How do we know that selective agonists are indeed selective?

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


Is there a resource to query gene expression similarity? Stratified by sex?

There are some similar resources, which at the same time do not mix the ingredients in the same way as your tool. Hope that pointing out the respective differences will help your rebuttal or resubmission! e.g.:

A similar web service is part of flyrnai, where tissue-specific expression can also be compared based on sex, and genes can be queried by the similarity of their gene expression profile to other genes.
A resource which has some conceptual relatedness regarding sex-specific similarity in gene expression, and which is also based on the GTEx dataset, has recently been published in the form of tables by Gershoni et Pietrokovski, BMC Biol, 2017.
A very nice and broad resource of high-quality gene expression profiles on individual tissues, but also on response to stimuli, is EBI GXA. Though the web interface only allows to query sex-specific expression profiles, computationally minded people could readily compute (dis)similarity between samples after downloading the (well-structured) data dump of EBI GXA.
A similar tool in terms of the visualization of sex-specific expression patterns is part of gtexportal, though it seems limited to displaying a single gene.


Hormonal terms Somatotrophin or somatotropin?

Yes

They are the same thing, and both are old-fashioned terms for what is now termed specifically growth hormone (i.e. not generically as in "a growth hormone"). It is clear from the Wikipedia entry for growth hormone that this is equivalent to somatotropin.

I could not find a specific scientific reference that states that the two are the same, but I present a line of reasoning based on a search for mention of the terms in books using the Google ngram.

The initial similarity in the curves in the left-hand frame reflects, I think the competing use of the terms when the hormone activity was first discovered. Eventually somatotropin won, although the use of growth hormone is much more common now (right-hand frame).

If you look at the books cited by the ngram in which somatotrophin is used, you will find that many are in the field of animal science, especially dairy science in relation to the lactogenic effect of the hormone. Years ago I worked in this area, and remember that growth hormone had such lactogenic effects.  Presumably somatotrophin stuck in this area, whereas somatotropin was more generally used, especially in human endocrinology.

General Dictionaries and possible reasons for variation

I am hesitant to quote non-scientific dictionaries on scientific topics, but in this case it is probably justified, and it also addresses the difference in meaning of ‘tropin’ and ‘trophin’, referred to in the question.

The Merriam-Webster online definition of somatotrophin redirects to:

  somatotropin
  variants: or less commonly somatotrophin

Chambers on-line only has somatotrophin, But my own 1994 printed edition has:

  somatotropin or somatotrophin a polypeptide growth hormone

My Chambers Dictionary iPhone app also has both.

And Saunders Comprehensive Veterinary Dictionary, 3rd ed. (2007), according to a citation in the Free Medical Dictionary, has:

  somatotropin, somatotrophin
  growth hormone

If you check the meanings of the two suffixes in Merriam-Webster:

  -trophic
  of, relating to, or characterized by (such) nutrition

Whereas

  -tropic
  1 : turning, changing, or tending to turn or change in a (specified) manner or in response to a (specified) stimulus
  2 : attracted to or acting upon (something specified)

It seems probable, therefore, that the original form was somatotrophin, but, either by confusion with the second definition of -tropic or a North American chemical aversion to ‘ph’ (as in sulphur/sulfur), somatotropin became dominant, except in the field of animal science. Perhaps that is why the Oxford Dictionary, both online and in my printed edition of 1991, ignores somatotropin completely. However you would have difficulty ordering somatotrophin from the chemical supplier, Sigma-Aldrich/Merck, whereas somatotropin is available.


"bead" on a string theory of genetics, source?

If the Cold Spring Harbor Laboratory is considered a reputable source (it should be), you can check out their Defining the gene page which has an overview of the beads-on-a-string theory, and how it was disproved by Seymour Benzer. You could also try to find Benzer's original paper, although it doesnt seem to be available online.

Related and possibly helpful:

Benzer's page on Cold Spring Harbor website
Evolution of Genes and Genes in Evolution - very interesting paper from 1959 on genes/genetics, look on the fourth page (marked 18) for the bead-on-string theory


How do you convert mtDNA sequences in FASTA to FSTAT format?

Check out PGDSpider. The inputs and outputs table indicates that it supports conversion between FASTA and FSTAT formats, among many others.


Cytokinesis is separate from mitosis.

What edition are you looking at?  To quote from the Fourth Edition:

  The cell cycle culminates in the division of the cytoplasm by cytokinesis. In a typical cell, cytokinesis accompanies every mitosis, although some cells, such as Drosophila embryos (discussed later) and vertebrate osteoclasts (discussed in Chapter 22), undergo mitosis without cytokinesis and become multinucleate. Cytokinesis begins in anaphase and ends in telophase, reaching completion as the next interphase begins.

The mouse-over definition of cytokinesis there is:

  Division of the cytoplasm of a plant or animal cell into two, as distinct from the division of its nucleus (which is mitosis)


Are there U-rich transcriptional pause sites?

Yes, there are: this is a feature of bacterial intrinsic termination. The mechanism of pausing is not as you describe, though.
In bacterial transcription, two forms of termination are recognised (to my knowledge):

Intrinsic termination, consisting of a hairpin and a stretch of Uridines.
Rho-dependent termination, consisting of a 'loading' site for termination protein Rho, and a pausing site, but not the stretch of Uridines you refer to.

If you were reading up on transcription in eukaryotes, or were reading about rho-dependent termination, that would explain why you found no mention of polyU tracts. When evolution provides many solutions to a problem, it can get tricky to keep on top of it all!
This lists a few types of termination, including attenuation which is fascinating, and does involve regulation dependent on the concentration of a substrate.
Intrinsic Termination
A palindromic sequence situated just before the termination site causes a hairpin to form in the nascent RNA inside the exit channel of RNA polymerase, if given time (and if anti-termination factors do not bind the RNA to suppress hairpin formation). It appears that formation of this hairpin "destabilises the elongation complex [RNA polymerase + elongation factors]", and is an irreversible step towards collapse of the transcription bubble and dissociation of the transcription machinery.
The polyU tract (~8nt long) proceeding the hairpin seems to have dual function: the A:U basepairing in the DNA:RNA hybrid is weak; the hybrid becomes less favourable. Since the hairpin (which is an RNA:RNA duplex) is adjacent to the RNA:DNA hybrid duplex in the bubble, they experience competition for formation. Weakening the hybrid duplex favours hairpin formation, which acts like a switch that separates most of the RNA:DNA duplex in the bubble - synthesis cannot proceed, and the unstable complex dissociates.
Also, the ployU seems to be responsible for pausing which allows time for the hairpin to form, but not for the reason you suggest:
The concentration of UTP in the cell is not unusually low. ATP concentrations are higher than other ribonucleotides since it is the cell's major 'energy currency', quite apart from nucleic acid synthesis. Hence I don't believe pausing can be explained as the polymerase waiting for UTP. The polyU tract probably acts as a 'back-tracking signal' to the polymerase, since the hybrid duplex in the catalytic site is weakened, and the repeated nature may be "slippery"(?). This back-tracking pauses the polymerase.

To summarise: The elongation complex passes the palindrome and reaches the polyU tract, where the hybrid duplex in the bubble is weak and tends to cause back-tracking/pausing. This allows time for the hairpin to form in the exit channel, which both unwinds the hybrid duplex further, and destabilises the elongation complex. The transcriptional machinery is now destined to dissociate and the bubble collapse: RNA is released from the DNA duplex.
It is interesting to note that intrinsic termination can be suppressed by proteins that bind the hairpin. In bacterial operons, where sets of (almost) concatenated genes are separated by intrinsic termination signals, the amount of read-through at each termination site determines the relative expression levels of each gene.
Rho-dependent Termination
Rho is a hexameric protein complex that is loaded on to the nascent RNA at a loading sequence. It hydrolyses ATP to move along the emerging RNA - apparently it "races" with the polymerase, and when it catches up to the polymerase, it causes termination. There are pause sites in the RNA which allow rho to catch up - these sites tend to be rich in A and U, so perhaps polymerase is slowed by destabilisation of the hybrid duplex - but it is nothing like the intrinsic terminator, since it depends completely on rho for termination.


Can anyone help confirm this tiny insect larvae?

Can anyone help identify this insect larvae?

This is a varied carpet beetle larva, which belongs to the species Anthrenus verbasci.

A. verbasci. larval form, left; matured beetle, right.

  The bed was searched thoroughly and no others were found, but is there likely to be more of them?

It's difficult to say, though, generally, ~40 eggs are produced at a time, and they can remain in the larval stage for 8 months to almost two years.

At any rate, the University of California Agriculture & Natural Resources, and this website, both provide solid information about this insect, and outline measurements that can be taken to protect your home from it.


The mechanism of aconitase classifies it as a lyase, even if (under most physiological conditions), the relative concentrations of substrates results in it catalysing the conversion of citrate to isocitrate. In short, it is not an isomerase because the substrate is released after each step.

As the mechanism of aconitase shows, it catalyses the conversion of either citrate or isocitrate to aconitate as well as the reverse reaction. This is similar to the reaction catalysed by fumarase, which is the reversible addition or removal of water.

Because the physiological concentrations of citrate is much larger than the concentration of isocitrate, aconitate overall catalyses the reaction from citrate to isocitrate, and does so via catalysing two lyase reactions.

Regarding the other part of your question, hydrolases are a completely different group of enzymes, and none of the reactions involved are related to hydrolases in any way.

While water is in fact involved in the reaction, it is not used in the process of hydrolysis. To be specific, hydrolysis (in its enzymatic/organic, and not chemical sense) requires that water be a substrate required to break apart a molecule A-B into A and B. Since the addition of water does not result in citrate/isocitrate being broken down into two smaller organic molecules, aconitase is not a hydrolase.


