What produces the strong odor of decaying dead animals?

Two compounds are specifically associated with the smell of decaying cadavers (Hoffman et al., 2009), namely:

1,5-pentanediamine (cadaverine), and
1,4-butanediamine (putrescine)

Cadaverine is produced by breakdown of lysin and putrescine by the breakdown of ornithine (Science ME). Both are nitrogen-rich compounds and particularly pungent-smelling.

Source: Science ME

Both compounds are also responsible, in part, for the smell of bodily fluids such as urine and semen, smell of rancid butter, bad breath and stinky cheeses (Science ME).

Forensic Science Central UK mentions that after death, the body begins to decay after about 5-11 days (after an initial phase of bloating). The putrid smells subside mostly after 10-24 days, although a rancid cheesy smell might persist due to butyric acid. Note that many factors will affect decomposition rates and will affect this time course. Moreover, trained police dogs may be able to sniff out minute amounts of putrescine and cadaverine long after humans cannot detect it anymore.

Note that, given the complex composition of animals and the complexity of the decomposition process, a host of volatile organic components are released during decomposition besides putrescine and cadaverine.

Reference
- Hoffman et al. Forensic Science International 2009; 186: 6-13


Why is the outer circle of human mitochondrial DNA ‘heavy’, whereas the inner circle is ‘light’?

The heavy strand is literally heavier than the light strand. The first, or at least one of the first, observations of this phenomenon was in this paper:

Corneo G, Zardi L, Polli E. 1968. Human Mitochondrial DNA. J Mol Biol 36(3):419-423.

They showed that alkaline denatured mitochondrial DNA separates into two bands upon ultracentrifugation in a cesium chloride gradient:

  Human mitochondrial DNA when centrifuged in alkaline CsCl in the analytical ultracentrifuge splits into two bands displaying densities of 1.727 g/cm3 and 1.766 g/cm3, respectively. The two bands appearing in the alkaline gradient correspond to the complementary strands of human mitochondrial DNA with a different GT/CA ratio... However, when an equimolar mixture of them is renatured by heating at 65°C for five hours in 2X SSC, a single band with a density very close to that of the native DNA is obtained. The latter experiment clearly indicates that the two bands correspond to the complementary strands displaying a bias in base composition.

The difference in molar mass (M) is due to a higher purine content (Pu) in the heavy strand (which are heavier than pyrimidines). This can be seen by tabulating the base composition of the RefSeq sequence of human mitochondrial DNA:

               A      T      G      C      Pu(%)   M(kDa)
Light Strand   5124   4094   2169   5181   44      5063
Heavy Strand   4094   5124   5181   2169   56      5174

R script if anyone is interested:

#uses Biostrings
light = readDNAStringSet("mtDNA.fasta")
heavy = complement(light)

comp = function(seq) {
  ll = as.list(alphabetFrequency(seq)[1, c("A", "T", "G", "C")])
  ll["%Pu"] = with(ll, (A + G) / (A + T + G + C)) * 100
  ll["M(kDa)"] = with(ll, (A * 313.2) + (T * 304.2) + (G * 329.2) + (C * 289.2) + 79.0) / 1000
  return(ll)
}

comp(light)
comp(heavy)


Why are hydathodes called hydathodes and not hydrothodes?

Dictionaries are your friend.  American heritage says "Greek hudōr, hudat-, water; see wed-1 in the Appendix of Indo-European roots + hodos, way, road."  Merriam-Webster says "International Scientific Vocabulary, from Greek hydat-, hydōr water + hodos road"


Why is a slow worm not considered a snake?

You are correct that the reason is similar to that of convergent evolution of the eye.

Both snakes and legless lizards are lizards (Squamata) that have lost their legs. However they have done so entirely separately much as octopus and human eyes have evolved entirely separately. An easier analogy is between whales and sea cows. Both are legless mammals but as they have evolved separately the must be given separate names.

Unfortunately it seems that the exact position of the snakes in the tree is unknown which makes this explanation less clear.

http://tolweb.org/Squamata/14933

However, the legless lizards (subfamily Anguinae) are within the family Anguidae, most of which have legs. This family is within the Anguimorpha, which includes even more species with legs. Just one small tip of the tree, with around 20 species is legless. On the other side of the tree, separated by many millions of years is the snakes (Serpentes).

A related question is why are snakes given their own name while legless lizards are just considered lizards without legs. This is partially due to the fact that there are so few species of legless lizard while there are thousands of species of snake. It is also probably due to cultural history. As snakes are dangerous to humans and prevalent in most inhabited areas of the world words for snakes are much older than the study of taxonomy. A western example is the snake in the garden of Eden. It is also important in Hinduism
and many other cultures/religions.


Found it. It's a case-bearing moth larva.


Are (baseline) high blood levels of melatonin associated with either circadian rhythm or mood disorders?

I found a recent PLoS article that said that none of hypochondriasis, depression, hysteria, psychopathic deviate, masculinity-femininity, psychasthenia, schizophrenia, or social intraversion (on the MMPI-2) "were associated with any melatonin parameter."

However, it does appear that "increases scores of Hypomania and Paranoia were associated with a shorter DLMO-DLMOff interval" (duration of melatonin production).

The only thing that concerns me are the significance and the effect size of the latter two results.  I can't tell whether they corrected for multiple comparisons or not.

Reference:  Burgess HJ, Fogg LF (2008) Individual Differences in the Amount and Timing of Salivary Melatonin Secretion. PLoS ONE 3(8): e3055. doi:10.1371/journal.pone.0003055


Why are prions in animal diets not destroyed by the digestive system?

Proteases are enzymes in your digestive system that help break down food, acting like molecular-sized scissors that cut up proteins.
Proteases have clefts, or subpockets, into which proteins fit, where the substrate (protein) gets cut.
Infectious or pathogenic prions are resistant to proteases, because of their three-dimensional shape, which hides away parts of the prion that would normally fit in proteases and which would cause the prion to be digested.
Prions that do not cause disease — normal prions — have a different three-dimensional shape that allow them to fit into proteases, and so they are not resistant to digestion:

A wealth of evidence contends that the infectious pathogen causing the prion diseases, also referred to as spongiform encephalopathies, is solely comprised of PrPSc, the pathogenic isoform of the prion protein (21-23). Both PrPSc and its normal cellular counterpart, PrPC, are encoded by a cellular gene (2, 19). Physical and molecular characterization of PrPSc and PrPC has failed to reveal any chemical differences between the two isoforms (32). However, PrPSc acquires distinctive conformational characteristics upon its conversion from PrPC. Whereas PrPC is soluble in most detergents and can be easily digested by proteases, PrPScis insoluble in detergents and maintains a protease-resistant core, designated PrP27-30, which polymerizes into amyloid (25).

Dr. Neena Singh also discovered that prions "piggyback" or attach to another protein called ferritin, as they make their way through the digestive system:

Disease-causing prions are thought to have passed into people when they ate beef from infected cattle, triggering the brain wasting condition called new-variant Creutzfeldt-Jakob disease, or vCJD. But researchers have not been sure exactly how prions enter the body.
To find out, Neena Singh and her team at Case Western Reserve University in Cleveland, Ohio, mimicked the process of eating and digesting infected meat.
They mashed up brain tissue that contained prions from patients who had a form of Creutzfeldt-Jakob disease. They then exposed it to a range of harsh digestive enzymes from the mouth, stomach and intestine, which normally break proteins into pieces.
Prions, which are known to be enormously tough, escape this attack almost unscathed, they showed, as does a second type of protein called ferritin, which stores iron and is abundant in meat. The two proteins seem to stick together, they report in the Journal of Neuroscience.
The researchers next added the digested slurry to a lab model of the human gut: a growing sheet of cells from the intestinal lining. By attaching fluorescent tags to the two proteins, they showed that they are transported through the cells hand-in-hand. "Prions probably ride piggyback" through the gut wall into the body, Singh says.

Attaching to ferritin may provide additional protection from digestion, insofar as this removes prions from the digestive system, where proteases are concentrated.


Visual phototransduction, neurons depolarization when no light: why?

Short answer
The reason for the depolarized state of photoreceptors in the dark is unknown as far as I know. It probably has its roots deep in the evolution of the eye.

Background
Indeed, photoreceptors are continuously active in the dark. A steady current flows through open channels (mainly Na+ ions). This current is called the dark current and it partially depolarizes the photoreceptor cell. The depolarized photoreceptor releases neurotransmitter (glutamate) to secondary neurons. Upon illumination of the photoreceptors rhodopsin molecules are isomerized to the active form and the photoreceptor cascade (Fig. 1) is initiated. This ultimately closes the cation channels in the photoreceptor's membrane, stopping the dark current.  This leads to cell membrane hyperpolarization and inhibition of glutamate release to the second-order neuron (Fig. 1).

Admittedly, I do not know why phototransduction exactly is organized this way. There is a lot known about the evolutin of phototransduction (e.g., Lamb et al., 2016), but why the dark current exists is unknown as far as I know. I surmise it is probably an evolutionary relic. Evolution eventually has to work with pre-exisiting features to generate new structures, or alter them. Simple photosensitive spots evolved into the complex eyes observed in today's vertebrates. Evolution thereby used what was there and that happened to be an energetically unfavorable 'NOT' gate.

Fig. 1. Phototransduction in photoreceptors. source: Kolb, (2012)

Reference
- Kolb, Webvision. The Organization of the Retina and Visual System (2012)
- Lamb et al., Molec Biol Evol (2016); 33(8): 2064–87


Why would deer continue to cross a river full of crocodiles even though some of them have been killed?

The reason for their behavior is that exactly the fact that even though some of them do indeed get killed, most of them survive -- what you have said.  The deer cross the river because that allows for the better continuation of the species rather than if they had stayed on the original side of the river. You could think of it this way: If there was a crowd of 5000 people crossing a field of grass and aliens were abducting them one by one, the actual chances of them abducting you are rather little.


How to remove bad lanes in ImageJ Westernblot analysis

ImageJ doesn't have a feature to remove individual lanes. But that shouldn't be a problem. All you have to do is draw the first lane correctly (I'm referring to size). Then press 1. Now, while the selection is still... selected, click inside it, but not on the number (where the cursor becomes hand), and drag it where you want the next lane. And press 2. And so on. Draw all your lanes.

