Is olfactory input processed by the thalamus? Is olfactory input processed by the thalamus? I know olfaction is the only sense that can bypass the thalamus, but are there cases where the input can project to the thalamus?

Short answer
Third-order olfactory neurons project to the thalamus and mediate conscious perception of odors.

Background
The human olfactory system is schematically depicted in Fig. 1. The olfactory system is indeed interesting, as it is the only sensory system in which the primary receptor cells project directly to the brain. The olfactory cells in the nasal sensory epithelium project via small, unmyelinated axons via the first cranial nerve to the olfactory bulb in the brain.

In the olfactory bulb, so-called mitral cells project to the olfactory cortex via the olfactory tract. Medial fibers project to the anterior olfactory nucleus and septal areas. Some others cross over to the contralateral olfactory bulb. Lateral fibers contact the primary olfactory cortex.

Now it becomes interesting - third-order neurons in aforementioned regions send projections to the dorsomedial nucleus of the thalamus, the basal forebrain, and the limbic system.

The thalamic connections are thought to mediate conscious perception of odor perception. The amygdala and the entorhinal area are neural components of the limbic system and may be involved in the affective and aversive components of olfaction.

Fig. 1. Olfactory pathway. source: Medscape


Can food swallowed when a person is upside down reach the stomach? If a person positions him/herself upside down and swallows food, will it reach the stomach against gravity? If so how?

The eminent @JanDvorak has basically provided the full answer, but yes, it is possible.  You can easily try this yourself, just lean off a bed and swallow something (small) and see what happens.  Peristalsis in the esophagus is responsible for moving food down into the stomach.  The big proof of this is that astronauts can eat when in space, when weightless.  Their food is moved into the stomach just fine.

It's easier to do it upright (peristalsis + gravity) as opposed to upside down (peristalsis - gravity) but definitely quite possible.


About sharks and how they find fish Other than olfactory senses do sharks use some kind of sense that uses electromagnetic waves? Is this similar to an electric eel? I saw a book with the cover statement 'Sharks never get cancer'. IS this possible or just 'quackery' ? Could being constantly 'bathed' in some kind of electromagnetic field cause pre-cancer cells ( that are already unstable) to be 'disrupted'?

Sharks sense their prey with the normal senses, they see, hear and smell them.

They have a remarkable sensitive sense of smelling, which enables them to sense highly diluted traces of prey. They can also use their smelling to determine the direction where a certain smell comes from. This is achieved by the timing in which the senses arrive in different parts of the sharks nose. See references 1 and 2 for more details.

While sharks have eyes which are similar to that of vertebrates, they have an additional reflective tissue called "tapetum lucidum" behind their retina, which reflects the light back and therefore raises the sensitivity of the eye. It seems that a lot of shark species are either colorblind (because they only have rod cells but no cones) or they had only one kind of cone cells which allows them only to see one color. For sharks it is obviously more important to detect objects than to see colors. See references 3 and 4 for more details.

The sense of hearing of sharks is also highly sensitive and is able to detect sounds from far away. See also references 5 and 6 for more details.

The most interesting sense of sharks is their electrosensory organ. This is also called Ampullae of Lorenzini which is a number of sensory cells along the head and which are able to detect the weak electric fields that exist around living animals. This sense only works on a very short distance. See references 7 and 8 for more details.

Finally sharks have the so-called lateral lines (which are present in most fish), which is an organ which detects movements and vibrations in the water around the shark. See the Wikipedia page for more information.

And for the sake of completeness (already quite nicely answered by @Susan in the comments), sharks do get cancer. All cures which are made from shark and claim to be able to treat cancer are pseudoscientific nonsense. This also endangers many shark species as they get radically overfished. See references 9 and 10 for more details.

References:

Smell and Taste
The Function of Bilateral Odor Arrival Time Differences in Olfactory
Orientation of Sharks
Microspectrophotometric evidence for cone monochromacy in sharks.
Vision and a Carpet of Light
Hearing and Vibration Detection
Functional anatomy of the auditory system in sharks and rays
The Shark's Electric Sense
Electroreception
Mythbusting 101: Sharks will cure cancer
Shark cartilage, cancer and the growing threat of pseudoscience.


What makes a good phylogenetic tree? How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees, what features would it have? Would it be highly reliable, well resolved etc? What other features are important to aim to maximise when it comes to improving phylogenetic trees?

A 'good' phylogenetic tree would be completely refined, properly binary, have high bootstrap support for all its branches, and reconstruct clades we think exist with high support values.

Generally high support values(there are other methods besides bootstrapping but that is a question for another time) is a measure of a good tree. There are other concerns, for example a tree that has no felsenstein zones is probably better than one that has lots.

We can know a lot more about trees than you suppose, though. Through simulation studies we can create datasets with a known phylogenetic history and then see how well the methods reconstruct the history. There are still problems(errors in the model used, just random error, ILS, HGT, other things) but mostly that kind of study tells us what good phylogenies look like.

It's very easy to generate a lot of different phylogenies. Using different methods, different models or approximation schemes, different genes or sequences from each species, or simply bootstrapping "new" samples from your existing dataset. A phylogeneticist usually has dozens of trees to choose from, which is a sort of crude bootstrap method itself. If trees look similar, they're probably pretty good. If they don't, you have a problem.


What is "contigs" in Picard's ReorderSAM? I've used BWA to map my NGS reads against the hg38 genome, and I have a BAM file. I'm not doing genome assembly, and my reference genome file has the human chromosomes. Thus, I shouldn't have "contigs". But...

  https://broadinstitute.github.io/picard/command-line-overview.html#ReorderSam

and quote:

  ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs

Q: What does contig ordering mean, for my whole-genome-sequencing experiment? In particular, what does matching the contig against a reference file mean?

I'm not familiar with picard and their reorderSam function, but as far as I know/understand from their documentation they mean this:
The ordering of the contigs while using a reference sequence.
Like this:

   Figure 5: Anatomy of
  whole-genome assembly. In whole-genome assembly, the BAC fragments
  (red line segments) and the reads from five individuals (black line
  segments) are combined to produce a contig and a consensus sequence
  (green line). The contigs are connected into scaffolds, shown in red,
  by pairing end sequences, which are also called mates. If there is a
  gap between consecutive contigs, it has a known size. Next, the
  scaffolds are mapped to the genome (gray line) using sequence tagged
  site (STS) information, represented by blue stars. © 2001 American
  Association for the Advancement of Science Venter, C. et al. The
  sequence of the human genome. Science 291, 1304–1351 (2001). All
  rights reserved. (source)

ReorderSAM (Picard)
So in Picard you have your INPUT (File), the reads in this file are then mapped on the REFERENCE (File). This can also be seen in their code:

// write the reads in contig order
109
            for (final SAMSequenceRecord contig : refDict.getSequences() ) {
110
                final SAMRecordIterator it = in.query(contig.getSequenceName(), 0, 0, false);
111
                writeReads(out, it, newOrder, contig.getSequenceName());
112
            }

(code source)

  ReorderSam reorders reads in a SAM/BAM file to match the contig
  ordering in a provided reference file

Some more background
There are two main approches two obtain a genome sequence:

  there are two "main" approches for this:  g. Second-generation
  sequencing technologies produce millions of short(a few hundred bp)
  strings of nucleotides (reads), which is ideal for resequencing when
  reads are mapped to a reference genome (reference-based assembly). De
  novo genome assembly based on second-generation sequencing is
  challenging due to difficulties with GC- or AT-rich and homonucleotide
  DNA stretches, which are under-represented in the sequencing output (source)

The characteristics of these are:
de novo

  no bias towards a reference genome
  no template to adapt to
  the    assembly is normally more fragmented
  it normally works better for large-scale/median scale differences (source)

reference mapping

  less contigs
  in most methods the reads that don't map are not used in the final sequence (this is also the case with reorderSAM: Reads mapped to contigs absent in the new reference are dropped
  you look what is similar to your reference genome
  SNPs and very small veriations are more easily positioned and compared among groups (source)

I would highly recommend to watch this short animation to differentiate between these two and understand what reference genome mapping is.


By what method do ants dissect and hold soil Not sure if this is the correct stackexchange site - please migrate/advise as you see fit.

I'm interested in the method by which ants "break off" a small amount of soil and then hold it in their jaws (?).

To clarify I know ants break off soil in small quantities, so that a single ant carries very little soil; I'm interested to understand what exactly how this happens. For example does the ant literally pick the soil directly, or does it brush it loose first etc. Further to this I'd like to know how the ant holds the soil. Is it akin to the soil being atop a palm, or more like being held between two hands?

Broader context: I'm looking into making a model of this type of soil movement and I wanted a more detailed understanding.

Short answer

Ants use specialized facial structures called mandibles to cut, shape and carry soil and other matter.

Background

you say "I know ants break off soil in small quantities, so that a single ant carries very little soil...". On the contrary I would say - Ants can carry relatively a lot of soil, as they can lift up to about 100 times their own body weight. In absolute terms, however, the weight carried is about 500 mg (Spectrum).

Source: The World's Best Photos

The structure that ants use to break off and carry soil are their mandibles:

Source: Tree of Life Web Project

Mandibles are specialized bodily structures typical for insects, and I quote from the University of Sydney website:

  The mandibles are the first pair of jaws in insects, moving laterally (i.e. from side to side) when in use. Mandible shape is strongly influenced by function and is therefore highly variable. For example a chewing insect will have strong tooth-shaped mandibles while in a sucking insect they will be thin and needle-shaped. Mandibles are used to cut, chew and tear food as well as to carry objects, fight and mould materials such as wax or soil.


Horned Mohawk looking insect. What is it? Any ideas? I didn't know any other way to explain it.

I live in Indiana, USA if that helps.

Someone said it might be a "stink bug" but I'm not sure and not willing to find out!

Its definitely a True bug (Hemiptera), and based on its distinct pronotum and small head I'm guessing its a Wheel bug (Arilus cristatus). It is a common species that is also found in Indiana.

They are aggresive predators and are part of the family Reduviidae also known as Assassin bugs. Assassin bugs have a painful bite, and they inject a toxin when they stab their victim (so humans should watch out). This is not a part of the world I know well though, and there might be similar closely related species that I've missed.

