texts: Why might the chirality of gastopods be dominantly dextral?

texts:
This wikipedia page on gastropods provides a definition of chirality, and briefly describes the genetic mechanisms behind why a shell is wound left (sinistral) or right (dextral) handed. It also mentions the fact that there are more species of gastropods that are dextrally wound than sinistral. What the page does not offer is why this might be so with regards to evolutionary pressures.

Does anyone have an explanation of why gastopod species have wound up dominantly dextral?

This question relates to my question about a specific species of gastopod that is found in equal proportion of both chiralities, and both in the question and answer there are suggestions of a chiral relationship between predator and prey and perhaps ease of mating. But it really doesn't answer my general question.

If it's a predator-prey pressure then is there any evidence across a larger sample of species that supports this explanation? Or of the left and right handed species of gastropods, anatomical evidence across a large number of species that shows mating advantages? Or likewise any other explanations that offer evidence?


texts: Phospholipid membrane fluidity if phospholipid had one type of fatty acid

texts: How would membrane fluidity change if the phospholipid membrane had only one fatty acid?


texts:
I found these "things" by chance on my wild strawberries which I grow in my organic garden. Basically, some strawberries are completely covered with them.

They're transparent, they have dots equally aligned and they don't move. I've tried searching for transparent slugs and worms and also faeces but to no avail.


texts:
Do sulfate reducing bacteria help during the formation of the mineral dolomite in low temperature environments?

Wikipedia says

  The actual role of bacteria in the low-temperature formation of
  dolomite remains to be demonstrated. The specific mechanism of
  dolomitization, involving sulfate-reducing bacteria, has not yet been
  demonstrated.

I wonder if someone has any updates on this. The reference given in the Wikipedia article is from 2000, from a source titled suspiciously "Journal of Conference Abstracts". Now it's 2013 and maybe someone else has found out something new.


texts: Has evolution made a mistake with prehistoric animals?

texts:
Let me start this by saying I have very limited knowledge in biology and evolution.

However, when visiting museums and watching documentary movies, I always get impression dinosaurs (and other animals in "dinosaur era") are very huge compared to today's animals, especially land animals.

So I wonder, was the this huge size actually an error in evolution?


texts: Why did many species of Homo and their ancestors evolve in East Africa?

texts: One thing I find interesting about the theory of evolution is the idea that Homo Erectus and Habilis evolved in Africa, began to spread around the globe, then was superseded by Homo Sapiens Sapiens which also evolved in Africa. Why did the vast majority of Homo species evolve in East Africa first?  What was it about Africa which encouraged speciation more than other areas?


texts:
I picked it this evening beneath an oak, in France, Nantes :

I tried an image search with Google, and it seems I picked a finger of a dead hand :)

What is its name, and is it edible?


texts: what is the difference between homozygous and heterozygous duplication?

texts:
In a genetic test result it's written

homozygous duplication

or

heterozygous duplication

Does it mean four copies of the same gene for homozygous duplication and three copies for heterozygous duplication?


texts: The TCA cycle intermediate Isocitrate dehydrogenase commonly undergoes point mutations in cancers. This allows IDH to reduce a-Ketogluterate to 2Hydoxygluterate, causing a reduction in pVHLs ability to hydroxylate HIF-1a, and a subsequent accumulation of HIF-1a. This leads to angiogenesis via VEGF. If the cancer cell is converting its a-KG away form the TCA cycle, how does the cell make up for the loss of TCA function, and subsequent ETC function for energy production? Why would the cancer cell prefer to lose high yield energy production in exchange for low yield energy production?


texts: I have a black tiny bug crawling all over the house

texts:
This bug is crawling all around the house it stays within the shadows and moves very very slow, i have never seen it jump or run, it just moves very slowly

P.S. those bugs as u can see are smaller than 1mm so it's hard to take better pictures but i will get better ones tomorrow

P.S. the hairs are not hairs they are wool from the carpets, i just got married in october 2014 and everything in the house is new, including the flat, it was built in january 2014.

Bug pictures with a 1 mm thick pencil refill

it is very similar to what's in this picture, but i couldn't take a picture of it because it's tooo tiny

I really need to know what it is so I can deal with it :(

Edit: once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles and I don't think it is a termite because I don't find any piles of eaten wood

EDIT 2:
More pictures:

-- Stage 1 --

-- Stage 2 --

-- Video for stage 2 --

I don't know what it is but I know that there is ones young in age i call them stage 1 they are unable to move

and there are ones I call stage 2 older in age and bigger in size and they can move and I think they can bite too

-- Insect 2 -- 5mm by 5mm

I found this one across the hall from the others and I do't know if it's related, i found it dead but I haven't sprayed that side with insecticides i sprayed the other side so it's possible that it was with the others but ran and died far from them.

EDIT: More photos

P.S. I found those moving in daylight (now)

when i blew a little air i think i turned it


texts: I recently read that the X-linked dominant disorder incontinentia pigmenti is lethal in males and homozygous females. Why is it so? Is there any other effect of this disorder on the body, other than random loss of melanin?


texts: How lion can carry the cub without harming it?

texts: We can see in the picture that lion is carrying its cub by the scruff of its neck without causing harm to it.


texts:
I have always drained and tossed the water from canned beans. My understanding has been that the water that canned beans are soaked and cooked in contains raffinose, the gas-causing sugars that humans can't digest. This University of Michigan page, referred to in the answer to an earlier question, says:

  Rinse beans thoroughly and never cook beans in the water they've
  soaked in. It's loaded with the gas-causing raffinose sugars.

And also advises:

  Drain and rinse canned beans. That will get rid of some of the
  gas-causing raffinose sugars (and almost half of the unwanted sodium).

Now that aquafaba is all the rage, though, I'm wondering whether my understanding is wrong. I understand that the bean water would taste mildly sweet and foam up so readily because of the raffinose. But it seems to me that aquafaba would lead to severe bloating and intestinal distress, as it relies for its properties wholly on the gassy and sugary nature of the bean water.

Am I mistaken in my understanding of the need to toss the water that one soaks or cooks beans in? Or is it just that fans consider the bloating and gas a price well paid for the delights of aquafaba?


texts:
[I striked through some passages that might be misleading, resp. where I have been misled.]

Is the following - very simplified - model biologically (or physically) plausible, explaining how spatiotemporal processing on dendrites works, especially how dendritic spikes and short-term potentiation modification of synaptic strength might work together? (I've read the wikipedia article on NMDA receptors but found it quite hard to digest. It's not a gentle introduction into the topic.)

Let the blue dots be two ligand- and voltage-dependent ion channels (eg. NMDA-gated channels) sitting on two synapses.

Let the green dot be a voltage-dependent ion channel that generates dendritic spikes.

Let the red dots be voltage-dependent ion channels that generate action potentials.

Without the green channel (generating dendritic spikes), two simultaneously synaptic inputs with depolarization V0 which sum up at the branching point of the dendrite would not suffice to generate an action potential:

But with it, two subsequent synaptic inputs (e.g. in two synchronous spike trains) would, because the postsynaptic response is stronger due to an additional voltage signal from the dendritic spikes.

At time  t2 another synaptic input and the dendritic spikes arrive at the blue channels. The resulting depolarization  V1 >  V0 suffices to evoke an action potential.

Is this picture correct in principle? Do such processes actually occur? Or are the real processes quite different? (Of course, they will be much more complicated and superimposed with other processes.) At least some NMDA receptors (which are ligand- and voltage-gated) sit on synapses.


texts: Snake with orange spots found in South Florida

texts: I found this snake near my doorstep. What species is it?


texts: Question about the basilar membrane mechanics (cochlea)

texts:
I am reading about the mechanics of the basilar membrane in the inner ear.
In various publications, it is said that, at a specific position on the basilar membrane,
the outer hair cells are activated by the amount of basilar membrane displacement
while the IHC are activited by its velocity.
As far as I know each position on the basilar membrane vibrates at a characteristic
frequency. Given that the to-and-fro movements have the same frequency at all sound intensities, isn't the velocity be directly proportional to the membrane displacement?
If that is the case, does this mean that the activation curve is steeper at higher frequencies?
Thank you!


texts:
The Varicella zoster virus causes chickenpox in children and shingles in adults.

It appears after the initial infection, it can go dormant in the nerve, and reactivate itself decades later.

In chickenpox - the symptoms are:

  characteristic skin rash that forms small, itchy blisters, which eventually scab over. It usually starts on the chest, back, and face then spreads to the rest of the body

In shingles - the symptoms are:

  a painful skin rash with blisters involving a limited area. Typically the rash occurs on either the left or right of the body or face in a single stripe.

My question is: What is the name of the property of viruses can activate a second time, with different symptoms?


texts: Evolution of the unique mating system of the scorpion Androctonus australis

texts:
Sperm transfer in the scorpion Androctonus australis involves a sclerotized spermatophore, which is formed in the paraxial organs of the male reproductive system. The right paraxial organ produces the right half of the spermatophore (hemispermatophore), and the left paraxial organ the left hemispermatophore. The hemispermatophores are mirror images of each other, and are always produced one pair at a time.

During mating activities, a sexually mature male locates a receptive female, grasps her pedipalps, and proceeds to drag her along in his search for a suitable substrate onto which the spermatophore will be glued. This search may last for several hours. When the male finds a suitable substrate, the hemispermatophores slide out of their respective paraxial organs, move past the genital atrium (where the hemispermatophores are glued together), and the spermatophore is attached to the substrate.

The spermatophore contains the sperm mass in a concealed vesicle so that sperm aren't dessicated. The male then pulls the female over the spermatophore, guiding her so that her genital opening reaches a position directly above the spermatophore. A brief struggle ensues and the female's rocking motion helps to engage the spermatophore with her genital operculi. Continued rocking by the female triggers spermatophore opening, and the sperm mass is transferred into her genital pore. The transfer requires a pressurized vesicle that forces the sperm into her genital pore.

