texts: Description of the paramaters in the packing parameter?

texts:
For a phospholipid, the critical packing parameter is given by:
$$P=\frac{v}{a_0l_c}$$
And I know that

$v$ is the volume of the hydrocarbon tail.
$l_c$ is the critical length of the hydrocarbon chains.
$a_0$ is the optimum surface area of the head group.

But what do these actually mean?

For example what is the volume of the hydrocarbon tail, since it can't be simply the volume of all the atoms that make it up else this would be negligible? What is the critical length of the hydrocarbon tail? And What is the optimum surface area of the head group?


texts: If it weren't for animals, insects, or people, would plants that produce seeds (nuts, fruit, etc) cease to exist?

texts: I gather that some would or could in theory still be successful, but don't most depend on takers to flourish?


texts: Would gargling with salt water every day increase blood sodium levels?

texts:
Would gargling and rinsing with salt water every day for a few minutes increase your blood sodium levels? Considering the fact that sublingual medication is a very effective way for introducing substances straight into your bloodstream very quickly.

Below's a link to a study on Pubmed about this issue. Does anyone here have access?
https://www.ncbi.nlm.nih.gov/m/pubmed/3474267/


texts: How is color information transmitted from the eye to the brain via the optic nerve?

texts:
I would presume that is has something to do with synapses and specific chemicals starting specific charges through the optical nerve's sub-components, and that this is somehow interpreted by the brain to configure an actual image; but in all honesty I have no idea.

The eye is obviously quite complex, and as I am not massively associated with all the terminology yet, I would be grateful for an answer in layman's terms.


texts: Definition of "Effective population size"

texts:
Could you explain to me, what is the meaning of "Effective population size ($N_e$)"?

I would appreciate an example as well.


texts: What regulates the timing of the motion of molecular machines during DNA Replication?

texts:
This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines.

I know that those big molecules moves using mechanical energy from ATP molecules and take advantage of the electric forces specially the hydrogen bonds, they also take advantage of the Brownian motion of water molecules around them.

From what is see, the green floating molecule triggers the whole process by attaching the purple one, then some electric equilibrium is disturbed so the {purple+green} molecule is attracted by the horizontal cyan molecule...etc.

But the problem is: does the green molecule attaches to this group in a periodic timing ? or in other words does the Okazaki fragments have the same lenght evertytime ?

Thank you in advance !


texts: Why is cold water more refreshing than warm water?

texts:
Obviously, the temperature of water does not affect its chemical composition. At least not in the ranges we are likely to drink it in. Yet it is clearly far more pleasant and refreshing to drink cool water than it is to drink tepid or warm water.

Is there actually any difference to the organism or is this just a matter of perception? Is cool water somehow more efficient at rehydrating a cell? In any case, surely by the time water reaches individual cells it will have warmed up to body temperature.

So, what, if any, is the difference between drinking cool and warm water in terms of its effect on the human (or other animal) body?

Extra bonus for explaining why the taste of water changes when it is cold.


texts: Mathematical models of gene editing using CRISPR

texts:
One confusing thing I have found when reading articles about possible CRISPR based gene therapy treatments in humans is that there is vey little discussion about what percentage of your cells will actually have their DNA edited, the rate at which the editing takes place, and how to quantitatively estimate how many edited cells would be needed to "cure" a specific disease.  (It's not so confusing how edits could be made to a small embryo, what's confusing is what is actually possible for grown patients)

Can someone provide a few basic facts that calibrate what is currently possible and what is needed.

For instance, is it currently possible to edit more than 50% of the cells of an adult  nematode (or more complicated organism) using CRISPR?  How long does it take (minutes, hours, days, weeks).

For the current list of human diseases that are possible targets for gene therapy, how many cells need to be edited for one of those diseases to be "cured" (hundreds, thousands, billions, etc)

But in general is there a name for the mathematical models that try to predict how many cells will end up being edited, how those edited cells will multiply and replace diseased tissue,  and how many edits are needed to generate a concentration of missing protein for a treatment to be successful?

cheers!


texts: Are humans the only species to suffer from impacted teeth?

texts: Many humans need their third molars (wisdom teeth) removed due to tooth impaction. Are humans the only species to suffer from this?


texts: How heavy are all foreign microorganisms in and on the human body?

texts:
I define "foreign microorganism" as a microorganism which is not produced
by the human body (not antibodies or leukocytes) including bacteria, viruses, fungi, biofilm aggregates or small lifeforms independent if they are benign or hostile.

Let's say I have currently a weight of exactly 100 kg. How much of it consists of organisms not belonging to me?


texts: Number of transcription factor genes in the human genome

texts: What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. cerevisiae? Additionally, does the proportion change between eukaryotes and prokaryotes?


texts: What's the difference between reaction norms and phenotypic plasticity?

texts:
I'm trying to understand better these two concepts, but I cannot see a clear difference yet.

Reaction norm: "set of phenotypes that can be produced by an individual genotype when exposed to different environmental conditions"

Phenotypic plasticity: "ability of individual genotypes to produce different phenotypes when exposed to different environmental conditions"

Are phenotypic plasticity changes temporary changes in genes; are they an extension of the reaction norm?


texts:
So there's a protein that binds to E7 viral protein, I want to remove a sub domain of the protein to see which exact domain the E7 binds to.

What is the procedure for this?

Edit: I believe the virus is HR HPV16. I need to know a method/procedure that can allow me to delete/mutate the NLS, CXXC ,BAH1 and BAH2 domains in the enzyme DNMT1


texts:
I am not quite sure how to write 100% out come for the phenotype ratio after using "Punnett Square". The result from the each alleles, the dominant allele completely(100%) took over the recessive allele.
How can I express my phenotype ratio?

(Let's say....Purple flower→dominant White flower→recessive)

Phenotype/ Purple flower 1: White flower 0
Phenotype/ Purple flower 4 :white flower 0
Phenotype/ Purple flower 4


texts: If birds are dinosaurs, then are mammals reptiles?

texts: I'm just curious - it seems generally accepted that birds are dinosaurs. If that's the case, then can we call all mammals reptiles? Can we go even further and call humans amphibians? And since single-celled bacteria were the precursor of all life, isn't just anything a bacterium?


texts: Why is pith of Cucurbits hollow when mature?

texts: What is the evolutionary significance of pith in cucurbits? Does it serve a function by being hollow? Or is it an evolutionary vestige? What function would it have had in its ancestors?


texts: Are there any genes (for any organism) for which we can say with confidence that they are over a billion years old?


texts: de novo gene synthesis vs cDNA library creation from plant RNA: Pros & Cons

texts:
What are the relative pros & cons of the following two approaches when one wants to insert a known, sequenced plant gene into a target host organism:

de novo gene synthesis vs
plant matter extracted RNA converted to a cDNA library

Specifically my gene of interest is approx. 2000 base pairs so de novo gene synthesis cost works to about $350. (please correct my estimate if I'm wrong)

While this isn't cheap, collecting plant samples, cryopreservation, digestion, extraction etc. aren't easy either.

Any other considerations when / why one may favor one approach over the other?


texts: Imidazoline receptor agonist in clonidine?

texts:
I am thinking which pathway is more important in hypertension, ADHD and withdrawal of clonidine:

alpha-2 agonist
imidazoline receptor agonist (maybe)

Alpha-2 is the classical one. Pubchem starts to have more more info about imidazoline receptors.

How does clonidine work in hypertension, ADHD and withdrawal?


texts:
My biology book says:

  No individual is immortal,except single celled organisms..

I think that such conclusion aries from the necessity of binary division in many single celled organism to reproduce.

Is the book's conclusion biologically correct and why?


texts: Does a bird nest out of its breeding range?

texts:
I have a book by the Audubon Society on building bird houses and for each bird they show a breeding, wintering and all year range.

Do the birds only breed in their breeding range, or in both breeding and all-year range?

For example, the northern flicker is shown as breeding in Canada, but its all-year range is in the United States. So, am I wasting my time building a bird house for a northern flicker in the United States which is south of the breeding range, but inside the all-year range?


texts: What are the differences between Signaler and Primer pheromones?

texts:
I have searched few authentic books and have found the following difference between them.

Signaler pheromone induces fast reaction in the recipient and the Primer induces slow reaction.

But I did not find any book that discriminates their function.

P.S. I have read Wikipedia and I'm not counting on it.


texts: Why didn't people taking up the Ice Bucket Challenge die?

texts:
I recently came across Vagal Inhibition. That article says,

  (5) Sudden immersion of body in cold water.

can cause vagal inhibition and ultimately death.

Recalling the Ice Bucket Challenge. Going by what the above article says, shouldn't many of the participants have had a vagal inhibition ?


texts: Does crude oil or kerogen contain ancient DNA?

texts: According to wikipedia by the formation of oil there are a lot of organic materials present including DNA. Is it possible that this DNA is conserved somehow for millions of years?


texts: What happens to apetite hormones like ghrelin and leptin when a person in coma?

texts:
Don't coma individuals feel hungry? If so, how does the brain senses this condition (as coma is caused by neural death or damage) and switches off gene expression of ghrelin and leptin.

Is there any research done on revealing the mechanism by which apetite hormones expression are shut down during brain death???

Thanks


texts: Why is there Turner syndrome if one of the X chrosomes is inactivated anyway?

texts: In females one of the two X chromosomes will condensate and turn into Barr bodies. So chromosome abnormality-free women will only have a single transcriptionally-active chromosome. Then why can abnormalities like Turner's syndrome still occur in the  presence of a single active X chromosome?


texts: What are the applications of predicting the structure of proteins?

texts:
Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure.

However, in predicting the structure of protein I haven't been able to find many use cases. In the omicsonline I was able to find a paper on Computational Methods for Protein Structure Prediction and Its Application in Drug Design:

  Most modern drug discovery projects start with protein target identification and verification to obtain a verified drug target. For structure-based drug design the three-dimensional structure of the protein needs to be determined experimentally by using either x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.

