Example of species that went extinct because of excessive hunting by non-humanoid predators? I was wondering if there were any species that went extinct for being excessively hunted/eaten by predators? I don't mean human hunting. For example, I wish to know if there's a species of frog that are now extinct, because they were driven to extinction by predation by snakes. In fact I'm also OK with examples where a species/class of plant or grass went extinct due to overgrazing? I want to know because I've always heard people say "Nature corrects itself" or "hunting is under control in the natural environment" etc. Is this argument valid?

The Brown Tree snake (Boiga irregularis) is responsible for five extinctions on the island of Guam. Some of these species existed only on Guam, while others exist elsewhere and so it is the Guam subspecies that has been lost.

Guam flycatcher (Myiagra freycineti). Last sighted in 1983.

Guam rail (Gallirallus owstoni) is extinct in the wild, but is now bred in captivity and has been introduced to the island of Rota.

Guam kingfisher (Todiramphus cinnamominus) is also extinct in the wild and exists only in a captive breeding program.

Guam flying fox (Pteropus tokudae). Went extinct in the late 1960's possibly as a result of the Brown Tree snake.

I had a suprisingly difficult time obtaining accurate lists of the Guam extinctions.

For an example of overgrazing leading to a local extinction, see St. Matthew island in the Bering Sea. The US Coast Guard introduced reindeer in 1944. By 1963 there were ~6,000. Without any natural predation to control the population, they are considered to have overgrazed, causing a population collapse to 42 by 1965 and no reindeer population by the 1980's.


Deliberately choosing one nostril to breath through James Nestor, on pp. 41-42 of his book Breath: the New Science of a Lost Art, claims the following.

The right nostril is a gas pedal. When you're inhaling primarily through this channel, circulation speeds up, your body gets hotter, and cortisol levels, blood pressue, and heart rate all increase. This happens because breathing through the right side of the nose activates the sympathetic nervous system, the "fight or flight" mechanism that puts the body in a more elevated state of alertness and readiness. Breathing through the right nostril will also feed more blood to the opposite hemisphere of the brain, specificially to the prefrontal cortex, which has been associated with logical decisions, language, and computing.

Inhaling through the left nostril has the opposite effect: it works as a kind of brake system to the right nostril's accelerator. The left nostril is more deeply connected to the parasympathetic nervous system, the rest-and-relax side that lowers temperature and blood pressue, cools the body, and reduces anxiety.

... Our bodies operate most efficiently in a state of balance, pivoting between action and relaxation, daydreaming and reasoned thought. This balance is influenced by the nasal cycle, and may even be controlled by it. It's a balance that can also be gamed.

A question on this site describes we only breathe out of one nostril at a time: at any given time, one of our nasal cavities will be more open than the other, and this switches back and forth every couple hours. For the most part, we are unaware of this. (At any rate, I was!)
I am very curious about Nestor's claim that the balance can be gamed. It seems that one could prepare effectively for a math exam by practicing right-nostril breathing, or for sleep by practicing left-nostril breathing. Is this the case?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681046/
Assessment of the Effects of Pranayama/Alternate Nostril Breathing on the Parasympathetic Nervous System in Young Adults
Result and Conclusion: This study showed that the parasympathetic tone was enhanced appreciably in the participants. The observations of this study suggest that the yogic exercise of A.N.B. influences the parasympathetic nervous system significantly.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978938/
Slow Yogic Breathing Through Right and Left Nostril Influences Sympathovagal Balance, Heart Rate Variability, and Cardiovascular Risks in Young Adults
Short-term practice of LNB improves vagal tone, increases HRV, and promotes cardiovascular health of medical students. Practice of RNB increases sympathetic tone and could jeopardize cardiovascular health.

There seems to be some evidence that this works.


Can Covid-19 (similarly to HIV) infect T-Cells? I'm interested in better understanding this Nature publication, discussing the potential for Covid to infect t-cells.

After describing the results they conclude:

"Based on the results of pseudovirus and live virus infection, here we proved that (1) SARS-CoV-2 could infect T cells, (2) SARS-CoV-2 infected T cells through receptor-dependent, S protein-mediated membrane fusion, and (3) infection could be inhibited by EK1 peptide."

Is this big news? I am not an expert but I believe that HIV's special trait is it's ability to infect CD4+ T cells. If this virus has this ability, does it mean it will have long-term effects like lymphocytopenia, which occurs in HIV?

As referenced the publication you shared, other human corona viruses also infect, but do not replicate in T cells, so it's not "Big News" in the sense of being a novel or unexpected finding. This also differs from HIV, which actively replicates in CD4+ T Cells. However, it does seem like CoV-2 patients have reduced T-cells after recovery, and that reduced lymphocyte levels during infection are associated with greater risk of mortality from COVID-19.

It doesn't seem like there's any evidence in the literature for long-term lymphocytopenia in recovered SARS and MERS patients, but it's still too early make any strong conclusions about long-term effects from the current outbreak.


Where do amino acids get attached to tRNA and where is it synthesized? Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere:

How exactly is tRNA synthesized? I realize that mRNA is synthesized through transcription and I know a lot about that. However tRNA is supposedly synthesized the same way but every time you read about transcription they just talk about how the mRNA then gets this and that...?

Where do the amino acids get attached? Is it in the nucleus or outside the nucleus?

Thanks.

A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step reaction that requires ATP. You'll find there's a unique splicing mechanism in tRNA that additionally splices out an anticodon intron which is abesnt in mature tRNA's:

The wikipedia article notes RNA Pol III generally recognizes internal control elements rather than upstream control elements as in a normal gene.

Source: Qiagen

Source: Molecular Cell Biology. 4th edition.

Addendum: I said in my post that tRNA is charged in the cytoplasm, this is somewhat true. In mammalian cells, we also see that tRNA are charged in the nucleus as well, and it might aid in the export of some of these charged tRNAs. (Source)


What is the length and number of the parts of a conformational epitope? I am interested in the question whether exposure to protein A might create antibodies that also bind to protein B.

I am wondering whether, if the antigen of protein A is a conformational epitope, it would still be possible to predict (or at least guess at) the reaction against protein B with only a sequence comparison.

This might be possible if the subunits are long enough and if there are enough of them, which is why I ask about their length and number.

I found this paper that analyzes 111 antigen-antibody x-ray crystal structures.

They find that in their dataset that "the large majority of Ag structures (86.5%) have CRS ranging from 20 to 229 aa." CRS stands for contact regions span which they define as "the minimum contiguous amino acid sequence containing all CRs of an Ag or Ab and represents the size of a complete structural epitope or paratope, inclusive of CR and the minimum set of supporting residues required for proper conformation." further on they mention that "The average and median CRS of all 111 Ag structures is 125 and 95 aa, respectively." and "the majority of the structures do indeed have epitope CRs that are clustered together in short, contiguous stretches ranging from 2 to 12 aa, longest contiguous sequence of CR being 5"

I hope this helps.


What are these tiny, swarming, jumping bugs? I built a small plywood box in my yard (on Long Island, NY, USA) for some stray cats about a year ago. I didn't bother waterproofing the box, and so over time the box has gotten damp.

About two weeks ago I started seeing small reddish brown bugs on the box, and in the food/water dishes near the box. Can anyone help identify them? Here are some details:

there are 100s of them
they're really small, the biggest ones are about the size of a sesame seed
they jump when disturbed, usually in an upwards direction
they don't seem to go on the cats
some venture 2-4 ft from the box to find food dishes on the ground (concrete patio)
they drown themselves in the water dish by the dozen
they're more active when it's warmer (~ 45°). When it's cold (25-35°) they mostly hide somewhere

All of this makes them sound like fleas,  but they're not fleas -- they don't jump as high or have the flat body of a flea. They actually look like arachnids. OK that makes them sound like baby jumping spiders - but I've seen baby jumping spiders at work, and these look different (they're reddish brown, not black, and they don't jump in an "across" direction, they jump upwards, kind of randomly). Maybe they're a different type of jumping spider, but why haven't they moved on? Why are they taking up residence on the box, instead of spreading out and going their separate ways like baby spiders usually do?

They're are about the size of a sesame seed so it's hard to get a good picture.

EDIT: new picture collage:

Very useful image updates! These are actually not arachnids but hexapods called springtails (order Collembola). Although springtails are often very tiny and hard to see without a lens, you happen to find some "larger" specimens. Specifically, these appear to be some species in the family Dicyrtomidae.

 Credit: M. Bertone (source)

Your species resembles the image of Dicyrtomina minuta seen here or Dicyrtomina saundersi seen here (though I can't be certain of these source's accuracy).

In general, springtails usually feed on decaying matter, and -- you guessed it -- they're known for their ability to jump!

  Springtails are so-called because they have a unique structure, the furcula, that allows them to jump for considerable distance relative to their tiny size. [source].

 Springing mechanism of a generalized springtail. Credit: Marianne Alleyne [Source]

According to NC State Extension:

  Rarely springtails may become exceedingly abundant and may congregate in heaps several inches high on driveways, sidewalks and poolsides.

Collembola.org has many excellent close-up images as well as detailed descriptions of nuances and sexual dimorphism seen in the Dicyrtomina group of springtails.


Why are female not competitive for reproduction like males? I have wondered if competition for mate among males and the race among sperm cells would result in healthy offspring,

why no such mechanisms exist among females and egg cells?

(Even females are genetically responsible for the offspring.)

As @Dexter said, there are examples of species where female compete for the access to the males but most often it is the other way around; males compete for the access to the females.

The reason for this discrepancy is mainly explained by Bateman's principle. Citing wikipedia:

  Bateman's principle suggests that in most species, variability in reproductive success, or "reproductive variance," is greater in males than in females. This is ultimately a consequent of anisogamy. Females, especially mammalian females, almost always invest more energy into producing offspring than males invest. Bateman's principle anticipated and is consistent with Robert Trivers's theory of Parental investment—in most species females are a limiting factor over which males will compete. This competition results in some males being more successful than others, leading to greater reproductive variance among males than females


B cell receptor editing If a B cell contains two mu chains and two lambda chains and is self reactive can it go back and rearrange its kappa light chains? I'm not sure if it can only try to rearrange its lambda light chains or if it can go back and try to rearrange kappa chains as well.

