Trying to understand reduction of color dimension in colorblind case I understand that dichromats have one of their cone missing/not functioning. And as for Monochromats, 2 or all of their 3 cones are missing/not functioning. And I read from Wikipedia - Color Blindness :

  Dichromacy occurs when one of the cone pigments is missing and color is reduced to two dimensions.

and

  Monochromacy occurs when two or all three of the cone pigments are missing and color and lightness vision is reduced to one dimension.

Since in the description they relate the cones with Red, Blue, Green (RGB) a lot, eventhough I'm fully aware that relation of cones and RGB is most likely for historical reason . I'd like to assume in this reduction from 3-dimensional into less dimensional colorspace dimension written in Wikipedia based on RGB colorspace.

This is original RGB colorspace in 3-Dimension

Question 1 : How exactly reduction from 3-dimensional to 2-dimensional or even 1-dimensional in colorblind case happen ? For example in Protanopia, would they lose the Red axis ? So only Blue and Green axis left ? (Any reference will be appreciated).

I also read this question If people with colorblindness lack one type of cone cells, shouldn't they be unable to recognize one particular color?. And it's written that Dichromats can match any color they see with some mixture of just two primary colors. Cones do not literally interpret colors. The three cones work together to encode a signal.

Question 2 : If cones don't really interpret any color in human color vision system. Is it wise that losing cone means reduce from 3-dimensional color into 2-dimensional by completely erase the corresponding color axis to the cone ?

[UPDATE]

For Question 1 :

Taken from the book Visual Transduction and Non-Visual Light Perception (p308),

Univariance, Monochromacy, Dichromacy, and Trichromacy

  If only one photoreceptor type operates, vision is monochromatic or reduced to a single dimension

  If only two cone photoreceptors operate, vision is dichromatic or reduced to two dimensions

and

  Most observers
  with normal color vision have three classes of cone photoreceptor and are therefore trichromatic.

So, I'm sure in my Question 1, they really refer to Young–Helmholtz Trichromatic theory. A theory when human color vision possess 3 types of cones thus they have three dimensions of color vision.

However, I still need some opinion related to Question 2. Any comments will be appreciated.

Let's start with a quick overview of the different types of dichromats in man:

Protanopes have no functional red cones. Red appears as black. Certain shades of orange, yellow, and green all appear as yellow.
Deuteranopes have no functional green cones. They tend to see reds as brownish-yellow and greens as beige.
Tritanopes have blue-yellow color blindness and lack blue cone cells. Blue appears green and yellow appears violet or light grey.

Now color vision can be modeled with the Hering model, where there are two opponent channels, namely red-green and blue-yellow. These opponent channels determine color vision. Because of these two limbs, color space is often represented as triangles, rather than cubes as in your post. Fig. 1 shows the color space in trichromats. In Fig. 2 the same is shown, alongside the three types of dichromatic deficiencies.

Fig. 1. Color space in trichromats. source: Lighting Analysis

Fig. 2. Triangles in trichromatic and dichromatic vision. source: Chartlr.


How does DNA from sperm fuse with DNA in egg? I see this statement all the time "half of our DNA (23 chromosomes) are from mom and 23 are from dad". Fine, but which chromosomes in our nucleus are from each parent? When I think of nucleus (before interphase), I imagine a total of 23 unique chromosomes and 23 copies of them. In the first cell after reproduction (zygote), does chromosome 1 from mom align with chromosome 1 from dad? When zygote divides (after S phase) do you now have 4 copies of the same cell? Since choromosome 1 from mom and dad is the same.
What role does crossing over play in all of this.
I have done lots of reading but nothing is helping me connect the dots.

First, to clarify on the number issue and parental origin of the chromosomes. For the moment, disregard crossing over. Then, you would begin with an adult somatic cell in the growth phase, having 46 chromosomes, two of each kind, that is, 23 pairs (assuming sex chromosomes to be of the same kind, including the case in males). Then, in the S phase, each chromosome replicates, creating exactly similar sister chromatids, each of these sisters being similar to the single chromosome the cell had in growth phase. Each of these chromosomes with two chromatids, sends one to each daughter cell, making the daughter cell exactly like their parents. In meiosis, after this step, one of each kind of chromosome separates into a gamete, so that instead of 23 pairs, each gamete has only 23 chromosomes, one of each kind. On fusion of two gametes, you would have the original configuration again.

Crossing over, just means that when the two chromosomes of a particular kind separate during meiosis, they exchange corresponding material. If no crossing over happened, the gamete would either have one of the two same-kind chromosome, or the other. But due to crossing over, you create a different set of genes on these two chromosomes, different from the ones fond elsewhere in your body. So if say two chromosomes of the same kind have genes $ABC$ and $DEF$, if no crossing over happened, the gamete would have either $ABC$ or $DEF$. But crossing over makes possible combinations like $AEF$, or $DEC$ etc.


How do G proteins move? G proteins consist of an alpha subunit and a beta/gamma subunit. These proteins are involved in various cellular signalling process.
From what I have understood, the alpha and gamma subunits have covalently bound lipid tails. That is, they seem to be directly connected to the cellular membrane. If this is the case, how do these protein subunits move?
I understand that the cellular membrane is flexible but I'm currently imagining a flying fox type scenario. This is where the alpha subunit is covalently bonded to one phospholipid and is now gliding down a cell membrane. I kind of find this hard to believe because it seems ridiculous (but fun!).
How do alpha and gamma protein subunits move if they are covalently bonded to the cellular membrane?

Interpretation of the Question
The question asks how the G-protein α- and βγ-subunits move, but does not state the context or circumstances of the movement. I assume that the question is, in fact:

How do the G-protein α- and βγ-subunits move apart and migrate
from receptor to target enzyme when their interaction is prevented by
the binding of GTP to the α-subunit?

False premise in the question
The problem envisaged in the question is that as the α- and γ-subunits have lipid moieties covalently bound to their amino acid chains, they are somehow part of the lipid cell membrane. This non sequitur may arise from a misunderstanding of lipid chemistry: the cell membrane is a bilayer the main constituent of which is individual molecules of phopholipids containing two long fatty acid chains and one polar organic phosphate (e.g. phosphatidyl choline) attached to a glycerol backbone. Other hydrophobic molecules (cholesterol, proteins with hydrophobic amino acids on their surfaces) can interact with these phospholipids.

The lipid moieties attached to the G-protein subunits are, in contrast, single palmitoyl or myristoyl fatty acid chains (in the case of the α-subunit) or farnesyl or geranyl (substituted fatty acid) chains (in the case of the γ-subunit). So the idea that they are somehow equivalent to the membrane phospholipids is incorrect.
How do they move?
As the lipid bilayer is fluid, its constituents can move within it, like ships on the sea. A review by Wedegaertner discussing G-protein trafficking illustrates this as shown below:

When the interaction between the subunits is prevented by GTP, they are free to drift apart in the membrane, like a boat cut loose from a ship at sea. The illustration shows them attached to the membrane by a single line representing the lipid group, but also considers evidence that they may move away from the membrane, presumably because the interaction is weakened on dissociation. Their movement is presumably random thermal motion in each case, as is that which leads to their reassociation after the GTP is hydrolysed.
However, as @BryanKrause mentions in his comment, it should be emphasized that the ability of the subunits to ‘float’ through the membrane (rather than ‘sink’ into the cytoplasm) facilitates their mode of action. They must first associate with the hormone/agonist receptor to receive the initial signal (or first messenger) and then move to interact with the target enzyme/protein which transmits the signal within the cell (e.g. through the second messenger cyclic AMP produced by the enzyme adenyl cyclase). See, for example, this Nature Scitable article.


Will meat rot in alcohol below freezing? I understand that freezing slows decay but I'm wondering what will happen if meat is kept in below freezing temperatures while submerged in a liquid that has a lower freezing rate, like alchohol?

A chemist's perspective:

Ethanol and water are miscible, meaning they are perfectly soluble in one another in all proportions. So given enough time, the alcohol will likely seep into the tissues and cells of the meat, and some water will seep out into the surrounding alcohol bath. The liquids might not equilibrate very well on a reasonable time scale, that is, the bath surrounding the meat could remain mostly alcohol with some water, and the tissues of the meat could contain more water than alcohol. This is because the biological barriers of the meat interfere with the diffusion of the fluids to reach a mixture of equilibrium proportions. However, in theory, cell membranes are permeable to ethanol, so given enough time soaking we might build up a useful concentration of ethanol within the meat.

Note that it doesn't matter so much what happens outside the meat - being bathed in a substance that remains a liquid below 0 °C won't necessarily stop the meat itself (well, the aqueous solutions within it) from freezing. That is why the considerations of solubility and permeability are crucial. As I said, for ethanol we have perfect solubility with water (miscibility), and possibly sufficient ability to diffuse throughout the organic catacombs of our meat. So, assuming ethanol can sufficiently perfuse the tissues and enter the cells, what would happen?

Water has a higher freezing point (not "freezing rate") than ethanol (0 °C > -114 °C). When you mix some ethanol into water, the freezing point of the solution will be lower than the freezing point of the pure water. The freezing point of pure water is depressed by the addition of ethanol. Here is some data on the freezing point of water solutions with different amounts of added ethanol:

(Note that the freezing point at 100% ethanol seems to be -111 °C according to this data; this should technically be freezing point of pure ethanol itself, so we would expect it to be the -114 °C figure I quoted earlier. But that small discrepancy between this experimental data and the traditionally accepted number will not affect our analysis.)

So, as you lower the temperature, the water-ethanol solution in the meat will begin to freeze. It will freeze at some temperature lower than normal because of the ethanol present. Note that the normal freezing point of water in meat is already going to be lower than 0 °C due to all of solutes inherent in such a biological system (ions, sugars, metabolites, maybe a few stray amino acids, etc). As it freezes, the water will freeze first and leave the ethanol behind.

