texts: Usually harmful mutations are those which disrupt a vital function, what you might call "passively" harmful. What about a mutation that makes a protein, which is not just useless, but actually toxic to its host?  Are there any known examples?


texts: How does the mutualism of figs and wasps exactly work?

texts:
I have just rudimentary knowledge about the mutualism of figs and wasps and would like to know how this works step by step.
Also how do humans use this mutualism? Do they support or hinder it at some points?


texts: Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

texts:
HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss.

I am only looking at a small (20AA) sequence and it is helical throughout.

Is hhpred still likely to pick up on subtle similarities in the basic secondary structure as it would in a folded protein sequence, or would simpler alignment be just as appropriate?


texts: Are bacterial RNA polymerases distributed evenly throughout the cell or localized?

texts:
Bacterial cells aren't internally compartmentalized with membranes (like eukaryotes). This naturally leads to an image of a homogeneous interior, but bacterial cytoplasm isn't homogeneous. Case in point, the DNA is localized in the nucleoid. If the cell goes through the trouble of putting all its DNA in one spot, having RNA polymerases everywhere would be pretty wasteful (even counterproductive). So, is the more intuitive image of bacteria, with RNAPols everywhere, right? Or are they localized? If so, how?

If species matters, lets primarily talk E. coli.


texts: classical conditioning paradigm for hippocampal learning

texts:
I wanted to know what a suitable classical conditioning experiment would be to analyze learning and memory capabilities in rodent models with respect to hippocampal long-term potentiation.

For example, I want to subject the animal to conditioning and test the behavioral readout at a certain time point after conditioning. Many , like fear conditioning experiments, are mostly attributed to amygdala processes.

I wish to know some classical conditioning task where I can understand primarily hippocampal processes.

Also is there a way to monitor hippocampal CA1-CA3 firing pattern after the training period or during the training ?

That is, I want to check if LTP will sustain after the training period or is there is any increased sustenance of LTP post training.

But if I am to do this electrophysiological experiment in hippocampal brain slices, how will I incorporate the conditioned and unconditioned aspect to this ?


texts: Validity of measurements of respiration in isolated mitochondria

texts:
I've recently read a couple of papers on exercise and mitochondria, in which state 4 and state 3 respiration rates and ROS production are assessed in vitro after exercise has been performed (i.e., rat heart mitochondria are isolated).

Question:

Given that it takes 1 hour for the mitochondria to be removed from the animal and isolated, that additional (saturating) substrate is added before respiration parameters are measured, and that the medium is saturated to the ambient oxygen concentration (much higher than in vivo), are this type of experiment valid to assess mitochondrial function in vivo in active animals? Opinions and/or pointers to resources that clarify how useful these measurements are would be helpful.


texts: Does Methanol cause similar intoxication as Ethanol?

texts:
Take two average healthy adult males weighing 80 kg. Neither has, ahem, developed their alcohol tolerance to any significant degree.

One imbibes 1 shot, 40 ml of 40% Methanol, and another 40 ml of 40% Ethanol (vodka) to empty stomach.

Now the vodka drinker should feel the drink going to their head, and he'd become just slightly drunk, and that's about it. No hangover expected from 1 shot of vodka, either.

What would be the effects on the Methanol drinker? Info on other effects would be nice too, but most importantly, would he become drunk, and how much compared to the vodka drinker?

If 16 ml of absolute methanol seems so much, that other toxic effects will dominate over "feeling drunk", then you can consider a smaller amount. The crux of the question is, does Methanol cause one to "become drunk" same way as Ethanol.

WARNING, just in case, to offset the casual tone of above question: Never drink anything which even just might contain Methanol! It's an easy way to die, or just go blind if you're "lucky"! It is not a useful way to get drunk or high, ever.


texts:
Do we have documented cases of animals purposely and consciously trying to end their own life? What leads to animal suicide, and is it preventable?

I've heard mixed answers from various biologists. Is anyone here capable of providing an answer?


texts: Why use two stop UGA codons instead of one in the spike protein mRNA for the BioNTech/Pfizer SARS-CoV-2 vaccine?

texts:
Unlike the SARS-CoV-2 virus, the BioNTech/Pfizer SARS-CoV-2 vaccine has two stop UGA codons  at the end of the Spike protein:
          V   L   K   G   V   K   L   H   Y   T   s
Virus:   GUG CUC AAA GGA GUC AAA UUA CAU UAC ACA UAA
Vaccine: GUG CUG AAG GGC GUG AAA CUG CAC UAC ACA UGA UGA
          V   L   K   G   V   K   L   H   Y   T   s   s
               !   !   !   !     ! !   !          !

What is the motivation behind using two stop UGA codons instead of one in the BioNTech/Pfizer SARS-CoV-2 vaccine?


texts: Is there any clear relationship between physical characteristics and patterns in the genome?

texts: Given that for example humans have five fingers on each hand, is there a region in the genome with a sequence of five similar subregions, one for each finger? Is the region on the genome that encodes for the right hand near another region that encodes for the left hand?


texts: Construct a restriction map of a linear fragment of DNA using the following data?

texts:
I've attempted to do the single digests, and the double digests, but cannot complete the map.... I've attached what I've done so far

DNA Sizes of Fragments (bp)

uncut DNA 900

DNA cut with EcoRI 500, 350, 50

DNA cut with HindIII 600, 300

DNA cut with BamHI 400, 300, 200

DNA cut with EcoRI + HindIII 350, 300, 200, 50

DNA cut with EcoRI + BamHI 300, 250, 200, 100, 50

DNA cut with HindIII + BamHI 300, 200, 100


texts: Do DNA supply houses maintain a watch list for dangerous oligos (Anthrax, Smallpox, etc.)?

texts:
The recent work by DeLoache, et al. on a synthetic opiate-precursor production pathway in yeast has generated a lot of scare stories in the media about people homebrewing heroin as easily as they would beer.

In connection with DeLoache and coworkers' research, the New York Times has claimed

  Their DNA could be put on a watch list, as sequences for anthrax and smallpox are, so any attempt to buy them from DNA supply houses would raise flags.

I have never heard of such a watch list, and a thorough googling turned up nothing relevant save for the NYT article itself. Does this watch list exist?


texts: (Non-expert-question) What exactly do chloroplasts do when they "convert light into chemical energy"?

texts:
Disclaimer: This question is kind of sprayed over biology, chemistry and physics.

Anyway, I had to learn more about photosynthesis recently, and although it is quite complex, I think I got it - except for one thing: Everywhere it is basically just said, that chloroplasts convert light energy into chemical energy. But seemingly no one is interested in how they do it. I couldn't find an explanation after some googling. Not even Wikipedia had something for me (at least nothing I was able to sort out of the technical jargon).

So my question now is: What exactly happens in this process? It'd be good if the answer wouldn't include to much jargon, because I'm not really experienced in the field. (Just the usual knowledge and a little more due to being interested in science in general).


texts:
[The following includes a) two specific questions (at the end), b) an attempt to capture a dispositional concept (excitability) in geometric and physical terms.]

I assume that "excitability of a neuron" is a reasonable concept (and measure) to distinguish neurons: there are (as will be seen) neurons that are more or less excitable (in a quantifiable way).

What does "excitability" mean?

Excitability $E$ may be operationally defined as the sensitivity of a neuron to excitatory synaptical inputs. Mathematically stated: as the (decimal logarithm of the reciprocal of the) proportion of excitatory synapses that must be simultaneously active (i.e. generate an excitatory postsynaptic potential, EPSP) in order to collectively evoke an action potential.

Let $N$ be the number of all excitatory synapses of the neuron, $n$ be the the minimal number of simultaneously active synapses that is needed to evoke an action potential:

$$E = \log \frac{N}{n}$$

If the proportion is 100% (all excitatory synapses must be active), $E =  \log (1) = 0$, if it's only 10%, $E=1$ (higher excitability), if it's 1%, $E = 2$, and so on.

How to determine $E$ for a given neuron? With the operational definition given above:

Count the actual number $N$ of excitatory synapses.
Estimate the minimal number $n$ of simultaneously active synapses that is needed to evoke an action potential (by repeated experiments).

Especially the second number $n$ will be quite hard to achieve experimentally. But there is an alternative way to estimate this number, given a simplified model of the neuron:

All synapses have equal (mean) distance $r$ to the axon hillock
(where the action potential is generated).
The EPSP generated at a synapse is $u$.
The EPSPs travelling from
the synapse to the axon hillock have a constant decay constant
$\alpha$.
The threshold value for action potential generation is $\theta$.

When $m$ synapses simultaneously generate an EPSP of size $u$, these EPSPs will sum up at the axon hillock to

$$ U = m\times u\times 10^{-\alpha r}$$

Only if $U \geq \theta$ an action potential will be generated, that is, the minimal number of simultaneously active synapses to generate an action potential is

$$ n = 10^{\alpha r}\ \frac{\theta}{u}$$

With this we can estimate the excitability $E = \log\frac{N}{n} = \log 10^{-\alpha r}\frac{N\ u}{\theta}$ by

$$E = -\alpha r + \log(N) + \log \frac{u}{\theta} $$

$\alpha$, $u$ and $\theta$ are more physical constants (more or less the same for all types of neurons?), $r$ and $N$ depend heavily on the arbitrary geometry/morphology of the neuron (especially do longer and more strongly branched dendrites have more synapses).

My specific questions are (please feel free to answer only with "yes" or "no"):

  Has the property of excitability (in the operational sense above) been investigated a) for single neurons, b) for morphological types of
  neurons?
  Is there an observed significant correlation between morphological type and excitability? Note that larger dendritic trees have larger
  $r$ (decreasing $E$) but also larger $N$ (increasing $E$).

(Final remark: The relation between $r$ and $N$ of a neuron is partially reflected in the structure – especially the degree of branching – of its dendritic tree.)


texts:
Can treatment of thrombus cause embolism, in case of very high blood pressure, that may even lead to a heart attack ?