The spermatophore originated in aquatic organisms, but it has undergone extensive modification for use in terrestrial organisms like scorpions. Which evolutionary developments caused the transition from an aquatic deployment of the spermatophore to a terrestrial deployment involving the various interdependent behavioral and physiological elements described above? Since the behavioral elements are invariant, they must be encoded in the genome just as the physiological elements are. A rigorous answer to this question necessitates the elucidation of a series of intermediate steps, each of which was driven by natural selection, and each of which involved a set of mutations whose overall probability was not prohibitively low. If one or more of the steps was driven by genetic drift, then we must take into account the fact that, although the time for fixation of a neutral mutation is shorter in small populations (such as occurs during a population bottleneck), there is less opportunity for mutations to appear in small populations.


texts:
I am doing an experiment on preservation of peas.

The first notable change to the peas over a period of one week is that they have changed colour from bright green to a dull colour... Why is this so?

The only test tube which did not have peas which changed colour was the one which was kept at 4 degrees Celcius in a fridge, so it probably has some relation to temperature...

Many thanks

N.B.: I know that the bacteria reproduce and could use the pea as their source of food, but how do they have any relation to the colour of the pea? I also put the tag "bacteria" and "thermodynamics" as I couldn't find any other related tags.


texts: Maternal immunity without prenatal vaccination?

texts:
It is recognized that antibodies from the mother provide a level of protection to infants. This is why mothers are often advised to get vaccinated when they're pregnant. However, does the vaccine have to be given during pregnancy or would a vaccine taken as a child-teenager, if still effective as an adult, function the same way?

I'll try to give an example to clarify. Suppose a person is fully vaccinated against Whooping Cough, at least based on the current schedule, but does not receive a pre-natal vaccination. Is it reasonable to suppose that if the vaccine is still effective and is causing the body to produce antibodies, that these maternal antibodies would be passed on such that the infant would still receive some protection that it would not receive had the mother not received the childhood vaccinations?

Further Detail
I am interested in this question because it could influence studies which look at rates of infection/cases in infants, in order to measure the effectiveness of cocooning. These studies assume that because these children are too young to be vaccinated, the vaccine cannot be influencing their susceptibility, except through cocooning. But if childhood vaccination results in a high enough IgG levels, that might not be the case, and so this result should be considered in such studies as this one.


texts: Features in individuals causing high population variation

texts:
As I understand it, a population with high variation is something sought after, since it makes the population better equipped to face a dynamic environment.

Then, I guess features in an individual which causes it's population's variation to be high, should be selected for (high mutation rate, other features.. ?).

If so, does this manifest itself partly as individuals preferring to mate with individuals from another population? (With genetic difference within reason, perhaps a norm for a proffered genetic difference between individuals)


texts: Why was the Davson-Danielli model rejected?

texts:
According to my textbook, Davson-Danielli's model of a phospholipid bilayer sandwiched between two layers of globular protein was incorrect. The nonpolar protein portions would separate the polar portions of the phospholipids from water, causing the bilayer to dissolve. Meaning, the Davson-Danielli model is not only incorrect, but it is also impossible.

I understand why the model is incorrect, but not why it is impossible. In my view, the nonpolar proteins would remain together in a micelle shape due to hydrophobic exclusion. Because of this, the phospholipid bilayer sandwiched on the inside would remain isolated from the water.

Why would a bilayer dissolve if the proteins were in contact with water and the phospholipids were isolated from the water?

I think that my confusion stems from many misunderstandings about the chemistry and structure of the cell membrane. In depth illustration of the error that my book mentioned would be most helpful.


texts:
I just read the answer to this question, and it got me thinking...

If the human brain (or any other brain) has a finite amount of storage, what would happen once the brain has taken in its maximum amount of information?

This is, or course, assuming that the individual can live long enough to acquire that much information.

I would take a guess that just like how we forget things all the time, the new memories would "override" some older ones.

Has there been any research or hypotheses on a brain's behavior once the its storage has maxed out?


texts:
How is energy acquired from ATP (i.e. What is the energy-releasing equation involving ATP plus water)?

I Would be grateful for the answer.


texts: Does the term "Biophysics" have two different meanings?

texts:
1.
Some sources (including  the current Tag-info at biology SE)  state; biophysics is the adoption of techniques / methodologies from physics to study biological systems.

The use of methods from the physical sciences to aid in the study of biological systems…

Bio-SE- Tag biophysics.

Biophysics or biological physics is an interdisciplinary science that applies the approaches and methods of physics to study biological systems…

Wikipedia (permalink).

Biophysics — the branch of biology that applies the methods of physics to the study of biological structures and processes…

Dictionary.com

2.
According to other sources, biophysics is the subject concerned with how the laws or phenomena of physics work in living systems.

“The subject of biophysics are the physical principles underlying all process of living systems.”

Google Book: Biophysics, An introduction, By Ronald Glaser (permalink).

Biophysics is a bridge between biology and physics. ... Biophysics looks for principles that describe patterns. If the principles are powerful, they make detailed predictions that can be tested. ---

Biophysical society

These two, although apparently quite similar (and I agree, have overlapping areas) basically indicate completely different things.
The first group of definitions refer to techniques and methodologies; such as “how does an electron microscope work?”, or “what could be the best strategy to separate membrane-lipids?”, or “how could you identify cells with the expression of certain RNA”; etc.
The second group refers to the physical principles applicable to living systems. Such as “why do phospholipids form a bilayer?” or “how do brain waves reach the scalp?” or “how does a humming bird move its wings when it hovers in a stationary manner?” or “what are the mechanisms working in the path of transport through phloem?”.
Now my question is: Is there a dual and different meaning, or use of the term ‘biophysics’?


texts: How does the value of K determine number of local optima in NK model?

texts:
BACKGROUND

The NK model of fitness landscape considers N states which can interact with K other states. For example N is the total number of genes in a haploid genome and K is the number of other genes that each gene may interact with.

In this article Kaufman says:

  The fully connected NK model yields a completely random fitness
  landscape. For K = N - 1, the fitness contribution of each site
  depends on all of the other sites in the sequence and therefore
  altering any site from one to the other value, 0-1, alters the fitness
  contribution of each site to a new random value. Thus the fitness of
  any 1-mutant neighboring sequence is completely random with respect to
  the initial sequence. The landscape is fully random. As was shown in
  Kauffman & Levin (1987), Weinberger (1988), and Macken & Pereison
  (1989), such random landscapes have very many local optima, on
  average, 2N/(N +1).

I did not read the references mentioned in the text but I read the related section in Kaufman's book: Origins of Order: Self-Organization and Selection in Evolution.

In the book he says that the fitness of a genotype can be ordered and given ranks; the probability that a genotype is fitter than its neighbours (local optima) is same as its probability of ranking higher than its N neighbours. So this probability:

$$P_m=\frac{1}{N+1}$$

and if each gene can have only two states lets say on or off then the expected number of optima with respect to one-mutants (i.e. the difference between a gene and its neighbour is just one mutation) would be:

$$M_1=\frac{2^N}{N+1}$$

What I don't understand is the role of K in this expression. This reason should be valid for any number of K (See the quote above). Even in the book this explanation is given in the case where K is maximum i.e. N-1. I can understand that K can affect the ruggedness of the landscape but can anyone explain how K affects the number of optima? (or are they just two separate statements written together, which is confusing me)


texts:
Below is a table of atmospheric composition. Could humans breathe if the average methane content of the atmosphere increased to 1%?

  Table 7a-1: Current Average composition of the atmosphere up to an altitude of 25 km.

Gas Name          Chemical Formula    Percent Volume

Nitrogen          N2                  78.08%
Oxygen            O2                  20.95%
*Water            H2O                 0 to 4%
Argon             Ar                  0.93%
*Carbon Dioxide   CO2                 0.0360%
Neon              Ne                  0.0018%
Helium            He                  0.0005%
*Methane          CH4                 0.00017%
Hydrogen          H2                  0.00005%
*Nitrous Oxide    N2O                 0.00003%
*Ozone            O3                  0.000004%

* variable gases


texts: Understanding F-statistics in population genetics

texts:
I am reading the classic Weir and Cockerham 1984 paper about $F_{ST}$ estimation. At the beginning (first page, right column), they define 3 statistics.

$F$ is the correlation of genes within individuals ("inbreeding")
$\theta$ is the correlation of genes of different individuals in the same population ("coancestry")
$f$ is the correlation of genes within individuals within populations.

They also state that the 3 statistics are related by

$$f = (F-\theta)(1-\theta)$$

I don't quite understand those 3 statistics and especially I don't understand why this relationship holds true. Can you help me with that?


texts: With an excess supply of nutrients, in how much time will the number of algae cells double in full sun?

texts:
I am growing algae in a container in my roof. It gets sunlight for the whole day as there are no clouds nowadays in my area. There is no lack of nutrients as I am constantly adding water mixed with organic waste. The dirt visible in the photos is from manure, which I added as fertilizer.

The water has become green and algae is deposited on top covering almost all of the surface area. There are no threads, so it is not filamentous.

Since there are probably several species of algae in it which I don't know, please tell me the doubling time of most common species.

Also, is there anything I can do to hasten the production of cells?

Below are pictures of the culture, as asked for.


texts: Does one memory cell take part in different memories? For example, both in the visual memory of a bird and a monkey?


texts: Would our body adapt to changes that are not in our DNA?

texts: If a person was to undergo a treatment or surgery at a very young age, that significantly reduced their final height, would the rest of their body adjust to the sudden change? If not; because our arms’ length is very similar to our height, would this give the person arms that weren’t proportional to the rest of their body?


texts:
There are numerous popular articles claiming that the wasp Apocrypta Westwoodi Grandi features an ovipositor tipped with zinc. You can find such an article here. You can watch an impressive video here. Beyond that, I have found information on the genus to be sparse.

Yet my question is, how metallic tissue can be formed. The popular article claims actual zinc was detected. It seems unlikely to me, these creatures consistently find a source of zinc to feed from, so as to deposit zinc in their tissue. Even so, I don't understand how this zinc can be made to deposit at a specific point. The article clarifies:

  With an x-ray detector and the electron microscope, they discovered the presence of zinc. It was only on the tips of the parasitic fig wasp’s ovipositors. Gundiah said, “We see it very consistently only at the tip and not anywhere else.”

