text:
How do biological communities at deep-ocean hydrothermal vents migrate between vents?
Much interest in the astrobiology community has been generated by the discovery of biological communities populating deep-ocean hydrothermal vents (i.e. "black smokers"). (1) These ecosystems rely on chemoautotrophic bacteria/archaea extremophiles as primary producers living at 40-80 C temperatures.
However, the lifetimes of these black smokers have been estimated to be of order 25 years. How  are these biological communities able to migrate to newer, active vent systems in conditions of extreme cold and high pressure?
(1) Lonsdale, P., 1977, Deep Sea Research, 24, 9

Interesting question.  I don't think the pressure would be a problem unless they have an air-filled cavity equalized to a lower pressure (which I can't imagine these organisms would have) or if the dispersal required rapid movement to other depths.  As far as I understand it, if you live in water and are filled with water then pressure is no big deal.

Yes, I am sure that the temperature would be more of a challenge.

I did some research on the topic and came accross this paper by Johnson et al. I am not a zoologist, so everything I write here is taken from the references paper.
The authors used genetics to estimate gene flow between different populations of limpets Lepetodrilus fucensis which is considered to be an endemic hydrothermal vent animal. They used a mathematical demographic model "isolation with migration" to estimate the migration of the animals across different biotopes.
The vents are distributed along the ridge segments and can be seen as small islands isolated by tens of kms from each other along the same ridge segment and thousands of kilometers between distinct ridges.
The results suggest that there is certain migration between the adjacent vent locations, that means that the flora of one vent can indeed survive the distance towards the next most proximal vent.

So, from now on is my pure speculation. Since the distance between single vents along the same ridge segment seems not be to so high we can suggest that these organisms are capable to resist the pressure and temperature on the ocean bottom while travelling from one vent to another...

I think you mean "fauna of the vent" rather than "flora".

Following up on Alexander's response, I read a little more on the subject by looking at some of the references in the Johnson et al. paper.
This paper  discusses an interesting case where researchers could study a hydrothermal vent ecology before and after a catastrophic eruption giving a "natural clearance" experiment. Since endemic organisms were eradicated, any pioneer species must come from other vent systems.
A number of species, in the form of larvae caught in larval traps, were observed to arrive at the vent. These species, including Cyathermia naticoides, Lepetodrilus spp and Gorgoleptis spiralis, arrived at a significantly different (P < 0.05, MANOVA and ANOVA) rate to the pre-eruption larval source population rate. Larvae of one gastropod species, Ctenopelta porifera, which had been seen only once pre-eruption, arrived in significant numbers post eruption. The source of these larvae may have been from a vent 300 km away.
These authors associate this change in the populations pre- and post-eruption with the specifics of the hydrodynamic transport processes operating in the region.
A more general sequence of vent re-population is given in this article.
However, the interesting thing for me was the significant, but changing fluxes of larval species at these deep-sea vents.


text:
Does current evidence support the use of resveratrol as an anti-ageing drug?
A while back there was a lot of noise about resveratrol, a naturally occurring phenol which was touted as a potential anti-aging drug due to its role in regulating the SIRT 1 gene. A number of studies suggested that it could extend the lifespans of model organisms such as D. melanogaster and C. elegans.
Has there been any follow up on this? Have there been any human trials?

It's worth noting that earlier this month a large body of resveratrol research was retracted:

The University of Connecticut, in what clearly seems like an attempt to get ahead of damaging news, has announced an “extensive”
  investigation into research misconduct involving one of its
  scientists, Dipak K. Das.
According to a press release, the university has notified 11 journals
  that published Das’ work about the alleged fraud. One area of interest
  for Das, a government-funded professor of surgery and director of the
  Cardiovascular Research Center, has been resveratrol, a substance in
  red wine that has allegedly been linked to improved cardiac health.

Retraction Watch's coverage has been pretty thorough and includes comments and citations:

UConn resveratrol researcher Dipak Das fingered in sweeping
misconduct case
So how peripheral was Dipak Das’ resveratrol
work, really?
Resveratrol fraud case update: Dipak Das loses
editor’s chair, lawyer issues statement refuting all charges

Yes, that was huge. Nevertheless, I know very honest people (in other institutions) that have found interesting results using resveratrol both in vitro and in animal models. Although a revisit of the literature will be needed, the field should not be ignored by the acts of one rotten lab.

I'm hesitant to upvote this answer. Much of the discussion on Resveratrol and proof of concepts of its pharmacodynamics don't come from Das's lab.

@bobthejoe someone needs to outline the evidence from other groups here as an answer then. I'll upvote a well sourced answer

If you search clinicaltrials.gov (maintained by the NIH) for "resveratrol", you'll find 44 clinical trials, many of them ongoing or not yet started.
A recent review by Smoliga JM et al states in the abstract:

"Although the supporting research in laboratory models is quite substantial, only recently data has emerged to describe the effects of resveratrol supplementation on physiological responses in humans. The limited number of human clinical trials that are available has largely described various aspects of resveratrol's safety and bioavailability, reaching a consensus that it is generally well-tolerated, but have poor bioavailability. Very few published human studies have explored the ability of resveratrol to achieve the physiological benefits that have been observed in laboratory models, although many clinical trials have recently been initiated."

Resveratrol has recently been shown to induce cellular senescence (at least at high concentrations, see here) which has the potential to accelerate ageing.  Senescent cells display and highly inflammatory phenotype which could damage tissues if not removed.  However, Resveratrol itself is rapidly metabolised and it may be these metabolites that have health benefits, but this needs to be researched further.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Why are amino acids in biology homochiral?
Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?

It's no answer, but Radiolab had a great discussion of chirality and the issue you've brought up. Worth a listen: http://www.radiolab.org/2011/apr/18/mirror-mirror/

@yamad.  The site you link to contains the line 'all living molecules are left-handed'. This, of course, is nonsense.

@TomD ha, fair enough. Oversimplifications aside, though, I still like the piece because my memory is that they do a good job giving an intuitive feel for what chirality is and its effects. Of course, its likely that they make more frustrating oversimplifications and I missed them or forgave them in my rapture that a popular show was willing to dig pretty deeply into an idea like chirality for entertainment purposes. Sometimes Radiolab makes major missteps, but in general, I think their stuff is pretty solid as far as popular accounts of tricky scientific concepts go.

I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very important pharmaceutical properties. I recommend this (1) review article if you are interested in the subject. It is also worth mentioning that D-alanine and D-glutamine are incorporated into the peptidoglycane of bacteria.
I read several papers (2, 3, 4) that discuss the problem of chirality but all of them conclude that there is no apparent reason why we live in the L-world. The L-amino acids should not have chemical advantages over the D-amino acids, as biocs already pointed out.
Reasons for the occurrence of the twenty coded protein amino acids (2) has an informative and interesting outline. This is the paragraph on the topic of chirality:

This is related to the question of the origin of optical
activity in living organisms on which there is a very
large literature (Bonner 1972; Norden 1978; Brack and
Spack 1980). We do not propose to deal with this
question here, except to note that arguments presented
in this paper would apply to organisms constructed from
either D or L amino acids.

It might be possible that both L and D lives were present (L/D-amino acids, L/D-enzymes recognizing L/D-substrates), but, by random chance the L-world outcompeted the D-world.
I also found the same question in a forum where one of the answers seems intriguing. I cannot comment on the reliability of the answer, but hopefully someone will have the expertise to do so:

One, our galaxy has a chiral spin and a magnetic orientation, which causes cosmic dust particles to polarize starlight as circularly polarized in one direction only. This circularly polarized light degrades D enantiomers of amino acids more than L enantiomers, and this effect is clear when analyzing the amino acids found on comets and meteors. This explains why, at least in the milky way, L enantiomers are preferred.
Two, although gravity, electromagnetism, and the strong nuclear force are achiral, the weak nuclear force (radioactive decay) is chiral. During beta decay, the emitted electrons preferentially favor one kind of spin. That's right, the parity of the universe is not conserved in nuclear decay. These chiral electrons once again preferrentially degrade D amino acids vs. L amino acids.
Thus due to the chirality of sunlight and the chirality of nuclear radiation, L amino acids are the more stable enantiomers and therefore are favored for abiogenesis.

BIOSYNTHESIS OF NONRIBOSOMAL PEPTIDES

Reasons for the occurrence of the twenty coded protein amino acids

Molecular Basis for Chiral Selection in RNA Aminoacylation

How nature deals with stereoisomers

The adaptation of diastereomeric S-prolyl dipeptide derivatives to the quantitative estimation of R- and S-leucine enantiomers. Bonner WA, 1972

The asymmetry of life. Nordén B, 1978

Beta-Structures of polypeptides with L- and D-residues. Part III. Experimental evidences for enrichment in enantiomer. Brack A, Spach G, 1980

Thanks Gergana. I'll follow some of this up. I can comment on the astronomy angle later.

Hope these papers are helpful. Let me know what you have found.

Because I was bored, I found and added links to the citations from "Reasons for the occurrence of the twenty coded protein amino acids"

The ribosome holds the peptide-bound tRNA and aminoacyl-tRNA in the right orientation to catalyze the peptidyltransferase reaction.
http://www.pnas.org/content/103/36/13327/F1.expansion.html
If the incoming aminoacyl-tRNA was the other enantiomer, the amino acid moiety would not fit properly into the ribosome active site.  In other words, the shape of the ribosome selects for specific amino acid enantiomers.  In abiotic mixes, the creation of amino acids and their polymerization is non-catalytic, and so there is no specificity or selection for certain enantiomers.
If you're asking the "biogenesis" question, then I think the answer is that we don't know the original selection, and it may just be chance.  But once biochemistry began making and using them, of course they were all the same.  But frankly "why not D-amino acids" makes about as much sense as "why not 22 amino acids, or 23, or 24, or 25?"  Because that's what happened.

