texts: Is it still true that C. elegans has no known natural viruses?

texts:
I read in a 2009 review that

  While mammals and C. elegans each have a single Dicer that makes both miRNAs and siRNAs, Drosophila has two Dicers: Dcr-1 makes miRNAs, whereas Dcr-2 is specialized for siRNA production. The fly RNAi pathway defends against viral infection, and Dicer specialization may reduce competition between pre-miRNAs and viral dsRNAs for Dicer. Alternatively, Dcr-2 and Ago2 specialization might reflect the evolutionary pressure on the siRNA pathway to counter rapidly evolving viral strategies to escape RNAi. In fact, dcr-2 and ago2 are among the most rapidly evolving Drosophila genes. C. elegans may achieve similar specialization with a single Dicer by using the double-stranded RNA-binding protein, RDE-4, as the gatekeeper for entry into the RNAi pathway. However, no natural virus infection has been documented in C. elegans. In contrast, mammals may not use the RNAi pathway to respond to viral infection, having evolved an elaborate, protein-based immune system.

Is it still true that no know natural virus infects C. elegans? And is this [thought to be] due to the effectiveness of its viRNA (virus-derived small interfering RNAs) immunity/defense mechanism?


texts: Natural killers cells in insects/ arthropods

texts:
I'm wondering if someone knowns anything about Natural Killer cells in insects or other Arthropods. Do they exist or are their any similar cells of the innate immune system that someone knows of?
Thanks a lot!


texts: What does the term 'bioavailability' mean?

texts:
From what I've read,

  Bioavailability is the degree to which food nutrients are available
  for absorption and utilization in the body.

How would you explain this with an example?


texts: What does the word specific epithet mean?

texts: Is the species for Rosa indica and Mangifera indica 'indica' as you can see is the same in both. What does this signify. It is obvious that it has different species as they have different genus.


texts: Do skin mites reproduce on human face during night?

texts:
I've seen this circulating on social networks:

I was wondering to what extent is it true. Do skin mites really get on the skin surface to reproduce? Why is it so?


texts: force required to do damage to child's leg/feet in collision

texts:
I'm currently working on a toy robot for a student project. Part of this robot is the fact that it will be moving around quite fast. As such hitting the child can and most likely will happen. As such we are obviously worried about safety. So what type of forces can a child safely withstand? The robot will most likely not be very tall (45 cm) and be shaped like the top half of a sphere, as such most collisions will happen with the shins or the feet.

I do hope this is in the correct  stack exchange and that this isn't supposed to go into a different stack exchange.


texts:
How do taxonomists classify breeds of organisms in a species? When talking in such depths about organisms (using RNA and DNA), don't they have to unavoidably do it?

I read in another question that all the breeds of dog we domesticate belong to the same species. But they (the dogs) certainly have very apparent differences. Don't they?

So how do taxonomists handle/consider these 'breeds'?


texts: Species identification - What is this "bug"

texts:
The title says it all. What the heck is it?

Edit:
I found this on my car, in Kansas city.


texts: Lungfish have a cartilaginous notochord, and a reduced cartilaginous skull. Is this feature to improve flexibility, or is there another reason?


texts: Forming a cladogram from a table of information

texts: Can someone please give me some tips or help me build a cladogram from the following table of information? The outgroup is Lancelets and the first derived character is vertebrae, followed by Lampreys and jaws I believe.  It’s not until after jaws I have trouble figuring out where to link up the organisms and traits. I’m assuming you cannot repeat or remove traits. When I look online the simpler examples do not help me much for this branching issue...I hope that made sense. It’s probably simpler then I think but I’m having a mental block with it. Any help would be great, thanks


texts:
What are the effects of addition of these chemicals to actively respiring cells ?
Which of them would lead to INHIBITION of aerobic respiration ? Would cytochromes be actually taken up by cells ?

a.addition of CO

b.addition of CO2

c.addition of cytochromes and flavoprotein


texts: Identifying flying insect from northern Poland / Baltic Sea area

texts:
Found during this year vacations at Baltic Sea (northern parts of Poland):

I don't have a picture containing other object, for size verification, but I'd say, that it was 3-4 cm long.

There were two interesting characteristics of this insect, that I haven't found in case of any other:

it was not flying / running away, when when being chased / waived by a hand; you actually had to snap it with a finger and sent it airborn, to make it fly away,
once touched by finger or upon falling from certain height it was pretending dead, but when you tried to remove "dead body" it turned out in most cases that it is alive and it was flying over.

This is all I can tell about this insect. Can someone help me with identifying, what species is it?


texts: Any tool to align whole genome sequence data to another genome and give exon regions a higher mark?

texts:
I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I want to use a tool that is aware of the annotation of exon and intron.

That is to say that matches in an exon region should have be given a higher weighting than matches in intronic regions.

Also, when a read pair maps to 2 exons, the insert size should be more flexible as the intron length can be vary among different mammals. Since the library insert is less than 2kb for short libraries, the more common situation should be one read on exon and another on intron.

This is different from RNA-seq as I am using WGS data of a whole genome, so both exons and introns are in the reads. And I want to align them to a human reference sequence.


texts: How do you keep track of past/new lab protocols?

texts:
Does there exist a list grouped my subject (e.g. 'microscopy') for keeping track of what protocols have been designed and used?

Closest I could find is http://www.protocol-online.org/ but it's fairly sparse and out of date.

Any recommendations/tips and tricks? Thanks!


texts: BMI limits in interpretation in people with high/low heights

texts:
In a study, I measure BMI of a large sample of adult people.

Among them, there is some who have very low and very high height.

As I can read on the internet (like here or even in the wiki, for instance), BMI is not relevant for very short or very tall people.

Some math professor even wrote an article with a "better" calculation of BMI, but with a very low impact in science world (didn't find it on pubmed) so it's not really peer-reviewed.

Let's take some examples, assuming "normal BMI" is 21:

for a 110cm tall adult, ideal weight is 25kg
for a 130cm tall adult, ideal weight is 36kg

These weights appear really low to me. Note that dwarfism cutoff is 145cm in France.

My question is then the following: How could I choose a cutoff on height to exclude BMI values ?

NB: I didn't find anything on pubmed nor on google scholar, but maybe I missed an important article


texts: Total dark deprivation at day-neutral plants

texts:
First of all, I am not a biologist.

Almost for a week, a question has come to my mind:
"Is it harmful ceaselessly exposing a plant to light?"
(I mean with natural & artificial light with proper spectrum)
I have been searching for a week, and I stumble upon many weird and wonderful things, and by them, I have become able to consider this topic more deeply, and refine my original question. However I have still not found the answer.
I am already familiar with these topics:

Light-dependent reactions
Light-independent reactions
Calvin cycle
Photoperiodism
Phytochrome
Cryptochrome
Long-day, Short-day, Day-neutral plants
Grow light

So my main question:
Does ceaseless light exposure with proper spectrum adversely affect a day-neutral plant?
As a layman I have started to fumble towards light-independent reactions, but I have not found strong claim. I have learnt that there are processes which taking place during dark phase, but are these reactions impossible in presence of light?
But probably there are other factors.

My resources were: Google, Wikipedia, (a tons of) academic paper, many article from Botanical Gazette, many blog & webpages about botany & greenhouses etc.


texts: Fasting gastric pH versus normal gastric pH

texts: I want to know if someone is fasting (no food or drink for a whole day) will they have a higher or lower pH than a person who is eating regularly? If so what is an estimate of both of those pH's in the stomach?


texts: Are Luteinizing hormone and Interstitial Cell Stimulating Hormone(ICSH) the same?


texts: Does more ATP present mean that a microbe can ferment more and decrease the pH?

texts: I noticed that EMP produces 2 ATP and EDP produces 1 ATP. Does that mean that if more ATP is present that would give more energy for fermentation and lowering the pH of a system?


texts: Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?

texts:
During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other when mentioning UAF or UBF, so I want to know if they are actually the same thing.

Another source of confusion is that Wikipedia has article for both:
https://en.wikipedia.org/wiki/Upstream_activating_factor

https://en.wikipedia.org/wiki/UBTF

Thanks in advance.


texts:
Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I assume they can bind long enough before disassociating)
However after doing some search on this topic, it seems that I am able to find only about 2 related papers. One of them seems to be from 1998, while the other one is more recent.

These articles suggest that it's doable. If this works, we'll be able to produce biopolymers with the sequence exactly as we designed, there would be massive applications, but I'm curious why it's not getting much attention, or why aren't there more papers related to this area?


texts: I know it is caused either by blood vessels beneath skin , or some pigment called "pheomelanin" . But what is it in fact?


texts: How to define "Quasifixation" in continuous approximation of finite population?

texts:
Background

Many models including the famous very first models derived by Sir Ronald Fisher in his early career, assume infinite population size. In an infinite population, an allele can rise in frequency (if its fitness is greater than the fitness of its counterpart(s)). This increase follows a logistic curve that never exactly reach a frequency of 1. Therefore, the term fixation does not apply to these model and in consequence the concept of quasifixation has been created.

Question

An allele is considered to be quasifixed if it reaches a frequency that is very close to 1. But how close? The decision is obviously arbitrary but when using a continuous approximation model in a finite population the question is necessarily raised and a decision needs to be made. How close should the frequency of an allele be to 1 so that it is considered to be quasifxed? The answer is probably a function of the population size $N$. What threshold do authors usually use in the theoretical population genetics literature? It would also be nice to have the definition of the author who first coined this term.


texts: How do place cells switch their response patterns when the subject moves to a different environment?

texts:
So I understand that place cells form a map of each environment the subject has been in and responds accordingly in each environment. Question is how do they switch to represent a different environment when the subject moves to a new environment? It seems unlikely that a different set of place cells represent each environment the subject has ever encountered because it seems that would require too many place cells (and since the cell counts in the hippocampus is I presume relatively fixed, "free" place cells run out at some point), so it must be the same place cells "remembering" different response patterns to different environment and responding accordingly in different environments.