How is the probability of Rh type inheritance calculated?

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

m  f
RR RR
Rr RR
RR Rr
Rr Rr

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

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


Transcription factors are an important cellular regulatory mechanism to control gene expression. The expression of TF is important for cell function, differentiation and also for responses to environmental signals.

We know quite a number of different TF, but only for a little part of them their exact function (in terms of which in which tissues they are expressed, when and which genes they regulate) and this is where the paper you read comes in.

They test for the expression of roughly 1400 TF in a number of different tissues, to see where they are expressed (figure 3 from the paper):

The group used micro-arrays to analyze the expression levels (in this case how much transcript from the genes is made assuming that this also translated). The quantification was done using the signal strength of the array - the more transcript you have, the stronger the signal is.

The expression of a certain TF in a specific tissues shows its involvement in gene regulation (either direct or indirect) there.


difference between transcriptional activator and general transcription factors?

Activators turn genes on - they help or promote RNA transcription of the gene.  Other Transcription factors may turn genes off (prevent or reduce RNA transcription).  Some transcription factors may promote or inhibit RNA transcription depending on their environment/context.

Transcription factors is such a generic term that anything can happen in practice.  They are generically supposed to interact with the polymerase, but if some were found to interact by attracting other transcription factors that would not be a surprise.

I think 20+% of human genes are transcription factors (that is just a guess we haven't been able to characterize more than a few of them.


HSV-1 has evolved mechanisms to thwart the immune system's surveillance.  A number of genes in the viruses genetic material code for proteins that can disrupt the process by which a cell alerts the immune system that it has a foreign virus within in it.

For technical readers, the reasons are described in the links above in detail.

For the non-biologist....

PART ONE  As you note in the question, HSV-1 can remain dormant in an infected cells for a long time.  In general, there is nothing for the immune system to respond to at this time.  So the infection persists in a dormant state.  Whats more, when it spreads, it can spread between cells, without entering the bloodstream.

PART TWO If the virus re-activates. In order for cells of the immune system to recognize and destroy a cell infected with a virus, the infected cell first chops up bits of the virus that are inside the cell and transfers these pieces (called antigens) to the outside of the cell so they may be presented  to immune system cells. At the same time, the infected cell attracts and activates immune system cells using 'distress' molecules.    However, HSV carries genes that make proteins that can thwart the presentation of antigens by a cell as well inhibiting the distress molecules that help activate an immune response.

PART THREE  What about antibodies ?  During the body's response to an HSV infection, antibodies can be produced and persist.  In many infectious diseases, antibodies can be protective as they mop-up any circulating virus and may prevent re-infection.  However, since HSV is already present inside cells, antibodies may have little effect in the reducing the amount of virus-infected cells in the body and may not prevent flare-ups.

Paradoxically, some of the symptoms of HSV flare-ups are due to the immune system's response!  (looking for a good reference)

The good news is that drug options to treat HSV have improved.


Why is offspring of identical twins not identical?

They are not identical for the same reason full siblings are not identical.

A simplistic Mendelian setup would be the following:

X1/X2 = Mothers
X3/Y = Fathers

That means the children could be:

X1/X3
X1/Y
X2/X3
X2/Y

So children born to two married couples composed of identical twins only have a 50/50 shot at being the same gender, much less have the exact same set of genes and express them in the same way.

Now, the simplistic view above only concerns 4 alleles - but the human genome is composed of thousands. By the end, the chances of genetically identical offspring from a set of identical twins is still very, very low.

And you haven't even began to include epigenetic variations, which often arise as a response to the environment! One cousin might be shorter due to their diet as an infant, one might have allergies the other does not depending on if they played outside as a child, and for non-Mendelian traits (incomplete dominance, co-dominance, phenotypes that rely on more than one allele [especially hair, eye, and skin color]) there's even more opportunity to introduce differences!


Where can I find the list of all tendons in the human body?

Your best bet is the Terminologia Anatomica, which is the international standard for anatomical terminology.

The 1998 edition is freely available. It lists only a few named tendons though, which is consistent with my experience as an anatomist: very few tendons are named separately from the muscles to which they are connected. Central tendon of the diaphragm, conjoint tendon, and calcaneal tendon are a few.

Otherwise, it's just "tendon of biceps brachii" (which actually has 2 tendons at one end and one at the other).

4,000 seems like a too high number to me. 2x the 640ish muscles plus some extra for multi-headed muscles and those with internal tendons or aponeurotic tendons seems like a more reasonable estimate.


How and why did bats and dolphins develop echolocation?

There are many conditions in which echolocation has evolved, and bats, dolphins, and even some birds (oilbirds) have evolved the ability to echolocate with different anatomical structures. Echolocation is a great example of convergent evolution, where a very similar feature is developed through very different stages in different taxa. Stephen Rossiter (from Queen Mary University of London) has uncovered that both bats and dolphins have similar mutations in a unique protein called "prestin", that increases hearing sensitivity. This could be a key step in developing the ability to echolocate.

Before a fully fledged echolocation system developed, fossil odontocetes seem to have developed high frequency hearing and sound production structures (for more details see research by Travis Park, Erich M. G. Fitzgerald, Alistair R. Evans http://rsbl.royalsocietypublishing.org/content/12/4/20160060 DOI: 10.1098/rsbl.2016.0060).

Instead of anatomical limitations (eyes on the side of the head) driving the development of echolocation, it seems to have evolved because it gives predators a competitive edge over visually oriented predators.


Why do animals use glycogen for their polysaccharide storage whereas plants use starch?

well glycogen can be broken down into sugars a lot faster, many more branches means many more ends to clip individual sugars off of, that's how you mobilize the sugar for use, it is clipped of the end of a strand. With many more branches glycogen can mobilize more sugar more quickly.  This is not important in plants but in animals that need to be able mobilize lots of energy in a hurry, glycogen works better. Additionally glycogen is a smaller molecule and easier to make, not surprising since glycogen is the ancestral condition for plants and animals.

As for why plants switched to starch, or more precisely gained it through symbiosis, starches folded crystalline structure makes it a higher density energy store but also slows its release, it is however more stable, which is important if you are going to be storing it for a long time. Animals would likely switch to starch too if they did not have to break it down to digest it, just because they take in so much of it. But since they have to break it down there is no real incentive the build it back into starch when glycogen has some advantages and quite frankly since the pathway is already there and evolution has a lot of "eh good enough".


Help in identifying an unknown Golden Worm/Larvae

These are larvae of the so called fungus gnat of the order Diptera. Fungus gnats are small flying insects that look sort of like mosquitoes but they don’t bite. In fact, adult fungus gnats live only about 7-10 days and do not feed. It is the immature larval form that can cause damage to your plants.

Source: https://www.projectnoah.org/spottings/30766835/fullscreen
I see, i'm Balinese too, you know everything things were rare are linked to myth.


Identify this roadside plant in Montserrat, Spain

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

 Photo: Macro63

 Photo: cc-by-sa-2.0 Bernard Dupont.


Classification of glycosidic anomeric bonds (alpha vs. beta)

Here's my interpretation, as far as I can get, which agrees with your deduction that both of the O-glycosidic bonds involve α epimers. (If the epimeric carbon has an -OH in the axial direction then this is the α anomer.)

Do you have the name of this compound?

Let's hope that a real glycobiologist comes along.

Supplementary
I'm now not sure that it is even possible to assign an anomeric state to the sugar marked as ?. There is no indication in the diagram of the presence of a -CH2OH substituent on the ring - it appears to have a methyl group instead. If that group was a -CH2OH then the putative anomeric C would indeed be in the α form since it is pointing in the opposite direction from the "-CH2OH" (c.f. the two galactose residues). If ? is a deoxy- derivative of a sugar then it may be that the convention still holds.


Why placental progesterone suppressed or drop before onset of labour?

Pregnenolone -the precursor of progesterone is principally converted to estradiol instead of progesterone.Thus the oestrogen:progesterone ratio increases prior to parturition.

  Fetal cortisol stimulates activity of placental 17 α hydroxylase/17, 20 lyase (CYP 17) enzyme, which catalyzes the conversion of pregnenolone to estradiol.

Confinement of the foetus in the uterus stimulates the stress responses.

  Stress leads to a rise in foetalACTH. The rise in ACTH causes production of cortisol from the foetal adrenal glands. The rise in foetal cortisol leads to an increased oestrogen:progesterone ratio by upregulating aromatase enzymes, which convert androgens to oestrogens. Cortisol also reduces progesterone production.


Why the C6 intermediate molecule in the Calvin cycle is so unstable

The question of why the molecule is unstable belongs to the realm of chemistry, which is not the subject of this list. Presumably the reaction for its hydration is thermodynamically favourable and there is a reaction mechanism which allows the reaction to proceed with a low activation energy.

The question of the existence of 2-carboxy-3-keto-D-arabinitol 1,5-bisphosphate and its role as an intermediate in the RuBisCO reaction was solved in 1986 and is no longer the subject of speculation. Its synthesis was described in a paper in Phil. Trans. R. Soc. Lond. B, which is behind a pay wall, but can be found in a post on ResearchGate.

In brief, they trapped this C6 compound in a more stable form with acid, and so could characterize it chemically. Its enzymic hydrolysis could then be studied at a slower rate.

The subsequent solution of the crystal structure of RuBisCO provided further confirmation of the reaction mechanism and molecular information on the role of the enzymic groups and magnesium ion cofactor. See, for example, the review by Gutteridge and Gettenby in Cell.

So the era of speculation would appear to be long past, and the account in standard biochemical texts such as Berg et al. — shown below — would appear to be reliable.