Now, if you misplaced a lane, click the rectangle selection tool, then click on the lane number while the cursor is a hand. It will be selected. If you're having troubles with this, use the shortcuts Ctrl+1 and Ctrl+2 or the menu Analyze - Gels - Select Previous/Next Lane to select between lanes. The cursor turns to normal. Click anywhere inside the lane and drag it on the right place.

If the first lane was bad and you want to remove all lanes, just go to Analyze, Gels and click on Reset.


Ok, this is more complicated than I first thought. I am pretty sure that we have an eukalyptus tree here. The species is more complicated, but I think it is likely Eucalyptus baueriana or one of its subspecies. To check this further, more detailed images of leaves, blossoms are needed. Check this image (from here):


Does cheese contain cells of animal stomachs?

Yes it is possible, filtering is unlikely to be fine enough to remove all cells (though the presence of intact cells based off of the culturing methods is unlikely), note though that modern methods of rennet extraction from stomachs are different than what you described. There are also non-calf rennet made with everything from fungi and bacteria to vegetables. Source


brain activity responsible for imagination

Edit: Added two studies to better show how different types of imagination tasks use different parts of the brain.

Imagination is a complex process that can use many regions of the brain. Insights into how our brain imagines have been gained through a number of studies. There is not an "imagination" area of the brain. Instead, different areas, and often several at a time, may be used depending on the type of imagination. I'll highlight a few examples here.

Ogino et al. (2007) asked 10 male participants to imagine feeling pain while watching pictures suggesting either pain or fear. Both pain and fear tended to activate an area of the brain called the anterior cingulate cortex (ACC), which helps to regulate blood pressure and heart rate among other basic nervous functions. Imagining pain activated not only the ACC but also another four areas of the brain were especially active. In comparison, fear tended to activate the ACC and the hypothalamus, which regulates the "flight or fight" response. Both sides of the brain were activated at the same time.

Boly et al. (2007) studied 12 brain-injured patients who where not capable of communicating. They were not in a coma. They were asked to imaging tasks involving spatial skills or motor skills. The two most common areas of the brain that were activated were the supplementary motor area, which helps to control movement, and the dorsal premotor cortex, which may contribute to movement and spatial coordination. (Wikipedia information so interpret cautiously.)

A detailed study was recently provided in a study by Schlegel et al. 2013. (An alternate version is here; both versions are open access.) Summaries of their work written for the general public can be found in Popular Science and Science Daily.

The scientists identified what they called the "mental workspace" which is not a particular region of the brain but instead is several different regions of the brain (from both sides of the brain) interacting together.

The researchers asked the study participants (9 males and 6 females) to select from a set of abstract shapes to assemble a particular target shape.  The target shape (the one the participants had to create) was a 2x2 grid. Each abstract shape that to be selected would fit one of the grids. So, four abstract shapes had to be selected to assemble the target shape. They also tested the reverse: Given a target shape, could the participants identify the four abstract shapes needed to make the target shape.

During the task, the researchers used functional magnetic resonance imaging (fMRI) to monitor brain activity. After the analysis of the fMRI results, they identified 11 distinct regions of the brain were active during the task.  In nearly all cases, the regions were active in both sides of the brain. However, I noticed that one region, the medial frontal cortex, only appeared to be active in the left side of the brain. This region was identified as one important component of the mental workspace for certain tasks.

The researchers concluded that four of the 11 regions were most important. You can see the regions of the brain in any four of the links above (and the abstract shapes in all but the Science Daily article). They argue that the interaction among the four major and seven minor regions contribute to our process of imagination.

Each of the three studies I highlighted requires the participants to perform different types of imgination tasks. Each type of task showed that different regions of the brain were used. Each type of task also required that several areas of the brain were used simultaneously during the imagination process. Together, these results show that no single part of the brain is used for imagination. Instead, many different areas are used, depending on what the person is imagining.

Citations

Boly, M. et al. 2007. When thoughts become action: An fMRI paradigm to study volitional brain activity in non-communicative brain injured patients. NeuroImage 36: 979-992.

Ogino, Y. et al. 207. Inner experience of pain: Imagination of pain while viewing images showing painful events forms subjective pain representation in human brain. Cerebral Cortex 17: 1139-1146.

Schlegel et al. 2013.  Network structure and dynamics of the mental workspace.  Proceedings of the National Academy of Sciences USA 110: 16277-16282.


Besides duplication as verification there are numerous other computational methods to ensure that the result is valid. Proprietary software is used for folding at home so one can safely assume that they check hashes on processors and files regularly. If integrity is broken (by a crash, memory corruption or God forbid injection) the software client side and server side trashes the result. One can imagine that faulty hardware or other problems can result in a ban from the servers.


Interestingly, treatment of mild pharyngitis before the advent of antibiotics wasn't too different from what it is today - it was (and still is) mostly symptomatic. First of all, viral pharyngitis, which is quite common (Hidreth et al., 2015), is not affected by antibiotics (no viral infection is), and they are not indicated in such situations. Second, mild and self-limiting bacterial infections, including pharyngitis, most often do not warrant prescription of antibiotics, as this leads to the growing problem of antibiotic resistance, which, according to the World Health Organization is "one of the biggest threats to global health." Many guidelines can be quoted, urging clinicians to prescribe antibiotics sparingly, but pharyngitis is so common (literally everyone has had it, multiple times) that one can simply turn to one's own experience - simply put, when you have a mild case of soar throat, your doctor doesn't give you antibiotics (if you even bother going to the doctor about it), most often you are advised to take only symptomatic medications (many of which are OTC). These most often include compounds with analgesic, antiseptic, and/or anti-inflammatory properties. Interestingly, such compounds were widely available long before the advent of antibiotics and even the pharmaceutical industry itself.

Menthol, for example, is a selective agonist of κ-opioid (Galeotti et al., 2002) and a modulator of GABBAa receptors (Watt et al., 2008), thereby eliciting analgesic and anaesthetic effects, respectively. Moreover, by disrupting bacterial cell membranes, menthol (and similar compounds, such as thymol, for example), elicit antibacterial activity, as well (Trombetta et al., 2005). Thus, wild mint, peppermint, and thyme are much more often indicated in cases of soar throat than antibiotics! Their use in the form of infusions and decoctions likely predates most, if not all, modern countries. Moreover, the analgesic and anti-inflammatory properties of willow bark, which are due to the salicylic acid contained therein, were known to Hippocrates (Norn et al., 2009), quite possibly dating back much earlier. Furthermore, it is known that caffeine potentiates the analgesic effects of many nonsteroidal anti-inflammatory drugs, including salicilic acid (Granados-Soto and Castañeda-Hernández, 1999). Unsurprisingly, this combination is often found in many modern drugs (many OTC), being marketed all over the world. Whether this effect was known before the advent of the pharma industry, however, is hard to say. Willow bark has been used as an analgesic and anti-inflammatory medication since ancient times, but coffee was brought to the West in the XVI century.

This is only a handful of traditional medications for pharyngitis, and I'm sure many more can be found, as well as many other treatments for many other conditions. The point is that treatments of mild pharyngitis were available before the advent of antibiotics, as a matter of fact, many of those treatments are still first-line therapy in most cases, even to this day.


Can GFP reporting be used to track localization of peptides in the ER, Golgi, and plasma membrane?

Historically speaking, the use of VSVG (Vesicular Stomatitis Virus G protein) labeled with GFP was indeed a practical method to define the secretory pathway. (@tyersome comment)

However, I am concerned that by the time everything is set up, the cell will be at steady state, which means GFP signal would be present throughout the secretory pathway, preventing me from doing this tracking.

Sec mutations in S.cerevisiae: Many biochemical pathways are initially identified owing to a particular mutation in the synthesis process. Recall Beadle and Tatum experiment and the logic they used to clarify the existence of 3 enzymes used in arginine metabolism.

(Image taken From https://www.chegg.com/homework-help/questions-and-answers/following-experiments-beadle-tatum-searching-mutations-disrupt-arginine-biosynthesis-pathw-q41797559)
A similar approach was taken back then to identify the distinct parts of the secretory pathway. Five different mutations in S.cerevisiae were identified named from A to E. Culturing all A to E mutated strains plus VSVG-GFP assay would clearly demonstrate the entire route.

(Image taken from https://slideplayer.com/slide/4382105/)
For example, even if the mutated class B, reaches the steady/equilibrated state, transport vesicles, Golgi, and the rest will not show the fluorescence activity (characteristic of VSVG-GFP) because all of the proteins have accumulated in the previous step(i.e budding from Rough ER)
Further Readings :
https://pubmed.ncbi.nlm.nih.gov/2188733/
https://www.sciencedirect.com/science/article/abs/pii/0092867481900647
MCB Lodish et al 8th edition chapter 14 section 14.1
https://www.nature.com/articles/35073068


Is all of the DNA used by genes (encoding DNA)?

The ENCODE consortium classifies human and mouse genome elements to try to answer this very question.
Work by ENCODE suggested up to 80% of the genome is functional in some way. In other words, by that upper-bound measurement, there is apparently more to DNA's role in biology than just encoding genes — there's a lot going on under the hood.