I am no biologist, but, to my feeble understanding the only alternative is that the so called zinc is actually synthesised by the body as a protein normally is. Surely no atomic reactions could take place in the wasp! :-p  Even teeth are mostly Ca5(PO4)3 OH, Calcium is found in plenty of our foods. Phosphorus is present in meats. But zinc? I totally don't understand it!


texts: Do women tend to have longer legs and shorter torsos than men?

texts:
I've always heard that women tend to have a greater leg length to torso length ration than men, and I think that my anecdotal observations of pedestrians of both sexes tend to confirm that.

However, now I read that is not the case:

  If they are the same height, she’s a lot “leggier” than he is. It looks as though women really do have long legs and short upper bodies for their height. (We’ll see later this isn’t the case.)

  (...)

  This observation is purely anecdotal, though. There are studies which measure the lengths of men’s and women’s legs, arms, upper bodies, and so on. These measurements show that women have shorter legs and longer torsos than men as a proportion of their heights.

So, at least, says a bicycle designer. And I suppose bicycle designers should know anatomy.

I have a cognitive dissonance here, since again, my eyes watching pedestrians tell me otherwise.

So - what is the truth?


texts: When purifying plasmid DNA after cloning, do you get endogenous plasmid in addition to your vector of interest?

texts: Since bacteria naturally contain plasmids, when you do a cloning experiment and purify the plasmids at the end, do you get plasmid naturally present in that bacteria in addition to your vector? The standard plasmid purification kits (miniprep, maxiprep, etc.) aren't sequence specific in their purification (they just seem to isolate all plasmids in the cells). I would assume you want a constant purity of vector. Otherwise, for example, you could have 2 vials of plasmid at 1 ug/ uL plasmid while one has 0.4 ug/ mL vector and another 0.8 ug/ mL vector which wouldn't be good for reproducibility. Or is it that the bacteria used for cloning are devoid of naturally present plasmids which would fix this issue?


texts: Difference between bacterial chlorophylls

texts:
I understand that bacterial chlorophylls are of the form a, b, c and d.
But i read in my textbook about pigments like bacterio purpurin and bacterio viridin; are they a part of the 4 types of chlorophylls and if not how are they different and what actually are they?


texts: How to learn and memorize animals classification to get an intuition about them?

texts: I would like to have a good intuition on how close is what animal to which one and how large each group is by number of species and population. I was wondering if there is a good website with good demographics and graphs that could help me memorize it because it's really so hard to make up the tree myself from wikipedia pages!


texts: Does gross production (P) and biomass (B) mean the same?

texts:
From fundamentals of ecology, Odum 2005:

  ... autogenic succession usually begins with an unbalanced community metabolism, where gross production, P, is either greater than or less than community respiration, R, and proceeds towards a more balanced condition, where P=R. The rate of biomass production  (B/P ) increases during sucession until a stabilised system is achieved, in which a maximum of biomass (or high information content) and symbiosis between organisms are maintained per unit of available energy flow.

Isn't gross production (P) same as biomass (B) ? I can't tell them apart, given that Biomass is the amount of matter living organisms (usually of a specific trophic level) of a given area at a specific time is made up of.


texts: How can I calculate alpha helix content from molar ellipticity?

texts: How can I calculate the alpha helix content (i.e. percent) in a protein from a given molar ellipticity of 222 nm, without using any software. I have tried the Greenfield-Fasman equation, but the answer doesn't seems to be correct.


texts:
I am studying the pathogenesis of atypia in cardiac cells where the etiology is most commonly irritation or infection and where the precancerous risk depends on the context of diagnosis.
This fact motivates me to think how they can generally arise, from superficial or stromal origin, and how - multifactorial and/or polygenic.
Cardiac tumours are mostly secondary (30x1) in comparison to primary tumours.
I am thinking the sources of these metastases.
I did not understand if benign tumours can be secondary such as myxoma. Therefore, I assume now that myxomas (superficial) and stromal origin can be secondary.
I am mostly interested in superficial changes of the heart in atypia.
It is interesting to notice that benign cardiac tumours originates from the left side of the heart mostly, while the malignant from the right side.
I am thinking the mechanisms here and how the myxoma could be related to the pathogenesis of stromal procesesses in the right part of the heart and the pacemakers' function (AV, SA).
It would be nice to understand the links between myxoma, AV and SA.

Myxoma in the left chamber

Benign.
Origin - superficial mostly in left atrium.
Pathogenesis - polygenetic and/or multifactorial. Mobile mass obstructs blood flow in chambers and cause an increase in pulmonary capillary wedge.
Myxoma (benign tumor of connective tissue containing mucus and gelatinous material) most commonly in left atrium, fossa ovalis in septum.
Imaging DX sound after S2 in ECHO and sometimes ECG; ECHO heterogenic mass.
Differential DX lipomas, rhabdomyomas, teratomas.

Stromal Processes

Malignant diagnostically mostly.
Right side of the heart mostly.
Most commonly haemangiosarcoma (= angiosarcoma).
Pathogenesis. There can be some pathways which are activating atypia such as lymphoma.

Myxoma and Stromal Processes?

I did not understand the link between these two processes.
The former resides mostly in the left side of the heart, while the latter in the right side of the heart.
Their link or their individual links to the pacemaking (SA, AV) would be nice to understand.
I am not sure if we can exclude Purkinje cells, although they reside physically far from the atrias because their low conduction frequency and because the myxoma is about benign tumor of connective tissue which would well reside there, probably even better energetically than in SA/AV.

Sources

DynaMed Plus Lymphoma, sarcoma, ..., visited 25-February 2016.
Orlandi A, Ferlosio A, Angeloni C, et al; Cardiac tumors. Pathologica. 2005 Jun;97(3):115-23.
Patient.co.uk. Visited 30.12.2014. URL: http://www.patient.co.uk/doctor/cardiac-tumours
Cleveland Clinic. Visited 30.12.2014. For Diagnosis. URL: http://my.clevelandclinic.org/services/heart/disorders/cardiac-
tumors
http://www.learningradiology.com/lectures/cardiaclectures/insideoutflash.swf, visited 13.1.2015.
Emilsson, Medscape. The Characterisation and Risk Factors of Ischaemic Heart Disease in Patients With Coeliac Disease.
P. e. a. Whorwell, DEATH FROM ISCHMIC HEART-DISEASE AND MALIGNANCY IN ADULT PATIENTS WITH CLIAC DISEASE. Institute of Cancer Research, Sutton, Surrey, United Kingdom: The Lancet, 1976, volume 308, Issue 7977, p. 113 - 114.

How can you describe the pathogenesis of Cardiac Atypia?


texts: I'm watching a sci fi series and a character who is a biologist claims "even on Earth there are species which is debatable if they should be classified as animals or plants". I looked for examples of this and I couldnt find any. Is this true? Are there species which is debatable if they should be classified as animals or plants?


texts: Can an upper forearm amputee correctly control the Median and Ulnar nerves

texts:
I'm an engineer who is looking to build a robotic hand for people without their upper forearm(from center of forearm in direction of hand), controlled by the Thalmic Myo(an EMG sensor). I am first checking for the idea's viability.

I was wondering if one who does not have their upper forearm can still send the correct nerve impulses for a desired hand movement through their Median and Ulnar nerves?


texts: Will the climate change help the trees to grow?

texts: I've heard several contradictory views and I'm not sure which factor do climatologists count with. Counting with all the effects of the current climate change (including changes of biotopes on places such as Siberia, as well as the higher percent of CO2 in the atmosphere), will the conditions help make better conditions for growing trees (I know the effect on biosphere is usually claimed to be synergic, e.i. for example coral reefs will have less CaCO3 to work with so they will make the global warming appear faster. So please consider just the average effect on trees)


texts: What is the advantage to neurons being asymmetrical?

texts: Does having a central axon and dendrites result in any advantage compared to if the neuron was symmetrical?


texts: The difference between Mast Cells and Basophils

texts:
While reading the Wikipedia article on Mast cells, I came across something that confused me. What is the major difference between a Mast Cell and Basophil?

They both seem to do the same exact function: triggering the inflammatory response. The only difference I can pick out is that Mast Cells are kept resident in a tissue while basophils move around.

Is this the only major difference?


texts: Using PGAL10 promoter to overexpress specific yeast genes: How to?

texts:
I was reading a poster about expression boosting for Artemesinin production in yeast and it had this line:

  PGAL1
  and PGAL10 have been used for the
  overexpression of all genes from the mevalonate
  pathway.

What exactly does this mean? I suppose these are promotors? http://www.yeastgenome.org/locus/S000000224/overview

But how exactly does one use them during cloning to boost expression?

Say that you wanted to over-express ERG10, the gene coding for the first enzyme in the MVA pathway. How does one go about using PGAL10 to do this during the cloning steps?

Link to the poster: https://ddd.uab.cat/pub/tfg/2014/119349/TFG_narcisferrerledo.pdf


texts: Calculating the canopy size (crown) of a newly planted tree at a future date

texts:
Assuming that one knows the maximum area of the canopy and the age of the tree when it achieves this. And given an initial canopy size from the nursery. How would I calculate the canopy size at a future date.

Whilst certain aspects of the growth are obviously variable... how would I model the growth over the year(s)? I'm looking for a simple formula that I could give to a user in a planning department to develop adaptive lighting solutions for trees in streets.


texts: Is there a comprehensive list of human circadian-like processes, hormones or gene expressions?

texts:
I'm reading this article onblood sugar and circadian rhythms and the following question popped into my head: a lot of articles mention various diurnal or circadian rhythmicity of biological processes. Is there a "master" list of hormones, gene expressions and other processes that the modern science recognizes as "circadian"?

In other words, is there something that can give reader a clear picture of what's happening at a certain (biological)time for a human and is expected to happen tomorrow at similar time?