As the very high Blood pressure may cause some of the enzymes not act completely on the thrombus and release emboli in the blood stream ?


texts: Question on kilobase - packaging of genomic material in viruses

texts: I have been looking up some information of SARS. Wikipedia says it is 29.7kb in length while 1kb is around 300nm. However, the microscope image on wiki shows the virus size <100nm. It doesn't make sense mathematically so that think I missed some knowledge. I hope this question qualifies to be posted on stackexchange. Thanks in advance.


texts:
I understand that based on their tertiary structure, intrinsic proteins have hydrophobic non-polar R-groups on their surface and that they 'interact with the hydrophobic core of the cell membrane to keep them in place'.

But how does the hydrophobicity of both the protein and the cell membrane prevent the protein from moving?


texts: Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes

texts:
In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as the DNA bases have the tendency to hydrogen bond. In DNA replication, this closing is prevented by single-strand binding proteins.

I have three questions regarding this:

In transcription, the pre-mRNA strand peels off the template strand in the wake of RNA polymerase. Why? There are just as well hydrogen bonds between the pre-mRNA strand and the DNA template strand as there are between the two DNA strands.
Why doesn’t the pre-mRNA stick onto the DNA indefinitely and block the non-template DNA strand from reattaching to the template DNA strand?
In DNA replication, why is it imperative that the separated DNA be stabilized by single-strand binding proteins? Won’t the replicated strand block the template strands from closing together?


texts: Which Hawaii bird makes this call at night?

texts: I'm on Big Island right now and keep hearing this bird starting at 6-7PM every night: https://voca.ro/18XEepbDmpCy. Which bird could it be?


texts: Do birds change their diet before migration?

texts: Migration takes up a lot of energy, so I am wondering if birds (in my case mallards) change their diet / food preferences in the weeks before migrating. Do they select for more energetic foods to fuel up, or do they just eat more of the same foods to gain enough energy?


texts:
Do you know an authoritative source for the approximate number of dopaminergc cells in the ventral tegmental area (VTA)?
Ideally I would like to know this for mice, rats, as well as humans, but one species alone would be a nice start. I have looked for this via google scholar and pubmed, but found nothing.


texts: How to measure growth of algae with colorimeter

texts: I am doing an lab for IB Bio and don't know how to use a colorimeter to measure growth in algae. The experiment I am doing will measure the effect of pH on algae growth. The algae will be taken from a fish tank and will include cyanobacteria, diatoms, and algae bloom. I don't know how the transmittance/absorption will relate to growth. I also don't know which wavelength of light to use. Help would be appreciated, thanks!


texts: How would one track a mineral nutrient in a plant in order to prove that nutrient has been re mobilized?

texts:
Before abscission - senescence of a plant structural components that contain mineral nutrients (E.g. Magnesium, Potassium...) are re-mobilized from the senescent tissue and used in other plant tissue for anabolic activities.
Could we design an experiment to prove this?
I was told that radioisotope method would work. We can detect the presence of the radioactive particle in one part at a time-point, but how would we know whether it is the very same particle that shows up elsewhere after abscission?


texts:
Can I ask you to help understand the meaning of "Non-primary hits" and "tags" in the following paragraph related to RSeQC:

The result table reports total number of reads (excluding nonprimary
hits) and tags (separate splice fragments of a read). Total assigned tags
indicate how many tags can be assigned unambiguously to the ten different
categories listed below.

Total Reads 49743155
Total Tags 63012643
Total Assigned Tags 57529077
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Group Total_bases Tag_count Tags/Kb
CDS_Exons 36821030 34763281 944.11
5'UTR_Exons 34901580 2856644 81.85
3'UTR_Exons 54908278 9772738 177.98
Introns 1450606807 8468986 5.84
TSS_up_1kb 31234456 94103 3.01
TSS_up_5kb 139129272 161914 1.16
TSS_up_10kb 249300845 217980 0.87
TES_down_1kb 32868738 789703 24.03
TES_down_5kb 142432117 1368378 9.61
TES_down_10kb 251276738 1449448 5.77
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =


texts:
There are currently only five species of monotremes remaining, and all of them are found in Australia. Additionally, I read a science article claiming that competition from marsupials essentially forced monotremes into the water, where marsupials couldn't follow without drowning their young.

Why are monotremes so rare? Are the traits that define a monotreme (such as egg-laying) inherently less competitive, or is their relative scarcity more of a quirk of fate?


texts: Lab technique to distinguish between single stranded and double stranded DNA?

texts: What lab techniques exist to differentiate between single-strand and double-stranded DNA?


texts: Why is one testicle larger than the other?

texts: Why is one testicle generally larger in humans? Just due to asymmetric development, or is there a hypothesis as to some utility it serves? I read that the different heights may be attributed to attempting to keep them from hitting against one another. Is there a similar guess to the purpose for the difference in sizes?


texts: Why are some animals so much more intelligent than others?

texts:
From what I found many biologists state that animals living in large social groups (elephants, primates, cetaceans etc.) have a tendency for improved cognitive abilities. Yet at the same time there are solitary animals with (suspected) high intelligence such as octopuses and plenty of social animals that fail our cognition tests.

What evolutionary pressures pushed certain animals towards such intelligence when their environments are so different while other animals in a similar environment show no exceptional cognitive skills?


texts: What functions other than spore dispersal does a fruiting body serve in a mycelial network?

texts:
I'm not exactly sure if this is the appropriate forum to ask this, so apologies in advance.

My question is both technical and general: what are the less obvious functions that the individual mushroom might serve in a network of mycelia. My knowledge of biology is pretty limited but I know that, for example, some mushrooms absorb radiation with some effects on the underlying network or that the network might generally shift itself underground overtime based on the signals that the individual fruiting bodies "gather" over their above-ground lifespan on.. whatever, humidity, predators, other conditions of relevance.

This is not to mystify it too much, but i'm really interested in the biological dynamic where a "node in the network" contributes something to the decentralized network, this probably sounds familiar, fungi are just the most obvious example. I was wondering what would be the term for this to begin with if there is one and if somebody could point me to some work on it at any level of resolution: from ecology to genetics or mathematics.

Thank you very much.


texts:
A family member saw this spider in her garden in the Cape Town area of South Africa. It's very attractive and I wondered what species it was?

Approx size is that it would fit roughly on a 3cm diameter circle.


texts: Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the protein eventually stop? Would it keep coding into the poly-A chain and insert a bunch of phenylalanine?


texts: How does HIV mutate into other strains while keeping their virulent phenotype?

texts: How does a virus like HIV mutate into so many strains, and yet all of them are  harmful to our immune system? What gives this virus the ability to mutate so efficiently?


texts:
I would like to make a double PCR with universal tailed primer. The first PCR would make a tailed amplicon. The second PCR would generate fragment labeled with fluorescent dye. Here is my protcole. Could you tell me if I am wrong ?

is my second PCR forward primer well designed to fit with the tail ?
What would be the ratio of primer to use if I want to merge the two PCR into one ?

Fist PCR ( works )

In bold, you have the tail M13(-20)

Forward : 5'-GTAAAACGACGGCCAGTTCTGCAGTTGTACTGAGTGAA-3'
Reverse : 5'-AAAGCGTGCAGCTGATATTT-3'

Mix for 1 sample

Water              = 15.8µL
MgCl2 (25mM)       = 18µL
Buffer (5x)        = 6µL
dNTP (4mM)         = 1.5µL
Forward(20pmol/µL) = 1µL
Reverse(20pmol/µL) = 1µL
GoTaq (5U/µL)      = 0.15 µL
DNA (50ng/µL)      = 1 µL

Second PCR ( not working = no fragment signal )

Forward : 5'-[FAM]-GTAAAACGACGGCCAGT-3'
Reverse : 5'-AAAGCGTGCAGCTGATATTT-3'

Mix for 1 sample

Water              = 15.8µL
MgCl2 (25mM)       = 18µL
Buffer (5x)        = 6µL
dNTP (4mM)         = 1.5µL
Forward(20pmol/µL) = 1µL
Reverse(20pmol/µL) = 1µL
GoTaq (5U/µL)      = 0.15 µL
DNA (50ng/µL)      = 1µL from my previous amplicon


texts: From a hosts point of view, which comes first, effect of toxins on pathways or identification of toxins by immune system?

texts: From a pure biology perspective, when a pathogen (gram-negative bacteria) affects a host by secreting toxins, what comes first, the effect of the toxin on the pathways or identification of the toxin by the immune system? A generalized overview would be very helpful.


texts:
Am a bit new to biology SE. My question is wether fucus is filamentous or collonial form of algea?Does a form of algea have to be collonial or fillamentous or it can be something else?
https://en.m.wikipedia.org/wiki/Fucus_vesiculosus


texts: Why there is Cp/Ct (crossing point) value for negative sample in COVID-19 RT-PCR?

texts:
I am from IT/ Engineering background and have some confusion in RT-PCR. So far my understanding we extract RNA from test specimens and transcribed it into complementary DNA (cDNA), and inside PCR DNA double helix is separated. Then primer a short nucleic acid sequence that provides a starting point for DNA synthesis with the target sequence and multiples the target DNA.
Since a higher cp value indicates a negative result but why negative results have cp value? Why it cross the threshold when it does have any target sequence (viral DNA)? Fluorescence is the measure of target DNA right??
In extraction, RNA is extracted does only COVID viral RNA is deducted? What happens to other viral and human RNA?
I have seen result were we have low cp value and test result is negative, the reason for this was because curve do not have Sigmoid function. I need more explanation on it.


texts:
I understand the different ways bacteria can undergo horizontal gene transfer (transformation, transduction (phages), conjugation (plasmids)).

Is there an experimental method to tell how a specific gene got into the host (during evolution)? For example if a gene A got into host X from species Y, is it possible to know how gene A was transmitted?


texts:
I'm researching the genetics of brain cancer, and finding a huge number of mutations in voltage-gated channels.  It stands to reason that some of this DNA damage is due to the DNA being transcribed heavily, or in an open chromatin conformation more often, leading to more breakage and damage due to environmental stress.

Of course, those are just guesses.  Does anyone know of any research papers in the area?


texts: What did Darwin mean by "degraded flowers"?

texts:
One of the chapters of The Origin of Species says that "Certain plants, belonging to the Malpighiaceæ, bear perfect and degraded flowers;" Full passage for context

Do you know which plant characteristic was he referring to? Is this morphological difference still recognized? Is there a new name for it?


texts: What is the role of increased cytosolic calcium concentration after firing, in neuronal cell bodies?

texts:
I've come across several studies in which scientists were investigating various questions related to neural activity by focusing on neuronal cell bodies using Calcium imaging. As this article suggests for example, cytosolic Ca concentration in the soma will significantly increase if the neuron fires. I understand the process behind this. But I'd like to find out if this somatic Ca increase has significant downstream effects inside the soma.

