texts: What compounds are consumed/produced by Staph. aureus grown on Mueller Hinton agar over time?

texts: I wonder what are the essential components on Mueller Hinton agar that S. aureus consumes and produces. I imagine there are preferred energy sources and as soon as those compounds run out the organism is changing to different ones. Did anyone ever measure a time series with Staphylococcus? Any references would be appreciated!


texts: Suitable writings for self-study in general biology/chemistry

texts:
I have recently commenced a graduate education in mathematics. Since I am currently attending extra classes in programming, which are not included in my education, my institution will not let me attend further courses in biology. Hereby, my question is simple:

What are suitable writings for self-study in general biology/chemistry? By general, I mean somewhat of an university-level introduction of mentioned fields.

My level of knowledge is slightly above "advanced" high school chemistry/biology.

(I apologize for my bad english, I'm Norwegian.)


texts:
I am wondering how can I control my converted DNA!
I converted my DNA with bisulfite then I amplified the converted DNA with specific primers of BSP and purified my product and finally sequenced the product!
In which step should I control my DNA? And what is the protocol?
thanks for any advice.


texts: What are the classical adaptations of amphibians?

texts: My question is about amphibians in humid or underwater environments. What biological adaptations can found in them, further what purposes do they serve?


texts: Why do neurons die so quickly (relative to other cells) when deprived of oxygen?

texts:
This question could be considered a follow-up question to Why is a lack of oxygen fatal to cells?, although the top answer there does not address why damage starts to pop in.

The answer says this:

  Neurons are also highly metabolically active, which means they
  generate more waste products. A buildup of nitrogenous waste products
  in the cell (and bloodstream) can be potentially fatal due to it's
  effects on pH (screws up enzymes and a whole slew of biochemical
  reactions)

But when the brain is deprived of oxygen, metabolism shuts down. So waste products aren't being generated anymore.

====

Basically I'm wondering - what causes neurons, in particular, to die so quickly (relative to other cells, like kidney cells) after they're depleted of energy?


texts:
I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change perspective - lots of genes that I would expect to be affected have the highest fold change values. However, from a q-value perspective very few of the results look promising, having q values > 0.05.

My question is, given 2 replicates, how is the q value calculated? Surely if there was high variance between replicates but the difference between experimental conditions was also large then the q-values would be correspondingly high?

In this case, can I, or should I, really trust the q-values?


texts: If there is more dopamine action in the mesocortical pathway in schizophrenia, then schizophrenics should always be in euphoric state. Instead, schizophrenics often lack motivation and do not experience pleasure. Why?


texts: Removal of the Initial Methionine in Venus for FRET

texts:
I'm working on building some FRET reporters.  In addition to a cleavage site (of varying composition from 15-18AA), a 1 AA linker, I'm using Venus and Cerulean.

Initially I was worried that 18AA would be too long, but it does in fact give a fair signal.  For reference, I believe the Förster radius (Ro) is 54Å.

I am now working on further optimization.  Does the removal of the intial methionine cause any problems for Venus if it is the second protein in the FRET pair?  The basic layout is:

Cerulean - Link - Cleavage - Link - Venus

And I'm wondering if cutting the Met from Venus might bring me 1 AA closer and therefore a slightly better signal.  I have seen it published both ways, and I was wondering if anyone had tried both or just knew theoretically that it wouldn't matter.


texts: What is going on with these buccal epithelial cells?

texts:
A pooled saliva sample from a 70 year old male. What is happening with these cells?

Are these cells undergoing normal apoptosis?

In the video, the cytoplasmic movement looks liquefied and jelly-like (A).

B looks more granular, with small vacuoles that seem to have bacterial activity in them (what could this be?).

Elsewhere in the sample were completely detached, intact nuclei.

Could this be indicative of diabetes? http://www.jdrntruhs.org/temp/JNTRUnivHealthSci1133-9277352_023437.pdf


texts: Reasons for a flower type to consume water faster than another?

texts:
This is an easy experiment where you put a white flower into a recipient filled with water and liquid watercolor, so that the flower gets dyed.

While doing this experiment for different types of flowers, and assuming equal ambient conditions, what would be the most important characteristics  (e.g. flower size, petal length, stem thickness, number of petals...) and the biological reasons for certain flower type to consume water (and get itself dyed) faster than another? (e.g., does a thicker stem mean the xylem is stronger?)

More specifically, I'm interested in comparing a rose like this and a carnation (like the one shown in comments) as an example to the answer.

(Note: I couldn't show a carnation sample image due to my reputation being lower than 10, but I'll update it as soon as I can).


texts:
I am reading on vasoconstriction on wikipedia. The article states that:

  When blood vessels constrict, the flow of blood is restricted or decreased, thus retaining body heat or increasing vascular resistance.

Why/How exactly is the heat retained when blood flow is decreased? Isn't it the case that when things slow down they generally get colder?


texts: Is there an adhesive that could used for larval fish?

texts: I am currently working on an experimental design that requires a larval fish (~ 4mm long) to be affixed on a metal wire tip on its dorsal side. Now, I was thinking of a glue or adhesive to do the job, but it doesn't have to be strictly these, anything that sufficiently attaches the fish to the metal wire tip would do. The glue/adhesive would have to work well on wet surface and, ideally, something that is not toxic. Any advice or ideas are welcome.


texts:
Can anyone summarize the mechanism by which when an object of a given temperature is placed in contact with, say, the skin on a human fingertip, the average speed of the particles of the object is converted into nerve signals to the brain?

If you can answer that, how about the format of how the temperature is encoded in the nerve signals?


texts: Do animals with very small eyes see microscopic objects?

texts:
I understand that many small creatures have very elementary eyes: they are not scaled-down versions of the human eye but as I understand it often just light-sensitive organs for detecting movement.
However, a mouse I would guess has an eye that is like the human eye but probably less than 1% the size. So does that mean that a mouse sees details that humans can't?
There has been recent evidence that ants might recognize their own reflections. Now, I know the structure of insect eyes is very different from mammalian eyes but if indeed they can recognize themselves in a mirror, that implies that their eyes can perceive very small details.
I could also imagine that things like wavelength mean that details of very small objects simply can't be perceived by bouncing visible light off of them -- that is why their are electron microscopes and so I could believe that mice, etc. can see bacteria, etc. any better than we can.


texts:
I have in my flat a plant which sometime make strange flowers. When the start it looks like plastic stars:

Then the flowers are opening after few days and looks like this:

The smell is a bit strange (I cannot say bad but definitively not good as other flowers). In general this plant does not need many watering and even I am in Switzerland, I guess it is living normally somewhere else.

For the size, mine is quite small (30 cm high but many wires) but my mother have a very long one along the wall (few meters).

Many picture with higher resolution are in my flikr gallery.

Anybody can tell me what is the name of this plant and where it lives normally?


texts: Could an exposure to a small amount of viruses result in an easier course of the disease?

texts:
According to Gunther Hartmann (Professor of Clinical Chemistry and Pharmacology at the University of Bonn) cited in this article (Süddeutsche Zeitung, in German)

  Die Zahl der Erreger hat bei Erstinfektionen Einfluss auf den Schweregrad der Erkrankung.

My translation:

  The number of pathogens during the initial infection affects the severity of the disease.

Leaving ethics aside I was wondering about the following:

Might it be an option to get infected by only a tiny amount, suffer only light symptoms and reach immunity (similar to a vaccination but probably more risky)?
Does the transmission path also affect the severity of the disease(inhaled vs. infected vs...)?

Edit: As Chris pointed out in his comment there is not enough research for Covid-19 yet so I would be also interested in findings from other viral infections.


texts:
If I want to turn teosinte into corn, using ancient methods like the Native Americans did, then how much time it takes, and what do I have to do?

For the sake of the question, let's assume that time is not a problem for me. Say I live 10,000 years. But of course, I prefer to have maximum efficiency. If I can get the result in 3,000 years, that's better than 5,000 years.


texts: Systematic difference of diversity between sister taxa?

texts:
When looking broadly at the tree of life, my feeling is that, after a divergence there is almost systematically one taxon that speciates way more than the other.

(There will have some approximations below it is not really the point of my question to discuss whether the urochordata is a sister group to the vertebrates or not.) Let's look at the kingdom Animalia for example:

Chaonflagellata vs "the others"
Sponges vs "the others"
Cnidaire and cténaire vs "the others"
Protostomia vs Deuterostomia (both are fairly equally diverse diverse! Some might not be happy with this claim!)...let's continue with the Deuterostomata
echinodermata vs chordata
cephalocordata vs vertebrata

etc ...

My questions:

Is there really a systematic difference in diversity between the branches?
Is this difference can be explained by chance?
Is it only a bias due to out ability to recognize more species in animals that look more like us (or a bias due to something else)?
Does it make sense to say: the more diverse is a taxon, the more likely it is that it gets even more diverse (because each species might have an equal chance to speciate or something like this)?


texts: Is one Short Tandem Repeat (STR) enough for a reliable identification?

texts: The lab simulates the analysis of just one STR in the genome. Would this analysis be sufficient for a reliable identification in real life? If not, explain what could be done using DNA to identify someone more reliably.


texts: Are there human-ingestible liquids that do not contain water?

texts:
My son asked me a question that stumped me: Is there anything a human can drink that does not contain water?

It stemmed from a conversation in beverages in general where I was pointing out that they all are based on water...coffee, soda, milk, etc.

That's when he asked if there are any beverages that don't contain water. Given that nearly all of the water and even solid food I could think of contains water, I couldn't come up with anything, but now I'm curious about it to so came here to ask the experts!


texts: How do beneficial features evolve in species without progressing through detrimental stages?

texts: I'm thinking in particular of wings on birds that would - I'm guessing - have to progress through stages during which they confer no particular advantage. Or is it that all evolved features must have followed a path of incremental benefit therefore imposing a fundamental limit on what evolution through natural selection can "achieve"? (features that are not beneficial while gradually appearing cannot be evolved)


texts: Why are Oxyuranus snake species named Taipan?

texts: It is interesting, why are Oxyuranus species called Taipan. The snakes are Australian but taipan looks like of Chinese origin word (it means big shot - important person).


texts: Start studying mathematical biology from basics

texts:
I am really passionate about theoretical and quantitative biology and I would like to build my future career around this topic.