It would be great to take a look at such list and see what are the major processes that recur on a time-sensitive basis in humans.


texts: I generally know how antibodies work by binding to antigens, but what is the specific purpose to being Y-shaped, as opposed to any other shape? Does this aid their function? Thank you.


texts: Mitochondrial donation - why is the second woman needed?

texts:
Mitochondrial donation or the latest case procedure describes that an egg of the second woman is used as a host with healthy mtDNA.

Being a complete layman I'm interested in whether it is a restriction of the method or some fundamental requirement. Is it in principle possible to replace broken mtDNAs of a mother with mtDNAs of a father, which are mtDNAs of his mother?


texts: From a purely biological perspective, how does an optimal human diet look?

texts:
There is hardly any subject as contested in the media as what humans should eat. Usually, such discussions are devoid of actual scientific reasoning, though they all claim to be backed by scientific studies (typically without naming those studies). The colorful spectrum of suggestions ranges from eating only bananas, to avoiding "refined" sugars and red meats, to avoiding meat altogether, to eating as much meat as possible etc. Clearly, many of them are completely contradictory.

From a purely biological, evidence-based perspective, how does an optimal human diet look? In particular, I'm interested in the following questions:

Is there a single diet that can be recommended to all humans, regardless of lifestyle, which only needs to be scaled in quantity (i.e. more physically active people should eat more of it) but not content?
Excluding diseases, does the optimal diet for an individual depend not only on their lifestyle but also on their genetic makeup?
Knowing nothing about their genetic makeup and living an average industrialized-society lifestyle, what is the best guess for what a human should eat?

Answers should be backed by solid reasoning and (ideally) references to verified (meta-)studies published in actual scientific journals supporting the claim. It seems strange to have to ask such a question, as one might expect it to have been answered thousands of times already, and of course it has, but the answers vary so wildly that I suspect I'm being fed hogwash mostly.


texts: Which animals can see (or feel) the Moon’s infrared radiation?

texts:
The luminosity (bolometric) of the Moon in infrared is several times greater that its luminosity in visible light. Moreover, it may be rather possible for the Moon to be obscured by some fog or haze which lets only the infrared radiation through. It is known that some snakes have “pit organs”, but the decent Moon’s infrared flux can, probably, be detected by something more crude. Can any other animal (than snakes) take benefit from its sensitivity to medium-wave infrared to see (feel) the Moon?

It is notoriously hard to find reliable information on the Moon’s infrared flux in Internet, although its density at Earth’s surface should be several µW/cm² (or tens mW/m²). My estimate is about 30 to 40 milliwatts per square metre under favorable conditions, which is probably not high enough to be detected with every pit organ (crotaline snakes are claimed to have threshold at about 107 mW/m²). Research on Agkistrodon contortrix (see graphs) states that 60 mW/m² and as little as 15 mW/m² (albeit not in infrared) produce a nerve response in receptors. On the other hand, pit organs are optimized for such localized and agile sources as small animals; some other sensory system might be more appropriate for nearly stationary sources producing more incident energy (heat).


texts: Tissue identification in vascular bundle sections

texts: I always have trouble differentiating the tissues in a vascular bundle. I specially cannot properly identify the vascular cambium and phloem. I know xylem vessel elements are large cells with thicker cell walls, that makes them clearly different from other cells in the vascular bundle. However, the difference between vascular cambium cells and phloem cells is unclear. I would like to know how I can identify these tissues accurately. A photomicrograph with marked borders would be appreciated along with explanation of cell appearance in these tissues. Thank you a lot.


texts: What is this fungus that is growing on my plant, and is it dangerous?

texts:
This fungus is growing on a plant in my front yard and I do not know if it is dangerous for my health or for the plants health. Can you please identify it? I live in Dominican Republic, a tropical island in the Caribbean Sea.

Here are some photos from my yard:


texts: What difference do trans and cis configurations of amide groups bring to the polypeptide chain?

texts:
Hi I was just wondering whether there would be any difference to the structure of the polypeptide chain, or any changes to a proteins characteristics, if it has more amide groups with a cis or trans configuration.

Apparently the trans configuration is more stable, so more amino acids with a trans configuration can be found within a polypeptide chain. Does this pose any significant characteristic to a protein, and if so what is this characteristic?


texts: Using DTNP to find free thiol groups on a protein

texts:
I've been tasked with using DTNB to find the number of thiol groups on a molecule of Bovine Serum albumin (BSA).

After measuring the absorbance, finding the concentration of TNB and calculating the concentration of the BSA, I've come out with a result of around 0.4 free thiol groups per molecule of BSA, which seems unlikely! There is either a free group or there isn't!

Yet, the implication from the demonstrator is that is is the correct result!

How can this be? Is it possible to get a value of less than one in an experiment like this?


texts: Two-fold cost of sex and r/K selection theory

texts:
This article cites a bunch of articles (I haven't been through them) that the effect of the two-fold cost of sex is "reduced" in stable environment or in K-selected environment. It says:

  [..] the infamous ‘two-fold’ cost may be reduced or, perhaps more accurately, more easily balanced in K-selected species. The ‘cost of males’ is with respect to reproduction. Abugov (1985) argued from life history theory principles that the two-fold cost of sex might be easier to pay with K-selection. The two-fold fecundity advantage of asexual reproduction is always a two-fold fitness advantage, regardless of whether it is in a K- or r-selected environment. However, a survival advantage is worth more under K-selection than under r-selection. Consequently, it is easier to balance the two-fold cost under K-selection if sexually derived genotypes have a survival advantage.

I think that k-selection, k-selected environment and stable environment describe (more or less) the same kind of environment. Let me know if this sounds wrong to you. Here is wiki for r/K selection theory

From the same article K-selection is defined as:

  K-selection might favour slower development, greater competitive ability, delayed reproduction, higher survival rates, lower resource thresholds, leading to ‘efficiency’ (rather than productivity) and constant population sizes at or near carrying capacity of the environment.

It sounds really strange to me. Can you please help me to understand why the two-fold cost of sex is lower in stable environment than in unstable environment?.


texts:
I have found the information: `In the absence of lactose, the lac repressor binds to the operator sequence on DNA and bends the DNA by 40 degrees. This blocks access of T7 RNA polymerase to the promoter site and thus prevents leaky transcription of your gene before induction.'
I am confuse about one fact.

When I add IPTG,  the lac repressor protein (from E.coli chromosome) can no longer bind the operator and native E. coli RNA polymerase begins transcribing, the T7 RNA polymerase gene engineered into its chromosome.

So if there is IPTG and lac repressor protein (from E.coli chromosome) can no longer bind the operator standing in front of the T7 RNA polymerase gene, why lac repressor protein still can bind to operator standing in front of the target gene from plasmid?


texts:
Viroids are described as short circular ssRNA with no protein coating.
Are there any analogous infectious particles that contain DNA instead of RNA?
If DNA viroids do not exist, is there an obvious reason for this?


texts: Can combining C3, C4 and CAM plants in a greenhouse/vertical farm increase the efficiency of plant production?

texts:
I am reading a little about different types of photosynthetic systems in plants because I want to learn something about plant production in greenhouses/vertical farms (I have no experience in this field).

Can combining C3, C4 and CAM plants in a certain way have positive effects on its production value? So for example C3 and CAM plants are planted in the same area close to each other and they have in some way a positive effect on each other because they use different methods for assimilating energy and thus one can bring down the energy use in the greenhouse/vertical farm.

This is an interesting article.
https://www.khanacademy.org/science/biology/photosynthesis-in-plants/photorespiration--c3-c4-cam-plants/a/c3-c4-and-cam-plants-agriculture

It explains the different aspects of the different plants very well. Maybe the best answer to my question is a simple: NO, because all 3 types of plants grow naturally in different environments, but I can imagine a system were energy that is gained from their photosynthesis at different times of the day can be shared among the plants and thus an increased energy efficiency can be reached. Maybe someone can


texts:
I have an ant nest in a jar. Whenever I want to observe them, I have to remove the cover and therefore put them in light - that scares them. They also can see shadow cast by myself.

I often throw in some food when I'm uncovering the jar.

I was curious if ants will ever remember that I'm not dangerous and that light means food.

If not, are there other things they can learn? Do they teach each other to hunt? Can queen learn things ants can not (queen has shown a lot of individuality compared to ants)?


texts: What is the purpose of back-crossing mice for multiple generations?

texts: Occasionally I will come across articles that refer to back-crossing mice of one strain onto the background other another strain (e.g., C57Bl6). They do not explicitly state the purpose for doing so, but I can infer that the change of strain is to relate their findings to what is already known using the new strain (e.g., C57Bl6). Usually the back-crosses are performed for 5-10 generations. Is this to try to remove (epi)genetic variation from the original strain relative to the new strain, or is it more about normalizing expression of a particular allelic variant (e.g., knocking-in a transgene)?


texts: How to isolate two plasmids from E. Coli strand?

texts:
I have an E. coli cell line I use to express a protein using a two plasmid system. One confers AmpR and one KanR.

For mutagenesis I would like to separate the plasmids to increase efficiency of the mutagenic PCR reaction. I was able to cure the cells of the KanR plasmid because it is low copy whereas the AmpR is high copy so I could easily grow the cells in ampicillin only and I ended up with only the AmpR plasmid. However I was unable to do the same to isolate the KanR plasmid.

My next idea was to run the plasmids through a gel and do an extraction. Since I didn't do a digest it was very hard to differentiate the bands and I ended up getting a negligible yield. I believe the plasmids were simply smeared through the gel due to tertiary structures.

My final hope is to perform a digest on the plasmids using a restriction enzyme that cuts each plasmid once. My concern is that I will not be able to get the stoichiometry correct due to the plasmids both being simulatenously present in vastly different concentrations.

