texts: Why do we have both on and off bipolar cells?

texts:
I have a question regarding the reason behind the 2 bipolar cells.
So, from my understanding we have both on and off bipolar cells and from the numerous diagrams I have seen, I find that most show a single cone attached to both an off and a on bipolar cell.
The on bipolar cell reacts in an inhibitory manner to glutamate and so if light hits a photoreceptor attached to this bipolar cell, less glutamate is released and so the bipolar cell will become depolarised.
The off bipolar cell is the opposite as it finds glutamate to be excitatory and so it will become depolarised in the dark.
My question is, in the light if a single cone has light presented to it, it will become hyper polarised and so will release less glutamate. If the bipolar cells attached to this cone have opposite effects as in one will become depolarised and one will become hyper polarised what is the reason for the off bipolar cell, why would we need that cell if it only becomes depolarised and doesn't result in anything?
A second question is, do the bipolar cells connect to corresponding ganglion cells for example, on bipolar cell connects only to on-centre ganglion cell? If so why is this?
Lastly, we also have single cones that connect to single bipolar cells. Are these cells on or off bipolar cells I assume they are on because if they were off we wouldn't be able to sense anything as the cell would be hyper polarised and so wouldn't cause the ganglion cell to reach an action potential. Is this thinking correct?


texts:
It is quite the old wives tale that drinking a hot drink cools you down. If you don't really think about it it does seem somewhat logical: increasing temperature will cause your body to try and cool down faster. This is of course flawed by the fact that you have increased your temperature before cooling it back down again.

I have had a bit of a look, but have been unable to find any evidence that addresses the fact that drinking a hit drink may make you feel cooler after sweating a little bit, rather than actually changing anything about your net temperature. Basically, is the 'cool down' just the placebo effect (you feel cooler because you think you feel cooler), or is there any evidence for a 'real' effect of hot drinks cooling you down? Or is there evidence that hot drinks do nothing at all except heat you up a bit before you come right back to the same temperature?


texts: I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it nomenclature Based on it, I try to figure out what is hsa-let-7a. As far as I understood, hsa refers to human but I expected a "mir" or "miR" after hsa but there is a word "let" .So my question is that hsa-let-7a is a name for a single mature miRNA or is it a name of a miRNA family(if there exists such a thing) ?


texts:
Could anyone help to identify the following small black fly please?

Here is some relevant information which may help:

Location: London, UK
Length: ~5mm
They are slow to react and drift lazily & silently around a room

After my own research, I thought it might be a fungus gnat, but I'm uncertain.

Hopefully, if the species can be reliably identified, I can then look to find out what attracts them and how to deter them.


texts:
With regard to nucleic acids with repeating residues, could anyone provide a description of what the following sequences are, and the key differences between them:

Poly(dA)
Oligo(dA)
Poly(A)


texts: How does repair take place on leading strand in eukaryotes?

texts:
I am currently reading molecular biology of the gene by Watson to develop an understanding of the mechanism of replication and repair.
Under the topic mismatch repair of DNA, they mentioned that eukaryotes lack a homolog of MutH. The repair takes place from the nicks developed on the lagging strand before ligase acts on Okazaki fragments.
How then does the repair take place on the leading strand as there are no nicks on the leading strand?
And also, because eukaryotes lack Dam Methylase, how does the repair system recognize which nucleotide of the mismatched pair is incorrect?


texts: What happens to tube nucleus of the pollen tube after fertilisation?

texts:
Background:
Pollen tube contains a vegetative cell and a generative cell. The vegetative cell contains the tube nucleus, and the generative cell contains two male gametes. The two male gametes fuse with the egg to form the embryo and with the polar nuclei to form the triploid endosperm in angiosperms.

Question:
What happens to the tube nucleus of the pollen tube after/during fertilization?

Research:

This site says that the tube nucleus disintegrates.
This article does not mention about disintegrating nor discuss anything about the fate of tube nucleus.


texts: Why honey bees built hive in perfect hexagonal shape instead of irregular shape?

texts:
Why honey bees built hive in perfect hexagonal shape ?

Due to Hexagonal shape, I can go near without any anxious or fear.( Apart from Honey bee's stings)

From this Question, Most creatures look like or tries to look like irregular to fear the other creatures to attack.


texts: Could old-style "inoculation" be used against COVID-19?

texts:
Before the first vaccination was invented, for smallpox, there already was a technique called inoculation or https://en.wikipedia.org/wiki/Variolation. Unlike vaccination where dead or modified viruses are introduced to the immune system without causing an illness, in those old-style innoculations, people were infected with real live smallpox viruses, but not through the normal infection mechanism (the mucus membranes) but through scratches in the skin. Apparently when the virus arrives in the "wrong" organ, it can't cause as much damage quickly, but still the immune system gets a chance to prepare antibodies for it - so at the end the individual does get sick, but it's a much milder version and not as deadly.

Could we do something similar for COVID-19, i.e., deliberately infect at-risk individuals in locations far away from the pulmonary system (e.g., scratches in the skin) hoping such innoculation will indeed cause disease but a milder and less deadly version?

Is there any reason, besides the ethical questions of how to test this approach, why such an approach might not work? (again, "work" here means reducing the morbidity rate. It will not reduce the number of people sick, unlike a proper vaccine - it should just reduce the number of critically ill and most importantly, the death rate).


texts: Is there a biological explanation for a 0.5 difference in allele size with PCR product?

texts:
CONTEXT

I am currently working on a set of diversity, this diversity in interspecific (within the same genus). I am using SSR markers, the primers were designed on one species and are working really well within the species (lot of diversity and difference between allele of 1 at least).
When trying them on the other species, I observe the normal non-amplification which could be due to mutation in the primer DNA sequence. But, for some genotypes I have been observing a new allele just between the two older ones (like the new one is 185.5 and the olders were 185 and 186.

QUESTIONS

Is that kind of observation frequent when using primers designed on other species?
I understand how a 1 pb difference could occur CACACA ==> CACCACA, but what could the biological explanations be for a 0.5 pb difference between alleles?


texts: What is this creature? Where can it be found?

texts: I recently received the picture below from a friend and began to worry. Does it really exist? What type of creature is it? What habitat does t live in and what is its range?


texts: What are these (eggs?) ? ( Location - India )

texts:
The picture can be zoomed in on clicking

Description:

There are 24 of them, each ovoid, 1mm long and attached to the switch's frame by suction cups connected by tubes. They are secured to the base and couldn't be brushed off with a stick. Found them in East of India.

UPDATE

The ovoid heads have reduced in number (17) and have turned brownish (10.04.2017). The number of ovoid heads are 11 now and two of them have a black spot at the proximal end (could be the eye spots of developing embryos) (13.04.2017). The bunch has 4 of them now (24.04.2017).

Research & Question:

Assuming those are eggs (resemble those of Green lacewing and with the changes observed it is evident), what group of arthropods have such stalked eggs other than Green lacewing?


texts: Why do fetuses have membranes between fingers and toes?

texts: Are the membranes present between the fetal fingers and toes a remainder of the phylogenetic evolution, or just a way organs do grow most easily?


texts: can magnesium bicarbonate be absorbed in the mouth?

texts:
Can Magnesium Bicarbonate be absorbed in the mouth?"
  Magnesium Bicarbonate occurs naturally in some mineral waters.


texts: What (if any) is the shortest evolutionary process observed by humans?

texts: So when I think of evolutionary processes, I think of it taking millions of years to happen. Like how humans evolved from monkeys or birds evolved from dinosaurs (I know that is super-duper simplified). Or how humans have parts that we don't need or use (the appendix, for example), but we don't have any records of a time when it was. But I wonder if there have been any evolutionary processes that happened on a human timescale or if we have evidence of something evolving in, say, thousands of years instead of millions? I think this would be interesting to learn about.


texts: Where should one start if they want to go about identifying phytoplankton and dinoflagellates?

texts: I'm a first year university student and I really need help on how to identify and recognize the different organisms observed in my water samples. Are there any good references/tips on how to?


texts: How much smaller is the diffusivity of a molecule in the retina as opposed to the vitreous of the eye?

texts:
I'm interested in the diffusivity of macromolecules inside the mammalian retina, relative to the vitreous.

For example is the diffusion coefficient for a macromolecule (protein, 50-150 kDa for example) 10 or 100 times smaller in the retina than the vitreous?

The diffusion coefficient for such a macromolecule is about 10^(-6) cm^2/sec in the vitreous - roughly that of a protein in water. I can't seem to find any information on how much smaller it would be in the retina, a tightly packed tissue.


texts: Are baby centipedes poisonous like the adults?

texts:
I know that centipedes have an appendage called "poison claw".But I am not sure if the same is there in the baby centipedes and if its functional like that of the adults.

So are baby centipedes poisonous like the adult?


texts: Which sample type is more proper for whole genome sequencing in AML patients? Peripheral blood or bone marrow?

texts:
I intend to perform whole genome sequencing in AML patients in order to find genomic abnormalities, particularly translocation and gene fusions. However, I am not sure whether it is better to obtain peripheral blood or bone marrow or if there is no significant preference between them.

Please, provide me with scientific resources to refer to.

Thank you in advance.


texts: How many Endogenous Retroviruses do we share with other primates?

texts: Is there a list of Endogenous Retroviruses that we share with other primates? I would like to map all (or most) of them into a hierarchy and see how it fits in our evolutionary branch.


texts: How does increasing the temperature increase the compound action potential in some nerve cell?

texts: In majority of nerve cells, action potential decreases with an increase in temperature.But a couple of papers I have looked at say some nerve behave in the opposite manner (https://pubmed.ncbi.nlm.nih.gov/20077389/). So I was wondering what the biology was behind it.


texts:
I was thinking about influence of ethanol on our brain.
We know, that ethanol can affect GABA receptors and increase flow of chlorine in our brain cells. So it makes signal weaker and slow our CNS activity down.

People with OCD usually take minor/major tranquilizers (and many other ofc.) that have similar effect.
I understand, that alcohol (ethanol) can't stay in our CNS as long as tranquilizers do and it also causes many bad influences, but if we put these bad effects away, could alchohol potentionaly help people with OCD for a short time?

I guess no, but i don't know much in neuropharmacology, so explain me please.