Therefore, since proteins are vital for maintaining the body are there any other use causes for predicting the structure?


texts: How to search for a DNA sequence in a genome on ENA (European Nucleotide Archive)?

texts: I have to do a search for small DNA sequences in the genome of an organism in ENA. I have the accession number and project id. However, I can't download the whole genome because of the download size and would prefer to do it online if possible. I have a rough idea of the part of the genome I wish to scan in, don't know if that's relevant.


texts: Which information can be extracted from time course RNA-Seq Data?

texts:
So I am very new to the area of biology so I am sorry if this is a stupid question.

I have RNA-Seq data carried out over a span of 100 days and I have gene expression data in the following format. Each expression value is the mean of
3 replicates.

           Day 1         Day 10     Day50     Day 100
Gene 1      12             42         35       12
Gene 2      50             53         23       100
.           .              .          .        .
.           .              .          .        .
.           .              .          .        .

so on, the above data is just something I came up with, but can you tell me what information I can extract from this type of data ? Such as differential gene expression. Thank you very much


texts: Can anyone identify whether or not these are bird or rodent mites?

texts: I found these on my patio furniture directly under a bird's nest that has hatchlings. Surrounding landscape is ivy so we do have raccoons and mice in the area.


texts: How do plasmids protect themselves against restriction enzymes?

texts: How do plasmids protect themselves from restriction enzymes released by bacteria (i.e., against bacteriophages)?


texts: How does evolution produce complex organs

texts: I've been wondering lately how evolution manages to produce complex organs. It is pretty obvious to me how evolution would select some minor traits like size, resistnce to illness or climate. There is a mutation where some organisms are slightly different and better traits are selected. However I cannot imagine how an organism will mutate to have lets say lungs at once and unless organism has a functional organ there is no reason for the trait to be selected. So how does evolution produce complx organs?


texts: If the xylem of a woody plant is composed of dead tissue, how does sapwood become heartwood?

texts: If the xylem of a tree is composed entirely of dead tissue, then that means the sapwood is dead. If so, how does it transform into heartwood, and what starts the process?


texts: Are humans not sexual dimorphic? Can genetic XY but SRY not expressed become pregnant?

texts:
My understanding was that XX/XY was how sex is determined in mammals, and so humans as well.

A science teacher posted this regarding transphobia:

  "I just commented this on a transphobic post that was all like, "In a sexual species, females have two X chromosomes and males have an X and a Y, I'm not a bigot it's just science." I'm a science teacher so I responded with this.
  First of all, in a sexual species, you can have females be XX and males be X (insects), you can have females be ZW and males be ZZ (birds), you can have females be females because they developed in a warm environment and males be males because they developed in a cool environment (reptiles), you can have females be females because they lost a penis sword fighting contest (some flatworms), you can have males be males because they were born female, but changed sexes because the only male in their group died (parrotfish and clownfish), you can have males look and act like females because they are trying to get close enough to actual females to mate with them (cuttlefish, bluegills, others), or you can be one of thousands of sexes (slime mold, some mushrooms.) Oh, did you mean humans? Oh ok then. You can be male because you were born female, but you have 5-alphareductase deficiency and so you grew a penis at age 12. You can be female because you have an X and a Y chromosome but you are insensitive to androgens, and so you have a female body. You can be female because you have an X and a Y chromosome but your Y is missing the SRY gene, and so you have a female body. You can be male because you have two X chromosomes, but one of your X's HAS an SRY gene, and so you have a male body. You can be male because you have two X chromosomes- but also a Y. You can be female because you have only one X chromosome at all. And you can be male because you have two X chromosomes, but your heart and brain are male. And vice - effing - versa. Don't use science to justify your bigotry. The world is way too weird for that shit."


texts: What do we know about the cellular structure, processes, environment, and immediate ancestors of the last universal common ancestor (LUCA)?

texts:
I am up for all scientifically sound speculations, and sources are highly welcome. I've looked into this quite a bit myself via scholar.google, the wiki article, and /r/askscience.

I'm really looking for more speculation about physical details of the organism, its environment, and its immediate ancestors.

e.g. How did they (referring to the LUCA and some immediate ancestors) acquire nutrients? What forms of mobility were available to them? How long was it until photosynthesizing organisms emerged?

mods: If this is too open-ended or too speculative, please let me know where I can redirect this question.


texts: Can anyone identify this strange creature? I live in a very urban part of Montreal, Canada. It wasn't moving (seemed dead) and although the image is huge, it wasn't as big as it seems (a couple of centimeters).


texts: Can anyone identify this spider? (greater Poland region)

texts:
This is in Poland, in the Greater Poland area, found a few days ago by a garage in the city.
I didn't have any coins on me to give a sense of scale, but the body is roughly 1.5cm long. It was dead when I found it.
I'm curious because I haven't seen any spider like this one during my stay here, they're all tiny specimens normally and this one really stuck out.


texts:
Here is an image of telomerase adding telomerase.

As we can see, the telomerase sort of binds to a bit of the existing "3' flanking end of [the] telomere" - it's almost half and half.

My question is, where did that existing telomere come from? And the telomere before that?

Essentially, the telomeres must have begun from some point on the chromosome/DNA, but how were those telomeres added if the telomerase has a preset RNA sequence that it uses to bind to specific nucleotide bases? Does our human DNA coincidentally end with TTAGGG as well or something?


texts:
The mountain blue bird build nests to attract females and exhibit aggression towards other males during breeding season. Which of the following is likely to give the birds maximal evolutionary fitness?

a) stronger aggressive behaviour only during egg laying

b) stronger aggressive behaviour during nest building rather than during hatching of eggs

c) stronger aggression when egg is first laid than during nest building

d) greater aggression during hatching eggs than during nest building


texts: Geographic/ethnic distribution of Neanderthal DNA in modern humans

texts:
There is a really good chance that various human populations have different levels of Neanderthal DNA in their genes.

And yet, the only thing I was able to find is the percentage of Neanderthal DNA in Europe, Asia and Africa.

Are there any studies with a finer resolution, such as regions, countries etc.?


texts: Are there examples of animals that live in groups, where all have the same role?

texts: For animals that live in groups, are there examples where all of them have the same role? For example, in animals we know there are bee queens or alpha, beta and omega mammals. But are there groups of animals where all the members have the same role? My question is aimed at 2 different groups actually, first animals in general (which includes reptiles, insects, etc.) and second to mammals only.


texts: Can an Ichthyologist identify this Canadian freshwater fish?

texts:
This will be very simple for a lot of you! But I been getting mixed answers about his catch. Is this a chinook salmon or brown spotted trout? Caught in Angus, Ontario, Canada. (Hwy 90 Bridge)

I appreciate the help!


texts: How often does pre-mRNA processing lead to midstream off-frame errors in eukaryotic mRNAs?

texts:
As I understand it, the splicing of introns from pre-mRNAs is not incredibly precise. I've only ever seen nucleotide position ranges given in any description of the involved processes. Since there is quite a bit of looping of pre-mRNAs during processing and given that involved proteins often have effects well downstream from where they bind, this intuitively makes sense.

However, this would be incredibly problematic if true. Most pre-mRNAs are more intron than they are exon. While the precise base offset for the bases padding the start and end of an mRNA are irrelevant due to the start and stop codons, the precise offset for cut locations is very important for any splicing between the start and stop codons. If the splicing of introns regularly lead to cuts that are 1 or 2 bases off (in addition to 0 or more whole codons that have been accidentally removed), then all eukaryotic cells should have lots of (junk) mature mRNAs that have the proper reading frame at their 5' ends but off frame codons at the 3' end or just for stretches in the middle.

Specifically, if pre-mRNA processing has mostly random cut locations in its splicing, I would expect only ${^1/_3}^{rd}$ of mRNAs to retain the reading frame of their parent genes from from start to poly-A. In turn, that would mean only about ${^1/_3}^{rd}$ of synthesized proteins have the proper primary structure. There's no way eukaryotes function with that much kludge running through them.


texts: Relationship Between Evolution and the Increase of Entropy of Earth

texts:
I was confronted by this question:

Biological evolution of life on Earth, from simple prokaryote-like cells to large, multicellar eukaryotic organisms,

A) has occurred in accordance with the laws of thermodynamics.
B) has caused an increase in the entropy of the planet.
C) has been made possible by expending Earth's energy resources.
D) has occurred in accordance with the laws of thermodynamics, by expending Earth's energy resources and causing an increase in the entropy of the planet.
E) violates the laws of thermodynamics because Earth is a closed system.

Answer:  A

However, I do not understand. Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased.

I would answer D... Where am I going wrong?


texts: It's been known for a long time that copper has antimicrobial properties, but if it is so potent, why does it seem to have no effect on human skin or really any large animal?


texts: What are the differences between a benign tumor and swelling?

texts:
What are the differences between a benign tumor and an injury related swelling?

And can swellings due to injury turn into a benign tumor?


texts: How to include multiple DNAs into a crystal structure

texts: I have a crystal structure (PDB 3OS1)that shows the interaction of PFV intasome with a substate DNA. I would like to replace the existing DNA in the intasome as well in the substrate with a longer sequences. What is the easiest way to do it. Thank you.


texts: Is there a difference between visual sensation and imagination in the brain?

texts:
How substantial is the difference between the neural signal associated with seeing an image and the imagination of that image? Surely, it can not entirely copy the pathway from the sensory organs to the emotional centers, but approximately how large is the common pathway for both processes?

Is there some principal difference in the neural pathway of these two processes, or is the imagined image just more of a slurred version of the visual image?


texts: Causes of the stochastic behaviour of voltage-gated ion channels

texts:
I came up with the following electro-mechanical model of a voltage-gated ion channel, resp. of its voltage sensor as described here and here. The voltage sensor is a bistable system with two local energy minima $E_1(V)$, $E_2(V)$, the first one indicating "closed", the second one "open":

From Bezanilla, The Voltage Sensor in Voltage-Dependent Ion Channels, p. 567. You can interactively explore a voltage-dependent energy surface here (schematically).

I created a spring model with Algodoo which looks like this (green: the voltage sensor (= a peptide subunit), white springs: keep it in place, blue: favours the closed state, red: simulates voltage, opens the gate):

(You can download the model here and explore it interactively with Algodoo.)

