What is the difference between Crossbreeding, Outbreeding and Outcrossing?

Answer in keywords

Inbreeding : related individual,same breed

Outbreeding

Cross breeding : between different breeds
Outcrossing : unrelated individual,same breed,no common ancestor

Detailed answer

Inbreeding it is a mating within the same breed between different superior male and superior female. Inbreeding between close relatives can cause inbreeding depression like decreased Vigour , fertility and productivity. It is therefore advisable to mte superior animals of different population of the same breed .

Outbreeding is mating between unrelated animals of same or different breeds.

Outcrossing is mating between unrelated animals of same breed with no common ancestor for at least 4 to 6 generation. Offspring formed from such a cross is called out cross .

Cross breeding is mating between superior animals of different breeds for raising new breeds for improving local breeds.

Please note: Outcrossing and
cross breeding are two types of Outbreeding.

If you have any further doubts please ask .
Hope it helps!!


Why aren't mammals and reptiles considered amphibians?

Some named groups are not monophyletic (see this post for definition if needed). Fishes do not represent a monophyletic group. Groups like "fishes" are completely awful to define but everyone would agree that no, humans are not fish!

Now, it is important to understand for many terms, there might have a scientific and a popular definition of the term. For example, when people talk about reptiles, they talk about turtles, snakes, lizards, squamates but they don't talk about mammals. Hence by "reptile" they don't mean "Reptilia". Have a look at the post If dinosaurs could have feathers, would they still be reptiles?).


The common scientific belief around 1900 was that the only dietary components needed to support life were protein, fats, carbohydrates, and salts.[1]  In 1912 Hopkins reported on experiments showing that "accessory factors" seemed to be needed.[1]  In 1916, some of the factors began to be characterized in the paper "The Relation of the Unidentified Dietary Factors, the Fat-Soluble A, and Water-Soluble B, of the Diet to the Growth Promoting Properties of Milk."[2]  The title itself designates two factors as A and B.  Lack of factor A seemed to be associated with various problems particularly with the eyes, and factor B with a condition similar to beriberi.  Before long, another factor was found that was associated with scurvy. In 1920, the literature had a confusion of terminology in use, and Drummond, using a variant of Funk's word, proposed:

  that the substances be spoken of as Vitamin A, B, C, etc. This simplified scheme should be quite sufficient until such time as the factors are isolated, and their true nature identified.[3]

It was only later that the factors became well characterized. Vitamin B came to be known to be a complex mixture, and its components took decades to be characterized.(Wikipedia)  As components of Vitamin B came to be known, subscripts were assigned.  Some of the subscripts were assigned to compounds that later turned out to not to be fundamental and essential, and so are no longer used. Vitamin B12 took a particularly long time to characterize.(Wikipedia)

The vitamins are now well understood, and each has a specific name unrelated to the vitamin naming scheme, yet the vitamin terminology continues to be used because it is well known and useful to people at many different levels of technical knowledge. The significance of the name of the B group of vitamins is that "B" follows "A" and precedes "C" in the alphabet, and the history of discovery is still embedded in the names we use.

[1]  Hopkins FG. Feeding experiments illustrating the importance of accessory factors in normal dietaries. J Physiol. 1912 Jul 15;44(5-6):425-60. doi: 10.1113/jphysiol.1912.sp001524. PMID: 16993143; PMCID: PMC1512834.

[2] EV McCollum, N Simmonds, W Pitz. The Relation of the Unidentified Dietary Factors, the Fat-Soluble A, and Water-Soluble B, of the Diet to the Growth Promoting Properties of Milk - Journal of Biological Chemistry, 1916

[3] Drummond JC. The Nomenclature of the so-called Accessory Food Factors (Vitamins). Biochem J. 1920 Oct;14(5):660. doi: 10.1042/bj0140660. PMID: 16742922; PMCID: PMC1258930.


Nature tends to turn against cancer not towards it. Cancer exists when cells begin to multiply with abnormal features, without correction. Cancer is the consequence of many many harmful mutations, which inhibit the correct reading of DNA.

Cancer takes time to develop, not months, but years. Also, babies don't have old tissues, so there haven't been as many divisions, or as many opportunities for mutations, as a 5 yr old or a 10 yr old has gone through.

Although rare, Neuroblastoma is a cancer that babies CAN be born with. Nerve cells develop early, week 5 of fetal development.

Perhaps someone else could talk more about the biological mechanisms which really make cancer more a reality for older organisms, but probablistically, it doesn't make sense that a newborn baby would have cancer.

I looked up these links, to try and address your question.

cancer in general
https://www.cancer.gov/about-cancer/understanding/what-is-cancer

why cancer takes time to develop
https://sites.duke.edu/missiontomars/the-mission/cancer/why-do-most-cancers-take-so-long-to-develop/

cancer in babies
https://blog.dana-farber.org/insight/2015/02/can-babies-be-born-with-cancer/


When does DIFFUSION occur and not OSMOSIS, and the otherwise?

But when does exactly osmosis occurs instead of diffusion?

These processes are not mutually exclusive. Both can happen simultaneously. Their rates depend on different parameters such as permeability of the membrane towards water and the solutes. A semi-permeable membrane has different permeability for different molecules. There are cases when one of these two processes may happen but not the other (again, a function of the parameters):

Osmosis+/Diffusion-
When there are no solute transporters expressed in the membrane of the concerned cell. For e.g. RBCs do not express the Sodium-Chloride symporter. It is expressed in the distal convoluted tubule of the nephron.

Osmosis-/Diffusion+
When the osmolarity of the cytosol is same as that of the ECF and the cell expresses ion channels. The action potential in a neuron would be an example of this phenomenon.


How many RNA-binding proteins can simultaneously bind on a single mRNA?

See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq.

Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression.

They show number of protein protected sites (PPS) per transcript but that is not a proper metric in my opinion. The number should be normalized with transcript length so that you get density of protected sites. From figure 4 (see below) you can roughly estimate that average PPS density is close to 0.6 which means that 60% of any RNA is expected to be protein bound.

  Figure 4

Other points to be noted:

Highly translated mRNAs will have multiple ribosomes on their CDS and
are likely to be more protected.
Sequestered RNAs in stress granules will also have high density of PPS
Footprint of different RBPs will be different. So number of proteins that can bind to a mRNA will differ between different RBPs.

Further reading:

http://dx.doi.org/10.1186/gb4153
http://dx.doi.org/10.1016/j.cell.2012.04.031
http://dx.doi.org/10.1016/j.molcel.2012.05.021


To obtain population related vcf files I created the respective (CEU, MKK, ...) samples list first using the samples file you can also download the 1000 genome ftp site.

grep CEU integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > CEU.samples.list

Then I installed vcf tools (https://vcftools.github.io/index.html) and used the vcf-subset command.

I got the commands from this faq page:
http://www.internationalgenome.org/faq/how-can-i-get-allele-frequency-my-variant/

I did not compute haplotypes from the files, but I read in another post, that you can do that with PLINK. Have you checked that?


Is there a bacterium that became a virus?

This virology site has a post about a 2017 paper about membrane-vesicled plasmids that act in ways that are theorized to be precursors to how viruses work:

It is likely that the plasmid-containing membrane vesicles are precursors of what we know today as virus particles. It is thought that viruses originated from selfish genetic elements such as plasmids and transposons when these nucleic acids acquired structural proteins (pictured; image credit). Phylogenetic analyses of the structural proteins of many enveloped and naked viruses reveal that they likely originated from cell proteins on multiple occasions (link to paper).
The membrane-encased Archaeal plasmid seems well on its way to becoming a virus, pending acquisition of viral structural proteins.

Though plasmids are not viruses and are not bacteria, bacteria are hosts for plasmids, and plasmids add indirectly to the genetic constitution of bacteria. Expression of plasmid genes can help bacteria survive hostile or extreme environments, and they reproduce along with bacterial chromosomes. Via the Wikipedia link:

Unlike viruses, which encase their genetic material in a protective protein coat called a capsid, plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host; however, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer.


What is meant by "alien" probe in a microarray?

It's a probe to detect external 'Alien' RNA standard, a synthetic mRNA commercialized by Stratagene/Agilent.

  The Alien RNA transcript is a ~500-nt, polyadenylated RNA molecule that
  is synthesized by in vitro transcription. The Alien RNA transcript is
  nonhomologous to all known nucleic acid sequences currently in public
  databases, as determined by BLAST comparisons against NIH sequence
  databases. https://www.chem.agilent.com/Library/usermanuals/Public/300602.pdf

As any other external standard, you spike in the same amount of Alien RNA standard in your different reactions and then using the Alien probe you can normalize for extraction efficiencies etc. It works not only for microarrays, but also for qPCR, RNA-seq etc.

If you didn't spike in any of it, I expect your probes giving very low signal that's probably why you thought about negative controls.


An allergic reaction requiring an epipen can be caused by swelling in the throat and/or bronchoconstriction (spasms decreasing the diameter of bronchioles). Bronchoconstriction can occur in the absence of soft tissue swelling in the lips, tongue and throat, and vs. versa.
Epinephrine reduces pharyngeal edema (swelling) because it is a potent vasoconstrictor in small arterioles and precapillary sphincters in most body organ systems. This is effected through alpha-1 adrenergic receptor activation. While the blood pressure and heart rate increase (due to beta-1 adrenergic effects), the permeability at the capillary level is decreased, relieving swelling.
At the same time, epinephrine relaxes bronchial muscle. It has a powerful bronchodilator action when bronchial muscle is contracted because it is a powerful beta2 adrenergic agonist.
Finally, epinephrine inhibits antigen-induced release of inflammatory mediators from mast cells, and to a lesser extent from diminution of bronchial secretions and congestion within the mucosa. Inhibition of mast cell secretion is mediated by beta2 adrenergic receptors.

Adapted from Simons. Kemp et al. World Allergy Organization Journal 2008 1(Suppl 2):S18-S26   doi:10.1186/1939-4551-1-S2-S18
Epinephrine: The Drug of Choice for Anaphylaxis--A Statement of the World Allergy Organization


How Plausible is Restoration of Cryonically Preserved People?

Largely implausible, mainly due to damage from freezing. This type of damage even happens when food is frozen (although flash-freezing decreases it).