Does anyone have any tips on how else I could isolate the plasmids? Or maybe does anyone have experience running a digest on plasmids with unknown concentrations? I really need help doing this. The mutagenesis project has been going on for months and this isn't even a molecular biology lab... so it's detracting time from main research goals!


texts: Which algorithm to find the evolutionary relation of 5 sequences?

texts:
After Multiple Sequence Alignment (MSA), data sets are produced on which models of evolution are used. I've seen in books that if there is strong similarity between the sequences then Maximum Parsimony (MP) is used, if that is low then Minimum evolution, and if there is very weak similarity then Distance based Method is used. However, all of these have their own cons.
Since character based methods are more reliable (as book), Can these methods be used even when there is low sequence similarity?
Are there any algorithm that builds the precise tree model without considering similarity of the sequences?


texts: On my one plants, this green worm is all over it, with white and yellow cocoons on the Leaves.


texts: Does anybody know what this shark is eating?

texts: Looking for a species identification on the orange fish that the shark is eating. The shark is a goblin shark filmed as part of the BBC's 'Legends of the Deep: Deep Sea Sharks'.


texts:
There is an attribute defined as DP (Total Depth) in VCF file format. For example, http://www.1000genomes.org/node/101.

What does this attribute mean? If I get a value of like DP=128. How can be that be interpreted?


texts:
I was reading my textbook and it says that breathing involves inhaling and exhaling but it doesn't say whether they happen simultaneously or sequentially.

Also is my overall understanding of breathing competent?  When you breathe in air, air ends up in the lungs passing through the nasal passages (heated, moistened, cleaned) through the pharynx, through the glottis through the larynx, through the trachea and into the bronchi and then into the bronchioles. Once air gets to the lungs, Is their already carbon dioxide in the lungs waiting to be expelled or will carbon dioxide diffuse into the alveoli and into the lungs when oxygen diffuses into the blood. And after this the carbon dioxide will be expelled?


texts: Does an FAD:FADH2 ratio exist in the cytoplasm? (similar to NAD+:NADH ratio?)

texts: I have learned about a lot of enzymes/proteins which are covalently bound to FAD, and use this as an oxidising agent. In vivo, FAD is (almost) always protein bound (very low concentrations of free FMN/FAD [source]). Would an "FAD:FADH2 ratio" make sense (if it isn't free)? I know that the NAD+:NADH ratios in the mitochondria and in the cytoplasm are important, same for NADP+:NADPH (e.g. low NADP+:NADPH ratio in cytoplasm makes the reducing environment for fatty acid synthesis). Is it the same for FAD?


texts:
I am trying to download the program FDist2 (Beaumont and Nichols 1996) for Mac but for some reason it appears that all the links I find are broken.

It appears that the program Lositan is an faster implementation of FDist2 but in my understanding Lositan works only through a GUI and not via the command line (and given the number of analyses I want to perform I need to be able to run this algorithm from the command line).


texts: What are the (statistically) normal pH levels in the most-outer part of human sexual organs?

texts:
What are the (statistically) normal pH values of the outer skin/epidermis of human sex organs (groin/crotch) in the male and female? e.g male testes, female vulva, male glans, the enveloping epiderm, etc. I was trying to find information to no avail.

Edit:

I googled different terms, like anatomical ph index map of the body, and couldn’t find any ph data about specific anatomical structures.

When I googled, I read through reiterations that the body has neutral ph mostly. Again, nothing anatomically specific.

Due to the ‘unique’ per structure microbiome, it does make sense to foresee a different ph, more to the acidic scale.


texts: Are there any enzymes synthesised by humans that specifically catalyse the hydrolysis of non-cyclic Imides?

texts: Imides or dicarbonyl amides are an interesting class of compounds that includes the pharmaceuticals thalidomide, aniracetam and a few other drugs. These compounds, however, are cyclic and I'm wondering whether there's an enzyme found in the human body that specifically catalyses the degradation of non-cyclic imides. I'm thinking that fatty acid amide hydrolase (FAAH) may catalyse the hydrolysis of non-cyclic imides at least as a minor metabolic pathway.


texts: Can anyone identify this garden orb weaver spider?

texts: Found in low foliage in Harare Zimbabwe. Argiope flavipalpis or A.levi


texts: Parallel Autonomic regulation of Cough and Runny Nose

texts:
I describe here the serous inflammation of runny nose.
Cough is mediated by Cough center.

I think Runny nose is also controlled by the autonomic nervous system and probably by some reflex.

Assume you have mild runny nose under Montelukast medication.
You have irritated cough (coughing so much you cannot sleep).
You stop the cough by codeine before sleeping.
You sleep at 30 degree angle.
Sometimes, you also feel that the runny nose stops i.e. complete relieve of runny nose in both nostrils and whole nose for about 30 seconds to a minute - perfectly clear nose and no serous inflammation - no symptoms of imflammation in the nose.

Then, it (serous inflammation) starts again - not like mucose running back - but the feeling of uneasiness in the whole nose starts again - then mucose can also continue to migrate from one nostril to another.
What is causing this kind of behaviour i.e complete relieve of of runny nose for about 30 seconds?
What is causing the stopping of serous inflammation in the nose?

I think the Runny nose can also be controlled by medulla oblongata because Codeine is blocking the cough center there.

I tried to achieve this behaviour by stimulating by lymphatic system in regulating breathing by abdominal muscles - lymphatic drainage massage - breathing inside with abdomen (not with thorax) and deeply exhale with abdomen).
At that time, I did not hear any creaky sounds in my throat.
After trying to stop the serous inflammation again, I heard them without managing to stop serous inflammation in both nostrils at the same time.

How is the control of Cough and Runny nose regulated by the autonomic nervous system?
Probably, some parallelism there.

Processes going on regulating Cough and Runny nose

reflex from medulla oblongata
sympaticus and parasympaticus (not sure about these)
possible parallelism of irritated cough and runny nose control


texts: Identify this gray spider with distinctive white mark

texts: I was out back in the garden tonight and found an extremely long strand of web running about 10 ft. At the end was a kind of spider I’ve never seen before. It’s about a .75-1 inch, fat body, with a distinctive white mark on its back. It was very docile while I took the pic. I’m in Austin, TX and this was night time. Any clues?


texts:
I live in Pittsburgh PA, the eclipse on Monday August 21 was only about 80% coverage here.  It was notably darker, but less dark then an overcast day. The night of August 21, had a low temp of about 70F.  On my daily walk the following day (Aug 22) there was notable amount of fallen leaves from the trees along my daily walk (mostly maple), by this morning (Wednesday Aug 23) the leaf fall has increased such that the grounds crews are out cleaning the leaves.

Did the eclipse make the leaves fall?


texts: At what temporal scales do forest structures change?

texts:
At which time scales do forest stand characteristics (i.e. stand density, species composition, & diameter distributions) change in a temperate European forest which is not managed?

Ideally, I'd like to conclude if a certain quantitative description (based on the variables I've mentioned above) of a forest stand is valid for e.g. 10 years or even 20 years.

A peer-reviewed reference would be ideal.


texts: How does a metronome help in controlling breathing rate?

texts: I'm new to the Bio/Medical field so kindly bear with me. I am doing studies on volunteers to formulate algorithms for evaluating Respiration rate from ECG and accelerometer data. I learned about this device when I read this paper. I'd like to know how exactly the metronome device helps in controlling the breathing rate, how is it to be used and precautions to be taken?


texts: Can a regulator genes be more highly expressed when it has more places to bind?

texts:
I am doing some research on small cell lung cancer and, from what I have found, many tumors show high levels of ASCL1, which is a regulator for neuroendocrine cell differentiation. However, no papers propose a mechanism for the higher levels of ASCL1. Instead, many of them refer to ASCL1 target genes with "amplified" enhancers and propose that ASCL1 may bind more frequently to these enhancer regions.

In general, if there are more places for the regulator to bind on an enhancer, is it possible that this is sufficient for the regulator to be more highly expressed?


texts: Is Bramble (blackberry bush) carnivorous?

texts:
I have come across this video which put forth the hypothesis that bramble actually qualifies as a carnivorous plant.  The observations that have led to the hypothesis are:
1. Sheep getting caught frequently in bramble
2. Sheep will die  without human intervention.
3. The rotting corpse of the sheep will nourish the plant for many days.
4. The thorns angle inward -- supposedly evidence for adaptation that helps trap prey animal.

I agree , on the surface it looks plain silly but that is a reflexive reaction, not an argument.  Is this a plausible hypothesis? If not , please give reasons.


texts: Why do we wake up after 6-8 hours of sleep ? Why don't we sleep for lets say 20-30 hours ? What mechanism is it that controls when to wake us up and how does it determine the moment that we should wake up ?


texts:
Calico cats are cats that have 3 fur colors and are always female or males two X chromosomes.
I've seen many cats that will have 2 fur colors (one of them is usually white) and another, third, color which is a darker shade of one of the other colors. As exampled in the pictures below (taken from the internet). Are those considered Calico cats?

(source: mirror.co.uk)


texts: What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?

texts:
From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011)

The metabolic profile reported here is unique to GTPCH deficiency or a defect in the GTP activator protein. While there is no known demonstrated defect in this protein, it would cause similar functional deficiency. Other enzymatic defects in the pterin synthetic pathway present with very different metabolic profiles.

I googled but could not find a particular "activator protein" that interacts with GTP cyclohydrolase I. Is this one of the GTPase-activating proteins? They must be numerous, and I haven't found one that was shown to activate GTP cyclohydrolase I.
At the same time, the authors use the definite article, as if this protein is known. I'm intrigued.
I found this paper, in which GTP cyclohydrolase I is said to interact with Rho-GTPase-activating protein 7 (also known as DLC1), but the paper does not say that this protein is an "activator", they merely list it as part of the putative transcriptome of GTP cyclohydrolase I.
Further, in the quote the authors say that "there is no known defect in this protein", but the OMIM page for DLC1 says that a defect was known from at least 2000, although it is related to cancer, not to the BH4 pathway.


texts: Thermodynamic noise determining gene expression?

texts: I'm wondering if and how thermal noise may randomly determine gene expression? Looking for cellular and 'transcriptional noise' one finds hints to diffusive cellular dynamics which rely on collisions between reactants (for example, RNA polymerase and DNA), see wiki. But the question is if there is any investigation that tried to assess also if and how also a thermodynamic link can be established, namely if the stochastic Brownian motion of molecules may also play a role in expressing randomly one or another patway? Any interesting papers to suggest?


texts: Does starch need to be cooked for human digestion ? Is the answer different for different starches; potato , wheat, corn, etc ?


texts:
Does knowing the sex of each of a couple’s first N children have any marginal value in predicting the sex of child N+1? By “marginal” I mean predictive power beyond other known effects, e.g., the race of the parents, the mother’s weight, season of birth (list from this presentation by Andrew Gelman).