Thanks.


texts: Why did the protein structure prediction accuracy in terms of GDT-TS decrease from 2008 (CASP 8) to 2014 (CASP 11)?

texts:
I read on https://doi.org/10.1038/d41586-020-03348-4:

Why did the protein structure prediction accuracy in terms of GDT-TS (Global Distance Test — Total Score) decrease from 2008 (CASP 8) to 2014 (CASP 11)?


texts: Does a full tear of the gluteus minimus tendon has any functional implications?

texts:
From what I read on Wikipedia, all functions of the gluteus minimus are mirrored by the gluteus medius. Additionally, the gluteus medius is larger than the gluteus minimus (see comparative images here), which leads me to believe that the gluteus medius is stronger than the gluteus minimus.

Subsequently, I would tend to guess that a full tear of the gluteus minimus tendon does not have any functional implications. I.e., a human might have a full tear of the gluteus minimus tendon without any limitation of their movements. Is my guess correct?


texts: Did migratory birds' ancestors live in the places of migration?

texts:
I was studying birds' migration as a type of instinctive behaviour. But my textbook points out that other than for warm climate and easy food, migratory bird migrate to places where their ancestors lived.

Is it a real point? Or the writers just made it up.


texts:
In most of the genome CpG sites are pretty much always methylated, but CpG islands are instead often unmethylated. This has been linked to the fact that they often are associated to transcripted genes.

What are the current theories on the mechanisms involved in this preferential demethylation?


texts: Reason behind formation of different shapes of cell

texts: I have always wondered how cells are modified to give them a specific shape. On what specific part of a cell does gene regulation act  for giving the shape ?


texts: Modeling intracellular interactions between sender and receiver bacteria

texts:
I am involved in a modelling task of a biological process described as follows:

--
"Objective: to model behavior of a sender receiver type system

The process goes as follows

Pre-signal [PS] is in media
Pre-signal diffuses into bacteria
Pre-signal binds to activator as a co-activator
Co-activator activator complex binds to DNA and starts transcription of enzyme mRNA
Enzyme mRNA is transcribed then translated into enzyme
Enzyme begins converting Pre-signal to signal [S]
Signal diffuses out of the cell into media
Signal diffuses into receiver cell from media
Signal binds to repressor inducing activation of reporter gene

Questions for model:

What concentrations of signal will be required to get a response from receiver cell?"

--

My questions are: what kind of mathematical/computational model or simulation tool is more suitable for this task? is it neccesary to model every step, or can some of these be ignored? I know the basics of ODEs, so I wonder if these are enough or something else would be required. Any other advice about how to go through the modelling is welcome.


texts: I was reading a research paper dealing with acute myeloid leukemia and the term "extracellular matrix pathway" came up. What does it mean? I found literature on extracellular matrix, but I'm not sure what the "pathway" indicates.


texts: Is Schoons Hard Shell muskmelon a hybrid?

texts: Would Schoon's Hard Shell muskmelon be considered a hybrid as I have read it was a cross between a Bender's Surprise and a Honey Rock.


texts: Do pigeons have the smallest legs-to-body ratio of any bird?

texts: Proportional to their size, do pigeons have the smallest legs of any bird?


texts: At what total rate is water used in metabolic processes over the entire biosphere?

texts:
A recent column on "The Straight Dope" website discussed the idea that water molecules are largely cycled around through the water cycle, and that therefore the water molecules that come out of your tap could have been drunk (and excreted) by the dinosaurs.  Cecil Adams (the author) points out a few flaws with this argument, namely that we've been burning fossil fuels for a couple of centuries and releasing water into the atmosphere, and that liquid water is constantly dissociating and reforming;  so it's not strictly true to say that every water molecule on Earth has been around since the time of the dinosaurs.

One thing that occurred to me in reading this article is that biological processes have also been consuming and producing water for many millions of years now;  this would be another mechanism by which water molecules can be "reshuffled".  Is is possible to estimate how much water participates in these processes (per annum)?  I know that there are estimates out there about how much carbon dioxide is produced/consumed by the biosphere, for example, but I'm not sure whether one can straightforwardly extrapolate from "carbon consumed" to "water consumed," and I don't know if there are other significant metabolic processes that consume/produce water molecules.


texts: Why is it that higher concentration of primers than the DNA template in PCR will favor the annealing of a template to a primer?


texts: What phenotypes can arise from gender-related aneuploidy?

texts:
Humans normally have 46 chromosomes (two copies - one from each parent - of each of the 24 chromosomes: [1:22] + [XX or XY]).

Aneuploidy is an abnormal number of chromosomes - Down's syndromes is an example of this, where individuals have an additional copy of chromosome 21.

I have read a little about gender-related aneuploidy, where individuals can have additional sex-specific chromosomes (for example XXY).

I was wondering what (roughly) the prevalence of the different combinations are, what the specific phenotypes are, and what (if any) medical complications can arise from these combinations, or indeed, what advantages could be conferred by the additional chromosome!

47,XXX
47,XXY
47,XYY

My question also stretches to whether the different combinations display a hermaphroditic phenotype?


texts:
From my understanding free radicals play a slight role in ageing.

In what ways are they so damaging, and can a restricted diet reduce production of free radicals?


texts:
Imagine being under a lot of stone age people and you are the only one who thinks something like "Hey I am a human being, and now I am thinking about this and that and maybe I change myself to become a better person". You would see the world in a totally different way. No one would understand your behaviour because nobody thinks about himself (self-aware) or sees the world as you do.

So my question is: How did we get self-aware? how did we develop this "feature"? And why did we develop this, how could the nature think that this would be an advantage?

There has to be a small "jump".
I mean, somebody has to be the first who thought about himself. Either you know (or think about) that you are a being or you don't. So you can't just be a little self-aware right?


texts: How can we define complexity in the context of biology?

texts:
Can somebody provide a definition of complexity in the context of biology?

Is it something of a personal opinion on the side of the user to decide precisely what s/he means by using the word complexity or is there something all biologists can agree upon? Is there any "standard" for the use of the term complexity or is such standard simply unattainable in our current level of knowledge and/or understanding of the living world?

To the moderator-I want to know What is complexity in biology?  in GENERAL, not only in the specific example of measuring it for an individual. One can argue complexity can be used to compare and even to "cast a vote" about the superiority or inferiority of many objects of study in biology, not just individual organisms. What about the complexity of an ecosystem, of a particular organ, of the interactions of macromolecules and so on. Are they not legitimate instances when the term complexity can be used without inferring to its meaning? This is the purpose of my question, not to merely measure the complexity of an individual. This is why I don't think it's duplicate of the question you mentioned. How is my reply?


texts: Can DNA rings, i.e. plasmids, form as Möbius strips?

texts:
I know that plasmids can be present in a coiled form, which keeps the DNA strands together when they degenerate, by forming catenases.

I was wondering, however, whether it has been documented to naturally happen or if anybody has ever successfully created a Möbius-strip plasmid. Technically, such a structure could readily form from a single circular strand of DNA, but the literature, as far as I have searched, has remained silent.


texts: Found this bug in my apartment in New York. Does anyone know what it is?


texts: PCR that worked previously is now only showing primer dimers and a smear on gel

texts: PCR amplification of a promoter sequence for gel extraction worked beautifully using Phusion HF enzyme with GC (higher error but less picky) buffer. However, DNA concentration from the gel extraction was too low, so I need to do it again. Now with all the reaction parameters the same it is not working. So far I am using the same Phusion enzyme stock and buffers, the same primers which worked before, the same proportions, and the same thermo-cylcer set up. I have extracted fresh genomic DNA to amplify from thinking maybe the DNA had degraded with no luck. I make a mastermix fresh before each reaction by combining the Phusion enzyme, nuclease free water, dNTPs from a 10mM stock, and the GC buffer mix. Any ideas would be appreciated.


texts: I currently work on gene networks and specifically, I analyze the brain gene regulatory network of an insect to understand its sexual behaviour. During a recent presentation, I got asked this question which I just couldn't really tackle in a good manner. The question was why do I study the brain gene network to understand sexual activity when I should be studying the gene network of a sexual organ, for eg: the ovary. I got out saying that since the brain decides behaviour, it would be much better to study the brain GRN. However, I got confused and would like to know if different tissue or organs in the same organism have different gene networks? Any idea regarding the theory is welcomed.


texts: What's Incomplete atrioventricular heart block (AV)?

texts: This is unclear for me and I can not understand differences between complete and incomplete atrioventricular heart block.also I want an electrocardiograph of incomplete atrioventricular heart block.


texts: Are there examples of animals that adapt to their environment very quickly? The phenomenon is called Phenoptic Plasticity

texts:
Evolution and speciation may take millions of years. This made me wonder if there is an animal that adapts itself relatively rapidly to its environment? I don't mean a simple adaptation like a change of a color by chameleons, but a real evolutionary change.

I've heard that some animals can adapt quickly to the environment like snakes (I am not sure they do). When they have a lot of water (e.g., a big river), they grow big, while the same species does not grow as big in a smaller water tank (small body of water). And when you take this animal to a bigger water it starts to grow quickly.  I want to be sure it is a snake or there is some other animals that evolve change like this...


texts: Atomic force microscopy: depth penetration?

texts:
What depth penetration can  one typically get with atomic force microscopes? (i.e. how far into the tissue can one image?). I have found numbers on acquisition times (minutes) and spatial resolutions (~nm), but what about depth?

Also, what is the sensitivity of AFM? (e.g. in moles)


texts: Why is assembling paired end illumina without any input parameters an important problem?

texts:
In one of the comments in this question about multiple sequence alignment, it was stated

  @5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any paired end illumina run optimally de novo without any input parameters.

What is a paired end illumina? How is optimally defined in this context? What are the usual input parameters?


texts: Why there is no fluorescent light from my DAPI-stained Hibiscus Rosa Sinensis Pollen?

texts:
I currently work with fluorescence microscope to observe generative and vegetative cells within hibiscus rosa sinensis pollen. I used DAPI to stain pollens but there is no light that indicate the existence of both generative and vegetative cells. I simply stained the pollens with 50 ppb DAPI without other procedure. I have referred this steps from Sexual Plant Reproduction textbook from Cresti and Tiezzi, here is the link : le.ac.uk/bl/phh4/openpubs/SPR_HH_pollen_stigma_crestiLR.pdf. From the book, it simply states "For DAPI staining, fresh or fixed pollen is stained on a slide in a drop of 0.005% DAPI (diamidinophenylindole), and the nuclei observed under a fluorescent microscope after 5-30 min (UV excitation, blue DAPI fluorescence).