Links:

Bug guide
Records in GBIF
Univerity of Florida: Entomology & Nematology

Some pictures:


Why do spiders have a leaf at the bottom of a piece of web? I've lately seen a lot of instances where a leaf is dangling from a piece of web coming down off a tree. What purpose/s does this serve for the spider? Is it some sort of mechanism for the spider to determine the wind / disturbances in that region?

I've seen a suggestion that it's to help act as a plumb during web construction to keep part of it tight, but do we actually know for sure?

Here's a national geographic image showing what I mean:

http://ngm.nationalgeographic.com/ngm/photo-contest/2012/entries/177963/view/

As far as I know, it has a practical effect. Spiders hunt for small insect and don't like when bigger animals damage their webs. So that they make the web visible for mammals, but in the way which doesn't prevent the prey from being caught.

I don't have reference for this, my colleague (entomologist) told me so.


How do metal ions acting as enzyme cofactors "find" their respective enzymes? Metalloproteins are metal-dependent proteins, i.e. they require certain metal ions (copper, magnesium, zinc, etc.) for their correct function in the body. Since proteins are manufactured inside cells by the ribosomes and metal ions are exogenous materials, i.e. are obtained from food, how would a metalloprotein and its respective metal ion find each other in the body? Are the metal ions taken inside all body cells? Does the meeting take place in the blood?

A quick Google search retrieved nothing useful.

The metal ions are transported across cell membranes by various mecanisms like channels, pumps or extracellular receptors for carrier protein.

The loading step mostly happens in the cell. Once transported inside, some ions just diffuse into their binding site on the protein; others, like iron, need a scaffold.

Some essential enzymes are metalloproteins, for example most ATP-using enzymes need magnesium; and the respiratory chain needs iron. Thus most cells will have transporters for these metal ions.


Why has grey hair evolved? A vast majority of humans get at least some grey hair as they age. As far as I know this applies to both genders and all races. Presumably this means that at least some grey haired humans have noticeable reproductive advantage, or maybe they had it in the recent past.

Theoretically, because this feature is so prevalent, there must be a strong evolutionary pressure to keep it. Am I right? If so, what is it?

Presumably this means that at least some grey haired humans have
  noticeable reproductive advantage, or maybe they had it in the recent
  past.

No it doesn't.  Natural selection is not that strong, it doesn't optimize every single possible physical trait towards maximum reproducing.

And as others have mentioned, having lots of grey hair usually happens after reproduction is over.  Historically, lots of women did a lot of reproducing before they had any grey hair.


In biosynthesis of cysteine and methionine, where does the sulfur come from? Methionine and Cysteine are the two amino acids containing sulfur. According to wikipedia, cysteine is built from methionine. However, the wikipedia also claims that methionine is synthesized from cysteine.
So, a chicken and egg problem (esp. since eggs are a rich source for those proteins). Where do living things get their sulfur to build these amino acids in the first place, in what forms is sulfur available biologically?

Microorganisms (and plants) make cysteine from serine using H2S as the sulphur source. Condensation of these two directly gives cysteine in some bacteria, but most often the reaction sequence is:

serine + acetyl-CoA >>> O-acetylserine + CoA-SH
O-acetylserine + H2S >>> cysteine + acetate + H2O

As you say, in terms of the sulphur, cysteine and methionine are interconvertible.
Animals rely upon their diet for methionine, and can make cysteine from that methionine.


Found this spider in my garden I found this guy in my backyard. I have no clue what he is, though I'm assuming it's a jumping spider after doing a little bit of searching.
For context, I live in Southern California, close to being right in between LA and San Diego. It's suburban, though there are a few reserves that are close by. It is incredibly small, probably no bigger than a dime. It's mostly orange and black with some rings of white on the legs. It's pretty hairy as well.
The only thing I'd like to know is if it's poisonous or dangerous, as I don't need my dogs getting sick or injured. If possible, I would also like some links for some background reading on it!

As Karl mentioned in his comment, this is a jumping spider in the family Salticidae.

Based on your location and the coloration, I would suppose this might be Phidippus adumbratus.

 Source: Wikimedia

You can see more pictures here and here.

I don't think the angle nor zoom quality of your photo can be used to definitively ID your specimen to species. However, as you can see in the photo above, P. adumbratus is not a bad candidate.

According to Edwards (2004) this genus is sometimes difficult to tell apart, but P. adumbratus can be distinguished from other Phidippus species as follows:

  Males can be distinguished from the closely related P. boei (and all other species of Phidippus in California except P. aureus) by the orange scales dorsally on both carapace and abdomen (P. boei is black with a red abdomen dorsally), although island populations have the OQ scales darker and reduced in number. P. adumbratus has a much longer, narrower embolus apical portion than P. aureus. Females can be distinguished from P. kastoni by the shape of the internal ducts of the epigynum; the duct heads are narrow in P. adumbratus (broad in P. kastoni) and the gland is visible as a rounded projection on the anterodorsal surface of the duct head (not visible in P. kastoni). Females are covered dorsally with orange or gray scales (usually with white abdominal spots), unlike the females of P. boei, which have a similar epigynum but are black in color without markings, or with red dorsal scales only on the abdomen (without spots).

If you'd like a much more detailed of description of P. adumbratus (or others in this genus), you can find whole-page detailed descriptions in Edwards's publication quoted and linked above.

A map of geo-referenced records from GBIF shows the occurrence of this species in southern California:

Edwards, G.B., 2004. Revision of the jumping spiders of the genus Phidippus. Occasional Papers of the Florida State Collection of Arthropods, 11.


How can a good SD / Kozak sequence enhance translation efficiency? In prokaryotes, if there is an mRNA with a good (almost the consensus sequence) Shine-Dalgarno (SD) sequence, ribosome proteins will bind to it.
In eukaryotes, ribosome binds to the 5' cap, then start sliding until it finds a good Kozak sequence and translation initiates.

Why will a good sequence (SD & Kozak) greatly enhance translation efficiency in both cases?  I can't understand this since translation is about the bases downstream of those sequences, I have no idea how they can exert effects on overall efficiency.

in eukaryotes, how can ribosome 'foresee' which is the best Kozak in a mRNA? E.g. there are 2 'AUG' in that mRNA and the first one has a better Kozak consensus. So how can ribosome 'know' the second Kozak is worse than the first, and start translation at first 'AUG', but not continue sliding towards the second Kozak?

Thanks

I would strongly recommend looking in more detail into available resources for SD and Kozak sequences, wikipedia basically answers these questions and has plenty of further reading if you desire to explore these questions.
At the same time, remember that these are statistical processes involving thousands of molecules, rather than deterministic processes happening at a single molecule. Thus, what changes with different sequences is a rate at which some step occurs (e.g. rate of ribosome assembly, rate of translation initiation, rate of start recognition); none of these steps will occur with 100% probability on every mRNA molecule.
What this means is that you can write down equations for kinetic models of translation, allowing us to apply principles of mass action and rates of reaction from elementary chemistry. Having a higher rate of ribosome affinity for a sequence is therefore similar in effect to just having more mRNA, in the sense that in both cases you will do more translation and make more protein.
Thus, it might be easier to use the terminology of "strong" and "weak" SD/Kozak sequences. A strong sequence has a high rate of reaction and a weak sequence has a low rate of reaction. Here, the "reaction" in question is ribosome binding, or translation initiation, or whatever process we're currently studying.
Now, as to the specific questions:

Sequences alter the rate at which downstream processes occur. So, e.g. a weak Kozak sequence will often simply not initiate translation, and the ribosome will fall off without translating anything. This will almost never happen with a strong Kozak sequence, so a strong Kozak is more "efficient" in the sense of more reliably leading to translation. A strong Shine-Dalgarno sequence increases the rate at which ribosome binding occurs.

Both ribosome binding and translation initiation are necessary for protein production, so if you increase the rate at which these processes occur, you increase translational efficiency in each case.

There is no "foreseeing". Think about this mechanistically. The ribosome scans 3' along the mRNA, starting at the point of attachment. Also, each ribosome attachment to an mRNA can only start one translation event. Once a ribosome stops scanning and starts translating, it does not recognize subsequent Kozaks.

Thus, if there is a strong Kozak sequence, then translation will almost always start at the strong sequence, and will never have the opportunity to start at a sequence further 3'. It is mostly only when a 5' Kozak is weak that further Kozaks get recognized at all ("leaky scanning"):

The first start codon closest to the 5′ end of the strand is not always recognized if it is not contained in a Kozak-like sequence. Lmx1b is an example of a gene with a weak Kozak consensus sequence.[22] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. Exceptions to the first AUG rule may occur if it is not contained in a Kozak-like sequence. This is called leaky scanning and could be a potential way to control translation through initiation.[23] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. (Wikipedia)

So it's not that Kozaks are required, necessarily. You just need some set of circumstances which increase the probability that the ribosome starts translating next to a start codon. The Kozak simply happens to be an efficient way to get a ribosome to start translating. The closer a sequence is to the consensus Kozak sequence, the more efficient it is, because the probability of translation initiation is higher.


All neuromodulators (dopamine, serotonin, acetylcholine, histamine, and norepinephrine) act only on metabotropic receptors? All neuromodulators like dopamine, serotonin, acetylcholine, histamine, and norepinephrine act only on metabotropic receptors?

Not all neuromodulators act only on metabotropic receptors. However, you are correct to observe that this is a general rule of thumb.

Of the substances you have listed:

Acetylcholine is not primarily a neuromodulator, but rather a "normal" neurotransmitter. As such it acts on both ionotropic and metabotropic receptors.
Serotonin - the one exception among the neuromodulators you have listed - acts on numerous classes of metabotropic receptors, but also on the 5-HT3 receptor, which is ionotropic.
All other neuromodulators you have listed act on metabotropic receptors only.

This tendency of neuromodulation to be metabotropically mediated is possibly a consequence of the nature of the neuronal function itself. Neuromodulatory systems do not per se relay information, but change how other information relays work. As such there is no need for the most rapid, temporal, coding (best achieved via the more rapid ionotropic signal transduction), and a slower coding may even be more efficient.


