texts: I have a list of miRNA IDs and a list of mRNA IDs and they are from Mus musculus species. I have converted the list of mRNA IDs to gene symbols by a list of data that was exist in NCBI and miRNA IDs list to gene symbols using Diana but I got in trouble because gene symbols on NCBI didn't match with the gene symbols that exist in Diana site. I think the problem is that naming of gene symbols doesn't follow a specific rule in different databases and are not standardized. Can anyone tell me a good way to transform both mRNA & miRNA lists to a platform for example unigene that would be unique in all kinds of databases?


texts:
Presumably, as a whale or seal dives, its lungs get compressed by the increasing water pressure, and it gets less buoyant.

Under this model, for a given amount of air taken in at the surface, the animal has a very specific depth D at which it is neutrally buoyant. Any deeper, and the lungs shrink, making it negatively buoyant. Any shallower, and the lungs expand, making it positively buoyant.

In other words, until it reaches depth D, the animal is positively buoyant. To get to depth D, the animal would have to do a lot of work swimming down, fighting against its own floatiness.

The amount of air that keeps you neutrally buoyant at 10 meters will inflate to twice the volume once you surface, keeping you pinned there. Speaking as a scuba diver, I can say that it would take a lot of work to dive back down to 10 meters. (We deflate our air vests at the surface and re-inflate at depth from our incompressible tanks, something animals don't have.)

For very deep divers like sperm whales, swimming down against positive buoyancy seems like a huge energy waste, the kind that one might expect wouldn't be tolerated long by evolution.

So do marine mammals do anything to compensate for the effect of fluctuating lung size on their buoyancy? One guess is that they actually exhale fully before diving, thus making lung buoyancy a small player in the overall body buoyancy. Another guess is that they compress the air with their chest muscles at the surface in order to sink. These are just guesses; I'd love to hear the real story.


texts: How does anaerobic burst-flight performance scale with mass?

texts:
Quails employ anaerobic burst flight to escape predators and the Quetzalcoatlus northropi have most likely used it during launch and climb out, then transition to soaring.

Now, I have read these papers, from Marden, Witton and  C.J. Pennycuick

I won't play pretend I really don't know that much about bird flight mechanics, so I easily got confused reading them.

How does anaerobic flight performance scale with mass?


texts: Could someone explain the join in the SARS-cov-2 genome at location 13468?

texts:
I am having trouble understanding the reference sequence for sars-cov-2, NC_045512.2

Three nucleotides equals one amino acid, right? But the nucleotide at position 13468 seems to be used twice, so the sequence starting at 13463 reads:

tta aac ggg ttt ... which translates to LNGF

However, according to the reference, the translation is LNRV, so it's read as tta aac cgg gtt etc - like the c is repeated.

The reference says "join(266..13468,13468..21555)" but how does this work and why?


texts: If we don't drink water for a long period of time(say,10 hours), as during fasting and then when we break our fast by drinking water why is it that our body starts sweating?


texts:
I'm located in Bologna, Italy, in the city center. I found this insect on by bean plants, I think it's feeding on their leaves.

What is it? The answer to this question suggests that it is a leafhopper, but I can't find the exact species. When approached, they seem to jump away.

 Altough related to the question I linked, I don't think it's a crosspost, because in that question I want to know primarily what's the solution to the problem of white spots on bean leaves, while here I ask for the exact species in the photo.


texts: Reference request for Sydney Brenner's "it might come in handy in the cretaceous" quote

texts:
In {1}, Richard Dawkins attributes a quote to Sydney Brenner without giving a citation. I'm preparing a publication on the same topic and if possible I would like to track down the original reference for the quote. Does anyone know the work (if it exists) in which Brenner made the argument Dawkins refers to?

Here is the text from Dawkins' paper where it is mentioned:

  It is all too easy for this kind of argument to be used loosely and unrespectably. Sydney Brenner justly ridiculed the idea of foresight in evolution, specifically in the notion that a molecule, useless to a lineage of organisms in its own geological era, might nevertheless be retained in the gene pool because of its possible usefulness in some future era: "It might come in handy in the Cretaceous!" I hope I shall not be taken as saying anything like that.

Edit: it looks quite likely that this is referring to something Dawkins heard Brenner say, rather than anything that can be cited. There is a footnote in {2} that reads:

  ...Brenner... has a sardonic wit to match his scientific brilliance. I once heard him lampoon the 'evolutionary foresight' fallacy by imagining a species in the Cambrian that retained in its gene pool an otherwise useless protein, because 'It might come in handy in the Cretaceous.'

So it seems likely that there is no citable source for the quote besides Dawkins' paper, but in any case it would be useful to know if there is a pre-1988 publication in which Brenner made a similar argument.

{1} Richard Dawkins (1988) The Evolution of Evolvability. In C. Langton (Ed.) Artificial Life, SFI Studies in the Science of Complexity. Addison-Wesley Publishing Company.

{2} Richard Dawkins (2009) The Greatest Show on Earth: The Evidence for Evolution. Random House.


texts: Why do some plant species have lobed leaves, while similar species in the same habitat don't?

texts:
Some plants have lobed leaves, like the English oak (Quercus robur), while other plants growing the same deciduous woodland habitats, and very often growing alongside oaks, such as the European beech (Fagus sylvaticus) don't have lobes. Here are two two leaves side by side for comparison:

These two species should be subject to most of the same evolutionary pressures. Why would one evolve lobed leaves, whilst the other has only tiny serrations?


texts: Will the N- or the C- terminal soluble domain be on the extracellular side?

texts:
Here is a homework question

A single-pass transmembrane protein is destined to be transported to the plasma membrane. In the wild-type protein, a lysine flanks the transmembrane domain on the N- terminal side, and a glutamic acid flanks on the C-terminal side. Both the N- & C-terminal soluble domains carry sequences that can by glycosylated by oligosaccharyltransferase.
After the protein is transported to the plasma membrane, will the N- or the C- terminal soluble domain be on the extracellular side?

My answer is

N-terminal with lysine will be towards the extracellular side and C-terminal will be towards the cytoplasm.

Does this seem right to you?


texts:
I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have >to be fairly substantial.
I'm interested in anything cell/DNA/molebio related with a mathematical connection. I >would prefer something other than mere statistical analysis, maybe something like >differential equations.
I have access to standard undergraduate lab equipment; assume that I'm able to procure all necessary materials and that I'm capable of performing the experiment. Thank you for the help.

As per the suggestion of shigeta below, I leafed through the links, and found gene circuits interesting. So, what exactly is a gene circuit, how are they modeled, and what are they used for?


texts: Can plasmodial slime molds be infected by virus?

texts: According to the definition, plasmodial slime mold consist of a "single cell" with thousands of nuclei. How would such a unique type of cell response to viral infection (if any)? Google search yield nothing.


texts: Why do red muscle fibres have more mitochondria than white muscle fibre but less ATP than White muscle fibres?

texts: This is a question given in my Anatomy book and I am really confused because logically the substance which have more mitochondria should have more ATP as mitochondria is the power house of cell.But the question contrast the logic.


texts: Why we have to damage our muscles to build them?

texts: I know that new muscle cells are made when actin fibers are disrupted. My hypothesis is that muscle mass is limited, from birth, and that nutrients (protein) are only directed to grow muscle when those muscles are actually used. Is this hypothesis true?


texts: Are SLC52A2 and GPR172A really the same?

texts:
The official HUGO gene nomenclature page says that GPR172A (Gamma-hydroxybutyrate receptor) and SLC52A2 (riboflavin transporter, member 2) are the same. The sequence reported by Andriamampandry seems to be the same, but I find no other evidence. Can anyone enlighten me?

(I'm wondering if I should add the SLC52A2 information to the GHB receptor Wikipedia page.)


texts: Where can I find the data on the geographical distribution of the species of Drosophila within various areas of the world?

texts:
Let X denote an arbitrary geographic area where drosophilas occur in the wild. I will need the answers to the questions of the following type:

  What is the three most occurring species of the genus Drosophila within X?

Where can I find the data on the geographical distribution of Drosophila species within various areas of the Earth?


texts: What's the meaning of the label MRE and a number like 162 or 600 in the names of bacteria?

texts:
I've stumbled across labels like E. coli MRE 162 or E. coli MRE 600 for different kinds of E. coli bacteria.

What's the meaning of MRE and the numbers like 162 or 600 in this context?


texts: Does the SMUG1 enzyme break single-stranded DNA?

texts:
The SMUG1 gene codes for the enzyme single-strand selective monofunctional uracil DNA glycosylase.  This enzyme can remove uracil from single-strand (unpaired) DNA.  (Uracil can occur in DNA due to deamination of cytosine.)

What happens when this enzyme removes uracil?  It seems what would be best is that a cytosine would replace the uracil in the DNA strand to restore the original DNA sequence, but I haven't found mention of this.  The alternatives would seem to be that the enzyme simply splits the strand into two strands by removing the uracil (which are then unconnected since this is single-strand DNA), or it joins the two adjacent bases together, deleting the uracil but keeping the strand intact.


texts: We are 7 billion human beings on the Earth. But how many mice are there? How would you estimate such a number?


texts: Genomic DNA resuspension after ethanol precipitation

texts:
I am having trouble resuspending purified human genomic DNA.
The genomic DNA is purified using phenol:chlorofom from ~ 1 mL of blood. After ethanol precipitation, I normally see a large pellet which is then resuspended in 150 uL of TE (10 mM Tris pH 8.0, 1 mM EDTA).

But the resulting DNA solution is extremely sticky.
There are the options I have tried:

1) Incubation at 37C for 1 hr to overnight

2) Incubation at 50C for 1 hr to overnight

3) Incubation at 65C for 1 hr to overnight

The 65C incubations for up to 3 hours do make the DNA solution less sticky, but in the mean times, cause increasing DNA smearing when running on agarose gel. After overnight incubation at 65C, the DNA solution is no longer sticky but shows extensive smearing on gel, indicating DNA degredation/fragmentation at high temperature.

I have also tried resuspending the DNA in 8 mM NaOH, then neutralise it with Hepes, but this doesn't help either.