The result is make me confused because there was no fluorescent light but only reflected light by pollen itself.

I will be very glad if anyone can suggests me what should i do or highlights an error in my steps.


texts: Would anything limit an "invasive species" T. rex introduction now besides equilibration with available prey or intervention by humans?

texts:
In the video Two-and-a-half billion T. rex roamed Earth, study finds contains a short explanation of the results in Science Absolute abundance and preservation rate of Tyrannosaurus rex by the corresponding author of the paper.
I'd like to understand better what is known about T. rex's adaptability and range of environments where it was thought to flourish. It's hard to imagine what things were like back then, so using modern flora/fauna and climate distributions as reference points will help me to understand this better.
Based on that knowledge and reference frame, I'd like to ask about the following Gedankenexperiment:
Question: Would anything limit an "invasive species" T. rex introduction now besides running out of food or intervention by humans?
Would they basically thrive over much of the Earth's surface and eat all the other mammals? Or without a supply of dead and rotting dinosaur cadavers would these giant scavengers with excellent olfaction quickly deplete a small region and die of starvation?
Currently there is not likely enough DNA to reconstruct a full genome nor a scheme to build and incubate a dinosaur egg for it (as far as I know), so we are not at any risk of this happening in the near future.


texts: Systematic anticoagulant injection after a CVA

texts:
Since most of the cerebrovascular accident are ischemic ones, would it be usefull to have anticoagulant everywhere (we already have  AEDs everywhere) so that everytime someone would have symptoms of a CVA we would be able to destroy the blood clot before any permanent damage to occur ?

On the other hand may it make the case of ruptured aneurysm getting worse ?

So what are the potential negative and positive effect of such a policy ?


texts: Difference between AjuA and ajuA in biosynthesis

texts:
I cannot for the life of me figure this out. In the following figure, you can find ajuA and AjuA for example.
I do understand that the lower-case ones are the genes. The arrows indicate the direction of transcription. However, what is the difference to the upper-case AjuA? The text speaks of subunits. How are the two related? When do I speak of ajuA and when would I be talking about AjuA?
I would also be happy if you could point me in the direction of some literature about the basics of this kind of notation.
PS: I do understand the mechanisms of the biosynthetic route and am familiar with the different domains in the modules as well as PKS and NRPS modules.


texts:
Is there any living organism that has the ability to remove and reattach body parts at will?

I'm not talking about regeneration (like in starfish). Say I'm chasing prey, and I decide that my tail will be a hindrance. So I leave it behind, and reattach it after the hunt.


texts: How long does it take for E. coli to shift feedstocks?

texts:
With our fermentations we're noticing that it takes an appreciable amount of time for E. coli (K12 variant) to change from being metabolically streamlined on amino acids to being metabolically streamlined to glucose.

How long does it take for such microorganisms to adjust to a new feedstock?


texts: Output of clustalo on (1.2.1) on ubuntu 14.04

texts:
I am trying to align the following 8 sequences using clustalo on ubuntu terminal using the following command. But I am not getting the right output.

clustalo -i sequence.fasta -o output.clu

My input file issequence.fasta with 8 sequences I downloaded from BLAST

My output file output.clu

The output I was hoping for outputOnline.clustal

Also I would appreciate if some can tell me how to share this kind of data in a question because obviously the way I have done is doesnot seem appropriate.


texts: Could habitat selection pattern be deformed in environment with low variability?

texts:
It is possible that strong (clearly visible) pattern of selection towards particular parameter is detectable only in environment with high variability (difference between used (red) and non-used (grey) space will be significant) whereas in sub-optimal environment used and non-used space do not differ due to low variability.

And if this is possible, is there any relevant study which focuses on such issue?

P.S. It seems to be very basic idea, however I could not find any relevant sources on this topic.


texts:
I've reading about proteomics and how it can be used with mass spectrometry to sequence digested peptides.

Reading this paper the author states (in box 2):

  peptide fragmentation induced by collisions with residual gas, and
  bond breakage mainly occurs through the lowest energy pathways - that
  is, cleavage of the amide bonds

Why is cleavage predominately at the amide bond? What makes the amide bond the lowest energy pathway?


texts:
I guess not, but it was discovered in 2000 so I don't know if we know enough about it. Are there people without ACE2 (angiotensin converting enzyme 2)?
It seems mice can survive, but that's not a proof on humans: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829150/


texts: Is drinking your urine an effective way to stay hydrated in a hostile environment?

texts: There are quite a few stories about people trapped or otherwise incapacitated resorting to drinking their own urine in an attempt to stave off dehydration, ignoring the long term consequences, my problem with this idea is that the main cause of death when dehydrated is kidney failure, resulting from the buildup of urea and uric acid when the body can't package those chemicals with water to execrate them. Because of this, I'm tempted to assume that drinking your urine (without somehow purifying it) is a futile action as you are consuming both the water and the exact chemicals you need to remove with the water. I'm however not confident with this analysis, so any sources on the subject would be appreciated.


texts: In reconstructions, how are various shapes of facial features determined from skull only?

texts:
I have seen reconstructions (with skin, eyes, muscles etc) of some first humans based on skulls and skeletons. But how can the shape of nose (protruding part), shape of eyelids, shape of eyebrow, hairline be determined base on the skull only?

Examples of these reconstructions:


texts:
I'm trying to understand what problem led to a development of kin selection.

The explanations I've found consist roughly of the following:

  The existence of some altruistic and cooperative behaviors in social
  insects like honey bees, the phenomenon of sterile castes formed by
  non-reproductive individuals that leave no offspring and the suicidal
  role of these insects in defending the hive, were traits that natural
  selection could not favor. Kin Selection | Nectunt

What I do not understand: Why could natural selection not favor the phenomenon of sterile castes?

From the perspective of the sterile worker: Since it can't reproduce, no strategy will affect the number of offspring it has (will always be 0). So there is no conflict with natural selection.

From the perspective of the queen bee: Her offspring consist of sterile worker bees and a new fertile queen bee. The worker bees improve the viability of the next queen bee. This is consistent with natural selection.

Therefore, I can't see the relevance of the worker bee sharing lots of genes with its sister queen bee. This seems to be nothing but an ancillary effect of the mechanisms of evolutionary change.
Imagine, the queen bee could produce worker bees without a genome (like a robot), or a genome that is not related to its sister queen bee, those worker bees would still show altruistic behavior.

What am I missing?


texts:
I found this insect in my garden

It's the first time I see this insect, so I'm wondering what it is.

It has blueish, purplish reflections, a head like an ant or wasp but it's the size of a thumb (4-5cm)

I am located in Hungary if it can help identify it


texts: Would chimpanzees and humans normally be in the same genus if we weren't so sensitive about it?

texts:
Listening to the BBC's radio program The Why Factor particularly poignant episode What Can Chimps Teach us About Politics? hosted by Professor James Tilley, I heard Professor Frans de Waal of Emory University's Yerkes Primate Research Center, and author of Chimpanzee Politics say:

  The differences are so small; normally we would put humans and chimpanzees in the same genus, but because of sensitivities in the human species we’ve not done that.

I'm wondering if this is an opinion, or arguably correct. I understand that taxonomy is an "evolving" discipline, but are there scientific arguments or viewpoints that would suggest that chimps and humans would be in the same genus if not for public, social or individual sensitivity to the idea?


texts: What is the name of this flower? The photo was taken in the Okanagan Valley, British Columbia

texts: This little flower was growing on dry ranchland in Kelowna, it flowered in April:


texts: How do prions cross the blood brain barrier?

texts:
How does the PrP scrapie protein maintain its confirmation while going through the GI tract? How does the PrP scrapie protein cross the blood brain barrier?

Wouldn't the host immune system recognize the prion as "not self" and attack it?


texts: Is fluoride toxic, and how worried should I be about it?

texts:
A recent flurry of "fluoride is bad!" posts are appearing on my social network news feeds.  Usually I can simply ignore them after a brief look, but this one, stemming from a recent article in The Lancet, isn't easy enough for me to understand and apply or ignore.

The posts link to a March, 2014 article, Neurobehavioural effects of developmental toxicity, from The Lancet Neurology, Volume 13, Issue 3, which has the summary (emphasis added):

  Neurodevelopmental disabilities, including autism, attention-deficit hyperactivity disorder, dyslexia, and other cognitive impairments, affect millions of children worldwide, and some diagnoses seem to be increasing in frequency. Industrial chemicals that injure the developing brain are among the known causes for this rise in prevalence. In 2006, we did a systematic review and identified five industrial chemicals as developmental neurotoxicants: lead, methylmercury, polychlorinated biphenyls, arsenic, and toluene. Since 2006, epidemiological studies have documented six additional developmental neurotoxicants—manganese, fluoride, chlorpyrifos, dichlorodiphenyltrichloroethane, tetrachloroethylene, and the polybrominated diphenyl ethers. We postulate that even more neurotoxicants remain undiscovered. To control the pandemic of developmental neurotoxicity, we propose a global prevention strategy. Untested chemicals should not be presumed to be safe to brain development, and chemicals in existing use and all new chemicals must therefore be tested for developmental neurotoxicity. To coordinate these efforts and to accelerate translation of science into prevention, we propose the urgent formation of a new international clearinghouse.

I don't have full access to the article, so I can't refer to the epidemiological study it says shows fluoride to be a developmental neurotoxicant.

What is a developmental neurotoxicant?
How strong is the research that claims fluoride is a developmental neurotoxicant?
What relationship, if any, does this report or research have with typical fluoride compounds used in US water treatment at the levels typically present in US water (sodium fluoride, fluorosilicic acid, or sodium fluorosilicate at 0.7 mg/L)?


texts: Algae or Lichen identification. Coastal BC, Canada

texts:
I have tried all books and internet resources I know of, but I still have no idea what this might be — a lichen or something else.