Fats as energy source As we know that the preferred source of energy for our body (source) are carbohydrates but heart muscle is an exception and need some explanation for this exception, that why the preferred source of energy for  or cardiac muscle are FATS?

Nice question! I've found a great article about fatty acid metabolism in heart muscle in healthy and disease conditions. As it is stated in this paper long chain fatty acids are utilized through beta-oxidation to meet the high energy need of continuous contraction. Beta-oxidation of long chain fatty acids produce far more ATPs than glucose. According to wikipedia:

For an even-numbered saturated fat (C2n), n - 1 oxidations are necessary, and the final process yields an additional acetyl CoA. In addition, two equivalents of ATP are lost during the activation of the fatty acid. Therefore, the total ATP yield can be stated as:
(n - 1) * 14 + 10 - 2 = total ATP or 14n-6 (alternatively)
For instance, the ATP yield of palmitate (C16, n = 8) is:
(8 - 1) * 14 + 10 - 2 = 106 ATP

While a single molecule of glucose produces 36 ATPs (under aerobic conditions)
Thus use of fatty acids (fats) in cardiac muscle is beneficial because of their higher energy concentration. Also it is noteworthy that this does not occur in isolation, so this is a response to contractile work and other competing energy sources (such as glucose, lactose etc). Also excessive uptake and beta-oxidation in disease conditions can even endanger cardiac functions. See details in the linked paper.


How does someone with red-green colorblindness see yellow on a monitor/television? I recently watched the video This Is Not Yellow explaining how red, green, and blue pixels can be used to create images of all other colors. Since yellow is created with red and green pixels, how is a person with red-green colorblindness (me, for instance) able to perceive yellow on a monitor?

Normal people see color due to the bellow mentioned combination of red, green and blue:

But due to genetic factors, The graph Distorts:

Now,If consider the normal Color code for yellow:

Yellow = R(255) + G(255) + B(0)

Or in other words

Max. Red + Max. Green + no Blue = Yellow

That means even if you can see a little of Red and Green, you can still a little deeper or lighter shade of yellow.

So Summing it up in the images:

Normal

Red ColorBlind

Green ColorBlind

Blue ColorBlind

Source:

Coblis — Color Blindness Simulator

A quick introduction to colorblindness


Why are there 10 base pair steps, not 16? In a biochemistry course I'm taking, the lecturer emphasised that there are 10 possible base pair steps; I've included a screenshot of a slide stating this. This confuses me, because I cannot work out why it's not 16; why are the 6 greyed out in the image not allowed (for example, CG stacked on CG counts, but GC stacked on GC doesn't)? TA|AT is listed as distinct from AT|TA, so it's not that the greyed ones are redundant.
I've found a couple of papers mentioning that there are 10 base steps, but not why. (I can't get hold of the lecturer.)
Thanks in advance!

Unlike RNA, where the sense of the molecule is unique, DNA is double stranded, with the two strands having the opposite sense. In the sense of chemical stability it odesn't matter, which sense is considered positive, and which is negative.
Thus, if we consider a base pair step WX|YZ, we have Y folowing W on the positive sense strand (W->Y), and X following Z in the negative sense (antisense) strand (Z -> X). This means that, if we labeled the strands differently, we would have Z->X on the positive strand and W->Y on the negative one, i.e., we would have base pair step ZY|XW. I.e., the general symmetry rule is
$$
WX|YZ \rightarrow ZY|XW
$$
In particular, this means that CG|CG is identical with GC|GC, whereas TA|AT is identical with itself, rather than with AT|TA.
Visually, this symmetries are obtained by rotating the image of the base pair step by 180 degrees, as can be readily seen in the image provided in the question.


Is it possible nowadays to artificially create an organism just by inserting organism's DNA into an artificial environment? Let's say we have a DNA of a bacteria and we want to recreate the bacteria just from this DNA. Is it possible nowadays to get this DNA and insert it into some artificial solution so that from this DNA a bacteria coulb be grown?

There may be technical issues that make certain genomes easier to transplant than others, but it can and has been done. Craig Venter's lab used such a transplantation technique to discover what minimum set of genes are required for viability in an engineered bacteria.


Embryonic cells, when can you detect them in vivo? (In order to do whole genome sequencing) I was wondering, when is it possible to extract cells (humans or mice) in order to sequence them and detect diseases.
Extra: Urine of the embryo in humans is excreted in the 16th week, so I guess that then it's possible to extract some embryo cells.

EDIT
In other words, when is it possible to grab enough DNA to know the full genome of the embryo without damaging it?
In order to sequence it and avoid most genetic diseases and regulate the weekly abortion limits.

Thanks

As usual, the answer is "it depends what you mean". There is a large existing field (prenatal genetic diagnostic testing) which trying to diagnose genetic diseases in fetuses using different technologies. These technologies are described more in points 2 and 3 below, whereas point 1 is a somewhat academic statement about the technical capabilities of genomic technology in pure research settings which are currently not really relevant for medical applications.

I can think of 3 different answers to the question as originally posed:

With currently available sequencing technology you can never know
the full genome sequence of a human well enough to see all the potentially damaging variants. The "finished" human reference genome in
fact has gaps and errors that are constantly being corrected. For
more information about what "finished" means, see here. Only one assembly of a telomere-to-telomere human chromosome exists as far as I know, and that's only the X chromosome. Even accepting that this best available technology is good enough, it also relies on things like the ability to isolate lots of high-molecular-weight DNA, which makes it very tough to do on the amount of cells you could get from a newborn without highly invasive procedures such as e.g. sampling fetal tissue in vivo. My guess is that even amniocentesis would be very hard to get good HMW DNA from.
With currently available sequencing technology you can however test
very early provided you used IVF, at least as early as the 100-cell stage
(probably earlier). This is a chancier method that will miss a lot
of information but gives you good enough info to diagnose
aneuploidies or other very obvious variants.
Alternately, you can screen cell-free fetal DNA as early as 7
weeks (or possibly earlier). However this does not involve
isolating cells so it is potentially not what you are thinking
about. It is somewhat better information than preimplantation
screening, but rather worse information than you can get from whole
cells.

Likely none of those are exactly the answer you want, but it's also a less simple question than it appears at first: a) getting cells is hard and probably not necessary for the current tech, and b) the tech isn't actually as good as generally advertised.


Difference between reciprocal inhibition and regular muscle movement? I was looking into a condition I have, anterior pelvic tilt, quite a bit. I ran into a website describing part of the issue as reciprocal inhibition. This was my confusion:

Reciprocal inhibition, defined by just about everyone, is the relaxation of muscles antagonistic to muscles currently contracting, and vice versa. How is this different from regular muscular flex? When we flex a muscle, don't the antagonistic muscles relax to compensate, same as in reciprocal inhibition? Thanks.

What is the difference between reciprocal inhibition and regular muscle movement?

Reciprocal inhibition is part of regular muscle movement. It is controlled by the stretch reflex controlled by the muscle spindle. It's an important part of a functioning muscle and spinal cord, and not pathologic at all. However, this same reflex, in an excessively tight muscle on one end of a joint, would cause an excessively loose muscle on another end of a joint.

Here is an image showing this reflex, from Brust Practice of Neural Science, Chapter 6.

I can't give you any medical advice on this site, so I can't put that in context, but I think that answers your biology question.


Isotretinoin and retinoid receptors in brain confusion? I am considering starting a treatment with Accutane(Isotretinoin), however I am not sure about what the effects on the brain are. Here are two studies that contradict each other:

http://www.ncbi.nlm.nih.gov/pubmed/11696672
The first one states that using an antagonist, they increased the rats' working memory. So logically, using the agonist (isotretinoin), it would cause a loss of working memory?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360864/
Here they state that not only did isotretinoin not have negative effects, but it actually had positive effects.

I am more inclined to believe that it has negative effects, because most anecdotal evidence says that it makes patients feel "foggy" and "forgetful". Can anyone please enlighten me? What exacly does this stuff do to the brain and is it irreversible?

The second study did not even examine the pharmacological effects the drug had on the brain. The researchers noted depression scores tended to increase while on the drug, but not in significantly significant way. Keep in mind the drug is clearing a disfiguring condition, so this novelty may interfere with the ability for measures to detect psychiatric issues.


How to obtain a list of proteins sorted by the ~1400 unique protein folds? The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB.  However, I do not see any method to access this particular data.

A list of each of the 1400 folds (just an id number, and/or a descriptor)?
For each individual fold (of the 1400), a list of PDB IDs for proteins which are known to adopt each individual fold?

If there is a simple way provided to do this it is very well hidden. The tedious and stupid way to do 1 (get a list of folds) would seem to involve rolling your own:

Go to http://scop.berkeley.edu/ver=2.07 (or whatever is the latest version).

Click on each of the 12 classes in turn. e.g. (a) all alpha proteins will take you to http://scop.berkeley.edu/sunid=46456 .

Save the source of each page as text.

Write and run your own parser to pull out the sunid () from the http://scop.berkeley.edu/sunid= and the description line if you wish. (This assumes you program.) I think this sunid is the fold id.

If you can than find some database or table that has PDB and sunid values in it, you can write another program to find the answer to 2.
Alternatively… (appended January 2021)

Download dir.cla.scope.2.07-stable.txt (or the latest version)
Save as a text file.
Open in Mircorsoft Excel. (Just dragging onto the app icon formatted it properly on my Mac. Your mileage may vary.)
You can just select the column with the ids, paste into another sheet, and then remove duplicates to get all the different fold ids. (Alternatively, you have about 276,000 entries to do with whatever you wish.)


Why are riboswitches mostly present in bacteria and not in eukaryotes? Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation.

Most of the known riboswitches are found in bacteria, there are few examples of riboswitches in eukaryotes. There are no classical riboswitches in humans as far as I know (there is one example, but triggered by a protein and not a metabolite), it seems that more complex organisms tend to use other methods of gene regulation.

Are there any known reasons for this? What are the drawbacks of regulating gene expression with riboswitches compared to using regulatory proteins? Is there an explanation for the lack of riboswitches in more complex organisms?