Could anyone shed some light on such known processes/pathways?

I've thought of one possibility based on an article that showed Calcium would upregulate mitochondrial enzymes, such as PDH and OGDC, responsible for TCA reactions. Considering that there's a coupling (source) between cytosolic and mitochondrial Ca concentrations, this could lead to a very quick increase in metabolic activity that covers up for the ATP loss related to neuron firing. However, I'm a bit skeptical about this idea. I'd think that the lack of ATP and low NADH/NAD ratio should speed up the TCA enough already and Ca might be more critical somewhere else instead.


texts: What is the limit of time resolution in fMRI?

texts:
I was reading about a few studies on estimating functional connectivity between brain areas using fMRI signals. However, as far as I know that fMRI has a very poor time resolution, roughly in the order of 1 second. Individual neurons communicate with delay less than 100 ms, and many brain functions happen within a second, in which case fMRI wouldn't have enough time resolution to determine if things happened simultaneously, or in a sequence at all. This problem would be even greater for causality analysis such as Granger causality framework.

So my question is, what is the theoretical, and practical limit of time resolution in fMRI on human?


texts:
What precisely is ecology? How does it differ from biology? Because I never studied biology after high school, please explain as if I were 10 years old. I only know that ecology is a subset of biology
I tried some dictionaries but they  didn't  adequately discriminate. I tried to find an explanation from a scientist: the following appears to claim that only ecology concerns some organism's external interactions with other entities? But how? Biology must also? For example, suppose that someone studies prions' interactions with humans, and not just prions. Then this is biology, not ecology?
Source: by  Matthew Fraser, PhD Candidate (Marine Ecology) at University of Western Australia

So what makes us fully fledged marine ecologist different from our biologist counterparts?  Well, I think that marine ecology is even cooler than marine biology because as marine ecologists we link what we know about the biology of a given species with other plants/animals and the environment as well. [...]
If we were splitting hairs, ecology is technically a form of biology, but I felt the need to write this post given how passionately I see some researchers stating that they are in one camp or another. [...]  But as an ecologist (albeit a biased one!) what gets me excited isn’t just finding out how the amazing plants and animals we find in the ocean work, but how they interact with each other and their environment, explaining why we see certain species in some places and not others!


texts:
From reading accessible information about tubers and taproots I recognize that the main differences between tubers and taproots (as well as a fibrous root system) are:

Shape
Different nutrient synthesis: Tubers contain less complex sugars than taproots

A possible third difference

As one who prefer a vegan diet in general I read a lot about B12; in many places (for example) Wikipedia, something like this was written:

  In the past, humans got Vitamin B12 from eating the roots of "short plants" that absorbed
  the vitamin from bacteria which produced it near to their roots.

This led me to assume that either tubers or taproots (as well as a fibrous root system) have Vitamin B12 absorption by dedicated receptors and if one has it and the other doesn't here is yet another difference.
An interesting side note: Tubers are always under soil while roots in general, aren't necessarily; as with aerial roots.

My question

What are the main differences between tubers and taproots?


texts: What determines the colors and patterns of a clam shell?

texts:
Earlier this week I was looking at some bivalve shells that had ornate patterns which ranged in color from a light orange-pink to a deep orange-red. Here is an image I found online that seems to be of the same type of shell:

The friend who was with me said, "I wonder where the color comes from." We were trying to look for two shells with similar colors, patterns, and approximately equal sizes, and it was hard, even though we were looking through a large collection of similar shells.

What determines this ornate pigmentation? Is it influenced by environmental factors such as the minerals in the water? Does it have anything to do with the age or health of the organism? Or is it purely genetic? Is this determined by the same basic biological principle that determines the color of human hair, or is there something different at work in shells?


texts:
At first I thought it may be related to physics.  You know, in one half of the day, the gravity changes, and the scale shows a different weight than the other.  Then at night, gravity intensifies, and you become slightly heavier.

But I'm a bit skeptical about that. Is that true?  That it's somehow related to gravitational fields?


texts:
Music is, of course, just a sequence of sounds. Sounds are vibrations in the air, which our ears detect. So why do we find certain sequences of sounds to be appealing? What makes us want to hear these sounds (turn on a radio, for example), or make these sounds on our own (sing/play an instrument)?

Heck, why do we even move our body strangely when we hear certain music (dancing)?


texts: Probability of carrying an autosomal recessive trait given both parents are carriers

texts:
I recently came across a question that asked for the probability of having a child with an autosomal recessive trait, namely cystic fibrosis. From various parts of the question, we can conclude that the father is definitely a heterozygous carrier and that the mother's parents are both heterozygous carriers. In this situation, the only way to produce a child with cystic fibrosis is if both parents are heterozygous carriers, and this will happen with a probability of $\frac{1}{4}$.

The part that causes confusion is figuring out the probability that the mother is a carrier.

One student reasoned that a cross between two heterozygous parents will produce a 1:2:1 genotypic ratio, so $\frac{1}{2}$ of the progeny will be heterozygous carriers. Therefore, the probability that the mother is a carrier is $\frac{1}{2}$ and the probability of producing a child with cystic fibrosis is $\frac{1}{2}*\frac{1}{4}=\frac{1}{8}$

Another student also referenced the 1:2:1 ratio but reasoned that since the mother is phenotypically normal, that the ratio is actually just 1:2 because there is no chance of being homozygous recessive. Therefore, the probability that the mother is a carrier is $\frac{2}{3}$ and the probability of producing a child with cystic fibrosis is $\frac{2}{3}*\frac{1}{4}=\frac{1}{6}$

These two answers are also found at this other question.

The last solution proposed is the most interesting. This student referenced the Monty Hall Problem, which is indeed somewhat related to this problem (read more about the Monty Hall Problem). Using the same ratio as above, we can conclude that there is a $\frac{1}{4}$ chance that the mother carries no alleles for cystic fibrosis and a $\frac{3}{4}$ chance that she does. The fact that she definitely does not carry two alleles does not change this probability. Therefore, the probability that the mother is a carrier is $\frac{3}{4}$ and the probability of producing a child with cystic fibrosis is $\frac{3}{4}*\frac{1}{4}=\frac{3}{16}$.

Out of these proposed solutions, which one is correct? And why are the others incorrect?

EDIT: To be clear, the solution I initially considered to be correct was the second one.


texts: Why would we overexpress Sir2 by overexpressing its hypomorph (dSir2-EP2300) in C. elegans?

texts:
Can't we just overexpress regular Sir2 in the paper? Rather than overexpress a reduced-function gene?

The paper is  Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.


texts:
Please see the following picture:

In my book, the author claims that these chromosomes are in metaphase (a metaphase stopped by cholchicin).
I don't understand why they don't have two chromatids...A chromosome looks, by everything I've learned, like TWO chromatids (http://i60.photobucket.com/albums/h1/GameMaster57/Chromosomestructure.jpg) and should be together in metaphase. These chromosomes only look like chromatids to me (1 of 2 pairs).

Have they been separated?

I am also asked to specify which chromosomes are from the father and which are from the mother. How would I go by doing that?

Thank you.


texts:
I was reading a course about DNA Supercoiling, and I stopped at this definition :

  [...] In the case of DNA, a topological property is one that is not affected by twisting and turning of the DNA axis and can only be changed by breakage and rejoining of the DNA backbone. (Source)

I didn't understand what they mean, can anyone clarify it please.


texts: Can any plant regenerate missing tissue?

texts: I have not yet found a plant that, when an insect eats a hole in one of its leaves, it can regenerate the lost tissue. Many plants will grow a new stem if the old one is cut, but it is not a perfect regeneration, and has no likeness in form to the previous stem. Are there any plants that can, even to a degree, regenerate missing tissue?


texts:
I smoke. For some reason, I've always had this idea that the pleasure of smoking works more or less like this: from the lungs, the nicotine reaches the blood, with which it travels to the brain, and there it does some difficult chemical stuff to make me feel all good. But that's also never made sense to me. I mean, the gratification is instant. I don't even inhale very deeply, and, momentarily, I feel the feeling for which I do the thing. I don't know how fast the blood travels -- I only know it varies -- but it seems impossible for it to travel this fast. Or is it?

Could you explain to me, a non-biologist, how it works?


texts: Are humans more adapted to "light mode" or "dark mode"?

texts:
I was discussing with a colleague about using dark-mode vs. light mode and remembered an article arguing that humans vision is more adapted to light-mode rather than dark-mode:

I know that the trend “du jour” is to have a dark mode for pretty much
everything, but look around the world is not dark with a bit of light,
it’s actually the contrary. And as the human has evolved its vision to
adapt to this reality, it’s asking extra efforts on many people.

Unfortunately, no reference is provided to support this claim, so I am wondering if this is just an opinion or there are some studies to support this.
Wikipedia seems to confirm this somewhat since we are adapting much faster to "light mode" transition than to dark mode one:

This adaptation period is different between rod and cone cells and
results from the regeneration of photopigments to increase retinal
sensitivity. Light adaptation, in contrast, works very quickly, within
seconds.

Also, some studies confirm that working using light mode is on average more efficient than using dark mode:

light mode won across all dimensions: irrespective of age, the
positive contrast polarity was better for both visual-acuity tasks and
for proofreading tasks.

I am looking for arguments coming from evolutionary biology to confirm (or not) the assumption that human evolution favors light mode.


texts: Can a protein kinase phosphorylate both a threonine and tyrosine residue?

texts:
I know that some kinases can phosporylate both serine and threonine residues because of their structural similarities, but can such a kinase phosphorylate a tyrosine residue as well?

If not, then why?


texts: I know that the pathway of nerve impulses during a reflex action is called a reflex arc. However, I want to know whether the term reflex arc can be called either a reflex path or simple reflex?


texts: What is this droplet of liquid that comes out of a mosquito?

texts:
I have been looking at pictures of different species of mosquito and several times I came across pictures where the mosquito seems to be secreting some kind of fluid.