So, inside the meat, you will see the meat freeze at slightly lower than normal, with some liquid remaining in the tissues which would be the ethanol. Outside the meat, in the bath of ethanol which has drawn some water out of the meat, you will see that water forming ice on top of the liquid, which will become purer and purer ethanol as the water freezes out of it. The process I just described is fractional freezing, and you may be interested to know it is how "ice beers" (Keystone Ice, Natty Ice, etc) are made more alcoholic.

Now, if the proportions of ethanol and water are just right, something interesting happens. Instead of the water freezing first and precipitating out of the ethanol, a special eutectic solution is formed that freezes all at once. (Perhaps you've heard of fractional distillation and azeotropes, the the boiling point analogue to fractional freezing and eutectic mixtures). On the graph above, the eutectic mixture is achieved at the very minimum value, around -118 °C. Note that freezing point of the eutectic mixture is lower than the freezing point of pure ethanol alone. Unfortunately, for the specific case of water and ethanol, reaching that special point of bonus freezing point depression requires the solution to be almost completely ethanol (about 93%). That would be the holy grail of lowering the freezing point of your meat, but it's likely not feasible to replace that much water with ethanol throughout the meat.

So, in conclusion: It's what happens inside the meat that counts. If you bathe meat in ethanol, a useful amount of ethanol may permeate the meat. The freezing point of the meat (rather, the aqueous solution within it) will be lowered the more ethanol perfuses it. In theory, you could even drop that freezing point below that of ethanol itself, but it would require replacing nearly all of the water with ethanol.


Does protein consist of repeating units of amino acids? I am currently studying the chapter called macromolecule. I get that a nucleic acid consists of repeating units of nucleotides, and I personally think "the repeating units" does not mean the nucleotdes are all the same, as nitrogen bases have four types either in DNA or RNA. How about the protein molecule. A protein molecule is made up of amino acids. However, I am sure about whether a protein molecule are made up of same and repeating units of amino acids. Theoretically, the R group in each protein is differed from one another. Therefore, does that mean we cannot state that a protein molecule is made up of repeating units of amino acids?

They are repeating units in the sense that all of the units are amino acids. The R group is different in different amino acids (it is not just different theoretically). The different R groups contribute to the different shape, structure, function of proteins, and if all were the same, then we would have a very limited range of proteins.You will still say it is composed of repeating units, since all units are amino acids, and there are no foreign groups between them.

Similarly, all repeating units of DNA/RNA are nucleotides, even if they aren't the same nucleotides.


Why do chickens not try to get up if laid on their backs? I've seen a few videos about chickens being laid on their backs for a few seconds after which the chickens stay in that position until they are turned over. Comments around the video suggested that lying on their backs is a very unnatural position for most birds and so they don't have any reflexes or instincts that would help them get back up. But this is only speculation. Why is that really happening?

Here's one video demonstrating the effect:
https://youtu.be/R9mzz9jxNsM

I've been told Chicken hypnotism is related to this.

This phenomenon is called tonic immobility. And those speculations you've mentioned are wrong: they do get back on their feet, only remain in that state for a prolonged time, which depends on the distance and eye contact with whoever laid the chicken on its back, as stated here.

From this experiment, it can be concluded, that this behavior in which the animal is immobile is a defense against predation, because most attackers sense motion primary.


Why do some people find vegetables so repellent when evolutionarily they should find them an attractive and thus tasty food? Why do certain people (especially kids) find vegetables so "repellent" when evolutionarily they should find them an attractive and thus tasty food?

I ask this question because if Darwin's theory of evolution is true then foods like vegetables that us human beings have been eating and attaining better health from eating for millions of years should have a taste that accordingly attracts us to them.

Evolution is not that simple. There is no selective pressure for a feature if it does not ultimately in some way benefit reproduction or the offspring. Vegetables are healthy for us now because we live much longer than we used to in an environment not dominated by us, and they contain many nutrients which help to sustain a healthy body beyond, say, 50.

However, if you imagine an average life span of around 30, it becomes clearer why evolution would favour foods high in energy over foods containing high amounts of micronutrients. Over such a time span, the long-term effects of a diet rich in fat and sugar do not develop significantly, but the energy supply is exactly what is needed to sustain bare life to the reproductive age.


To what extent is prion aggregation responsible for Alzheimer's disease? I was intrigued by a description of prions as a factor regarding 'Mad Cow Disease', the epizootic threatening the cattle stock of the United Kingdom and France predominantly.

Understandably, the prion, a misfolded protein causes neurodegenerative damage through inducing an aggregation of prions into a complex capable of converting functional proteins. Disregarding Creutzfeldt-Jacob disease, thus far believed to be a Dementia characterised by the accumulation of prions, I simply seek clarification as to whether the onset of Alzheimer's disease should have a direct correlation with an aggregate of misfolded proteins.

Nota Bene

Although the hypothesis regarding the accumulation of amyloid-derived diffusible ligands, toxic oligomers, may be associated with the prion causing Bovine Spongiform Encephalitis, if any further clarity regarding the direct correlation between these two events in humans would be appreciated.

To What extend is prion aggregation responsible for Alzheimers's disease?

Until recently, there was no 'hard evidence' implicating an infectious, self-propagating protein or prion (proteinaceous infectious particle) in Alzheimer's disease, or any convincing evidence that  a prion-like mechanism  is involved in this disease.

However, I quote from a recent review (Alzheimer’s and Parkinson’s diseases:  The prion concept in relation to assembled A$\beta$, tau, and alpha-synuclein) by a leading researcher in the Alzheimer's field:

  Transcellular propagation of protein pathogens, reminiscent of the spread of viruses, represents an unprecedented concept of disease. It is now known to extend beyond CJD [Creutzfeldt-Jakob disease], to include AD [Alzheimer's disease]  and PD [Parkinson's disease], which are the most common neurodegenerative diseases.

Pruisner,
 who
 received a Nobel prize
 for his work on prions ('a new biological principle of infection'), was one of the first to suggest that neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease, like Creutzfeldt-Jakob disease (CJD), may be due to a prion, or to a prion-like mechanism. He points out that over 80% of these diseases are sporadic, late-onset, and involve proteins present since birth (see
 A Unifying Role for Prions in Neurodegenerative Diseases
 ).

However, there  is one caveat.  The prion causing CJD, scrapie and kuri may be transmitted from one individual to another, and there is no evidence that Alzheimer's disease or Parkinson's disease may be so transmitted or  are in any way infectious.

What is Alzheimer's disease?

Alzheimer's disease is a neurodegenerative disease, and a disease of ageing, that causes severe dementia worsening over time. It affects 10% of those over 65 years of age, and 50% of those aged over 85  years. There is no known cause, and no known cure.  It is the leading cause of dementia, ahead of Parkinson's disease.  Most cases of AD are sporadic, but a small percentage have a genetic origin (familial AD).

The disease was first described (On certain peculiar diseases of old age)  by Alois Alzheimer in 1906. After histochemical analysis, Alzheimer described  two characteristic abnormalities in the postmortem brain of a 51-year old woman :  the (extracellular) neuritic plaques and the (intracellular) neurofibrillary tangles.

There is a very nice picture of both neuritic plaques and neurofibrillary tangles in Fig 1(A) of Goedert (2005).  For a great summary of the history of AD and references to the above summary, see  A Century of Alzheimer's Disease (2006) by Goedert & Spillantini.

What are the neuritic plaques?

Neuritic plaques are extracellular structures primarily composed of  a small peptide of (usually) either 40 or 42  amino acids known as  the amyloid-$\beta$ ($\beta$A), where the '$\beta$' refers to their tendency to form beta sheets.

This small peptide arises by proteolysis of a much larger protein of unknown function, the amyloid precursor protein (APP). The APP is a trans-membrane protein with  a single membrane-spanning segment, where the N-terminus (28 amino acids) is extracellular. Two proteases are responsible for generating $\beta$A :   $\beta$-secretase and $\gamma$-secretase

Peptide bond cleavage by   $\gamma$-secretase  occurs within the membrane-spanning region of APP and components of this proteolytic complex (the presenilins) are 'major players' in the Alzheimer's story.

It is thought that A$\beta$ is a 'normal' brain peptide, that is it does not arise from 'aberrant' proteolysis, but its function is unknown (Goedert & Spillantini, 2006).

Finally, mutations in the APP gene are known to cause familial AD, but account for only a minority of cases. (Goedert & Spillantini, 2006).

So, the structure of the neuritic plaques is known. They consist of a small peptide of unknown function derived from a much larger trans-membrane protein of unknown function.

And the neurofibrillary tangles?

Under the electron microscope, neurofibrillary tangles have a ribbon-like appearance called paired helical filaments.  It is now known that these structures are composed of a single protein, microtubule-associated protein Tau, or Tau protein  in an aggregated and hyper-phosphorylated state. There is  a very nice picture (electron micrograph) of a paired helical filament in  Fig 1(B) of Goedert (2005)

What is Tau Protein?

Tau is a 'normal' brain protein characterized by Kirschner and colleagues (see here and here)  as a microbutule-binding protein, long before its role in Alzheimer's disease was realized.

In humans, it consists of six isoforms generated by differential mRNA splicing of the transcript from a single gene, and 'imperfect repeats' within the amino-acid sequence are thought to be responsible for microtubule binding.

Mutations in the Tau gene are not known to cause Alzheimer's disease, but are responsible for very rare neurogenerative diseases (taupathies ) such as frontotemporal dementia  (FTD) (Goedert, 2005)

In the 'native' state Tau is phosphorylated, and is considered an intrinsically unstructured protein, (there is no crystal structure available), and it is now accepted that  'hyper-phosphorylated' Tau is the major structural component of the paired helical filament of Alzheimer's disease.

I simply seek clarification as to whether the onset of Alzheimer's disease could have a direct correlation with an aggregate of misfolded proteins

This is where things get interesting.  There is no doubt that aggregated proteins are involved in AD. The case of Tau and $\beta$A attest to that, and the paired helical filament could be considered a misfolded state.  Can either of these proteins act  as a prion and transmit the misfolded state?  That is, can Alzheimer's disease be considered a prion disease, where a 'rogue' form of a protein transmits its 'rogueness' to 'normal' proteins?