At first glimpse, I thought it was something man-made and unnatural, but then I looked closer and saw how it appears to be attached and growing. It grows on exposed rocks well above the high tide. The photo is taken in late March, on northern Vancouver Island. It's loosely attached to the rock.

It was somewhat abundant around the general area (within of a few km), but I haven't seen it elsewhere - although I'm not from BC so there might be a lot of this around.

The water droplet in the lower right corner give a rough sense of scale.

Edit:
Adding another photo in which I just noticed a streak of white, which I included in original resolution.


texts: Missing 4 $\ce{H_2O}$ (per glucose) in Cellular Respiration... Where can they be?

texts:
I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $\ce{H_2O}$ molecules. Generally, cellular respiration is written thus :

$\ce{C_6H_{12}O_6 + 6O_2 + 6H_2O -> 6CO_2 + 12H_2O}$

Yet studying the reaction on a molecular level, I realized that the water molecules just don't add up to be six! (on the left side) What I obtained from my textbook and Wikipedia is that (per 1 glucose molecule)

(Glycolysis) (in the reaction that 2-Phosphoglycerate(2PG) forms Phosphoenolpyruvate(PEP)) 2 molecules of $\ce{H_2O}$ are out of the reaction
(TCA cycle) (in the reaction that combines Oxaloacetate and Acetyl-CoA to form Citrate) 2 molecules of $\ce{H_2O}$ are into the reaction
(TCA cycle) (in the reaction that Citrate form Cis-Aconitate) 2 molecules of $\ce{H_2O}$ are out of the reaction
(TCA cycle) (in the reaction that Cis-Aconitate form D-Isocitrate) 2 molecules of $\ce{H_2O}$ are into the reaction
(TCA cycle) (in the reaction from Fumarate to Malate) 2 molecules of $\ce{H_2O}$ are into the reaction

These sums up to a net of (only) 2 molecules of $\ce{H_2O}$ into the process of glycolysis and TCA cycle... additional 6 molecules of $\ce{H_2O}$ comes from oxidative phosphorylation. Then, where can the remaining 4 molecules of $\ce{H_2O}$ possibly be?


texts: Why is oxaloacetate made in the mitochondria?

texts:
I'm looking at the gluconeogenic pathway:

Pyruvate is shuttled into the mitochondria from the cytosol, converted to oxaloacetate by pyruvate carboxylase, converted to malate which is then shuttled out of the mitochondria, and then converted back to oxaloacetate in the cytosol.  Why is the mitochondrial step necessary?  Why can't pyruvate just be made into oxaloacetate in the cytosol?


texts: why can a queen wasp sting many times but a worker bee can only sting once?

texts: wasp queen and workers can each sting you several times but a bee can only sting you once. As all of the stings have barbs on them, how can this happen?


texts: What is the number of influenza strains occurring at a given time?

texts:
My question was initiated by reading on mock-up influenza vaccines. I understand that the manufacturer pre-prepares a certain vaccine and tries to get it tested and ready before it is actually needed, by taking a novel virus strain that has infected a few people, and could potentially cause a pandemic.

My questions:

How many different influenza strains are there at any given time at one geographical spot (say, one US state? - narrow down at will). I always thought there would be just one novel strain appearing each year, explaining why people get sick time and again of the 'same' virus. However, the mock-up virus vaccine production seems to imply there are various strains occurring at once?
Do influenza strains vary on an annual basis, or is it a continuous process (like evolution), and is a new strain re-named after it becomes potentially dangerous (like speciation?) - i.e., what is an influenza strain? It seems, given the vaccine preps, that various strains occur at once, and strains survive for extended periods? Any hard evidence for these indirect assumptions?

And as a side -

Do vaccine manufacturers prepare a whole bunch of mock-up influenza vaccines on a yearly basis just awaiting to identify a dangerous strain and start manufacturing it once people get sick? Or are mock-up vaccines combined into a cocktail mix containing many strains and are these cocktails re-vamped annually? Or is a yearly shot necessary because immunity only lasts a year?
I might have to re-post this last question at Health.SE as a dedicated question, but since related to above I prefer to leave it here for now. Grab me in chat if need be!


texts: how did we breed after the fusion ? and why can't we bread with chimps?

texts: after the chromosome fusion happened to one of our ancestors, how did he breed ? if he was allowed to breed because the chromosomal differences were still not very big back then, why can donkey and horse breed then ? ain't we supposed to be able to breed with chimps as well ?


texts: What are the most efficient heat exchange sites on the human body?

texts: Where on the body would be the best place to achieve the greatest cooling effect with a "cooling undergarment"?  Concentrated over the kidneys, groin, inside the wrists, back of the neck?


texts: I have a gene sequence with 15 alternative splicing forms. I want to design a siRNA for 1 isoform, I select the exon intron junction that is unique for this isoform, and I must design siRNA for this sequence or this unique isoform, but this sequence has a similarity with another sequence when I blast it, also this sequence doesn't have features for siRNA design. With this condition how can I design siRNA for my sequence?


texts: To characterise diameter of capillaries in organs

texts:
I know that there exist Continuous capillaries (skeletal muscle, adipose tissue, connective tissue, pulmonary circulation), Fenestrated capillaries (small intestine, renal glomerulus, exocrine glands), and Discontinuous capillaries (sinusoids; liver, spleen, bone marrow and hypophysis).

However, I am not sure how to characterise these.
The diameter of capillaries is different for each.
I have not managed to find any figure which present the relationship of diameter of these capillaries.
I have reviewed books Guyton, Pocock and Lange.

What are the diameters of capillaries in different organs?


texts:
I've been translating a text listing some analytical laboratory equipment, and found that some fellow translators translate the Russian word "автоматическая пипетка" (avtomaticheskaya pipetka, which literally means "automatic pipette") as "pipettor".

I consulted the producer's website and found that the proper word for my particular model (thankfully the model code was mentioned) was indeed 'pipette'.

However, in case I come across a Russian 'pipetka' that really means "pipettor", how to distinguish between the two? Maybe the terms are largely synonymous?

Bear with me, I'm not a specialist in this sphere. I googled and found a discussion on Reddit that shed little light for me.


texts: What are important temperature breakpoints for plant distributions?

texts:
I am working on a climate classification system. Some previous works like Koppen and Trewartha use temperature breakpoints of 18℃ monthly minimum of daily average to delimit tropical climates, and 0℃ monthly minimum of daily average to distinguish subtropical from continental (Koppen only).

The first question, is there any scientific basis for these specific temperature breakpoints?

As an example of what I am looking for, I want to point out something in plant distributions in the area of the world I'm most familiar with; the South of the US. In Atlanta, where January averages are 6.3℃ and lows are 1.3℃, most of the natural trees you see around are either conifers or deciduous hardwoods (Oaks, hickories, yellow poplar (Liriodendron tulipifera) and sweetgum (Liquidambar styraciflua). However, towards the coast in New Orleans 11.9℃/7.1℃ or Savannah 9.8℃/3.7℃, there are a lot more evergreen non-coniferous trees. If you look at the (very similiar) distributions from Wikipedia of evergreens such as southern magnolia, live oak, or swamp laurel oak, you can see that there is a cline where the coolest month-averaged daily temperature goes below around 6-8℃ where these evergreen plant no longer grow.

So the general second question is, are there temperature breakpoints that are significant in controlling what sorts of plants can actually grow in an area?


texts: Why does my gel have such poor resolution?

texts: Brand new user to bio stack exchange here. I ran this gel (0.9% agarose, run starting at 60V then to 105V over ~30-45 min) with DNA samples containing 20uL of DNA and 1X tracking dye in each of the wells. I do not know why the resolution of this gel is so poor. I'm assuming it's from DNAse activity, as this is what my lab tech said it probably was. I'm pretty sure I did everything right regarding the procedure. I'm not sure what other info I could provide, other than the samples were prepared and stored at -20C a week prior to the gel being run. Here's a picture of the gel below.


texts: Do animals get Post Traumatic Stress Disorder after escaping from a life threatening situation out in the wild?

texts:
Can animals come down with PTSD in the wild by themselves? For example, would a gazelle that nearly pulls away from a cheetah at the last second and heard the cheetah's jaws clamping down at air right behind it's tail, show symptoms of stress and anxiety after the event?

And if not, why can we as humans succumb to these kinds of disorders, and not animals in the wild?


texts: A very long time ago, I happened across research into using an oxygenated liquid in the stomach and or intestinal  cavity.  I wondered what further results came about of that research, and am having difficulty finding anything on it.   Is anyone aware of it and it and or  can point me to articles and or research papers done?


texts:
Which was the most recent common ancestor between mammals and birds?

Form a rapid google research I could not find good answers. This site seems to imply it was at least 250 milions of years ago. This scientific article mentions 600 milion years but the sentence is a little unclear.


texts:
My daughter Stella and I found these bones on the shore of Port Phillip Bay, Victoria, Australia.

The smaller, barbed bone is attached by a hinged joint that allows it to move through just over 90 degrees. The photos show it at its two extreme positions.

The photos include an Australian 20 cent coin for scale (29mm diameter).

Can anyone identify what kind of bones these are, and which species they come from?


texts: Applying Constraint Programming to sequence alignment/analysis

texts:
My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, areas that have been dominated by statistical methods.

So can you give me examples of some research problems suitable to be approached as constraints satisfaction problems?

Note: By constraint programming I also include more flexible paradigms like weighted constraint programming, where a solution may violate some of the constraints.


texts: How many Watt-hours can an electric eel produce in a day?

texts:
Electric eels are cited as being about to produce about 860 watts of energy. But I haven't been able to find information on how long they can sustain their charge.
https://www.youtube.com/watch?v=y9wktSQdyaE
In another question, it was shown that they can continually power a Christmas tree, albeit the lights flicker, just when it's hanging about and doesn't appear to be defensive. This suggests that it has some ability to sustain a low level of current... so I'd be surprised if there is no study that has measured the potential Wh. Sadly, I cannot find it.
Does anyone know any estimates for the energy an electric eel can produce over the course of a day?


texts: What's the lowest atmospheric pressure a tardigrade can remain active in?

texts: I'm not asking what atmospheric pressures they can survive (we now they can survive the vacuum of space) I'm wondering at what point a deficit of atmospheric pressure would cause them to enter one of their various states of metabolic suspension.


texts: Why do Kupffer cells not attack malarial sporozoites?

texts: During malaria, why don't Kupffer cells (hepatic macrophages) attack  the Plasmodium sporozoites and stop schizogony, thus saving us from the disease?


texts:
The consensus seems to be no, but I see conflicting evidence.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5361427/

Supernumerary human hair cells—signs of regeneration or impaired development? A field emission scanning electron microscopy study

The combination of scarring and proximity to the supernumerary cells suggests it is regeneration and not just misplacement.
Do adult mammalian cochlear inner hair cells regenerate?


texts:
The follicles in the thyroid, intake iodine and bind them onto the tyrosine rings (attached to the thyroglobulin). This produces either MIT or DIT (tyrosine rings with 1 or 2 iodines attached respectively).