From the wikipedia page on place cells: "In a different environment, typically about half the place cells will still have place fields, but these will be in new places unrelated to their former locations."

Muller, R. U.; Kubie, J. L. (1987). "The effects of changes in the environment on the spatial firing of hippocampal complex-spike cells". The Journal of neuroscience : the official journal of the Society for Neuroscience.


texts: I understand multiple origin bubbles; DNA polymerase only synthesizes DNA from 5' to 3' and all that. But what I don't understand is why it has to be in fragments. Yes, DNA is anti parallel, and so the DNA elongates in opposite directions, since DNA polymerase can only go one way. But why not go on just like the leading strand? Why not continue happily along the DNA template continuously but in fragments?


texts: Determining sequence of oligoribonucleotide

texts:
Oligoribonucleotide X was treated with phosphatase (for removal of 3'
  and 5' - terminal phosphates), then with RNAase T1, which cleaves all
  phosphodiester bonds located in a 3' position of guanosine in a
  5'-specific manner.

  As a result, oligonucleotides L, M and N were generated in equal
  amounts. Each of them was further treated with phosphatase and
  subjected to alkaline hydrolysis. Results are listed in the table
  below.

  Then experiment was modified: oligoribonucleotide X after treatment
  with phosphatase was hydrolyzed with RNAaseP, which cleaves all
  phosphodiester bonds in a 3'-position of pyrimidines in a 5' -
  specific manner.

  This hydrolysis yielded five products in approximately equimolar
  concentrations: uridine monophosphate, cytidine monophosphate and
  oligonucleotides P, Q and R. After resolution of the mixture and
  alkaline hydrolysis of these oligonucleotides data listed in the table
  below were obtained.

My thinking : G can not be at the 5' end otherwise we would get a single Guanosine also in the first experiment. G can also not be at the second last from 3' end as we have not got any singles. We have got A and C in a duplet and so they must have been at the 3' end.

I also have trouble understanding the significance of "mole/mole of oligoribonucleotide".

I am trying to fit  in other results but am unable to do so.
A GOOD HINT WILL BE APPRECIATED MORE THAN A DIRECT ANSWER.

Thanks


texts: Image Dataset for Cardiac cells for Mus musculus?

texts:
I'm working on developing a transfer learning model to detect cells in a culture using microscopic images.
for that i require data set of images having microscopic images of various cell types. Is there any such database present? Any open source research work having  microscopic images of cardiac cells that can be used?


texts: Proteome patterns between treated and control cells

texts:
We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only one pair (one treated and one untreated) sample for each experiment. We want to see which proteins are differentially expressed (minimum 1.5 fold up/down).

First approach: We have compared protein levels of all 4 treated (as a group) with the 4 untreated (as a second group). There is of course variability between all experiments, because of the nature of the cells. We have a list of the proteins that are differentially expressed as a result of the treatment, however this list is not very long.

My question is (second approach): Can we compare the proteins levels pairwise for each experiment (treated vs its respective control) and make 4 corresponding lists, and then compare these four list using a statistical tool and find which proteins are consistently up- or down-regulated? DO you think that these two different approach will generate different lists of the affected proteins?


texts: I would like to get suggestions for the books related to General time reversible model of evolution and Felsenstein model etc. Specifically the mathematical treatment of these topics and concepts related to general balance and detailed balance etc. Can someone point out any books, links etc related to these.


texts: What factors are known to affect evolution?

texts:
My understanding is that the possible mechanisms of evolution are:

Environmental changes
Cultural/mating preferences
Population Immigration
Genetic Mutation

Am I missing anything? I've heard that population shifts within a existing populaces will effect evolution, but imagining the most simplicity scenario, it's hard to see why the would make a difference.


texts: What is the origin of the name "λ phage"?

texts:
The lambda bacteriophage which infects E. coli was first discovered by Esther Lederberg  in 1950.

However, in the earliest paper on the lambda phage that I could find, I was unable to find the reason behind why the phage was named after the Greek letter λ.

Is there a source (by Lederberg or previous scientists) that mentions the etymology of this phage?


texts:
Suppose I want to provide "smart" (AI, meaning extraction etc.) search over many published papers (specifically, biological) to simplify researchers' live.

Now, I have access to my university library that contains text of many papers from different sources, including those with payed subscription.

Is it legal to download all papers, analyse them and provide search without disclosing full text of the paper, only small part of text or image and with proper citation?


texts: What evidence gives clues to the physiological basis for conversion disorder?

texts:
Conversion disorder has a set of DSM diagnosis criteria, which, among other things, includes ruling out all neurological disease.

However, as the media has shown us (and one could argue a biased portrayal), many of these young people in Le Roy, NY who were diagnosed with conversion disorder have exhibited tics and starts that are highly reminiscent of Tourette's Syndrome, which is thought to have some basis in pathology of the basal ganglia (and perhaps the thalamus and frontal cortex).

Granted, the issue is being looked into as having an environmental cause, so I can understand how the diagnosis may be reshaped, but I'm more curious about the initial diagnosis of "mass hysteria".

If this syndrome causes real physical symptoms and yet is "psychogenic", through what physiological means is the disease acting?  Why would ruling out a neurological basis be a valid criterion?


texts: Writing methods section on PCR amplication in a paper

texts:
Considering that I am writing a paper for a journal, could the following phrase be understood? or should I put the 'step-by-step' way by giving numbers?

PCR Amplification and sequencing

PCR reaction for sequencing with universal primer  ITS5: F: (5’TCCTCCGCTTATTGATATGC3’ and ITS4:R: (5'TCCGTAGGTGAACCTGCG
C3'), including 5,8S rDNA region (White et al 1990). Amplification condition  was performed in a 25 ml reaction volume and consisting of 10 µL nuclease free water, 12.5 µL Tag green master mix, 0,5 µL forward primer, 0,5 µL reverse primer, 0,5 µLDMSO, 1 µL template. Mixture solution  was amplified by PCR machine (Biorad). Thermal cycle programmed for 90 seconds at 95°C as initial denaturation, followed by 35 cycles of 30 sec at 95°C for denaturation, 30 sec at 55 °C as annealing, 90 sec at 72 °C for extension, and final extension at 72 °C for 5 min. PCR products were examined by electrophoresis  at 100 V for 30 minutes in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker used DNA ladder 1 kb.  Electrophoresis gel was soaked in ethidium bromide for 30 minutes then visualized in UV light.


texts: Reliability of SARS-CoV-2 tests - false negatives

texts:
This is about the entire process from sample collection through transportation to lab processing and assessment. In Canada, we are seeing about one COVID-19 test in 10 produce a positive result. Can we be confident that the number of false negatives is negligible? There have been reports of issues potentially occurring at every step which could result in a false negative, from failed collection of the sample to degradation of the sample in transit, to perhaps process or reagent issues in the lab.

Also, is there any possibility of the virus mutating in such a way that what makes it COVID-19 from a public health point of view remains the same but its genetic identity changes enough to no longer be recognized by the existing tests?

Is the testing process from end to end reliable enough that we can trust the reported result be it positive or negative?


texts:
I'm so confused. I used to think Xanthosine is Xanthine with a ribose instead of H but it appears to me as if it isn't. If you look at the picture in top-right of its wikipedia page you will see that the Imidazole is reversed from the picture in here also the picture in the bottom of this page in additional images section is like the second one. I'm sorry if didn't use the right chemical terms! I'm no chemist. Also I while I was searching I saw different images for Adenine and Guanine where the Imidazole loop was reversed in some by reversed I mean like the position of NH and N was reversed with respect to the Benzene loop!

P.S. It would be great if you could also teach me the correct way to ask this question by means of the chemical terms I should use.

P.S.S I hope it is not a wikipedia problem!


texts: Action Potential Distribution On Synapses

texts:
This is a biology+physics question. Since there is no biology section, I am asking here.

In brain, when a neuron reaches to threshold value, it fires an action potential. In most graphics, that is shown as 40 mV. An example is

Neuron's this potential reaches to all synapses where this neuron is connected to, and chemically transferred to other neuron and transformed into electric charge again.

My question is, because in artificial models not shown, if that whole 40 mV is distributed to those synapses according to synapse strengths, or do all synapses take a total 40 mV which is like creating a potential while it is not there?

Another small question is if the collected potential is stored in neuron if it cannot reach to threshold value like a capacitor in circuit?


texts:
All right, I was reading article on nutrition, that focussed on content analysis of pastry-like food product for kids. I have to say that I am not sure this article would pass the imaginary smell test, although it didn't raise any serious red flags, except one.
Among other things, this article said that oxidation means inflammation. It said this in connection with use of rapeseed oil in said product, saying rapeseed oil is less saturated and therefore more likely to oxidize. It then implied, that when this oxidation takes place in the human body, it leads to inflammation.
Now I am no biology, medicine, or nutrition specialist, but if something is still stuck in my head from high school biology, it is that inflammation is the physical manifestation of our immune system fighting off infection, no? Apart of some autoimmune reactions, I don't see how ingesting rapeseed oil could cause inflammation.

So my question is this: is it really possible to safely say: "oxidation = inflammation"? Or is it total nonsense? Or is there some theory that could support such claim and how reliable is this theory? Isn't it just one of those hypothesis disguised as theories?

Said article is in Czech, otherwise I would link it for you.

EDIT: Article link here, you can try it with Google translate :)


texts: I know that it is common to say, "use hot water when washing your hands" or when you've got a cut, "wash your hands with warm water," etc. I was wondering, why is this the case? Since bacteria grow in warm environments, you would think that it might be beneficial for bacteria. Is this just another myth or is this actually true?


texts:
I found this stunningly beautiful Fly in a graveyard in Point Lonsdale Australia.  Can someone tell my what type it is Please.

It was wide as my thumbnail about 3cm long.


texts:
I'm naturally thinking this is a bee, but I cannot find it anywhere in any insect identifiers. I caught this picture on top of my doorway, it's about 1 1/2 inches in length, and its torso seems to be coated in a layer of hair, and the rest of its body is narrow. The thick layer of hair may or may not be accurate, I didn't want to get too close to it, but that's how it appeared at least.