I've just got my bachelor's degree in biology (ecology) but scince I've had only one math class through the years, my math skills are very poor, so I have problems in understanding even simpe models. My main interests are population dynamics, adaptive dynamics and game theoretical models of social conflicts.

I would like to improve my skills, but I have just no idea where/how to start. Could you give me some advice about textbooks or online resources?

I have almost no knowledge in the field of math, I am interested in resources for complete beginners. And I would also appreciate any suggestions about skills/topics I should master if I am interested in these biological phenomena.

Thank you!


texts: Where do the lysines come from during ubiquitination?

texts:
I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from?

Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine available on each of the additional Ub added to the chain? After the first Ub is added onto the target protein, does the E2/E3 complex still have to bind each time a Ub is added to the chain?


texts: Basic Modelling in Quantitative Genetics

texts:
I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a very simple model. I welcome any explanation of some other classic model of the evolution of quantitative traits.

Scenario

Consider a haploid population of constant size $N$. The fitness of the individuals is determined exclusively by a single quantitative trait $z$. $l$ loci codes for this trait. The genetic value at each locus adds up to give the quantitative trait $z$. The mutation rate at each locus is $\mu$. A mutation changes the genetic value at any given locus by $+ \Delta z$ with probability $\frac{1}{2}$ and by $- \Delta z$ with probability $\frac{1}{2}$. If you prefer to consider the effects of a mutation to be drawn from a normal distribution with mean $=0$ and variance $= \sigma^2$, please feel free to do so. The fitness $w(z)$ of an individual is given as a gaussian function of its quantitative trait $z$

$$w(z)=\exp\bigl(-Vz^2\bigr),$$

where $V$ is the strength of selection. The optimal phenotype is $0$, that is $w(0)=1$. The larger is $V$, the more severe it is to be at a given distance to the optimal phenotype. If you want to assume that the fitness $w(z)$ is some other function of the trait $z$, such as the even more simple $w(z)=z$, please feel free to do so. For simplicity, we assume no environmental variance on the quantitative trait.

Questions

What is the equilibrium mean fitness $\bar w$ of the population?

What is the equilibrium genetic variance (=phenotypic variance) for fitness $w$ and for phenotype $z$?


texts: Are there any mutagens that can undo the mutations they cause?

texts:
I was reading a section from my textbook about tautomeric shifts, and it seems to suggest that there are some mutagens that can be directly responsible for the phenomenon. The section is mainly describing spontaneous mutations as opposed to induced mutations, and examples of mutagens are mentioned. However, the author explicitly states that the sort of changes made to DNA due to spontaneous mutations also occur at a higher rate during induced mutagenesis.

If a tautomeric shift can occur due to mutagenic activity, is it possible for the mutagen to undo and "correct" the mutation by reversing the shift? If so, what kind of chemicals or physical mutagens (e.g. radiation) would be involved?


texts: For how long can a person drink sea water?

texts:
How long could a person of lets say 18 years be able to drink sea water without getting too much into trouble ? Or can a person drink it without noticing that it is a very bad idea ? I don't mean in just 1 drink session but like can one manage a day or two ? Can one drink it and go to sleep and be still healthy (although very thirsty) in the morning ?

(this is just a hypothetical question, I'm not a scientist at all, I'm not sure what tags to use actually)

Additional brainstorming:

kidney failure
any other organ failure
dying of thirst
...


texts: How to name a case of convergent evolution where the same mutation is involved in both lineages?

texts:
Definition of Convergent evolution - from Wikipedia > Convergent Evolution

  Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function, but that were not present in the last common ancestor of those groups.

Examples

-- Lactase --

Humans have evolved the ability to digest lactose at adult age twice; once in Europe and once in Africa. Different mutations are involved in European lineage and in African lineages.

Source: Tishkoff et al. (2007)

-- White fur --

Beach mice and mammoths have both evolved white fur independently. The same mutation is involved in both lineages.

Source: Römpler (2006)

Question

Is there a term to differentiate convergent evolution that involves the same mutation in different lineages from convergent evolution that involves different mutations in different lineages?


texts: How do transport/carrier proteins rotate during facilitated diffusion?

texts:
In my book, it is written that when a molecule binds to the carrier protein then the protein rotates and releases the molecule inside the cell. I want to know how is this possible. Wouldn't the surrounding phospholipid molecules or other proteins hinder its rotation?

EDIT

The rotation axis is in the plane of membrane

Source : http://ncert.nic.in/ncerts/l/kebo111.pdf (page 177, Third paragraph)


texts: If aging is due to accumulation of damages in DNA, then shouldn't the DNA in gametes also be damaged and so the next generation should be borne old! How does gametes avoid this DNA damage accumulation?


texts: Does frequency of eye blinking reveal anything about human biology/nervous system?

texts:
I'm looking at an output of a single dry sensor EEG headband with the sensor positioned above left eye. As a side effect of it's placement, the device picks up eye blinks, and some eye motion as changes in the amplitude of the raw output waveform. It is clearly visible, and I can probably detect it algorithmically.

My question is - does frequency of eye blinking (not controlled) reveal anything about the state of (autonomous?) nervous system, or processes that take place within the brain? For example, what is the difference between blinking involuntary X times per minute versus Y times per minute for the same individual? Does blinking get suppressed in response to some stimuli, like loud noises, speech, etc?

I appreciate your input!


texts: Do different acids have different effects on the enamel of our teeth?

texts: Do different acids or acidic solutions corrode the enamel of our teeth at different rates or in different ways? Are these effects present even when controlling for pH?


texts: Could potatoes that have been refrigerated for 142 days still sprout?

texts:
I know that potatoes can still sprout even after being refrigerated, but could you refrigerate them for 142 days still use them as seeds to grow more plants after that?

As for the temperature of the fridge, look at this.
 Considering that, what would be likely?

What about frozen or hermetic potatoes?

If anyone's wondering why I'm asking such a strange question, here's why.


texts: Location of microbes causing eliminated diseases

texts: Do eliminated diseases like polio, smallpox etc still exist in locations they have been eliminated from or in the wild or did we just make them go extinct like the dodo?


texts: Melatonin production, sleep, and "cyan light"; how might this finding be possible?

texts:
The BBC News article Cyan colour hidden ingredient in sleep describes research that suggests melatonin levels as measured in saliva could be affected by the presence or absence of cyan color in a displayed screen, even when the color balance was adjusted so that the difference was not visibly perceptible.

The colour cyan - between green and blue - is a hidden factor in encouraging or preventing sleep, according to biologists.
University of Manchester researchers say higher levels of cyan keep people awake, while reducing cyan is associated with helping sleep.
The impact was felt even if colour changes were not visible to the eye. (emphasis added)
The researchers want to produce devices for computer screens and phones that could increase or decrease cyan levels.

Is cyan going to keep you awake?

I am guessing that this even possible because color perception comes through the sensitivity of three (or four?) color channels and so two different spectra can appear to be the same color. An example might be that a green wavelength might appear to be the same color as the mixture of a blue and a yellow wavelength if properly adjusted.
But if the two stimuli are adjusted to have the same or similar mix of signals in the individual's color receptors, how might the melatonin production still be affected?
edit: According to Wikipedia, monochromatic light would have a wavelength in the range of 490 to 520 nm, and if you wanted to create a visual impression of cyan, you'd use a mixture of Green and Blue channels:
Wavelength    490–520 nm
Hex triplet   #00FFFF
sRGBB         (r, g, b)   (0, 255, 255)


texts: How mosquitoes get their food and survive?

texts: How do mosquitoes find and get their food? For how much time can they survive without food?


texts: Have there been any studies on 'surf balls'? (not related to surfing)

texts:
I know the title sounds like something else, but I'm actually wondering about these things, which are also apparently called 'whale burps':

This one was found on a beach on Lake Michigan.

Does anyone know if any scientific studies have been done on these? If so, can you refer me to them?


texts: How does an increase in CO2 concentration affect Photosynthesis and Transpiration

texts:
I noticed a strange thing in my book. At one place it says that an increase in CO$_2$ concentration in the outside air decreases the rate of transpiration but at the other place it says that an increase in the level of CO$_2$ in the environment increases the rate of photosynthesis?
Can we reconcile between these two statements? I don't think so because both the processes mostly take place through the stoma so how is it possible that when transpiration decreases photosynthesis increases ?How ?


texts: Measurement of glucose concentration in the human brain

texts: If I want to measure the exact glucose concentration in a human brain then how can I proceed to do that? Is there any technique or assay to do that?


texts: Can the human gut work with other type of gut bacteria?

texts:
I was wondering if the human body would be capable of functioning with, say, cellulolytic bacteria in their gut (instead of or in addition of their current bacteria), like that of ruminants and if they'd be able to digest cellulose thanks to it.

Couldn't find any papers on that, only on the implantation of faecal matter from a healthy gut to a sick one, nothing interspecific.


texts: can self-fertilization in flowers be called asexual reproduction?

texts: Suppose a flower having both male and female reproductive parts is self-fertilized then can this be called asexual reproduction...?I'm quite confused cause in this case the fusion of male and female gametes do take place but again the gametes are from the same parent....please help.


texts: Is it biologically possible for an adult's eye color to change?

texts: Can it be that the adult eye can change color? Specifically my question is about a unilateral color change, such that the color of one eye remains constant, while the other changes color over time. Can this happen? Or can it be related to light-scattering, or an illusion of some sort?


texts: Why was cotton chosen to grow on the moon?

texts:
The choice of plants for the first lunar ecosystem is a bit unusual.

They are growing cotton, rapeseed and potatoes.