Background info: the light chain is the smaller of the two types of polypeptide chain in an immunoglobulin molecule. There are two classes of light chain known as the kappa and lambda light chains. During B-cell development the light chain genes rearrange. First one kappa gene is rearranged; if this doesn't produce a functional protein then the kappa gene on the second chromosome is rearranged; if a functional protein is still not produced then the lambda gene is rearranged one chromosome at a time until a successful rearrangement is produced.

The short answer is no.
Here's a review article with some evidence:

B cell receptor editing in tolerance and autoimmunity
Section: Receptor Editing in Mice with Conventional Autoantibody Transgenes
If multiple κ rearrangements fail to yield a suitable L chain, the κ
locus undergoes rearrangement to a non-coding gene called RS in mice
(RS is referred to as the κ deleting element in humans). RS
rearrangement results in either deletion or inversion of Cκ,
consequently inactivating κ L chain expression on that allele. In cell
lines with λ rearrangements, one or usually both κ alleles are
deleted, whereas in κ-expressing B cells the fraction of RS
rearrangements is approximately 15%.

In summary: After a point with (probably multiple) κ rearrangement failures, both κ loci (usually) get deleted, leaving only λ. So if a B cell expressing a BCR with λ is self-reactive, it won't have the chance to rearrange its κ.
However, there's a lot more involved. For one, it's possible to get a functional and non-self-reactive λ chain BCR without repeated κ rearrangement failures.
Since the quoted passage might be confusing out of context, I'd like to mention briefly that your question's description of light chain recombination is very simplified. In reality, there are many additional mechanisms involved and many different paths to get a functional κ rearrangement, a functional λ rearrangement, neither, or even both. Moreover, there's a lot we don't know, since we learn one experiment at a time, and we can't always directly measure what we'd like to.
First, rearrangement has been observed to occur simultaneously in  κ and λ. This fact might explain why it's possible to get a functional λ chain BCR right away as mentioned above. Second, allelic exclusion (between both κs and both λs) doesn't always work as you and I might expect it to, and a developing B cell can express different BCRs simultaneously (even one with κ and the other with λ). Third, due to receptor editing, a B cell has multiple opportunities for a functional κ chain rearrangement on a single chromosome, meaning that neither λ nor the second κ is needed despite an initially nonfunctional κ rearrangement.
I highly recommend reading the review article!


What are the biochemical processes occurring when food spoils? Let's assume for a minute that microbes themselves and their direct toxic products (i.e. endotoxins) aren't toxic to humans. Let's also discount any innate immune responses the body mounts against the invading microbe (i.e. inflammation and production of cytokines).

What happens to food molecules (mechanistically) as it spoils and what deleterious effects do these "spoil products" have on the body if ingested? I'm looking for compounds that can result from the spontaneous breakdown of food or the byproducts of microbial metabolism (that is NOT a "direct" toxin) that is harmful to the body.

For example, do the proteins in food break down into some toxic nitrogenous substance?

During putrefaction of animal tissue, lysine is decarboxylated into cadaverine and arginine is decarboxylated into putrescine. These compounds are deemed to be toxic.

A serving of meat contains 8 g of protein, corresponding to 640 mg lysine and a little bit less of arginine. Let's go straight and say that a spoiled meat serving contains 640 mg cadaverine and a little bit less of putrescine.

In rats, the acute oral toxicity for both polyamines is around 2000 mg/kg, let'assume that this is valid for humans also. According to these rough calculations, to have an acute toxic effect, a 70kg man that is resistant to the direct toxic effects of microbes, should eat 140 grams of cadaverine, corresponding to 218 smelly rotten meat servings.

[composition and toxicity data taken from wikipedia]


Is it possible for a person to become "reinfected" with the same strain of a virus? If a person contracts a virus, viral conjunctivitis for example, is it possible for the individual to become "reinfected" with the exact same strain of the virus once the person has it treated and the symptoms have gone away? I am a nursing student and am fascinated with virology, but my basic microbiology class did not go very in-depth on the subject.

The nature of infectious agents is that they transmit between organisms. This means that they have reservoirs outside a single host, and hence of course encountering the exact same strain twice is possible if this strain leaves the body and at a later stage is carried back to it. This could typically happen for example with influenza or common cold viruses, spreading from one child to other children at school and later being carried back to the original child through them.

The reason why the child will not develop another illness when being exposed to the same virus again is the adaptive immune response: After the first infection, immune cells specific to a pathogen will proliferate and differentiate both into effector cells to destroy the pathogen, and into memory cells. These can mount a much stronger immune response much faster when they come in contact with the same (or a structurally very similar) pathogen, meaning that a secondary exposure usually does not result in a proper infection and illness. Of course, this mechanism doesn't work properly for anyone with a compromised immune system.

In most cases where a viral disease develops repeatedly, this is due to evasion mechanisms. For example in some viruses, those antigens which tend to be targeted by immune systems have high mutation rates. In this case the "same" virus is actually a mutated strain which causes the same illness, but "looks" different to the immune system, and so the memory cells don't respond. Again, influenza is a great example. The reason why we get flu again winter after winter, is because this virus tends to mutate over the year with relatively low infection prevalence. Then during the winter, when the conditions are favourable for flu infections, typically only a small number of strains cause epidemics - because we were maybe immune to last year's influenza, but this year's has mutated antigens which our immune systems do not recognise yet.


Crossing over and exon shuffling? Campbell Biology 10e, in discussing the functions of introns, writes:

  The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of a process known as exon shuffling. Introns increase the probability of crossing over between the exons of alleles of a gene—simply by providing more terrain for crossovers without interrupting coding sequences. This might result in new combinations of exons and proteins with altered structure and function. We can also imagine the occasional mixing and matching of exons between completely different (nonallelic) genes. Exon shuffling of either sort could lead to new proteins with novel combinations of functions. While most of the shuffling would result in nonbeneficial changes, occasionally a beneficial variant might arise.

Hitherto, I had perceived crossing over as the shuffling of alleles between two homologous chromosomes, not of parts of alleles. That is, breaks in the DNA during synapsis would occur in between loci, not within them. Am I wrong to think that? My books tell me that, with regards to evolution, sources of genetic variation include mutations and genetic recombination. Genetic recombination includes random fertilization, independent assortment of homologs, and crossing over, yet it is only mutations that can produce new genetic material. If exons were crossed over, then new alleles would be formed, would they not? Is this a type of mutation? (I do not recall studying such a specific case of mutations.)

Crossing over primarily happens because of homologous recombination (HR). From the molecular point of view, it can happen between any homologous regions and it is not necessary that an entire allele has to be crossed over. During the process of HR, a DNA double strand break occurs. This is followed by resection (exonucleolytic degradation of one of the strands — 5'→3', from the break-point) by the MRX complex which leads to formation of ssDNA ends. The length of these ssDNA ends dictate the total length of crossover region.

   Taken from: Branzei, Dana, and Marco Foiani. "Regulation of DNA repair throughout the cell cycle." Nature reviews Molecular cell biology 9.4 (2008): 297-308.

This length can be from around 1.5kb to over 10kb depending on the repair kinetics with possibly an average of 3kb (more than half the cases) [1, 2]. Therefore, the author speculates that the probability of intra-gene crossover would increase with increase in intron length. However, in my knowledge, there are no recent reports to validate this hypothesis.

Edit:

Going back to the original question. It is not necessary that entire alleles are crossed over. Generally the genome has some recombination "hotspots" flanked by what are known as LD (linkage disequilibrium) blocks. An LD block need not cover an entire gene, as observed by Twells et al. (2003)[3] :

  LD breaks down in the region LRP5 g.5257T → G–LRP5 g.28149C → T, in
  intron 1 of theLRP5 gene. A second block of very strong LD
  (‖D'‖ > 0.9) is observed, LRP5 g.28149C → T–LRP5 g.45704G → A,
  spanning 17.6 kb of intron 1 to intron 3 of the LRP5 gene.

References:

Chung, Woo-Hyun, et al. "Defective resection at DNA double-strand breaks leads to de novo telomere formation and enhances gene targeting." PLoS Genet 6.5 (2010): e1000948.
Zhou, Yi, et al. "Quantitation of DNA double-strand break resection intermediates in human cells." Nucleic Acids Research (2013): gkt1309.
Twells, Rebecca CJ, et al. "Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene." Genome Research 13.5 (2003): 845-855.


Can anyone identify this small shrub? Has white flowers Small shrub in adelaide south australia garden.

Looks like the common olive, Olea europea.  Cut into one of the fruits and see if there is a stone/pit, which will confirm.  You can search online for images to compare (use the Latin name as your search term).


Why are fruits so large compared to their seeds? Why do many plants produce such large fruits(apples and strawberries,for example) if those contain only relatively small seeds?

The short answer: Fruits are large compared to seeds because humans have made them large.

In the natural environment, there is a different set of evolutionary pressures. A fruit has to be able to successfully propagate itself using its seeds, while commercially farmed fruit is usually cloned via vegetative propagation. Therefore, the commercial farmed fruits do not need large seeds to propagate, since they are cloned by the farmers. In many cases, their seeds are actually nonviable (i.e. they will not grow when planted).

For example, this is a wild banana, before being selectively bred by humans. As you can see here, the seeds are enormous compared to those in commercial Cavendish bananas.

Similarly, this is a wild strawberry compared to its commercial farmed variant.

Fruits with large seeds don't appeal to consumers, and therefore farmers who sell fruits with large seeds will get a poorer return on investment.

Therefore, farmers who plant the fruits which appeal the best to consumers by being the easiest to eat (small seeds) will reap the greatest profits.


Enzyme\Protein amounts in cancer I am searching for source, that providing information about enzymes\proteins, in different types of cancers, that their amount in cell is significantly higher - comparing to normal, healthy cell.