What is this?

PS - Found in Kentucky, and I'm not sure why one pic shows wings and the other one doesn't...


texts: We are trying to figure out what kind of bug this is? It appears to have larvae on its back it is not dust and debris.


texts: why not classify organisms based on genetic distance?

texts:
When learning about "families of animals" in mid-primary school, my son asked me if there is not a better way to classify animals than by looking at them (they were taught that animals are grouped into families based on what covers the skin (hair, feathers, nothing), number of legs, the way they breathe, etc.).

He was wondering if there would be a more quantifiable way of grouping them (this is my wording). I told him that since all animals share the same genetic coding principles, we could try to calculate how different their genetic material is, and derive a "distance". This would allow grouping animals in possibly novel ways, and maybe have some of them cluster in "families" (possibly different from the existing ones).

After having played my role of super-hero-dad, I now wonder if this makes sense? (and if so - is it used? and if so - why still using some classifications from centuries ago?)


texts: Why is one phase of a plant dominant (Alternation of generation)?

texts:
In plants, there is the alternation of generation.

In nearly all land plants, one phase of the two possible phases is dominant--namely the sporophyte.

The "dominance" over the other phase can be seen in the following ways:

The gametophyte organism depends on its sporophyte progenitor, while the sporophyte organism is fine without the other.
The sporophytes are more structurally complex, larger and longer lived.
The sporophytes carry out more activities/functions and receives more subjective attention.

I want to know if there is an evolutionary reason why alternation of generation, one phase is dominant. Here are some guesses:

Zipf's law: as one of the two phases got more complex (start doing more complex jobs) It became more convenient and more likely for that phase to acquire other functions, causing the complexity of that phase to increase with a sort of positive-feed-back-loop, while it became more beneficial for the other phase to depend on the other more and more, to reduce its complexity.
Chromosomal difference: the sporophytes of plants are diploid while the gametophytes are haploid, perhaps one of the two configurations is more efficient?
The sporophyte generation "reproduce" asexually, perhaps this allows it to have a little "head-start" in accumulating non-sexually reproductive functions and became more complex as explained in 1.


texts: I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have some experience how much of sample can I sequence in one run (by coverage around 30) and if it is really for this price?


texts:
I have a question. Given a molecule A and two isoforms of a gene X, Y, and the knowledge that A targets X. Can I infere from this anything about whether A targets Y?

As a motivation think about Furosemide (= A) and SLC12A1, SLC12A2. From Drugbank I know that Furosemide targets SLC12A1, and from KEGG I know that Furosemide targets both genes. I wonder whether I can infer the KEGG knowledge already from the Drugbank knowledge...

Best,
Alex :)


texts: How bad is ethidium bromide in your plasmid for downstream applications?

texts:
I want to transfect Adipose Derived stem cells using a clone of my own. My problem is that I get a lot of contamination (not only genomic, but due to the nature of the technique, I get undesired products I haven't been able to get rid of).

So I was thinking about running a gel with my plasmid DNA samples and gel purify my desired bands. I don't know, however, if Ethidium Bromide contamination in my sample would be a problem or if a regular gel extraction kit gets rid of it.


texts: Does antidromic conduction occur in the brain under normal conditions?

texts:
So I am reading a book on neuroscience and they mentioned in passing that the action potential is capable of travelling in either direction along the axon (orthodromic vs antidromic), The wikipedia antidromic article states that the effect is often used to confirm connections in laboratory experiments.

What I'm now wondering is if the phenomenon has been observed with normally behaving neurons in situ (as normal as a neuron under experimental observation can be anyway) and therefore possibly needs to be factored in when modelling neurons in software or is it safe/justified to treat the information as only flowing in one direction (orthodromic)?


texts: Is extreme cladism a mainstream position in the species debate?

texts:
In the philosophy of biology it has been claimed many times that a popular position regarding the question of what species are, among biologists, is cladism. For my current purposes, the defining trait of cladism is captured in the following quote:

According to cladism, a species becomes extinct whenever it sends forth a new side species. (LaPorte 2004, 54)

So, for example, if Homo floresiensis is truly a species, and it derives, via a speciation event, from Homo sapiens, then, after the speciation, there is no Homo sapiens: there is Homo floresiensis and a new species, very similar to sapiens. In general, whenever there is speciation the mother species disappears.

I am under the impression that this description of the situation is not the one most mainstream biologists would endorse. I take it that a more common description would be one under which, if a number of Homo sapiens get isolated in an island and go on to form a new species, Homo sapiens exists both before and after this speciation event. I would like to know whether cladism, described as above, is really a popular position, or whether I am right about what most biologists would say about the relation between floresiensis and sapiens.

It might also be that biologists declare themselves cladists when explicitly theorizing about the nature of species, but fall back to a less extreme form of cladism in the actual practice. Evidence in favour of or against this possibility (coming from biology, not the philosophy of biology) would also be appreciated.

As Noah has pointed below, what I have called extreme cladism might be very far from cladism, as usually interpreted. This is precisely the kind of claim I would like to see substantiated.

  LaPorte, Joseph. 2004. Natural Kinds and Conceptual Change. Cambridge University Press.


texts: I noticed a tiny spot with weird shape on the shoot of a plant (Variegata), and there are many others on other branches. I wonder what is it, this is a cropped picture of it, Thank you!


texts:
Background

In all eutherian (mammals excluding the marsupials), the female (who is $XX$ for the pair of sexual chromosomes) inactivates one of her $X$. This is called dosage compensation. This inactivation occurs at a given time during the development when randomly one $X$ is silenced. The daughters of this cell inherit the $X$-inactivation pattern epigenetically, which results in some part of a tissue having the maternal $X$ inactivated while others having the paternal $X$ inactivated (daughters of some other cell which silenced the paternal $X$). This process yield to the famous turtoiseshell coat in female cats.

Question

In short

Assuming X-inactivation occurred in the lineage of the oogonia/oocytes, when does the X-inactivation and X-reactivation occur in the lineage of the oocytes?

A bit developed

Are the X inactivated as well in primary oocytes? If not, is the $X$ inactivated in the secondary oocytes in a primary follicle? If not, did the diploid mother cells of the secondary oocytes have one $X$-inactivated? If yes, did all diploid mother cells of oocytes have the same $X$ inactivated (inactivation occurred relatively early in the development or is there an imprinting) or did the mother cells of oocytes differ in the $X$ they have inactivated (inactivation occurred relatively late in the development)


texts: Architecture of lamellae in trabeculae in spongy bone

texts: It is easy to find the architecture of lamellae in osteons in compact bone, they're layers of collagen fibers and each layer alternates in the angle the fibers are oriented. Is the lamellae in trabeculae similar, and the main difference that there isn't a central blood vessel to supply the bone cells with nutrients, since that is done trough the marrow instead?


texts: What species is this large bug? (South India)

texts:
I found this bug in South India. What species is it? The tiles in the picture are 5x5 centimeters each. The bug was moving relatively slowly and didn't seem to fear me much.

I tried asking it directly, but it kept claiming to be a feature.


texts:
I'm having problems with data analysis here.

I have flow cytometry data being collected on a Fortessa, and when I import them into FlowJo 8.7, all of my fluorescence values are systematically 10X lower than they are on the cytometer. No idea what's going on here, anybody can help? If you want screenshots and photos of the data, I'm happy to post them up.


texts: How does fluid pass through the glial limitans into the subarachnoid space?

texts:
I have often heard that the cerebrospinal fluid (CSF) and interstitial fluid (ISF) are in free exchange. Because the CSF eventually drains (predominantly) into the dural venous sinuses, ISF's ability to access the subarachnoid space actually allows the brain to eliminate metabolic waste products that would otherwise remain the parenchyma. ISF presumably accesses the subarachnoid space, mixes with the CSF, and eventually, through arachnoid granulations, drains via the dural sinuses.

While that is fine and dandy...there are two layers that the ISF must first pass in order to access the subarachnoid space: the glial limitans and the pia mater.

How does ISF pass through the foot processes of astrocytes, which comprise the glial limitans? Does the H2O remain largely in the parenchyma while waste metabolites are selectively transported across the astrocytes and into the small spaces between the glial limitans and pia mater?


texts: Are neurotransmitters part of the endocrine system?

texts: I was speaking with a substitute teacher of mine, and we were discussing whether neurotransmitters are part of the endocrine system or not. My class just spent an entire semester on the topic of the endocrine and nervous systems. From my knowledge, they are not part of the same system, because they function very differently and they are not activated by the same triggers. Does anyone have any info on this subject? I am interested what the case is an why.


texts: How many centrioles/basal bodies are there in multi-ciliated cells throughout the cell cycle?

texts: I thought there were only two centrioles per cell, that convert to the basal body at some point during the cell cycle. I also thought there's one basal body per cilium, so I'm not clear on where the other basal bodies are coming from. I'd like to know the distribution of basal bodies and centrioles throughout the cell cycle in multi-ciliated organisms/cells.


texts: Are gizzard muscles voluntary or involuntary?

texts:
I started raising chickens this year. They have amazing appetites, and I often wonder what eating is like for them. They have no teeth, so they don't chew their food as they eat it. They do seem to have some sense of taste, because they often bite off a bit of something and then spit it right back out. But the only equivalent of chewing for them occurs in their gizzard. Because the gizzard is pretty far down the digestive tract, I would assume that it's an involuntary muscle. But all chewing being unconscious for them also sounds kind of crazy.

I'm trying to discover the answer to this question on the internet and I'm surprised that the answer hasn't been easier to find. Does anyone here know? Do birds masticate unconsciously?


texts: What's superposition and thread in RosettaCM?

texts:
I'm a beginner in structural biology.
I had a question while reading a paper on RosettaCM.
What does RosettaCM's superposition and thread mean?
I googled it.
As a result, the following results were obtained.