To behave stochastically - i.e. the probability of being open $p(V) \sim e^{-\Delta Q(V)/kT}$ which presupposes a thermal equilibrium - there must be fluctuations that can lift the system above the energy barrier between the two energy minima.

My question concerns the source of these fluctuations in the real ion channel: are these thermal (mechanical) fluctuations (e.g. other molecules hitting or tearing the sensor) or are these fluctuations of the membrane potential?


texts: Do seeds use cellular respiration when they are germinating?


texts: Which of the response is faster? voice or hand action?

texts:
After taking certain stimuli and making the the decision to do certain action, which one response (output) (out of 2 possible output-ways, voice and hand-movement) would act faster?

For example lets say I'm playing a car video game that can be controlled by voice.

If i say "left" it will turn left and so on.

If I'm controlling that car by hand then I could just steer to the left.

So, if i'm not considering energy required for hand to move and all.

Which will get the signal to my brain faster, my mouth or my hand?


texts: What causes rashes to appear in specific parts of the body without a site specific trigger?

texts: Why do rashes appear randomly at highly specific locations (and not others), without location specific triggers? Like, if it's a systemic issue, then it should be distributed to other areas on the body too.


texts: Why does drinking milk lead to increased fractures?

texts:
Milk has always been associated with strong bones due to the high amount of protein and calcium in it. Yet reading it up on wikipedia,

  A study published in The BMJ that followed more than 45,000 men and 61,000 women in Sweden age 39 and older had similar results. Milk consumption in adults was associated with no protection for men, and an increased risk of fractures in women. The risk of any bone fracture increased 16 percent in women who drank three or more glasses daily, and the risk of a broken hip increased 60 percent. It was also associated with an increased risk of death in both sexes.

My question is:

Why did this happen? Can someone explain the biological reason of this observation?

Even though milk really does provide large amount of calcium and proteins yet isn't is contradictory that the fracture rates increase?

This is the aforementioned study.

Michaëlsson, K.; et al. (2014). "Milk intake and risk of mortality and fractures in women and men: cohort studies". The BMJ. 349: g6015. doi:10.1136/bmj.g6015.


texts: Can Helicobacter pylori be eradicated naturally?

texts:
This question is not to discuss whether substances that have anti-H. pylori activity work or not, or to discuss the pros and cons of such but from a medical perspective.

Assuming that one is able to control, reduce, or eliminate H. pylori via foods containing natural anti-bacterial activity targeted at H. pylori without the consumption of antibiotics, what is the possibility of reinfection or an overgrowth with H. pylori?

  In this study, the bactericidal activity of Korean and Japanese wasabi roots, stems and leaves against Helicobacter pylori were examined... All parts of wasabi showed bactericidal activities against H. pylori strain NCTC 11637, YS 27 and YS 50.

My questions are:

If this method was carried out in vivo and the results were found to be consistent with the research mentioned above, what is the chance of developing resistance to H. pylori?
Will developing resistance prevent recolonization of the stomach lining with H. pylori?

Bactericidal activity of wasabi (Wasabia japonica) against Helicobacter pylori


texts: Toxic Metals and Oxidative Phosphorylation

texts: I was reviewing the toxicity of certain toxic metals, specifically cadmium and their effect on Oxidative Phosphorylation and Cellular Respiration, I have found that metals such as cadmium inhibit certain antioxidant enzymes such as catalase, resulting in oxidative stress as a result of excess of Reactive Oxygen Species or free radicals, I also have come across information that states that toxic metals can bind to the mitochondria and interfere with oxidative phosphorylation, possibly in the electron transfer change or in another way. I was wondering if anyone is aware of the other ways in which cadmium interferes with oxidative phosphorylation as it bonds with the mitochondria, or if attaching to antioxidant enzymes IS actually binding to the mitochondria.


texts: What motivates children to start walking?

texts:
Crawling is a way we first learn to translocate but  , in all our lives, there comes a point where naturally try standing up and try to walk.. but why? What really pushes us over the edge to start walking?
When we first start walking, usually we fail many times but still we have this natural motivation learn walking despite the failure. Is this some sort 'intuitive' intelligence which babies have? To be more specific I can't imagine a baby to consider the pros and cons of walking vs crawling and then logically argue to himself/herself that learning how to walk would be something worthwhile to spend his mental resources on.

Reference video


texts: Can the psychology of a person alter his immune system and health?

texts:
Can the psychology of a moderate aged person alter his immune health? because I have read many a times about the different types of linkages between nervous system and immune system.

Can someone outline the general facts about what is understood in this relationship from which i would gain some knowledge?


texts: What is the name of the appendage that mantis shrimp use to rub their eyes?

texts: In this short clip, you can see the mantis shrimp using some sort of feathery arm/claw to rub its eyes. Looking at a diagram here, it appears possibly that it's using maxillipeds. Someone with knowledge of crustaceans (the behavior is probably not unique to mantis shrimp) would be appreciated.


texts: anyone can help identify this aquatic microganisms?

texts:
I extracted from fish excretion and at 400x
At the moment i have yet to try any medication because i don’t know what this is. Can someone who has seen this before share the light? thanks!


texts: Classification of glycosidic anomeric bonds (alpha vs. beta)

texts:
In the process of studying for my upcoming biochemistry exam, I have stumbled over the classification of glycosidic bonds. I want to be able to distinguish $\alpha$- from $\beta$-glycosidic bonds. Unfortunately, even after reading through this page, I don't really understand how to go about classifying the bonds in e.g. an oligosaccharide.

(Source)

Now, I am inclined to say that both of these anomeric linkages are of type $\alpha$, because the O-glycosidic bond is axial to the respective sugar rings. Is that a correct way of reasoning?


texts:
Strictly speaking, what is the definition of cDNA?  This confuses me, since usually it is said to refer to DNA that is complementary to mRNA.  Is this correct?  Is it restricted to mature mRNA?

I also find directionality very confusing.  As I understand it, mRNA has a sequence equivalent (less introns, after splicing) to the so-called 'coding strand' of DNA.  Does this mean that cDNA made from mRNA, at least before treated with a DNA polymerase, is also complementary to the original genomic DNA?  Is this the better definition (I have seen this used as well, though the first definition seems far more common).

Lastly, as I understand it each chromosome has a forward and reverse strand, defined by convention, but that the 'coding' strand of a given gene is random.  This seems counter-intuitive... is it just because both strands are equivalent?  Does it introduce complications in terms of the cell 'knowing' which strand is the coding strand for a gene?

The most upvoted reply to this question (http://www.biostars.org/p/3423/) confused me even further.  I feel the same way as 'Onefishtwofish' does, in the replies.  Can anyone clarify?


texts: The primary source for Erich von Holst research for minnow forebrain and shoaling

texts:
I am trying to find the primary source of information about the experiments of Eric von Holst, mentioned by Konrad Lorenz in the book “Das sogenannte Böse: Zur Naturgeschichte der Aggression”/“On Aggression”. The essence of the experiment is widely known and retold in many tertiary sources.

Quoting from a secondary source: under the chapter “Die anonyme Schar”/“Anonymity of the flock” from Konrad Lorenz.

"Ein Fisch, der, aus welchen Gründen immer, in bestimmter Richtung
zu schwimmen beginnt, kann ja nicht umhin, in Bälde aus dem
Schwarm heraus ins freie Wasser zu geraten und gleichzeitig damit
unter den Einfluß aller jener Reize, die ihn in den Schwarm
zurückzuziehen trachten.
...
Man kann ganz kribbelig werden, wenn man diesem Treiben
zusieht, und man kann nicht umhin, an der Demokratie zu zweifeln
und Vorteile in der Rechtspolitik zu sehen.
...
Er [Erich von Holst] operierte einem einzelnen
Fischchen dieser Art das Vorderhirn weg, und in diesem stecken,
wenigstens bei diesen Fischen, alle Reaktionen des Schwarmzu-
sammenhaltes.
...
Das operierte Tier war eben durch seinen Defekt eindeutig zum Führer geworden.
"

"A fish which begins, for any reason, to swim in a certain direction cannot avoid leaving the school and thus finding itself in an isolated position. Here it falls under the influence of all those stimuli calculated to draw it back into the school.
...
Watching these indecisive actions one almost begins to lose faith in democracy and to see the advantage of authoritarian politics.
...
Erich von Holst removed from a common minnow the forebrain which, in this species, is the site of all shoaling reactions. The pithed minnow sees, eats and swims like a normal fish, its only aberrant behaviour property being that it does not mind if it leaves the shoal unaccompanied by other fish.
...
By virtue of his deficiency the brainless animal had become the dictator!"

The many-hour search for the words "elritze vorderhirn schwarm erich holst"/"minnow forebrain shoaling erich holst" gives only biographies and obituaries of Eric von Holst and secondary/tertiary / damn knows what sources.

Could it be that with all due respect to Konrad Lorenz it was a false quote or a stretch? Did anyone dig up primary sources?


texts: Can anyone tell me what type of snake this is?

texts: I found this snake in my garden and I'm wondering what type of snake it is! It was around 1 metre long and I'm in Lincolnshire UK.


texts: What is the difference between [Clinical Trials as Topic] category and [Clinical Trial [Publication Type]] category in pubmed?

texts:
Dears in biology stackexchange community, I hope that everyone is fine.

I am using pubmed in my current review. My focus is about an application on the scope of Clinical Trial. When I used MeSH for narrowing my research scope on Clinical Trial, I got two different categories which I cannot find any clear difference between them. They are:

Clinical Trials as Topic
Clinical Trial [Publication Type]

However, when I search on the two different categorises, I found very different resulted papers. That means that there are a difference between the two categories where my ignorance is.

Could you please tell me what is the difference?

Possible examples of two queries:
1. ("Clinical Trial" [Publication Type]) AND "Prostatic Neoplasms"[Mesh]
2. ("Clinical Trials as Topic"[Mesh]) AND "Prostatic Neoplasms"[Mesh]

Many thanks to you for your time, in advance.


texts: Who are humans' closest relatives, after primates?

texts:
This question here addresses the controversy of whether humans are more closely related to bonobos or chimps.

My question is - which group of animals are are closest relatives, beyond primates? Or which group of animals are all primates most closely related to?


texts:
In "Variation under Domestication", Darwin makes several references to the concept of true breeding:

  They believe that every race which breeds true, let the distinctive characters be ever so slight, has had its wild prototype.