Some pathways that exist in cancer in much more higher amounts.

For example - Telomerase.

Is there some sort of database for this information?

Yes. The dbDEPC 2.0 database for example.
If you want to extend your search to pathways the best database I know of is the KEGG.

There are multiple databases out there. You might want to look at this wikipedia page.

By the way what you are looking for is called a cancer proteomic signature.


How do we know that selective agonists are indeed selective? Suppose we know that compound X is a selective agonist of receptor Y, meaning that it binds only this receptor Y and no other. But how do we know this that it doesn't bind some another receptor? I suppose that screening for the binding strength of a given ligand to all known receptors would be very tedious and not feasible.

Unfortunately, it's really hard in the general sense. Even for FDA-approved drugs with well-characterized mechanisms of action, the binding profiles are incomplete.
For GPCRs, it's you can run your compound(s) against a full panel of many GPCRs. For example, the PDSP (Roth Lab) can test for binding against multiple GPRCs using radioligand binding assays. See: https://pubmed.ncbi.nlm.nih.gov/23235874/, Figure 2 in particular. Most receptor binding assays are competitive, meaning they detect the displacement of known ligands. This is inherently limited because your compound could bind to a different site -- even a novel site.
You'll notice that in Figure 2, the GABA A receptor was conspicuously missing. One of the reasons is that binding is subunit-specific, which is another complication -- many receptors are oligomers, and it's often hard to prepare them for the assays.
For many well-known enzymes, there are specific activity assays available. These measure the level of a reaction product (often by fluoresence). This of course doesn't rule out binding without activity, and these assays are not available for all enzymes.
Another class of assays measure changes in potential across a membrane. For example, the FLIPR assay for GABA A receptors (https://pubmed.ncbi.nlm.nih.gov/31127604/). These tend to be very time-intensive and expensive, they're limited in the number of receptors, and of course they can't detect binding without activity.
As a last resort, you can use pull-down assays. One of the popular methods is immunoprecipitation (IP). You make an antibody that's selective for your compound and use to cross-link to any protein your compound might be binding to. Then these proteins get pulled out with your compound. These are generally very time-intensive and expensive, and they can need a lot of tweaking. And, of course, they won't detect all proteins your compound might bind to.
It's currently impossible to show that a compound is completely selective. To show that it's "likely" to be very selective, you can expect to invest a year or more for one compound.
But! To take a first stab, you can check out commercial assays offered by Eurofin (ex https://www.eurofinsdiscoveryservices.com/cms/cms-content/services/in-vitro-assays/gpcrs/binding/). They have a GPCR panel and a number of activity assays. Unfortunately their services are quite expensive.


How does the Platypus grow before it eats? From this fascinating documentary on monotremes it is mentioned that the Platypus is born less than 1 cm in length, but has doubled its size by day three when it begins to nurse. How does the animal grow before feeding?

Surely by conservation of mass there must be some alternate process by which materials are being processed and absorbed by the young animal. Does it absorb nutrients from the air or surrounding environment? Sucking on dirt? Osmosis?

The video is quite old and they knew a lot less about the species then.  They probably had to make some guesses.  Any modern reference I find doesn't mention any waiting period before nursing.

It seems to me that were this the case it would be very explicitly studied by now as it would be a real oddity for a mammal.  And we love platypus oddities.

Interestingly, the platypus doesn't actually have teets to be suckled on.  Instead the milk is expressed through their skin and into grooves on the belly that the newborns can drink from.


What is this insect wing, based on its vein pattern? I've heard that it's possible to identify insect species uniquely based only on the vein patterns of their wings.  Is this true?  If so, what is this?

The image is taken from an unsolved Internet puzzle game from a few years ago.  (The creators of the puzzle are no longer to be found, so I can't ask them).  I believe the wing is probably from some species of cicada, but I couldn't be sure, and if possible I'd like to know what particular species of cicada.
Also, is there any kind of formal classification/notation for insects' wing venation?  Might shed some light on what the puzzle makers actually meant by the dratted thing!  (You can remove this bit, or I can, if it's considered to be asking two questions at once.)

There is a way to classify insect wings: the Comstock-Needham system.
From Wikipedia:

The Comstock–Needham system is a naming system for insect wing veins, devised by John Comstock and George Needham in 1898. It was an important step in showing the homology of all insect wings. This system was based on Needham's pretracheation theory that was later discredited by Frederic Charles Fraser in 1938.

The system assigns names to the enlarged longitudinal veins of the wings and provides subnumbering for different branches of those veins. The system also names cross-veins and cells (transparent areas between veins) relative to the major longitudinal veins.
Again, according to Wikipedia:

the major longitudinal veins are named:
> - costa C, meaning rib
> - subcosta Sc, meaning below the rib
> - radius R, in analogy with a bone in the forearm, the radius
> - media M, meaning middle
> - cubitus Cu, meaning elbow
> - anal veins A, in reference to its posterior location

The cells are named after the vein on the anterior side


Incubation time of Antarctic Phosphatase in lab Antarctic Phosphatase is used to catalyze the removal of 5' phosphate from DNA. If I'm using it in the lab on a sample of 1-5 micrograms of digested DNA, how would I figure out how long to incubate the sample at 37 degrees Celsius?

For 5' extensions or blunt ends, incubate the sample for 15 minutes at 37 degrees Celsius.

For 3' extensions, incubate the sample for an hour.

https://www.neb.com/protocols/1/01/01/vector-dephosphorylation-protocol


Please identify bird call / animal call What species is making this sound?

You can hear it from the opening samples of this song: Earthgarden by Nada (2003).

I wish to study the frequency distribution of the bird call.

Sounds like a Curlew (Numenius arquata).

http://www.british-birdsongs.uk/curlew/
https://www.youtube.com/watch?v=q7V25M0szqU


What is the identity of this flower found in Mavericks Beach in Half Moon Bay, California, USA? Please help identify this flower I saw in Mavericks Beach in Half Moon Bay, California. It was smelling soooo good, you can feel from distance. I want to buy and plant in my garden.

Thank you,

Based on the habitat, color, and size that lupine looks like Coastal bush lupine (Lupinus arboreus).

Please note that Coastal bush lupine can be invasive, so be responsible about where you plant it!

You can also learn more about this plant and its growth requirements from the California Native Plant Society

Images for comparison:


Do swarms show intelligence? Can you think of collective and swarm behaviors as "intelligence"? Would such a concept apply to a) ant colonies and b) fish swarms?

Intelligence is something which has to have a definition, and there are many, but I would cautiously say no.

The reason that I say this is because swarming behavior can be largely reproduced by a simple set of rules - matching distance to your neighbors and direction and speed as well.  To me this really removes any intention or even conscious element to swarm behavior although its clear individuals do make decisions, they don't have to be more intelligent than a mouse looking for food or other kinds of animal behavior.

That being said, others have literally built definitions of intelligence inspired by swarming - a decentralized sort of mind which makes decisions based on the interactions of component individuals.  You could argue that our own brains are a similar sort of ensemble, and therefore no more different than our own intelligence if we look closely enough.

So take your pick really.


Glycolysis - ATP production In glycolysis, 2 ATP molecules are produced from each triose phosphate molecule (to give a total of 4 ATP produced; 2 net produced as 2 were initially used up in the reaction).

I don't understand how this would be the case, as each triose phosphate only has one phosphate group available to form ATP from ADP, meaning that one ATP is produced per triose phosphate. I know this cannot be the case as this would mean a 0 net production of ATP defeating the purpose of glycolysis, but i can't get my head around why.

out of curiosity, would the other remaining two phosphates that are required come from other sources, i.e. 2 phosphates + the 2 phosphates already from the two trios phosphate molecules to give us the 4 ATP molecules (2 net ATP)

Many thanks in advance.

The other two phosphates come from inorganic phosphate* in solution (Pi — in my diagram below) at the glyceraldehyde phosphate dehydrogenase stage. (Two, of course, because there are two molecules of triose.)

This is covered in Berg et al. Section 16.1.5.

*The term inorganic phosphate is used because there are various different anions in solution derived from phosphoric acid, depending on the pH. At physiological pH the predominant species is the double-negativly charged, monohydrogen phosphate.


How is the probability of Rh type inheritance calculated? I found somewhere on the Internet that, if parents are both Rh-positive, their children have 93.75% chance of being RH-positive and 6.25% chance of being RH-negative.

My question is: How is this calculated?

There are four possible parental genotype combinations (R = Rh+ allele, r = Rh- allele):

m  f
RR RR
Rr RR
RR Rr
Rr Rr

Only the last can produce Rh- offspring. The probabilty that the Rr Rr combination leads to a rr genotype in the F1 generation is $1 \over 4$. Since there are four combinations, the probability that the Rh+ parents are Rh Rh is also $1\over4$. Thus the probability of the offspring to be Rh- is $${1\over 4} \cdot {1 \over 4} = {1 \over 16} = 0.0625$$ Thus, the probability of Rh+ in the F1 generation is $$1 - {1 \over 16} = {15 \over 16} = 0.9375$$

Note: This is the rationale behind the values you state in your question. I am pretty sure that these four combinations are not equally distributed in a population. You would have to need to know the allele frequencies.


Which organs need to have fluid compartments in order to develop properly? I am a student, slightly struggling with the new concept of fluid compartments. I know that there are two main types of fluid compartment, extra and intracellular fluid. I also read that most organs need to have these fluid compartments (established by cell-cell adhesions within tissues) in order to function and develop properly.
My question is what type of organs require these fluid compartments? Would it be the kidneys and the intestines for example?
thanks

Organs consist of different tissues and cells. To function properly each cell needs intracellular fluid. All cellular processes (energy metabolism, signal transduction) occur in aqueous environment, otherwise the required chemical reactions could not take place. Extracellular fluids provide nutrients to the cells and also information from other cells or organs. It can be divided in three categories:

Interstitial compartment: between tissue cells; provides nutrients and helps the cells to communicate within a tissue or organ.
Intravascular compartment: content of blood vessels; transports nutrients, information and immune cells within the body e.g. from one organ to another.
Transcellular compartment: all spaces in the body where only a small amount of fluid is present, normally between organs.