The term structural superposition refers to rotations and translations performed on one molecular structure to make it match another structure or structures. Inherent in the definition of structural superposition is an assumed measure of structural similarity. The optimal superposition is the one in which this similarity measure is maximized. Alternatively, one can define superposition in terms of a difference measure, such as root-mean square deviation ( RMSD ). In this case, the optimal superpositon is one in which the RMSD is minimized. The program ASH uses the former approach with similarity defined by the NER score.
Also, implied in any superpositon is an alignment, or mapping, between points in one structure (usually atoms) and those in another. Sometimes alignment and superpositon are used interchangeably.

Is this correct?
I also think of threads as part of a protein segment, is this correct?
In other words, in Rosetta CM's 1-step Global Superpotion, after aligning, the templates are stochastically determined, and the unselected templates are superposed so that RSMD is smallest.
Furthermore, the superposed template is a thread.
Is the above correct?


texts: How do you remove DNA/RNA from plastics?

texts: I want to know how to make plastic containers free of DNA & RNA? this is just for knowledge


texts: Was the mitochondrion or chloroplast first?

texts: I still don't  know if the mitochondrion or chloroplast was first? I've looked for it on the internet and in various books but haven't found anything. Does anyone have the answer and a theory which backs up this answer?


texts: MAPK signalling pathway initial conditions

texts:
I would like to know the initial conditions and locations of the chemical reagents in the MAPK cascasde.

I'm going to plug this information into a reaction diffusion simulation.

From reading various papers I have gleaned the following:

[MKKK]total = 100nm; [MKK]total = 300nm; [MAPK]total = 300nm

MKKK]total = [MKKK] + [MKKK-P]
[MKK]total = [MKK] + [MKK-P] + [MKK-PP]
[MAPK]total = [MAPK] + [MAPK-P] + [MAPK-PP]

Ras-GTP seems to have an initial concentration of 30 nM and seems to start at the nucleus.

ppMAPK seems to have an initial concentration of 0.

I can't figure out where the rest of the reagents start and what thier concentrations are. People always seem to miss this out from their work...

Thanks


texts: What kind of insect does chirp like this?

texts: I live in Japan. Recently I hear chirp coming from Wisteria floribunda at every night. Please check this sound that I uploaded for this question.


texts: Identifying whether amino acids are hydrophobic or hydrophillic

texts: How do you figure out whether an amino acid is hydrophobic or hydrophilic? (other than memorization) I know that it has something to do with the R groups of the amino acids, and that polar molecules are hydrophilic, while nonpolar molecules are hydrophobic, but that's about it. Please give a simple answer, I don't need too much information other than an easy way to tell.


texts:
Why do I not have any cells left in my positive panning plate after transferring from the negative panning plate during immunopanning? I am trying to purify retinal ganglion cells from postnatal rats and use a Thy1.1 antibody harvested from a hybridoma cell line supernatant in the positive panning plate.

Following transfer of the cell suspension from the negative to the positive panning plate there are no cells in the pre-trypsinization supernatant, nothing stuck to the panning plate, and no cells in the post-trypsinization supernatant so I have no idea where they could have gone. Checking the negative panning plates however shows that there are many cells stuck to those plates, so could my RGCs have been lost at some point during the transfer and when?

Thanks v much in advance for your help.


texts:
A prototrophic Hfr strain of E. coli with the genotype trp+ purB- pyrC+ is conjugated with an F- strain with the genotype trp- purB+ pyrC- . The trp gene is known to enter last. The following numbers of recombinants were isolated:

trp+        purB-    pyrC-       [0]

trp+        purB+    pyrC+       [44]

trp+        purB+    pyrC-      [132]

trp+        purB-    pyrC+      [224]

Draw a genetic map that shows the order in which these genes are arranged and the distances between them.

I started off by making these assumptions:

trp+        purB-    pyrC-       0  (the lowest #, must be double recombinant(DC)

trp+        purB+    pyrC+       [44](must be single recombinant(SC)

trp+        purB+    pyrC-      [132](must be single recombinant(SC)

trp+        purB-    pyrC+      [224](the highest #, must be parental(P)

Now since i know which one is DC and which one is P I can find the middle gene:

trp+        purB-    pyrC+  (224)- P

trp+        purB-    pyrC-  (0)-  DC

The only gene that varies is pyrC thus PyrC is the middle gene.

Consequently, the distance from trp-->PyrC=(DC+SC)/400=(0+44)/400= 0.11 or in map units it becomes 11

similarly, the distance from pyrC->pur B=(0+132)/400=0.33 or 33 m.u.

and here's the part im confused about: I only have 1 parental and i cant make the cross to figure out which is  trp-->PyrC and which is  pyrC->pur B. Even though i'm confident i got the right numbers how do i figure which one is 11 and which one is 33???

ps: I know it's a silly question after solving 99% of the problem it just that im used to do mapping with 2 parentals that i get lost when there is only 1 parental.

EDIT:

I actually figured it out, its not a regular genetic mapping problem but the bacterial genetic mapping(in particularly High resolution mapping). Thus, all the steps above are correct and answering my own question the way to figure out which direction it goes is just to compare the parentals given:

trp+ purB- pyrC+

_X_____X____X___

trp- purB+ pyrC-

(NOTE: ignore the trp minus since we solve for it)

doing the crossovers will yield the same results listed above,its just that it's more precise way to know which one is trip --->pyrC and which one is pyrC--->purB

PPS:SMC Bio 22 students doing problem set 1 in the future, you can thank me later.


texts: Are intestinal and pancreatic lipases different?

texts:
For explaining the action pancreatic lipase, my book wrote this equation:-
$$fat\space particles + lipase\rightarrow fatty\space acid + glycerol + lipase$$
But for intestinal lipase, my book has a different equation:-
$$fat\space particles + lipase\rightarrow monoglyceride + fatty\space acid$$
So, did my book make a mistake or are intestinal and pancreatic lipases different?


texts: Does Pseudomonas aeruginosa have any common name at all?

texts:
Pseudomonas aeruginosa is the fifth most written about¹ binomial name of all species. I'm having trouble coming to terms with the possibility that such a well researched and studied organism has never been given a shorter vernacular name. I can't find one listed anywhere.

Is there any short common name for it? Even a colloquial one? Maybe a pet name common to microbiologists or students in the labs of some particular region? I'm mostly interested in English but how about in other languages?

I am aware it can be abbreviated to P. aeruginosa. I don't consider that a common name. Pseudomonas by itself refers to a genus of around 191 species.

¹ "most written about" meaning mentioned in the most books or volumes of Google Books' English corpus (ngram data), according to my own research. The top five are: Homo sapiens, Escherichia coli, Staphylococcus aureus, Candida albicans, Pseudomonas aeruginosa.


texts: Cigarette consumption dose-response function WRT health outcomes

texts:
I'm curious how health risks (mortality, lifetime probability of cancer, etc) change with cigarette consumption.  Specifically, treatring cigarette consumption like a continuous variable, rather than a binary for "smokers" and "nonsmokers".  I've got access to academic literature, but I'm not a doctor or a PhD health researcher.  This article states in the abstract that the dose-response relationship between cigarettes and incidence of lung cancer is linear.  This website (CDC) states that "smokers" have a 25-fold increase in risk of lung cancer.

How to reconcile the two?  The latter reports odds ratios, which means that they did a logistic regression, which means that the raw logistic regression coefficient was 3.2.  If the average smoker smokes 20 cigarettes a day, and the dose-response relationship is linear, then the relative risk for someone who smokes one per day should be exp(0.32) = 1.37.  So someone who smokes one cigarette per day would be 1.37 times more likely to get lung cancer than someone who never smoked (on average).

Is this a reasonable estimate?  I can certainly understand why public health types wouldn't promote this sort of conclusion, as smoking one cigarette can be a slipper slope to smoking a lot more cigarettes.


texts: What decides between the synthesis of eumelanin and pheomelanin on a biochemical level?

texts:
MC1R is a very well known gene where a loss-of-function mutation will cause the synthesis of pale/redish pheomelanin instead of black/brown eumelanin. MC1R is only a receptor which doesn't directly participate in the synthesis. it affects the expression and transcription of several important enzymes for melanin synthesis (Tyrosinase, TYRP1, TYRP2).

In one study (Ito, 2003) they proposed that increased tyrosinase activity and decreased cysteine levels would promote the snythesis of pheomelanin. Since MC1R controls the expression and transcription of tyrosinase I think it makes that mainly the increased tyrosinase activity is responsible for the decision between eumelanin and pheomelanin.

The question is whether this is correct or false or if we just don't know yet.


texts: What kind of mushroom is this, and is it edible?

texts:
I found these growing on the side of some trees (mostly birch) in my local forest in Gothenburg, Sweden, and was wondering if you could help me with identifying them.

I think they smell of aniseed however my wife thinks they smell of farm animals!

The spore-trace turned out white, if that aids with identification.


texts: Inbred mice has no severe phenotype outcome?

texts: Why does 20 generation of inbred mouse have no particular strange phenotypes, but on the contrary, when on purposely inbreed dogs or tigers for specific phenotype cause severe deformation of the bone structure or cranial structure?


texts: Does a piezoelectric organic substance exist?

texts: that contracts rapidly, in 10 seconds or less, by .5mm or more, when bombarded by electrons as from a cathode ray tube? or expands? could either be living tissue or dead organic matter.  thanks!


texts: I'm trying to get a very in-depth idea of the ecosystem of Pleistocene Europe, somewhere around 40,000 years ago, and I can't seem to find what types of foliage (other than the obvious grasses and lichens) grew in that place and time. I'm particularly interested in the species of tree that were present; can anyone help?


texts: Spatiotemporal patterns in neural networks

texts:
It turns out that my work in nonlinear dynamics directly maps to a close variant of the Integrate and Fire model. My model produces spatiotemporal patterns that resemble foam. I have to stress that this is  the result of an exceedingly simple model of neuronal activity.

The plot below visualizes the voltage levels of a network of neurons. Yellow is high, purple is low.

