texts: Why is it often the case that an enzyme is favorable only towards one direction of a reaction and not both directions?

texts:
In class when we're studying enzymes like amylase or protease it only works well when you're using it to break down compounds like polysaccharides.  I'm just curious but why is it not possible for enzymes to work efficiently in a reverse reaction?  I mean a formula like

$\ce{amino\ acid + amino\ acid + energy<=>H2O + protein}$

does imply that our reaction can go both ways , right?  But why is it that the enzyme favors the catabolic reaction?


texts: What would "N" and "V" stand for in DNA barcoding?

texts:
I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:

...CCGATCTNNxxxTTT...TTTVN

where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.

As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.

So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?


texts:
Frequently I have experienced sore joints during a bad bout of influenza. I understand that during time of sickness, white blood cells are deployed in the blood stream. I also believe that white blood cells originate or relate to bone marrow. I'm wondering if there is a relationship between each of these

My question is: What is the biological reason that some viruses cause sore joints (eg flu)?


texts: Do voltage-gated calcium channels affect neuronal conduction speeds?

texts: We have a hypothesis that a drug may block the voltage-gated calcium channels (VGCC) in annelid worms. We are wondering whether there are any correlations between VGCCs and neuron conduction velocities.  If there are fluctuations in calcium ion contents, would there be any changes in conduction velocities? Or if the channel is blocked, would it block the entire action potential along the worm's giant axon?


texts:
I was reading about the Placebo effect and came across this little story:

  The roots of the placebo problem can be traced to a lie told by an
  Army nurse during World War II as Allied forces stormed the beaches of
  southern Italy. The nurse was assisting an anesthetist named Henry
  Beecher, who was tending to US troops under heavy German bombardment.
  When the morphine supply ran low, the nurse assured a wounded soldier
  that he was getting a shot of potent painkiller, though her syringe
  contained only salt water. Amazingly, the bogus injection relieved the
  soldier's agony and prevented the onset of shock.

https://www.wired.com/2009/08/ff-placebo-effect/

I also read that Morphine specifically lessened the effects of shock:

  Only when it is severe, or when a severely wounded or injured person must be moved quickly (as from a wrecked vehicle or aircraft) it is wise to give Morphine at once. It may not always relieve the pain entirely, but will certainly lessen shock.

https://web.archive.org/web/20140420133119/http://www.med-dept.com/morphine.php

So, how do painkillers prevent wounded soldiers from going into shock and dying? What physiological mechanisms are responsible? Is it something to do with blood pressure? Heart rate? Pain itself?


texts:
I'm reading an article about MLPA (Multiplex ligation-dependent probe amplification) and I got stuck on this sentence:

  The advantage of splitting the probe into two parts is that only the ligated oligonucleotides, but not the unbound probe oligonucleotides, are amplified.

The principle I don't understand is why won't the unligated oligonucleotides be amplified? As is my current understanding of the PCR, the primers should normally anneal and produce fragments which would end at the end of an oligonucleotide (at the "ligation site" - so they would be shorter, but they should be there), am I wrong?


texts: What animal / insect carcass is this? (Victoria, Australia)

texts:
During a hike on a mountain in Victoria, Australia, I came across this unusual shedding in one of the small rainwater pools. The pool looks small, but was developed long enough to have several insect species thriving in it such as water fleas and others of which I'm unsure.

This was the only shedding found and no other large insects or animals were found in this pool.


texts: Why does sexual selection evolve beautiful features?

texts:
I have a very raw understanding of sexual selection:

Say a group of females of a certain species "like" some feature of a certain groups of males; by "like" I mean some behaviour that makes this group of females tend to mate with males having this feature, then the females are selecting their genes which make them feel appealed to males with the feature, and then this process becomes exponent since the group of females becomes bigger and forces the population of males to have this feauture, until an equilibrium is reached. I know this also happens with the roles interchanged.

My first question is, why do females tend to like males that have high amounts of these features, more than the average in the population?

My second question is, why do the end products of these selections are such beautiful features? Perhaps this may sound a little arrogant but I don't understand how an animal can appreciate this beauty, I suppose this is to make some sort of selection of healthy males.

Thanks


texts: Strange looking mushroom found in a dead tree

texts:
I'm trying to identify this mushroom my sister found at her campus' lawn. It is brown, looks somewhat like a turtle or a brain and is growing inside of a dead tree trunk. Geographically the campus is in Haifa, Israel in case that helps. Any ideas?

Images:


texts: Does parental conflict lead to genes combining important functions with functions only advantageous for one of the parents?

texts:
In a sitation of a mother-father conflict of interests, the mother might use epigenetics to turn off some genes only advantageous for the father's genes and not her own. I thought a logical father's contra-strategy would be to bind the functions only advantageous to him to some of the genes crucial for them both, so that the mother couldn't turn these genes off.
Is there any evidence for a similar mechanism of "taking some genes hostage" in a situation of a conflict of interests?


texts: Why is black eumelanin black even though it consists of black AND brown molecules?

texts:
In dogs,eumelanin consists of molecules of DHI and DHICA. DHI and DHICA are made from dopachrome. DHI through DHI oxidase and DHICA through DHICA oxidase also known as TYRP1. When TYRP1 has a mutation through which it loses its function, mostly DHI is produced which gives brown eumelanin.
Now, if TYRP1 is functional, are both DHI and DHICA produced? If no, why not? If yes, why does the eumelanin appear black and not a dark brown?


texts: (How) does coppicing fundamentally alter tree growth?

texts:
I am interested in adding the ability to model coppice tree production to a model of perennial crops (Miguez et al 2008)..

Implementing the biomass pools and allocation parameters required for tree growth is relatively straight-forward.

However, it is not clear to me if it will be necessary to account for any changes in growth form and physiology (e.g. allocation, allometry) associated with coppice management.

Are there any models that explicitly model coppice regrowth? Are there any particular issues that I should consider?

Fernando E. Miguez , Xinguang Zhu, Stephen Humphries, German A. Bollero, and Stephen P. Long. GCB Bioenergy . 2009 . Volume 1 Issue 4, Pages 282 - 296 (link)


texts: What is the lowest common denominator of cancer?

texts: What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?


texts: Is a nature possible where animals do not kill each other?

texts:
like the title suggests, i always wondered if its possible that nature would work without animals killing each other. Where they just eat plants. Like one special plant for each animal. If they eat to much of them away they also will stop multiplying to much, so there will never be too much of one species etc, terefore balance. I am sure there could be other controlling mechanism for balances.

:)


texts: I found it on the wall, it was calm for 15 minutes. Central Europe, Hungary. Never seen anything like this. I have two more pictures.


texts:
These have been popping up all over our yard in South Western Australia. I have been digging them out before they mature as I have small children. But with 7 acres I can only check so much.
My question is: Is it possible to eliminate them as being harmful mushrooms from this picture before seeing them at maturity?

Some have been growing in isolation, others in clusters.

Note: a few weeks ago, from near this spot, I removed a white mushroom on a stem with its cap still closed and white gills when I opened it. I have also found a few different types of puffballs around


texts: Rate-determining steps in enzyme catalysed reactions

texts:
According to my chemistry book, there are 3 simplified steps within an enzyme catalysed reaction:

S + E → ES
ES → EP
EP → E + P

Where S is substrate, E is enzyme, ES is enzyme substrate complex, EP is enzyme product complex and P is product.

It is my understanding that at first, when substrate concentration is low the rate determining step is step 1, as this is the slowest step in the mechanism.

When you increase substrate concentration to a certain level, where there are no free enzymes remaining to bond with them, adding more substrate will not make the reaction faster, so the order has become 0 with respect to substrate conc.

Is the rate determining step now 2 or 3? I thought it would be 3 as that is the step that frees up more enzymes which could go on to catalyse more reactions. My book says that it is step 2, as "it depends on how fast the ES can convert into EP". But surely this step won't free up more enzymes to catalyse reaction further?

Is the book correct? Can anyone help me understand this?


texts: Who/where has the advocado genome been sequenced?

texts: I have read several places that the genome of the advocado has been sequenced in mexico but i am not sure at what university or persons involved.


texts: Fluoroquinolone mitochondrial and genomic DNA adduct

texts: What could be possible consequences of covalent bond mitochondrial and genomic DNA adduct by Fluoroquinolones, our study was done by Fluoroquinolone Toxicity Study NFP. All 50+ participates who took Ciprofloxacin and Levofloxacin were positive. In vitro study showed DNA adduct after 3.61 min. We are FQAD victims not scientists. We would like to know what may be consequences of DNA adduct.


texts: How does Serotonergic (5-HT2A mediated) Psychedelia work?

texts: How does serotonergic (5-HT2A specific) psychedelia work? I've read that there are some theories that it might involve the induction of a glutamate release in certain regions of the brain involved in perception.


texts: In electron transport system the final acceptor of proton is?

texts: My lecture notes say that the answer to this is inorganic phosphate  (iP)..and the question is about proton not electron so the answer can't be oxygen. But I don't understand how is the answer iP


texts:
Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species.

Let's say I have a protein alignment downloaded from Ensembl (coming, for instance, from this Ensembl tree).

This gene is present in some other "NCBI species" that I would like to include in my tree (for instance, Stegastes partitus, with available genome and present in the NCBI database but NOT in the Ensembl database). Indeed, if I manually blastp asip protein sequence of D. rerio (extracted from my Ensembl multifasta protein alignment) onto nr database parsed for S. partitus, I find this sequence, corresponding to the first blast hit. Perfect! And I can manually append it to my initial protein tree.

Where the problem starts is that I don't have one gene and one NCBI species but many of them (let's say p genes and n NCBI species). I already have an Ensembl protein multifasta file for each of my p genes.

My question is: is there an easy way to append to each of my p multifasta files the corresponding homologous protein sequence(s) for the n "NCBI species"?

Thanks for any insight!


texts: Why doesn't the human skin grow back exactly how it was before being damaged?

texts:
Very simple: Why (and how) is regenerated skin different from original ?