In the case  of Tau, it has been shown that extracellular Tau aggregates can "transmit a misfolded state from  the outside to the inside of a cell, similar to prions" by inducing fibrillization  of intracellular Tau .  In addition, aggregated intracellular  Tau can transfer to other cells. (Propagation of Tau Misfolding from the Outside to the Inside  of a Cell)

Testing of the hypothesis that prions or a prion-like mechanism is the cause of AD is a very active field and much more detail and discussion will be found in Goedert (2005).

What are the other 'players' in the Azheimer's story?

There are many 'players' in the modern understanding of AD.  Two further important ones are the presenilins and  apolipoprotein E  (APOE).

What are the presenilins?

Presenilins are part of the $\gamma$-secretase complex, a protease that cleaves trans-membrane proteins including APP. Mutations in the presenilin-1 gene are the  most common cause of familial AD; presenilin-2 mutations also known to cause AD. (See  Goedert & Spillantini, 2006).

And apolipoprotien E4?

A risk factor for sporadic AD is inheritance of the  ${\epsilon}_4$ allele of apolipoprotein E (APOE), a protein of fat metabolism,  but the molecular basis for this is a complete mystery.   (Goedert & Spillantini, 2006, Goedert, 2005). Inheriting a single copy of the APO-$\epsilon_4$ gene more than doubles the  likelihood of developing AD; inheriting two copies increases the risk by 12-fold (see Smith, Dana, 2018)

In what looks like a major advance, gene editing has been used to convert a  APO-$\epsilon_4$  phenotype to one resembling 'normal'  APO-$\epsilon_3$.  For a great recent article, see Scientists Fix Genetic Risk Factor for Alzheimer’s Disease in Human Brain Cells by  Dana Smith (2018).


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 ?

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.


How do bumblebees and hornets avoid the negative effects of inbreeding? I just learned that all hornets and bumblebees except for the queen die at the end of the year and the queen starts a new nest in spring.

But that means the next generation of queens have only brothers to breed with.

Should this lead to severe inbreeding, which over a couple of years would cause serious problems for survival?

Queens do not generally breed with their brothers, but with males from other nests. In the life cycle of bees (and other social Hymenoptera), new queens are born late in the season along with haploid male drones. These all leave the nest and disperse in the landscape to find mates to reproduce with. After mating, all males die and the queens overwinter to start new colonies next spring. The situation is therefore not all that different compared to other annual, semelparous (single reproductive event) species, since you have population mixing before mating and reproduction.

Here are a couple of mechanisms that bees avoid inbreeding:

Population mixing before reproduction (see above).
Inbreeding avoidance
That queens prefer not to mate with close relatives has been shown in several species, see e.g. Foster (1992) and Whitehorn et al (2009).
Polyandry
Each queen generally mates with several males (regulary more than 10 in honey bees, see Palmer & Oldroyd, 2000) and stores their sperm to fertilize eggs during the next year, which means that workers and the queens of next year will have different fathers (increasing genetic variability).

References:

Foster. 1992. Nestmate Recognition as an Inbreeding Avoidance Mechanism in Bumble Bees (Hymenoptera: Apidae). Journal of the Kansas Entomological Society 65(3)
Whitehorn et al. 2009. Kin recognition and inbreeding reluctance in bumblebees. Apidologie, 40(6)
Palmer & Oldroyd. 2000. Evolution of multiple mating in the genus Apis. Apidologie 31(2)


The properties of benign tumours Do benign tumours have no functioning apoptosis mechanisms ? If so what stops benign tumours from excessive growth? Also can a benign tumour have a functioning apoptosis mechanism?

Benign tumors can absolutely have mechanisms available to them to commit to and carry out apoptosis.  An example of this would be benign prostatic hyperplasia, in which the balance of apoptotic and proliferating cells is offset, but apoptosis is still occurring, simply at a lower comparative rate than the proliferation.
Benign tumors can therefore be caused either by excessive proliferation or inadequate cell death; evidently, a complete failure of programmed cell death in many tissues would result in a tumor, benign or no.

Source:

Kyprianou N, Tu H, Jacobs SC. Apoptotic versus proliferative activities in human benign prostatic hyperplasia.  Hum Pathol. 1996 Jul. 27(7): 668-75.


Can someone identify this tree from the Pacific Northwest? A tree at my house in Seattle, Washington, USA has these leaves. Can someone tell me what it is?

It looks similar to a Cotinus coggygria, which is a shrub that we call a Smokebush in the UK. But given your location, it could be Cotinus obovatus, known as American smoketree.

See http://dendro.cnre.vt.edu/dendrology/syllabus/factsheet.cfm?ID=415

The leaves will start green and progressively change colour to deep reds in the autumn with sprays of pink-purple flowers in the summer that from a distance look like smoke, hence the name.

Here are some images I have found on the web.

http://www.cirrusimage.com/tree_American_smoke.htm

http://allthedirtongardening.blogspot.co.uk/2012/08/smoke-tree-smoke-bush-coninus.html


Short dated spontaneous ringing in ear What causes very high pitched sound in one's ear?

Spontaneous ringing is caused by When the outer hair cells put energy back into the vibration, which is known as positive feedback. The process is meant to amplify very quiet sounds more so than loud ones. Normally this works, and you would not notice the sound. But occasionally, the amplification level of one or more outer hair cells will go awry and as a result, the whole system will erupt into spontaneous oscillation.

When this occurs, it becomes audible to us. We perceive it as a ringing in the ear, or “sudden-onset ringing tinnitus see here”. As with most of our biological systems, there are quite a few homestatic control mechanisms (negative feedback) which exist to correct the problem and get rid of the oscillation. It takes about 30 seconds for this mechanism to begin, and then sends messages which suppress the ringing. After the message is sent and received, the tinnitus percept begins to fade away.  You can tell when this reaction has taken place as its often accompanied by a slight reduction in hearing sensitivity (like background or ambient noise we hear suddenly getting quieter), followed by a feeling of fullness in the ear. It usually takes about a minute for this process to fully complete.

Sources:

Wikipedia. Wikimedia Foundation. Web. 30 Jan. 2016 (https://en.wikipedia.org/wiki/Tinnitus)
"What Causes Spontaneous Ringing In Our Ears?" Zidbits. Web. 30 Jan. 2016.
"What Causes That Spontaneous Ringing in Your Ears?" Sciencedump. 2015. Web. 30 Jan. 2016.
"Tinnitus." [NIDCD]. Web. 30 Jan. 2016. (http://www.nidcd.nih.gov/health/hearing/pages/tinnitus.aspx)


Why are Arabidopsis plant seeds being sent to the moon and not other seeds? The latest Chang'e-4 rover brings an entire ecosystem with it, including Arabidopsis plant seeds and silkworms.

My question is: why Arabidopsis? Is this question conclusive without having to ask Chinese sources, such as just by having an educated guess as regards to the plant's own qualities?

Without speculating further about specific decision making processes, Arabidopsis is the standard model organism in plant biology, similar to the mouse for mammals, the fruit fly for insects, C. elegans for nematodes, etc.

It's the first plant to have its genome sequenced, it's commonly used in undergraduate laboratory experiments in part because it grows very fast, etc.

If you were going to choose a plant arbitrarily for a research project, it might as well be Arabidopsis, I'd say it would be the default against which other options would be considered.


Is there an evolutionary advantage to crying when sad? It seems as though the act of crying when sad does nothing to relieve that sadness. Is there an advantage to crying from an evolutionary perspective, or is it the end result of a different process? Also, why is there the same physiological reaction of crying when in sadness or in pain?

First, here is a link to an article that discussion the answer to your question:
Why Cry? Evolutionary Biologists Show Crying Can Strengthen Relationships

The original article to which it refers can be found here:
Emotional Tears as Biological Signals

To speculate a bit on Jez's question, crying in adults could be a result of our possible Neoteny. Crying in infant animals is extremely common as a way to elicit attention and sympathy from the mother. If we are neotenous apes, crying could be a left-over behavior that was seized by evolution, instead of being discarded.


Is this bacteria or fungi? I've been growing bacteria on an agar plate and after putting the dishes in the incubator, this is what I saw. I'm new to bacteria identification, and is this just contamination by fungi or is this actually bacteria colonies? I suppose it is fungi, but what about the white, round white circles on top of the fungi(the top, left picture), is that bacteria colonies?

It's probably mostly fungal contamination if you did not sterilize and left the container open. This video on how to isolate bacteria better may help: https://www.jove.com/video/3064/aseptic-laboratory-techniques-plating-methods

Good luck!


How does UV light damage the DNA when the chromosomes are deep inside the cell? When UV light falls on the skin it has to go through the cell membrane and the nuclear membrane to reach the chromosomes. So it looks like that the DNA is protected but it probably isn't. Won't membranes be damaged first and the so that the cell dies before the DNA is affected and is replicating wrongly (if it is damaged too)? Or is DNA just really much more vulnerable than cell membrane?

UV Rays kill the cells by damaging the DNA. UV lights do not disrupt the cell membrane. If a cell is exposed to UV light, it creates THYMINE dimers (bond). Thymine dimers are the actual disruption in the kinks of DNA. UV exposure to skin is proportional to the cell damage.

P53 is a gene product which takes care of fixing cell damage. However it has a tolerance. If the damage is less, P53 sends damage repair machinery. If it's non-fixable, then P53 directs the cell to programmed death.

More UV exposure, more thymine dimers causing more cells to die (cell death). If the damage is not extensive, then that may cause cancerous cells (Result of cell damage).


Did human hairs actually evolve from scales? What is the evolution of hairs? Did they evolve from scales?

From a little research I have been able to find some of the hypotheses and speculations but no papers expressly confirming or denying the matter.