Why did the Chinese scientists choose them? Is it because of their ability to thrive in such an environment or because of their possible  contribution to sustaining life in long space missions?


texts: Can there be multiple EPSPs with constant current injection to a neuron?

texts: I am performing a current clamp experiment and measuring the change in membrane potential of a neuron with different current injections. A constant current of 50pA is injected to the neuron for 100ms. The current is not enough to cross the threshold for the neuron so there are no action potentials. But will the neuron have multiple EPSPs in this setup?


texts: Spider with brown zig zags on abdomen and black head

texts:
Found this spider roaming around my room the other day.. can someone tell me the species?

Location: Central KY, USA

Also, here's a video of him moving around in a glass candle lid, where you can get a really good look.


texts: How is magnet based bead capture used for indexing-first ChIP-seq?

texts:
The context for this question can be found in this paper by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they

sort cells
sonicate chromatin
immobilize chromatin on Dynabeads with anti-H3 antibody
index chromatin (barcode)
pool samples
perform H3K4me3 ChIP
sequence

I am interested in the purpose of step 3 and how that contributes to step 4. What could be the purpose of essentially adding another IP step?

The Supplementary Materials (where all the methodology is described) mentions that "magnet based bead capture was used to efficiently add, wash and remove the different master mixes used in the indexing process." I'm somewhat confused as to how this adds efficiency, as I thought barcoding prior to sequencing is typically performed as a ligation step without selection (they perform the H3K4me3 ChIP after the indexing step anyway, so why select for histone H3 chromatin first?).


texts: How does lactulose cause the removal of ammonia from the colon?

texts:
Lactulose is also used to reduce the amount of ammonia in the blood of patients with liver disease. It works by drawing ammonia from the blood into the colon where it is removed from the body.
[Source]

How is ammonia removed from the colon?
From the quote above it sounds like ammonia removal must be some other mechanism than absorbing it into the blood, correct?


texts: What kind of microscope should be used to view biological structures (such as spores) roughly 5 µm in length?

texts:
I would like to be able to identify genera of fungi based on the shape, size, and colour of spores. So the requirements are:

Must be able to view a 5 micrometre object clearly with reasonable resolution
Must be true colour
Must facilitate the measurement of an object within reasonable accuracy (500 nanometres would be nice)
Should be inexpensive (\$100-\$400) fingers crossed
Bonus: Be able to take photos

What type of microscope do I need? What magnification/resolution? Is there a good rule of thumb relating size of object with magnification?

How do I find and purchase a decent microscope after defining my requirements? Any tips?

Blue light is ~450 nm, so does that mean I will not get very good resolution?

(For the sake of context: I have absolutely no formal experience in biology, but I have recently taken an amateur interest in mycology and might enrol in an undergraduate course as part of my degree at some point.)


texts: Why does strenous exercise cause vision of "lights"?

texts:
I had a hard climb a week ago. I got so tired then any time I closed my eyes I saw these lights inside my head. I see these lights almost every time that I run fast or some thing like that. What are they and where do they come from?

Here is a picture I drew using Photoshop ;)


texts: Why is an A-U bond less stable than an A-T bond?

texts:
I have encountered the following fact many times, but have not yet encountered a possible explanation for it. Will you please help me understand the molecular mechanism by which the bond between Adenine and Thymine is more stable than the bond between Adenine and Uracil?

Thanks in advance


texts: How to remove protein contamination in plasmid isolation.

texts: I have already tried phenol chloroform extraction, isopropanol precipitation, did not work. It is giving high 280 reading.


texts: Is "TATA signal" synonymous with "TATA box"?

texts:
In the text I'm translating I have a diagram of an expression vector. It has a lot of marks, and one says "TATA signal". I googled and found the expression "TATA box".

Are these expressions fully synonymous and interchangeable?

From Wikipedia:

  Considered to be the core promoter sequence, it is the binding site of either general transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase.

So basically "TATA box" serves as a signal to the transcription machinery that says "transcribe this"?


texts: How exactly does alcohol solution kill or neutralize viruses?

texts:
To reduce the risk of infection by viruses (including 2019-nCoV) the CDC suggests:

Wash your hands often with soap and water for at least 20 seconds. Use an alcohol-based hand sanitizer that contains at least 60% alcohol if soap and water are not available.
Avoid touching your eyes, nose, and mouth with unwashed hands.
Avoid close contact with people who are sick.
Stay home when you are sick.
Cover your cough or sneeze with a tissue, then throw the tissue in the trash.
Clean and disinfect frequently touched objects and surfaces.

To my knowledge most alcohol-based hand sanitizers use ethanol. In clinical settings sometimes isopropanol is also used.

Question: How exactly do alcohols, especially ethanol and isopropanol provide some disinfecting action against viruses? Are the virus particles simply dissolved? What happens?


texts:
Richard Feynman mentions in the third chapter of The Feynman Lectures:

  So the real system is in the GDP-GTP transformation; in the dark the GTP which has been stored up during the day is used to run the whole cycle around the other way. An enzyme you see, does not care in which direction the reaction goes, for if it did it would violate one of the laws of physics. 1

Which law of physics is Feynman referring to and how would it "caring" violate it?

Chapter 3 Vol. I of The Feynman Lectures, just search for "violate"


texts: Why does sequence of amino acids presented on the Catalytic Site Atlas from a given protein differs from the sequence on the RSCB Protein Data Bank

texts:
I wanted to compare the amino acid sequence of enzymes for this project I'm working on and need to compare them at their catalytic site. For that, I went to the Catalitic Site Atlas to get the information on the catalytic site, but since they don't offer an easy way for me to download the structure data programmatically I downloaded it from the RSCB PDB by downloading the fasta sequence. When checking for the catalytic sites it wasn't matching what the CSA was telling me and that's when I realized that they are different files. Take for example the 3nos, the CSA presents the following sequence:

MGNLKS...

While the PDB presents the following sequence:

PKFPRV...

Why aren't they the same sequence if it's the same protein?

Sorry if it's a noob question, I'm not a biologist, just a computer scientist who happens to like bioinformatics.

Important info:

The CSA data comes from here while the PDB data comes from here


texts:
Reading from the internet, I've come across quotes that said stem cells have the potential to replicate indefinitely. However, there are other sources that say cells that are specialised will have their telomeres shortened each time the cell undergoes cell division until it renders them unable to reproduce.

I would like to ask if stem cells that replicate in terms of self-renewal will have their telomeres shortened as well to a point where they can only renew themselves a set number of times before they cannot undergo cell division anymore.

Thank you.
[P.S. I'm no biology student, just a curious person seeking answers, hence do forgive me if this is supposedly a basic question. I've tried looking online for answers but it seems quite difficult to get a satisfactory or targeted answer.]


texts: Why do some fruits have their seeds disintegrated

texts:
Sometimes I'd come across a Lychee or a Naseberry whose seeds are kinda disintegrated.. in a thick powdered form, either completely or partially. What could cause such a thing? And is the fruit with such seed harmful?

I wish I had pics to show but it happens rarely.

Here's a normal Lychee with normal seed:

And what I sometimes find in place of the solid black seed is something that has the texture like this wet dirt:

but obviously more like the seed itself that has disintegrated into a thick wet powder.


texts: How can different ion channels of the same type have different cell responses?

texts: The NMDA receptor is an ion channel and contributes to synaptic plasticity and memory. It is said that calcium ion flux through the receptor is critical for this mechanism. However, there are other ion channels that let calcium ions into the cell, how come they don't contribute to synaptic plasticity (to my knowledge)?


texts: At school we were told on scale of 0 through 1000 the animal kingdom ranges from amoeba the simplest/primitive being at 0, and Humans the most complex animals at 1000; what are the equivalent complexity species (?) in the plant kingdom? What is the least complex plant, and the most complex?


texts: Clarifying distinction between genetic recombination , translocation. and transposition

texts:
Having thought about the distinciton between these terms I have come up with the following definitions, are these correct?
Translocation describes the relocation of a chromosomal segment to a different position in the genome.
Recombination is the same except:

it usually describes a non-pathological process involving balanced, reciprocal relocation of homologous DNA segments. Translocation is its accidental counterpart.
Translocation usually related to endogenous DNA. Recombination is a broader term that can describe the incorporation of external DNA in bacteria such as transformation or transduction.
The term can be used even more broadly to include independant assortment, which also effectivley acts to "Reshuffle" genetic material.

Transposition:

essentially a special case of translocation which occurs as a result of transposase enzymes acting on mobile genetic elements.

Thanks for your help!


texts: Are all known germs benign in small enough quantities? i.e. Why do we wash our hands?

texts:
We know that we wash our hands because germs can get into our body through the nose, the mouth, the eyes, cuts, etc. But I doubt we can completely clean our hands of germs every time we wash them, down to the individual bacterium or virion, even if we use anti-septic soap. So chances are, even if we keep up with our hygiene, germs still get into our body, only in very very small quantities. So here are some questions:

In theory, is there a dividing line where we can say "ok, at this non-zero count of bacteria or virion, there is still (an arbitrary probability) that a normal healthy person won't get sick" for every germ known to man? If not, are there germs that are known to cause havoc in a healthy person even if he comes into contact with a single individual bacterium or virion?
Do we know a certain trend based on the classification of the germ?
How about the most commonly found germs (whichever they are)?
How about some of the most feared, but not so common, virii known to man, like HIV, ebola, SARS?

I think that without being able to answer some of these questions, especially #3, hygiene would be nothing but a ritual activity (because "it just works").


texts: Why is thrombin time (TT) normal range longer than prothrombin time (PT)?

texts: Reference range for the TT is longer than that of the PT.


texts: (Web)app to search metabolic/signalling pathways

texts:
I'm looking for an application where you can find pathways by selecting a chemical occurring in it.

So, for example,
selecting 6-phosphogluconolactone brings up the pentose phosphate pathway or any other where it occurs as an intermediate or product.

Same could be possible for endocrine or any other signalling. The target organism is human.