As we know we lose skin cells that becomes the dust in out homes and it always grows back to full thickness right ? So when I have a cut, I imagined it to heal provisionally with whatever possible and then after some time to replace itself with the normal skin that is coded in my chromosomes. So why doesn't it do that ? Scars remain and the color is always different from the neighbor parts.

Update:

Why we get scars?
What about skin transplants ?
Why doesn't skin actually grow/replace itself?

Update 2:

(I've been thinking) Skin has lots of different layers, right ? So when an area is damaged does it regenerate all layers or just one for being simple and efficient (in "hope" the subject will take precautions not to damage this part of body again, so that regenerating everything back to 100% would be overkill) ?
I'm not a scientist, I have only the basics from school, so I'll probably not understand most of the technical terms
also I'm more interested about an explanation that goes towards the "survival of the fittest" rule, and not so much about the biochemical reactions in our bodies (because it was just some random mutation that turned out to be the better choice for us → why?)


texts: Indian tropical fruit trees and fruit bearing

texts:
Most Indian tropical fruit trees produce fruits in April-May. The best possible explanation for this is

  optimum water availability for fruit production.
  the heat allows quicker ripening of fruit.
  animals have no other source of food in summer.
  the impending monsoon provides optimum conditions for propagation

This was asked in a competitive examination, and being a mathematician with interest in plants, this caught my attention. Please note that this was asked in aptitude section, and I feel it more aptly belongs this SE, correct me if I am wrong.

My thoughts:

April-May is summer in (tropical) India (where I live, Kerala) hence optimum water availability looks out of option.
Considering fruit production being a part of process of propagation, though this is a favourable factor, I doubt if it is a determining factor
Animals help disperse the fruits, and less availability of food may be a favouring factor attracting animals to fruits, it is not a determining factor.
which for me looks like the factor influencing increased fruit production more than the other two.

Sorry for the layman language, I would be grateful if someone can correct me if my reasoning is wrong and explain it more precisely (preferably in layman language, though I can understand some botanical terms)


texts:
Most drawing and 3D modeling tutorials show the iris to be concave. But all the diagrams I Googled show the iris is at best flat, otherwise even a little convex (discounting the optical distortion in photographs). So is it concave or convex?

Edit: Just to be clear, the question only concerns the concavity of the iris. The reason I mention drawing and 3D modeling here is that because it's such a common practice to make the iris explicitly concave in a somewhat exaggerated way, which is at odds with countless profile diagrams of the eye that I could google.

For example, this video (at about 5:52) even says that "it is convex according to anatomical diagrams, but I like to draw it as if it is concave". Or in this video (at about 7:46), the modeler pushed the concavity of the iris quite far, it's like a deep indent.


texts: Would two species of yeast with similar genome sizes have the same number of genes or chromosomes?

texts:
Similar organisms generally have similar genome sizes. Given this, would two species of yeast have the same number of genes and chromosomes?

Edit: Fixed with thanks to @daniel-standage


texts:
This exercise was given by my professor but I am struggling to understand the solution.

A PCR is performed on the following sequence (in order to replicate the chain and thus have a greater quantity of DNA so to be able to analyze it):

The main sequence belongs to a horse and differences are indicated below with dna belonging to a cow.

1) Choose appropriate primers in order to analyze some lasagna, which is suspected to contain both horse and beef.
Given Solution:
The primers should be:

I understand how these primers would work in this case, but why not just have the second pair of primers which would make it possible for the whole chain to be analyzed at once?


texts: Does the palate truly house the sense of taste?

texts:
Source: Your “palate” is the roof of your mouth, and by extension, your sense of taste.

I was reading Etymonline's entry for palatable {adj.}, which cites and derives from palate {noun}:

  ... Popularly considered the seat of taste, hence transferred meaning "sense of taste" (late 14c.), which also was in classical Latin. ...

Are the quotes above factually right about mouth anatomy (I ask NOT about language here)? Or was this an outdated wrong idea?

Footnote: Did the etymology become corrupt? I heed the Etymological Fallacy.


texts: Why does our hair turn white before we get old?

texts: White hairs are considered a sign of old age, but they often occur in young boys. I want to ask why my hair is turning white? And why black hair turns white?


texts: How was it discovered that flouride helps stop tooth decay?

texts:
Apparently flourinated water helps stop tooth decay. So I have some quesions about this.

Firstly how does it stop tooth deacy?

and

Secondly, how was it found that out of all the chemicals, it is flouride that stops tooth decay and nothing else?


texts:
Trying to understand Photosynthesis better. I understand the NADP+ is reduced to NADPH in light dependent reactions and NADPH is then recycled back into NADP+ in the Calvin cycle. What I don't understand is where does the NADP+ come from initially?

Specifically I am asking with regards to its presence in the stroma within the chloroplasts of a plant cell. Where do plants get NADP+ from in order to assist in the production of sugar?


texts: Acid/basic chemicals that can be used without extraction hood?

texts:
I need to use some meat dissolvent for my thesis, I’m working in forensic anthropology, but in my university, we are not allowed to use those which might be extremely harmful (such as HF or HCl due to the fumes).

Friend of mine suggested me to use CaO and KOH, since you only need normal lab equipment. Do you have other suggestions that might come in handy?

Thank you! All the help I can get is really appreciated


texts: What is this red orange insect with black dots found in Japan?

texts:
I searched with picture to Google, and they suggest it might be

Fire-coloured beetle

I also went through the list of insects from this page, http://www7a.biglobe.ne.jp/~yabuyama/koucyuumoku.html, it is in Japanese. The bug that looked like the one in picture the most was a ベニカミキリ (latin name: Purpuricenus temminckii), but it did not have the black dots, and it seems too small.

The insect was found near a pond in a Japanese garden in Fukuoka, Kyushu in June. I do not recall the size of it, but I think it was somewhere between 1cm and 3cm long.


texts: How does plasmid pcr amplifcation work exactly?

texts:
Suppose that you have an unwanted gene in a plasmid vector and you want to get rid of it in Gibson assembly. I get the whole concept behind using the primers and essentially making copies that exclude the pink region but what is the first step required to separate the plasmid and editing the plasmid?
Do you just use heat to separate the circular plasmid and then add the primer and expect a polymerase to go around the circle and make a copy without the unwanted gene? Does a circular plasmid even separate into single stranded DNA like a linear DNA??  How does the primer even access the strand in the plasmid DNA in the first place?
I haven't found a clear animation nor diagram on how this exactly works and was hoping for someone to answer this. What enzyme opens up the circular plasmid without the restriction enzyme and adds the base pairs to make copies without the unwanted gene. Please refer to the figures below for what I am trying to ask. And thank you in advance. In short how do you go from "PCR backbone" to "PCR product BB with no insert"


texts: Identifying whether ELISA kits are authentic or fake

texts: What methods can be used to determine whether they are authentic or fake?


texts: Forward versus backward numerical simulations in population genetics

texts:
My question is closely related to this post.

There are a number of existing platforms to perform numerical individual-based simulation in populations genetics. An almost exhaustive list of such platforms can be found here.

Some program (like NEMO or SFS_CODE for example) perform forward simulations while some others (like SIMCOAL2 for example) perform backward (coalescence) simulations.

I am asking for a general comparison between those two methods.

Is one faster than the other? Why? (Intuitively I'd expect backward simulations to be faster).
Does backward simulation allow for simulating selection, recombination, gender-specific mutation rate, complex demography, etc..
Why/when would one use a backward/forward simulation model rather than the other type of model?


texts: What neuro-motor diseases cause the lower esophageal sphincter (LES) to malfunction?

texts:
Please note: This question is neither homework nor seeking medical advice. I'm simply asking for a factual, objective, biological explanation of the various neuro-motor diseases/illnesses that can act as the underlying cause to LES malfunction.

The primary function of the lower esophageal sphincter (LES) is to prevent stomach acid from backwashing into the esophagus. This sphincter is an involuntary muscle, and so, for it to malfunction (unable to fully or properly close), it must be the result of an underlying neuro-motor (autonomic) disease or condition.

What such condition attacks this sphincter/valve, thereby causing it to malfunction and not operate properly? How exactly does this condition effect the sphincter biologically/neurologically?

Update

Looks like the Vagus Nerve (10th Cranial) innervates this sphincter, so I guess the question is: What neuro-motor diseases attack the Vagus Nerve or cause it to malfunction?


texts:
I know that being basophilic or acidophilic corresponds to affinity to certain dyes used in microscopy.

What i want to know is what characteristics of the cytoplasm can we infer from its basophilic property? Does it give us any idea about its different compartments relative abundance, or practical features of the cell? Can we predict how acidophilic and basophilic cells differ in their life and roles?

Thanks for help.


texts: What I mean is, during long term potentiation (LTP) or long term depression (LTD) for a particular memory, do the strengthening and/or weakening of neuronal connections only occur in a small patch of neurons or regions spread out in the cortex?


texts: Why do workouts cause your muscles to feel heavy?

texts:
I know that muscle activity causes your muscles to build up lactic acid. Is this the specific reason that your muscles begin to feel heavy? How does this relate to the healing or inflammation process for muscles, or does it?

Thanks!


texts:
I captured a picture where ants feeding on Chili peppers also, I was shocked.

Actually this peppers is one of the best way to get rid of ants is to prevent them from ever considering from home.


texts: blue/white screening - results are opposite as expected

texts:
We inserted GFP-gene into plasmid Bluescript SK+, transformed E. coli with this construct, and then plated on an agar plate with Ampicillin and X-gal to do a blue/white screening. We got blue colonies and white colonies, and normally the white colonies are considered positive for the insert and the blue ones are negative for the insert.
The problem is that the results we got are actually the opposite. If we look at the plate under UV-light, we see that ALL the blue colonies are fluorescent, which means they actually produce the GFP, and ALL the white ones are not!! How would you explain this??
Thank you

Edit: i thought that maybe the insert could be in frame with lacz', so we get fusion proteins. However this doesn't explain why we got white colonies which are not fluorescent


texts: How fast animals habituate to wearing shoes

texts:
You probably have seen hilarious videos of dogs wearing shoes for the first time. Animals usually very uncomfortable and try to "shake it off", as they seem to consider shoes be some sort of sticky dirt.