Case for Abundant Functional Genomic Elements.
Genome-wide biochemical studies, including recent reports from ENCODE, have revealed pervasive activity over an unexpectedly large fraction of the genome, including noncoding and nonconserved regions and repeat elements (58⇓–60). Such results greatly increase upper bound estimates of candidate functional sequences (Fig. 2 and Fig. S2). Many human genomic regions previously assumed to be nonfunctional have recently been found to be teeming with biochemical activity, including portions of repeat elements, which can be bound by transcription factors and transcribed (79, 80), and are thought to sometimes be exapted into novel regulatory regions (81⇓⇓–84). Outside the 1.5% of the genome covered by protein-coding sequence, 11% of the genome is associated with motifs in transcription factor-bound regions or high-resolution DNase footprints in one or more cell types (Fig. 2), indicative of direct contact by regulatory proteins. Transcription factor occupancy and nucleosome-resolution DNase hypersensitivity maps overlap greatly and each cover approximately 15% of the genome. In aggregate, histone modifications associated with promoters or enhancers mark ∼20% of the genome, whereas a third of the genome is marked by modifications associated with transcriptional elongation. Over half of the genome has at least one repressive histone mark. In agreement with prior findings of pervasive transcription (85, 86), ENCODE maps of polyadenylated and total RNA cover in total more than 75% of the genome. [emph. added]

However, people outside the ENCODE consortium have criticised this research with very strong language, such as in this article by noted critic Dan Graur:

Actually, the ENCODE authors could have chosen any of a number of arbitrary percentages as “functional,” and … they did! In their scientific publications, ENCODE promoted the idea that 80% of the human genome was functional. The scientific commentators followed, and proclaimed that at least 80% of the genome is “active and needed” (Kolata 2012). Subsequently, one of the lead authors of ENCODE admitted that the press conference mislead people by claiming that 80% of our genome was “essential and useful.” He put that number at 40% (Gregory 2012), although another lead author reduced the fraction of the genome that is devoted to function to merely 20% (Hall 2012). Interestingly, even when a lead author of ENCODE reduced the functional genomic fraction to 20%, he continued to insist that the term “junk DNA” needs “to be totally expunged from the lexicon,” inventing a new arithmetic according to which 20% > 80%. In its synopsis of the year 2012, the journal Nature adopted the more modest estimate, and summarized the findings of ENCODE by stating that “at least 20% of the genome can influence gene expression” (Van Noorden 2012). Science stuck to its maximalist guns, and its summary of 2012 repeated the claim that the “functional portion” of the human genome equals 80% (Anonymous 2012). Unfortunately, neither 80% nor 20% are based on actual evidence.

Other critics, including Sean Eddy, focus a great deal on what is called the C-value paradox: Given a genome of a certain size, if it was all functional — or a lot of it functional, as the ENCODE consortium has claimed — then it would all be under evolutionary pressure, i.e., you'd expect certain mutation rates to occur, but they don't. Evolutionary biology would say about 5-10% is functional, I believe, based on how much selection takes place and where. So those critics would say (and have had indeed said) a lot of negative things about results reported by ENCODE.
I suspect that the true answer, if there is one, depends on what one defines as functional and as evolutionarily conserved, by what means you measure it, and what the balance is between functionality and conservation. You pick your definitions and processes, and you accept the compromises and limitations that go along with those choices.
Caveat: I am a contributing author to ENCODE papers released in Nature in 2012.


The below structure circled in green clearly is part of the stomach antrum. The location is correct, and the mucosal folds are characteristic. Kerckring valves of the small intestine and semilunar folds of the colon both look different.


That's the gladius (also known as pen) of a cephalopod, probably a squid. The gladius is an internal remnant of the originally external shell of cephalopods.

According to University of California Museum of Paleontology:

  Members of the Coleoidea are probably the best known of the Cephalopoda, as this group contains the squids (Teuthoidea) and octopuses (Octopoda) [...] The majority of coleoids are squid species, and most of these animals are torpedo-shaped, fast moving, and have a thin, flexible internal shell called a pen.

And according to the Tree of Life project:

  Other cephalopods have other types of shell remnants. The gladius lies within a sac, the shell sac, which secretes it and to which various muscles attach. The gladius has a variety of shapes and thicknesses, is composed mostly of chitin and is located in the dorsal midline and generally extends the full length of the mantle.

Here is one similar to yours:

Sources:

http://www.ucmp.berkeley.edu/taxa/inverts/mollusca/cephalopoda.php
http://tolweb.org/accessory/Cephalopod_Gladius_Terminology?acc_id=1955


Help identify this red/black Vietnamese insect

Dasypogon is a genus of robber flies in the family Asilidae.

Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Diptera ,
Family: Asilidae
Tribe:Dasypogonini
Genus:Dasypogon.

84 species belong to the genus Dasypogon. Among these, this one is Asilidae Dasypogon diadema.


Why don't weak detergents lyse the nuclear membrane?

First, an important fact   about non ionic detergents- {1}They have a hydrophilic head group that is uncharged and are preferred for their ability to break lipid-lipid and lipid-protein interactions. They have limited ability to break protein-protein interactions and are often referred to as non-denaturing detergents and are used to isolate biologically active membrane proteins.
Generally, moderate concentrations of mild (i.e., nonionic) detergents compromise the integrity of cell membranes, thereby facilitating lysis of cells and extraction of soluble protein, often in native form.
An example would be Triton X-100. {2} Non-denaturing detergents such as Triton X-100 have rigid and bulky nonpolar heads that do not penetrate into water-soluble proteins; consequently, they generally do not disrupt native interactions and structures of water-soluble proteins and do not have cooperative binding properties. The main effect of non-denaturing detergents is to associate with hydrophobic parts of membrane proteins, thereby conferring miscibility to them.
The following article is about the same protein insolubility that I have written above, but in the nuclear membrane of chicken RBC’s. {3}

Protein has been selectively extracted from isolated chicken erythrocyte nuclear envelope by (1) dilute MgCl2/Triton X-100 followed by (2) concentrated MgCl2/Triton X-100 solutions. Certain proteins appear to be selectively dissolved in the first solvent and may occur in the nuclear envelope primarily as lipoproteins. Among the proteins insoluble in the low MgCl2/Triton X-100 wash, as well as in 500 mM MgCl2 without Triton previously used in the preparation of the envelope fraction, the quantitatively major polypeptides dissolve in a combination of high MgCl2 and Triton X-100. Further, much of this dissolved protein precipitates when the MgCl2 concentration is lowered by dialysis. The insolubility of these proteins appears to result from a combination of ionic and hydrophobic interactions and may explain the resistance of nuclei to various manipulative procedures including nonionic detergent washes.

The conclusion is that the protein insolubility of these detergents is what makes the nucleus resistant. You know that the phospholipid bi-layer is common for both- the cell membrane and the nuclear membrane. But underlying the inner nuclear membrane is the nuclear lamina, a fibrous meshwork that provides structural support to the nucleus. The nuclear lamina is composed of one or more related proteins called lamins.
Coming to your last question, using the example of Triton X-100 and leukocyte cells, a paper says: {4}

Leukocyte membranes except the nuclear envelope were solubilized in a buffer that contained 1% Triton X-100.

Which means that all membranes- including mitochondrial, dissolve in the detergent because they do not have an additional protein layer in them, like the nucleus does.
1-http://www.genotech.com/protein-research/detergent-accessories.html
2-https://www.thermofisher.com/in/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/detergents-cell-lysis-protein-extraction.html
3-https://pubmed.ncbi.nlm.nih.gov/999948/
4-https://link.springer.com/article/10.1007/BF00554425


What information can Uniprot give me about phosphorylated forms of proteins?

You were looking in the wrong spot. The PTM section you clicked on is for post-translational modification databases such as PhosphoSite. To get the actual modified residues, click on "PTM/Processsing" (sic) further up the page and then select "Modified Residue", and in your results table you'll get a list of all phosphorylations, glycosylations, acetylations, etc.


Is it unusual for a child to be diagnosed with diabetes?

Short Answer

Type 1 diabetes is commonly diagnosed in children; type 2 diabetes is more common overall and is much less likely to be diagnosed in children, though possible.

Longer Answer

Type 1 diabetes is caused by damage to the pancreas and depends on environmental and genetic causes, most often leading to autoimmune loss of the insulin-producing beta cells in the pancreas. Type 1 diabetes occurs because insulin levels themselves are low. It commonly begins in childhood, and is also sometimes referred to as "juvenile diabetes" although it lasts life-long. Type 1 diabetics often take insulin to replace the insulin they are not producing.

Type 2 diabetes, by contrast, is caused by reduced insulin sensitivity and develops over time (lack of insulin can also eventually occur). Obesity and other lifestyle factors are strong influences on the development of type 2 diabetes, though genetics can also play a role. Type 2 diabetes is most often diagnosed in adults (and is also referred to as adult-onset diabetes, though it is also possible to occur in children), increases with age, and is overall more prevalent than type 1 diabetes, so this is likely where your community's surprise comes from.


Function of heparin and dextran sulfate for removing proteins

See here.

Histones are basic proteins (cationic, high pI) because they are required to interact with polyanionic DNA at physiological pH. Heparin and dextran are polyanions which form insoluble salts with the cationic histones.(Dextran is a polymer of glucose. In dextran sulphate it is derivatised with sulphonate groups creating a polyanionic material.)

Immobilised heparin is sometimes used as an affinity matrix for purification of DNA-binding proteins like transcription factors.


Attachment of muscles during molting in insects

You can find a concise answer here in a section from The Insects: Structure and Function  by R. F. Chapman, eds. Stephen J. Simpson, Angela E. Douglas. 5th Edition. Cambridge University Press.

In essence the source says that the muscle attachment to the cuticle is maintained during the moulting process, while the new cuticle is formed under the old cuticle.

  As a result the insect is able to continue its activities after apolysis during the development of the new cuticle. The connections to the old cuticle are broken at about the time of ecdysis.

Connections to the new cuticle are formed at the same time as the old ones are broken.


What is the right spelling for this agar?

The first word is ok, there is agar called Gonoline, the second one is probably Euroline and there is an agar with this word too (Liver IgG Euroline).

I've found both of them on the Italian site, probably the are not one, but two agars.


lifespan of Nautilus compared to other cephalopods

On a basic level, the difference in lifespan is due to the fact that the nautilus has a vastly different reproduction strategy from other living cephalopods.  While most other cephalopods exhibit a rather extreme form of r-Strategy reproduction, the nautilus is, relatively speaking, a K-Strategist.  To explain, r-Strategy is when a species produces many offspring, but puts relatively little investment into each one under the expectation that most will die.  K-Strategy, on the other hand, produces relatively few offspring, but put much greater investment into each one.

As you stated, in most cephalopods, sexual maturity triggers a shutdown of the digestive tract, as they put all their energy into reproduction, during which one spawning episode will result in hundreds or thousands of eggs.  After fertilizing the eggs for males, and for females after laying those eggs (allowing for a delay of a relatively short incubation period in some species, including most or all varieties of octopus), the adults die, having produced enough young to guarantee the next generation.  This lifestyle of a single massive reproduction event before dying is called semelparity.

