Exome data can be used to determine both somatic point mutations and copy number variations.  The limiting element for the power of detection for both is read count (how many reads per gene).

Exome data:  Exome data uses a reference (for a trio, that would be parents; for cancer, that would be a paired normal sample from blood or non-invasive tissue) in order to determine if a certain point is mutated or not.  Next-generation sequencing is prone to sequencing errors, so having a high enough read count is essential to properly calling a somatic mutation.  Even so, issues with highly repetitive sites can make this difficult.

Using exome data for copy number is happening a lot nowadays.  The number of reads is used as a proxy for how many copies exist, and the balance of alleles at any given gene tells you whether there has been loss of heterozygosity.  Of course, with exome data, you aren't getting truly genomic data.  But there is enough coverage using the exome to pick up the big events.

CNV data: Copy number analysis is now conventionally done using a high density SNP (single nucleotide polymorphism) array.  These are designed to be biallelic, and come in two types.  First are the copy number SNPs, which are designed to give the best information about copy number.  Then there are the genotyping SNPs, which give information about loss of heterozygosity.  Often, SNP array data is higher quality, but this is determined by your platform.  Newer platforms have extremely high coverage of the genome and can allow you to really pick out focal changes.

These arrays, based on manufacturer's recommendations, are not meant to be used for somatic mutation calling.

As far as bioinformatic pipelines, you can use similar tools for each.  For example, the Aroma package in R has pipelines for both Exome & SNP array data.  GISTIC 2.0 from Broad can be used to find focal copy number changes.

A word of caution: It is always best to validate what you find in one platform with another.  I recently worked on a paper that used both Exome sequencing and SNP array data to determine copy number.  Using GISTIC, there were no focal peaks that matched.  The broad chromosomal trends were the same, and that's what the group reported.


Is this a spider caught on video floating its web between trees?

If you're saying you think this is a spider riding air currents to travel from tree to tree, sorry, but I don't see it. If it's actually moving from one side of the drive to the other, it would have to be moving relatively quickly to cover that distance (about 20 feet according to the video) in only a second or so. If it's just being blown by the air, it seems to me like it would have to have been fairly windy to have moved that quickly, or be capable of directed flight.

It seems more likely to me that's it's just a particle of dust or similar material floating close to the camera. The reflection of the IR light causes it to appear much larger and causes the shape to appear more regular than it truly is. If it's actually a much closer to the camera, only light breeze would be required to show this behavior. There's a strand of web clearly visible near the camera, and perhaps this is indeed something caught in another strand web and dangling down in front of the camera—heck, it could actually be a small spider, but it appears dangling from a web near the camera rather than floating between trees.

I couldn't tell you exactly what it is, but it seems more likely to me that be a trick of light and perspective than a spider floating from one side of the drive to the other.

Disclaimer: I'm not an expert in arachnology or videography. These are just my thoughts on the video.


How can synonymous mutations lead to cancerous or tumorous phenotypes?

I think you assumed that synonymous mutation means silent mutation. But this is not correct.

From Wikipedia (synonymous mutation) :

  Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations, however this is not always the case. Synonymous mutations can affect transcription, splicing, mRNA tranport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent

From wikipedia (Oncogene):

The proto-oncogene can become an oncogene by a relatively small modification of its original function. There are three basic methods of activation:

A mutation within a proto-oncogene, or within a regulatory region (for example the promoter region), can cause a change in the protein structure, causing

an increase in protein (enzyme) activity
a loss of regulation

An increase in the amount of a certain protein (protein concentration), caused by

an increase of protein expression (through misregulation)
an increase of protein (mRNA) stability, prolonging its existence and thus its activity in the cell
gene duplication (one type of chromosome abnormality), resulting in an increased amount of protein in the cell

A chromosomal translocation (another type of chromosome abnormality)

There are 2 different types of chromosomal translocations that can occur:

translocation events which relocate a proto-oncogene to a new chromosomal site that leads to higher expression
translocation events that lead to a fusion between a proto-oncogene and a 2nd gene (this creates a fusion protein with increased cancerous/oncogenic activity)

the expression of a constitutively active hybrid protein. This type of mutation in a dividing stem cell in the bone marrow leads to adult leukemia
Philadelphia Chromosome is an example of this type of translocation event. This chromosome was discovered in 1960 by Peter Nowell and David Hungerford, and it is a fusion of parts of DNA from chromosome 22 and chromosome 9. The broken end of chromosome 22 contains the "BCR" gene, which fuses with a fragment of chromosome 9 that contains the "ABL1" gene. When these two chromosome fragments fuse the genes also fuse creating a new gene: "BCR-ABL". This fused gene encodes for a protein that displays high protein tyrosine kinase activity (this activity is due to the "ABL1" half of the protein). The unregulated expression of this protein activates other proteins that are involved in cell cycle and cell division which can cause a cell to grow and divide uncontrollably (the cell becomes cancerous). As a result, the Philadelphia Chromosome is associated with Chronic Myelogenous Leukemia (as mentioned before) as well as other forms of Leukemia.

You might be especially interested in the second point (An increase in the amount of a certain protein)

Therefore, there is nothing impressive to find some synonymous mutations that are involved in oncogenes.


Does melatonin change the appearance of humans?

Melatonin is a hormone produced by the pineal gland located in the brain, and its production is inhibited by light to the retina and permitted by darkness (reference). It has a lot of effects on the body (reference) but I will stick to just discussing its apparent effects on aging and skin.
Melatonin works as an antioxidant and helps in removing free radicals from the body (reference). Research has shown that free radicals could damage the skin (reference), so I would have to conclude that melatonin could have a part to play in maintaining the beauty of your skin.
It is a known fact that melatonin levels in the body decrease from age, and its decrease has been correlated with some of the effects of aging (reference). As you have mentioned in your question, there is research proving that melatonin could decrease the effect of aging in rats (reference). Also melatonin was found to increase the youthful rhythmic activity in a shrew (reference). In the paper titled melatonin and skin aging it has been stated that

In UV-induced solar damage, melatonin distinctly counteracts massive
generation of reactive oxygen species, mitochondrial and DNA damage.
Thus, there is considerable evidence for melatonin to be an effective
anti-skin aging compound.

Moreover in the paper titled "On the Role of Melatonin in Skin Physiology and Pathology", it has been proposed that

Melatonin (synthesized locally or delivered topically) could
counteract or buffer external (environmental) or internal stresses to
preserve the biological integrity of the skin and to maintain its
homeostasis.

So in conclusion, I would have to say that melatonin does have a lot of positive effects on the skin but, given that it is a hormone and there are side effects (reference), it should be used in moderation.


What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination?

The answer to your general question is 'it depends':

A lot of RNA localisation to the ER and mitochondria happens co-translationally (based on the protein targeting sequences), so these mRNA actually depend on translation to be localised. However, RNA localisation to mitochondria can also happen due to targeting sequences in the mRNA 3'UTR - in these cases translational repression would be possible, but it's unlikely and I don't think anyone ever checked it in this particular case. (see i.e. this review)
the translation of many mRNAs that are actively transported along the cytoskeleton is inhibited during transport, either by specific RNA binding proteins or larger RNP (ribo-nucleo-protein) complexes (see another review).

There are also bound to be some specific mRNA that have very specific regulation mechanisms and others that are exceptions.


The new DNA study showing that we have two DNA codes and not only one unique code

Perhaps you are referring to so-called "duons" (dual-use codons) discovered by Stergachis et al.. This paper was published a bit more than six years ago. A recent paper within the last 2-3 years references duons implicated in photosynthesis.

Duons essentially extend the idea that conserved coding DNA encodes proteins, but can in fact also preferentially encode sites which bind transcription factors, at the same time. DNA can code proteins as well as code that controls regulatory regions, which in turn are switches that control how proteins get made.

Disclaimer: I am a contributing author in the linked Science paper.


In the basic model of protein synthesis the events involving tRNA and amino acids are as follows (see any standard text, e.g. Lodish et al. section 4.4):

An amino acid is attached to the appropriate tRNA (the one with the anticodon that recognizes a codon for that amino acid) by one of twenty specific amino acyltRNA synthase enzymes in a reaction requiring ATP. This is called charging or aminoacylation of tRNA.
The tRNA corresponding to the mRNA codon is brought to the ribosome by an elongation factor (EF1) and the peptidyl transferase activity of the large ribosomal subunit catalyses the formation of a peptide bond between the growing polypeptide chain* and the amino acid of the tRNA, releasing deacylated tRNA.

I am unclear why you are concerned with this problem, but if there were two alanine codons in the mRNA, in theory after a particular discrete tRNA molecule had inserted the first alanine it could be recharged by the aminoacyl tRNA synthetase and then be used to insert the second alanine. However the concentration of tRNA molecules in the cell needed to support protein synthesis is such that the actual probability of this same discrete molecule being used, rather than another tRNA carrying alanine, is remote.

*A real-life complication is that a polypeptide chain has to be initiated by an initiator methionine-tRNA that is distinct from the methionine-tRNA that inserts internal methionines (see Lewin et al. section 4.5).


Do the left half and right halves of the diaphragm undergo the same displacement during breathing?

A short answer is that the displacement of the right and left part of the diaphragm during breathing may not be the same.

ASYMMETRY

Thoracic diaphragm (Wikipedia):

  In humans, the diaphragm is slightly asymmetric—its right half is
  higher up (superior) to the left half, since the large liver rests
  beneath the right half of the diaphragm. There is also a theory that
  the diaphragm is lower on the other side due to the presence of the
  heart.

Genetic specification of left–right asymmetry in the diaphragm muscles and their motor innervation (PubMed):

  The diaphragm muscle is essential for breathing in mammals. Its
  asymmetric elevation during contraction correlates with morphological
  features suggestive of inherent left–right (L/R) asymmetry.

EXCURSION

Excursion (displacement during breathing) of the right and left part of  the diaphragm may or may not be the same, which may differ from case to case.

Manual evaluation of the diaphragm muscle (PubMed):

  In most cases, the diaphragm shows a symmetrical respiratory excursion
  of ~2–10 cm...

Imaging of the Diaphragm: Anatomy and Function (RadioGraphics):

  The excursion may be somewhat asymmetric and there may be a slight
  delay or lag on one side, typically the right.