I could only find short clips of dogs wearing shoes for the first time, but I would like to know, how fast dogs, or other animals, will learn that shoes are an integral part of their feet and continue with normal stride?

From AllDogBoots, it seems that teaching dog to walk in shoes will take up to 4 days and a lot of treats.


texts: Would BMP7 introduced to a Petri dish with cartilage cause chondrocytes to replicate?

texts:
Chondrocytes are the cells that make up cartilage. As I understand it, the best growth factor that signals replication of chondrocytes is Bone morphogenetic protein 7.
If supplied with a sufficient source of nutrients and a growth factor, would those chondrocytes begin to replicate?
If you prepare a Petri dish full of blood and cartilage and add BMP7, would the cartilage start to grow? Are those two questions the same?


texts: I generally see it written that there are three types of neurons, classified by projection: (1) sensory neurons, (2) interneurons, and (3) motor neurons. Now, in the CNS, I don’t think there would be sensory or motor neurons, seeing as they connect the PNS to the CNS. Does that mean, then, that all the neurons in the CNS are interneurons? I remember my biology teacher telling me not all neural pathways involve interneurons, so that suggests to me that the CNS consists of other neurons as well. What neurons would these be, if they are existent?


texts: What are the absolute facial features which features sexual dimorphism in humans?

texts:
Apart from beard and moustache, is there any facial feature that would help to distinguish between men and women?

It is said that men have square, rectangular or oblong face and women have oval,diamond or heart shaped face.

Also men are said to have thicker eyebrows, widely spaced eyes and prominent eyebrow ridges while women have longer eyelashes.

Again, men have wider mouth and women have fuller lips.And men have sharp jawline while women have rounder jawline.

This list can be extended further. However, there are several exceptions to the above mentioned generalization.

So,how can we instinctively determine biological sex(male or female) of someone just by looking at the face?


texts: Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

texts:
I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm.

I tried the nearest neighbour algorithm with RNA and salt concentrations as described in a respective paper (thermodynamic table used as in paper below from: Freier et al 1986). Yet, the values largely differ (execute code below to see).
I tried all seven salt correction methods provided by Biopython, still I never get close to the values generated by siRNA design algorithm for the same 7-mers.

Can someone tell me how accurate Biopython's melting temperature nearest neighbour algorithm is? Especially for short oligomers like my 7-mers? Is there maybe something I am implementing wrong? Any suggestions?

Values derived from executing sample input:
http://sidirect2.rnai.jp/
Tm is given for the seed duplex of the guide strand: bases 2-7

Literature:
"Thermodynamic  stability  and  Watson–Crick
base  pairing  in  the  seed  duplex  are  major
determinants  of  the  efficiency  of  the
siRNA-based  off-target  effect"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602766/pdf/gkn902.pdf

from Bio.Seq import Seq
from Bio.SeqUtils import MeltingTemp

test_list = [
('GGAUUUG', 21.5),
('CUCAUUG', 18.1),
('CAUAUUC', 8.7),
('UUUGAGU', 19.2),
('UUUUGAG', 12.2),
('GUUUCAA', 14.9),
('AGUUUCG', 19.7),
('GAAGUUU', 13.3)
]

for t in test_list:
    myseq = Seq(t[0])
    tm = MeltingTemp.Tm_NN(myseq, dnac1=100, Na=100,   nn_table=MeltingTemp.RNA_NN1, saltcorr=7)  # NN1 = Freier et al (1986)
    tm = round(tm, 1)  # round to one decimal
    print 'BioPython Tm: ' + str(tm) + '  siDirect Tm: ' + str(t[1])

# Output:
>>> BioPython Tm: 10.1  siDirect Tm: 21.5  # GGAUUUG
>>> BioPython Tm: 8.2  siDirect Tm: 18.1   # CUCAUUG
>>> BioPython Tm: -2.0  siDirect Tm: 8.7   # CAUAUUC
>>> BioPython Tm: 8.2  siDirect Tm: 19.2   # UUUGAGU
>>> BioPython Tm: 1.3  siDirect Tm: 12.2   # UUUUGAG
>>> BioPython Tm: 4.4  siDirect Tm: 14.9   # GUUUCAA
>>> BioPython Tm: 9.0  siDirect Tm: 19.7   # AGUUUCG
>>> BioPython Tm: 2.1  siDirect Tm: 13.3   # GAAGUUU

Question first asked at stack-exchange: https://stackoverflow.com/questions/30037939/biopython-big-discrepancy-calculating-rna-melting-temperature-over-literature


texts: I just bought this plant from flower shop, after it flowered it was very beautiful red flower, can anyone tell me what is this flower?


texts: Why do glial cells of the retina become more abundant the closer they are to the optic nerve?

texts:
I am doing a project on expression of GFAP in the zebrafish retina. GFAP is a marker for glial cells.
I have found that the glial cells are more abundant the closer they are to the optic nerve at the middle of the eye. This may just be because the cells are more tightly compacted here than at the edges of the eye...
But I am wondering if it may have something to do with the glial cells being involved with neuornal processes, and the optic nerve being the transmitter of signals from the eye to the brain?


texts:
I am currently doing some work on modelling the effects of treated nets usage on mosquito populations. Nets do not retain their maximum efficacy forever. They lose their chemical efficacy after about three years and all that is left is the physical protection offered by the net which I estimate to be 20% of the original efficacy.

I am trying to model this behaviour. I need continuous function over the interval $[0,1095]$ which decreases slowly  from 1 when $x=0$ and asymptotically approaches 0.2 when $x \rightarrow 1095 $.

I tried an ellipse of the form $y=\sqrt{1-\dfrac{x^2}{(1095)^2}}$, but i realized the function is equal to zero when $x=1095$ which is not what i want.

Any help will be appreciated. Thank you.


texts: What is the maximum potential sucrose concentration of plant sap? What keeps plants below this potential?

texts:
I am interested in identifying the maximum potential dissolved sucrose (%w/w) that plant sap could have, and which (biological, physical, chemical) factors constrain the observed sucrose concentrations.

For example, sugar maple has one of the highest sucrose contents at 6%, and the solution also contains fructose, glucose, organic acids, minerals (K, Ca, Mn, Zn, Na, Cl), amino acids, volatile organic compounds, phenols, enzymes  (according to Wikipedia), and most sap flow occurs when temperatures cross the freezing point each day.

Is there a way that I can calculate this theoretical maximum from "first principles" of organic- or bio-chemistry, or is this a question better suited for empirical study?

this is a biological application of my question at physics.SE


texts: If targeting a certain daily water intake, do you have to compensate for beverages that promote diuresis?

texts:
Please forgive my ignorance on the topic and I hope this is a "on topic" question here. It was a toss up between this SE and Physical Fitness SE but I want a more scientific answer.

I came at a impasse in a conversation with another fitness enthusiast. They stated that if you are targeting your water intake during the day then drinks with a diuretic effect (tea/coffee) count negatively towards that water intake total.

So, is it true that one should over-compensate if drinking these diuretics? Or does the water content of drinks like coffee and tea balance out or even positively hydrate you?


texts: What is/are the molecular differences between HDL and LDL cholesterol?

texts: Why exactly is HDL-cholesterol good for us and LDL-cholesterol bad for us. It has been well-established that LDL-cholesterol is associated with atherosclerosis and that HDL-cholesterol helps remove excess LDL-cholesterol from the circulation. From a biochemical view, however, what is the difference between the molecules that causes this difference?


texts: I found those mushrooms in my garden in Luxembourg and I was wondering what species they might be.


texts: Potential between endolymph/cytoplasm and endolymph/perilymph

texts:
I am studying for an exam and there is something I can't seem to understand. My textbook says that the endolymph contains 150mM potassium, 2mM Na+ and 130mM Cl-. The perilymph contains 5mM potassium, 140mM Na+ and 110mM Cl-. "Thus" the electric potential between perilymph and endolymph is +80mV (endolymph being positive).

I can see that there are chemical gradients but why is the endolymph so much more positively charged than the perilymph?


texts: Why didn't Escobar's hippos introduced in a single event die out due to inbreeding

texts:
Today I read a BBC Report about how Pablo Escobar had once imported 4 hippos (1 male, 3 female) into his estate in Colombia for his private zoo. After his downfall, while other species were shipped out, hippos were considered too big to move and expected to not survive.
However, to the surprise of all the hippos are thriving and are so numerous that there have been calls to cull them. From the report:

Numbers are projected to only get bigger. [Colombian biologist Nataly] Castelblanco and her
peers say the population will reach over 1,400 specimens as early as
2034 without a cull - all of them descended from the original group of
a male and three females. In the study, they envisaged an ideal
scenario in which 30 animals need to be culled or castrated every year
to stop that happening.

My understanding is that since there was only 1 male, the gene pool would be limited and lead to lot of inbreeding in the descendants. This would cause population to not explode because some individuals would be unfit to survive.
Why has this not happened in case of hippos? Is it because there are 3 females (probably unrelated to each other) which keeps gene pool large enough? Or can mutations explain this phenomenon? Would results have been different if originally 2 females had been moved and only 1 retained?
EDIT - I have just found that current population is maybe less than 100 individuals which though big is not massive.
EDIT2 - I have edited the question title to keep focus on the hippos although a general answer would be welcome.


texts: Is this trial that reversed aging in humans worth taking seriously?

texts:
In September 2019 Fahy et al. published results from the TRIIM (Thymus Regeneration, Immunorestoration, and Insulin Mitigation) trial. Their stated goals were to investigate whether they could restore the immune systems in eight healthy older men (ages 51 - 65) using a combination of recombinant human growth hormone, dehydroepiandrosterone and metformin. While they achieved impressive on-paper results partially restoring the thymus, the most impressive result came from their epigenetic measurement of aging of subjects in the trial.