Then the DIT joins with either another DIT or a MIT to form T3 or T4. This makes sense.

But it seems to me, that there could be a MIT attaching to another MIT, forming T2. Why doesn't T2 get created?


texts: Why are chickens passive when their eggs are taken?

texts: Most species don't seem enthusiastic when their eggs are taken, yet on farms with domesticated hens, they seem more passive when their eggs are harvested. Why does this occur?


texts:
I read in a chemistry book that a steroid is a class of lipids, and that the fat-soluble vitamins like vitamin D are part of steroids. So is a fat-soluble vitamin a lipid?
This makes me confused as the lipid nutrients seems to contain vitamins which make another type of nutrients.


texts: Is the ringing sound in the ears caused by dying ear cells?

texts:
I was recently watching the movie "Children of Men" (great movie) by Alfonso Cuarón. Now in a certain scene, the lead actor happens to be nearby a loud explosion. Later, when he complains about the 'ringing-sound' in his ears due to the explosion, a co-actor replies:

  Julian: You know that ringing in your ears? That 'eeeeeeeeee'?    That's the sound of the ear cells dying, like their swan song. Once it's gone you'll never hear that frequency again. Enjoy it while it lasts.

How true is that statement?
Do the ear-cells really die after such an incident?Can you really never hear that frequency of the ringing-sound again?


texts: The speed of blood may vary from one place to another and may be quite low in the tiniest vessels compared to the biggest one. What is the speed of blood while exiting a normal human heart?


texts: Why isn't Fluorine, or Neon, the final electron acceptor in cellular respiration?

texts:
I'm a Chemistry student learning about periodic trends. I know that in (many organisms') cellular respiration, oxygen serves as the final electron acceptor due to its high electronegativity.

However, applying the periodic trends, fluorine is more electronegative than oxygen, and the noble gas neon even more so than fluorine. Why aren't either of these the final electron acceptor? I know that in some organisms, the final electron acceptor is sulfur. But I've never heard of it being fluorine or neon. Why?


texts: How can tree branches grow upwards against gravity?

texts:
I saw this tree in front of my room with those branches, and I asked myself why they didn’t grow downward in the direction of gravity since that would be easy for them? And I came to the conclusion that they are seeking sunlight. Is there any research which explain how they can do that?

I found that this mechanism is called Gravitropism (Tree Branches grow against gravity, while roots grow into the soil in the direction of gravity) but I didn’t find a clear explanation.


texts: Is there an advantage to linear chromosomes?

texts:
The DNA copying enzymes have a hard time working to the end of a chromosome. For circular chromosomes this is not a problem, since there is not a sharp 'end'. However, for a linear chromosome, without extra mechanisms in place, a bit of DNA is lost off the end of the chromosome after each replication. Because of this, eukaryotes have a telomere to cap off their chromosomes.
In most cells of a mutli-cellular organism, this telomere is slowly worn away after each reproduction leading to apoptosis. Cells that need to reproduce indefinitely such as germ and stem cells have to invest in extra mechanisms to replenish the telomere. For multi-cellular eukaryotes I can see how this might be usefull (for instance as a cancer counter mechanism). However, multi-cellular organisms evolved from single-cell eukaryotes.
I cannot see a reason for wanting apoptosis in a single-cell organism. However, single cell eukaryotes (say yeast) still have linear chromosomes with telomere caps. What advantage did linear chromosomes provide single-cell eukaryotes to offset the extra investment in reparing the telomere?

Related questions

What is the advantage of circular DNA in bacteria?


texts: I found this photo in a local news page. The page claims that this fish is a new species that was found by a Malaysian fisherman. Is this true or is it a known fish and already has a name?


texts: How are micelles formed from the byproducts of emulsification in fat digestion?

texts:
It is known that fat droplets are made into emulsion droplets via the addition of bile salts. It is then said that the emulsion droplets are made into micelles through some sort of lipase, which can be absorbed and transported to different cells through the LDL and HDL pathway.

My question is what is the biochemistry for transforming emulsion droplets into micelles? How does water, lipase, and other factors make these micelles?


texts: How might gene clusters like the lac operon evolve?

texts: The obvious answer for a gene cluster is gene duplication and mutation of one or both genes. But the genes in the lac operon seem not be so functionally/structurally similar (as compared to the Hox gene cluster, for example), so I was curious as to how they ended up physically associated in the first place.


texts: Is Aspergillus clavatus an unicellular organism?

texts:
I could not find the piece of information form Burton Human Parasitology -book and not by Google.
Yeast is divided to two phylums: one of them is Ascomycota.
Aspergillus clavatus belong to the given phylum.
Yeast is unicellular.
So it is possible that Aspergillus clavatus is unicellular.

Can you tell whether the Aspergillus clavatus is an unicellular orgarism or not from the following picture?

I need to find unicellular parasites that cause damage of brain. The fungus causes patulin so hemorrhaging of brain, but should still be unicellular to meet the criteria.


texts:
Body size: 30mm
Location: Poland, in the middle of a large meadow
It was flying and landed directly on my cap :-)

After consulting wikipedia it look similar to some of Tenebrionoidea but can't find an exact match.

Help!


texts: Why is there a layer of moist lining the inner walls of alveoli?

texts:
I'm taught that the walls of the alveoli are moist, so gaseous oxygen molecules can dissolve into this water. This then allows the dissolved oxygen (liquid state) to diffuse faster from the alveoli into the bloodstream through the basement membrane.

However, why is it faster for gaseous oxygen to first dissolve in water (transitioning into liquid state) then diffuse through the basement membrane and dissolve into the blood stream than for gaseous oxygen to directly diffuse through the basement membrane and then dissolving into the blood stream?

The second mechanism would eliminate the need for the moist layer lining the alveoli wall.

Is there some physical or chemical explanations to this phenomenon?


texts: Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

texts: I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have written a code for the backbone alone (i.e) to construct cartesian coordinates of each atom in backbone from the respective internal coordinates(without side chains). However I got to know that this can be done in a software (maybe in PyMol or VMD). I am completely a beginner in this field of biochemistry/bioinformatics/biophysics. Does it really possible to do this in software like PYMOL/VMD? I'll be very happy if I can do this in python itself. I want to generate cartesian coordinate of a given tetrapeptide for all possible Ramachandran angles (within the allowed region)


texts: Could trees be engineered to produce rainfall-nucleators?

texts: Scientists are using genetic engineering to make trees produce more terpenes. Is it possible to genetically engineer trees to produce more hygroscopic volatile organic compounds? These trees could be used in drought areas to create more rain.


texts: is there a difference in meaning between the terms "bone architecture" and "bone structure"?

texts:
I'm wondering whether "bone architecture" and "bone structure" mean the same thing, or whether they refer to two different concepts.

In this article - http://rheumatology.oxfordjournals.org/content/48/suppl_4/iv3.full - bone microstructure and bone microarchitecture are mentioned in the abstract in a way which makes them sound like they are the same thing. Also, they seem to be used as synonyms in the rest of the article.

This website - http://www.doitpoms.ac.uk/tlplib/bones/structure.php - discusses cortical vs cancellous bone under "structure and composition of bone" while other sites often discuss the same thing under the heading "bone architecture".

So am I right in thinking that the architecture of bones and the structure of bones are synonyms and that either term can be used when referring to osteoporosis? Thanks.


texts:
So we know that our sperm and egg cells get set aside relatively early so that they aren't going through unnecessary cell divisions and causing DNA damage or telomere shortening, but since each new generation starts from one cell each generation has germ cells that have divided more than the previous generation's germ cells.

So, does this have an effect on age?

Is a second generation baby technically older than a first generation baby due to these extra cell divisions, or is telomerase and DNA repair able to keep each generation at the same relative life span?


texts:
I found this microorganism in a wet moss sample taken from my backyard in Richmond, Virginia (USA). I took some pictures of it at 40x, 100x, and 250x. I'm not entirely sure what it is, but I think it's some kind of rotifer based on it's behavior. It anchors onto a piece of moss while hunting. It stretches out to catch food, and once it's caught something, it snaps back into itself.

Any ideas as to what this is?


texts: Are heterozygotes always fitter than homozygotes? Can inbreeding be beneficial?

texts: Inbreeding is mostly not very good because when there is a 'disease' in one allele, the other could/would take over the function. But when you have two of the same genes/alleles, do they, or could they have advantages? Can inbreeding be beneficial?


texts:
I was reading this site which broached comedones, an esoteric word to me; so I thought to look up its etymology which I find exceptionally singular and peculiar (I would have never guessed that the word originated from to eat up !) :

  Etmyonline: "blackhead," etc., 1866, from Latin comedo "glutton," from comedere "to eat up" (see comestible). A name formerly given to worms that devour the body; transferred in medical use to secretions that resemble them.

Footnote: ODO also offers an etymology.


texts: If flies avoid IR light, many places can be kept free from flies using IR light. We see insect repellers in many restaurants, but they don't seem to work well. Can IR be a safe & effective alternative?


texts: Why dont "growing degree days" have units of degrees Celsius (or do they)?

texts:
From Wikipedia:

  Growing degree days (GDD), also called growing degree units (GDUs), are a heuristic tool in phenology. GDD are a measure of heat accumulation used by horticulturists, gardeners, and farmers to predict plant and pest development rates such as the date that a flower will bloom or a crop reach maturity.

GDD is calculated as $\frac{T_{min}-T_{max}}{2}- T_{base}$ - so a quick check of the units would indicate that they are in the same units as T, i.e., degrees C. However, they are usually presented without units.