I am wondering is these patterns are relevant to the computational neuroscience community. To this end, I am looking for literature describing spatiotemporal patterns in (preferably biological) neural systems.

I am especially interested in any work that  proposes metrics that characterise such patterns since this would allow for a quantitative comparison with my results.

Forgive me is this seems trivial to you, but coming form complex systems theory I did my best and found nothing.


texts: Simply question, do snail show when it's raining because they like it or/and need hydration and food or are they showing up just to escape somewhere, because they're scared of drowning?


texts: How does a RNAP locate a specific gene? For instance, growth hormone has to be produced and the RNAP has to locate the gene. But the promoter (TATA box) will also be present infront of all cistrons. So how does the RNAP choose the specific gene? Are the promoters specific for specific gene?


texts: Why do some organelle (like ER and Golgi complex) cannot be seen under microscope during cell division?

texts: I have recently read in a book that organelles like ER (endoplasmic reticulum) and Golgi Complex cannot be seen under a compound microscope during cell division. Why does this happen, and where do the organelles go during that time?


texts: What is the present tense verb form of apoptosis?

texts: For example, if I want to say something along the lines of "this signaling pathway causes a cell to go through the process of apoptosis", but I want to shorten the phrase "go through the process of apoptosis" to one word, what would that word be? I've been saying "apoptose" so far but I'm not sure if that's correct.


texts: How to Determine the Most Conserved Sequence from BLAST Result?

texts:
I used BLAST to find the best aligned DNA sequence to my query sequence.  The BLAST result shows a number of sequences that it calculated to be the best aligned sequences to the query sequence that I give.  Each of those aligned sequences have an e-value score representing the best hit by chance.

My question is how can I determine if the query sequence is highly conserved with the aligned sequence, or not?  Can I determine that by saying the sequence with best hit e-value (lower e-value) is the one that is highly conserved? or are there other concepts that I need to consider in this case?

I appreciate your help!


texts: Can oncogenesis happen without apoptosis pathway being affected?

texts: Has there ever been incidences of one or more cancerous cells having all it's cell-death pathways and apoptosis mechanisms intact and functional?


texts: Why only able to close one eyelid? Genetic reason?

texts: Eye-dominance is a critical thing with bows: right-eye-dominant is recommended to do the aiming on the right eye here otherwise inaccuracy. This made me think whether all people are even able to do this. I have seen people who can only close one eye or two eyes at the same time but not two eyes separately. What is the factor determining this? Is this determined by genes, learning or by something else? Is it possible that the other side of the eye muscles are missing because they have not been needed for the survival? I discussed missing muscles with my medical friends and they mentioned that there are muscles that some people do miss such as in hands because they are not essential for survival. I don't know whether certain muscles in face could be missing with some people or is this just learning thing?


texts: Identify this giant green moth(?) with great taste?

texts:
One evening in late February I sat down to eat dinner after a day of hiking in hills around New Taipei City and discovered that someone else shared my taste in clothes. A very large green moth-like insect had landed on my pants with a green floral pattern. The inset in the first photo shows that the body was about 5.5 centimeters long. Included are additional cropped top, side and front photos, the top one without flash for a better appreciation of the colors.

It frightened me at first because it was just sitting there and I have no idea how long I'd been walking around with it. After it's photo shoot I brought it outside and located some bushes and was able to convince it to move. It seemed quite sluggish though it wasn't very cool yet (I estimate perhaps 22 C)

Can anyone identify this obviously style-conscious insect, and speculate why it was lethargic and not interested in flying away?


texts: Can a brown recluse bite lead to diabetes?

texts:
Ok, I realize that this question may seem crazy at first glance. I would agree. Also, this does deal with a medical diagnosis, however, as I'm more concerned with the explanation behind it, I figured it fit in this category the best. Feel free to move this question (or suggest a better bit) if this is incorrect. On to the question...

Apparently (according to a friend of mine) this person woke up in the morning, could barely move, had a bite-like sore/mark and went to the hospital. Doctor said it was a brown recluse bite and as a result of the incident, this person now has Type 1 diabetes.

It really doesn't matter how (the result is still living with diabetes), but I'm fascinated by this incident and, being neither an expert on spider nor diabetes, I would like to know if this is plausible and, if so, how?

I realize that (1) approximately 80% of brown recluse bites are misdiagnosed and (2) I will never have access to their medical records, but let's operate under the assumption that this was as reported.

From what I've been able to find, in very rare cases, brown recluse venom can result in viscerocutaneous lexoscelism, which may lead to acute kidney failure... but through my research, I can't seem to link that to diabetes (the converse is easy, as diabetes is one of the leading causes of kidney failure).

What (if anything) am I missing?
Is there another response to Lexosceles toxin that can lead to diabetes?
If this isn't possible, what could be an explanation that would cause diabetes but look like a brown recluse bite to a doctor?


texts: What are the various types of protein-protein interactions

texts: I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?


texts: Which was the first DNA-based genome to be sequenced?

texts:
The Wikipedia article on phi X 174 states that:

The phi X 174 (or φX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA-based genome to be sequenced.

But, the article in Wikipedia on Whole Genome Sequencing states:

The first whole genome to be sequenced was of the bacterium Haemophilus Influenzae

So as bacterial genomes are DNA-based, I am confused as to which organism was the first DNA-based one to be sequenced.


texts: Can human mRNA be translated in vitro by prokaryotes?

texts: As the genetic code is universal, can mRNA from a human cell be correctly translated by a prokaryote in a in vitro translation system?


texts: What is the speed of blood in when flows through the fingertip?

texts: What is the average speed of blood as it flows through the index finger on the right hand?


texts: Can anyone advise me a literature supporting the claim that Encephalitozoon cuniculi is an aerobic organism? I have seen papers saying otherwise, but also I was told that this is not quite true.


texts: Are there any "in vivo" DNA replication fidelity assays?

texts:
I haven't been able to find a way to assess the fidelity of DNA replication in vivo as opposed to in vitro. I was wondering, would it be possible to find this by sequencing the DNA of individual cells after they have replicated a certain number of times?
For example, could you:
(1) Have a cell replicate N number of times in vivo
(2) Sequence the DNA of a cell that went through 0 replications and the DNA of a cell that went through N replication
(3) Compare the errors between the DNA of the two cells
(4) Determine the error rate of DNA replication for each cell division by counting how many different base pairs are in the cell that went through N replications and factoring in the error rate of the DNA polymerase being used in PCR
Please let me know if this is feasible, if it has been done before, or if there is another way to do this. Any help is much appreciated.


texts: What would cause bands to appear lower on a nonreduced SDS-PAGE gel?

texts: I have a protein gel and I'm comparing the reduced with the non-reduced gel. On the reduced gel, I have a few shorter bands but these bands appear with low intensity. In the non-reduced gel, I'm seeing more of the shorter product? What would case the protein to run "smaller" in the non-reduced conditions?


texts: What is the radius of the Ora Serrata and lens in rabbits?

texts:
I'm interesting in estimating the surface area of the hyaloid membrane connecting the vitreous and aqueous chambers. This is a crude estimate however i'm struggling to find parameter values for rabbits.

I have estimated in humans the radius of the Ora Serrata, measured from the
centre of the lens, to be 1 cm. The radius of the lens to be 0.5 cm, giving the surface area of the region between the two to be roughly 2.36cm^2.


texts: How is a very small quantity of poison able to kill a large organism?

texts:
Take cyanide for example: it prevents mitochondria from producing energy in form of ATP but, in the process, it binds with it and hence it's spent.

It's theorized that half a gram of cyanide can kill an average adult human. How is this possible? There surely is more than half a gram of mitochondria in an adult human. So, if cyanide molecules bind and hence get spent so fast, how are they able to kill so many cells so fast and continuously?

Is it something to do with the amount of molecules in half a gram of cyanide being several times higher than the amount of cells in one gram of human tissue?


texts: Why do cells in the cerebral cortex act as interacting nonlinear oscillators?

texts:
I'm not a biologist, but I'd like to know something about EEG analysis.
In particular, I have read that EEG signal derive from cells in the cerebral cortex and hippocampus. And that these cells act as many interacting nonlinear oscillators.

I'd like to understand why they are oscillators and why their behaviour is nonlinear. Many thanks for the help!


texts: Why must DNA be packed into chromosomes during mitotic phase?

texts: Why does DNA have to be packed into chromosomes? Why can't DNA just divide itself evenly?


texts: Why does snow not stick to the fur of wolves and some breeds of dogs?

texts:
This question made me wonder, why for example wolves don't suffer from these "paw snowballs"?

  (...) but after a few miles on the trails in soft snow, he often develops snowballs between his paw pads - usually one big one right in the middle. (...) I have heard really bad snow buildup can lead to raw/bleeding paw pads.


texts: Where are the genes of proteins that make the electron transport chain of mitochondria?(are they in in the nucleus or they are in the dna of the mitochondria itself?) Thanks for this answering system by the way


texts: How are cells that have died replaced by new ones?

texts:
I'd like to have a clearer picture how cells that have died are replaced by new ones.

I assume the following:

Normally, when a cell dies it will be replaced by a new one of the same type.
It will be replaced by the division of another cell (of the same or another type). One copy remains where it is and keeps its type (for later use) and the other one possibly travels to its target location (where the died one has lived) and possibly changes its type (during travel or after arrival).

My questions are:

Are these assumptions essentially correct? Or are they overly simplified?
What are possible distances between the regenerating dividing cell and the target location? I assume some static cells will be replaced in situ, possibly skin cells. Others may be regenerated far away, especially floating cells, like blood cells.
If the distance is large: How does the regenerating cell know it has to divide? And how does the regenerated copy know where to travel to?
When one of the copies of the regenerating cell starts to travel,why doesn't the other?
Are there cases where the regenerating cell is already of the same type as the cell that has died – and so are its two copies?
What about the (programmed) lifetimes of the regenerating cells?

I hope these questions - which would give me one consistent picture - can be answered in one comprehensive answer.


texts:
Afaik GMO products are not a real risk to health of course if they do not contain toxins.

