way to put them on that doesn't destroy hands, hearts, and dreams?

To clarify, the hard part is putting the blue stoppers in the tubes in the first place. Once they go thoroughly in, we can crimp them with our hand crimping tool. Since the time I posted this, I find a (little) better luck using a piece of cloth / putting the cap and the glass vial between a vice. With too much pressure, I actually broke a vial and glass shattered everywhere. The best way to put them in is with a twist, but that usually comes with an expense of bruised hands after extensive use.

Wish I had a camera on me, but they look somewhat like this:


texts:
From evolution point of view can we explain as to why mothers care about child rearing more than fathers? Is it Social phenomenon or genetic phenomenon?
Are mothers hard wired to take care of children more or they are socially forced to do so?


texts: What do "reduced antipredator defense" and "reduced antipredator vigilance" mean?

texts:
The book BIOMAT 2010 (International Symposium on Mathematical and Computational Biology, edited by Rubem P. Mondaini) mentions the terms reduced antipredator defense and reduced antipredator vigilance.
Can you help me to make sense of them?


texts: Is there evidence to suggest that nutrients in vitamin capsules are not as readily absorbed as the same nutrients in whole foods?

texts:
I recently fell ill with a cold, and began to take a vitamin C capsule each day to help my immune system. When I noticed no change in my condition, I began to incorporate an abundance of citrus into my diet instead of taking the capsules. When I ate the citrus my condition began to improve markedly.

The ingredients listed by the vitamin manufacturer are:

Ascorbic Cellulose Gel
Hydroxypropyl Cellulose
Croscarmellose Sodium
Stearic Acid
Magnesium Stearate
Silicon Dioxide

Not excluding the possibility of coincidence, I was was intrigued. Has evidence been published to suggest that nutrients in whole foods like vitamin C in citrus fruits are more readily utilized in the body than nutrients in vitamin capsules?


texts: What is the frequency of double-hets between parent and child?

texts:
Say both parent and child are genotyped for all SNPs. In this setup we are only looking at variant positions between one parent and child - so neither parent nor child are homozygous reference (no AA/AA) in the millions of positions we are studying.

Assume all variants are biallelic and there is no de novo mutation (no AA/BB or BB/AA)

P    C
AA   AB
AB   AA
AB   AB
AB   BB
BB   AB
BB   BB

What is the fraction of AB/AB among these possibilites?

We are looking at all positions in the genome so the minor allele frequency (MAF) of B allele varies. You can choose whatever B frequency you like.


texts: Can inhibition of lymphocytes migration be a direct cause of chronic inflammation?

texts:
Here is the original slide:

I am thinking about the "cord factor" sentence in a more general case.

Assume you inhibit Leucocytes migration.
How does this lead to accumulation of macrophages in the site of infection?


texts: Will bacterial promoter without either -10 or -35 sequence allow no transcription?

texts:
I have a strong constitutive promoter on a plasmid inside of E.Coli, which expresses a gene. Having either -10 or -35 sequence modified to random sequence, will it ensure zero transcription from that promoter?

Thanks.


texts: Why is defibrillation in asystole ("flat line") useless?

texts:
In most popular medical dramas, when a patient has a cardiac arrest and "flatlines" the doctors many times use a defibrillator to "shock the heart back into rhythm'. I know that actually, the proper protocol is CPR and epinephrine (if possible), and that you should shock rhythms such as ventricular fibrillation. But why doesn't shocking the heart in asystole help?

If anyone could please explain, that'd be great.


texts: How to recognize a conserved motifs of the protein

texts: I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids sequence of this protein. But if I know this protein from another organism and the structure of this protein is known, then I can compare both of the sequences and conclude something, right? what I mean, is that there is no specific sequence corresponding to, for example, helix-two- turn-helix motif, and that I can take this sequence, check if my protein has it and say that there is helix-two- turn-helix motif or not. I can do this only by comparison to the protein which structure is already known, right?


texts: Major effects on cells grown with 5% FBS supplemented media instead of 10% FBS?

texts:
I maintain a few cell lines in the laboratory (industrial R&D) that I use regularly for experiments. I realized today that the media i prepared for the week on monday was only supplemented with 50 mL of FBS into 1 L of DMEM, instead of the usual 100 mL that i usually do. I was in a hurry and absentmindedly didn't add the second 50 mL autopipettor's worth.

My cells are fine morphologically but I think they're growing a bit slower than usual, my guess is due to the 1/2 concentration of all the FBS growth factors, etc. Are there any other effects that would be pronounced in these?

I understand that it will be apples to oranges to do compare results with these cells to, say, an experiment done with a batch of cells grown in complete (10% FBS supplemented) media.


texts: How can we digest lactose even though it has Beta glycosidic linkages?

texts:
I have Read that we cannot digest cellulose because we do not have enzymes to digest Beta glycosidic linkages in Cellulose

Then how is it that we have an enzyme called Lactase to digest the Beta glycosidic linkages in lactose?

Also If we have evolutionarily developed Lactase ,Why didnt we develop "Cellulase " too ?


texts: What is the average volume of the human Psychic tear? ("emotional tear")

texts:
My goal is to find out the volume of the average human "emotional tear" (Psychic tear - sadness, happiness), specifically when crying. I found a lot of information about Basal tears (constant lubrication), as well as Reflex tears (when slicing onions), but nothing about the volume of Psychic tears.

I should mention that in a 2016 study Is it possible to cry a river by the University of Leicester, the volume of one average tear that was used is the same as the volume of the average Basal tear - 6.2 micro liters. (Volume of Basal tears was also determined to be 6.2 micro liters in another study I found online)

I have a slight doubt that the average Psychic tear has the same volume as the average Basal tear, which is approximately 6.2  micro liters plus/minus 2 micro liters.

Could it be that both types of tears have the same average volume, and it is only the flow intensity that is different?