Calling for Free Online Data for Paediatric ECG?

I recognize this was asked like 7 months ago, but in case you're still looking for a good resource:

I used a CD of heart sounds that is called something like "Harvey Heart Sounds," which I got with the purchase of my stethoscope.  If you can find a copy of this, I found it an excellent tool when training to recognize the differences.

These are good heart sounds: http://depts.washington.edu/physdx/heart/demo.html

If you were looking for something other than the sounds themselves, then I'm not sure if you're asking about.  There are all sorts of good ECG references, especially Dale Dubin's EKG Interpretation book.  And Kablunde was the cardio textbook I used, which I liked.


One long standing hypothesis of cancer formation is that it originates in a 'wound that never heals'.  I was about to add that there is little hard evidence for wounding as a significant cause of cancers but Google found this fascinating report on Marjolin's Ulcers
 which I had never heard of.   Whether it was the wound or a comorbid virus or something else.....

You may also want to search the current thinking of how a chemically inert 'irritant' - an asbestos fibre - can cause mesothelioma.


Does a breastfed infant gain immunoprotection due to intramuscular vaccination of the breastfeeder?

Vaccinating the mother or a breastfeeder to provide immunization for the baby through breastfeeding is not proven nor recommended by health authorities.

If a mother is vaccinated intramuscularly or any other route, it will anyway pass IgA and IgM, and to a much lesser extent IgG antibodies to the baby through breastmilk but it is not proven to confer specific immunity against all pathogens.

And as per your other question, a child from a mother who hasn't had any infection/vaccination with Hepatitis A and hasn't passed any IgG through the placenta will not be conferred immunity against Hepatitis A even if it is breastfed from a woman who had the infection or was vaccinated against Hepatitis A.

There are other ways a mother's breastmilk can induce immunity (cell immunity) this is currently under research and it has been proven to confer immunity in animal models in recent studies but is still not a medical recommendation in humans (studies in pups regarding passing immunity through foster breastmilk for candida albicans , tuberculosis and helminth infections).

What is already proven is that breasfeeding and vaccination of the baby does provide with a more robust vaccination response so that is why breastfeeding and vaccination to the baby at the same time are encouraged.

Maternal Milk T Cells Drive Development of Transgenerational Th1 Immunity in Offspring Thymus

Pre-conception maternal helminth infection transfers via nursing long-lasting cellular immunity against helminths to offspring


Protein-coding introns in mitochondrial genomes

Mitochondrial genomes differ greatly in size, coding potential and even whether they are circular or linear. Mammalian mitochondrial DNA is small (11–28 kbp) and intronless. However the mitochondria of certain other organisms range up to 1000 kbp in size.

Certain sponges (demosponges) with large mitochondrial genomes contain type I introns and type II introns.  Although introns were initially thought to have no other function than to separate exons, the introns of certain nuclear genes have been found themselves to contain genes. This turns out also to be true of some of the mitochondrial introns. To quote from then introduction to a paper I found through an internet search:

  Most Group I introns encode homing endonuclease genes (HEG) and/or
  maturase of the LAGIDADG † family, while most Group II introns encode a
  reverse transcriptase (RT).

These introns are found in genes such as that encoding cytochrome oxidase subunit 1 (COI).

† This appears to be a misprint for the LAGLIDAD mutases, which are also endonucleases, and are involved in splicing the introns in which they reside.


The black and white colours on the front and the grey back as well as the overall shape make me think it could be a badger. Given the location, it could be the European badger (Meles meles). The size matches, and badgers are omnivorous, so they can eat meat.


Which is a good methodology to find out a domestication process?

Yes, everyone use SNPs today for such analysis. Some RADseq is probably the way to go.

Detecting selection is not an easy task as many technics exist which differ by their assumptions and by the applicability. You should probably try to find papers having done the same type of analysis with the same types of data and eventually talk with authors. Your lab might already be experienced in such analysis.

What test to detect genomic signatures of selection? might help but the suggested algorithms are mainly for the analysis of within species variation. Procedure like mcdonald-kreitman test and other more advanced methodology to detect selection over a phylogeny (such as OUWIE if you have phenotypic traits) might be of interest. You could also simply use some rank tests when having many independent domestication events. The exact methodology you end up using very much depend on your data (how many independent domestication events do you have for example, do you have phenotypic traits, ...).

  compare them with the species that gave them origin

Do you really have sample of the ancestor? Most of the time people simply consider a non-domesticated descendant of the non-domesticated common ancestor. Don't make the mistake of considering an extant lineage as if it was a descendant. This extant lineage evolved too!


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


Found it!

Seems to actually be the pupae phase of the common drain fly - psychoda spp.

Looks like I'm going to be routing or replacing the pipes in that house.

Thanks.


Can life occur from a fertilised egg cell, in which both the egg and sperm possess an extra copy of a chromosome?

There are many ways to answer your question, I'll try a couple.

First, extra chromosomes in humans are commonly deleterious. However, there are known rare forms of tetrasomy that are not lethal, see Wikipedia on tetrasomy. Note that the causes of tetrasomy are rare events, so they are typically occurring in just one of the original gametes, not both; for it to happen in both would require a rare event paired with another rare event - not saying this is impossible, just less likely.

Polyploidy in other organisms, particularly plants, is both common and normal, see Wikipedia on polyploidy.


Minimum infective dose is the minimum number of infectious particles that causes infection/illness in 50% of those given that dose.

Practically this is only really measurable in a controlled laboratory setting, but one can estimate it for real world circumstances as well.

It isn't easy to know how exactly the probability will vary around the MID - there are too many factors related both to the individual and the pathogen to make simplistic assumptions (like assuming each individual infectious particle has an independent probability of leading to infection). It is typical that higher initial exposure (particularly for foodborne illness, but seems to be an issue with SARS-CoV-2 and other respiratory viruses as well) leads to more severe illness, however.


Calculating number of amino acids in mRNA

I think I have this figured out. Had to do some math. With our 4 nucleotide system, the number of possible codons is 43 = 64. That is number of nucleotides to the codon length power. The question asks us to determine codon length while giving us the number of amino acids and an upper limit on tRNAs. Using the same formula,  #Nucleotides(Codon-Length) = #Codons, we must find a combination of nucleotide number and codon length that gives between 20 and 40 codons.

                               Codon Length
Nucleotides    1         2        3        4        5
     2         2         4        8        16       32
     3         3         9        27       81       243
     4         4         16       64       256      1024
     5         5         25       125      625      3125
     6         6         36       216      1296     7776
     7         7         49       343      2401     16807

So using this table we see that a few different combinations of Nucleotide number and codon length will fit in that range. A 2-nucleotide system could work if each codon was 5 bases long. A 3-nucleotide system could work with 3 base long codons. A 4-base system cannot work, it goes from less than 20 to more than 40. A 5-base system can work with 2 base codons. A 6-base system can also work with 2-base codons. 7 or more bases fails because even a 2-base codon will make more than 40 codons.

A codon length of 1 nucleotide would require at least 20 nucleotides, so it would not be a good answer.

5 is probably the correct answer because it works with the shortest codon length, though I don't know how you'd get base pairing with an odd number of bases. Perhaps the 5th base pairs with itself. A 6 base system can also work with the same codon length and wouldn't need a self pairing base. However that table shows several combinations could work, so this question might have been to see how you defend your answer.


Spike protein production by mRNA vaccines?

I am asking this question to understand whether the cells which are
used to create spike proteins are attacked by the immune system.

Yes, that is the aim of RNA vaccinations!
But don't worry, that's a good thing, as can be concluded from this review-paper, that emphasizes the advantage of RNA vaccinations to invoke cellular immune response:

Although subunit vaccines have been used successfully to elicit
humoral immunity against a wide variety of pathogens, they fail to
induce cellular immunity which is required to eradicate the
intracellular pathogen reservoir of many chronic diseases, including
viral infections such as HIV or hepatitis C.

Basically, the idea is that presented antigens from traditional vaccines are inclined to be presented via MHC2, rather causing humoral immunity, while after RNA transfection, cellularly produced peptides can also be presented on MHC1, causing cellular immunity.


Does a woman contain all the genes needed to make a man?

Human female cells contain most of the genetic information required to make a male, but they do not contain a critical component: The Y chromosome. This is a relatively small chromosome. Wikipedia claims we have identified around 200 genes on it to date, compared to estimates of 20,000 - 25,000 genes overall in the human genome.

Importantly for your question, only other males contain and make full copies of all the genes on the Y chromosome. The Y chromosome does not cross-over* with the X chromosome during meiosis when producing sperm cells, which keeps the Y genes isolated, except for rare exceptions (e.g. gene translocation). So those genes are passed down the male line only. The SRY gene is just one of the genes encoded uniquely on that chromosome, so something else is definitely missing - the question could be re-phrased "how important to being a functional male are the unique genes other than SRY unique to the Y chromosome?"

The linked question (an experiment on mice that produced XX "males" by finding an alternative trigger to the SRY gene to induce male development) demonstrates that in terms what we might consider a physical male specimen, the Y chromosome probably contains a minority of critical unique features. The mice developed into apparently complete physical males. That means genes outside of the Y chromosome cover most of the body development plan for both males and females.

However, such XX males will in most mammal species not be fully functioning males - the missing genes do make a difference. One outcome is infertility - biologically speaking, XX males do not possess a key male function, the ability to mate with a female to produce offspring. There are missing genes related to sperm production.

Human XX males - as in developmentally male - do occur naturally. This can be caused by gene translocation - specifically the SRY gene moves to the X chromosome in a sperm from the father (potentially other Y genes will move in the same event). The symptoms that present with the syndrome vary, but give some indication of which critical components are missing.