One theory displayed in "The evolution of mammalian keratinized structures" (abstract only) is that mammalian hair developed along the following pathway:

Hair follicles develop between reptilian like scales.
A granular layer formed in the pilosebaceous canal (see diagram of modern human skin)
The granular layer extended into the epidermis.  I read this as the point where scales started to more resemble mammalian skin.  It is suggested that this was as a result of a need for increased flexibility and agility.
Hairs began to protrude through the follicles (as seen in rat tails today).  Adaptations to organisms living in cold conditions led to the production of wool to help conserve heat.

So this paper would suggest that hair production evolved separately from but parallel to the movement away from reptilian scales.

"Some Speculations on the Evolution of the Vertebrate Integument" (Paul F. A. Maderson) suggests an entirely different origin of hairs.  He proposes that hairs ultimately evolved from sensory appendages that were involved in the detection of temperature in early synapsids.  The extension of these micro-limbs into hairs was selected towards as a result of their thermally insulating effect by-product rather than for their sensory role, however.


Are neurons roughly a magnetic dipole? I would like to make a simulation (concerning genetic evolution) and I want to use a very simplistic model of neurons.

I don't really care there are different kinds of neurons, I don't care much that the extracellular field is different at axons-dendrites and initially, I don't even care that the spike is transferred through the axon. What I really want to know, is whether I can approximate (very roughly) the field with a magnetic dipole pointing at the direction of the axon. Or are the directions of the MF and the axon unrelated?

I have looked around for some image depicting such a relation, but I didn't find any. Is there any resource of some kind available?

Yes, neurons can be modeled as magnetic dipoles.  In fact, that is the basis of MEG.  Here is an example of a paper that instantiates a computational model of magnetic dipoles in order to explain MEG data Neural mechanisms of transient neocortical beta rhythms: Converging evidence from humans, computational modeling, monkeys, and mice.


What is the active site (not metal binding site) of tyrosinase and other monooxygenase/oxidoreductases? On https://www.uniprot.org/uniprot/P07524, tyrosinase is shown as a monophenol monooxygenase. However, the UniProt database only shows a metal (copper) binding site, when there is presumed to be an actual active site that performs the reactions, other than the metal binding site. Are there any clues to find the actual reaction active site for a monooxygenase? Please include the sources, if there are.

Tyrosinase uses two copper ions as cofactors. The copper binding site is the enzyme active site.

The active site of the crystal structure of tyrosinase from Streptomyces sp. (PDB code: 3AWT) is shown below. Note the two copper ions (coordinated by active site histidine amino acid residues) and an oxygen atom (of a water molecule) bound to the copper ions:

Matoba et al. (2011) J Biol Chem 34: 30219-30231.

  The Cu(II)-soaked crystal structure of tyrosinase ... possesses two
  copper ions at its catalytic center.


Relationship between membrane current and voltage in neurons Depolarization of neurons leads currents of different magnitudes flow in or out of the cell, and the Sodium and Potassium currents can be separately plotted (Purves):

Caption: Relationship between current amplitude and membrane potential,
taken from experiments such as the one shown in Figure 3.2. Whereas the late outward
current increases steeply with increasing depolarization, the early inward current
first increases in magnitude, but then decreases and reverses to outward current
at about +55 mV (the sodium equilibrium potential). (After Hodgkin et al.,
1952.)

Here we see the dependency of the currents (early: Sodium, late: Potassium) on membrane potential.

What I was wondering was this: It looks like the dependency of the Sodium current on the membrane potential is very non-linear.
However, experiments which assess the amplitude of injected current on excitatory postsynaptic potentials (EPSP) state that the amplitude of EPSPs are proportional to the injected current. How is this consistent with the non-linear current/permeability changes of Sodium? Is the Sodium current linearly dependent on voltage (and vice versa) before the action potential threshold is reached?

This is a bit of a strange way to plot out these data, I think Figure 3.2 is easier to understand, but basically these are data plotted from early voltage-clamp experiments trying to walk you through how the Hodgkin-Huxley model was developed.

They step the voltage to a particular point and look at the current. There are two phases to this current: an early transient and a later plateau.

The shape of the "early" component ultimately results from the multiplication of two functions: the gating curve of the voltage-gated sodium channels and the reversal potential for sodium around 50 mV. If the voltage gated channels were simply open all the time, you would just have a straight line through +50mV, it would follow the right-side shape of the curve. The left-side of the curve is due to more channels opening as you depolarize more.

For the late component, which comes from voltage-gated potassium channels, all of the dependence is on voltage, because the plateau is at a point where all the potassium channels are open. You will also notice, however, that the slope changes a bit in time: it's steeper at the higher voltages, because the potassium channels open more quickly (and also sodium channels inactivate; the combination of the two would make it hard to separate them here).

Your picture is a bit different from these traces plotted in time: figure 3.3 is showing the peak of each component as a function of the voltage step. I think it would be better to present 3.3 as a series of data points rather than a smooth curve to make this more obvious.

Note that the actual numbers here are a bit different than one would see in a mammalian cell, because these original experiments used the squid giant axon which has some differences in voltage dependence, gating, and ion concentrations.

The reason sodium and potassium can be seen separately in these voltage clamp experiments is because:

A) Sodium channels open really fast early on, and then inactivate

B) Therefore, in the long term the potassium current dominates the sodium current.

If you blocked the potassium current and VG sodium channels didn't inactivate, the "early" part would look like a mirror image of the "late" part of the voltage-clamp traces. As-is, the early component is mostly sodium but also includes some voltage-gated potassium current as well that cancels it out and makes it appear smaller than it would otherwise be.

If you look at the late curve in your original figure, it's mostly straight from the point that all the K channels are open. For the late component, the K permeability is at max by -30mV so after that it's all linear from driving force. The little curve at the bottom up to about -30mV is the range at which not all the K channels are open, otherwise it would be a completely straight line, and it would reverse at the K reversal potential instead of asymptoting around zero. But it's not exactly zero because there is also some leak which is mostly potassium, and that does reverse around the K reversal.


How does methamphetamine (meth) damage neurons? Meth is considered to be neurotoxic by forming reactive oxygen species and oxidizing the neurons. But unlike dopamine, which, by the way, is neurotoxic due to ROS induced dopaminergic stress, meth does not have any oxygen atom, and thus cannot be the direct cause of ROS.

So, how exactly does meth exert its neurotoxic effects?

Nice question! I will directly begin with the process through which methamphetamine causes damage to neurons, putting in as much details as are known, and adding appropriate citations wherever required.

Methamphetamine (METH) is known to act by increasing concentration of dopamine in brain1. When excess of dopamine is produced, it causes oxidative damage to axon terminals2. This is because direct oxidation of dopamine leading to quinone formation3, iron-catalyzed dopamine metabolism via Fenton reaction4, and metabolism of dopamine by monoamine oxidase-A5 contribute to production of superoxide and hydrogen peroxide.

Methamphetamine is known to increase concentration of glutamate. This (supposedly) happens as: high concentration of methamphetamine D1-mediated striatonigral GABAergic transmission, which in turn activates GABA-A receptors in substantia nigra pars reticulata (SNr), leading to increase in GABAergic nigro-thalamic activity which increases corticostriatal glutamate release6 (since I can't explain all those terms in a single answer). Now, excessive glutamate activates the glutamate-activated NMDA and AMPA receptors which, in turn, increases activity of nitric oxide synthase7. Activation of nitric oxide synthase generates reactive nitrogen species which create an oxidative stress8.

Oxidative stress is further increased because of depletion of antioxidant enzymes due to methamphetamine itself9. Now, the oxidative stress has to be manifested somehow. This is done by lipid peroxidation and protein carbonyl formation10, and also by specific nitration and nitrosylation of proteins important for monoamine synthesis and release, including VMAT-2 and tyrosine & tryptophan hydroxylase7,11,12. Oxidative modification of these proteins restricts their activity and contributes to their degradation, thus playing a major role in neurotoxicity. Researches substantiate the significant contribution of oxidative stress to the neurotoxicity of substituted amphetamines antioxidant treatments have also been shown to be neuroprotective against the damage produced by methamphetamine or methylenedioxymethamphetamine13,14,15.

P.S.: oxidative damage is not the only way through which methamphetamine causes neurotoxicity. Other possible ways include altered metabolism16, damage to mitochondria17, peripheral organ damage18 due to oxidative modification of hepatocellular mitochondrial proteins19, activation of microglia in striatum, cortex and hippocampus20, etc. Also, cannabinoids are known to suppress inflammatory processes and damage during methamphetamine exposure21. But since this is out-of-scope for this question, I won't go into their details.

References:

 1. Cadet JL, Brannock C, Jayanthi S, Krasnova IN (2015). "Transcriptional and epigenetic substrates of methamphetamine addiction and withdrawal: evidence from a long-access self-administration model in the rat". Mol. Neurobiol. 51 (2): 696–717. doi:10.1007/s12035-014-8776-8. PMC 4359351Freely accessible. PMID 24939695.

