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If a non-mammal is starved of oxygen for some time, how long would it take the animal's neurons to die?
This is a follow-up question to Why do neurons die so quickly (relative to other cells) when deprived of oxygen?.
I'm particularly interested in the case of reptiles, octopuses, and other invertebrates. Could it be that mammalian neurons are especially oxygen-demanding compared with the neurons of other animals?

I believe, it mostly depends on external parameters rather then organism type. The humans could revive after up to 72 hours of clinical death with specific treatment, while under normal conditions irreversible damage occurs after 5-10 minutes. Some frogs, for example, can survive being frozen for several months.

Medically, recovery of brain function after 3 minutes of oxygen deprivation at body temperature is rare.
Further down here in 1 it indicates that at lower temperatures the time can be much longer.  At 13C, the record is 80 minutes for people.  Animals cooled to 0C have a record of recovery of three hours!  Not sure how much like themselves they feel after that though...


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How reversible is decerebrate posturing caused by brain stem damage?
This is a follow-up question to How likely would Abraham Lincoln be to survive his wounds today?

You don't have to see a CT scan or autopsy to know if the brainstem is
injured (directly or indirectly), if it doesn't work right.
The description of the first doc at the scene mentioned that Lincoln
was not breathing, and one pupil was dilated (the latter a clear and
unequivocal sign of dysfunction of the third cranial nerve or the
upper brainstem, from where it comes). Unfortunately, the second doc
described the enlarged pupil being the right one (it's extremely
unlikely to have been one and then the other - one of the doc's was
probably mistaken as to the side).
By 3 hours after injury, both pupils were fixed and dilated, and
Lincoln showed extensor (decerebrate) posturing - again, all signs of
profound brainstem dysfunction (but not yet brain death, though pretty
close to it).

Now, what is decerebrate posturing? See http://en.wikipedia.org/wiki/Abnormal_posturing#Decerebrate

Decerebrate posturing is also called decerebrate response, decerebrate
rigidity, or extensor posturing. It describes the involuntary
extension of the upper extremities in response to external stimuli. In
decerebrate posturing, the head is arched back, the arms are extended
by the sides, and the legs are extended.[6] A hallmark of decerebrate
posturing is extended elbows.[12] The arms and legs are extended and
rotated internally.[13] The patient is rigid, with the teeth
clenched.[13] The signs can be on just one or the other side of the
body or on both sides, and it may be just in the arms and may be
intermittent.[13]
A person displaying decerebrate posturing in
response to pain gets a score of two in the motor section of the
Glasgow Coma Scale (for adults) and the Pediatric Glasgow Coma Scale
(for infants). Decerebrate posturing indicates brain stem damage,
specifically damage below the level of the red nucleus (e.g.
mid-collicular lesion). It is exhibited by people with lesions or
compression in the midbrain and lesions in the cerebellum

Okay - the context is here: http://en.wikipedia.org/wiki/Abnormal_posturing#Decerebrate. I'll add another quote for it.

The decerebrate posturing is a sign of major brainstem dysfunction.
The reversibility of this state (which is considered to be very critical and hardly reversible) depends upon the origin of the brainstem dysfunction.
The primary brainstem dysfunction means that the brainstem was directly damaged (by a bullet) and there is no way that this can be quickly reversed. This is exactly the case here and there are no chances that the brainstem might recooperate with time.
The secondary brainstem dysfunction may be caused by cerebral edema and thereby dislocation of the brainstem towards foramen magnum, where the brainstem is coned. The coning of the brainstem can be reversible if the brain edema is treated quickly and effectively (by administration of diuretics in the intravenal catheter.
With brainstem regaining its normal functions the decerebral posture will eventuall resolve and depending upon the residual brain injury the recooperation of the brain function (and compensation) may be almost entire.

source: Stack Exchange

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How correlated are proximally related CpG sites in human DNA?
Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together.
I can only find one paper that states this empirically (1), that 90% of CpG sites within 50bp of one another are in the same methylation state - see below graph.

However this study is quite dated now (in the fields of epigenetics at least), and is very general.
I would like to know whether CpG's in different regions of the genome are more/less likely to be correlated than in other regions (say, exons vs. promoter regions). It would also be interesting to know whether the correlations change with age, and whether this is related to any disease processes?
Thanks for the input.

Eckhardt, et al, 2006. Nature Genetics. doi: 2010.1038/ng1909

I've got to dash off so I won't be able to give a fully in-depth answer today, but this basically boils down to the concept of CpG islands.  Something like 70-80% of CpGs are methylated in humans, so if they were randomly scattered around the genome there is already a pretty high chance nearby CpGs are in the same state.  However, because of CpG islands, CpGs of similar state are indeed grouped together, depending on promoter activity (to simplify things a bit).
That being said, if you look for articles that cite your article, a plethora of useful references show up.  In particular, this bad boy has a handy figure 1 which displays the overall landscape.  Maybe that's too broad of a view, but in general, like methylation patterns cluster together; otherwise, there'd be no such thing as a methylation pattern!  This paper has a neat figure which sums it all up nicely:

Basically, it's usually high-methylation or low-methylation; rarely is there anything in between.  There's a lot more in there so I'd recommend going through some of them; I'll try to get back to this later.

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Is there any evidence that soft tissue can be preserved for 65m+ years and if not what hypotheses exist to explain it?
I read an article on howstuffworks.com and they mentioned how we have found soft tissue in dinosaurs. According to the article even Mummies and Mammoths have no soft tissue left. Is there any evidence that soft tissue can remain intact this long even under perfect conditions? and if not what are some hypotheses that could explain it?

Science is not at the stage of imaginative hypotheses. We have the natural experiment of DNA recovery from geological strata that are easily and precisely dated, for example by 14C. From the fact that, as you look at older rocks, you see less useful DNA, the highly likely conclusion is that DNA is unstable in time. There is less fossil DNA in warm, humid places, pointing to a few explanations. There are DNA fossils dating more than those 65 million years, but they were in places where mammoths could not get (say, salt deposits that form today's mines).

Schweitzer et al. (2007) studied soft tissue preservation in a number of specimens, including an 800-1000 year old moas, 300,000 year old mammoth and mastodon, and 65 million year old *T. rex. and Triceratops. The oldest specimen was a 78 million year old Brachylophosaurus. Their goal was to try to find common environmental conditions that favor soft tissues preservation in fossils. As of this study, they have not been able to identify a single common environmental factor that seems to favor soft tissue preservation. They did note, however, that the specimens from which they could extract soft tissue (with varying success) were from fluvial sandstone environments, meaning sandy rivers. They (so far) could not extract soft tissue from terrestrial mudstone or marine environments.
Note that Schweitzer et al. did successfully extract soft tissue from the mastodon. The conditions required for mummification are probably not conducive to soft tissue preservation.  Here is a good blog article on one of Schweitzer's previous studies of soft tissue preservation.
The importance of extracting soft tissue from fossils cannot be overstated. Based on Schweitzer's work, her and her colleagues (Organ et al. 2008) were able to develop a phylogeny that incorporated both mastodon and T. rex. The used the amino acid sequence from collagen, a protein that is abundant in soft tissue. She and her colleagues repeated the analysis (Schweitzer et al. 2009) and included Brachylophosaurus, a hadrosaur. As predicted by morphological and other evidence, the mastodon was most closely related to modern elephants and the two dinosaurs were most closely related to modern birds and alligators.
Here is the phylogenetic tree derived from Schweitzer's 2009 study. Mammut is the mastodon. Brachylophosaurus and T. rex are the two dinosaurs.

Literature Cited
Organ, C.L. et al. 2008. Molecular phylogenetics of mastodon and Tyrannosaurus rex. Science 320: 499.
Schweitzer, M.H. et al. 2007. Soft tissue and cellular preservation in vertebrate skeletal elements from the Cretaceous to the present. Proceedings of the Biological Society of London B: 274: 183-197.
Schweitzer, M.H. et al. 2009. Biomolecular characterization and protein sequences of the Campanian hadrosaur, B. canadensis. Science 324: 626-631.


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Can neurons divide if somehow centrioles are introduced in nerve cells?
I am a biology student, so i know that centrioles are required for cell division, and i also know that nerve cells lack centrioles.
My question is that if somehow compatible  centrioles were introduced to the nerve cells, would their division be possible?

Welcome to Biology SE! I think it would be helpful for people to know your understanding of mitosis and meiosis. Since you say you are a biology student, how much of cell division have you studied?

Please read about cell division and what happens there first and then rephrase your question. Adding centrioles alone wouldn't certainly be enough.

Induced Pluripotent Cells
https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell?wprov=sfla1
You should probably look into this. This introduces what is called iPSCs, which are stem cells derived from adult cells.
What it is is that  they use signals that are found in embryonic cells, and the adult cells revert from their differentiated form into cells that can become virtually anything.


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Synthetic construct with multiple ORFs not expressing
I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation by different cis-elements (2-3 different cis-elements can be studied simultaneously).
The construct is like this:
SmaI-RES1-CMV-RES1’-GFP-MCS1-SV40PA-Linker-RES2-CMV-RES2’-RFP-MCS2-SV40PA-Linker-RES3-CMV-RES3’- YFP-MCS3-SV40PA-ΔLinker-SmaI

where:
RES1 = KpnI [GGTACC]
RES1’= SalI [GTCGAC]
MCS1 = EcoRI+BamHI [GAATTCTGGATCC]
RES2 = ClaI [ATCGAT]
RES2’= NheI [GCTAGC]
MCS2 = SpeI+HindIII [ACTAGTAAGCTT]
RES3 = XbaI [TCTAGA]
RES3’= PvuI [CGATCG]
MCS3 = NotI+SacI[GCGGCCGCGAGCTC]
Kozak consensus sequence = GCCACCATGG
Linker (100bp) = AATTCTGGATCCTGCAGCTTATAATGGTTACAAATAAAGCAATAGCATCACAAATTTCACAAATAAAGCATTTTTTTCGAATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGC

GFP, RFP and YFP are fast turnover variants with MODC pest sequence. I took the sequences for these proteins from Evrogen website. I took the Sv40 polyA signal sequence from one of their vectors in order to avoid any event of incompatibility. Kozak sequence was also taken from those vectors only. The total size it ~4.8kb. For CMV promoter I took the standard sequence used in most vectors.
With this vector I could clone any post-transcriptional regulatory sequence between stop codon and SV40PA, and could change promoters as well.
With the CMV promoter and no 3'UTRs I see a very faint expression of GFP, but could not see any RFP expression. I used pMaxGFP and dsRed as a control for filter sensitivity.
I transfected the plasmid in Hela and Neuro2a and at various concentrations (1-5μg) using lipofectamine. The controls express well (transfected 1μg each) but I see very faint GFP expression and dont see any RFP expression.
I checked the sequencing QC report given by the company and there were no indels or other mismatches. I am clueless about why the construct fails to express.
Is the linker a problem; is 100bp not sufficient ?