In the pictures one can clearly see that the mosquito both secretes transparent fluid and blood.

What kind of fluid is the transparent stuff? Could it be plasma from the host's blood?
Why does the mosquito do it?


texts: Natural examples of XOR functions at the cellular level

texts:
We can often think of cells as a sort of circuit on macromolecules, and can show that they can accurately and robustly implement functions like $\text{MAJ}(x_1,...,x_n)$ (return $1$ if more than half of $x_1,...,x_n$ is $1$ and $0$ otherwise) under natural conditions (Cardell & Csikász-Nagy, 2012).
Not all functions are created equal. $\text{XOR}(x,y)$ is a boolean function that is $1$ if exactly one of $x$ or $y$ is $1$ and $0$ otherwise (i.e, if $x = y$). It is often generalized to a multi-input function parity (or odd) as $\text{ODD}(x_1,...,x_n)$ which returns $1$ if an odd number of $x_1,...,x_n$ is $1$. Notice that this is superficially similar to $\text{MAJ}$ but is doing its counting in base 2, which one would expect to be easier for say finite state machines.
However, in some ways, this sensitivity makes the function much more difficult to the point that Valiant (2009) writes:

[Parity] appears to be biologically unnatural. That is exactly the prediction of our theory, which asserts that evolution cannot be based on the evolvability of [the class of functions parity belongs to]

Synthetic biologists used to agree to some extent, with Tamsir et al. (2011) writing that the closely related XNOR (i.e. $\text{XNOR}(x,y) = 1 - \text{XOR}(x,y)$) is empirically impossible to implement. However, they were proven wrong when Bonnet et al. (2012) implemented XNOR among many other amplifying gates by exploiting the structure and process of transcription. Unfortunately, this is an example from synthetic biology, and I really want to learn ones (if any) that occur naturally.
Are there any examples of XOR or related gates implemented (without human engineering) at the cellular level? Are there any naturally occurring molecular pathways that compute something similar to parity? (i.e. something similar to the majority result, but for a more 'sensitive' function) I am primarily interested in empirical demonstrations, but I would be satisfied with theoretical examples that are appealing to biologists (i.e. not something purely comp. sci. like P-systems or something).

References
Bonnet J, Yin P, Ortiz ME, Subsoontorn P, & Endy D (2013). Amplifying Genetic Logic Gates. Science, 340(6132): 599-603. PMID: 23539178
Cardelli L, & Csikász-Nagy A (2012). The cell cycle switch computes approximate majority. Scientific Reports, 2: 656. PMID: 22977731
Tamsir, A., Tabor, J. J., & Voigt, C. A. (2011). Robust multicellular computing using genetically encoded NOR gates and chemical wires. Nature, 469(7329), 212-215.
Valiant, L.G. (2009) Evolvability. Journal of the ACM, 56(1): 3-22.


texts:
I want to know if, as a baby chick grows inside the egg, does it excrete waste?

If it does excrete waste, does the waste just sit inside the egg with the chick, until the chick cracks open the egg and gets out?


texts:
I tend to see terms amino acid, acid stable amino acid, and free amino acids used often in the field of nutrition, but they are sometimes used interchangeably which confuses me.

I know that:

amino acid is a general term to describe organic compounds that encompass both essential and non-essential amino acids.
free amino acids is a general term for amino acids that are not broken down from a protein source; instead it exists in its original form 'freely'.
acid stable amino acid ... no idea

Is that right (correct me if I'm wrong)? What is the larger relationship amongst all three terms? Would consuming a free amino acid be better than one from a protein, or from an acid stable amino acid? Why would one choose to consume a particular class of amino acids over another?


texts: Has any flying creature evolved into a sea creature?

texts:
I am talking about a creature that has evolved true flight.
Has any such creature evolved into a sea creature, that permanently dwells on water (like fully aquatic fish) and doesn't come out? According to the theory of evolution, many sea creatures of the deep past evolved into land animals and some of them went a step further, evolving flight. I am talking about the reverse process, excluding semi-aquatic or semi-terrestrial animals.


texts: Why was Achromobacter xerosis removed from the NCBI taxonomy?

texts:
The Global Catalogue of Microorganisms lists a bacterium called Achromobacter xerosis which is mentioned in several papers and patents. It once existed in the NCBI taxonomy database, with ID 216898. However, it is no longer there - going to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=216898 just yields a "No result found" page.

Why was this species removed from the NCBI's taxonomy? I haven't managed to find any documentation on why the NCBI would purge a species from their database, nor can I see any obvious reason to do so.


texts:
Of what species is the following creature?

I expect it would be a Cephalopod living in not too deep water with a tropical climate (Brazil?). However, I can not find any information about what species it actually is.


texts: What would the presence of a hub metabolite in a metabolic pathway signify?

texts:
Say I have a metabolic pathway, consisting of multiple metabolites and reactions. On analyzing the pathway I find that among all the metabolite, one metabolite is the hub metabolite (hub metabolite is the metabolite such that maximum number of reactions involve that particular metabolite).
What is the significance of this metabolite or of this pathway?


texts: When did humans or their ancestors gain the instinct to take shelter?

texts:
I was going to ask if seeking shelter in a constructure dwelling or natural formation was instinctive to modern humans or if it is a learned sociatal behaviour.  By shelter I mean seek routine issolation from elements by being "inside" some structure or formation that encloses the individual or group on multiple sides and above.  A small shelter would be expected to trigger Claustrophobia and being outside of a shelter would be expected to trigger Agoraphobia in people that experiance such conditions.

It was highlighted that "nest building" is considered a part of a shelter instinct.  I am looking for when this behaviour develops not just during child rearing (as many birds do) but routinely (as great apes do with bedding).  Unlike forming a bed in an open space it seems common place for modern humans to form their beds inside a shelter and to choose to perform many other actions in this shelter such as eating.

Perhapse the first part of that should be to ask if there are any current or recent groups of poeple that do-not routinely occupy a shelter?
Many nomadic peoples seem to go to the trouble of transporting shelter with them but perhapse some do not if there is not an environmental driver to do so.

Not knowing where to look I did some searching and found a couple of websites that dicuss human instincts but not all of them list sheltering as instinctive so perhapse that is still debatable?

Herding but not sheltering is mentioned on Wikipedia.  Shelter is mention in this Harvard Business Review article about How Hardwired Is Human Behavior? but it seems that we could learn to shelter driven by other instincts.  This website was one of the more prominant ones to list seeking shelter as instinctive but I would not call it a reliable source.

Following on from that would be the harder question of when did the instict to shelter first evolve in humans or an ancestory of humans if it is instinctive?
I am not looking for a calendar date but whether there is some point in the ancestry where it is possible to say these early humans did prefer indoors and these ones did not.  We often hear about finds being located in caves which suggests those humans were sheltering in the cave.  I would accept those as signs of habbitation inside a shelter.

It seems obvious that other mamals like Rabbits and Foxes instinctivey live in burrows or dens either perminantly or following a "Nesting Instinct" but it is not so clear for humans it seems.  I could find more references to humans having a "Nesting Instinct" so perhapse that is where the instinct began or maybe it is the limit of it in humans.  There are examples of nesting or sheltering in fish speacies to so it is clearly something that develops multiple times in evoluionary processes, unless the Nesting Instinct is common all the way back to some aquatic species long ago for our line.

Sorry this is a bit rambling and not well resurched.  I have no background in biology, sociology or the study of human evolution so I am a bit stumped as to where I would begin to look for an answer.

I did look into the H2DB from a suggested similar question but noting in there seemed obviously linked to shelter to me besides "conditioned place preference (CPP)" & "housekeeping ability".  Housekeeping being a predominantly female trait could suggest a genetic factor in shelter, possibly from earlier "nesting" instincts?  Although I would have thought both male and female might have some protection of mate & young instincts beyond those for our habbit of forming herds or family groups.


texts: Why do seagulls hit the ground with their feet?

texts: In several occasions I saw some seagulls standing still and pretend as if walking that is they hit the ground with their feet. It always happens on the soil and not for example on the sidewalk. I am wondering why they do this. Sometimes, from a distance, I see they pick something up from the ground and eat it. Do they do this to simulate the sound of raining and encourage the earth worms to come to the surface?!


texts: In which of the following diseases structure of haemoglobin produced is normal but their amount reduced?

texts:
The options provided are-

Chronic blood loss
Sickle cell anaemia
Haemolytic anaemia
Thallasaemia
Transfusion reactions
               -

*Q-15: pg-785; **Review of Medical Physiology - William F. Ganong;    International 22nd Edition***

Here, the answer provided is (4), i.e Thallasaemia...
My point is that, Thallasaemia is essentially a genetic defect resulting in mutation of either alpha or beta or both the chains, thus rendering the structure of haemoglobin fragile....the disease as far as I know don't cause any reduction in blood volume...

According to me option (1) i.e chronic blood loss is more feasible as in case of diseases resulting from nematodes like Hookworm (Ancylostoma duodenale)....

So, where am I wrong???


texts: What are the white eggs growing from a black stem on the Napa cabbage plant?

texts:
Are they fungal or eggs?
Can't find anything like this in the internet


texts: Boys born in excess - how can the nature draw from non-natural distributions?

texts:
The probability of a newborn baby to be a boy is not exactly 50% but a bit more. I have been given the explanation that it is because boys act more self-destructive during the early ages and so the distribution evens out during time. But how can the nature know beforehand that boys should be made in excess?

It would make sense that the nature followed natural distributions in its choices like uniform, gaussian, exponential etc. but this seems not to be the case. What are the motivations and mechanisms to deviate from natural distributions? Can you come up with another examples of such "non-natural behaviour" in nature?


texts: Can environmental pressures affect genes in one generation?

texts:
Environmental pressures are the catalyst of evolution. Pushing a species to adapt to changes therein. My question is can these mechanisms cause significant adaptation over one generation(parent-> child). My thinking is the pressure of the equivalent of human trauma in a species(depending on neurological and biochemical makeup of said species) would be enough to induce genetic influence.

If not, what is the minimum theorized timeframe for environmental pressures to act?

Edit: This is not a duplicate, the previous question is about one animal's lifetime


texts:
I have these insects in a very old wooden floor. I would like to know whether they are possibly termites, and if not, what they are.