More feasible approaches for avoiding death would include machine-replacement parts, lab-grown transplants, neural backups, and regenerative gene modifications. I'm surprised no one has considered studying hibernation and how to add similar genes to humans that would enable hibernation.


Was there ever a very first Homo sapiens?

No. It is important to distinguish "species" as a human system of classification, and "speciation" as a biological process. Except in cases like chromosomal speciation (changes in ploidy), speciation takes a long time. Probably thousands of years between some initial restriction of gene-flow, and fixation of a specific identifiable trait, present in all individuals of a species, and not present in any others. As a human system of classification, the taxonomists who define species would all understand that speciation is a process that occurs over time, although they may make some arbitrary distinction for convenience. For example, a node on a cladogram symbolizes an instantaneous process of species bifurcation, but this is understood to be an unrealistic simplification.


Can someone identify this stinging plant?

I think it is a common stinging nettle, Urtica dioica. It is a native to Europe, Asia, northern Africa, and western North America and is the best-known member of the nettle genus Urtica. As commented by others, your geographical location would be helpful to obtain a more accurate identification.

Like other stinging nettles, it is unpleasant to the touch, but harmless. Just be patient. The redness and burning/itching will disappear. If the pain gets serious or other complaints arise, go to your GP.

Stinging nettle. Source: Health Direct.


Removing a restriction site and introducing other at its place

The recognition site for EcoRI is GAATTC, and the enzyme cuts after the first base. See this picture from NEB:

The overhang is: AATT, which is supplied by your oligo and fits into the overhang. If the next nucleotide whould be a C than the site would be recreated, since its a G its not. The new sequence of the old EcoRI site is GGATTG which is not recognized by EcoRI.

One technical note: To avoid religation of the digested DNA which carries this site, I would treat it with alkaline phosphatase to remove the phosphate end at the 5' end of the DNA.


Why is Lamarck's evolutionary theory considered incorrect?

In science theories are tested by experiment evidence and, as scientific knowledge progresses, how they can be accommodated in the framework of knowledge. In brief, there is no evidence to support Lamarck’s idea (Lysenko is notorious for his falsification of such evidence during the Soviet era to fit with Stalin’s philosophy), and the subsequent discovery of the molecular basis of heredity provided a requirement for the theory to show how changes in somatic cells could affect the DNA of the germ cells. No such evidence has emerged.

It is true that there are epigenetic effects, but none so far support Lamarckian postulates of the giraffe neck variety.

Finally, a word of advice. Don’t waste your breath on this list with arguments of the sort “Doesn't the latter contradict the evolutionary theory itself”. This is not a philosophical debating society, but community that is concerned with the factual basis of science. If you have never studied molecular sciences, stay away — or ask questions in the course of genuine attempts to acquire knowledge in this area.


What is an efficient way to spike 10-50 cells to a culture

If you are you working with primary cell cultures or cell lines may be you could do this when cells are in suspension, after tripsinization, mix them well with a 5mL serologial pipete in a falcon 50mL tube and plate to a 100mm2 with a final volume of 7mL. And finaly draw an eight with the plate in the hood more than 3 times to mix them well.

Edit: For the addition of 10-50 cells, count these cells with trypan blue, and do a 1:100 dilution, for example if you have 1e6 cells in 10mL you could take 0.01 mL (10 microliters) to get 1, 000 cells

And then you add the 0.01mL into 1mL of cell media to get 1 cell per 1 microliter, and then if you wanna get 10 cells, take 10 microliters, and so on


If you have a cat carrier then trying to intice it inside with some food would be a good idea. Try to contact your local wildlife vet for information on whether they would be willing to treat the animal. If you think it may be injured then I wouldn't reccomened handling the bird as you may hurt it further, but if you do need to then handle it by placing both hands over the wings in order to pick it up (https://www.rspb.org.uk/birds-and-wildlife/advice/how-you-can-help-birds/injured-and-baby-birds/if-you-find-an-injured-bird/) . In addition the bird could have gotten used to its injury and learned to live with it so you could monitor it for a bit and see how it's getting on. Hope it turns out alright.
If you live in the UK here is some advice from the RSPB: https://www.rspb.org.uk/birds-and-wildlife/advice/how-you-can-help-birds/injured-and-baby-birds/sick-and-injured-birds-faqs/#:~:text=For%20most%20injured%20birds%2C%20place,how%20you%20can%20help%20it.


Are there testosterone receptors in female mammary tissue?

The female mammary gland tissue contains androgen receptors (testosterone is an androgen). So this tissue is sensitive to androgens, and they inhibit the estrogen-induced proliferation. The inactivation of the androgen receptor on the other hand leads to an accelerated growth of the pubertal mammary gland and to the upregulation of estrogen receptor α expression in female mice. See references 1-3.

And the androgen receptor also seem very important in the formation of the nipples, as testosterone here directs apoptosis in the forming breast tissue. Mice without a functioning androgen receptor were born without nipples. See reference 4 and 5 for details.

To answer your question shortly: Yes, androgen hormones (among them testosterone) have a profound influence on the female mammary gland.

References:

Testosterone inhibits estrogen-induced mammary epithelial
proliferation and suppresses estrogen receptor expression.
Minireview: The Androgen Receptor in Breast Tissues: Growth
Inhibitor, Tumor Suppressor, Oncogene
Androgen receptor inactivation resulted in acceleration in pubertal
mammary gland growth, upregulation of ERα expression, and
Wnt/β-catenin signaling in female mice.
Hormone Action in the Mammary Gland
Specificity of tissue interaction and origin of mesenchymal cells in
the androgen response of the embryonic mammary gland.


Vaccine efficacy
Pfizer's target measures for efficacy (see the study on clinicaltrials.gov) seem to be:

Confirmed COVID-19 in Phase 2/3 participants without evidence of infection before vaccination

Confirmed COVID-19 in Phase 2/3 participants with and without evidence of infection before vaccination

From Pfizer's study plan (VE = vaccine efficacy):

VE will be estimated by 100 × (1 – IRR), where IRR is the calculated
ratio of confirmed COVID-19 illness per 1000 person-years follow-up
in the active vaccine group to the corresponding illness rate in the
placebo group from 7 days after the second dose. VE will be analyzed
using a beta-binomial model.

(note: they also have other time windows and checkpoints in their analysis plan; which one is reported will shift from press release to press release as they get more data. If you are interested in the details the study plan also describes the planned interim analyses, and some of the press releases discuss deviations they've made from their original interim plans in consultation with regulatory agencies)
This measure is called relative risk, and can be written like this:
%InfectedPerTimeplacebo = NInfectedplacebo / (NStudiedplacebo * AverageFollowUpTime)
%InfectedPerTimevaccine = NInfectedvaccine / (NStudiedvaccine * AverageFollowUpTime)
Efficacy aka VE = %Infectedvaccine / %Infectedplacebo
If you assume risks are the same in the placebo and vaccine groups (they "should" be, but might vary if, for example, people who experience vaccine side effects change their behavior) and the average follow-up time is the same (they should be approximately the same, because they are giving the vaccine and placebo to patients enrolled at the same time), this ratio would tell you that a vaccine efficacy of 95% means that if you took 20 people who would have had a positive test after the placebo, you would only expect 1 of them to test positive if they instead got the vaccine.
Population vs. individual statistics

Put very simply: is it 100% effective in 95% of the population, or 95% effective in 100% of the population?

These are population-based measures. They can't say anything about efficacy in particular individuals by these outcome measures. For example, there is no way to know from a study like this whether the vaccine is 100% effective in 95% of the population, or if it raises the infective dose in everyone by some amount which causes the number of people exposed to this critical viral dose in their environment to decrease by 95% (or some other effect with the same end result).
Other approaches like challenge studies, where vaccinated individuals (or animal models) are intentionally exposed to a certain dose of the virus, can help understand the individual effects of vaccination, as can indirect measures of immune response like antibody titers. These approaches have other drawbacks, however (safety, translating animal results to humans, translating a given immune response to an infection chance, etc).
Beyond just 'vaccine efficacy': disease severity, real-world efficacy
These particular outcomes also say nothing about disease severity. It could be that the people who do test positive despite getting the vaccine get just as sick as the sickest people who don't (interpretation would be that the vaccine protects mostly against mild illness). It could also be the reverse, and that people who get the vaccine and still test positive have a milder illness than they would have otherwise. Efficacy defined by this relative risk ratio does not say anything about this, it only compares positive vs negative rates.
An additional note: these numbers report efficacy in the trial environment. "Real-world" effectiveness (the same measure of effect, but in real world use rather than under trial conditions) might depend on other factors such as differences in the people enrolling in trials vs the general population (both in terms of things like age and preexisting conditions as well as behavior and exposure risks), failure to administer the vaccine properly (including improper storage), failure to complete both doses in timely fashion, etc. This measure of effectiveness also refers only to "primary" effectiveness. One would expect that if enough people were vaccinated, the effect on the population could far exceed the primary effectiveness, because not only do vaccinated individuals have a lower chance of infection, but everyone else in the population also has a lower risk if there are fewer people available to transmit the infection.


Walkingsticks, like that in your photo, belong to the insect order Phasmida (also sometimes called Phasmatodea). The species in your photo belongs to the family Pseudophasmatidae. Texas has two species documented for this family. One is Anisomorpha ferruginea, commonly called the dark walkingstick or northern two-striped walkingstick.  The other species is Anisomorpha buprestoides, commonly called Florida stick insect or two-striped walkingstick.

According to W.S. Blatchley's Orthoptera of Northeastern America (1920), pg. 145, A. ferruginea has narrow stripes and is a bit shorter than A. buprestoides, which has broad stripes. Based on the appearance of the stripes in your photo, I'd say you have A. buprestroides.


Technically, higher main magnetic field strength doesn't mean more resolution.  There are three parts to the scanner: 1) main magnetic field, 2) gradient coils and 3) RF coils.

The main magnetic field strength (1.5T, 3T, 7T, 9T, the last two typically more for research) determine more of the signal to noise (in a very simple sense).  This is static - it doesn't ever change.

The gradient coils are what determines the resolution and the rate of switching is the biggest determining factor. There are limits on what they can switch at when used on humans as they can cause peripheral nerve stimulation, vertigo, nausea, metallic tastes etc.