Why is this?


texts: Why is only the donor's antigen seen during a blood transfusion?

texts: I am a high school student and I am a little confused that why only donor's antigen matters during blood transfusion? for e.g if the donor's blood is O- so it means that it will antibodies against all antigens so if he donated blood to say some A+ blood group then those antibodies will attack on that antigen and agglutination will occur, isn't it? At first I thought may be the antibodies do not work outside our body then later I heard of passive immunity so this thought is not correct then what's the correct reason?


texts: Do primitive lymph nodes exist in 12th week embryo?

texts:
Someone told me that primitive lymph nodes do not exist during this week.
However, others say they can.

Here is a picture about inguinal lymph nodes from here.
No primary lymph nodes are visible (like circular) at 56th day:

When are the primitive lymph nodes formed?


texts:
I would like to ask how i can search in blast against UNIPROT (TREMBL PLUS SWISSPROT) for a selected organism. In the BLAST site there is no option about UNIPROT(only Swissprot), and in the uniprot site i cannot limit the results only in one organism(E.COLI).
THANKS A LOT!!!


texts: Can scientists create totally synthetic life?

texts: This particular question has been of a great deal of interest to me, especially since it dives at the heart of abiogenesis.


texts: Why is there no U3 snRNP in the spliceosome complex of transcription initiation?

texts: snRNP U1,U2,U4,U5,U6 are present in the spliceosome but there is no mention of U3.


texts: Effect of flask position in shaking incubator affects growth kinetics

texts:
During some cultivation experiments for my bachelor thesis I noticed that in liquid culture my bacteria (E. coli) grew differently, according to the position in the shaking incubator.

Because the goal was just to induce protein expression at a given OD, I altered the position of the flasks in the shaker, so the cultures were at a similar OD and I could add the IPTG to all of them at the same time.

Now I wonder if someone else noticed this phenomenon (Literature to cite would be great, I couldn't find anything until now) or if I did something wrong. Maybe it's also known and ignored for longer times?
The cultures more in the back of the incubator grew faster, so I think it's because of temperature alterations when opening the incubator to draw samples for growth kinetics, but I'm not sure about this at the moment.

Thank you for helping me :-)


texts: How do ants get oxygen in deep colonies?

texts: With ant colonies getting to be +7 feet deep, how does oxygen renew that deep for their respiration demand?


texts: Why is sugar absorbed very fast into the blood stream?

texts:
Recently, I heard from a pregnant person I know that immediately after she eats something sugary/sweet, the baby starts kicking and moving around, as if reacting to the sugar. She told me (unscientifically) that sugar gets absorbed fast into the bloodstream (and then into the baby), faster than protein for example, which takes a couple of hours to be digested.

However, I know that both sugar and protein must go through the digestive system until the small intestine to be absorbed into the blood. This is done through mechanical action (peristalsis), as well as chemical digestion. Yet I was wondering how there is such a big time difference between the digestion of sugars versus proteins if the path to the bloodstream is the same.

I did a little bit of research and found that there are some glucose transporters in the cheeks, which could explain how glucose is absorbed so fast (in the same way alcohol is also absorbed fast through the cheeks too).

I wanted to ask if theres any other reason or way in which sugar is given so fast to the foetus when ingested by the mother?


texts: Pyruvate dehydrogenase: Apparently anomalous NAD/FAD redox reaction

texts:
Below is the mechanism for the reactions of the pyruvate dehydrogen complex, which oxidatively decarboxylates pyruvate and transfers the acetyl group to coenyzme A for further metabolism in the Krebs cycle.

The key point is that after $\ce{FAD}$ has reoxidized the dihydrolipoamide, the resulting  $\ce{FADH2}$  is reoxidized by $\ce{NAD+}$, which is reduced to $\ce{NADH}$.
I find the chemical energetics of this difficult to understand. According to standard tables of redox-potential for half reactions, $\ce{FAD}$ is a stronger oxidising agent, and a weaker reducing agent, than $\ce{NAD+}$, which is why it used in the succinate dehydrogenase reaction, for example. How, then, can it reduce $\ce{NAD+}$?
If $\ce{FADH2}$ is really able to reduce $\ce{NAD+}$ it should generate as much ATP in oxidative phosphorylation after oxidation of succinate to fumarate, despite the relatively low free energy change for that reaction. But that is absurd.


texts: What is actually systematics? What is the difference between it & taxonomy?

texts:
In the last century, even during the past decades of the present century, students of systematics could not have thought of any fundamental distinctions among Taxonomy & Systematics . These terms appeared to them more or less synonymous and hence often misunderstood until G.S.Simpson(1961) analysed each of the terms separately & gave a comprehensive definition of each term and its workable areas so that their underlying fundamentals became clear.

This is what I found in my book. But what is actually Systematics? And what is the difference between it and taxonomy??


texts: Why PPD test in patients without M.tuberculosis often slightly positive?

texts:
I got this question which I interpret as

  Why PPD test in patients without M. tuberculosis often have slightly positive PPD reaction i.e., a lifelong slightly positive skin test reaction?

because slightly positive -phrase does not make so much sense to me.
I first thought it is about false positiveness, but it does not make sense.

I am reading Murray Microbiology book.
It says there

  [An alternative to the PPD skin test,] is in vitro IFN-gamma release
  assays. The tests use immunoassays to measure IFN-gamma produced by
  sensitised T cells stimulated by M.tuberculosis antigens. If an
  individual was previously infected with M.tuberculosis, exposure of
  sensitised T cells present in whole blood to M.tuberculosis-specific
  antigens results in IFN-gamma production.


texts: Can enzymes catalyze thermodynamically unfavorable reactions?

texts: Can biological enzymes catalyze thermodynamically unfavorable reactions? I read that an enzyme lowers the activation energy of a reaction by offering an alternative reaction pathway with a lower activation energy, however the ΔG of the reaction is unchanged. If enzymes can do this, then how exactly does this work?


texts:
I found it in Brittany, in my kitchen. It was about 3cm in width and 5 in length.

Is it dangerous ?


texts: How to get Bacteria to attach to an Object?

texts:
I have cultured Cyanobacteria (in a media) in a beaker. I want that bacteria to attach to a cloth (e.g. Carbon). My current method is using a syringe to slowly push the bacteria to one side of a cylindric tube and exist through the other end. The cloth is placed stationary inside that tube throughout the process.
Is there a way to get more bacteria to attach to the cloth? (e.g.maybe adding something to the cloth)


texts: How do you obtain specific mRNA transcript levels for comparison from a Hi-Seq dataset?

texts:
I have HiSeq data from mice exposed to two conditions. I would like to answer the following question: "Is there a significant difference in mRNA transcript levels when comparing condition A to condition B?"

To answer this question, do I have to map my HiSeq reads to the reference genome to determine expression values or is it acceptable to use a small set of reference sequences of interest (approx. 50)? These particular sequences are not annotated on the reference genome. What are the downsides to not mapping to the genome?


texts: I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro boundaries). I've tried performing several database searches with the sequences, but each search produces a set of different unrelated hits. How would one go about using this info to confirm the exon shuffling hypothesis? Any tips are appreciated. Thanks!


texts: Comparing BLAST and the Smith-Waterman algorithm

texts:
I've been asked: how does BLAST improve dynamic programming accuracy?

I do know that BLAST is based on heuristic approach that approximates the Smith-Waterman algorithm and that the Smith-Waterman is too slow for large databases but more accurate.

Can someone settle my conflict?


texts: How often does bacterial transformation happen?

texts:
I have been reading:

  M. Dröge, A. Pühler, W. Selbitschka, "Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies", Biol. Fertil. Soils (1999) 29 pp221–245  [PDF]

I am not a biologist and am trying to get a feeling for how often prokaryotes make changes to their chromosomal DNA.

How often is plasmid DNA successfully incorporated into chromosomal DNA?

I would like to estimate either the number of gene changes (or, failing this, base pair changes) that a bacterium makes per unit time. Or, equivalently, the mean time between such changes.


texts: How can one accurately diagnose the cause of human hearing loss without surgery?

texts:
In a human, if you were to avoid a tympanotomy (surgical examination of the middle ear), how could you distinguish between a blocked Eustachian tube, a ruptured eardrum, or a perilymph fistula?

For instance, take the situation where a young man (suffering from a common cold) blew his nose violently, became dizzy for 1 minute, and then reported loss of hearing in one ear of about 40%.  What would your diagnosis be, possible treatments, and expected outcome?


texts: Equilibrium and Metabolism: Can cells exist at STATIC equilibrium? What about dynamic equilibrium?

texts:
I understand that in closed systems, once reactions reach equilibrium, they can no longer be used to power other reactions. If a cell was a closed system (which it is not), being at equilibrium would mean that it's dead, for it needs a continuous input of energy from the environment.

I know that the cells are open systems, and my teacher mentions that cells can never be at equilibrium. But, I am confused because can't cells be at dynamic equilibrium (where rates of reactions = rates of products)? So my next question is: can the cells not exist at static equilibrium? I am not quite understanding the differences between equilibrium, dynamic, and static. And, when something is at dynamic equilibrium, why does this mean that the concentrations of reactants and products are not necessarily equal?


texts:
T cells are known for their ability to bind multiple antigens, owing to the degeneracy of the recognition sites on their receptors. [I] When examining the structure of the T cell receptor, we can observe the ɑ and β chains which have a highly variable region, in their extracellular domain:

From what I understand, TCR degeneracy means that one receptor can bind to different antigens.

In comparison, the B cell receptor consists of a recognition site that contains a membrane-bound isotope of immunoglobulin. Again, from what I gather, variation in both the Ig on B cells and the TCR occur as a result of genetic recombination. [II]

Question:

Does the membrane-bound Ig in the BCR exhibit the same degeneracy as TCRs? Does variation caused by V(D)J recombination work the same way for both these receptors?