Are there animals which produce their own colour pigments`?

Although no expert in this field, I think this question is interesting and I would like to put forward some tentative answers.

In a general evolutionary sense one might regard coloration as a secondary feature of living things — especially animals. Their primary concern is to obtain energy, synthesize structural components, reproduce etc. So the metabolism that evolves under this pressure is such as to allow them to do these things. Colour is not a primary concern. Pigments are complex molecules, and enzymes are only likely to evolve to produce them if there are already reasonably complex precursors available. I know little about plant biochemistry, and would welcome improvement of this answer, but it would seem to me that (1) plants have more complex or different metabolic pathways than animals, such as those for synthesizing chlorophyl, and (2) the pathways for producing pigment precursors are more widespread, perhaps because coloration affords a greater advantage to plants — for pollination etc.

There does appear to be pigment synthesis in animals — an article on pigmentation in bird feathers can be found on the website of The Cornell Lab, for example. That states that the pigments in bird feathers are based on three types of compounds: carotenoids (red or yellow), melanins (black to reddish brown and pale yellow) and porphyrins (pinks, browns, reds and greens).

Two of these are related to compounds the birds synthesize themselves from amino acids — melanins for skin pigmentation, and porphyrins for haem. However, it appears that carotenoids are not synthesized by the birds that employ them for coloured feathers, but are acquired from plants in their diet.

Finally, one might argue that producing colours by optical effects has certain advantages over the use of pigments, namely that they are ‘tunable’ — can be modulated or turned on and off.


Something is antigenic because it acts as an antigen - it binds to an antigen receptor in the immune system (antibody, B-cell receptor, T-cell receptor, etc.). While the concept of "foreign" in immunology is often (incorrectly) equated with antigen, that is not the case. For example, there are many chemicals one could think of that are foreign (non-self), but don't usually raise immune responses - nylon, for example.

The difference between an antigenic and non-antigenic peptide is that the antigenic peptide, when presented in the correct circumstances, can raise an immune response. This means that, theoretically, the exact same peptide sequence can be both antigenic and non-antigenic depending on the environment - whether it's being presented in an immune-suppressed environment, for example. However, it's more common to classify antigenic potential based on whether it's possible for the substance to raise a response in an otherwise "normal" immune environment.


Short answer

The concepts dominance, additivity, epistasis, recessivity and others are all specific to a given phenotype. Here you are getting confused because you are considering two different phenotypes at once.

Slightly longer answer

By definition, if an allele is recessive, then in the heterozygote state, the phenotype of interest is just like the homozygous dominant. An important point in the above sentence is "the phenotype of interest". A given locus may show a pattern of simple dominance-recessivity for a given phenotype but may show a completely different pattern for another phenotypic trait.

Let's consider your example of sickle cell anemia. For the phenotype which is the disease, sickle cell anemia has a simple dominance-recessivity relationship. However, for the phenotypic trait which is fitness (yes, in quantitative genetics, fitness is often modelled as a simple phenotypic trait), sickle-cell anemia shows (environment dependent) heterozygote advantage. Also, the fitnesses of the two homozygotes differ greatly.

Note that, in reality, very few loci show cases of perfect recessivity dominance.

EDIT

You are considering two (or even three) phenotypes.

First Phenotype: Fitness

Fitness shows overdominance (with highly unequal fitness for both homozygotes).

Second phenotype: Disease

Double mutant are sick, the others aren't. Perfect dominance-recessivity (although if I am not mistaken heterozygotes individuals have some restriction when it comes to scuba diving if I am not mistaken)

Third phenotype: Shape of hemoglobin

If the heterozygote hemoglobin is shaped just like the healthy homozygote, then there is dominance-recessivity. If the shape differs (which might be causing malaria resistance, I don't know), then there is some partial dominance going on.


From IUPAC Goldbook:

  A loosely defined term for substances of biological origin that are
  soluble in nonpolar solvents. They consist of saponifiable lipids,
  such as glycerides (fats and oils) and phospholipids, as well as
  nonsaponifiable lipids, principally steroids.

That means that lipid does not mean any hydrophobic molecule.
Lipids can be amphipathic as you already know about fatty acids.

Glycerol is not a lipid; neither is it hydrophobic. Glycerol, if to be classified into one of biomolecular classes, it would be that of monosaccharides (in the form of sugar alcohol like sorbitol and xylitol).


Are all genetic disorders inherited?

Not all individuals with a genetic disorder inherited that disorder. Some genetic disorders are caused by spontaneous mutations.

  Is cancer a genetic disorder?

Yes. The seminal paper by Hanahan and Weinberg, the Hallmarks of Cancer, is a good place to go to get a sense of what we understand cancer to be. This paper is quite influential and has its own wikipedia page. These authors wrote an updated review in 2011. Re: your question as it relates to cancer, yes, genetic changes result in tumorigenesis. Cancer is a genetic disorder of cell populations. One can view cancer diagnosis and treatment from the framework of cancer as a metabolic disease, but this adds to, rather than subtracts from the framework of cancer as a genetic disease.

  Are other diseases caused by spontaneous mutations genetic disorders?

Yes. Achondrodysplasia is one illuminating example. It is a form of dwarfism caused by a mutation in the FGFR3 gene. It does follow mendelian autosomal dominant inheritance patterns, but in 80% of cases, the mutation is, in fact, acquired spontaneously (that is, not present in either parent). As noted by @Eff in the comments, Down syndrome, Trisomy 21 (and other chromosomal abnormalities, e.g., Turner, Kleinfelter, Patau, Edwards) are other common examples.


What is the point of Meiosis II, considering Meiosis I already produced haploid cells?

After meiosis I, those n=23 chromosomes have two chromatides. Meiosis II just separates them into single chromatides.


Any good website/book to understand protein folding and enzymes?

Okay, so for introduction the 4 levels of protein structure (each level influences the levels after it):

primary (1st): the order of amino acids.
secondary (2nd): alpha-helicies and beta-sheets
tertiary (3rd): complex 3d structure
quaternary (4th) : 3rd+ non-protein elements (ions, co-factors etc)
and / or multple subunits interact. Not every protein has this kind
of structure.

I think the first does not need any explanation.

The secondary structure is where amino acids form 2D structures: alpha-helices or beta sheets. From wikipedia on a-helix and b-sheet

  The alpha helix (α-helix) is a common secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier (i+4 \rightarrow i hydrogen bonding)

  The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins. It is less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.

Pictures are from here, that is a great site that explains basic protein strucutre in a quite understandable way.

These secondary structures are important because they can from motifs with specific functions like DNA binding, interaction surface with other proteins. The aforementioned wiki sites have detailed info. These secondary structures and motifs serve as building block for higher order functions. Between motifs "loose" non-structured parts can be found to allow for flexibility.

Tertiary structure:
This is the level where complex 3D geometric structure is defined. The aforementioned 2D structures are packed into domains - a single functional element of a protein. A single protein can have multiple domains and the relative position of these domains result in the tertiary structure. The domains themselves are connected with loose regions that do not show any high order structure and provide flexibility between the domains. Flexibility is necessary for conformational changes.

The quaternary structure is where non protein elements and / or multple subunits are involved. For example the positioning of the heme group in hemoglobin. Or when monomers from dimers, trimers etc. so in general when mature proteins get together to form a larger complex.

Here is a great image about the different structure levels:

source: https://dopeahmeanbio.files.wordpress.com/2013/03/333.gif

So now onto the "how" part :)

As I mentioned in the beginning all levels influence the levels after it. So the amino acid sequence predestines the 2D structures to be formed. The secondary structures themselves are formed by amino acid forming hydrogen bonds with each other. This process occurs "naturrally", so by the inherent properties of the amino acids. At the third level disulfide bonds stabilize the structure. This is also a naturally occuring event. Also binding ions, co-factors, etc also stabilizes the protein strucutre.

The folding process can also be supported by chaperon proteins, These proteins can actively "twist" the polypetide chain using ATP as energy source. They can "sense" if there are hidrophobic amino acid chains facing the outer surface of the protein, a thing usually avoided because these amino acids need to face inner surface of the protein where they can avoid water - this is energetically better. This signal (outward facing hidofobic AAs) indicate that either the protein is un/misfolded or it is damaged because of for example heat - that denatures ("unwinds") proteins.

Finally the wiki page on protein folding if you need more. I hope this helps.


How DNA programs the first cell in womb into a human

The short answer is: "Nobody knows yet." The slightly longer answer is that different species use different mechanisms. In amphibians and insect the oocyte, or egg, produced by the mother, has a polarity such that some macromolecules are enriched in different regions of the egg. The best characterized examples are localized RNAs, but there could be other signals as well.  In nematodes the site of sperm entry at fertilization determines the polarity of the cells, which then leads to asymmetry, etc.

In mice, our closest approximation to humans, the early cells after fertilization all seem equivalent, but as the number of cells increases the cells on the inside of the ball and the cells on the outside start to choose different differentiation pathways. There can also be signals from the extraembryonic environment (i.e., the womb).


Do experiences shape actions of insects? Animals?

"Simple" insects like fruit flies can learn to associate odors with food, e.g. see here for a pretty classic example. Drosophila even show some kind of depression which is acquired. Their sexual experiences even shape their alcohol intake.

You will find similar examples for other model organisms as well.
So, yes, simple animals behave differently in response to previous experiences.


Why do Kupffer cells not attack malarial sporozoites?