I know that many claims that some variable can predict a child have been accused of resting on shaky statistics (see the presentation linked to above). But the sex of preceding children seems like it could be a strong predictor.

UPDATE: answering fileunderwater's question

  Can you expand on why (by what mechanisms) you think that it could be a strong predictor? Male sex-chromosome bias in sperm?

Yes, sex-chromosome bias was my first thought. I almost focused my question specifically on that but the fact that I saw maternal weight listed as a predictor in the Gelman presentation made me think there might be other relevant factors that I wouldn't think of. So I broadened the scope of the question.


texts:
When collagen is digested is it broken up into usable components that the body can use to produce its own collagen?

What evidence is there that supplementing with collagen type I & II etc.. can help connective tissue disorders?

What evidence is there that supplementing with collagen from animal products is not useful?


texts: Do antigens protrude through the capsule/slime layer in prokaryotic organisms where these features are present?

texts:
In prokaryotic organisms that have a slime layer or capsule, do intrinsic/extrinsic proteins and other molecules that could be used as antigens protrude through the capsule?

I assume that they must in order to maintain their function for the cell, yet am struggling to suggest another way in which the presence of a capsule/slime layer could serve as a defence against phagocytosis?  Unless the slime layer directly resists lysosomal activity after the pathogen has been recognised and engulfed?

On a related note, could the flagella of an organism (which must protrude through the capsule as above) trigger an immune response on its own?


texts: How do porcupines keep from pricking each other while mating? It seems like they would constantly be scratching each other.


texts: Why to use transgenic mice in ALS models?

texts:
In ALS mice model with mutant SOD1 - there are use of transgenic mice, with insert of human mutant SOD1.

Why is that? Why not to mutate directly mice SOD1 ?

In transgenic mice, after few generations these human gene thrown out and not present any more.. Why thrown out? Is the second question.

Looking for an answer for a while. Thanks a lot.


texts: Expected $\mu$ and $\sigma^2$ for a phenotypic trait, given heritability h and known parental phenotypic measures?

texts:
Say a measurable phenotypic trait has mean $\mu =0$, variance $\sigma^2 = 1$, and heritability $h$, meaning that h*100% of the variation in the population is caused by genetic variation and (1-h)*100% is caused by environmental factors whether shared or unshared.

We define "standard environment" as an environment in which the contribution made by each environmental feature, whether shared and unshared, is at the population mean for the contribution made by that feature.

Clearly if we take individuals in the population at random their expected mean measurement is 0 and their expected standard deviation is 1.

But say we have two parents whose phenotypic measurements for the trait are respectively $p_1$ and $p_2$. Then what will the expected mean and standard deviation for their offspring be if their offspring's environment is standard? I am interested in the general case, but even an answer only for the case $p_1 = p_2$ would be helpful. I would also be interested to know whether the answer might reasonably be expected to vary according to whether the parental phenotypic measurements are or are not significantly different from what would be expected from their own genes.

From a "pure mathematical" point of view, the answer is "we can't tell", because for example the expected mean measurement might be 0 for all individuals except those who have both parents with genes determining an expected measurement greater than 3 or smaller than -3. So please make (and state if possible) whatever assumptions seem reasonable.


texts: Has an artificial symbiotic relationship ever been created?

texts: Have 2 organisms ever been introduced to create a symbiotic relationship that doesn't occur in their natural environment?


texts: How come our thyroid glands don't suffer awful mutations (or do they)?

texts:
I was listening to a lecture by my Biology professor and he said that the thyroid gland contains radioactive Iodine which can break down and create reactive Oxygen species (because ionizing radiation from the Iodine interacts with water in the human body).

So, shouldn't the thyroid gland suffer awful double-stranded chromosomal breaks constantly? Shouldn't we be suffering mutations in the thyroid gland all the time?

Thanks!!!


texts: What is "irrational" drug/molecule design?

texts:
Both the papers "Directed evolution: the 'rational' basis for 'irrational' design" by Tobin et al. and "Rational and 'Irrational' Design of Proteins and Their Use in Biotechnology" by Nixon et al. reference the concept of "irrational" drug design, but never formally define it in their text.
Is there a formal definition of what makes a drug design process "irrational"? What is the meaning of the term "irrational" in this context?

Nixon AE, Firestine SM. Rational and "irrational" design of proteins and their use in biotechnology. IUBMB Life. 2000;49(3):181-187.
Tobin MB, Gustafsson C, Huisman GW. Directed evolution: the 'rational' basis for 'irrational' design. Curr Opin Struct Biol. 2000;10(4):421-427.


texts: What is the expected amount of DNA shared by first cousins and the people between them in a family tree?

texts: What is the expected amount of DNA that is shared by all of the people between first cousins, including the first cousins, in a family tree?


texts:
I am reading this paper, which shows that a Human Endogenous Retrovirus (HERV) K provirus is present at the orthologous position of gorilla and chimpanzee genomes but absent in the human genome.

If it's not present in the human genome, why is it still called a HERV? Should it not just be an endogenous retrovirus?

(I am not a biology student, so I might not have understood the idea of a provirus/retrovirus entirely.)


texts:
Does a woman's G-spot actually exist? Are there any research studies?

Links:

G-spot (Gräfenberg spot) at Wikipedia
U.S. gynaecologist says he has found the G-spot


texts: How do scientists transfer the specific DNA in Optogenetics?

texts:
I'm a bit new to genetic modification and I was wondering in Optogenetics (a field in neuroscience) how the scientists transfered the desired DNA strand from the light-sensitive ion channel opening cell (I forgot the name) to the specific neuron that will grow these cells sensitive to green light and trigger an action potential in the neuron? (open the neuron ion channels)

I don't understand how scientists know exactly which strand of DNA to cut from the source and where to put it in the target. I mean, if scientists can do this, why not cut the legs growing part of my DNA and insert in a butterfly and boom, you have a butterfly with legs, no?


texts: During human ageing, which immune cell sub-types are most affected?

texts:
It is now well established that human ageing is accompanied by an increase in systemic, low-grade (chronic) inflammation, sometimes termed inflammaging (Franceschi, 2007). This is in part due to more global changes to the body, including an increased number of senescent cells, but of interest to me currently is the change in the composition of the circulating immune cell sub-types that may either cause, or be affected by, the increase in 'global' inflammation.

I imagine the answer to this question is a study that samples individuals of different ages and separates the various leukocyte fractions. Using this it could be determined which immune sub-types are over-/under-represented in the aged, and at what age the changes occur (e.g. monocyte numbers may decrease from age 40, whereas neutrophil numbers may increase...). I have done some fairly extensive research, but have been unable to find a study that has done this - however it seems likely that it has been performed. Thanks.


texts: Do carrier proteins constantly open and close or do they only work when a substance binds to them?

texts:
What causes carrier proteins to change shape ?
Do they need energy to change shape? If that is true, how are they involved in Facilitated diffusion ?
By changing shape, do we always mean opens from one side and closes from another ? (they all work by changing shape right ?)
once they transport a molecule from inside to outside, do they return to their original shape instantly or do they need to transport a substance from inside to the outside to return to their original shape ?
and finally, are all co-transport proteins carrier proteins ?


texts: How do penicillin resistant bacteria grow slower in the presence of penicillin?

texts:
We put 2 flasks inoculated with Bacillus cereus in 37⁰C: one with 100μg/ml penicillin +  50μg/ml chloramphenicol and the other without penicillin. We found that the OD is higher in the one without the penicillin. These strains are supposedly penicillin resistant as verified by growing them in a test-tube containing penicillin (5mg/ml) at 30⁰C. It contradicts my hypothesis that they should have the same growth rate because of the $\beta$-lactamase secretion that would destroy the penicillin. I can't find any explanation in the web.
help me


texts: Strand representation in the DNA version of the Genetic Code

texts: A Wikipedia entry entitled DNA Codon Table states that the codons presented in the table are on the ‘sense strand of the DNA’. But what is the purpose of this, if the sense strand doesn’t code for anything? It stated that it is used a lot in computational biology, what exactly is the use of it in that field?


texts:
I've been looking for the average width (at widest point) of the average American male body but couldn't find it anywhere so far.

When I say "widest point", I mean that if you draw a rectangle (that gives X for width and Y for height) around the whole body, all of it should fit inside the rectangle, whether the shoulders are wider than the hips or vice-versa. I'm looking for the average value of X (arms against body).

If the hips are the widest point inside the rectangle, the width should contain the width of the hands that are against them.

Do you have (or know where I can find) that information?


texts:
I photographed a dragonfly but can't really identify the species using http://www.libellen.tv/. Are there any other resources I could use?

The pictures were taken in early June, around 11:00 next to a lake at 1700 meters above sea level. The pictures were taken in the Alps in Austria.


texts: Does sleep in humans re-structure based on the expected sleep time?

texts:
I've read about anecdotal evidence that human brain has a fairly good internal clock that can be used to judge the amount of time that has passed. I'm wandering if there are any mechanisms in the human brain by which the brain can make adjustments to biological processes, based on the expectation of getting so many hours of sleep in the upcoming night. In this case, an alarm clock is not used.

For example, a person typically sleeps for 8 hours a night. On one day, that person realizes that he/she will sleep for only 5 hours that night, has there been any studies that demonstrate that the person's sleep would be "different" from the regular sleep? Will the person's sleep on that night be just a "cut short" version of regular sleep, or will the sleep be restructured to accomodate sleep time restriction?

For example a person's normal sleep cycle is 90 minutes long, so in 8 hours there would be about 5 complete cycles. Would there be any observable adjustments to the sleep cycle length or the amount of deep/REM sleep within the cycle, if a person expects to sleep only 5-6 hours or 10+ hours?

