Is there any research paper state the pros and cons for human to be taller?

People with Shorter height may outlive Taller ones.

It is a statistically established fact that they are more successful in terms of money,
as the study published Journal of Applied Psychology, (Vol 89(3), Jun 2004, 428-441).
But, still in the health, the counterpart succeed over the former.

  The Effect of Physical Height on Workplace Success and Income: Preliminary Test of a Theoretical Model.

  Author: Judge, Timothy A.; Cable, Daniel M.

  In this article, the authors propose a theoretical model of the
  relationship between physical height and career success. We then test
  several linkages in the model based on a meta-analysis of the
  literature, with results indicating that physical height is
  significantly related to measures of social esteem (p = .41), leader
  emergence (p = .24), and performance (p = .18). Height was somewhat
  more strongly related to success for men (p = .29) than for women (p =
  .21), although this difference was not significant. Finally, given
  that almost no research has examined the relationship between
  individuals' physical height and their incomes, we present four
  large-sample studies (total N = 8,590) showing that height is
  positively related to income (β = .26) after controlling for sex, age,
  and weight. Overall, this article presents the most comprehensive
  analysis of the relationship of height to workplace success to date,
  and the results suggest that tall individuals have advantages in
  several important aspects of their careers and organizational lives.
  (PsycINFO Database Record (c) 2012 APA, all rights reserved)
  Source: http://psycnet.apa.org/journals/apl/89/3/428/

Long back in 1975, the relationship between breast cancer and height had been nearly established.

  Breast Cancer Incidence and Nutritional Status with Particular Reference to Body Weight and Height

  Author: F. de Waard

  Cancer Res 1975;35:3351-3356.

  Summary The epidemiological literature on breast cancer is reviewed with particular emphasis on the possible etiological role of
  nutritional status as reflected by weight and height. The results of a
  prospective study and preliminary results of a population-based
  case-control study seem to indicate that body size or body mass rather
  than overweight (obesity) is a risk factor. A considerable proportion
  of the differences in incidence between the Netherlands and Japan can
  be explained by differences in body mass. The biological mechanisms
  mediating nutritional status and breast cancer are believed to be of
  an endocrinological- metabolic nature.

Primarily the investigators started with overweight problem but they have found a better correlation with height. They have concluded:

  A further lead to biological mechanisms might be derived
  from the fact that several endocrine and metabolic functions
  (e.g., basal metabolic rate and cortisol production rate)
  seem to correlate better with body surface area than with
  body weight. The rationale for using surface area is often
  lacking except for the fact that it is estimated from both
  weight and height.

Height and cancer risk are fairly clearly linked, with a 16 per cent higher relative risk for every extra 4 inches of height.

The answer may lies in the metabolic rate:

  For one, taller people tend to weigh more than shorter people, even if
  their BMI isn’t any higher. For another, poor nutrition and stress can
  stunt height growth, and higher calorie diets have been associated
  with increased height. And that doesn’t even begin to take into
  account the psychosocial variables like increased income, education,
  and socioeconomic status.

Other Diseases

On the contrary, in a study examining cardiovascular disease risk and height in men found that men who were taller than 6′ 1″ (185 cm) had a 35% lower risk of having a heart attack than men who were shorter than 5′ 7″ (170 cm). Every inch a man gained in height resulted in a 2-3% decrease in heart attack risk.
In a study in among, Israeli civil servants, shows height was also associated with lower stroke risk. Taller people are more likely,around 76%,  to suffer from recurrent blood clots.

LINKS:

http://blogs.discovermagazine.com/crux/2013/11/08/is-being-tall-hazardous-to-your-health/#.U79p3vmSzQJ
http://scienceblog.cancerresearchuk.org/2011/07/21/height-and-cancer-risk-%E2%80%93-the-long-and-short-of-it/


Is the Common Cold an Immune Overreaction?

Can someone die of the common cold?

No.
The common cold is a clinical syndrome restricted to upper respiratory tract involvement. By clinical syndrome, I mean it is the constellation of symptoms (rather than the consequence of a specific pathogen). As you mention, these symptoms are the result of the immune response, rather than tissue damage or compromised function as a direct effect of a pathogen or its toxin (e.g., the watery diarrhea in cholera).