Indeed the process is even more interesting than thought: sporozoites actively attack Kupffer cells and let themselves get eaten! In a 2001 research, Pradel et al found that sporozoites pass through a layer of Kupffer cells in order to enter hepatocytes for the next stage of their life cycle. They observed that in rat liver cells, Plasmodium berghei and Plasmodium yoelii sporozoites attach to and enter the Kupffer cells, but not the sinusoidal endothelia. During experiment, the number of intracellular sporozoites kept increasing for upto 12 hours, unlike hepatocytes and other non-phagocytic cells which were invaded in vitro for only the first hour of parasite exposure. The sporozoites entered the Kupffer cells via endocytosis in specialized vesicles which did not interact with lysosomal markers. From Kupffer cells, sporozoites traversed to hepatocytes where they developed into exoerythrocytic schizonts. In another 2015 research, Cha et al concluded that the sporozoites interact with CD68 receptor on the surface of Kupffer cells for endocytosis. In short, sporozoites literally pass through Kupffer cells without letting Kupffer cells doing any harm to them. See this diagram for illustration:

EDIT: What happens in Kupffer cells during traversal of sporozoites remains unkown to some extent. However, Frevert et al, 2008 has shown that sporozoites render Kupffer cells insensitive to pro-inflammatory stimuli and force them towards apoptosis (aka programmed cell death or "cell suicide"). This happens as sporozoite-exposed Kupffer cells are stimulated by lipopolysaccharide or IFN-$\gamma$, causing down-modulation of TNF-$\alpha$, IL-6 and MCP-1 and upregulation of IL-10. Nuclear factor NF-$\kappa$B is also activated, which causes apoptosis in Kupffer cells (Punsawad et al, 2014). However, if Kupffer cells are activated, in particular by immunization caused due to high antivody levels, they may phagocytoze the sporozoites and thus prevent their traversal (Krzych et al, 2015).

References:

Pradel, G. and Frevert, U. (2001), Malaria sporozoites actively enter and pass through rat Kupffer cells prior to hepatocyte invasion. Hepatology, 33: 1154–1165. doi:10.1053/jhep.2001.24237
Cha, S.-J., et al. CD68 acts as a major gateway for malaria sporozoite liver infection. J. Exp. Med., July 2015 DOI: 10.1084/jem.20110575
Klotz C, Frevert U. Plasmodium yoelii sporozoites modulate cytokine profile and induce apoptosis in murine Kupffer cells. International journal for parasitology. 2008;38(14):1639-1650. doi:10.1016/j.ijpara.2008.05.018
Viriyavejakul P, Khachonsaksumet V, Punsawad C. Liver changes in severe Plasmodium falciparum malaria: histopathology, apoptosis and nuclear factor kappa B expression. Malaria Journal. 2014;13:106. doi:10.1186/1475-2875-13-106.
Frevert U, Krzych U. Plasmodium cellular effector mechanisms and the hepatic microenvironment. Frontiers in Microbiology. 2015;6:482. doi:10.3389/fmicb.2015.00482.


Flicker fusion threshold for insect eyes

"The flicker fusion frequencies of six laboratory insects, and the response of the compound eye to mains fluorescent ‘ripple’" (Miall, 1978) touches on flicker fusion thresholds for six different insect species commonly used in laboratory settings:

  Locusta migratoria, Periplaneta americana, Saturnia pavonia, Antheraea pernyi, Glossina morsitans and Drosophila hydei.

I also found this paper: Potential Biological and Ecological Effects of Flickering Artificial Light (Boyles, 2014) that includes an exhaustive literature search of flicker-fusion thresholds and other related data for many species (including insects). If you're looking for an authoritative source, I'd say that this is it (as there doesn't seem to be a database with this information).


What is the origin of the name "λ phage"?

The original paper from Lederberg from January 1953 (see reference 1) indeed doesn't mention the origin of the name, but the paper in reference 2 does. It says:

  The isolation of λ was first reported in 1951 by Esther Lederberg
  (119), then a Ph.D. student at the University of Wisconsin, and later
  was described, in greater detail, in a 1953 Genetics paper by Esther
  and Joshua Lederberg (120). The discovery was accidental, when a
  λ-sensitive strain of Escherichia coli K-12 (W518, obtained after UV
  irradiation) was crossed with its parent. The mixture yielded plaques,
  and the source of the virus was the K-12 parent. W518 cells that
  survived infection became stable lysogens which, like the K-12 parent,
  were immune to superinfection and which released unaltered phage.
  Although the Lederbergs were initially opposed to the notion, crosses
  between lysogens and sensitive cells led them to suggest that λ
  prophage was chromosomal and linked to gal. Joshua Lederberg recalls
  that he was convinced, from earlier work of Burnet and Lush (21), that
  lysogeny was a real phenomenon but that he “fully expected lambda to
  be a [plasmid]—in fact the term lambda was modeled after Sonneborn's
  kappa [in Paramecium; see reference 156 for a recent review], so it
  was quite a shock to discover the contrary.” (In fact, years later
  Hideo Ikeda and Jun-ichi Tomizawa [98] showed that prophage P1, unlike
  λ, is a plasmid and not part of the host chromosome!)

The mentioned kappa particle in Paramecium is an inheritable cytoplasmatic symbiont and the Lederbergs thought of something similar for their discovery. My assumption here is that lambda was the next greek letter, hence the name. The publication in which Sonneborn describes Kappa can be found in reference 3, a short historical overview on the discovery of Kappa in the review in reference 4.

References:

Genetic Studies of Lysogenicity in Escherichia Coli.
Little lambda, who made thee?
Mating Types in Paramecium Aurelia: Diverse Conditions for Mating in
Different Stocks; Occurrence, Number and Interrelations of the Types
R-body-producing bacteria.


Estimation of tissue-partition coefficients and clearance for liposomic nanoparticles

Regarding the tissue partition coefficient, Li et al. said:  "By using such a parameter, it is assumed that there is the same transfer kinetics of nanoparticles from blood into tissues as from tissues back into blood circulation, and an equilibrium of concentrations between blood and tissue exists. These assumptions may not be appropriate for nanoparticles."

Physiologically Based Pharmacokinetic Modeling of Nanoparticles
Mingguang Li, Khuloud T. Al-Jamal, Kostas Kostarelos, and Joshua Reineke
ACS Nano 2010 4 (11), 6303-6317
DOI: 10.1021/nn1018818

However if you are set on using a tissue:blood partition coefficient (Kp), Yun and Edginton have done a review of 6 in silico methods for determining Kp for small molecules.  You may be able to extrapolate to nanoparticles.

Yun, Y.E., Cotton, C.A. & Edginton, A.N. J Pharmacokinet Pharmacodyn (2014) 41: 1. doi:10.1007/s10928-013-9342-0

Finally, if you are looking for data to help determine a partition coefficient, there is an excellent review of liposomal doxorubicin pharmacokinetic data in animals and humans here.

Gabizon, A., Shmeeda, H. & Barenholz, Y. Clin Pharmacokinet (2003) 42: 419. doi:10.2165/00003088-200342050-00002


Does repolarization of muscle fibers mean that the muscle bundle is relaxed?

No, macroscopically human muscle works by oscillation. This means that when a muscle is contracted (isometric contraction), some fibers alternatively contract through the actin/myosin process while some others relax at the same time. The end result is that the muscle as a whole keeps the same length, although it still does consume energy to stay in that state. That is why you get tired after some time of isometric contraction. To directly answer your question, it means that muscle in isometric contraction state will have some fibers depolarized, and others in resting state at any moment.


How can a polar molecule pass through polar channels of proteins in the cell membrane?

The molecule won't "stick" to the polar amino-acids for at least three reasons :

The amino-acids might not all be on the same plan, so their is always a force pulling the molecules transiting trough the channel in one direction (in or out the cell)
When  a flux is established, the repulsion forces between the molecules will force them to go in a direction, meaning that a coming molecule will basically push the ones already engaged in the channel.
For an ion or a protein, the water molecules constituting the hydratation shell of the molecule can't always follow it into the channel, so the water molecules present at the end of the channel (entry and end being relative to the direction of the flux) will more or less pull it outside the channel, as it is thermodynamically more stable to have a shell.  The fact that water molecules are able or not to follow the molecule depends on the size of the channel.

It's worth noting that water is itself a polar molecule, and that it can selectively cross the membrane thanks to channels called aquaporins.


Ammonium sulphate precipitation assay pH dependence

I think it would affect some proteins, but ammonium sulfate precipitation usually requires such large amounts of salt, that you would have to add a lot of base to adjust the pH.

When I have done ammonium sulfate precipitation, its to take a rough cut of proteins out of a whole cell/whole organ lysate - its more like a hammer than a pair of tweezers as far as protein purification is concerned.  I would rather use a charged plastic resin or a sizing column if I were to care about the isoelectric purification.


What do nerves have to do with feeling nervous?

As buzrw's first comment states, most nervousness is primarily a sympathetic nervous system response.

There are also neurotransmitter imbalances involved with anxiety, especially in anxiety disorders.  The NT are dopamine, serotonin, and norepinephrine.

I want to clarify buzrw's comment on nerve cell regeneration, as I am unsure if he is stating it's proven to exist or to not exist.  "Primary neurons are not readily mitotic..." makes me think it's the latter.

Neuroregeneration is proven. Mayo Clinic has good information here and this is a well-phrased simplified answer here.

It is more commonly seen in peripheral nervous system, as the central nervous system has limited capabilities to regenerate.  Mostly it is regrowth of severed axons of  cells, and differs between different nerve cell types.  There are other types of regeneration as well.  They involve many physiological processes we're only starting to understand, such as the role of neuroligin.  Without getting too technical, there is a lot that can be done to help stimulate and guide the regrowth of some neural damage, but there are still chasms in our knowledge in the fields of neurology and psychiatry.


educational sources for learning biochemistry

There are several reference books for biochemistry, some more readable than others. I personally recommend two of them: (1) Lehninger et al. Principles of Biochemistry and (2) Voet, D., Voet, J., et al. Fundamentals of Biochemistry: Life at the molecular level. Both books contain the most important and basic features of each subject. The chapters are generally well written. I have to say that, from my own experience, I consider that Voet's book is more enjoyable, given that some of the sections of Lehninger's can be a bit tricky. Whichever book you choose, make sure you get relatively new editions. Good luck!
As a side note, even though biochemistry is one the first proper biology classes one takes in undergrad, there are some background requirements. Taking organic and inorganic chemistry courses before is important and some understanding of thermodynamics will certainly come in handy.


Do large animals often evolve into smaller animals?