Fahy et al. had successfully reversed aging in their subjects according to four epigenetic measures of aging. The effect size was large: each measure indicated an average gain of over 2 years after 1 year of treatment.

In other words, if hypothetically a subject was 60 years old at the beginning of the trial, both chronologically and epigenetically, then by the end of the year they would be 61 years old chronologically but less than 59 years old epigenetically.

Of the epigenetic measures of aging, GrimAge is thought to be the best available predictor of lifespan. From the paper introducing GrimAge,

  Using large scale validation data from thousands of individuals, we demonstrate that DNAm GrimAge stands out among existing epigenetic clocks in terms of its predictive ability for time-to-death, time-to-coronary heart disease, time-to-cancer, its strong relationship with computed tomography data for fatty liver/excess visceral fat, and age-at-menopause.

Fahy et al. demonstrated a mean age reversal of 2.16 years after 1 year of treatment according to the GrimAge measurement (see Table 1 in the paper).

Fahy is reportedly spearheading a new trial, called TRIIM-X (see this part of his recent TEDx talk). He hopes to investigate the effects of a modified version of the same treatment with the benefits of a larger trial and a more diverse set of participants.

The skeptical side of me has a question:

Is a reversal of the epigenetic clock good evidence that aging was reversed, or is there a good theoretical reason to think that you can reverse the epigenetic clock without reversing “true” aging and thus increasing lifespan?


texts: The most annoying thing for me about being cold is a runny nose. Is there an advantage to having a runny nose when cold? What does having a runny nose achieve?


texts: What does the term "recruitment of T-cell" mean?

texts: With respect to the article, what does the term "recruitment of T-cell" mean? Who recruits T- cell? Does recruiting T-cell mean the T-cells get a sense of directionality to get activated by the APC's?


texts: After reading the question why do I only breathe out of one nostril I realized that breathing out of both isn't common. I have always breathed out of both, and when I get a stuffy nose, or a runny nose, it's on both sides. If only one side is stuffed, I'll just lay on my side a bit to even it out until I can breathe out of both again. I've always though that was totally normal! What does it mean that my autonomous nervous system is not alternating my breathing?


texts: Where can you find the quantities of each amino acid of a particular protein or food?

texts:
Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information?

Is there a freely accessible database online with these statistics? Or, one that contains something for each protein from which this could be derived? (and if so how?)


texts: What are the "minimum requirements" for a single cell?

texts:
I saw a description of the "minimum requirements" for a cell at http://creation.com/origin-of-life in the section called "What are the minimum requirements for a cell to live?" and I'm wondering if this is scientifically accurate - and if not - what are the real requirements?

[note/warning - the link above is to a creationist site - I'm only quoting this source because I'm trying find the science involved and I didn't find other sources talking about all the necessary pieces. I'm not trying to promote creationism with this question so please don't attack the source or me for bringing it.  If you can find a non-creationist source which outlines these requirements, I'll be happy to update the question and remove this source.)

In summary it lists the requirements as follows:

cell membrane
way of storing information (DNA)
way of reading 2. to make components needed

RNA polymerase
gyrases to untwist DNA
ribosomes to make proteins
(a few others I omitted b/c I don't know if they're really important)

means of creating fuel (ATP synthase)
a means of copying the information for reproduction

The context of the question is similar to Can scientists create totally synthetic life? and a question I wrote What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?.

I'm trying to understand what would be involved in making a cell from scratch. Somehow I found this source but I don't know if it's accurate.


texts: Why did we evolve to be able to see this specific set of wavelengths only?

texts: It is understandable that life didn't evolve the capability to sense all wavelengths of light, it simply didn't need it. My question is, why did it evolve the set of wavelengths it has, for example, the human visible range is 390-700nm, so why couldn't it be a different set of wavelengths, like, (say) 300-620nm? Is there a reason for it?


texts: How do Apes get their Omega 3s in the wild given so few plant sources? Are they able to convert it to DHA?

texts:
Given so few plant sources(around 6-7) of ALA, how do Apes get ALA in the wild?

Are they able to convert it into DHA in satisfactory amounts?


texts: What equipment would one use to modify a virus?

texts:
Would anyone be so kind as to give me a few examples of the equipment involved when modifying a virus? Otherwise my novel may end up reading

Eva entered the lab and modified a virus.

Not much back story there!


texts: Have we succeeded in building a living organism from inanimate material?

texts:
Following the Miller-Urey experiment where we were able to produce organic compounds with basic primitive atmospheric gases, high potential and water in a closed system. Have we been able to create a living organism fully functional with only inanimate material (dead material, or atoms, or anything that is not coming from a living organism such as a clone, or already existing DNA)?

I mean building a living organism from scratch. Are we able to do this?


texts:
I have a list of gene name in a file

CHRNB2
EGR2
GCK
KRT14
LMNA
FGF3
TK2
ABCC8

How can I map them to uniprot ID ?
P.S I tried Uniprot "ID mapping" (from-"GENEID" to-"UNIPROTKB AC"), but it couldn't map.
Please suggest me what to do.


texts: Why not surgically resect the tumor before CAR-T cell therapy? Won't that be more efficient?

texts: If CAR-T cell therapies suffer from tumor antigenic escape, why not just resect the tumor via surgery, leaving behind a small number of cancerous cells, and then wipe them out with CAR-T cells? The small number of cancerous cells may reduce the chance of too many cancerous cells escaping CAR-T cell cytotoxic killing that may cause tumor regrowth.


texts: Generate full dimer from monomer with C2 symmetry?

texts:
I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?structureId=2PJY.

How can I generate the PDB for the full dimer?

I am comfortable with PyMol, so an answer using PyMol is preferred.


texts: How selfish is Dictyostelium slug formation?

texts:
Dictyostelium is a slime mold which is well known for having a single cell free living phase and other some conditions (e.g. when food is scarce) for forming communal piles of cells called 'slugs' which migrate as a proto animal.  Eventually the slug can turn into a fruiting body with a stem and a nodule of spore forming cells at the top.  The spores can then be carried off by the air and seed dicty further away.

Apart from being amazed at the seeming ability to form amoebic, animal, plant and seed like forms, there must be a lot decision making happening at the formation of the stalk and fruiting node at the top.

So my question is: what is the current thought about how cells compete in the mexican hat and stalk formation to be at the top of the pile?  Its pretty altruistic of the cells in the stalk to do this - some web pages say they die, is that right?  Links to references after 2007 or so would be appreciated unless it's all been decided.

By analogy its always been pretty altruistic of 99% of our bodies to let our gonads reproduce, but we are (approximately) homogeneous genetically.  In the wild is slug formation heterogeneous?  How does genetic diversity influence slug and fruiting body formation?


texts:
Never saw them before, they appeared suddenly , the day my father died.
Place is Serbia in Europe.
Does anyone know what are these birds?


texts: Which one is true about sunflowers, "follow the sun across the sky" or "always face east"?

texts:
Which one is true :

Sunflowers follow the sun across the sky.

Or...

Sunflowers always face east.

Or are there 2 kinds of sunflowers with different behaviours?


texts: Are chromosomal and plasmid DNA in the nucleoid?

texts:
I know plasmid DNA is not part of the chromosome, according to my textbook, but can you still class it as being part of the nucleoid?
Also is chromosomal DNA in the nucleoid?


texts: What is the difference between an active and inactive T helper cell?

texts:
1- Are all inactive T helper cells "T memory cells" ?
2- Is there anything such as active T memory cells ?
3- I have noticed that there is also a third type of T helper cells but i dont know what it is called. They are used in the beginning of the humoral response process (they bind to initial APC cells and then divide producing active t helper cells and inactive t memory cells). How are these different from the active and inactive T helper cells ?


texts: Linkage and LD: quantitative or qualitative?

texts:
My understanding is that the concept "genetic linkage" can be expressed in quantitative form, like:

A predisposing gene X was found in close genetic linkage to Y.

And that linkage disequilibrium (LD) is a quality, like being pregnant, you are either in LD or your are not:

A predisposing gene X was found in close genetic linkage to Y and in
linkage disequilibrium with Z.

Is this correct?


texts:
Googling, I find two different explanations for why earthworms tend to surface after a rain.

This page from UCSB, for example, gives both answers, contradicting itself:

The first explanation is that worms can breathe fine when it's wet underground, but surface after rain because it's their only chance to surface without drying out:

  Worms, like all other animals need to breathe, but since worms do not have mouths, they have a different way they breathe. Worms breathe directly through their skin, but they can only do so if their skin remains moist. Deep down in the soil, where worms typically live, it is normally moister than the surface. For this reason, worms prefer to live underground. After it rains, the surface becomes wet enough to support worm life, so they can come above ground to explore new areas more quickly. Fun fact: worms actually don’t come above ground after it rains to avoid drowning. Earthworms can live underwater for approximately two weeks. Thank you very much for your question!

The second answer is that worms drown if they stay under ground after a rain

  Worms are animals and, like you and me, they require oxygen to live. Instead of breathing air though their mouth into lungs, worms absorb oxygen from the air across their skin. Worms eat dirt. They burrow into the soil and normally live underground, where they are protected from the sun and so won't dry out. If you've ever played in the dirt by digging holes, you probably noticed that there are small holes or tiny pockets of air. The worms use that air, and the air that enters through their burrow holes, to breathe. When it rains and the dirt absorbs a lot of water, those air holes disappear, and the worms' burrows fill with water. If the worms do not come to the surface during a heavy rain, they will suffocate. Likewise, if they do not return to the soil after the sun comes out, they will dry out and die.

Which of these two is correct?


texts: Has DNA communication/interaction at a distance been empirically demonstrated?

texts:
I recently had a discussion with a statistician in my school about memory. Among other things, he told me that it has been experimentally demonstrated that when one extracts DNA from any organism and then induces a stressful condition on that organism, the same effects on DNA can be observed both in that organism and the DNA sample that was extracted before the stressful condition. From what I could tell it is as if he was suggesting that DNA has some kind of a telepathic property that enables this phenomenon.