However, with nautiluses, each mating results in only about a dozen eggs.  These eggs are much larger than the eggs of any other cephalopod, have a considerably longer incubation perios, and by extension, the hatchlings start out larger and better-developed.  However, technically, nautiluses aren't true K-Strategists, like humans or whales, which have only one offspring at a time and put a massive amount of investment into that offspring.  Instead, they are more like cats or dogs, Median Strategists, who fall somewhere between the extremes.  While for r-Strategists like other cephalopods, semelparity can produce enough young to ensure the survival of the species, this is not the case for Median or K-Strategists.  Instead, they must reproduce multiple times over the course of their life, a strategy called iteroparity.

While in all cephalopods, the gonads are destroyed by the process of reproduction, in nautilus females, the gonads regenerate after spawning, allowing them to mate again the next year.

It should also be noted that despite this, the nautilus spends a relatively small portion of its life sexually mature.  It takes roughly fifteen years for a nautilus to reach breeding age.

While my knowledge of genetic engineering is pretty much limited to what appears in the news, based on this information, it seems like to lengthen the lifespan of other cephalopods to be on par with that of a nautilus, you'd have to completely change the way they reproduce and the rate at which they mature, which I tend to suspect is beyond our current abilities.


Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?

Note: This is NOT my field. However, given @biogirl's question, it appears that there aren't many people in this field in the first place. From what I can gather, here are the reasons why I think it has been difficult to study.

I. The lac operon has strong polarity. By this I mean that when the lac operon is induced, lacZ (the first gene in the operon) is translated much more than lacA (the last gene in the operon). Measurements have recorded the molar ratio of $\beta$-galactosidase : thiogalactoside transacetylase (the protein products of lacZ and lacA) upon induction of the operon at 3:1 to 5:1; i.e. when the lac operon is induced 3 to 5 molecules of $\beta$-gal are produced for every one of the transacetylase. If you factor in the relative length of each of these proteins ($\beta$-gal is 1024 a.a.s, transacetylase is 203), it works out that lacZ is being translated at least 10 times faster than lacA when the lac operon is induced. Sidney Altman's lab has attributed this to the fact that there is a cleavage site between lacY and lacA where RNAses can cleave the nascent mRNA transcript, removing lacA from the operon and reducing the production rate of transacetylase. So it appears the cell needs quite a bit less lacA than lacZ---if indeed they need it at all, see point 2---which makes it harder to study.

Sources: Brown JL, Brown DM, Zabin I. (1967). J Biol Chem. 242(18):4254-8.

Li Y, Altman S. (2004). J Mol Biol. 339(1):31-9.

II. lacA seems to provide only a small fitness advantage under somewhat contrived conditions. In A paper from the 70s researchers presented competition experiments between $lacA^{+}$ and $lacA^{-}$ strains in media with $\beta$-galactosides as the only carbon source. For 50 generations there was no competitive advantage of one strain over the other (ratio of $lacA^{+}$ : $lacA^{-}$ stayed at 1). When after 50 generations the researchers added a lot of IPTG, a non-hydrolyzable $\beta$-galactoside, $lacA^{+}$ outcompeted $lacA^{-}$; the absolute fitness of wild-type:mutant could be calculated to be $\approx 1.05$. This means that the wild-type produced 105 cells for every 100 produced by the mutant. I am not a population geneticist, so I don't know if that is a large value or not. For comparison, I used to work in cyanobacterial circadian rhythms, and the absolute fitness advantage for having a circadian clock with the same period as the light-dark cycle in the environment works out to $>1.11$, which is twice as advantageous as the one reported for $lacA^{+}$ over $lacA^-$. In any case, the experimental situation in which $lacA^+$ has a competitive advantage seems rather contrived: growing with $\beta$-galactosides as the sole carbon source with a significant amount of non-hydrolyzable analoges around gumming up the $\beta$-galactoside metabolic machinery.

Source: Andrews KJ, Lin EC. (1976). J Bacteriol. 128(1):510-3.

My read from these observations is that the physiological role of lacA is challenging for a biologist to untangle due to the small size of its effect on bacterial physiology. Fitness advantages of 5% may certainly be useful on evolutionary timescales, but they suggest that the benefit afforded by the enzyme will be very hard to discriminate from noise or other confounding factors in the system. The fact that lacA production is much lower than lacZ in times of lac operon induction also would make it hard to measure.

A postdoc I used to work with advised me, "don't go looking for 2-fold changes in biology," by which he meant don't spend too much time on questions where the size of the effect you are looking at is minor and very difficult to distinguish from noise, bias, measurement error, or other confounding variables. Obviously there are limitations to this advice; a lot can be learned from the the combination of several seemingly minor effects that have big cumulative consequences for an organism. But as a rule of thumb, it's so hard to get strong results when your effect size is so small that going after small effects is justifiable only if you have a good reason to believe there is some profound, fundamental biology behind them. My view is that the consensus of the scientific community up to this point has been that untangling the role of lacA in the lac operon and more broadly in bacterial physiology would involve too much work for too little payoff.


I am not sure but I think it is water leaf plant ( called sambar cheera ).If you see other pictures, the leaf and flower color matches but I am not sure as I do not know how the flower looks when it is bloomed ( in your picture).
You can see this site http://papanasini.blogspot.in/2012/02/cylon-spinach-sambar-cheera.html

I got a picture of the above-mentioned plant from my house, unfortunately, it is not having flowers and I will get back when it will have one.

Hope this helps!


Why does NAD+ become reduced if it gains a hydrogen proton?

You are correct that reduction is simply a gain of electrons. This results in a decrease in oxidation number.

You know that NAD+ is reduced by this process because it starts off with a positive charge (+1) and ends up with a neutral charge (0).

The reducing agent that is donating the electrons is the hydrogen. More correctly, the electrons come from the hydride (H-).

The hydride is represented by 2 electrons on this redox diagram:

As you can see, the reduction reaction transfers a proton (H+) and hydride electrons (H- or 2e-) to NAD+. One electron goes to the nitrogen, and the other to the carbon where the proton binds. More details on the redox reaction of NAD can be found here.


@another 'Homo sapien' is basically correct, and what they were getting at, is that in just the F1 generation, you're right, any recessive traits are masked. However, if you continue this onward, in subsequent breeding, recessive traits are unmasked. (This is basically why inbreeding is a bad thing).

If we use the traditional Punnet square method for determining genotype:

if A is a Brown-eye dominant allele, but a is a blue-eye recessive allele:

F1:

You can see that a single recessive allele is now present in 50% of the offspring of a given pair of parents.

Now, if in F2, we assume that 2 of those recessive offspring were to mate, the recessive gene would be unmasked in 1 quarter of the offspring (statistically speaking), and 50% would be carriers.

F2:

Now it gets a little more complicated. Our double recessive F2 member has blue eyes phenotypically, they aren't just a recessive allele carrier.

F3:

So, if in F3, our aa mates with another aa, (ignoring spontaneous mutation for simplicity) it should be obvious that all of their offspring in F3 would have blue eyes (and I can't quickly find a Punnett square in Google showing this).

However, if our aa now mates with an AA (homozygous dominant brown), we will get 100% offspring with a heterozygous Aa genotype - in other words, all blue eye carriers, but with brown eyes phenotypically.

If aa mates with a heterozygous individual though (Aa), we have the following:

And thus, 50% blue eye individuals, with 50% brown heterozygous dominant. And so on and so forth, ad infinitum.

Hopefully that explains how a recessive allele can go to fixation despite only occurring once.


Development and function of spindle neurons

The spindle-shaped brain cells you refer to are called von Economo neurons —named after the man who first described them  (source: Smithsonian).

In humans, von Economo neurons reside only in the anterior cingulate cortex (ACC) and the frontal insula (FI) (Allman et al., 2011). These two regions are particularly active when people experience emotion and they are reportedly important for "self-monitoring," such as noticing bodily sensations of pain and hunger, or recognizing that one has made a mistake. The ACC seems broadly involved in nearly every mental or physical effort (Smithsonian). By contrast, the FI may play a more specific role in generating social emotions such as empathy, social awareness, and self-control (Allman et al., 2011), but also trust, guilt, embarrassment, love, and even the sense of humor Smithsonian).
Humans and the great apes (chimps, bonobos, gorillas and orangutans) have von Economo cells. Lesser primates, such as macaques, lemurs and tarsiers, do not. That means the neurons evolved in a common ancestor of all the great apes about 13 million years ago, after they diverged from other primates but well before the human and chimp lineages diverged about six million years ago (Smithsonian). However, elephants and whales have them too, possibly explaining their complex social behavior (Allman et al., 2011).
I couldn't find literature on the development of these cells in children. Note, however, that, as far as I know, the presence of these cells can be only detected using microscopic techniques, i.e., on coupes of post mortem tissue (e.g., Santos et al., 2010)). This will make research in infants and children difficult.

References
- Allman et al., Ann N Y Acad Sci (2011); 1225: 59–71
- Santos et al., Brain Res (2011); 1380: 206 – 17


Why do the sick and unhealthy trees leaf out first in spring?

Trees that have been dormant over the winter exist on nutrients stored in their roots during fall. When a tree has been damaged or diseased, it may not have been able to store enough nutrients before winter, or may not have enough stored to heal the damage/disease. If the damaged/diseased tree has depleted its winter root stores, it must leaf out (earlier than others of its species) and resume photosynthesis in order to have enough energy to attempt healing itself.


Definitely a nymph of some species of true bug (order Hemiptera), most likely in the suborder Heteroptera (i.e., the shield bugs, stink bugs, assassin bugs, etc.) and family Pentatomidae.

For example, see these photos of nymphs of similar species:

 From L->R: Podisus maculiventris, Troilus luridus, Glaucias amyoti, Cosmopepla lintneriana, Carpocoris purpureipennis, Murgantia histrionica

Using yet another species, Piezodorus lituratus, as an example, you can see how a Pentatomidae nymph typically develops to maturity:

 Source

As to your species...

This site lists Cosmopepla lintneriana, Chinavia hilaris, Podisus placidus, Chlorochroa rossiana, and Sehirus cinctus as species of Pentatomidae that live in Utah. None of their nymphs looks quite right, though your specimen reminds me most of a stripe-less Podisus. That might be a good jumping off place for further digging...