Your question brings up several important issues with regards to the evolution of body size. The rationale for concluding that the ancestral mammal had a small body size is that all of the taxa in that area of the tree tend to be small. In contrast, if all of those taxa had been cow-sized, then the most parsimonious conclusion would be that the ancestral mammal was cow-sized.
Identification of ancestors is difficult
Identification of a fossil species as the most recent common ancestor of a pair of sister taxa is exceedingly difficult. The way that different species are diagnosed in fossils in by their unique derived characteristics (autapomorphies). So if a fossil is found with no autapomorphies, then it is plausibly an ancestor (i.e., at the split between two sister taxa). Some would argue that if you don't find any autapomorphies, then you just haven't looked closely enough.
Cope's Rule
The idea that lineages tend to evolve toward larger body size is known as Cope's Rule, named for the paleontologist Edward Drinker Cope. The success of Cope's Rule has been highly variable, with some lineages following and others not (Polly, 1998).
Some clades following Cope's Rule

Early reptiliomorphs (Laurin, 2004)
Pterodactyloidea (Hone and Benton, 2007)
Most Cambrian-Devonian marine invertebrates (Novack-Gottshall, 2008)
North American canids (Van Valkenburgh et al., 2004)
Mesozoic birds (Hone et al., 2008)

Some clades not following Cope's Rule

Early stegocephalians (Laurin, 2004)
"Rhamphorhynchoid" pterosaurs (Hone and Benton, 2007)
Mesozoic birds (Butler and Goswami, 2008)

Note that many results depend on the methods used.
Evidence from experimental evolution
Several studies have addressed body size evolution in vertebrates both directly and indirectly. MacArthur (1944a, 1944b) directly selected for large and small body mass in laboratory mice. Within 8 generations, mean body masses had increased or decreased by over 50%. Even when body mass is not directly selected upon, mass can change in a correlated way. Selection for high levels of voluntary activity has led to an approximately 25% reduction in body mass.
Based on these studies, evolution of body size (larger or smaller) is certainly possible within relatively few generations.


What is difference between plastid, chloroplast and mitochondira?

Plastid is a general term for an organelle which consists of Chloroplasts, Chromoplasts, Leukoplasts/Amyloplasts and Apicoplasts.

Chloroplasts (Chloro = green) are involved in photosynthesis; they express Chlorophylls and have the thylakoid structures which are involved in the electron transport chain that results in ATP formation during the light reactions of photosynthesis. As it is obvious chloroplasts are found in the green parts of the plants such as leaves. Chloroplasts also have the enzymes of biosynthetic pathways involved in carbon fixation.

Chromoplasts (Chromo = colored) express more of other pigments and less of chlorophyll. Neither do they have thylakoid structures. Therefore they are not involved in photosynthesis. When fruits ripen, the chloroplasts differentiate to chromoplasts. Flowers also contain a lot of chromoplasts.

Leukoplasts (Leuko = white) do not have any pigments and usually carry out biosynthetic processes. When they store starch they are called amyloplasts.

Apicoplasts are found in parasites like plasmodia (causes malaria) and are vital for their survival. The Apicoplast is involved in biosynthetic pathways but the precise importance of it remains unknown.

The mitochondrion is a very different organelle and has a different evolutionary origin. Mitochondria, like Chloroplasts, produce ATP from an electron transport chain but use chemical substrates (NADH, flavin etc) rather than light as a source of initial energy. Mitochondria are thought to be an outcome of an endosymbiosis between an ancestral eukaryotic cell and an $\alpha$-proteobacterium. Chloroplasts, on the other hand have descended from a Cyanobacterial endosymbiont. Therefore the structure of mitochondria is very different from that of chloroplasts.

Chromoplasts, leukoplasts, amyloplasts and apicoplasts have lost the photosynthetic ability. Similarly, there are variants of mitochondria which use different electron acceptors (other than oxygen) and some are just incapable of ATP synthesis.

  Are there any plant sequence database for each of them (plastid,
  chloroplast and mitochondira)?

Chloroplast genome database: {link}

I don't know of a separate plant mitochondrial database but you can see this resource called MitBASE.

NCBI also has the organellar DNA sequences.

  Can we separate as chloroplast, mitochondria, platid sequence from
  whole genome assembly?

Usually the organellar genomes will assemble as separate contigs when you sequence from the whole cell DNA prep. By homology it is possible to say if the contig is a mitochondrial or chloroplast DNA. But the best way would be to experimentally isolate the organelles and sequence their DNA.


All cases of same species grooming I know of involve animals with a certain amount of dexterity. For example (images from wikipedia):

Macaw beaks:

Primate fingers:

Even ponies rubbing each other:

In all of these cases, the animals involved have the right tools for the job. fingers, beaks and prehensile lips can all close in on a parasite and remove it with precision. how exactly would you expect a shark to do this (image from the guardian)?

Sharks can and do rub themselves against rocks to get rid of dead skin but they simply don't have the tools for the kind of detail work that the smaller fish can do for them. The same applies to other fish. I think you will find that at least in most cases, fish that use client species to groom themselves wouldn't be physically able to do the same job themselves. It's all a matter of the right size and the right tools.

Note that this is pure speculation, I have no references to back this up, it just seems reasonable. I would not be surprised if some fish did actually indulge in social grooming, it's just harder for the reasons outlined above.


Unfortunately, this is not a fossil, but a pseudofossil: a pretty deposit of iron or manganese called a dendrite.


What is the distinction between F' plasmid and R plasmid?

If I understand the nomenclature correctly, an R plasmid is just any plasmid containing an antibiotic (R)esistance gene (eg. Amp, Kan, Cm, etc.). It's a bit of an outdated name from when people didn't know how exactly the plasmids conferred such resistance.

An F-plasmid is any plasmid that contains the genes necessary for (F)ertility, eg:horizontal gene transfer via the tra operon.

The two do not have to appear together -- eg: Many F plamids will contain resistance genes (along with other random chunks from the genome), but resistance doesn't always have to be part of the payload. Likewise, it is common in labs to build pure resistance vectors that lack any horizontal transfer capability in order to select for particular clones.


These enzymes are named by the bacteria and the strain from which they are isolated. For BamHI this is Bacillus amyloliquefaciens strain H. In the beginning the enzyme was named BamI, which was later changed to BamHI.

See these two references:

Isolation of a sequence-specific endonuclease (BamI) from Bacillus
amyloliquefaciens H.
Recognition sequence of specific endonuclease BamH.I from Bacillus
amyloliquefaciens H.

The same is true for all the other restriction enzymes, so is EcoRI the first restriction endonuclease isolated from Escherichia coli strain R.


Knockdown of long noncoding RNA (lncRNA) - how is it done?

Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the RNase H enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.

UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I found this paper to quote:

  Although we (Fig. 3A) and others (42, 49) have used siRNA to knock down NEAT1 lncRNA and although the knockdown of strictly nuclear RNAs has been well described (53, 54), we remained concerned that because NEAT1 is mostly a nuclear RNA (55), it may not be very efficiently targeted by the RNAi machinery. Nuclear RNAs, however, are proficiently targeted using complementary antisense (AS) oligodeoxynucleotides that recruit nuclear RNase H activity to degrade the RNA (56). Hence, we also employed complementary AS oligodeoxynucleotides to knock down NEAT1 lncRNA in HIV-1 NL4-3-infected Jurkat cells (Fig. 4C, left). The AS approach reduced NEAT1 (Fig. 4C, left) and increased HIV-1 p24 production (Fig. 4C, right), providing results consistent with those from siRNA-mediated knockdown of NEAT1 (Fig. 4A and B).


Peptide oxidation bias during sample preparation for LC-MS/MS

I know this was posted a long time ago and I'm not sure if you have found your answer but I am an author on two of the publications you  andcite can offer some insight.
1.) Methionine oxidation, unlike cysteine oxidation, is irreversible without the action of a dedicated enzyme or catalyst. Neither TCEP nor DTT is able to reduce methionine sulfoxide. The only reducing agent that I know of that is strong enough to reduce methionine sulfoxide is MMA.
2.) The in-vitro oxidation of methionines during sample preparation is a well documented issue in LC-MS/MS analysis and it is known that the majority of in-vitro oxidation occurs during peptide digest as well as during electrospray ionization. The strength of the effect is highly variable and dependent on how long you digest proteins. For a typical overnight digest we observe effects that range from 0%-400%, depending on the peptide.
3.) The use of 18O labelled blocking reagents is the only currently available method that can prevent the accumulation of in-vitro oxidation. I'm the first author on the publication you cite and would be happy to send you a copy if you email me (jbetting@ur.rochester.edu) I have also been working on improved methods using the same general strategy and would be happy to share those with you after publication


How can I detect which antibody is produced by the B cell?

The major antibody in the second exposure is IgG and in the first exposure it is IgM. IgG and IgM would be produced by Plasma Cells, which are effector B-Cells activated by Cytokines.
If you want to see which antibodies (not just antibody types) are produced by the B-Cell, I would suggest transforming a GFP gene into a Naive B cell and using a Restriction Endonuclease and DNA Ligase to insert the GFP gene to the 5'-end of the Constant (C) region of the Antibody producing gene. Then, you could see which Antibodies are produced by B-cells since the Antibodies would fluoresce.
Note: I am currently in high school so I don't have much experience with Immunology, so there might be a few things wrong about my answer. However, I tried my best to answer the question. Hope this helps!!


Brain regeneration - book recommendation

Neural regeneration is addressed broadly in this chapter from a book published in 2013 (though I would say for a topic such as this, you're probably going to want to read primary literature or recent, less comprehensive reviews in addition to any book chapters published in the few years):

Neural Regeneration by Melissa M. Steward, Akshayalakshmi Sridhar, Jason S. Meyer, published in New Perspectives in Regeneration.

The chapter includes two sections on stem cell therapy and one section on reprogramming of somatic cells to neural lineages.


When the sister chromatids are joined in the centromere, why is it stated that the number of chromosomes is 46 and not 72?

When I was learning genetics for the first time I have also found naming the two chromatids joined at centromere as chromosome a little bit strange. The number of DNA molecules and their behaviour in cell cycle seemed to me more important for understanding of genetics.
What you need to understand.is the term chromosome predates knowledge of DNA structure. The name literally means colored (chromo) body (soma). It is an object visible under the microscope when using specific dye. In metaphase two chromatids joined at centromere look like a single object - a chromosome. Sometimes the two chromatids of one chromosome are so close together it is difficult to tell them apart. In anaphase the chromatids separate and one object (two-chromatid chromosome) visibly splits to two objects (single-chromatid chromosomes of daughter cells)


Identifying structures from anterior end of dissected prawn

I guess you got your antero-posterior axis wrong. If I am correct then anterior is right and posterior is left in your image. In that case the black structure should be the cerebral ganglion and the red should be the heart. See the image below.