I am thinking to try silica/glassmilk beads based methodology. Will genomic DNA captured in silica beads be easier to elute and resuspended without the "sticky" issue.


texts:
Why do marine animals have fins?
Why do Marine animals have fins.


texts: Better population models than the logistic equation

texts:
For modelling the population of a single species in a region, the logistic equation is used

$$ \frac{dN}{dt} =kN\Big(1-\frac{N}{K}\Big) $$

where $N$ is the number of organisms, $K$ is the carrying capacity, and $k$ is a constant.

However, for most real primary consumers, in the absence of predation, the population usually deviates from the standard sigmoidal curve in two ways

The population typically overshoots the carrying capacity before decaying again to the carrying capacity
The population usually oscillates around the carrying capacity, rather then remaining constant

Are there any better mathematical models for describing growth mediated by density dependent factors of primary consumers in the absence of predation?


texts:
I read in Thomas Myers book Anatomy Trains:

  Although the muscles themselves have attachments within the anterior
  compartment to the tibia, fibula, and interosseous membrane, the next
  station for the SFL [Superficial Front Line] is at the top of both the medial and lateral side
  of this track, the tibial tuberosity

  Continuing in a straight line upward is no problem: the quadriceps
  begin their upward sweep here with the
  subpatellar tendon. The SFL  includes the patella, the large sesamoid bone designed to hold the SFL away from the knee joint
  fulcrum so that the tissues of the quadriceps have more leverage for
  extending the knee.

I can't find the term subpatellar tendon in my anatomy book. What does it refer to? Is it the patella ligament?


texts:
This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer.
What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is converted to 1D representation in SMILES(Simplified molecular-input line-entry system)? two properties I found that gets neglected are linkages,interaction properties. By properties I meant isomeric count,isomeric threshold etc. Are there anymore properties that gets neglected?


texts: How much does the distance between a transcription factor binding site and a promoter influence transcription?

texts:
Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an activator binding site and a promoter - would placing the binding site closer to the promoter lead to significantly stronger activation, or more robust system behavior?

In some genomics-related models I saw authors assigned weights to binding sites based on position (orientation and distance from the promoter); the general idea was that binding sites farther away could have a weaker influence on transcription. This can be modeled e.g. by decreasing the binding affinity. But that was genomics, and I'm unsure how much of that has any relevance in smaller scale plasmid constructs.

For example, suppose we have a highly specific binding site (e.g. a TALE binding site) upstream of the promoter:

In Fig.1, the binding site A is only e.g. 40 bp away from the promoter. In Fig.2, it is e.g. 5000-7000 bp away. Should I expect this to make a noticeable difference? Would the same apply if it would be a constitutive promoter, with a repressor instead of an activator? What about more complex networks, could the answer change?


texts: How do scientists discover a new antigen and its epitope?

texts:
I've found some database on the internet that list all discovered antigens and their epitopes.
So how do scientists discover a new antigen? Do they try to inject them into the body to see if it causes an immune response or not? And finally if it's an antigen, how do they know their epitopes?


texts: Why is my peripheral vision better for seeing in the dark?

texts: I often walk around my house at night with the lights turned off and one night I noticed that looking straight at an object with very little light available made the object disappear from sight but if I directed my visual else where I could clearly see the object in my peripheral


texts: Do you know which is this small flower in Asturias?

texts:
Was located in the Turón valley on Mieres, Asturias, Spain (https://goo.gl/maps/BMwyfWtiSdw). Found it at 900 meters of altitude. The plant is just about 8 cm high maybe. All the ones I've found were alone. Just one flower from a couple of leaves.

Kind of reminds me of a Cyclamen?


texts: Pyruvate oxidation - where did the hydrogen come from?

texts:
As shown in the diagram above, NAD+ is reduced and becomes NADH by gaining two electrons

Now, where did the hydrogen come from?

In the diagram, pyruvate has 3 hydrogen, but it still has 3 hydrogen in acetyl CoA.


texts: Why aren't D-amino acids used in proteins?

texts:
Possible Duplicate:
  Why are amino acids in biology homochiral?

Why are only L-amino acids used in protein construction, and not D-amino acids?


texts: Why do germs live longer on surfaces than on skin?

texts:
After looking up how long germs live for on surface, I came across lots of resources that explain how long germs live on different surfaces.

A common pattern is that germs survive longer on cold/hard surfaces than on skin.

Why is that?

Wouldn't skin be a much more hospitable environment than something like a desk?


texts:
It seems that many nutrition experiments [directed at human diet] are carried on laboratory mice. Is there any justification that nutrition that is good or bad for laboratory mice will also be same way applicable to humans ?

I wonder because mice and humans, although both being mammals, are separated probably by tens millions years of separate evolution.  By the "mammals" logic, dolphins, cows, wolves, and goats, all being mammals, shall have same diet as mice ?

Sometimes one man's food is another man's poison (lactose differences for example, due to genetic differences). That's man to man, same species. On what is "transfer of nutritional information" from species to species based ?

2) Was it ever established, or the opposite, that all humans have same best diet. Other than known lactose metabolism difference.


texts: How long can you store tissue on 4°C before B-cell extraction and culture?

texts: We receive tissue regularly and extract B-cells for culturing, studying differentiation and survival with diffenet stimulation conditions. However, often the tissue arrives late afternoon and might be put in FCS at 4°C overnight before cell aextarction. I'm not sure however if such storage would impact the viability or functionality of B-cells later on during the culture.


texts:
I read that

  Doherty and Zinkernagel found that MHC- heterozygotes present more
  antigens to the immune system than homozygotes; yet, the infected
  heterozygous mice in their experiment all died, apparently from
  overresponsiveness.

Can MHC-heterozygotes be more susceptible to autoimmune disorders and allergies because there is a tendency of over responsiveness ?


texts: How does DNA resolve on size exclusion resin?

texts:
We generally have a good idea of how DNA separates using agarose gel electrophoresis, how well does DNA resolve on a SEC resin like superose? I get the impression that salt influences where it elutes.

Is it possible to compare the molecular weight of DNA and where it elutes to the molecular weight of proteins and peptides and where that elutes?


texts: Why do cats like enclosed spaces (e.g. boxes) so much?

texts:
A recent article doesn't reach a firm conclusion, but offers two possible explanations.

  Hiding is a behavioral strategy of the species to cope with
  environmental changes and stressors.

It keeps the cat at a comfortable temperature.


texts: Oscillatory electrical system using a chain of neurons

texts:
Many daily activities that we perform are result of inbuilt oscillatory circuits in our body. For example walking, breathing, heart beat, blinking, etc. The coding and decoding of stored memory also happen via controlled oscillations. The link http://en.wikipedia.org/wiki/Neural_oscillation contains information about neural oscillations. It says in here that a single neuron, an ensemble of neurons and activity of brain may exhibit synchronised oscillations. It is also said that these oscillatory circuits can control all the parameters of oscillations i.e. frequency, phase and amplitude.While above are true for neurons as a part of bigger systems, my question is related to study of isolated neurons.
There are many instances of studies of artificial neural circuitary created on a customized substrate(Micro Electrode Array) by masking techniques. Also there are loads of ongoing research to study the simple neural circuits in temporal and spatial domain by electrical interfacing of semiconductor and nerve cells using Field Effect Transistor(FET).

I want to know if these kind of oscillations are unique to some special kinds of neuron? Is the control of oscillation parameter possible in every neurons and isolated neurons? Can a neuron or any other cell exhibit change in action potential independently? Do other cells except neuron and pacemaker cells exhibit oscillation? Can a single neuron exhibit memory?
Can a simple circuit like below generate oscillations?
Suppose I culture the neurons on a substrate in a controlled way such that one neuron is connected to only one other neuron in a linear fashion and the last neuron is connected to first. Assuming we supply the ions if there is loss, can a clock pulse of varying frequencies be generated, where the frequency is the function of the no. of intermediate neurons and their length.

It would be a great help if somebody can provide information about softwares to simulate simple neural circuits (If available).


texts: What happens to potassium after an action potential?

texts: If I understand right, after repolarization, much of the potassium is outside the membrane and much of the sodium / calcium is inside. How does it get back to the original concentrations (i.e. potassium inside and sodium/calcium outside)?


texts:
I know that so much fats running in the bloodstream could deposit in arteries, harden forming a plaque and cause atherosclerosis. But what about veins (which are formed from same types of layers as arteries) and capillaries?

I googled a bit but everything was regarding arteries.

Is it because veins have a much wider diameter than arteries that even if some fats deposit they won't clog it?

And for capillaries, they are much smaller so shouldn't they be more vulnerable to this?

In addition, I guess since one of the lymphatic vessels functions are to transport fats from  capillaries in villi to bloodstream, how are they adapted to prevent deposit of fats as they carry out the transportation?

N:B I'm just an OL biology student, and also horrible at chemistry


texts:
I'm not a biology expert, but I have often wondered about the following facts of life:

All mammals have precisely 5 fingers on each of our 4 extremities. Granted, some may not be seen, but the bone structure of 5 fingers is there in all mammals, from whales to bats to humans. This, I guess, tells me that changing the number of finger bones is, genetically speaking, fairly difficult (as it never happened during the evolution of mammals.

On the other hand, pigs have 12 nipples, dogs have 6, and humans have 2. Pigs have 44 teeth, dogs have 42, and humans (the lucky ones) have 32. This, I guess, means that it is easy to change the number of teeth in a species, as this happened often during the evolution of mammals.

My question is this: What is the reason behind this discrepancy? Why is it that much easier to change one thing and not the other? And a subquestion: why do we still have 32 teeth when the 4 wisdom teeth cause nothing but trouble? Wouldn't having only 28 teeth be an evolutionary advantage?


texts: Figure out which is the risk allele from SNP in GWAS article

texts: I do neuroimaging research, and am interested in dabbling in genetics. I am trying to create an anxiety risk profile score from several SNPs shown to correlate with measures of anxiety in past GWAS studies. However, many of the GWAS studies, such as this one (https://www.biorxiv.org/content/10.1101/540245v1) don't seem to explicitly state which allele was the risk allele (i.e. which allele was positively correlated with anxiety). It's likely that in most cases the minor allele is the risk allele, but I don't want to assume this. Am I missing something in the text of the example manuscript, or would I need to contact the author to find this out?


texts: Ancestral states of sex determination system

texts:
Most (maybe all?) species that reproduce sexually have either genders (anisogamy) or mating types (isogamy). There exist today many different type of sexual determination system. There is a whole complicated continuum from species where the gender is exclusively determined genetically (genetic determination system, GSD) to those where the gender is determined by the environment (environment determination system, ESD).