Now, I am not a biologist (and neither was he) but I am heavily suspicious of this idea. Also, when I asked him for a specific paper on that, he simply told me that there are many and that it is fairly easy to find them. However, my efforts to find anything on google scholar were fruitless so far.

So I want to know: Is such a thing possible and have there been any experimental studies on that?


texts: What are the types of interactions in biological network (protein networks)?

texts: In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, phosphorylation, dephosphorylation, glycosylation, ubiquitination, and methylation. I want to know more about these interactions. Is there a particular source from where I would understand what these interactions mean in depth?


texts: Where can I find SSR and/or SNPs that locate RC1 genes in Soybean?

texts: Where should I look to find SSR and/or SNPs that locate RC1 genes in Soybean?


texts: What is a good method to test the effect of gibberellin concentration?

texts:
I was just wondering what a good method would be to test the effect of gibberellin concentration on growth. I know it is prevelant in many flowering plants but am unsure as to what would be suitable. I have been looking into tepary beans as one but am unsure as to how exactly I would measure 'growth'/the effect of gibberellin.

Thanks!


texts:
Are there species that occupy several roles in the food hierarchy?

By role, I am referring to producer, primary consumer, secondary consumer, tertiary consumer, quaternary consumer and so on.

Examples of more specific questions

Are there species that are both primary and secondary consumer?
Are there species that are primary consumer, secondary consumer and a tertiary consumer?
Are there species that are both producer and primary consumer?


texts: What proves that speciation is a pairwise process?

texts:
I have been asked this questions by many biology students and even non-biologist without a pretty straightforward answer to give. We are quite accustomed to phylogenetic trees where a common ancestor becomes two different species and these new species become, each one, two more. But, Why is not possible that a species might divide in three different species? Or four? Or more?

What arguments support this conception of the evolutionary process? Also, if somebody has a good article explaining this, please provide me with the link or citation so I can refer my fellow biology students to it.


texts:
In the book "The Kaizen Way" by Robert Maurer, I've read the following:

When we’re sitting, our muscles go into a form of hibernation, causing
our bodies to shut down the enzyme (called KK1) that breaks down some
of the fat in the blood.

However, when I tried to google "KK1 enzyme", I got nothing about any enzyme. I mean, I got this website and this article, but they don't contain the name "KK1" at all.
What was meant by that? Is it scientifically accurate?


texts: Why do flipped cockroaches sometimes lose their heads?

texts: Sometimes I see in my house there are flipped cockroaches whose lose their heads. I used to have a cat, but there is no pet in my house anymore so I think it's only ants can be involved in this. But if so, the headless cockroach should be preyed already. Is there any explanation for this?


texts: What is the change in ratio of histone to protamine in men with infertility called?

texts:
I am neither a biology researcher nor a student. In a paper (written by a biology researcher) I am translating into English, there is the following statement which, according to the text, must have a name and I fail to find the English name:

  It is showed that in men with infertility histone to protamine ratio changes and the change is called ...

What is the change called? I guess it's something unnatural/abnormal.


texts: What is the most difficult feature to explain evolutionarily?

texts:
I wonder what are examples of organs/structures/behaviours/cooperation that evolutionary biologists themselves find most difficult to explain -- to explain how they could appear evolutionarily -- within known mutation rates, generation frequency, and known time frames.
Excluding issue of appearance of life itself.

Knowing rates of mutation and generation cycle (and population size), it would be possible to estimate time needed for appearance of new feature.

Thus it would be possible to spot counter-examples, such examples that are probabilistically beyond possibility to appear in given evolutionary time. Are such examples known ?

I might be naive, but I think some rare behavioral trait can be a candidate, behavior that does not trigger even once in a lifetime of organism, on average, that triggers really rarely.


texts: Risks of latent viruses that reside in ancient genomes under research?

texts:
Some interesting research in reactivating mammoth genetic material (https://www.nature.com/articles/s41598-019-40546-1) made me wonder what risks are inherent (or are not inherent) in reviving older genomes that may have integrated latent viral code?

Are there potential biohazards in this line of research, where dormant viruses that have otherwise gone extinct (along with the extinct host) and which now may have the potential to be reactivated? Not just in terms of zoonoses that infect across species, but also viruses that infect modern animals that are more closely related or have relatively common ancestry (e.g., from mammoth to elephant).

Could a disease be brought back via this kind of research? Or are the conditions for waking latent viruses from starting material of this kind just not possible to recreate in a lab setting?

Edit: To clarify what I mean by potential biohazard in relation to this question: Experimental conditions result in a latent virus going into lytic phase. The virus is a communicable pathogen; it spreads outside the laboratory environment; it causes sickness or death to living organisms to the extent that it creates a public health, ecological, or other crisis of significance. For background, please also see: Cambridge, The Free Dictionary, and Wikipedia.


texts: How is the human oxygen absorption dependent on the concentration of oxygen in respiratory air?

texts:
I just wanted to calculate the theoretical time span in which I could survive (conscious) in my apartment without letting the air on the inside exchange oxygen/carbon dioxide with fresh air. During my calculations I came to the point where I was unsure, if the oxygen amount already consumed, influences the future O2 absorption and consequently the CO2 production.

In this hypotetical scenario, I assume that the air in my apartment is homogeneous and ideally mixed, thus measuring the same level of oxygen anywhere on the inside. Furhter I assume that all of my rooms are completely empty, hence having volume of the living space * room height * oxygen concentration as my initially available oxygen amount. (I tried to be independent of the air pressure by using standard values for consumption depending on concentration and calculate how long it would take for the oxygen level to drop below/carbon dioxide to rise above a specific threshol (depending on what gets lethal first) ).

I asked this particular question and not "How long can one survive in a closed room...", because I have not found a useful answer yet considering the oxygen/carbon dioxide concentration, but the absolute amount of these gases in it.

In case it would be helpful/necessary: I am not familiar with biochemical, metabolic reactions and have not studied in this field before.

Thanks in advance.

PS: If you think, another stackexchange community would be more appropiate, please comment.


texts: How does one determine the sex ratio of a ZZ and ZW cross?

texts:
In Campbell's Biology Chapter 14-15, Mendelian Genetics & The Chromosomal Basis of Inheritance, question 12 reads:

12) In birds, sex is determined by a ZW chromosome scheme. Males are ZZ and females are ZW. A recessive lethal allele that causes death of the embryo is sometimes present on the Z chromosome in pigeons. What would be the sex ratio in the offspring of a cross between a male that is heterozygous for the lethal allele and a normal female?

A) 2:1 male to female

B) 1:2 male to female

C) 1:1 male to female

D) 4:3 male to female

E) 3:1 male to female

The correct answer is A. In my Punnett square, there were two male and two female so shouldn't the answer be C?


texts: In what range do humans generally interpret sound best?

texts:
I am currently working on a speech recognition frameworks. A generally used feature used in speech recognition are MFCC features, which uses the mel scale to extract features with.

The mel scale visualises how humans interpret different frequencies of sound compared to each. The graph shows that by linearly increasing the frequency from 0 -1000 will the sound/pitch be interpreted as linearly increasing. When the frequency is linearly increased beyond 1000 hz, is the sound not interpreted as linearly increasing but logarithmic increasing.

How MFCC make use of this:
When training the system, are audio files processed using band pass filters with center frequencies that are mel distant, meaning that they will be (somewhat) linearly increasing at the beginning and end up being logarithmic increasing.

How do I interpret this:
It seems to me that the human auditory system is very susceptible to sounds the range 0-1000 and not much above, but 1000 hz isn't much and I guess conversation must in somewhat higher range. So why are humans more susceptible to sounds in these ranges?


texts: What is the distinction between deoxyribonucleases and restriction enzymes?

texts:
Both deoxyribonucleases (DNases) and restriction enzymes are endonucleases (some DNases can be exonucleases).

They both break the bonds between nucleotides. Therefore, what is the difference between the two?

My original thought was that restriction enzymes, unlike DNases, cut at specific sequences of DNA. Then this raises the question of whether restriction enzymes are just a category of DNases, but I have found no sources to back that up. Also, according to this Wikipedia article:

  There are more than 900 restriction enzymes, some sequence specific and some not...

This further erodes the distinction I had created between the two types of nucleases.


texts: What soft tissue separates bones of toes?

texts:
I need to know a little about the "knuckles" of toes; specifically the 4 areas that separate the 5 proximal/metatarsal joins.

I'd like to know the terms for areas that might be damaged if the width of the foot were to be repeatedly compressed there. Is there even a name for just the general "knuckle area"?

Thanks


texts:
Now when i was studying about thalassemia, I read that anaemia is its major characterstic. I can understand that fact. But it was also written that the skin gets pale.

  Wikipedia says that the skin turns yellowish.

I want to ask firstly is it that the skin gets darker when the affected person is exposed to sun and is otherwise pale?

And also why does the skin turn yellow/pale in the first place? Does that have to do something with Iron?


texts: Examples of animals who 'forget' their offspring

texts:
Occasionally on the news I read about young children dying in hot cars on a sunny day. Usually the article reports that the parent(s) 'forgot' about their children still being in the car.

Obviously natural selection would select against a trait where parents forget about their dependent offspring or their whereabouts. However, I can imagine that under certain circumstances and on the fringe of the bell curve for offspring-caretaking, this occasionally happens.

Are there documented examples of animal species (preferably mammals or birds) who truly sometimes 'forget' about taking care for their dependent offspring, or forget their whereabouts?

Disclaimer:
I'm aware of possible anthropomorphism in this question. With 'forgetting' I don't mean behavior such as abandoning offspring at the age where they need to become independent, or accidentally being separated from their young.

Here's an example of what I would file under forgetting:

A parent feeds their young every two to three hours. One day, they go out to find food, but get distracted by something interesting (let's say a mate). They spend a day frolicking around with the mate, and eventually return to their young. On return, they find out one of the young has died due to starvation, and they are visibly surprised / startled / upset about this.