In plant cells, is water stored only in the vacuole?

One of the properties of "storoge" is that in can be filled or empied when needed. Contents of cytoplasm and all organelles are aqueous solutions so all of them contain quite some water. However, thease solutions need to maintain precise concentration of many solutes in order to facilitate proper enviroment for various biological processes. Therefore, radical changes in amount of water in cytoplasm would be detrimental to life of the cell. Vacuole is not as sensitive and it can expand or shrink and act as a sort of water availibility buffer for the rest of the cell.


Feeling warm and cool breezes - how does it work?

You have many different types of sensors in your skin; you probably feel the pressure of the air moving past your hand in addition to the temperature.

The temperature increase in your hand due to collisions isn't very significant, you have to be going at really high speeds to encounter that phenomenon (spacecraft reentry would be an extreme example, for example see this wikipedia page).

Temperature changes due to evaporation are probably most significant (this is why even warm air blown from a fan can feel cool, especially if you are perspirating), as well as the temperature of the outside air around your hand compared to the air inside the car.


It's a type of centipede.

Based on the long legs, I would bet on something like that:
http://en.wikipedia.org/wiki/Scutigera_coleoptrata

Or at least a Scutigeromorpha http://en.wikipedia.org/wiki/Scutigeromorpha#Scutigeromorpha


Is there evolution in humans since the first homo sapiens sapiens

We continue to evolve all the time: http://www.npr.org/2013/09/27/226837803/modern-humans-still-evolving-and-faster-than-ever

  For those who think the forces of natural selection no longer apply to modern humans, paleoanthropologist John Hawks would urge you to reconsider. In recent times — that's 10 to 20 thousand years, for a paleoanthropologist — Hawks says we've picked up genetic variations in skin color, and other traits that allow us to break down starch and digest cheese.

Homo sapiens sapiens is over 100,000 years old and we have changed in many ways since then, as noted in the above NPR article!

I'm not sure we can say there is a "first" homo sapiens sapiens -- the change from one species to another is gradual.  You may know that mixing red and blue gives purple, but at what points do we officially have red, purple, or blue when mixing different levels of red and blue?


The confusion here is quite common (at least it was quite common among my students): the "segments" in a tapeworm like Teania, properly called proglottids, are not really segments, or metamers.

According to Hickman et al. (2001), in the chapter 17, Segmented Worms:

  Body segmentation, or metamerism, in annelids is not merely an external feature but is also seen internally in the repetitive arrangement of organs and systems and in the delimiting of segments (also called metameres or
  somites) by septa. Metamerism is not limited to annelids; it is shared by
  arthropods (insects, crustaceans, and others), whose metamerism may be
  homologous to that in annelids, and also by vertebrates, in which it evolved independently.

Some pages before, in chapter 14 (Acoelomate Bilateral Animals), the authors say:

  Some zoologists have maintained that the proglottid formation of cestodes
  represents “true” segmentation (metamerism), but we do not support this view. Segmentation of tapeworms is best considered a replication of sex organs to increase reproductive capacity and is not related to the metamerism found in Annelida, Arthropoda, and Chordata (see pp. 193 and 371).

I'm citing Hickman, but all zoology books I'm aware of (Ruppert-Fox-Barnes, Brusca & Brusca, etc...) will say the same: segmentation is synonym of metamerism, and Plathyhelminthes (including Teania) are not segmented animals.

Source:

Hickman, C., Roberts, L., Larson, A., Ober, W. and Garrison, C. (2001). Integrated principles of zoology. 1st ed. Boston: McGraw-Hill.


Which organism has the smallest genome length?

Since you said plant/animal/anything, I offer the smallest genomes in various categories...

(Kb means Kilobases, Mb means Megabases. 1 Kb = 1000 base pairs, 1Mb = 1000Kb)

Smallest plant genome: Genlisea margaretae at 63Mb (Greilhuber et al., 2006)
Smallest animal genome: Pratylenchus coffeae (nematode worm) at 20Mb (Animal Genome Size DB)
Smallest vertebrate genome: Tetraodon nigroviridis (pufferfish) at 385Mb (Jailon et al., 2004)
Smallest eukaryote: Encephalitozoon cuniculi (microsporidian) at 2.9Mb (Vivarès & Méténier, 2004)
Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003)
Smallest bacterial genome: Carsonella ruddii (endosymbiont) at 160Kb (Nakabachi et al., 2006)
Smallest genome of anything: Circovirus at 1.8Kb (only 2 proteins!!) (Chen et al., 2003)

Refs...

Chen, C.-L., Chang, P.-C., Lee, M.-S., Shien, J.-H., Ou, S.-J. & Shieh, H.K. (2003) Nucleotide sequences of goose circovirus isolated in Taiwan. Avian Pathology: Journal of the W.V.P.A. 32 (2), 165–171.
Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S. & Barthlott, W. (2006) Smallest Angiosperm Genomes Found in Lentibulariaceae, with Chromosomes of Bacterial Size. Plant Biology. 8 (6), 770–777.
Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431 (7011), 946–957.
Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H.E., Moran, N.A. & Hattori, M. (2006) The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella. Science. 314 (5797), 267–267.
Vivarès, C.P. & Méténier, G. (2004) Opportunistic Infections: Toxoplasma, Sarcocystis, and Microsporidia. In: World Class Parasites. Springer US. pp. 215–242.
Waters, E., Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proceedings of the National Academy of Sciences of the United States of America. 100 (22), 12984–12988.


JMol "calculate HBONDS": which atom is the donor/acceptor?

I dont know about JMol, but this can be easily done with UCSF Chimera.

I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond

I kept the default values and selected Write information to reply log

Then clicked OK

On the structure the H Bonds will be identified with a coloured line.

To view which is the donor and acceptor go to: Favorites > Reply log

An output of the reply log is below:

H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ASP 12.A N    GLU 25.A OE2  no hydrogen  3.012  N/A
HIS 13.A N    GLU 25.A OE1  no hydrogen  3.338  N/A
HIS 13.A ND1  ASP 12.A OD2  no hydrogen  2.835  N/A
LEU 14.A N    TRP 70.A O    no hydrogen  2.934  N/A
TRP 15.A N    ARG 23.A O    no hydrogen  2.866  N/A
...
120 hydrogen bonds found

As you can see the donor and acceptor has been identified as defined in the header line.

If you wish, the information can also be written to a file by selecteing Write to text file in the FindHBond window.


Coracoid vs. Coronoid - Etymology/Naming Choice?

It appears that both naming conventions originate with Galen, the Greek physician, almost 2000 years ago (for example, see: Singer, 1952).

Although the precise motivations behind the naming conventions aren't entirely clear, it seems that the origin of the coracoid naming convention is quite simple: Galen thought it looked specifically like a raven's beak, as you state, rather than the beak of some other bird.

Fortuine (2000) seems to suggest that the origins for both words originally applied to beaks of different birds, which implies that Galen may have thought some bone structures looked like beaks of one bird, and other bone structures looked like the beaks of another bird, so he used the corresponding terms of description. Specifically, "korōnē" may have referred to a crow or cormorant (I feel like the cormorant link makes more sense, though both are supported by Arnott (2007) - it may not be possible to know how the distinction was applied from surviving texts), as well as referring to a hooked shape. The same source mentions several other bird-derived terms, including the coccyx resembling the beak of a cuckoo and "rostrum" used more generally for beak-like structures.

Today, coronoid and coracoid may sound similar enough to be easily confused by students of medicine. However, giving these different bones distinct names does allow for some useful shorthand, such that one need not refer to the "coronoid of the scapula": I would assume, though I'm not sure if it is possible to find a good reference on this, that this is the motivation to keep things as-is, besides of course the history.

References

Arnott, W. G. (2007). Birds in the Ancient World from A to Z. Routledge, New York.

Duckworth, W. L. H., & Lyons, M. C. (2010). Galen on anatomical procedures: the later books. Cambridge University Press.

Fortuine, R. (2000). The words of medicine: sources, meanings, and delights. Charles C Thomas Publisher.

Singer, C. (1952). Galen's elementary course on bones.


This is one of the most intriguing questions of eukaryotic evolution. As far as I know and have read, the autogenous theory is not accepted. There are quite some reviews on this topic. Also there is a wonderful book by Nick Lane on mitochondria called Power Sex and Suicide. You would be interested to read it.

There are no sufficient evidences for the evolutionary transition from prokaryotes to eukaryotes which somewhat suggests that this was some kind of quantum jump. For example:

There are no microfossil records for the evolutionary intermediates
Almost all eukaryotic features including organelles, syngamy, nucleus etc emerged simultaneously

So to answer how it exactly happened is quite difficult.

As for the autogenous theory; it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without an organelle like mitochondria i.e. a prokaryote as large as a eukayotic cell wouldn't survive. You may check this post.

There are eukaryotic cells that lack mitochondria (eg. Entamoeba histolytica ) or have one with reduced functionality. However, these are not intermediates in evolution but have lost the functionality in a retrograde manner.

There is one more evidence to support the endosymbiosis theory:
There is this observation that organelles that are less numerous in a cell have retained more of their genome compared to those with the organelles that are surplus numbers (eg. plastids vs mitochondria). This is called the Limited Transfer Window Hypothesis which reasons that the organelle to nuclear gene translocation would have happened because of organellar injury and the likelihood of a cell tolerating one is higher if there are more number of organelles.

This article suggests an alternative view that predatory bacteria like Bdellovibrio could have settled in a prokaryotic host. There are other cases of bacterial endosymbiont in a larger bacteria (I need some time to mine up the reference. Read it a while back) but these are not the the ancestors of eukaryotes.


What would cause proteins to get stuck in the stacking layer of a SDS-Page gel

At the interface of the stack gel and resolving gel is a pH change and a change in gel density.  If you feel certain that your protein is not crosslinking so much that it can not enter the gel than I would think about the pH of the sample and the effect of Cu ions on the stacking effect of the stacingk gel.  Is your sample the normal blue color (indication of pH) when you load it (compared to other samples you load)?  Are you overloading the gel?  I have seen overloading cause the effect you describe because the proteins get concentrated to a very high degree before entering the resolving gel.  Could the Cu ions be affecting stacking itself?