But how about cancer cells? Like say rhabdomyosarcoma which is more or less a muscle cancer found also in cows.

Likewise, meat breweries use stem cells, but wouldn't cancer cells just grow faster?


texts: Is there a way to prevent an HIV infection after exposure to HIV infected Blood?

texts: If a person is accidentally injected with blood from an HIV+ person, is there a treatment option that can keep the person from developing an HIV infection?


texts: Can you use a microscope without an eyepiece?


texts:
I've been reading through Paulsson (2002) and I am not sure what he means by "lineage selection" in the second to last section. The paper deals with plasmid replication, and mostly concentrates on the contrasting pressures from two levels of selection:

intracell selection - competition between plasmids in a single cell. A plasmid can undergo a cis-mutation and over-replicate, resulting in a higher intracell fitness than the focal plasmid. The plasmids reproduce.
intercell selection - competition between cells. Cells with a heavier load of plasmids will take longer to reproduce, and plasmids that produce a heavy load will have lower intercell fitness. The cells containing plasmids reproduce.

In this context, what does the third level of selection -- lineage selection -- mean? What reproduces? How do the lineages split or interact?
My guess
Does lineage selection simply mean group-selection on separate colonies of cells? In that case, how are new lineages formed? I would expect this group level to select for zero levels of plasmids (since they place no loads on the cells and thus these groups of cells will grow the fastest), but Paulsson (2002) suggests the opposite:

lineage selection could favor plasmid traits that help the population of plasmid-containing cells to fight plasmid-free cells.

Is there a more detailed discussions of this available than the one section in Paulsson (2002)? Neither the unit of selection nor either the evolutionary or genetic lineage Wikipedia articles address my question. The first only mentions lineage in passing, and the second two don't discuss models of selection.

References
Paulsson, J. (2002). Multileveled selection on plasmid replication. Genetics, 161(4): 1373-1384.


texts: How to select a microscope for deep microscopy? Specifically for Deep Learning/ML model development

texts:
I am new to biology and microscopy. I am a data scientist. I am faced with a question on selecting a good microscope that enables automation of scanning the slides. And cellular object detection using deep learning.
Considering, my lack of background I am only looking at the resolution of scanned output and the ability of the microscope to provide images that can integrate with a workflow that I am about to develop. As one of the first applications, I am looking to detect sperm cells stained with Christmas Tree stain (head = red/pink, tail = yellow/green) using brightfield microscopy.
What are the other criteria I should worry about? What questions should a data scientist ask?
Any general advice will also be valuable.


texts: Fluorescence assays to identify protein concentration without adding a large peptide sequence?

texts:
I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. However, GFP and its cousins are very large proteins that would change the properties I'm targeting for purification, making them non-starters.

Is there a tag that through fluorescence, colorimetrics, etc. can be used to quantify concentration of a single protein while minimally altering chemical/physical properties of the protein for purification?


texts: How to refer to person-derived and place-derived species names

texts:
Are there words that categorize latin specific epithets by how they're derived? Specifically, I was wondering if there exist adjectives to refer to:

Person-derived species names as in Nothura darwini (these could be "eponymic" or "eponymous" perhaps, but that seems grammatically wrong )

Place-derived species names as in Amolops hongkongensis (would these be "toponmyous", or maybe "loconymous"?)


texts: Differential Scanning Calorimetry for bacterial membranes

texts: I would like to study the freezing and melting of bacterial membranes and would like to use Differential Scanning Calorimetry (DSC) to obtain the glass transition temperature of the membrane. However, I am unsure where to find such protocols describing the process. Could someone please tell me how to use DSC for bacteria such as E. coli?


texts: If re-boiling does not curdle the milk, can that be taken as an indicator that the milk hasn't developed the bacteria (and their toxins)?

texts:
Usually when left in hot temperature, the milk curdles (which I know when I boil it and it starts separating).

If the re boiling does not curdle the milk, can that be taken as an indicator that the milk hasn't developed the bacteria (and their toxins)?

This is the milk that I use.
http://www.amul.com/products/amul-taaza-info.php


texts: the macrophages are pretty known well for antigen presenting process and to present the antigens which are bound to pathogens unlike exotoxins (which are free) the pathogen first should be digested and destructed and derive the antigenic portion and present it to T cells then stimulate the B cells to make antibodies. If the macrophages can destruct and digest the pathogen to derive the exact antigenic portion so then whats the need of humoral immunity to be activated because they have already destruct and kill the pathogen if your answer is that the pathogen gets knocked out quickly by antibodies for the second if they invade,so there are millions of other infecting agents every day         invading our body and are omitted by the first line defenses?


texts: An offspring is 23 chromosomes of mother and 23 of father, if one of the mate learns say music after the birth of their first child— will their second offspring have better music skills than former? about my knowledge of biology, so far I read about DNA, Genome, chromosomes and genetic engineering, I am an engineer by profession.


texts: What does it mean by “end effects can be ignored”

texts:
I have been reading a book ( Statistics for Biology and Health) and i encountered many of following bold text.

Consider a long DNA sequence of length N, where N is assumed to be
so large that end effects can be ignored in our calculations.

In Shotgun sequencing also the saw similar thing :

The fragments are assumed to be taken at random from the original
full-length sequence, so that if end effects are ignored, the left-hand ends
of the fragments are independently distributed with a common uniform
distribution over [0,G].

What does " end effects can be ignored " means?


texts: Are added yogurt cultures harmful to the gut?

texts:
I have read somewhere that the live culture added to yogurt acting as "healthy" gut bacteria are actually synthetic and harmful.

Any truth to this? If so, what are some alternatives to getting good gut bacteria?


texts: Genetic information storage and the extent to which it controls appearance/structure

texts:
So there are often articles about cloning from a small piece of tissue etc.

My question is (two actually) Is the Complete information about entire organism's structure stored (as in duplicated) all over the body? And is everything actually stored/based on DNA information, such as number of hairs you have including their position and texture. That would be a lot of information, I mean just taking hair as an example and its quantity and position, but there are also things about every aspect of structure, from bone composition, to position of organs, veins etc. None of it is random (ignoring mutations aspect) and all of it has to be "programmed" in initially. How can this be possible when the number of specifications is so huge?


texts: How well does it actually work to surgically reroute the optical nerve?

texts:
Two publications, Roe et al, 1992[1] and Metin & Frost, 1989[2], describe results pertaining to the ability of a region of cortex to process information from a different sensory mode than the one that it normally does.

Specifically, they describe studies in which:

input from the retinas of newborn rodents was rerouted, by
surgical methods, to parts of the cortex other than the visual;
the rodents were allowed to mature;
the responses of cortical cells in the new target region to visual stimuli were assess.

Now it's 20 years later, so I'm sure there have been many others.

Something of which these publications seem to make no mention is the behavior that developed in the test subjects. For example, did they appear to be completely blind from a behavioral standpoint?

Is anyone aware of any publication, relating to these studies or other, similar experiments, which addresses this question?

Roe AW, Pallas SL, Kwon YH, Sur M. 1992. Visual projections routed to the auditory pathway in ferrets: receptive fields of visual neurons in primary auditory cortex. Journal of Neuroscience, 12(9): 3651-64.
Métin C, Frost DO. 1989. Visual responses of neurons in somatosensory cortex of hamsters with experimentally induced retinal projections to somatosensory thalamus. Proceedings of the National Academy of Sciences USA, 86(1): 357-361.


texts: Does gene editing have any technical cross-species limits?

texts:
How far could you go in cross-species gene editing?

Is it possible for example to introduce plant genes into human DNA and vice versa?

Question: How is gene editing limited by the "donor" and "target" species?


texts: How do chemists calculate the existence of billions of organisms?

texts:
So the packaging of Bio-Cultures Complex says that it contains a minimum of a billion viable organisms per capsule.

How has such an estimate been drawn?

Have they counted a smaller amount and then multiplied it?


texts:
In many grasses, tillers develop roots at their nodes etc.. Those roots can hit the ground and subsequently anchor in the soil, so eventually the tillers end up like something that is very hard to separate from stolons (I often see this in Agrostis gigantea).
Are there objective criteria for separating tillers and stolons at all times?


texts: How do processes of one osteocyte establish contact with processes of the adjacent cells within the mineralized matrix?

texts: Are the processes and canaliculi formed and contacts established after the osteocytes are embeded in the matrix or are they formed during the embedding process itself. Is there any evidence to suggest either?


texts: What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?

texts: What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association with a report generation.


texts: What was the first known organism to exhibit muscle growth based on activity?

texts:
Being able to grow bigger muscles to match an organism's personal habits seems like a pretty nifty feature since most organs grow to one specific size, aside from some stretching.

Was this a feature as long as muscle tissue has been around? If not which species had the ability first?


texts: Experiments on abiogenesis in laboratories

texts:
Has any scientist created an organism in a laboratory using the primitive kind of Earth's environment, like the one used by Miller, etc.?

I read that protobionts (coacervates and microspheres) have been created in the lab by Alexander Oparin and Sidney Fox respectively. I also read that these were not 100 percent living.


texts: Why is the body cooled during cardiac surgery?

texts:
When undergoing cardiac surgery, the heart is disconnected from the blood circulation and blood is passed through a heart-lung machine and cooled so that the body temperature of the patient is reduced.

I understand that this would slow down metabolic processes but how exactly does slowing down these processes benefit the patient?

Thanks for answering!


texts: How are light sheet microscopy 3D images and their computed sections built up from stacks of 2D images?

texts:
The iBiology Techniques video Microscopy: Dual-View Inverted Selective Plane Illumination (diSPIM) (Hari Shroff) describes light sheet microscopy and the improvement in resolution by introducing dual-view (two cameras) capability.

What's happening is that the object is moving randomly in 3D, and so for each frame, the stacks are used to generate a 3D image, and then it is de-rotated to synthesize a view in a plane fixed to the object, rather than the microscope.