And:

  I crossed some white fantails, which breed very true, with some black barbs.

Before diving into the book, I never heard of the term, so I looked it up and found this definition in the Wikipedia article on Zygosity:

  A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes. The cell or organism in question is called a homozygote. True breeding organisms are always homozygous for the traits that are to be held constant.

But this is rather technical and it's not the kind of explanation I would give to a child.

What is true breeding, in simple terms? When is breeding not considered true?


texts: What is the distribution of gene polymorphism levels across human genes?

texts:
Of the approximately 19,000 human genes, about how many have one allele that occurs with appreciable frequency in the current human population, how many have two alleles, and so on? (By "appreciable frequency", I mean, say, is found in at least 1% of the population, which seems to be the rule of thumb for classifying a gene as polymorphic in the population.)

I'm not looking for an exact breakdown for every single number of allele variants - I'm just curious, does the typical human gene have only one (frequently found) allele? Or two, as is often implied in elementary genetics texts? Or five, or 10, or 100? What does the approximate distribution look like?

According to the Wikipedia article linked above, the most polymorphic genes known are those coding for the Major Histocompatibility Complex (MHC), with the HLA-B HLA-DRB1 loci having 200 significant alleles, so I guess 200 is the upper end of the spectrum. (Although I don't know whether "the HLA-B HLA-DRB1 loci" refers to a single gene or several, so maybe 200 alleles is higher than any single gene has.)


texts: How similar do proteins have to be to trigger the same immune response?

texts:
The title really says it all. How precise or vague is the immunity we get from vaccination or from having encountered a germ before?

Is it about protein parts that are recognised if they are identical? Full proteins? Which kinds of mutations break the recognition and which don't?


texts: What are good data on the Human Metabolic Model and where can I get them?

texts:
Trying to get a good SBML representation of the Human Metabolic Model for use in Flux Balance Analysis and drug targetting (i.e. gene knockout) simulations.

What are good sources for these data?

Thanks very much!


texts: Can you eat enough to make your stomach explode?

texts:
Background

After eating a large meal last night, I noticed that my tummy had significantly enlarged. After that, I started wondering if eating too much could cause a stomach to explode. Could this actually happen?

Question

  Are you able to explode your stomach by eating too much? Can it pop or break?

I assume your body would just regurgitate the extra food.

  What if you held in the regurgitation? Then would you explode?


texts: How is the Energy Systems Language used in ecology?

texts:
Is the Energy Systems Language useful in systems ecology? It is developed by Howard T. Odum, "the father of system ecology", to make analogies between ecological systems and electronic circuits. But how far this analogy remains correct? What important results have been found from it? Is it widely used by ecologists in other subfields? If yes, then why isn't it applied to other fields?

Related: What are the branches of system ecology?


texts:
what do curly braces in sequence motifs stand for?
e.g. in

RTCRYBN{4}ACG

what is N{4}? moreover, i notice that in TRANSFAC matrix notation the N{4} is completely omitted:

NA  Abf1p
XX
DE  RTCRYBN{4}ACG
XX
P0  A     C     G     T
01  0.500 0.000 0.500 0.000 R
02  0.000 0.000 0.000 1.000 T
03  0.000 1.000 0.000 0.000 C
04  0.500 0.000 0.500 0.000 R
05  0.000 0.500 0.000 0.500 Y
06  0.000 0.333 0.333 0.333 B
XX
P1  A     C     G     T
01  1.000 0.000 0.000 0.000 A
02  0.000 1.000 0.000 0.000 C
03  0.000 0.000 1.000 0.000 G

moreover the MEME suite's transfac2meme completely ignores the second chunk of the matrix after the P1 row.


texts:
What is the evolutionary reason behind sharing the same path for food and air?

For example, we have a nose and lungs, yet they are linked by the pharynx, which is shared with the mouth and oesophagus.

Wouldn't it make more evolutionary sense for the nose + lungs to have their own "path", while the mouth and stomach have a separate system? This would prevent "choking", allow for breathing while eating/drinking, etc.


texts: What does it mean for an enzyme to be "constitutively partially active"?

texts:
I am reading a paper* about the link between the enzyme GSK3 and autism, and I have come across the following statement:

Unlike many kinases that require a signal to be activated, GSK3 is
constitutively partially active; therefore, signals impinging on GSK3
can either decrease or increase its activity.

I am not sure what it means for an enzyme to be constitutively partially active, and I have tried Googling it but have not found any results. Any insights are appreciated.

* Mines MA, Yuskaitis CJ, King MK, Beurel E, Jope RS. GSK3 influences social preference and anxiety-related behaviors during social interaction in a mouse model of fragile X syndrome and autism. PLoS One. 2010;5(3):e9706.


texts:
(sorry if the title seems like flame-bait - but it's a real question).
I'm trying to understand what could have come before the first cell (What are the "minimum requirements" for a single cell?)

From what I've seen, the presented chemical evolution (aka abiogenesis) process centers around self-replicating RNA that gets trapped inside a lipid-based protocell and then somehow turns into a functioning cell.  But it seems like a giant leap to go from that situation to the most basic cell we know about.

Instead of starting from basic molecule and trying to get more complex, what if we take a simple cell (which is actually really complicated) and try to get more simple - try to take out some of the pieces. Work our way backwards. The problem is, I don't know what pieces you can take out. It seems there are several molecular systems that need to be functioning for cell to be viable.  Once you start to imagine a cell without them, it seems the cell will not be able to survive or replicate.

My question is, what would the step just before a "minimum cell" look like?  Are there pieces we can take away and it would still be able to survive and replicate?

** Edit **

Based on some of the discussions in the comments, I wanted to clarify what I'm asking. This is a bit long - but hopefully it will help.

Evolution is a process in which replicating systems transfer beneficial permutations to 'offspring'.  Usually the term is applied to "biological evolution) (meaning something living - from a cell to more complex organism) but I've also heard people refer to "chemical evolution" which is the process in which atoms combine to make molecules and amino acids and the amino acids combine to make RNA which can replicate.  Or fatty molecules combine to make a lipid membrane, etc.

In this process to get to something more complex, you have to have gone through a simpler stage.  To arrive at RNA, you had to have a system that would first produce nucleic acids.  If the first life was in the oceans, you needed something that could survive in and out of water before you now have creatures on dry land.  Each stage has to have a predecessor.

Generally question of the origin of life start at the raw materials and work their way towards the more complicated.  Most of the discussion I've seen basically end with RNA in lipid cells + billions of years = a prokaryote.  The difference between RNA in a protocell and a working basic cell is vast and I haven't seen an explanation on how to bridge that gap.

I'm approaching the question from the opposite direction.  If we take the most basic, simple prokaryote cell - what came before it? Even such a simple cell is in actually very very complicated (semi-permeable membrane, nucleoid, ribosomes, cytoplasm, etc..) There are so many interconnected pieces that it seems are only valuable when working as a whole. Eg, could I have had a cell without ribosomes and then some how it mutated to have ribosomes?  It seem not, because a cell without ribosomes would never have survived/replicated.  The same with other components.. if I have some precursors without that piece, it would never have survived long enough to mutate to now have that component.

So my question is what could the predecessor to a basic cell have been, considering its complexity and the seeming interdependence on the pieces for the cells survival?

I hope that helps explain the question better - thanks for any insight you can provide!


texts:
What factors determine the melting point of a fatty acid?

Chain length
The number of methylene group
The ionized state of the fatty acid
Its degree of saponification
Its ability to alter the entropy of water


texts: Absent gene expression from one of two vectors co-transformed into the BL21(DE3) strain of E. coli

texts:
I've been trying to express two proteins in the BL21(DE3) strain of E. coli.

One gene is in a pCR2.1 vector and the other in a pET-expression vector. When I induce with IPTG and run on an acrylamide gel I only get the protein encoded in the pCR2.1 construct. If I transform the BL21(DE3) cells with each vector independently (only one of the plasmids in the cells) I can get expression for either protein.

Does anyone have any Idea why I wouldn't be able to induce expression from the pET vector in the double plasmid strain but can induce expression from either vector in single plasmid strains?


texts:
I am studying human gross anatomy in order to produce an anatomically correct CGI model of the human body. As part of this, I'm attempting to understand the different features that define the topography of the skin. One class of features is the creasing of the skin, which appears to manifest both on a large and small scale (illustrated in figure 1 of [2]) with variation about the body. In my reading, I have found [1] which catalogues the major creases and only [2] which briefly discusses the smaller creases and cites paywalled articles. Since this topic seems particularly obscure, it would be good to have a definitive summary of this topic. Therefore:

What are the different types of skin creases?
Is there terminology that distinguishes the larger and smaller creases?
How are they distributed about the body?

[1]: Mallouris, Andreas & Yiacoumettis, Andreas & Thomaidis, Vasilios & Karayiannakis, Anastasios & Simopoulos, Constantinos & Kakagia, Despoina & Tsaroucha, Alexandra. (2012). A record of skin creases and folds. European Journal of Plastic Surgery. 10.1007/s00238-012-0774-3.
[2]: Wong, R., Geyer, S., Weninger, W., Guimberteau, J.‐C. and Wong, J.K. (2016), The dynamic anatomy and patterning of skin. Exp Dermatol, 25: 92-98. doi:10.1111/exd.12832


texts: What does the term 'glycogen mobilisation' mean?

texts:
I read that glycogen is a mobilised store of glucose:

Glycogen is a readily mobilized storage form of glucose. It is a very large, branched polymer of glucose residues (Figure 21.1) that can be broken down to yield glucose molecules when energy is needed. Most of the glucose residues in glycogen are linked by α-1,4-glycosidic bonds. [Source]

When looking online, mobilisation refers to something that is capable of movement.
I think glycogen mobilisation has something to do with glycogenolysis but not sure how to easily define glycogen mobilisation.
How would you define glycogen mobilisation in the easiest definition?


texts: Red flower with yellow star in center with fig-like leaves

texts:
This plant has red flowers with a yellow star in the center and has fig-like leaves.