 2. Schmidt CJ, Ritter JK, Sonsalla PK, Hanson GR, Gibb JW. Role of dopamine in the neurotoxic effects of methamphetamine. The Journal of pharmacology and experimental therapeutics. 1985;233:539–544

 3. Graham DG. Oxidative pathways for catecholamines in the genesis of neuromelanin and cytotoxic quinones. Molecular pharmacology. 1978;14:633–643

 4. Yamamoto BK, Zhu W. The effects of methamphetamine on the production of free radicals and oxidative stress. J Pharmacol Exp Ther. 1998;287:107–114

 5. LaVoie MJ, Hastings TG. Dopamine quinone formation and protein modification associated with the striatal neurotoxicity of methamphetamine: evidence against a role for extracellular dopamine. J Neurosci. 1999;19:1484–1491

 6. Mark K. A., Soghomonian J.-J., Yamamoto B. K., High-dose methamphetamine acutely activates the striatonigral pathway to increase striatal glutamate and mediate long-term dopamine toxicity. J. Neurosci. 24, 11449–11456 (2004)

 7. Eyerman DJ, Yamamoto BK. A rapid oxidation and persistent decrease in the vesicular monoamine transporter 2 after methamphetamine. J Neurochem. 2007;103:1219–1227

 8. Imam SZ, Islam F, Itzhak Y, Slikker W, Jr, Ali SF. Prevention of dopaminergic neurotoxicity by targeting nitric oxide and peroxynitrite: implications for the prevention of methamphetamine-induced neurotoxic damage. Annals of the New York Academy of Sciences. 2000;914:157–171

 9. Jayanthi S, Ladenheim B, Cadet JL. Methamphetamine-induced changes in antioxidant enzymes and lipid peroxidation in copper/zinc-superoxide dismutase transgenic mice. Annals of the New York Academy of Sciences. 1998;844:92–102

 10. Gluck MR, Moy LY, Jayatilleke E, Hogan KA, Manzino L, Sonsalla PK. Parallel increases in lipid and protein oxidative markers in several mouse brain regions after methamphetamine treatment. J Neurochem. 2001;79:152–160

 11. Kuhn DM, Aretha CW, Geddes TJ. Peroxynitrite inactivation of tyrosine hydroxylase: mediation by sulfhydryl oxidation, not tyrosine nitration. The Journal of neuroscience : the official journal of the Society for Neuroscience. 1999;19:10289–10294

 12. Kuhn DM, Geddes TJ. Peroxynitrite inactivates tryptophan hydroxylase via sulfhydryl oxidation. Coincident nitration of enzyme tyrosyl residues has minimal impact on catalytic activity. The Journal of biological chemistry. 1999;274:29726–29732

 13. Gudelsky GA. Effect of ascorbate and cysteine on the 3,4-methylenedioxymethamphetamine-induced depletion of brain serotonin. J Neural Transm. 1996;103:1397–1404

 14. Sanchez V, Camarero J, O’Shea E, Green AR, Colado MI. Differential effect of dietary selenium on the long-term neurotoxicity induced by MDMA in mice and rats. Neuropharmacology. 2003;44:449–461

 15. Fukami G, Hashimoto K, Koike K, Okamura N, Shimizu E, Iyo M. Effect of antioxidant N-acetyl-L-cysteine on behavioral changes and neurotoxicity in rats after administration of methamphetamine. Brain research. 2004;1016:90–95

 16. Pontieri FE, Crane AM, Seiden LS, Kleven MS, Porrino LJ. Metabolic mapping of the effects of intravenous methamphetamine administration in freely moving rats. Psychopharmacology. 1990;102:175–182

 17. Burrows KB, Gudelsky G, Yamamoto BK. Rapid and transient inhibition of mitochondrial function following methamphetamine or 3,4-methylenedioxymethamphetamine administration. European journal of pharmacology. 2000;398:11–18

 18. Smith DE, Fischer CM. An analysis of 310 cases of acute high-dose methamphetamine toxicity in Haight-Ashbury. Clin Toxicol. 1970;3:117–124

 19. Moon KH, Upreti VV, Yu LR, Lee IJ, Ye X, Eddington ND, Veenstra TD, Song BJ. Mechanism of 3,4-methylenedioxymethamphetamine (MDMA, ecstasy)-mediated mitochondrial dysfunction in rat liver. Proteomics. 2008;8:3906–3918

 20. Pubill D, Canudas AM, Pallas M, Camins A, Camarasa J, Escubedo E. Different glial response to methamphetamine- and methylenedioxymethamphetamine-induced neurotoxicity. Naunyn-Schmiedeberg’s archives of pharmacology. 2003;367:490–499

 21. Yiangou Y, Facer P, Durrenberger P, Chessell IP, Naylor A, Bountra C, Banati RR, Anand P. COX-2, CB2 and P2X7-immunoreactivities are increased in activated microglial cells/macrophages of multiple sclerosis and amyotrophic lateral sclerosis spinal cord. BMC neurology. 2006;6:12


Does the mesoderm evolve from the ectoderm or the endoderm? I know the embryos of most animals develop into 3 germ layers. However primitive animals, such as Cnidarians, only have 2 germ layers - they lack a mesoderm. Therefore the 3rd germ layer must have evolved from cells which originally differentiate to one of the two more basal germ layers.

So my question is - does the mesoderm evolve from the ectoderm or the endoderm? Meaning, during embryogenesis, which cell type is the first to differentiate from the other two - the ectoderm or the endoderm?

In human,the mesoderm doesnot develop from the endoderm or the ectoderm.It develops from epiblast of the bilaminar germ disc stage.

During the week 3 of development, the epiblast of the disc invaginate and divide rapidly to form the cells of the endoderm.The division is rapid enough to replace the hypoblast layer.

Even after the endodermal layer has formed, the epiblast continues to divide at the region of the invagination.The divided cells migrate between the epiblast(soon to be the future ectoderm) and the newly formed endoderm to form the mesoderm.

REFERENCES:

Langman's Medical Embryology (13th edition) T.W. Sadler
website


Help identifying tiny jumping bug I've found a few of these bugs hanging out on my desk. There aren't many. Maybe 5-10 at any given time. Are they a type of springtail? I couldn't find an image in searching that made me say, "That's it!"

Any help is appreciated!

Thanks!

Those are springtails. Order Collembola. You can find yours here on BugGuide. https://bugguide.net/node/view/258362


Are there examples of animals that adapt to their environment very quickly? The phenomenon is called Phenoptic Plasticity Evolution and speciation may take millions of years. This made me wonder if there is an animal that adapts itself relatively rapidly to its environment? I don't mean a simple adaptation like a change of a color by chameleons, but a real evolutionary change.

I've heard that some animals can adapt quickly to the environment like snakes (I am not sure they do). When they have a lot of water (e.g., a big river), they grow big, while the same species does not grow as big in a smaller water tank (small body of water). And when you take this animal to a bigger water it starts to grow quickly.  I want to be sure it is a snake or there is some other animals that evolve change like this...

The snake example you provide is a single animal that adapts itself to its surroundings. Adaptation is similar, yet very different from evolution. Adaptation happens on a short timescale (as little as seconds, to perhaps years, but within a single life time, without substantial changes in DNA other than, perhaps, epigenetic ones), while evolution may occur over the course of millions of years or more, and likely involving gross changes in appearance and hereditary material. I am not entirely sure what you are exactly after.

A striking example of adaptation is the fish Tilapia, an invasive species of fish (Fig. 1) that is capable of sustaining fresh water as well as sea water environments. The transition from one medium to the other is mediated by gross changes in endocrinology. Your specific snake example on size adaptation seems, however, unsupported based on non-scientific websites at least.

Fig. 1. Nile Tilapia. Source: Sea EX

If you are after examples of swift evolution -There is a nice example of the Waterlily Beetle, Galerucella nymphaeae (Fig. 2), that shows striking host-race formation, i.e., the same species of beetle shows clear adaptations (on an evolutional scale) dependent on which plant it has been found. It has been shown that these beetles extracted from different plants (Nymphaeaceae versus Polygonaceae) showed strong morphological and ecological differentiation to their different host plant families. Beetles from Nymphaeaceae were significantly larger and had disproportionally larger mandibles than beetles from Polygonaceae. It is argued that these differences are adaptations (on an evolutional scale) to the tougher leaves of the Nymphaeaceae, which has been linked to genetic differences. In addition, females showed a strong oviposition preference, and all beetles showed distinct feeding preferences for the host family from which they originated. Moreover, these host preferences resulted in clear differences in survival: survival was 2 to 11 times higher on the natal host family than on the alternative host family.

Fig. 2. Waterlily Beetle. Source: Wikipedia.

Exactly how fast these beetles have adapted I am unsure of, but the interesting thing is that these beetle races are not geographically separated by a natural barrier like a sea, a mountain range etc. Instead, they live side-by-side, but have adapted to a specific host plant.

Reference
- Pappers, Evolution in action: Host race formation in Galerucella nymphaeae. PhD thesis (2001), Radboud University, Nijmegen, the Netherlands


Are there any (chemical) processes occuring inside a seed while it's in a dormant state? If a seed were in a glass jar without a chance of germination, are there any (chemical) processes occurring inside the seed while it sits there?

My intuition tells me no since my understanding of seed dormancy tells me that dormancy serves as a delay mechanism to increase the chances of survival of the plant.

I deductively reason that dormancy prevents germination by pausing all reactions (processes) in a seed until a combination of conditions triggers the process that initiates germination.

I've done some research online but I can't find anything to support the "pausing all reactions” portion of my statement which would answer my question.

We can consider two processes that a seed might care about:

(1) Ordinary chemical reactions that just happen in the cytoplasm of the seed cells. It's very hard to stop chemistry! Even in the freezer, chemical reactions occur (slowly). This is why long-term storage of biological specimens is generally in an ultra-cold freezer (-80C). Chemical reactions could degrade DNA and proteins and prevent seed germination, so seeds take steps such as drying to reduce the chemistry going on. But, clearly this just slows down the reactions, as seeds of all types gradually lose their ability to germinate (some faster than others). Spore-forming bacteria are the most successful organisms in this regard: they drastically dehydrate the interior of the spore and surround it with a highly protective coat, and there is evidence that some can literally remain viable for millions of years.

(2) Seed metabolism: enzymatic reactions and the normal biochemistry of the cell. "Dormancy" means in part that seed cells shut down processes like transcription and translation and minimize their metabolism. But, research suggests that the metabolic activity of seeds is not zero - among other things, there are active enzymes that are involved in repairing damage to DNA and proteins.


What can you tell about a person, having only their whole genome as information? Well, the question is in the title, no explanation need.

I've had a little encounter with this question in the past few months so I'm updating here...

The overall answer is 'really a lot about some things, but not as much as you'd like to think about others.'    There is a scientific genome interpretation 'contest' that has been going on for the past few years called CAGI (Critical Assessment of Genome Interpretation).  This is meant to be a cutting edge set of challenges and its worth looking them over.  Last year there was in particular one challenge - answering questions about ten individuals given only a list of traits and their genome sequences.