Knowing that genders (and mating types) evolved several independently, what seem to be the ancestral states of sex determination system? Where the first sexually reproducing lineages GSD or ESD? Does it differ between lineages?


texts: Is there any biological support for the concept of "chakras"?

texts:
Is there any support in modern biology for the ancient concept of "Chakras"?

I've seen the concept of 7 chakras linked to the major endocrine glands in the human body (pineal,thyroid, adrenal, testes, etc). This makes some sense, however, I've seen other numbering start to talk about 14, 21, etc number of chakras, which makes me skeptical.  Are chakras real?


texts: How's the membrane potential restored to resting state after hyper polarisation?

texts: I have known for so long that Na+/ K+ pump restores the membrane potential. But as it pumps in 2 K+ for every 3+ Na+ moving out how can it make the membrane potential less negative when the net result is one positive charged ion moving out?


texts:
I saw a caterpillar in my bathroom. It's about 2 inches long and 3/4 inches in diameter. It has long (about 1 inches) long hair on his body.

I live in eastern India, Asia. I don't know if it was alive, as I didn't see any remarkable movement.

Are they dangerous? Do they bite? How to get rid of them?


texts: The effect of Atrazine on the LDR in Photosynthesis

texts:
The herbicide Atrazine causes inhibition within the Qb site in the D1 protein of photosystem 2.   Given this information, would Atrazine’s inhibitory effect halt the production of oxygen or ATP first?

Given that water is oxidized indirectly by P680+ and the build up of intermediates caused by inhibition in Qb  would not allow P680 to deposit its extra electron into the beginning of the electron transport chain, water would not be oxidized/split into 2H+ and (1/2)O2 because P680 would not become P680+.   So this inhibition would halt the production of oxygen, correct?

Given that, I would say that the production of O2 would be more immediately halted than that of ATP, especially since ATP synthase would continue to function until the electrochemical gradient between the stroma and thylakoid space was spent, and would not be immediately affected by inhibition in Qa (although the electron transport chain which maintains the electrochemical gradient would be compromised and thus indirectly ATP synthase would be affected).

Is my reasoning correct?


texts: Hybridization in Darwin's finches is rare or frequent?

texts:
I've talked to a couple of researchers today and read recent articles on the subject of hybridization of Darwin's finches. I'm confused about the consensus in the scientific community.

First, I was reading about hybridization in systems where adaptive radiation occurred. I came across this Honeycreepers paper: Knowlton, J. L., D. J. Flaspohler, N. C. R. Mcinerney, and R. C. Fleischer. 2014. First Record of Hybridization in the Hawaiian Honeycreepers: 'I‘iwi ( Vestiaria coccinea) × ’Apapane ( Himatione sanguinea). The Wilson Journal of Ornithology 126:562–568.

In this paper they are saying:

  The Galápagos finches, for instance, hybridize frequently both within and across genera (Grant et al. 2004, Grant and Grant 2008).

But in the resources they cite, here is what I found:

  Rare hybridization between the species, occurring partly as a result of misimprinting on song (Grant
  and Grant 1998)

From Grant, P. R., B. R. Grant, J. A. Markert, L. F. Keller, and K. Petren. 2004. Convergent evolution of Darwin's finches caused by introgressive hybridization and selection. Evolution 58:1588–1599.

  Hybridization was rare at the level of individuals: only
  a few percent of all offspring are hybrids

From Bell, G. 2015. Every inch a finch: a commentary on Grant (1993) 'Hybridization of Darwin‘s finches on Isla Daphne Major, Galapagos’. Philosophical Transactions of the Royal Society B: Biological Sciences 370:20140287–20140287.

  Hybridization was always rare.

From Grant, P. R. 1993. Hybridization of Darwin's Finches on Isla Daphne Major, Galapagos. Philosophical Transactions of the Royal Society B: Biological Sciences 340:127–139.

  Hybridization occurs rarely (less than 2% of breeding pairs) but persistently across years, usually as a result of imprinting on the song of another species.

In Grant, B. R., and P. R. Grant. 2008. Fission and fusion of Darwin's finches populations. Philosophical Transactions of the Royal Society B: Biological Sciences 363:2821–2829.

Did I miss something, or is hybridization rare and not frequent? Maybe frequently is so vague that it includes, rare?


texts:
Phylogenetic trees with >2 branches on a node are polytomic, and polytomy can appear on trees for two reasons. Firstly a lack of information in the data prevents proper resolution within a clade, called soft polytomy. Alternatively, hard polytomy may exist, this is when there truly is a simultaneous split from one lineage (species) in to more than two. Yang states that "it may be argued that hard polytomies do not exist" but makes no citation or attempts at theoretical discussion. Are there any papers which discuss the theoretical possibility of hard polytomy and any evidence of it occurring?

Image from http://biology.fullerton.edu/biol404/phylo/polytomies.html


texts: Why there aren't any pandemic diseases by prions?

texts:
Learning biology in school, I became interested in the fact that there aren't any diseases by prions which are globally infectious (as far as I know), unlike diseases by viruses (ex. COVID-19, SARS etc.) or by bacteria (ex. plague, ...). Why is it?
cf. Here are some my hypothesis

Prions are not efficient pathogens because they don't have DNAs.
Such prions are not yet discovered or does not exist.
There exists lots of people who are immune to such diseases.

Are there any answers to the questions? Or is there any answers?


texts: Antibacterial soap impacts on septic system?

texts:
What impacts do antibacterial soaps have on septic systems?

I know that septic systems rely heavily on bacteria (especially regarding the breakdown of wastes by bacteria), so it seems as though antibacterial agents surely could do some harm to septic systems. Is that the case?

One of my students in my Environmental Science class asked me this question, and it seemed very much worthwhile to post the Q&A to Bio.SE!


texts:
The image below is taken from a molecular biology textbook.

It is not clear to me that what is happening at the two writhe crossings matches up with the numbers provided.

Is there  a problem with this example? And if not, is anyone able to explain (without using Calugareanu's Theorem, i.e. $\text{Lk}=\text{Tw}+\text{Wr}$) why the linking number is $23$? When I give the two strands orientations and half the sums of signs of crossings, I do not get $23$.


texts:
I often use BONAP's North American Plant Atlas, for researching plant taxa ranges.

  BONAP maintains relatively complete phytogeographic and related botanical databases for all free-living vascular plants found in North America (north of Mexico). For over four decades, we have worked collaboratively with many federal and state government agencies, private groups and individuals across the continent to produce and edit our databases

It generates incredibly useful range maps, and I can search by higher taxa (i.e., genus) to investigate many species based on their ranges at once. For example, Fagus:

However, I have so far been unable to find a similar online atlas (or any range-map query tool) for insects.

Does anyone know of any similar range-map resources for insects?

I'm most interested in maps for the US, but global maps would be incredibly awesome :)


texts:
I just found this little guy crawling on me after coming in from the garden in Northern VT.  We live in a narrow grassy valley in a pretty wooded area.

This bug was crawling up my neck and when I tried to sweep him away he clung the way a tick does.  He also has a very flat profile and kind of a "hard" feeling body, but otherwise bares no resemblance to a tick.

I took this photo with my phone so it's not great.  The eyes are distinctly roundish and black. His mouth parts were visible and moving around slightly, but while I watched him he didn't appear to be trying to bite into me.

That's all I've got.


texts:
Glycolysis yields 2 net ATPs. However, gluconeogenesis (lactate->pyruvate->glucose) costs 6 ATP, with a total net loss of 4 ATP.

Does the body not care about the net loss because of the potential energy from glucose to yield up to 38 ATP?


texts: Imagine a gene with  $n$ exons and $m$ introns. How many proteins are possible from that gene? Would all the proteins be isoforms?


texts: How likely will 2 normal bacteria "attack" each other if they infect the same parts of your body?

texts:
I read this interesting article online about how deadly bacteria are known to attack other deadly strains of bacteria.
https://www.google.com.sg/amp/s/phys.org/news/2013-02-deadly-bacteria-remarkable-precision.amp
I am wondering how normal bacteria that infect us like those that cause strep  throat and so on also have the capabilities to attack other bacteria and how feasible it is to use this as a treatment for bacteria infections by introducing harmless strains od bacteria to fight pathogenic versions (maybe like probiotics?)


texts: How do duplicate brain regions (ex: left/right amygdaloid body) operate together?

texts:
I frequently hear talk about parts of the brain like "Amygdala" or "Hypothalamus", so I looked them up in an app called "essential anatomy". What I see is that there's mirror symmetry, and most of these glands/nuclei are actually mirrored in two halves of the brain.

I'm trying to understand how two halves of nuclei like amygdala work together. For example, it is frequently said that Amygdala processes fear response. If it was a single nucleus, it is conceptually easy to comprehend, but what about a "multi core" nuclei with two halves? Which half would process the fear response?

Additional questions to help clarify this question:

Are duplicate nuclei connected through some nerves, making up a single organ?
Is there a dominant/non-dominant relationship between halves (like dominant hand)?
Or do nuclei fulfill identical role within different brain halves (right half gets scared, then left half gets scared)?

Here's an image that prompted my curiocity - it is a 3D model of nuclei that sit on top of brain stem and under white matter.


texts: Assays for detecting RNA binding with protein

texts: In a project I'm working on, we are designing a system where specific RNAs bind to proteins - an important part of this is to test whether the RNA binds when we modify the proteins in some way. What assays are there to test whether a specific (or non-specific) RNA is binding to a protein?


texts: How does alzheimer's affect an octopus, particularly relating to their multiple brains?

texts:
From what I have read, Octopus' have multiple brains rather than a single one like in humans. They are also affected by alzheimer's, and so an interesting question arises:

Do Octopus' get alzheimer's in one brain, or are all affected, and can they shut off a single brain if it gets the disease?


texts:
There is a theorem in the Intelligent Design literature called Basener's ceiling.  It states that all evolutionary algorithms that attempt to optimize some fitness function will eventually reach a plateau where complexity no longer increases.  This is seen in practice when engineers and computer scientists try to use algorithmic forms of evolution.