There seems to be nothing about this online after several hours of research. Any help would be greatly appreciated. Thank you.


texts: Do our ears or brains gradually adapt to noise pollution?

texts:
Having lived in various places all over the world for the past 9 years of my life, one thing stood out to me throughout this time, and now in particular. From a quiet place on the countryside in Sweden, I moved to Manchester for my studies. When I first arrived there, I felt the city was very noisy, a feeling which gradually reduced as I presumably got used to the noise levels there. From Manchester I moved over to Saitama in Japan, an enormous city right next to Tokyo with a considerable amount of noise during the day, and buildings that have little to no sound insulation. With the exception of particularly loud noises, I again adapted to the sound levels in the country, which at the time, I felt was no more than a natural response in terms of how much attention we pay to the noise. If I'm distracted by work or other activities, I have little reason to dwell on the sounds of driving cars and talking people.

The thing I couldn't explain purely by the 'paying attention' argument however was when I moved back to the Netherlands, to an apartment with excellent sound insulation. My apartment is located in front of a somewhat larger road, and cars pass by almost consistently. However, when I moved in I could barely hear these cars driving past, something that stood out to me as fairly pleasant. I thought a little bit of ambient music would kill the sound of these vehicles driving past altogether.

Now skip ahead one month, and I can hear the cars almost as if I'm standing next to them, an exaggeration of course, but the sound is much clearer than it was when I moved in. I know that nothing has changed in terms of insulation and I know that no windows are open. Strangely the only thing that appears to have changed is the clarity in which I perceive this noise, as none of the other people whom I've asked seem to share the same opinion (that is, that the noise has grown louder). This made me wonder - does our hearing adapt to noise pollution, and if so, how does it work?


texts: Defining Resistance and Sensitivity Thresholds for IC50

texts:
I have a dataset containing IC50 data for each of my cell lines and up to 80 drugs. Basically for each drug I want to be able to define an IC50 threshold where if a cell line has an IC50 above that threshold it is resistant, and if it is below that threshold it is sensitive.

I'm trying to think of the best way of doing this: I was thinking of taking the median for each drug as the threshold but I realize that's quite crude. Are there any more robust statistical techniques I could use to define such a threshold for each drug?

Thanks!


texts: Why is there low hepcidin levels in hemochromatosis?

texts: If hemochromatosis is iron overload and there is excess iron in the blood, why does the liver reduce hepcidin secretion (which increases the iron uptake) furthering the worsening of hemochromatosis?


texts: What are the disadvantages of forbidding flights to and from the African Ebola region?

texts:
After looking through the available Stack Exchange sites, this one seems to come closest to the appropriate place to ask...

Popular opinion, including my own, is that banning flights to and from the Ebola-ridden portion of Africa would protect us overall. I understand it would increase pressure on that region, making it more chaotic and less conducive to tracking people, so that eventually it could "explode uncontrollably" out of that region in a year or whatever time frame. Sanjay Gupta explains this briefly in Jon Stewart's (at points hysterical) report.

The disadvantage of allowing free travel to and from these regions, as I see it, is that the disease spreads much much faster, and to many many more disparate locations. This is because of the variety of places where each passenger comes from. And also the flight crew and plane itself, which affects all future passengers.

I'd appreciate more educated opinions. I'm far from it, regarding these issues, as are many Americans.


texts: How can I verify my true genetic relationship with my close relatives with simple physical traits?

texts:
Question
I don't know if it is ethical to ask a question like that, but I would like to know every simple physical trait that I can observe on me, my parents and my siblings which are regulated by a single or really low number of genes.  I don't want any disease-related traits, just simple traits that could illustrate genetic relatedness.

Already done search
During my research I've found about:

Hair on the second phalanx which is controlled by a single gene and absence of hair being recessive. (Recessive means you need two copies of the allele to have the trait absence of hair!) So if both parents have the trait absence of hair (on second phalanx), every child must have it as well.
Merged ear lob is also a recessive trait.

These are some for which I am not sure of the underlying genetics.

Hair in V on the forehead
Presence of dimples
Able to make a U with tongue
Able to detect Phenylthiocarbamide (PTC)

Don't hesitate to answer with references

EDIT: This site is saying that both hair in second phalanx and merged ear lobs are not as simple as they seemed...

Question: What trait can I use to illustrate genetics?


texts: Why is glucose our primary source of energy?

texts:
Is there any evolutionary reason for glucose being the "main" molecule used as a source of energy, beginning with glycolysis and subsequently cellular respiration (after being converted to two pyruvate molecules)? Or did this particular biochemical pathway arise "by fluke" early on in the history of life?

A colleague of mine told me that it was because as shown below, all of beta-D-glucose's hydroxyl substituents are all equatorially positioned (when in the correct chair conformation), which lends to its general stability.

Image taken from the Wikimedia Commons.

Could this have played a factor in the beginnings of energy metabolism, and if so, why?


texts: What's the duration between the binding of adrenaline to β-AR and the first translated protein?

texts:
Binding of adrenaline (epinephrine) to the β-Adrenergic receptor leads to formation of cAMP (via G protein activation), activation of protein kinase A and subsequently to the expression of specific genes related to glucose metabolism.

How long does it take (in units of time) until translation of the first protein related to the adrenalin binding event is completed?

EDIT: I can accept a reasonable guess at the time scale (+/- factor of ten). Also, it can be also any another kind of ligand/receptor system.


texts: Can I pellet DNA back from dissolved state?

texts: I have a dissolved plasmid pellet in water. Can I pellet it again by centrifuging it at 13000 rpm? If not, why?


texts: What coastal creature leaves braid-like trace that has clear landing and take off points?

texts: 6/29 around 8 PM EST (within 40 minutes after downpour) the depicted trace was found in swash zone at Jacob Riis Park in NY. For reference the boot size is 12.


texts: Why is ethanol osmotically active if it can enter through the plasma membrane easily?

texts:
This has been bugging me for a while, and I can't seem to find an answer to it, and I am sorry if I am asking a lot with this question(s). Firstly, I keep finding sources suggesting that ethanol is osmotically active, but I also know that ethanol can enter the cell readily through passive diffusion, and some sources also say it uses transport proteins - what causes osmotically active behaviour, then?
Secondly, and this is very closely linked to the above, why do cells shrink in the presence of ethanol of high concentrations, if it is able to enter readily, unlike, say, ions? The mechanism seems to be far more complex than I have found regarding simple osmosis for ions and such.