Location: Toronto
Size: 4ft tall by 3ft wide
Date: July 25th, 2020

What is it?


texts: Ran-GEF facilitates an exchange of GDP for GTP in the formation of Ran-GTP in the nucleus as part of gated import of proteins. Would I be correct in calling Ran-GEF or Ran-GAP coenzymes?


texts: Cancer cells and their ability to avoid the immune system

texts:
Since cancer cell retain their ability to trigger the immune system from their pre-cancerous state and any condition that causes an auto-immune reaction in a specific area of the body will attack any cells in that area then could an auto-immune reaction actually attack any cancer cells in that area also?

Noting that regular human cells are not able to avoid 'attacks' by an auto-immune response so the normal cells can not pass on any 'strategies' for avoiding an auto-immune disease attack to any cancerous cells they 'turn into'.. Is all this possible?


texts: How does taking drugs speed up the development of drug resistant or viruses?

texts:
First, here is what I know:

Some infectious illnesses, such as HIV or Hepatitis B, can be treated with the help of some drugs. The problem is that the virus sometimes undergoes mutations which grant resistance to the drug.

First question : Is it so far right?

Secondly, what is not totally clear is why taking drug does speed up the development of the drug-resistant version of the virus. In my point of view, the drug resistant virus will develop anyway with or without taking drugs. I don't see what taking drugs changes. Is it like an intra-competition between the different mutated versions of the virus and in this case, taking drug will eliminate all the mutated versions that are not drug-resistant and, this way, favour the development of the drug-resistant versions?


texts: Do alternative start codons code for methionine after transcription?

texts: There is some literature which shows that all start codons code for methionine. However, in the standard genetic code, the alternative start codons clearly code for leucine. Does that mean these codons will code for leucine when they are encountered during translation (after start codon has been initialised and translated).


texts: I have question about cholesterol, as I know we can get cholesterol using vegetables and meat, so what is good and what is bad ?


texts:
I googled it, It didn't helped me a lot.

So Why cancer disease is named after sun signs ?


texts: What are the requirements for a spectrometer to be used in biological research?

texts:
Suppose one would do spectrophotometry on biological materials. What would be the minimum requirements for the measuring device so that the results could be published in a reputable journal? I suppose that two important properties are

resolution of the spectrum (would e.g. 25 nm be enough? 15 nm? 5 nm?)
measurement error (10%, 5%, 1%, ..?)

What else (if anything) should be taken into consideration?


texts: Do effects of caffeine on human body change with habitual use?

texts:
I've been reading about homeostatic nature of a lot of neurobiological processes - the brain is trying to maintain a balance by desensitizing receptors, re-uptaking and breaking down neurotransmitters.

With this in mind, I'm interested in what happens to the receptors in the brain with chronic use of caffeinated beverages.  Let's say an occasional caffeine drinker likes the cognitive boost of caffeine and starts to consume it habitually/chronically - every day. Will the caffeine drinker experience the same effects day after day, or will the effect change over time?

If there is a change in how the body responds to caffeine, are there any time frames that can be used to estimate when the change takes place - is it X days/weeks of habitual use?

Thank you for your input!


texts: How to keep Paraffin Sections from falling apart?

texts:
I've been trying to make 5 uM sections of injured mouse spinal cords and stain the tissue with Luxol Fast Blue and H&E. At first I was removing the bones from around the spinal cord, but the tissue just fell apart after I got it on the slide. I think because it had been severely damaged.

I thought I might be able to hold the tissue together better if I kept the bone, so I took a spine and decalcified it with 500mM EDTA for 1 week and tried again. But the bone tissue just pulled away from the spinal cord.

These were some of my better images. I have many others that are even less intact. I see the tissue fall apart on the slide during the drying step, after I put the section on the surface of a water bath and catch it on the slide. I have seen some sections spread all the way across the slide. I suspect it has something to do with water getting trapped under the paraffin section and not drying correctly.

How can I improve the procedure to keep the tissue in 1 piece?


texts: What do repopulation and expansion mean in stem cell biology?

texts:
I was studying a lecture on the effects of cytokines on hematopoiesis, and it uses these two terms often in the context of the effects of regulators on hematopoietic stem cells:

All repopulating bone marrow HSCs express a fibroblast growth factor (FGF) receptor that supports HSC expansion
TPO may has a role in promoting the survival of repopulating HSCs, however, it contributes to both generation and expansion of HSCs during definitive hematopoiesis.
Etc.

I looked online and honestly struggled to find any form of a definition on these two terms. They are used awfully alot though which makes it kinda weird too frankly.


texts:
Can one be immune to the new coronavirus?

Another question is what is the exact definition of "being immune". Does it mean that even when the virus enters my system, it cannot multiply?


texts: Are there neurons that can sense light shining in your ears?

texts: I know someone who bought earphones that shine light in you ears. According to what he was told, there are neurons that sense light and then make you feel wide awake when activated, which seemed like snake oil to me. Apparently the pineal gland may be able to sense light and it does secrete melatonin - a sleep regulating hormone. I'm still sceptical though as its stuck in the middle of your brain. Would shining lights in your ears be able to have any effect on how awake you feel?


texts: What is this plant with hardened fruits on the beach in Mozambique?

texts:
We saw these near the Barra and Tofinho beaches in the Inhambane province in Mozambique, in July. They were hard and leathery and dry to the touch, long past something resembling edible fruit.

Anybody have an idea what they might be? (just curious)

Edited: Here is some context around the tree.


texts: Spread of malaria from an infected person

texts: If a person is infected with malaria, how can that person be a part of spreading malaria? As in, if a female anopheles mosquito sucks blood out of that infected individual, how is it possible that malarial schizonts will be only sucked by the mosquito and not pure blood? The point is, out of such a huge volume of blood, how can only malarial parasites enter the suckling mosquito?


texts: Geographic regions as subpopulations/demes

texts:
I am developing a computational simulation for DNA barcoding. One of the parameters in my simulation is the number of subpopulation/demes, which I label as $K$. Most studies that use DNA barcodes tend to focus on a single geographic region.

My question is: is it valid to presume that a single geographic region is equivalent to a single subpopulation/deme?

For example, if the focus was on cichlids of Lake Malawi, would it be a safe assumption that Lake Malawi comprises a single subpopulation/deme?

Eventually, I would also like to incorporate migration rates into my simulation, but these are very difficult to estimate without accurate data on $F_{ST}$.

Any insight would be most helpful and is warmly welcomed.


texts: Specific mechanism behind lethality of yellow coat color in mice

texts:
Our high school genetics chapter has some extra information about L.Cuenot. It only covered his research, and the fact that mice homozygous for yellow coat color would die before birth. It was an example of a lethal allele.
We have learned about sickle cell anemia, thalassemia, and hemophilia. All of them had a specific reason/mechanism which caused damage. For example, it's not the shape of the red blood cell in itself which is problematic, it is the fact that it can't carry enough oxygen. Therefore the cell will die off much quicker than normal cells.
I asked few of the biology teachers why the yellow coat color was lethal, but they couldn't provide any answer.
My question is, what causes the mice to die before birth?
Links to relevant articles or excerpts from them are highly appreciated.


texts: Can a macrophage differentiate back into a monocyte?

texts: I know that monocytes differentiate into macrophages when they enter the tissues, but do macrophages stay in those same tissues for the remainder of their lifespan, or do they differentiate back into monocytes and re-enter the bloodstream at some point?


texts: Is apparent competition a suitable term in situations where one species is not negatively affected?

texts:
When two prey (or resource) species share a common predator (consumer), they can be in apparent competition. An increase in one prey species can increase the common predator density, which negatively influences the other prey species.

A textbook (Molles, Seventh edition, ISBN-10: 0077837282) gives an example of apparent competition that confuses me. It gives another definition "one species facilitating populations of a predator or herbivore of the second species." Thus, one of the species does not have to be consumed by the predator/herbivore.

The specific example is that there are two plant species. Species A becomes the habitat for the herbivore (but is not consumed by the herbivore). Species B is consumed by the herbivore. Therefore, an increase in species A will increase the herbivore density and has negative effects on species B. I thought that to form an apparent competition relationship, it has to be mutually negative relationship (-,-).  In this example, there is no mutually negative relationship. Furthermore, the plants do not share the common herbivore.

This is simply a definition question. Different sources have variable definitions, but is the example really considered an apparent competition?


texts: Using anatomical terms for human organs and parts of plants

texts:
I know how to apply anatomical directional terms (e.g., dorsal/ventral, anterior/posterior, etc.) for animals as a whole (bipeds and quadrupeds).

Recently, I've been studying plant physiology, and I came to know that the upper surface of a leaf is the ventral surface and the lower surface of the leaf is the dorsal surface. I cannot understand how these terms are applied to plants and leaves.

I've also seen anatomical directional terms being used for body organs such as the brain.

I want to know how anatomical terms are applied for parts of plants and body organs.


texts: How Many Generation We can Run a Mycelium of Pleurotus ostreatus/Pearl Oyster?

texts:
I am able to grow mycelium successfully on the spent coffee grounds. And mycelium is successfully fruiting once/twice on the same substrate. I am cloning by taking mycelium from the existing one (which is fruiting at present) and transfer to the new jar and run it for 8-10 days and use it in new box for fruiting next generation.

What I am growing is 4th generation(I mean the transfer cycle).

As I am Newbie, I have done some sort of research and started with a master spawns (got it from govt. mushroom labs). But I am not able to understand one thing is.
Is it ok to clone using mycelium or do I need to do spore cloning or need to go for master spawn spawns now and then or its ok to continue to nth generation and keep eating the fruits.

Is there any serious issues with my cloning?


texts: Does amount of sperm affect fitness of baby?

texts:
If there's a 3 day ovulation period in which to have intercourse, would it be better (to create a more fit/healthy baby) to have sex once and ejaculate more sperm than have sex three times with reduced sperm count?

You would think that the more sperm ejaculated at once would result in much more competition to reach the egg, leading to a more fit spermatozoa, and presumably a more fit baby.

If the egg is fertilized during a lower level ejaculation, a less fit spermatozoa can fertilize the egg since there's less competition. Meaning a less fit baby?