Edit:

To respond to Tyersome's comment: I have done plenty of searching and research. I haven't been able to find anything, neither in the scientific literature nor pop-culture websites / books. When you Google 'animal parenting' you'll find plenty of examples of various species who abandon their young (such as harp seals or rabbits) or who don't care for their own young (such as cuckoos), but these are 'deliberate' actions across an entire species, not examples of accidentally forgetting.


texts: I'm quite curious on how animals view incestual pairings. Given there are enough mates around, i have quite observed that most females (subjects are dogs, cats, pigeons and chickens) would go choose another mate that is not a direct family member (parent, sibling, offspring). How does this work? Is it instinct to not favor family members or does it still revolve around who's the fittest mate?


texts: Is the ACh receptor more permeable to sodium ions?

texts:
The AChR is permeable to sodium and potassium ions only and has a reversal potential of 0mV.

However the Nernst potentials for sodium and potassium ions is ~ +60mV and -88mV respectively. Taking a simple average of these two potentials would give an expected AChR reversal potential of -14mV; but that is not what we see.

My question is whether the reversal potential is pulled up to zero because of a greater conductivity to sodium than potassium ions, and if so, how the AChR selectivity filter achieves this.

Thanks!


texts: What species of tree is this (found in Navarre, Spain, many tiny flowers)?

texts:
It was planted within the urban area of Pamplona, Navarre, in Spain. It does not seem like it's native to the area, since no trees like it are found in nearby forests. Its size is of 7-9 meters, while its leaves were commonly 4-5 cm long. It was spring when these photos were taken. It had a great number of tiny, dark flowers. It also showed tumor-like growths where the trunk begins to branch.

[


texts: Why do human have continuously-growing hair on their head?

texts:
Why do hair continuously grow on human heads, while the same doesn't happen on other parts of the human body? Where there are hair, they only usually grow to a fixed length; but they seem to have no limit (or at least a much higher limit) as long as the head is concerned (and the face, in men).

Why does this only happen on humans? When did it start happening? What kind of evolutionary advantage could there be in overly-long head hair, so that humans have them while other primates and mammals don't?

I know there are various questions around about why humans have much less body hair than other mammals; mine is related but different: why are we the only species with so much hair on our head, to the point that they might even become inconvenient if we don't cut them?


texts:
There are two conflicting things I have heard. One more anecdotal:

  Wasps can smell when you are afraid of them

The other from reading popular science magacines:

  Humans don't produce any pheromones

As far as I know, a pheromone is a smell produced to communicate with members of your own, but also other species. From my understanding these two statements are mutually exclusive.

So: Can wasps smell if a human is afraid?

Any answer with sources is appreciated.


texts: I wonder if it's possible to pet a domestic crow, or an owl. Do birds respond to grooming as cats or dogs, for example? If so, then how does one pet a bird?


texts:
I was in my garden a few days ago and found the flower shown in the pictures.
Can anybody tell me what this flower is?

Location: Germany / northrhine westfalia
Date: February 2017
Season: Winter

[Edit]:
My neighbour thinks it is a Anemone hupehensis (en.wikipedia.org/wiki/Anemone_hupehensis), could be right.


texts: Hydrophobic elution times in ionic exchange columns

texts:
What would the order of elution be of say Gly, Val, Leu?

My argument is that hydrophobic residues will try and get away from the resin and the more hydrophobic the residue is the faster it will elute. This seems to run contrary to the steric argument however, where larger residues would take longer to elute. Which argument is right?


texts: Among the 6 secretion systems in bacteria, can these 6 ways be sorted out in the order of how harmful it is to the human host? Like say type 3 is highly virulent so that comes first, but I don't know about the rest of the systems. Being a computer science student, I have failed to understand the Wikipedia article to derive this order. Does a discrete order even exist? Can anyone answer this question?


texts: Can someone help me interpret these charts on fluorescent polarization?

texts:
I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a: https://elifesciences.org/articles/28909#fig2

It seems fentanyl was tagged with PE and the proteins (Fen49 and 2QZ3) were tagged with FITC. Fen49 binds with fentanyl and 2QZ3 doesn't but I don't know what about these charts tells me that. Is it the blue specks scattered all over 2QZ3's graph? I'm also confused about the bar graph next to it representing mean fluorescence - does it represent the binding affinities of these proteins/mutations to fentanyl?


texts: Does DNA polymerase always go the same direction?

texts: I read that mutations are more likely to occur on "the strand that DNA polymerase replicates discontinuously". Does DNA polymerase always replicate the same strand discontinuously and, if so, how/why?


texts: Are the y-axis values informative when performing biolayer interferometry?

texts:
I am currently reading  an this article by Alexandra C. Walls et. al.
I would like to ask a question about a graph that is being used in the article and I wanted to know if my analysis was correct.

I was wondering if for the Binding Response versus Time graphs of SARS-CoV-2 (panel A), and SARS-CoV-1 (panel B), can we infer that SARS-CoV-2 was more adept at binding to the human ACE2 because the y-axis has larger numbers than for SARS-CoV-1? If not, why not?


texts:
A year or so ago, a spider that may have been a recluse, wolf or hobo (or anything visually similar), crawled up onto my bed. We locked eyes for a moment, and then it charged at me.

I don't recall whether I killed it or captured and released it, but it is definitely the most aggressive spider I've ever encountered. In fact, I've never known any spider to proactively attack (large mammals such as myself).

Is this a normal or even precedented behavior (in common species of spider in the U.S.)? Is there any specific reason that a spider might behave this way?


texts: How does Pox virus duplicate it's genome? Does it bring DNA polymerase or RNA polymerase into the host cell?


texts: RT-PCR: Not seeing how it can measure mRNA expression levels

texts: From my understanding, in RT-PCR we start off with an mRNA molecule, use the enzyme reverse transcriptase to create a cDNA copy (hence creating a double-stranded mRNA / cDNA hybrid), degrade the mRNA, and finally create a complementary strand to the cDNA with a DNA polymerase. If we're ultimately creating DNA and it's being duplicated at each cycle, how are we able to deduce the original quantity of mRNA in our sample? It seems like we would need to combine it with some other method, but a lot of sources I'm seeing seem to imply that RT-PCR alone is enough to "quantify" the amount of mRNA in a sample. Any thoughts on this are welcome


texts: How quantitative is the theory of evolution right now?

texts:
We developed complex structures like eyes and brain, whose mechanisms rely on specific species of molecules and relevant chemical reactions. But we did not develop an enhanced night vision, the ability to fly, or a built-in silicon-based integrated circuit.

As I understand, we did not develop the latter set of abilities because they are either not so much needed, cost too much energy to be beneficial, or that they required so many information to be coded into our genome that it would take forever for the mankind to produce sufficient mutations. But could this be quantified? Can we tell if a species will develop a specific character, based on the environment they're in?


texts:
If instincts are passed on through genetics, how is that information encoded in DNA?

For example, spiders instinctively know how to spin webs. Does that imply that the algorithm for web spinning is directly encoded in spider DNA?


texts: As a team of undergraduate researchers we are looking to transform two genes of interest into our competent E.coli cells. Both of these genes are in separate plasmids and we would like to put them into one E.coli cell. Is it possible for a cell to uptake two plasmids in one transformation process? If the last question is impossible, is it possible to transform a cell and then transform the colonies produced by that transformation? Thank you very much.


texts: Why does low sequence diversity cause sequencing problems

texts: When sequencers are processing sequence fragments, if there is little diversity at a particular bp locus this can cause problems for the sequencer. I have the superficial understanding that when a flow cell contains a significant percentage of a single base on any given cycle, it has difficulty deciding what base is present in each sequence. Why is this?


texts: Is co-transport within a cell active or passive transport?

texts: ATP is used to actively transport H+ out of the cell against the concentration gradient. The H+ & sucrose cotransporter, for example, then uses this proton gradient for transport. H+ goes back into the cell with the gradient (passively) with concomitant sucrose transport across the membrane. Is this active or passive transport?


texts: I have a fig tree with ripe fruit. There are many birds in it including woodpeckers ( red-bellied  ), don't know if he is eating fruit or bugs. The birds have eaten holes many fruits and some juice drips out. Do humming birds drink this available juice ?


texts: Single Nucleotide Polymorphisms and diseases

texts:
I am writing a report on how Single Nucleotide Polymorphisms occurring in each of these regions:

Transcription factor (TF) binding sites
Epigentic signals
Splicing variants
MicroRNA binding sites
Coding regions

can cause diseases.   Related literature suggestion from you or just informations that you know would be grateful


texts: How can I measure the population growth of yeast?

texts: I will soon have to carry out an experiment. I want to estimate the rate of growth of a population of yeast, although I don't know if it is possible to at least estimate the number of yeast bacteria in a set yeast population. Does someone know of a way this can be carried out? Thanks.


texts: What is the current consensus, if any, about why long term potentiation is not clearly correlated with learning?

texts:
I was watching a video where a professor said that according to some experiments, Long Term Potentiation (LTP) is correlated with better learning, while in yet other experiments, LTP is correlated with poorer learning.

Are there any models that explain this phenomenon? What's the current theory on this?


texts:
Could someone tell me what the species of this beautiful insect is? Location: Chennai, India.

Thank you!


texts: Ideas for microbiology lab. Antimicrobial properties of cutting boards

texts:
I am an undergraduate student in Biology and I am trying to design a microbiology lab that will takes 3 weeks to carry out (1-2 day each week). I am going to examine the antimicrobial properties of cutting boards. So far I have determined that I will use bamboo vs plastic and dish-soap vs disinfectants. I will be using two bacterial strains E.coli and S.epidermis.

Week 1: MIC (Minimal Inhibitory Concentration) assay of disinfectants and soap and prepared LBA (lysogenic Broth Agar) plates for viable counts during week 2.

Week 2: Inoculated cutting boards wait 30, 60, and 120 mins wash with various products then swab cutting boards with sterile swab, place swab in test tube with saline vortex and plate the resulting liquid on LBA. Count CFU (colony forming units) during the week.

Week 3: This is where I'm stuck the experiment has to last three weeks but I'm not sure what other tests I could carry out on the third week.