You get higher accuracy and more timely control at a post translational level (think about the time it takes to affect a pathway with cofactor stimulation compared to gene expression stimulation). You also have more points of control throughout the pathway if you affect activity post translationally allowing for a more complex interaction between stimulating and repressing factors.


What's a segmented copy number profile I am studying copy-number variation. I am reading

  C. H. Mermel, S. E. Schumacher, B. Hill, M. L. Meyerson, R. Beroukhim, and G. Getz, “GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers,” Genome Biol., vol. 12, no. 4, p. R41, 2011.

Here, it is written that

  Segmented copy number profiles represent the summed outcome of all the SCNAs [somatic copy number alterations] that occurred during cancer development. Accurate modeling of the background rate of copy-number alteration requires analysis of the individual SCNAs. However, because SCNAs may overlap, it is impossible to directly infer the underlying events from the final segmented copy-number profile alone.

It is not clear to me how a segmented copy number profile represents the summed outcome of all the SCNAs. Is it because different alterations can be present in the same sample, or can alter the copy-number in different moments, or both?

And, do they overlap spatially, temporally, or both?

Yes, one sample can contain different alterations. For each patient there is typically one tumour specimen that is removed. That specimen may be divided up into several samples (e.g. one for DNA sequencing, one for RNA sequencing, one for methylation microarray, and one for copy-number variation microarray), however each sample contains thousands of individual cells and two adjacent cells may have different CNVs (depending on their clonal ancestry, etc.). In other words, a tumour is a heterogeneous collection of cells. For some tumour types there can even be healthy cells mixed in.

The term in the literature is clonal evolution, there is a nice image in this article: Tumor Heterogeneity


Identification of an Australian pigeon in the NT This pigeon was spotted in Darwin, NT, Australia. I am not able to solidly identify it using my books or google searches. My best bet is a Torresian Imperial Pigeon (Birds of the NT website).

Your bird appears to be an Imperial Pigeon of the Ducula genus. Based on the limited angle of the lone picture of your specimen, my best guess as to the species is the Torresian Imperial Pigeon (Ducula spilorrhoa).

The species is a relatively large, pied species of pigeon found in various habitats (forest, woodland, savanna, mangrove and scrub) in Australia (including in the Northern Territory where you saw your specimen), New Guinea and nearby islands.
You can see more pictures, videos, and calls here, as well as additional info here.
Your specimen is unlikely the closely related  Pied Imperial Pigeon (Ducula bicolor) because:

D. bicolor is a  Southeast Asian species

D. bicolor has a bluish grey beak, whereas your specimen and D. spilorrhoa both have a yellow beak.
Note: Your specimen is also unlikely Ducula subflavescens because the feathers are white and not yellow, and it is unlikely Ducula luctuosa because that species is endemic to only a few islands.


What determines a successful protein expression in E. coli? Some proteins express well in a heterologous host; others- don't. A few requirements are known to determine the protein expression, like a strong promoter (like T7) for transcription and a strong ribosome binding site for translation. I am working with a protein, which consists of 2 subunits - alpha and beta. Both of them are on a plasmid with T7 promoter in front of the beta subunit (i.e. the construct is T7 promoter, CDS for beta subunit, CDS for the alpha subunit). The beta subunit expresses well, but the alpha doesn't. Do you thing this has something to do with the local environment (promoters, RBSs, etc) and how much does it depend on that? How can I increase the protein expression?

One important aspect when expressing a protein from a different organism in E. coli is that the codon usage of the original organism is likely different from the codon usage of the E. coli used for expression (Codon usage bias).

Though the genetic code is degenerate, not all codons are equal. They might encode for the same amino acid, but organisms tend to favor specific codons over others and the tRNAs for those codons tend to be present in different concentrations. When you now have a lot of codons in your sequence that are very rare in E. coli, the expression will suffer because the tRNA for those codons is not present in high enough concentrations to sustain the translation.

There are two ways of compensating for that, either you get your E. coli to produce more of the rare tRNAs, or you optimize your sequence to use different codons. For the first solution you can buy certain E. coli strains that contain plasmids encoding the tRNAs that are rare in E. coli, one of those strains is e.g. the Rosetta BL21 strain.

For optimizing the codon usage there are several companies offering to synthesize optimized sequences. There are also tools available online, but I have no direct experience with those.

The optimization is also not as easy as just using the most prevalent codon every time, it has been shown that optimizing the codons to match the translation speed in the original organism can enhance the expression yields. For some proteins, pause sites during the translation might be necessary to ensure proper folding. If the protein doesn't fold correctly it will be quickly degraded and your yield will suffer. This is described in the article "Heterologous Protein Expression Is Enhanced by Harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host" from Angov et al.

You'll find a nice overview about the whole topic in the article "You're one in a googol: optimizing genes for protein expression" from Welsh et al.


How did interspecies reciprocity involving cleaner wrasses originate? The small bluestreak cleaner wrasse (Labroides dimidiatus) will approach a much larger fish (for example a grouper such as Cephalopholis miniata), enter its mouth, and spends several minutes cleaning its teeth. How did this behavior evolve? Wouldn’t the first cleaner wrasse that was bold enough to approach a larger fish have been immediately eaten? Since, in this encounter, the behavior of both fish isn’t learned, it must be encoded in their genomes. How could the appropriate coding gradually evolve?

Cleaner wrasse don't only clean within the mouth; although some species may specialize towards mouth-cleaning, it's likely that this behavior began with cleaning elsewhere on the fish's body.

Some studies (e.g. Bshary, 2003) suggest a large effect of cleaners on fish populations/diversity, so it seems that there are strong selective pressures for evolving behavior permissive to cleaning fish.

The cleaners themselves seem to have evolved cleaning traits on many occasions (see Baliga & Law, 2016). Although there are some obligate cleaner species, it's more common for cleaners to clean as juveniles, and the most common transition between cleaner behaviors is from non-cleaners to juvenile cleaners.

Therefore, it seems like the first cleaners were very small fish outside the typical prey target size of the cleaned fish. If there is strong selection towards individuals who tolerate these small, non-prey cleaners, it's reasonable to expect that this behavior could expand towards larger cleaners, and eventually to the more extreme versions of the behavior like allowing cleaners in the mouth.

Baliga, V. B., & Law, C. J. (2016). Cleaners among wrasses: phylogenetics and evolutionary patterns of cleaning behavior within Labridae. Molecular phylogenetics and evolution, 94, 424-435.

Bshary, R. (2003). The cleaner wrasse, Labroides dimidiatus, is a key organism for reef fish diversity at Ras Mohammed National Park, Egypt. Journal of Animal Ecology, 72(1), 169-176.


Why might food go bad in an oxygen-free environment? I was recently watching a video from the International Space Station (Making a peanut butter sandwich in space), and I noticed he mentioned that a tortilla kept in an oxygen-free environment could last up to 18 months. Impressive, but it got me thinking: Why would some foods ever spoil if kept in a state where molds would not be able to grow? Would it be that other micro-organisms in things like the moisture present in the food eventually take their natural toll? Just a curious thought I had while watching through these awesome ISS videos.

Thanks for any answers!

First of all, you assumed that this tortilla went bad after 18 month, not that austranaughts just decided to eat it?

More importantly, there is thing called anaerobs. Just like your muscle don't use oxygen in times of acute stress (force requirement), so there are organisms that don't care much about oxygen. As it happens in muscle, it happens in yeast during fermentation when sugars are turned into alcohols and released energy is used to propel molecular machinery. So, if there are sugar molecules on tortilla, there are still microbes that willing to prosper on it.


Importance of knowing GC Content of an organism I was looking at the GC content percentages of few organisms. I also know calculating the GC content percentage. But, what I want to know is, what information would we get., let us suppose if human genome has 40% of GC in the genome.

Does it help us compare the number of genes between different species, for example, a bacteria has less GC content than human, so does it mean Human produce more genes than bacteria?

or Is it that the 40% of the genome,has coding regions in them and more genes are found in those regions? What is the number "40%" actually indicate us?

Please help me understanding the concept. Would be thankful your answers and suggested reading.

EDIT: My question is what does knowing percentage of GC content help us knowing? If the GC content is 40%, does it correlate to number of genes in the genome?
Regards,
Prakki Rama.

Interesting question. The GC-content seems to evolve over time and it also seems that the GC-content of coding regions is higher than for the surrounding non-coding regions (see reference 1). If there is a specific function for this higher GC-content or not is (if I understand this right) debated among the groups which do research in this field. Have a look at the references (and probably also their references) to decide on this:

Both selective and neutral processes drive GC content evolution in
the human genome.
Integrating genomics, bioinformatics, and classical genetics to
study the effects of recombination on genome evolution.
Recombination Drives the Evolution of GC-Content in the Human Genome
GC-Content Evolution in Mammalian Genomes: The Biased Gene
Conversion Hypothesis
Contrasting GC-content dynamics across 33 mammalian genomes:
Relationship with life-history traits and chromosome sizes


Why do orcas eat only the tongue of whales, liver of sharks, etc.? I noticed that although killer whales are clearly the top predator living in the present oceans, some of them appear to be very picky with their meals.

After spending hours hunting down a whale, pretty much the only thing they eat is the tongue. I'm not sure how that satisfies their hunger, especially considering how long and arduous the hunt took.

Then there are orcas hunting sharks and eating virtually only the liver. For such a dangerous prey, is such a delicacy worthwhile? I mean, what happens if they're starving after the hunt?

Any relevant comment will be greatly appreciated. Thanks!

Killer whales have a wide range of prey. They hunt in coordinated packs called pods. They are very organized on a hunt and each has a specific job prior to the kill.

Where the confusion might be coming from is that different pods have different habits. It is true that Orca's have been witnessed eating only the tongue, this is not the norm. They tend to eat the tongue first because it's muscle, with lots of protein. Plus, they like the tongue, as we like a good steak. However, in most cases they will consume as much of a whale (typically baleen, or blue whales) as they desire. In fact, whalers hate them because they will follow whaling ships and wait for the fishermen to harvest a whale. They will then rush in and gorge themselves. Another case of them only eating the tongue is when they are well fed. In this case, they can afford to be picky and may only eat the tongue. Oh, by the way, the average tongue is the size of an elephant. So, it's no small meal.