As you can see, there are many species with similar nymphs, and various instars within species even have fairly great variation.

I can't find a great match yet, but I can keep looking. I'll update if I find one.


It sounds pretty much like a fox squirrel (or better: as masked face fox squirrel which are found in Alabama).
They look like this (taken from this website):

There seems to be quite some variation in terms of fur color, some animals are more greyish:

Taken from here, this website also contains some additional information.


External "lungs" that process your blood the same as your real lungs do - would that stop your need for breathing?

A device that fits your description does seem to exist, namely an ECMO machine that delivers extracorporeal membrane oxygenation (Fig.1 ). It is defined as:

[A] machine [that] pumps blood from the patient’s body to an artificial lung (oxygenator) that adds oxygen to it and removes
carbon dioxide. Thus, it replaces the function of the person’s own
lungs. The ECMO machine then sends the blood back to the patient
via a pump with the same force as the heart, replacing its function.

The response of patients to ECMO appears to be variable (Crotti et al., 2017):

As the physiologic cardiorespiratory variability is increased in this condition, the dynamic interaction between patient respiratory activity and extracorporeal system function affects the clinical management. The effect of extracorporeal CO2 removal on patient respiratory drive is variable and not always predictable, with some patients responding to CO2 removal with a decrease in respiratory rate and effort and other patients demonstrating a persistently high work of breathing independent on CO2 unload.

Breathing and undoubtedly the exaggerated gasping for air after heave exercise is related to the concentration of CO2 in the blood that's monitored by the brain. Those chemoreceptors basically measure the pH of the blood. However, pulmonary pH receptors exist and a multitude of other physiological mechanisms are at play to keep the level of O2 in check . I happily refer to Brinkman et al. (2020) for an overview on O2 and CO2 homeostasis.

Fig.1. ECMO. source: University of Iowa
References
- Brinkman et al., StatPearl
- Crotti et al., J Thorac Dis. 2018 Mar; 10(Suppl 5): S661–S669


Why would a flower evolve such that a particular pollinator cannot pollinate it?

I think the explanation by the interpreter is most appropriate. The definition of species is a particular category of organisms capable of reproduction among themselves. Thus pollen of a particular species must fall on the stigma of the same species. But pollinators visit all species of flowers (as they never visit Biology Stock Exchange, thus ignorant of the definition of species) which bears nectar and the entrance is big enough to let them in.

The flowers in your question increase their chance of pollination by reducing the varieties of flowers a particular pollinator can visit. Lets make it simpler (or even more difficult for those who don't like mathematics!)...

Suppose there lives 4 humming birds and 4 bees in a oasis...both are too lazy to visit other oasis in search of nectar. One morning 4 flowers bloom in that oasis...2 wild flowers you mentioned and 2 wide mouthed flower of some other species.  Now 1 flower of the wild species can be visited by 4 bees (as humming birds can't enter the flower). One flower of the other species can be visited by 4 bees and 4 humming birds. This large number of pollinators for the second type of flower reduces its chance to be visited by a pollinator that visited a flower of the same species. Whereas for the wild type flower the possible number of pollinators are very few (only 4)...so the chance of one bee visiting two flowers of the same species is very common and so is the chance of it getting pollinated.

In this way these flowers increase their chance of pollination by modification of their shape.


The coefficient of relationship between you and your uncle is 25% (see wiki > coefficient of relationship for more info).

However, the percentage of similarity depends on the genetic diversity in the population of interest. If you were studying a population of fully homozygous clones (no genetic diversity), then no matter what the coefficient of relationship is between any two individuals, they would still be clones and therefore perfectly similar.


If all B cells are present at birth, why should the primary response to an infection take longer than the secondary response?

These so called virgin B-cells (becase they never had contact with their antigen) which are present in your body only have random B-cell receptors (when secreted, these are the antibodies), mostly of a relatively low binding affinity. These B-cells undergo division, re-arrangement and somatic hypermutation of the B-cell receptor and clonal selection. Only cells producing high-affinity antibodies survive this selection process and build later the pool for the memory cells and the plasma cells. It is like in the image below (from here):

Using this approach we have a big pool of low affinity antibodies (which somewhat fit). These are then used as the basis for the elaboration of a population of high affinity (perfectly fitting) antibodies, which target only the pathogen. And the antibodies are available relatively fast.


Complete genetic linkage does occur in some cases.

Most of the Y chromosome (present as a single copy in males of many species) does not recombine with the X chromosome. Any genes in this non-recombining region, the "male specific Y" (which is 95% of the Y), will be "completely linked", in other words, they cannot be broken apart by recombination and are inherited as a single unit.

Non-recombining region of the Y marked as NRY from this paper.

The closer two genes are, the higher the general tendency for them to be co-inherited. When co-inheritance is non-random the genes are in linkage disequilibrium. The genetic linkage between genes is measured in centimorgans.

I'm not aware of any completely linked genes in recombining parts of the genome. By definition there is some distance between two linked genes (otherwise it's one pleiotropic gene). Therefore, if recombination is possible, then it is possible for them to become unlinked at some frequency, even if that frequency is extremely small (I could be wrong though, but scholar searches have given me nothing). There are, however, cases of very tight linkage between genes (1, 2, 3).

Note that factors other than genetic linkage can affect linkage disequilibrium.


Question about equilibrium potential formula

That quasi-travesty is the Nernst equation in $\log_{10}$ for a positive monovalent ion at physiological temperatures (37 degrees celsius), but they've hidden all that from you. Shame on them.

The canonical form of the Nernst equation, for an ion $S$ is

$$
E_{S} = \frac{RT}{z_{S}F}\ln{\frac{[S]_{out}}{[S]_{in}}}
$$

where $R$ is the gas constant, $T$ is temperature expressed in Kelvin, $F$ is Faraday's constant, and $z_S$ is the charge of ion $S$. This is the actually useful form of the equation that can be used for any ion for any temperature.

The Nernst equation is a limiting case of the Goldman-Hodgkin-Katz equation for a single ion. The Nernst equation is useful for directly determining the equilibrium potential of a single ionic species. The GHK equation is used for determining the reversal potential of a membrane or channel in multi-ion cases.

Note that the terms "reversal potential" and "equilibrium potential" are not synonymous, except in the case of a single ion system. The reversal potential is where the direction of current switches. An equilibrium is when net ion flux is zero (although, in a living cell, it is more appropriate to call even this situation a steady state). If membrane were only permeable to one ion, the reversal potential will be at the equilibrium potential (given by Nernst) for that single ion. However, when there are several permeant ions, usually none of the ions will be in equilibrium at the reversal potential--that is, all the ions will have a measurable flux across the membrane even though the sum of those fluxes (weighted by permeabilities) is zero at the reversal potential.

Converting natural log to log base 10, you can use the identity $\log_b{a} = \frac{\log_{10}{a}}{\log_{10}{b}}$, which gives

$$
E_{S} = \frac{1}{\log_{10}{e}} \cdot \frac{RT}{z_{S}F}\log_{10}{\frac{[S]_{out}}{[S]_{in}}}
$$

In the case of sodium ions (Na+) at 37 degrees (physiological temperature), $T$ is 310 and $z_S$ is +1. Substituting in these values, we have

$$
E_{S} = 2.303 \cdot \frac{(8.3145) (310)}{(+1) (96485) }\log_{10}{\frac{[S]_{out}}{[S]_{in}}} \\
E_{S} = 61.5 \text{ mV} \cdot\log_{10}{\frac{[S]_{out}}{[S]_{in}}}
$$

YAK uses a less common form of the Nernst equation in membrane physiology which uses the Boltzmann constant directly and deals with elementary charges instead of moles ($R = N_A k_B$). It is a wonderful exercise to derive the Nernst equation from the Boltzmann equation,

$$
\frac{p_2}{p_1} = \exp{(-\frac{u_2 - u_1}{k_BT})}
$$

where $p_i$ is the probability of a particle being in state $i$, and $u_i$ is the energy of state $i$. All it takes is some rearranging and keeping careful track of the units.


In real life, round and tall are dominant traits in pea plants, which would make C and D both correct.  I don't think people are expected to memorize the traits of pea plants, so the question ought to tell you somewhere which traits are dominant.  There must be an error in the question as printed.


The uniqueness of irises and fingerprints are, as you said, limited to the number of possible permutations of irises and fingerprints.

A similar problem exists in computer science, and is known as a hash collision. Given sufficient samples, there will always be a collision for a hash of finite size. However, the sample space is sufficiently large for iris and fingerprint analysis for this to not be a problem.

A typical iris analysis system produces 2048 bits of entropy, while a typical fingerprint analysis system produces about 82 bits. Even accounting for the birthday problem, the information space is large enough that the chance of a given false positive is sufficiently low to prevent a random person from passing fingerprint/iris authentication.

For comparison, the current world human population is 7.2 billion, or slightly under 33 bits. The risk of a hash collision occurring is small enough to be negligible.

Of course, side-channel attacks against such biometric systems are relatively simple, but that's another issue altogether.


How allele is related to trait that is more complex than two cases (ex. height)?

You are absolutely correct that many traits are not "digital", but "analog". In genetics, these are usually called quantitative traits. Such traits generally do not follow Mendel's laws of inheritance, but are said to have "complex inheritance". Most traits (phenotypes) in biology at the level of whole organisms probably have complex genetics; height is a classic example.

It is thought that complex traits arise by the combined actions of many genes (via their encoded proteins), while Mendelian inheritance occurs when phenotypes happen to correspond to the activity of a single gene. For very complex traits like height, many functions of the body might be involved, so the number of genes that may have some effect on the trait can be very large, but the effect of any single gene on the trait is likely small. In general, it is not understood exactly how genes contribute to the trait in such complex traits, so a phenomenological/statistical approach is used where the trait is modeled as some simple function of the genotype which is fit to data.  Wikipedia's page on quantitative genetics has more information on this.

In addition, traits may of course be affected by environmental factors as well as genetics. Height for example is strongly affected by having access to good nutrition. See this article for some discussion.

For traits with complex genetics, the underlying genes are generally difficult to identify, and for along time we have known almost nothing about the genetics of traits like height, obesity and diabetes. Since the early 2000's, massive efforts have been put into mapping the genetics of such complex traits by brute force --- measuring the effect of all genes on the trait in a very large number of individuals, in so-called genome-wide association studies. These have revealed a large number of genes over the past decade, but as expected each has only a small effect on the trait.