Did the company synthesize the sequence as above or did they codon optimize it for a species?  You can really mess up folding if you're not careful with translation gradients.  Also where did you put the Kozak sequence?  I couldn't tell from the question.  Need to make sure we have everything in the right order, gene start-stop, etc.

i just gave them the sequence.. it is codon-optimized for mammalian expression. Kozak sequence was obtained from the ORF source i.e Evrogen vector.. Kozak sequence is overlapping with the start codon and I just took the entire sequence from start of kozak sequence to stop codon

I have used an GFP+RLuc plasmid before that had linker just shy of 100BP, so I don't think that's the issue.  Have you done any westerns or northerns to see if you're getting some kind of read-through?

no.. I dont have the antibody or the primers/probes yet.. I have also tried electroporation.. no great difference.. I'll try it once more and see.. Point of using GFP was to have a direct readthrough

GFP antibodies are not too hard to run across.  I might try and see what your base level of expression is.  Otherwise the only way I know to go above CMV in expression is to use T7.  And then you have to worry about your T7 source.

I m not sure if it is a weak expression because of the promoter.. CMV promoters are quite common and give high expression.. I wonder if this is the case with CMV, how will I use other promoters like Tet-On and UAS... i guess their efficiency is less than CMV

let us continue this discussion in chat

@AtlLED: would you summarize the points that you mentioned in an answer.. it might be useful for others too..

I'm afraid there's not much of answer but back to the bench with you! (That's why it's called re-search).
There are several factors that could be playing a role here.  You could have transcriptional or translational read through.   You should check your sequence and the cells you are going into to make sure you aren't getting Amber (UAG) suppression.
Before you do anything, you should check your DNA of all your groups.  Run it uncut on a gel and make sure the majority of the DNA is super coil.  The next easiest thing to check is translation problems.  Get an GFP antibody, possibly a few that recognize different epitopes, and see if your GFP is coming out the right size.  It may not be processed correctly or folded correctly.
You can run into problems by optimizing the sequence.  First, synonymous mutations can cause folding variants (1).  Second, you might be causing a hair pen or other disadvantageous secondary or tertiary structure.  If you can't detect any problems in your Western, you might consider doing a Northern to trouble shoot the transcription.
If you rule everything else out, and you are just getting poor expression, then the only way I know to boost over CMV is to use T7.  The problem with T7 is always going to be what use for a source.  If you can use BSR/T7 cells and you can get your hands on them, they work great.  Otherwise you're looking at a T7 plasmid or MVA-T7 as common sources.  The plasmids never lead to a great deal of expression in anyone's hands I've ever known.  MVA-T7 works, but to say that it confounds things would be the under statement of the year.

Re-search That's perfect.

Can't take credit for that one.  Heard it back in the 90's from an advisor, and I'd bet he didn't come up with it ether.

It never had the time or resources to modify the vector and eventually gave up this project. I am accepting this answer as it summarizes all issues and would be useful for others who seek to work on synthetic biology.


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How is phenol antiseptic?
What makes phenol an antiseptic, is it because of its acidity which may increase the proton concentration at cell membrane? I am unable to figure out the exact mechanism.

The main reason for phenol being antiseptic is it's effect on proteins which it denaturates. It also causes leakage of cellular membranes. See the paper in reference 1 for some details and a load of references. They say in the section on phenol:

Phenolic-type antimicrobial agents have long been used for their
  antiseptic, disinfectant, or preservative properties, depending on the
  compound. It has been known for many years (215) that, although they
  have often been referred to as “general protoplasmic poisons,” they
  have membrane-active properties which also contribute to their overall
  activity (120) (Table (Table22).
Phenol induces progressive leakage of intracellular constituents,
  including the release of K+, the first index of membrane damage (273),
  and of radioactivity from 14C-labeled E. coli (242, 265). Pulvertaft
  and Lumb (386) demonstrated that low concentrations of phenols
  (0.032%, 320 μg/ml) and other (nonphenolic) agents lysed rapidly
  growing cultures of E. coli, staphylococci, and streptococci and
  concluded that autolytic enzymes were not involved.

Reference:

Antiseptics and Disinfectants: Activity, Action, and Resistance


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Multi-nucleated cells: advantages and examples?
This question arises because I saw that monocytes and leukocytes are commonly called 'mononuclear cells' in the scientific literature. The implication of course being that other immune sub-types are multi-nuclear!
I know of granulocytes (e.g. neutrophils) that are classed as 'polymorphonuclear' because their nuclei are segmented, and can alter their shapes, and muscle cells that fuse together to form one long cell (muscle fiber) with multiple nuclei. What other examples of multi-nucleated cells are there?
I am also interested in the advantages gained by cells having multiple (or segmented) nuclei?

Technically, all the granulocytes (neutrophils, eosinophils, and basophils) have multiple lobes/segments, not multiple nuclei. Syncytia in cardiac muscle cells is important for coordinated contraction. Not sure about the rest..

@jello yes I realize that polymorphonuclear does not mean multiple nuclei, but 'mononuclear' does imply that 'ploynuclear' cells exist, and I am sure that muscle fibres do have multiple nuclei, because multiple cells fuse together. I'm interested to know the advantages of multiple nuclei, and what other cell types have it. Thanks

Another example of multinucleated cells is osteoclasts, which are specialized derivatives of macrophages that degrade bone matrix.  They form by fusion of mononucleated progenitors and can accumulate many nuclei in a single large cell.  In cell culture with mouse macrophages, it's common to obtain individual osteoclasts with 50-100 or more nuclei each.

Can you back your answer up with a reference?

Multinucleate cell angiohistiocytoma (MCAH)
Osteoclasts
muscle fiber
granulocytes
Types of giant cells
A.  Physiological giant cells:
•   Osteoclast
•   Megakaryocytes
•   Striated muscle
•   Syncytiotrophoblast
B.  Pathological giant cells:
•   Langhan's giant cell
•   Foreign body giant cell
•   Touton giant cell
•   Tumor giant cell
•   Warthin–Finkeldey giant cell
Liver cells
Skeletal muscle
Some cardiac muscles

As such, your answer is incomplete because you haven't mentioned any advantages. It also needs references.

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During human ageing, which immune cell sub-types are most affected?
It is now well established that human ageing is accompanied by an increase in systemic, low-grade (chronic) inflammation, sometimes termed inflammaging (Franceschi, 2007). This is in part due to more global changes to the body, including an increased number of senescent cells, but of interest to me currently is the change in the composition of the circulating immune cell sub-types that may either cause, or be affected by, the increase in 'global' inflammation.
I imagine the answer to this question is a study that samples individuals of different ages and separates the various leukocyte fractions. Using this it could be determined which immune sub-types are over-/under-represented in the aged, and at what age the changes occur (e.g. monocyte numbers may decrease from age 40, whereas neutrophil numbers may increase...). I have done some fairly extensive research, but have been unable to find a study that has done this - however it seems likely that it has been performed. Thanks.

From my Immunology notes:
*Decrease in hematopoietic stem cells resulting in a reduction of Affector cells. Erythroid and myeloid progeny cells don't seem to be affected.
*Fewer pro-B cells, resulting in fewer affector B-cells.
*Lymphoid progenitors in the bone marrow and thymus mature.
*Lymphocytes in secondary lymphoid organs.
For the Innate system:
*Neutrophils have a reduced capacity for Oxidative bursts, Batericidal activity, and Chemotaxis.
*Macrophages have a reduced capacity for phagocytic activity, oxidative bursts, and MHC II expression (which impairs their ability to present antigen and initiate CD4 Helper T-Cell responses).
*NK Cells have a reduced capacity for Cytotoxicity, proinflammatory cytokines and chemokines,and proliferation in response to IL-2. However, the total number of NK cells increases.
The sources: Both clinical (it was at a teaching hospital) and Aging and Immune System, Chapter 33 of the class text: Cellular and Molecular Immunology

Does the textbook give any information on the different stages of the decline? I.e. at what ages the various changes occur, whether the adaptive immune response is affected more-so? Thanks for the answer though - will have a look for that chapter.

30 and 60 were the major milestones mentioned in my notes, where an increased prevalence of cancers and diseases (respectively) become significant. However, that's probably due to the architecture of the studies the authors drew the numbers from and not any natural impetus.
My personal guess would be that after 30 it's just a downward sigmoidal curve without any "hard" ages that signify major shifts in immunological makeup.


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Cyanobacterial photosynthetic oxygen yield
I am somehow not convinced that biotic factors are solely responsible for creating 21% of atmosphere (around 40 million moles of oxygen).
There may be additional issues here. Since cyanobacteria produced oxygen, it should have developed antioxidant machineries. By the time cyanobacteria flourished, some dependent heterotrophs must have evolved and they also would need antioxidants, as they are expected to thrive in close proximity to the autotrophs. There is a likelihood that aerobic respiration co-evolved with biotic oxygenesis. This would have further delayed the build up of oxygen in the atmosphere.
Does anyone have an idea of what is the photosynthetic oxygen production rate per gram biomass of cyanobacteria? Since photosynthesis must have happened mostly at the surface of the water (limnetic zone), the total biomass would be restricted. Then it might be possible to calculate the time required to achieve the oxygen levels of 21%.
This measure can indicate whether the current theory is plausible or not.