I don't believe static field of 20T etc would be a problem, though there is not much research to prove or disprove that.  The problem would be moving into that field as that will cause the same types of effects as the gradient coils switching.  Even for 7T, one must not run into the scan room as it can cause peripheral nerve stimulation (and some other effects). Currently, I believe the strongest full body human MRI scanner is 10.5T. Another article talks about 11.7T human scanners (one of them is a "head only" scanner. It also has some nice pictures).


Why do COVID19 serology tests focus on the nucleocapsid while vaccine efforts focus on the spike?

The vaccines will be directed towards a protein/epitope of the virus that creates the most robust immunogenic response, in which the defense system will create an array of antibodies to confer immunity, those antibodies will have to NEUTRALIZE the virus upon entry.
In the case of SARS-CoV-2, the majority of research shows that neutralizing antibodies are directed towards the S1, S2 and RBD proteins which are all part of the S protein.

In this same line, the fact that the body creates antibodies directed towards other components of the virus doesn't mean that they are protective. So creating a vaccine towards those components wouldn't be useful at all.

The reason why those serologic tests target the N protein is probably due to the fact that is highly antigenic. But I'm sure I've seen tests that also target the S protein.


Your vocal chords vibrate to produce a tone, but your mouth shapes that tone into the sounds that make up voice. If your vocal chords fail or are removed, the electrolarynx can be used to vibrate the throat for you, but your mouth still needs to shape that sound into words. Because the electrolarynx produces a mechanical buzzing vibration, you get mechanical buzzing words. This is similar to how the talkbox works with electric guitars, the guitar sound is piped through a tube into the musicians mouth, they have to shape that sound into words with their mouth. Go listen to Peter Frampton for a good example.


C-myc/anti-myc Ab Interaction with Fusion Proteins

After some further research, I found papers reporting successful co-immunoprecipitation experiments with POI-myc-His fusion proteins.

Moreover, I figured the signal sequence will be cleaved by signal peptidases which will leave the c-myc tag exposed on N-terminus with only an extra residue. I don't think that one extra residue will create a problem.

Here's the tool I used to figure out where the signal sequence will be cleaved:
http://www.cbs.dtu.dk/services/SignalP/

Here are the references for POI-myc-His experiments:

DOI: 10.1016/j.cub.2006.08.085
DOI: 10.1073/pnas.97.2.668


How is histamine useful against allergies?

Histamine is produced in allergic reactions. - True

Histamine is produced against allergic reactions - False

Okay. Lets get a few things right here first. An allergy is an inappropriate immune hypersensitive response. It is something, we are not supposed to have. A small harmless pollen grain, in normal people shouldn't initiate an allergic reaction.

IgE antibodies are produced against an allergen. These attach their Fc ends to the mast cell. When these antibodies are cross linked by the antigen, degranulation of the mast cell ensues which release various mediators one of which is histamine. So there is a lot of histamine produced in allergic reactions and common antihistaminics like cetirizine and terbinafine act by blocking histamine receptors thereby reducing its biological effects.

So, allergy is a bad thing. The whole IgE, cross linking, degranulation and histamine release wouldn't have happened in a normal person. Histamine isn't going to protect from allergies. It is the cause of allergic effects. Hence the antihistaminics work. You might know that if you have taken a cetirizine during a rash or severe sneezing.

So if allergy is a bad thing, what is the normal physiological role of IgE?

IgE has a role to play in the immune response against parasites where a similar mast cell degranulation process happens.

And if histamines are causing the allergic effects and allergy is bad, what is the normal role of histamine?

Histamine has several roles to play. One is that it is produces as a part of immune response by basophils and mast cells. It also is a neurotransmitter and also is important is gastric acid secretion physiology. The various functions of histamine have important pharmacological considerations while talking of antihistaminics.

Reference : Kuby, Immunology 6th Ed.


How do DNA-binding proteins recognize the correct DNA base pairs?

There are different kinds of DNA binding domains; the ones involved in base identification in the major groove can differentiate between different base pairs of the same nucleotides i.e. AT vs TA because they bind to functional groups on a nucleotide and not the base-pair per se. The stereochemistry i.e. which nucleotide is in the major groove, is important. The location of the nucleotides in the major groove also is a factor (Figure 1).

  Figure 1: DNA sequence identification by Helix-Turn-Helix transcription factor. This is the example case of the Engrailed protein in Drosophila. Reproduced from Paro and Sauer (1992) [1].

You can see that Adenine is recognised differently than Thymine. In many cases such as that of zinc finger proteins (ZF), sequence identification usually happens for dinucleotide pairs such that each finger (a modular unit) can identify a di/tri-nucleotide (Figure 2,3). An array of fingers in case of ZF and helices in case of Helix-Turn-Helix motifs can recognize a unique stretch of DNA sequence (which is certainly more unique than individual base pairs). Usually the binding of the fingers are co-operative which leads to increased affinity and specificity of the protein-DNA binding [2,3]. Analogous mechanism may exist for other kinds of DBD too (I haven't specifically looked for that). Moreover, many DNA motif binding proteins oligomerize, which is again co-operative. This increases the specificity and the overall binding kinetics becomes sigmoidal and thresholded (see Hill kinetics).

Binding mechanisms are best understood for ZF proteins that led to the development of zinc finger nucleases which was one of the first modern methods of targeted genome editing [4] (though they have now been obsoleted by CRISPR-Cas system).

  Figure 2: DNA sequence identification by zinc finger proteins. This example considers the Zif268 protein. Reproduced from Paro and Sauer (1992) [1].

  Figure 3: A more detailed depiction of Zif268-DNA interaction. Reproduced from Durai et al. (2005) [4].

References:

Pabo, Carl O., and Robert T. Sauer. "Transcription factors: structural families and principles of DNA recognition." Annual review of biochemistry 61.1 (1992): 1053-1095.
Krishna, S. Sri, Indraneel Majumdar, and Nick V. Grishin. "Structural classification of zinc fingers SURVEY AND SUMMARY." Nucleic acids research 31.2 (2003): 532-550.
Lee, Juyong, Jin-Soo Kim, and Chaok Seok. "Cooperativity and Specificity of Cys2His2 Zinc Finger Protein− DNA Interactions: A Molecular Dynamics Simulation Study." The Journal of Physical Chemistry B 114.22 (2010): 7662-7671.
Durai, Sundar, et al. "Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells." Nucleic acids research 33.18 (2005): 5978-5990.


Bird ID (greenish passerine, Sacramento, CA)

You probably found a Yellow Bellied Flycatcher, which is weird because they are mainly midwest.


Do PC-12 cells have to be stored in nitrogen?

The temperature at which nitrogen evaporates is about −195°C. Given the considerable difference in temperature between the current freezer and nitrogen vapor, I'm inclined to say probably not.

I suspect that it may be dependent on what exactly you are using the PC 12 cells for. Without knowing more detail about the situation, I would do my best to get ahold of some liquid nitrogen for your samples as soon as possible. When in doubt, it is always best to follow procedure.

Until you can acquire nitrogen, -80 is still far better than room temperature. Be sure to take note of the discrepancy in your notes and hope for the best.


Tissue plasminogen activator is a serine protease consisting of approximately  530 amino acids and about 13% carbohydrate.

This enzyme is made up of five domains performing different functions. The finger domain and the two kringle domains are involved in the binding of t-PA to fibrin, whereas the epidermal growth factor domain is responsible for activating EGF receptor. Kringle 1 also help in transport of this molecule via liver's endothelial cells. Kringle 2 also helps in binding with inactive plasminogen. The serine protease domain cleaves the plasminogen at  Arg561-Val562  and activates it into plasmin.

(Image Source: https://www.researchgate.net/figure/Structure-and-functions-of-tissue-type-Plasminogen-Activator-tPA-A-Structure-of_fig1_284797342)

Plasminogen is the precursor for synthesis of protease plasmin. Plasminogen is converted to plasmin by cleaving Arg561 and Val562. The  activated plasmin is formed by making disulfide-linkage between these two polypeptide chains.

The heavy chain  is at the N-terminal and light chain is at C-terminal.  The activation takes place by removing the signal peptide and activation peptide  by autolytic cleavage. This activation peptide is released from the N-terminal  to convert Glu-plasmin to  Lys-Plasmin. The active site which plays role in binding with fibrin is situated on the light chain.

(Image Source:  https://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/plasmin.html)

So, this proteolysis only produces one working peptide sequence, as the peptide bond cleaved and then amino acids are again joined by disulfide bond. And this peptide bond between arginine and valine is at 561/562 instead of 560/561 according to various sources.


Answer the questions in one word with help of clues and images given

Since you have apparently tried to answer the question here is my interpretation. I list the six pictures (numbered from top to bottom) and link four of them to an answer.

1 - yeast cells?

2 -  ash tree section (c)

3 - rotifer (b)

4 - muscle fibre??

5 - bacteria? (a)

6 - Leeuwenhoek's microscope (d)

According to the WP page on van Leeuwenhoek he did describe the banded pattern in muscle, but there is no mention of yeast (although he would have had no trouble seeing these cells if he could see bacteria).

It's a very odd question.


Is Schoons Hard Shell muskmelon a hybrid?

Goldman surmises that Schoon's Hard Shell is a variant of the Bender, so would have been bred from the Surprise, Irondequoit, and Tip Top, all of which were from the Sill's Hybrid.
In that sense, I suppose it's a hybrid. I'm guessing that you're asking because you want to know if you can save the seed; that is, if Schoon's Hard Shell will breed true or will lose its characters in subsequent generations.
I can't find any specific detail on that, but given that it's sold by Seed Savers Exchange, I'd guess that it is a good candidate for seed saving, as long as you make sure it's not crossing with related species in your garden. Seed to Seed has detailed info on melon seed saving.

Goldman A. 2002. Melons. Artisan Books (p. 76)

Whealy K. 2012. Seed to Seed. Chelsea Green Publishing (p. 103)


Metrics to analyze branch lengths in phylogenetic trees

There are a variety of measures of tree similarity implemented in the TreeDist R package. (Your phylogenies appear to be from the R ape package, so hopefully you are somewhat familiar with R.)
Other tools include treedist from Joe Felsenstein, which computes Robinson-Foulds and the Branch Score Distance (which sounds closely related to your interests, described in this paper). You can see that software page for a lot more information.
For a practical description of the different tree comparison metrics you can see this article.
I would suggest taking a look at the manual and the multiple vignettes associated with the TreeDist package to learn more about how exactly those metrics work. There appear to be a wide variety of metrics in there that I have never heard of, such as clustering entropy or split entropy or Nye similarity.
This package also includes tools for making visualizations of differences, such as that shown below:


Is there nutrient absorption in the large intestine of hindgut fermenters?