Is there anything like this in existence?


texts: Does the genetic expression of specific physical traits ever correlate to behaviour?

texts:
Over at skeptics, there were a couple questions asked as to the correlation of specific physical traits in relation to personality/behaviour.  For instance, the simian line as well as red hair.  Now, I did my best to answer these questions, with what I understand as there being a long history of people attempting to correlate external physical characteristics with behaviour (see the disgraced "art" of phrenology for instance).

However, in answering the simian line question, I did come across some weak correlations.  It got me to wondering if this is an area of exploration in terms of perhaps one gene sequence for a physical trait somehow being tied with another gene sequence for behaviour.

So, do any physical characteristics being expressed through genes correlate to behaviour?


texts: Resource for finding what proteins bind?

texts:
I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. What online resources exist for finding out what a given protein binds or otherwise interacts with?

I am aware of Uniprot and Phosphosite which have proved useful but I am wondering if there are others that I am not aware of.

Again: the question I am trying to answer is "which proteins from list A interact with proteins from list B and vice-versa?"


texts: What happens to the brain during sleep versus unconsciousness?

texts: How does being unconsciousness differ from being asleep and whether it causes breaks in consciousness?


texts:
Just out of some weird thoughts, can a microbe (any single-celled organisms, accepting answers for both prokaryotes and eukaryotes) ingest too much food (e.g. via absorbing too much involuntarily because the surrounding has too much of it,or via phagocytosis) and retain part of it somehow?

Being "overweight" can be characterized by larger than average cell size/mass, presence of numerous intracellular food reserves (like glycogen?). I am guessing these (increasing cell mass and food reserves) would likely happen to some extent. But do these changes affect reproductive fitness (readiness to cell division) of the microbe? (In humans, we can safely say that being overweight is detrimental to reproductive fitness.)

For instance, What would happen when microbes are over-supplied with energy-rich and carbon-rich molecules but not the other nutrients (e.g.NPK)? And once it is switched back to a "stoichiometrically/nutritionally normal" diet, would it likely have a higher/lower reproductive fitness (compared to microbes normally-fed the whole time)?


texts: which signalling pathway is involved in cancer?

texts:
Columnar epithelial cells from the colonic mucosa are studied to identify abnormalities in cell signaling pathways. Abnormal epithelial cells from colonic adenocarcinoma are shown to have a mutation that blocks hydrolysis of GTP-bound active RAS. Normal columnar cells have active RAS protein that undergoes hydrolysis to the inactive GDP-bound form. Which of the following signaling pathways is most likely abnormally stimulated in the carcinoma cells?

a. Jak-Stat Pathway
  b. MAP kinase pathway
  c. p53
  d. Both a & b

I think its MAP kinase pathway because RAS is part of MAP kinase pathway that ultimately leads to transcription and expression of genes but if GTP is not hydrolyzed then RAS will be constantly activated leading to continued gene expression that may lead to cancer but I am not completely sure about it because p53 is also a tumor suppressor gene.


texts: In a vertebrate chimera, are particular organs homogenous genetically?

texts: I have read that a chimera is an organism with two or more sets of DNA, with every cell having one of the sets. Is it possible and common for the two or more sets to be present in the cells of a single organ? I'm confining my question to vertebrates because I don't remember much about the biology of invertebrates from high school, but please don't hesitate to add anything interesting about them.


texts: How much natural genetic variation is there between bacteria of the same species?

texts:
There are lots of questions about how and why there is genetic variation between organisms of the same species, but I haven't been able to find a numerical value for the expected amount of genetic variation.

Let's say we have two different samples of MRSA252. We sequence these samples and get the full genomes of ~3 million base pairs each. What percentage of these bases would we expect to be different (assuming there is no sequencing error)? I figure it will be about 1%, but I haven't been able to find a source.

I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria. An academic source would be much appreciated.


texts:
I have been growing B16F10 Mouse Melanoma cells. I need to extract the genomic DNA and do PCR to amplify a specific region. However, no matter what temperature or magnesium concentration I use, I have no luck.

I obtained mouse DNA from someone who was genotyping mice. I tested the PCR oligos with that DNA, and the reaction worked, so it's not an oligo problem.

The genomic DNA had poor 260/230, about 0.6. I thought the EDTA levels may have been high, so I did an isopropanol precipitation to clean it up. This made the 260/230 ratios about 2.1. But the PCR still didn't work.

What I had noticed during the precipitation however was that the DNA pellets were gray to black. I assume this is melanin, because the cells are melanoma cells, and turn black.

Could this melanin be a problem in PCR?


texts: Ambiguity about the relation between membrane potential and concentration gradient in neuron cells

texts:
I am stuck in an ambiguity about the equilibrium potentials of neuron cells. The following text is picked up from khanacademy website:

In one part it is said that:

We'll start out with K at a higher concentration inside the cell than in the surrounding fluid, just as for a regular neuron. (Other ions are also present, including anions that counterbalance the positive charge on K but they will not be able to cross the membrane in our example.)

If potassium channels in the membrane open, K will begin to move down its concentration gradient and out of the cell. Every time a K ion leaves the cell, the cell's interior loses a positive charge. Because of this, a slight excess of positive charge builds up on the outside of the cell membrane, and a slight excess of negative charge builds up on the inside. That is, the inside of the cell becomes negative relative to the outside, setting up a difference in electrical potential across the membrane.

As potassium continues to leave the cell, separating more charges, the membrane potential will continue to grow. Thus, the building membrane voltage is an increasing force that acts counter to the tendency for net movement of potassium ions down the potassium concentration gradient.

Eventually, the electrical potential difference across the cell membrane builds up to a high enough level that the electrical force driving K back into the cell is equal to the chemical force driving K out of the cell. When the potential difference across the cell membrane reaches this point, there is no net movement of K in either direction, and the system is considered to be in equilibrium. Every time one K leaves the cell, another K will enter it.

In another part it is said that:

The electrical potential difference across the cell membrane that exactly balances the concentration gradient for an ion is known as the equilibrium potential. Because the system is in equilibrium, the membrane potential will tend to stay at the equilibrium potential. For a cell where there is only one permeant ionic species (only one type of ion that can cross the membrane), the resting membrane potential will equal the equilibrium potential for that ion.

The steeper the concentration gradient is, the larger the electrical potential that balances it has to be. You can get an intuitive feeling for this by imagining the ion concentrations on either side of the membrane as hills of different sizes and thinking of the equilibrium potential as the force you'd need to exert to keep a boulder from rolling down the slopes between them.

I concluded the two following information from the above text:

The closer we get to the equilibrium state, the membrane potential
decreases because the concentration gradient decreases. (The steeper
the concentration gradient is, the larger the electrical potential
that balances it has to be)
The closer we get to the equilibrium state, the membrane potential
increases, because positive ions leave the cell.

How to solve this paradox?


texts: Is there any danger in putting a magnet in your ear (next to your brain)

texts:
I recently bought some wireless earbuds that fit right in my ear, so they're very small.
But the method it uses for charging is magnetic, so it has magnets built into the earbud.

I was wondering if there's any danger in keeping a magnet in your ear for many hours every day? I'm not sure if it would affect things in your skull/brain.


texts: What is phenotyping of blood during transfusion process?

texts:
Thallaesemic patients are advised to have only "phenotypically matched blood".I mean the transfusion problems arise mainly due to "grouping problems" like mismatch b/w ABO & Rh+/- so what do this phenotyping mean? Isn't "grouping" of blood enough?

Statutory declaration- the link provided in the q is only to clarify in which context the q is asked & nothing more, like promoting Egyptian Gov. Health Service...(or any other CRAZY INTERPRETATIONS like that)**


texts: Why are tumor suppressor genes recessive?

texts:
In my Intro. to Biochemistry course, we have been studying cancer. The professor has pointed out that tumor suppressor genes are "recessive" while proto-oncogenes are "dominant". Since only one mutation is necessary to turn a proto-oncogene into an oncogene; while two are needed for the malfunctioning of tumor suppressor genes, why is this not the other way around (i.e. tumor suppressor genes dominant; proto-oncogenes recessive)?

All help is greatly appreciated.


texts: Is body energy production and consumption cyclical?

texts:
If we look into how energy is produced by the humans, it always involves some kind of periodicity: fuel combustion rotates engines, water rotates turbines, nuclear chain reactions heat up water, which rotates turbines, dynamo machines, etc.

So that means that with a few exceptions humans produce most energy (electricity) using rotation or some kind of cyclical rotative movement (as it proved to be the most efficient way of doing that).

Now what if we look at the human body? It is producing the energy from the food that we consume, converting carbs and proteins into glucose, which is then broken down into carbon dioxide, water and ATP. This ATP is then used in chemical reactions that are needed to contract the muscles or to send impulses within the brain.

The question is: Does anybody know – are those chemical reactions also cyclical in their nature? And if not, what's the common dynamical property (pattern) that can be observed in them all, if any?

Thank you and sorry for the long intro, but I thought it's important you know where I come from.


texts: What does it mean to "nucleate multi-protein complexes"?

texts:
I am reading an article about the mTOR signalling pathway and I have come across the following:

mTOR nucleates at least two distinct multi-protein complexes, mTOR
complex 1 (mTORC1) and mTOR complex 2 (mTORC2).