As for sharks, it's pretty much the same scenario, however, there are many cases of Orca's only eating a great while shark's liver. The reason they target the liver (and they do it with surgical precision) is because it contains large amounts of a compound called squalene. Squalene is important to synthesis of certain chemicals in the Orca's body. They will also target the heart, as well. The attacks of great white's is a more recent trend among killer whale pods. They are quick learners and once they feel the benefits of these organs, they will then focus on the sharks when their bodies tell them they need the squalene. Of course, they don't know that. They just know they feel better and stronger after consuming GWS organs.

There may be pods out there that tend to have these habits (outlined above) more than others. Resident pods (staying in one area) seem to be calmer and are not as likely to have the tongue activity, but it is the residents that are often that which kill the GWS's for their organs.

Transients are far more aggressive than residents. They are likened to pack wolves and will do some extremely cruel things (by human standards). These are the one who are far more likely to eat only the tongue of a whale. It could be that since the shark organ habit hasn't been happening for very long, it's the residents who figured out the connection between health and these shark organs.

Another factor that could come into play is that scientists/marine biologists tend to believe that there are different species of killer whales. This may play a role in dietary habits as well.

Killer whales are the top (known) predator in the water. While a much larger whale, or GWS could potentially kill one, they are typically no match for a pod and will instead steer clear and only fight if no other alternative presents itself.

I hope this helps. I'm no expert, I've just done my research.


Can anyone identify this tiny insect? Very high magnification, size of a very small ant. Found in Menorca, spain

That's a barklouse, order Psocoptera. https://en.wikipedia.org/wiki/Psocoptera
It's very hard to identify those to species in a picture.


How to calculate virus titre from qPCR I harvested some lentivirus from 293T cells and want to titre the result. I infected 293T cells on a well plate with 400,000 cells per well which I infected with virus stock, and 1 in 10, 100 and 1000 dilutions (as well as a few uninfected wells). After 72h incubation I trypsinised the cells and used FACS to titre first, but 293T do not express the promoter under which GFP is located in some samples and hence these do not appear on FACS. As an alternative, I extracted the genomic DNA from all samples using a QIAGEN DNeasy kit (also the samples which I was able to titre by FACS already) and then performed qPCR on them.

I used the ABI PRISM 7000 SDS: http://www.cgenetool.com/products/abi_prism_7000.shtml

Included on the PCR plate were:

Number standards: 1000, 10k, 100k, 1m copies
Samples in triplicate
No-template controls as well as untransduced controls

Each of those was doubled, once with primers and probe for WPRE (an element specific for the lentivirus) and once with primers and probe for beta-actin (a housekeeping gene present in all cells).

The results returned by the machine include for each well the cycle at which the threshold fluorescence was crossed - along with the automatically calculated quantity of copies (which the software calculates from the standards I assume).

Since I named the triplicate samples identically, it also automatically calculated the mean quantitiy among each triplicate (practical, eh?). I checked if there were any outliers which should have been excluded from the means but everything was fine.

So now for example I have a result of 700k for the quantity of WPRE in sample A. The quantity of beta-actin in sample A was 6.82 x 106. The transfection was 400,000 cells per well, sample A was transfected with 10uL of viral stock diluted 1:100.

How do I calculate the virus titre per mL from this?

I have been given the formula: WPRE Qty / (b-act Qty*0.5) * cells in well (400k) * dilution factor (100), but am struggling to figure out a) why b-act Qty is divided by 2, b) whether the result would be virus titre per uL or per 10uL (transfection volume) and c) how beta-actin can have almost 107 copy numbers consistently across all samples when there were only supposed to be about 105 cells...

I have 2 doubts here.

You obtain your viruses from the media whereas Actb measurements can be performed only in the cell lysates.
Actb is just a reference to normalize for the cell count: higher the cell count higher will be the viral titre because of higher number of infected cells. But that is immaterial if your aim is lentiviral transduction where you are only interested in obtaining titre values and not measuring the efficiency of its formation.

You can simply do qPCR with the media sample and the standards and regress the measured Ct values of the samples to obtain titres.


Is the male bee's penis homologous to the female bee's stinger? Considering that when a bee stings it loses its stinger and dies, this is similar to the male drone losing its penis and dying after copulation. It also seems similar that each event basically rips the abdomen open. Are the two structures a homologous pair?

After a little bit of digging I was able to find a couple of facts that seem to verify that the drone bee's penis is in fact homologous to the worker bee's stinger:

This Wikipedia article about the stinger that says a honey bee's stinger is "a modified ovipositor as in other stinging Hymenoptera".

This book (actually about soil arthropods) states very specifically that, "The ovipositor, with which the female lays her eggs, is homologous to the male's penis.".


Can someone please explain the following jargon to a layman I was reading an article on a substance called apigenin:

  Apigenin can inhibit both aromatase and 17β-hydroxysteroid dehydrogenase (17β-HSD) with the inhibition of 17β-HSD being unique to apigenin and 3 other tested flavonoids (chrysin, genistein and naringenin)[22] and apigenin possessing an IC50 of 300nM (0.3μM). The IC50 of Apigenin on aromatase is approximately 2.9μM (most potent tested flavonoid on aromatase was 7-Hydroxyflavone at 0.21uM, outperforming the reference aminoglutethimide at 1.2uM[22]) and both of these enzymes are involved in testosterone synthesis at different stages.

Does this mean that higher apigenin potentially yields higher or lower levels of testosterone? I guess I'm unsure what the implication of "inhibits" is.

So I can definitely explain what "inhibits" means and what that implies, but I think the answer as to what apigenin is actually doing to testosterone levels is somewhat complicated. I wasn't able to find a study looking at steroid levels in vivo following apigenin administration, so this is based solely on a quick look through the biochemistry and cells biology available.

17β-HSD is an enzyme that catalyzes a reaction (meaning it makes the chemical reaction happen more quickly than it would by itself) that converts androstenedione to testosterone. If it is inhibited, that means that the enzyme is no longer able to catalyze the reaction. Therefore, inhibition of this enzyme should prevent the synthesis testosterone, and reduce its levels, since less testosterone will be made.

On the other hand, aromatase is an enzyme that converts androgens, namely testosterone and its aforementioned precursor androstenedione, into estrogens. So, one would expect inhibition of this enzyme to lead to increased testosterone levels, as less testosterone and androstenedione would be converted to estrogens, meaning more testosterone and its precursor are left unchanged.

So, it seems we have some competing actions. Based on the paragraph in your question, apigenin's IC50 for 17β-HSD is 0.3 μM, and its IC50 for aromatase is about 2.9 μM. That means that when the concentration of apigenin is 0.3  μM, the enzyme activity of 17β-HSD is cut in half, but it must be at a concentration of 2.9 μM to do the same to aromatse's activity. So, it is about ten-fold more potent at inhibiting 17β-HSD than aromatase, at least in the assays used above. That would suggest that at concentrations significantly below 2.9 μM, apigenin would inhibit 17β-HSD but not aromatase, resulting in a decrease in testosterone. However, once concentrations became sufficiently high to allow for inhibition of both enzymes, things would get more complicated. Depending on the relative amounts of both enzymes, how much access apigenin was able to get to each, and what the cellular steroid composition was prior to inhibition, you could imagine relative testosterone levels to go either up or down. However, I would be inclined to suspect that testosterone levels would in fact decrease in the long run, since eventually existing testosterone stores would be depleted, and the inhibition of 17β-HSD would prevent the creation of new testosterone.

However, if we look at the paragraph in the article immediately following the one you quoted, there is a summary of a study done in cells that found that apigenin actually increased testosterone levels by blocking the TBXA2 receptor. This inhibited a signaling cascade that normally decreases testosterone synthesis, so the end result was an increase in steroidogenesis/testosterone production.

So, I suspect things are actually somewhat complicated and the best way to know would be to test in vivo


Why does 4-thiouracil labelling to map RNA-binding proteins cause a T-C change? I am now reading a paper about the purification and identification of mRNAs and its RNA binding proteins by using UV crosslinking and immunoprecipitation. I came upon this sentence which puzzled me

  Up to 28% of all uridines present in 3' UTRs showed diagnostic T-C
  changes in the protein occupancy profiling sequence reads. This number
  is reasonably high, considering observations that typically only one
  of a few uridines in RNA binding sites when substituted by 4SU,
  crosslinks to proteins.

What I do not understand is why does 4-thiouracil (4SU) labelling in the cell show T-C changes. Would the uracil-adenine base pairing not be affected?

How does the 4SU labelling really work?

The technique used in that paper is called PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation; see Ascano et al., 2012 and Spitzer et al, 2014). This technique involves substituting uridine (U) with 4-thiouridine (4SU) or substituting guanosine (G) with 6-thioguanosine (6SG). The rationale behind using these modified bases is that they improve the efficiency of RNA-protein crosslinking. Moreover, PAR-CLIP uses 365nm UV instead of the 254nm UV used in the conventional crosslinking. However, the crosslinking process causes the loss of the sulphur atom causing the U to be read as C during reverse transcription. Likewise, 6SG gets read as A.

  Ascano et al., 2012


Are there nerves in the umbilical cord? I have always imagined that cutting the umbilical cord after birth might be painful. But I have always been confused about who would feel the pain and why. It occurred to me that the mother or the infant could only feel pain if they had nerves connected to the umbilical cord.

Do either mother or infant have nerves running into the umbilical cord that carry nociceptive information?
If not, is there a reason why no pain receptors are present?

Short answer
There are no functional nociceptors present in the umbilical cord.

Background
Having had the opportunity to cut the umbilical cord of one of my kids, I can anecdotally confirm neither newborn nor mother gave any sign of pain during the procedure. That is, when cutting the umbilical after the birth of a full-term baby. The only person clenching his teeth was dad :)

In fetuses at gestational age of 18-36 weeks no stress response was noted after puncturing the umbilical (Teixeira et al., 1996), indicative of the absence of pain receptors connected to the baby's brain.