So all organs need these fluid compartments to function properly. The only organ where this is different is the skeleton. But the bone building cells (Osteoblasts) also need extra and intracellular fluid to build a scaffold of collagen. Only after that, they can fill up the interstitial space with hydroxylapatite.
The kidneys clean up the blood and excrete the waste via the urine which occurs in aqueous environment. The intestinal tract absorbs nutrients which are solved in water. Hence, saliva and gastric juice are produced when you ate something.

So every organ needs fluid compartment to do its job. So does the whole organism to make sure all organs are working together (via blood circulation and nervous system).


Can you identify this Illinois wasp? I live in northern Illinois and had these guys appearing in my room. No facial markings and they seem non agressive.

About 2cm in length with off white u shaped markings below it's waist and a single white line a few segments down.

It looks to me as Potter Wasp (or mason wasps), the Eumeninae, are a cosmopolitan wasp group presently treated as a subfamily of Vespidae, but sometimes recognized in the past as a separate family, Eumenidae.

Since there is no more info provided and image is not sharp I cannot be 100% sure.


Sensory adaptation regarding smell and hearing Imagine the scenario. My friend and I are playing a game of chess near a highway. Initially, I notice the sound of the highway. While I'm playing chess, however, I do not notice it. After the game my friend asks me if I can hear the highway, and I regain my ability to notice it. This seems to be different for smells.
If we were playing chess in a room filled with garbage, the smell would gradually fade away. If my friend asked me if I could smell the garbage, I would not be able to smell the garbage as severely. What is the cause of this difference?
It seems that visual and touch follows the same pattern as hearing. What makes smell unique?

Adaptation occurs in every sensory system. For example in vision there is the motion after effect that occurs through adaptation of visual neurons in the cortex. Also, the visual system strongly adapts to low and high lighting conditions through light and dark adaptation. The tactile system also shows substantial adaptation, as touch receptors in the skin fail to convey information after prolonged stimulation (you won't feel a watch/ring/band aid etc after wearing it for a while). For example, mechanoreceptors in the skin such as the Pacinian corpuscles fail to transmit tactile stimuli when activated for a prolonged time. The auditory system also adapts to loud sounds by cortical mechanisms as well as  peripheral mechanisms through the middle ear muscles. Lastly, as you correctly identified, the olfactory system adapts to stimulation as well through metabolic mechanisms that decrease the responsiveness of chemical receptors. The list of adaptational mechanisms provided is not comprehensive, but I just used some obvious examples to show that adaptation occurs in all the senses in a variety of ways. In fact, one of the hallmarks of any physiological intact sensory system is the capability to operate over a wide range of stimulus levels. For example, vision operates over a range of intensities differing 8 orders of magnitude, while hearing operates in an intensity range of 1013. To maintain such an impressive range of input intensities sensory systems have to adapt at various levels. As an analogy, the same applies to your photo camera in which the exposure time has to be regulated in order to take pictures under different lighting conditions.

So to come back to your suggestion that smell cannot be revived after continued stimulation while it can be revived with other senses is not true I think. The attentional revival you are talking about is not so much adaptation but has more to do with the attentional shift, which may occur with any sensory modality.


Calculating Possible Combinations of Bases in a DNA Strand of a Given Length In my Biology class we were asked this question:

This DNA strand consists of eight pairs of nitrogenous bases. How many different sequences of eight bases can you make? Explain how you found your answer.

I guessed either 28 or 8!. Apparently, the answer is 8! ÷ 24. I asked my teacher, but she did not know the answer. Does anyone know why this would be?

At each base, you can have 4 different bases (A,T,C or G). Therefore for the first base there are 4 possibilities, namely

A
T
C
G

For the first two base pairs there are $4^2 = 16$ possible combinations

AA
AT
AC
AG
TA
TT
TC
TG
CA
CT
CC
CG
GA
GT
GC
GG

For the first three bases, there are $4^3$ possible combinations. For 8 base pairs, there are $4^8 = 65536$ possible combinations. $2^8$, $8!$ and $8! + 2^4$ are all wrong.


What is the cause of "imbalanced" linkage disequilibrium? With perfect linkage disequilibrium ($D' = 1, R^2 = 1$), you might have the following table of counts for the alleles:

    B     b
A  100    0
a    0  100

With "partial" linkage disequilibrium ($D' < 1, R^2 < 1$), you'll see something like this:

    B     b
A  100   25
a   25  100

But I've sometimes seen the following "imbalanced" linkage disequilibrium ($D' = 1, R^2 < 1$):

    B     b
A  100    0
a   50  100

What gives rise to this sort of situation, where aB occurs, but Ab never does? Is there a name for this phenomenon? Which is a better measure of linkage disequilibrium in this case, the normalized LD coefficient $D'$, or the squared-correlation $R^2$?

This can occur if the Ab genotype is lethal, i.e. you won't observe individuals with a Ab genotype.

Allele lethality is a common mechanisms that can explain non-mendelian inheritance of a trait.

For the question of which LD metric to use, this is tricky. Under the assumption that allele lethality is indeed at play, you observed perfect haplotypes, so D'=1 wouldn't be incorrect. Yet the correlation coefficient is also correct in the sense that SNP A is not a perfect proxy for SNP B.


What happens during a Raynauds episode? Raynaud's phenomenon can be a serious health issue, as the blood flow to the extremities, mainly the fingers is compromised, causing fingers to blanche, and then turn blue. Severe Raynaud's can cause gangrene in illnesses like progressive/ diffuse scleroderma.

I am not asking about connective tissue disease per se, but what occurs during an actual Raynaud event (for a better way of putting it), not what precipitates the condition to occur within a particular person and not another.

what are the underlying biological processes that cause the blood flow to be compromised like this?

The Raynaud phenomenon is a recurrent vasospasm that is associated with cold temperatures and emotional stress [1]. Excessive vasoconstriction leads to hypoxia. The cause of vasoconstriction is a hyperactivation of the sympathetic nervous system [2] and probably the lack of parasympathetic response. The mechanism is thought to involve both central neural issues and peripheral impairment (subclinical polyneuropathy) [3]. The resulted chronic hypoxia leads to pain, atrophy and sometimes even ulceration [2].

References:

Bakst R, Merola JF, Franks AG, Sanchez M. Raynaud's phenomenon: pathogenesis and management. J. Am. Acad. Dermatol. 2008 Oct;59(4):633-53. doi: 10.1016/j.jaad.2008.06.004. PubMed PMID: 18656283.
Wikipedia contributors, "Raynaud's phenomenon," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Raynaud%27s_phenomenon&oldid=613954124 (accessed June 27, 2014).
Koszewicz M, Gosk-Bierska I, Jerzy G, Bilińska M, Podemski R, Budrewicz S, Adamiec R. Peripheral nerve changes assessed by conduction velocity distribution in patients with primary Raynaud's phenomenon and dysautonomia. Int Angiol. 2011 Aug;30(4):375-9. PubMed PMID: 21747356.


Why are bats the source of dangerous coronavirus pandemics? Why do coronaviruses come from bats?

I mean, why precisely coronaviruses and not (for instance) herpesviruses?
It looks like bats host more zoonotic viruses (per species) than rodents, although they don't develop any sign of disease.

The article above says that rodents host more zoonotic viruses than bats overall (68 against 61), but at the same time most of the latest pandemics originated from bats.

It also seems that bats could be involved in the maintenance of ebola viruses.

My question is: why did these major pandemics originate from bats and not from rodents, although rodents host more zoonotic viruses overall?

We should also take into consideration that human-rodent interaction is usually more likely than human-bat interaction, except for people who consume bats (like Chinese people; this would (partially) explain why both SARS and 2019-nCoV developed in China).

The preponderance of links between bat and human pathogens has led to a debate about whether bats disproportionately contribute to emerging viral infections crossing the species barrier into humans (26–30). Given the diversity of the Chiroptera order (Figure (Figure1),1), we may simply see more bat viruses because there are so many (>1,300) species of bats (31). However, even when accounting for the fact that they make up ~20% of extant terrestrial mammals, bats are overrepresented as reservoir hosts of pathogens with a high potential for spilling into human populations (32, 33). In fact, no known predictors that have been described to impact the likelihood of crossing the species barrier, including reservoir host ecology, phylogenetic relatedness to humans or frequency of reservoir-human contact, explain this pattern (32). Thus, why bats are such a frequent source of pathogenic human viruses remains a tantalizing mystery.

--Going to Bat(s) for Studies of Disease Tolerance

Other references that debate whether bats are special, generally conclude that they might somehow be, and argue about causes, include

Brook CE, Dobson AP. Bats as ‘special’ reservoirs for emerging zoonotic pathogens. Trends Microbiol. (2015) 23:172–80. This may be the best of the group, going into more detail and including more recent data
Dobson AP. Virology. What links bats to emerging infectious diseases? Science (2005) 310:628–9.
Wang LF, Walker PJ, Poon LL. Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? Curr Opin Virol. (2011) 1:649–57.
Olival K, Epstein JH, Wang LF, Field HE, Daszak P. Are bats exceptional viral reservoirs? In: Aguirre AA, Ostfeld R, Daszak P, editors. editors. New Directions in Conservation Medicine. Oxford, UK: Oxford University Press; (2012). p. 195–212.
Luis AD, Hayman DT, O'Shea TJ, Cryan PM, Gilbert AT, Pulliam JR, et al. . A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci. (2013) 280:20122753.