I am not sure what is meant by "mTOR nucleates 2 multi-protein complexes". From the paper, I understand that mTOR is a component of the mTORC1 and mTORC2 complexes. I have read the definition of 'nucleate' online and it means to either "to form into a cluster" or "to act as a nucleus for". However in the context of this article, I am not clear about what is meant by "nucleates" in the above statement. Any insights are appreciated.


texts: What type of moth is this that was on my wall in Spain


texts: At what point during an organism’s lifespan do mutations occur?

texts:
I’m a software developer and I’m implementing something called a Genetic Algorithm. I would like some input on when during an organism’s lifespan mutations occur.
Genes mutate throughout the lifetime of an organism. When do the bulk of mutations, which would effect the offspring of an individual, occur? Do most mutations happen at conception and early adolescence, or do a significant number happen between adolescence and parenthood?


texts: Is this a legitimate teratoma for a human pluripotent stem cell assay?

texts:
I can't quite make out this teratoma:

                                    [Source: FIG 3B]

I can kind of guess at ectoderm, mesoderm and endoderm structures based on generalized textbook developmental biology references but it looks like the stain was messed up. Shouldn't a hematoxylin-eosin stain be blue and red? Is this a legitimate confirmation of germ cell development from human pluripotent stem cells?


texts: What can we expect when we culture a mould in a liquid?

texts: I am currently running a short project in my school, where I am trying to look into the biodegradation of dyes from textile effluents using Fursarium sp. Most of the articles that I have read uses a spore suspension as the seed, because it is easy to quantify, and also perhaps reproducible. Well, I was thinking about how vegetative cells, may have different metabolic traits, so what can I expect are the results if I use the vegetative cells as the seed? Also, if I were to use the vegetative cells as the seed, is it considered semi-quantitative if the seed (vegetative cell) is retrieved on an agar plug of equal diameter?


texts: How many cells need to be damaged before a human can feel it as pain?

texts: I'm guessing the answer to this question is rather large. Skin cells die all the time, it seems, and that never registers as painful. But suppose you rupture or otherwise destroy a group of cells, say in the dermis or something, which enough precision to be able to specify the exact count. How many would you have to destroy before it would be perceptible? What if you add a delay between the destruction of each cell in the group? If it was staggered in time, would that make it imperceptible again?


texts:
Can someone comment on this article which claims that biologists have been misleading the masses when they compare the genome of humans and chimps
https://yaqeeninstitute.org/daniel-haqiqatjou/can-islam-object-to-evolution/


texts: Why haven't modern grass based crops overrun wild grasses?

texts:
Modern grass based crops are significantly superior to wild grasses, they grow faster, are stronger stemmed, have larger leaves and higher seed yields in terms of individual seed size, giving germinating seeds a significant head start vs other wild breeds.

I've heard time and again that GM crops will escape into the wild with potentially devastating consequences, out-competing wild plants for space and destroying biodiversity.

So why hasn't this happened already? Our crops are already GM (albeit through different methods and over a much longer time)

Edit:
I have seen the odd crop plant growing in the wild, amongst other grasses, but rarely more than one or two clumps of wheat or barely grass amongst a sea of wild grasses.


texts: What determines the pathway of a neurological signal?

texts:
My question is about the neurological signals. In our body when a signal, for example a hearing signal from hair cells, is built, it goes through a lot of neurons and it passes a lot of synapses. I am wondering how it doesn't lose it's correct path and chooses the right way to auditory cortex? I mean what are the features of a neurological signal that shows it the correct way?

In other words, how can a neurological signal be created and sent through a chain of neurons to the brain, how can it 'know' when entering a synapse contacting multiple neurons which is the correct one for going through it?


texts: Arsenic (V) Reduction to Arsenic (III) by Microorganisms

texts: I am currently doing research on arsenic toxicity in microorganisms, and I learned about arsenic (V)/(III) cycling. Arsenic (III) (usually in the form of arsenite) is generally 50 times more toxic to biological life; however, most bacteria (or at least some) reduce the less toxic arsenate into arsenite. I just do not understand why these organisms would reduce arsenate into something more toxic. This doesn't seem to be an accidental reduction in which the microorganism mistook arsenate for phosphate, as there are plasmids specifically encoded with genes that reduce arsenate. Why is this happening? How would this be an advantage in these organisms and not a disadvantage?


texts: Would biotechnology in agriculture actually decrease biodiversity, as many people say? Does it have to?

texts:
I've heard the claim that because farmers would be using the same seed, you would end up with an entire crop population that could be susceptible to a disease. Like if you had a diverse population of potatoes, not many of them could become blighted, but if you have only one kind of potato on your farm and that kind is susceptible to Phytophthora infestans, then all your potatoes would become blighted.

I was wondering:

Is this really how it works? Like once a seed with a desired characteristic is found, is it cloned? Or would they implement the same gene into many different crops?
If they do clone them, why couldn't they implement the same gene into a diversity of crops? Is it too costly?
Could one use mutagenesis to create diversity? If the seeds are cloned, could a certain number of the seeds be modified to try to account for natural diversity?


texts: Why does Stereology use Systematic Random Sampling?

texts:
I am a student of Neuroscience and in all my textbooks and lecture notes it is written that in Stereology, Systematic random sampling (SRS) is used to obtain sections.

Why it's that and not any other type of sampling? For example, why do we not use completely random sampling? What are the advantages of SRS over any other type of sampling when applied to stereology?


texts: determining meaning of basic biological keywords about C. elegans

texts:
First of all I have to say that I have no biology background since I'm a undergraduate computer science student. Nowadays, for my research I need to use some of the databases related with bioinformatics (modENCODE and NCBI-GEO). Currently, I'm searching RNA-Seq data and I have found the following one in modENCODE website which is stored in NCBI-GEO database.RNA-Seq data

In the description part of it, it is written that:

  Synchronized L1 worms cultured at 25degC for about 91 hrs to a point
  at which ~100% worms are resistant to 1% SDS treatment. Illumina
  sequencing of C. elegans dauer daf-2(el370) sample 2-1 DauerDAF2-2-1
  polyA+ RNAseq random fragment library This sample is available through
  the modENCODE DCC (www.modencode.org) as: DauerDAF2-2-1 Local library
  name: DauerDAF2-2-1 Quality values are ASCII encoded Phred + 33.

Regarding with this paragraph, I want to ask that, what is C. elegans dauer daf-2(el370) . I've searched on the internet and I have found that dauer is kind of development stage of C. elegans. However, I could not find any information about the daf-2(el370) part (Actually all I found was that daf-2 is name of a gene of C. elegans). Actually, my primarily concern is whether this RNA-Seq data contains the C. elegans' whole transcriptome or it contains only mRNAs related with daf-2 gene.


texts:
Often, in science, when we have evidence that doesn't fit our paradigm, we bend it until the paradigm collapses.

Although there is plenty of decent evidence for evolution, is there anything that does not fit the evolutionary paradigm? Is there any biological evidence that is not suggestive of or seems to disprove evolution? Or is everything merely hunky-dorey?


texts: Enzyme kinetics: recommended literature to grasp the concepts better

texts:
I have had a few biochemistry courses, but I still feel confused and a bit scared each time they try to explain and apply enzyme kinetics or even chemometrics in different situation during class. On our last lecture we had kinetics regarding:

Pingpong reactions (with two substrates A, B):
$V_0 = \dfrac{K_{cat}[E]* [A][B]}{K_m^B [A] * [B] * [A][B]} $

General reactions (with two substrates A, B):
$V_0 = \dfrac{K_{cat}[E]* [A][B]}{K_m^B [A] * K_s^A * [B] * [A][B]} $

And we also had something about analyzing the "principle component" in multivariate data, from enzyme kinetic measurements (as effect of e.g. pH of temperature).
I really don't understand this, or how I would apply this - or analyze my data if I have two substrates.
Question: In general, is there a good web site which goes beyond the normal Michaelis menten analysis, or a very good book which explains both the basic and more complex scenarios regarding analysis/application of enzyme kinetics for biochemists?


texts: Suppose a sperm fertilized a 2nd polar body( haploid) is there a chance of somewhat normal development?


texts:
What would be the resultant by-products of a completely decomposed dead skin cell?
What would be the size of each of the by-products of a decomposed dead skin cell? How long would it take for a dead skin cell to begin to decompose?
I am curious because anything below the 10 micron range can enter the alveoli of the lungs and cause emphysema. I have had eczema since early childhood, and therefore have breathed in more dead skin cells and by-products of dead skin cells than those without eczema, principally during sleep.

The epidermis, the outermost layer of the skin, sheds corneocytes. Corneocytes are 30-50 micrometers in diameter. http://www.nanoscience.de/richter.old/corn.html


texts: Why does muscle blood flow decrease during exercise?

texts:
My questions semi-relates to these two items: Where does extra blood come from to fill your muscles during exercise? , and Blood pressure during exercise .

While reading Exercise Physiology by Dr. Brooks, I've come to the following quote, which is a bit puzzling to me:

  Muscle blood flow increases exponentially with metabolism. At maximum exercise, some vasoconstriction occurs in active muscle in order to maintain blood pressure. Maximum muscle blood flow is largely determined by the amount of active muscle. The larger the portion of active muscle mass, the less total muscle blood flow.

Questions:

Why is it that the larger the active muscle mass, the lower the total muscle blood flow? I'd expect it to be greater.
Say that I am doing the bench press, does that qualify as an exercise with large active muscle mass?


texts: How many different chains exist within a specific pdb file?

texts: More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many different chain identifiers exist there?


texts: Where can I find a cannabinoids profile of hemp strains?

texts:
For my web article, I need to find out the content of individual cannabinoids in hemp strains, specifically for Kompolti, Carmagnola and Purple Haze. I mean the content of all the components, not just THC and CBD.
Do you know of any website that provides this information?
Thank you for answer


texts:
So I was looking over some genetics question and came across this data set.
In Fruit fly Drosophila melanogaster, there is a dominant gene b+ for grey body color and another dominant gene c+ for normal wings. The recessive alleles (b,c) of these two genes result in black body color and curved wings respectively

The question was asking about the calculation of the recombination frequency. To me Ada's data set makes sense as the parental type offspring numbers are higher than the recombinant offspring. However, Donald's data set doesn't. Is there any way a recombinant offspring could be in a higher proportion than the parental type offspring?


texts: What is the meaning of a selection regime in this context?

texts:
"Our second approach was based on modeling adaptive regimes
across a phylogeny for each of the groups in our study using an OU
model. We especially focused on the lineage leading to humans, and
tested whether a shift in the selection regime was inferred on this
branch. Under the OU model, species evolve through various selection
regimes that map to branches on the phylogeny. The goal is to characterize the regimes across the tree, and to assess whether a shift in selection regime occurred on the branch connecting Homo to the
other primates."

taken from:
Nunn, Charles L., and David R. Samson. “Sleep in a Comparative Context: Investigating How Human Sleep Differs from Sleep in Other Primates.” Wiley Online Library, John Wiley & Sons, Ltd, 14 Feb. 2018, onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.23427.


texts: What are these little creatures on the fish?

texts:
I'm not a fisherman, but I just caught a cod fish (my first one) and found a lot of strange little creatures all over the fish:

What are those? Are they harmful to the fish, or to the human?