They are about 4 mm in length (and I've had difficulty taking a picture with a standard camera, I may be able to get a better one in a couple of days). This one is dead and may have been crushed a little. Another sign of their presence is little heaps of wood dust appearing with a periodicity of 24-48 hrs, which are about 1 cm in diameter.

Following the indications of @usr137, I think it's rather an ant, indeed it has a slender mid-portion of the body, corresponding to detail (4) in this termite/ant comparative:

But they are much smaller than the ranges I find for carpenter ants (6—19 mm).


texts: Can the absorption of vitamins be enhanced?

texts:
Are food additives like vitamins better absorbed when you mix them among fruits?

I heard that secondary substances in fruit promote the absorption.


texts: How do birds influence brood sex ratios?

texts: This paper concludes that birds can adaptively modulate brood sex ratios. How do birds modulate brood sex ratios? Are they somehow able to influence the sex of their young? Or once young are born, do they provision one sex with more food so that the other sex does not survive?


texts:
The bacterial flagellum uses rotation for generating forward motion, just like a helicopter main rotor does. Helicopters must utilize a secondary rotor to avoid self-rotation due to preservation of angular momentum. Alternatively they can have multiple rotors rotating at opposite directions. But all flagella rotate in the same direction.  Does this mean that the bacterial cell rotates in the opposite direction?

If so, what is the typical frequency of such rotation? Shouldn't the rotation disturb sensing and nevigation in the environment by the cell?


texts: What factors have led to selection for intelligence in crows and rooks?

texts: The Corvidae family could include some of the smartest species after primates. What could be the factors that differentiate them from other species of birds that have determined their potential for intelligence? The only explanation I found mentions their "juvenile gangs" but many other birds are more social and less intelligent.


texts: I am trying to identify this insect on a hibiscus plant. Google googles is unable to identify it.


texts: Why sigmoid curves appear in quantitative analysis of many biological phenomena?

texts:
I know two examples:

1-The binding of hemoglobin to oxygen (binding of oxygen to one site of hemoglobin induces conformational changes which increase the affinity of the other sites for oxygen - the curve could be interpreted as transition from a low affinity T sate to a high affinity R state). The plot can be seen here

2-The denaturation of DNA by temperature (when one segment of the double helix opens, base stacking is disrupted, making the denaturation of the rest of the molecule easier); Another plot

The two examples I gave were actually of positive cooperative phenomena, that is, the occurence of a first event favours the next events. There is also the titration curve, which is a sigmoid, but I don't think it's correlated.
I'm asking that because I found it amazing that the same sort of curve appeared in the study of such different subjects.
Are these examples somehow correlated, that is, for which sort of phenomena sigmoid curves are expected?


texts: Can I simply take the trend of heart rate amplitude to get breathing rate in an ECG?

texts:
I processed an ECG signal using findpeaks in Octave. Then, I plotted the amplitude of the "peaks" found by that function and got the followinge result (original unprocessed ECG signal on top, simple plot of "peaks" on bottom).

If I analyze the "peaks" signal, I get a frequency of about .07 Hz, which translates to about 14 events per minute. This correlates nicely with breathing rate. Is that really the breathing rate that I found, or am I jumping the gun? I've heard this may be referring to a "DC Drift"?


texts: Sequence between PolyA signal and PolyA tail

texts:
Between the polyadenylation (PolyA) signal (AAUAAA in humans) and the start of the polyA tail, there is a short sequence of about 10~20 (G/U rich) bases, is there a special term for it?

Image credit: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175714/


texts: How are colors outside the standard RGB color scheme perceived?

texts:
I found this image in a German book about biology. It's called DIN 5033 and represents the RGB color scheme.

What colors are outside the RGB scheme, i.e., in the black areas of the picture?


texts: Is there a kind of 'rule' which decides whether the male of female is bigger?

texts: In human race usually males are larger than females, and probably is this for all primates. But some animals there are the females bigger, but what determines whether the male or female should be bigger. Is this just random with no logical system as evolution can be or are there some marks which indicates that it is better that the female should be bigger?


texts: How does one determine intracellular concentration?

texts:
The TL;DR version

Is there a fast way to determine what the cell environment of a particular cell (E.g RBC) is? (in terms of solute/ionic concentration)

I'm not sure if the question belongs here, but hear me out. I was doing revision and I kept coming across the line "put the cell in a solution which has the same solute/ionic concentration to prevent the cell from bursting or shrinking"

I get that concept, basically it's sort of replicating the internal environment of the cell with the buffer/solution so that the cell feels "at home."

Then my question is, how does one go about finding out how much exactly for each cell? I would think different cells have different internal environments and I don't believe that scientists actually just have stock solutions of buffers ranging from 0.00001M to 100M and trying every single solution until they find the perfect concentration.


texts: In endochondral bone formation, why does only hyaline cartilage get ossified to form bone?

texts:
There are three types of cartilage: hyaline, fibrous and elastic cartilage.
Fibrous cartilage does not have perichondrium...so it does not take part in ossification because perichondrium needs to develop into periosteum.
Hyaline cartilage has more matrix in comparison to elastic cartilage. Hence, during ossification the quicker spreading of calcification of the matrix will lead to the death of the chondrocytes which will develop into osteoprogenitor cells. Is my theory correct?


texts: Why am I finding peculiar B cell population when pbmcs are cultured for 3 days with CD40L?

texts:
While performing intracellular cytokine assay on B cells, I am finding a peculiar population.
I use 2*10^6 cells for studying each functional marker. The pbmcs are cultured for 72 hours, with CD40L dose being given in 0 hour after plating and BFA in the 48th hour. When analysed, I am getting two CD19+ populations from the lymphocytes. Can anyone enlighten me about what actually is happening?


texts: How do (marine) cells not lose potassium?

texts: Eukaryotic cells keep a sodium-potassium gradient across their external membrane. The concentration of potassium ions is about 5mM outside the cell. Although the potential gradient keeps most of these ions close to the membrane, won't some of these ions diffuse away from the cell/organism? Over long periods of time, wouldn't cells 'dry' out of potassium? I guess the same sort of question can be asked about phosphate.


texts: What liposaccharides are represented by the O-group designations of Salmonalla serovars in the Kauffman-White classification scheme?  I mean to ask, how do the numbers in a Sal serovar (1, 9, & 12 for Enteriditis, for example) describe the oligosaccharide(s) present on the cell membrane?  Continuing said example, does 1, 9, 12  indicate three different types of liposaccharides, or one type of oligosaccahride containing three distinct features?


texts: Is there any advantage to one blood type over another?

texts:
All humans can be grouped into ABO and Rh+/- blood groups (at a minimum).  Is there any advantage at all to one group or the other?  This article hints that there are some pathogens that display a preference to a blood type (for example Schistosomiasis apparently being more common in people with blood group A, although it could be that more people have type A in the areas that the parasite inhabits).  Is there any literature out there to support or refute this claim or provide similar examples?

Beyond ABO-Rh, is there any advantage or disadvantage (excluding the obvious difficulties in finding a donor after accident/trauma) in the 30 other blood type suffixes recognised by the International Society of Blood Transfusions (ISBT)?

I'd imagine not (or at least very minimal) but it would be interesting to find out if anyone knows more.


texts: What is the name of this moth and why does it have an extra wing?

texts: Moth of length 15mm. Seen in Kerala, India on March 2019. Third Unusual wing part visible. Without mobile flash the colour of moth visible is completely black.


texts: Comprehensive biology or anatomy wordbank

texts: I teach A&P for bio non majors. I have a special needs student whose accommodation requires a word bank for any anatomy identification questions I have on the exam. I would like to present the student with a 'master wordbank' (presumably hundreds of words in length) that would act as a word bank for all the exams in the course. I'm surprised to be unable to find much of anything online. Has anyone seen something like this?


texts: Question about radiation and how it affects biological systems

texts:
I'm doing research on the effects of radiation, and specifically UV, X-Ray and Gamma radiation, on biological systems at the cellular level and beyond. I understand that radiation types can be classified by their wavelength, with the gamma radiation being of the shortest wavelength and thus highest energy.

How does this measure of wavelength relate to the unit rads, or radiation dosage? And how do they both affect the survivability of cells? I can understand that the lower the wavelength, the higher the energy and it will affect the cells more adversely at those levels, but how does rads relate to that?


texts: Covid-19: Is it possible to get to r0 < 1 through social distancing measures?

texts:
I'm trying to wrap my head around some of the information I'm reading about how to fight Covid-19  and conflicting opinions about how much "social distancing" is required to avert a disaster, or whether social distancing works at all. (I am a data scientist, not a biologist or medical professional)

First I want to check if some of my assumptions are correct or not:

Flattening the curve doesn't reduce the overall number of infections, only the average rate of infection for a given time period, e.g. Flattening the curve doesn't take you from 1000 infected people to 100 infected people, it takes you from 1000 infected people in a week to 1000 infected people in 3 months (numbers are just examples):  True or False?
The purpose of social distancing is to flatten the curve, not to reduce the number of overall cases: True or False?
If $r_0 > 1$ than growth is exponential: True or false?
Sub-exponential growth can only happen if $r_0 \leq 1$: True or false?
Flattening the curve cannot reduce exponential growth in number of cases to sub exponential growth, it only leads from steep exponential growth, e.g. $r_0 \approx 2.5$ or $r_0 \approx 3$, to "not so steep" exponential growth $r_0 \approx 1.5$ or $r_0 \approx 1.2$: True or False?

Assuming 1-5 are correct, here are the more complex questions I am trying to figure out:

Can social distancing (without hard quarantines, tracking as many cases as possible, and instantly isolating any new cases discovered, etc...) actually lead to $r_0 < 1$ and therefore reduce the number of infections as opposed to just spreading them out to a manageable rate?
I think the answer is "No", because of small world network theory: The majority of people respect prefect social distancing, i.e. they maintain zero social contact with anybody outside of their immediate family and the the people they interact with for procuring life essentials. Because the number of people who cannot practice social distancing due to their essential role in society (grocery and pharmacy employees, health care professionals, law enforcement, etc...) will still experience very high transmission rates, a small world phenomenon occurs, where the average chain of transmission is still very short between any two individuals in an impacted area. What is wrong with this line of reasoning?
In general, is $r_0 < 1$  achievable without a cure, a vaccine, herd immunity, or the ability to track infections with very high accuracy and isolating them instantly?


texts: How much of the entire blood in the body blood flows to the breast (while resting). If you know the percentage or absolute values , as well as the total cardiac output, I would appreciate it answers or referrals to publications or tables. Thanks.


texts: Any examples of a group of micro-organism that continuously spans two or more species classifications?

texts:
Are there any examples of a group of micro-organisms where two different, established species are designated and these two groups meet all aspects of the definition of species (perhaps can not reproduce with each other?), but it turns out that there is a continuous distribution of occurences of this group such that they can reproduce "locally" with nearby members?