  There are a number of standard models for the evolutionary process of
  mutation and selection as a mathematical dynamical system on a fitness
  space. We apply basic topology and dynamical systems results to prove
  that every such evolutionary dynamical system with a finite spatial
  domain is asymp- totic to a recurrent orbit; to an observer the system
  will appear to repeat a known state infinitely often. In a
  mathematical evolutionary dynamical system driven by increasing
  fitness, the system will reach a point after which there is not
  observable increase in fitness.

Biological evolution is the same as an evolutionary algorithm in the relevant aspects.  It is a search to optimize reproductive fitness, where the fitness function is just the fact of survival or lack thereof.

How then is evolution able to make organisms continually increase in complexity, as history shows, despite Basener's ceiling?


texts:
How and why did Fair Meiosis evolve?

I can hardly think that it provided a fitness advantage to the individual carrying the mutation. Why would it? Or did it evolve through lineage selection? Or was it some kind of pre-existing characteristic of meiosis that have no energy cost and therefore never disappear?

UPDATE:

I call fair meiosis the process of meiosis in which each chromosome has an equal chance of transmission.

I'm trying to make my questions clearer.

Is there any selection pressure in favour of alleles causing a fair meiosis? If yes, why? It doesn't seem to me to provide any advantage to the individual carrying this allele.


texts: How can grass-fed livestock generate fat?

texts:
How can herbivorous cattle get fat? These animals eat only grassy substances, think of cattle, buffalo, goats etc. For example, wheat grass contains 0% fat, and its nutritional value is limited to carbohydrates and fibers. Still, livestock can have substantial (10%) fat content and give milk with lots of fat on top of it.

Where does that fat come from?


texts: How does one calculate Rx/a in population genetics?

texts: The ratio of sex-linked to autosome mutation frequencies (R) is Rx/a =(2/3)(2+ α)/(1+ α) for X-linked genes and Ry/a = 2 α /(1+ α) for Y-linked genes. How does one calculate Rx/a, in order to find α?


texts: According to Gray's anatomy, cartilage is avascular but in a recent class, my teacher told me that there is vascular supply but it is confined to upper surface only. So, I'm confused that who is correct.


texts: Are there examples of selection on males influencing female phenotypes?

texts:
I've been studying selection on female body color in a sexually dimorphic species and am intrigued by the possibility that selection on males, whether it be through sexual or natural selection, may influence the color of females. I think pleiotropic interactions may lead to this, or maybe some sort of genetic linkage.

A hypothetical example may be that selection for red dewlap color in anoles results in more melanic females.

I'm having trouble finding examples of this but I think it's a real phenomenon. Does anybody know examples of this occurring in a sexually dimorphic species?


texts: Can you please help me identify this insect?

texts:
I have been trying to get rid of this bug and need help to identify it.
I found this in my bedroom first.

I don't think this is a bed bug as I saw it fly. It is black with some white spots on it.

Any suggestions on what it could be are greatly appreciated.
Thank you!


texts: Can lysozyme also lyse gram-negative bacteria and if yes, how fast?

texts: Lysozyme attacks peptidoglycan, which are found in Gram-positive bacteria. I know someone who uses lysozyme to lyse Escherichia coli, which is Gram-negative. How is that possible? Can lysozyme lyse all bacteria, independently of their Gram status? Does anybody have information on how long I should leave lysozyme in a bacterial solution for it to be effective?


texts: What does sympathetic and parasympathetic 'tone' mean?

texts:
My professor's lecture notes say that " The basal rate of firing is called “sympathetic tone” and 'parasympathetic tone"  , but a table I found on the internet  says that the parasympthetic system has no tonic activity.

Does saying the ANS has tonic activity mean that it sends impulses continuously and at a low rate to effectors? How is the ANS considered rapid then?

On Euroform Healthcare
It is written that without the sympathetic and parasympathetic tones, we would not be able to regulate the activity of organs or bring it up and down, I don't understand why that's the case ?

I'm very new to this whole topic (ANS) so please go lightly on me.


texts: Does imprinting occur at different life stages?

texts:
For example, consider the offspring of a bird species. Can offspring get imprinted by other individuals of the same population at various life stages (e.g., hatchling, nestling, fledgeling, juvenile)?
If you have any literature, please send the links.


texts:
If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the approximate doubling time in hours?

My colleague says it should be around 200 hours. But I don't understand how they reached to this conclusion, can anyone explain this to me please?

Thanks


texts: Is there such thing as a generic "metabolic type"?

texts:
A while ago I picked up a book called "Eat right for your metabolic type". The book discussed the effects of the endocrine system on the overall shape and the speed of metabolism.

The book outlined few major metabolic types:

Adrenal
Thyroid (hypo/hyper)
Muscular

The book proceeded to discuss the overall shape of the body, including shape of fingers to help identify the metabolic type and give suggestions on which foods to avoid for a particular type.

The book then gave examples of effects of foods on metabolic types - for example an Adrenal type who eats too much sugar would crash and compensate for this by sleeping.

Since I can no longer find that book in print, I'm interested if there's really such a thing as a metabolic type that can be easily identified ? Are there indeed some foods that people should avoid eating?


texts: Anyone know what this bug is? (Southern California)

texts:
I found it in Southern California on the fringes of the Mojave Desert. They seem to have nests similar to ant hills but don't look like any ant I've ever seen. They seem to have shown up within the past week or so and have their nests near some big red ants (Camponotus castaneus I believe) though the ants don't seem to be eating them. They are around the same size as the little black ants (Monomorium minimum), but unlike ants they seem to get blown around by the wind. There were hundreds of them around and had several apparent nests. They were also climbing all over a wood fence nearby. I was able to get a picture, hopefully it is clear enough to make out the bug in. You can see a few of them on the gray rock.

The only thing I could think they might be is some kind of termite or something. Are they harmful, and if so, how would I deal with them?


texts: Can Inositol triphosphate (IP3)-mediated Calcium release on its own cause membrane depolarization?

texts:
This is about smooth muscles.
I know that the Voltage-operated Ca²+ channels on the smooth muscle membrane can be opened by membrane depolarization to threshold. I also know
that this depolarization in question can be brought about by opening of receptor-operated calcium channels on the plasma membrane.(1) What I am curious to know, however, is whether the Ca²+ released into the cytoplasm (sarcoplasm) when say IP3 binds to its receptor on the Sarcoplasmic reticulum can (on its own, without any other thing happening) cause depolarization of the membrane potential to threshold and subsequently lead to opening of
the Voltage-operated Ca²+ channels on the muscle cell plasma membrane.
I am asking this because most often, the IP3-mediated Calcium release is discussed almost entirely as an accessory pathway for Calcium release, being only able to supplement an existing Calcium current.
(1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652144/#!po=4.24837


texts:
What causes the crease through the pericarp of a drupe fruit (peach, nectarine, olive)?  It may just be in exocarp as @Ilan pointed out, but I assumed (perhaps wrongly), that the division continued through the pericarp.  I'm also not sure if this true generically for drupe fruit, so I'm not sure which phylogenetic step down to take.  Olives for example have a divot that seems to extend from the stem down, but it stops well before the midline of the fruit in most cases.

I assume the crease has something to the initial genesis of the fruit tissue, but I haven't found any arguments on it's formation.  A more technical term might be "cleavage," but that was after some searching and not coming up with more certain term.

Botany is not my strong suite, but I recently entered into a collaboration where we will be making some recombinant alpha viruses (which is within my strong suite) that will infect drupe tissue.  Finding good pathology papers has been difficult, and they tend to be specific (not trying to imply that's bad).  Can anyone point towards a reference text/article on the genius of drupe fruit if the cause of the "crease" is not clear?  Disruption of the crease seems to be a particular phenotype of infection for some strains, and I'm searching for the correct terminology and mechanisms that might be effected.

If I can get permission I will include photos of an infected vs control peach.  In the mean time to clarify what I mean, the line that seems to transverse from one poll to the other of the fruit:

Peach:

Nectarine:

On the sea mango it is pronounced, but on most other mango it seems like just a slight marking along the exocarp:

Even the coconut seems to have at least one:


texts: Primer Design with Primer-BLAST over specific site

texts:
I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site.

I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward primer should span chr12:25398285.

However, I'm not sure how to restrict the design to accomplish this. Thanks.


texts: I need help identifying a completely unknown plant for my biology class

texts:
I know two things about this plant
1 is that it does not need to be watered for a long time because it has been able to survive in my schools greenhouse for quite some time without water and 2 my teacher says she "thinks" it blooms purple or pink flowers.
Thank you in advance for any help given!


texts:
There is no AAMI 12-lead ECG databases available online.
All of them have problems.
I and my friends finally finalised our tests with St Petersburg.
It is not AAMI.

So the next step is to search any ECG databases with some leads (at least lead 2) with ECHO data.

Is there any AAMI standarded ECG databases with ECHO data?
This data need to be from the same patient.


texts:
I have seen in textbooks referring to ds RNA and ssDNA.
How a RNA can be double stranded and likewise how a DNA can single stranded  and if they do exist why are there names not interchanged?


texts: Is resource partitioning a type of character displacement?

texts:
Question

Imagine two related species. They prey on the same species but avoid competition by feeding at different times of the day. Is this a type of character displacement?

Thought

On one hand I have the  Galapagos Finch example, which is typically used to illustrate character displacement. But since resource partitioning is more behavioral than anatomical, is resource partitioning a subset of character displacement or a rough overlap or none?


texts: Can I tell my antioxidants intake based on nutrition facts labels?

texts:
The recommended daily intake of fruits and vegetables is 5-10 portions (url), in order to meet the "required antioxidant levels" (dark-leaf green vegetables, berries, cruciferous vegetables, ...).

Can I measure my antioxidant intake based on nutrition facts label, instead of counting vegetable portions?

Adding up the total intake of vitamins A, C, E and magnesium may not be representing because they are not necessarily the "major players" (additional significant players are CoQ10, alpha-lipoic acid, l-carnitine, acetyl-l-carnitine, n-acetyl cysteine).


texts: What would be the fate of protein made from D-amino acids after ingestion by humans?

texts:
There are some natural peptides made of D-amino acids, rather than the L-amino acids normally found in nature. It is now possible to chemically synthesize artificial proteins made of D-amino acids.