Edit: it's caught on Faroe Islands


texts: Is it possible to live without health problems sleeping one day and not the other?

texts:
Basically, I want to know if it would be humanely possible to sleep one day, skip the next, sleep, skip, sleep, skip, etc, with a 8 hour sleep time.

If you need any extra information, let me know.


texts:
I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows:

bowtie2 -x $REFERENCE -f $TARGET -S $TARGET.sam

The version 2 of bowtie complains with the following:

Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because length (0) <= # seed mismatches (0)
Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because it was < 2 characters long
Warning: skipping read 'ORIGINAL: GGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAG' because length (0) <= # seed mismatches (0)

Note that bowtie (version 1) is pleased by my FASTA! Here's a snippet and what bowtie says:

>ORIGINAL: GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
>ORIGINAL: ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
>ORIGINAL: GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGCT
AATGGGAGTGAAAATCTCCGATGAGCAGC

# reads processed: 471409
# reads with at least one reported alignment: 464583 (98.55%)
# reads that failed to align: 6826 (1.45%)

Now I'm at loss. Can anyone see what I'm doing wrong here? Can I trust anyway bowtie2 when it finishes and outputs how many sequences are aligned?

Thanks!


texts:
Can aflotoxin presence be inferred from the mild discolorotion at the middle parts of a hazelnut?
For instance, how likely is it that the hazelnuts pictured below contain Aflotoxin?

P.S.: these hazelnuts were fried before packaging in a vacuum sealed plastic bag. ( I am not sure whether the color change in the middle part comes from fungal activity (e.g., aflotoxins) or from the frying process?)


texts: What is this discarded exoskeleton from?

texts: This morning I was looking round the garden and found this sticking out of a pit in patch of soil, next to the wall of the house (in a trough sort of thing). I came to the conclusion it must be part of an insects exoskeleton that was discarded or part of a pupae. Can anybody identify what this belongs to? My location is in the south-west (Wiltshire region) of Great Britain. I'm just interested in what exactly I've found!


texts: Trouble amplifying microsatellites using a 3 primer protocol, positives in negative controls

texts:
I'm trying to collect microsatellite data using primers developed on a related species but instead of having primers with fluorescent dye already on them, I'm trying to attach an M13-dye to the forward primer which also has an M13 tag on its 5' end. I am having some difficulties though because my negative control bands look identical to the positive bands, regardless of annealing temperature and MgCl2 concentration, and the bands seem too large for it to be primer-dimers, it seems like genomic DNA.. it's about 100-150bp.. so I'm not sure what is going on.
Before somebody suggests that it is contamination - I started over at a whole different lab bench, different pipettes, pipette tips, reagents, ordered new primers, thermocycler, everything, but the problem did not go away. Since I'm still optimizing the microsatellite primers I also ran a test using some invertebrate COI which I have positive results from in the past, and included a little bit of each reagent into each reaction instead of DNA, and I got a very strong band at the M13-dye. This was brand new, reordered after the last batch had this problem, suspended with TE and diluted with nuclease-free water. I am wondering if it has to do with the gel sybr-safe filter? Or the UV illumination for visualizing the gel? I am grasping at straws, please help or let me know if you have the same problem. The dye is just M13 labeled 6FAM: 5'-/56-FAM/TGTAAAACGACGGCCAGT-3' from IDT


texts: What is the subcellular location of synthesis of non-essential amino-acids?

texts:
What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this?

I thought the whole point of DNA is coding for how to synthesize proteins and that it is the mechanism of genes expression. Triplets of nucleotides are codes of amino acids and that is the granularity that cell works with.

Now it turns out cells knows how to synthesize more than half of the 20 amino acids, in humans, and I do not see, in the web, good texts of how it is done, where, and how that is coded.

Thank you for helping to shed some light.


texts: Looking to study botany, some general advice

texts:
I've been doing some hydroponics lately and I've noticed I don't have much insight about how plants really work under the hood, I would like to have the full picture and understand more about it.

My primary interest is to apply botany knowledge on my hydroponics projects, not to get a job/degree. But, I do understand that studying among my peers is a rich experience, reason why I'm considering this kind of training instead of just grabbing a book.

However, I'm not sure how extensive is the study of botany, if I need a degree in X before starting it, etc.

Also a good book is welcome.

Thanks.


texts:
I know that growth is an irreversible increase in mass or overall size of a cell, organ or whole organism. I also found that growth occurs due to the net result of anabolism and catabolism.
My teacher said;
           When anabolism > catabolism - growth occurs
                 Anabolism = catabolism - no growth
                Catabolism > anabolism - negative growth
But on searching about this negative growth, I couldn't find any information. What is this negative growth? Where do you see it?


texts: What would be the best dredging/trawling tools to collect macrofaunal priapulids?

texts: Title says it all. I've been searching for the best way of collecting macrofaunal priapulids and would like advice on sampling methods and particularly sampling tools. Since large priapulids are usually found in low densities any form of grab-sampler would probably be inefficient and a dredge/trawl would be preferred. Any ideas on what tool(s) would sample at the right depth and filter efficiently?


texts: Its there a gene or genes for intelligence?

texts:
I don't know almost nothing of genetics but I felt a little interested in the subject of genetics and its role in intelligence and i found to reports that talk about certain genes that contribute to intelligence

https://www.nature.com/news/smart-genes-prove-elusive-1.15858 https://www.newsweek.com/how-be-smart-intelligence-linked-500-genes-large-new-study-842454

What I don't understand is if only some people have this 500 genes or all human population has this genes?


texts: Infant Death Adjusted Historical Human Lifespan

texts: I had found a good paper at one point to describe this but I can't seem to locate something similar now. I am looking for a manuscript that describes average human lifespans throughout history/prehistory especially adjusted for infant and child deaths but it would be nice if there was un-adjusted data as well. Does anybody know of a reference with this information?


texts: Why is the liver the only internal organ of the human body to regrow?

texts:
Related to my earlier question, "How does the human liver regrow?", am curious as to why the liver is the only major organ that has this capability?

Why is it that other major organs, such as the heart and lungs etc are not able to regrow in the same fashion?


texts:
What is a cognate enhancer sequence?

While reading a paper (1) presented at a journal class in graduate school, I encountered this sentence:

  HIF-1 binds to its cognate enhancer sequence, the hypoxia-responsive
  element (HRE), and induces the expression of various genes related to the adaptation of cellular metabolism to hypoxia (the switch from oxidative to anoxic respiration),16 escaping from hypoxia (invasion and metastasis of cancer cells),17,18 improvements in hypoxia (angiogenesis)19,20 and the resistance
  of malignant tumors to chemo as well as radiation therapy.

(1) Is Wikipedia's definition of an enhancer correct for this case? Then does 'cognate' mean "related to, tending to be found together", whereas "sequence" means there's a chain reaction that occurs?

Y Zhu et al, "Involvement of decreased hypoxia-inducible factor 1 activity and resultant G1–S cell cycle transition in radioresistance of perinecrotic tumor cells" Oncogene (2013) 32, 2058–2068


texts:
Is this statement applicable to any known plant/region combinations?

  Plant species X, Y, and Z are truly indigenous to region R. Other "immigrant" species can be destroyed by drought or harsh weather, but these species will always be part of the region R.

(all species in question are "benign" - like wheat; please disregard climate change and other global disasters like nuclear wars).

PS. Background: I heard this statement (with specific X,Y,Z,R) attributed to a "leading botanist" (probably 20th century), but I don't really see how this can be true (my biology education ended in high school though; I am a mathematician by training).


texts: I am aware that certain organs in the body have specific pH environments to increase the activity of their enzymes. I'm also aware that enzymes only work at certain pHs due to the configuration of the amino acid in their active site and the way this is altered as the pH is changed. What I want to know, however, is why their amino acids are as they are to begin with - has it got to do with the substrate molecules they react with? Particular reference to catalase would be helpful.


texts: Are all prokaryotic promotor regions the same, or do they differ depending on the product of the transcript?

texts:
Are all prokaryotic promotor regions the same or do they differ depending on the protein encoded by the mRNA being transcribed?

What I am thinking is that if activator proteins are a method of transcription regulation, then shouldn't promoter regions differ so that activator proteins have an effect on the  expression of a specific gene?

Please tell me if this is correct, or if I misunderstand something.


texts: How do the X and Y chromosomes synapse during the zygotene stage of when they have almost no homology between them?


texts: What is the meaning and significance of extreme pathways

texts:
Can someone please explain me what extreme pathways are? I found this definition in this article:

  Extreme pathways are a unique and minimal set of vectors that
  completely characterize the steady-state capabilities of genome-scale
  metabolic networks.

Now, frankly speaking, I did not understand the head or tail of this definition? What is steady state? What does it mean by steady state capabilities? Can someone please explain me in a simpler way?
PS: I am a computer Science student


texts:
I am having some difficulty understanding a few things about genetic recombination, in part because of confusion from different diagrams in books.

First of all, I wanted to verify whether I have understood correctly: It seems to me that when homologous chromosomes (which at this point are as sister chromatids joined at the centromere) join during the zygotene/pachytene stage, only one of the chromatids from each homologous chromosome form synaptonemal complexes with one of the chromatids in the other chromosome. Is this correct? Then only one of each of the chromatids is involved in the DNA recombination...