Mollusk shells found on typical east coast (US) beaches can range from days old (the animal that made the shell died recently) to thousands of years old.  Some shells in our state, North Carolina, have been dated as 40,000 years old.  A high number of "seashells" found on east coast beaches are from mollusks that lived in the marsh on the back side of the island.   The presence of these shells on ocean beaches provides evidence of island migration - the island has moved landward over the marsh until what was once the marsh is now the ocean shore.  Once buried in the sand, the shell is well preserved until erosion uncovers it.  Occasionally, fossilized shells are washed up on beaches after having been dislodged from offshore limestone deposits - these shells can be millions of years old.

-Richard -
Carolina Ocean Studies


Is it the theory of the 5 senses obsolete?

It depends who's counting and according to what criteria.

Some neuroscientists argue that smell and taste are one sense because altering one produces substantial changes in the other.

Conversely, if you break down the senses to receptors, you get at least 5 different for taste and 1000 or more for smell.


Why do people perceive blood pressure as the force that moves the blood forwards (see details)?

In the vascular system, pressure is what moves blood forwards, at least in an analogous manner to voltage...just like voltage, pressure itself doesn't move things, but a pressure gradient does. You are correct that the pressure applies in all directions, but the resistance of the blood vessels means that the pressure can only be relieved by flowing in one direction: down the pressure gradient.

Although blood pressure is often medically reported at a single site(i.e., 120/80mmHg), this is only the pressure in the larger vessels. The pressure originates from the heart forcing blood out into the major arteries, and the compliance/elasticity of those vessels keeps a sort of "reservoir" just like a capacitor would in an electrical circuit. The pressure drops over time from systolic to diastolic as that reservoir drains out into the body.

Importantly, and most relevant to your question, blood pressure also drops significantly through space, through the arterioles and capillaries, down to near zero in the venous system:

(from https://legacy.owensboro.kctcs.edu/gcaplan/anat2/notes/APIINotes5%20cardiac_equations.htm)

This pressure drop occurs for the same reason that you get a voltage drop over a resistance in an electrical circuit: the rules of Ohm's law for electricity are analogous to the Poiseuille's Law for fluids.

Sidenote: there are some exceptions to the pressure drop over space in the arterial system because of hydrostatic pressure (i.e., the pressure from gravity, for example see this question, though the better answer is definitely not the accepted one or the one with the most up-votes). However, that hydrostatic pressure difference is offset by gravity in the same direction, so you can effectively ignore it. It is also much less significant once you get to the smallest vessels.

I'm not sure where you got the quote in your example:

  Veins contain a lot of valves because the blood pressure inside them is low.

..but I would say this statement isn't really false, though it could be stated better and the full causation is missing. Veins use valves because a lot of the pressure in the veins is coming from muscle contractions that squeeze the vessels from the outside, not from a pressure wave caused by forced blood volume from the heart. Venous valves ensure that the flow caused by this external pressure travels in one direction.

The Wikipedia page on hemodynamics may be helpful, though I noticed some poor wording in a couple places; any physiology textbook from a major publisher should be a good reference as well.

For a more "ELI5" answer, if the concepts I discussed so far are foreign, try this: In the arteries, blood is moved because the heart fills the big vessels with lots of blood, and the only place it can go is through the vessels into the capillaries. However, because the capillaries are all so thin and skinny, it takes a lot of pressure to push through them, and all the pressure is lost by the time you get to the veins.

So how do we get blood back to the heart? Well, we could try a vacuum, and have the heart "suck" blood back the way it "pushes" out the other side. However, this would collapse the veins. You can suck through a plastic straw because its rigid, but if you make it less rigid, such as by crushing a section, when you suck it will collapse, and sucking harder won't help the situation. Not good!

Okay so it's better to pump, but all the vessels are so small it would be hard to have them each have their own pump. So instead, the veins go through and around various muscles, and when those muscles move, the veins get smushed. Imagine you have a hose full of water, and you jump in the center...oops! Water goes out both ends! Okay, what if you put your hand over one side? Now it only goes out the end you want. That's essentially what a valve does: only lets the flow go one way when things are squeezed. Then the blood stays in the next compartment and over time works its way back to the heart.


Why might food go bad in an oxygen-free environment?

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

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


It is mainly determined by the OCA2 gene, but it also likely involves several other genes, including TYR, TYRP1, HERC2, and several others. To complicate things further, it is not a "mutant/wild type" trait, but multiple normal alleles can be found in the population, and it is believed that the sum of these single nucleotide polymorphisms (SNPs) determine the final phenotype.

I took the info from a 2004 review by Sturm and Frudakis and a more recent paper from Liu et al, 2009


Is plastic just as good for you as corn?

The part of the corn kernel that is visible in human feces is the outer coat of bran called the pericarp (see this image). This is a common structure in cereal grains like corn and wheat.  However, the bulk of the corn kernal is starchy endosperm, which is readily digestible by humans and provides carbohydrates and vitamins A and C.  The non-digestible (by humans) pericarp does help to keep fecal material soft.

Plastic bags do not provide those same benefits. Studies on human consumption of plastic bags are lacking, for obvious reasons.  However, marine organisms like sea turtles unfortunately consume large amounts of plastic debris (Derraik 2002). Bugoni et al. (2001) found that plastic debris caused mortality for 13% of the green turtles in their study. A review of 408 leatherback sea turtle autopsy records by Mrosovsky et al. (2009) found plastic inside 34% of turtles. The mortality in the sea turtles may be due to the accumulation of plastics in the gut which can block movement of food, alter feeding behaviors, and prevent absorbtion of nutrients.

If humans were to consume chopped up plastic bags, the evidence suggests that instead of receiving the same benefits as we do from whole kernal corn we are much more likely to be harmed. Eat your corn, recycle your plastic.

Literature Cited

Bugoni, L. et al., 2001. Marine debris and human impacts on sea turtles in southern Brazil. Marine Pollution Bulletin 42: 1330-1334.

Derraik, J.G.B. 2002. The pollution of the marine environment by plastic debris: A review. Marine Pollution Bulletin 44: 842-852.

Mrosovsky, N. et al. 2009. Leatherback turtles: The menance of plastic. Marine Pollution Bulletin 58: 287-289.


What, if anything, would prevent flying fishes evolving to be capable of extended flight?

As AMR said, fish are tied to the water by their respiratory systems. Bats and gliding mammals and herptiles don't have that limitation. Fish have an advantage over mammals and herptiles in that they're generally streamlined. On the other hand, they're adapted to "flying" in a denser environment and might therefore be a little heavy for flight. Also, I wonder if the need to keep their skin moist might present a problem.

Nevertheless, flying fish are halfway there. Just imagine if lungfish - which can survive out of water for long periods - were adapted for gliding.

P.S. I posted this as a comment by mistake, then deleted the comment.


The following study shows evidence that UVB does damage plant DNA.

Rousseaux et al. Ozone depletion and UVB radiation: Impact on plant DNA damage in southern South America. Proc Natl Acad Sci U S A. 1999 December 21; 96(26): 15310–15315.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24816/


How can I determine the purity of cells isolated from rat brains if I cannot use FACS, Immunohistochemistry or SEM anaysis?

You can do qPCR for certain markers from the extract. GFAP for astrocytes, Tuj1 for neurons, Myelin for oligodendrocytes etc and calculate their percentages to have an estimate of the relative populations. If you are quite used to microscopy and studying these cells then you can identify the different populations of cells with normal light microscopy as well; this is not quantitative and is susceptible to bias.


How long does a mosquito take to land on a host, bite, and fly off?

That's an interesting question and not easy to answer. I haven't found data for humans but from experiments with mice. They analysed how the mosquito actually bites, probes for the blood vessels (not all bites are successful) and finally sucks bloods. In their research  they observed feeding times between 150 and 329 seconds, depending on the size of the blood vessel. The mean feeding time was 240 seconds. It also depends on the age of the mosquito, older mosquitos suck longer. To this comes the time for probing (mean time 142 seconds) and the time before the mosquito starts probing after it landed (mean time 6.5 seconds). This totals to about 389 seconds (or roughly 6.5 minutes) total time after landing. This data can be found in table 1 of reference 2.

This is pretty interesting, they also show videos of the mosquito probing the skin for a blood vessel. You can find a pretty nice summary in the first reference and the original paper in the second:

Here’s What Happens Inside You When a Mosquito Bites
Visualizing Non Infectious and Infectious Anopheles gambiae Blood
Feedings in Naive and Saliva-Immunized Mice.


This insect might be Bactrocera dorsalis.

It looks similar to this species based on the characterstic yellow spots, shape of the abdomen, as well as the light brownish orange stripes on the abdomen.

I had arrived at this conclusion by reverse-image searching the second picture that you have posted and observing the thorax and abdomen patterns. This image shows a very similar pattern as shown in your second picture:

The Wikipedia article has quite some stuff to say,

  Bactrocera dorsalis is a species of tephritid fruit fly that is endemic to Southeast Asia, but has also been introduced to Hawaii, the Mariana Islands and Tahiti. It is one of the major pest species in the genus Bactrocera with a broad host range of cultivated and wild fruits.

Considering that you had found this insect in Pune, it makes a lot of sense to conclude that this is, in fact, the insect that you have found.


Is it possible in modern biology to make any person's identical twin (or genetical clone) using his DNA?

I will assume that by "identical twin", you refer to "clones". Individuals who share the same genetics but of course do not necessarily share the same womb. I won't pay much attention in detail epigenetic modification nor in the length of telomeres.

While it has never been done for ethical reasons, we would probably be quite able to make a clone of a human being. We can take a cell from an individual, make it totipotent again, like a zygote and then, insert this zygote into a woman's uterus. The resulting individual is a clone and therefore have identical genetics, just like two identical twins. Similar technics have been used to clone Dolly the sheep.

We cannot, however, modify the DNA in all cells of a living individual to make this individual a perfect cone of another one.


Is there a map of the individual motor axons in the limbs?

No it is not possible to map axons at that fine of a scale between individuals.

You mention a possible use for controlling bionic arms. There are a bunch of problems with that approach.