References:

[I] https://en.wikipedia.org/wiki/T_cell_receptor

[II] https://en.wikipedia.org/wiki/V(D)J_recombination

[Images] http://what-when-how.com/acp-medicine/adaptive-immunity-antigens-antibodies-and-t-cell-and-b-cell-receptors-part-2/


texts: What is the mechanism of oxygen uptake in E. coli?

texts:
How does E. coli uptake oxygen? Most of the literature I found is concerned with response to oxygen level supplied in the medium, as opposed to how much is actually transported inside. Can they shut down the oxygen uptake if required? For example, to avoid damaging effects of reactive oxygen species.

There exist bacteria which die in presence of oxygen (strict anaerobe), while some use oxygen when available but also can survive in absence of it (facultative anaerobes, like E. coli). Are there bacteria which cannot consume oxygen for metabolism, but when exposed to oxygen they don't die, rather simply discard the oxygen and carry out fermentation? In a sense, they are strict anaerobe (their mode of metabolism is anaerobic), but they can still survive in presence of oxygen in environment.


texts: How to measure the length of mitochondria from z stack fluorescent microscopy image?

texts: I have been working on yeast cells to analyse the effect of DNA damaging agents on mitochondrial structure. I have imaged my culture treated with MMS for a period of 6 hours and while observing the images, I suspect there is fragmentation of mitochondria in later point of time. So, I am wondering if I can get measurements of mitochondria using z stack images.


texts: What causes motor laterality/ side dominance?

texts:
I would like to understand what leads up to motor laterality, or side dominance of motor skills.
I made this assumption that it depends on neuroplasticity and the side in which one first learns the motor skill; whereas the more you practice, the more you strengthen that side. I appreciate your time and patience. Thank you; can't wait to discuss.


texts: Did vertebrates diverge from other deuterostomes via neoteny?

texts:
Question: Is there any research corroborating my suspicion that vertebrates diverged from other deuterostomes via neoteny (the attainment of sexual maturity while still in larval stage)?

Context: Most echinoderms have pelagic, bilaterally symmetric larvae, while the adults are not bilaterally symmetric (except for sea cucumbers) and live on the sea floor. The same is true for tunicates, which are supposed to be the sister group to vertebrates.

Adult echinoderms also have very reduced nervous systems, although I am not sure whether the larvae have more advanced nervous systems than the adults. For tunicates, which are more closely related to vertebrates, the nervous system definitely does degenerate when transitioning from pelagic larvae to sessile adults.

Echinoderms are also one of the few clades of bilateria, except for vertebrates, which have endoskeletons. And of course, echinoderms, tunicates, and vertebrates are all deuterostomes.

In contrast to tunicates and echinoderms, the MRCA of vertebrates is thought to have resembled a lancelet, which is pelagic and which has a more advanced nervous system than adult tunicates or echinoderms. In other words, it seems like ancestral vertebrates retained larval features into adulthood, and then just grew bigger in size.


texts: Is it possible to have cancer and normal blood count at the same time?

texts: Does cancer always cause abnormal full blood count? I've read on the internet that some people who had advanced cancer, also had normal blood count. I can't find anything on the internet about this topic.


texts: Is 100% antibacterial resistance possible?

texts:
The quest to develop antibacterial and antibiotic substances has often been described as an arms-race, as bacterial life develops resistance, requiring us to develop novel agents which can effectively kill said microbes.

My question is: is it at all possible for a single microorganism to develop resistance to everything we can possibly develop?

There is only so much information-capacity in microorganism DNA to encode the means of resistance to various substances. If we climb the arms-race ladder high enough would a highly-advanced bacteria somehow "forget" how to defend against penicillin, for example?

...or are we utterly boned?


texts: How does formaldehyde cause protein-DNA crosslinking?  I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less polar solvent causes the DNA and protein to pull more tightly on each other than their pull on the solvent, but I haven't been able to find an answer online.


texts: What percentage of a complete Denisovan genomes lives on in the union of the sets of overlapping pieces in extant humans

texts:
In studies like this one mapping out distributions around the world or the analysis described in this article (suggesting a contribution from a non-Denisovan but Denisovan-like unidentified hominin to Melanesian populations, various single digit percentages are given of an average as high as 6%.

One complication in talking about this is what we mean by percent. Just through shared DNA we'd have over 99%, if we knew which DNA was shared. There are surely other complications, like how do you count repetitions toward the percentage, etc. But I mean to ask what percentage of  DNA that is DNA descended from introgressions adds up to, if you put together the different and overlapping pieces various people have.

I realize it may also be hard to pin down exactly what one would mean by a Denisovan genome -- as I said one of the linked articles suggests there may at least one Denisovan-like hominin species represented in the introgressions.

Note: Someone already asked this about Neanderthals.


texts: What is the cause of the packaging capacity limit of recombinant adeno-associated viral (AAV) vectors?

texts:
I am working with recombinant AAV and I am puzzled by the limit of their  packaging capacity (around 5Kb ssDNA), that is really a huge drawback for gene delivery.
I have tried to look more in deep into this problem but I couldn't find any paper that could clarify what is the reason of this limitation. Is it the size of the capsid or something else? I suppose that it is the size of the capsid but there are smaller capsids able to accommodate more DNA so it could be due to other factors. Either way, I could not find the proper literature to solve my doubts.
Do you know the answer? Or, can you point me to good papers on this topic?


texts: Can we digest food as well as herbivores

texts: I heard some guy say that we can't digest plant food as well as herbivores. Which seems weird to me seeing as how humans can survive without any nutrient deficiencies besides b12 on only plants but we would pretty much just die of nutrient deficiencies on a carnivore diet. Can someone show me how we can't digest plant food as well as herbivores?


texts: Does the two-state gene expression model apply to constitutive genes?

texts:
Wikipedia defines constitutive genes as

a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when needed.

I don't have a strong theoretical background biology/molecular biology, and I am currently studying gene expression analytically, specifically the two-state model of gene expression, where a gene can be on the 'ON' or 'OFF' state.
From this definition I get the understanding that constitutive genes are always in the 'ON' state, although I am not sure if that is the case since other sources describe constitutive genes as genes that are expressed at a relatively constant level, which could still be a gene fluctuating between 'ON/OFF' states.


texts: What is the significance of and biological mechanisms demonstrated in lac operon?

texts:
I would appreciate it someone could explain clearly how the genes in the lac operon of E coli are activated to allow the bacteria to metabolize lactose?

The part that I really don't understand is the activation of the lac operon.  A good answer would make clear to me how the introduction or removal of lactose from the envirnment activates and deactivates the different genes there.

Also, what are the specific functions of each of the genes (lacA, lacI, lacY, lacZ).

I am in AP Biology and I will not see the light of day again if I do poorly on this test. Please help!


texts: Do humans have a "dominant" neurotransmitter system/sensitivity within their brain?

texts:
I've recently heard a podcast, in which Dr. Helen Fisher suggests that there are "4 broad personality types", and each one is associated with a particular neurotransmitter:

The corresponding Platonic thinking style, Keirsey temperament type (according to some readers, not Fisher herself), and color can be seen in parenthesis.

Explorer (creative; Artisan temperament, yellow) = dopamine
Builder (sensible; Guardian temperament, blue) = serotonin
Director (reasoning; Rational temperament; red) = testosterone
Negotiator (intuitive; Idealist temperament; green) = estrogen/oxytocin

I'm interested if there's indeed scientific evidence to support that for different people their affinity for a certain neurotransmitter is increased to such degree that it manifests in a noticeable difference in personality?


texts: Absorption ratios 260/280 and 260/230 for RNA

texts:
I extracted RNA from different cell lines, an I want to perform reverse transcription and then PCR. To get good results, in which range should the absorption ratios 260/280 nm and 260/230 nm be? And what is the idea behind measuring those ratios?

I got values for the 260/280 ratio from 2.1 to 2.13 and values for the 260/230 ratio from 0.98 to 2.01. Are these values acceptable, and what information can I gain from them?


texts: Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?


texts: What is the difference between nucleotide polymorphism (θ) and nucleotide diversity (π)?

texts:
In my population genetics book (see reference at bottom) they define them as:

Nucleotide polymorphism (θ): proportion of nucleotide sites that are expected to be polymorphic in any sample of size 5 from this region. Of the genome. $\hat{θ}$ equals the proportion of nucleotide polymorphism observes in the sample (S) divided by $a_1 = \sum_{i=1}^{n-1} \frac{1}{I}$. If n= 5, $a_1 = \frac{1}{1}+ \frac{1}{2}+ \frac{1}{3}+ \frac{1}{4}+ \frac{1}{5}=2.083$
Nucleotide diversity is the average proportion of nucleotide differences between all possible pairs of sequences in the sample. In R, I came up with that code which is in accordance with what is in the book.

   data # Only polymorphisms
   total.snp # This is the total number of sites that were looked (e.g. 16 might be polymorphic over the 500 sites that we've looked at. So 484 sites are monomorphic)

   n = nrow(data) # Number of samples
   pwcomp = n*(n-1)/2 # Number of pairwise comparisons
   for(i in 1:n.col){ # Compute the number of differences in the samples that are polymorphic
     t.v = as.vector(table(data[,i]))
     z = outer(t.v,t.v,'*')
     temp= c(temp,sum(z[lower.tri(z)]))
   }

   pi.hat = sum(temp)/(pwcomp*total.snp) # Nb of different pairwise comparison/(nb all pairwise comparison * total nb of loci (polymorphic or not))

In the book, they say

  On the other hand, there is a theoretical relation between θ and π that is expected under simplifying assumption that the alleles are invisible to natural selection.

In summary θ = π with this assumption and large sample sizes.

So what is the difference in the
Why are we calculating both
(what could they tell us)?

Hartl, D. L., & Clark, A. G. (1997). Principles of Population Genetics (3rd ed.). Sinauer Associates Incorporated.


texts: What is the role of CRISPR-dCas9 in gRNA-dCas9 transcription regulator complexes?

texts:
In this paper1, I read that mutant versions of Cas proteins such as a deactivated Cas9 (dCas9) are used alongside a guide-RNA (gRNA) to form variants of CRISPR tool that can function as transcription regulators.

Since the mutant Cas9 has lost its nuclease functionality, the mutant gRNA-dCas9 complex can "block" transcription factors such as RNA polymerase from binding a certain gene, hence repressing transcription or elongation.

Another way that dCas9 can regulate transcription is by "carrying" another transcription factor - be it an activator or repressor - and this can be done by engineering a dCas9 fused to the other transcription factor of choice.