If such proteins were ingested by individuals, how would they be metabolized and what consequences would they have?


texts:
Of the 192 target genes, 79 map to a significant eQTL or pQTL in at
  least one dietary condition.

is the line for a paper "Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population"

As far as I know an eQTL is a SNP (particular genotype) affects gene expression. How can I map then a gene to an eQTL? A gene is a sequence on a reference genome. Genotypes of one specific gene are just variations of the sequence of this specific gene. So, a gene itself cannot be an eQTL, a specific genotype (with a variation) can be, right?

So, how can it be possible that one gene (let say GENE22, location: 10-100) is mapped to eQTL(SNP within GENE22, location: 12) in one dietary condition but is not mapped to eQTL in another dietary condition if we are still speaking about the same gene and the same location of an eQTL? So, I am not quite sure what they mean or what they mapped there.


texts: Might new bones evolve from soft tissue?

texts:
I wonder how bones evolve where there are none. (This is the question, read the sub-questions as examples :) )

Lets take an elephant as an example. If it was adaptive for the elephant, could bones somehow evolve in their soft-tissue trunks? If so, what tissue would they develop from?

Perhaps the sheet of cartilage in their ears are more likely to somehow calcify and become a new bone?

And would then several connected bones and joints evolve from the new bone tissue?

Is it very rare for new bones to evolve from scratch? Or, do today's bones entirely trace back to the set that evolved in early tetrapods?


texts: I'm sure by the nature of this question you will come to know my amateurish knowledge in biology. During mitosis, they simply state that the organelles just replicate...while we are provided somewhat detailed information regarding the division of the cell. How do the nucleus and the other organelles divide? Mitochondria used to be prokaryotes apparently so do they divide by binary fission? while we're on that what exactly are the organelles composed of? There is a spike in protein production during interphase...so how do the organelles even go about dividing?


texts: Can a human be made with ovum but without sperm?

texts:
This article says that scientists were successful in making a mouse using only a sperm and no egg (ovum). The article also states that this procedure could be applicable to humans.

However, I want to know why didn't they try with only an ovum?

Can a human be made only with an ovum, i.e. without sperm?


texts: What evidence is there that common PCR DNA purification kits can isolate DNA from pathogens engulfed in macrophages?

texts:
I have previously asked a more general question about how PCR sequencing reaches all possible DNA targets here. I want to ask more specifically now: what evidence is there that common PCR DNA purification kits can isolate DNA from pathogens engulfed in macrophages?

Specifically what such a KIT would have to achieve is to destroy the double lipid cell membrane of a macrophage and destroy the cell walls of engulfed bacteria or fungi. (The latter of which even contain chitin)

I am looking for as specific evidence as possible proving that if one takes a whole blood sample and employs a purification KIT, any microorganism's DNA engulfed in a macrophage should be isolated. Please allow me to say that I am looking for evidence beyond just the manufacturers specifications. I would like to find publications, book chapters or other written statements that specifically show and discuss how isolation techniques work on the barriers I mentioned or even better how they work on intra-cellular micro organisms. Thank you!


texts: Why is contractile vacuole absent in parasitic protozoans but present in free living protozoans?

texts: I know that contractile vacuole helps in osmoregulation of protozoans and some nitrogenous wastes are also excreted through it. Since contractile vacuole plays an important role in protozoans, why is it absent in parasitic protozoans? I could not find the logic behind this.


texts: Why the name coined for MARKUP LANGUAGE for SBML?

texts:
I'm get the confusion about  SYSTEM BIOLOGY filed.  SBML is refer to as SYSTEM BIOLOGY MARKUP LANGUAGE why we should called as MARKUP LANGUAGE? In HTML,XML and other field Mark up language mean particular function is declare into the Angular bracket like <H1> for Heading Tag this is displayed on the browser. Markup Language was actually developed for Wep application.

In other words, MarkUp language only displayed what we want., not display the simple mathematical function. Like, I need add function 1 + 1 which is display on the browser Markup language is not add, which is done by the CGI programming Like PERL,PYTHON, javascript.

So, in SBML(System Biology MarkUp language) Tools are not only display the what we want it? and It is not run on the browser? So why we called it is MarkUp Language?


texts:
Looking for values of the average human body density on the Internet, one often finds the values of 0.98 for male, 0.87 for female. Other values are 0.985 for male and female. However, I can find no scientific reference confirming these values.

Instead, I found multiple articles giving numbers closer to 1.05 for male and 1.03 for female (Durnin and Womersley, 1974). The difference probably comes from the air comprised within the lungs, but I do not know how much it can change the density and how full our lungs are in average. Would anyone have a reliable reference on this matter?

Ultimately, I would like to understand the effect of breathing on the floating in water and compare this effect for male and female. I would like to see if it can account for women tending to float, even after deep expiration. It upsets a friend in her diving lessons. :)


texts:
I am mapping some reads to a reference genome (hg19). I used bamtools to have the percentage of mapped vs unmapped reads.

Total reads:       1150004
Mapped reads:      1052983  (91.5634%)
Forward strand:    624067   (54.2665%)
Reverse strand:    525937   (45.7335%)
Failed QC:         0    (0%)
Duplicates:        0    (0%)
Paired-end reads:  1150004  (100%)
'Proper-pairs':    1046208  (90.9743%)
Both pairs mapped: 1049400  (91.2519%)
Read 1:            575002
Read 2:            575002
Singletons:        3583 (0.311564%)
Average insert size (absolute value): 534.479
Median insert size (absolute value): 215

My question:

What represent exactly these unmapped reads? What information do they tell us? How can we analyze them?

Thanks


texts: It seems so simple that if my brain can tell my right hand to do something, then it should be able to tell equally well to the left ? This seems like a pretty major evolutionary advantage. Why haven't we evolved so during millions of years ?


texts: Ratio of bleach to water required to disinfect COVID-19?

texts:
I am confused about the needed ratio of bleach to water required to disinfect COVID-19 from surfaces.

The guide on CDC states that: https://www.cdc.gov/coronavirus/2019-ncov/community/home/cleaning-disinfection.html

  Diluted household bleach solutions can be used if appropriate for the surface. Follow manufacturer’s instructions for application and proper ventilation. Check to ensure the product is not past its expiration date. Never mix household bleach with ammonia or any other cleanser. Unexpired household bleach will be effective against coronaviruses when properly diluted.

  Prepare a bleach solution by mixing:

  5 tablespoons (1/3rd cup) bleach per gallon of water or

  4 teaspoons bleach per quart of water

This is a 2% ratio. My problem is that it is not clear what "bleach" means. Chemically I guess it's Sodium hypochlorite. What's not clear is that what is the strength of the solution I can buy in shops.

Wikipedia states that bleach in stores can be anything between 3-25%.

Does CDC recommend the final strength of Sodium hypochlorite : water to be 2% or "bleach in stores" : water to be 2% (which can be anything between 0.06% - 0.5%

Disregarding this confusing CDC direction: What is the scientific recommendation for the required sodium hypochlorite : water ratio needed for disinfecting COVID-19 from surfaces?


texts: Identification of the bug on the curry leaf- Delhi, India

texts:
I found this bug on my curry leaf in early morning. Which bug is this?
Size- 1-2 cm
Habitat- Delhi, India.
The bug was on one of the curry leaf of the curry plant pot in my residential balcony
Time- 7:00 am


texts:
Liver is the most resilient of the human organ (on par with or next to skin). A very interesting experiment on liver regeneration is here. Even if two-thirds of the liver is removed, the remaining liver would regenerate to recover the full volume and function.

Cirrhosis of liver is a condition where excessive fibrosis occurs shattering the architecture of the liver. The blood vessels and the parenchymal cells of the liver get constricted into narrow spaces causing portal hypertension and fall in the Liver Function Test parameters (albumin level falls, clotting factors fall leading to spontaneous bleeding, bilirubin level rises causing jaundice, etc...). It can be either congenital or acquired. Cirrhosis is considered an end stage liver disease.

In the end stages of cirrhosis the only treatment option available is liver transplantation.

Question:

Why is partial hepatectomy (removal of part of liver) not a treatment option for end stage liver disease (cirrhosis of the acquired variety)?


texts: What do you call mRNAs that translate to the same protein?

texts: For example AUAACC and AUCACG in distinct mRNAs may both be translated to the same dipeptide Ile-Thr.


texts: What is the reason behind high resting membrane potential of pacemaker cells?

texts: Pacemaker cells have high resting membrane potentials of -50 to -40 mV, whereas normal cells have their resting membrane potential around -70 mV. Which ions, and what kind of channels are responsible for the high resting potential of pacemaker cells?


texts: Why the scent of mouth gets dirty after not eating for a long time?

texts: After a long time of hard workout,not eating and nervousness makes your taste and scent of mouth very uncomfortable and bad why this happens and is there any way to prevent it?


texts:
I highly doubt that fruit flies or their larvae can digest any plastic used in everyday products. But are there any documented cases where they attempted to eat plastic? I ask this because last Sunday I was setting up a Wii U at my grandparent's house. It had been in this plastic bag that has been sitting in the same room for about three weeks because I only use it at other people's houses and is never set up in my house. This plastic bag was similar in shape and size to many re-suable grocery bags that supermarkets distribute, example Whole Foods. But this bag was made entirely out of plastic. Of course I don't know what type because it wasn't recyclable. It was also more rounded on the edges. Okay, here comes the biology part. I took the Wii out and there were light-brown, rice-shaped and approximately rice-sized "things" on some of the controllers, the power adapter and on the inside of the bag. There were a couple of fruit flies flying around when I took everything out. This immediately led me to believe that the "things" were fruit fly larvae, or dead larvae. I came to this assumption because in the past few weeks there have been more fruit flies than normal in my house, probably because of compost staying inside for too long (in a container in the kitchen sink) and a few too many rotting bananas that weren't eaten or disposed of for a while. And after seeing two or three live flies flying around the controllers I assumed that's what it must be. When searching for fruit fly larvae on Google Images the best picture that represents what I'm describing is this. There were also smaller brown dots where the larvae were and in some places they were not. I don't know what these are. They are smaller than 1mm in diameter. I understand that the flies probably thought that the bag was a dark and safe place to reproduce, but there are two things that I could not figure out, and they seem to be related. One of the Wii remote controller's strings (handles?) was dark brown and slightly wet. It looked like it had been soaking in muddy water. I was very confused by this. I took the bag outside to try and empty it but the supposed larvae were stuck to the inside of the bag. What did fall out of the bag that I missed before was a black ball about two inches in diameter that was also slightly wet upon touching it and was apparently plastic. There were a couple larva on it as well. The bottom of the bag looked like it had some plastic removed from it. This led me to believe that larvae had eaten some of the bag and detached it from the bottom. And somehow this ended up in the form of a ball. (Not a perfect sphere, but round.) I really wish I had taken more time and examined it more to confirm that it was from the bag. I don't have pictures of any of this because everyone was pressuring me to throw out the bag and clean off the equipment, apparently not caring about what actually happened. I also don't have pictures of the Wii remote string because I cut that off and threw it away as well. I later realized that I should have taken pictures because it is so difficult to describe. I began thinking of explanations for each part of what happened. My hypothesis is: Fruit flies in our house reproduced until there were too many to be sustained by the amount of food that was available. This probably happened when there were no bananas left or compost had just been taken outside. Some found the bag which was dark and safe, so they reproduced there. There wasn't any food for the larvae so they tried to eat the plastic that they were on but couldn't digest it, so they died.