Not all animals have the same mechanism. Birds have W and Z chromosomes (with males being ZZ and females ZW). Yet other animals do not use genetic switches, but environmental ones. In those cases, the female does contain all the necessary genetic information to create a male. In cases where there is parthenogenesis (production of offspring without fertilization), then this can be fully demonstrated.

* Technically there are some small regions, about 5% of the Y chromosome, which do cross-over with X, called the pseudoautosomal regions. At the time of writing the linked article mentions 29 genes found in these regions.


Can SIRS occur without Sepsis from Infection?

According to the classification of sepsis, it is SIRS with a suspected or known source of infection. By definition therefore, sepsis without SIRS is not sepsis but SIRS can exist without sepsis. In all fairness though, SIRS can exist if you run for a while (elevated heart rate and respiratory rate by themselves qualify for a diagnosis of SIRS).

Sepsis is however not the same as a bacteraemia which may be caused even by brushing your teeth (although the bacteraemia in this case is transient).


Miroux and Walker (1996) Over-production of Proteins in Escherichia coli: Mutant Hosts that Allow Synthesis of some Membrane Proteins and Globular Proteins at High Levels. J Mol Biol. 260: 289–298

The authors report on problems of over-expressing membrane proteins in E. coli using a T7 (pET) system. They isolate mutant strains which show improved levels of expression compared to the parent strain, BL21(DE3). In their Table 1 they document levels of expression of 17 proteins including, as a control, GFP. GFP was found as a combination of soluble and inclusion body protein at a level of 37 mg L-1 in BL21(DE3) and 140 mg L-1 in one of their mutant strains (C41(DE3)). The highest level of expression that they observed was 300 mg L-1 for bovine OSCP.

Unfortunately the authors document neither the total protein content, nor the cell density of the cultures that they analysed.

Let's assume that the cultures were 10e9 cells mL-1 = 10e12 cells L-1.

According to this source (citing Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. Vol 1. pp. 14, ASM Press 1996), the dry weight of an E. coli cell is 2.8e-13 g

The generally accepted figure for protein as a fraction of dry weight in E. coli = 0.55

I calculate from these numbers a value of 1540 mg protein L-1. For the three protein expression levels described above this means:

GFP in BL21(DE3) = 2.4%

GFP in C41(DE3) = 9.6%

bovine OSCP in C41(DE3) = 19.4%

I conclude (from these numbers, and from personal experience) that overexpression levels are highly variable, and are going to be strain and protein-dependent. Values in the range of 1-20% total cell protein may be anticipated.


What's the effect of oxygen deficit on plants?

During the daylight, the plant is photosynthesising faster than it is respiring so there is no net uptake of oxygen (the oxygen of course being produced in the as part of the photosynthesis).

Of course, this only applies for tissues where photosynthesis is occurring.  In the roots of the plant, oxygen must always be present in the surrounding soil/growth medium for respiration.  Therefore if there is no oxygen in the roots then the root cells will be unable to produce ATP from respiration and consequently die.  This will eventually lead to the death of the entire plant as it is unable to take up nutrients due to the lack of a functioning root network.

This is the cause of plant death when soil is waterlogged - the water fills spaces in the soil that would otherwise contain air (i.e. oxygen).

Certain plants (often crop plants), rice being given as an example in the comments below, are able to survive being waterlogged and the resulting low oxygen supply. However they can only do so in the short term.  Rice plants in particular have adaptations that allow the transport of oxygen from the aerial parts of the plant down to the roots.  This does of course mean that the rice can not survive being totally submerged for an extended period of time.  Plants such as rice may have better adapted anaerobic fermentation pathways that become the main producer of ATP when aerobic respiration has arrested thus allowing them to better cope when transiently submerged than other plants.

Molecular strategies for improving waterlogging tolerance in plants


Which fishes produce alarm signals to warn other group members about in coming predators

Here are some fishes produce alarm signals as sounds.

members of family Pamadasyidae-the grunts.

the family scaridae e.g.—Parrot fish.

sea catfish Galeichthyes felis

gafftopsail catfish

Indian loach

Trigger fish

Epinephelus striatus

For mor information see the link. http://www.fishfarmingtechniques.com/fish-structure/specialized-organs/sound-producing-organs/sound-producing-organs-in-fishes-specialized-organs-fisheries/13563


Why does weight loss lower blood pressure?

Weight gain increases blood pressure, the reason for this process is due to the effect of hormone called Leptin.

Leptin is made by fat and circulates in the bloodstream to reach the brain, where it acts as a signal for energy reserves, adjusting both energy expenditure and the sensation of hunger – hence it is sometimes referred to as the ‘satiety hormone’.
The group showed that some obese people who were lacking the hormone leptin because of a genetic disorder had low blood pressure despite being very heavy. This was also the case for people lacking the gene for the leptin receptor in the brain, meaning that the brain was unable to respond to the hormone.
Reference

The team lead by Professor Michael Cowley, Monash University, Australia, in collaboration with Professor Sadaf Farooqi, from the University of Cambridge, UK suggests that the leptin signalling is necessary for obesity-induced increased blood pressure. The clinical studies in severely obese humans showed that these observations are relevant to humans.

Professor Cowley said: “High blood pressure is a well-known consequence of obesity. Our study explains the mechanism behind this link, showing that leptin, a hormone secreted by fat, increases blood pressure.”
Professor Farooqi, from the Wellcome Trust-Medical Research Council Institute of Metabolic Science added: “We now know that leptin regulates both our weight and our blood pressure through its action on the brain. Targeting this action could offer a useful way of helping people fight obesity and associated problems such as high blood pressure and heart disease.”
Reference

It is thought that Leptin's only task is to activate the sympathetic nervous system connected to the brown fat and there by directly burns energy. But it is also behind the activation of sympathetic nervous system of heart and kidney, thereby increase the blood pressure.

Genetic and drug experiments in mice, they have pinpointed an area in the mouse brain that increases blood pressure when it is exposed to high leptin levels.
This region is called the dorsomedial hypothalamus, and is thought to be involved in controlling energy consumption. Their findings show that high levels in leptin do indeed boost blood pressure, via this brain region.

Reference
http://ndt.oxfordjournals.org/content/15/8/1115.full.pdf+html


How does frame-shift mutation not absolutely ruin the organism?

First of all, for a frame shift mutation to occur nucleotides (not amino acids) are either deleted or inserted into the sequence.  Read about details on this wiki page. Here's an image about frame shifts.

On panel A a new stop codon is formed  (TAG is trasncribed to UAG that is serves as stop codon during translation) thus the result is an abnormally short protein.

On panel B the codon 37 is swapped to a G thus the TA from the codon 38 is shifted left by two resulting in the new codon GTA.

On panel C exactly 3 nuleotides are deleted thus codon boundaries do not change, but a codon and the amino acid encoded by it is completely deleted.

On panel D 4 bases are deleted thus the T form codon 171 and the C from 172 are merged with the G from 170.

source: the linked wiki page.

It does not affect the choromosome in the way you describe because genes are separated and are independently transcribed (with some simplification). Every gene has its own translation  start that determines the correct frame in that gene If you think of a chormosome as a chapter of a book and the genes are paragraphs, you can see that deleting letters or words may scrable one paragraph, but the others are not affected by this because they have their own boundaries.

EDIT:
During translation the ribosome reads the mRNA in the form of triplets. When a single nucleotide is deleted then the whole sequence from that point shifts to the left by one thus the first letter of the subsequent triplet gets mixed into the frame where the mutation happened (the same goes for insertion but the sequence is shifted to the right). This causes the change in the meaning of the triplet, and can ruin stop codons that would affect the translation of the mRNA but not the transcription of the gene to mRNA.It is important to understand that transcription is a countinous process and the DNA is transcribed from base to base not in triplets, and that transcriptions stop is not encoded in the from of stop codon.


In general, xenobiotic biotransformation (i.e. processing the xenobiotics aka drugs - detoxing the body) is accomplished by a limited number of enzymes with broad substrate speciﬁcities. In humans, for example, two cytochrome P450 enzymes— namely,CYP2D6 and CYP3A4 — metabolise over half the orally administered drugs currently used. (Gonzalez and Tukey,2006).

The various different CYP enzymes can act on various different foreign organic compounds with varying levels of efficiency. The CYP enzymes oxidise these organic molecules adding on -OH groups to make them more solube and thus more easily excreted.

Grapefruit contains compounds known as furanocoumarins that block the CYP3A4 enzymes. These compounds do this by irreversibly binding to the CYP3A4 enzymes, putting them out of commission. Like the wikipedia article says it takes about 24 hours for the CYP3A4 enzymes to return to normal levels after the average glass of grapefruit juice is consumed. During this time your body’s ability to process drugs for elimination is decreased because CYP3A4 is the main CYP enzyme for processing many drugs and toxins.

You might think that this could be used to reduce the dose for a drug, but the amount of furanocoumarin in your blood would vary widely (grapefruit isn't uniform in it's concentrations) and CYP3A4 levels vary between individuals.
 If you tried using grapefruit juice or another source of furanocoumarins to do this you'd be reduced to guessing how much of your prescribed drug is safe to take. Blood levels of the drug may rise, resulting in the risk for new or worsened side effects. it can essentially cause the normal, dose of a therapeutic drug to act like an overdose by increasing the bioavailabilty of the drug in your body. Better not to risk it.