Some of these points are addressed briefly at http://hoopermuseum.earthsci.carleton.ca/stromatolites/OXYGEN.htm and again at http://www.scientificamerican.com/article.cfm?id=origin-of-oxygen-in-atmosphere

This is a study on the O2 production rate of one of the fastest growing species of cyanobacteria. The theory is not just someone's idea, it's a conclusion made from trends which were discovered during the course of conducting countless experiments.

thanks. I asked this question a while back. There is also a nice recent article in nature about the Great Oxygenation Event


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Predators on the Galapagos
I understand that in many isolated islands, such as the Galapagos, there are no large predators. I find this observation interesting because it has been suggested that the lack of predators unleashes the evolution of new and bizarre species.
However, as new species evolved there (and increase their size, with respect their ancestors), why no small predator species evolved into a large predator species? Or can new predators evolve from herbivorous animals?
This may be a difficult question, because we may not  know the natural history in such great details. More specifically, I wonder if, in general, there is some pressure against the selection of predators or if there are counter examples which show that small isolated islands evolved their own apex predator.

Larger predators need a large range on which to find potential prey. An island might be bigger than the normal range of a predator, but too small to support a large enough breeding population (because of inbreeding, and because a brief lack of food, disease, or other insult could wipe out the entire population, rather than just a few individuals).

Interesting point. Are there fossil evidences of extinctions in islands due to that? Of course let us exclude humans and their pets and pests.

Not such a simple and clear pattern
What you are talking about is called insular dwarfism. The process is not as straight forward as you seem to think it is. It is not systematic that insular islands evolve toward reduce sizes. In fact, the opposite of insular dwarfism, insular gigantism (which is related to Foster's rule) has also been observed.
In any case, there seems that islands often bring selection pressures of size but the causes are numerous. I think wikipedia does a descent job at screening over the existing explanations.
Wiki > insular dwarfism > Factors influencing the extent of dwarfing

For both herbivores and carnivores, island size, the degree of island isolation and the size of the ancestral continental species appear not to be of major direct importance to the degree of dwarfing.4 However, when considering only the body masses of recent top herbivores and carnivores, and including data from both continental and island land masses, the body masses of the largest species in a land mass were found to scale to the size of the land mass, with slopes of about 0.5 log(body mass/kg) per log(land area/km2).[7] There were separate regression lines for endothermic top predators, ectothermic top predators, endothermic top herbivores and (on the basis of limited data) ectothermic top herbivores, such that food intake was 7 to 24-fold higher for top herbivores than for top predators, and about the same for endotherms and ectotherms of the same trophic level (this leads to ectotherms being 5 to 16 times heavier than corresponding endotherms).[7]

Wiki > Insular gigantism > possible causes

Large mammalian carnivores are often absent on islands because of insufficient range or difficulties in over-water dispersal. In their absence, the ecological niches for large predators may be occupied by birds, reptiles or smaller carnivorans, which can then grow to larger-than-normal size. For example, on prehistoric Gargano Island in the Miocene-Pliocene Mediterranean, on islands in the Caribbean like Cuba, and on Madagascar and New Zealand, some or all apex predators were birds like eagles, falcons and owls, including some of the largest known examples of these groups. However, birds and reptiles generally make less efficient large predators than advanced carnivorans.
Since small size usually makes it easier for herbivores to escape or hide from predators, the decreased predation pressure on islands can allow them to grow larger.1[a] Small herbivores may also benefit from the absence of competition from missing types of large herbivores.
Diagram displaying the change in size of weta species in two ecosystems. The size and population of wetas are affected by predation. Rats introduced on the mainland began to prey on wetas, reducing their population; wetas shrank in response. On an island isolated from predation, such as Little Barrier Island, wetas have a dense population and have grown to a massive size. Insular species of giant wetas are the only ones not facing extinction. As wetas grow over time, bird predation declines.[citation needed]
Benefits of large size that have been suggested for island tortoises include decreased vulnerability to scarcity of food and/or water, through ability to survive for longer intervals without them, or ability to travel longer distances to obtain them. Periods of such scarcity may be a greater threat on oceanic islands than on the mainland.4
Thus, island gigantism is usually an evolutionary trend resulting from the removal of constraints on the size of small animals related to predation and/or competition.5 Such constraints can operate differently depending on the size of the animal, however; for example, while small herbivores may escape predation by hiding, large herbivores may deter predators by intimidation. As a result, the complementary phenomenon of island dwarfism can also result from the removal of constraints related to predation and/or competition on the size of large herbivores.[6] In contrast, insular dwarfism among predators more commonly results from the imposition of constraints associated with the limited prey resources available on islands.[6] As opposed to island dwarfism, island gigantism is found in most major vertebrate groups and in invertebrates.
Territorialism may favor the evolution of island gigantism. A study on Anaho Island in Nevada determined that reptile species that were territorial tended to be larger on the island compared to the mainland, particularly in the smaller species. In territorial species, larger size makes individuals better able to compete to defend their territory. This gives additional impetus to evolution toward larger size in an insular population.[7]
A further means of establishing island gigantism may be a founder effect operative when larger members of a mainland population are superior in their ability to colonize islands.[8]
Island size plays a role in determining the extent of gigantism. Smaller islands generally accelerate the rate of evolution of changes in organism size, and organisms there evolve greater extremes in size.[9]

Dwarfing refers to species evolving towards a smaller size. This is not the case of Galapagos where predators didn't become smaller... Is seems that they just didn't arise!

There actually are some terrestrial predators on the Galapagos Islands. Notably, there are four species of birds of prey on the islands: the endemic Galapagos hawk (Buteo galapagoensis), and three other birds with a wider distribution, the osprey (Pandion haliaetus), the short-eared owl (Asio flammeus), and the barn owl (Tyto alba). This is actually pretty typical for islands, even Hawaii and New Zealand have a number of native bird of prey species, even if they lack predatory terrestrial mammals or large terrestrial reptiles.
In a broader sense, the reason why there aren't a lot of predators on small islands is because there aren't enough resources for them to sustain a breeding population. A carnivorous animal on average requires ten times as much resources in the environment to support them than a herbivorous one due to energy that is lost from plant to herbivore and herbivore to carnivore, which results in carnivores either existing at very low densities across islands and easily going extinct. This is thought to be one reason why carnivorous mammals rarely successfully disperse to islands: they do disperse, but the islands they arrive on can't sustain them.


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How do proteins get into the blood stream?
So I'm asking this in reference to the injection of insulin, which is commonly done subcutaneously (in the hypodermis, a fatty part of skin). Now I know proteins usually get into the blood when digested through the stomach/intestines - but I was wondering how they manage to get into the blood when injected into muscles/fat? I know there are capillaries pretty much everywhere, but from what I've researched proteins are too large to get through capillary walls.
That begs the question then, how do proteins manage to get into the blood stream when injected? I can't really envisage large capillaries, because surely they'd have huge holes in them or whatever to allow large proteins like insulin in. Any help on this one? Cheers

maybe from lymphatic capillaries(they have larger pores) ... I am not sure....

Found the answer - the lymph capillaries. I've not researched them too in depth but from what I've read thus far, their job is to essentially pick up fluids not picked up by the blood capillaries. They have walls that allow proteins to enter but make it very hard for fluid to flow out.
Wiki states that an average of 20 litres of blood gets processed each day by the blood, with roughly 17 litres through the blood capillaries/system (1), with the remaining 3 litres through the lymphatic system.
These are also prevalent around skin. 70% of lymph capillaries are found near the skin (2).
1) http://en.wikipedia.org/wiki/Lymphatic_system
2) http://www.lymphnotes.com/article.php/id/151/

Could you expand on this slightly to make it more useful for people viewing it in the future?

Apologies, didn't see the comment above suggesting the lymphatic system, and have done a bit more research so edited.


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Can Anyone Identify This Insect?

I keep seeing these bugs on a wall in my house in Istanbul (Turkey) walking up and down generally during evening and night. They are about 1 mm long and have a brownish color. I see more of them through late hours. Does anyone know what they are called?

I don't recognize it, but it might be possible to identify this insect using an automated species identification program.

Related: Bug Identification: Tiny Bugs in Fairport NY, What are these tiny, swarming, jumping bugs?, Help identifying tiny jumping bug, Taxonomy: Categorising Collembola, What kind of small insect is this?, Unknown aquatic larvae

Those are collembolans. Common name, springtails. Do you have a potted plant nearby? They are completely harmless.
Here is an example:

(picture from bugguide.net

Could you please add, why  you think these are collembolans?

SIze and shape. See https://biology.stackexchange.com/questions/54878/taxonomy-categorising-collembola

Agreed. The picture is poor but it looks very much like a typical springtail


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What kind of scorpion is this?
This is in Nevada; it's about the size of a tooth pick in length.

(click to enlarge)
What kind of scorpion is this?

Welcome Samantha. Please take our [tour] and refer to thee [help] for guidance. I've edited to make the image work, which will apply once approved. Please tell us how big the toothpicks are in your part of the world as they vary quite a bit in size over the international community which visits here.

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


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How did the Chromosome #2 Fusion propagate?
There is strong evidence that chromosome 2 in humans is a fusion of two chromosomes of a common ancestor of chimps and humans as explained at wikipedia here
Was it necessary for the common ancestor with fused chromosome 2 to mate with another creature whose 2 chromosomes fused in a similar manner?
If yes, what would their offspring look like? would they also need to mate within themselves or could they mate with the chimp population?
if possible, also, how in the world could a genetic disadvantage take over the population? doesn't this contradict natural selection?

Was it necessary for the common ancestor with fused chromosome 2 to
  mate with another creature whose 2 chromosomes fused in a similar
  manner?