I have divided this answer into a section on horse and rabbit. While there are many other hindgut fermenters, these species are good illustrations of  different ways hindgut fermenters can digest and absorb nutrients from their food.

Horse

As you know, absorption of "nutrients" occurs along the intestines, but at varying degrees at different sites. Most compounds are primary absorbed in the small intestine of the horse. This includes protein, glucose (soluble carbohydrates), fats, calcium, and magnesium.

Any carbohydrates that are not absorbed in the small intestine reach the hind gut. Here they are fermented by bacteria to short-chain volatile fatty acids  (VFAs) and lactic acid. Horses can use the VFAs (propionate, butyrate, and acetate) as an energy source, but a diet too high in grain can also lead to excessive lactic acid production in the hindgut, and as a result the horse may experience colic.  As your question pertains to the hind gut, a nutrient of main concern is therefore volatile fatty acids.

The hindgut of the horse is very long and developed. To review with the anatomy of the horse hindgut, it consists of the caecum, ventral colon, dorsal colon, transverse colon, descending colon (or small colon), and rectum.

In a study in 1974, RA Argenzio et al. determined that among the parts of the horse hindgut, most VFAs were produced and absorbed in the ventral colon, 8-12 hours after feeding. This is depicted by the graph below, which shows a large negative net production of VFAs after 8-12 hours (i.e. more VFAs absorbed than produced). Note that the caecum and dorsal colon are also important sites of VFA production and absorption.

The hindgut is also an important site for phosphorus absorption in the horse, unlike many other species that primarily absorb phosphorus in the small intestine. This is thought to be because most of the dietary phosphorus in the horse in phytin phosphate, which must be exposed to the enzyme phytase produced by the microbial flora in order to be absorbed. Studies such as Schryver et al. (1972) and T. Matsui et al. (1999) have shown that most phosphorus is excreted by the small intestine and caecum, and most is absorbed in the dorsal colon and small colon. The figure below from Schryver shows the net absorption of phosphorus on the various experimental diets. Note that this is oriented opposite to the VFA figure above; absorption is positive rather than negative on this graph.

Rabbit

To begin with the rabbit anatomy, you will note that the colon of the rabbit is much less developed than that of the horse. However, both are hindgut fermenters, and what they do have in common is a very large caecum.

As in the horse, much of the digestion and absorption of nutrients occurs in the small intestine. This includes protein, fats, and simple carbohydrates (glucose), as well as some vitamins.

Also like the horse, the digestable material not absorbed by the small intestine passes to the caecum, where it undergoes fermentation by the microbial flora. The large fibrous material passes directly to the colon, where water is absorbed and forms hard faecal pellets, while the small digestible material passes through reverse peristalsis into the caecum. What is different in a rabbit to a horse, however, is that the about 8 hours after feeding, the caecal material is packaged into a small pellet called a caecotrophe. As or shortly after the caecotrophe is excreted, the rabbit re-ingests the caecotrophe. As this food has been digested once already, the small intestine is better able to absorb nutrients from it.

As an example, important nutrients that are able to be absorbed due to caecotrophy in the rabbit are the B vitamins such as niacin, riboflavin, folate, and cobalamin (vitamin B12). One of the early studies on this topic is Kulwich et al. (1953).

Summary

The reason for the difference between the horse and rabbit is fundamentally an anatomical difference. Both species have a large caecum which enables fermentation of plant matter. However, the horse has a long, voluminous colon in which it can absorb many nutrients, but they will lose protein and other nutrients in this process because the colon is less adapted to absorb them. In coprophagic (rat) or caecotrophic species (rabbit), they do not have as long a colon, but can absorb vitamins and proteins lost in the faeces during the second pass through the gastrointestinal tract.

An excellent and very detailed review of the gastrointestinal tracts and nutrient absorption in a variety of species is this freely accesible paper by Stevens and Hume, "Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients."

References

Argenzio, R.A., Southworth, M., and Stevens, C.E. (1974) Sites of organic acid production and absorption in the equine gastrointestinal tract. Am. J. Physiol. 226:1043-1050.

Bugaut, M. (1987) Occurence, absorption and metabolism of short chain fatty acids in the digestive tract of mammals. Comp. Biochem. Physiol. 86B(3):439-472.

Hornincke H., and Bjornhag, G. (1980) Coprophagy and related strategies for digesta utilization. In Digestive Physiology and Metabolism in Ruminants, 707-730. Avi Publishing, Westport, CT.

Kulwich, R., Struglia, L. and Pearson, P.B. (1953) The effect of coprophagy on the excretion of B vitamins by the rabbit. J. Nutr. 49:639-645.

Matsui, T., Murakami, Y., Yano, H., et al. (1999) Phytate and phosphorus movements in the digestive tract of horses. Equine Vet. J. Suppl. 30:505-7.

Schryver, H.F., Hintz, H.F., Craig, P.H., Hougue, D.E. and Lowe, J.E. (1972) Site of phosphorus absorption from the intestine of the horse. J. Nutr. 102: 143-148.

Stevens, C.E., and Hume, I.D. (1998) Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients. Physiological Reviews, 78(2):393-427.


How does rate of evolution/innovation scale with population size?

Interesting question (+1) but not that easy to answer. I'll give a try!

First, the rate of evolution and rate of adaptation are two different things.

There are two main thing processes that quantitatively differ in populations of different sizes. 1) population-wide mutation rate and 2) genetic drift.

1. Population-wide mutation rate

Large populations create more mutations at each generation and therefore if the rate of evolution or the rate of adaptation is limited by the genetic variance, then one can expect large population to have higher rate of evolution and higher rate of adaptation.

--> Large populations may have higher rate of evolution and higher rate of adaptation

2. Genetic drift

However, small population have higher drift, resulting in a higher probability of fixation for new neutral (or slightly deleterious) mutations. It results that a small population will fix (fixed: frequency = 1) a higher proportions of the new mutations through time than large populations.nActually the probability of fixation of a neutral mutation is \frac{1}{2N}. Therefore, the rate at which neutral alleles fix is $\mu\cdot 2N \frac{1}{2N} = \mu$, where $\mu$ is the mutation rate. So, the rate of fixation of neutral alleles is independent of the population size.

--> Small populations have more drift but this doesn't necessarily yield to higher rate of evolution

Other and comments

Shifting balance theory

If adaptation is limited by the genetic architecture, that is, only mutation of very big effect on phenotype can be advantageous, then small population have the advantage to be able to accumulate slightly deleterious mutations, so that they can get off a local peak on the adaptive landscape and eventually manage to evolve toward a new higher fitness peak.

--> Small population may have higher rate of adaptation

Population-wide mutation rate vs genetic drift

Weighting the relative importance of rate of production of neutral (or quasi-neutral) mutations (See population-wide mutation rate above and the probability of fixation of neutral (or quasi-neutral) mutations (See Genetic drift above) depends also on the probability distribution of mutational effects (=probability distribution of the effect on fitness of a given new mutation).

Ceteris Paribus

The comparison between large and small populations are dependent on the state of other parameters. So even when saying all else being equal (ceteris paribus), we need to know what these other parameters are equal to, in order to answer the question because there are interactions between populations size and other parameters in explaining the rate of adaptation and rate of evolution.

Other impact of population size on genetic features

Population size has many impacts on various genetic features, such as pattern of genetic diversity, distribution of per locus Fst between subpopulation, and other things. This paper is likely of interest


The Relationship between Copper and Alzheimer's Disease

I found your second reference online, which says

Hydrogen bonds are disrupted by the process of partial unwinding which induces structural changes such as loosening of base–base interaction, base tilting and destabilization of the DNA double helix leading to DNA denaturation [17]. The destabilization was due to most probable binding sites in DNA such as Cu2+ to N7 of guanine and N3 of cytosine in line with our present results and with the predictions of Eichhorn and Clark [18], [19].

With this in hand, we can Read The Friendly References.  #18 is on PMC and gets the first look - they say "perhaps the structure is"

The other references are less helpful for me right now - #17 is a paper from 1971 that's not online and never will be, and #19 talks about histone H1 blocking the copper interaction.
Now what I see here is only unwinding, and is dependent (as proposed) on the presence of G-C base pairs in the sequence.  So far from what I've seen, this is based at interactions at around 0.1 mM in in vitro studies, so I feel like it is possible a physiological situation could involve a completely different mechanism.
After writing the above, I found the other paper in Young Scientists Journal - it is quite a remarkable thing to consider.  The author is a 12th-grade student from Panama who was doing (among other things) a circular dichroism study and molecular docking with Discovery Studio 3.5.  Statistics is lacking and the experiments aren't very well integrated, and the model from the software, which doesn't agree with the image above (it doesn't bind a ring nitrogen in the cytosine), doesn't seem to be tested by the lab data.  Despite the sophistication of the software I'm afraid I'm about as skeptical as I was the first time.  Still, there is some Ph.D.-level thought there, using some methods that American undergraduates rarely access, conducted by a university in Panama with support from an Indian research institute.  Educationally, fascinating.
But I don't see much support for the interpretation in that paper that the DNA coils more tightly.  The fluorescence experiment suggests a competition between copper and ethidium bromide, but knowing what actually happens is another story.  The CD study ... well, some shifts are identified, one one way and one the other, but I don't see how they prove the DNA is coiling more.  But maybe I'm missing something!


How do plasmids protect themselves against restriction enzymes?

The strains that we use in the lab have defective restriction machinery.

In the case of DH5α it is mostly because of the endA1 and hsdR17 mutation. The former mutation eliminates an endonuclease that can degrade plasmids and the latter one eliminates the restriction system.

Check this.


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

Ony a few protein kinases can phosphorylate all three amino acids — these are classified as dual-specific kinases (EC 2.7.12.1). Examples are APK1 from Arabidopsis or MEK kinases in mammals.