Thanks for the answer @KAM. However, i don't buy your criticism of the biogenesis aspect to the question! Sure,it may have been that "by chance" L-amino acids got selected, but the fact that all life now only uses L-aminos is intriguing. Given an equal probability of L and D aminos, this suggests that life only arose one from L-aminos, or that L-amino life managed to outcompete and eradicate D-amino life. Either possibility sends us in interesting directions.

But, you still get an upvote ;-)

As far as I know, it is unknown why we only see left-handed and not right–handed amino acids. A recent article speculates that the weak force could be responsible for a tiny asymmetry in energy levels between the stereo-isomers. However, if the effect is tiny, its hard to see why it should have biological implications. In 2004, Tamura and Schimmel showed that RNA has a preference for L-amino acids, whereas mirrored RNA has a preference for D-amino acids. They conclude:

These results suggest the possibility that the selection of L-amino acids for proteins was determined by the stereochemistry of RNA.

So the next question is: Why do we observe only one kind of RNA? It could just be by chance, that a polymer of one RNA configuration became self-replicating.

The chirality of RNA enforces the chirality of amino acids, neat. I wonder if there is mirror RNA out there, because the penalty for being mirrored is lower? (is it lower?)

The normal results of an attempt to assemble proteins with mixed chiral amino acids is a protein that fails to fold.
The general assumption due to this result is a choice has to be made very early on to use all right-handed or all left-handed amino acids. There doesn't seem to be any particular reason to choose one way over the other except for prevalence.

Using only 1 chirality for the ecosystem simplifies protein formation and folding frameworks. In theory, you could have a codon system with 40 distinct values (and 24 redundant values): glycine, stop codon, and left/right variations of each other amino acid. However, the proteins and nano-"machinery" required to support this would be crazy complex. It's much more efficient to build around 1 chirality and stick with it.
Alternately, you could have enzymes specifically designed to flip proteins of the "wrong" chirality depending on species.
With that in mind, an ecosystem with different species having different amino acid chirality would be digestive chaos. If you eat a dextro-protein steak, your digestion will break the proteins into... dextro amino acids. Best outcome: they fail to absorb and get flushed down the toilet. Worst outcome: they get absorbed and your cells use them to make proteins - causing severe folding errors, nonfunctional proteins, and a host of untraceable health problems that would likely get misdiagnosed as a spirochaete infection (wide-ranging health problems that aren't limited to a specific region and have no discernible pattern).

Addendum: your immune cells might identify nonfunctional/malformed proteins produced from consuming dextro-amino acids as dangerous foreign matter/invaders, causing widespread allergies

Most answers to the question of homochirality have considered the reason (if any) for amino acids in proteins being L rather than D. i.e. Why L? I have nothing further to add to that discussion.
A couple of answers have addressed the question of why there is not a mixture of L- and D- amino acids in proteins, i.e. Why all L? Two distinct arguments have emerged. I shall consider them in turn, and attempt to develop them a little further.
@Joshua stated that “the results of an attempt to assemble proteins with mixed chiral amino acids is a protein that fails to fold”. I think one can cast this more precisely in evolutionary terms. The α-helical secondary structure component of proteins probably arose early as it involves only the protein backbone, rather than the particular amino acid side-chain. Nevertheless, it is not possible to substitute a D-amino acid in an α-helix of L-amino acids, without disrupting the structure. Hence one can suppose that homochirality was necessary for the creation of standard ‘building blocks’ for early protein development.
@KAM has considered the question of the stereochemistry of the active site, specifically that of the peptidyl transferase. The stereochemistry of the active site of the interaction of enzymes with their substrates is a strong argument for homochirality, but it struck me that this needs to be addressed before peptide-bond formation — in the synthesis of the amino acids themselves.
It turns out that I was late to the party. In the 2002 edition (I haven’t checked earlier ones) of the text book, “Biochemistry”, by Berg et al., section 24.2.2 of the chapter on amino acid synthesis is entitled:
A common step determines the chirality of all amino acids
Amino acids are synthesized, directly or indirectly, via reactions catalysed by transaminases (aminotransferases) which convert keto-acids to amino acids:
Oxaloacetate → Asp → (Asn, Met, (Thr→Ile), Lys)
Pyruvate → (Ala, Val, Leu)
Phosphoenol pyruvate → (Phe, Tyr, Trp)
α-Ketoglutarate → Glu → (Gln, Pro, Arg)
3-Phosphoglycerate → Ser → (Cys, Gly)
Ribose 5-phosphate → His
These transaminases have a similar active site involving a lysine and arginine residue and use the cofactor, pyridoxal phosphate. The reaction mechanism (below) may appear a little complex, but the step at which the chirality of the amino acid is determined is the conversion of quinoid intermediate to external aldimine:

To quote from Berg et al. (from which the diagrams are taken):

The chirality of the amino acid formed is determined by the direction
from which this proton is added to the quinonoid form. This
protonation step determines the l configuration of the amino acids
produced. The interaction between the conserved arginine residue and
the α-carboxylate group helps orient the substrate so that, when the
lysine residue transfers a proton to the face of the quinonoid
intermediate, it generates an aldimine with an L configuration at the
Cα center.

So it would seem more likely that the stereochemistry of the active site of peptidyl transferase was an evolutionary response to the existing homochirality  of amino acids, rather than vice versa.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is there any convincing evidence for the existence of nanobacteria?
The existence of nanometer scale microorganisms has been proposed and used explain several phenomena  including morphological structures in a martian meteorite (ALH 84001) and implication in the formation of kidney stones (1).
Is there now any consensus in the biology community whether these are biotic or abiotic in nature?
(1) Kajander EO, Ciftcioglu N (1998) Nanobacteria: An alternative mechanism for pathogenic intra- and extracellular calcification and stone formation. Proc Natl Acad Sci U S A 95: 8274–8279

There are two convincing papers (1,2) arguing that the observed "nanobacteria" are in fact mineral/protein complexes and not any living organisms.
In (1) Martel and Young created very similar looking particles from calcium carbonate in vitro. The calcium carbonate precipitations can even look similar to dividing cells:

After 5 days of serum incubation, a white precipitate formed and
  adhered on the bottom of each flask. When examined by scanning
  electron microscopy (SEM) and transmission electron microscopy (TEM),
  the precipitate was seen to consist of particles with a size ≈500 nm
  (Fig. 1 A, B, and E), an observation consistent with normal bacterial
  morphology, which peaks at one particular size specific to the strain
  on hand. Some forms resembled cells undergoing division (Fig. 1 D,
  arrow).

One strong argument against those nanobacteria being living organisms is that they don't seem to contain any nucleic acids. Of course non-DNA based organisms are theoretically feasible, but that would be an absolutely extraordinary discovery.
The autors of (1) also observed these particles after filtration through a 0.1um filter. They argue that this size could not be sufficient to contain all the cellular machinery bacteria need:

Because an earlier workshop commissioned by the NAS had suggested that
  the minimal cellular size of life on Earth must exceed 200 nm in
  diameter to harbor the cellular machinery based on DNA replication
  (19), it is unlikely that nanobacteria represent living entities
  unless they contain some other type of replicating mechanism.

(1) Martel J and Young JD, Purported nanobacteria in human blood as calcium carbonate nanoparticles. PNAS 2008, 105(14):5549-54
(2) Raoult D. et al., Nanobacteria Are Mineralo Fetuin Complexes, PLoS Pathog. 2008, 4(2): e41.

It would be very illustrative if you could post the actual figures shown in these papers.


text:
How are the boundaries of a gene determined?
What statistical processes and methods are used by geneticists/molecular biologists to know where one gene starts and one ends?

What does the "basic" tag refer to?

I thought that the question was more of a foundational one to seed the group, so I tagged it basic . If that's not protocol, please feel free to remove.

Just to clarify: we’re talking about protein-coding genes here, right? There are many more for which the methods are completely different.

@KonradRudolph could you perhaps reference the other gene types and methods? Thanks.

@ghchinoy Just as an example, I’m currently working on tRNA genes and since they’re using a different polymerase their promoter and termination site look markedly different. The same is true for all the other non-coding RNAs and then there are things like pseudogenes and LINEs/SINEs (those are not usually considered genes but due to their similarity to non-coding RNA genes they complicate the analysis). Still, there actually are bioinformatical methods to find those genes. They predominantly use motif search as far as I know.

I know of only one naive approach to determining the boundaries of a gene : RACE-PCR. There are two kinds, 3' and 5' RACE, which allow to find the respective extremities.
The rationale is the following :

You perform a reverse transcription of the transcript of interest using a specific primer. At this step you have a specific single stranded cDNA.
Then you add a stretch of identical nucleotides called the homopolymeric tail in 5' of the cDNA.
Finally you perform a PCR using one specific primer and one universal primer that recognizes the homopolymeric tail. You can sequence your amplified cDNA and find where it is located in the genome with a 1 bp resolution.

For the 3'RACE, the concept is the same but the poly-A tail is used instead of generating it yourself with the terminal transferase.
See this paper for a detailed protocol :
 Sambrook J, Russell DW. 2006. Rapid Amplification of 5’ cDNA Ends (5'-RACE). CSH protocols 2006.
Also, the corresponding wikipedia article gives you more details about what is happening at each step, but beware, there is an error : it is said that for the 5'RACE, the terminal transferase appends the homopolymeric tail in 3' while it appends it in 5'

-1: that may be a good approach to see the boundaries of an ORF (to be honest, you don't always need a RACE, a simple PCR may work as well), not of a gene. What about promoter and regulatory elements? Also, what is the advantage compared, say, to a bioinformatics approach after sequencing?

@nico : so, with the definition you provide, a gene has no boundaries.

@nico : Ok, I see your point, but I don't think the OP had this definition of a gene in mind. Also, I totally agree that new technologies such as RNA-seq give you a more comprehensive answer for genome annotation.

we can discuss for hours about the correct definition of a gene, but I don't think there is much to discuss about the fact that the promoter is part of a gene. And by retrotranscription of mRNA you don't get the promoter.