Sources:

Gonzalez FJ, Tukey RH: Drug metabolism, in Goodman LS, Gilman A, Brunton LL, Lazo JS, Parker KL (eds.): Goodman & Gilman’s the Pharmacological Basis of Therapeutics. New York: McGraw-Hill, 2006, pp. 71–91. [I'm afraid I unable link you directly to it]

Textbook - Toxicology - the basic science of poisons, Cassarett & Doull (A PDF version of the textbook can be found here: https://ilmufarmasis.files.wordpress.com/2011/07/casarett-and-doulls-toxicology-the-basic-science-of-poisons7th-ed.pdf)
Half-remembered undergraduate lectures.


What is a synonym of the word design that can be used in context of evolution?

Although not ideal, "adaptation" is more appropriate than "design" as a noun describing something that has come about in an evolutionary context, even though not all evolution is adaptive.

In writing, though, I would not phrase it as you have, rather I would change the agency from something evolution does as some sort of "entity" which makes it sound like a goal-driven "designer" with whatever words you use, and instead say that "Eyes evolved from simpler photosensitive groups of cells." Eyes deserve the agency, because having eyes is what would improve the survival of an organism versus eyeless conspecifics and increase the proportion of eyed individuals in the next generation (I hope my simplification of the eye-evolving process as if eyes are a simple Mendelian trait isn't too distracting here, I mean it mostly as metaphor), rather than eyes being a "goal" of something called evolution.

Similarly, you would not say "Chemistry makes water from hydrogen and oxygen," rather you would say something like "Hydrogen gas reacts exothermically in the presence of oxygen gas to produce water." There is no agent "chemistry," that is just the word we use to describe the set of processes in the universe that govern how molecules/atoms/subatomic particles interact. Similarly, "evolution" is not an agent who does things.

One place I would differ in this guidance is in talking very big picture, such as saying that "evolution produced the wide variety of species present today"; in that example, there isn't anything more local to act as an agent, and it's appropriate to refer to the evolutionary process as a whole.


Perhaps it was a species of velvet ant (a type of wasp from the genus Dasymutilla). The females lack wings, and it appears like what you describe and vaguely see in your image.

Here are some photos:

Photo 1 Source

Photo 2/Information Source


Why does the direction of endolymph flow oppose direction of body motion?

The endolymph inside the ear, like any kind of matter, has mass and so is subject to inertia.  This means any change in speed and direction will be resisted.  The ear and semicircular canals themselves are fairly solidly connected to the rest of the body and so accelerate smoothly.  But since endolymph is fluid, it cannot be brought up to speed as fast, so it lags behind in moving.  So, as the ear moves forward, the endolymph stays behind and so in relation to the ear, flows backward.

This is like what you experience when a car or airplane accelerates: you "flow" backwards into your seat as the vehicle surges forward.


How sterile is sterile when working with nucleic acids to prevent contamination?

Short answer: Yes

Long answer: Depends what you are working with.

DNA: If you are working with DNA, its pretty stable and you can usually get away with a 70% ethanol wash/autoclave (mainly to prevent contamination and obtain consistent results). EDIT: Read Chris's answer also below

RNA: If you are working with RNA well.. whatever you did for DNA doesnt apply anymore. You have to take it to the next level.  You will need to replace everything, you'll need nuclease free water, tubes, reagents and whatnots. Throw out ethanol and bring in RNAZap, DEPC water or something like that.

  An RNase free environment is essential when working with RNA samples. There are two main reasons for RNA degradation during RNA analysis.

  First, RNA by its very structure is inherently weaker than DNA. RNA is made up of ribose units, which have a highly reactive hydroxyl group on C2 that takes part in RNA-mediated enzymatic events. This makes RNA more chemically labile than DNA. RNA is also more prone to heat degradation than DNA.

  Secondly, enzymes that degrade RNA, ribonucleases (RNases) are so ubiquitous and hardy; removing them often proves to be nearly impossible. For example, autoclaving a solution containing bacteria will destroy the bacterial cells but not the RNases released from the cells. Furthermore, even trace amounts of RNases are able to degrade RNA. Note that RNAses are present everywhere (skin, reagents, normal plastic etc).

  Therefore, it is essential to avoid inadvertently introducing RNases into the RNA sample during or after the isolation procedure.

Remember that following microbiological aseptical techniques is usually good practice (and a requirement) when working in a molecular biology lab.

There are excellent guides available online for working with RNA:

I took the above paragraph from here:
http://www.bioline.com/us/rna-hints-and-tips

Life tech has a few more tips for you: https://www.lifetechnologies.com/uk/en/home/references/ambion-tech-support/nuclease-enzymes/general-articles/working-with-rna.html

Here is a good pdf to have in your labbook as a reference sheet:http://genomics.no/oslo/uploads/PDFs/workingwithrna.pdf

If this scares you , that's good because when working with RNA there are a million things that can go wrong the first few times you try it. You have to be very careful, and adapting a cavalier attitude such as not bothering is going to come back and haunt you at night...


Correlation between threat and odour, taste

The compounds that smell bad to us are often the same ones produced by the anaerobic metabolism of bacteria, such as hydrogen sulfides or butyric acid. These types of compounds are the ones that make excrement and rotting food smell bad, and if something is giving is giving off a lot of them it's a pretty good signal to not put it in your mouth. Vomit also has quite a lot of butyric acid in it, so we may be particularly sensitive to it.

Plants produce toxic compounds to stop herbivory, many of them taste bitter. Alkaloids are often toxic and uniformly bitter, terpenoids are another example.

There's nothing obviously different from a chemical perspective in chemicals that smell bad. Butyric acid is just a 4 carbon chain with a couple of oxygens on the end and reeks, while the compound propanediol (which is 4 carbons with an oxygen on each end) is used in deodorants. If a compound has a strong smell or taste to us, it is because that compound has been important to us during our evolution. That doesn't mean it's a perfect indicator; cheeses can stink and be totally edible, but that's because the compounds in that cheese usually are a sign of something dangerous.


Would modifying the human microbiome to digest cellulose be worth it?

You really need to understand how cellulase would effect metabolic systemic homeostasis before anyone can answer that. It's an interesting question. At first glance, one could consider that cellulase would allow disproportionate glucose intake, ultimately making fat a smaller % part of the diet. If unchecked, this could lead to a reverse Randal effect inhibiting fatty acid metabolism thus altering adipokine synthesis leading to a range of negative, if not, species detrimental effects such as reduced capacity for reproduction (as an example between altered biosynthesis and crosstalk between leptin and estrogen). This may have presented a problem for early humans, because in essence, cellulose could have acted as the very first mcdonalds convienience if we were capable of digesting it. I'm sure I'm missing many complications that would have occurred if early humans had this capacity, but it's a nice thought experiment.

And regarding the mathematical induction, forget about it, you can't induce a conclusion on potential alterations within the mammalian digestive system from only the enzyme kinetics of cellulase found in bacteria.


Is there a tool to find the action of an enzyme in a metabolic pathway?

I think the KEGG pathway database may be of some use to you.

Link is here: http://www.genome.jp/kegg/pathway.html

This a database of manually drawn pathway maps, I have used the site myself and it is very useful in determining if your enzyme is in a pathway and where it lies in it. This is assuming though, your enzyme is in the database and has been mapped.


How to do a blast search for similar sequences?

As stated in the comments here, there is no complete genome sequence for avocado as of yet, though people appear to be working on it.

However, there are a large number of ESTs and doing a BLAST of their translations with the tomato PPO sequence (tblastn) gives some hits.

Here is a link to that BLAST.

  However there are no matches, which may be because it is a different species with a slightly different sequence?

This is precisely the problem that BLAST was designed to solve.


Yes. Sick people are occasionally administered vaccines. But you need to keep in mind the mechanism of action of vaccines.

Broadly speaking, there are two types of vaccines.

Active immunization works by exposing the immune system of an individual with a pathogen (be it organism or derived proteins, etc). This type of immunization results in development of adaptive immunity in the individual, with long lasting effect; but it can days or weeks to fully develop.

On the contrary, passive immunization works by directly administering protective agents (antibody, etc). This will provide the individual with almost immediate protection; but will not lead to development of adaptive immunity, and thus will be short-lived.

You may find this wikipedia article informative.


Good model for comparative genomics in relation to temperature adaptation

As a starting point I would suggest you look at genomes of thermophiles and hyperthermophiles (organisms that thrive at upwards of 40 °C and 60 °C respectively), which are often found near underwater volcanos or hot springs.

For instance, one could do a genomic analysis of the archaean Methanocaldococcus jannaschii, comparing it to mesophilic species of Methanocaldococcus or Methanococcus. This organism is well studied, and genomic information for this organism is readily accessible.

Some studies have been done comparing the genomes of mesophiles and thermophiles. For example, Zheng and Wu (2010) found a correlation between GC content in coding/noncoding regions and temperature conditions.

At the other end of the spectrum you could examine psychrophiles (organisms that grow at low temperatures, −20 °C to +10 °C). However, few of these organisms are obligate psychrophiles, meaning many can thrive at higher temperatures as well and thus may not be suitable for your purpose.


Why would a single celled organism evolve to be multi-celled?

How did multicellularity evolved?

It is an ongoing field of research - Some insights about the origin of multicellularity

This is a big ongoing field of research. To start with an example, there was relatively recently (2012) an important article by Ratcliff et al. that shows that yeast can quickly evolve multicellularity under selection on the speed they sink to lower water layers. This article is one among many others and is far from being able to explain everything we would like to understand about the evolution of multicellularity. Typically, I think that this yeast species had a multicellular ancestor and we might think that this species would already have fixed alleles (=variants of genes that is fixed meaning that the whole population is carrying this variant today) in the population predisposing this species to easily (re-)evolve multicellularity. Also, they may have kept some standing additive genetic variance in their genome from their past and they would therefore very quickly respond to selection as they don't need de novo mutations. (Sorry if this last sentence was slightly technical).