I would like to add that my confusion may also be due to conflicting information I am getting, whether the cell shrinks or grows (or does one then the other), so it is hard for me to even picture if the solution acts as if it is hyper- or hypotonic.

SECOND EDIT: Seems that there is evidence from some sources that suggest ethanol can affect the osmolarity of the solution without itself being "effective", whatever that means. Something to do with the lipid membrane. Again, I keep editing this so people might... possibly... have something to go off when answering this.


texts: How do organophosphates affect kidney function?

texts:
Many organophosphates, besides inhibiting acetylcholinesterase, can also permanently inhibit the enzyme neuropathy target esterase, leading to nerve damage. NTE also happens to be found in the kidneys, and is involved in osmolyte production. Have organophosphates been known to affect kidney function through the inhibition of NTE in the kidneys? If so, how?
Source:
Gallazzini, M., & Burg, M. B. (2009). What’s New About Osmotic Regulation of Glycerophosphocholine. Physiology, 24(4), 245–249. doi:10.1152/physiol.00009.2009


texts:
I'm trying to understand the purpose of different clinical trial phases, and the following question comes into my mind :

  Do pharmacodynamics and pharmacokinetics of the drug in animals are the same as in human?

The reason I asked this question is that our professor said that pharmacodynamic and pharmacokinetic studies are performed during pre-clinical studies (in animals), as well as during clinical trial's phase 1. The answer I was thinking about is that animal's physiology cannot be the same as human's physiology, thus, pharmacological profils should be different.

I just want to know more about this and feed my curiosity.


texts:
Anyone knows of a table with average concentration that can be found in  white blood?

Something like:

Neutrophils - 80%
Mast cells - ?%
Dendritic cells - ?%
B cells - ?%
Helper T cells - ?%
Killer T cells - ?%
Natural killers - ?%
Others - (whatever is left)
(the sum should be 100%, of course :))

Also: are helper T cells and killer T cells visually different? I can only find pictures of T cells, but not of each. I am also unable to find pictures of natural killers. - Thank you!


texts: Are Flippase Recognition Target sites read through during transcription?

texts: I believe it is quite straight forward, but if i have a FRT site following the last exon of a gene (with the stop codon removed), would the transcription factors read through the FRT site and transcribe whatever follows it, or would transcription be halted?


texts: What is the purpose of eletrowetting on microfluidic chips?

texts: I am doing a college BioMed project to make disease models and I have seen that Electrowetting-on-dielectric chips (EWOD) are widely used in the making of organs-on-a-chip, but I have yet to understand its advantages over continous-flow or droplet-based microfluidics.


texts: What is Environmental Robustness? Is it different from plasticity?

texts:
Hansen (2006) in his review uses the concept of environmental robustness independently of the other concepts of robustness (at pages 139 and 140) without defining it.

How is the term environmental robustness usually defined?

The concept of robustness (aka genetic robustness) can be further decoupled into mutational robustness, developmental robustness and maybe some others. I think envirnmental robustness is one of these sub-categories of (genetic) robustness.

Intuitively, I understand environmental robustness as something that is very close to plasticity in the broad sense. What I call plasticity in the broad sense is any phenotypic response to an environment whether or not the response is adaptive or not. Therefore, plasticity in the broad sense is adaptive plasticity + non-adaptive plasticity. I would intuitively think that a genotype is environmentally robust if the phenotype it produces varies little with environment, that is if this genotype has low plasticity (in the broad sense). Am I using a more or less standard definition of environmental robustness?


texts: How the conjunctivitis virus spread just by seeing a person's eye who is infected

texts:
Conjunctivitis or 'pink eye'.

I have a few questions on conjunctivitis. When I was suffering from conjunctivitis, my doctor advised me to wear sunglasses so that no one else gets infected.

I wonder how it happens that if someone looks into an infected eye, then there is a chance for that person to also get infected. Specifically, why does this apparently happen only when we see an infected eye?.

Another question I have is why does our eye get watery when we see the eyes of an infected person?.


texts: How much decibel can a fish produce with swimming?

texts:
I am talking about any sound that is produced by the movement of the body of a fish when it propels itself forward. Can this sound, if any, be recorded with a decibel meter? If so, how much decibel are we be talking about?
I understand that a goldfish probably doesn't make allot of noise, but what about a super fast sailfish or a whale?


texts: Does any specific property decide which DNA strand acts as leading strand template?

texts: Of the two strands of DNA, the one that unwinds in the 3' to 5' direction constitutes the leading strand template, with the other strand of course acting as the lagging strand template. Is there any specific property - such as a specific base pair sequence present on one of the strands - which decides that that strand shall be the leading strand template - whereas the second strand with the complimentary sequence will be the lagging strand template? What decides, in other words, which of the two strands will be unwound in the 3' to 5' direction (effectively rendering it the leading strand template and the second strand the lagging strand template)?


texts: What creates the feeling of 'excess' blood pressure to an area of the body?

texts:
If I hang upside down, and feel blood rushing to my head, what structures are actually responsible for me "feeling" this excess flow of blood? Baroreceptors? Mechanoreceptors? Something else?

Regardless, how does this process actually work? How do I "feel" excess blood pressure to a certain area of my body?


texts: Which human cells have the longest and shortest lifespan?

texts: Which cells in a human have the longest lifespan? Which cell has the shortest lifespan?


texts: Blood Pressure: Significance of difference between systolic and diastolic

texts:
I wanted to understand what is the difference between systolic and diastolic readings of blood pressure. I understand 120-80 to about 100-60 is considered normal but does the difference in the two values in the reading hold any significance?