There are various software in which you can enter your sequence (let's say the whole genome sequence) and it can identify for you the putative open reading frames (ORFs), i.e. the start codons and the stop codons. Then, by using these putative genes, you can do a sequence alignment by using BLAST and then, based on the scores you can confirm that those are really ORFs. As this being the statistical approach, you can then verify your results in the wet lab, like agrimaldi suggested.

But how do those software determine gene boundaries? What are they looking for that is indicative of a gene boundary?

Maybe another question should be started specifically about what programmatic techniques are used? Maybe with a bioinformatics tag.

@RichardSmith They are basically looking for start codons (ATG, GTG) that define the beginning of the open reading frame (ORF), and stop codons (TAG, TAA, TGA), that define the end of the ORF, and also checks whether the number of bases between the start codon and the stop codon is devisible by 3.

@ghchinoy Yes, that could be interesting, but I don't think it is more complicated than I already explained to Richard. You can of course add a few more "checks" the software can do, like the length of the ORF.

If your goal is to define the boundaries of the transcription unit (the part of the DNA that is transcribed) the above answer is accurate, although many people merely use homology to cloned cDNAs rather than RACE reactions.  This approach has the benefit of defining alternative splice forms at the same time.
If your goal is to define the "ends" of the gene, it can only be done empirically and functionally because control elements (boundaries, enhancers, etc) are impossible to recognize using informatics, and even if one finds enhancers, it's not certain that those enhancers are used with specific genes.  Some genes can be millions of base pairs long, so have hundreds of others genes interspersed.  The "gold standard" for defining the boundaries of genes is to rescue the loss-of-function phenotype of a mutation with a transgene that contains the gene of interest.  If the DNA that is transformed back into an organism can recover the wild-type condition of a mutation of a gene, it is assumed that all of the important parts of that gene are within the transgene.

Generally speaking you sequence the genome and then search for clues. There are usually specific sequences preceding a gene that help the translational equipment know "hello this is where we begin" as well as regions where proteins can bind that are used to enhance or inhibit translation of the gene.
Computers can be programmed to search through the sequence and bring up possible candidates for people to look at more closely.


text:
Why can you graft two unrelated cacti successfully, but you cannot do this on garden trees?
Any cactus can be grafted onto any other cactus, and even the most unlike of them grow together. My latest graft was a Schlumbergera truncata scion on an Opuntia microdasys rootstock. This kind of graft is always successful. Why can't garden trees be grafted in a similar way, between genera?

Firstly, different genera of trees can occasionally be successfully grafted. For example, quince, genus Cydonia, may be used as a dwarfing rootstock for pear, genus Pyrus.
However, it is true to say that this is the exception rather than the rule.
In the case of plants in the family Cactaceae, I would suggest that grafting is usually successful for two main reasons:

Genetic similarity. Plants in the family Cactaceae while known to be morphologically often very different, have relatively little genetic diversity. This will increase the likelyhood of a successful graft.
Ease of aligning vascular cambium. This is required for a successful graft, and in Cacti this is quite easy to achieve since the cambium is clearly visible when you prepare the scion and stock.

It is also possible that Cacti readily form callus tissue, which would also aid in the grafting process.
Nyffeler, R., 2002, doi: 10.3732/ajb.89.2.312 Am. J. Bot. 1 February 2002 vol. 89 no. 2 312-326

just to add my link.  This guy has patiently grafted 11 fruit to a single tree.  http://inventorspot.com/articles/lemon_tree_japan_bears_eleven_ki_9572

Interesting. However, it looks like they are all from the same Genus - Citrus.


text:
Do we know abiogenesis only happened once on earth?
Do we know that abiogenesis happened only once on earth? Do biologists know that all life originates from a common ancestor?
If so, is this considered a sign that abiogenesis is rare even in under generous conditions like a habitable zone?

No, we don't. Abiogenesis has never been observed, ever, so it must be rare. There are a lot of questions about this; searching the tag will get you plenty to chew on. :)

Does this answer your question? Is abiogenesis possible today? (Just one example of many.)

Also for abiogenesis to be noticed, it will have to evolve  completely different structures and metabolic pathways (non-carbon based or non-DNA,non-RNA based) to avoid competition for resources. Otherwise it might also be dismissed  as  a result of general evolution.

we have some evidence all extant life has the same origin due to codon mapping, but there could easily have been several competing life linages on the early earth. indeed all life extant life could come from the merging of different simple lineages.

We don't even know IF abiogenesis happened on Earth, let alone how many times. Most evidence suggests that all Extant life on the planet evolved from a universal common ancestor, but that isn't necessarily evidence that abiogenesis is rare. For one thing, if multiple branches of life arose independently, they would likely still utilize similar resources, thus competitive exclusion could take place. And what counts as rare may also be subjective. What's rare on the scale of recorded history may not be so rare on cosmic timescales.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
What insect is this with 'horn' at the side?
Found this interesting insect hiding behind the thin branch of flower (the diameter of the branch is 3-4mm) in my garden in Kuching, Sarawak, Malaysia

@Karl Kjer It's most likely a Leptocentrus taurus, even though the perspective in the photo doesn't allow to observe the prominent dorsal thorn.
https://www.flickr.com/photos/some_soul/15316794326
https://indiabiodiversity.org/observation/list?count=0&hasMore=true&max=10&offset=0&sort=lastrevised&taxon=72846&view=list
Ants are always trying to come in contact with these mimic treehoppers for collecting the sweet juices secreted by them. Maybe the OP can confirm that.

That is a treehopper. Order Hemptera, family Membracidae. I looked on a site for membracids of Malaysia, and could not bring it to species-level. But I am confident that it is a membracid. This family is characterized by sometimes bizarre protrusions of the pronotum.
https://en.wikipedia.org/wiki/Treehopper


text:
What creature is this?

Found on a beach in Brisbane, Australia. Only a few cms of it was visible but I dug the rest of it out, it was about 20cm in length.

That is a Priapulid worm, also known as a "penis worm". In its own phylum, Priapulida. https://en.wikipedia.org/wiki/Priapulida

Thanks, I would never have worked it out as it is quite different looking from the other photos of Priapulid worms available through google search (i.e. I couldn't find an example of a similar looking specimen). Thanks for helping.


text:
Do plants have distinctive DNA genomes from each other like humans do?
Can exact same species of plant have a distinct genome from others of same exact species growing nearby or in a different place/country etc. ?
Can a leaf be traced to the the exact plant based on DNA if we were to be given DNA of the "parent" plant of the leaf, and two test plants' DNA of exactly the same species?

It's kind of an interesting question. The answer is yes for sexually reproducing species of plants, but plants that reproduce clonally can form massive genetically identical colonies

probably yes for both sexually and asesually reproducing plants as well as i am taking a wild guess on cloned species also, because of natural and artificial mutations.

Short answer: Yes!
Now for the longer answer. Yes, they do have distinct genes in general, but what you may see as different plants can also sometimes be clones. For example Quaking Aspen Trees which commonly grow in clonal colonies.
If you had a massive database of genetic material from plants you would be able to trace it. You may be able to, by doing sampling, work out where a sample was located geographically.

We need to distinguish plants which replicate by sexual reproduction from those who reproduce asexual.
Due to the higher recombination rate in sexual reproduction it should be easy to find your plant to which the leaf corresponds to. Because you can see lot of single nucleotide polymorphisms and maybe other changes in the DNA unique to the plant whose leaf you found.
If your plant species reproduce by vegetative reproduction it could be more difficult because you can not find a lot of DNA changes making your plant unique. But since there are some mutations in DNA from vegetative reproducing plants (see here and here) you probably should try to find them.


text:
What is this black insect?
  I found it in my computer but I don't know what it is

Please provide your location and the approximate size of the bug you found. Thanks.

It appears to be a Boxelder bug, which are common in areas of North America with maples, ash, or other host trees:
 (photo by Katja Schulz via Wikimedia Commons)

A hemipteran, yes, but the OP's specimen has quite different color patterns than the species you suggest. Can you explain the difference in colors or provide stronger support for why Boisea trivittata is the correct answer despite these morphological differences?


text:
Symbiosis of Pseudomonas Fluorescens
Have a modest background in molecular biology and presently considering a project that requires some knowledge of botany.  Specifically, I seek details on the epiphytic relation between the microbe pseudomonas fluorescens and flowering plants such as the orchid and rose.
    * What would be the relationship?  Commensalism or Mutualism?
    * What is the nutrient source for Pseudomas? Life Span?
    * What becomes of the metabolic end products from Pseudomonas?
    * Does the plant alter its surface properties to accommodate Pseudomonas?


text:
What conditions should I use for Gel Red staining?
What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often indistinguishable. We have tried both pre- and post-staining, together with varying concentrations of Gel Red.
Any advice about how to fix this problem?

Are you sure it's the staining, and not the gels themselves that are the problem?

What wavelength and filter set are you using for visualizing your gels?

I have had success with 1.5% agarose gels in TBE pre-stained with gelred.  I use a 10,000x stock solution of gelred sold by http://biotium.com.  I visualize the gel on an old fotodyne UV transilluminator.
After melting agarose in the appropriate volume of TBE in a microwave, I let it cool to about 50 C (I can touch the flask with the back of my hand without snatching it away) and then add the appropriate volume of stock gelred.
For a 30 mL 1.5% agarose gel:

mix 0.45g agarose + 30 mL 1x TBE
microwave until agarose solution boils and clarifies
let cool to around 50 C
add 3 uL gelred
swirl the mixture
cast the gel (don't forget comb)

This typically works for me.  I run the gel in a 1x TBE buffer at around 120 volts.

i've also had the best resolution with pre-stained gels.  Even so, its better to take long time exposures of the gels on UV sometimes.  Hi Mac!