I couldn't find information about pain in the mother, but I cannot imagine that the maternal central pain centers are being connected to the umbilical, which would be pretty extraordinary. This, because long-distance neural connections are rarely, if ever, established in adult humans. Also, I haven't heard any reference to the mother feeling pain because of injury to the umbilical cord. For example, knots in the umbilical cord, or cords wrapped around the fetus' neck due to excessive movements of the fetus are never noticed by the mother, and are only revealed during ultrasounds.

Note, however, that the umbilical cord is innervated by cholinergic neurons that are thought to be involved in the control of blood transfusion to the fetus, but presumably do not carry sensory information to either fetus or mother (Ellison, 1971).

References
- Ellison, Am J Anat (1971); 132: 53-60
- Teixeira et al., The Lancet (1996), 347: 624


What product of cellular respiration creates an acid when in solution with water? What product of cellular respiration creates an acid when in solution with water?

Topic question really, haven't been able to find a direct answer.

Cellular respiration itself, defined as the activity of the respiratory chain complexes I -- V (including ATP synthase), is not acidifying. On the contrary, free protons are captured during ATP synthesis, so cellular respiration acts to raise pH. But then ATP synthesis is always matched with ATP breakdown in reactions that utilize energy (muscle contraction, for example), and ATP breakdown liberates the captured protons again. So the complete cycle of ATP turnover is pH neutral. (For more information, see for examplle http://www.ncbi.nlm.nih.gov/pubmed/6298937)

The activity of the TCA cycle, on the other hand, produces CO$_2$ when oxidizing carbohydrates, and CO$_2$ dissolved in water is slightly acidic (pK$_a$ = 6.3) and so tends to lower pH. This is the main acidifying effect of oxidative metabolism. In animals, the CO$_2$ generated is of course released via the lungs, so the amount of CO$_2$ dissolved in body water is (more or less) constant, and therefore pH is stable.


Do non-enzyme catalysed reaction pathways exist? Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google.

I have almost no background in biology, and am only studying certain topics from a mathematical perspective.

If by enzyme you mean "protein" aka polypeptide, than there are such things as catalitic RNAs. Those are molecules of RNA that facilitate chemical reactions but don't change themselves (definition of catalyst). I think that, based on the discovery of such RNAs, it is now believed that life might have started from or with the help of catalytic RNAs (please forgive the speculative tone, see self-replicating RNAs).

You might find this article interesting: The Road to Non-Enzymatic Molecular Networks, which describes non-enzymatic networks. The problem with searching this topic is that most current publications, seem to me, to concentrate on way to transfer enzymatic reactions into inorganic catalysis systems--because those systems can be more clean and easy to expand--than purifying enzymes for biotech.


Serological assays measuring antibody response Given that an appropriate immune response to a bacteria may be thwarted in an individual, including not producing all of the antibodies which are known to occur in people who have been infected, or producing insufficient amounts of antibodies specific to a bacteria --- Are all serological tests using antibodies as a basis for detection of a systemic infection inherently flawed? In this instance, I'm assuming appropriate application of a test and competent laboratory methodology. But, equally important, what criteria can routinely be used to consider the efficacy of a particular antibody test, across the board.

Antibodies used for serological tests are performed in vitro, and are not required to be effective for eliminating the pathogen. For an infected individual, antibodies may play a role in neutralization, opsonization, or activating the complement system (checkout Janeway's Immunobiology for more details). There are a number of reasons why antibodies may be present and not trigger an effective response down these pathways.

For example, E. Coli O157:H7 produces Shiga toxin and there are immunoassays to test for the presence of the toxin in feces (1). Only low amounts of the toxin is needed to cause disease. Antibodies against the toxin have been seen in individuals with the disease, suggesting the toxin is not a strong enough challenge for an immune response Discussion of (2).

You could go case-by-case for each of the immunoassays and see why their targets are difficult to turn into therapeutics.


Blood Pressure: Significance of difference between systolic and diastolic I wanted to understand what is the difference between systolic and diastolic readings of blood pressure. I understand 120-80 to about 100-60 is considered normal but does the difference in the two values in the reading hold any significance?

I have read some text here and here.

The difference between systolic (the upper number) and diastolic (the lower number) pressures is known as the pulse pressure:

  Systemic pulse pressure = Psystolic - Pdiastolic

For a typical blood pressure reading of 120/80 mmHg the pulse pressure is therefore 40 mmHg.

It is proportional to stroke volume, the amount of blood pumped from the heart in one beat, and inversely proportional to the compliance or flexibility of the blood vessels, mainly the aorta.

A low (also called narrow) pulse pressure means that not much blood is being expelled from the heart, and can be caused by a number of factors, including severe blood loss due to trauma, congestive heart failure, shock, a narrowing of the valve leading from the heart to the aorta (stenosis), and fluid accumulating around the heart (tamponade).

High (or wide) pulse pressures occur during exercise, as stroke volume increases and the overall resistance to blood flow decreases. It can also occur for many reasons, such as hardening of the arteries (which can have numerous causes), various deficiencies in the aorta (mainly) or other arteries, including leaks, fistulas, and a usually-congenital condition known as AVM, pain/anxiety, fever, anemia, pregnancy, and more. Certain medications for high blood pressure can widen pulse pressure, while others narrow it. A chronic increase in pulse pressure is a risk factor for heart disease, and can lead to the type of arrhythmia called atrial fibrillation or A-Fib.


Where in the digestive tract are melatonin pills dissolved? Same question for gelatin capsules I want to do a blind controlled experiment on myself to learn whether melatonin pills have any effects on me. I bought some empty gelatin capsules. I am going to fill some of them with rice and put pieces of melatonin pill in others.

Melatonin pills instruction says I should take it 30-40 minutes before going to bed. Now I wonder if the timing is the same when stuck inside gelatin capsules. Also is it possible that melatonin pills stuck inside capsules will get to a later stage of the digestive tract than they should and thus will not work.

Unless specially coated or formulated, most pills break apart in the stomach. Note: "break apart", not necessarily absorbed.

Take a gelatin capsule with rice or melatonin and immerse it in warm water. Massage gently with your fingers. Watch the clock.

When the rice is fully exposed, or the melatonin starts to break apart and dissolve, add that amount of time to the instructions. Be sure to take it with at least 4 ounces of water.


Oxygen in the earth’s atmosphere If CO2 only makes up about 0.04% of the earth’s atmosphere how do trees and organisms in the ocean produce oxygen to 10% of the earth’s atmosphere?

A very long head start
To elaborate on Drake Johnson’s comment, CO2 used to be much higher in concentration. During the Great Oxygenation event, when cyanobacteria (ancestors) began photosynthesizing, they converted much of the CO2 into O2, driving CO2 concentrations down as they drove O2 up.


Is the complement system a part of innate or adaptive immunity I've been reading about the complement system, as part of the human immune system. The complement system is introduced as part of the article on innate immunity on Wikipedia. This classification makes obvious sense in the case of the alternative pathway, which is obviously not dependent on any specific pathogen.

However, I'm confused about whether this is an appropriate classification for the classical pathway (and, therefore, the system writ large) since the classical pathway is activated by antigen:antibody complexes and only by certain antibody isotypes (IgG and IgM). It is, therefore, to some extent pathogen specific and it is also, clearly, activated by and dependent upon the humoral immune response (generally classed as part of adaptive immunity).

So, in short, is it best to classify the complement system as part of the innate immunity (and, if so, why is that?), or would it be better to restrict ourselves to the observation that it is, to a greater or lesser extent, part of both types of immunity?

Yes, the complement system is part of the innate immune system. It can be activated by the:

classical pathway (activated through bound IgM and IgG molecules but
also by DNA, collagen (both are usually not available freely outside
of cells) and c-reactive protein)
lectin pathway (activation by binding of mannose through the mannose
binding lectin on the cell surface)
alternative pathway (activation by the constant hydrolysis of the
complement component 3 (or C3) in an antibody independent way)

My guess here would be, that the classical activation via antibodies is evolutionary younger than the other two possibilities which act more directly on bacteria and do not depend on the availability of specific (at least to some degree) antibodies. The Wikipedia article on the complement system is pretty extensive.


Why the "cfr." in 'Cirrhipathes cfr. anguina' and not "cf."? Recently I stumbled upon the species name Cirrhipathes anguina. In the literature it is often mentioned as Cirrhipathes cfr. anguina. What does cfr. mean? Does it carry the same meaning as cf.?

Edit: If the same, why is cfr. used in this case and not just .cf?

It's the same as cf. Both abbreviate confer-- meaning the specimen has most of the defining features of the species indicated, and the ID would likely be confirmed with comparison to reference material.

Ref: Sigovini, M. et al. 2016. Open nomenclature in the biodiversity era. Methods Ecol Evol. 7: 1217-1225. http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12594/abstract


Why is there an increase of diagnoses of Lyme disease? On the Center for Disease Control page for Lyme disease, you can see the progression of reported cases of Lyme disease from 2001 until 2016 and see that over time, there are more reported cases of Lyme Disease.

I am wondering if there is an actual increase in incidence or if, perhaps, there is an increased awareness of the disease causing doctors to be more likely to test for it (and diagnose it) than they were in 2001.

Is there any information supporting one or the other?

One of the opinions expressed on the CDC website is that the increase of diagnosis of the Lyme disease could be accounted to expansion of ticks:

  Since the late 1990s, the number of reported cases of Lyme disease in the United States has tripled and the number of counties in the northeastern and upper Midwestern United States that are considered high-risk for Lyme disease has increased by more than 300%. One explanation for this trend is that the ticks that can transmit Lyme disease have expanded their geographic range and are now being found in places they weren’t seen 20 years ago. --Rebecca Eisen, Ph.D. (source)

I have also found a report containing another possible explanation:

  Areas of patchy woods, which are very common in cities and suburban and rural areas, may have higher populations of Lyme-disease carrying ticks than forest fragments, which generally have fewer species than continuous habitat. This is because some species thrive in smaller places.