Any advice would be greatly appreciated thank you.


texts: How protein denaturation affects digestion?

texts:
Which one of these is a) easier to digest, b) more nutritious (in whatever sense):
1. scrambled egg,
2. raw egg.

Bascially is "denatured protein are worse than not denatured" a myth, or not?


texts: Use cases of RNA secondary structure prediction

texts: I'm an undergraduate currently writing a thesis on RNA secondary structure prediction, specifically building upon analysis done by the RNAStructure and Unafold software packages by modifying certain algorithms here and there. I'm actually not a biologist, however. I've taken all of my classes in physics and computer science, and I sort of stumbled into my current research, and since it seemed to be a good fit for my skill set I stuck with it. However this leaves me curious of a motivation for my current work. Why is RNA secondary structure prediction important and what are some of its applications?


texts:
I am reading the following journal paper and I have come across the following statement:

Overexpression of GSK-3β significantly increases motile mitochondria
in a Tau protein-dependent manner. However, GSK-3β does not alter
mitochondrial velocity or mitochondrial run length.

I understand what mitochondrial velocity is but I am not sure what exactly is meant by mitochondrial run length. Any insights are appreciated.


texts: Diffusion coefficient of cells in blood?

texts:
What's the diffusion coefficient of white cells in blood?
Is it well defined, or are cells too large and few as to be treated as particles in this context?

P.S. I have tried to look this up, but what I find inevitably is about diffusion coefficients of molecules inside cells, which is not what I want.


texts: How do I homogenise a small pellet of 10 to 50 cells within less than 50 µL?

texts:
I have a problem with declumping/ homogenising bacterial cells in small volumes (10 to 50 µL). I know that I can get all of my cells out of the tube, but they are still stuck together and won't form separate colonies on an agar dish.
I know that because when I take the last 50 µl from a 1 ml tube and put it in a new tube and mix the 50 µL with a larger volume (e.g. 100 µL), we get a higher CFU count.


texts: Does Acromegaly cause actual expansion of the zygomatic(cheek) bone

texts:
Acromegaly is a disorder in adults involving excess growth hormone production. Since epiphyseal fusion has already taken place in most bones of adults , this does not cause an increase in stature. Certain features of the face such as the jaw may be changed due the fact that the flat bones, such as the maxilla do not undergo epiphyseal fusion and may enlarge.

Several reports describe a prominent zygomatic arch due to arcomegaly, such as this. As I understand ,the zygomatic bone cannot enlarge due to its being fused in adults.

Can acromegaly cause an actual enlargement of the underlying zygomatic bone ?


texts: What processes regulate the sex of offspring?

texts:
It is known that some species are more likely to born male than female (and some maybe vice versa). I understand that it is due to evolutionary perspective (average number of adult males is close to that of females), I want to know about how it is regulated.

What I thought is that spermatozoa are made by half as Y and half as X chromosome. Then mitosis and meiosis and the probability that one of them will die is equal for both types. So, somewhere I feel lost.

Also, can it be regulated by female body or not? According to this paper claiming that hormone levels in women affect the likelyhood to born son. Possibly it is just because they choose males that are more likely to have more Y spermatozoa than X, but if it is some chemical mechanism to regulate that I'd like to know.

I'm not asking only about humans, mechanisms can be similar in almost all mammals. I'm not asking about other species: I know some are regulated by temperature, etc. This question is only about mammals.


texts:
When performing normalization of real time PCR results, I found two ways of doing it:

In my lab they follow the next layout: $\text{Efficiency}^{-(CT\ _{\large\text{interest gene}} - CT _{\large\text{ housekeeping}})}$ each time controls with controls and treatments with treatments. Then they divide the all values (treated and controls) each with controls.
On the other hand I found another way to normalize that follows this steps: $\text{Efficiency}^{(CT_{\large\text{control}} - CT_{\large\text{treated}})}$. Then you make the same for the normalizing gene and divide the first by the last.

The values obtained are similar but not exact. Also I noticed that first algorithm gives rather different values for most diluted when performing a standard curve.
Which is correct?


texts: Where can I find extensive information on animal blood types and transfusions?

texts: I'm interested in doing research on different animal blood types, including blood transfusion across different species. What are some resources you could recommend for me?


texts: How does paracetamol interfere with immune system?

texts:
Paracetamol is used to reduce body temperature when it is to high. The high body temperature (fever) is known to be an indication that immune system fights against an infection.

In this context I have two related questions:

Is high body temperature one of the mechanisms of immune system to suppress an infection or it is just a side effect?
If it is just a side effect, does paracetamol remove it by decreasing the intensity with which immune system fights with an infection or not?


texts:
I was wondering that how does shell of garden snail "grows " with growth of snail.
Small snail possess shell as its size but as it grows shell grows. How do they enlarge cavity inside shell?


texts:
This may sound like a silly question, but I have been wondering about this for a while. I live in a suburban neighborhood with a lot of trees. A lot of trees means birds and squirrels. You can hear them all day and cant leave the house without seeing them.

So why dont we see dead birds and squirrels more often? I only really see them after they have been hit by a car.

My first thought was that nature was just really efficient at cleaning them up. Flies, foxes, and maybe birds of prey get to them before I notice. But that would have to be awfully efficient. When I see a dead squirrel in the road it can take weeks for the sun and the flies to remove it entirely. A fox would have trouble getting in to my backyard (lots of trees but it is fenced in), and I rarely ever see a hawk or a falcon in my area.

My second thought was that there may not be as many birds and squirrels as i think. Yes, there are a lot of them, but maybe I am seeing them same ones over and over again? Squirrels dont really travel THAT far from their homes so maybe I just see the same 10 squirrels all of the time, which makes me overestimate their numbers.

There is a store near my house that always has hundreds of pigeons hanging out in the parking lot. They fly up to the power lines and occasionally fly down for what I assume is left over food or trash. Im guessing they arent there at night, but during the day you can always see them. Why wouldnt you see more dead pigeons in an area with so many pigeons? I know they have relatively long lifespans but still, some of them must die of unnatural causes

Does anyone have any idea where they go?


texts: Why does this oxygen duration chart have increased times above 30,000 FT MSL?

texts:
This oxygen duration chart from an airplane shows the amount of time a pilot can be on oxygen at a specified altitude (in 1000s of feet).  For example, the chart shows two pilots able to cruise at a cabin altitude of 35,000 FT MSL for 182 minutes using a diluter demand system or 192 minutes using 100% oxygen.
I have one question.

Why does the oxygen duration chart show increasing times above 30,000 FT MSL?


texts: Separate DNA fragments with very different size (oligo and lambda-DNA)

texts:
I am running a ligation reaction to one of the sticky ends of lambda-DNA.

The oligo for the ligation is 25 bp (10x excess), whereas lambda-DNA is 48 kbp. I would like to recover the lambda-DNA and discard the unreacted excess oligo.
Given their vastly different molecular weights, they should be easy to separate, but I could not find a standard methodology online.

I do not want to run gel and my total sample volume is 0.5 mL. There are some filtration columns that may work, but the input volume is only 25 uL (I have 20 times that).

I don't have to get rid of all the oligo, having slightly more lambda-DNA than oligo at the end would suffice.

Which simple protocol may work in this case?


texts:
As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops.

I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs.

My interest is in knowing what other enzymes will create DNA loops with no DNA motif biases from a DNA extraction.

This is a follow-up question to this one, as ultimately I would like to know if there could be any ways of optimizing the process of DNA circularization of very long stretches of human (or mammalian) double-stranded DNA, from several kilobases to megabases, by first creating stable DNA loops that leave two DNA ends close by for a more effective ligation process.

Any ideas?


texts: Why does ostrich and other birds like pigeon swallow stones?

texts: I have read in my book that birds swallow stone to help in their digestion process. What is the need of swallowing stones? And how does it aid them?


texts: What are the ants underneath leafs in my garden doing?

texts:
So a few days ago I spotted a couple of ants underneath some leafs of a major branch of a tree in my garden. Yesterday I had the impression the amount of leafs being occupied by ants has increased a lot what then made me curious. So I spent quite some time yesterday observing one of the minor branches the ants had been very active on by that time. What I figured so far:
Underneath each leaf the ants are gathering, is an insect that looks sort of similar to a fruit fly (gonna call it fruit fly for simplicity, despite it certainly is something different).
Around that insect are varying amounts of dots, which could be eggs or larvae. The ants seem to collect something from the larvae and also seem to be interacting with the fruitfly.

At some point I spotted on the far end of the minor branch 2 living fruitfly. They seemed to be not capable of flight despite having wings. So I concluded they must just have been hatched. They seemed to try escaping the branch, as they pretty directly were just running up all the branch. Having almost made it from the minor to the major branch, the 2 fruitfly came across an ant, which immediately attacked both of them on contact. I was expecting the ant to carry them away then. While being attacked, both fruit fly tried to hide in the attatchment point of a leaf. The ant was circling around the attatchment point of the first fruitfly I was wondering why it did not carry that fly away, since it could clearly geto to that fly. After roughly a minute the ant turned back to their hide, having fully ignored the second fly, after attacking it once, and also leaving the first fly motionless at the attatchment point it was trying to find cover in.
But what happened a few minutes later is what left me astonished.
A few minutes after the 2 fruitfly had been attacked, roughly at the same time, they started moving again. But different then before (kinda looked as if they had been injured but not killed by the ant). They did not seem like trying to escape the branch anymore. But just slowly moving to the next leaf in range continuing for 1 to 2 centimeters going underneath the leaf and then stopping there. Pretty much being in a position, as a fruitfly is positioned underneath the other leafs, where the ants are gathering .
After like 4 or 5 hours 1 ant for the first time scouted the leaf these 2 flys went on. And in fact, other than attacking them again, this ant interacted with the 2 fruitfly1 like the ants under the other leaves interact with the fruitfly positioned on those leaves.