I have read some text here and here.


texts: When a Lysosome's bonding sites all get bonded to, what is the most resource and energy efficient way to handle the used Lysosome?

texts: Let's say a Lysosome that bonds to a hazardous material to neutralize it has all bonding sites used up. would it be more safe / efficient to excrete the entire Lysosome / hazardous material molecule or to bring it to a certain organelle / organ to unbind the material and send it for excretion and then have the Lysosome available for use again? In which way do Lysosomes in nature commonly handle this problem?


texts:
I was studying development of chick but didn't understand what is cytoplasmic localization. My book says:

  After third cleavage , the rest of the cleavages are irregular and completely delimited cells are formed all over the germinal disc which is termed as blastoderm. This outcome of cleavage called cytoplasmic localization helps seal the developmental fate of each cell's descendants.


texts: How to calculate the number of folds present in a protein

texts: Suppose I have number of PDB files of proteins. How can I get the number of folds present in these proteins? Is the fold count derivable from the PDB files? If so, how?


texts: Can you identify this mold? (Aspergillus?)

texts:
I took some macro pictures (see below) of some black mold growing on wet straw. I noticed this creature that I think to be Aspergillus niger, but looks bigger than the one depicted in many pictures (the fruiting body is visible by naked eys) and since I am not an expert mycologist, I would like to ask the following questions:

Do you think it is Aspergillus niger?
If not what it is?
Is it dangerous (toxic/poisonous/infective) to keep it growing for the sake of making pictures?

Update. I am still getting this mold infection running on some of my cultures. Eventually, I managed to add some extra pictures.


texts: difference between ischemia and oxygen-glucose deprived medium

texts:
Ischemia is roughly defined as insufficient blood flow to a specific region of the body and in the literature it is generally considered as causing oxygen and glucose deprivation in the tissue and therefore cells. Can we induce ischemia by depriving cells from oxygen and glucose in the medium or does it require more than that and ischemia is more complicated?

edit: i know the definition of ischemia maybe i should have said 'mimick' instead of 'induce'. Anyway, here is the better version of my question:

Ischemia is defined as blood flow shortage in a tissue and it is one of the main causes of non-apoptotic cell death. In an article i was reading, the authors claim that they induced ischemia in the glucose-serum containing medium. Does this mean they deprived the cells from oxygen and thus mimicked ischemia? Is this the way to create ischemia in a cell culture? What other ways can there be? Should not cells also be deprived from glucose?


texts: How to calculate apparent diffusion coefficient (ADC) with example?

texts:
Can someone give an example calculation for the apparent diffusion coefficient (ADC)?

There appears to be multiple ways that this can be calculated, e.g. as discussed here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166577/


texts: Accumulation of Na⁺ and Ca²⁺ in the myocardiocytes while having acute heart failure

texts: Why is it necessary to have accumulation of sodium and calcium ions in the myocardium cells while having acute heart failure? Normally, at resting membrane potential, sodium and calcium are more outside of the cell than inside, then I expect to see them enter less to the cell than to expect from them to enter and not exit.


texts: What will happen to transcription if histone acetyltransferases are removed from a eukaryotic cell?

texts: If HATs are destroyed in a eukaryotic cell, how will gene expression level be affected? Will all gene expression be affected or just be slowed down and most gene will still be expressed?


texts: What causes DNA gel electrophoresis bands to swirl?

texts:
I recently ran a gel on a new system and came out with something I've never seen before.

I loaded the first three wells with a ladder in the first and an uncut plasmid in the next two. There are no bands, just swirls all over the gel.

It's a 10 cm gel, 0.7%, and I ran it at 80 v for 1.5 hours. Part of the new system is the buffer, lithium borate,  which I've never worked with before.

Any ideas as to why this is happening?

Edit: thank you for your answers. I followed the regular protocol closely and used the same bottle of buffer for both making and running the gel. I did this twice and got similar results both times.

I had the power supply tested and discovered that the voltage may have been fluctuating between 77 and 83 volts during the run. Could this have caused it?


texts: Does Penicillium roqueforti produce penicyllin?

texts:
I have recently discovered that blue cheese is produced with Penicillium roqueforti. As I know that some Penicillinum sp. produce penicyllin I wonder whether it is produced by P. roqueforti too?

The Wikipedia article does not mention penicillin, it mentions "compounds that can be employed as antibiotics" instead.

However the article on P. glaucum also do not mention penicillin, while P. glaucum is mentioned in the article on the history of penicillin.


texts: I live in South central Indiana, US, and these have just started appearing in the grass in my yard. I just bought this house last fall so I've never seen them. Anyone know what they are? Are they harmful to dogs?


texts:
I'm a junior math major starting to take his first courses in Algebra, Analysis, Topology, Nonlinear and Partial Differential Equations, etc.

I am just considering my career options at this point and somebody told be biotech/biology could have some interesting work. So I have come here to hear some advice if that is okay! Is there anything highly mathematical about the search for anti-aging or achieving the whole "biologically immortal" thing? I just don't know about any of this stuff so please inform me :)

PS: I also know Prob/Stats at a decently advanced level. So there's that too. Thanks!!


texts: How to understand Aposematism and Batesian mimicry

texts:
EDIT I want to understand the reason for intense animal colors. I.e. I don't want to understand the variety of the colors, just the intensity.

The Wikipedia page for Cethosia biblis says, the intense colors are a "warning" to enemies, which means the enemy is warned by the colors that eating that butterfly may result in death.

  [...], while the intense color of the dorsal sides of the wings is a warning
  to predators that the Red Lacewing has a bad taste, deriving from the
  poisonous host plants of the caterpillars.

In general it would make sense to me, that animals have learned something like "intense colors means danger". Although, I don't know how good animals recognize colors, but that would be another question.