One of the first traits that we usually refer to when talking about the evolution of multicellularity is the presence of sticky proteins allowing individual cells to paste to each other.

Some insights about the evolution from simple multicellular to more complex multicellular

Then, we could talk about more complex multicellular and argue how do these simple multicellular evolve into some more complex organisms. A common argument is that multicellular can have specialized cells are very could at doing what they're doing as they are specialized. Also, some level of complexity is thought to have raised due to the fact that multicellular organisms tend to have smaller population size than unicellular (see Lynch and Conery, 2003). It is important not to confuse evolution of complexity with the evolution of multicellularity although these two notions are somehow related.

What do you mean by multicellularity?

The evolution of multicellularity can be discussed in the context where sister cells form an organism together or when unrelated cells (among the same species or even cells from different species) come together to form an organism. Also, the multicellularity can be discussed at a different level depending on how we want to define multicellularity. Is a stack of cells reproducing individually, working for their own benefit a multicellular? Do we need a division of labor? Do we need a division between germline (reproductive caste) and soma line (non-reproductive case)?

How many times did multicellularity evolve independently?

Some people consider that there are multicellular bacteria (biofilms) but we will avoid discussions that are based on limit-case definitions. Let's talk about eukaryotes. Most Eukaryotes are unicellular and multicellularity evolved many times independently in eukaryotes. To my knowledge, complex multicellularity however evolved only (only?) 6 times independently in eukaryotes.

Metazoa (animals)
Ascomyceta (fungi)
Basidiomyceta (fungi)
Viridiplantae (green plants)
Florideophyceae (red algae)
Laminariales (brown algae)

Model organisms and interesting cases to study multicellularity

There are a bunch of specific clades that are particularly interested in studying multicellularity because they present transition states. For example Volvox is a chlorophyte genus and the species in this clade present different stages of multicellularity; Some species are exclusively multicellular, some form small groups, some create big colonies, some have some division of labor and some even have separation between the germline and the soma (Some castes don't reproduce). (ref1, ref2, ref3, ref4, ref5, ref6). Yeasts are also a good model organism for studying the evolution of multicellularity.


When do the spindle fibers attach to the chromosome

Your confusion comes from the inconsistent terminology in the literature. The attachement of the spindles to the chromosomes happens in the Prometaphase [1, 2]. The name already suggests that this is not one of the classical phases is cell division, but lies somewhere between Pro- and metaphase. Wikipedia states:

  Prometaphase is sometimes simply included as part of the end of prophase and early metaphase.

If you really need to stick to the classical scheme of pro-, meta-, ana- and telophase, I would personally suggest to treat the attachement (not the formation!) of spindles as a part of the metaphase.


variation in expression accounted for a SNP -- what's a usual percent?

eQTLs (expression quantitative trait loci) are variants that affect the expression of one or more genes.

There have been several 'genome-wide' studies of SNPs that directly affect expression. The actual effect sizes are hard to pin down in most of them, but in the supplementary data for this paper is a list of the SNPs with the largest effects and coefficients of determination.

There are several common SNPs (cis-acting) that account for >50% of the variation in that genes expression in this (European) population cohort. That being said, that vast majority of variants account for much less variation in the expression, but this is to be expected.

I therefore can fully suppose that a disease-linked SNP could affect the expression of a gene to that degree, particularly if it is an oncogene or tumour suppressor.

Reference:

 Wood AR, Hernandez DG, Nalls MA, Yaghootkar H, Gibbs JR, Harries LW, Chong S, Moore M, Weedon MN, Guralnik JM, et al.. 2011. Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Human molecular genetics 20: 4082–92.


Western blot, though is a commonly used technique and is relatively simple to do, has some issues:

Low throughput: it is difficult to analyse multiple proteins simultaneously
Limited cross comparability: since antibodies to different proteins can have different affinities, they cannot be compared with each other.
Low sensitivity
Not very quantitative

LCMS addresses all the above limitations of western blot. It is also possible to do targeted proteomics i.e. study just some few proteins instead of the entire proteome.
An LCMS system has a high initial setting up cost but a relatively lower run cost. However, the mass spectrometer has to be maintained and it is not an easy job; you basically need a facility and a dedicated technical staff.

  Which one would you recommend and would you do both for validation?

Which technique to use depends on what you really want to see and what resources you have at hand. It is a commonly practised approach to do a western blot for re-validating a few selected genes identified from LCMS experiment, which is just to prove that the result can be obtained using another technique too.


Insect ID, found in shower, northeast USA

That is a silverfish (Order, Zygentoma). The most common species of household silverfish is Lepisma saccharina. Details can be found here. https://en.wikipedia.org/wiki/Silverfish
They are relatively harmless.


Average molecular weight (MW) of a ribonucleotide = 340g/mol

Size of RNA = x

MW of RNA = 340*x g/mol

moles of RNA needed = y * 10⁻¹² moles (1 picomole = 10⁻¹² mol)

mass of RNA needed = 340*x*y*10⁻¹² g

Conc of RNA = 10*10⁻⁹ g/µl `(1ng =10⁻⁹g)

Volume needed for y picomoles = (340*x*y*10⁻¹²)/10*10⁻⁹ = 0.034*x*y µl

If your RNA is biotinylated then add the MW of biotin to MW of RNA


What are evolutionary implications of contraception and reduced childhood mortality rates worldwide?

Before the introduction of contraception, humans conceived quite a lot of babies (there was little to do to avoid that), but the population was kept in check by very high childhood mortality rates. This mortality rate ensured that only the fittest survived.

Woh! Let me stop you there. No, high rates of childhood mortality do not ensure that whom Natural Selection is acting upon are the "most fit." That title is given to individuals who are able to survive long enough to breed.

Many, many conditions that affect humans do not interfere with a person's growth or ability to perform physical or intellectual feats - but can definitely reduce or completely eradicate a person's ability to reproduce. These individuals are evolutionary dead-ends, and thus - while they survive in the environment - are not "fit" in the context of this topic.

  What are the implications of reducing childhood mortality rates worldwide on human evolution? Maybe evolution is a wrong term to use here. Would it be fitness as species?

What it means is that populations will rise. As populations rise and intermingle, alleles get spread around. Perhaps rarer alleles become more common, or more common alleles become rarer. We're talking about Hardy-Weinberg equilibriums in the allele frequencies. However, with populations large enough true equilibriums are impractical to reach.

The more pragmatic explanation is that more mutations will arise, they'll be passed around, rare mutations will see more exposure, and humanity - in a very general sense - becomes more diverse genetically until a Selective Pressure is applied. Until there's a detriment to having a particular gene, there isn't a need to eliminate it from the population.

Your example is children who are too weak at birth to live outside of an NICU for their first few months - well, because we're capable of providing such care, until that care goes away it's not negatively affecting us. If it comes with an additional cost - say that, for whatever reason, premies can't digest mother's milk until the 8-month mark, then Natural Selection would pressure humans to evolve so that only 8+ month or older babies are born.

There's no evidence of significant pressures in human populations at this time, though. At least not in politically stable and technologically apt countries, although in areas undergoing long-time drought or other dangers it is seen. Sickle-Cell Anemia is though to be an adaptation to rising Malaria rates - which was quite fatal until medication was devised to treat it in the last 50 years or so (not even a blip in evolutionary terms).

  Is there any evidence that people who lived in a world without contraception and with high childhood mortality rate were more physically or mentally fit?

Not that I can think of or find easily. While there are detriments associated with being born prematurely, and some evidence that women waiting until they're late 30's and men until they're 60 or older can negatively affect their gametes and consequently the development of any children born from them - it's been such a short time since the introduction of hormonal contraception and modern medicine that we may not see results tangible results for hundreds of years. Although condoms have been around for several hundred years, and there's been no associations with condom use that I can think of.

In the short term, what it has done is affect the ethnic diversity of countries. For the first time ever, Hispanic births have outnumbered Caucasian births in 2012 in the United States. Other countries, mostly European countries, are seeing declines in birth rates - which means their populations will decline with age or be compensated for by immigration. Higher birth rates, however, are associated with lower income brackets or very religious communities - both of which are associated with ethnic Minorities, at least in the United States. So while minority populations have more kids, they do so on fewer resources which may negatively affect their children in the long-term, whereas higher-earning segments of the population might have fewer children later in their lives, but can provide a much more stable environment and opportunities to continue that success.

One thing that hormone-centered birth control has done, however, is eliminate rape as a viable form of passing on one's genes. As gruesome as it might be to consider, pregnancies as a result of rape can produce "fit" offspring. It is a legitimate reproductive strategy in nature, and is in humans... unless the woman is using contraception. In the long-term this will probably show some interesting results (nominally an enhanced "Female Choice" effect - which is already evident in human evolution), but nothing right now.

It's also worth considering the ability for humans' increasing abilities to manipulate our own genome. At this point, we're nearly able to remove detrimental genes at-will and replace them with more effective versions. Because of this bio-engineering ability, the generations after ours might never be susceptible to inherited diseases - or they might all hop on the trendy "genes" and end up completely identical to each other. That's part of the fun of being human, though; we're very messy when it comes to Evolution. We tend to muck things but up good. :)


What does it mean to have different "metabolism"?

There are differences in metabolism, and the "calories in" part is the one which differs more than the "calories out" part.

People do lose different amount of calories for the same action, but for mostly mechanical reasons. If a 50 kg person walks up a mountain at 3 km/h, and a 100 kg person walks up the same mountain at the same speed, the 100 kg person will expend more energy, because they did more work. And then there are slight differences in how we do our movement - some people's gait is more efficient than others', and uses less energy. But this is not really interesting for the explanation of having it easy/hard to lose weight.