This is way longer than I wanted to it to be...
So it comes down to these questions:
1. Would fruit flies lay eggs where there is no food?
2. Would fruit fly larvae attempt to consume something that clearly wasn't food?
3. What are the small dots on the adapter?


texts:
Coding sequences of genes have a certain degree of evolutionary conservation, so that comparisons based on sequences (BLAST, HMMER etc) can be informative. Generally speaking, the more two species are phylogenetically close to each other, the more their genes will be similar to each other. To add to that, different genes will have different degrees of sequence conservation - for instance, histons are very conserved and so on.

Do these considerations hold true for untranslated regions of genes (both 5' and 3')? To what extent can an alignment of UTRs be meaningful? Are there any very conserved UTRs as there are very conserved CDS? I know that there are some conserved motifs in 5' and 3'UTRs, but what about the overall sequence?


texts: Ill effects of urea and NH₃ on metabolism

texts:
What exactly does urea do that harms our body? Does it interfere with our cellular processes or disturbs the colloidal onchotic pressure of our blood?
I have heard that NH3 damages the brain. What does it actually do?


texts: Are the Chromosomes organized in any meaningful way?

texts:
So my major is in pharmacy but both my master and my (currently in progress) doctoral degree are both in theoretical chemistry. My thesis is about quantum chemistry and proteins, but it has a certain amount of phylogeny and evolutionary biology such that I've had to learn some phylogenic analysis methodology and have had my share of experience using sequence databases and analysis tools around the web. Although I do not focus particularly in the human genome, or even human proteins for that matter, I got myself thinking about a rather curious question.

I am by no means a specialist in molecular and evolutionary biology, but I do understand that chromosomes and genes come up in the population by several mechanisms. Now, it is interesting to me that all the information regarding biological sex in humans is contained within a single chromosomal switch, the Y chromosome. Given that fact, I asked myself

"Do we have some order in the arrangement of our genes in their chromosomes?"

So now I turn that question to you people, who seem to be more well-equipped to tackle theses questions than I certainly am. Forgive my ignorance and indulge my curiosity!

[EDIT FOR CLARIFICATION]

Okay, clarifying some points that were raised in the comments:

The question is about whether there is a pattern in the organization of genes into chromosomes. For example, the Y chromosome clearly contains a lot of genes associated with sexual dimorphism in humans. I was wondering if chromosomes in general follow that general pattern. If, for example, Chromosome 1 contains such and such kinds of genes, as if it had hints of an overarching "theme" to it.

Is that clearer?


texts: I'm wondering if only humans, or only mammals have antibodies and immune system. Obviously humans and dogs have (we vaccinate both) and in my head makes sense since we're so genetically similar to all mammals that we all have antibodies. Do all synapsids, or even amniotes have antibodies as part of their immune system? Do plants have antibodies or insects?


texts: How is it decided that one drug is better than others by X times?

texts:
I read in Tortora and Derrickson that :

  Enkephelins are 200 times powerful than morphine in their analgesic effects.

I wonder how exactly researchers arrive at a number (like 200 here). I also want to know what exactly is meant by "powerful".


texts:
It is said that

"When a virus or a pathogen enters the body, the immune-response produces Y-shaped proteins called antibodies to bind to the pathogen or virus".
"Also it is possible to extract antibodies from the blood."
Since antibodies are proteins, is it possible to sequence their structure ?
If the answer to point-3 is Yes, then can't coronavirus antibodies be sequenced, more antibodies be produced from this sequence on a large scale, and then these are administered to the infected people ?

I would like to know any challenges to the above mechanism like "difficulty in figuring out the correct antibody or so" ? Thanks!


texts:
Found this in a rural area next to the road last month and I wonder what is it?

From my searches I think it is a strawberry bush but I'm not sure and any help would be appreciated, thanks!


texts: What is the scientific name of Japan's (other) national flower, the chrysanthemum?

texts:
In my notes, I had Japan's royal chrysanthemum listed as Chrysanthemum japanense, but I just discovered that name has either been retired or it was never valid to begin with. (Or did I just misspell it?)

A little research uncovered Chrysanthemum sinense var. japanense, though I haven't yet learned anything about it. "Var." means "variety," indicating that it's a domesticated hybrid, right?

Then I learned that Chrysanthemum sinense is a synonym of Chrysanthemum moriflorium - and there's a Chrysanthemum moriflorium var. sinense.

At any rate, I'd like to establish the correct scientific name of the chrysanthemum species that represents Japan. Am I correct in assuming it's Chrysanthemum moriflorium? And, if you know anything about the history behind the royal emblem, do you know if the Japanese specified a particular subspecies or cultivated variety as their royal emblem?


texts: How many primary oocytes in human female body at birth?

texts:
https://discovery.lifemapsc.com/library/review-of-medical-embryology/chapter-4-gametogenesis-oogenesis

In the above site, I see that:

  About 2 million primary oocytes are found in the ovaries of a newborn
  femal Many regress during childhood so that at puberty about 30-40
  thousand remain. Only about 200-400 of these ever reach full maturity
  after puberty and are expelled at ovulation during the female's
  reproductive life

http://www.pnas.org/content/107/22/10280.full

Also, from this site, I see that

  Human ovaries contain follicles as basic functional units. The total
  number of follicles is determined early in life, and follicle
  depletion leads to reproductive senescence. Human follicles begin
  development during the fourth month of fetal life, and each human
  ovary contains ≈400,000 follicles at birth.

From my understanding, there is one oocyte inside one follicle. So, two number should be the same. Why there is a big difference? Or my understanding is just wrong?

PS. I am doing research for my sci-fi, I didn't learn this topic in any college, sorry if this is a silly question.


texts:
The major gene of the Y-chromosome is SRY. Would it be possible to get the X-chromosome and add SRY to create a "fuller" Y-chromosome?

What advantage does the skinny Y-chromosome give an individual anyway? Females only use one X-chromosome (via the Barr body) so they don't seem to gain as much from having the pair.


texts: Do Class A biosolids count as organic fertiliser?

texts:
Does Human Waste, which has been treated at least twice to remove pathogens & remove stink, still count as organic despite it passing the EPA's class A standard?

If so, does this mean that none-GMO crops grown in this fertiliser are still organic?

Thank you to those that take the time to answer.


texts: Why reaginic antibodies are absent in these types of syphilis?

texts:
According to Textbook of Microbiology and Immunology
2e, Subhash Chandra Parija, pg.no; 375

  These(reaginic) antibodies do not appear in early primary syphilis, latent acquired syphilis of long duration, and late congenital syphilis. Therefore, Venereal Disease Research Laboratory (VDRL) and other tests may show false negative reactions during these conditions.

Isn't latent syphilis detected by presence of reaginic antibodies? Then why is it said that it does not appear in long duration?
Why antibodies are not produced in late congenital syphilis?


texts: Confusion about read counts distribution in RNA-seq

texts:
While reading old DESeq paper (Anders and Huber 2010) I came across following line.

  If reads were independently sampled from a population with given,
  fixed fractions of genes, the read counts would follow a multinomial
  distribution, which can be approximated by the Poisson distribution.

I am unable to grasp this line. Why would read counts follow multinomial distribution? My guess would have been Gaussian distribution. Can anyone explain this?


texts: Does catching a cold give you an "effective" advantage against future colds?

texts:
By effective advantage I mean that if I catch a cold now and then recover fully, does this actually reduce my probability of catching a future cold. I understand that the body can build up anti-bodies and such, but pathogens also have the ability to mutate and I would assume that anti-bodies levels decrease over long periods of time. I am not a biologist! So feel free to correct my poor assumptions.

Thus taking those factors into account, are there models or data to argue that catching a cold gives me a future advantage over avoiding the cold altogether?


texts: Nerve fiber responses to intense stimuli

texts: Can one instantaneous, high-intensity stimulus performed on a nerve fiber generate a series of action potentials? Or are nerve fibers limited to one response action potential, no matter how intense the stimulus?


texts: When DNA polymorphism occurs mutations can take place.  If these mutations occur in the germ cell and do not destroy its capability to reproduce, it is said that the mutation might move on to the next generation. My book says it might lead to allele sequence variation. But what does it mean?


texts: The number of nipples (breasts) a species has?

texts:
Only mammals have mammaries and mammary glands.

What evolutionary factors determines the number of mammaries (nipples/teats/breasts) a species has?

Is it always an even number?


texts: Can a hairpin (stem loop) within a transcript stall a eukaryotic ribosome?

texts: Is their evidence of RNA secondary structure causing a stall in translation within a eukaryotic cell?


texts: Identifying a spider from my childhood memory

texts:
Once, as a child, I found a spider in my parents' garden. I remember catching it in a jar because I thought it looked unusual, but I never figured out what kind of spider it was and unfortunately didn't get any pictures. I've been looking for it in books and on the Internet since, based on memory, with no luck.

This was twenty years ago now, and I realize my memory of it may not be good enough to identify it now, but here's trying.