As defined (see, e.g., Cecil Medicine Ch. 369), this clinical syndrome cannot lead to death.

  The common cold is an upper respiratory syndrome of rhinorrhea and nasal obstruction, frequently accompanied by sore throat, sneezing, and cough.

Can the viruses that cause the common cold cause death?

Yes. Many viruses that cause the common cold also cause other clinical syndromes that can cause death. This occurs when viral replication moves to the lower respiratory tract. As an example, influenza viruses are responsible for 25 - 30% of common colds (see Bennett, Principles and Practice of Infectious Disease, Ch.58). When it moves beyond the upper respiratory tract, influenza is responsible for substantial mortality. Other virus families that are responsible for both a common cold syndrome and lower respiratory tract syndrome in immunocompetent individuals (e.g., bronchiolitis, pneumonia) include parainfluenza virus, metapneumovirus, adenovirus, and (rarely) coronavirus. Rhinovirus, responsible for 40-50% of common cold cases, is uniquely unsuited to lower respiratory tract involvement, because of its preference for the cooler environment of the nasal mucosa, replicating best at 33 C (Murray Medical Microbiology, Ch 56). However, in individuals with Severe Combined Immunodeficiency (SCID), lower respiratory tract involvement does occur. There are a number of case series reporting death due to lower respiratory rhinovirus. This is an example.

Can the common cold lead to serious illnesses other than lower respiratory tract involvement?

Yes. Other morbidity can occur as a result of the immune response that produces the common cold syndrome. Rhinorrhea and congestion can progress to a viral rhinosinusitis, a separate syndrome with its own complications, or a secondary bacterial infection, which can lead to bacterial sinus involvement and/or bacterial lower respiratory tract infection. Otitis media is another common complication, especially in children, and has its own potential complications. Asthma (and, generally speaking, most lung diseases) can also be exacerbated by what would otherwise be a simple common cold and predisposes to lower respiratory tract involvement. Asthma does deserve special mention, because rhinovirus associated exacerbations can be fatal, but this is a consequence of asthma rather than a common cold syndrome. Further discussion of these syndromes are beyond the scope of the question, but are discussed briefly in the chapters referenced above.


Questions in Regards to Isolating Promotor Region for Recombinant DNA Techniques

If you are performing sticky end PCR you do not need any restriction enzymes at all.

Design primers for your acceptor plasmid to 'linearize' it at the ATG and add a unique 4 nucleotide on the full length forward and another unique on on the full reverse primer. Design your promoter fragment primers to have compatible overhangs to that of the vector. And to answer your question: you will have very very poor yields if both are not perfectly complementary.

You will need to phosphorylate the full length primers for the promoter because primers are usually not phosphorylated at the 5' end. Do your PCR, anneal and ligation as per normal.

But if I were you I would switch over to Golden Gate cloning, our lab did a year ago and I have not regretted it one moment.

Edit:
I have added a diagram below. There was one thing which I overlooked in my original answer: You can get a direct repeat of the overhangs when the two longest products of each annealing reaction combine in a blunt end ligation but that should not affect your expression too much. However I still think that sticky end PCR is not the best way out of this. Blunt end ligation, gibson or my favourite: Golden Gate are all much more powerful techniques


Which organisms have their cell wall made of polysaccharides and amino acids?

The correct answer is Monera.

It is so because their cell wall is made up of peptidoglycan.

  Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid. Attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer.

Fungi is wrong because its cell wall is made of chitin which lacks amino acids.

  Chitin $(C_8H_{13}O_5N)_n$ is a long-chain polymer of an N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world. It is a characteristic component of the cell walls of fungi, the exoskeletons of arthropods such as crustaceans (e.g., crabs, lobsters and shrimps) and insects, the radulae of molluscs, and the beaks and internal shells of cephalopods, including squid and octopuses and on the scales and other soft tissues of fish and lissamphibians.