As with other enzymes, the residues at the substrate binding site determine which substrates can be accomodated there. Structures or Ser- Thr- and Tyr-kinases are available for inspection, should you wish to explore them.


What determines the fate of a cell with respect to differentiation?

Cell differentiation, cell fate and cell mapping is an interplay of accessible evolutionary strategies/programmes and responses to dynamic environmental cues such as specialized hormones (e.g. morphogens) and physical parameters and constraints. That is putting it very broadly. It is a complex issue, if L. Wolpert's PLOS assays are any indication. I compiled a few links to get you started.

Specifically, reappraising the topic of your cited classical experiment are R.Moore et al:

  The classical cell sorting experiments undertaken by Townes and
  Holtfreter described the intrinsic propensity of dissociated embryonic
  cells to self-organize and reconcile into their original embryonic
  germ layers with characteristic histotypic positioning. Steinberg
  presented the differential adhesion hypothesis to explain these
  patterning phenomena.....

(Source: Robert Moore, Kathy Q. Cai, Diogo O. Escudero, Xiang-Xi Xu, Cell Adhesive Affinity Does Not Dictate Primitive Endoderm Segregation and Positioning During Murine Embryoid Body Formation, Genesis. 2009 September; 47(9): 579–589)

Regarding: ...without something taking the lead and actively coordinating...

On a hunch that you are not talking about complexity, attractors and polarity, I would like to share a few words. You may completely disregard them if you'd like.

My personal experience (from my country) is that few biologists delve into "that" branch of EvoDevo, because a profound understanding involves calculus, modeling and a knack for theoretical biology. Yet, afaik few struggled comprehending the evolutionary logic of making an organism based on Albert's book chapters alone.

See:

Reaction–diffusion system
Cell fate determination
Fate mapping
Asymmetric cell division
Pattern formation
Alberts Molecular Biology of the Cell describes this very well (can be accessed online for free)

I personally recommend G.Müller's authored/coauthored papers:

(open access)
http://homepage.univie.ac.at/gerhard.mueller/publications-papers.html

Disclaimer: I am not specialized in the field of EvoDevo or Theoretical Biology.
Views expressed here are my own.


Why proteins are not visible on my membrane after ponceau staining?

From what you say, I can only give a few advices:

For the quantification, make sure your sample does not contain any substances which disturb the assay. The Bradford assay is for example sensitive against SDS or DTT. See here for more details. This prevents you from loading a sample without enough protein.
Make sure that you really have protein on your gel. Run a gel as normal and then stain it with Coomassie Blue (it cannot be used for western afterwards).
Don't loose your sample - this happens easier than most people think.
Make sure your transfer works. This can either be done by using pre-stained ladders (which are helpful anyway) or by doing Ponceau Red staining. This can be washed off with water and doesn't disturb downstream applications.
Depending on the type of membrane you are using, they might need pre-treatment. PVDF membranes are extremely hydrophobic and need to be activated in methanol.


Where do biologists get information about mouse genes?

Hi Potion and welcome to Biology Stack Exchange and biology in general!

To answer your questions, these changes do not occur. The authors of the publication have engineered "new" genes (also called transgenes in this context).

They have done so by fusion a portion of a of another gene (also called domain) to the beginning or the end of the sequence of the catalase gene. If your gene of interest is localized to a given organelle (for example mitochondria), you can also swap the domain which is responsible for the targeting to this particular organelle with one from a different gene you know goes for let's say peroxisomes.

If you want to know more details for this particular work I encourage you to check the supplementary material here: https://science.sciencemag.org/content/sci/suppl/2005/06/23/1106653.DC1/Schriner.SOM.pdf

Hope that helps!


Is Insulin-Glucose dynamic Lotka-Volterra?

Is the standard Lotka-Volterra (LV) model an exact fit for insulin-glucose (IG) dynamics? No. Can a similar model built on the same principles capture most of the essential features of the IG dynamics? Absolutely.

How to capture most of the insulin-glucose dynamics using a slightly modified Lotka-Volterra model

We can figure out how to change the LV equations to fit the IG dynamics by figuring out how our assumptions have changed. Like Daan mentioned, neither insulin nor glucose undergo self-reproduction. So we'll drop those terms from the equation, and we'll represent an influx of glucose (as from, say, a meal) as a simple time-dependent linear spike. Your rate equations will now look like:

$\frac{dx}{dt} = \alpha[t_{gi} < t< t_{gf}]-\beta x y$

$\frac{dy}{dt} = \delta x-\gamma x y$

where $x$ is glucose concentration, $y$ is insulin concentration, and $[t_{gi} < t< t_{gf}]$ is equal to 1 if the current time $t$ is greater than the time when the glucose spike starts $t_{gi}$ and less than the time when the glucose spike ends $t_{gf}$, and is equal to zero if the time $t$ does not meet this condition.

Simulation of insulin-glucose dynamics using the above LV model

I ran a simulation of the above model in Matlab, and here's what it looks like:

The basic features of the insulin-glucose dynamics from the example graph the OP posted are present. Just like in the real system, first the glucose spikes, then the insulin spikes after a short lag, then they both return to baseline.

With some small improvements, the LV model can capture the dynamics of the infamous "sugar crash" phenomenon

Now for the really cool part.

As can be seen on the OP's graph, glucose levels tend to fall somewhat below their baseline following a large glucose spike. This is the physiological basis for the sugar crash that people sometimes get a little while after eating something really sugary like a candy bar. Regardless of whether the psychological symptoms actually occur, the dip in glucose levels is a real thing.

In order for a model to be considered "good", it has to be able to capture these kinds of complex but important phenomena in their underlying systems. The glucose dip did not show up in my original LV model, so the question is, can the model be modified in a simple way so that it will capture the dip? Let's take another crack at it!

Part of the problem with trying to study phenomena related to baseline levels using the previous model is that the baseline levels of both insulin and glucose are effectively fixed at 0 in that model. We can set the baseline levels by adding what's called a zeroth-order production term (essentially a fixed constant that isn't multiplied by the concentration of anything) to each of our rate equations. The rate equations now look like:

$\frac{dx}{dt} = \alpha[t_{gi} < t< t_{gf}]+\epsilon-\beta x y$

$\frac{dy}{dt} = \delta x+\eta-\gamma x y$

where $\epsilon$ is the 0th order glucose production term, $\eta$ is the 0th order insulin production term, and everything else is exactly the same.

Simulation of insulin-glucose dynamics using the "dip-enabled" LV model

Again using Matlab, I ran a simulation of the "dip-enabled" LV model:

and this time the dip shows up.

Notes:

-The term with the times in it is called an Iverson Bracket.

-You could make this model more physiologically relevant by using a more complex function for the glucose spike, but for simplicity's sake we'll stick with a linear function. A smoother function, like for example a Hill function, would probably help to reproduce your original graph of the IG dynamics.

Matlab code

function dxdt = insulin_glucose_birth_death_dxdt(t, x, kip, bip, kid, kgp, bgp, kgd)
dxdt = [kip*x(2) + bip - kid*x(1),
    kgp*(t>1 && t<2) + bgp - kgd*x(1)*x(2)];
end

function [t,x] = insulin_glucose_birth_death_odesol(tspan, x0, kip, bip, kid, kgp, bgp, kgd)
opts=odeset();
[t,x]=ode45(@(t,x)insulin_glucose_birth_death_dxdt(t, x, kip, bip, kid, kgp, bgp, kgd), tspan, x0, opts);
end

function [t,x] = insulin_glucose_birth_death_plot(tspan, x0)
%run with:
%   tspan = [-10, 5];
%   x0 = [0,0];
%   [t,x] = insulin_glucose_birth_death_plot(tspan,x0);

kip = 2;
bip = 0;  % set to .01 for the "dip" simulation
kid = 1;
kgp = .1;
bgp = 0;   % set to .1 for the "dip" simulation
kgd = 50;

[t,x] = insulin_glucose_birth_death_odesol(tspan, x0, kip, bip, kid, kgp, bgp, kgd);

figure(gcf)
hold on
plot(t, x(:,1), 'b', t, x(:,2), 'r')
legend('insulin','glucose')
xlabel('time')
ylabel('concentration')
axis([0 inf -inf inf])
hold off
end


What exactly happens if during translation, an amino acid is not present?

Point to know : aminoacyl-tRNA binds to mRNA its not just t-RNA..

So if there is no Amino-acid there is no aminoacyl-tRNA of that aminoacid.. so if there is no aminoacyl-tRNA, the anticodon of tRNA doesn't form a bond with mRNA, so the protein production halts (until the Amino acid produced).

If the protein is not formed within a certain long time, the premature protein folds itself and breaks. Then a molecule (example: ubiquitin for certain type of bacteria) attaches to this premature protein and marks it for degradation.

But there are still chances of protein production with slight mutations.

Mutation: tRNA with the same anticodon and different aminoacid can easily bind to the A site of the ribosome in the absence of the correct aminoacyl-tRNA, so the protein production doesn't stop in this case but the protein has a mutation with different aminoacid.


This actually depends on how your tap water is warmed.
If you have a personal water heater, which is connected to your tap with non-corrodable pipes, then there is essentially no difference.

However, if the heating comes from a common source, then it would be very difficult to verify that the heater-tap connection does not contain any corrodable pipes. In this case, it might be better to not use the warm water for direct drinking, especially if the building is old.

A 7-year old house should not have lead pipes installed, since the Canadian Plumbing Code has banned lead pipes since 1975. As such, I believe that your warm water is safe to drink.

  The National Plumbing Code allowed lead as an acceptable material for pipes until 1975 and in solder until 1986. All provinces and territories use the National Plumbing Code as a basis for their own regulations.


Finding steady state concentration given half life and production rate

tl;dr besides making this a bit harder than necessary, your main problem is that you have confused the lifetime (average time to removal of a molecule), not the half-life (time until half of the molecules are removed, which is $\ln(2)$ times the lifetime ...) Wikipedia has some formulas ...

You can translate the problem into a differential equation (not as scary as it sounds):

$$
\frac{dB}{dt} = \underbrace{1000\vphantom{\frac{1}{200}}}_{\textrm{production}} - \underbrace{\frac{1}{200} B}_{\textrm{removal}}
$$

The only tricky part here is recognizing that if the lifetime is 200 s, a fraction 1/200 of the existing molecules will be removed per second.