By now (over 12 hours later) the 2 fruitfly are still there I just checked and the small fruitfly that was only being attacked once, disappeared. The other one still being at the very same spot it moved to yesterday, tho. I would consider them being dead. But I am not even sure about that.
So what exactly are the ants I observed there doing?
If any other pictures would be helpful ask for it, I can take them later today.
Also I have a speculation what it could be that was going on here, but not sure if that would anyhow improve this OP.
Oh, since I can't identify the species, it might be useful to know at least: this is happening in Bavaria - Germany

1 well with 1 of them, the other that had just been attacked once, was simply being ignored


texts: Is there a strong reason to be sceptical about the "cured HIV patient" being reported by mainstream media?

texts:
There's a story going round the news about a baby that was, apparently, cured of HIV using a cocktail of drugs at an early age. The story piqued my interest, but details seem scarce. One of the main things I've seen being refuted about it is the difficulty in proving that (a) the child actually had HIV in the first place, and (b) that the child is really fully cured.

I've seen the following arguments:

Western Blot tests on young children are practically useless, since they test for antibodies. The child will likely have antibodies passed down by the HIV+ mother, regardless of whether the child has HIV. The test will show the antibodies, which may be mistaken for an active immune response from the child. As such, there will be a high false-positive rate on such tests.
Using PCR to attempt to identify a lack of HIV is flawed, since it may lay dormant in a small colony of T-cells until a secondary immune response is triggered, causing a new outbreak. As such, it is very difficult to show that a patient is "cured".

Are these arguments valid? Are there any other reasons to be sceptical about the claims? Any other information that might be useful in understanding the case?


texts: Which cultivated plants produce most nectar for pollinators?

texts:
Pollinators are important for many crop types (e.g. wikipedia list), but I am wondering how important the crops are to feed the pollinator. Obviously, some of the crop plants provide much more food than others, and the plants that depend on pollinators for their reproduction will be likely to attract the pollinators with pollen, nectar, or both. But I am not sure that I can use the dependance on pollinator as an accurate estmator of the quantity of nectar that is actually available for pollinator.

I can think of the rapeseed as being very rich in nectar, but are there other "nectar rich" flowers ? For instance, what about sunflower, potatoes, peas ,sugar beet, mustard, flax, lucern, clover, maize, wheat...

To sum up, I would like to have a list of the most common European cultivated plants that produce a reasonalble amount of nectar accessible to insect pollinators. (rem : I've asked a similar question about pollen, and maybe the answer is the same, but as far as I understood some plants have more pollen and some plants have more nectar.)


texts:
Well I have noticed that almost all of the babies cry after birth, but some of them (1 to 1,000,000? births) don't cry. So, we have:

Why is this happening (the cry after birth)?
Also why animals babies don't cry when they are born, but human babies cry? I have noticed that many mammals such as giraffes or chimps don't cry at all (The chimp only makes it's ordinary sounds).
Are there any special genes that humans have and animals not?


texts: Improving transformation efficiencies- induce supercoiling?

texts:
From my limited knowledge of science, I know transformation can be one of the hardest step in cloning, and that a large amount of research/trial and error has been done to improve on this step. I've heard electroporation is the most efficient technique, though I have no reference, and of course the cell, media and duration all have vital parts to play in the process.

However, I've never heard of supercoiling as an important factor. Size of the plasmid plays a large part in transformation, so intuitively it makes me think supercoiling the plasmid prior to transformation would improve the efficiency. I thought transformation was simply DNA diffusing through holes, but are parts of the plasmid required to bind/interact with the host?

Why aren't we suggested we supercoil prior to transformation? I have several thoughts but I'm just guessing:

Is it because gyrase can disrupt the integrity of DNA?
Or is it that it's just an expensive enzyme and the gain isn't worth it?
Or perhaps supercoiling reduces efficiency of subsequent plasmid preps/transcription (though wouldn't the host's natural enzymes supercoil anyway?)


texts: How does epigenetics affect the birth conditions via alcohol?

texts:
Recent study has shown that epigenetics can play role in male-caused infertility and it cites for example studies which showed an enhancing of silent genes when drinking alcohol. Since the study argues this as a reason to the negative newborns' conditions, it has to act negatively on the organism somehow.

I would call an epigenetic influence on the fetuses an influence that is meant to prepare the fetus on the change in the conditions. Does the evolution of the enhanced genes any relate to the alcohol consumption, or is it just a negative coincidence?


texts: How is bilateral asymmetry determined in embryonic development?

texts:
What are the mechanisms that ensure consistent left-right asymmetric placement of various internal organs (heart, liver, etc) or consistent left-right asymmetric development of paired organs (brain, etc.)? At what level, and how comprehensive is our current understanding about the underlying mechanisms?

(It seems to me a mirror image is just as good as the original one in terms of fitness and functionality. But why only one specific LR asymmetry prevails? Maybe this is a misguided way to think about the problem but that motivated to ask anyway.)


texts: Why doesn't CAS9 cleave the original CRISPR sequence in the bacterial genome?

texts:
CAS9 is the RNA-guided endonuclease that cleaves DNA as specified by the RNA sequence and is used to target viruses that infect bacteria. So why doesn't this RNA+endonuclease combo also cleave the original CRISPR spacer sequences (which also have the same DNA?). Is it the same reason that the bacterial genome is methylated (and hence protects from restriction enzymes)? Does methylation also make a difference to CAS9 as it does to restriction enzymes?

This actually was a doubt asked to Eric Lander in this lecture.


texts: Are Triceratops and Eotriceratops similar enough to be considered as the same genus?

texts:
Everybody knows Triceratops, the horned dinosaur from Late Cretaceous North America, who lived 68-66 MYA.

In 2007, Eotriceratops xerinsularis was named and described (Wikipedia). It lived in (what is now) Canada about 68 MYA. It is a little bigger than Triceratops but in many aspect very similar, e.g. they both have long horns and solid frill, and postcranial skeleton. Gregory S. Paul, in his Princton Field Guide to Dinosaurs 2016, suggested putting Eotriceratops xerinsularis in the same genus as Triceratops, renaming it to Triceratops xerinsularis. I find this suggestion appealing, but I know Paul's taxonomy is unorthodox and not mainstream (e.g. I do not agree with the thesis that Torosaurus is merely a full adult Triceratops).

So the question is: can Eotriceratops xerinsularis be put in the same genus as Triceratops and is this suggestion is plausiable enough?


texts:
What would happen if I drink lactic acid?

I use lactic acid to clean an espresso coffee machine and I wonder what injuries could occour drinking it.


texts: Are bronchioles and alveoli covered by respiratory epithelium?

texts: Which parts of respiratory apparatus are covered by respiratory epithelium and which are covered by other kinds of epithelium?


texts: A question about the clarity of certain terms

texts: In the Red Queen's depiction, a population must evolve just to be able to survive its ever-evolving natural enemies.  I'm trying to refer to a state in which many natural enemies have evolved adaptive advantages against individuals in the population (as opposed to a state in which most individuals in the population are able to survive their natural enemies with little difficulty).  When parasites have evolved adaptations that are dangerous to most individuals, I say they are virulent.  When predators have evolved adaptations that are dangerous to most individuals, I say they are well-adapted.  Is this clear?


texts: During the process of crossing over, Why is the maximum possible recombination frequency between two genes equal to 50% and not more than that?


texts:
The heart pumps the blood to supply tissues and kidney always filters the blood to remove urea,extra water and etc. And all these are vital,so the kidney is as important as heart:
and my question is:
Why is heart failure treated as more critical than kidney failure?


texts:
Animals can survive without eating if nutrition is injected directly into their blood.

Can the equivalent be done with plants? By injecting carbohydrate rich nutrient solution, either without photosynthesis or in addition to photosynthesis.


texts: How do Opioids Stimulate a Histamine Release?

texts:
Histamine is a neurotransmitter that also has peripheral functions such as the regulation of gastric acid secretions, allergic responses, etc. I know that opioids stimulate a release of histamine but I want to know how?

What exactly I would like answered is:

Which of the opioid receptors are involved in the histamine release that opioids stimulate and to what extent are they?
How does the activation of the opioid receptors in question lead to a release of histamine?
Are there any ways of suppressing the histamine release stimulated by opioids without compromising the analgesia they elicit?

I would like an answer, not just links. However I would like you to cite journal articles, although a formal reference list is not required so long as I can easily find the link to the abstract/full article.


texts: Why can't Turner Syndrome occur in males?

texts: In Turner Syndrome, one X chromosome is missing, meaning that the resulting egg or sperm has 22 chromosomes (without pair) and the 23rd chromosome is missing.  If this develops in an egg, and a normal sperm carrying a Y chromosome fertilizes that egg, then due to presence of a Y chromosome, can a male with Turner Syndrome develop?


texts: Small, brownish bird with reddish spot around eyes

texts:
This bird was seen in the Bourgoyen-Ossemeersen nature park, Ghent (Belgium) on December 3rd 2016. It is about the size of a common chaffinch.

We couldn't get a very good picture of it, unfortunately. What is the species of this bird?


texts:
When CO2-levels are to low plants start to photorespirate instead of photosynthesise. This cost them losses in energy, and adds CO2 to the atmosphere instead of O2.

I wonder if the photorespiration is entirely "bad" for the plant or is there any beneficial outcome as well?


texts: Are all endocrine glands associated with common human feelings?

texts:
I was looking at endocrine glands and found it interesting that a few of them have some very understandable feelings/mentalities associated with them.  In particular:

Gonads: arousal/romance
Pancreas: hunger (glucose)
Adrenal glands: fight or flight
Pineal gland: sleepiness (melatonin)

Of course, there is a lot more complexity to how these glands work and what they do, but I find the notion of being able to empathize with a part of the body interesting.

As a counter-example, if something is wrong with my spleen, there may be feelings associated with that (ie pain), but they aren't so profound as things like hunger, fear, and arousal.

Anyways, my curiosity here is: do all endocrine glands have a feeling associated with them?

Here's the list of all glands:

Pituitary gland
Thyroid gland
Parathyroid glands
Adrenal glands
Pancreas
Gonads
Pineal gland

Also, I know this is a silly question, but please bear with me here.  It's piqued my interest, and I just want to fulfil some curiosity.