Is there a simple way to understand how these image stacks are processed to obtain a smooth 3D reconstruction that can then be sectioned computationally? Is there some kind of interpolation or modeling of structure at the limit of the depth resolution?

Rather than a complete explanation, which would likely be fairly mathematical and in depth, a simpler explanation plus a reference or link to a more in-depth description might be a better way to help me get on the right track.


texts: How many smaller muscles compose the interosseus muscle in the human hand?

texts:
When looking at Wikipedia, I read that the interosseus muscle is actually composed of 3 muscles, but on the French Wikipedia, they talk about a 4th muscle.

So how many interosseus muscle components are there, 3 or 4?


texts: Have lumping/splitting criteria for animal genera historically depended in practice on how similar they are to humans?

texts:
This is a history of science question, hence the history tag. I've heard it claimed that if genus Homo had not included our own species, then objectively the genus would have included multiple other living primate species, such as chimps, gorillas, and orangutans. This seems like a hard claim to evaluate, since AFAIK there are no absolute criteria for how to split or lump species into genera. However, I think one way to get at it is the following.
Some animal species, such as beetles, were historically seen as being lower on the medieval chain of being, and others, such as dogs, were higher. If this caused a bias, then we should see that, for example, the number of species per genus would be higher for animal species that were more distantly related to us. Or we might be able to get at this by looking at, for example, the distance T1 back in time to our most recent common ancestor with a certain genus, and see if that correlated with the distance T2 back in time between different species in that genus.
Is this actually true at all?
Or does this actually correlate more with whether the species is extinct and whether it's important or familiar to us? I've heard it said that if dogs had been known only from fossils, then they would have probably been split into many different species.


texts:
First of all,I am very bad at biology. So please bear if it sounds elementary.

I heard about lasik operation for reshaping cornea.

Assume the patient is suffering from myopia implying lens is thicker than expected.So if i think logically ,to correct the lens thickness ,lens must be reduced.

In lasik, do they cut the lens's tissue.If yes what happens to the part that is cut and if no then how exactly lens thickness is reduced?


texts: Steroid hormones: how do they travel through the cytoplasm (not just the blood plasma) if they're hydrophobic?

texts: I get that steroid hormones need hydrophilic plasma protein carriers (eg albumin, TBG) to travel in the plasma because they're not soluble in the plasma. However, I don't see any sources talking about how these hormones can then traverse through the (presumably also hydrophilic) cytoplasm to get to their receptors either in the cytoplasm or nucleoplasm. Anyone have any clarifications on this?


texts: ID a marine creature found on a beach on the US east Coast

texts:
While walking on a marshy beach, I found this creature. It has no eyes, no feet, no fin, no gills. The only thing I know is that the skin lightly contracts. I found at least three of these. It is basically carried around by water.

Found this on a Maryland beach, roughly 150 miles east of Washington D.C.


texts: What is the current state of research on the relationship between sponges, ctenophores, and other animals?

texts:
I've been reading about the basal taxonomy of animals recently, and it seems as though there is some controversy surrounding the classification of sponges, ctenophores (comb jellies), and all other animals. One proposal has it that sponges form a monophyletic group, sister to all other animals. Another proposal is that sponges are polyphyletic, with the rest of the animals descended from some group of sponges or another. A third proposal is that in fact ctenophores are the sister group to the rest of the animals.
What does the current state of research on this topic look like? What are the arguments for and against each view? Is there a general consensus?


texts: Is bacillus strain 2-9-3 really 250 million year old?

texts:
I've read that in the last decade (I believe) some scientists discovered a microorganism, which they dubbed bacillus strain 2-9-3, in a crystal of salt that they think is 250 million years old and that started replicating when put in favorable conditions.

Is this really an example of the longest surviving life form?

Could someone confirm this is true and scientifically validated and provide some info and references that can be understood by non specialists. I'm a telecommunications engineer so I can understand general scientific approach and I have a basic understanding of chemistry and biology, but no formal or specific training on the subject.


texts: How does BH2 reduction to BH4 need only one NADPH molecule?

texts:
Dihydrofolate reductase (DHFR) reduces dihydrobiopterin (BH2) to tetrahydrobiopterin (BH4). Someone told me that this reaction needs only one NADPH molecule (I am not sure if this is correct), namely, NADPH provides one hydride atom and becomes NADP+.

Could someone explain to me how is this possible? How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?


texts: What is this small black bug found in Turkey?

texts: What species is this? It was found in Turkey. It was dead, I did not kill it.


texts: What is the best way to clean plastic flasks that have been used for cell cultures - is virkon a good idea?

texts:
When you use cultures e.g. insect cells, which are infected with virus one way to clean the (plastics) shake flasks is with virkon. Which is the most effective way to clean your flasks in order to extinguish the virus?
Also, is it effective to use SDS in order to denatured the virus proteins?


texts: How does a fertilized egg form 23 pairs of chromosomes?

texts: I am always confused about this...so when one cell which has 23 pairs of chromosomes undergoes the two meiotic divisions it produces four cells containing 1 chromatid of every chromosome pair so when this fertilizes the opposite gamete (of course it has also one chromatid of each chromosome pair) when they are fertilized they make one 23 chromosomes because 23 chromatid from one and 23 from other and they will form 23 chromosomes not 23 pairs of it, so my question is how they form 23 pair of it or to make it homologue..please clarify with some pics??...tnx


texts:
I was searching literature related to neurilemma and oligodendrocyte and came across these lines from WP (Neurilemma)

  Oligodendrocytes do not have neurilemma because excess cytoplasm is directed centrally toward the oligodendrocyte cell body.

I tried tracing more scholarly articles in this  context but I wasn't satisfied.

So my question is: Why doesn't oligodendrocyte produce neurilemma. Any  reference articles would also help.


texts: What is the common ancestor of humans and trilobites?

texts: I have always been immensely fascinated by trilobites. What is the single common ancestor of humans and trilobites? Do we know? Do we have a name for it? Have we identified it?


texts:
DNA motor will rotate during transcription instead of reciprocal.

What others will rotate?
Does it rotate in a fixed sense?
Why do they rotate?


texts: Is it possible to estimate the age of a wasp nest by its size?

texts:
Long story, but briefly I am debating knocking down a paper wasp nest. I don't want to kill the wasps, because (1) they're beneficial wasps, and (2) I would not have even known they were there, except I came face-to-face with the nest (~1 foot) and they didn't act remotely aggressive at all (karma).

My concern is that I've been out of town for a couple weeks, and I don't know if the nest has been under my deck all year and they were actually relatively sedate, or if the nest has developed recently. I mow regularly, and my big concern is that the noise of the mower and weed eater is going to agitate the wasps into stinging.

The wasp nest is under my deck, and my dog crosses the deck to get to the back yard frequently. I also have a toddler, but we generally play with him in the front yard, which is separated from the back yard by a fence.

So, tl;dr - A wasp nest is a little smaller than a baseball and covered in about 15 wasps. Has this nest been under my deck all year (and I can mow without worry as I have in the past), or has this nest sprung up since I stopped mowing (about 2 weeks) and I should remove it before I mow again?


texts: I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a conspecific?


texts:
There are a couple of papers and "lots" of anectodal evidence which imply that mushroom hunting does not have any adverse effects on the fungi, neither short nor long term. One of the counter arguments for that is that some fungi developed deadly toxins and what reason do they have other than stoping animals from eating them?
So, I had this discussion recently and I raised this point. I was told that many compounds that fungi produce do nothing for the fungus and they are producing them just because they are not costly enough to be cut by evolution. I don't find this argument particularly compelling, so I was wondering whether we know anything about the function of such compounds, say amatoxins.
Do they have any function other than killing us? Are they used by the fungus for anything during its life cycle? Do they kill insects or larvae? Do we know anything about them?


texts: How to explain the colour of these scots pines?

texts:
I would like to know why the trunks of scots pines have a particular colour, at least in Estonia, as shown here.

The bottom part of the trunks is darker than the upper part. What could explain this?

Thank you for your help!


texts: Is there any database with RNA classification?

texts: I am looking for a database that would provide classification of various types of RNA - information about its structure, function, etc.


texts: What are some useful (starter) metrics to use on phylogenetic trees?

texts:
I'm doing a computational biology project in which I simulate evolution under different inheritance rulesets and I am generating phylogenetic trees (beautifully visualised in Python with ete3).

My question is: where can I find and test out some simple metrics that can describe these trees in terms of 'branchy-ness' (you can tell I'm not a bioinformatician or phylogeneticist!). I'm looking for kind of mean-field descriptors of the trees. Kind of like degree distribution for networks.

My specific goal is, like in network science, trying to see if I can differentiate between different rulesets that created the tree by examining the [statistical] properties of the tree itself.


texts: First life forms to evolve controlled flight

texts: What was the first living organism able to fly in the skies and control their direction , not just Aeroplankton like bacteria and viruses carried by the winds but something  like an winged  insect or fish  or  something  similar,  and when did it evolve?


texts: Why are the organs for reproduction and urinary excretion combined?

texts:
We eat food for getting energy to our body parts, and we excrete the wastes through urine, feces, and perspiration.

Why has nature combined the urinary tract with the genital system (urogenital system) in humans?


texts: In my city, there is a unique tree, with thorns all over it. I would like to know - what species is this?


texts: Effect of the Marcus Theory on Photosynthesis

texts:
As far as I know, the Marcus Theory explains the rates of electron transfers in reactions as a function of differences in free energy between the product/reactant's potential well.

Furthermore, there is the so called inverted region which is often said to be important to explain effects as the photosynthesis. Sadly, I do not see the connection here. The inverted region seems to reduce the transfer rate in the backwards reaction but not in the forwards reaction which creates a net reaction flux. But how can this be explained by the Marcus Theory? I tried to read several sources which claimed to talk about this online, but apparently missed the crucial point.


texts:
These little flying fellows seemed to have made themselves a small nest in the crevices of the roof of my house (I live in Poland). I don't know if this makes a difference, but I do live near a small park.

I'm wondering if this is a house sparrow or something else.