Like @kmm says, at the fine level there is a ton of variation.
I think you are failing to appreciate just how many axons there are, even going to a particular muscle; while each muscle fiber only gets input from one axon, there are thousands of fibers in a single muscle.
The EEG-based approaches to prosthetic control are most relevant when there is a problem with spinal function, for example caused by an injury. In this case, there is no connection between the motor neurons and the brain.
Axons often degrade if their targets are damaged. Therefore, if a hand is lost in an accident, for example, the neurons projecting to the muscles of the hand will atrophy.
If the axons themselves are in place, there are already prosthetics that operate based on muscle contractions in existing muscles. It takes some time to train users to use these devices, but most movements you make involve all sorts of muscles you may not realize are involved, and it is quite possible for brain plasticity to allow muscles in, for example, the shoulder, to control a bionic hand after an amputation.

If for some reason the issues I raised don't apply, there is another alternative: mapping. You don't need to know which axons you want information from, you only need to be able to record their activity (which you will need anyways to operate the prosthetic). Record the activity while the patient tries to move their finger, for example: now you know the signal you should transduce into a finger movement. The technical challenge, then, is being able to isolate that signal from all the other signals from all the other axons in the same nerve. This challenge is related to, though not precisely the same as, the challenge of isolating a signal in the EEG.


What is the name of this beautiful insect?

This is indeed a true bug (Hemipteran) in the infraorder Pentatomomorpha.
As Arthur Frost said in his comment, exact identification is difficult for those of us on the other side of the world.

However, a fortuitous series of internet rabbit holes may have led me to a very similar looking specimen.

Homoeocerus striicornis and Homoeocerus angulatus appear to be quite similar in appearance to your insect, and so I would not be surprised if your insect was at least in this genus (see here for more pictures) within the "leaf-footed bugs" family (Coreidae).

I'd say Homoeocerus angulatus is more likely only because the sightings maps on inaturalist show this species being found in Singapore.

I can't say that any incredibly reputable or peer-reviewed resources in English online provide definitive support for this identification, but this is at least a step in the right (a?) direction.


I don't know if they are classified as organs, but basically, blood vessels match the criteria for being organs.

Quoting SIU School of Medicine:

  Blood vessels are basically tubular organs found within other organs.

Biology Reference states the same:

  Even the glands within the integument can be considered organs; any gland is primarily secretory epithelium surrounded by connective tissue for support and protection. Likewise, the blood vessels and nerves in these organs are organs unto themselves.


Why do we have to move in the cold for higher chance of survival?

As with any evolutionary "why" question, most any answer will likely involve some speculation. But we can still think about what we do know in relation to the question.
First, lets think about thermogenesis in humans. As your questions mentions, humans move to stay warm. This is because the conversion of chemical energy (in the form of ATP) into kinetic energy in our muscles is inefficient, resulting in some of the kinetic energy dissipating in the form of heat (instead of moving your body). Shivering is actually a cold-induced reflex that helps our body maximize the amount of chemical energy converted into heat through skeletal muscle contraction. So, in a sense, you body does "know" how to invest in generating heat without moving (without moving as much at least).
A different mode of non-shivering thermogenesis in mammals is mediated by a specialized type of fat called brown adipose tissue or brown fat. This brown fat is used by some animals to generate heat during periods of hibernation. However, adult humans tend to have very little of it. Human infants on the other hand, carry can carry quite a bit (up to 5% of total body weight). This could relate to a number of factors that make infants more sensitive to cold than adults, including having less developed skeletal muscles that are unable to generate much heat though movement or shivering.
It seems like one reason we can't generate heat very well without moving is that we don't carry much of this brown fat around. So, why don't we then? It could be that it's just energetically expensive, and those resources can be better spent elsewhere. Or maybe there could have been some negative health effect associated with carrying excess brown fat in adults. Whatever the reason, it comes down to a lack of selective pressure to maintain this extra tissue into adulthood.
But there's one other, more behavioral solution that might be worth consideration (although it's purely speculation at this point). In most naturally occurring scenarios where the body would be approaching a state of hypothermia, simply staying put and waiting for the temperature to change will seldom be your best chance for survival, even if you are doing burpees to stay warm. In order to ensure continued survival, one may need to actively change their condition of being in an environment that's too cold to maintain sufficient body heat. Humans are pretty good at changing their immediate circumstances. It might involve getting up and finding/building shelter, gathering fuel to make a fire, or migrating to someplace warmer. But in any case, it would require some amount movement accompanied by a cognitive motivation to move. Feeling less cold seems like a powerful motivator to me. If we had more robust means stationary thermogenesis, it's possible that we'd be able to survive a longer spell out in the cold just by conserving our energy a bit better, but that might not be the most effective survival strategy given the situation. Calories and liquid water can be hard to come by in extremely cold environments, and waiting for some other physiological need to motivate action might be less advantageous than proactively moving around to alter one's state of being too cold. Just a thought.


Small worm living in some kind of cocoon, what are these animals?

This little dude is not a Caddisfly, but a true moth,  Tinea pellionella, a case making clothing moth.  Confusing because they do resemble caddisfly larvae cocoons more so than those of their own family (Tineidae).  Sort blurb Here:

  "The brown-headed larva spins a silken case that is open at both ends. The case in the above image is covered with fine sand and debris, and superficially resembles a caddisfly case. The flattened case is about 10-11 mm long (3/8 to 1/2 inch). When crawling, the larva's head, thorax, and three pairs of legs protrude out of the case, and drag it along. According to Internet sources, the larva feeds on a variety of material, including hair, fur, silk, felt, feathers, woolen clothing, upholstered furniture and carpets. It apparently prefers darkness and soiled clothing, and is not fond of synthetic fabrics, such as nylon and polyesters."


Formation of ammonia from air and moisture

If you're absolutely sure it's Ammonia ($NH_3$) you're smelling, it's probably from you.

Ammonia will not spontaneously form at any significant rate from the air. Molecular Nitrogen ($N_2$) is extremely stable.

What can happen is that during marathon-type activities, muscles turn from carbohydrates (which are later converted into glucose and enter into the Krebs Cycle) as an energy source to proteins themselves.

One of the waste products of protein catabolism is Ammonia, which is excreted in your sweat if the body can't convert it into Urea ($CH_4N_2O$) quickly enough:

  Ammonia forms with the oxidation of amino groups (-NH2), which are removed from the proteins when they convert into carbohydrates. It is a very toxic substance and only one nitrogen atom is removed with it. A lot of water is needed for the ammonia excretion.


How does the immune system fight scabies mites?

Found from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535073/

In addition to being a physical barrier, the skin is an immunological barrier63. The skin immune response is vital in wounding and infection and also modulates the commensal microbiota that colonizes the skin. Keratinocytes continuously sample the microbiota colonizing the skin surface through pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), mannose receptors and the NOD-like receptors. These receptors recognize pathogen-associated molecular patterns (PAMPs) including flagellin and nucleic acids, as well as lipopolysaccharide from Gram-negative bacteria, mannan and zymosin from fungal cell walls, and peptidoglycan and lipoteichoic acid from Gram-positive bacteria. The activation of keratinocyte PRRs by PAMPs immediately initiates the innate immune response, resulting in the secretion of antimicrobial peptides (AMPs), cytokines and chemokines. Beyond effecting an adaptive immune response, AMPs also directly kill bacteria, fungi and enveloped viruses64. Therefore, there is a constant interplay among keratinocytes, immune cells and microorganisms that is modulated by AMPs, cytokines, chemokines and microbial peptides.

While mites certainly are not fungal, viral, or bacterial, you can extrapolate the mechanisms required to prevent mite infestation being similar to those referenced above. Hope this helps!


Prothrombin time when extrinsic pathway is turned off

In order to understand the importance of both pathways, you first need to be clear about what is meant by them respectively. Clotting activation from tissue factor (TF) is known as the extrinsic pathway, so you've got that one right.

The intrinsic pathway doesn't involve FX

The intrinsic pathway does not (as often misunderstood) refer to the clotting cascade downstream of factor X (FX) which involves FV, FVIII and thrombin. Rather, the intrinsic pathway is a system which is able to initiate the clotting cascade without any tissue factor being present. It is triggered by the assembly of high molecular weight kininogen, prekallikrein and FXII on collagen. This is also known as contact activation, and sets off a small cascade producing active FIX (FIXa), which can then assemble with circulating FVIIa in order to produce FXa and thereby set off the rest of the clotting system.

The extrinsic and intrinsic pathway are separate ways towards a "common pathway"

So think of it this way: The extrinsic pathway produces FXa in one way (TF), the intrinsic pathway produces FXa in a different way (HMWK+prekallikrein+FXII). There isn't really any interaction between these two. Once FXa is produced from either of these two, it will start to set off what you could call the "common pathway", i.e. it will produce thrombin, which will activate co-factors that will then lead to more production of FXa and propel the entire thing forward faster and faster until it reaches what we know as the thrombin peak.

The intrinsic pathway is not important for haemostasis in humans

Aside from this, you should know that the intrinsic pathway exists, but it doesn't bear much significance in a living human. This is demonstrated by genetic FXII deficiency - you would expect it to produce haemophilia if FXII and therefore the intrinsic pathway was important (just like FVIII and FIX), but it doesn't (read here: http://en.wikipedia.org/wiki/Factor_XII#Role_in_disease).

The principle behind the initiation pathways and the common pathway

So to summarise: You fell victim to a misunderstanding and a bad explanation on that site you linked. The extrinsic pathway doesn't "turn itself off", and the intrinsic pathway doesn't "take over". What really happens in a human is that the intrisic pathway doesn't really do anything. Rather, the extrinsic pathway will produce a little bit of active FXa. But that is enough to produce a little bit of thrombin. And that bit of thrombin will then produce small amounts of FIXa and co-factors (FV and FVIII). These will start to produce more FXa, which will produce more thrombin, which will produce more FIXa and co-factors, and so on.

What the article you refer to is trying to mention are the inhibitory systems that will be set off alongside all of this. Think about it - if thrombin increases its own production perpetually, how does it know when to stop? These systems which ensure that clotting does stop are known as anticoagulation pathways. They are just as amazing as the coagulation pathways themselves, and they are extremely well-geared towards shutting off exactly the right clotting factors at exactly the right time, to ensure that a clot forms in the wound but only there and nowhere else.