I lack the sophistication in biology to know the best possible words to use here so some guidance is welcome, and since the concept of species classification has been around much longer than genome sequencing and analysis, the topic itself draws on concepts from several different centuries.

So I've draw a simple diagram with a 1-D simplified "spectrum" of genetic difference, whereas of course it would likely be multi-dimensional.


texts: Are there examples of now-living species where one is descended from the other?

texts:
I'm not a biology person so please forgive me if this question is formulated badly :)

I'm curious. Are there any species that has an ancestor species that is still alive today?


texts: PEG-silane treatment: why incubate for 18 hours at 60 degrees Celsius?

texts:
I am conducting a biochemistry-related experiment and I have been unable to understand a step which is commonly performed.
My aim in this step is to apply a PEG (Polyethylene glycol) silane layer.

After immersing indium tin oxide (ITO) slides in a PEG-concentration, the slides are incubated for 18 hours at a temperature of 60 degrees Celsius.

Can you tell me why the incubation is performed? And why for 18 hours and at 60 degrees Celsius?

Thanks a lot in advance!!


texts:
Can identical twins have different genders (as in biological sex)?

I thought they should have absolutely the same genes. If they can, what caused it? I'd assume it MAY be because of errors in cellular division at conception.

Thank you.


texts: Time required to evolve advanced chromatophores in octopuses and squid?

texts:
Do we have any idea how long it took primitive Coleoida to evolve from non-color changing organisms to color changing organisms?  Granted, not all coleoidans can change color (vampire squids are good example), many of them do.

(Coleoida is the subclass below Cephalopoda that includes all squid, cuttlefish and octopuses.  Nautilus' are excluded.)


texts:
Which of the following statements about photosynthesis is true?

a.  Photosynthesis is an energy consuming process

b.  The light-dependent reactions produce the energy-rich compounds that are used up in the light-independent reactions.

c.  The light independent reactions can only occur in night

d.  Photosynthesis and respiration cannot take place together in plants

I think both c and d are incorrect, but I'm unsure whether a or b is the correct option.

The reason why I think a is correct is that sunlight is used during photosynthesis and b because the hydrogen of $NADPH$ produced during light phase is used to combine with $CO_2$ by utilizing ATP (which again was produced in the light phase ) to make $C_6H_{12}O_6$ in the presence of enzyme Rubisco.

Which of the following is true about photosynthesis?

a.  Rate of photosynthesis is directly proportional to concentration of $CO_2$ in the air.

b.  Photosynthesis takes place only in the visible spectrum of the electromagnetic radiations.

c.  Rate of photosynthesis would be highest under the green light

d.  Structure of leaf has no effect on the rate of photosynthesis

Here I am also stuck between either a and b.

The reason why I think a is correct is that when $CO_2$ concentration increases the rate of photosynthesis also increases until the concentration reaches 0.1 % and it could be b because photosynthesis takes place in the presence of sunlight, not any other radiation.


texts: How does action potential conduct across a branch in a neuron?

texts:
As the action potential travel in the dendrite towards the cell body, it will encounter many branches. What happens at the branch? What makes it go to the cell body instead of other dendrite?

Also, as the action potential travel from the axon to its branches, does it go to only one or all terminals? If it goes to only one terminal, how is it decided which terminal it has to go?


texts: How do you write genotypic and phenotypic ratios?

texts:
If two homozygous recessive parents are crossed, I know that all of the offspring will be homozygous recessive as well. Would you write the genotypic ratio as 0:0:4 then and the phenotypic as 0:4? (Does order matter? i.e. compared to 4:0)
Also, if the results are 2 homozygous dominant and 2 heterozygous, is it necessary to put the zero for recessive (2:2:0) or would 2:2 be fine?


texts: Is there a way to quantify in vivo cholesterol transport rates?

texts:
I have always had trouble grasping the physiology of lipoprotein cholesterol transport. The "standard" description found in the literature is that liver synthesizes cholesterol which is carried in "forward" transport to peripheral organs by VLDL (and LDL?), while "reverse" transport is mediated by HDL. Most tissues can synthesize their own cholesterol as well (which makes one wonder what cholesterol transport is needed for in the first place). The figure below sums it up (shamelessly taken from this review).

My question: what are the net rates of transport (fluxes) in this system?

Does the liver actually provide net cholesterol to pheripheral tissues, or is it the other way around? Or is the net close to zero? I can imagine this differs between peripheral tissues, some might be net producers and others may be net consumers, but reviews typically lump everything except the liver together as "the periphery". Perhaps some tissues become net cholesterol producers in certain situations, and consumers in others?

I can't find any data on this in the literature (reviews tend to focus on molecular details of lipoproteins, receptors etc.) but this is not my field and I'm sure the data is out there somewhere. I imagine people have done isotope tracing studies to quantify the rates of transport.


texts: What is the lifecycle of hanging woody vines?

texts:
In the first ten seconds of this video, you can see a vine that appears to have started its life 60 feet up in a tree and has now grown down almost close enough to touch the ground. I have seen similar vines that do make it to the ground and start curling around, but don't sink roots. Why do they create this long woody stem? Or do they start at the bottom, grow up the tree, and then release their roots somehow so they can swing free? They're sometimes not wrapped around the trunk at all, just hanging from the very upper branches, as if their seeds found purchase there and started stealing nutrients to grow. Is that possible?

I have swung from these in several locations in Wisconsin and Iowa. They're very tightly attached.


texts: Can a bacterium express a virulence gene and not produce toxins and what may be the cause of this?

texts:
I am preparing a seminar on viable but non-culturable (VBNC) state in bacteria, mainly foodborne pathogens and I just saw this line in a journal article by Lothigius et al that "the expression of the virulence gene in VBNC cells does not necessarily indicate the cells will produce toxins". Any explanation on what this statement means?

Lothigius, Å., Sjöling, Å., Svennerholm, A.-M., & Bölin, I. (2010). Survival and gene expression of enterotoxigenicEscherichia coliduring long-term incubation in sea water and freshwater. Journal of Applied Microbiology, 108(4), 1441–1449.


texts: What's the use of RNA editing in kinetoplast?

texts:
The genes of the mitochondrion (kinetoplast) of some Kinetoplastida - e.g. Trypanosoma brucei, the parasite which causes African sleeping sickness - are "encoded" in a way that the pre mRNA requiries partially heavy editing (insertion and deletion of Uridines) by the editosome (a RNA/Protein complex) until it can be translated to the correct proteins.
The information where to insert and remove Uridines is contained in small gRNA also part of the mitochondrial genome.

However this whole thing seems kind of unnecessary to me. Why did evolution not get rid of the surplus/missing Thymidines in those Genes? What's the use of this?


texts: When can we know if one develops immunity (to SARS-CoV-2)?

texts:
I've been thinking for this for a while. It seems there's no ethical experiment to perform to check if immunity is actually developed (the obvious experiment would be to expose someone that have recovered from the infection, but that's unethical).
My idea is that lack of immunity would eventually result in observation of reinfected subjects and one should be able to estimate the likelyhood of that. An experiment would for example be that if we study a set of subjects over time and at one time 1% are infected and later when these have recovered we at a later time find that 1% are infected then perhaps 1% of these would be expected to be among those that were infected the first time (unless immunity has developed).
How did we realize that we get immune to measles, chickenpox and mumps for example?


texts: What would classify those findings of the University of Sheffield experiment as aliens?

texts:
It's in the news that some experiment was able to capture some alien specimens during a meteor shower:

http://www.ibtimes.com/aliens-are-here-scientists-say-they-have-proof-alien-life-there-should-be-plenty-skepticism-1408322

Despite all the skepticism that has already been said about this finding, what would be a proof that such specimem came from outer space? Is there any established protocol to assure that some form of life didn't come from Earth?


texts: Are the 5 digits of all land vertebrates an accidental number?

texts:
All land verterbrates except some frogs have 5 fingers on hands and feet.

The first vertebrate lizards came out of the water and had 7 fingers ( -370mn yrs), and then 6 fingers, and after 30 million years, all their descendents had 5 fingers on both limbs.

someone told me "5 is much more of an accidental number", so if all land vertebrates had 7, then 6 fingers, why did that get selected to 5?


texts:
I heard somewhere that when we want to do a repetitive movement of one finger (ex the index) . Our brain (in a very crude way) sends a first message to move all the fingers, and then a second message to hold the fingers that we don't want to move.

The person who said it, was explaining about brain evolution and the fact that the old reptilian part of our brain is the one that send the first message and the higher brain sends the second message.

So is that true ?
If so, do other parts of our brain work like that too? For example more complex behaviors, like sexual mate choice?


texts: Meat and mushroom allergies, why are they so rare?

texts:
There are a lot of food allergies, but for some reason not to meat (mammalian meat or poultry) or mushrooms. I've googled a bit, and now I know that one can actually have a meat or mushroom allergy, although the odds of that are very-very small. Why is it so?

Is it because both meat and mushrooms are usually cooked and that kills potential allergens? What about undercooked or raw food like portobellos or carpaccio and steaks?
Or is it because animal tissues are so similar to ours and so are better digested? What about mushrooms then?
Is it something else?

Also, are there any data of what types of meat and mushrooms are most allergic?


texts: By what mechanism does elevated homocysteine level cause endothelial dysfunction and damage?

texts: It has been stated that elevated homocysteine level causes endothelial dysfunction and damage. By what mechanism does this happen? Why is it the endothel where elevated homocysteine causes problems?


texts: Antihistamine's effect on insulin secretion and tiredness?

texts:
Antihistamines are known to cause tiredness.
The essential hormones of the body are insulin (glucose), parathyroid hormone (calcium) and aldosterone (Na-K ATPase, sodium).
I am thinking how this tiredness symptom can come.
There are so many different antihistamines so I am confused about the mechanism how they cause tiredness.