Of course not.  People with balanced translocations have kids with people with the wild-type chromosome arrangement all the time.  Such people have some fertility problems, due to problematic meiosis leading to more inviable gametes, but they can still reproduce.
Someone already mentioned Robertsonian translocations to you in your previous question.  Didn't you look it up?

would they also need to mate within themselves or could they mate with
  the chimp population?

What chimp population?  There were no modern chimps when the fusion happened.
Look, you could ask a million questions here, and still learn nothing.  This board is helpful for people who have a good, accurate framework of the facts of biology, but who want specific holes in their knowledge base filled.  I don't think that's you.  I think you think you know the right answers to your questions, based not on science, but on other things, have imbibed or made up a whole slew of very wrong stuff about biology, and are asking questions here expecting people to confirm your wrong beliefs, trying to trick people in to confessing that mainstream biology is wrong, and you are right.
Picking at one bit or another of evolutionary biology is not going to help you.  You need to start by assuming that a lot of what you think you know about the scientific facts is wrong, and learn the real stuff.  It is not at all easy to get wrong information out of our brains, but until you do, this exercise isn't going to educate you much at all.

you wrote "What chimp population? There were no modern chimps when the fusion happened.". correct - my mistake. I  meant "common ancestor". frankly, I am surprised by your reaction. in all honesty, if I thought I knew the answer to my question, I wouldn't be asking it here. I fully realize there is much I don't know and that is why I am asking, hoping to get an honest answer.


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If some humans inherited 3% of Neanderthal DNA, why are we 99.9% same genome?
Many sources say that humans are 99.5 to 99.9 percent the same.
Also some sources state that some humans have 3.4% Neanderthal DNA and some don't share those genes.
Why is that?

Please search past questions on the list (neanderthal, african, denisovian etc). I am sure this has been asked before, but have not time at the moment to find it for you.

3% and 99.9% are from different calculation method.
20% (a rough estimation, might be wrong) of neanderthal DNA survived in the modern human genome, but it is 'diluted' by the human population,  which lead to 2 percent of neanderthal DNA in each human genome. This is the number 3%.
But how can we know it's neanderthal DNA?
If DNA fragment contains several neanderthal special SNP (single-nucleotide polymorphism), we will treat it as neanderthal DNA. (Based on linkage disequilibrium, the inference is reasonable.) The fragment might of tens of thousands nucleotides, but the difference are just one or two base.
But when we compare two human, we calculate the difference at nucleotides level, rather than DNA fragment. This is the number 99.9% come from.
If we have the complete genome of neanderthal and human, by comparing them at base level, the similarity might be great than 99%, I suppose.


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What selective factors drove the evolution of lactose in lactation?
As far as I can determine, lactose, and the monosaccharide galactose have few biological uses outside of mammalian lactation.  It not only required enzymes for its production, but enzymes in offspring for its digestion, suggesting that it serves some specific purpose.  Yet intuitively, it seems like it would have been significantly easier to just concentrate glucose from the blood or generate a disaccharide readily found in the diet like sucrose, for which digestive enzymes already existed.
What drove the evolution of lactose in mammalian lactation?

Galactose is also an important component of the oligosaccharides that are added to glycosylated proteins.

As it happens someone has just published a theory about this. To save you following the link, I reproduce the abstract below.
I must admit that I had never realised that lactose is synthesised within the organelles of the secretory pathway (β4-galactosyltransferase is a Golgi enzyme and α-lactalbumin is, of course, a whey protein, so is in transit through the pathway). This may go part of the way to answering your question: by having a disaccharide that is made within the Golgi, the cells of the mammary gland will effectively partition their glucose metabolism between the cytoplasm and that destined for secretion as lactose (transported into the Golgi lumen).

Mammalian milk or colostrum contains up to 10% of carbohydrate, of which free lactose usually constitutes more than 80%. Lactose is synthesized within lactating mammary glands from uridine diphosphate galactose (UDP-Gal) and glucose by a transgalactosylation catalysed by a complex of β4-galactosyltransferase and α-lactalbumin (α-LA). α-LA is believed to have evolved from C-type lysozyme. Mammalian milk or colostrum usually contains a variety of oligosaccharides in addition to free lactose. Each oligosaccharide has a lactose unit at its reducing end; this unit acts as a precursor that is essential for its biosynthesis. It is generally believed that milk oligosaccharides act as prebiotics and also as receptor analogues that act as anti-infection factors. We propose the following hypothesis. The proto-lacteal secretions of the primitive mammary glands of the common ancestor of mammals contained fat and protein including lysozyme, but no lactose or oligosaccharides because of the absence of α-LA. When α-LA first appeared as a result of its evolution from lysozyme, its content within the lactating mammary glands was low and lactose was therefore synthesized at a slow rate. Because of the presence of glycosyltransferases, almost all of the nascent lactose was utilized for the biosynthesis of oligosaccharides. The predominant saccharides in the proto-lacteal secretions or primitive milk produced by this common ancestor were therefore oligosaccharides rather than free lactose. Subsequent to this initial period, the oligosaccharides began to serve as anti-infection factors. They were then recruited as a significant energy source for the neonate, which was achieved by an increase in the synthesis of α-LA. This produced a concomitant increase in the concentration of lactose in the milk, and lactose therefore became an important energy source for most eutherians, whereas oligosaccharides continued to serve mainly as anti-microbial agents. Lactose, in addition, began to act as an osmoregulatory molecule, controlling the milk volume. Studies on the chemical structures of the milk oligosaccharides of a variety of mammalian species suggest that human milk or colostrum is unique in that oligosaccharides containing lacto-N-biose I (LNB) (Gal(β1 → 3)GlcNAc, type I) predominate over those containing N-acetyllactosamine (Gal(β1 → 4)GlcNAc, type II), whereas in other species only type II oligosaccharides are found or else they predominate over type I oligosaccharides. It can be hypothesized that this feature may have a selective advantage in that it may promote the growth of beneficial colonic bacteria, Bifidobacteria, in the human infant colon.


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Number of elongating RNA polymerases on a gene
I'm interested in knowing how many Pol II molecules are simultaneously transcribing any given gene. There are RNA pol II ChIP-seq (phospho-S5) data for different cells but these come from pooled cell samples. So the different peaks on any given gene would be the average of the cell population. Single cell ChIP-seq data would help but I can't find any.
The other way to check this is to calculate transcription rates of different genes, normalize with copy number and divide by the elongation rate of the polymerase on that gene. However, elongation rate is not unique for all genes.
Is there any resource – paper or raw data, which would help me find the answer to the question?

Regulation of RNA polymerase II activation by histone acetylation in single living cells by Stasevich et al. provides detail on how they were able to determine the number of elongating RNA polymerase II for a given gene array. The issue I had with the paper is that they used a ~1.8Mbp tandem repeat as their target, so they really upped the probability of seeing activity. You may be able to do similar for your gene of interest, but there may not be enough signal to tease out your data.


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Please help ID this possible fish skull
Found on the shoreline of a tributary of the upper part of the Chesapeake bay in Maryland:

More pictures here
ichthyology??

I suspect you're going to need better pictures from multiple angles to have a chance at an answer; from this view it isn't even clear you have a skull.

I don't disagree. I'm having trouble posting pics....it is definitely a skull. I will create a link to the other pics. Thanks for responding.! Please look if you have time. I have been collecting mammal skulls for quite some time & I am stumped.

Here is the link to more pictures.  Any opinions are greatly appreciated.  It's driving me nuts                                https://photos.app.goo.gl/Cg8t4Ttsde4oDDDg7

I think that's ichtyology because it's probably a fish, the comment says herpetology,

Similar to this https://biology.stackexchange.com/questions/74087/what-type-of-bird-skull-is-this

Thanks for your input

I've fixed your image link — in the future you should be able to avoid this kind of problem by entering each link on a separate line.  ———— I recommend uploading some more of your pictures — questions with clear images from multiple angles are more likely to get useful feedback! ——— To me this looks like it might be part of a turtle skeleton rather than a fish skull, but that's really just a guess.

yes an ichtyology forum is not suitable for fish IDs cos ichtyos dont know that kinda thing as well as this forum does.


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When did the term "non-avian dinosaur" come in common use?
When I first learned about the prehistoric (mega)fauna that we now commonly call non-avian dinosaurs they where just referred to as dinosaur. I am trying to figure out when we made the collective switch in articles and literature to the use of "non-avian dinosaur".
Merriam-Webster provides us with a definition and indicates that the first known use is in 1988. But that does not indicate it was in common use nor general knowledge that birds are a descendant of dinosaurs which means we need to distinguish between avian and non-avian dinosaurs.
So can someone help me find when the trend to the more specific non-avian dinosaurs got started?

Don’t you mean when did it become common knowledge that birds are NOT the descendants of dinosaurs? People used to think they were so, and this was the mistake that occasioned the invention of the term you reference. It depends when you started reading Robert Bakker's explorations of dinosaur endothermy starting in 1968. Most of the dinosaurs — both the avian ones and the non-avians ones — went extinct at the K-Pg boundary. Most dinobirds died then and only one tiny branch of them survived: the little, ground-not-tree-dwelling but flighted toothless ones with beaks for cracking open seeds.

@tchrist ?? Of all the life that survived the KT event, only birds are descended from dinosaurs. Doubt they ate seeds, termites are more likely. It's believed that all mammals that survived were insectivores.

@PhilSweet Birds are a kind of dinosaur in the same way that humans are a kind of great ape. That's different from saying something like reptiles are descended from  amphibians.

The term non-avian dinosaur is usually taken to be a term used in chronological classification schemes. There are three systems of classification that share some terminology and supplement as needed with unique terms. You can base all branching on the known fossil record. Or you can base some of it on hypothetical lineages, Or you can look at timelines and dateable events and use terms that relate to specific chronology. Non-avian dinosaur basically belongs to the third system.

@tchrist birds did not become entirely toothless until well after the K-Pg extinction.

@John Thanks for the quite interesting correction.