  White-footed mice, for example, are more abundant in forest fragments in some parts of the country, likely because fewer predators and competitors remain there. These mice are particularly abundant in patches smaller than about five acres, which could spell trouble for people living nearby: the mice are the main carriers of Lyme disease-causing bacteria. In the eastern and central United States, Lyme disease is contracted via blacklegged ticks that feed on infected mice, then transmit the bacteria when the ticks bite people. As a result, says biologist Felicia Keesing of Bard College in Annandale, New York, Lyme disease is concentrated in areas where people live near forests with blacklegged ticks.

  Keesing, scientist Richard Ostfeld of the Cary Institute in New York and other researchers found that smaller forest fragments had more infected ticks, which could translate to more Lyme disease. Forest patches that were smaller than three acres had an average of three times as many ticks as did larger fragments, and seven times more infected ticks. As many as 80 percent of the ticks in the smallest patches were infected, the highest rate the scientists have seen. These ticks may also be infected with other emerging diseases--Babesiosis, Anaplasmosis and Powassan encephalitis--therefore, forest fragmentation might also be contributing to other serious illnesses, Ostfeld says.

  "Our results suggest that efforts to reduce the risk of Lyme disease should be directed toward decreasing fragmentation of deciduous forests of the northeastern United States, particularly in areas with a high incidence of Lyme disease," says Keesing. "The creation of forest fragments smaller than five acres should especially be avoided."

EDIT: Another article on Vox also provides some possible explanations including the global warming, reforestation of farms and increase in the number of deers (caused by hunting protections).


Extracting cell-free DNA Has anybody had any success in extracting cell free DNA from plasma without using expensive kits? I've already spent a lot of my own blood trying to use standard phenol/chloroform methods with very minimal yield. I know it's possible that since I am not pregnant and don't have cancer (I hope) my blood may not have a large quantity of cell free DNA to begin with but I'm afraid to start using precious experimental samples until I'm confident I have a technique that will work.

For some background, cell free DNA is DNA that is circulating in the plasma (as opposed to the majority of DNA which is cellular). This has become an exciting new way to analyze fetal DNA from a mother's blood without doing a dangerous amniocentesis. There's also strong evidence that tumour DNA can also be found in some abundance this way (most studies seem to be with prostate cancer).

Qiagen has a kit for sale to extract this DNA but it is pretty expensive and I would still think that phenol/chloroform would give me a high (if less pure) yield. There is a paper in Cancer Biomarkers 2013 by Mazurek et al that claims that compares methods and shows a reasonable yield with this method but I haven't reproduced it. Has anybody here had success and if so what modifications did you use? Is it just time to move on to using samples that are more likely to have larger amounts of cell free DNA?

To note: I have no personal experience with this protocol. I am forwarding this paper, passed on to me by a colleague

There are many kits and methods available that don't rely on Qiagen. Or alternatively, if you ask them nicely, they do heavily discount their first kit you buy off them as a sort of trial (as they dont do samples).

However, to answer your primary question, are you adding a detergent and heat denaturing your samples first before phenol-chloroform (Triton/Heat/
Phenol)?

  Blood samples for CFDNA
  analysis are collected into EDTA tubes and held at/or below RT
  (18 °C–22 °C) for no more than 2 h before separation of plasma.
  Plasma should be separated from whole blood samples by double
  centrifugation (800 g and 1600 g for 10 min, separately), avoiding
  leukocyte lysis. We prefer to isolate CFDNA immediately after plasma
  separation to minimize the effect of prolonged storage. Otherwise,
  samples should be aliquoted into small portions and stored at −70 °C
  before extraction because fragmentation of CFDNA might be caused by
  repeated freeze–thaw cycles

  For the THP method, 500 μl of plasma/serum was mixed with 5 μl Triton X-100
  (Sigma-Aldrich, UK) and heat denatured at 98 °C for 5 min. Samples were placed on ice
  for 5 min, then extracted with an equal volume of phenol–chloroform–isoamyl alcohol
  (25:24:1, v:v:v) (Sigma-Aldrich, UK) and centrifuged for 10 min at 14,000 g. The
  aqueous phase was precipitated overnight with 1/10 volume of 3 M NaOAc and 2.5
  volume of 100% ethanol at −20 °C. The DNA pellet was washed with ethanol, air-dried
  and resuspended in 50 μl of ddH2O.

  In the THP protocol, 98 °C incubation was used to inactivate
  PCR inhibitors and denature proteins in plasma/serum samples.
  Different times and temperatures were tested before choosing this.
  Since we had noticed substantial DNA contamination in SDS, Triton
  X-100 was used in the protein solubilization step. Direct conventional
  PCR was performed successfully on heat-denatured samples
  and able to detect 25 ng/ml DNA, indicating that this simple
  procedure offered sufficient protein digestion and inhibitor elimination
  for PCR analysis. The THP protocol gave a significantly
  higher yield of pure DNA solution for qPCR analysis than the
  QIAamp kit. The THP protocol showed high efficiency even with
  small DNA fragments as low as 100 bp.

You might want to read this:
Xue, Xiaoyan, et al. "Optimizing the yield and utility of circulating cell-free DNA from plasma and serum." Clinica Chimica Acta 404.2 (2009): 100-104.

A quick search of google scholar also revealed a few other papers you might be interested in:

Fleischhacker, Michael, et al. "Methods for isolation of cell-free plasma DNA strongly affect DNA yield." Clinica Chimica Acta 412.23 (2011): 2085-2088.

UPDATE:

After reading this (Fong, Siew Lee, et al. "Comparison of 7 methods for extracting cell-free DNA from serum samples of colorectal cancer patients." Clinical chemistry 55.3 (2009): 587-589.) which gives about 7 protocols (sadly without any references for some reason) I went hunting for  came up with this:

  DNA was extracted from 1.0 ml plasma by phenol-chloroform method with slight modifications.
  One ml of plasma was treated with 1x SDS/Proteinase K solution (0.5 mg/ml) (1:1), incubated
  overnight at 56 °C followed by phenol-chloroform (4:1) treatment and centrifuged at 7 000 rpm.
  The upper layer was transferred into fresh 15 ml centrifuge tubes and the same step was repeated
  again; DNA was precipitated by adding glycogen (0.1 µg/µl), ammonium acetate (7.5 M) and
  absolute alcohol. DNA pellet was obtained by centrifuging at 7 000 rpm; was washed with 70%
  alcohol at 10 000 rpm, dried and finally dissolved in TE buffer at 56 °C and stored at -20 °C until
  further use.

You can read about the above method here: Singh, Deepika Misra1 Renu, and Monisha Banerjee. "A simple and reliable method of obtaining fetal DNA from maternal circulation; its accuracy and sensitivity."

Also, if its available to you, it might be worth it:

Gahan, Peter B., ed. Circulating Nucleic Acids in Early Diagnosis, Prognosis and Treatment Monitoring: An Introduction. Vol. 5. Springer, 2014.


RNA secondary structure comparison Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common sec. structure/shape.

You can use R-coffee of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession1. R-coffee can align RNA sequences taking into account structural information:

1 The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being simply ridiculous, this also affects other programs you might want to pipe your data to. For example, I wanted to pipe t-coffee alignments to an alignment viewer and I had to parse out his effing name in order to be able to do it.


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

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

Oxygen is actually not needed in the Krebs cycle - it is needed in the electron transport chain that is downstream of the Krebs cycle to regenerate NAD+ from NADH. NAD+ is a co-enzyme and acts as an electron carrier in oxidizing reactions at various positions in the Krebs cycle. However, note that without O2, NADH accumulates and the cycle cannot continue as it needs NAD+ to run.
Krebs cycle - No O2 needed:

Electron transport chain - O2 needed to regenerate NAD+ essential for the Krebs cycle:


What is the evidence that australopithecines were bipedal? Before the discovery of Australopithecus afarensis in the 1970s, most anthropologists believed that an increase in brain capacity had preceded bipedal locomotion. However, this reconstruction of the Lucy skeleton shows that the A. afarensis was bipedal even with a brain size of around 400 cc.

But the actual Lucy skeleton does not include feet, and only has two partial leg bones.

How do anthropologists determine, based on the bones preserved, that A. afarensis was bipedal?

Mainly because of the characteristics of the pelvic joint with the femur and the foramen magnum (the hole the spinal cord uses to connect with the encephalon). Also, there are more specimens other than Lucy, and there also exist fossil footprints (for instance the Laetoli footprints). All this evidence points to a bipedal walking.

Source: http://www.talkorigins.org/faqs/homs/pelvis.html

As you can see, the Asutralopithecus pelvis resembles human pelvis more than chimpanzee's (wich is adapted to a primarily quadrupedal movement).

Source: https://web.archive.org/web/20160817080843/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Primates.html

In this image you can see the position of the foramen magnum in a typical pure quadrupedal mammalian, such as a dog. The foramen inserts in the posterior part of the cranium. In the human, the foramen inserts in the base of the skull, due to de erected position. In chimpanzees, which have quadrupedal march, but can also display some bipedal movements, the foramen is slightly displaced towards the basis of the cranium, in an intermediate position between both.

Source: http://www.fcnym.unlp.edu.ar/museo/educativa/serypertenecer/principal/australopitecinos.html (Spanish)

In this image it shows the foramen in chimpanzees, Australopithecus and modern humans, and you can see that the position in the second is at the base of the skull, just like in Homo.

It is assumed that the bipedal locomotion is an adaptation to the savanna environment, where trees were rare. Bipedalism also allows a better visual field and it has more energetic efficiency.


What are limiting factors for intron length? For predicting genes from a sequenced genome, you need to set a maximum intron length. How long can introns get in animals? Is there some limit?

I think the above values (500-750 kb) are wrong.  http://www.bioinfo.de/isb/2004040032/ shows that most introns are less than about 10 kb (and personal experience in Drosophila confirms that - I've rarely seen an intron bigger than about 5 kb).  There are some very large ones, but since it's nearly impossible to detect the splicing reaction, particularly if they're very large, it's not clear whether they are spliced as one BIG intron or are instead recursively spliced (in little steps, as in http://www.genetics.org/content/170/2/661.full.pdf+html).  I think its safe to say that we don't know how long the biggest introns can be.