Keep in mind I'm NOT asking about the chance of getting pregnant, I'm talking about the fitness/health of the baby. Obviously having sex once instead of three times decreases the chance of getting pregnant.


texts: Long-term potentiations that last for a lifetime

texts:
One reads more often than not that

long-term potentiation has been reported to last for as long as several weeks
LTP is persistent, lasting from several minutes to many months

and most sources seem to explain mechanisms of LTP that just last as long - from hours to days to weeks to months. Only rarely it is explicitly mentioned that such-and-such LTP lasts for years or a lifetime, and most authors seem to hesitate to make such claims.

But there are memories (and learned skills) that can be retrieved many years and even decades later, even though not (consciously) used in the meantime.

I have no idea how this kind of "really long-term potentiation" is explained. Three options come to my mind:

The long-term potentiated synapses and the "memories" related to them have actually been used in the meantime (just "unconsciously" or in completely different contexts) and thus been re-newed and re-strenghtened every now and then.
They degraded but have been re-newed without having been used, but by some other mechanisms than "normal" LTP.
They actually did last for such a long time (i.e. didn't degrade) - and the authors just hesitated to claim it (because they could not prove directly).

Is one of these three explanations the correct one, or is there another one?


texts: Can a person survive on blood in place of water?

texts:
This question: Can you get enough water by eating only fish? asks if a person could survive on fish alone. Can a person survive on fish and/ or blood alone of any species if stuck at sea or animal blood as a last resort where there is no water or fire?

Obviously if it was a fresh water fish there is water, but there are fresh water mud skippers that can breathe air and the water to tainted to drink in that case a fresh water fish blood maybe safer than the water. https://chemistry.stackexchange.com/questions/115901/what-can-i-eat-that-will-help-metabolize-blood

Desalination would be the best way to process the blood but this is in emergency situation scenario.

From @PTwr Comment's Link: If you drink blood regularly, over a long period of time the buildup of iron in your system can cause iron overload. This syndrome, which sometimes affects people who have repeated blood transfusions, is one of the few conditions for which the correct treatment is bloodletting. https://what-if.xkcd.com/98/


texts: Workflow for batch analysis of ROI in histology samples

texts:
This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via BLOB detection).  I am hoping to get every airway epithelium annotated as an ROI so I can get colorimetric/masking data from the ROI.

That's the simply stated goal, but there are several issues along the way.  The imager we are using produces files in the MRXS format.  Satyanarayanan group's work at OpenSlide has been great in the initial hurtles of exporting the files into very large tiled TIFF files (~2-5GB each, under JPEG compression, generating a few hundred a week).  This has it's own bugs, but the mailing list has been solid.

Given a very large series of very large tiled TIFF files, what is the best way to train a BLOB (or other) detection method to find an ROI?  Using small images, I've gotten acceptable mapping with WIKA, but every time I try on larger images I run into errors and corruptions (when I don't run into memory limits).  Is ImageJ the best choice for this?  If so which plugins would you recommend trying?  I've used what comes FIJI and I've been exploring over others.  LOCI will load ~80% of the image correctly then run into tiling problems.  Given that you can't choose the ROI strictly on color, but human's can quickly ID it, I think a computer will be able to.

I have two systems I'm trying this on:

64-bit Ubuntu, 32GB RAM, FX-9590 processor
64-bit Windows 7, 16GB RAM, 2x E5430 processor

The Win7 machine is the one required for the imager, and I'm trying to do the analysis on the more powerful Ubuntu box.  Deroulers et al produced an interesting work on the subject, however, my group hasn't been able to implement the system as of yet.

I would prefer an open solution, but a proven solution with propitiatory software would also be acceptable.

I thought the over-arching question would fit here, but if people think I should break it up and put smaller questions on SO, I will.  I'm just not sure we're tackling this the best way from slide to graph.


texts:
Back story.

Watched an episode of Arctic Air, (season three episode six), where they are practicing and hoping to become a licensed search and rescue airline.

Anyhow; two hikers gets attacked by a grizzly bear and whilst one get killed the other manages to throw himself off a cliff and ending up with his leg pinched under a rock. He also has big lacerations on his chest from the grizzly. Finally he manages to send a distress signal.

Though not licensed a team travels out to asses the situation. As they find the wounded climber they start to help. First they clean the lacerations by pouring alcohol over them, and then lay some bandages on top. After a while the injured man complains he is thirsty, and they give him water.

TLDR;/Question If I recall correctly one should not give water to a trauma patient. They can have internal bleeding and/or, as in this case big external wounds which likely has caused quite some blood loss.

Liquid will, IIRC, cause some bad effect on the re-production on blood, and might also affect existing blood.

Am I correct in this? If so; what happens and why should one not give liquid to the patient?

Guess there could be some situations where liquid is proper. E.g. patient has been laying in exposure to sun for N hours and dehydration might also cause ill effects... ? (Kidneys, blood-pressure, plasma?) But that might be a negative in any case if one suspect internal bleeding?


texts: What is the difference between "lineage restriction" and "differentiated" in terms of stem cell biology

texts: Is there a subtle difference between these two concepts or are they basically the same thing? When I mean differentiated, I don't mean terminally differentiated.


texts: Why isn't the sticky bud plant more widespread

texts: Why isn't the sticky bud plant (Galium aparine) everywhere around the world? Because to me it seems that it has the best method of seed dispersion/transportation (wiki link: https://en.wikipedia.org/wiki/Galium_aparine)


texts: Can you see the coloration of Sinosauropteryx with the naked eye?

texts:
In 2010 this beautiful fossil of Sinosauropteryx was put under microscopic examination in order to determine the colors of the preserved melanosomes. It was determined that the feathers were reddish brown with white stripes going down the tail and a white underbelly.

Is it just a coincidence that that's exactly what I would have guessed by looking at the color of feathers in the fossil? Am I falling prey to
hindsight bias? Or is it the case that the feathers are so well preserved that their color is visible to the naked eye?

By Sam / Olai Ose / Skjaervoy from Zhangjiagang, China - Dinosaurs!, CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=4209411


texts: Is sequencing error a function of the nucleotide being read?

texts:
Checking out on Google Scholar, I can see that for Illumina (just to consider one example) the sequencing error rate is of the order of 0.001-0.01 per nucleotide.

Talking about sequencing error, let's consider mismatches (substitution of one nucleotide by another) only. Knowing the "true" nucleotide at a given position, is it as likely to be read as any other specific nucleotide during a mismatch or are there bias? For example, if the true nucleotide is A, is it more likely to be found being as a G (as they both are purines) than a T or a C? Are some nucleotides more likely to be misread than others?

I am hoping the answer won't depend too much on the sequencing techniques.


texts: Continuous EEG: Where does pronounced power peak at 38 Hz come from?

texts:
I'm pretty new to EEG analysis. I measured EEG on six scalp positions over night. When I plot the power of the frequencies, I get the following:

What I want to explain (and didn't manage to) is the origin of the 38 Hz peak in my case.

The most important steps to arrive at my graph were (using Python-MNE):

band-pass filter of data (1 to 45 Hz)
resampling from 512 Hz to 200 Hz

Then for every of the six channels:

cut recording into consecutive segments of 2 sec duration

exclude segments if:

maximum allowed voltage step of 50 µV is exceeded
activity is lower than 0.5 µV
maximum and minimum amplitude exceed +/- 200 µV
maximum absolute difference of values in the segment > 200 µV

further:

retain only segments that are ok for all electrodes
randomly choose 15 such good segments (all electrodes) from every participant
calculate FFT for every 2 sec time segment for every electrode and participant
calculate mean of all these FFTs
plot

My question is: is someone familiar with such an artifact at 38 Hz? Where could it come from? These are the things I already checked:

it is pronounced in every participant
it is pronounced in every electrode
eye movements are unlikely since this peak is there after filtering out horizontal eye movements via ICA
electrical devises are unlikely since they should peak at 50 Hz
it is pronounced when segments are 6 sec instead of 2 sec
I also used a notch filter at 50 Hz instead of the bandpass filter, with the following result (here the individual 15 segments are shown, but the 38 Hz peak is still there):

Does someone have an idea where this feature could come from?


texts: RNA polymerase Sigma subunit: transcription factor, coenzyme, or what?

texts: Studying prokaryotic transcription, it seems that the α2ββ′ω core enzyme + the sigma (σ) subunit comprise the ‘holoenzyme’ required for prokaryotic transcription. In traditional enzyme nomenclature, this would indicate that the α2ββ′ω is the ‘apoenzyme’ and that the sigma subunit is the cofactor or coenzyme. However, I’ve not been able to find any sources that clarify whether or not the sigma factor is indeed a coenzyme (not cofactor since that has to be non-organic), and if not what it actually is and why. Any clarification would be appreciated.


texts:
A controversial concept in Biology "Group Selection", has caused confusion and conflict amongst scientists since the since the mid 1990s. The more general realm of study is termed the "unit of selection" discussion.

Definition

A simple working definition for "group selection" (edit/discuss this!) is:

  "Selection for traits that would be beneficial to a population of units at the
  expense of an individual unit possessing the trait" (here)

Question

  "What examples of group-selection are there?"

To add more structure, perhaps answers would consider the following details:

Organism/Species in question
Unit that experiences cost in fitness
Group that experiences benefit in fitness
Group-selected trait
Explanation

Forward Example (trait whose presence benefits the group)

Organism: Homo sapiens, Humans
Unit: Cells and their genes
Group: Collection of all cells in one individual Human body
Group-selected trait: anti-cancer traits, e.g. apoptosis (programmed cell death) via p53 ("guardian angel" gene that "kills" cancerous cells)
Explanation: Apoptosis is costly to the perspective of a cell, since it kills the cell and its genes. This enables the individual as a whole to live for long enough to mate and yeild offspring. Fitness of cells relative to other cells in the body is reduced, but fitness of the genome as a whole of that individual is increased relative to other individuals of that population -as a result of cancer-directed apoptosis.