Here is what Google Ngrams has:

This suggests that the mid-70's are the first recorded instance, but it wasn't until the 90's that it began to gain use. What defines "common use" is up to you.

The understanding that bird are dinosaurs was not a sudden realization but a slow accumulation of evidence and convincing scientists along with the rise of cladistics and phylogenetics making such clarification useful. so this is probably the best answer you can get.


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Mammal size and capillary wall thickness
How does capillary wall thickness vary with the size of the animal?

Background/context of question:

Of the following, Figure 1 is most consistent with the fact that, in general, smaller mammals have:
A] thicker capillary walls than do larger mammals.
B] a more rapid metabolic rate than do larger mammals.
C] smaller surface area/volume ratios than do larger mammals.
D] capillaries of more variable cross-section area than do larger mammal

My working:
Of the following, Figure 1 is most consistent with the fact that, in general, smaller mammals have:
A] thicker capillary walls than do larger mammals.
B] (correct answer) a more rapid metabolic rate than do larger mammals. This is correct because a smaller animal has a higher surface area to volume ratio and hence radiates/loses heat quicker, and so must metabolise food quicker to keep their temperature up.
C] smaller surface area/volume ratios than do larger mammals. This is wrong as a smaller object has a higher surface area per volume
D] capillaries of more variable cross-section area than do larger mammal
My issue: I am trying to work out why A and D are wrong.
I can't find anything on the Internet about how capillary wall thickness (Answer choice A) or capillary cross sectionn (Answer choice D) vary with animal size.
If I was going to have a guess based on the stimulus:
For Answer choice A : From the graph, we know smaller animals have less oxygen partial pressure (as they lie to the right) and less HB saturation (as their curves lie to the bottom). If capillary walls were thicker, I would think this means that the oxygen partial pressure would be GREATER. I.e. if I think of a really thick walled balloon, it would be more difficult to blow up and increase in volume (and hence, have a higher pressure) than a thin walled balloon. However, as I know C is the correct answer, A (and my reasoning above) must both be wrong.
For Answer choice D: I don't really know how variation in cross section would have an effect. Maybe by providing a bottle-neck and increasing pressure in that way?

I believe your problem lies in understanding the oxygen dissociation curve. The higher the need for oxygen (e.g. because of metabolic rate or physical activity), the greater the shift to the right. So generally, increasingly smaller animals, having increasingly higher metabolic rates, have curves that shift progressively to the right. Capillary wall thickness is fairly constant in mammals: about one cell thick.

Thanks @anongoodnurse ! That explains why I couldn't find anything about the capillary wall thickness and animal size relationship ; I assumed as A wasn't the answer that the opposite i.e. that LARGER mammals have thicker capillary walls was true (rather than them being equal).


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Where to archive web citations for molecular biology article?
In 2013 I wrote a scientific paper in the field molecular biology. I needed to quote some webpages which I feared might disappear, e.g. amazon sales offers (it was a food related topic). So I archived them at Webcite (wecbitation.org), because it was recommended to me as an appropriate place for biosciences.
However, they stopped accepting new submissions. Where should I archive now ?

You can use the Internet Archive's Wayback Machine to get "permanent" links (as permanent as anything is on the internet) to just about any webpage, and I believe you can request indexing for pages that aren't already in the archive. Wikipedia uses this functionality for permalinks, for example.


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Why does methylation not occur in viral DNA?
Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?

Are you mostly interested in bacteriophages ?

Contrary to the question title, viral DNA can be methylated.  See for example Bonvicini et al. 2012. (1) and Hoelzer et al. 2008 (2).
Hoelzer et al. give a review of the presence and role of cytosine methylation in DNA viruses of animals:

To understand the impact of cytosine methylation on the viral life
  cycle and the evolution of base composition, the particularities of
  each virus will need to be considered. Differences will inevitably
  exist between actively replicating viral DNA and that which is
  integrated into the host genome. The type of viral persistence will
  also be of importance. The integration of adeno- or polyomavirus DNA
  into the host genome is usually a terminal process since the viruses
  cannot liberate their genomes and are therefore no longer infectious.
  The evolutionary roles of methylation in these cases will likely
  differ from those seen in other viruses, such as Herpesviruses, which
  can liberate their genome after periods of latency. But differences
  may also exist between large and small viruses—with many larger
  viruses encoding their own replication machinery and additional
  proteins which modify host cell processes and immune responses. The
  susceptibility of the viral genome to methylation and immune
  recognition will also be affected by other factors, such as the
  location of replication within the cell and the specific intracellular
  trafficking route.

Viral DNA methylation has mostly been studied in large DNA virii, and the extent of methylation may be related to repression of viral replication. Bonvicini et al. writes that

Epigenetic mechanisms, and in particular the impact of cytosine
  methylation at CpG dinucleotides on the viral life cycle have been
  mainly studied for viruses that can establish latency and undergo
  reactivation, such as viruses in the Herpesviridae family, or for
  viruses that can integrate their genome into the host genome such as
  Retroviridae or Papillomaviridae. In general, a correlation has been
  found between the extent of CpG dinucleotides methylation of viral
  genomes and viral quiescence [24]. Scarce information is on the
  contrary available on the possible occurrence and role of methylation
  for actively replicating viruses

Methylation played different roles for different types of organisms throughout evolution. For bacteria, methylation protects against self-digestion of DNA by restriction enzymes. In eukaryotes, methylation assumes many different roles (e.g., mutation-rate regulator, gene expression regulator, chromatin structure regulator, etc.). Insects have very little methylation and it is not entirely clear what they use it for. Viruses don't encode for methyltransferases that modify DNA. However, when a virus integrates into a host genome that is methylated, the viral DNA usually assumes the methylation pattern of the integration locus.


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Role of dam methylase in bacteria
In bacteria, an enzyme called dam methylase (Deoxyadenosine methylase)  methylates adenines (A) in the sequence GATC in the new strand formed after replication.
What role does this methylation play?
I read that it has something to do with proofreading. If this is so, then how?

The dam methylase has three different functions:

Correction replication errors, since the new DNA molecule
is only hemimethylated (the old strand is methylated, the newly
synthesized is not). Since the proof-reading only takes place on the
new strand, errors introduced during replication can be corrected.
Regulation of replication: The ori of the chromosome is methylated to ensure that is only replicated once.
Regulation of transcription: Methylation of GATC sequences promote the transcription of genes.

For further details see the references.
References:

The great GATC: DNA methylation in E. coli
The dam and dcm strains of Escherichia coli--a review.
Dam methylation: coordinating cellular processes.


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Is the Andraka pancreatic cancer test real?
In the wikipedia article about Andraka's pancreatic cancer test there are some controversial statements.
On one hand there are many glorious words about the method, also some awards, also some astonishing comparisons with other methods.
On the other hand, there is no proof, and also some evidence against its efficacy.
Also, I can't find any signs of Andraka's test in reality. For example, there is no such product in drug stores.
What is the proof or evidence that Andraka's method is really working and can feasibly exist in the near future?

Its mentioned in the Wikipedia article: None of the articles was published peer-reviewed and the replication of the results showed they were not significantly different from healthy persons.

Then what does award mean?

That some people, who probably have not much knowledge of scientific processes were impressed enough to award a price.

I think "fake" here implies that Andraka willfully misled people to earn the prize.  I don't think that is likely and speculating on it would be outside the scope of the site.  If you want a better explanation of the ways in which the method may not work as well as originally proposed, then you should re-word your question to reflect that.

@KennyPeanuts I have reworded my question. I don't care Andraka's motivation, only the reality of the method matters.

Basically, Andraka's method measures mesothelin. There's two key questions being asked about it (as it stands right now), falling into two categories:
1) There is some doubt as to the significance of serum mesothelin levels as a biomarker in pancreatic and biliary cancers. Some studies (e.g. Sharon et al (1)) suggest that there is no significant difference in levels - others (e.g. Hassan et al (2)) suggest that mesothelin may be a valid biomarker in some conditions but not others.
2) There are questions around the test itself. Andraka's work is promising and quite impressive. There are, however, some claims about it are being made that there's just not the evidence to support. I suspect that any fault for this lies with the journalists reporting on the story or PR people for various companies or institutions. The device may stand up to clinical trials and testing and be as revolutionary as it's claimed to be, but it does need to be fully tested.


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Why isn't there T2 thyroid hormone?
The follicles in the thyroid, intake iodine and bind them onto the tyrosine rings (attached to the thyroglobulin). This produces either MIT or DIT (tyrosine rings with 1 or 2 iodines attached respectively).
Then the DIT joins with either another DIT or a MIT to form T3 or T4. This makes sense.
But it seems to me, that there could be a MIT attaching to another MIT, forming T2. Why doesn't T2 get created?

What makes you think that T2 doesn't exist? I did a search for "T2 thyroid hormone" and got several papers as hits ...

I think you've already answered your own question. DIT = 'T2', so yes, it gets produced.

ok so it appears T0, T1, T2, T3, T4 actually all exist, except T0, T1, T2 are simply byproducts of synthesis and don't do anything.

In fact, there are two T2 hormones, depending on the position of iodine atoms on the thyronine backbone molecule [5].
One of them, 3,5-diiodothyronine (3,5-T2) is the most active of all thyroid hormones with a relative T4 potency of 8 to 15. Thereby, it is 2 to 5 times as potent as T3. Its plasma concentration is rather low, however, being 0.2 to 0.37 nmol/l [1–3]. It is weakly bound to plasma proteins and has a short half-life [7, 8]. 3,5-T2 seems to be a risk factor for atrial fibrillation [3], and it is able to suppress pituitary thyrotropin (TSH) secretion [4]. It is upregulated in critical illness (NTIS/TACITUS) [1, 3, 6].
The second isomer, 3’,5’-T2 is an inhibiting thyroid agent that is able to block the activity of deiodinases and receptors for thyroid hormones, similar to reverse-T3 (rT3) [5].