I don't think you should need to vary the concentration of the GelRed.  Mine came with instructions for the exact concentration and how to dilute.  Optionally salt can be added, which I did, and it has worked for me.
I have only done this with Post-staining.  1-2.5% agarose with TAE.  Used a 10,000x solution from Phenix research. The gelred stock and working solution needs to kept in the dark.  I am assuming you have a transilluminator and (optional) filters to visual though. GelRed has similar excitation and emission [wavelength] properties as EtBr, so a standard transilluminator and filter should work without any changes.  It will not be visible with the naked eye.
That being said there are a ton of things that can go wrong in casting the gel, eletrophoresis, staining, and visualization.  If bands are visible but just blurry I was suspect there is more of a problem with either the gel creation or eletrophoresis though. Make sure agarose is completely clear and cooled down a little before pouring. Otherwise voltage is one of the main things I have noticed that can have significant affects on how sharp or blurry bands appear.  You might try different % gels and different voltages.  There are formulas that can help you estimate the best value for each of those.


text:
What is Curved DNA?
CbpA is DNA binding protein found in E. coli and binds non-specifically to curved DNA (Cosgriff et al., 2010), when the bacterium is in a static phase of growth.
The use of "curved DNA" confuses me. Is the term "curved DNA" essentially the same as "Circular DNA"?

Cosgriff, S. et al. Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA. Mol. Microbiol. 77, 1289–1300 (2010).

It might be useful to link the source where you read the term, it could provide additional context that would be helpful for answering the question.

I've provided a link to the reference and unipot

it is not necessarily circular - the transcription factors usually require a curvature that is much greater than what a plasmid will have, and the requirement can show up on eukaryotic proteins as well.  DNA binding proteins will cause a local loop or curvature that fit the transcription factor.
The classic picture is for the Gal and Lac repressor proteins which bind 2 strands simultaneously, causing a loop in the DNA.
Reference: see fig 1 in:
http://genesdev.cshlp.org/content/3/5/606.full.pdf+html

I'm hardly an authority on this topic, but I distinctly recall an amazing report the mid-1990s of the co-crystal structure the yeast TATA binding protein in complex with DNA.  The structure shows that TBP bends the DNA axis by approximately 80 degrees, presumably in order to expose bases and improve recognition.  The structure is available at RCSB: http://www.rcsb.org/pdb/explore.do?structureId=1ytb . (Make sure you check out the Jmol view.)
Thermodynamically speaking, bending DNA would require energy. Therefore, DNA that was pre-bent (e.g., due to auxiliary binding proteins or composition bias) would improve binding.
So, I suspect that in the context DNA binding proteins, "curved" refers to the static curvature of unbound DNA or to the bending of DNA upon binding in order to facilitate recognition.

I never heard of the term until today but a quick search implies that certain DNA sequences are more pliable than others. Most notable is the Widom sequence which binds to Histones. It is also noted that DNA isn't a free floating polymer but that there is also some directionality in its bend. It seems that the concept is bested explored in this review: Curved DNA.


text:
Why is offspring of identical twins not identical?
When identical twins marry identical twins, the children of the couples will be full genetic siblings but why are they not genetically identical?

I think we need more information. What is the evidence for your assertion?

Apparently this phenomenon (twins marrying twins) is called "quaternary marriage." Useful to know because (1) you can change the title of your question to be more precise (and maybe get better answers to your question); and (2) you now have a starting point to dig around to find answers.

They are not identical for the same reason full siblings are not identical.
A simplistic Mendelian setup would be the following:
X1/X2 = Mothers
X3/Y = Fathers
That means the children could be:
X1/X3
X1/Y
X2/X3
X2/Y
So children born to two married couples composed of identical twins only have a 50/50 shot at being the same gender, much less have the exact same set of genes and express them in the same way.
Now, the simplistic view above only concerns 4 alleles - but the human genome is composed of thousands. By the end, the chances of genetically identical offspring from a set of identical twins is still very, very low.
And you haven't even began to include epigenetic variations, which often arise as a response to the environment! One cousin might be shorter due to their diet as an infant, one might have allergies the other does not depending on if they played outside as a child, and for non-Mendelian traits (incomplete dominance, co-dominance, phenotypes that rely on more than one allele [especially hair, eye, and skin color]) there's even more opportunity to introduce differences!

Exactly. And then there is crossing over that will produce even more variability.

Let's not forget possible environmental influences on development.

There was actually a 1960s TV sitcom based on the notion of identical cousins. It was called the Patty Duke show. In reality the only way to have cousins that look alike would be through a quaternary marriage. That is when twins marry other twins. The children from the two marriages would technically be 1st cousins yet genetically they would be siblings as well. In other words, it would be impossible to figure out who the biological parents are based on the DNA alone since the parents (being identical twins) would share the exact same genetic material. The truth is the Patty Duke show scenario is highly unlikely. Patty and Cathy could not be identical cousins because the only way we get identical offspring is when a fertilised egg splits into two cells. Those identical cells grow into identical twins. So there would be a strong resemblance between Patty and Cathy but the odds of them looking like identical cousins is unlikely. More likely they would look like fraternal twins. Patty would indeed look like Cathy but you could tell the difference between them just as you could between any pair of sisters. The cousins wouldn’t look identical but they wouldn’t look like cousins. They would look like sisters.

Hi Toussaint, welcome to Biology.SE! Nice anecdote! It would be useful to add reference for the "scientific" part of your answer and improve the formatting for better reading.


text:
Strange behavior of a DNA gel
I ran a PCR product of ~300 bp on a 2% TAE-agarose gel for 30 minutes. I used Sybr-safe as a DNA stain. Voltage was 80V.
When I imaged the gel, the DNA on the bottom half of the gel, including the ladder had disappeared (it showed no bands). The DNA in the top half looked-clear and well-separated, but the bands on the bottom were somehow missing.
What could be the reason? I've never encountered this before.
I know it's not due to gel overheating - I ran the gel in the cold room and when it was done it was cold to the touch.

If you use pre-staining, the stain migrates as well in the electric field and this can lead to some parts of the gel being unstained. This would look pretty much like you describe, the ladder being invisible as well points strongly to that part of the gel just being no stained properly.
It sounds a bit unlikely with your running parameters, I've only seen that with a very long running gel, but I also haven't used pre-staining for quite a while now. Ethidium bromide is positively charged and migrates in the opposite direction as the DNA, I have no experience with Sybr-Safe though and don't know if it behaves the same as EtBr in this regard.

I looked it up and the website does say sybr safe runs away from migrating DNA. I might have been off with the timing and this fits, thanks.

@Drosophila I'd just try to stain the gel again, if this was the reason the DNA should be visible then.

Yeah, I threw out the old gel but I ran a new one at a higher voltage and shorter time. It worked. I'll check your theory when I get some free time

Jut for reference, with 20min@100V running time I usually get the bottom ~1.5cm of the gel Sybr-Safe free.


text:
Why do antacids have a special importance when taking lactulose?
“Before taking lactulose, tell your doctor and pharmacist what prescription and nonprescription medications you are taking, especially antacids, antibiotics including neomycin (Mycifradin), and other laxatives.” (Quote from here)
Why do antacids have a special importance when taking lactulose?

Other laxatives can exacerbate the effects of lactulose, leading to diarrhea, and could eventually lead to dehydration and general GI issues.
Neomycin and antacids in general raise the pH of the gut, making it more basic, and reducing the peristaltic movements. Lactulose, meanwhile, is broken down to primarily lactic acid (if I recall) in the gut, and creates a more acidic environment. The acidic environment increases peristaltic movement in the bowel, and in turn the patient eliminates waste.
If you are on concomitant antacids or other drugs that raise the pH of the lower gut, you are reducing the effects of lactulose, and in a worse case scenario, making the constipation worse.

So are you saying that antacids raise the pH of the lower gut, the acidic environment in turn inhibits the breakdown of lactulose into acidic metabolites?
I guess that then less water is retained in the bowel than would be without an antacid, making lactulose less efficient against constipation.

The antacids don't necessarily inhibit the breakdown of lactulose, but they counteract the effect that would be caused by a more acidic environment in the gut. Acidity = increased peristaltic (bowel) movement. So the gross amount of acidic product from the lactulose might still be the same, but it is being neutralized to some extent by the alkaline products of the antacids.

Many thanks for your answer. In the main text you wrote “antacids … raise the pH of the lower gut”, in your comment “alkaline products of the antacids”. Isn't that a contradiction? Do I misunderstand something?

pH <7 is acidic, pH > 7 is basic/alkalinic, so the antacids (calcium carbonate, etc) would raise the pH, making it more alkalinic and less acidic, hence the "antacid"


text:
How does the body measure dehydration?
What, physically, does the body do to measure it? I assume it's measured by how how turgid or plasmolysed certain 'sample cells' are, or water concentration in the blood,

What is the way they use to measure it?
What do the receptor cells that do the measuring actually do that is variable with water concentration, etc.

This article reviews the subject but I can't access it. http://www.nature.com/nrn/journal/v9/n7/full/nrn2400.html perhaps someone has access to nature neuroscience and can relay the details, good luck!

From Wikipedia entry on thirst:

In the mammalian brain, the posterior surface of the hypothalamus
  forms the front wall of the third ventricle (a cerebrospinal
  fluid-filled cavity) and clusters of cells (osmoreceptors) on this
  surface, notably in the organum vasculosum of the lamina terminalis
  (OVLT) and subfornical organ (SFO), signal this cellular dehydration
  to other parts of the brain, and thirst is experienced. Destruction of
  this part of the hypothalamus in humans and other animals results in
  partial or total loss of desire to drink even with extremely high salt
  concentration in the extracellular fluids.1

The entry on osmoreceptor says in part:

When the osmotic pressure of blood changes (i.e. it is more or less
  dilute), water diffusion into and out of the osmoreceptor cells
  changes. That is, they expand when the blood plasma is more dilute and
  contract with higher concentration.