Edit: It turns out people do use more complicated definitions of "intrinsic" and "extrinsic" - the problem being once again that everybody can define words as they like. This is rather based on the distinguishing of the two ten-ases, TF-FVII (extrinsic tenase) and FIX-FVIII (intrinsic tenase). In this understanding, the physiological process does indeed start off by the extrinsic pathway (i.e. mechanisms which generate extrinsic tenase), which will kick off the amplification cascade of the intrinsic pathway (i.e. which produces intrinsic tenase). It is true that this way, the contribution of the "extrinsic pathway" is minor once the "intrinsic pathway" is active, but even so, it does not "shut itself off". What turns the extrinsic pathway off is the layer of material which gets deposited on top of the exposed subendothelial surface, preventing access to TF!


Is it possible to give a person an allergic reaction in a very specific place?

Depends on the kind of allergic reactions you want to create. If your target tissue is skin epithelium sure you can.

That's actually the way the skin allergy test is all about: The physician tries a wide variety - last time I did it were 28 well known kinds - of substances in liquid form (drops). If an allergic reaction is caused, the physician takes note. Even very small quantities can cause allergic reactions.

These tests are usually made in a secured environment (physician's office, hospital, etc) at a very low level which most of the times, if result is positive will cause just an irritation. The level of irritation will be self-explanatory, so even a non trained patient can understand what is going on.

Not sure if that what you were asking though.

Best Regards,

pa


Why are the genomes of some trees so large?

This study of the recently sequenced pine species states that 82% of genome is repetitive. This is characteristic of any complex genome, including humans. Such sequences have often been considered "junk DNA", though any scientist will tell you that just because we don't know its purpose doesn't mean it doesn't have one. That said, a good portion of repeats are due to transposable elements, effectively intracellular parasites, whose only purpose is presumably self-amplification and are more often than not deleterious. These interspersed repeats make up ~45% of the human genome. That paper mentions that, based on sequence homology, ~65% of the pine's genome is made of these repeats (that's 15 billion base pairs).

It's interesting that, even though the pine's genome is ~7 times larger than a human's, it has only twice as many predicted genes. The pine tree has ~50 000 hypothetical genes but only ~16 000 are what the authors call high confidence. When the human genome was first sequenced, there were ~35 000 hypothetical genes but now, some 10 odd years later, there are only ~21 000 predicted genes. It seems too early to compare the two. This also brings up the important point that the number of genes is not necessarily related to organismal complexity: the worm C. elegans has ~20 000 genes.

From the paper:

  The large genome size has primarily been attributed to an extensive contribution of interspersed repetitive content (Morse et al. 2009; Kovach et al. 2010; Wegrzyn et al. 2013). Assembly of the Norway spruce genome has shown that LTR retrotransposons in particular are frequently nested within the long introns of some gene families (Nystedt et al. 2013). In addition, there is evidence for gene duplication, pseudogenes, and paralogs, although the extent of these is not clear (Kovach et al. 2010; Pavy et al. 2012).

I have never heard of the hypothesis you mention (not that that means anything), but it seems to me that it's far to early to tell.


What is the exact reason for the stickiness of Fibronectin?

Fibronectin interacts with diverse substrates which reflects its non-specificiy and its interaction with hydrophobic substrates is better suggesting that the adsorption is dependent on hydrophobic interactions.

  Does Fibronectin stick to the other proteins or rather to "free areas"
  of the surface?

It can stick to both as you can see from the table. However, its binding to hydrophobic materials like polystyrene and PVC is the most efficient.

  which parameter is the best to vary?

Note that there will be a lot of free regions in the substrate. You cannot block all the sites unless you use a high concentration of fibronectin. So the best parameter to vary would be the concentration of fibronectin. You may also use fibronectin-BSA mixtures as their mutual binding is not that great (A stepwise method would be nonetheless better). You can also vary the adsorption time (see the figure below) but that is not as easily controllable as concentration. Since fibronectin does not bind to agar, you can also block some sites on your coverslip using molten agar (or agarose).

Reference:

Klebe, Robert J., Kevin L. Bentley, and Robert C. Schoen. "Adhesive substrates for fibronectin." Journal of cellular physiology 109.3 (1981): 481-488.


Which grows slower: the thumb nail or the pinky nail?

I did some research and found out that it is actually the pinky that grows the slowest. See the decadal reports of Bean on fingernail growth or:

Gupta, Gita Rani, et al. "Human nail growth pattern and medicolegal aspect." (2005).


Have creatures ever evolved to become less intelligent?

Unfortunately, measuring intelligence (assuming we would have a strict definition) is not a thing that can be done from fossil record or genetic data. The only thing one can do is to compare brain mass (or at least size of the cranial cavity) from fossil record. In this regard, no need to go very far for an example, humans are an example. From wikipedia

  The evolutionary history of the human brain shows primarily a gradually bigger brain relative to body size during the evolutionary path from early primates to hominids and finally to Homo sapiens. Human brain size has been trending upwards since 2 million years ago, with a 3 factor increase. Early australopithecine brains were little larger than chimpanzee brains. The increase has been seen as larger human brain volume as we progressed along the human timeline of evolution (see Homininae), starting from about 600 cm3 in Homo habilis up to 1500 cm3 in Homo sapiens neanderthalensis which is the hominid with the biggest brain size. The increase in brain size topped with neanderthals; since then the average brain size has been shrinking over the past 28,000 years. The male brain has decreased from 1,500 cm3 to 1,350 cm3 while the female brain has shrunk by the same relative proportion.

Note however, that wikipedia does not cite any reference and I failed to find one!

Note, also that one should not confound cranial cavity (the thing that is actually measured) with brain size and more importantly no confound brain size with intelligence. Wikipedia goes on saying

  However it is argued that another essential element of brain evolution in humans is rearrangement (Hoffman et al. 2004). Larger brains require more wiring, but more wiring can become inefficient (Hofman 2001). The brain has therefore become reorganized for efficiency. Furthermore, the average body size of nethanderthals was larger which led to bigger brain size (see Brain-to-body mass ratio).

I could not find the Hofman papers but I probably just did not look hard enough (and am a bit tired right now)! One might want to read Healy and Rowe 2007 for a criticism of the inference that can be done from measures of cranial cavity.


Why do Type II Restriction Endonucleases cleave at palindromic sequences?

Short Answer

  The palindromic symmetry of the restriction site allows a dimeric
  enzyme to bind the DNA in a manner that bends the double helix in a
  way that facilitates the endonuclease reaction.

More Detailed Answer

The ‘palindromic’ nature of the recognition/cleavage site of restriction endonucleases, such as EcoRV (illustrated here) results in a form of symmetry (A) that allows a dimeric enzyme — that forms a tunnel — to bind symmetrically at that site in the DNA (B).

This binding causes the DNA to bend (C) bringing a catalytic magnesium ion into a position in which it can interact with phosphate of the phosphodiester bond that is being cleaved (D). (The dimeric nature of enzyme allows force to be exerted at two points, to produce the bend. Compare bending a thin pipe over one’s knee, applying equal force with both hands.)

Methylation of the adenine nucleotide in the recognition sequence prevents hydrogen bonding of the enzyme to the DNA. DNA lacking the recognition site is not cleaved by the restriction enzyme because it does not bind specifically to the protein so that the magnesium ion remains too far away.

Reference

This answer is based on chapter sections 9.3.2 and 9.3.3 of Berg et al., which is available online at NCBI Bookshelf and is well worth reading in full. There is also a PDB Molecule of the Month item on this, although unfortunately the bending of the DNA is not apparent in the images there.

Comment on Last Two Sentences of Question

There is no particular “advantage for bacteria”  other than “it works”.  So I think the last sentence is looking at things from the wrong perspective.


Kinesin-5 / cytoplasmic dynein spatial density distribution in neurons

It is possible to tag molecular motors with fluorescent proteins. It may impede with its movement but as this paper describes, a variant can be created that doesn't have cargo binding ability.

  Constitutively active kinesin motors can be generated by truncations
  that remove autoinhibitory and cargo-binding regions of the
  polypeptide. For this work, we generated KHC(1-560) (Figure 1A), a
  dimeric motor that has been well characterized in vitro and in vivo
  [16],[18],[19]. KHC(1-560) motors were tagged with three tandem copies
  of monomeric Citrine (mCit), a variant of enhanced yellow fluorescent
  protein (FP) (Figure 1A), and expressed in COS cells (Figure 1B).
  Single Kinesin-1 motors were tracked in live cells using a modified
  TIRF microscope (Figure 1C) in which the angle of illumination was
  varied to enable deeper imaging as described [17]

However, if your objective is just to determine the density distribution of Kinesin and Dynein in a Neuron, you can simply fix the cells and do IHC staining for the motor proteins followed by high resolution imaging.


can a bacterial protease inhibitor cocktail be used for Western Blotting involving HUVEC cells and HT-29 adenocarcinoma cells?

In general, leupeptin (a cysteine, threonin and serine protease) and aprotinin (sometimes called Trasylol; trypsin inhibitor) are included in most mammalian cell lysate buffers. Whether you need them is really up to your protein of interest: if you know how it gets degraded in vitro, then you should be fine with inhibition of just those proteases. If instead you want to preserve as much protein as possible, then you should add them. Should you not use them, then yes, those proteases will degrade some of the cell proteins.

The good news is that you can buy aprotinin and leupeptin individually and supplement them to the necessary concentrations for a working lysis buffer.


Why is the species-diversity of deadly parasites greatest in the tropics?

The diversity of parasites shows a gradient with increasing diversity from the poles to the equator. Several reasons have been brought forth to explain the latitude-dependency of parasite diversity:

An increased diversity overall around the equator; species diversity in general is greater in the rain forests and hence more hosts are available and thus more parasitic species can develop that target specific hosts;
Larger amounts of precipitation and higher temperatures around the equator may favor the development and transmission of parasites (Nunn et al., 2005);
Increased available energy overall around the equator (Guernier et al., 2004).

References
- Guernier et al., PLOSone (2004): 0020141
- Nunn et al., Diversity and Distrib (2005); 11: 249–56