It was not so easy it turns out - simply looking up variants and cross referencing them to the literature led to poor predictions.  Glaucoma, asthma, migrane, irritable bowel syndrome, color blindness, lupus, lactose intolerance are examples from a list of 40-odd contest questions.  If you register onto the site you can get some of the results or there is a paper reporting the results, only four labs tried the challenge and the accuracies were sometimes not great, topping off with Rachel Karchin's lab with an AUC of 90%.  Even some of the phenotypes you think are easy are not a simple lookup.  Genetics is not as pre-determined as we think.

While we are good at inferring our history and geneology on the other hand.  A reasonable example of this is the 23andme analysis.  They have a lot less information about you than a complete genome sequence, but they do seem to make the most of the 0.0001% of the genome that they do have.

They have a nice lookup of some of the hereditary disease data that is available.  "Increased risk of skin cancer" or for Alzheimers are only chances and its never clear how much your actual lifestyle has impact on 44 outcomes, but its there.

What they also have is your ancestral analysis which is crazy interesting. it shows where your maternal and paternal lineages come from and how strong.  they have a very pretty heatmap of the continents for this.  National Geographic's DB is probably more sophisticated and ancestry.com also does this.  This is pretty cool.

Also included things like curly hair, color of skin eyes and hair.

Like SimaPro says they are described in OMIM.  OMIM stands for 'online mendelian inheritance in man' and all the straightforward directly inheritable traits we know of are listed there.  its worth taking a look. There are not a lot of known single mutation genetically inheritable conditions.

If the genome sequence includes methylation, then some other traits which are epigenetic, not genetic but would also be determined from a genome sequence.  Most famous example of this is MEST which will give an indicator of whether you are a doting parent or not.


What is the distinction between chemokines, cytokines, interferons and interleukins? They all seem to describe molecules of similar function and many people seem to use them interchangeably.

Also please include any other similar molecules if I've forgotten any in the list above.

Cytokines is the general class of molecules to which chemokines, interferons, interleukins and others belong. Biologists dispute whether something is a hormone or a cytokine, but generally the consensus goes with if it's to do with immunology it's a cytokine or if the resting concentration is in the picomolar range, but that's a very rough distinction.

Chemokines are molecules that drive cellular chemotaxis. That means they make cells move towards a desired place. Generally chemokines refer to immune cells and there's loads and loads of them.

Interleukins are anything which are messenger molecules between immune cells (inter- means between and -leukins means leukocytes/white blood cells). They're typically denoted by IL + number. However the interferon and tumour necrosis families come under interleukins too in most people's opinion. The interferons are a special group that typically inhibit viruses by making cells non-permissible to viral replication. They also do a few other things like activate macrophages or promote Th1 response, which both also interfere with viruses but there is bacterial overlap. The TNF family is a bit weirder as some are interleukin-like but others aren't as much. TNF-alpha (the classic one) is involved in macrophage maturation. However not all interleukins are strictly between white blood cells, as IL1 acts on the hypothalamus among other leukocytes.

See the problem is everything is a bit grey because most cytokines (if not all) have more than one role and there's never consensus in the world of immunology when it comes to cytokines because more and more keeps getting discovered.


What is the close and related genome used for in Gene models? all

I am a little bit confused about using the related genome or reference genome.

When we have a reference genome, we can do alignment. Also we can do the assembly.

Can you give some more reason why a related genome can help to improve gene model ?

And if we do use a related genome, what kind of problems or caveats may occur there ?

Why a related genome helps:

1) Alignment of the reads first and assemble next.
 2) The gene-space is already predefined ( the genes and their co-ordinates are already known), so if your assembly is fragmented or missing a portion of the gene information, that can be accomodated with reference genome.

Limitations: Rather than assembling your own genome, you are forcing the reference genome to be part of your genome assembly. If at all, any differences are there, they are washed out, when you do a reference assembly.


Apart from nerve cells and muscle cells, what types of cells do not undergo mitosis in adult man? Neurons and muscle cells in adult humans do not have the ability to divide by mitosis, so they can not repair themselves and their cell cycle remains in the interphase. I’m looking for more cells with this feature. Are there other cells with this inability to undergo mitosis in humans or in plants?

In an adult human:

Do nervous cells ever undergo mitosis?
I wonder if all muscle cells do not undergo mitosis or if this inability only applies to cardiac and skeletal muscle cells.

To answer the numbered questions:

In general, neurons never divide by mitosis. However, I believe you may have unintentionally misphrased your question; there are functional neural stem cells in the adult human brain as well, and these are believed to give rise to new neurons throughout the lifespan of an individual. They have only been found in specific parts of the brain, though, such as the SVZ and the subgranular zone of the hippocampus (Gonzales-Perez 2012; Behnan et al. 2017). It also bears noting that following an external insult (such as DNA damage, oxidative stress, hypoxia), even terminally differentiated neurons can re-enter the cell cycle and go as far as to replicate their DNA, but this tends to result in apoptosis or arrest at the G2/M phase; such aberrant re-entry into the cell cycle is more frequent in brains afflicted by neurodegenerative diseases (Frade & Ovejero-Benito, 2015). In addition, the possibility to induce neurons to proliferate and form cancers has been demonstrated in retinal cells in mice (Ajioka et al. 2007).
Correct; as with neurons, muscle cells (myocytes) lack the ability to undergo mitosis. But again, I believe what you really want to ask is whether or not muscles maintain a pool of stem cells that can replace lost cells. The answer to this is yes—there are stem cells within skeletal (Wang, Dumont & Rudnicki 2014)  and smooth muscles (Majesky et al. 2011) that proliferate in response to damage. According to some studies there are stem cells in the adult heart as well, although their regenerative capacity appears to be very low (Bergmann et al. 2009).

If your intention was indeed to ask about which cells are unable to undergo mitosis, then the answer will likely be a very long list, as no terminally differentiated cell type undergoes division under normal circumstances. This would, for example, include all different blood cell types (erythrocytes, megakaryocytes, neutrophils, eosinophils, basophils, B-cells, T-cells, natural killer cells, mast cells, macrophages), most skin cells (e.g. keratinocytes, melanocytes), epithelial cells (such as those that form the intestinal lining) and such. This would likely include most if not all of the cell types listed here that do not have the "(stem cell)" note next to the links (although I did not confirm this by checking the literature on them).

References:

Ajioka, Itsuki, et al. "Differentiated horizontal interneurons clonally expand to form metastatic retinoblastoma in mice."
Cell 131.2 (2007): 378-390.
Behnan, Jinan, et al. "Identification and characterization of a new
source of adult human neural progenitors." Cell death & disease 8.8
(2017): e2991.
Bergmann, Olaf, et al. "Evidence for cardiomyocyte renewal in
humans." Science 324.5923 (2009): 98-102.
Frade, José M., and María C. Ovejero-Benito. "Neuronal cell cycle: the neuron itself and its circumstances."
Cell cycle 14.5 (2015): 712-720.
Gonzalez-Perez, Oscar. "Neural stem cells in the adult human brain."
Biological and biomedical reports 2.1 (2012): 59.
Guo, Dayong, and Lynda F. Bonewald. "Advancing our understanding of
osteocyte cell biology." Therapeutic advances in musculoskeletal
disease 1.2 (2009): 87-96.
Majesky, Mark W., et al. "Vascular smooth muscle progenitor cells:
building and repairing blood vessels." Circulation research 108.3
(2011): 365-377.
Wang, Yu Xin, Nicolas A. Dumont, and Michael A. Rudnicki. "Muscle
stem cells at a glance." (2014): 4543-4548.


Can plants yield two more molecules of ATP from glycolysis? Since 2 ATP are used to convert glucose to glyceraldehyde 3-phosphate in glycolysis, can plants bypass this step of ATP investment since they produce glyceraldehyde 3-phosphate directly from the Calvin cycle?

If yes,  what would be the final yield of ATP.

If not,  why not?

Plants produce ATP in the ‘light reaction’ of photosynthesis.
The purpose of the Calvin cycle (the ‘dark reactions’) is to produce glucose, for which it uses some of this ATP to provide the energy to make carbon–carbon bonds.
Glycolyis in plants functions to produce ATP from reserve carbohydrate etc. when ATP is not available from photosynthesis, or in tissues, that do not have sufficient ATP from photosynthesis.

So this question makes no physiological sense†, as it is based on a misunderstanding of the purposes of the differ metabolic reactions in plants. The answer is not that it cannot happen, but that it would not happen — the regulatory mechanisms that prevent futile cycling of pathways would come into operation.

† It is analogous to saying that the liver can perform gluconeogenesis, and so can produce glyceraldehyde 3-phosphate. So can the liver bypass this step...


Is there variability in genetic combination from the same sperm and egg combination Given a single sperm and a single egg, is there more than one resulting DNA combination they can form given the same human process of combining that genetic material. That is if I have the  DNA off an egg sequenced and the DNA off a sperm sequenced, can I programmatically determine the DNA of the child formed by that egg and sperm?

Assuming we know the haplotype of the ovule and the haplotype of the spermatozoid, then the genotype of the future egg is perfectly deterministic. This is true to the extend that none of the following rare events occur:

mitochondria could be inherited from the father as well
mutations in the broad sense (see here for definitions) may occur outside an event of mitosis or meiosis
The egg might pick up random sequence floating in the environment

Of course epigenetics elements might vary but this is another discussion.


(How) does coppicing fundamentally alter tree growth? I am interested in adding the ability to model coppice tree production to a model of perennial crops (Miguez et al 2008)..

Implementing the biomass pools and allocation parameters required for tree growth is relatively straight-forward.

However, it is not clear to me if it will be necessary to account for any changes in growth form and physiology (e.g. allocation, allometry) associated with coppice management.

Are there any models that explicitly model coppice regrowth? Are there any particular issues that I should consider?