You take a list of SNPs and a list of gene expression values and you plug it into something like this: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

  So, how can it be possible that one gene (let say GENE22, location: 10-100) is mapped to eQTL(SNP within GENE22, location: 12) in one dietary condition but is not mapped to eQTL in another dietary condition if we are still speaking about the same gene and the same location of an eQTL? So, I am not quite sure what they mean or what they mapped there.

The SNP is associated with expression level changes in that gene for one dietary condition but that same SNP is not associated with expression level changes in another dietary condition. Its possible that the SNP never appears in samples from the other dietary condition.


What happens when you mix type A with type B blood (and v.v)

The blood type of people is determined by proteins which are anchored into the surface of the red blood cells. Cells can either express the A, B, A and B or no marker, resulting in the blood groups A, B, AB and 0. People which have a certain blood type (for example A) have antibodies against the other blood type (in this case B).

This will lead to the attachment of antibodies against the subtype which you don't have (so B for people with A and vice versa) on the transfused blood cells and their lysis. Depending on the amount of blood transfused, this can also lead to a very serious immune reaction. This works like in the figure below (from here):

To avoid this reaction a sample of the blood, which is about to be transfused is mixed with blood from the patient before the transfusion takes place. This looks like this:

For more information look here:

Acute hemolytic transfusion reaction
Transfusion reaction - hemolytic
Genes and Blood Type
Adverse reactions to transfusion


Among terrestrial plants, roots have two major functions - obtaining water (as well as nutrients) and anchoring plants in place. (However, roots may have other important functions as well.) Aquatic plants obviously don't have a problem obtaining water. So roots presumably function primarily as anchors.

There are rootless planktonic plants that float on the surface of water bodies. However, aquatic plants like cattails and water lilies are probably a little more discriminating in their habitat preferences. Imagine a rootless water lily being blown by a hard wind into a patch of water lilies, which block out the sun.


Skin Colour in "Northern" Regions of The earth

Melanin reduces the skin's ability to make Vit D due to reduced UV penetration. This is a disadvantage in northern areas where people get less sun light, and also need to wear heavy cloths to keep warm which adds to the problem. People in Sunny regions have the opposite need as there is more than enough UV light exposure, but they run the risk of developing skin cancer, which is why having melanin provides an evolutionary advantage in these regions.

Interestingly, in the Arabian Gulf region, there is currently an epidemic of Vit D deficiency especially among those with dark skin. Although there is plenty of sun light, people tend to avoid the harsh sun almost completely by commuting strictly in cars and avoiding walking outdoors during the day. Car windows (and glass in general) are opaque to UV rays, therefor reducing the skin's ability to produce Vit D, and forcing many locals who adopt such lifestyle to take oral Vit D supplements.

Here is a link with some references to confirm the medical link between Vit D deficiency and lack of sunlight exposure:

https://www.webmd.com/food-recipes/qa/how-can-dark-skin-lead-to-vitamin-d-deficiency


What signals histone methyl transferases to function?

Histone methylation is regulated by a variety of of events, including transcriptional activation and repression, relative location of the histone in the chromatin (pericentric or not, hetero- vs. euchromatin, etc.), X-inactivation, the cell's point in the cell cycle, and others. A variety of signaling pathways can lead to the (in)activation of HMTs. I found this table at cellsignal.com listing known methylation sites, along with literature references. Elsewhere on the site is this graphic, which shows some of the same info in a different way, and also has links to data at PhosphoSitePlus with links to the protein of interest. If you dig around, you can find all sorts of pathway and experimental information. For example, if you look up PRMT1 (human), you get a brief description of the protein and what pathways it's involved in, as well as links to all sorts of other info. On the histone side, a look at Histone H4 (human) allows you to look at individual modified residues (I picked K21-m2) and find all sorts of literature links and information about experiments used to determine its function.

PS: I'm not affiliated with Cell Signaling, I just think they have a ton of useful protein information, kind of like NEB for mol bio stuff...


What is the mechanism that directs myosin walking?

Good question that got me waist-deep in PubMed. It appears that the directionality of myosin motors is due to the angle at which the actin-binding catalytic domain is attached to the neck region. This review by Vale and Milligan, 2000, sums up the "unzippering" of the neck region that contributes the force for the movement (a video from the review adapted for Alberts' textbook is also informative).