It also describes how the kidney measures chlorine anion flow through some nephrons, which triggers a cascade of messenger molecules resulting in increased blood levels of the hormone angiotensin, which also results in thirst messages originating in the hypothalamus.
1Derek A. Denton (8 June 2006). The primordial emotions: the dawning of consciousness. Oxford University Press. pp. 118–19. ISBN 978-0-19-920314-7.
2Walter F., PhD. Boron (2005). Medical Physiology: A Cellular And Molecular Approach. Elsevier/Saunders. ISBN 1-4160-2328-3. Page 872

How do osmoreceptors work? That is, how and by what is the 'swollenness' of the osmoreceptors measured, and how does this turn into an electrical signal?

Dehydration results in decreased blood volume (hypovolemia) and in slight decrease of blood pressure. The body recognises dehydration by these ways:

Baroreceptors in the aorta detect the drop of blood pressure - this results in activation of the sympathetic nerves and the release of adrenaline from the adrenal medulla - this leads to constriction of the arteries ad increased heart rate.
Volume receptors in the heart atria detect hypovolemia - this result in the secretion of the antidiuretic hormone from the pituitary gland - this results in water retention in the kidneys.
Osmoreceptors in the hypothalamus detect increased blood osmolality - this triggers the release of the hormone ADH.
Juxtaglomerular apparatus in the kidneys detect decreased perfusion, what results in the renin-angiotensin-aldosterone release cascade, which results in water retention in the kidneys.

All these mechanisms are activated in the compensated hypovolemic shock.


text:
Is it more likely to develop a throat-ache at night?
I have noticed that I rarely develop phlemmy throat-aches in the daytime, but often notice them after I have been sleeping.  Is this a recognised phenomenon?  Could it be because viruses or bacteria aren't being flushed out by food, water and vibration of the throat from speaking or that one's immune system is lower at night? If it is the latter, why is this?

It's because your mouth and tongue are stationary at night, so you don't move the slowly-drying saliva around to lubricate tissues. The mucous tissues dry out, resulting in greater friction with muscle movements (like swallowing), and your body is slightly dehydrated after 6-10 hours without water. If you've ever undergone surgery where they intubated you (stuck a tube down your throat to ensure air supply), afterwards it's a very similar feeling to waking up with a soar throat because your throat dries up and the anesthesia prevents muscle movements.
Your immune system actually works better at night and requires rest to work efficiently. Bacteria and viruses don't really care about the time of day, although the muscles of the larynx do ensure that the mucous layer is continuously circulated. The continual circulation helps prevent debris and bacteria/virii from establishing themselves, although the magnitude of the effect isn't on the same scale of other tactics taken by your body.
Several factors can affect mucous/phlegm/saliva production - including infections, hydration levels, environmental temperature, smoking habits, diet, environmental humidity, and lots more. If it's a constant trouble, you can try drinking more water during the day, a steam humidifier, or talking to your doctor.


text:
Do siblings have a bias toward believing they look different from each other?
Anecdotally, I have observed (myself included) that siblings tend to think that they look less similar to each other than an unrelated observer would say. Is there any experimental data to back this up, or am I completely wrong?

if they did, I think it would be due to the fact that we don't look at ourselves so much as we see others.

Would this be better in http://cogsci.stackexchange.com

You are not completely wrong but not completely right either. Some siblings tend to think they are less similar to each other, even twins. It may or may not have scientific reason, but it has sociological reason behind it. Every people in our society want to have their own separate identity and they do not want themselves to be compared with others even with their siblings.It might be also due to the result of fact that, siblings pass times with each other so often that they notice distinct differences in both their characteristics and look while ordinary people, looking at them for the first time, can not notice the differences. This is related to the reason why we can not sometime recognize people from any particular race or ethnicity at first look.

Can you add references to support these statements?


text:
How can a plant become resistant to glufosinate?
From Wikipedia, the mode of action of the non selective herbicide Glufosinate is:

Phosphinothricin is an glutamine synthetase inhibitor that binds to the glutamate site. Glufosinate-treated plants die due to a buildup of ammonia and corresponding decrease in pH in the thylakoid lumen, leading to the uncoupling of photophosphorylation. The uncoupling of photophosphorylation causes the production of reactive oxygen species, lipid peroxidation, and membrane destruction.

Now, in this article from the University of California (Weed control, management, ecology, and minutia), it states:

Researchers in Malaysia reported a few years ago on a population of goosegrass resistant to glufosinate in vegetable and orchard systems (Lee L J & Ngim J (2000). A first report of glyphosate-resistant goosegrass (Eleusine indica (L) Gaertn) in Malaysia. Pest Management Science, 56, 336-339).  For a number of years this was the only reported case of resistance to this herbicide.

What would have to happen in the weed for it to become resistant to this chemical/mode of action, and what would initiate this process?

Can you add real citations (Author, year, journal, volume, page) or links to the PubMed (or where ever this can be found)? Than we can have a look at the articles without having to find them first.

I think a general resistance strategy is to pump the offending molecule out of cells. I don't know if that applies here, but I wouldn't be surprised.

@Chris still looking for those

Phosphinothricin is a metabolite from the bacteria Streptomyces viridochromogenes which has a protein called phosphinothricin N-acetyltransferase (PAT). This Protein inactivates the phosphinothricin which is the reason why S. viridochromogenes is not dying from it. If you want a plant to be resistant to phosphinothricin you can add the gen for the PAT protein to the plant genom.
This is also described in this paper about herbicide-tolerant crobs.
An explanation for the resistant goosegrass could be that somehow it got the gen for PAT, maybe by horizontal gen transfer from S. viridochromogenes.
In your case the publication which is cited in your source contains another possibility. "We hypothesize that reduced herbicide translocation is responsible for resistance to both glyphosate and glufosinate in these populations"

Yes, this looks to be correct. Mind adding a reference or 2 before I accept?

I learned this in university this semester, but I'll try to find the publications :)
There could be other explanations to your question


text:
Why do some mammals not have testes in a scrotum?
Coming from an evolutionary approach, Is the only purpose of a scrotum to regulate the temperature of the testes?
Knowing all mammals are warm blooded, shouldn't all mammals have testes in a scrotum?

Having descended testes is a derived characteristic within mammals; monotremes and the Afrotheria (including elephants) all retain the ancestral character state (Kleisner, et al., 2010)2. Among those mammals with descended testes, these can be ascrotal or scrotal. Testicular descent is hypothesized to have only occurred once within Mammalia, with the ascrotal Laurasiatheria. Descended ascrotal testes are found in cetaceans, phocid seals, hippos, tapirs, rhinos, and some bats. Descended scrotal testes are found in horses, pigs, camels, and Carnivora.
Since basal mammals would presumably have to regulate testicular temperature just as much as derived mammals, the temperature regulation hypothesis seems to not hold up. So the real question is: why have a scrotum? One hypothesis has to do with evolution of fast locomotion (e.g., galloping).
According to Frey (1991, 40)4:

The strong flexions and extensions of the vertebral column during
gallop should cause intense fluctuations of intra-abdominal pressure.
Fluctuations of intra-abdominal pressure severely impede continuous
flow of blood in the abdominal veins. Periodically reduced venous
drainage resulting in fluctuations of intra-testicular pressure would
impair the process of spermiohistogenesis, which is dependent on an
absolutely constant pressure within the testis.

Chance (1996)5 suggests that the temperature hypothesis might represent a secondary adaptation:

Because in the human male, scrotal testes function optimally at
temperatures below that of the body, much speculation, and a
considerable amount of research, has gone into attempting to see what
(metabolic) advantage might accrue from this lower temperature,
without considering the possibility that this is a secondary
adaptation to an enforced external position.

Kleisner, K., Ivell, R., and Flegr, J. 2010. The evolutionary history of testicular externalization and the origin of the scrotum. J Biosci 35:27-37
Frey, R. 1991. Zur Ursache des Hodenabstiegs (Descensus testiculorum) bei Säugetieren. Z Zool Sys Evolut-Forsch 29:40–65
Chance, M.R.A. 1996. Reason for externalization of the testis of mammals. J Zool 239:691–695

What about dolphins or marine mammals? Do they have ascrotal testes?

@GabrielFair This has more than you will ever want to know about mammalian penises and testes, but the answer is no, cetaceans and seals do not have scrota, presumably an adaptation for being streamlined.


text:
Why would taking antibiotics increase stamina and energy?
I often hear that people who are taking antibiotics experience wild fluctuations between feeling full of energy and completely alert but soon after feeling impossibly fatigued and sick.
Does this have anything to do with the antibiotics being used by the body as anything? For example as a hormone or as a source of nutrition?  Is this this a reported side effect when used for other infections?

Mono is caused by the Epstein-Barr virus.  The antibiotics won't do anything to fight against that, anyway.  Sometimes antibiotics are given to fight the strep throat infection that can accompany mono.

ah didn't know that. Well, they tell me its mono... haha

can't really answer this, but I wanted to mention that there are some stimuli that can make you feel full of energy. There are anecdotes that drinking some radioactive isotopes also make some people feel great.  See "The Great Radium Scandal" by Roger Macklis in the August 1993 issue of Scientific American.

I have never heard about this phenomenon from my patients or professors at the Medical School, but this is a possible mechanism that comes to my mind.
One of the classification for antibiotics takes consideration the effect on bacteria. Two possible effects are either stopping the proliferation (and letting the immune system to kill those that are currently present in the body) or killing bacteria directly.
The second approach is obviously more effective but has one big disadvantage: massive death of bacteria leads to the massive release of their toxins that are normally trapped within they bodies (so-called endotoxins). The symptoms you describe as "impossible fatigue" match exactly the symptoms of bacterial intoxication -- and this can increase upon the antibiotics intake.
Depending upon the bioavailability and pharmacokinetics some antibiotics might not kill all bacteria "on the first run" and the symptoms of intoxication recur several times with decreasing severity of manifestations.