Read http://en.wikipedia.org/wiki/SDS-PAGE.  Specifically the section on buffer systems.  You might want to try a different buffer system.

Finally, you could try an acetone precipitation to try to remove the Cu ions and other chemical and see if that helps.


Are there any DNA base sequences that are fully conserved between the genomes of all humans?

In 2004 Bejerano et al. identified "481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes". These were found to be mostly in/around genes related to RNA processing, which is perhaps unsurprising given that it is such a primitive/inherent biological process.

Bejerano's paper has been cited over 500 times on Scopus, with numerous papers reporting variants in such regions that cause diseases such as colorectal adenocarcinomas.

So few conserved regions exist because there is plenty of redundancy in the genome; many genes functionally overlap with others, and many genetic variants are 'silent' - they have no effect on the phenotype. Having this variability is advantageous in Darwinian terms because this increases the evolvability of the species.

There are many regions of very high homology between individuals (protein-coding regions are highly conserved even between species), but there will still be natural variation; each mutations effect will be dependent on the rest of the genome. Genes work together to produce a working organism - they do not each code for a little 'bit', and therefore a change in one portion of the DNA may be 'balanced' by a change elsewhere.

It is only in 'ultra-conserved' sequences that mutations are presumably incompatible with life because the process is so finely-tuned and indispensable.


What do we mean by distribution of species?

Welcome to Biology.SE!

  Species distribution is the manner in which a biological taxon is spatially arranged.

In the specific sentence you suggest, it seems that the term species range would have eventually be a little bit more appropriate though. The species range is the delimitation over space where individuals are found. The species range is just the maximum value in every possible direction of your species distribution.

Note however, that we often don't care too much about such semantic details (the sentence sounds correct to me).

Next time, please specify where you get the citation from 1) because context often matter and 2) because it is a copy right issue to not cite your source.

Same as above in simple terms

The term species distribution (and species range) describe the geographical locations of individual of the population (of a species). We are talking about a single species here. The term distribution takes the same definition than it does in statistics if you are used to it.

Imagine you have a population of oak trees. You can position every single individual tree over space Consider the drawing

Each individual is represented by a circle. The blue line represents a river.

Description of the species distribution: There are no individuals south east of the river. There is a clutch of high density at the north west of the study area.

Description of the species range is given by the red circle

The difference between species range and species distribution does not matter much for your purpose. The point is that you understand those terms are concepts describing the geographical locations of individual of the population (or the species if you prefer)


Why are low throughput methods more trustable for protein interaction?

This article is a bad example, it has been retracted. See here.
But this doesn't matter for the methods.
This is usually done by so called "genome wide association studies". There you compare the regulation of your group of interest with a "normal" group to find genes which are differently expressed. This is something we did: We overexpressed a transcription factor in a cell line and compared it to the untransfected cell line, which doesn't have this factor. The comparision brings up differently expressed genes. This is either done with microarrays or today more like by ChIP-sequencing (let me know, if you want to know more, I can go into the details).

When you analyze such data, you first cut-off all data, which is below a certain threshold to be sure, that you reduce the number of false positives. A low threshold for the recognition of changes means that you are more likely to have false positive genes in your final list. This might happen due to changes in the cell or the conditions, secondary effects and so on. And you will also have signals, which appear statistically and which are false positive.

If you choose your threshold too high, you will reduce the number of false positives, but on the downside you will also generate false negatives, since you refuse genes which only have a relatively low change but are real. The balance between this is not always easy. As a rule of thumb usually everything which changes at least twofold in expression is used (unless you control better).

Even when filtered, the output of the experiment will still contain some false positives. Then you will also record some secondary effects, meaning that you gene of interest regulates a second, which regulates a third. Since both will come up in the analysis, it will look like that the third gene is regulated by the first (and not the second, as it would be correct). And these are the reasons why usually every intereaction between two genes (or better: Between a protein and a gene when talking about a transcription factor or two proteins) needs to be verified in the wet lab. And this is work, which can be pretty hard.


How do the antibodies in colostrum survive the infant’s digestive system?

There are two main differences between adults and newborn babies which allow the passage of antibodies (while maintaining the activity) through the stomach and the resorption in the gut.

The digestive activity of the stomach in newborns is still immature and needs to develop. This results in almost no production of hydrochloric acid (which is responsible for the very low pH in the stomach). It can take up to two years to until the pH in the stomach of children reaches the level of adults (see chapter 5 in reference 1).  Because of this higher pH much more proteins (and other components of the milk like anti-microbial proteins, carbohydrates and lipids) can pass the stomach unaltered.
The other really important feature of newborns is their much greater permeability of their intestine. This allows an efficient transport from the antibodies into the blood stream and where they provide protection. See references 2 and 3 for more details.

References:

Breastfeeding and Human Lactation
Antibodies in  Milk
Intestinal permeability in the newborn


Which poison makes seastars inedible to possible predators?

Asterosaponins are the class of compounds - they have a cholesterol like organic core.

Apparently, these saponins make pore-forming complexes with Δ5-sterols of cell membranes, and so are deadly to all usual kind of life, including bacteria and fungi. Quote:

  Starfish and sea cucumber cell membranes are resistant to their own
  saponines due to the presence of Δ7- and
  Δ9,11-sterols, sulfated Δ5-sterols, and
  β-xylosides of sterols instead of the free Δ5-sterols.


First of all, cold and flu viruses are not 'simple viruses', and they are not harmless. They kill tens to hundreds of thousands of people every year.

Secondly, this would depend highly on the risk group that the virus falls in. The NIH sets strict guidelines on who can handle infectious agents. Unfortunately, I can almost guarantee you that no one is going to give you even risk group 1 plant viruses, and they are certainly are not going to give you cold or flu viruses. Risk groups range from 1 to 4. To handle risk group 2 viruses, for example, you are expected to do so in a BSL-2 or higher laboratory, and anyone maintaining stocks of virus is going to do a hefty check of you and your 'facilities' before shipping you anything.

Furthermore, even if you did obtain the virus, you would need to store it or maintain stocks of the virus in tissue culture. Its not like you can just get an eppendorf tube of virus in saline and expect it to survive in your refrigerator at home, and its not like companies are shipping virus willy-nilly to anyone.

That being said, and at the expense of sounding self-righteous, there is really no reason for you to obtain virus particles. You should start by getting a book on virology and reading it. There is plenty of learning material both visual and written out there, and all I will say is if you don't already know how to culture virus or where to obtain it, you shouldnt be doing so, and no one is going to give it to you.

CDC Biosafety in Microbiological and Biomedical Laboratories: http://www.cdc.gov/biosafety/publications/bmbl5/BMBL.pdf

WHO Laboratory Biosafety Manual: http://www.who.int/csr/resources/publications/biosafety/en/Biosafety7.pdf

NIH guidelines recombinant nucleic acids: http://osp.od.nih.gov/sites/defaul/files/NIH_Guidelines.html

I think its great that you are interested, and it sounds like you are interested in histopathological changes caused by virus, so I have included some nice histo pictures below

Syncytia (Herpes Simplex Virus type 1)

Clearer example of syncytia

Characteristic owl-eye (Cytomegalovirus)

Distemper virus inclusion body

Coronavirus particles with 'crown' of surface glycoproteins

Budding HIV virus particles from the plasma membrane

Bacteriophage T4 escape by lysis

Papillomavirus

Rous-sarcoma virus

Tobacco mosaic virus


Its pretty well established that there are photoreceptors in cells besides the cones and rods in the retina of the eye.  Humans and most animals have four light receptor genes known (so far).  In addition to Rhodopsin - there are the short, med and long wavelength opsin genes.

While they are mostly expressed in the retina of the eye, they can be found in many other tissues as well. The first image from GeneAtlas below shows the relative amount of RNA found for short wavelength opsin in a variety of tissues - its expressed in immune and nerve cells ( cyan and forest green respectively) relatively well too.   This might imply that neurons are light reactive.  Compare that to that of medium wavelength opsin, which is primarily much more common in the retina.

This is not a psychosomatic effect.  Light receptors in the skin are known to help with seasonal affective disorder - shine a bright or blue light behind your knees.  These receptors are not connected to optical nerves, and so you don't get any image from them, but the information can affect your biochemistry anyway.

The idea of unconscious receptor inputs from other parts of the body probably applies to many sorts of receptors.  This last year there has been a great deal of interest in taste receptors which are expressed in the gut.  They can taste sweetness and other flavors a second time and register the gustatory response in the brain.  Its not a conscious input, but it registers in the brain in MRI.

Why would evolution do this?  It seems to me that this is a new way of looking at the individual life of a cell and makes a good deal of sense.  If every cell has all the genes' DNA why wouldn't a little bit of receptor expression be found in any cell which could use the information?  The conscious processes of the brain probably only take in a small fraction of the information that is sent in and there maybe hundreds of other such senses from various parts of the body to integrate, only a fraction of which we are aware of.

In addition, there are probably lots of cases where receptor signals are only used locally by cells that are sensing their local environment.  It really doesn't make sense that the individual cells must blind themselves.  Individual bacteria and fungi have scores of receptors.  It makes sense that cells that are part of an organism would have as many or more senses as well.


Would it be correct to state that any biological difference between the sexes has to be found in the Y chromosome?

"Blame" is a strong word.  The human Y chromosome has only a few dozen protein-coding genes.  One of the most important, for males anyway, is SRY, the sex-determining region.  This is a transcription factor that is responsible for modulating the expression of other genes; those genes need not be on the Y chromosome.  SOX9 for example is itself a transcription factor, is upregulated by SRY, and is found on chromosome 11.  Most of the genes associated with maleness are found elsewhere.  Moreover, once the testes form, they can be potent secretors of hormones that cause a number of physical changes.  So is SRY to blame, or SOX9, or the testes?  It depends on how direct you want your genes to be.  If you're blaming SRY you're not wrong, but at that point you might as well blame fate.

Oh, and there are epigenetic differences between the sexes.  You could also make some arguments about the Xist gene responsible for X-inactivation in females.


Does ingestion of alcohol with methylphenidate make it act more like dexmethylphenidate?