But poisonous animals don't have necessarily intense colors. E.g. Sydney funnel web spider is very poisonous, but doesn't have intense colors, while on the other side some very intense colored butterflies are not poisonous like explained here. As a result, the explanation given in the wikipedia article doesn't make sense to me. I estimate it very unlikely, that animals learned something like "intense colors means danger", because there are of course examples where this is not true.

Therefore, I don't think the "Golden poison frog" has survived because his enemies recognize his intense colors and conclude "eating this frog will result in death" are hence hesitated to eat him.

My question is: Why does wikipedia say then, the intense colors of Cethosia biblis are a warning for their enemies?

PS: I just found the correct terms for my thoughts ("aposematism" and "batesian mimicry" and are reading now the appropriate wikipedia article. I didn't knew them when I've asked this question.

PPS: to avoid confusion: @DavidBlomstrom answered this version of my question https://biology.stackexchange.com/revisions/42554/2


texts:
This image has been posted on the Wikimedia Commons

This spider is about 3~4cm long. It was found in the middle of tomatoes plants in a garden, in the center of France, Clermont-Ferrand. Photo taken in the early days of August. It would be interesting to specify the species on Wikimedia Commons.

Please let me know if you need other information.


texts: "Heterozygotic expection" - when heterozygote differs from both homozygotes, but homozygotes are similar

texts:
For simple 2-alleles genetic model {a,A} and corresponding quantitative trait Q is typically true that

Q(aa)>=Q(aA)>=Q(AA)

or conversely

Q(AA)>=Q(aA)>=Q(aA).

For example, dominance means that Q(aa) < Q(aA)=Q(AA) , recesivity Q(aa)=Q(aA) < Q(AA) ; in additive models Q(aa) < Q(aA) < Q(AA) etc.

The situation when Q(aA)>Q(aa)~Q(AA) is atypical in biology ("heterozygotic expection ?", "uncooperative alleles ?"). Known example is HBB gene (heterozygotic form gives resistence to malaria but homozygotic mutation form is sickle-cell anaemia). But this is weak example only, because f is evolutionary advantage, not a measurable  phenotypical or biochemical trait.

QUESTION 1: Are there any systematic reviews about this atypical phenomena? (about "heterozygotic expection")

QUESTION 2: Is there a standard scientific term for this phenomena?


texts: Understanding the configuration of channels in the 10-20 EEG montage

texts:
In a typical 10-20 system there are 21 electrodes placed on the scalp. However, this does not mean there are 21 distinct "channels" or voltage sources.

I've heard that some of these electrodes are "reference" electrodes, while others are "active" electrodes. Sometimes electrodes can setup in a "bipolar" or "differential" fashion.

How many actual channels (that is, distinct input sources) will there be?
What's the difference between reference and active channels?
How does this bipolar/differential setup work differently than a "normal" setup?

Update

Here is my updated understanding based on @Christiaan's answer below:

time (t)    F2v    F3v        F2-F3         F3-F2
=================================================
1           2      1            1             -1
2           3      6           -3              3
3           5      3            2             -2

So, if my understanding is correct, then at time t=1, the voltage of the F2 electrode might be, say, 2 (units; volts, microvolts, whatever), and the voltage of the F3 electrode might be 1. If F2 is the arbitrary active electrode, then the potential difference between F2 and F3 is 2 - 1 = 1. But, if F3 was the active electrode (and F2 the reference), then the potential difference would be the inverse (that is, 1 - 2 = -1).


texts: Why does RNA alone go into the aqueous phase when treated with phenol-chloroform at lower pH? At a neutral or basic pH, both DNA and RNA would escape into the aqueous phase. So how is DNA held back at acidic pH?


texts: Which cryogenic vials and caps are ideal for storing glycerol stocks?

texts: There are internally threaded, externally threaded, natural caps. For the vials, there are skirts, star-footed, and various bottoms. Why do any of these things matter?


texts: Can one talk about deacetylation of a promoter rather than associated histone?

texts:
I am confused on a detail in a paper I am reading and am not sure whether I am misunderstanding the wording or misunderstanding the concept.  I am including the whole abstract of this paper for background:

Epigenetic regulation of uterine biology by transcription factor KLF11 via posttranslational histone deacetylation of cytochrome p450 metabolic enzymes.
Zheng Y, Tabbaa ZM, Khan Z, Schoolmeester JK, El-Nashar S, Famuyide A, Keeney GL, Daftary GS.
Abstract:
Endocrine regulation of uterine biology is critical for embryo
receptivity and human reproduction. Uterine endometrium depends on
extrinsic sex steroid input and hence likely has mechanisms that
enable adaptation to hormonal variation. Emerging evidence suggests
that sex steroid bioavailability in the endometrium is determined by
adjusting their metabolic rate and fate via regulation of cytochrome
(CYP) p450 enzymes. The CYP enzymes are targeted by ubiquitously
expressed Sp/Krüppel-like (Sp/KLF) transcription factors.
Specifically, KLF11 is highly expressed in reproductive tissues,
regulates an array of endocrine/metabolic pathways via epigenetic
histone-based mechanisms and, when aberrantly expressed, is associated
with diabetes and reproductive tract diseases, such as leiomyoma and
endometriosis. Using KLF11 as a model to investigate epigenetic
regulation of endometrial first-pass metabolism, we evaluated the
expression of a comprehensive array of metabolic enzymes in Ishikawa
cells. KLF11 repressed most endometrial CYP enzymes. To characterize
KLF11-recruited epigenetic regulatory mechanisms, we focused on the
estrogen-metabolizing enzyme CYP3A4. KLF11 expression declined in
secretory phase endometrial epithelium associated with increased
CYP3A4 expression. Additionally, KLF11 bound to CYP3A4 promoter GC
elements and thereby repressed promoter, message, protein as well as
enzymatic function. This repression was epigenetically mediated,
because KLF11 colocalized with and recruited the corepressor
SIN3A/histone deacetylase resulting in selective deacetylation of the
CYP3A4 promoter. Repression was reversed by a mutation in KLF11 that
abrogated cofactor recruitment and binding. This repression was also
pharmacologically reversible with an histone deacetylase inhibitor.
Pharmacological alteration of endometrial metabolism could have
long-term translational implications on human reproduction and uterine
disease.
Citation:
Zheng Y, Tabbaa ZM, Khan Z, Schoolmeester JK, El-Nashar S, Famuyide A, et al. Epigenetic regulation of uterine biology by transcription factor KLF11 via posttranslational histone deacetylation of cytochrome p450 metabolic enzymes. Endocrinology. 2014;155:4507–20.