What I remember best was its abdomen, which was a dark metallic blue and sort of rectangular in shape. Its body was probably about 1.5 cm long, without the legs, and maybe 1 cm wide or a little less (I was a child, things look bigger when you're small.) It was found in a garden in the suburbs of Copenhagen, Denmark, sitting on a bed sheet drying in the sun. It left only a few strings of web, almost like a bridge, from the bottom of the jar to the lid where it had escaped during the night because the lid wasn't sealed. I never found it again or saw another spider like it.


texts: Structures of cyclodextrin complexed with small ligands

texts: For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, mol2, etc) complexed with small molecule ligands, such as cholesterol and even smaller. Right now I could only find on the PDB database some proteins complexed with cyclodextrin, but no structure of cyclodextrin with small ligands, could you help me?


texts: LAMP (isothermal amplification), hydroxy naphtol blue , disodium salt" or just hydroxy naphtol blue?

texts:
I am reproducing this work on LAMP (isothermal amplification)
Article A new visually improved and sensitive loop mediated isotherm...
,
but I am a bit confused  about the difference between "hydroxy naphtol blue", and "hydroxy naphtol blue , disodium salt". They hav a very huge difference in price. One is 470 USD and 40 USD for the same aliquote.  Or for LAMP there is no difference?
E.g. Price for HNB
https://www.sigmaaldrich.com/catalog/product/mm/104593?lang=de&region=CH&gclid=CjwKCAjw4rf6BRAvEiwAn2Q76quMK0jzJnsEL5Dsjh_rwYhGCz_Foj5ybiH4o8vNCZQ8S53qkaiA9RoCisIQAvD_BwE
and HNB disodium salt
https://www.sigmaaldrich.com/catalog/product/sial/219916?lang=de&region=CH


texts: Does octopus eye presents the equivalent of fovea in primates?

texts:
I'm working on a simple computational model of Primate eye:  as we know, it presents a central part, the fovea, that is very rich of receptors in comparison with eye periphery. I'm wondering if other species eye, like octopus, present a similar structure: a central fovea.
Thanks


texts: What is the term for toes that pull together with an upstep?

texts:
I fairly recently learned the term digitigrade, to describe the anatomy of a creature that stands on its toes rather than on the flat of its foot, like cats and birds.

I'm trying to narrow that down a little more now. Some animals like a cat or dog (or us), the toes are fairly static as they walk. Contrast that to the toes of a bird where on the upstep the toes... pull together, for lack of a better description, and spread apart as they step down on the foot, as shown in this video.

What is the proper term used to describe that motion and style of walking, or that type of functional foot, where the toes pull together and then spread apart as the foot goes up and down?


texts: How are chromatids correctly segregated during mitosis?

texts: In my book this is described as happening by kinetochores depolymerising from their attached microtubule spindle, then being dragged towards the spindle's centrosome by a dynein protein. I can understand this, but what it does not seem to answer is how different copies of chomatids beome attached to the correct spindles in the first place (i.e. spindles connected to opposing centrosomes). How does this work?


texts: How to determine continental ancestry group (race) with transcriptome data obtained with RNA microarray?

texts: Say I have a whole genome expression data (transcriptome) for some sampled human tissue. Is this data sufficient to find out the continental ancestry group of a donor?


texts: Time required for RNA precipitation in ethanol

texts:
I precipitated bacterial RNA during 1 hour at -80ºC after depleting rRNA with Ribo-Zero kit.

Does more time lead to better results?


texts: What's the evolutionary reason behind decussation?

texts:
A bunch of stuff in the human nervous system decussates. Optical information inputs from the eyes cross over in the optical chiasm. Multiple sensory and motor pathways cross-over before ascending the spinal chord or within the brain stem.

What's the current hypotheses being explored for justifying this anatomical phenomena?


texts: Where can I find DNA decryption research?

texts:
What is the name of the science that studies the mathematics of DNA?

Where can I learn about maths, statistics, types of code, numbers, patterns and graphs for genes and information found in DNA?


texts: Can elephants trumpet when they have water in their trunks?

texts: I am writing a fun story about elephants and want to know if elephants can trumpet or at least, make noises when they have water in their trunks, like when they are drinking water. Thanks for your help!


texts: Does ingestion of alcohol with methylphenidate make it act more like dexmethylphenidate?

texts:
Methylphenidate (MPH) is a dopamine and norepinephrine reuptake inhibitor. It is the racemic mixture of d-MPH and l-MPH. According to the binding profile info on Wikipedia, based on studies, it is at least 6 times more potent at inhibiting the dopamine transporter (DAT) than the norepinephrine transporter (NET).

The dextrorotatory enantiomer, d-MPH, is said to be the main responsible for the therapeutic response of methylphenidate, and to be "much more bioavailable than levomethylphenidate when administered orally" (this paper from 1999 is given as reference). I read it "can be anticipated to be twice the strenght of the racemic product". One distinct property of d-MPH is that it is much less selective for DAT inhibition as opposed to dl-MPH - in fact, it is a bit more potent at inhibiting the NET (at a ratio of about 1.2 - 1.3) compared to the DAT).
The way I see it, this may have clinical significance since dopamine reuptake in the prefrontal cortex is mainly carried by the NET, since DAT expression is significantly lower in this region of the brain [1] [2].

The Wikipedia article also states that "Coingestion of alcohol (ethanol) also increases the blood plasma levels of d-methylphenidate by up to 40%". It references this study from 2011.

What I want to know is: Does that all mean that the ingestion of alcohol, when taking (racemic) methylphenidate can actually make it more potent, at least at lower doses?
Of course, alcohol has an increased activity effect on GABA receptors, which complicates things.

Thanks


texts: Why African species are larger in size compared to other parts of world?

texts:
Why are African species larger in size compared to other parts of world?

Best Example: African elephants are very famous for Giant ears.

So many African Animals listed in Guinness World of Records. (Source)


texts: When is an anatomic entity named "laterale" vs. "lateralis"?

texts:
I'm trying to learn the latin names of anatomical entities and I have a hard time remembering whether it's "Os cuneiforme laterale" or "Os cuneiforme lateralis".

In that case it's "laterale". But in a case like "Nervus cutaneus antebrachii lateralis" it's "lateralis". What's the logic here? How do I remember the right one?


texts: Living organisms with properties similar to both plants and animals?

texts:
Is there any example of currently living organisms that shows close resemblance to both being a plant and an animal?

What is the plant with the closest possible resemblance to animals, and
What is the animal with the closest possible resemblance to plants?


texts: Doxorubicin's intercalant and topoisomerase inhibition in leukemia?

texts:
I am thinking the role of doxorubicin's pathways in cancers such as leukemia and lymphoma:

topoisomerase inhibitor and inhibit DNA activity
intercalant - intercalant DNA bases and inhibit DNA activity

I am interested in which of these mechanisms are most relevant in leukemia and lymphoma.

How does doxorubicin work in leukemia and lymphoma?


texts: How to put a gene under the control of a regulable promoter?

texts:
Suppose I have a hetrologous (eukaryotic, plant) gene sequence that I want to express in E Coli under the control of a regulable promoter (say the lac promoter induced by IPTG) how exactly does one add the promoter sequence upstream of the gene?

Are there any tools to do this?

e.g. Say this is the gene itself, what sequence modification is needed to put it under the control of the lac promoter? The goal is to induce overexpression of the protein coded for by the gene on addition of IPTG to the medium (if I understand the strategy correctly)

atggctaccg ataatgacag ctctgaaaac cgtcgtatgg gtaattacaa gccgtccatc       60

tggaactacg acttcctgca gtccctggct acccgccaca atatcatgga agagcgccac      120

ttgaaactgg cggagaaact gaaaggccag gtgaagttta tgtttggtgc cccgatggag      180
.................................................................
gagccgttcg tgacgttcaa cctgaacagc gttcgtggtt cccatttctt ttacgagttt     1560

ggtgacggtt tcggtgtgac gaatagctgg accaaggttg acatgaagag cgtcctgatt     1620

gatccgattc cactggatga agaataatga                                      1650


texts: Has Epipremnum aureum lost its ability to reproduce sexually?

texts:
In this recent question the shy flowering nature of Epipremnum aureum (Golden Pothos) was discussed:

Where can I find a picture of the inflorescence of Epipremnum aureum (golden pothos)?

To summarize: (1) The two first and only observations of the plant flowering date back to the 60s and (2) genetic analysis yields a potential explanation for why the plant is so rarely flowering

Question: Is this sufficient evidence to conclude that E. aureum has lost its ability to reproduce sexually?

(Triggering thought: It is very unlikely that two specimens flower simultaneously, at a distance from each other that allows pollination, that pollination actually takes place and that the seeds germinate and successfully grow into new plants)


texts: Is an adaptation against impact of fall a factor in babies' bones' structure?

texts: Obviously, babies' bones need to be flexible to get through the pelvic bone. But is that the only reason? Could it be that as babies aren't able to maintain stability, they need bones less prone to damage?


texts: What is the incentive for plants to add rich nutrients to food?

texts: As we know fruits are good sources of vitamins and minerals. What is the incentive for plants to add so much of vitamins and minerals to fruit pulp. My thought is that  seeds would need is some protection, and why waste rich nutrients and vitamins by adding it into pulp?


texts: Do human cells contain only one copy of the genome?

texts:
Does each cell contain only a single copy of its genome? Or are there ever 'extra' copies present.

Reason behind question: Wondering whether gene mutations could be corrected by referencing a 'backup copy'.. If such a thing exists..


texts: Has synthetic biology created new plants or animals as of 2013?

texts: I've seen a Ted.com talk where the speaker suggests that modern science can create new micro organisms, like bacteria with a pre- defined new set of traits. But has anyone create a new species of plants or animals using synthetic DNA yet? If so, what are their names?


texts: why is DNA better for storing genetic info while RNA better for transmission of it?

texts: I do know that RNA cannot be used for transmission since it is unstable, but how does it prove to be a better transmitter of genetic information?


texts: Why do mammalian red blood cells lack a nucleus?

texts: How did the red blood cell in humans get to lose its nucleus (and other organelles)? Does the bone marrow just not put the nucleus in, or is it stripped out at some stage in the construction of the cell?


texts: Are resonances the reason receptors work?

texts:
From Visual phototransduction - Wikipedia:

  When struck by a photon, 11-cis retinal undergoes photoisomerization to all-trans retinal which changes the conformation of the opsin GPCR leading to signal transduction cascades which causes closure of cyclic GMP-gated cation channel, and hyperpolarization of the photoreceptor cell.