References

Pinna G, Meinhold H, Hiedra L, Thoma R, Hoell T, Gräf KJ, Stoltenburg-Didinger G, Eravci M, Prengel H, Brödel O, Finke R, Baumgartner A. Elevated 3,5-diiodothyronine concentrations in the sera of patients with nonthyroidal illnesses and brain tumors. J Clin Endocrinol Metab. 1997 May;82(5):1535-42. PMID 9141546. https://pubmed.ncbi.nlm.nih.gov/9141546/
Lehmphul I, Brabant G, Wallaschofski H, Ruchala M, Strasburger CJ, Köhrle J, Wu Z. Detection of 3,5-diiodothyronine in sera of patients with altered thyroid status using a new monoclonal antibody-based chemiluminescence immunoassay. Thyroid. 2014 Sep;24(9):1350-60. doi: 10.1089/thy.2013.0688. Epub 2014 Aug 1. PMID: 24967815. https://pubmed.ncbi.nlm.nih.gov/24967815/
Dietrich JW, Müller P, Schiedat F, Schlömicher M, Strauch J, Chatzitomaris A, Klein HH, Mügge A, Köhrle J, Rijntjes E, Lehmphul I. Nonthyroidal Illness Syndrome in Cardiac Illness Involves Elevated Concentrations of 3,5-Diiodothyronine and Correlates with Atrial Remodeling. Eur Thyroid J. 2015 Jun;4(2):129-37. doi: 10.1159/000381543. PMID 26279999. https://pubmed.ncbi.nlm.nih.gov/26279999/
Pietzner M, Lehmphul I, Friedrich N, Schurmann C, Ittermann T, Dörr M, Nauck M, Laqua R, Völker U, Brabant G, Völzke H, Köhrle J, Homuth G, Wallaschofski H. Translating pharmacological findings from hypothyroid rodents to euthyroid humans: is there a functional role of endogenous 3,5-T2? Thyroid. 2015 Feb;25(2):188-97. doi: 10.1089/thy.2014.0262. PMID 25343227. https://pubmed.ncbi.nlm.nih.gov/25343227/
Hoermann R, Midgley JE, Larisch R, Dietrich JW. Homeostatic Control of the Thyroid-Pituitary Axis: Perspectives for Diagnosis and Treatment. Front Endocrinol (Lausanne). 2015 Nov 20;6:177. doi: 10.3389/fendo.2015.00177. PMID: 26635726; PMCID: PMC4653296. https://pubmed.ncbi.nlm.nih.gov/26635726/
Langouche L, Lehmphul I, Perre SV, Köhrle J, Van den Berghe G. Circulating 3-T1AM and 3,5-T2 in Critically Ill Patients: A Cross-Sectional Observational Study. Thyroid. 2016 Dec;26(12):1674-1680. PMID 27676423. https://pubmed.ncbi.nlm.nih.gov/27676423/
Louzada RA, Carvalho DP. Similarities and Differences in the Peripheral Actions of Thyroid Hormones and Their Metabolites. Front Endocrinol (Lausanne). 2018 Jul 19;9:394. doi: 10.3389/fendo.2018.00394. PMID: 30072951. https://pubmed.ncbi.nlm.nih.gov/30072951/
Köhrle J, Lehmphul I, Pietzner M, Renko K, Rijntjes E, Richards K, Anselmo J, Danielsen M, Jonklaas J. 3,5-T2-A Janus-Faced Thyroid Hormone Metabolite Exerts Both Canonical T3-Mimetic Endocrine and Intracrine Hepatic Action. Front Endocrinol (Lausanne). 2020 Jan 8;10:787. doi: 10.3389/fendo.2019.00787. PMID: 31969860; PMCID: PMC6960127. https://pubmed.ncbi.nlm.nih.gov/31969860/


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Refuge impact on growth rate
I have a question related to the refuge effect in ecological models. The assumption is that the population of hosts/prey is divided into two groups. One group consists of individuals that are safe from parasitoids/predators and another group consists of individuals that are exposed to parasitoids/predators and can get parasitized. Does it affect the growth rate in the sense that hosts that are in refuge have a bigger growth rate than those that are not in refuge? Are there some known experimental results, some papers or books that deal with this topic?

The answer to this depends a lot on what kind of question you're asking. Adding more context/clarifying your question might help you get more useful answers.
If you run a short-term experiment starting with the same population sizes in each region, and little mixing between populations, the protected population must grow faster (given that the protected region is the same in every way as the exposed region except for being protected from natural enemies).
Of course, if you don't have enough statistical power (there isn't very much predation even in the exposed region, or your population counts are not very accurate, or there is lots of other random variation in the growth rate) then you might not be able to detect this difference.
There are lots of potential confounding effects:

how smart are the prey? Do they preferentially move into the refuge (in which case the protective effect of the refuge might be overestimated)?
... or do they prefer places with lower conspecific densities (in which case they might preferentially move out of the refuge as predators remove conspecifics in the exposed region; you might underestimate the protective effect of the refuge)
or do conspecific densities affect survival or fecundity in other ways? (If the protected individuals die less from predation, this might be compensated by other effects of crowding.)
how do the natural-enemy (predator/parasite/parasitoid) densities respond to changes in host density?
are the refuge and the protected area really identical in all other ways? If this is an observational study, maybe the prey species is already making a tradeoff between areas on the basis of predation risk balanced with some other benefit (such as greater resource availability)

There is a lot of research about all of these complexities (you might start by doing a literature search on "ideal free distribution" and "predator", or "landscape of fear"; however, most of this research is about short-term redistribution rather than long-term growth rates)
If none of these complications is occurring (in particular, no other environmental differences and no differences due to host densities in each area) then we could also say that the fitness (i.e., expected number of lifetime offspring) of hosts in the protected area would also be expected to be higher than that of hosts in the exposed area (this might be what you mean by "growth rate").
You might want to dig into the literature on marine protected areas, where researchers consider how population dynamics work inside and outside spatial regions where fishing is excluded (which is similar to protection from predators or parasites).
From a very narrow mathematical biology perspective, if the two populations are coupled (i.e. individuals can move back and forth between refuge and non-refuge areas), then there aren't separate growth rates for the two subpopulations — in the long run, both will grow at the same (exponential) rate as the whole population (discounting density-dependent effects). Consider the simplest possible model:
$$
\begin{split}
N_e' & = (r-p-m)N_e + m N_p \\
N_p' & = (r-m) N_p + m N_e,
\end{split}
$$
where $N_e$ and $N_p$ are the "exposed" and "protected" population sizes (and $N_e'$, $N_p'$ are their derivatives/instantaneous growth rates); $r$ is the intrinsic growth rate (in the absence of predators); $p$ is the per capita predation rate; and $m$ is the migration rate, the per capita rate at which individuals move back and forth between protected and exposed areas. (This model is horribly unrealistic because it assumes that all of the per capita rates are constant — neither the intrinsic growth rate of the prey, nor the attack rate of the predators, nor the behaviour of the prey, can change as the population densities in both regions change.)
We can do the typical mathematical analysis of this system:

find the Jacobian of the system

$$
J = \left(
\begin{array}{cc}
r-p-m & m \\
m     & r-m
\end{array}
\right)
$$

calculate its eigenvalues, $r-m - \frac{p}{2} \pm \frac{\sqrt{4 m^2 + p^2}}{2}$
conclude that the overall population size (and both components) grow, asymptotically, at an exponential rate given by the largest eigenvalue (the positive root above), unless $m=0$ (in which case the protected population grows at rate $r$ and the exposed population grows at rate $r-p$).
if you want to know the relative contribution of the two subpopulation densities to the whole population (attained asymptotically), calculate the eigenvector associated with the dominant eigenvalue and scale its magnitude to 1.0.

Great explanation, thanks a lot!


text:
What do lower case nucleotides mean in this gene sequence?
The following table (image linked below) shows promoter sequences recognized by different sigma factors. The sequence given for, e.g. sigma B is "GTTTaa"; why are the "a"s lowercase?

(from "A sigma factor toolbox for orthogonal gene expression in Escherichia coli", Bervoets et. al. 2018)

How would we know, without reading the paper, which you can do yourself? It is in no way a standard convention, as some databases have all nucleotides in lowercase.

The case refers to the degree of conservation of a particular nucleotide in the consensus sequence. Highly conserved nucleotides are written in uppercase. At positions where the sequence varies, the most common nucleotide is given in lower case. That said, I'm not sure what the cut-off would be between "highly conserved" and "most common" and, in my opinion, is something that should be explained in the paper (though, in this case, it does not appear to be). There may be some convention I am unaware of.

@canadianer Can you make that an answer rather than a comment?

@BryanKrause Okay, though I don't particularly like ending an answer with "I am unaware".

Here's a link to the paper, for those interested: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829568/ No mention of what the frequency cutoffs are for conserved-bases/less-conserved-but-higher-than-background-bases, but contacting the authors may help with getting specific percentages. (That's what the contact info is for!)

The case refers to the degree of conservation of a particular nucleotide in the consensus sequence. Highly conserved nucleotides are written in uppercase. At positions where the sequence varies, the most common nucleotide is given in lower case. That said, I'm not sure what the cut-off would be between "highly conserved" and "most common" and, in my opinion, is something that should be explained in the paper (though, in this case, it does not appear to be). This paper, for example, uses uppercase where a base is conserved in four of the five sequenced promoters. There may be some convention I am unaware of.


text:
How is plasmin formed from plasminogen?
In Ganong's Review of medical physiology it is mentioned that plasminogen is converted to active plasmin when tissue type plaminogen activator hydrolyses the bond between Arg560 and Valine 561. Can anyone show the molecular mechanism ? What happens to the two different parts of the hydrolysed chain.

I'm a bit unclear what you mean by "molecular mechanism" - are you looking for the mechanism of the cleavage itself? The change in conformation that makes plasmin active while plasminogen is inactive? The general principles or those specific to this particular protein?