Is it possible to conduct scientific research without actually getting close to the sample/specimen? For example, I have never get closed to a whale. The only source I have is research from who has get close to it. If I read their research and find a new thing, would my "discovery" be scientific? If yes, can you give some example of such research?
There is a related question in Philosophy SE: “Dinosaurs did exist once”. Is it knowledge or is it only justified belief? However this question is more about the knowledge directly produced by field researchers, while in this question I focus more on researchers who can only access secondary research. Plus that dinosaurs extincted, so in a sense I and a paleontologist are equal: neither of us can have direct experience to a living dinosaur. But whales are still living, and that equality is gone. So maybe the threshold for scientific research between a living organism and an extinct one is different?
See also: Is it possible to have a scientific review of a method if the author doesn't have direct experience of it?
Some may say this question is opinion-based. But there are good subjective questions as well.

It depends on one's field - whether what you study actually requires first-hand knowledge of the experimental subject and the methods of dealing with or not. Moreover, one could invert the question and ask, whether a field, based solely on the knowledge of the experimental subject, can be considered science?
Theoretical physics/chemistry/etc.
In some sciences, such as physics, there is traditional division into experimentalists and theoreticians - the former are people who actually work in a lab, but who limit themselves to very basic statistical analysis of the phenomena observed. The latter are providing deeper, model-based, analysis of the data and description of the phenomena. Very often their work is not tied to any particular experiment, bordering on very abstract math. Looking at the list of the Nobel prize winners in physics one can easily convince oneself that this work is no less valuable than the experimental work.
Similar division exists in other fields, e.g., one can freely talk about quantum/theoretical/computational chemistry.
Computational biology, bioinformatics, biostatistics, epidemiology, population genetics
Although biology is relatively young science, the times when it was frowned upon by physicists as mere stamp collecting have long been gone: evolutionary theory and epidemiology have been put on a firm mathematical footing, and the explosion of genomic data in the last couple of decades has ushered in the professions of bioinformatician and computational biologist - all complete with designated job descriptions and advanced university programs. Less noticeable, but no else widespread is the observation using modern technology - such as video and sound recording - every conference features a few talks like this, related to swarms of insects, flocks of birds, or behavior of whales (incidentally, whales have been extensively studied in connection to tracing enemy submarines. The analysis of the data is often done very far away from the sea.)

All science is either physics or stamp collecting. - a quote attributed to Ernest Rutherford, but likely of even earlier origin.


What is a detailed chemical explanation for describing how an enzyme may lower the activation energy of a reaction? If you can provide some sound reasoning that touches on tertiary structures of proteins and does not use a lot of advanced chemistry jargon that might be really helpful, especially for an intro biology student.  I think my problem is that activation energy is lowered by an enzyme and I know how its like on the Gibbs Free Energy diagrams.  However I think I've been taking this as an axiom and I'm not really sure why.

BACKGROUND

We should first understand what activation energy really is and what does Arrhenius equation mean. For any chemical reaction to happen you need to break some existing bonds in order to form new bonds. Breaking existing bonds consumes some energy; in other words you have to convert the reactant to an active form which undergoes a reaction readily. The energy that is required to do so is called activation energy.

It is essential to note that activation energy is an empirical term because it does not actually consider the reaction mechanism. The above example of bond-breaking and re-formation can happen in many ways. Some mechanisms may require less activation energy than the others.

The Arrhenius equation denotes the relationship between reaction rate and activation energy:

$$k=Ae^{-\frac{E_a}{RT}}$$

where $k$ is the reaction rate constant, $A$ is the Arrhenius constant (an arbitrary proportionality constant), $E_a$ is the activation energy, $R$ is the universal gas constant and $T$ is the absolute temperature.

This equation tells you that the rate of reaction decreases with increase in activation energy and increases with increase in temperature.

The temperature indicates the internal energy of the system i.e. the movement of molecules. Collision between molecules is essential for chemical reaction to happen and increased temperature increases the chance of collisions (due to higher molecular movement).

How do enzymes lower activation energy of a reaction?

They either do that by increasing the chance of interaction between the reactants or diverting the reaction to follow a different mechanism that has a lower activation energy.

As you know, the enzyme binds to the reactants and forms a complex. This effectively brings the reactants closer thereby increasing the probability of their "collision" which in turn increases the reaction rate. This can be further extended to the level of molecular orientation. The analogy presented by AMR in their comment is great. It is one of the mechanisms by which the free energy of the system would increase — by reduction of entropy. Clamping the substrate in place can expose its reactive groups to the co-reactants, thereby allowing the reaction to proceed faster.

In most other mechanisms of enzyme catalysis, the functional groups in the enzyme active site react with the substrate to form intermediates and these intermediates which have lower activation energy give rise to product faster than the substrate in absence of the enzyme.

It is to be noted that this entire process of catalysis adds a few extra steps to the actual reaction (binding,  formation of intermediates etc). The catalyst would be effective only if these combined rates are still faster than that of the uncatalyzed reaction.


Why do coliform bacteria smell so bad? I have done multiple cultures of E. coli bacteria and related species over the course of my education. Almost every time, they had this revolting smell. However, other organisms used for genetics experiments (eg. Saccharomyces cerevisiae) rarely have a bad scent, if a scent whatsoever. My question is, what is it about the coliform metabolism that produces such a pungent and revolting odor? Any and all answers are appreciated.

E. coli and other bacteria metabolize tryptophan into odoriferous skatole and other indole compounds.

If you're culturing these organisms in medium that contains tryptophan, that may be what you're smelling.


What if $rB=C$ in Hamilton's rule? Hamilton's rule states that if $rB>C$ then a gene giving altruistic behaviour will increase in frequency in the population. What would happen if $rB=C$? Will an individual perform the altruistic act?

I agree with @Amory in the sense that Hamilton's rule is not a rule that applies to each specific individual and explain their behavior (or other traits). The Hamilton's rule describe the direction (and not the dynamic) of how a social traits evolve. A social trait is any trait which does not only affect the fitness of its carrier but also affect the fitness of other individuals in the population. Theoretically, all (or almost) traits are actually somehow social traits.

$RB>C$ is a simplistic way of looking at Hamilton's rule which might bring you to some confusion. This formula makes more sense to me by replacing $B$ by $\frac{dw(x,y,z)}{dx}$ and $C$ by $\frac{dw(x,y,z)}{dy}$. $w(x,y,z)$ is the fitness function of a focal individual expressing trait $x$ and interacting with an individual drawn from a subpopulation expressing trait $y$ (expected value of the probability distribution of trait expression of individuals in the subpopulation) in a population expressing trait $z$ (expected value again). In the particular case where there is no population structure $y$ equals $z$. $\frac{dw(...)}{dx}$ describes the partial derivative of the fitness function according to the variable $x$.

Therefore the Hamilton's rule can be rewritten as:

$$R\cdot\frac{dw(x,y,z)}{dx}>\frac{dw(x,y,z)}{dy}$$ where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$.

Altruistic behavior evolves if (but not "if and only if") this rule is respected. Hope this reformulation of Hamilton's rule helps a bit understanding it.

In the special case where $R\cdot\frac{dw(x,y,z)}{dx}=\frac{dw(x,y,z)}{dy}$ then, the trait of interest is not selected (neither counter selected). Therefore the trait will evolve under genetic drift alone. While the allele frequencies are modified by drift, the Hamilton's rule might (or might not) differ from the equality and then the trait would not be neutral anymore.


Hibernation, Metabolism and Aging People are beginning to seriously research space travel applications of therapeutic hypothermia, specifically for reducing metabolism and stress on humans traveling to Mars.

It seems that as you decrease the temperature, the metabolism decreases. My question is regarding the relationship between ageing and metabolism. Do we have any data that answers the question if lowered metabolism also lowers the rate of ageing?

I'm wondering if these hypothetical astronauts going to Mars are actually losing 6 months of their lifespan in an unconscious state, or is their ageing rate being lowered as well? And by how much?

For the sake of simplicity, let's ignore the effects of radiation on ageing during the travel.

Therapeutic hypothermia certainly is an extremely useful short-term treatment for hypoxic and ischaemic injury to tissues (caused by loss of blood flow and/or oxygen) and is part of the protocol for treating people in intensive care who have had out of hospital cardiac or respiratory arrest as well as being used during heart surgery in cardiopulmonary bypass. In addition there is currently research into treating people who have just had heart attacks and strokes, both conditions where there is acute loss of blood flow due to a clot.

However, there is little evidence as regards use of chronic (long term) hypothermia to prevent aging. While severe hypothermia does suppress cellular respiration and slow down metabolism and bodily function, it also often causes other abnormalities such as:

Disturbances in cardiac conduction that can lead to cardiac arrest
Markedly reduced blood flow to skin and limbs which can lead to tissue death in fingers, toes, etc.
Clotting dysfunction (haemorrhage if there is any injury)
Pulmonary oedema - fluid in the lungs causing inability to oxygenate and/or ventilate the blood
Increase in infections

There is, however, quite a lot more evidence in regards to slowing down cell ageing from oxidative stress using diet energy restriction and this has been replicated in rodents.

In other words, there really isn't any good evidence at this stage in regards to long term hypothermia, but currently, given the high risks of cardiac dysfunction and death, without invasive monitoring and intervention (such as in an ICU) it is not feasible.


Does Cholestyramine (CSM) raise Tyramine levels? This is a layman's question.

Will ingesting Cholestyramine (CSM, the resin, in powdered form to be specific) raise tyramine levels?

I am asking because Cholestyramine clearly has "tyramine" in its name, so i don't understand the chemistry behind all this and/or how this interacts with the body.

Thank you.

I'm not sure why "tyramine" is in the name "cholestyramine", but the molecular structure of tyramine is not present as part of the molecular structure of cholestyramine. Specifically, in tyramine the amino group is on the beta-carbon from the ring, and in cholestyramine the ammonium group is on the alpha-carbon (note the different number of points between the ring and the nitrogen in the line structures provided). I find it highly doubtful any reasonable metabolic reactions by the body could generate tyramine from cholestyramine.

Cholestyramine molecular structure

Tyramine molecular structure


Is there a surface or body cavity that does not have epithelium? Is there any surface in the (human) body that is not covered with epithelium?

Short answer
Edit with credits to anongoodnurse: As far as I know, every bodily surface and cavity is covered by epithelia.