My question is on the fourth-to-last sentence of this abstract specifically:
"This repression was epigenetically mediated, because KLF11 colocalized with and recruited the corepressor SIN3A/histone deacetylase resulting in selective deacetylation of the CYP3A4 promoter."
This sentence seems to say that SIN3A/histone deacetylase is deacetylating the CYP3A4 promoter itself (i.e. it is deacetylating a region of DNA directly).  However, shouldn't a histone deacetylase be deacetylating a histone, not a region of DNA?  Am I misunderstanding the mechanism?  Or is "deacetylation of the CYP3A4 promoter" really a short-hand way of saying "deacetylation of a histone that is associated with the CYP3A4 promoter"?
Thanks in advance for your help!


texts:
I'm struggling to find a reference for the mass or density of a human (monkey or rabbit would also work) retina.

I'd appreciate any help!


texts: What is it called when there is natural truncation selection?

texts: Truncation selection is when a breeder selects for animals that exhibit a value for a trait that is above a certain threshold.  What is it called when nature selects for a value of a trait that is above a certain threshold?  I want to say natural truncation selection, but I don't see any mention of that.  To clarify, what I mean is, what is it called when, as a result of natural selection, all perish but those with a value for a particular trait that exceeds a particular threshold.


texts: What is the name of this big plant with a purple trunk and green to purple berries?

texts:
I have photographed the following plant in our garden in Pittsburgh, PA.

Do you know the name of the plant?


texts: Aerobic vs anaerobic respiration comparison

texts:
The following graphs compare glucose decomposition in yeasts (in anaerobic vs aerobic conditions respectively)

My question is, why doesn't the first one look like a straight line as the second one does? Don't they actually follow similar processes?


texts: Ni-NTA purification, problem with the chaperone protein

texts:
I'm trying to purify the protein by Ni-NTA affinity chromatography. It seems that my protein (size about 54 kDa) is co-purified with chaperone protein (probably GroEL  - as the band is around 57kDa).
I tried the method where 4M glycerol and ATP is added to the wash buffer 1 and then I incubated this with the resin for 2 hrs in 4C, but it did not help.
Has anyone met such a problem before? I will be grateful for any advices.


texts: I would like to generate T2/T1 phage resistant Stbl3 E Coli to use in virus production. Is there a plasmid somebody has used that confers resistance, or is this done another way?


texts: Does antibodies get produced in female body against sperms?

texts: Our immune system produces antibodies against any foreign particles entering our body.In female body  sperms are a foreign particle .Does females produce antibodies or some sort of chemical resistance against these sperms?If so how come sperms able to survive this?Is it because there a huge number of sperms entering female body?


texts: Why do sloths come down from the trees to defecate?

texts:
I'm under the impression that most sloths exhibit this behavior, but why? They are slow moving and so have no way of escaping from predators when on the ground. Not to mention the energy they expire to break from their normally sedentary lifestyle.

They may only have to defecate and urinate once a week, but it strikes me as an unnecessary risk.  Why not let gravity do all the hard work?


texts: Does my nearsightedness come into play when creating light outlines in the distance?

texts: After looking at a light and closing your eyes, you see an outline of the light. I was curious how my nearsightedness would come into play. I look at a light in the distance without my glasses on and close my eyes, would I be able to distinguish the light shape better than if directly looking at the light?


texts: Why do genitals feel frozen when freefalling?

texts: I don't want to add much more about that. Since childhood I noticed a chilling effect, even when doing rollercoaster-type activities.


texts: Is Zeiss Primo Start microscope worth the price for student use?

texts:
I study physics but I have got interested about biology too. Surfing around the web, I have found out that in buying microscopes one needs to decide between the cheaper no-name brands vs. the four big ones: Zeiss, Nikon, Leica, and Olympus.

From the four big ones, only Zeiss delivers directly to my country. The price for Primo Star with phototube and Full-Kohler illumination is 1.8k euro or 2.3k usd. It has only bright-field optics but dark-field (if I got it correctly) is easy to add, as well as phase-contrast.

Anyway, I was wondering how much I would get out of the scope as a home user. I would probably do plant biology. I would also like to learn some staining techniques.

How difficult it would be to run some mini-studies at home? Do research? I would know about imaging quite a lot..

(There was some other similar questions but they did not mention home use.)


texts: Hhhmz! A hummingbirds flew past me while I was in the garden and yet, it still managed to halt perfectly in front of a blooming flower nearest to me. Just as soon I began to wonder, how fast do hummingbirds fly and in which way do they achieve their flight in addition to their distinctive hum.


texts: Definition of Linkage Desiquilibrium (LD)

texts:
According to wiki, linkage disequilibrium $D$ equals

$$D = x_{11} - p_1\cdot q_1$$

where:

$$
        \begin{matrix}
        \text{Haplotype} & \text{Frequency}\\
        A_1B_1 & x_{11}\\
        A_{1}B_{2} & x_{12} \\
        A_{2}B_{1} & x_{21} \\
        A_{2}B_{2} & x_{22} \\
        \end{matrix}
$$

and

$$
        \begin{matrix}
        \text{Allele} & \text{Frequency}\\
    A_{1} & p_{1}=x_{11}+x_{12} \\
    A_{2} & p_{2}=x_{21}+x_{22} \\
    B_{1} & q_{1}=x_{11}+x_{21} \\
    B_{2} & q_{2}=x_{12}+x_{22} \\
        \end{matrix}
$$