The point is that the amount of food we intake is determined by our hunger, and our hunger is determined by hormones. Then, the amount of fat we store is also determined by hormones. If your body "thinks" you should be putting on weight, and you go on a calorie-reduced diet, it won't just start complementing the missing energy from the fat stored in your adipose tissue. Rather, it will continue diverting some of your food intake to make more fat storage, all the while rationing the energy available for other activities: making you feel tired so you don't move much, shutting down some luxurious, energy-hungry processes in the brain, mostly the ones associated with higher mental functioning, and making you feel hungry and cold so you will be more motivated to seek out food and eat. The hormones which regulate these processes are many, most of them are poorly understood, some are probably not yet discovered (orexin, one of the main hunger regulating compounds, was only discovered sometime in the last 5 years I think), and we really don't have a complete picture of everything that is involved. It is a complex mesh of finely balanced homeostatic systems which interact with each other and the environment.

The people who say that it is as simple as "calories in, calories out" are right. They are right in the sense that, if you just observe a human being and measure their energy household, you will be able to document the amounts of energy consumed, expended and stored, and the energy consumed will equal the energy consumed plus the energy stored.

But to derive from this that we are talking about a passive overflow system and, if we reduce intake, storage is also reduced, is a big leap of faith and has been proven wrong again and again. Living systems are actively reacting to any influences from outside, by mechanisms much more intricate than simple mechanic rules. Mechanics tells us that if I push you, you will fall over; experience tells us that if I push you, you will brace yourself so you don't fall over, and then try to stop me from pushing you by using words, force, or whatever else you have at your disposal. Our physiological systems are the same way. They like the situation they have chosen to be in as much as you like standing upright. If somebody comes from outside and tries to forcibly change their status quo, they do whatever they can to 1) resist and retain the status quo, and 2) stop the outside force if possible.

As for the difference in metabolism: the hormone systems of different people are differently "tuned". For example, eating pure glucose causes insulin production to spike, and excess insulin causes glucose to be removed from the bloodstream, plus a handful of other effects. But the size of the insulin spike is different in different people. Also, the extent to which cells react to elevated insulin is different. When the reaction becomes dangerously weak at even high insulin levels, we say that it's a pathological variation, and call it "metabolic syndrome". If goes really towards zero, it's called diabetes type two. And this is an example about just one of the hormones connected to metabolism and the distribution and use of energy in the body.

On a simpler level, there is no difference in metabolism where physical energy calculation is concerned. Expending one molecule of ATP will let the same number of Na+ ions to move the same distance along a nerve dendrite, across humans. But this level is not really interesting when it comes to gaining or losing weight.


What is the difference between hsa-miR-33a and hsa-miR-33b?

They are paralogs i.e. they have high level of sequence homology. They may have the same seed sequence too (see this). The paralogs can have same targets if they have same seed sequence but it is not essential in all cases. However, the extent of homology required for this kind of classification is poorly defined. miRBase still follows the guidelines mentioned in this (quite old) article:

  When such a candidate is so similar in sequence to the known miRNA
  that the probe designed to detect it would surely cross-hybridize with
  the known miRNA, criterion A need not be satisfied, and the candidate
  can be annotated as a variant form of the known miRNA, provided that
  the candidate itself meets criterion C, and there is also very high
  confidence that one of these paralogs is a confirmed miRNA (i.e., its
  classification is supported by at least three of the listed criteria).
  When there are two or more mismatches between the miRNA paralogs such
  that probes could differentiate between the species on Northern blots,
  criterion A must be satisfied experimentally. Sometimes partially
  overlapping cDNA sequences are identified from the same locus; these
  are assumed to represent differentially processed products from the
  gene.


Yes.  Both fruits and seeds often possess stomata as well as chloroplasts, which have been shown to be quite important in many cases for seed and fruit development.  It makes sense when you think about it.  If these vital components of the plant can make some of their own energy, rather than relying entirely on sugar reserves produced elsewhere (especially given how much sugar your average fruit has to produce), this would be a vastly more efficient system.  If you are interested in a more detailed look at fruit and seed stomata, the following paper should make for a good starting point:

https://www.jstor.org/stable/2442508?seq=1#page_scan_tab_contents

The authors of this paper conducted an in depth investigation of the structure and functions of the fruit and seed stomata present in a number of species within the Eschscholzia genus.  It's an interesting read.


Can anyone identify this insect from India?

This is definitely a bug - as indicated by the characteristic body form and the segmented (it should be five) antenna. My guess here is that this is Nezara viridula, also known as the "southern green stink bug" or the "southern green shield bug".

See this image (from here):

Besides being a pest for agriculture, they are harmless and not toxic, although they can spread a stinking substance when threatened, hence their name. You can find more about them here and here.


Why doesn't muscle strength depend on its length?

It's simply that the fibers are arranged end-to-end. If you simplify this down and imagine a single muscle fiber you have actin and myosin like this:
ligament-|actin-myosin-actin-myosin-actin-myosin

If you think of this as a strand of cotton pulling on a weight (ligament). Each group only pulls along the length, so the strength is not multiplied, but rather related to the strength of the individual fibre.
In reality muscles are stacked into bundles, which are much stronger as all the fibers can contract pulling with the strength of the multiple ends. Like this:
         |actin-myosin
         |actin-myosin
ligament-|actin-myosin
         |actin-myosin
         |actin-myosin

This is like the multiple strands of cotton making up a rope, the strength comes from having lots of them distributing the load.
This is something called physiological cross-sectional area, which describes the strength of a muscle by estimating the cross-section of the muscle across its thickest part.


Do different emotions produce different tears?

Basal tears

  are always in our eyes to serve the purpose of lubricating, nourishing, and protecting the eyes.

Reflex tears

  protect the eyes from irritants, including wind, smoke, or onions.

Tears produced by emotion

  Although these tears contain higher levels of stress, such as ACTH and enkephalin, and endorphin and natural pain killer, they can also work by directly calming the iris down while signaling the emotional state to others.

Secretion of tears

  The lacrimal gland, located in the outer part of the upper eye, is constantly secreting a protein-rich, antibacterial liquid. This fluid goes from the outer edge of the eyeball toward the cornea and lubricates the entire eye surface every time we blink.

Sources:

http://archopht.jamanetwork.com/article.aspx?articleid=625096
http://www.sciencedirect.com/science/article/pii/0002939481906516


You should try another housekeeping gene like GAPDH since the very definition of these genes is that they shouldn't change with your treatment


What's the relation between Kinase, Phosphatase and ATPase, GTPase (GTP/ATP)?

Enzyme names usually refer to the substrate of the enzyme, i.e. the molecule or chemical group that the enzyme targets and then removes or modifies.

Kinases are enzymes that add phosphate groups, usually to other proteins. One of the older enzyme classes that have a more "creative" name. Phosphatases remove phosphate groups.

In signalling pathways, kinases often transduce signals and phosphatases shut them down when their job is finished.

ATPases and GTPases target ATP and GTP respectively and catalyse the removal of one phosphate group by hydrolysis, the product being ADP or GDP. This makes them a type of phosphatase.

Many proteins are ATP/GTPases but have different names because there's a more significant function to name them after. Usually the ATP/GTPase function serves to deliver energy for the main function. Your impression might be caused by an enzyme which is both a kinase and an ATPase because it transfers phosphate groups from ATP to a target protein.

Enzymes that target ADP/GDP and add another phosphate group are called ATP/GTP synthases (rather than kinases).


Terminology for quantitative response of T cells to antigen complexes

It means that a dendritic cell only needs between 1 and 100 antigen–MHC complexes on its surface in order to activate a T cell.


How to interpret this PubChem record of L-Alanine

The PubChem format description is not that easy to find:
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/pcsubstance.asn.html

And the ASN file linked here:
https://pubchemdocs.ncbi.nlm.nih.gov/data-specification

  I am correct in saying that the numbers in the 'element' array are corresponding to Atomic Numbers?

Yes, 1 is hydrogen, 6 is carbon, 8 is oxygen, etc.

  And these atomic numbers are assigned to ids from the corresponding indexes in the 'id' array?

in your example, "atoms": {"aid": [1, 2, 3,  ...,  13], "element": [8, 8, 7, ..., 1]},, the the ID of the first atom would be 1 and element 8 (oxygen), the third atom: ID 3 and element 7 (nitrogen).

  Am I correct in saying that these represent the x, y, and z coordinates of atoms in the corresponding index of the above elements array?

Yes

  What are aid1, aid2, and order?

aid1 and aid2 are the atom identifiers. order is the bond type.

  These arrays are 12 entries each so each must represent 1 bond between two atoms. But what do the number values correspond to? How should they be interpretted?

For example aid1 = [1, 2], aid2 = [3, 4], order = [1, 2] would mean a single bond between atom 1 and atom 3 and a double bond between atom 2 and atom 4.

Good examples of implementations:

PubChemPy
pubchem_2d_structure_json_to_svg.py


How much heme is in cooked pork and beef; why is cooked pork ("the other white meat") not red?

Yes.
Pork has substantially less heme than beef (Cross et al. 2013).

As to why the red colour is lost, it is due to the Maillard reaction, by which the iron in the myglobin is oxidized from Fe(II) to Fe(III).  This results in a colour change in the meat (Tamanna & Mahmood 2015).

Sources:

Cross AJ, Harnly JM, Ferrucci LM, Risch A, Mayne ST, Sinha R. 2013. Developing a heme iron database for meats according to meat type, cooking method and doneness level. Food Nutr Sci 3(7): 905–913.