Now we have to solve this at equilibrium: $dB/dt =0$. We get
$$
\begin{split}
1000 - \frac{B}{200} & = 0 \\
1000 & = \frac{B}{200} \\
B = 200000
\end{split}
$$

Or you could memorize Little's Law: steady state = arrival (1000/s) $\times$ lifetime (200 s).


Mechanism for earthworms to get into a roof gutter

I would say that the reason why a given organism reaches a given space relies on four main factors:

Morphology and physiology: can that organism reach that place physically?
Food distribution: is there enough food to reproduce and spread in that specific spot?
Habitat: does that habitat fulfill its environmental/physiological needs? Is it environmentally safe for that species?
Abiotic factors: wind, water, etc...

I know it's a very general answer, but consider that the main goal of every organism seems to be to survive, spread and reproduce as much as we possibly can.

For example, if the gutter accumulates moss, earthworms will most likely crawl up the wall and into the gutter to feed on the precious organic matter. Also, gutters, due to its function, tend to be wet at times, and earthworms need a moist environment, so it seems like an ideal spot for them (earthworm climbing up).

  Live worm dropped by an overflying bird

Seems likely too: the term ornithochory defines seed dispersal by birds. I guess it could also be applied to dispersal of other animals (at least anthropochory can be applied to both seeds and reproductively capable animals dispersal by humans, in this case, earthworms being transported by the bird's beak). I think the most likely scenario in this case is food availability and a good environment to proliferate and make more earthworms (mostly because it would take a couple of clumsy birds to drop their prey on top of your gutter to establish an earthworm colony up there although it depends on the specific earthworm species and whether it is parthenogenetic or not, of course, but still within the realms of possibility).

When it comes to species distribution, it normally tends to be a mixing of different mechanisms rather than one single specific mechanism.


This issue is addressed in this review by Cordaux et al, 2011, along with other, similar strategies.

The simple answer is that these types of bacteria are efficiently spread from females of the species they infect to their offspring; by inducing unfertilized eggs to develop into females, they increase their transmission efficacy.


Why does renal artery stenosis lead to activation of Renin-Angiotensin system?

So why does narrowing of the renal artery cause a decrease in blood pressure, and not increase?

It doesn't. It causes an increase.

If the blood flow to the kidney is decreased for any reason (for example, hemorrhage or dehydration), the kidney is one of the organs that will protect it's perfusion by causing an increase in BP through the renin-angiotensin-aldosterone system (RAAS).

Very briefly: decr. blood flow -> renin secretion by juxtaglomerular cells -> conversion of serum Angiotensinogen into Angiotensin I (+ ACE) -> Angiotensin II => elevated BP (by a host of mechanisms).

If there is renal artery stenosis, the kidney will try to compensate for this (locally) reduced blood flow by activating the RAAS. The kidney doesn't 'know' that the blood flow/pressure is only locally reduced. It will cause systemic hypertension as a way to increase it's blood flow.

Atherosclerosis is a whole different ball of wax.


Is our color vision calibrated to sky, vegetation, and blood?

Short answer
Color vision is not based on a calibration to the sky, vegetation and blood. The current leading theory of the development of trichromatic vision in humans is based on the foraging of fruit in our primate ancestors.

Background
The places of red, green and blue wavelengths in the spectrum are physically defined and, therefore, not arbitrary; see this question on Biology SE.

Before continuing, it is good to mention that trichromacy (the presence of red, green and blue cones in the retina) is typical for primates. For example, dichromacy (<500 and >500 nm cones) is the most common configuration in mammals. The split in red and green photopigment in primates developed relatively late in evolution (30-40 mln years ago), inferring trichromacy in primates from a dichromatic ancestor. Note that many avian and aquatic species may be tetrachromats or up (4 or more photopigments) (Nathans et al. 1999), with the mantis shrimp featuring no less than 10(!) different photopigments (Cronin & Marshall, 1989).

It is believed that the red-green-blue system in primates has evolved due to its benefits for identifying fruit on a background of foliage, and to assess the ripeness of fruits. The food of monkeys typically consists of fruit, and young leaves. Young leaves are light-green, while ripe fruits are often yellow (e.g., bananas) and orange (e.g. oranges, mangos) (Osorio & Vorobyev, 1996). Unripe fruits typically contain chlorophyll and resemble the color of foliage (green). Hence, to discern ripe, nutritious fruits (yellow-orange or 570-620 nm) from foliage (green or 495-570 nm - frequencies mentioned were copied from wikipedia), it makes sense to have good resolution in the red-green area. The red opsin has its maximum at 530, and the green at 560 nm. The blue has its peak a lot lower at 425 nm (Nathans et al. 1999). Hence, the red and green opsins, which evolved late in evolution, are both right in the "ripe fruit area" and have absorption spectra very close together. Hence, there is a lot of color sensitivity (high color resolution) in the red-green area, which covers reds, oranges, yellows and greenish colors. This gives primates a very high sensitivity to recognize fruits, and especially ripe fruits in a green background. The resolution in the green-blue range is smaller (blues, purples).

As a background: color vision in trichromats works by color opponency, and specifically a yellow-blue and red-green color opponency. This means there exists no yellowish blue hue, or a reddish green (De Valois & De Valois, 1993). The red-green opponency means that we have exquisite sensitivity in the red-green pathway, as red cones suppress green cone output and vice versa. In other words, there is a high color acuity in the red-green area that helps to recognize fruits.

As a side note: The trichromat color vision scenario in primates supports the notion that cats (for example), being predators with dichromatic vision, do not benefit from being able to identify ripe and unripe fruits, as mentioned by @GoodGravy. In contrast, cats need excellent night vision and motion sensitivity, being nocturnal hunters. Indeed, color vision versus night vision, and color vision versus high motion sensitivity are both trade-offs that do not go hand in hand (Kelber et al, 2002).

References
- Cronin & Marshall, Nature (1989); 137-40
- De Valois & De Valois, Vis Res (1993); 33(8): 1053-65
- Kelber et al., Biol Rev (2003); 78: 81–118
- Nathans et al., Neuron (1999); 24(2): 299–312


No, Hemes are not proteins. They are porphyrins (large organic molecules) which are composed of four pyrrolic groups linked together. In the middle the coordinate the iron atom which is responsible for the activity. The combination of heme and iron is called a prosthetic group or co-factor. They are bound by the protein.

The image shows the Heme B from the Wikipedia.


Measuring the density of surface antigens

Do you mean to count numbers of both antigens and receptors in live cell?

Possible ways:

FRET (unlikely to work)
imaging of receptors with single molecule resolution
western blot to roughly estimate amount of receptors
single cell proteomics techniques (not very suitable)


Meaning of "Domain with function to find" (FIIND)

I was pretty certain @David's comment was spot on, that this was some one-use funny acronym from just this paper, but a search of Google Scholar suggests that it has indeed been propagated sufficiently to have meaning beyond this paper, while also originating, as these things do, in some clumsy one-off usage.

One of them gives a clear definition that is consistent with what you supposed:

  The acronym FIIND (domain with function to find) was coined several years ago to indicate a highly conserved protein region with unknown function[4]

D'Osualdo, A., Weichenberger, C. X., Wagner, R. N., Godzik, A., Wooley, J., & Reed, J. C. (2011). CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain. PloS one, 6(11).

The paper they cite (reference 4 in the previous quote) is in fact this one:

Tschopp, J., Martinon, F., & Burns, K. (2003). NALPs: a novel protein family involved in inflammation. Nature reviews Molecular cell biology, 4(2), 95-104.

...which probably looks familiar since it is in fact the paper you started from. Importantly, though, this is not a generic term for a domain with unknown function, it's a specific domain which was known to be highly conserved (and since found in several other proteins) - it's just that it's specific function was at the time unknown.

This paper is a recent review of NLRP1 that may also be useful and has some discussions of what has been found of the functions of the FIIND:

Mitchell, P. S., Sandstrom, A., & Vance, R. E. (2019). The NLRP1 inflammasome: new mechanistic insights and unresolved mysteries. Current opinion in immunology, 60, 37-45.


Identification of that red and black bug

This looks like Graphosoma italicum (aka G. lineatum; it is a stinkbug):

Graphosoma italicum had been regarded as either a subspecies, or a mere synonym to G. lineatum.
G. italicum can reach a length of 8–12 mm (0.31–0.47 in). The body is almost round, with a large shield. The basic color of the upperside of the body is bright red, with wide black longitudinal stripes. The pronotum has six black bands. The antennae are black. Also the sides of the abdominal segments (connexivum) are red with many small black spots. The legs are black.
Wikipedia

I think you are right that they are mating. Here is another picture of the species mating:

ibid

(Despite it saying that the legs are black, they are clearly striped in some specimens, like in your picture.)
It's found in France, according to Honeyguide.


Using evolutionary algorithms in molecular biology?

The first thing that springs to mind is modeling and simulating the evolution and specificity determinants in protein - protein binding. You can easily include an experimental  part and make it as big as you like (the bigger, the better). For a useful set of physiologically important protein - protein interactions and background info on the specificity and affinity determinants in those systems, see Ivanov et al., 2017 and Ivanov et al., 2016, and the references therein.


determining genome-wide exogenous binding of pathogens to host genome?

The techniques used to do this are ChIP-seq and ChIP-chip.

Basically, you

let the pathogen bind to the (highly replicated) DNA
cut up the DNA into little random pieces by sonication
enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen
sequence the thus enriched DNA
map the sequenced fragments back to their original location on the genome.

Wikipedia has a nice picture explaining this process in a little more detail:


Is my RNA-seq experimental design correct to use it for SNP calling?

Using RNAseq for SNP analysis is not the best tool available for several reasons. First, you will only find SNP in genes that are expressed (you need more than 120 reads per SNP in your experiment). Second, you will only find SNP in coding regions of the genes. For your particular experiment, where you have a pool of 60 individuals per sample, it's another drawback because you'll have 120 alleles in your sample (without knowing the allele combinations of the individuals).

Of course you can still try to find SNPs that are present in your phenotypes, but real GWAS kind of analysis is in my opinion not possible.