E. Coli metabolization of paracetamol For my science fair project, I did an experiment on how paracetamol and ibuprofen affected the growth of bacteria. By day 5, however, parts of the paracetamol blackened (image below). I am wondering if E. Coli can metabolize paracetamol and if so, what operon in the K-12 genome is responsible for this.

EDIT: I realized it may be metabolizing other ingredients in the medicine I used. I am including a list of the ingredients in the medicine I used.

Acetaminophen 160 mg in each 5 mL (duh)

Other ingredients (33.015873 mL):

Anhydrous citric acid
FD&C red no. 40
glycerin
high fructose corn syrup
microcrystalline cellulose and carboxymethylcellulose sodium
purified water
sodium benzoate
sorbitol solution
sucralose
xanthan gum

I thought it might be the fructose, but is the byproduct really black? Still confused...

Sorry that my answer is not a real answer, but this would be a good starting point for some more science.

Several of the questions you might ask and could answer (with some more experiments):

Does this happen in plates without E.coli?
You have a contamination on the right side, perhaps also on the black part. Could this be the culprit? Only half the plate is black, the rest is (still?) red.
You used a paracetamol tablet with red dye and a lot of sweeteners, does the same thing happen if you use one without the red dye? A dye would be a likely source, because it already contains an absorbing moiety. It only needs to be slightly modified to absorb different wavelengths.
What kind of agar are you using exactly? There are many kinds, often selecting for certain types of micro-organisms, with indicators for pH or other colored markers to detect and identify strains.

For your metabolic question you can take a look at https://ecocyc.org/ where you can find a database with all known metabolic pathways for E.coli K12. Unfortunately I couldn't find anything for paracetamol (or synonyms) but you could try to see if it produces a colored product for any of the additives.


What are the differences between isozymes, allozymes and isoforms? As far as I have understood

Isozymes are derived from different genes but perform similar functions
Allozymes are derived from the same gene but different loci, functionally conserved
Isoforms are a result of post transcriptional modification of the same gene, I am not sure for its functional conservation.

Are there anyother things to know about them?
Thanks

You have the basic idea:

Isozymes come from different genes but carry out the same enzymatic reaction.

Allozymes come from the same gene - i.e., the gene at a particular point on the chromosome; but chromosomes come in pairs, and the allozymes come from the 2 different chromosomes in the pair.

Isoform proteins ["protein variants"] are from the same gene, but they can have the same or different functions, depending on how they are spliced = which exons are included, and in what order. There's a nice picture in the Wikipedia article "protein isoform."

Here are Wikipedia links:

Isozyme - Wikipedia
https://en.wikipedia.org/wiki/Isozyme
Isozymes (also known as isoenzymes or more generally as multiple forms of enzymes) are enzymes that differ in amino acid sequence but catalyze the same chemical reaction.

Alloenzyme - Wikipedia
https://en.wikipedia.org/wiki/Alloenzyme
Alloenzymes (or also called allozymes) are variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus.  ...These are opposed to isozymes, which are enzymes that perform the same function, but which are coded by genes located at different loci.

Protein isoform - Wikipedia
https://en.wikipedia.org/wiki/Protein_isoform
A protein isoform, or "protein variant" is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences. While many perform the same or similar biological roles, some isoforms have unique functions.


Does the testicle's temperature increases with the body temperature during a high fever? The testes is the male sexual organ. It is positioned outside the abdomen along with the scrotum. I would like to know if its temperature is independent from the body temperature due to its location.

The question is quite vague. Please specify for clear answer.
However, although testicles are out of the body, but a part for sure. Due to pyrogen attack when the body temperature increases, literally the temperature of the testicles should be increased but clear research has not been found yet.
Please specify your question.


Are some polyketides enzymes? I am currently reading a "book" (rather an article) called "Protein Modelling & Molecular Docking: Modeller, Autodock".

The abstract starts with the following sentence :

  Polyketides are a large family of complex enzymes synthesized by
  polyketide synthases.

Before reading this article, I knew nothing about polyketides. I looked it up online, and I saw that they were secondary metabolites, which adds up with the rest of the article. However, I could not find any mention of some polyketides being enzymes, hence my question:

Are some polyketides enzymes or is this a simple mistake in the article ?

You are correct.  Polyketide synthases (PKS) are the enzymes that synthesize polyketides.  PKS are derived from fatty acid synthases via evolution.  Polyketides are of great interest becaus many are of important medical use.


How could 45 milligrams of a substance equal 4,500 micrograms? In this book, the author repeatedly states that 45 milligrams of vitamin K2 equals 4,500 micrograms.  I thought 1 mg = 1000 mcg.  How could this be?

This is a typo.  In the text he states:

  ... only 0.120 milligrams (120 micrograms) of MK-4 ...

So, he knows the correct conversion.

Then:

  ... the "same" product is almost 40 times more potent in one country
  ...

40 times 120 micrograms is 4800 micrograms -- which is close to 4500.

So, that suggests that the (4,500 micrograms) in the table is correct and that the 45 milligrams is a typo.

It should read 4.5 milligrams.


Does Darwin's Theory of Evolution refute Terence McKenna theory "Stoned Ape" theory of human evolution? I haven't read it but I'm asking for a quick answer.

As far as I know, Terence McKenna's theory of evolution in humans main concept is that a hominid has tried in their diet psilocybin mushrooms, and the experience they integrated changed their mind in a way that led to "us."

Briefly the "Stoned Ape theory" posits that psychoactive Psilocybin mushrooms in the diet of pre-Homo sapiens primates catalyzed the change Homo sapiens.  It suggests that the mushrooms conveyed selective benefits to consumers of the mushrooms, dissolving the 'egos' of our ancestors and allowing them to form communities.  It may also be sexual stimulant, goes the theory and so may have conveyed an advantage there.

I think this theory is not terribly popular now, but it is difficult to refute or to prove.  The only real proof would be to take a hominid or any other species and give them the fungus and see if they become intelligent.   Just because this has not happened does not disprove the theory.  the only other way to prove this really would be to have a time scope and look back and see what happened.  Its a similar question as to how life emerged on Earth.  We have some interesting evidence but conclusive proof is going to be hard to get.

I found a large collection of supporting evidence.  Even the definition of human intelligence and whether it is so unique is subject to debate.  Certainly there are other primates who appear to be as or more social than we.  I think other theories seem as or more likely.

Darwin's theory of evolution doesn't refute many theories of how something happens in evolutionary history.  The Panspermia hypothesis is taken quite seriously at this point - could it be that life originated elsewhere then was introduced here by meteorites.  The origin of Species doesn't have a lot to say about that.  I think the same is true for the emergence of human intelligence, which at this point we believe is unique on Earth.  Hard to make an irrefutable theory based upon a single example.


Purpose of the conversion of 3-PGA to G3P in the calvin cycle? 3-PGA ($\ce{C_6H_7O_7P}$) is converted to G3P ($\ce{C_6H_7O_6P}$) before it is able to be made into glucose, with an expansion of 6 ATP and 6 NADPH. My question is why this process is needed and why the loss of 1 oxygen atom decides whether a sugar molecule can be synthesized into glucose. My take on this matter is that if they incorporate 3-PGA directly into glucose, they can save time and also energy in the form of ATP and NADPH.

Nice question! To see what trouble that extra oxygen can cause, lets get to the core of the reaction i.e. Calvin-Benson cycle; one step at a time. To start with, have a look at the detailed Calvin-Benson cycle (following image taken from here):

As becomes quite clear from this image, the actual use of Glyceraldehyde-3-phosphate is at the step of formation of Fructose-1,6-bisphosphate. Yet, we don't know why we cannot use 3-Phosphoglycerate instead at this step. For that, lets go a step further and see how the concerned enzyme, fructose-1,6-bisphosphate aldolase/phosphatase (aka aldolase), works.

Since the full article is behind a paywall, lets get a sneak peak into it. See this image1:

Pay attention to the steps where G3P enters i.e. steps between b and c. Even without entering into details of the mechanism, we get two factors which can prevent 3PGA from being utilized in this reaction:

Steric Hindrance: replace the terminal -H with -OH of G3P in the first image in your mind. You can clearly see that this would cause some steric hindrance and prevent formation of covalent bond between DHAP and G3P.
Formation of Geminal Diol: again, replace the terminal -H with -OH, but this time in the second image, in your mind. You get geminal diol in the resultant molecule, which is famous for its reactivity and instability. Thus, by adding 3-PGA instead of G3P in the reaction, we might end up with unstable molecules that cleave themselves up. I hope this is what you were looking for.

Reference: Juan Du, Rafael F. Say, Wei Lü, Georg Fuchs, Oliver Einsle Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase Nature 478, pages 534–537 (27 October 2011)
doi:10.1038/nature10458


Can methylisothiazolinone/methylchloroisothiazolinone (MI/MCI) behave as bacteriostatic in low concentrations? Wikipedia mentions this as a biocide. It also mentions that low concentrations of certain bacteriocides is bacteriostatic. (I am assuming that biocide and bacteriocide play the same role, here.)

Hence, the question. (The only information I can find about MI is with regards to allergies.)

Yes, MI/MCI can behave as a bacteriostatic at low concentrations.

Check out table 1 in this paper: The Mechanism of Action of Isothiazolone Biocides. For a bunch of different isothiazolones (including the two you're interested in, though they call them MIT/CMIT instead of MI/MCI) it gives the Minimum Inhibitory Concentration (the concentration at which the isothiazolone acts as a microbiostatic) and the Minimum Biocidal Concentration (the concentration at which the isothiazolone acts as a biocide)*.

It's my understanding that basically everything that can act as a bacteriocide can also act as a bacteriostatic at a lower concentration. At low concentrations bacteriocides will kill some cells while leaving others alive in a stochastic (ie random) fashion. At some concentration this stochastic killing will balance out with the natural growth rate of the bacteria, and so thus act as a bacteriostatic.

*It should be noted that the paper lists these values for isothiazolone activity against yeasts, but the results would likely follow the same trends for isothiazolone activity against bacteria, since "CMIT/MIT has broad spectrum efficacy versus bacteria, algae, and fungi" (from the above cited paper).