I understand how the dCas9 can block the binding of another transcription factor to repress transcription initiation or elongation, but what is the point of fusing another transcription factor with the dCas9? It seems to me that in this scenario, the dCas9 is just a passive carrier of the transcription factor that is actually doing the job, so why can't the transcription factor be fused with the gRNA instead, so that it can directly affect transcription when the gRNA forms complimentary base pairs with the target gene, instead of it being on a passive dCas9?

 1. Jusiak, B., Cleto, S., Perez-Pinera, P. and Lu, T.K., 2016. Engineering synthetic gene circuits in living cells with CRISPR technology. Trends in biotechnology, 34(7), pp.535-547.


texts: How do I generate a phylometric tree given species names?

texts:
I have a list of species. I want to put those names into a tool and get back a visualized tree that includes names of shared order, suborder, family and genus.
Is there an existing tool that does this job for me or do I need to program my own solution?

(The solutuion in the other thread only shows the name of the species but not order/suborder/family/genus)


texts: What is an example of a plant species that is a halophyte with seeds that germinate quickly?

texts: I’m doing an experiment on the effect of salt concentration on the germination of seeds from halophyte plants. What would be an example of a species that is suitable for such an experiment? I would prefer a species the seeds of which germinate relatively quickly under not very difficult conditions.


texts: Which species of Hemiptera is this preimago, seen in 2015 in Rome?


texts:
In the history of animal evolution, both the Cnidarians and the Echinoderms have radial symmetry, according to this cladogram:

Source: http://www.cpalms.org/Public/PreviewResourceLesson/Preview/45851

Do both groups having this feature mean radial symmetry evolved twice?


texts: Where can I find anthropometric data for different ethnicities?

texts:
I get that this is a sensitive topic, but please trust me, the very reason I'm asking is because I want to represent a people properly.

There's a video game where peoples of different ethnic backgrounds appear. Those people are automatically generated with full 3-dimensional models, that are to look realistic. It follows a simulated gene structure: there's about a hundred genes, for stuff like shape of the cheekbone, hip width, eye, skin and hair colour, et cetera; each with their own alleles, and they get inherited by offspring of those characters, so you get children that look like their parents, even when they are of mixed race.

Now, every "ethnicity" (e.g. Mongolian) in the game has a template determining the alleles that occur in that ethnicity's population. It is quite a clever system. And as I am modifying the game, I want to add a new ethnicity. Specifically, Native Mesoamerican. I want to go about this objectively; looking up photographs of Nahua people and eye-balling it from those references will not be very accurate, and it will not do justice to the people I want to put in the game. What I need is a dataset of anthropometry, of human phenotypes as found in a specific native population; of the exact way people commonly look. The more detailed, the better.

The best source I have found so far is the Handbook of Middle American Indians, of which the 9th volume deals with physical anthropology. However, the book is not fully digitally accessible, unlike its sister work, the Handbook of South American Indians. I am prepared to buy the book, but given that it is from the 1970's, and given that I like my wallet, I first want to ask if there's any open sources, and more modern ones, that people here know of.

And at risk of sounding even more insensitive: a comparative dataset or study of ethnicities beyond just Mesoamericans would be most helpful, because it allows for comparison with the ethnicities already in the game. That's why I'm asking the question generally.

Note: I'm new to this SE. I'm not sure if this question would be better suited here, or in Worldbuilding, or perhaps Open Data. Feel free to correct me.


texts: Are there specific theories as to what causes cold[-water] muscle cramps?

texts:
The field of what might cause cramps is quite contested with a lot of controversy around the heat/dehydration cramps, but I find it surprising that no specific theories appear to have been proposed (or tested) while swimming, usually in cold[er] water. There's one governmental site that does acknowledge cold and cold water in particular as a risk factor. I for one never get cramps in a pool/water over 18 degree C, but I am quite likely to get them below that, no matter what I do in terms of stretching, drinking etc. (There's one other site that mentions that "muscle spasms" occur during cold-water shock, below 15 degreed C.) Am I correct that no specific theories have been proposed or tested for cold-related cramps?

Interestingly, the cutoff temperature I found experimentally for myself is perhaps reflected in one article:

  during swimming at a water temperature of 18 [deg] C, it is noted that
  esophageal and muscular temperatures tend to decrease, below 37 [deg] C. [3 refs cited for this fact]

So below 18 C water temperature it appears that consistent cooling of the muscles occurs. So I guess one could ask, equivalently, why muscle cooling [below 37 C] can lead to cramps.


texts: What kind of fish is this, caught in Cape Coral, Florida?

texts:
What kind of fish is this?

It was caught in the canal in Cape Coral, Florida. The canals are clean brackish water — a mix of saltwater from the Gulf of Mexico and freshwater from the Caloosahatchee River — but the canal where the fish was caught has gulf access so it should be saltwater. The fish was about a foot long, a little less maybe.


texts: Concentration of degenerate primers should you dilute to?

texts: I'm a little embarrassed to ask but when you have for example four degenerate primers and the end protocol says that the final primer concentration should be 10 µM working stock, should you make the primers 10µM total (2.5 µM each) or 10 µM for each degenerate primer?


texts: Core Biological concepts explained to a Computer Scientist?

texts:
I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as:
Evolution, Selection and Variation, to a Computer Scientist? I am looking for something in the middle. I read Futuyma's book and was very useful, but I would like an explanation I can relate with my background, something to start building "bridges"...

Bibliography suggestions are welcome.


texts: Are Young Girls Stronger than Young Boys?

texts:
According to "common wisdom" the average man has, as a proportion of his body weight, 50% more muscle mass than the average woman. This is in addition to how the average man is several inches taller than the average woman and thus has a larger body mass to take that proportion out of.

Notice the above is phrased in terms of men and women as opposed to boys and girls. I am interested in how strength compares at a younger age. If we took the average ten-year-old boy and the average ten-year-old girl $-$ before the first growth spurt of puberty $-$ and compared their proportional muscle masses, how would they compare? Have any studies been carried out?

Looking for information online about this nets me a hundred accounts from men who remember how, as children, they lost every fight with their older sister. The problem here is that in any contest between siblings (twins excluded), the older sibling most likely has a height and mass advantage. So it's hard to say much about proportional muscle masses.

My guess is that if we took twins Bill and Roberta then they would have similar muscle-mass proportions up until about age 10. From then Roberta would have a growth spurt and increase proportional (as well as absolute) muscle mass due to extra testosterone (in addition to extra estrogen). A few years later Bill would have a growth spurt and increase proportional muscle mass to exceed Roberta's. But she would still be stronger than him, until he caught in terms of height.


texts: Does the 'President' have 2 Billion Leaves?

texts:
The world's second-largest known tree, the President, in Sequoia National Park is 3200 years old and is said to have 2 billion leaves (Source: https://youtu.be/vNCH6uhB_Bs?t=59).

Is this correct? And how was this number arrived at?

In other words, how is such an insanely large number possible?


texts: Where is the H+ ion in this step of glycolysis coming from?

texts:
(from Fundamentals of Biochemistry by Voet, 5th ed.)

In this step of glycolysis, I'm not seeing where the $\ce{H+}$ ion on the product side is coming from. It seems to me that the G3P's aldehydic H is replaced by phosphate, and that H is given to $\ce{NAD+}$ to make NADH. So where is the extra $\ce{H+}$ coming from?


texts: Are genotypes with the same two alleles equivalent even if the alleles come from different parents?

texts:
I am looking at the following question

  If $m$ alleles may occur at a given locus, how many distinct diploid genotypes are possible at that locus?

The obvious answer is that there their is $m$ possible paternal alleles and $m$ possible maternal alleles so the solution is $m^2$. However this considers inheriting allele $a$ maternally and allele $A$ paternally as the same as inheriting $a$ paternally and $A$ maternally.

If they are considered distinct we have double counted all matchings apart from matchings where the same allele is inherited maternally and paternally so I think the answer to the question if $Aa$ is the same as $aA$ would be $\frac{m(m-1)}{2}+m$

My question is which if any of my interpretations is correct?

Thanks in advance


texts:
A biologist wrote to me:

... C- or N-terminus,... For example, a C-terminal tryptic peptide like AGWRGSDSHSR, would be...

I don't have any idea what that is. When I google the term ("C-terminal tryptic peptide"), nothing obvious came up. What's that? Why AGWEGSDSHSR is a "C-terminal tryptic peptide"?


texts: Is there a theoretical maximum on the number of sexes a given species can have?

texts:
Background: To the best of my knowledge, most sexually-reproducing species of organism have two sexes, although there are also sexually-reproducing species of organism (flatworms come to mind) which have only one sex. (Depending on one's definition of sex.)

Many species of fungi are both sexually reproducing and apparently have more than two sexes. (Depending on one's definition of sex.)

There are also species of lizards with more than two biologically determined "gender morphs". It is even more debatable than in the case of fungi whether these morphs should be considered separate "sexes" or not, since their mating compatibility network is bipartite.

Question:
Is there a theoretical maximum on the number of sexes a given species of organism can have?

Elaboration:
There would also be a lot of different possibilities -- already with three sexes, one can imagine at least two different means by which sexual reproduction could occur -- any one of three combinations of two individuals from two distinct sexes (most likely in "rock-paper-scissors" fashion), or the combination of three individuals from all three distinct sexes.

How, for example, might either of these two scenarios be maladaptive compared to sexual reproduction of two individuals in species with two or fewer sexes?

I am asking about species with more than two sexes/mating types in general, not necessarily about situations where more than two sexes are involved in a single reproductive event. (Contrast with this related question.) I am also not restricting to animals, or even multi-cellular organisms, or even eukaryotes, since these restrictions might affect the answer. (Contrast with this related question.)

Note that this answer to the second related question implies that we should expect the mating compatibility network of anisogamous sexually reproducing organisms to be bipartite. But note that, as in the example of the side-blotched lizards, this doesn't necessarily preclude having more than two sexes, nor does it give a theoretical maximum to the number of possible sexes. And since I don't want to necessarily restrict to anisogamous sexually reproducing organisms (i.e. isogamous ones would also be fine), then that answer also does not provide a theoretical maximum for isogamous sexually reproducing organisms either.