Over the years since this question was posted, gut flora research has become mainstream. Could the elimination of gut flora cause a statistically significant increase of nutrients in the blood stream? Could that be a source of the proposed effect?

"There are antibiotics which contain carbohydrates, such as Gentamycin and Streptomycin (the aminoglycosides). These must be the antibiotics that could account for this phenomenon."
My conjecture that the carbohydrate moities contained within aminoglycosides account for the high energy is incorrect. Aminoglycosides are NEVER metabolized by the body, they are excreted out into the urine UNCHANGED. See here: http://www.ebmedicine.net/topics.php?paction=showTopicSeg&topic_id=43&seg_id=839
And even if it were possible to metabolize the carbohydrate molecules within them, the energy released would be far less than the energy consumed to break their linkages in the first place, thus placing a negative energy balance on the body, and thus, not providing the burst of energy that is apparently observed after taking antibiotics.


text:
Harmless virus?
Is it possible for a virus to live symbiotically with its host?
Is the human body plagued with viral infections that do negligible harm, or even serve a beneficial role?

It is possible for viruses to live in mutualistic relationships with their hosts, these associations are often overlooked due to the devastating effect that many viruses can have.
To give an example in humans, when HIV-1-infected patients are also infected with hepatitis G virus, progression to AIDS is slowed significantly (Heringlake et al., 1998; Tillmann et al., 2001). Also hepatitis A infection can surpress hepatitis C infection (Deterding et al., 2006).
There are many other notable examples within plants, fungi, insects, and other animals, reviewed by Shen (2009), and Roossinck (2011), in two excellent papers.
The table below, summarises some beneficial viruses across all organisms, and is taken from Roossinck (2011).

References

Deterding, K. et al., 2006. Hepatitis A virus infection suppresses hepatitis C virus replication and may lead to clearance of HCV. Journal of Hepatology, 45(6), pp.770-778.
Heringlake, S. et al., 1998. GB Virus C/Hepatitis G Virus Infection: A Favorable Prognostic Factor in Human Immunodeficiency Virus-Infected Patients? Journal of Infectious Diseases, 177(6), pp.1723 -1726.
Roossinck, M.J., 2011. The good viruses: viral mutualistic symbioses. Nature Reviews Microbiology, 9(2), pp.99–108.
Shen, H.-H., 2009. The challenge of discovering beneficial viruses. Journal of Medical Microbiology, 58(4), pp.531 -532.
Tillmann, H.L. et al., 2001. Infection with GB Virus C and Reduced Mortality among HIV-Infected Patients. New England Journal of Medicine, 345(10), pp.715-724.

That aphids require a particular virus to be present in order to develop wings, is one of the most amazing things I've ever learned in biology.

I have asked about Herpes virus suppressing HIV here: http://biology.stackexchange.com/q/1365/238

As mentioned in this question , Adeno-associated virus is often used for gene therapy.  This is due largely to its predictability when injecting genes (1), however it is also used as it is not implicated in any human pathology. As it is a replication deficient/helper dependent virus, natural infection is much less likely.
The human immune system does mount an immune response against wild-type AAV, as Alexander Galkin discusses regarding an engineered AAV here. Despite this, I think that AAV does meet your criteria for a 'harmless virus' , even if it is unlikely to infect without human encouragement.

(1)  Kotin RM, Siniscalco M, Samulski RJ, et al. (1 March 1990). "Site-specific integration by adeno-associated virus" . doi:10.1073/pnas.87.6.2211 .


text:
How does this illusion work?
I found this image on Google+

If you shake your head you can see a portrait of a person. Can anyone explain how the image is constructed in the brain?

If you zoom in on the image, you can see that it is not just composed of black vertical lines, but also has pixels with different gray tones in the white areas. When you move your head sideways, you perceive the gray tones more.
If you were to remove the black lines, you could see the face clearly. Initially I thought that by blurring the gray shapes when your head moved, they became more visible as they seemed larger. On reflection though I think that actually what's happening is that the high contrast between the black lines and the mostly white background causes your perception to adjust so it doesn't easily see the mid tones. This is because we have a low dynamic range in our vision (relative to absolute brightness, but compared to camera CCDs we have a high dynamic range) - we have to adjust the light sensitivity to compensate for the overall brightness of the image. This is called brightness adaptation. There's a good free textbook for further reading about this at Utah U's Webvision.
When you move your head, the black and white lines blur together which makes the overall brightness appear to be the average brightness of the black and white. So against that background your light sensitivity increases and the areas where the pixel tone is different from the average - the gray pixels of the face - start to stand out.
By reducing the brightness you can see the faint image in the background much more clearly...

Nice answer. Thanks a lot. Just one thing, you said the high contrast between the black lines and the mostly white background causes your perception to adjust so it doesn't easily see the mid tones Does this phenomenon have a specific name? Can you provide references?

Added terminology and a reference. Sorry I couldn't find any good review papers - it's not my field at all. Perhaps a human biologist can contribute better references.

As additional info: The blurring of the black and white areas is not primarily caused by the movement. The eyes can only focus a very small area of the field of view. The rest is perceived in low detail. This can be visualized easily. When you move your head and keep the focus on the image, the  portrait appears with low intensity. But when you focus an area next to the picture, you can see the portrait without moving your head at all.

Actually you can also see the portrait simply when looking from a distance (especially if you have myopia), without moving your head.


text:
Would ovoviparous to viviparous mutation have been gradual? How would that work?
It seems unlikely that an ovoviparous ancestor of mammals long ago could have had a viviparous offspring in a sharp one-generation dividing line, but what would be the gradual steps between egg birth and live birth? Are there any examples of answers to the first question today? It seems that marsupials are a different thing altogether, not something in between egg laying and live birth (no modern mammal's ancestors aren't believed to have marsupial-style birth in their evolutionary history, right?)?

I happen to have seen a talk by an anthropologist who was working on this (i can't reference them here i'm sorry to say - forgotten her name).  I can only give an example from their work...
If you look at old world and new world primates, there is a large difference between the gestation time.  If you look at the table in the link, lemurs have half the gestation time that humans and gorillas have.
What I can recall is that the lemurs placenta lacks many of the structures that primates have (see section 5).  The lemur placenta is supposed to be primitive and a lot more like an egg sac which was internalized as opposed to a more articulated womb that primates have.  So her thesis was that eggs would start out being internalized and subsisting only on their own internal structures, still isolated from the mother, then later placental structures would come about that nourish the fetus and enable it to enjoy longer gestation and better development pre-partum.
The stage I'm describing is only the divergence between primitive wombs and 'more advanced' wombs in the sense that they were capable of supporting the fetus for 9 months rather than just 4.  That development happened over about 30 million years.  The divergence of mammals is thought to have happened about 270 million years ago.
So the rough answer would be hundreds of millions of years for the whole shebang, but internalized eggs and live birth would be a relatively smaller amount of time.


text:
Identify this roadside plant in Montserrat, Spain
Photographed in April; growing abundantly on the side of a rocky path in Montserrat, Spain.  Up to maybe 1 foot (30 cm) in height.

This plant is in the genus Euphorbia, which is a large and diverse group.  The members take wildly different forms, but the general form of this plant is shared by many Euphorbia members.  I'm not sure of the species, but think it is most likely Mediterranean Spurge, Euphorbia characias:
 Photo: Macro63
 Photo: cc-by-sa-2.0 Bernard Dupont.


text:
Please explain to me the difference of molecular weight in g/mol versus dalton
From my studies i thought so far that:
1 NA * Da = 1 * NA  mu = 1 g,
However since 2019 SI says that one dalton is only approximately one gram per mol
1 NA Da  ≈ 1 g/mol
This makes sense if I consider the definition of :
1 Da as 1/12 Mass of Carbon-12
while MW of 1 * C 12 is 12,0107 g/mol
However this leads to differences in mass calculation for molecules:
lets say for ssDNA PhiX genome of a length of 5386bp I calculated 1664042 g/mol but 1664051 Da MW leading to a difference of ~ 9 Da
so my question is how should i calculate and report molecular weights from now on to not include errors resulting from the change made by the International System of Units
can anyone explain to me or hint me to a publication or similar on how to correctly do mass calculation ?

This is a chemistry question and should be moved to SE Chemistry.

For practical purposes, the answer is that it doesn't matter. The example you give corresponds to a relative difference of approximately 0.00054 %. Depending on your pipetting skills, the volume you are trying to pipette and the pipette you use, your accuracy will be at best within a few percents of the intended volume.
If this helps convince you, try calculating the volume you need to pipette with both molecular weights: the difference will show only after several decimal places, that you would need to round anyway because the pipette only goes to two decimal places (assuming you are using a typical 10 uL pipette).
In addition, you can consult the Gilson Guide to Pipetting, section Tips for Mistake-Free Pipetting (page 23 in the edition I got at the time I wrote this), to learn about common causes of inaccuracy when pipetting and, more interestingly, how much variation they incur. You will see that they all amount to a lot more than the inaccuracy incurred by using an approximate molecular weight in your calculations.

Yes in actual practical terms this wont make a difference, even in microvolume work >0.1μl. However my question is more aimed at theoretical ideas, and if there is any guideline or strong opinions on how to use Da or g/mol in the future..


text:
Do TADs derive from operons?
TADs (Topologically associated domains) are DNA sequences in the eukaryotes genome (except plants) that are between two sequences named "Insulator". The genes in TAD just are affected by enhancers and suppressors that are in the same TAD.
This structure can be seen in operons that exist in bacteria. Is there evidence to say that TADs derived from operons?