Tissue plasminogen activator is a serine protease consisting of approximately  530 amino acids and about 13% carbohydrate.
This enzyme is made up of five domains performing different functions. The finger domain and the two kringle domains are involved in the binding of t-PA to fibrin, whereas the epidermal growth factor domain is responsible for activating EGF receptor. Kringle 1 also help in transport of this molecule via liver's endothelial cells. Kringle 2 also helps in binding with inactive plasminogen. The serine protease domain cleaves the plasminogen at  Arg561-Val562  and activates it into plasmin.

(Image Source: https://www.researchgate.net/figure/Structure-and-functions-of-tissue-type-Plasminogen-Activator-tPA-A-Structure-of_fig1_284797342)
Plasminogen is the precursor for synthesis of protease plasmin. Plasminogen is converted to plasmin by cleaving Arg561 and Val562. The  activated plasmin is formed by making disulfide-linkage between these two polypeptide chains.
The heavy chain  is at the N-terminal and light chain is at C-terminal.  The activation takes place by removing the signal peptide and activation peptide  by autolytic cleavage. This activation peptide is released from the N-terminal  to convert Glu-plasmin to  Lys-Plasmin. The active site which plays role in binding with fibrin is situated on the light chain.

(Image Source:  https://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/plasmin.html)
So, this proteolysis only produces one working peptide sequence, as the peptide bond cleaved and then amino acids are again joined by disulfide bond. And this peptide bond between arginine and valine is at 561/562 instead of 560/561 according to various sources.


text:
Has electrical activation, rather than mechanical tension been investigated as a direct trigger for hypertrophy?
Three of the most common theories for what induces hypertrophy are mechanical tension, muscle damage and metabolic fatigue.
The prevailing theory at the moment is that mechanical tension is the main mechanism for inducing hypertrophy, with the other two possibly playing a smaller role. [1]
More specifically, activation and mechanical tension in high threshold motor units (type 2 fibres) induces hypertrophy, whereas activation of low threshold motor units (type 1 fibres) induces little to no hypertrophy.
The theory is that the muscle cells have a mechanism whereby they sense being physically stretched, which triggers off the hypertrophic cascade.
It seems that mechanical tension would highly correlate with activation. In that,  when electrical signals from the nervous system are telling the muscle to contract, a stronger electrical signal would result in greater contraction and therefore greater mechanical tension.
My theory is that an alternative mechanism could be that the muscle cells sense high levels of electrical activation in type 2 muscle fibers, and it is this which directly triggers the hypertrophic cascade, rather than the cells sensing being physically stretched.
Has any research been conducted as to whether it is the electrical activity itself which triggers the hypertrophic cascade rather than mechanical tension?

An answer for this should be relatively easy to find. If it were so, repeated electrical stimulation should induce muscle mass increase without mechanical load. Does it?

My theory is that this would only be the case if the electrical stimulation is strong enough, and necessarily occurs in high threshold motor units.

It doesn't matter what your theory is. What does the research say? I gave you ample terms to do an effective search.


text:
A cup of milk dregs has turned a deep blue color. What is growing in it?
Ok, so yes this is gross and all. But it was too amazing to me to keep to myself. I left a cup with a small amount of leftover milk from "honey bunches of oats" out for like 2-3 days and this is what I found:

It's a shiny (might I say pretty?) paint-like shade of turquoise. Can anyone identify what is growing is cup or shed light on what happened? I've never seen milk go off like this before.


text:
Tree ID request
We have a small tree (more like a shrub) in our village in North Eastern Anatolia, and it is known for its local name which is not Turkish. Even worse, I don't know which language it is, but most likely there are Armenian, Georgian, maybe Russian influences in the regions' language. So I cannot find it in literature.
It is spelled as "syr-sun-syllic". Its fruit has a name too, that is pronounced like "lyllic". It gives red and round fruits in autumn, which are edible.
Here are some photos.

It is said to be "lonicera iberica" by http://nhm.co.uk, which has edible fruits.

In addition, it gives fruits in autumn.

could you describe the flowers and the fruit? the way the leaves grow reminds me of honeysuckle (Lonicera).

What's the local name?

It is spelled as "syr-sun-syllic". Its fruit has a name too, that is pronounced like "lyllic". Our villages have more words that are not Turkish. Even the villages called with their non turkish old names by the peasents. I think probable languages affected us are armenian, georgian, maybe russian etc.

Nope it is probably not a honeysuckle.

It has a layered trunk and one can easily tear them off by hand.

The leaves are indeed similar to lonicera (honeysuckle). How do the flowers and fruit look? What color, size and shape do they have? Do they grow solitary or in groups? Any info might help (and a picture would be fantastic).

Its fruits are small red rounds and are eatable.

Interesting. Red and round rules out Eucalyptus, that does have opposite-leaves and a peeling bark. Honeysuckle has red and round fruits but afaik they are not edible.

It is said to be lonicera iberica by nhm.co.uk, which has edible fruits.

@AhmedBilâl You should post this as an answer. Posting answers to your own questions (if you find them) is encouraged in the StackExchange network. Then your questions is also removed from the unanswered queue.

It is said to be lonicera iberica by nhm.co.uk, which has edible fruits.

It would be nice if you could expand this answer and add a picture of the plant. Additionally it is always good to not give just a one-line answer but one, that stands on its own and explains stuff.


text:
Models of quorum sensing for multi-agent systems
Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model of quorum sensing that abstracts away from the details of the mechanism implementing it inside the agent, but keeps the key inter-agent properties like diffusion rate, range, and timing.
Is there a standard abstract mathematical model of quorum sensing used by biologists?
I am not interested in the particulars of a specific organism, but would like a general model I could apply to capture the 'gist' for any organism that relies on quorum sensing for part of its behavior.

Bernardini et al. (2007) provided an extension to P-systems incorporating the basics of quorum sensing, and Romero-Campero & Pérez-Jiménez (2008) have used their approach to model bioluminosity in vibrio fischeri. This approach is conceptually appealing to me, but that is because I am predominantly a computer scientists. Although P-system can be used for modeling biological systems (Ardelean & Cavaliere, 2003), they still feel fundamentally computer-science-y and are typically not published in orthodox biological venues. This makes me suspect there is a more standard approach among biologists, probably via dynamic systems and diffusion equations.

It may not be what you are looking for, but there is a quorum sensing model available here at the EBI repository.

I found this paper[1], which might be relevant; it uses is a more chemically inspired approach. Another paper[2] also might be interesting, it takes a more dynamical systems approach.
My personal instinct would be to use ordinary differential equations: generate a population of cells in random positions, assign each cell levels of any relevant molecular species, and come up with a list of ODEs that describe the rates of change of the species in a particular cell in terms of gene expression, degradation, and diffusion. You should then be able to simulate the time evolution of the system just by solving the (large) system of ODEs given your initial conditions. Something like the approach in this paper[3] (read the supplemental info), only your cells would move around during the simulation, rather than remaining still as part of a tissue. The implementation would get thorny, because you would have to accommodate the motion of the cells as you solve the ODEs. I imagine that this could be accomplished by simply treating the initial positions of the cells as part of the system's initial conditions and then defining the ODEs that govern the rate of change in each dimension (either randomly, or perhaps they move in a coordinated manner) so that this aspect of the system can evolve during the integration.
References:

 Rai N, Anand R, Ramkumar K, Sreenivasan V, Dabholkar S, Venkatesh KV, Thattai M. 2012. Prediction by promoter logic in bacterial quorum sensing. PLoS computational biology 8: e1002361.
 Chiang W-Y, Li Y-X, Lai P-Y. 2011. Simple models for quorum sensing: Nonlinear dynamical analysis. Physical Review E 84.
 Lubensky DK, Pennington MW, Shraiman BI, Baker NE. 2011. A dynamical model of ommatidial crystal formation. Proceedings of the National Academy of Sciences of the United States of America 108: 11145–50.

Since the accepted answer is nearly a decade old, I'm adding a new answer to address a recent piece of research that presents a good framework for modeling quorum sensing over small distances.1
First, the authors consider two types of signal diffusion systems.

Absorbing -- the signal molecule is imported into the recipient cell, where it interacts with its receptor to induce a response. This process is irreversible (the signaling molecule is "used up" once imported). Many peptide-based quorum sensing systems found in Gram-positive bacteria are absorbing systems.2
Non-absorbing -- the signal molecule interacts with a receptor on the surface of a recipient cell, inducing some response cascade. The signal then dissociates and diffuses into the intercellular space, where it can interact with other recipient cells. Examples of non-absorbing systems include autoinducer networks in Vibrio species 3 and acyl-homoserine lactone quorum sensing systems in Proteobacteria.4

Next, they made three modeling predictions, and tested each prediction in synthetic communities grown in microfluidic chambers. Their model organism, B. subtilis, was transformed with signal-recipient gene pairs from both absorbing and non-absorbing systems, though the bulk of their paper is spent discussing the less well-studied absorbing modality.

Signal response in signal-receiving cells ($Y$) is inversely proportional to their distance from the signal source boundary ($x$) and is a function of the communication range ($\lambda$). For a absorbing systems, the authors define $\lambda$ as "...the distance from the boundary of signal producers over which the signal response reduces one order of magnitude ... on a natural log scale". Unsurprisingly, they predict absorbing systems to have much shorter signaling ranges than non-absorbing systems, assuming a high signal uptake rate among recipient cells.

$$Y(x) \propto e^{-x/\lambda}$$

In absorbing systems, communication range ($\lambda$) is a function of signal diffusion rate ($D$) and signal uptake rate ($\alpha$). Using the Stokes-Einstein equation 5 and an estimated radius of 0.5 nm for small peptides, the authors estimate that signaling molecules diffuse through water at a rate of ~
400 μm2s-1.
$$\lambda ≅ \sqrt{\frac{D}{\alpha}}$$

In both absorbing and non-absorbing systems, the signal concentration (and thus the signal response $Y$) is related to the width of the cluster of signal-producing cells ($W$). Simply, more cells produce more molecules. For non-absorbing systems, the signal concentration is unbounded. However, the concentration of signaling molecules in absorbing systems saturates when the cluster radius is larger than $\lambda$.

$$Y \propto W^2$$
The authors find experimental justification for each of their model predictions (I suspect the predictions wouldn't have been included in the paper, otherwise). For the nitty-gritty math behind their models and other assumptions / simplifications, read Section 2 from the supplementary discussion, Mathematical modeling of quorum-sensing designs. An excerpt:

While bacterial communities consist of cells, we use a continuous framework to model the community. That is, instead of modeling cells that produce and receive signal molecules explicitly, we simplify the model by assuming a constant production rate per unit volume and a decay rate per unit volume of the community.