According to Hartl and Clark, linkage disequilibrium $D$ equals:

$$D = x_{11}x_{22}-x_{12}x_{21}$$

Question

Can you please prove that these two formulations of linkage disequilibrium are equivalent (assuming that they are equivalent)? If they're not… Do we use different definitions? What are their respective meanings?


texts:
I'm writing a thesis on bioinformatics and looking for drug-target databases. I'm implementing a open-source application for a tool called Cytoscape and so far I've used a open-source database called DrugBank to retrieve drug-target data, but I've read a paper on a database called Drug2Gene that combines multiple open databases into a unified format. The paper is from 2014, but all websites are down and I was wondering if someone here knows of any other databases/resources that does this and is maybe up-to-date? I want to utilize as much open-source data on drug to target relation as possible to provide a simple way of accessing all these resources. Drugbank is regularly updated and a good source, but with so many different databases with a decreasing overlap of data I was happy to stumble across Drug2Gene database only to realize I can't get it and it's probably not up-to-date.

I will be very thankful for any tips as I'm purely a Informatician and feeling helpless in finding thing related to biology.

Source: Drug2Gene paper


texts: What is the name of this plant with Fig-like leaves & mulberry look like fruits?

texts:
Location: Napa, California

Size: It's 20' tall now.


texts: What is the origin of "melting" in molecular genetics?

texts:
I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that they're referring to the separation of DNA from the double stranded form to single strands.

Maybe it's just because chemistry isn't my thing, but when I think of melting I think of a solid gaining enough energy to become a liquid. How did the term melting come to apply to DNA in this way? Does the term melting have a more general definition in terms of thermal chemistry?


texts: Population where most of the newborns die soon?

texts: Is there an ecological name to describe a population of organisms where most of the newborns die after birth without reproducing? The population as a whole keeps growing, however, because there are enough individuals that manage to reproduce.


texts:
What is the correct meaning of cytogenetic notation "inv(4)(p13q22)" ?

Inversions at chromosome 4, at the p arm 13 is inverted AND at q
arm 22 is inverted

OR

Inversions at chromosome 4, the p13 is
Swapped with q22


texts: How to build a trimeric protein structure from monomeric PDB file?

texts:
Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full structure in COOT, SWISS-PDBviewer or pymol?

Here is a link to the protein complex I am looking at

I would appreciate: Guidelines on how to do this (preferably in coot, pymol or Swiss-PDBviewer), or referral to a tutorial that actually goes through this would be great!

For reference: I found some descriptions on how to "build/merge" with Swiss PDB viewer here. And in threads from this discussion I found descriptions of how to do it with other molecular graphic tools as well (although I don't completely understand it)

What I have tried: In the tutorial for the SWISS-PDBviewer ( link ), I am able to follow some of the instructions, but I can't follow them for long:

I upload three of the same PDB file in SWISS PDBviwerer (they are layered on top of each other)
I can access/see the layers in the "layers info"
I am told to open the "text icon" to see the PDB text file, and look for "mtrix" rows - which should come right before the "atom" rows. As cited from the instructions:

  " Scroll down the pdb file until you find MTRIX lines (they are just
  before the ATOM lines). You can see 9 lines MTRIX. They represent
  three transformation matrices, and allow you to build the
  non-crystallographic symmetries of the protein"

I cannot find the "mtrix" rows in the PDB-text file, and am very unsure of how to follow the next instructions (link) after this as well. I am not able to click anywhere in the text file, then I get the error: "sorry can't recognize any clickable information under this pointer..

This is what I see above the "atom" row:


texts: How reversible is decerebrate posturing caused by brain stem damage?

texts:
This is a follow-up question to How likely would Abraham Lincoln be to survive his wounds today?

You don't have to see a CT scan or autopsy to know if the brainstem is
injured (directly or indirectly), if it doesn't work right.
The description of the first doc at the scene mentioned that Lincoln
was not breathing, and one pupil was dilated (the latter a clear and
unequivocal sign of dysfunction of the third cranial nerve or the
upper brainstem, from where it comes). Unfortunately, the second doc
described the enlarged pupil being the right one (it's extremely
unlikely to have been one and then the other - one of the doc's was
probably mistaken as to the side).
By 3 hours after injury, both pupils were fixed and dilated, and
Lincoln showed extensor (decerebrate) posturing - again, all signs of
profound brainstem dysfunction (but not yet brain death, though pretty
close to it).

Now, what is decerebrate posturing? See http://en.wikipedia.org/wiki/Abnormal_posturing#Decerebrate

Decerebrate posturing is also called decerebrate response, decerebrate
rigidity, or extensor posturing. It describes the involuntary
extension of the upper extremities in response to external stimuli. In
decerebrate posturing, the head is arched back, the arms are extended
by the sides, and the legs are extended.[6] A hallmark of decerebrate
posturing is extended elbows.[12] The arms and legs are extended and
rotated internally.[13] The patient is rigid, with the teeth
clenched.[13] The signs can be on just one or the other side of the
body or on both sides, and it may be just in the arms and may be
intermittent.[13]
A person displaying decerebrate posturing in
response to pain gets a score of two in the motor section of the
Glasgow Coma Scale (for adults) and the Pediatric Glasgow Coma Scale
(for infants). Decerebrate posturing indicates brain stem damage,
specifically damage below the level of the red nucleus (e.g.
mid-collicular lesion). It is exhibited by people with lesions or
compression in the midbrain and lesions in the cerebellum


texts:
I read somewhere that recently some people are trying to use harmless bacteria that live symbiotically in humans to express some portions of antigens of the harmful ones. Some people have raised concern that continuous exposure to the same antigen may lead to adaptibility of immune system to that epitope and render it useless when the germ actually comes.

Can't we use the same procedure for exposing some parts of MHC of the donor to the recipient before transplantation, so that, by the time the real transplant is done it may become adapted ? How much time would it take for this to occur ?