I added ethanol to my TRizol RNA extraction

My answer is based on my experience in the lab and something like a best guess - it may or may not work. But given the fact that added 100µl of ethanol to 500µl of total volume and since water and ethanol mix completely, I would give it a shot.

I don't think that the ethanol would change the polarity of the solution so much that phase separation is inhibited. The only thing that I can image is the contamination of the aqueous phase with traces of phenol, so I would probably clean up more carefully and do an additional NaOAC/ethanol precipitation at the end of the procedure. If you expect a small pellet with little nucleic acids, add some glycogen to get a better outcome there. I would appreciate it, if you could comment on your experience (and the outcome) when you try to save you sample.


Is induction and derepression the same thing?

Induction is an effect of a stimulus on the cell. During an induction of gene expression a gene is expressed in response to a stimulus.

De-repression is a mechanism of gene regulation which may lead to expression of the corresponding gene. The gene can be expressed via direct activation as well. The action of CAP on lac operon would be an example of direct activation. There are several other examples too.


Is it possible to perfuse chemicals into brain after removal from body?

Of course it is possible to perfuse an organ once it has been removed from the body. It is probably unwise to do so with the brain as the delicacy of the structures and high levels of lipids make rapid fixation necessary and difficult. I think the major obstacle is the speed at which the brain could be removed with arteries intact and then perfused as ultrastructural changes occur rapidly once ischemia (oxygen deprivation) begins.


Homology modelling of protein with two identical subunits in its quaternary structure

For anyone who will struggle with this problem in the future: The trick is in reading WHOLE of the manual, NOT submitting the whole sequence/badly segmented sequence, and in NOT attempting to input the same subunit twice. It is necessary to upload subunit FASTAs separately as a hetero target, and each subunit ONLY ONCE (so A,B,D,E for A-B-D-A-E receptor), and then search for templates: most probably there is a template with your quaternary structure uploaded somewhere already, and if not, you can choose preferred arrangement afterwards.


Are the cytosol and extracellular fluids electrically neutral?

Membrane potentials are caused by different concentrations of ions on opposite sides of membranes in micro-environments along the membrane. The membrane can be, overall,  electrically and chemically neutral with small areas that have differences in electrochemical gradients.

For cells to produce these potentials they have proteins embedded in the lipid membrane. Ion pumps are the main players in creating potentials and gradients; through active transport (the use of ATP) the protein moves ions from one side to the other. When the concentration of that area of membrane is at one concentration the proteins are held in one conformation (active or inactive) and when the gradient is changed or meets a threshold the protein changes conformation and becomes activated or inactivated. So the actual electrochemical gradient dictates when the proteins are transporting.

There are also other proteins/messengers that are produced which can interact with the transmembrane proteins that keep them in one configuration or another to facilitate the production of an action potential. Once again, when this specific concentration is met the signaling molecule/transporter will become inactivate or activated.

This is just stuff I recall from some classes. Honestly, wikipedia is a fine general knowledge source. And more detailed than my explanation.  http://en.wikipedia.org/wiki/Membrane_potential#Ions_and_the_forces_driving_their_motion


Phospholipid membrane fluidity if phospholipid had one type of fatty acid

Cell membrane doesn't have just phospholipid inside.

Components who influence fluidity in cell membrane are:

1) Fatty acids length
2) The grade of unsaturation of these fatty acids
3) Presence of cholesterol

So, if composed of just fatty acids, excluding every other component (carbohydrates, channels proteins and, mainly, cholesterol), the answer would be yes, its fluidity will change drastically.


If a venomous snake somehow gets it's own venom in its body, will it be affected by it?

An excellent question.  This fun mental floss article addresses that question, but from the perspective of one snake biting another snake:
Snake on snake violence

“The conventional wisdom is that they have circulating antibodies in their blood,” says Stephen Mackessy, Ph.D., a Professor of Biological Sciences at the University of Northern Colorado and an expert in venomous snakes. “This would protect them from their own venom, as well of venom from another snake in their own species.”
Hypothetically, if a speckled rattlesnake bit another speckled rattlesnake, the immunity they’ve built from being exposed to low levels of their own venom—kept in glands behind their eyes and secreted when they bite—would protect them from a fatal wound. (Even though the glands are closed, they still contain blood vessels that allow the venom to circulate in their system, causing mild exposure, Mackessy says.) But a speckled rattlesnake that meets up with a cobra might have a different day entirely.

The same principle should apply to venom ingested in dead prey. Antibodies against the venom would protect the snake. For what it's worth, I think your way of phrasing the question is more interesting and relevant than the way it was phrased in the mental floss article.


Oocytes, or immature female eggs, develop in the fetus's ovaries during pregnancy. This graph (U. New South Wales) shows the oocyte population over time in a human female:

Although the x-scale is kind of confusing (months when negative, years when positive), you can see that the fetus has all the oocytes it will ever have at the peak 18-22 weeks after conception. Since age 0 is birth, meiosis in a woman happens long before she is born.


Why does so much variation exist within species?

First of all, your assumption is incorrect: those are not genotypes and they do not occupy specific niches. You are talking about phenotypes (eye colour) or in the case of acne, not a trait at all.

I'll answer the question I think you're asking: why does biological variation exist?

Variation is constantly being generated by mutation, errors in the replication of the genome of an individual. If a mutation occurs in the gametic cells, it affects the genotype of the offspring. By affecting the genotype, it may or may not have a discernable effect on the phenotype. Where a gametic mutation isn't fatal, it has a chance of becoming established in the population when that mutant individual breeds. That chance is increased the further along the gradient from harmful to beneficial that effect of that mutation is.

Variation also exists because development responds to environmental factors, not just genetics. Different individuals grow in different environments, and have unique combinations of factors influencing many traits.

The reason variation persists is because, except under conditions of extreme selective pressure or genetic bottlenecks, many traits have no impact on survival or fecundity (reproductive success) or are determined only partly by genetics. Height, for example, only has a very slight impact on fecundity within quite a broad range of heights. It is partly genetically determined, and partly determined by environmental factors such as diet (Eckhardt et al. 2005), exposure to toxins during development, muscular development etc.

If height were the key factor in human mate selection, we might see a gradual reduction in the range of heights, and a gradual increase in average height. However, what we see in reality is that height has changed through human history in concordance with economic factors like social status, inflation and war (e.g. Steckel, 2001), suggesting that nutrition is a major determinant.

I know it wasn't your choice of example, but for more detail on the effects of natural selection on human height, see this question.


Short answer
It all depends on how you look at $k_\text{cat}$ and enzyme concentrations

Long answer
The effect of an uncompetitive inhibitor on $k_\text{cat}$ can be interpreted in two ways.
Interpretation 1:
This is followed in the lecture series mentioned in the question.
See the video https://youtu.be/rNBEUGYu034 from 7:37 to 11:01 minutes. The instructor says:
... the turnover number basically describes the ability of that active site to actually transform the substrate molecules into the product molecules per unit time. Now because when the inhibitor is not bound to that particular enzyme-substrate complex, the active site's ability or efficiency to change that substrate to the product doesn't actually change, we see that the $k_\text{cat}$ value in uncompetitive inhibition also doesn't actually change...
Mathematically, $k_\text{cat}=\frac{V_\text{max}}{[\ce{E}]}$ (where $[\ce{E}]$ is the concentration of enzyme, excluding that which has been inactivated by inhibitor). Now, uncompetitive inhibition reduces both $V_\text{max}$ and $[\ce{E}]$ by the same factor. Thus $k_\text{cat}$ remains unchanged.
Interpretation 2:
Some people do things differently. They regard $k_\text{cat}$ as $\frac{V_\text{max}}{[\ce{E}]}$, where $[\ce{E}]$ is the total concentration of enzyme in the mixture (including inactivated forms). In this treatment, the uncompetitive inhibitor reduces $V_\text{max}$ but $[\ce{E}]$ stays the same. Thus $k_\text{cat}$ is reduced.
Qualitatively, the enzyme in the mixture is now a combination of active and inactivated forms, and thus has lower "efficiency" overall, i.e. lower $k_\text{cat}$.


RNA seq: Should non-infected units be used for RNA-seq?

It will dilute your signal if you have a pool of samples +/- the parasite prepared as one library prep. It is always better to maximize the number sequencing libraries (usually cost prohibitive) and extract RNA from samples you are confident exemplify the condition of interest, and an equal number of control samples to maximize your statistical power.


What allows for no selection pressure against non-coding DNA?

A) Here's the thing about evolution - just because something might have an adaptive benefit does not mean that trait will evolve ; this is contingent on the occurrence of the necessary mutations to produce a phenotype in the first place.

B) There are multiple copies of the transcriptional machinery (RNA pol, Transcription Factors) - numbering in the tens of thousands when you are talking of the core transcriptional machinery.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC84381/

The 3d structure of chromatin , as well as the large amounts of the core transcriptional machinery, prevent there from being too much adaptive benefit to losing large amounts of noncoding DNA.

C) Thirdly, there are suggestions that enhancer promoter contacts, which can greatly facilitate transcription, may be in some part at least determined by sequence motifs in the loops that bring together enhancers and promoters ; so there would be costs associated with losing ncDNA en masse. See www.nature.com/ng/journal/v48/n5/abs/ng.3539.html

D) Indeed, even when one looks at repeat elements derived from endogenous retroviruses, there are those that are of functional significance; Syncitin (which actually codes for a protein) is responsible for trophoblast fusion + placenta formation (See https://www.ncbi.nlm.nih.gov/pubmed/10693809 )  , and there are multiple repeats that themselves serve as enhancers of interferon response genes. See https://www.ncbi.nlm.nih.gov/pubmed/26941318


Can/Have cancer cells be/been used in stem cell culture lines?

Cancer cells can be and are used in cell culture. HeLa cells were the first human cell line to be grown in culture and they were derived from a cervical tumor.

That being said, Cancer cell lines would not necessarily be used for stem cell work. They have sustained too many mutations to study the type of questions that stem cells are used to study, though as MattDMo points out, teratomas, tumors that originate from stem cells, can be used in stem cell research as a model for Stem Cells in culture. Also, they could never be used for therapeutic purposes.

As for viruses, HeLa cells were used by Jonas Salk to develop the polio vaccine, so cancer cells are used in viral research.

Edits in italics.