Fernando E. Miguez , Xinguang Zhu, Stephen Humphries, German A. Bollero, and Stephen P. Long. GCB Bioenergy . 2009 . Volume 1 Issue 4, Pages 282 - 296 (link)

According to Deckmyn et al (2004), the primary effect of coppice management is that the fraction of total biomass in roots is relatively higher after coppicing, and that a substantial fraction of carbon in roots (~20% of root mass) is reallocated aboveground to support shoot growth in the spring following coppicing.

Because of this large re-allocation, coppiced plants are able to grow more rapidly (and reach canopy closure sooner), than seedlings (Ceulemans et al 1996) it is important to consider that canopy closure (maximum leaf area index) occurrs more rapidly after coppicing

Deckman et al, 2004 Poplar growth and yield in short rotation coppice: model simulations using the process model SECRETS. Biomass and Bioenergy doi:10.1016/S0961-9534(03)00121-1

Ceulemans et al, 1996. A comparison among eucalypt, poplar and willow characteristics with particular reference to a coppice, growth-modelling approach Original Research Article
Biomass and Bioenergy, Volume 11, Issues 2–3, Pages 215-231 doi:10.1016/0961-9534(96)00035-9


Why is muscle force more dependent on cross-sectional area than on fiber length? I was looking up why smaller animals are proportionally stronger than larger animals. The answer that comes back everytime is that muscle force depends on the number of muscle fibers, which is proportional to the cross-sectional area of the muscle.
However, I don't understand why muscle force wouldn't depend on fiber length.
I'm not a native english speaker, so I'll try my best to articulate my reasoning in the most concise way possible.

Force is exerted by the myosin motors. Force is therefore proportional to the number of myosin motors.
The number of myosin motors is proportional to the fiber length.
The number of myosin filaments is proportional to the cross-sectional area.
Then, muscle force is proportional to muscle volume, and therefore to muscle mass.

What am I missing ? Why is muscle fiber length not that important to muscle force ?

Thank you in advance for your help.

Here is a thought experiment that might help. Consider a single muscle fiber as being like a rope. Granted, a rope won't shorten on its own, but if you think of an isometric muscle contraction, then it's closer to what is happening when a single fiber contracts.

Now think about two situations:

You double the length of the rope. Does the total force that the rope can hold get larger, smaller, or stay basically the same?
You halve the length of the rope by doubling it up (so two ropes instead of one). Does the force that the rope can hold get larger, smaller, or stay basically the same.

So lining up more fibers in series is like making a longer and longer rope. It's still basically as strong (or weak) as a single rope. But when you bundle more ropes, increasing the cross-sectional area, the overall force that they can hold increases.

I'm not sure why a thought experiment needs citations, but here you go:

The canonical source for discussion of muscle fiber architecture is Gans C. 1982. Fiber architecture and muscle function. Exerc Sport Sci Rev 10:160–207.


Do all gene mutations in pathogens lead to more harmful consequences for humans? It seems that the concern we always hear is that bacteria and viruses mutate to dodge our treatments either through random mutations or survival of the fittest. Do harmful living things ever mutate to become not harmful?

Mutations are random; the (pathogenic) bacteria (or any living being) will randomly acquire mutations that may be beneficial, deleterious or neutral to its fitness. Only beneficial and neutral mutations will survive the selection. Random mutations and survival of the fittest are not two independent mechanisms. The random mutations can alter the fitness as I mentioned and natural selection ensures the survival of the fittest.

Many pathogens have reduced genome (number of genes) compared to their free living relatives (Weinert and Welch, 2017). This is because they lack most of the genes required for synthesis of different metabolites required for survival. They rather obtain these metabolites from the host and hence they have the parasitic lifestyle. It is not possible for the pathogens to acquire that many genes to stop being pathogenic and become a free-living organism. It may be possible via lateral gene transfer wherein a bacteria may obtain an entire gene (or a set of genes) from another bacteria but the likelihood of that happening to convert a pathogenic bacteria to a non-pathogenic bacteria is negligible.

It is certainly possible that pathogens might lose the activity of some of the pathogenic genes (for example those required for toxin production) due to mutations. However, they may no longer be efficient pathogens and would be outgrown by the others who still retain those genes.


Why can't gametes of one species fuse with that of the other species? I have read that gametes of one species cannot fuse with that of another? For example the sperm of a dog can't fuse with the ova of a cat or a horse?

The implied subject of your question is the prezygotic barrier and is one of the possible determining mechanisms of speciation, the others being temporo-spatial (meaning different time or place), behavioral, and mechanical (the organisms don't fit together, physically).

Fundamentally, this means that gamete cells of each organism are chemically incompatible. While the details specific to each species vary, we can take a look at a few examples to illustrate the point.

In order for eggs of Arbacia Punctulata to attract sperm of the same species they secrete a specific chemoattractant peptide we call Resact (a selection of different species' chemoattractants can be found beyond the former link), which is adapted to diffuse well in seawater. Sperm then follow the chemical gradient in the direction of the egg, which is called positive chemotaxis. Resact doubles as an activating peptide for that species' sperm. Pycnopodia helianthoides starfish, which also reproduce through broadcast spawning, use an attractant we call startrak. Internally fertilized animals use roughly the same mechanism to guide sperm through the reproductive tract, though with different chemical adaptations specific to their evolutionary history.

Once the sperm reaches the egg, an acrosome reaction leads to the fusion of the two gametes into a potential zygote (for the reason why I say potential, see  Speciation by polyploidy). The chemistry of this reaction also varies between species.

In summary, the reason is this:

A change in gamete chemistry (chemotaxis, activation, reaction, adhesion) alters the chances of successful fertilization between one or more members of the same species.
Thus, the altered group reproduces more often within itself than it does with the parent group, allowing it to grow in population.
Changes in the altered group further reduce the chance of success with the parent group.
Eventually, the chances of the altered group successfully mating with the parent group are practically zero.

This process is, of course, typically assisted by one or more of the other aforementioned mechanisms. Where two species are capable of producing offspring and successfully do so, you get hybrid speciation.

Further reading

Study.com - Speciation II: Prezygotic Barriers
Recognition of Egg and Sperm
Egg and sperm recognition systems during fertilization


Is human "sperm warfare" a concept supported by biology? I've recently read the "Sperm wars" book by Robert Baker. It deals with human sexuality and infidelity. The main premise of the book is that  human male has different kinds of sperm:

Regular sperm for fertilization
Toxic sperm that kill competitor sperm (similar in concept to white blood cells)
Slow, inactive sperm to block channels in female cervical filter

According to the author, when a female engages in infidelity or group sex, the sperm actually "goes to war" killing competition and preventing passage through cervical filter.

Are there are indeed different kinds of functional sperm in humans, and are their functions involved in sperm competition / warfare? In other words, does human sperm not only fertilize the egg, but also to block passage of competitor sperm and even kill it?

I wanted to respond to your question because while I don't know very much about this particular subject myself, I did have the pleasure of attending a talk by Robert Martin, author of How We Do It (https://www.amazon.com/How-We-Do-Evolution-Reproduction/dp/0465030157/ref=sr_1_2?ie=UTF8&qid=1492260860&sr=8-2&keywords=how+we+do+it).  In the talk and in his book he does address this topic (and the book Sperm Wars) and basically says that while it was a highly influential idea, the underlying science isn't reliable.  He argues that evidence suggests that humans have not evolved under multi-male types of mating systems. There is a lot of evidence to back this up, and revoke the idea of "killer sperms."  Check it out and see what you think!  If anything it is an interesting read.


Proteome patterns between treated and control cells We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only one pair (one treated and one untreated) sample for each experiment. We want to see which proteins are differentially expressed (minimum 1.5 fold up/down).

First approach: We have compared protein levels of all 4 treated (as a group) with the 4 untreated (as a second group). There is of course variability between all experiments, because of the nature of the cells. We have a list of the proteins that are differentially expressed as a result of the treatment, however this list is not very long.

My question is (second approach): Can we compare the proteins levels pairwise for each experiment (treated vs its respective control) and make 4 corresponding lists, and then compare these four list using a statistical tool and find which proteins are consistently up- or down-regulated? DO you think that these two different approach will generate different lists of the affected proteins?

If I understand you did a treatment to some cells and compared them with non-treated ones. Instead of running the four experiments at the same time, you did one treated and one untreated at a time. Then you did proteomics for each sample. Is the treatment the same in all four experiments?

Edit after the further comments of the OP: So, since the four treated samples are the same and the four untreated also (same conditions except from the treatment and the treatment is the same), then the way to go is as what your collaborator did.

Identification and quantification of the detected proteins is one thing and every sample of the four are replicates. Comparison between the two conditions is another thing.
The software he uses for ID can combine the same samples and already perform the statistical analysis, so the list you have now has higher credibility in terms of the proteins it includes and their levels for your cells when they are treated or not.

Using only one of your replicates, although it might give you different number of detected proteins or different amounts of each, has lower credibility, because it's only one sample out of four. In plain words, the presence or absence or the amount of a protein might be an artifact or insignificant.

What has to be clear is that the comparison between treated and untreated conditions is done after you have received the statistically correct list of detected proteins.

Thus, and in accordance to what I had said before the edit, if you take the list for each treated sample and compare them with any of the lists of the untreated ones, it will lead to conclusions that won't be as statistically significant as when you combine all treated together and all untreated together (as your colleague did). In plain words, your conclusions will have a higher chance to be wrong.

Every statistical analysis you do yourself for each sample should eventually lead to a similar consensus as your colleague got using the statistical analysis of his software.

As a sidenote, considering how many types of proteins are in a cell, now that you have a quite short list might not be a bad thing at all and you can proceed by:

Concluding that the treatment had minor effect in the proteins that you expected it would affect (if they are not present in your lists as significant different)
Trying to understand, identify and hypothesize on the role of the proteins that made it in your comparison threshold, as they have a much higher probability of being indeed different between the two conditions.

Splitting the samples in your analysis might have a point if the conditions of the experiment were not exactly the same or the treatment level is different etc. In that case you could split the samples accordingly, but that would definitely reduce your certainty level for your conclusions.