Thank you for your input!


texts: Re-stain slice using a different secondary antibody?

texts:
I stained a free-floating ~300uM brian slice using 4 different 1º antibodies (rabbit, chick, mouse, rat).

For the mouse primary, I mistakenly used an Alexa-350 secondary, when I should have used 594.

The microscope we have in lab cannot detect the 350 fluorophore, so I'm wondering if I can re-stain the slice with the anti-mouse 594 secondary.

Thanks for your advice !

[cross-posted in reddit/labrats]


texts: Entropy increase or decrease in an reaction

texts:
My question is how would you tell if the product of an reaction has more or less entropy than the reactants?

For example, in glycolysis, when glyceraldehyde-3-phosphate becomes 1-3 bisphosphoglycerate, BPG has less free energy and more entropy than G3P. Anyone able to give me a rundown as to how you would know? Thanks in advance.


texts: how long would oxidation of ammonia solution to nitrates take?

texts:
A hot topic among amateur chemists is making nitric acid from ammonia. While not as useful, im interested in making nitrate salts from ammonia as well.
A simple idea is to just infect ammonia solution with soil bacteria and add some fresh grass as source of other necessary nutrients for bacteria. If kept at optimal temperature, how long can i except the process of forming ammonium nitrate to take?


texts: Extinction of species with extant descendants

texts:
From what I've seen, species such as Homo heidelbergensis which have extant descendants are classified as extinct, which makes sense as far as it goes.

However, given that species exhibit a continuum of development throughout time, does that mean that for any given extant species and their ancestors there is an "extinction line" which moves gradually forward as small changes in the "current" gene pool render the ancestors from a given time no longer capable of producing fertile offspring with the "current" species and thus shunts them out of the current species and into the extinct species immediately proceeding it?

Additionally, does that mean that there might have existed a species (say, for argument's sake, H. heidelbergensis) with a genetic distribution such that some of them would be capable of producing fertile offspring with the "current" descendant species (in this example, H. sapiens) and some of them not, thus rendering half of the species effectively extinct and the other half not (at least, not yet)?


texts:
If cut a cut down the middle, both halves are symmetrical.

Why is it that most animals are symmetrical?

Is there an energetic reason for this? (as in, it is energetically favorable to create the same thing twice instead of making something new)


texts: Are there any drawbacks to having immutable DNA during lifetime?

texts: Imagine that there is a way to prevent cell DNA from being changed once zygote has been formed. Would this have any negative effects on the target organism? Does DNA change during the lifetime as part of normal operation, or DNA changes are always due to mutations or malfunction?


texts: I'm generating random molecules I would like to know if they are able to pass through the cell membrane. Are there any ways (preferably computational) to predict cellular uptake of an organic molecule which is about 55 atoms?


texts: Has the protein composition (with identification) in honey and other honeybee byproducts been studied?

texts:
I am interested in studying honey and other honeybee byproducts.  I have not been able to find sequence or structure records for any of the contents of honey.

In particular, I want to study the protein sequence and structure and the amino acid compositions within honey.

Has any of this data been produced and published in any databases or research papers?


texts: Is Infra Red light safe to use on your scalp?

texts:
I own an Anodyne Infrared therapy device which I use to treat ligament/tendon/muscular pains and it works nicely.

I see other infrared products used to combat hair loss (e.g. https://www.amazon.com/dp/B01B29PCUU), but I don't know the nuances of different infrared devices. Is it safe to use the device intended for the above uses on my scalp? I'd rather not purchase a separate infrared device for my scalp if I own the necessary technology already.


texts: Is arachnophobia connected to lower immunity against spider toxins?

texts: Are arachnophobics more subceptible to toxical effects coming from spider toxins?


texts: ABO allele frequencies: Why use the EM algorithm?

texts:
In textbooks and lecture notes and slides posted online, determining allele frequencies using blood type information (ABO), under the assumption of Hardy-Weinberg equilibrium, is accomplished using the EM algorithm. It seems to me, though, that this problem can be solved using basic algebra: If $a$, $b$, $o$ are the frequencies of the $A$, $B$, and $O$ alleles, respectively, and $p_A$, $p_B$, and $p_O$ are the proportions of the population in question displaying blood types $A$, $B$, and $O$, then

$$
p_A = a^2 + 2ao,\quad p_B = b^2 + 2bo,\quad\text{and}\quad p_O = o^2.
$$

Inverting the third equation gives $o$ in terms of $p_O$:

$$
o = \sqrt{p_O}.
$$

Plugging that into the first equation and rearranging, we get the quadratic equation.

$$
a^2 + 2\sqrt{p_O}a - p_A = 0
$$

Solving using the quadratic formula and throwing away the negative solution, we get

$$
a = \sqrt{p_O + p_A} - \sqrt{p_O}.
$$

Symmetrically,

$$
b = \sqrt{p_O + p_B} - \sqrt{p_O}.
$$

Thus, we've solved for the allele frequencies $a$, $b$, and $o$ with only basic algebra.

In the standard textbook case in which $p_A = fa = 186/521$, $p_B = 38/521$, and $p_O = 284/521$, this gives

$$
a \approx 0.21,\quad  b\approx0.05, \quad\text{and}\quad o\approx0.74,
$$

which is close to what you get after a few iterations of the EM algorithm.

Question (finally): If the above calculation is correct (if not, please let me know!), what is a "simplest" non-synthetic (real data, from the literature) example of an allele frequency computation from phenotype data that actually requires a sophisticated technique like the EM algorithm?


texts: Is there any disease in common between human and insects?

texts:
I am not asking about disease transferred by insects.

I am wondering is there any disease that commonly make both human and insects sick?


texts: In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

texts:
I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis.

I also understand cloning can be a bottleneck in Sanger sequencing - and partly prompted the development of NGS methods.

But doesn't PCR do just that, make multiple copies?

What am I missing?


texts:
Recently, kinesiology tape has become popular, especially in CrossFit. I have also noted its' use in the NFL, and I want to say Tennis as well.

What beneficial effects does this tape offer our bodies (muscles, joints)?  Is there any definitive proof of its' benefits? Can there be negative effects? I don't foresee any, but if it does something to your body, I could see a possibility of prolonged use causing some kind of alternate effects.


texts: Sleep deprivation relation to growth rate and mental health in adolescence

texts: Do sleep deprivation and its timing affect growth rate and mental health in adolescents? If so how much sleep is enough for teenagers?


texts: How do you turn a minimal CIF description into a complete one?

texts:
I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition.  This page provides a batch script that I may be able to tease apart to suit my needs, but I thought there was a way to do this from within the CCP4 Program Suite GUI/job manager.

Maddeningly, I see in my project job history a couple "dictionary" jobs where I did this, but I utterly forgot how I set them up (forgive the asinine names):

When I try to use the Monomer Library Sketcher (under Refinement/Restraint Preparation) and open a CIF ("mmCIF") file, nothing happens.

Also under the sketcher, I can severely abuse the "Load Monomer from Library" and it looks like I get the right thing:

However, when setting up the above, it throws "Error: can't read "monomer_lib(code,n..." warnings, then when running it generates the Geometry file (seemingly successfully) then says that Libcheck failed when trying to create the coordinate file.

If there are other solutions, I'd be interested as well.  I've used PRODRG to create CIF files before with its draw tool, but it can be a bit clumsy, it ignores how I drew my double bonds, and it creates new names for all the atoms.


texts:
What I Think I Know: Hydrophilic and hydrophobic things repel each other. Since the cell membrane contains hydrophobic tails, it is difficult for hydrophilic molecules to pass through the cell membrane.

Question: Why don't the heads of phospholipid bilayers repel hydrophobic molecules? In other words, if the phospholipid membrane has both hydrophilic and hydrophobic portions, why do only the hydrophobic portions act as repellents?

Stipulation: I need a quotation from a textbook, university, or other credible source.

Evidence of Prior Research:

Why lipophilic molecules can pass phospholipid bilayer, in spite of 2 hydrophilic layers?: This question has a comment that links a graph from a textbook. I can't understand the graph by itself. There are no other references.

Understanding what passes through and doesn't pass through the plasma membrane: All references discuss the topic, but none answer the question.

I understand that this topic is addressed quite frequently, but the question I'm asking is never answered. Texts tend to say something like, "Ions can't get through the core because of their charge" and completely gloss over the concept of lipids getting through the heads. Please don't dismiss this as a homework question that I didn't take the time to research. This is my second try asking this question (on this site); I have spent hours trying to find an answer.


texts: Complexity in creating transgenic animals (e.g., mice)

texts: Many papers I have seen describing transgenic rodent models (and presumably applicable to other model organisms) involve the knock-in, or modification to, a single gene, possibly two genes. With respect to recombineering techniques, what prevents targeting multiple genes in a single organism? For instance, if I wanted to simultaneously knock-in some genes and knock-out others within the same mouse, would I be forced to generate individually modified transgenic lines and then do some "fancy" breeding to generate the multiple-modified mice?


texts: Why do urine have a chemical smell after drinking a lot of alcohol (red wine)?

texts:
When I've been drinking a lot of red wine my urine starts to have a chemical smell. How do that urine differ from normal urine?
Is that chemical smell a sign of liver issues? When I was younger I don't remember my urine having that smell after or during drinking lots of alcohol.


texts: How can cells produce antibodies despite error-checking mechanisms in their genomes?

texts: How can immune cells produce so many different kinds of antibodies with different variable regions if there are so many mechanisms inside the cells that try to keep the DNA sequence as constant as possible (i.e. prevent mutations, which are actually necessary to create the different kinds of antibodies)?


texts: Are there oligocellular organisms in nature and, if so, what are they like?

texts: I'd think protozoans can be oligocellular, but I haven't found any examples, and I'm curious to know what is the minimum number of cells an organism can have other than a single cell.


texts: Why do rod cells not recover after bleaching upon exposure to bright light?

texts:
I'm confused as to why, when exposed to bright light, rod cells cease to function.