Background
Epithelial tissue is a sheet of cells that covers a body surface or lines a body cavity. There are two types of epithelium in the human body:

Covering and lining epithelium forms the outer layer of the skin; lines open cavities of the digestive and respiratory systems; covers the walls of organs of the closed ventral body cavity.
Glandular epithelium surrounds glandular tissue.

Hence, the entire the bodily surface is covered by some sort of epithelium. Even the eye is covered with squamous epithelia (thanks to anongoodnurse for pointing this out).

And while acknowledging that an absence of evidence is not evidence of absence, I believe that there is no surface on, or cavity in the body not lined with epithelium.

Fig. 1. Epithelial lining of bodily surfaces. source: Ternopil State Medical University


Pipetting damage to cells I'm curious how much damage is potentially inflicted by shear stress by pipetting. I know that syringes used for stem cell injection can cause a lot of damage. However, to what extent does this happen with P20 and P200 pipette tips? Understandably the shear modulus of bacterial cells is significantly different from that of cancer cells, which will be different from that of stem cells.

This is an excellent question, I have been training people to culture cells for about 12 years and students have a hard time grasping this and appreciating the importance etc.

What cells are usually experiencing during pipetting is analogous to a crowd of people trying to fit through the doorway of a building. Shearing during pipetting  is certainly a legitimate concern in cell culture. You will notice its negative effect on viability most explicitly when pipetting cells in freezing
 medium (containing DMSO) following a thaw. Until their DMSO concentration drops their membranes are weaker & more fluid. That's why you pipette the frozen cells drop-wise to the fresh medium, to be especially gentle at this point.

Prokaryotic cells such as the above mentioned TOP10 cells are treated with Calcium chloride and glycerol which has essentially the same effect on their walls and membranes. Hence pipetting should be delicately performed after thawing these cells as well.

With that being said, if you compare the sensitivity of prokaryotic and eukaryotic cells to shearing, eukaryotic cells are profoundly more sensitive.

For individuals using competent bacteria for sub-cloning and other routine uses, killing a small percentage of of your cells is not that important. However if you are using the transformation to generate cDNA libraries it's very important that you have a titer sufficiently representing the transcriptome the library is composed of.

In these instances using a more premium competent cell, adhering to correct temperatures and minimizing pipetting is essential. This is why many are taught to swirl the DNA the with the competent cells, rather than the harsher alternative: pipetting up-and-down.

The four most important factors that contribute to cellular shearing are, and in order form most to least contributory:

Diameter of the bore in the pipette tip, the smaller the more shearing.
Speed at which the suspension is passing through the opening of the tip. The faster the more damaging.
Size and rigidity of the cell. Larger cells are more prone to damage.  Cells with a murein wall are less prone to damage.
Concentration of cells. Cultures that are more concentrated are more prone to damage.

Because the make up if the cell itself is so influential on the amount of damage, and because of the enormous variety of cells; designing a representative experiment to assess damage would be very difficult and  laborious.

Finally,  the variety of tips and seriologicals is also enormous. However if one were to attempt to assess this it could be done:

Choose a representative variety of cell lines, choose a representative variety of pipettes. One would probably want to use a robotic pipette to be able to  evaluate incrementally assigned speeds and pressures. Look at different culture concentrations,  phases of the growth curve, time between pipetting and analysis, distance between the exiting fluid and the culture etc, etc.

I think a very successful analysis method would be using propidium iodide and FACS.

After your experiment which will cost a lot of time and $, I think you will find common sense rules: keep pipetting to a minimum and use wider tips whenever possible.


Whole genome amino acid composition tool? I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes.

I've looked in MeSH terms database but I'm a bit lost when I search for "Genetic Code" and Software.

I'm looking for an output like this one:

I have written a script that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript.

You will need to install the Bio::EnsEMBL::Registry Perl module, see here for instructions. The script also uses the Math::Round module, everything else should be installed by default with your Perl distribution. Finally, the script expects to be run from a Unix/Linux operating system.

Example run

 ensembl_get_codon_count.pl human > human.csv

Example output

Gene Name   Gene ID      Transcript ID  Ala_GCC Ala_GCC_% Ala_GCA Ala_GCA_% Ala_GCG Ala_GCG_% Ala_GCT Ala_GCT_%
CRLF2   ENSG00000205755 ENST00000400841    6       40        6      40         0       0         3       20

In the example above, the transcript ENST00000400841 of the human CRLF2 gene, contains a total of 15 Alanine residues, 6 of which are coded for by the GCC codon (40%), 6 by the GCA codon (40%) and 3 by the GCT codon (20%). The GCG codon is not used (0%).

This is a cut version of the output, the actual output lines are much longer since they include all codons and there will be one line per protein coding transcript.

This script should at least get you started since it will provide you with the raw data needed to perform your statistical analyses. If you use it in published work, I would appreciate it if you could let me know (my email is included in the script) and perhaps mention me in the acknowledgements :).


What is the name of this plant with leaves having two different shades of green? I am trying to find the name of this plant. I am attaching the relevant images. Thank you for your help.

Location: Hyderabad, India

So after searching a bit, I think this plant is of the genus Ficus:

I am still unaware of the species but the nearest I could find was Ficus retusa. I hope I have been of help.


How would real-time blood glucose monitoring work? Is it possible to perform real-time blood glucose monitoring using a wearable non-invasive device (similar to a fitness band measuring heart rate)? I'm aware that there are some devices in the market developed by medical companies but most of them require you to stick a needle in your body and it also requires you to switch needles and reapply it every few days.

How can blood glucose be measured in a non-invasive way?

If you browse the on-line patent data bases - either www.uspto.gov or www.freepatentsonline.com for "glucose monitor" you'll find there are at least half a dozen technologies that have been proposed including the most non-invasive technologies such as using light - similar to the pulse oximeters used in hospitals to measure the pulse and PaO2 through the skin to more invasive methods that periodically pump small samples of blood outside the body for chemical or optical analysis. But in terms of accuracy, the best way to measure BG is by some means that can analyze arterial blood in vivo.

Companies that are trying to develop these devices are shooting for accuracies better than 12 mg/dL, but that's very hard to do with the noninvasive methods. There is a very new technology that uses a contact lens as the sensor, measuring from the iris and transmitting to remote electronics for processing, but that's still probably year's away. I believe the best products that are available today may be those developed by Dexcom in San Diego, CA. See their website here: http://www.dexcom.com/

The journal Science just published its year end Breakthroughs and that includes an article that shows hope in restoring the B cells in the pancreas for type I diabetics see http://www.sciencemag.org/content/346/6216/1444.full . This of course is the best solution - a cure. I hold hope scientists are less than 5 years away from that goal.


Gene transfer between Gram positive and Gram negative bacteria? How does transfer of genetic material occur between Gram positive and Gram negative bacteria?

Have a look at this two links:

Exchange of genetic information
and
Gene transfer between distantly related bacteria

Especially the second should answer a lot of questions.


What is the best way to analyze non-quantitative mass spec hits from an immunoprecipitation pull down? I am studying a nuclear protein and want to come up with a list of potential proteins that it interacts with. From the nuclear fraction of 293T cells, I did an IP (immunoprecipitation) to pull down my protein and submitted whatever I pulled down for a mass spec analysis. I also did an IP with a non-specific antibody as a control. I got a huge list of hits, and I'm not sure how to prioritize them. I can manually remove the hits that also came down with the non-specific antibody, those are obviously just sticky proteins. I looked around Pubmed for ways to prioritize non-quantitative mass spec hits, but I'm not sure if any of them would work in my case. All of them require multiple mass spec repeats - I can do that if I need to, but would like a way to look at my initial data more intelligently.

If they are available, talk to the people who analysed your data. Using their knowledge is intelligent.

I will assume two critical steps are completed. First that your results have been searched correctly. I will also assume that the peptide and protein identifications have been filtered to provide a false discovery rate of 1:100 at each level.

You can remove all the proteins that were identified in your affinity purification control. Another option is to use the Contaminant Repository for Affinity Purification (the CRAPome) which provides a formal framework for removing contaminant proteins. It is a nice resource if your data are compatible.

The remaining proteins are what you have to work with, this is the

  list of potential proteins that [your protein] interacts with.

Prioritise these proteins based on the biology of your experimental system. If the list is small work through the function of each protein and assess how it fits with the biology you are researching.

To assess the potential functional links between the proteins you can create an in silico network. Markov clustering can highlight the presence of functionally distinct groups of proteins within a network. String, linked above, can do this. Centrality measures can indicate the presence of proteins with the potential to influence the behaviour of the network.

For larger lists you can also assess the function of the proteins in the list by performing a functional annotation enrichment analysis. There are many other things you could do but the primary goal is to keep biology at the forefront of your efforts.

Finally you mention that repeats are necessary. Analysing the data is time consuming. If this was a test run verify that the test was successful and then run the replicates. Time spent analysing incomplete data can be spent completing the data set or ensuring the right data is collected. Quantitative data can be very useful and with care shotgun proteomics approaches can provide quantitative data but the people who run the machine need to be consulted when quantitative data is required.


Identify little green long legged bug Discovered attempting to hide on bathroom sink handle at night, though bathroom light had been left on.

Barely reacted to attempts to capture it at all. No flying. No jumping. Just really slow crawling.

Found Eastern US. 2017/11/18

The photo is not high quality, but the shape and size of the insect definitely point towards it being the nymph of some species of assassin bug (order hemiptera, family Reduviidae).
See this as an example:

Specifically, your specimen looks similar to one found in a home in Virginia.
The genus is likely Zelus, and based on it's greenish hue, I'd say it's an individual of the eastern US's most common species of Zelus, Zelus luridus (Pale Green Assassin Bug).

 Source: Christine Hanrahan

Nymphs are solid green, wingless, and with narrow bodies

The most reliable feature to distinguish this species from others is the pair of spines on the rear corners of the pronotum. These spines are long on the lighter colored individuals and shorter on ones that are darker. It can also be distinguished by dark bands on the distal ends of the femurs, but these can often be too light to be easily seen. [Source].