What is this large brown bug with pincers?

You probably have a specimen of a stag beetle.

In Europe we have a very big one: Lucanus Cervus
but it seems to be absent in US.

Then I found an interesting web-site referring to the different stag beetle and mentioning the link to the European one.

In this above site, they mention you have to look into the antenna and as they are not very visible on your picture I think it would be difficult to define precisely what is the exact taxon of the one you found.

For specifically Massachussets region, I found this interesting link.

and they refers to Lucanus Cepreolus, but I would not be 100% sure it is this one as the antennas are not present on your picture.

References

http://beneficialbugs.org/bugs/Ground_Beetles/stag_beetles.htm
http://bugguide.net/node/view/3104/bgpage
http://www.insectidentification.org/insects-by-type-and-region.asp?


Can photosynthesis take place if the plant is kept in ice cold water or not?

Biochemically, it appears it can, as some Algae can. The question is then whether there are any real plants who do it.


Australian Tree Identification - maybe pine?

Native cherry, Cherry ballart or Cypress cherryn belongs to the sandalwood family of plants.

http://en.wikipedia.org/wiki/Exocarpos_cupressiformis


High frequency human genetic oscillators?

Here are some examples:

electric oscillators:

neural activity
cardiac automatism (0.8 ... 1 Hz)

mechanical oscillators (as a result of neural activity):

heart beats
breathing (0.2 ... 0.3 Hz)
intestinal peristaltic waves
vocal chords activity (up to a few kHz)
muscular spasm (pathological)

chemical oscillators:

insulin variation in concordance with glucose intake
endocrine oscillations
menstruation
feedback enabled metabolic pathways

See this Wikipedia page too: http://en.wikipedia.org/wiki/Oscillation#Human

When it comes to genetic oscillators, some of them follow circadian rhythm.

  A typical proliferating human cell divides on average every 24 h. This division timing allows cells to synchronize with other physiological processes and with the environment. The circadian clock, which orchestrates daily rhythms, directly regulates the cell division cycle and is a major synchronizing factor [5].

Immune system:

  In every single cell an oscillator goes ticking through a molecular clock operated by transcriptional/translational feedback loops driven by the rhythmic expression of circadian genes. This clock gene machinery steers daily oscillations in the regulation of immune cell activity, driving the periodicity in immune system function [1].

Glucose homeostasis:

  The master circadian clock, localized in suprachiasmatic nucleus (SCN), regulates multiple metabolic pathways, while feeding behavior and metabolite availability can in turn regulate the circadian clock [2].

Retina:

  ... the retina itself possesses intrinsic circadian oscillations, exemplified by diurnal fluctuations in visual sensitivity, neurotransmitter levels, and outer segment turnover rates. Recently, it has been noted that both central and peripheral oscillators share a molecular clock consisting of an endogenous, circadian-driven, transcription-translation feedback loop that cycles with a periodicity of approximately 24 hours [3].

But there are others which don't.

  Genetic oscillators are ubiquitous regulatory motifs in the molecular control circuits of living cells. Prominent examples include the cell cycle and cellular signaling [4].

The frequency is much lower in some human cells [6]:

Cell Type      Process    Time
______________ __________ ______________________
fly embryo     mitosis    8 minutes
bacteria       mitosis    20 minutes
yeast          mitosis    2 hours
human skin     mitosis    20 - 24 hours
human sperm    meiosis    about 64 days
human liver    mitosis    1 year or more
human egg      meiosis    up to 40 years or more
human nerve    mitosis    never, once mature

References:

Vinciguerra M, Borghesan M, Pazienza V, Piepoli A, Palmieri O, Tarquini R, Tevy MF, De Cata A, Mazzoccoli G. The transcriptional regulators, the immune system and the the circadian clock. J. Biol. Regul. Homeost. Agents. 2013;27(1):9-22. PubMed PMID: 23489683.
Chrościcki P, Usarek M, Bryla J. [The role of biological clock in glucose homeostasis]. Postepy Hig Med Dosw (Online). 2013 Jun 20;67:569-83. doi: 10.5604/17322693.1053906. PubMed PMID: 23799401.
Ramsey DJ, Ramsey KM, Vavvas DG. Genetic advances in ophthalmology: the role of melanopsin-expressing, intrinsically photosensitive retinal ganglion cells in the circadian organization of the visual system. Semin Ophthalmol. 2013 Sep 6;28(5-6):406-21. doi: 10.3109/08820538.2013.825294. PubMed PMID: 24010846.
Davit A. Potoyan and Peter G. Wolynes. On the dephasing of genetic oscillators. PNAS 2014 ; published ahead of print January 27, 2014, doi:10.1073/pnas.1323433111
Samuel Bernard and Hanspeter Herzel. Why Do Cells Cycle with a 24 Hour Period? Genome Informatics 17(1): 72{79 (2006).
wiseGEEK.org. How Long Does it Take for Cells to Divide? (accessed 21.07.2014)


A first (and obvious) approach is the use of cellulose agar in order to isolate all the celluloltic bacteria in the sample. Be careful, however, since the nutrient requirements of some of those microbes may be higher and then they won't grow with only cellulose (they may need some other compounds, like a nitrogen source). Be careful with fungi, too.

If you have the proper equipment, it would be ideal to extract DNA and analyze the environmental rRNA 18s sequences. With this, you should be able to know if your bacteria is present in your sample. If so, proceed with the previous steps.

Once you had a set of suspected colonies, you must proceed with more specific culture media (wich would depend of the exact bacteria you're looking for. For example, if you're looking for Clostridium, you should try to grow your sample in an anaerobic jar and test the ability to reduce sulphur). With this approach, you may reach a point where you can't differenciate similar species. At this point, mollecular characterization is the best option, with the use of rRNA 18s again. Note that the mollecular approach, while relative expensive, can be performed in every step, so you can combine cultures and DNA analyses at will.

Lastly, if you're looking for an specific bacteria, it would be useful to know wich one is, so the community can give you more accurate responses.


Will tagging a protease with HlyA for secretion inactivate the protease?

Unless someone has actually done this specific fusion and reported on the activity, this question won't have an answer. I can't find anything about proline aminopeptidase fusions, but enzyme-HlyA fusions have been done that retained activity similar to the wild-type protein (examples: cutinase, β-lactamase). Your fusion might work fine or folding might be disrupted after secretion (either by the tag itself or by the absence of chaperones, if required). In other words, you need to try it yourself.

Bacillus subtilis is commonly used for secretory protein production and may present another/better option.


When two amoeba cells form from one amoeba, does spindle fibers form?

Amoebas undergo binary fission, which is a much more simplistic process than mitosis. In binary fission, the duplicated chromosomes simply separate as the cells is pulled apart.  There are no spindle fibers used in this method of cell division.


In the PR segment of an ECG, how come there's no current flowing?

I'd suggest reading the rest of the Wikipedia article on EKG rather than focusing on the particular cartoon you are using right now, because that cartoon does not depict the dipoles that are measured.

The key interpretation that you are missing is that the signals measured are not voltage differences between intracellular compartments of the heart (like between the atria and ventricles, or between the depolarized and polarized part of one compartment), but a moving dipole created during polarization changes.

As the atria depolarize, there is a wave of negative extracellular charge as positive ions enter cells, creating a dipole: there is more negative charge at the most recently depolarized point than ahead of the wave where cells haven't yet depolarized. This is the signal you measure. If you were to pause this process at any moment, those extracellular charges are free to move and the potential dissipates quickly.

There is too much conductivity in the extracellular space for the dipole to be maintained without the rapid polarization changes that occur when ion channels open. You can think of this as a high-pass filter; the amplitude of the dipole measured would approach zero as the speed is reduced regardless of static differences in intracellular voltage measured against some reference.

This is what happens during the brief "pause" between atrial and ventricular contraction: there is still a dipole, but it is much smaller as it travels through the AV node than in the muscle and would only be measurable from local electrodes. You begin to see the signal again once the ventricles contract.

http://umdberg.pbworks.com/f/Hobbie-EKG-1.pdf may also be useful.


Are we naturally born right or left handed or ambidextrous?

tl;dr

Yes!

Is handedness determined before birth?

Without thinking of whether handedness is genetically or environmentally defined (see below), is handedness decided before birth?

Hepper et al. 1991 and DeVries et al. 2001 show that handedness can be inferred from from fetal position and hand usage. Typically, looking at what thumb is used for sucking is good indication of handedness.

Is handedness heritable?

The question

  [A]re we naturally born right or left handed?

can sometimes be understood as

  Is handedness genetically determined?

or in more concrete terms as

  Is handedness heritable in humans?

If it is not obvious to you that this is your question, then you probably don't understand the concept of heritability! Then you should have a look at Why is a heritability coefficient not an index of how “genetic” something is? first and then come back here to read the results.

There have been a large number of studies on the question, unfortunately most of them were very small studies with small sample size. Medland et al. 2008 is pretty large scale twin study which report a heritability of 0.24.

In other words, yes handedness is heritable. To be more accurate, 24% of the total variance in handedness is explain by additive genetic variance. Yet again in other words.

The cooperation-competition hypothesis

On the evolution of the handedness in he human population you might want to hear about the cooperation-competition hypothesis. For that, you should have a look at this TED-ed video. As you watch this video, you'll probably be interested in reading the wikipedia article on frequency-dependent selection.

Thanks to @Mockingbird for pointing out to this video.


Can a virophage potentially be used to cure a viral disease?

There are few enough virophages occurring in nature that I don't know if there's a clear and compelling case for them being potentially therapeutic.

In principle however, the answer is yes, though they may suffer from the same problems that bacteriophage treatments have suffered during their history - difficulty in preparation, extreme species specificity, and fairly daunting regulatory hurdles. While viral diseases don't have the "Or we could just use antibiotics, which work" out which made bacteriophages less popular, as far as I know there's not been a suggestion of widespread virophages against human pathogens.


After some more searching, I think stumbled across the answer. It appears to be an…

Eriophora ravilla:

Source BugGuide.net.

This species appears to have quite a diverse range of colors, and even thought I haven't found one that quite matches mine, the other similarities (the large abdomen, the stripe down the back, the four 'dimples', and the dark first leg segments) are enough to convince me. However, if anyone else can shed some light on this, I'd appreciate it.