Reverse Example (trait whose absence benefits the group)

Organism: Cervus elaphus, Red Deer
Unit: Individual red deer and their genomes
Group: Isolated population of red deer and the population gene pool
Group-selected trait: Lethal potential of antlers (e.g. sharp single antler instead of two blunt antlers).
Explanation: Consider a one-antlered stag, whose single antler is imbued with a jagged edge and is the product of a point mutation in his genome. During a rut he is able to win against other males as his antler inflicts potentially fatal injuries. This allows him to mate many females and have many offspring - however this leaves the population at risk of becoming extinct since the mating season would either have too few males to form a rut, or due to deleterious inbreeding defects in the next generation.

Links

Wiki: http://en.wikipedia.org/wiki/Group_selection
History: http://ib.berkeley.edu/courses/ib160/past_papers/beroukhim.html
Published Review: http://arxiv.org/abs/1204.6491

Of course do not feel restrained in your answers by the above suggestions - the point is to discuss the topic and learn!


texts:
I read on https://en.wikipedia.org/w/index.php?title=Nail_(anatomy)&oldid=863800434#Growth:

  Actual growth rate is dependent upon age, sex, season, exercise level, diet, and hereditary factors.

Why does the exercise level impact the nail growth rate?


texts: Does transcription terminate at the end of antibiotic resistance genes on the Duet expression plasmids?

texts:
I am working with the pETDuet and pRSFDuet plasmids to express RNAs under control of the T7 promoter. On these plasmids the antibiotic resistance genes (Amp for pET, and Kan for pRSF) are downstream of the T7 promoter site where I cloned in my genes. The Amp and Kan genes are transcribed in the opposite orientation of the T7 promoter and since these genes are downstream from where I inserted my genes, readthrough transcription from the resistance genes would result in a sequence complementary to the RNA sequence I wish to produce. My question is: do the antibiotic resistance genes in these plasmids have a built in transcription termination mechanism?
I have used the ARNold tool: http://rssf.i2bc.paris-saclay.fr/toolbox/arnold/index.php to look for Rho-independent terminators at the 3' end of the antibiotic resistance genes and in the region downstream. There was one hit for the pETDuet plasmid but nothing for the pRSFDuet plasmid. There were no hits for the  pCDFDuet or pCOLADuet plasmids either. My sense is hairpin terminators were not specifically incorporated to stop transcription downstream of the antibiotic resistance genes. The other possibility is the antibiotic resistance genes terminate in a Rho-dependent manner, is this known to occur for the Amp and Kan genes?


texts:
When staining transciption factor proteins with fluorescent antibodies (Alexa, etc.), why are the fluorescence signals stronger in the nucleus as compared to fluorescence signals in the cytoplasm (in context of transcription factor-activation?)
Is it simply spatial localization, that more fluoresence-marked proteins are at the same place, or are there other factors related?


texts:
After I planted some spring mix lettuce a couple of years ago, nothing survived except for this plant.  It doesn't look like any of the leaves that I am used to.  Does anyone know what it is?  Is it edible?  I am located in East Tennessee.

Thank you for any help you can give!

I just posted some more photos with measurements. The total length from base of the plant to the end of the leaf is about one foot. These plants have no flower growing from the base, however there is a separate plant nearby in the mix that does have flowers. I included a photo of it in case it is related. The original plant in question has leaves that are mostly smooth (some have tiny white or clear hairs on the backside or stem...some are smooth). They are almost as thick as spinach leaves.


texts:
Problem
A transmembrane protein has 1000 aa. The 5th aa is found on the external side of the cell membrane. It interacts with the aqueous environment outside the cell. Amino acid 90 is inside the membrane bilayer. Aa 100-600 are intracellular, and 200-400 make a tight ball with minimal exposure to the aqueous cytoplasm. Amino acid 979 is found on the extracellular side of the protein where it forms a weak ionic bond with Cl-.

a. Can you draw the protein and mark positions of all mentioned aa in it?

b. What are the properties of these amino acids?
￼￼￼￼￼

I dont necessarily want/need the exact answers to these questions, rather i would like some guidance in what principles i would need to understand and conceptualize to attack this problem. Thanks all !


texts: How does 'phosphorylation of glucose' maintain concentration gradient in membrane transport (facilitated diffusion)?

texts:
Our book explains how glucose from the blood plasma gets inside red blood cells via facilitated transport.

It states here in the book that the glucose will be transported inside by a carrier protein. Then the glucose will be phosphorylated by ATP. The phosphorylation of glucose molecules maintains the concentration gradient. This prevents the glucose from diffusing back to the blood plasma.

Based from my current understanding, concentration only change when the number of dissolved molecules changes.

My question is, "How can phosphorylation maintain the concentration gradient if it doesn't change the number of molecules inside the red blood cell?"


texts: Why is there no toxic effect on the bulbuls feeding on Cascabella thevetia (oleander) nectar?

texts: I have a huge Cascabella thevetia by my house and I know that its sap and fruits are extremely poisonous.However I have seen red vented bulbuls and wasps feed on its nectar.Also this confirms it but doesnt specify nectar infact it says plant parts...The same source says the poison affects vertebrates and the birds are definitely vertebrates.So why it doesnt affect them?


texts: How to replace intron region in a plasmid?

texts:
I'm considering working with the plasmid pRFHUE-eGFP and would like to replace the gpdA intron (which is the eGFP promoter region) with a promoter from another organism.
What would be a good strategy for replacing the intron if I already have the other gene in-hand?
Would I cut out the fragment between the SalI and SmaI restriction sites and then insert the new promoter with compatible overhangs there?


texts: How is RNAse contamination in RNA based experiments prevented?

texts:
Does anyone have any suggestions to prevent RNAse contamination when working with RNA?

I tend to have issues with degradation regardless of whether I use DEPC treated / RNAse free water and filtered pipette tips.


texts: Which brain regions are D1 dopamine receptors expressed, and which brain regions are D2 dopamine receptors expressed?

texts:
This is a follow-up question to If D1 receptors stimulate adenylate cyclase (through GPCRs) and D2 receptors inhibit it, then why do mutations in both have similar effects?.

As a further question - I'd like to ask: do D1 dopamine receptors have the same (excitatory) effect everywhere in the brain? And do D2 dopamine receptors have the same (inhibitory) effect everywhere in the brain?


texts: How pulmonary vasculature removes embolism?

texts:
This book says:

  Pulmonary vasculature removes emboli before they reach into systemic circulation.

I can speculate that if the emboli are made of fat or clot then our body could degrade it but how does it removes air emboli?

Wikipedia without any citations just states:

  Gas bubbles arising from decompression sickness are generally formed in the venous side of the systemic circulation, where inert gas concentrations are highest, the bubbles are smaller at first and they are generally trapped in the capillaries of the lungs where they will usually be eliminated without causing symptoms.

Could anyone provide a reliable source for it or a satisfying explanation?


texts: Why Milky serum in diet rich with Triglycerides?

texts: When we eat the meal rich with triglyceride our muscle or blood after seperation of the serum the color of the serum will be milky. What is causing to happen in our serum ? Milky serum (lipemic serum)


texts: Is the Insulin Receptor Considered an Enzyme?

texts: Can we consider insulin receptor an enzyme? In other words, does the insulin receptor have enzymatic characteristics?


texts: What's the purpose of colorful mushrooms' caps?

texts:
What's the purpose for many mushrooms to have colorful caps? Is not it is in their interest to hide as well as possible? Or there are mushrooms that propagate by being eaten, like fruits?

Why not all the mushrooms are poisonous?


texts: What is the difference between the two? I see them frequently listed together in conference descriptions but can't seem to find anything that clearly explains the difference.


texts:
I was wondering can multiple HIV virus infecting same T cell ?
Coz in flu virus they have SA to cleave of those sialic acid residue preventing re-infection of the same cell by other viruses to maximize the amount of cell get infected.
I was wondering is there any mechanism found in HIV virus like what found in flu virus to prevent re-infection of an already HIV-infected T cell.

(little bit more about HIV virus that is irrelevant to the question, coz i was told that there is some HIV possible to hide in our body, but then i don't understand what it is the meaning of this hiding? Q1:Is the "hiding" refer to the genome of HIV that integrated into T cell. some of these infected T cells circulating in the blood Q2: will some of them reside in lymph node? Q3: and what make these infected B cell proliferate so to keep these B cell with the hiv genome long existing? will the virus transform these T cells into self proliferating? but will that be like cancer cell uncontrollably proliferating or well controlled?)

Thank you everybody


texts: Applying drugs to brain via scalp (transdermal)

texts:
Many medications are intended only for the brain, but are taken orally. Hence <10% finds its intended target, while the remaining >90% is at best wasted, and at worst causes unwanted side-effects.

Valproate is a classic example; it is medicated as an antiepileptic, but only a small fraction crosses the brain blood barrier to make it into the brain. Because of this, a large dose is required, and unwanted side-effects are common.

However, certain (small molecule?) drugs (e.g. Ibuprofen) can be applied transdermally.

For a drug intended for brain tissue that allows transdermal application, is there any sense in applying on the (preferably shaved) scalp?

Is this a known mechanism of administration? If so, does it have a name?

Is there any way of correctly scaling the dosage? For example, if experiment shows that 50% of substance X taken transdermally reaches the bloodstream, if it is administered to the scalp is there any way of figuring out how much ends up in the brain and how much ends up in the rest of the body?
Since this is a tricky and obscure question, may I also ask this: how to go about finding an answer to this? Where else can I ask?


texts:
Is there an on-line database that will enable one to find the genetic distance between two species?

I'm vaguely aware that there are various metrics used that may give different results, but I'm looking for a database that can be used to derive any of these metrics.


texts:
This photo is from Guide to the Six Kingdoms of Life under Archaebacteria:

It's not obvious to me where I can find archaea in this photo, although the website seems to indicate it's clear.