I understand that exposure to bright light bleaches all of the rhodopsin, but...so what?

Why doesn't the bleached product (opsonin/retinal) simply get re-synthesised back into rhodopsin as it does in dim light, and therefore continue the cycle and enable impulses?


texts: Quinone A, Quinone B, Ubiquinone, Plastoquinone: whats the difference?

texts:
I am getting very confused about this. My understanding so far is that ubiquinone is used as an electron (and proton) carrier in oxidative phosphorylation in the mitochondria whereas plastoquinone is the carrier in the light dependent reaction in photosynthesis in chloroplasts. My guess is that these carriers are similar because it is a highly conserved carrier that was present in many of the original life forms (including those that formed chloroplasts and mitochondria).

My first questions are:

is the above distinction correct?
do we find ubiquinone and plastoquinone elsewhere in cells, other than in mitochondria and chloroplasts, or in other prokaryotes?

Then I am not sure about quinone a and b. My lecturer said that quinone b is present in photosystem II and it accepts the two electrons from the lysis of H2O and then it accepts two H+ ions from the stroma to enter the membrane of the thylakoid

But I have also read that it is plastoquinone which shuttles the H+ ions in the thylakoid membrane in the form of plastoquinol. So could it be that quinone B turns into plastoquinone on accepting the electrons, and plastoquinone accepts two H+ ions to form plastoquinol?

If so, how is the quinone B from photosystem II replenished?


texts: Can a protein go outside of nucleus after go inside with nuclear localization signal (NLS)

texts: To make a protein (for example Cas9, GFP...) able to enter the nucleus, we need to add a NLS tag for it. So will it able to go outside the nucleus after get inside ?


texts: What is the difference between endomysium and sarcolemma

texts: They both are lining of muscles so how can we differentiate these two? Please answer in simple terms.


texts: What was the breakthrough behind the “sudden” feasibility of mRNA vaccines in 2020?

texts:
Several sources describe the initial failures in the realization of a successful mRNA vaccine. E.g., this 2017 article from Stat describes the following problem faced by Moderna while working on one of their mRNA vaccines:

The safe dose was too weak, and repeat injections of a dose strong enough to be effective had troubling effects on the liver in animal studies.

Another Stat article describes a similar challenge:

In animal studies, the ideal dose of their leading mRNA therapy was triggering dangerous immune reactions — the kind for which Karikó had improvised a major workaround under some conditions — but a lower dose had proved too weak to show any benefits.

The work by Karikó was conducted before Moderna and BioNTech were founded, so it does not seem to be the breakthrough that led to feasible mRNA vaccines. I am also aware that one of these companies, Moderna, is secretive about its technology.
However, I would like to learn, at least at a high level, the reason mRNA vaccines are a viable option against COVID-19, while earlier attempts to develop them against other diseases, such as Crigler–Najjar syndrome, were unfruitful.

I am aware of Why weren't mRNA vaccines clinically tried earlier?, which was closed for being opinion-based. However, my question is specific to the biological mechanism behind the breakthrough that enabled feasible mRNA vaccines, so is objective and within the scope of this site.


texts: Does the body use radio frequencies in the range of frequencies used in mobile phone networks?

texts:
I read something related to the biological effects of "mobile phone radiation". It was not as far from reality as one might expect with this topic. The context was about the acceptable distance of mobile phones to the human body. Mobile network operators specify minimal distances of some cm.

I was surprised to read that the human body actively uses electromagnetic waves in or near the frequencies used by mobile phone networks.

Is that true?
Or partially true?
Or at least plausible?

German source: https://www.diagnose-funk.org/themen/mobilfunk-anwendungen/mobiltelefone/smartphone-nicht-in-koerpernaehe-benutzen

Relevant section translated (paragraph above the image):

  Human body cells also communicate via electromagnetic vibrations, such currents are measured, for example, in the case of a cardiac ECG or brain EEG. The mobile radio signals are in the frequency range of the body's own vibrations. It is therefore not surprising that electromagnetic radiation can disrupt brain waves, heartbeat and other body functions. The health risks posed by high-frequency electromagnetic fields (EMF) have been sufficiently researched and documented. Diagnosis: Radio documents this on the website www.mobilfunkstudien.org


texts: Using ion-exchange chromatography to purify DNA from a cell extract - Is DNA more negatively charged then RNA?

texts:
When applying this method we have a glass or plastic column of resin which is positively charged. Then we pour cell extract into the column in order to capture the negatively charged particles which include DNA.

After that we gradually add salt which neutralizes the molecules. But it does this gradually so strongly attached DNA molecules fall last while RNA and proteins fall first.

The question is why does DNA have a greater negative charge than RNA ?


texts: Is there a standard format for plant community composition data?

texts:
FIA has a nice database of forest Inventory data, this would be great except that it does not seem capable of handling data from non-tree species (e.g., grasslands, wetlands).

Is there a standard database or flat-file format for collecting plant community data (e.g., biomass, cover, dbh as appropriate)?


texts: DNA replication - how many times and when does it occur?

texts: I’m currently learning about DNA replication in both prokaryotic and eukaryotic cells. And my lecturer has mentioned that replication is a once in a lifetime activity. And I’m not sure what this is implying because I’ve searched up that DNA replication occurs during cell division (cell cycles), which occur repetitively as organisms develop.


texts: How do we know the brain flips images projected on the retina back around?

texts:
Why do we turn images upside down again rather than dealing with them directly, still vertically rotated after passing through our lens?

I don't see how that would cause any problems, and how we'd ever be able to figure out if we are presented with flipped images after getting used to interacting based on visual input, whether flipped or not.

What am I missing?


texts:
I’ve heard that HIV developed from SIV, etc.

I’ve also heard that most species (including most monkeys) can’t get a common cold like humans.

So then what causes infections to be able to travel across species, or vice-versa?

For the sake of the question, I’ll narrow the scope. Let’s say we have a virus that can infect humans but not infect close human relatives, like Chimpanzees. What about that virus biology or animal biology causes that difference?

I know with some animals it’s about body temperature or skin composition, etc. But humans and chimps are physically pretty similar. Is it all about the immune differences?


texts: Why are pharmacology studies so experimental?

texts:
I am a med student, and as far as I see from our pharmacology lectures, pharmacologists work almost completely experimental. Quite typically they take a substance (e.g., from nature), they add, change or remove some chemical groups, and then they test it (either with high throughput screening or on animals), for example to see whether the new drug is active or not. To me, this sounds a bit indirect.

Ideally, we should know exactly what we are targeting, and then custom-make a new drug. For example, if we know which receptor (the 'lock') we wish to activate or inhibit, why do pharmacologists not simply design a fitting key (a plug to block, or a substrate-resembling activator) to the specific lock?


texts: I've found this insect in my apartment and I don't know it could be bed bug or not. Could it be hazardous and what are the ways for getting rid of it?


texts: Concentration of caffeine in physiologically relevant setting

texts:
Caffeine is known to overcome G2/M (and possibly other types of) cell cycle arrest through its effects on DNA repair machinery and is used as a positive control in studies of cell cycle arrest. In this paper, for example, researchers use concentrations of caffeine in the 1-4 mM range to overcome nocodazole-mediated arrest. Is this a physiologically relevant concentration?

I found a lot of interesting caffeine data including the LD50 (estimated to be around 150-200 mg/kg) but have not been able to turn up any good numbers on reasonable concentrations that might be found in a human.


texts: Is it possible to use microalgae to produce food and live on it?

texts:
I know microalgae have not less protein and starch, grow quickly, require less. So, is it possible to use them for producing food (replace rice and wheat) and live on it?

Currently, I only saw people eat it as an extra-nutrition.


texts: Serotonin activity with short 5-HTT promotor region and depression

texts:
So after reading a few studies (1,2) it seems that a shorter promotor region for the serotonin transport protein may be associated with increased likelihood of developing depression after stressful life events.

I'm still an undergrad but this would seem like it would lead to less transcription of the protein leading to more serotonin at the synapse. My understanding is that this should then lead to some sort protection against mood disorders not the increased likelihood of them like the studies suggest. Is someone able to explain what I'm missing here?

Thanks,

Zane


texts: Alan Turing was treated with estrogen-analog, though he was gay. Shouldn't it actually increase his female-like desires?

texts:
Alan Turing was a great mathematical genius of all the time, as well was a homosexual-male. However, the biography of Alan Turing on Wikipedia ( Permalink ) tells that :

  Turing was convicted and given a choice between imprisonment and probation, which would be conditional on his agreement to undergo hormonal treatment designed to reduce libido. He accepted the option of treatment via injections of what was then called stilboestrol (now known as diethylstilbestrol or DES), a synthetic oestrogen; this treatment was continued for the course of one year. The treatment rendered Turing impotent and caused gynaecomastia,fulfilling in the literal sense Turing's prediction that "no doubt I shall emerge from it all a different man, but quite who I've not found out".

Though upon modern medicine, probably Turing needed no medication; but medicine (and politics) of that time; needed to prescribe some medication for Turing.

Well. But why they've chosen an Estrogen analog? Shouldn't that actually increase Turing's female-like needs and behaviors? Or maybe it indeed increased the homosexuality in Alan Turing unintentionally or intentionally?


texts: Which is the correct term haploid daughter cells or haploid parent cells?

texts:
Meiosis 2 begins with 2 haploid parent cells and ends with 4 haploid daughter cells (gametes). Gametes from the opposite sex can now merge together and fertilize.

If I were to refer to a specific haploid daughter cell merging with another to produce a zygote; are these daughter cells from Meiosis 2 still called 'daughter' cells or are they now called parent cells?


texts: I only found chemotroph and photoroph examples of life, but are there organisms that can use a temperature gradient to convert energy?


texts: What software/approach to use to build a graph based on microarray gene expression correlation?

texts:
What software to use to build a graph based on microarray gene expression mutual correlation?

I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more reliable robust software or R/Python tutorial on how to make a graph with gene-nodes and edges built on the rule of significant (p<0,05) positive and negative Pearson/Spearman correlations.