On one of the photos I could swear these look like common sparrows, but on another (the one where the wings are apart) it seems like a different species. It also seemed larger than a sparrow, but is hard to tell due to the distance at which I've seen the birds and the photos were taken. One other notable feature was that they seemed very loud...

Any help?


texts: Why is the human ear most sensitive to 4000 Hz tones?

texts:
Human hearing sensitivity is dependent on frequency, which can be visualized by equal-loudness (iso-loudness) contour plots. An example is given below (Taken from here).

This plot shows that a tone with around a 4 kHz frequency (minima above) needs the least amount of actual energy in order to be percieved well as compared with a tone of any other frequency, while on the other hand it shows that tones of frequencies below 100 Hz and above 19 kHz need to have a lot of energy for us to percieve it.

My question is, how does one explain the clearly uniform/persistent fluctuations in these iso-loudness contours? Why are our ears most sensitive to 4 kHz tones, and why is there a "shoulder" in the contours at about 7 kHz? My first guess would be for proper perception of human speech - but the characteristic frequency of human speech is around 80 - 260 Hz!

EDIT:
My question is similar to this previous question, but it is a bit different in detail (they are only concerned with the overall dip, whereas I'm concerned with the dip, the shoulder, etc.). Moreover, that question has no accepted answer.


texts: Overall, for the most part, which is more important--capturing prey or surviving predators or parasites?

texts:
For animals in nature, does selection intensity tend to be stronger upon abilities used against parasites or predators or abilities used against prey?  Any empirical reports would be appreciated.

I understand that it would depend somewhat upon the species and the time, but I'm asking about a typical generation in most species.


texts: What are those visual and auditory reflex controlled by the midbrain?

texts: The midbrain is a centre for certain visual and auditory reflexes. But what are those reflexes exactly? My study book says that these reflexes are, e.g., responsible for moving the eyes to view something as the head turns. But I don't quite get it. What is the difference between those reflexes controlled by the midbrain and those mediated by the spinal cord?


texts: How is the protease inhibited by lopinavir different in SARS-CoV-2 compared to SARS-CoV?

texts:
The protease inhibitor lopinavir, originally developed as a cure against AIDS and HIV, has been shown efficient against SARS Coronavirus SARS-CoV.

  Dayer M R, Taleb-Gassabi S, Dayer M S. Lopinavir; A Potent Drug against Coronavirus Infection: Insight from Molecular Docking Study, Arch Clin Infect Dis. 2017 ; 12(4):e13823. doi: 10.5812/archcid.13823.

Why is Lopinavir not efficient against SARS-CoV-2? Is there a difference in the gene encoding for the protease?


texts: How essential is vitamin B3 to the diet?

texts: I know this might seem contradictory since by definition a vitamin is an essential part of the diet but I have read that nicotinamide, a form of vitamin B3, can be synthesised from L-tryptophan. Is it possible for a person to synthesise all their vitamin B3 requirements from one's dietary intake of L-tryptophan?


texts: Which nervous system is the Sensory system a sub-unit of?

texts:
I'm wondering about this because on one hand, the actual sensory information from something such as sight or sound transmits to the brain, which is part of the central nervous system.

On the other hand, the actual muscles that control eye movement but have absolutely nothing to do with processing incoming information are part of the somatic nervous system, meanwhile the actual motion of tissues within sensory organs can also be involuntary.


texts: Sickle-cell trait : Why is only one type of beta chain found in any one hemoglobin molecule?

texts:
I was reading a textbook (iGenetics, 3rd edition page 71), and came across the following passage:

  Homozygous bS bS people make Hb-S, the defective hemoglobin, with two
  normal a chains specified by wild-type a-globin genes and two
  abnormal b chains specified by the mutant b-globin bS allele: these
  people have sickle-cell anemia. Heterozygous bA bS people make both
  Hb-A and Hb-S and have sickle-cell trait. Because only one type of b
  chain is found in any one hemoglobin molecule, only two types of
  hemoglobin molecules are possible—one with two normal b chains, the
  other with two mutant b chains.

(Emphasis mine)

My question is: Why is only one type of beta chain found in any one hemoglobin molecule? Or is this statement simply false?

I did search biology SE for similar questions, and found this one, but it is phrased poorly and the only answer does not address my question.


texts:
Fluoride is a common active ingredient in tooth paste to prevent dental caries. It is also added or removed from the water supply in some communities for the same reason, but in children only.

My understanding is that the fluoride in tooth paste reacts with minerals in saliva then bonds to the tooth enamel. The fluoride in water is ingested and is somehow added to the developing bones and teeth of growing children, to the benefit of making decay resistant teeth.

What is the biochemical pathway of each process? A perfect answer will also discuss fluorosis and when that occurs and why.


texts: How to incerase the efficiency of co-immunoprecipitation?

texts:
immunoprecipitation recently. My main problem is i am getting very clean and my target protein only (as you see in the lane 3,4,5,6) but when i reduced the NP40 concentration to 0.05 percentage i could see enriched pattern in the IP pull down (lane 1 and 2). but the main problem is that i can same pattern in the control also. I am using my lysis buffer for the washing also (2 times washing with lysis buffer 10 mins at cold room followed by 2 times with 1X pbs). I am Using Mag Strep "type3" XT Beads (Incubation 4 hours in cold room with beads).

Lysis buffer:
20mM HEPES-KOH pH 8
15 -per glycerol
150mM KCL
0.2 per NP40 (I reduced to 0.05 per)
1 mM DTT
1X protease inhibitor cocktail

Can anyone help me with this. Should i change the washing buffer what about the stringency. What are the other factors that could increase the efficiency of the co-IPs. I am trying to optimize the protocol. This is human cells.


texts: Relationship between turgor pressure and osmotic pressure?

texts:
I would like to know if there is a relationship between osmotic pressure (inside and outside of a cell) and turgor pressure. If so, is there a way to formalize it mathematically?

Thank you in advance,
Eorn


texts: Knockdown of long noncoding RNA (lncRNA) - how is it done?

texts:
I don't work at the wet lab and don't know all the details about the knockdown techniques.
My question is:
How lncRNA knockdown is done?
For example - you have lncRNA that is functional in the nucleus. How is it possible to do knockdown using iRNA if interference happens only in the cytoplasm?
Sorry if there is biology related misconception in my question.


texts: Is APB an antagonist of the mGluR6 receptor?

texts: APB is a glutamate analogue specific to the mGluR6 receptor of ON retinal bipolar cells. It is used in research into receptive field processing by blocking the ON channel. Why is it not called an antagonist?


texts:
I'm a high school student in a third-world country (Algeria).

My problem is with the way we are been taught biology. It's all about memorizing facts and procedures from a textbook without any application whatsoever due to the unavailability of laboratory equipments(there are some but they are either expired or useless).

My question: does this way of learning have any benefits at  all? Are we even learning?

I know what a lipid is because I've read its definition, but, is this enough? Is it enough to only read a paragraph that describes lipids and then see a model of it in order to know  what a lipid really is? Would it be useless if I go to a laboratory, extract some cholesterol, study its characteristics and see it with my own eyes to have a rough idea of what it is?

I've been seriously thinking about dropping out of school because I think the world doesn't need another indoctrinated kid who knows a bunch of facts and want to  earn some money with that knowledge.


texts: Cells created using differently aligned proteins

texts:
I remember reading that scientist were making cells (I assume bacteria), that used differently oriented proteins to create a whole new class of life. Because apparently right and left aligned proteins don't interact in same way, cells made in such manner would behave similarly but couldn't be interacted with differently aligned bacteria/virus.

However I can't find any proof this story was true? I could be wrong about details. Is there a similar mechanism that would allow a whole case of twin (contain DNA, and most molecules that regular cells posses) cells that couldn't interact with existing bacteria?


texts: Why is down syndrome more common than other trisomies?

texts: Why is Down syndrome more common than say trisomy 18? Is chromosome 21 easier to replicate? Or is it because those babies are more viable?


texts: There are two of these trees, growing in old fence rows, along my yard, in central VA, Augusta County, Shenandoah Valley.  They have smooth, leathery leaves, pale wood, quite hard to cut, and tough to break.  The close ups are of some limbs I trimmed, yesterday. The biggest is about 10 inches in diameter, and perhaps 40 feet tall.  Branches tend to grow strangely hooked elbows that send branches off into strange directions, which makes trimmed limbs tangle and hook together.  This is what the foliage looks like in mid September.


texts:
Years ago, when I lived in Greece, I saw crows from a close distance, but never with this peculiar colouration. Today I saw two individuals, both with these gray parts.

Location: Austria, Vienna. Pretty much in the city centre. Specifically Altes AKH Hof 2 near the rear yard of the department for East Asian studies.

Time: I am not sure. Probably before my lecture (around 10am) or after it (12am). I'll see, whether I find the timestamp of the picture anywhere.

Size: Now, at this I am really bad. I would say roughly the length of my boot, which is a 47-48 European continental size.

Behaviour: nothing interesting. Two of them came, stalked around the benches, did not make sounds and as far as I remember were gone quickly. They were not afraid of people.

My guess is Corvus cornix , but I have always been bad at identifying birds.

EDIT:
Unfortunately, I didn't see the linked answer. But had I seen it, I would probably have assumed my bird wasn't Corvus cornix. The plumage  in the linked answer looks significantly more colourful. Whether you want to mark it as duplicate or not, I am fine with your decision, since I have little practice in identification. However, I find the answer here more detailed when it comes to differentiating C. cornix from other corvids. The linked answer only states the results. The answer here teaches us what to look for!


texts: I have always been taught that enzymes can catalyze both the forward and reverse reaction, and will increase the reaction rate in both directions. I understand that the thermodynamics of the reaction are not altered by the enzyme, but I have yet to find a good answer / example for an enzyme that actually does this. (E.g. can a nuclease join DNA together if the products are in excess? Can a protease form a peptide bond?) I am having difficulty finding a resource online that actually justifies this claim without just saying "Yes enzymes work both ways."