From the physics point of view, does this mean the proteins in the eye are combinations of oscillators, each of them in charge for a specific wavelength, so that if one oscillator resonates with the photon, the signal is produced? In general, does all receptors work this way? Note that physical oscillators should have exponential or sinusoid functions. See this Photography question: How to capture a swinging pendulum?


texts: Is studying chemical and physical properties of chemical substances that make up organisms really a task of molecular biology?

texts:
I have read in a high school textbook that (translated into English by myself): "Branch of science that concerns itself with studying chemical and physical properties of substances that make up organisms is molecular biology".

Is this statement accurate? From what I understand, molecular biology deals more with "biological processes at the molecular level", and so it would be biochemistry, or maybe even "standard" organic chemistry, that would study chemical and physical properties of such substances, not molecular biology.


texts: Would the microgravity "shape-shifting" bacteria effect have anything to do with bacteria growing in a host?

texts:
Phys.org's news article Why bacteria 'shapeshift' in space describes a recently published study Phenotypic Changes Exhibited by E. coli Cultured in Space, Zea Luis, Z. et al, 2017, Frontiers in Microbiology 8:1598, doi: 10.3389/fmicb.2017.01598.
The Phys.org article summarizes some of the results:

Because there are no gravity-driven forces in space like buoyancy and sedimentation, the only way the ISS bacteria can ingest nutrients or drugs is through natural diffusion, said Zea. The large decrease of the bacteria cell surface in space also decreases the rate of molecule-cell interaction, which may have implications for more effectively treating astronauts with bacterial infections in space.
The new study also showed the bacterial cell envelope—essentially its cell wall and outer membrane—became thicker, likely protecting the bacteria even more from the antibiotic, said Zea. The E. coli bacteria grown in space also tended to form in clumps, perhaps a defensive maneuver of sorts that may involve a shell of outer cells protecting the inner cells from antibiotics, said Zea.
In addition, some of the E. coli cells also produced outer membrane vesicles—small capsules that form outside the cell walls and act as messengers for cells to communicate with each other, Zea said. When cells with such vesicles reach a critical mass they can sync up to initiate the infection process.
"Both the increase in cell envelope thickness and in the outer membrane vesicles may be indicative of drug resistance mechanisms being activated in the spaceflight samples," said Zea. "And this experiment and others like it give us the opportunity to better understand how bacteria become resistant to antibiotics here on Earth."

I'm wondering how likely the following part of the quote from the corresponding author is to be true: "...which may have implications for more effectively treating astronauts with bacterial infections in space."
If I understand correctly, *ll of the effects related to growing in space that are described seem to be related to growing in a liquid culture medium, not inside a mammalian host. I'm not sure a bacteria which has infected an astronaut or other mammal in space will experience any difference in conditions if the host is in microgravity vs being in normal gravity. The differences seem to be specific to transport mechanisms in the culture medium, and not to any effect of weightlessness on the bacteria themselves.
Am I missing something?


texts: Why facet cells/umbrella cells of uroepithilium are sometimes multinucleated?

texts: Why do are they multinucleated and why only some cells, why not all?


texts: How can we calculate the minimum sustainable number of the panda population?

texts:
I have a degree in Biology so I'm a little embarrassed that I never learned this, but...

How do we know 1600 Pandas isn't enough?

I know that we have historical numbers (although I couldn't find them) which show the population has declined, but we also know the usable habitat has declined and it would be foolish to not consider that when trying to replenish the wild population. It seems to me that if there's only 1600 Pandas in the wild, that's probably the right number. How do we know it's not?

I will accept answers about other endangered animals, if they show how we can calculate the approximate "appropriate" number for a species.


texts: What are the effects of combining rapamycin with dietary restriction?

texts: Are the effects additive or subadditive? In many ways, rapamycin acts like a CR mimetic, but even CR can only go so far.


texts: If there are three different alleles to a gene, is it possible that the first is dominant to the second, but recessive to the third?


texts: Why didn't Mendel ever see the recombination?

texts:
I saw a video on youtube of a professor saying it's because of the quantity of peas. So Mendel would never have published his work if by any chance he had found a pea with recombination.

Someone can explain to me in a dummie way the reason?


texts: Where is DNA during the process of RNA extraction using Trisure?

texts:
Where is DNA during the process of RNA extraction using Trisure described here? Given that DNA is also a nucleic acid, should I expect the isolated RNA to also contain DNA? However, Bioline claims RNA 'with
virtually no genomic DNA contamination'.


texts:
Here's a picture:

That's pretty much it, besides that it was found in Vienna, Austria.

Edit: Thanks to Magne Flåten; it's called Hausmutter in German.


texts:
Suppose a person wears the specs of power -6D, the far point for that person is 16cm.
But the near point of normal eye is 25cm.

So, is the near point of a  person with myopia (having far point less than the near point of normal person) also changed ?


texts: Is eye colour of Drosophila a polygenic trait or an X-linked trait?

texts: I have seen examples of various eye colours in Drosophila and they have been described both as "X-linked" and "polygenic". I thought these were mutually exclusive. Is Drosophila eye colour polygenic or X-linked?


texts: How are subspecies defined, in contrast to species?

texts: When should a taxon be considered to be a subspecies of a certain species, and when as a different species? Are there some general guidelines how to assign a specific taxonomic status to a taxon?


texts:
Why is the Krebs cycle considered a part of aerobic metabolism if molecular oxygen is not involved in any of the reactions in the cycle?

I originally thought that Krebs cycle was aerobic metabolism because it is in the process that oxygen is the final electron acceptor, but my teacher claims that glycolysis is anaerobic so what makes the Krebs cycle aerobic?


texts: Why does low temperature make RuBP, GP and TP concentrations fall in Calvin cycle?

texts: In my A level revision guide and places on the internet it states that at low temperatures levels of RuBP, GP and TP all fall. However I don't quite understand how this is the case, because as far as I can see, a reduction in temperature would give the molecules less kinetic energy and reduce the rate of reaction of the enzymes and so there would be no change to relative concentrations, because everything is slower all equally. Could anybody explain to me why all three decrease in concentration at low temperatures?


texts: Bioinformatics tool for "pairwise alignment" of complementary sequences?

texts:
I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate efficiency of binding. After thinking about it, I'm essentially looking for "the opposite" of BLAST, in that BLAST looks for regions of similarity in sequences in the same orientation, while I'm looking for  regions of complementarity in sequence in the opposite orientation.

Does such a tool exist?

EDIT 1

To clarify, I'm looking for a tool that can detect the most optimal regions of complementarity in two sequences when both are aligned as such:

  5' TCGAAUAACTCGTCUGAUGAGUCGCUGAAAUGCGACGAAACCGTTAACGGA 3'

  3'   GTTTTACGCAAAGCAGCGTAAAGTCGCTGAGTAGTCACTTTAATGAC   5'


texts: What is the probability that a gamete will only contain father's chromosomes

texts:
As it is depicted in most textbooks, cross-over does not occur between the two "outer" sister chromatids. By independent assortment during Meiosis I, there is 1/2^23 chance that all father's chromosomes, with one pure father's chromatid, will end up in the same daughter cell. Does this mean that roughly one in eight million people does not have any genetic material from one of his grandparents or is there some more independent assortment during Meiosis II, which makes this outcome extremely unlikely? (more like 1/2^46)

More generally I would be interested in the probability that a gamete will contain more than 60% ,70%, 80% ... of only one of your parent's genes.


texts: If your body can slow down your metabolism, why doesn't it do that all the time?

texts:
I've read that in cases such as in anorexia or a lack of food, the body slows down the metabolism to preserve the little food it does get. If it can do this, though, why doesn't it keep your metabolism slowed, preserving energy? Are there effects to slowing down your metabolism?

Edit: I read it in various realistic fiction books about anorexia, which claimed to have accurate medical information. One was Wintergirls, by Laurie Halse Anderson, where the girl with anorexia says she has a slow metabolism, and her doctor mother says something to the effect of "your body's slowed down your metabolism because it thinks you're in a famine."


texts: How many end segments does the axon of a typical cortical pyramidal cell have?

texts:
I tried to do some research - starting with a Google search for "typical axonal trees" - and found the following pictures:

source

source (axons are red)

but didn't find a concise answer to this and some related questions:

  How many end segments (which don't branch anymore) does the axon of a typical cortical pyramidal
  cell typically have. I guess it's a much smaller number than the
  number of end segments of a typical dendrite, but how large is it
  roughly: some tens, sometimes less than ten?

I'd like to exclude from this question the typical axonal "end trees" which branch into the axon terminals.


texts: Biology and dna samples to determine parental lineage

texts: How could you use nuclear and mitochondrial DNA samples run through electrophoresis to determine parental lineage.


texts: gene duplicated on genome but is different

texts:
I've been looking at a miRNA cluster on a genome and I found it three times. The first two are right next to each other and look exactly the same, the third sequences is on a different scaffold of the genome and is both shorter and has a number of mismatches with the first two sequences.

Is there a particular name for this? The first two are most likely some sort of gene duplication, but I'm not too sure on what to call the third,

Thanks


texts: Why does the 'Positive-inside Rule' exist?

texts:
Gunnar von Heijne's Positive-inside Rule seems to have been around for a couple of decades and underpins a lot of what we know about transmembrane topology. It is used to predict the topology of a given transmembrane domain, typically a helix.

My question is what are the physicochemical, or biochemical explanations for this rule? Although the literature talks about it in depth and has many examples of the rule being employed, I can't seem to find anything about the "behind the scenes" explanation.


texts: What is the source of the fat in adipose tissue?

texts: I have heard the opinion that all of it comes from de novo lipogenesis of carbohydrates, but I'm skeptical. Is there evidence either way - either that dietary fat definitely gets stored in the adipose tissue, or that it never does, and all of it is from carbohydrate transmutation?


texts: How can I list genes present on a given series of bands?

texts:
My question is related to this one. My interest relate to this deletion:

  del(7)(q11q36)[12]

as defined by ISCN.

I would like to access a list of the genes found on the bands 11 to 36 of the 7th chromosome in humans. How can I do that?


texts: Can insects or mosquitoes be astonished(shocked)?

texts:
Can insects like mosquitoes get astonished by sudden happenings?

Background

I missed hitting a mosquito on a wall with great force. However even though I missed hitting it, it was dead.

So I wonder if insects can reach death or at least astonished by sudden happening, or lead to something like cardiac arrest.

Hope it isn't a noob question :)