Question: Where in this photo can I find archaea?


texts: Chickens roosting, is it sleep or torpor?

texts: At night when they roost, do chickens experience a state of sleep (meaning do they move from NREM1 to NREM2, NREM3 and REM) or are they in a state of torpor (reduced metabolic rate and decreased physiological activity)?


texts: Haplodiploid species that are not eusocial

texts: Haplodiploid species need not necessarily be eusocial and eusocial species need not be haplodiploid (reference). Everywhere I look its been mentioned in general terms that some species of bees, termites and wasps are haplodiploid but not eusocial. What are some specific examples of haplodiploid species not being eusocial? I was specifically interested in bees but examples from other species are also welcomed. Thank you in advance.


texts: how to calculate dilution factor and CFU

texts:
I'm very confused
I did a bacterial experiment where i added 5 grams to 70ml of distilled water that contains 10g of fresh meat. I left it in a sampler container over 24 hours then i cultured bacteria from the broth using an incubating loop onto nutrient agar. I left them to culture then observed 29 colonies of bacteria.
I observed 1 bacterial colony under a light microscope and counted 19 bacterias.
How do i calculate the dilution factor and CFU?
i need to calculate how many bacterias were on the agar plate?
please help!


texts: Is transition more common than transversion during the evolution of duplicated genes?

texts:
Transitions are base mutations of purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T). Transversions are purine to pyrimidine or vice versa (A <-> C, A <-> T, G <-> C, G <-> T). And it is well-known that transitions are more common than transversions in the populations.

So what is the condition in the evolution of duplicated genes? Suppose a gene A is duplicated with two copies A1 and A2 in the same genome (not two alleles in different sets of chromosomes, or the same gene in two different cells/organisms). At first A1 and A2 had the same sequence, but then they went through an evolution process and each got some mutations. Now let's check the sequence of A1 and A2 again, are the differences between A1 and A2 mainly transitions instead of transversions?

Although I think it would not be surprising to find that transitions are more common in this condition, I've searched some papers focusing on the evolution of duplicated genes to look for some support. However, they mainly discuss what happened to their functions instead of sequences.


texts: How would you identify the independent variable in an experiment where it isn't specified?

texts:
I know that the above question is broad, but I specifically want an answer in terms of the following investigation - all of question 3 (ONLY) of this paper.

The independent variable, according to this mark scheme is the presence of hidden food in the cage to which the rats are released. How am I to identify this if it's not stated that the investigation investigates the ability to learn with the presence of hidden food.


texts: It is said that the coronary artery that gives the posterior descending artery(PDA) determines if the heart is right dominant(most cases) or left dominant. Is there any reason to this? Why PDA?


texts: Thousands of Reporters Integrated in Parallel (TRIP) barcodes

texts: Has anyone worked with constructing barcodes for TRIP? How does constructing of barcodes work in general? I don't seem to be able to grasp the basics of constructing these barcodes.


texts:
The mole-like golden moles.

The hedgehog-like tenrecs.

The shrew-like sengis.

The rodent-like hyraxes.

The anteater-like aardvarks.

The whale-seal-hybrid-like sirens.

The tapir-like proboscideans.

All these mammals, diverse in appearance, actually belong to one superorder, called Afrotheria.  Which raises the question — what are the anatomical characteristics common to all afrotheres?


texts: Antiparallel DNA Strands - Error Correcting Code?

texts:
Let me quote Wikipedia.org:

"The two strands of DNA run in opposite directions to each other and are thus antiparallel."

There is a practice or method used for error correction with regard to parking tickets: First the number plate is written down from left to right, then again but in reverse (right to left) order.

So my question is: to what extent does the antiparallelity of both DNA stands constitute an error correcting code?


texts: Do people of the same height walk at the same speed?

texts:
I'm working on a project that concerns movement and the human body. Before I begin to experiment, I need an answer to a question I'm sure has an answer, but doesn't Google well.

What I need to know is firstly whether I can assume that if people have the same height, they will also have the same leg length?

Secondly, if two different people have an identical height, will they take the same amount of time to cover the same distance when running at the same speed, regardless of their unique technique for running?

An Example:

Say I'm with a friend, we're both 6 feet tall exactly, we both get on to treadmills side-by-side and set it to a speed of 7.5km/hour.

Will we be moving exactly the same body parts at the same time - will our feet land on the treadmill at the same time?

Is there a possibility that people of the same height do not have the same leg length? If so, how likely is it on average?


texts: Can conventional PCR amplify DNA from different organisms from a specimen in a single step?

texts:
I've understood so far that in conventional PCR, the most abundant DNA/genotype present in the speciment at the beginning of the reaction is selected and esponentially amplified. So that cPCR are likely to miss mixed infections.

But I had 1 case in which when I sequenced the PCR product I got in BLAST 100% similarity for 3 different species at the same time. Is this suggestive of a mixed infection?


texts: Is there a reason for the choice of E.coli as a model for many bacterial systems? Other bacteria such as B.subtilis are also used, but why is E. coli preferred?


texts:
I know that a diplobacillus is a bacillus bacteria that has a buddy 'attached' to it.
What I haven't been able to determine is exactly how is it 'attached'? Are their cell membranes fused - are they even touching? If they aren't fused, what keeps them together? Also, does this make diplobacillus a multi cellular organism because there are multiple cells in this organism?


texts: What does the species name 'fistula' mean?

texts: Cassia fistula is tree with yellow flowers. As a medical student what amazes me is that the word fistula implies other meanings. A fistula, at least in medical science refers to a tract with two epithelial openings.


texts: Why does the intelligence of an animal correlate with the brain to body mass ratio more closely than to the mass of the brain itself?

texts: It seems counterintuitive that a large animal with a large brain is likely to be less intelligent than a small animal with a medium size brain. It would make more sense if the intelligence of the animal correlated simply with the mass of the brain, since there is more tissue to use for cognition - yet it is the ratio of brain mass to body mass which seems to matter more. Why is this?


texts: Why can't diamine oxidase be supplemented?

texts:
I've read from an academic article that diamine oxidase cannot be supplemented  but it had no explanation as for why. I am curious as to why this?

  Food rich in histamine or red wine may cause allergy‐like symptoms
  such as sneezing, flush, skin itching, diarrhoea and even shortness of
  breath. The suspected reason is a diminished histamine degradation
  based on a deficiency of diamine oxidase. As diamine oxidase cannot be
  supplemented, a histamine‐free diet was implemented to reduce
  histamine intake.


texts: I get regularly get déjà vu - but I know it's not a memory recall - I always think it's from a dream

texts:
My apologies if this is not the right forum for a neuroscientific/psychological question, especially not one coming from personal experience. Please close/move as appropriate :)

Doubtless we're all familar with déjà vu - people invariably describe it as the feeling of recalling their current situation from memory, as though they're repeating something they've experienced in real-life before.

I've regularly had this experience - it happens about once every month or two, the experience never lasts more than 5-10 seconds, and it can be unnerving. However my experience is different from what others always describe: when I'm having an episode I know I'm not re-experiencing something I've done in real-life before, instead I have this feeling that I'm experiencing something I've had in a dream before - a dream premonition, not a memory of real-life. After the experience fades I return to normal and recognize that I have no dream-memories of whatever it is I just experienced - a false feeling of post-hoc premonition.

My father reports the same as well, that he has times where he swears he's "seen this before in a dream" instead of a momentary false memory - he named the experience "breaking a dream" - no-one else seems to using the same terminology as my dad so searching for that online comes up blank. I do see very rare reports online of similar experiences but we "false-dream" deja-vu subjects are definitely in the minority.

I'm curious where my (apparently inherited) ability to slightly discern deja-vu experiences from false memories might come from, and how this "false dream-memory" vs "false real-life memory" difference has a basis in neurology.


texts: Can a pathogen be totally resistant to the human immune system?

texts:
Can a pathogenic organism be totally resistant to the human immune system? For the purpose of this question, the organism in question must cause a disease.

Examples of organisms that would qualify as totally resistant:

Pathogenic organisms that are completely undetected by the immune system while the disease that they cause runs its course.

Pathogenic organisms that, even if detected, are completely invulnerable to the immune system. For instance, macrophages and other immune cells would not be able to destroy even one cell of such an organism.

Is it possible for such a pathogen to exist? Are there any such pathogens?
(For the purpose of this question, the HIV and diseases that only manifest in immuno-compromised individuals do not count)


texts: How would homologous recombination and mutations affect speciation?

texts:
I'm wondering how homologous recombination and mutations can affect how speciation can occur from one species (so that 2 will be created).

I'm doing research and I found that different mutations and genetic combinations occur in two geographically separated populations which can lead to speciation.

I know recombination can result in different genetic combinations, but how does that factor into a phylogenetic tree? Wouldn't recombination technically play no role in leading to evolution?

My (sort of) guess is that say recombination creates a population with a lot of AA genes and the other population, say by chance (genetic drift), has a population with a lot of aa genes.

We know A and a differ by perhaps a few SNPs, so on average, the two populations would become slightly different from one another due to genetic drift and geographic separation.

Do I have the right idea here? I'm not 100% sure how recombination during prophase I would affect recombination. Hoping someone can clarify this for me or provide some new insights.

Thank you!


texts:
I am doing an experiment where I have treat the cells with a drug and calculate their counts. I would like to know if is bad to trypsinize the cells in consecutive days i.e. twice within 48 hours. How much time do the cells need to attach again on the surface of the flask? I want to know if I can treat them with drug the same day I add trypsin for counting.

Thanks.


texts: Is a wild-type strain more "fit" than its mutant strains?

texts:
Question's context

In the context of a presentation on mathematical models for antibiotic-resistance bacteria research, someone mentioned that wild type strain (WT) are expected to be more fit than mutant strains.

Assume that there is one WT introduced to an environment E (no drugs present), and consider the WT mutates, yielding a certain number of fit-enough mutant strains.

Question

Is WT expected to be the ONLY strain to persist in the long run?

How common is this scenario?

What about co-existence?

Examples and references for beginners will be very appreciated.

My context:
Please note that this may be a very naive question, and I may even be using the wrong terminology, given my background on mathematical modeling and a very, very basic knowledge on evolution.

Thinking about dynamical systems, I would have guessed that coexistence would be possible, so I didn't understand how strong was such an assumption.


texts:
I'm pretty sure there's a spider in my ear. I feel it move and hear the scratching (i blame my cat for playing with bugs in the bed). I've gone to the doctor, but all they do is flush my ear with water and it never works. I've decide to just wait for the damned thing to die.

How long will it live in my ear without coming out? How quickly will it die if i flush my ears with peroxide once a day?

any other advice for how to get the stupid thing out?