The short answer is "no".
Operons have very closely coupled regulation, even in eukaryotes. The classic operons are polycistronic, meaning that transcription of adjoining genes occurs as part of the same process.
TADs on the other hand are merely (not always very well defined) regions in between insulators, as you say. They probably have some common regulatory context, but it is nothing like the direct coupling observed in operons.


text:
Any Ideas what this insect might be?
A year ago my family and I were in Tanzania on vacation. Upon returning to our home in Alaska my wife found a small stowaway in her luggage. Feeling sorry for the poor creature we put it in a container, gave it some green leafy things to eat, some water and some paper towels pieces to hide/burrow under - thinking that its life span would be a few days/weeks and short of flying back to Tanzania this was the best we could do.
Skip ahead a year and he/she is still with us... every few days we change its food, change its bedding, and make sure it has something moist to get water from. We even took it on vacation this year to Florida and back because trying to explain how and why to take care of our friend to a neighborhood kid may work for pet cats or hamsters but we were afraid Mr. Bug might not survive.
Since we are coming up an a full year of bug sitting we are wondering what is it ? And should my daughter plan on taking it to college with her when she leaves in 6 years ?

Given how long you've had the critter, and looking at the photo, I think you have a beetle larva here; you may be "sitting" for some years yet (once you see it pupate there will be less than a year [I think] left, and the resulting adult will be much easier to identify ... if it gets that far you may want to follow up with more pictures).

FYI: please do not travel with insects. This is how nonnative species get spread -_-

I agree with Arthur. It is a beetle larva. I don't agree with forestecolgist. Most non-native species spread as unintended hitchhikers in commercial shipping, or as intentional introductions.

Topview and bottom view photo would be appreciated

@Karl I wasn't trying to suggest that personal luggage was the (i.e., the primary) way that invasives are spread -- Just one such way that it can happen. So no one should willingly and knowingly enable it to happen.

Could you please add the length of your pet?


text:
Life without DNA?
I'm by no means an expert in the field, merely a curious visitor, but I've been thinking about this and Google isn't of much help. Do we know of any lifeforms that don't have the conventional double-helix DNA as we know it? Have any serious alternatives been theorized?

What is considered alive? This is a good question. I think it is safe to define something as alive when it is (1) capable of sustaining and replicating itself and (2) able to interact with its environment.

Irregardless if viruses and prions are "alive", those that we know cannot survive in a word without RNA/DNA.

I agree with @Poshpaws it is great question

To follow up what mbq said, there have been a number of "origin of life" studies which suggest that RNA was a precursor to DNA,  the so-called "RNA world" (1). Since RNA can carry out both roles which DNA and proteins perform today. Further speculations suggest things like a Peptide-Nucleic Acids "PNA"  may have preceded RNA and so on.
Catalytic molecules and genetic molecules are generally required to have different features. For example, catalytic molecules should be able to fold and have many building blocks (for catalytic action), whereas genetic molecules should not fold (for template synthesis) and have few building blocks (for high copy fidelity). This puts a lot of demands on one molecule. Also, catalytic biopolymers can (potentially) catalyse their own destruction.
RNA seems to be able to balance these demands, but then the difficulty is in making RNA prebiotically - so far his has not been achieved. This has lead to interest in "metabolism first" models where early life has no genetic biopolymer and somehow gives rise to genetic inheritance. However, so far this seems to have been little explored and largely unsuccessful (2).
edit
I just saw this popular article in New Scientist which also discusses TNA (Threose nucleic acid) and gives some background reading for PNA, GNA (Glycol nucleic acid) and ANA (amyloid nucleic acid).

(1) Gilbert, W., 1986, Nature, 319, 618 "Origin of life: The RNA world"
(2) Copley et al., 2007, Bioorg Chem, 35, 430 "The origin of the RNA world: co-evolution of genes and metabolism."

There actually was a study where they were able to create (using theoretical early Earth conditions) two of the four RNAs. Though I always have a tough time finding the video interview for it I did find this. http://www.wired.com/2009/05/ribonucleotides/

There has been a recent report on Science, which had much return in the general press, in which a bacteria was identified that could live in an environment where arsenic was subsituted to phosphorus (one of the components of DNA, forming the backbone of the double helyx).
This is the original paper:
A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
and the commentary appeared on Nature
Arsenic-eating microbe may redefine chemistry of life
There is, however, much critique on the methodology used in the paper, and on whether arsenic would really be incorporated in DNA instead of phosphorus.
Science published several of these critiques in an Editor's Note
And here you will find the Response of the Authors
Other than that... well if you consider virus as life-forms, there's plenty that do not have double stranded DNA, but have instead single strand DNA or single strand RNA or double strand RNA.

I am also sceptical - but fascinating if correct !

I don't want to get too deep into the controversy over this study, but from reading the paper myself and talking to others, the weight of current opinion is certainly against the arsenic result.

yamad, is the prevailing scepticism possible to summarize for those of us curious about the result?

@KatieBanks, this is not my field so those interested should read the 8 critiques. One main criticism, though, is that their As+/P- medium has sufficient trace phosphorus to support the growth they attribute to arsenic incorporation. The authors argue that their As-/P- control, which shows no growth at all, indicates that it isn't just trace P supporting growth. This is a good point, but this still doesn't really require an interpretation that As is incorporated into the DNA. Their other data has also been criticized for insufficient purity in their samples/preps.

this was debunked: http://news.nationalgeographic.com/news/2012/07/120709-arsenic-space-nasa-science-felisa-wolfe-simon/

@woliveirajr the original papers can be found here: GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism and Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells. However, I wouldn't go as far as saying they "debunked" the study, just gave better explanation for their results (i.e. applied the scientific method).

Also: http://www.ncbi.nlm.nih.gov/pubmed/22798070

It depends whether you call prions a life form, but prions do not make (direct) use of DNA to propagate themselves. They force other proteins into a misfolded protein state.
Again, the question remains whether prions should be considered "alive".

The question of them being alive is moot; prions are ultimately dependent on DNA for their propagation as the host must generate additional substrate for them to turn over.

That is the reason I put "direct" between parentheses. Strictly speaking, prions do not make use of DNA to propagate. However, as you indicate, there is definitely room for debate.

Prions can't however change any protein into a misfolded state... they are a misfolded state of the PrP protein, which is normally synthetised by the organism, and for which a gene exists.

Luckily they can't. However, keeping the question above in mind, I don't think that this is of any relevance.

This recent Cell paper mentions a ribozyme (RNA enzyme) that ligates two oligonucleotides into itself. Given a sufficient source of input oligonucleotides and the correct conditions, it can catalyse its own replication and undergo Darwinian evolution, and can be thought of as a rudimentary form of RNA-based life.
The authors hypothesise that ligase-based RNA replicators could have been the first RNA replicators, which were later replaced by the now-standard polymerisation:

A somewhat different approach relies on RNA enzymes with RNA-templated
  RNA ligase activity to join oligonucleotide substrates to form
  complementary RNA products. It has been proposed that the first
  replicating, evolving systems on Earth operated by this mechanism and
  only later came to depend upon residue-by-residue polymerization

It should be noted that RNA ribozyme polymerases already exist, but many of them require proteins in addition to the RNA structure.


text:
Do goldfish really have a 5 second memory span?
I heard that when people place goldfish in another tank, they just forget where they where previously? True or False ?

There's already a question about this on Skeptics: http://skeptics.stackexchange.com/questions/6474/do-goldfishes-have-a-two-or-three-seconds-memory

@MadScientist, nice link! Why don't you write it up as an answer?

My answer might sound unscientific, since I haven't had tanks filled with goldfish. However, I have had fish and other pets over the years, including cats, turtles and a very sick lizard. I have a scientific background, and on this strength, I will report based on personal observation, albeit with a small sample size.
My fish always "knew" me. When I approached the tank, they knew it was their "feeding person", and even when they were not getting fed, left what they were doing aside and came to the surface to "greet" me, or more likely, impending food. I even experimented by asking others to walk up to the tank and saw that most of them did not respond in a similar fashion, although sometimes they did. With me, I enticed the same reaction every time, even  after a new tank was populated or new additions were made.
This makes me conclude fish, and goldfish, which I did keep, have "better than expected" memory.
When they are put in a new tank - well, I suggest you move to a well crowded city that is new to you, and see how long it takes for you to get your orientation right.
Hope it helps.


text:
What are the constraints when growing an artificial brain?
Are there any experiments on growing artificial brains from brain tissue?
What are the constraints? Will such tissue grown to the mass greater than that of human brain surpass it in intellect or it would need additional conditions?

Please try to clarify your question, it's not entirely clear to me what you are asking. We're also far, far away from anything near growing a functional brain in the lab, so this question might be close to unanswerable.

It is already very difficult to grow neurons in culture, let alone having them form a brain.

You may want to look into the study of embryology.  A jumping off point to get some search terms (as this is a huge area) would be http://en.wikipedia.org/wiki/Neural_development_in_humans.  For a more microscale view, look into http://en.wikipedia.org/wiki/Axon_guidance

A term from counting bacterial colonies comes to mind as an answer to this question: TNTC (too numerous to count).

The comments above are quite relevant -- we are years / decades away from growing functional brains in the lab, so there are probably innumerable constraints that we have likely not even thought of yet.
That being said, you might find this paper interesting: "Adaptive flight control with living neuronal networks on microelectrode arrays" [1]. The authors are able to succesfully culture rat neurons and electrically interface with them in order to control pitch and yaw in the XPlane flight simulation software.  It's a very crude system compared to an actual brain, but it's able to successfully use cells as rudimentary living neural networks. If you consider this to be a successful "artificial brain," then your constraints are all the ones associated with culturing neurons.
[1] DeMarse, et. al 2005


text:
What is the lowest pressure at which plants can survive?
What is the lowest pressure at which plants can survive? How the plants behave in a Martian-type atmosphere? Is there any plant that can survive such atmosphere?
Can a lichen grow at Martian pressure?

Are you referring to total air pressure or partial pressures of oxygen and carbon dioxide?

Lichen is not a plant though.