How are there alternative initiation codons? According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the mechanism of translation initiation in the absence of the canonical tRNAfMet.

Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNAfMet (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable interaction. But apparently, only two-bases-interaction between the start codon (GUG, UUG) and the fMet-tRNA anticodon are sufficient for the initiation of translation (1). I will look more into the literature.

1. Initiation of translation in prokaryotes and eukaryotes


How does further hybridization affect fertility? Numeruous scientific sites state that hybrids (like mules) are infertile. On the other hand, ligers are known to mate with both tigers and lions and still have viable offspring.

So my question is: if the hybrid is fertile in the first generation, does further mating with either of the parents' species somehow affect its offsping's fertility?

For example: if liger mates with tiger let the odds to produce viable offsping be 50%. If this offsping further mates with tiger, are odds the same or are they lower / higher?

Some first generation hybrids[f1] are viable and fertile, but when they mate with each other or back to either parental species[P}, the successive generations[f2] are sterile or feeble.  this concept is known as hybrid breakdown.  This is often seen in hybridized forms of domestic crops.  I am aware that some female tiger/lion hybrids are fertile, but I'm unaware of successful breeding of the f2 generations.  It could be a case of hybrid breakdown.

Article about hybrid breakdown in rice

Hybrid breakdown in Cichlid Fish


What is the symbiotic relationship between truffle fungi and their host trees? I understand that truffles share a symbiotic relationship as they reside among the root systems of host trees, but I cannot find any material that specifies the details of such a relationship. In other words, what exactly do truffles get from their host trees, and what do they provide in turn?

A truffle is the fruiting body of a subterranean Ascomycete fungus, predominantly one of the many species of the genus Tuber. Truffles are ectomycorrhizal fungi and form symbiotic relationships with the roots of several tree species including beech, birch, hazel, hornbeam, oak, pine, and poplar.

Mycorrhizal symbiosis is a mutualistic association between a fungus and the roots of a plant (usually a tree) in which (typically) the fungus obtains energy in the form of carbohydrates from the plant, and the plant gains the benefits of the mycelium's higher absorptive capacity for water and mineral nutrients, partly because of the large surface area of fungal hyphae, which are much longer and finer than plant root hairs, and partly because some such fungi can mobilize soil minerals unavailable to the plants' roots. The effect is thus to improve the plant's mineral absorption capabilities.

Based on the quote below from the website of a truffle nursery in Australia (http://trufficulture.com.au/what_are_truffles.html), it sounds like truffle symbiosis is a completely standard mycorrhizal symbiotic relationship.

  The truffle coats the tips of the tree roots to form mycorrhiza which
  act as an extension of the tree's root system. The tree provides the
  truffle with a source of photosynthesised carbohydrates, and in return
  the fine, thread-like filaments (mycelia) of the truffle, extract and
  trade soil minerals and nutrients which would normally be unavailable
  to the tree. Thus the mycorrhiza is able to increase the effectiveness
  of the trees roots, enabling the tree to grow in soils which would
  normally be too nutrient deficient to support them.


Would a vial of anticoagulated, warm blood attract mosquitoes? Would mosquitoes feed on free blood as an easy source of nutrients? They home in on veins by means of infrared light (heat detection). Also, blood needs to be in liquid form. So would they feed on anticoagulant-treated blood kept at 37oC? Or is there some physiological phenomenon that mosquitoes necessarily need to pierce something to draw in blood?

I am asking this, because just keeping a vial of blood at the end of a room might save us from mosquito bites.

According to wikipedia they locate "prey" by detecting CO2 and some other compounds, so I don't think mosquitoes will actually find the blood unless they're accidentally right on top of it.

And for your reason: if you have the equipment to regularly draw some blood, keep it at 37 C and have some anticoagulants on hand, you might be better off using some tried and true anti-mosquito tech (nets, insecticides, preventing them to breed in the local area).

Or maybe this: https://en.wikipedia.org/wiki/Mosquito_laser


Factor causing Methicilin-resistance in MRSA? I think the main reason is the natural selection that is causing methicillin-resistance.
However, I am not completely sure what this means practically.

Here, the original question:

MRSA was isolated in the throat secretion of patient hospitalized with bronchitis. Which of the following
statements best characterizes this microorganism?

a. its MIC is increased to methicillin, but not to penicillin
b. methicillin-resistance is associated with production of β-lactamases
c. Methicillin-resistance is caused by changes in configuration (mutation) of PBP

What is the right answer?

I think you can normally think about similar pressures leading to extended-spectrum beta-lactamase (ESBLs) and  methicillin/oxacillin-resistant Staphylococcus aureus (MRSA).

Going to the core of your question:

"Currently, the reported mechanism of methicillin resistance in S. aureus is the production of a distinctive penicillin binding protein 2a (PBP2a), which exhibits low affinity toward β-lactams"

But to really read on it you need to back to Liu et al.

Again Todar's is a great source for a good broad reading on staph including MRSA.

Response to Edit [inclusion of full question]:

TSDR: The answer is C.

Let's break down the three options given in the question and learn about MRSA along the way.

  a. its MIC is increased to methicillin, but not to penicillin

First, for people who may not know, MIC is short for minimum inhibitory concentration.  Simply, the MIC is a basic measurement of how much of any given agent is need to stop the growth of a bacterial colony.  Often we think of current medical antibiotics when thinking of MIC, but even simpler things like table salt and sugar have a MIC for a given species.  Thus this sentence is making the assertion that the bacteria found in the patent have an increased resistance to methicillin but not to penicillin.  This leads us to ask the obvious question:

Can Staphylococcus aureus (staph going forward) be methicillin resistant but not penicillin resistant?

This is a bit of a trick question, but let's break it down to the needed components: What is Methicillin, what is/are penicillin(s), and how are staph resistant to them.

First that it should be noted that penicillins can actually refer to a whole class of antibiotics which all use β-Lactam and the specific set of antibiotics:

  benzylpenicillin (penicillin G), procaine benzylpenicillin (procaine
  penicillin), benzathine benzylpenicillin (benzathine penicillin), and
  phenoxymethylpenicillin (penicillin V). (from wiki)

It should be noted that more correct way to address the whole class of antibiotics would be β-Lactam antibiotics, not penicillins, and that if you wanted to talk about more specifically penicillin derived compounds you would be discussing penams.  For even further clarification, penicillin as drug most likely refers to benzylpenicillin, and for the rest of this answer I will use penicillin to refer to benzylpenicillin.

Thus we should think of penicillin as an early antibodic that work by preventing the dividing/genesis of cell walls and certain organelles via binding to penicillin binding proteins (PBPs).

Methicillin is also a β-Lactam antibiotic, and it's MOA is similar to penicillin.  It was developed/discovered after penicillin and was seen a answer to Gram-positive bacteria that were breaking down penicillin via β-lactamase.  Methicillian still works by binding to PBPs, but it escapes the bacteria's counter to penicillin.

This leads us to address how penicillin resistance and methicillin resistance commonly occur in staph.  First, many staph strains and other bacteria use β-lactamases to breakdown antibiotics so they no longer can bind to PBP's (1).  But methicillin is particularly suited by its side chains to not be degraded by β-lactamases.  In their ground breaking work on the subject, Hartman and Tomasz identified that methicillin resistance was not in the acquisition of a β-lactamase, but in a mutation in PBP's that prevented methicillin binding (2).  There they tested 4 strains of staph, two were methicillin resistant (MR), and two were methicillian susceptible (MS).  You will note that all but 1 didn't have β-lactamase activity, and where more susceptible to penicillin than methicillin (ibid).

BUT this does not mean that MR strains are not also penicillin resistant, instead it shows that the resistance can be independent of each other.  Therefore "A" is wrong because it tries to draw a correlation that is not there.  In reality many MR strains are also β-lactamase positive.

This also address the problem with "B."  While it is possible that a β-lactamase could bind to methicilin and lead to degradation of the antibiotic, the main mechanism of methicillin resistance is the mutation of PBPs (ibid, 3), in particular BPB2a (4, 5).

We are then left with the task of figuring out why "C" is the correct choice.  Indeed "C" is the given reason for the failure of "A" and "B," but we can still go deeper into how and perhaps why BPB2a mutated.

For that I think it is best that we turn back to Chambers' review of the subject.  Forgive my over quoting, but it's done so well there and the text is now open.

  Methicillin resistance is associated with production of a novel PBP
  that is not present in susceptible staphylococci. Resistant strains of
  S. aureus produce an additional 78- kilodalton PBP (Fig. 1), termed
  PBP2a or PBP2' (assumed to be identical for the purposes of this
  review), that has a low binding affinity for beta-lactam antibiotics.

...

  PBP2a is highly conserved. Limited proteolysis of PBP2a from unrelated
  strains of S. aureus (123) and coagulasenegative staphylococci (31),
  whether homogeneous or heterogeneous, generates remarkably similar
  peptide fragments.

...

  Presumably PBP2a can substitute for essential PBPs when these have
  been saturated by drug and can perform the functions necessary for
  cell wall assembly (22, 122).

...

  In some strains, PBP2a is inducible by beta-lactam antibiotics and its
  production differs according to growth conditions (34, 122, 125, 159).

Unfortunately, they didn't quite have the staphylococcal cassette chromosome mec (SCCmec) figured out at that point.  The genetics is quite complex.

How does MRSA genetically accomplish resistance?

As we already established, the resistance comes from the production of an alternate PBP, PBP2a.  SCCmec is interesting for several reasons.  First of all, it's much larger than a plasmid, and contains information for several genes.  That's why it's called cassette chromosome.  Further it normally incorporates into the same part of the genome in staph, in an area know as OrfX (6).  This means that even during horizontal transfer, that the cassette has to direct it's integration into the genome, which is exceedingly uncommon, or at least there are not many other know examples (7, 8).  This cassette can be spread horizontally between staph, and even with other species (ibid, 9).  Even if the integration site (integration site sequence, ISS) is slightly different, this specificity is carried out by cassette chromosome recombinases (ccr), wich are also on SCCmec (8).  This is carried out by ccr-medated recombination of the target chromosome, and further details on the process are considered outside the scope of this question.