Does the ingestion of alcohol, when taking (racemic) methylphenidate can actually make it more potent?

It is the 2011 study you've mentioned that answers most of the question.

In the study, ethanol co-ingestion with racemic MPH elevated maximal plasma levels of d-MPH by up to 40%. The participants reported greater stimulant effect after alcohol + MPH than after MPH alone (Table 2).

Now, the completely different question is if such combination of alco + MPH is also beneficial and safe.

Also:

  MPH–ethanol coabuse has been widely reported in both annual Drug Abuse
  Warning Network data and the clinical literature.


Is it possible to stop yourself from going into shock?

There are different types of shock: hypovolemic, cardiogenic, anaphylactic, septic, neurogenic, etc.

Can you prevent yourself from going into shock by virtue of pure willpower? No. You cannot override the body's reactions to decreased oxygen to the brain any more than you can will yourself out of the flu.

The early signs of hypovolemia (blood loss), though, can be confused with those of vasovagal syncope (simple fainting). Both involve dizziness/lightheadedness, cool or clammy skin, and a decrease in blood pressure. However, with hypovolemia, your heart rate increases to compensate for the lowering of blood pressure (which eventually leads to shock), whereas with vasovagal syncope - which can occur with sudden fear - your heart rate drops, which is what causes your blood pressure to fall.

Passing out due to blood loss depends in part on how rapid the blood loss is (the more rapid, the earlier on might pass out) and the volume lost. To lose enough blood to pass out, a healthy, normally hydrated person would need to lose about 2 liters of blood (or 20% of one's blood volume); maybe 1.5 liters if it happens quickly enough.

Regardless of whether it happens slowly or quickly, if enough blood is lost, shock will ensue. No amount of willpower will stop it.

Interestingly, the sight of blood or having your blood drawn are frequent triggers of vaso-vagal syncope.

What you experienced is commonly called pre-syncope: the feeling of lightheadedness as though one might blackout, but consciousness is preserved.

Vasovagal syncope
Hypovolemic shock
HEMORRHAGIC SHOCK


Are there lifeforms that have more than 2 sexes?

There exists something like multiple sexes in fungi, but it's a bit complicated.

First of all fungi don't actually have anything that represents the two classical animal sexes, phenotypically their reproductive cells are all equal (they have isogamic reproduction).
However there can be certain alleles in some fungi species (sometimes multigenic, sometimes not), that restrict sexual reproduction to other fungi with a different variant of that allele, these alleles are therefore called mating types. It is however important to note, that almost all fungi can also reproduce asexually (by basically cloning themselves).
In general all of the mating type systems always require only 2 individuals to (sexually) reproduce, it just can't be 2 individuals with the same type.

In their simplest form mating types resemble the male/female sex we often see in animals: for some fungi (e.g. yeast) there exist exactly 2 forms of the mating type allele (called a and $\alpha$), so basically they have '2 sexes' (though genetically/biologically the difference is MUCH smaller).

There are however also much more complicated mating type systems:
Some species of the Basidiomycota or Agaricomycotina groups have a tetrapolar mating type, which is composed of 2 independent alleles (with 2 variants per allele this would already results in 4 different 'sexes'). Additionally they can have many more than 2 forms for each of the alleles (up to hundreds), which leads to (ten-)thousands of different mating type combinations (or 'sexes').


Questions about what a productive cough actually is and where it comes from

When I'm sick with a productive cough, what is the stuff I'm coughing up (?)

If we're talking about a productive cough, you're most likely coughing up mucus, which is a thick (highly viscous) liquid that functions as both a lubricant to the internal behaviors of the body, as well as a defense against foreign particulates from getting too far within the body (e.g., breathing in dust through the nose and preventing it from traveling into the lungs).

  is it coming from my lungs (?)

Mucus is produced all throughout the respiratory tract by mucosae. However, since you're talking about coughing up mucus (as apposed to it running from your nose), it's probably originating from the lower respiratory tract. So, yes!, it's quite possible that the mucus is coming from your lungs.

  how come it doesn't hurt a lot and trigger a violent cough like if I got even a single drop of water down the wrong hole (?)

Hmm.. I think this is a bit more difficult to address. First off, as previously mentioned, mucus has a much higher viscosity than water does. Because of this, it could be that water more violently moves around while being coughed up, whereas mucus may remain more intact, thus causing less (increased) agitation.

It could also be that, because the trachea (the "wrong hole") isn't as accustomed to coughing as the esophagus is, then increased sensativity is experienced (relative to what's felt when coughing within the esophagus).


How can I convert plate reader measurements of Pichia pastoris OD to cells per ml?

From a technical perspective, for the FlopR package you mention (and I believe also for Jacob Beal's protocol) you can simply change the bead size and perform a new calibration. The only information that you need is the bead count at each point of your calibrant curve.
However, using calibration beads of a given size assumes that your cells will remain approximately the size of the beads for the duration of your experiment. We know that cell size and shape vary based on growth phase, antibiotics etc. [1] This can cause substantial misreporting of cell counts but is currently brushed under the carpet. I would suggest that if your Pichia change significantly in size or shape during their growth, it would be worth using a range of beads sizes and attempting to calibrate different growth phases of your samples against beads that correspond to cell size at during that phase.
[1] K. Stevenson, A. F. McVey, I. B. N. Clark, P. S. Swain, and T. Pilizota, “General calibration of microbial growth in microplate readers,” Sci. Rep., vol. 6, no. 1, p. 38828, Dec. 2016.


Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks

I was in a car accident age 19. Jaw was wired shut, food access was limited to one broken front tooth. It was liquid diet or nothing.
 So, I drank a lot of foods in liquid form, ( soups, etc. ) and a lot of Gerber's baby foods, and just about anything that could be pulverized in a blender.
 I gained weight like crazy. About 15 pounds in 2 months.
 The body takes advantage of having the harder work of digestion done for it. One of the advantages of cooking food is it's easier to digest. It is believed by some that such benefits to our life are the reason humans became the dominant force on this planet.


What animals have a blood-brain barrier?

It appears it is all vertebrates.

"All vertebrates started out with a glial blood-brain barrier 4–500 million years ago"

  All extant vertebrates have a blood-brain barrier (BBB), a specialized layer of cells that controls molecular traffic between blood and brain, and contributes to the regulation (homeostasis) of the brain microenvironment. ... The barrier is formed by vascular endothelial cells in most groups, but by perivascular glial cells (astrocytes) in elasmobranch fish (sharks, skates, and rays). It has been unclear which is the ancestral form, ... we conclude that the ancestral vertebrate had a glial BBB. This means that an endothelial barrier would have arisen independently several times during evolution, and implies that an endothelial barrier gave strong selective advantage.

So, all vertebrates have one; in some fish, it is composed of glial cells rather than endothelial cells.

However, insects do have something similar:

"Evolutionary conservation of vertebrate blood-brain barrier chemoprotective mechanisms in Drosophila"

  Insects also possess protective neural barriers, but they differ anatomically from vertebrates (Figure 1). Drosophila melanogaster (Dm) has an open circulatory system that is separated from the CNS by a thin layer of glially-derived epithelial cells (Treherne JE, 1972; Carlson et al., 2000; Stork et al., 2008), making the Dm humoral/CNS interface topologically much simpler than the vertebrate BBB. However on a cellular level, the vertebrate and insect BBBs share many common features.


Do animals only breathe through one nostril at a time like humans?

The post linked by @Remi.b says

  The nasal cycle is a natural ultradian cycle (see here and here. Not only is it present in humans, the nasal cycle has been observed in rats, rabbits, domestic pigs, cats and dogs (see references in Eccles 1996).

Proceeding to Eccles 1996 (p. 372):

  The nasal cycle is not only limited to the human nose, as it has been found in the rat and rabbit [31], the domestic pig [32, 33], the cat
  [34] and the dog [35], and appears to be a universal phenomenon at least in all mammals and possibly other animals.
  ...

  Bojsen-Moller F, Fahrenkrug J. Nasal swell bodies and
  cyclic changes in the air passages of the rat and rabbit
  nose. Anat 1971; 110: 25–37.
  Eccles R. The domestic pig as an experimental animal
  for studies on the nasal cycle. Acta Otolaryngol (Stockh)
  1978; 85: 431–436.
  Campbell WM, Kern EB. The nasal cycle in swine.
  Rhinology 1981; 19: 127–148.
  Bamford OS, Eccles R. The central reciprocal control
  of nasal vasomotor oscillations. Pflügers Arch 1982;
  394: 139–143.
  Webber RL, Jeffcoat MK, Harman JT, Ruttimann UE.
  Demonstration of the nasal cycle in the beagle dog. J
  Comput Assist Tomogr 1987; 11: 869–871.

A Pubmed search for '"nasal cycle" animal' gets a total of 18 hits, including refs 32 and 35 above, as well as

  Spontaneous nasal oscillations in dog. A mucosal expression of the respiration-related activities of cervical sympathetic nerve. Asakura K, Hoki K, Kataura A, Kasaba T, Aoki M. Acta Otolaryngol. 1987 Nov-Dec;104(5-6):533-8.
  Proceedings: Studies on the nasal cycle in the immobilized pig. Eccles R, Maynard RL. J Physiol. 1975 May;247(1):1P.

A bit more digging forward & backward through citations finds the article on cats (also by Eccles):

  R. Eccles & R. L. Lee (1981) Nasal Vasomotor Oscillations in the Cat
  Associated with the Respiratory Rhythm, Acta Oto-Laryngologica, 92:1-6, 357-361, DOI: 10.3109/00016488109133272

You might find more if you poke around (Google scholar/Pubmed, look at citations backward & forward, try search terms like "'nasal cycle' bird" or "'nasal cycle' reptile"), but at this point I doubt that anyone's bothered to check this in non-mammalian animals ...


How do DNA, enzymes, hormones etc. reach their proper cellular locations?

The answer given by Sadegh gives a general correct broad view. But one part of the puzzle is missing, which is molecular recognition.

Molecules bind to each other via physical/chemical interaction like forming hydrogen bonds, electrostatic interactions and other mechanisms. The sum of all interaction defines the strength of the binding. If molecules have enough interactions, they stick together otherwise not.
Mind that all these interactions have a range of action (a field). Like with magnets, two opposite magnetic poles attract each other at a distance, before they get in contact. Imagine a small molecule getting close to a receptor, if they are "magnetically" compatible they will be attracted toward each other.