Most myosins move towards the plus end of actin, but myosin VI moves towards the minus end. The neck region of myosin VI attaches to the head region at a different angle than conventional myosins and this is the apparent reason for the change in direction preference (see Figure 1 in review by Rodriguez and Cheney, 2000; also Volkmann and Hanein, 2000; Masuda, 2008).

And for your entertainment, an awesome movie of myosin V walking by Kodera et al, 2010 on YouTube.


Why did many odd-toed ungulates become extinct?

there are two suborder under perissodactyla that are still suvival, Hippomorpha and Ceratomorpha. many perissodactyla species become extinct may bacause the member of perissodactyla animals have sample stomach, compared with artiodactyla, so after the plant change on the earth, they cannot adapt it. and also hinting was one part of reason.
http://en.wikipedia.org/wiki/Odd-toed_ungulate


Single channel refers to the system used to detect the labelled probes.  A single channel array, as shown in this slidedeck (slides 6-8) uses one type of molecule for detection.  In the example, (slide 8) the optical label is phycoerythrin.   Contrast that to a double channel array (e.g slide 7) that uses a "green" or "red" molecule used to label probes.  Detecting two different labels requires two channels, one to detect red and one the the green.   The key to using two (or more) labeling molecules is to ensure that your detection system can discriminate between the light spectrum emitted by each of the labels.   Many modern microarray readers have designs that handle multiple labels.
When you see single channel results, they often have colors.  The color is a pseudo color representation of the intensity of the emission of single-color label, which is due to how much probe has bound to the array at that spot.


There are many studies that have used RNAi against the plant parasite M. incognita. The fundamental idea is that RNAi is directed against one of the vital genes of this nematode. Since, RNAi causes downregulation of the target gene, the nematode dies (or becomes ineffective in infecting) because of the loss of function of these important genes. As you might know about the process of RNAi, dsRNA (or hairpins) are cleaved by Dicer and the small single stranded RNA products, called siRNAs, associate with Argonaute proteins to form RISC (RNA induced silencing complex). The RISC will cleave RNAs complementary to the siRNA.

If you see any of these articles you will notice that the dsRNA is not injected into the nematode; it is expressed in the plant. Nematodes (such as this one and C.elegans in which it is quite well studied) can take up dsRNA from the environment via the RNA transporters present in their cell membranes (See this post).

Now, coming to your question on "Why do RNAi pathway proteins exist in the nematode when they can cause them harm?"

endo-siRNA and miRNA mediated silencing pathways have critical roles in the nematode development and other miscellaneous functions (See this review). As you already know, RNAi can also serve as a defence against dsRNA viruses.

It is us, humans, who have exploited this pathway to develop tools for molecular biology and for targeting parasitic organisms. There is certainly a likelihood that the host plant may express the dsRNA against the nematode during the course of the evolution of its anti-parasitic defence system (it is however not the case now). Not just RNAi, there are many other examples of endogenous pathways of a pathogen being exploited to kill the pathogen.


How many ommatidia does a honeybee have?

4700 - 5400, according to Somanathan et al. (2009). They base their reported values on two other papers.

Reference
- Somanathan et al., J Exp Biol (2009); 212: 2448-53


What is the effect of exendin on beta-cells?

I recently tested exendin on INS1e cells in an Edu incorporation assay (similar to BrdU incorporation) to observe if this compound induces proliferation of the cells.  Compound incubation was for 24 hours.  I saw no incorporation of EdU with this compound over untreated levels.  In addition, during the assay I look at overall cell number with a DNA stain, but I did not see any effect on total cell number with exendin (ie, if it were toxic the total cell number should go down which I have observed with other compounds).


Do we have enough diversity of antibodies to overcome almost any antigen?

As my answer is quite big I've highlighted the different regions I answer your question.

Intro and basic info

I take it you know how antibodies are made, but as a quick recap they're made by VDJ recombination of a limited but still quite numerous pool of genes which are recombined randomly, and then further recombination occurs by hypermutation of certain segments particularly in the regions that identify antigens.