Tamanna N, Mahmood N. 2015. Food Processing and Maillard Reaction Products: Effect on Human Health and Nutrition. International journal of food science 2015: 526762. doi:10.1155/2015/526762


Do individual mammal hairs absorb water?

Researching this answer took me to some strange literature, but it appears to suggest a little bit of both (at least for human hair, which is porous, implying that some water can suffuse through the cuticle into the cortex). For example this paper looks at the impact of this effect on drug testing.

There's also a few papers in cosmetics science journals describing various elements and effects of increased hair porosity, but I was unable to find one primary citation which characterised the trait.


What kind of changes "stays" in the neuron after the nervous impulse happened?

TL;DR: There are many ways a neuron can change after a neural impulse happens including calcium influx, long term potentiation and depression, and G-protein coupled receptors. While not an exhaustive list by any means I'll give a brief summary of some mechanisms I know best.
Calcium Entry
There exist calcium channels that open in response to a variety of signals be it voltage depolarization (voltage gated calcium channels), neurotransmitter acetylcholine (Nicotinic-Receptor) or Both depolarization and Neurotransmitter binding (NMDA receptor). There is much more calcium outside the cell than inside the cell. Once inside the cell calcium binds to EF-hands in various calcium-binding enzymes like calmodulin. When calcium binds to the EF-hands of the calmolulin protein it activates and from there can interact with the other enzymes responsible for cell signaling and the effects can be quite diverse depending on what the neuron is responsible for doing and the specific signaling cascade it sets off.
LTP/LTD
I'll focus on the NMDA receptor(excitatory Glutamate/Glycine receptor) in the CA1 region in hippocampus. LTP (or Long Term potentiation) occurs when a synapse (connection between neurons) becomes stronger, meaning the post-synaptic neurons response to the same stimulus from the pre-synaptic neuron is stronger after LTP has occurred. LTD (or long term depression) is the opposite effect where a neuron's response to the same stimulus is weaker after LTD.
The LTP whole process is dependent on calcium entering through the NMDA receptor channel. When both glutamate and glycine are released pre-synaptically they open the channel,  allowing calcium ions to flow into the cell. However, If the voltage in the post-synaptic membrane is too low, Magnesium will get stuck in the channel blocking calcium (and the other ions too!). If the neuron has previously been stimulated and depolarized, by another neurotransmitter/receptor system like AMPA the voltage will be positive enough to pop the magnesium out of place and allow calcium into the cell.
Once calcium is in the cell it is bound to calmodulin which then binds to CaMKII (an enzyme activated by the calcium/calmodulin complex). This will cause a long and complicated signaling cascade which results in AMPA (the other excitatory glutamate receptor in the post-synaptic region) to be phosphorylated causing it to be more active. Furthermore the signaling cascade can cause an increase in AMPA receptor creation and subsequent insertion into the post-synaptic membrane. This of course results in LTP.
Many rules in biology one quickly finds exceptions and caveats to nice rules of thumb (In fact I learned of a few just by preparing this answer!) LTD (long term depression) can occur in the hippocampus as well, and is dependent on the influx of calcium! As paradoxical as that seems, there is a negative feed back loop dependent on the levels of calcium ions inside the neuron, such that strong pre-synaptic stimuli create LTP (potentiation) and weaker (lower frequency) stimuli cause LTD (depression) and rare or intermittent stimuli cause no response. (see this and this for reference).
G-Protein coupled Receptors
G-Protein coupled Receptors are more of a general family of proteins than a specific example. They are metabotropic receptors (meaning they do not allow Ion's to flow through them). Rather when bound they release an G-Protein, which like calmodulin binds to other enzymes and activates them allowing them to do their job. They  can respond to many different neurotransmitters (or more generally ligands) and can do lots of different tasks depending on the  on what type of G-Protein it releases.
I'll give the muscarinic(M2) receptor for acetylcholine as an example. This receptor is found in the heart and responds to acetylcholine release from the Vagus nerve. When the GCPR binds to the acetylcholine it releases its G$\beta$ unit and it binds to potassium ion channels in the heart. This causes the outward flow of potassium ions thus lowering the voltage( hyper-polarizing the heart cell).
Furthermore G-coupled proteins can even induce changes in how many are present in the membrane (i.e. they are self regulating). These are produced by internal signaling cascades and are thought to be the reason for tolerance of drugs. Take for example the $\mu$-opioid receptor (activated by morphine, heroine and other similar compounds). These drugs will induce changes in how well the protein response to the morphine and if enough exposure then the cell will actually take the receptor back into the cell body and thus off the membrane in a process called endocytosis. (source here)
Literature reviews worth reading include (all open access):

Calcium signaling
NMDAR meditated LTP/LTD
GPCR's


Why do grapes not pea shrink when placed in strong sugar solution?

Well, without the details of your experiment to cross-check with the sugar and H2O content of your average grape, I'd say the saturated solution probably approximated the natural molarity of sugar in the grape. At least to the point it didn't make any advese effects noticeably on your time scale.

That seems the most apparent solution to me. I suppose it's also possible (though I don't know the mechanics behind it) that hypertonic solution might have acted as a preservative - similar to jam. It's not just water which will attempt to reach an equilibrium, but all compounds that can pass through the membrane - perhaps sucrose/fructose/glucose can do so, maintaining the structural integrity of the grape.

Both are guesses until you reveal more information, though.


What are all possible vectors for unicellular human parasites?

Based on my course material, I managed to get the following list:

Malaria - Plasmodium falciparum, p. malariae, p. vivax, p. ovale - female anopheline mosquito
Babesiosis - Babesia devergens, babesia microti - tick ixodes ricinus
Balantidiasis - Balantidium coli - waterborne
Coccidiosis & toxoplasmosis - Eimeria species - waterborne
Toxoplasmosis - Toxoplasma gondii - waterborne
Amoebic dysentery - Entamoeba histolytica - waterborne
Periodentitis - Entamoeba gingivalis - oral-oral contact
PAM - Naegleria fowleri - waterborne
GAM - Acanthamoeba species - waterborne
BAE - Balamuthia mandrillaris - waterborne
Trichomoniasis - Trichomonas vaginalis - sexual contact
Trypanosomiasis - Trypanosoma brucei gambiense, trypanosoma brucei rhodesiense - bite of a tsetse fly
Leukopenia - Leishmaniasis specieses - different genera of sandflies: Plebotonus & Lutzomyia

Waterborne means that the parasite is transmitted to the host through contaminated food, water or hands, or by swimming in warm pools or mud pools, for instance.


Where do the antibodies that trigger the specific immune response come from?

First: What your teacher says about the free floating antibodies is not correct. The first contact with a new antigen to generate specific immunity is done by naive B cells which have a membrane bound B cell receptor and their effector T cells. This contact can either happen directly or by the presentation of the antigen to the cell by antigen presenting cells (APC).

Short answer:
These naive B cells are present in our body without antigen contact, but are not highly specific.

Long answer:
Our body has the possibility to express a vast variety of different antibodies - estimations go up to 10 billion different antibodies which the human body can produce, each of them capable of binding a different antigen (see reference 1).

To begin with, naive B cells express antibodies as a membrane-bound version, the so called B cell receptor. The antigen specificity of these receptors is random and occurs before the individual had contact with the antigen. These receptors bind a wide variety of different antigens, more or less good. This is the so-called affinity of the receptor (or the antibody) against an antigen.

Upon binding of an antigen, the B cells get activated (if the receive a co-stimulatory signal from a T cell). When activated, the cells starts to proliferate and to differentiate, as shown in the figure below (from here).

Basically, the cells start to re-arrange the genes which are responsible for generation of the variable region of the antibody (the part which does the actual binding of the antigen) to generate highly specific high affinity antibodies to the antigen and then mature into relatively short lived plasma cells, which produce big amounts of antibodies and long lived memory cells. The later are dormant in the body and get reactivated, when the body is challenged by the same antigen, against which it already produced highly specific antibodies.

When re-exposed to an antigen, the antibodies in the blood stream bind to the antigen and mark it for phagocytosis. The phagocytes will then take up the antibody bound antigen, process it and present parts of it on their surface to B/T cells. This either starts the process of selection and clonal expansion as described above or if there are specific memory cells, these cells will proliferate and differentiate into antibody producing plasma cells.

The initial process of adaptive immunity takes about two weeks until highly specific antibodies are available, if you only have to "wake up" the cells from the memory pool, this will take a few days. This is also how vaccinations work.
See also the Wikipedia page on Antibodies for much more details.

References:

Development of the immunoglobulin repertoire.


Are antihistamines considered to be psychoactive substances?

Short answer
First-generation anti-histamines are psychoactive, second-generation equivalents may not be*.

Background
According to WHO, psychoactive substances are:

  [...] substances that, when taken in or administered into one's system, affect mental processes, e.g. cognition or affect. This term and its equivalent, psychotropic drug, are the most neutral and descriptive term for the whole class of substances, licit and illicit, of interest to drug policy. ‘Psychoactive’ does not necessarily imply dependence-producing, and in common parlance, the term is often left unstated, as in ‘drug use’ or ‘substance abuse’.

Antihistamines are used to treat allergies. First-generation antihistamines readily cross the blood-brain-barrier and have been associated with performance deficits on tests of attention, working memory, vigilance, and speed. By contrast, second-generation antihistamines that do not readily reach the brain do not have these side-effects (Kay, 2000).

Since attention, working memory and vigilance are mental cognitive processes, first-generation antihistamines fall into the classification of WHO as being psychoactive.

Reference
- Kay, J Allergy Clin Immunol (2000); 105(6-2): S622–7

Note
*I am not an MD and data on 2nd generation drugs are based on a single study with a limited number of tests. Consult a medical professional for prescription of the appropriate treatment.