References

van Gestel J, Bareia T, Tenennbaum B, Dal Co A, Guler P, Aframian N, Puyesky S, Grinberg I, D'Souza GG, Erez Z, Ackermann M, Eldar A. Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities. Nat Commun. 2021 Apr 19;12(1):2324.
Neiditch MB, Capodagli GC, Prehna G, Federle MJ. Genetic and Structural Analyses of RRNPP Intercellular Peptide Signaling of Gram-Positive Bacteria. Annu Rev Genet. 2017 Nov 27;51:311-333.
Papenfort K, Bassler BL. Quorum sensing signal-response systems in Gram-negative bacteria. Nat Rev Microbiol. 2016 Aug 11;14(9):576-88.
Schuster M, Sexton DJ, Diggle SP, Greenberg EP. Acyl-homoserine lactone quorum sensing: from evolution to application. Annu Rev Microbiol. 2013;67:43-63.
Miller CC. The Stokes-Einstein law for diffusion in solution. Proc Roy Soc. 1921;106:724.


text:
How can a chromosome translocation in somatic cells lead to disease?
Looking at this picture...

(source: nih.gov)
...I get the impression that the part of chromosome is attached to other chromosome, but it is not mutated. When we assume that all genes in the translocated part are intact and can still make mRNA, my question is:
How can a chromosome translocation in somatic cells lead to abnormality or disease?

The concept of "in somatic cell" that you recently added to the post is a little unclear to me, probably just because I am not aware of any particular example. Can you cite an example of an abnormality/disease that you are interested in?

https://en.wikipedia.org/wiki/Chromosomal_translocation#Role_in_disease

Thank you. I think what you mean by "in the somatic cell" is actually "for the balanced carrier". I tried to expand on my current answer. Let me know if that make more sense now.

You can't assume that all genes remain intact. What if the translocation break occurs inside a gene and inactivated it? And what if that gene is a tumour suppressor.

In the Down syndrom typically, the translocation does not induce (usually; see later) any disease. We call someone carrying the translocation a "balanced carrier". The problem arises after, at the moment of segregation.
When balanced carriers reproduce
Consider someone who has a translocation as you showed. You showed only one chromosome of each types (1N), below are the 2 chromosomes (2N). On the below image, the person with the translocation is assumed to be mating with someone who does not have the translocation.

The balance carrier is usually healthy. As a consequence of this translocation a kid has probability 1/4 to be "normal", 1/4 to have the translocation (and therefore to eventually have offspring with trisomy/monosomy) and a probability 1/2 to have trisomy/monosomy.
Balanced carrier
Citing from wikipedia:

Most balanced translocation carriers are healthy and do not have any symptoms. But about 6% of them have a range of symptoms that may include autism, intellectual disability, or congenital anomalies. A gene disrupted or disregulated at the breakpoint of the translocation carrier is likely the cause of these symptoms.

Indeed, even a balanced carrier can be affected by the translocation. Gene regulation network is often quite complex and separating a gene from its regulatory region can eventually have important impact. It is also possible that the break point occurred in the middle of a gene (or a regulatory sequence).
I think that one cannot say much more about why a balanced carrier can be sick in a general form. We'll need to go case by case and ask specifically what are the genes and regulatory processes involved in the disease. However, it is easy to conceptualize that moving genes around can affect the genetic network and the expression of genes.

Thanks for this fantastic explanation. This make complete sense in case of Meiosis but my original question was intend to chromosomal translocation in somatic cells. If you can add some detail about somatic cells chromosomal translocation  I will accept it as answer.

Let us know if you feel like the updated answer (based on you updated question) does not answer your question?

You have made an incorrect assumption-- that all the genes on both chromosomes necessarily remain intact. It's possible that they do, and the the translocation is harmless.
But the transition point could be within a gene. This would usually lead to that copy of the gene becoming inactive, which can cause diseases just like any other loss-of-function mutation.
Alternately, the translocation can fuse two genes in a pathogenic way. While this might seem fantastically unlikely, the fact that the translocations are non-random means that there are patterns that recur frequently. The BRC-ABL fusion (https://en.wikipedia.org/wiki/Philadelphia_chromosome) is one of the most common causes of childhood leukemia. The fusion protein is constitutively active because the regulatory domain of the original protein has been replaced.
Finally, a translocation could separate a promoter element from the gene it controls, which could cause aberrant expression of that gene. The promoter element could also wind up proximal to a different gene and cause aberrant expression of that gene.


text:
How are amino acids neutral at physiological pH?
Amino acids with non‐ionizable side chains are zwitterions when they are at physiological pH, pH 7.4. This is what my book says. But I do not understand why. The Pka for a carboxyl group is around 3 and the pKa for an amino group is around 9. So the isoelectric point should be around ( 9+3) /2 = 6 for an amino acid with no ionizable side chain. At pH 7.4 it would be slightly negative, would it not?
Also what exactly is a basic amino acid? Is that an amino acid that has a PI value of more than 7?
Thank you.

You are right, most of the amino acids have pI around 6, so they are slightly negative at pH 7.

Calculating approximate isoelectric points for amino acids and peptides

The isoelectric point depends on the amino and carboxylic-acid groups and the groups of the side chain. E.g. lysine has an amino group on the side chain, so it has a pI of 9.74.

If an amino acid has two amino groups and only one carboxyl group (like arginine and lysine), then they are positively charged (++ vs. -) at neutral pH. On the other hand, if amino acids have two carboxyl groups and only one amino group (like glutamic acid and aspartic acid), they are negatively charged at pH7 (-- vs. +). You are not correct that the groups are truly neutral. The carboxyl group is negatively charged in a solution much higher than the pKa of the carboxyl group (which is pH 2.48 for arginine). Same is true for the amino groups (pKb is at pH 11.5 for arginine). So, at pH 9.5, the ratio of the positively charged amino group to a neutral amino group is 100:1 (at the pKb it would be 50:50). At a pH of 4.48, the carboxyl group of arginine would be 1:100 negatively charged, versus neutral. So, at pH7, all of the carboxyl group is negatively charged (COO-) and all of the amino groups (2 of them) are fully positively charged (NH3+). Net charge is plus 1, in the case of arginine at pH7.

At pH 7.4 a carboxyl group is mostly present as COO-, while an amino group is present as NH3+. So when a molecule has both groups, such as an amino acid, the molecule as a whole is neutral. As it is a Zwitterion (equal + and - charges) the hydrogen can also flip flop between amino and carboxyl group. Making the molecule 'truly' neutral as both groups are not charged.
A basic amino acid has a basic group such as an amino group (Arginine) on its side chain.

The truly neutral (no positive charge on the amino group and no negative charge on the carboxyl group) does not really exist, since pH7 is far away from the pK of the individual groups (amino and carboxyl). Probability is much less than 1:100.

Technically yes, most amino acids will be slightly negatively charged at physiological pH. But we need to understand what that means. Let's take alanine as an example. Any individual alanine molecule can either be uncharged or have an integer net charge- it's either protonated or it's not. You will never find a "partially charged" alanine molecule. However, if you have a bunch of alanine molecules in solution physiological pH, they won't all behave in exactly the same way at exactly the same time. One molecule may have a protonated N-terminus while another has a deprotonated N-terminus. At physiological pH, the C-terminus is pretty much completely deprotonated, so we just have to pay attention to the N-terminus. We can use the Henderson-Hasselbach equation to figure out what percentage of alanine molecules will have a protonated (positively charged) N-terminus and what percentage is deprotonated. pH = pKa + log(deprotonated/protonated).  If we substitute in our known numbers, we get 7.4 = 9.5 + log(deprotonated/protonated)
Therefore -2.1 = log(deprot/prot) and 10^-2.1 = deprot/prot = 0.008. That means that out of 1000 alanine molecules, about 8 of them are deprotonated and therefore negatively charged. The other 992 are zwitterions. So for all intents and purposes alanine is neutral at physiological pH.

Please add some references to your answer.


text:
Transcription Factor expression level
Could someone explain me in detail what is meant by "TF expression LEVEL", what does it represent and how is it measured? This is for example used in figure 3 of this paper: A census of human transcription factors: function, expression and evolution.

Where did you find this expression?

@Chris In scientific litterature, I am trying to understand a paper on the topic. Google gives more than 15o.ooo results containing the exact expression "Transcription Factor expression level". Any ideas what it means ?

I understand that. Can you link the paper in quest and probably also say in which section it is? That may make the answer easier.

http://www.nature.com/nrg/journal/v10/n4/full/nrg2538.html see Figure 3, for example

Transcription factors are an important cellular regulatory mechanism to control gene expression. The expression of TF is important for cell function, differentiation and also for responses to environmental signals.
We know quite a number of different TF, but only for a little part of them their exact function (in terms of which in which tissues they are expressed, when and which genes they regulate) and this is where the paper you read comes in.
They test for the expression of roughly 1400 TF in a number of different tissues, to see where they are expressed (figure 3 from the paper):

The group used micro-arrays to analyze the expression levels (in this case how much transcript from the genes is made assuming that this also translated). The quantification was done using the signal strength of the array - the more transcript you have, the stronger the signal is.
The expression of a certain TF in a specific tissues shows its involvement in gene regulation (either direct or indirect) there.

Thank you ! What does it mean for a TF to be expressed in a tissue ? Does it mean that it participates in gene transcription in the cells of this tissue ?

Yes, either directly in the expression or indirectly in its regulation. Transcription complexes are often very big.