I like your question!
Low surface pressure on Mars (averaging 600 Pa or about 1/170 of Earth's at sea level) is only one difficulty that an organism would have to contend with. In addition, mean surface temperatures are ~210 K (- 63 °C), the surface ultraviolet flux is extremely high (no ozone layer) and an aridity comparable to the Atacama desert. On the plus side, a 95% CO2 atmosphere might promote photosynthesis.
So, higher plants are extremely unlikely to prosper on Mars. Purely in terms of pressure, experiments suggest that at 1/10 Earth atmospheric pressure vascular plant transpiration increases significantly. So much so that they enter into a drought response which often leads to plant death.
However, lichens may be another matter. These are often adapted to low precipitation/pressure environments such as high mountains. Indeed, this article addresses exactly your question (sadly it is not open access). The authors suggest that the lichen Xanthoria elegans experiences no loss in vitality after 22 days exposure to laboratory Mars-like conditions (low pressure, low temperature etc.)!
Having skimmed this article I am frankly amazed (and slightly dubious) at the result. However, it should be noted that they only ran the experiment for 22 days, applied no ionising radiation (to simulate the high UV flux) and make little mention of the precise metabolic state of the lichen. If it has entered into cryptobiosis (cessation of metabolic processes) then it can't exactly be regarded as prospering.

de Vera et al., 2010, Astrobiology, 10, 2, Survival Potential and Photosynthetic Activity of Lichens Under Mars-Like Conditions : A Laboratory Study

No, the lowest pressure at which plants can survive is not around 0.47 atm.
It is 0.07 atm or less in the case of ryegrass. And it's the total pressure. Not partial pressure of one of the constituent gases.
See this article:
https://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/19860010460.pdf

Short answer : around 0.47 atm
World's highest plants discovered growing 6 km above sea level
If this Air Pressure Calculator is to be believed that should be 0.47 atm, so for plants 'the lowest pressure at which plants can survive is around 0.47 atm' seems to be your answer.
The air pressure on Mars is 0.00628 atm, so no, plants can't survive on Mars, if they could then we'd certainly find them far above 6 km on mountains on Earth.
Howsoever
It does seem that some of Earth’s toughest life could survive on Mars.
The life in that article that (not only) survived (but flourished in) the environment in the chamber (which included the atmospheric pressure of Mars) where Lichens & Cyanobacteria.
Neither of those are plants though.

Cyanobacteria are bacteria.
lichens are a composite organism incorporating a fungus & algae or cyanobacteria.
Algae are plants, but it's in a lichen, not a standalone plant, it's not clear from the article any of those lichens were algal rather than ones with cyanobacteria either.

But (that bit of pedantry aside) it would seem the answer to your second question is yes.
A lichen can grow at Martian pressure.
So there are examples of life that clearly can survive lower pressures than 0.47 atm.
But actual plants don't seem to be among them.

... almost 8 years later..
A newer experiment with a timespan of 1.5 years on another one lichen species suggests that there is

.. a minor resistance potential of the lichen Buellia frigida towards
  Low Earth Orbit and Mars analogue conditions effecting the survival
  potential and the resistance of the symbiotic organism

due to a DNA damage.
Source: "DNA damage of the lichen Buellia frigida after 1.5 years in space using Randomly Amplified Polymorphic DNA (RAPD) technique" Backhaus et al, 2019 Planetary and Space Science
So the answer is possibly "no" until we find some Martian lichen.

It looks like this study is mostly showing the effects of radiation exposure in space rather than atmospheric pressure.


text:
Can visual acuity be improved?
Is it possible to completely cure myopia using natural methods (i.e. not with Lasik etc.)?.
I have seen websites claiming that exercising the eyes will help improve eyesight.
Is this true?

What is perfect vision?

@Kevin: 20/20 vision I guess (see http://en.wikipedia.org/wiki/Snellen_chart )

While there is no such thing as perfect vision, growing evidence from Asia shows that looking often at distant objects (which one does naturally when being outside) can stop myopia progression. Vice versa, progression appears to increase when myopic children mainly live indoors.
D. J. Park, N. G. Congdon: Evidence for an "epidemic" of myopia. In: Annals of the Academy of Medicine, Singapore. 33, 1, Jan 2004, 21–26. PMID 15008557. (Review).
K. A. Rose, I. G. Morgan et al: Outdoor activity reduces the prevalence of myopia in children. In: Ophthalmology. 115, 8, Aug 2008, 1279–1285. DOI:10.1016/j.ophtha.2007.12.019. PMID 18294691.


text:
Can genetically modified genes jump to bacteria in the eater's intestine?
The Guardian ran an article a while back talking about GM gene's jumping to bacteria in an eater's intestine. Has other research confirmed this phenomenon?

It is intestine, not stomach. Also, I love how the article says that because it can happen in certain conditions for bacteria that live in bees guts "The research - which has yet to be published and has not been reviewed by fellow scientists - is highly significant because it suggests that all types of bacteria could become contaminated by genes used in genetically modified technology, including those that live inside the human digestive system.". Talk about hurried conclusions.

Isn't the phrase "genetically modified genes" kind of tautology?

I just want to point out that the Guardian article you refer was published in 2000. 12 years later, these putative results have not been published yet.

@MartaCz-C: I guess it was intended to be GMO's genes

No.
There is nothing special about a piece of GM DNA when compared to any other random piece of DNA. If this phenomenon happened at any detectable level, we'd have found eukaryotic DNA in bacterial genomes/plasmids long before the introduction of genetically modified crops. And that would be front page news in the field of horizontal gene transfer! Which has many talented people in it!

Do you have any references to back that up?

A basic molecular biology textbook plus one in microbiology would be sufficient to provide the details of the mechanisms described by Amy +1.

@Casebash You're asking me to prove a negative. I think the onus would be on you to provide evidence otherwise. For what it's worth, the wiki entry on horizontal gene transfer gives a pretty good overview of the mechanisms we know about: http://en.wikipedia.org/wiki/Horizontal_gene_transfer

Also, this textbook chapter: http://pathmicro.med.sc.edu/mayer/genetic%20ex.htm

Of far greater concern is the transfer of genetic material between bacteria in which antibiotic resistance is conferred. The firmicutes in your poop is not at all the same genetically speaking as the firmicutes in my poop. Polymorphisms and genetic transfer have changed members of the gut microbiome and that leads to differential extraction of energy from the ingested food and differential behavior with respect to antibiotics.

Apparently transfer between prokaryote and eukaryote (in both directions) has been detected:
http://www.biomedcentral.com/1471-2148/11/276/abstract
http://www.sciencedirect.com/science/article/pii/S0888754311001959
http://genome.cshlp.org/content/19/8/1441.abstract
Some numbers I'd like to know are the rate of pro<->eu HGT detection /versus the rate of looking for it/ (i.e. 3 confirmations in 300 attempts would be more impressive than 3 confirmations in 30,000 attempts).

Hi and welcome to biology SE. Please use the buttons above the editor window to insert links and it is better to include the title, authors and journal of your cited articles. That said, I have downvoted your answer because i) you link to 3 articles showing HTC between virii and eukaryotes (even if one of them seems to think that the Hz-1 virus is a prokaryote!) and ii) the existence of HTC between eu- and prokaryotes does not answer whether it would be possible for such a transfer to occur in the very hostile environment of a mammalian gut. In short, you're not answering the question :).


text:
Why do the feet of the Gecko Lizard not stick to Teflon surfaces?
I have noticed that lizards feet can stick to walls but not to Teflon surfaces?
Why is that?

Gecko feet have been the focus of a lot of research over the past 10 years.
Their ability to walk up vertical or even hanging from ceilings is attributed to tiny branching hairs growing from the pads of their feet.  The hairs branch down to the size of 100s of nanometers and its believed that this gives them large surfaces at the molecular scale, giving them a strong van der Waals adhesion force.

Teflon, being hydrocarbon chains covered with 'hard' electronegative flourine atoms doesn't provide the same attraction to the hairs, as van der Waals forces rely on mutual polarizability of atoms in close contact. That is to say, electronically fluffy atoms can stick together more readily.

Nice simple straightforward explanation. +1 for "electronically fluffy atoms"! :)


text:
Why does the mixture of infant formula with saliva provide an ideal breeding ground for disease-causing micro-organisms?
From: http://www.nal.usda.gov/wicworks/Topics/FG/Chapter4_InfantFormulaFeeding.pdf

Discard any infant formula remaining after a feeding. The mixture of infant formula with saliva provides an ideal breeding ground for disease-causing micro-organisms.

Why is this so? Doesn't Saliva contain anti-bacterial properties?

Doesn't Saliva contain anti-bacterial properties?

Yes, in particular some IgA antibodies and lysozyme, but there are also plenty, and I mean plenty of bacteria in your mouth at any given point; we do, after all, still have to brush our teeth!  In fact, animal (including human) bites should be treated lest they lead to sepsis.  Those bacteria would love all the magnificent nutrients in infant formula.  Contact with an infant's mouth will introduce bacteria to the formula, as will exposure to air, contact with your hand, and anything else it experiences.  As an example, in the past few years, there have been some cases (from China, I believe, someone correct me if I'm wrong) of formula contaminated with bacteria, which were more than happy to stick around.

Consider also that the neonatal immune system isn't yet fully working. In fact, one of the reasons breastfeeding is important is transfer of IgA from the mother. Even when antibody production starts after 4-6 months, they don't bind as well.
"In addition to quantitative differences in antibody production during early life versus adulthood, there are also qualitative differences. IgG and IgA responses to pathogens, although inducible, are relatively weak during the first year of life, being short-lived and of low avidity." (Jaspsen et al., 2006)

Whether infant formula or food for adult consumption - should be discarded if there is salivary contamination since there is universal presence of microorganisms in saliva. These act as culture media and the microorgnisms rapidly degrade the food, not to mention the selective overgrowth of pathogenic microorganisms.