Indeed, molecules in the bloodstream (like the Follicle Stimulating Hormone) flow all around the body. However, not all the molecules end up in all the cells. That is because cells have specific receptors on the surface that bind selectively their target. In the case of the Follicle Stimulating Hormone, some cells, like the Sertoli cells or the granulosa cells have the right receptor able to bind that specific hormone.

In the case of a drug targeting the liver, the drug gets assimilated or injected into the bloodstream, it travels all around the body but it is retained by specific molecular interactions only (mostly) in the liver. It is not that the drug knows where the liver is, it is just forced to pass through it and then it is retained by it. The drug passes also through the lungs, but it has no affinity for them so it doesn't get retained.

Inside the cells, it occurs the same. Molecules pass all around, but they do not stick to anything unless a specific protein/receptor/enzyme is found.

There is an intricate network of interactions both inside and outside the cells, molecules randomly flow throughout this network bouncing on each other until they find the binding partner and they stick to it.

Randomness is not the only factor. Brownian motion occurs, but molecules are also actively moved by different chemo/physical stimuli causing the network of interactions to be in fact extensively regulated.

For example, during the cell cycle, the cytoskeleton is actively remodeled to favor the flow of certain molecules in determinate directions (look metaphase). The cell can also alter its own permeability, actively influencing the influx/efflux of a variety of molecules.

At the body level, the circulatory system itself forces the flow in a specific direction (from the stomach to the liver for example).

The fact is, that there are mechanisms to selectively control the flow of the molecules at any level in the body, from organs to tissues, to single cells and inside subcompartments of the cells. The topic is complex but very well understood.

I suggest a big dive into this book if you really want to get a grasp on how biological systems work.

UPDATE: As suggested by @WYSIWYG, the picture would be more complete adding a very short note (the topic is way to broad to be extensively discussed here) on chemokines which are a perfect example on how cells can respond to concentration gradients. Chemokines act as a chemoattractant to guide the migration of cells. Cells can sense the concentrations of chemokines in the surrounding environment and, usually, move toward the source of the signal following the increasing concentrations of the signal molecule. In general, it cannot be overstated the importance of chemical gradients during embryogenesis, inflammation and countless other events. Gradients effectively indicate to cells the path to follow.


How are physiological reversal potentials (or ion concentrations) of neurons measured?

There are various methods to determine the intracellular ionic concentrations. One method is to register action potentials by the fowling method: inject a Voltage Active dye VAD (something like a -2di Anepp or s similar dye) into the cell or tissue and using an Optic Mapping System register the Action potentials and then determine the intracellular ionic concentrations by Nernst equations.

We could also register Action potentials by "ion-sensitive glass electrodes method" by introducing ion-sensitive glass electrodes directly into the interior of the cells. The problem with these electrodes is that they cannot register very low ionic concentrations especially of Calcium. And so the above method is superior using  VAD.


Is there any reason for the variation in mitochondrial DNA size?

One of the contributing factors the size of the yeast mitochondrial genome are 'selfish' mobile genetic elements termed homing endonucleases genes (HEGs).  These genes are typically found in introns that encode site-specific DNA endonucleases.  These endnoclueases cleave the HEG- alleles during yeast mating leading to DNA recombination using the HEG+ allele as template.  I suspect over time as organisms became more complex and HEGs become unable to mobilize they would become fixed in the organisms genome.  Upon being fixed there is no selection pressure to maintain the open reading frame of the HEG or the intron its encoded within (ref).  This causes the eventual loss of the HEG and intron since they provide no real benefit to the organisms genome.

I don't know how much of the yeast mitochondrial genome is taken up by these introns.  I believe that there are 4 of them in yeast some of the introns also require reverse transcriptase for splicing and mobility.  Other fungal species can have many more introns and sometimes weird things like introns embedded within introns.


Is ebola non-contagious until symptoms appear? Why?

First, confirmation from the World Health Organisation:

  The incubation period, that is, the time interval from infection with the virus to onset of symptoms is 2 to 21 days. Humans are not infectious until they develop symptoms.

But

  People remain infectious as long as their blood and body fluids, including semen and breast milk, contain the virus. Men who have recovered from the disease can still transmit the virus through their semen for up to 7 weeks after recovery from illness.

They also state that deceased people may still transmit the virus via body fluids.

As to why the patients become infectious only when symptoms show, there are several related ideas.  For example, from the CDC:

  Ebola virus enters the patient through mucous membranes, breaks in the skin, or parenterally and infects many cell types, including monocytes, macrophages, dendritic cells, endothelial cells, fibroblasts, hepatocytes, adrenal cortical cells and epithelial cells. The incubation period may be related to the infection route (i.e., 6 days for injection versus 10 days for contact). Ebola virus migrates from the initial infection site to regional lymph nodes and subsequently to the liver, spleen and adrenal gland.

According to Dr. Ray Schilling:

  Ebola virus disease has an incubation time of 8 to 10 days where the person may complain of some tiredness, but is not sick yet. This is the time when the Ebola virus multiplies. It  paralyzes the immune system and distributes itself through the organ system.

From there, the symptoms and effects of Ebola are fast, according to the article "Ebola Virus Pathogenesis: Implications for Vaccines and Therapies" (Sullivan et al. 2003):

  Ebola virus replicates at an unusually high rate that overwhelms the protein synthesis apparatus of infected cells and host immune defenses


Does the Rayleigh formula apply to electron microscopes or only light microscopes?

This is more than likely better asked in physics SE, however since you contextualized it biologically somewhat I will answer it here.

You are correct in your concern. The Rayleigh Criterion and the associated calculations(Rayleigh Scattering) are talking about the minimum separation of 2 light sources to resolve a given object. From this we are able to derive nice metrics like resolution and so forth. As you say, this describes the resolving of light wrt to the diffraction limit.

In order to calculate the resolving power of an SEM or TEM you need to do a different set of calculations.

First, the theoretical limit of EM microscope resolution is given by the De Broglie Wavelength of the accelerated electrons. However, as with the calculations for the Rayleigh Criterion, there are other factors to consider. For a full walkthrough see this. You take Abbe's equation for resolution in a perfect optical system, and take account of the other factors at play(optics for example).


Is it true that oxygen has a diffusion rate in air 10,000 times greater than in water?

Yes, according to calculations presented here and here the conclusion is that:

  The O2 diffusion coefficient in saturated air (15% oxygen) is 5,700 to 10,800 times greater than in water (60°C and 20°C respectively).

And here is a paper using this difference to investigate the transfer of O2 through the tracheal system of a click beetle.


What is the role pyruvate carboxylase in lipogenesis?

Okay so pyruvate carboxylase is a ligase-class enzyme, meaning it forms covalent bonds. What we see is that pyruvate is carboxylated into oxaloacetate by pyruvate carboxylase, here's our proposed reaction,

What this does is replenish mitochondrial oxaloacetate levels, because when we switch into lipogenesis, TCA intermediates must be shuttled into the cytoplasm for forming triglycerides, like so,

Also here, page 2, they go into how the production of NADPH is coupled to acetyl group export and how PC must perform the aforementioned function to keep substantial flow maintained. Block quoted them for ease of access,

  As shown in Scheme 1, the
  generation of NADPH is coupled to the transport of mitochondrial
  acetyl groups into the cytosol for fatty acid synthesis.
  Acetyl-CoA is generated in the mitochondria by the oxidative
  decarboxylation of pyruvate, and, after condensation with oxaloacetate,
  acetyl groups are transported to the cytoplasm as citrate,
  which undergoes ATP-dependent cleavage to yield acetyl-CoA
  and oxaloacetate. This pathway requires a continuous supply of
  oxaloacetate, which is produced by the activity of PC. AcetylCoA,
  a building block for the synthesis of long-chain fatty acids,
  is then converted into malonyl-CoA by acetyl-CoA carboxylase
  (ACC). Meanwhile, the oxaloacetate generated in the cytosol
  from citrate is reduced with NADH to malate, which in turn is
  oxidatively decarboxylated in a reaction catalysed by NADP+-
  dependent malate dehydrogenase (‘malic enzyme’; EC 1.1.1.40).
  The pyruvate thereby produced is taken up by the mitochondria
  and carboxylated to give oxaloacetate, while the NADPH
  generated is used in the pathway of fatty acid synthesis.


Why is an HIV infection considered "incurable"?

The reasons why HIV is "incurable" (a misnomer) are legion:

HIV is a retrovirus, which means it inserts its own genome into the host cell's genome.  You must therefore kill each and every infected cell to rid the body of the virus.
HIV is a lentivirus, which means it has a long incubation period, so it can "lay low" before symptoms are readily detected.
HIV infects CD4+ helper T-cells, macrophages, and dendritic cells, which are responsible for mediating the host immune response.  Thus, it infects specifically the cells we need to fight an infection.
HIV drastically reduces the number of CD4+ T-cells.
HIV has a number of viral proteins that prevent some of the body's antiviral mechanisms
HIV can infect via cell-free (large number of particles, low infection rate) or cell-to-cell (low number of particles, high infection rate) routes.
HIV is wildly variable.  It has a small RNA genome (about 10kb) that mutates very rapidly.  Given the number of viral particles produced each day during infection — well over 1 billion — every single base is mutated every day.

I'm simplifying matters a bit — you should just read the en.Wikipedia article for your own research — but that's a rundown of some of the reasons why.


How to prevent HL-60 cell contamination?

The single most likely reason for the contamination is that your frozen stock is contaminated. Assuming you've been properly trained in cell culture, you're working in a correctly-maintained biosafety cabinet, your reagents are all sterile (has your media been sterile-filtered after adding FBS, etc.?), and the incubator is clean (water bath pan has been autoclaved, sterile water with biocide/fungicide added to it, entire incubator wiped down and all removable parts autoclaved periodically, etc.), then stock contamination is the most reasonable answer. Try thawing earlier passages than you have been working with, or order a new vial or two from ATCC or whoever your cell vendor is. Make sure your pipetors are clean, and you're using sterile filtered pipet tips.