The actual gene that encodes PBP2a is called mecA.  But as we mentioned above, PBO2a production can be induced and regulated.  It is likely less favorable to produce it in the absence of antibodies, and after serial passage of bacteria in antibiotic free broth, you find that PBP2a expression can drop drastically.  Therefore regulatory and other useful proteins encoded by SCCmec.  When placed in a β-Lactamase environment, MecR1 causes a single transduction cascade to start transcription of mecA (10).  Conversely, MecI provides a negative feedback loop to MecR1, and in the absence of β-Lactamase, will lead to the down regulation of mecA (ibid, 11).  The actual action of MecR1 is to cleave MecI, thereby remove the suppression of mecA by MecI.  I actually learned something new when reading the wiki on MRSA, but didn't do further research on the subject:

  mecA is further controlled by two co-repressors, BlaI and BlaR1. blaI
  and blaR1 are homologous to mecI and mecR1, respectively, and normally
  function as regulators of blaZ, which is responsible for penicillin
  resistance. The DNA sequences bound by MecI and BlaI are
  identical; therefore, BlaI can also bind the mecA operator to
  repress transcription of mecA.

This represents the general pattern of resistance of MRSA, but there is a rich diversity in the particulars of how each strain manages expression.  Two of the main identifiers are how the mecA gene complex and ccr gene complex are configured (carriage).  The other two identifiers are the ISS and whether or not the ISS is repeated in the target chromosome (and how many times it's repeated) (8).  If we just consider the mecA and ccr carriage, then we get a great summary from IWG-SCC (ref 8):

  The mec gene complex is composed of mecA, its regulatory genes, and
  associated insertion sequences. The class A mec gene complex (class A
  mec) is the prototype complex, which contains mecA, the complete mecR1
  and mecI regulatory genes upstream of mecA, and the hypervariable
  region (HVR) and insertion sequence IS431 downstream of mecA. The
  class B mec gene complex is composed of mecA, a truncated mecR1
  resulting from the insertion of IS1272 upstream of mecA, and HVR and
  IS431 downstream of mecA. The class C mec gene complex contains mecA
  and truncated mecR1 by the insertion of IS431 upstream of mecA and HVR
  and IS431 downstream of mecA. There are two distinct class C mec gene
  complexes; in the class C1 mec gene complex, the IS431 upstream of
  mecA has the same orientation as the IS431 downstream of mecA (next to
  HVR), while in the class C2 mec gene complex, the orientation of IS431
  upstream of mecA is reversed. C1 and C2 are regarded as different mec
  gene complexes since they have likely evolved independently. The class
  D mec gene complex is composed of mecA and ΔmecR1 but does not carry
  an insertion sequence downstream of ΔmecR1 (as determined by PCR
  analysis).

And

  ccr gene complex.The ccr gene complex is composed of the ccr gene(s)
  and surrounding open reading frames (ORFs), several of which have
  unknown functions. Currently, three phylogenetically distinct ccr
  genes, ccrA, ccrB, and ccrC, have been identified in S. aureus with
  DNA sequence similarities below 50% (Fig. 2 and 3). The ccrA and ccrB
  genes that have been identified to date have been classified into four
  allotypes. In general, ccr genes with nucleotide identities more than
  85% are assigned to the same allotype, whereas ccr genes that belong
  to different allotypes show nucleotide identities between 60% and 82%.
  All ccrC variants identified to date have shown ≥87% similarity; thus,
  there is only one ccrC allotype. We suggest describing their
  differences as alleles by using previously used numbers, e.g., ccrC1
  allele 2 or ccrC1 allele 8.

All of this is nicely summarized in their table:

\begin{array} {|r|r|r|}
\hline
SCCmec ~type  &ccr ~gene ~complex  &mec ~gene  ~complex \\
\hline
I &1 ~(A1B1) &B \\
\hline
II &2 ~(A2B2)&A \\
\hline
III &2 ~(A3B3)&A \\
\hline
IV &2 ~(A2B2)&B \\
\hline
V &5 ~(C)&C2 \\
\hline
VI &4 ~(A4B4)&B \\
\hline
VII &5 ~(C)&C1 \\
\hline
VIII &4 ~(A4B4)&A \\
\hline
\end{array}

To sum up, methicillin-resistance is caused by the encoding of a novel PBP, PBP2a, along with other factors, which is both genetically stable and transferable via the use of SCCmec.

References:

(1) Pathak A et al. High prevalence of extended-spectrum β-lactamase-producing pathogens: results of a surveillance study in two hospitals in Ujjain, India. Infect Drug Resist. 2012;5:65-73. doi: 10.2147/IDR.S30043. Epub 2012 Apr 5. [Note that many of the great sentinel studies on drug resistant bacteria occur in the massive hospitals in India].

(2) B Hartman and A Tomasz. Altered penicillin-binding proteins in methicillin-resistant strains of Staphylococcus aureus. Antimicrob Agents Chemother. 1981 May; 19(5): 726–735.

(3) Liu, H. et al. Detection of borderline oxacillin-resistant Staphylococcus aureus and differentiation from methicillin-resistant strains. Eur J Clin Microbiol Infect Dis. 1990 Oct;9(10):717-24.

(4) Tawil N. et al. The differential detection of methicillin-resistant, methicillin-susceptible and borderline oxacillin-resistant Staphylococcus aureus by surface plasmon resonance.  Biosens Bioelectron. 2013 Nov 15;49:334-40. doi: 10.1016/j.bios.2013.05.031. Epub 2013 Jun 4.

(5) Chambers HF. Methicillin-resistant staphylococci. Clin Microbiol Rev. 1988 Apr;1(2):173-86.

(6) Huletsky A et al.  New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J Clin Microbiol. 2004;42(5):1875-84. DOI: 10.1128/JCM.42.5.1875-1884.2004

(7) Schoenfelder SM et al. Success through diversity - how Staphylococcus epidermidis establishes as a nosocomial pathogen. Int J Med Microbiol. 2010 Aug;300(6):380-6. doi: 10.1016/j.ijmm.2010.04.011. Epub 2010 May 6.

(8) IWG-SCC. Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements.  Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7. doi: 10.1128/AAC.00579-09. Epub 2009 Aug 31.

(9) Stürenburg E. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations.  Ger Med Sci. 2009 Jul 6;7:Doc06. doi: 10.3205/000065.

(10) Jensen SO and Lyon BR. "Genetics of antimicrobial resistance in Staphylococcus aureus". Future Microbiol 4 (5): 565–82. doi:10.2217/fmb.09.30. PMID 19492967

(11) Oliveira DC, de Lencastre H.  Methicillin-resistance in Staphylococcus aureus is not affected by the overexpression in trans of the mecA gene repressor: a surprising observation. PLoS One. 2011;6(8):e23287. doi: 10.1371/journal.pone.0023287. Epub 2011 Aug 2.


Identifying a tree with an image I have trouble identifying a tree that I saw on a vacation. This is the image:

I would like to know the name of the tree, I only know that its not European.

The fruit strongly resembles immature lychee (Litchi chinensis). Since I have only seen the fruit, I cannot comment on whether the flower looks correct. The flowers appear to be slightly different from those in Wikipedia, especially in the number of "stamens"(?) per flower.


What is this spider hunting in the tree in the night? I took the following picture of this spider in northern Switzerland (alt: ~700m) with macro flash/lense.

The picture was taken during the night in a cedar tree (Thuja occidentalis).

It's look like Sac Spider (Clubiona lutescens) to me.

Source: http://ednieuw.home.xs4all.nl/Spiders/Clubionidae/Clubionidae.htm


Why are humans so variable in appearance Most animals look almost identical to their peers. To distinguish lions we record the spots on their face; with whales we look at the blemishes on their tail or flukes. In other words, we have to try hard to distinguish one lion from another.

In the case of dogs, we have created many different looking breeds - but within each breed they look the same: one poodle looks very much like the next one.

On the other hand, with humans we have not only the different races (cf. dog breeds), but even within one race no two people are alike. And, not only are the faces different, the body shapes vary equally much. We use face and body shape (and voice) to recognise each other. Most other animals use smell or sound.

I thought the reason for our uniqueness might be that, with civilisation, we are not constrained us to look the same. However, even in hunter-gatherer tribes each person looks different from every other one.

So what is it in human evolution that made us unique in this regard? And, are we unique? I cannot think of any other species with as much variation as ours, but are there others?

Because we as humans are really really good at picking up small differences in humans and really really bad at detecting them in anything else.

Animals are often quite good at telling each other apart, far better than humans are, birds in particular are known for this. Just because you as a human are bad at it does not mean they are.

There is a pretty strong evolutionary pressure for humans to be able to tell other humans apart and not much of an advantage for being able to tell two lions apart. We need to be able to tell mates, rivals, relatives, and strangers apart easily. We don't need to differentiating one black bird from another.

We also spend a lot of time around other humans, so we are more familiar with their differences, but the same thing happens to animal researchers whale researchers who spend a lot of time around whales can easily tell two whales apart at a glance. this is also part of the reason some people have trouble telling individuals from a different "race" apart, they are to unfamiliar and uninterested to spot differences. Or the way a car guy can spot the difference between two models at a diffrence but someone else might not.

You see the same effect chimps can tell each other apart but can't tell humans apart, unless they spend a lot of time around humans then they can. They can also match voice to face meaning the can recognize both.

Then of course you have the fact you are focusing on vision, try to tell two people apart by smell and you will likely fail but a dog will have no problem with it. likewise many monogamous song birds can identify their mates from song along, just as we recognize others by voice, penguins are another example. Humans are very visual creatures so much of our identification ability relies on vision we see the same thing in other visual species, animals tend to use whichever sense are their dominant ones. Saying organisms are more visually similar because organisms with far worse vision than humans can't tell them apart by vision alone is simply an unreasonable conclusion.