Histamine acts on parietal cells of stomach via H2 receptors to stimulate hydrogen ion secretion - cephalic phase.
Excess of antihistamines can lead to decreased acidity of stomach so change in conversion of pepsinogen into pepsin.
So less pepsin breaking down peptides and proteins.
Body has to do something else to break those components - and this consumes much energy and makes you tired.
Small mucus food mass stays in the intestines.
Delayed absorption.
Nutrients needed so liver has to work and make essential things - amino acids and something else.
Some waste management also may happen - because of tiredness.

Changes in blood sugar level.
Delayed most probably after food intake.
Very fast and fast insulin secretion mechanism starting during wrong times - all of the sudden.
So less insulin secretion cumulatively:

very fast mechanism - change of permeability of membranes (Na-K ATPase and sodium channels) reacting during times when not suitable - long after food intake
fast mechanism (phosphorylation of different things) happening more, since sympaticus apparently is not so inhibiting here
slow and very slow mechanisms however preferable (increased permeability of amino acids and mitoses)

So I think the tiredness of antihistamines is because of the increased amount of active fast mechanisms of insulin secretion, while less very fast mechanisms.
To carry the raw food mass in the intestines also require much energy.

What is the physiological mechanism behind the tiredness of excess antihistamines?


texts: Can ingesting substances that are produced by the body cause a permanent withering of the organs that produce the substance?

texts:
This question is about substances such as insulin and some vitamins that the human body is able to produce on its own.

Some substances that are produced by the body are also present in various body building supplements.

What I wanted to ask is, is there evidence that ingesting these types of substances for prolonged period leads to (permanent?) withering of the organs that produce the substance?


texts: What waste products do cells secrete in culture, and at what rate?

texts:
I am designing microfluidic chips for mammalian cell culture. One aspect I am interested in modeling is the rate at which I must renew media to ensure that:

Cells receive enough nutrients
Cytotoxic waste products are removed before they reach concentrations that would be detrimental to the cells.

Number 1 is fairly easy. Numbers for glucose uptake rate, for example, are available for many cell types. Number 2 is proving more challenging. I cannot find articles that detail secreted metabolites, including their secretion rate and the relationship between their concentration in media and toxic (or other) effects on cells.

Are there any resources out there on quantitative assessment of secreted metabolic waste?


texts:
For human genetic mapping several different types of markers are used:

RFLPs (Restriction Fragment Length Polymorphisms)
VNTRs (Variable Number of Tandem Repeats) such as mini- and microsatellites
SNPs (Single Nucleotide Polymorphisms)

What are the pro's and con's of using each type?

Do any of these markers have a specific functionality in human genetic mapping, or can they all be used for the same purposes?


texts: Why do dog's eyes glow green on a photo?

texts:
Taking my current profile picture as a prominent example:

This photo has been taken with flash. As I gather, this is the same effect that makes a human's eyes glow red on photos, namely the reflection of the flash at the choroid and then passing back through the retina.

The retina is full of bloodvessels and the blood inside them gives the reflected light it's reddish color.

If it's the same effect, why is the color different?


texts: What kind of predators do the snail's shell protect against?

texts:
Growing a shell is a significant material and energy investment for a snail. They have lots of predators which can easily eat them, having beaks which can pick them out or teeth strong enough to break the shell. Those which are not big enough to have a strong enough jaw, are small enough to be able to reach inside the shell.

Why do snails still have shells? Is there a large group of animals which cannot eat snails because of their shells, and would be able to if the snails had no shells?

I'm thinking of commonly known land snails.


texts: Can different cell lines of same type symbolise samples from different patients in ChIP-seq?

texts:
Can I simulate different patients by using different cell lines of the same cell type and from the same tissue? Can I also study apoptosis in an immortalised cell line?

I have a gene X (transcription factor) which from wet lab experiments induces apoptosis in  cell type A (endothelial cells) and proliferation in cell type B (smooth muscle cells).

I want to address this differential behaviour using ChIP-seq of antibodies against gene X.

I do not have enough patient samples and I wish to purchase immortalised cell lines to perform ChIP-seq with 4 biological replicates per condition: untreated control and over expression of X.

I plan each biological replicate to be a different cell line of the same cell type and preferably the same tissue. Is it possible to have such?

I will also be very grateful if anyone provides me a link or good article containing the best practices in planning for a ChIP-seq experiment.

Thanks in advance.


texts: Do humans emit more carbon through respiration or defecation?

texts: Where does most of the carbon we ingest go? I understand that a large amount is exhaled as carbon dioxide, but what percent is defecated (and theoretically deposited in the ground)?


texts: What is the meaning of "The Molecular Basis of Disease"

texts: What is the exact meaning of The Molecular Basis of Disease? I have one assignment which involves presenting Molecular Basis of a Disease. I am not really sure what points to add.


texts:
According to this article, only about 1% of all humans are ambidextrous:

  About 90 percent of people are right-handed, says Corballis. The
  remaining 10 percent are either left-handed or some degree of
  ambidextrous, though people with "true" ambidexterity—i.e., no
  dominant hand at all—only make up about 1 percent of the population.

Less dominance is observed in other animals, as indicated by this article:

  Bill Hopkins, at the Yerkes Regional Primate Research Center in
  Atlanta, USA, has made even more contentious claims in recent years,
  asserting that his captive chimpanzees exhibit a 70% right-handed
  preference for many tasks requiring manual dexterity, a rate that
  rises to almost 98% for very specific tasks, like the precise over-arm
  throwing of objects. However, for everyday food-related tasks (like
  cracking nuts or digging out honey), the rate remains closer to 50-50.

I am wondering if there is any theory that explains why ambidextrous persons are so rare. As a totally layman when it comes to biology it seems that this would require a more complex brain to wire all the complexity to both members and this would be rarely justified (virtually all tasks can be done without being fully ambidextrous).

Question: Why are ambidextrous persons so rare?


texts: In histidine structure , full protonation gives a structure with only the double bonded nitrogen having been protonated in the ring and not the single bonded nitrogen. Why is that?


texts: Value of r (intrinsic rate of natural increase)

texts:
What is the current value of 'r' (instrinsic rate of natural increase) in India? How do we calculate it?

My book says that In 1981, the r value for human population in India was 0.0205. But this link (https://www.google.co.in/amp/knoema.com/atlas/India/topics/Demographics/Population/Rate-of-natural-increase%3fmode=amp) says it was around 22.50 in the year 1981. Such big discrepancies are a query.


texts: What is the difference between influenza A and B viruses that causes their distinct seasonal patterns?

texts:
I recently learned from an answer at health.SE* that influenza B tends to occur later in the season compared to influenza A. According to the graph in that answer, during this year’s flu season the peak for influenza B was mid-March, compared to late December for influenza A. I’m wondering why this is. What are the virological factors that account for this difference?

*Now public!


texts: Does a human body age at any place at the same rate or can there be big differences?

texts:
Aging can be caused by bad working mitochondrion, stacking of protein, shortening of telomers etc.

Now all our organs and materials have their own kind of cells, but are they equal vulnerable for aging by eating (which is the main cause of aging).

Probably there are some differences. For example the liver would get much more aged when drinking a lot of alcohol then one would get grey hair, because it is the task of the liver to break down toxic proteins etc.
But can in general be said that the aging of the body goes equal throughout the whole body, or are there more/many special patterns for each organ which are dependent on the kind of food is taken?

So for example a person can have very 'young' intestines but a very old milt or can a person get grey hair but all other organs are very young?


texts:
According to Wikipedia and many other sources, women live substancially longer than men (over 5 years in the U.S.).

Men can reproduce for much longer than women.  So longer living men would have the most offspring, while the longevity of the women would be more or less irrelevant in reproducing.  These offspring would be the product, on average, of men and women where the men are older than the women.

So why do women live longer than men?  Am I misinformed, or what don't I get?


texts:
I barely know anything about biology and realize that this might be a stupid question, but I'll ask anyway! I know that species "transform" into other species through the process of evolution. Many species around today still co-exist with the species in which they evolved from, right? Actually, is it correct to say that all species coexist with some common ancestor?

Anyway, my question is; if the monkeys that we evolved from are still around today, then where are all the in-between species. Are there still early humans, like Neanderthal's or Hominids or what have you still roaming around some where?

If all early forms of humans are gone, is it because the more modern humans had a greater evolutionary advantage? But wouldn't these less modernized humans have those same advantages over the less evolved monkeys?


texts: What is the difference between a myofibril and a myoblast? (In skeletal muscle)

texts:
I read that a muscle fibre (myofiber) is formed when myoblasts fuse.
https://teaching.ncl.ac.uk/bms/wiki/index.php/Skeletal_muscle#:~:text=The%20multinucleate%20feature%20is%20established%20in%20myogenesis%20where,cells%20%28each%20muscle%20cell%20is%20one%20muscle%20fibre%29.
On google I saw that a muscle fibre is formed from many myofibrils.
https://biologydictionary.net/myofibril/#:~:text=Myofibrils%20are%20long%20filaments%20that%20run%20parallel%20to,are%20made%20up%20of%20repeating%20subunits%20called%20sarcomeres.
Does that mean that myoblasts and myofibrils are the same thing?


texts: The Wikipedia entry for Ion states "A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space."  Cells pumping ions across membranes is very common so can someone help me understand what context might be implied by the quote?


texts: Why doesn't mitochondrial DNA accumulate damage over successive generations?

texts:
From what I recall, mitochondrial DNA is very susceptible to damage from oxidative stress because it is a site where free radicals are generated and their DNA isn't packed into chromatin like nucleic DNA is. How then is it possible that mitochondria can stay in-tact when it is repeatedly passed on to offspring?