Leading on from my previous point, I think this would mean that in the final four zygotes that are formed, there are four different chromosome possibilities: the maternal chromosome (call it m) which has not had any recombination events; the maternal chromosome M whih has had recombination events with the paternal chromatid. Then the corresponding paternal chromatid p and chromatic which has undergone recombination event P. Is my understanding correct here?
Also, I have seen in some diagrams there is a single chiasmata forming between the homologous-chromosome chromatids and in other diagrams I have seen more than one chiasmata. I think the one chiasmata picture is a simplification and there can in fact be more than 1 crossing over point between the chromatids of homologous chromosomes.
Finally, if it is so that only one of each pf the sister chromatids is involved in recombination between homologous chromosomes, is there a a preference as to which chromatid this is, or is it random?

I realise that if both of the sister chromatids undergo these recombination events, then many of my questions would be redundant! However from the books I am looking at now, it seems that only one chromatid undergoes these crossings over...


texts: Do other young mammals turn their backs to their parent when upset?

texts: I have noticed that upset toddlers turn their back to someone who wronged them and huff. Most adults don't do this, so I don't know how this could be a learned behaviour. Do other animals express this behaviour? I do not see how this could be specific to culture.


texts: In my biology textbook, it says that plants grow towards light because auxin is laterally transferred from the light side to the shaded side, so more auxin stimulates growth and hence the plant bends towards light. My textbook also specifically states that light doesn't destroy auxin. Yet, recently I searched online and find that light will actually destroy auxin by photo-oxidation. I am confused, can someone tell me which is the correct mechanism (or both)? Thanks!


texts: What is the oxygen carrying capacity of reticulocytes?

texts: What is the oxygen carrying capacity of immature red blood cells, or reticulocytes? Is there any difference between oxygen carrying capacity of mature and immature red blood cells?


texts: What evolved to produce sweetness, plants or consumers?

texts:
I couldn't find an existing answer on this site, although I may be wrong.

What evolved to produce "sweetness", a pleasant reaction to the presence of sugar?
(A) Plants, using it to lure in consumers and spread seed
(B) Animals / consumers, which used sugar as a vital nutrient, to identify nutritious food, or
(C) Neither of the above; something else?


texts: What causes knuckle "popping" and the feeling of relief that comes from it?

texts:
Many people like cracking their knuckles. I have always been curious about it.
What happens when we crack knuckles?

What creates the POP sound?

Why do we get a relief-like feeling after doing it?


texts: Why do our limbs and other body parts get numb/feelingless and then they start to tickle?

texts:
Why do our limbs (legs, arms) get numb/feelingless when they are under prolonged pressure or when one has crossed his/her leg while sitting for a long period?

After we move it to a more relaxed or natural position numbness goes away and we get the really strange and hard to bear tickles. Why does the numbness go away by doing this and why do why get these odd tickles?


texts:
From what I read on wikipedia they are made of collagen. Collagen is just a protein. Right? How is this collagen structured (I imagine like fibers). Aren't there cells in this fibers as well?

From this picture:

Is the pink stuff the collagen? and the purple stuff the tenocytes?

If someone can expand on this with a picture preferably, it would be great.


texts: Why do we value species that are on the brink of extinction?

texts:
As I understand, biodiversity has two benefits:

Species might be a functional part of the ecosystem, e.g. balancing other species' numbers or beeing part of the foodchain.
Species with diverse abilities make sure that "life as a whole" can adapt to changing environments.

These hold true for most species currently alive. For species that have only a few thousand or even a few dozen exemplars left, neither function seems to be achievable. Yet there is a wide consens in protecting such species - what's the reasoning?


texts: Why does human hair grow and behave differently depending on its location?

texts: Why does human hair behave differently depending on its location? For instance, head hair grows to an indefinite length, but eyebrows maintain a particular length and appearance. Head hair and eyebrows may exhibit balding, but not ear, arm, nose, and facial hair (etc). Why is this so?


texts: The effect of depth on net primary production in aquatic ecosystems

texts: The figure shows the relationship between the water depth and net primary production (=P-R). I want to know why the production (P) initially increases with water depth near the surface? I have seen similar relationships from other sources but never seen a clear explanation.


texts:
Do fingerprints change as we grow from child to adult? Most notably, what is the effect of the increase in surface area of palms and fingers on the finger print? Does the finger print simply increases in size, and/or does the pattern change?

And what about old age? As the connective tissue in dermis get lax, how is the fingerprint affected?


texts: How does natural selection explain sexual display?

texts:
As I understand it, animals sometimes grow more vibrant colors, bigger feathers, elaborate dances, build shiny nests, all to impress the other sex. However, these are all superfluous to survival -- any nutrition or energy spent developing these attributes or conducting these rituals are no longer usable for hunting or child rearing, for example. Given the same animal who does one of these wasteful practices versus the same animal who doesn't, in theory the latter should have the advantage in its chances of passing its genes down.

Why is it then, that sexual preference grows towards these wasteful growths and habits, rather than ignoring these sexual displays for sheer survival efficiency?


texts: How are collagen fibers in skin aligned with respect to skin surface?

texts: I read in one paper that collagen fibers in dermis are randomly oriented in direction with respect to the skin surface. I can't locate that paper now. However, I came across this paper that indicates that collagen is always aligned parallel to the skin surface (page 3). Which one is correct?


texts: What is the probability of fixation for a mutant under fluctuating selection?

texts:
Here is an answer which explains how one can model the frequency of an allele that is under fluctuating selection (the selection that varies through time).

Not, thinking about fluctuating selection, there exist several derivations of the probability of fixation of an allele present at frequency $p$ with selection coefficient $s$ in a finite population of size $N$. For example, Kimura (using diffusion equations) approximated the probability of fixation $P_{fix}$ to be

$$P_{fix}≈\frac{1-e^{-4Ns} }{1-e^{-4Nsp}}$$

How to model the probability of fixation (in a finite population) of an allele that undergoes fluctuating selection?

I welcome one to answer by using whatever type of fluctuating selection. It might be an alternate of $s_1$ (uneven generation) and $s_2$ (even generation) or $s(t)$ might be a sinusoidal function of the time $t$ (in generations). Or $s$ might be drawn randomly from some distribution.


texts: What does 'half life' of a protein mean?

texts:
Why do we use the term 'half life' for proteins?

Here is a link to some information regarding this question, but I am unable to infer it.


texts: Do Scrubjays weigh peanuts by picking them up?

texts:
I have been feeding scrubjays where I live (Monterey, California) with peanuts in the shell.
Something interesting I've noticed them do is, after I've laid out a selection of peanuts for them, they pick them up in their beaks and seem to be determining which one they want to fly off with. I have seen them first eye them all for a couple of seconds, then pick one up, shake it in their beak as if listening or "weighing" it, then picking up another one, or even three, and then going back to one of the previous ones and flying off with it.
What are they doing? Weighing them? "Counting" how many nuts are in the shell? Listening for something?
Here is one "in the act":


texts: Medium preparation, using calcium hydroxide instead of potassium hydroxide

texts:
As the question states, I am interested in growing alkaliphile bacteria. I have seen many media use KOH, mainly to neutralize, and was wondering if it is possible to change this to Ca(OH)2?
Is there a reason KOH is used instead of any other alkali solution to neutralize media?


texts: Is the appendix a vestigial structure in all vertebrates?

texts: In humans the Appendix is a vestigial organ. Does it serve no apparent purpose in all the vertebrates that have one?


texts: Why do men have a higher hematocrit (red blood cell count) than women?

texts:
The hematocrit, also known as packed cell volume (PCV) or erythrocyte volume fraction (EVF), is the volume percentage (%) of red blood cells in blood. It is normally 45% for men and 40% for women.

so,Why do we have hematocrit for men?

First,I thought it might be caused by different hormones but I couldn't find adequate evidence to prove this Hypothesis.Therefore I decided to share it.


texts: If a non-mammal is starved of oxygen for some time, how long would it take the animal's neurons to die?

texts:
This is a follow-up question to Why do neurons die so quickly (relative to other cells) when deprived of oxygen?.

I'm particularly interested in the case of reptiles, octopuses, and other invertebrates. Could it be that mammalian neurons are especially oxygen-demanding compared with the neurons of other animals?


texts: Hardy-Weinberg Equilibrium: To compute probability of finding two siblings (random mating)

texts:
I've been working a little with M. G. Bulmer's Principles of Statistics (Dover, 1979) and cannot see how to properly compute half of one question. This should be a basic probability computation, but I am not getting the same answer as the book's suggestion.

Here is the question (Chapter 2, Problem 2.4): If the three genotypes (i.e., AA, Aa, aa) are all distinguishable, find the probabilities that a) a pair of siblings and b) a pair of unrelated individuals will appear the same when p=q=.5.

The book offers .59 for a) and .38 for b). I can get b correctly, but I don't understand how to properly compute part a).

This does not seem like a complicated exercise!


texts: Does opponent process happen in the retina or in the brain?

texts:
I understand that both the Trichromatic Process and the Opponent Process take place in human vision.
Trichromatic Process is widely accepted to happen in the retina,
however I heard differing accounts of where Opponent Process happens - in the retina or in the LGN.


texts:
There certainly are poisonous plants, but I was wondering, whether there are venomous specimen, too?

First, I thought the stinging nettle could be one such. After all, it's common knowledge it "applies a toxin upon touch". However, reading about the mechanics it seems that the injection is actually a much more passive procedure, which would render the plant poisonous, wouldn't it?

So what are some venomous plants?


texts: Do neurons feature a collective "resistance" to firing too often beyond the refactory period?

texts:
My understanding is that neurons are prevented from firing too often by a 2-part refactory period: an immediate inability to fire again for a period of time followed by an increased threshold for firing for an extended period of time.

My question is simply whether or not there is an additional "collective" aspect of the refactory period or other mechanism which prevents too many firing based on frequency within a period of time. In other words, the refactory period as I understand it is the same each time a neuron fires, regardless of whether or not it has repeatedly fired as often as possible for a period of time before hand. I'm asking whether there's a mechanism that takes into account how many times the neuron has fired within x timeframes collectively to prevent further firings or weakens the output, sort of like a "resistance" (in which case it would be a mechanism having more to do with the synapse than the action potential / refactory period).