I can already see one drawback : In emergency transplants, this can not be used due to time factor. Can you see any other drawbacks ?


texts: Statistician confused about exact SNP data type

texts:
I'm from a statistical (not biological) background, and I'm very confused about what exactly is the "data" associated with a SNP. Below, I'll explain things as best I can--please correct me if any point is wrong or otherwise unclear. Assume we're working with humans, since the following will change depending on the species. (Assume all cases of interest are biallelic.)

When a locus has an allele on least one chromosome, the measurement AA, Aa, or aa is called a SNP (pronounced "snip"). Therefore, using statistical language, SNPs are three level factors--this is the data associated with a SNP. As said earlier, if the factor has 1 level (ie it's only aa or only AA) then it's not a SNP.
Sometimes for humans it seems like people say a SNP is actually just one allele (so a two level factor, a or A). How is this possible? Do people sometimes only measure one allele instead of both to get the genotype?


texts: Is it true that cats can drink sea (salted) water?

texts:
Found somewhere in the Net, that cats can drink sea (salted) water.

This fact seems to me as being urban legend, not true (because the purpose of water in body apparently implies it should be clear).

What is true and how to explain?


texts:
1) What happens in the ovary and in the bloodstream that brings about this change in the uterus?
2) Why does the level of FSH decrease and remain at a relatively low level during the luteal phase of the cycle?

For 1 I was thinking: So estrogen levels increase and the follicle matures which first cause menstruation and then the lining reforms??
For 2 I was thinking: the follicle has already ruptured by the luteal phase


texts: Where can I find the metabolic network for the human erythrocyte?

texts:
Where can I find the metabolic network of the human erythrocyte (red blood cell), in SBML format? The red blood cell metabolic network is a model that's usually employed in the literature [see refs below] to demonstrate mathematical techniques of analysis of metabolic networks.

Despite this common use, I haven't been able to find a metabolic network of the human erythrocyte in SBML format, which is commonly employed for these networks (for example, in the BiGG database, http://bigg.ucsd.edu/) because it is easy to use with the COBRA package (http://opencobra.sourceforge.net/).

So, anyone can tell me where I can find an SBML model of the metabolic network of the human red blood cell?

References where the red blood cell metabolic network is used:

Wiback, S. J., Famili, I., Greenberg, H. J., & Palsson, B. Ø. (2004).
Monte Carlo sampling can be used to determine the size and shape of
the steady-state flux space. Journal of Theoretical Biology, 228,
437–447. doi:10.1016/j.jtbi.2004.02.006
Braunstein, A., Mulet, R., & Pagnani, A. (2008). Estimating the size
of the solution space of metabolic networks. BMC Bioinformatics, 9, 240. doi:10.1186/1471-2105-9-240
Jamshidi, N., Edwards, J. S., Fahland, T., Church, G. M., & Palsson,
B. Ø. (2001). Dynamic simulation of the human red blood cell
metabolic network. Bioinformatics, 17(3), 286–287.
Kauffman, K. J., Pajerowski, J. D., Jamshidi, N., Palsson, B. Ø., &
Edwards, J. S. (2002). Description and analysis of metabolic
connectivity and dynamics in the human red blood cell. Biophysical
Journal, 83(2), 646–662. doi:10.1016/S0006-3495(02)75198-9


texts: Why do monocots have eustele in the roots instead of protostele like dicots? I thought the roots don't need the strength of eustele because the roots are supported by the soil. So what is the evolutionary reason for the eustele in the roots of monocots?


texts:
I need help: I would like to prepare an HEPES solution, without using the powder. It is possible? I remember that I did it once, but maybe I'm wrong...does someone know a protocol for HEPES preparation without using a powder? thanks!!

I need It for morpholino dilutions. 5mM, ph 7.6.


texts: If mantis shrimp have 16 photoreceptors then how many other colors on the spectrum are there?

texts: Mantis shrimp have 12 to 16 photoreceptors and humans have 2, and in rare occasions even 3. But if mantis shrimp can see 16, how many other colors are out there? How many photoreceptors is possible? How much of the spectrum is not ever going to be seen by any creature ever?


texts: Toxicity of stannous fluoride in toothpaste?

texts:
I recently purchased a new brand of toothpaste, and when I looked at the medicinal ingredients, it listed stannous fluoride 0.454% w/w, instead of the regular sodium fluoride. I was a bit concerned because I thought that tin was toxic to humans, and that it might be absorbed in the mouth.

A couple of studies like this one say that stannous fluoride is great, and I can't seem to find any studies on how toxic tin ions are to humans, but on Wikipedia it says that stannous fluoride readily forms tin metal and ions in water. Should I be worried?

  Readily soluble in water, SnF2 is hydrolysed. At low concentration, it forms species such as SnOH+, Sn(OH)2 and Sn(OH)3−. At higher concentrations, predominantly polynuclear species are formed, including Sn2(OH)22+ and Sn3(OH)42+. Aqueous solutions readily oxidise to form insoluble precipitates of SnIV, which are ineffective as a dental prophylactic.


texts: What is this worm like animal found on a well water filter?

texts:
This was found in the water filter on a private water well that feeds a house in southeast Colorado, USA. The well has hard water, and is shallow (25’). There are several of these creatures all over the filter. They range from 3mm-5mm long.
The picture is of the water filter. In a video we have of them on the filter they move their arm like appendages.


texts: Plant cell question in age 12 science test Part II

texts: I'm a parent and I think the teacher had been a bit harsh with marking most of these questions but can someone help me answer the very last question on the paper please (where someone has written SP against it). Is the answer mitochondria?


texts:
How is the primer present in the daughter, leading strand replaced? I've circled the primer in question.

I don't see how this primer can be replaced by DNA polymerase; there is no free 3' end for DNA pol to act on.

My book, however, says there is no telomere problem with the leading strand.

Other sources say there is a telomere problem.

So what is it?