I would have thought that an accumulation of errors would cause them to malfunction over time.


texts: Why does DNA need to be pure for restriction enzymes to act on it?

texts:
My textbook states: “In order to cut the DNA with restriction enzymes, it needs to be in pure form, free from other macromolecules. Therefore DNA isolated from other chemicals of the protoplasm like carbohydrates, lipids and proteins via techniques of DNA isolation.”
My question is, why does DNA need to be alone? Won’t restriction enzymes work if there were a DNA molecule in a sugar solution? I understand that the DNA has to be freed from cell membranes and walls for restriction enzymes reach the DNA but how does the presence of other macromolecules hinder DNA’s digestion of a restriction enzyme?


texts: Indicators of Ras binding domain (RBD) activity in Ras effector proteins?

texts:
Ras family based small GTPase proteins usually have a Ras binding domain (RBD) in their effector downstream proteins like Raf. Roughly Ras proteins cycle between active(GTP-bound situation) and inactive(GDP-bound) states. So what information is passed onto RBD when Ras protein is active in a Ras:Raf complex. It is well known that Switch-I , Switch-II root mean square fluctuations(RMSF) of inactive Ras protein is very high. In the active Ras case the Switch-I RMSF falls by making that loop rigid.

So my question is that is there any observables like RMSF of RBD region indicate the "activity" of effector molecule(like that of Raf). In other words how do I understand that the RBD region is active/inactive (say from simulation perspective or experimental perspective) ?

Please suggest me any related references or links.


texts: What percent of biology study is dedicated to species-specific subjects like ecology and evolutionary biology?

texts: I'm thinking of studying biology, especially ecological and evolutionary biology. Could you give an estimate for me, what percentage of current standard biology study at university contains information about these subjects, and not theoretical biology? What percentage of the study is dedicated to species-specific subjects?


texts: One Sample, Different Methylation Values

texts:
I'm hoping that somebody here can explain this unusual result that I'm getting with some pyrosequencing data. I have bisulphite converted a few samples a couple of times over the years for different projects. Recently I was collecting some of this disparate data together and I noticed that when the same pyrosequencing assay was used on these samples, those that were converted later had decreased methylation at the CpG sites of interest compared to the initial bisulphite converted samples. The original conversion was in 2010 and the repeat conversions were in 2014/2015. The assays are the same and it's difficult to blame this on PCR amplifying one clone over another since I've done technical replicates on each aliquot. Even the 2010 converted sample has the same result in 2015 that it did in 2010 but this is different from the 2015 converted sample.

We are using the same kit (Qiagen) for bisulphite conversion and haven't made a major change to our procedure (we follow the Qiagen protocol without modification). Has anybody noticed this phenomenon before? Is it possible that stored DNA would experience methylation changes? It seems more likely that the issue is technical but I'm having trouble figuring out exactly what that technical issue is.


texts: Is there any parasitoid that preys on something other than arthropods?

texts:
Besides fungi, most parasitoids seem to be arthropods themselves, specifically insects that undergo complete metamorphosis. This makes sense, as feeding on a living body poses different challenges from finding one for offspring.
However, parasitoid hosts seem to exclusively be arthropods themselves. Why is that? Could it be due to the specific respiratory and circulatory systems of arthropods? Are there any exceptions?


texts:
I’m finding contradicting methods of   Fructose  transfer to blood

page no 264(10)One of which saYs fructose is absorbed by simple diffusion

And another sources like this say that fructose is absorbed by facilitated diffusion

I Believe that second source is true but still which one is correct ?


texts: Question about different gametes that can be produced

texts:
I have a question from a past exam that asks the following:

"For the organism of genotype AABbCcDDEe (homozygous for 2 genes, heterozygous for 3 genes), how many different types of gametes will be made if the C gene and the E gene are linked on the same chromosome while the remaining genes are all on different chromosomes?"

However, I have no answer key, and these answers are the choices:

A. 2

B. 3

C. 4

D. 8

E. 9

Here's my approach to the question:

We have 5 traits, and each trait consists of 2 alleles. To make functional gametes, each gamete must receive one of each allele so that it can survive. Clearly, for AA and DD, there's only one choice: A, and D.

However, for Bb, Cc, and Ee, things are a little different.

C and E are linked on the same chromosome. c and e are on different chromosomes. Therefore, a gamete can have either CE, or c and e. Similarly, a gamete can have either B or b.

Therefore, shouldn't we be able to create 4 different types of gametes?:

ABCDE, ABcDe, AbCDE, AbcDe

So wouldn't the answer be C. 4?

Please show me any mistakes I might be making, or any gaps in my understanding. This would be very much appreciated.

Thank you!


texts: Preparation of dihydroxyacetone phosphate from glycerine by fermentation

texts:
I read on Wikipedia that
dihydroxyacetone (DHA) can be obtained from fermentation of glycerin. I would like to obtain dihydydroxyacetone phosphate (DHAP) for a science experiment but, since I'm 15, I cannot purchase it.

So I'm gonna have to make some if I want it.

With that being said, how do I properly ferment it, and how do I phosphorylate it? (I have phosphoric acid at home, maybe that would do the trick...)


texts: Gene & Protein nomenclature: N-Myc, c-Myc, et. al

texts:
Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins?

I think I know that for genes, we use an italic font and for proteins, we use a regular font.

I think I've also learned that for human, all letters are in uppercase (eg. SHH) whereas for mouse, only the first letter is in uppercase and the remaining letters are in lowercase (Shh). (From http://en.wikipedia.org/wiki/Gene_nomenclature)

But I'm stumped with all the other "tags" (in quotes because that's how they seem to be used and I don't know how else to think of them) that I see floating around gene and protein symbols.

For example, Myc (MYC?).

I see these three articles in uniprot.org:

http://www.uniprot.org/uniprot/Q99417 for C-Myc

http://www.uniprot.org/uniprot/P04198 for N-myc

http://www.uniprot.org/uniprot/P12524 for L-Myc

These proteins are all in human, and yet their recommended names are not all caps; what's up with that? But even more confusing to me are the "C-", "N-", and "L-" letters prefixed to them. What in the world are those supposed to be indicating?

Are these all fundamentally different proteins (coded by different genes), but maybe related somehow to each other (thus the common three letters, 'myc' even if they are not all the same case and not all upper case as I thought was supposed to be the case in human), and they are just given these "C-", "N-", and "L-" tags to distinguish one from the other? Does one tag indicate an oncogene or a proto-oncogene? Why do I sometimes see "c-Myc" and other times, "C-Myc"? Does the case of the "C-" mean something? Is there some kind of key or legend I can look at to get answers to all these questions? I've found some explanations in Scott Gilbert's Developmental Biology textbook, but it still doesn't give me all the answers I seek here

I just want to understand how these tags and symbols are being used because it seems to me that when I read research papers (of which I've read many), they are used by different authors in different papers in ways that are not consistent with each other. Either that, or else I'm missing something very basic, which is why I'm asking here.

Thanks in advance for any help.


texts: How come only a handful of animals can do photosynthesis?

texts:
As far as I understand, all the energy that living beings rely on comes from the sun. It's processed by plants in photosynthesis. These plants are consumed by herbivores, which in turn are consumed by carnivores. Energy trickles down that way, with photosynthesis being the crucial basis for all the other layers.
A couple of days ago I was wondering, how come animals don't do photosynthesis? This story talks about a few exotic animals that can do photosynthesis, but they seem to be an edge case.
It seems like there's a rule of thumb: Iff a creature can do photosynthesis, it can't move. Why is this so? Wouldn't it be beneficial for a herbivore-like mammal to be able to create sugars directly from sunlight? They wouldn't have to graze at all, just find water and sunlight. It's possible they'd have an easier time avoiding predators and expanding into more territory.
Can you think of a good reason why such creatures never became mainstream?


texts: Do green algae form obligate symbioses with fungi?

texts: I understand that obligate symbioses means that the two organisms cannot live without each other and are in a symbiotic relationship, but do green algae from this with fungi?


texts: Mechanism of Octoxynol-10 as a preservative in vaccines

texts:
I noticed that the Fluarix Quad flu shot this season contains Octoxynol-10 rather than Thimerosal as a preservative. I am not expert in this area, so I did a Google search of "Octoxynol-10", and noticed that it has lysing properties and so speculated that this must be how it would kill any bacteria present and thus act as a preservative. Nonoxynol-9 is an active ingredient in anti-spermicides, I speculate for the same reason.

My question is: What does the Octoxynol-10 do when injected into my muscle tissue? I speculate that there may be some lysing of my cells. Perhaps only the cells with very thin membranes lyse? bacteria, sperm, nerve?


texts:
I have 10 samples of some food or other things and I need to know, if it contains amylase. I already ran an experiment with storch and iodine, but I have to make it right and my experiment must not be right.

List of samples:

Saliva (I know this one)
Banana peel (inner side)
Corn
Sponge biscuit
(http://www.kaloricketabulky.cz/fotografie-velka/f1136aba2e11082a/piskoty-detske-kulate.jpg)
Tomato
Banana (dried)
Bread
Potato peel
Ketchup
Milk

Thank you very much!


texts: Why does mud therapy work by some pain related diseases?

texts: Apparently, some users here agree there is no ion exchange through the skin. Mud therapy has some therapeutic effect for pain related diseases. As an anecdotal example, I experienced pain relief by treating my sport injury using mud therapy. If it is not ion exchange, then what is the mechanism behind mud therapy?


texts: Do insects respond to the detection of dead insects?

texts: Are there insects that change their behavior upon detecting the nearby presence of other dead insects? If there are, can you provide an example?


texts: Are the transcription factors Oct4 and Oct3, who are encoded by the POU5F1 gene, actually the same protein, or alternative spliced products from said gene?


texts:
What is inclusion forming unit load? I found it when reading this article.

What does this measure and what information can be gained form it? Does this represent the amount of bacteria within a person? What's the difference between inclusion forming units and colony forming unit?

I am from a mathematical background, so can someone please explain these in simple terms?


texts: Why does insertion of transmembrane domains occur in the rough ER?

texts: To elaborate on that question, why in the secretory pathway does the insertion of transmembrane domains into the membrane occur in the rough ER as the protein is translated and threaded across the ER membrane? This is the answer to a problem from a science textbook. I thought that integral proteins are first produced in the rough ER, modified in the Golgi apparatus, and then shipped in vesicles that fuse with the cell membrane. If that's the case, wouldn't insertion of the entire protein into the membrane happen when the vesicle fuses with the cell membrane?