How does genetical variability works on bacteria? I'm very Lay in biology, but I was studying the subject and the following problem emerged:

It's known that all bacteria are unicellular beings, and their reproduction it's asexual. Besides of that the indiscriminate use of antibiotics leads to the development of more severe infections, because of a process of natural selection and survival of the most resistant. How do we explain this process considering that asexual reproduction doesn't generate genetic variability, besides mutation? Why do we have this differences, if asexual reproduction generates clones?

The question is based on the false assumption that sexual reproduction creates genetic variance. If we neglect epistasis, then on average segregation and recombination do not increase genetic variance within the population.

All 3 of the following processes present in some bacteria lineages do increase the amount of genetic variance:

conjugation
transduction
transformation

You should have a look at the wikipedia articles.


Variation of length of circadian rhythm in humans in absense of time reference Are there any studies which show the range of the length of circadian rhythms for people that are removed from actual time, (Eg no sunset/ sunrise, no clocks or other reference of time)?

For example, what proportion of people tend to have a natural 30 hour rhythm or greater?

I ask because I would like to know if it is a possible cause of insomnia, how likely insomnia is caused by this, and if this knowledge might in some way lead to solutions for insomnia

This might be the study to which you refer in your answer, the people tested averaged a daily cycle of 24 hours and 11 minutes with a surprisingly small variation in their rhythms:

  The variation between our subjects, with a 95 percent level of confidence, was no more than plus or minus 16 minutes, a remarkably small range.

Worth noting they were all healthy and so it doesn't tell us much about insomnia.

This study about insomnia in adults with ADHD shows that circadian rhythms of insomnia sufferers aren't so much longer as delayed (for sleep-onset insomnia anyway). Figure 2 might be of interest, showing that insomnia sufferers have significantly delayed melatonin production.


Osmoregulatory Acclimatization in amphibians If a frog is gradually exposed to increasing concentration of salts can they acclimatise or will they die of exosmosis ?

It will depend on how quickly the salinity is raised and to what level.  Two studies (Karraker 2007, Karraker et al. 2008) looked at the effects of road salt (used to reduce icing on roads in winter) in the spotted salamander, the wood frog (a small frog), and the green frog (a big frog). Their studies showed that survival decreased, especially for larval individuals, as salt concentration increased. Deformities in embryos and larvae increased with salt concentrations$^1$.

Another study (Shpun et al. 1992) showed that a few species of frogs and toads that could tolerate high levels of blood plasma urea concentrations could also tolerate elevated levels of NaCl in their environment (but not all species that had high urea tolerance could tolerate high environmental salt concentrations.)

There would naturally be an upper limit of salt tolerance in amphibians, especially if they are not able to retain or regain water at a rate they are losing it to the high salinity environment.  The studies suggest that higher salinities do decrease survivorship and increase deformities. While they may acclimate to the short term, I would question long term adaptation unless the rate of salinity increase is very gradual.

Footnote

They made their salt solutions based on conductivity, measured as microsiemens. For lab experiments, they made salt solutions that varied from 5 µS (control) to 3000 µS. These translate to 1 mg/L to 945 mg/L Cl$^-$.  In the field, they measured salt concentrations that were more than 3000 µS.

Literature Cited

Karraker, N.E. 2007. Are embryonic and larval green frogs (Rana clamitans) insensitive to road deicing salt? Herpetological Conservation and Biology 2: 35-41.

Karraker, N.E. et al. (2008). Impacts of road deicing salt on the demography of vernal pool-breeding amphibians. Ecological Applications 18: 724-734.


Cloning a gene of an organism with an nonsequenced genome What would be the best protocol to clone a gene about 5kb in size? The genome is not sequenced, but the gene itself very similar to orthologous genes of organisms with known sequences.

I assume that we are talking about eukaryotic genomes which are split into introns and exons. Depending on what you want to do with your cloned gene, you need different strategies. The method is based on the assumption that the gene sequence has only very little differences to the known sequences of other organisms.

If you want to express your gene from a vector, you need to find the right processed mRNA which is then processed into cDNA and then cloned. Here two strategies are possible: If you have a gene, which is strongly expressed, you can design a primer primer (based on the orthologous sequences) which is anchored in the poly-A tail and has a gene specific seuqence next to it. With this it should be possible to amplify your gene specifically and isolate it. If the gene is not strongly expressed (the resulting amount of cDNA would be very small, since there is no amplification involved), I would opt for making cDNA from total mRNA (use anchored polyA primers) and then amplify the sequence from the cDNA pool with two primers (again based on the orthologous sequences) to amplify the gene sequence. I would go for TA-cloning here, since you do not know, which restriction enzyme recognition sites are present on your gene.

When you need the complete sequence containing introns and exons, there are two possible strategies. First you can use primers to amplify the gene and subsequently clone it. Then it is possible (and this is probably what I would do) to use a set of primers which bind to the end of the gene (and also the reverse strand) to amplify the sequences at the end and then sequence these PCR products. This gives you the exact sequences at the 5' and 3' end of the gene and allows you to include possible regulatory sites, since you then can design exactly matching primers for this region. Again, I would go for TA cloning.

And finally you could start by sequencing the whole region based on homologous sequence primers first and then with primers designed on the newly analyzed sequences. This is the most exact way, but is also costly and takes some time (since you need to make new primers after each round of sequencing until you are done).


What is the role of a chemotroph in an ecosystem? Chemotrophs are bacteria that synthesize ATP based on favorable REDOX reactions. This solves the problem as to how they can survive. But what exactly is their function in an ecosystem? For example, can they provide nutrients for algae?
I want to know if we can cultivate chemotrophic bacteria to provide nutrients for plants. This way, we could grow them in a place like Mars where the soil is made of a lot of inorganic material. I was especially interested in algae because some species can provide a lot of nutrients humans need.

Chemotrophs are usually found in extreme environments where they can be the source of all energy for the ecosystem also called the primary producers. Deep-sea hydrothermal vents are a great example of a chemotroph primary producer and support the growth of large eukaryotes like the tubeworms (Below). The chemotrophs supporting life at the vents can oxidize Sulfur to create ATP.

But chemotrophs don't just have an impact on these small ecosystems, they are actually responsible for earth-scale geochemistry affecting all life. (Cool paper on that here). The reason why chemotrophic bacteria are usually not found in "normal" environments with algae is simply competition. A heterotroph using hydrocarbons will occupy a niche faster and more efficiently than any chemotrophic bacteria.
You are definitely right on the Mars soil question, where chemotrophic bacteria could be used to fix carbon or nitrogen and solubilize nutrients for future plants on mars. But maybe some cool chemotrophs are already living there!


How to determine the relationship of competition or cooperation? I am currently studying the interaction of Twitter memes (two or many), such as competition and cooperation. Is there any model or method in biology that can identify the types of the relationship, such as competition or cooperation?

I have heard the Lotka–Volterra equations, but when I begin to dig deep, I found that it is still not suitable.

Species interactions

Generalities

Species interact. Species actually interact a lot. One can classify species interactions into categories based on the effect that the interaction has on their fitness (≈ reproductive success). Here is a table of possible biological interactions (comes from [wiki][1]), where a + indicates "beneficial", a - indicates "detrimental" and a 0 indicates it has no effect on fitness.

Different terms exist for a given relationship. Typically, antagonism is often called parasitism.

Note about symbiosis

Different authors use the word symbiosis differently. From wikipedia:

  The definition of symbiosis is controversial among scientists. Some believe symbiosis should only refer to persistent mutualisms, while others believe it should apply to any type of persistent biological interaction (i.e. mutualistic, commensalistic, or parasitic).[6] After 130+ years of debate,[7] current biology and ecology textbooks now use the latter "de Bary" definition or an even broader definition (i.e. symbiosis = all species interactions), with the restrictive definition no longer used (i.e. symbiosis = mutualism)

Blurry limits

Generalities

It may seem pretty obvious that two species should have either one type or another type of interaction. However, the reality is often more complicated than that. An interaction might fall in one category under one set of environmental conditions and fall under another category under another set of environmental conditions. In addition to that, it is not uncommon that due to selection on the host genes due to the presence of a parasite, the host evolve so to tolerate the presence of the parasite up to the point of actually having a lower fitness in the absence of the parasite.

Example of environment-dependent interaction type

Consider an animal that is host to an algea. The host is providing shelter to the algea while the algea is providing sugar (produced through photosynthesis). If there is no light or if the enviroment is loaded with sugar, then the host has no gain of hosting the algea. In such case, the algea may even be parasitic. If, however, there plenty of light and there is few nutrients in the environment, then the algea and the host have a mutualist relationship.

Example of the evolution of a parasitic interaction

Consider for example a snail which is infected by a parasite. Let's assume (I think it is a real world example but I am too lazy to find out a reference) that the parasite need the snail to be eaten in order to reproduce in the body of the predator. In order to improve the chance of its host to be eaten the parasite is selected so to diminish the thickness of the snail's shell. In response to that, there is selection (which intensity depend also on the proportion of infected snails in the population) for having thicker shells. But now, snails that are not infected have shells that are so thick that the can't move as fast as they'd need to forage. So, by the end infected snails may have a higher fitness than non-infected snails. And therefore the interaction between the snail and its parasite is not a parasitic interaction anymore but a mutualistic interaction.


How can chromatin state be measured? I have some RNA-Seq data and I'd like to align it to the physical genome and see which sections of chromatin are geometrically open and being transcribed.  The data are already sequence-aligned, and every Google search I do for tools that might help ends up sending me down a rabbit hole.  What computational tools have helped you?

Starting out with RNA data is great, since you already have fully spliced entities, despite  being in a different dynamic regime.

As the chromatin landscape itself is dynamic and High throughput data exploration has only begun in the last decade, consider the following tools and results with care...

You may find the following tools helpful:

Archalign , Publication (didn't work well during my day of trials)
Ensembl chromatin-state map data (See the database layout, Regulatory Build, and the lincRNA
genes in the web-interface of the Ensembl databases)
HaploReg, Publication (the most recent)