Do neurons feature a collective “resistance” to firing too often beyond the refactory period?


texts: Does regulate always mean suppress when it comes to heteroreceptors?

texts: Do heteroreceptors always suppress the release of the neurotransmitter they regulate upon their (the heteroreceptor's) activation?


texts: After a bacterial infection is dealt with, do any of that colony of bacteria remain?

texts:
Suppose that I get a bacterial infection, which my immune system deals with. Are there any remnant bacteria, or are they all gone? Now consider the same scenario, but having been treated with a full course of antibiotics - are there any bacteria left alive? Now suppose I take a partial course of the antibiotics - enough to reduce the bacterial population to a level that my own immune system can deal with by itself. In this last case, if I beat the infection, is there any chance of bacteria having evolved resistance to those antibiotics, or are they all dead?

I ask having recently read an article claiming that conventional wisdom on antibiotics might not be as useful as once thought.


texts: Tiny dark-colored bug ID in Amman-Jordan

texts:
I live in Amman-Jordan and I keep finding this bug species on my walls. I saw four till now on the walls of another room. A little bit bigger than the first one.

Click on all photos to open full-sized image:

With cm ruler:

I also have a video, but don't know how to post it.


texts: Why don't neurons die during a stent procedure in the brain?

texts: Stents are used to provide scaffolding to the blood vessels. When they are used in arteries or arterioles in brain, won't neurons die because of lack of oxygen during procedure?


texts:
I was discussing this with my brother. I'm pretty sure I read somewhere that they can move.

Thanks

EDIT: By movement I mean long distance migration (preferably within the brain only).


texts:
According to wikipedia on chimeric genes:

  These mutations are distinct from fusion genes which merge whole gene
  sequences into a single reading frame and often retain their original
  functions.

I am not totally sure I understand the statement. My interpretation is that a fusion gene is caused by a translocation of DNA in a single gene; therefore, it "retains their original functions". This is different from a chimeric gene where DNA from two or more different genes are translocated to a new location to form a completely new gene.

Is my interpretation correct?


texts: Hardy-Weinberg applied to three alleles and stimation of allele frequencies

texts:
I have this equation:
Corresponds to HW in equilibria with three alleles:

$(p+q+r)^2=1$

Expanding the square results:

$p^2+2pq+r^2+2pr+q^2+2qr = 1$

I need to separate homozygous and heterozygous, that means:
$2pq+2pr+2qr=1-p^2-q^2-r^2$

How I can use a equivalence similar to $(p=1-q) or (q=1-p)$ in two alleles to resolve the last equation?


texts:
I have come across a map and a part of it looks like this:

Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate the reaction that converts alpha D-glucose Glucose to Glucose-6P. Since an arrow exist from alpha D-Glucose to Glucono-1,5-lactone, i am assuming that such a reaction exist. But could not locate it. I clicked on the arrow marked in blue in the picture, but could not find the desired reaction.(alpha D glucose and beta D glucose are different compounds)  What is the reaction and how is it possible to find the reaction from the map?
NB: The arrows are clickable so are the circles that denote the compound.


texts: Which metazoans host anaerobes to aid in digestion? Do any host oxic digestive tracts?

texts:
Many metazoans (e.g., mammals, insects, earthworms) have anoxic digestive tracts that are colonized by anaerobic microbes that perform portions of digestion of food for the host.  Some other metazoans (e.g., porifera/sponges) rely on intracellular digestion.

I'm wondering, which metazoan taxa (I suppose we can keep it at phyla level) host digestion that is aided by anaerobic microbes, which do not, and are there any that have digestive tracts that host aerobic microbes instead (though that seems unlikely since they'd likely completely consume the food for themselves)?

We could start by addressing a partial list of the most well described metazoan phyla (plus a few of particular interest to me).  Perhaps no one will have the knowledge/expertise for each of these phyla - in which case we could have a community answer that is built on over time.

porifera- sponges
cnidarea - jellyfish, corals and sea animals
platyhelminthes- flatworms
nematoda- round worms
rotifera- worm-like animals
bryozoa- small aquatic animals
brachiopoda- lamp shells
phoronida- tubeworms
anelida- segmented worms
mollusca- soft bodied animals including chitons, snails
arthropoda- insects and others with hard, segmented bodies
echinodermata- starfish
hemichordata- acorn worms
chordata- primarily vertebrates
placozoa - simplest non-parasitic multi-cellular animals
Ctenophora - comb jellies
tardigrada - water bears
loricifera - tiny shelled sediment dwelling animals


texts: Can HIV be transmitted via breastfeeding?

texts: If a pregnant women is HIV positive and she is treated with medicines to deliver a normal child,can she transfer the HIV virus back to her normal HIV free child by colostrum?


texts: Can MHC class I be used for presenting peptides of extracellular origin by non-professional APCs?

texts:
Wikipedia says that: "The antigens presented by MHC class II are derived from extracellular proteins (not cytosolic as in MHC class I)."

So does this mean that MHC class I cannot be used for peptides derived from phagocytosis by non-professional APCs? (i.e. peptides that of extracellular origin?).

For example, when non-professional APCs that can undergo phagocytosis (Eosinophil, neutrophil, dendritic cell) engulf bacteria, will they present their antigens using MHC I although the peptides are of extracellular origin? or will they not present any MHC at all? thanks!


texts: Should we be looking for extra-terrestrial life on comets?

texts:
I have just read What elements are a possible basis for life? and I find myself wondering whether instead of seeking advanced life-forms at remote locales a La SETI, and perhaps fundamentally differently, we ought to be looking for similar microscopic life forms on comets that pass off-and-on.

Granted, a comet may be near absolute 0 for a lot of the time, but microscopic life-forms are known to be capable of surviving lean periods by using a cyst, for instance. As far as the rest is concerned, comets probably contain some amount of ice, and hence water, too. Similarly a comet's sprint around the sun could provide some limited amount of gravity/mass too.

So, should we be looking for life on comets?


texts: Strange fast growing mushroom like entity

texts:
I found this in my lounge today.
This room was cleaned less than 48hours ago, with no sign of this growth.

We sweeped and mopped, using the same floor cleaner we always do.

The two images below is of the same corner, but with the growth lifted in one image.

The consistency is like a fungus or mushroom and can probably be removed from the wall as one piece without much effort.

One of the walls close by do suffer from damp on occasion, but we have been in this house for over two years and have not had anything like this appear.

Please help!


texts:
Grapefruit juice contains furanocoumarins, which irreversibly inhibit CYP3A4.  For this reason, when one is taking certain medications it is necessary to not eat grapefruits because the inhibition of CYP3A4 can reduce how much of the drug is metabolized before it can get used, resulting in an overdose.   It apparently takes 24 hours after eating a grapefruit before the enzyme level is 50% and up to 72 hours for it to be completely normal.  So, it seems that eating one grapefruit a day would substantially impair one's CYP3A4 levels indefinitely.

Wikipedia says, the purpose of CYP3A4 is "to oxidize small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from the body."   It seems like inhibiting CYP3A4, from a biological standpoint, would reduce one's immune system or at least the ability to tolerate and eliminate certain toxins.   Are there other enzymes that take up the slack, or is there something in grapefruit itself which does the job instead, or is a daily grapefruit just a bad idea?  What are the effects of extended inhibition of CYP3A4?  Will the body perhaps build up a tolerance or immunity, or (perhaps with negative effects) pump out more CYP3A4 to try to compensate?


texts: How much does sprayed water remove bacteria?

texts:
I was quite skeptical about some company claiming that their device was able to suppress 99.99 % of bacteria.  Then I read a report testing the germicidal effect of their device, from a large and independant testing laboratory.

The device was tested against a number of bacteria, including Salmonella, Escherichia coli, Staphylococcus aureus, or Listeria.

They incubated contaminated Petri dishes, then used the device, then incubated the Petri dishes again.  It appears that the test samples had a CFU level log-reduced by 4 to 6 (i.e. the number of bacteria is reduced by a factor of 10,000 to 1,000,000) in most cases when compared to control samples, which supports the claim.

However the device implies spraying water, to which the control samples have not been subjected.  I am curious about how much this simple spraying may affect the results.

Would rinsing the dishes with sprayed water significantly reduce the amount of bacteria ?


texts: Looking for a gene in my raw genetic data. What are the possible causes for this?

texts:
Obviously, I barely know what I am talking about.

But I want to find the "MUC5B promoter polymorphism rs35705950" in my RAW genetic data from 23andMe. (see this paper  http://www.ncbi.nlm.nih.gov/pubmed/23695349)

I think rs35705950 is the SNP number...   When I search I get no results.

When I search for MUC5B I get 9 results, but the SNP numbers doesn't match.

My question(s)

Is it possible that I just don't have this gene (rs35705950)?

Does 23andMe not have ALL of my genetic information?

Am I doing something wrong or misunderstanding what I am looking for?


texts:
If an element, ion or molecule is found in a cell is it possible to tell which method of transport was used? for example if a hydrogen or sodium ion was found in the cell could you tell if it got there by diffusion, or facilitated diffusion, or endocytosis, pinocytosis etc? If not could you at least narrow down the number of transport methods it could have used?

I'm very interested in which substances are let throught the cell membrane and by which method.


texts:
I was reading an article, when I read a sentence saying, His mother ... nearly died less than three years later during Mathers' 73-hour birth.

What does mean by 73-hour birth?


texts:
In the study of supercentenarian woman here, it was found that all her blood cells are formed from only two stem cells (ancestor stem cells).

How scientists can distinguish cell ancestors?

Aren't all genes of one body identical?

If there are somatic mutations, which are increasing while lifetime, then how they could know, that there are more ancestor stem cells in childhood? Shouldn't it be less mutations and cell lines less distinguishable?

May be stem cells only can be counted in oldness.

Then how is it possible to know, that there are 20000 of stem cells at birth?