What is Hypermutation?

Hypermutation occurs after the original antibody is made in order to perfect it. The same mechanism I talk about in moulding antigens below. It is exactly what it says: a high rate of mutation compared to that of the low rate in cells normally. When B cells are activated because they've met their antigen to which they respond (cognate antigen), they undergo somatic hypermutation. While the B cells undergo somatic hypermutation, the genes which code for the antibody are mutated so that the antibody binds to its cognate antigen with a different specificity. If it binds better the B cell gets to live, if it doesn't bind or it is worse then the B cell dies.

Moulding antigens

What we cannot do is the other way around. We can't recognise an antigen and then make an antibody to it, because recognising the antigen requires an antibody. What we can do is once we've recognised the antigen, then mould the antibody so it is a better fit. How we do this is by B cells mutating their antibodies and competing which binds better. However, B cells just don't have the knowledge to see an antigen and think a tyrosine residue at this position will be perfect to change my shape to this configuration - that's really complex stuff!

Do antibodies recognise every molecule?

Antibodies are made to essentially every antigen which is very costly in terms of energy as you mentioned. In fact, the number of genes that make antibodies are thought to be the perfect amount as to protect us without being too numerous so that it is not only too costly, but we have so many different antibodies the chance of ever finding the right B cell is so low we die before we manage. This is because of the way antibodies are mass produced, in the typical pathway of new antigens, firstly a T cell must recognise the antigen then B cells that produce an antibody that binds to the antigen (rarely in the same region, and may not even be to a protein antigen).

So these two paragraphs highlight the limitations and answer your first question. Antibodies are so diverse that we can expect quite a few to recognise every pathogen, but not every single possible antigen will have a cognate antibody. Diversity without so much diversity that it becomes redundant. The second limitation is that antibodies will ideally not form if they recognise self (our own proteins etc.) Which leads on to your next question.

What if a pathogen makes antigens that look like our own proteins?

Autoantibodies are made but are typically non-pathogenic (i.e., they don't cause harm). Certain HLA/MHC polymorphisms that make us likely to form autoreactive T cells, also make us make autoreactive antibodies. Interestingly, this increases our risk of autoimmune diabetes but ALSO makes us more resistant to infection by HIV. This can be practically seen in the DQ8 polymorphism. This is a perfect example to illustrate the answer to your second question. Ideally, pathogens which have antigens similar to our own would not be detected. HIV wraps itself with an envelope of our own lipid membrane for this purpose, and the best neutralising antibodies are often self-reactive and therefore are those that failed elimination.

However even these pathogens are going to do something or make something that isn't something our cells usually do. This is how the body finds and targets cancer cells (in a way), they do things our own cells won't typically do like make the wrong proteins or wrong amounts etc. Thus cancer cells and pathogens can be targeted by our cells that find something that isn't self (CD8 cytotoxic/killer T cells). As for pathogens, we all make MHC/HLA which is unique to us and pathogens could never manage to invade and make the specific HLA/MHC that we do, so our body also targets missing HLA/MHC.


What is the effect of Montelukast on the amount of IgE in blood?

I was interested in this question because I have always been a little confused about allergic responses, so I did some rather superficial research (i.e. I looked at some Wikipedia pages). As far as I can see there is no reason to think that Montelukast will have any effect upon IgE levels.

Montelukast is a leukotriene receptor antagonist. It is used to treat allergies and asthma.

Leukotrienes are lipid signalling molecules that are used by cells to regulate immune responses. One role of leukotrienes is to promote contractions in the smooth muscles lining the bronchioles. If they are over-produced they can cause inflammation in the airways leading to symptoms of asthma. Since leukotrienes act through a receptor, an antagonist of that receptor such as montelukast can reduce their effect.

IgE is involved in allergic responses because it interacts with Fc receptors on the surface of certain cells such as mast cells. If the IgE molecules are associated with one another through Ig-antigen interactions this leads to clustering of the Fc receptors which triggers an intracellular signalling pathway leading to mast cell degranulation - the release of histamine by fusion of storage vesicles with the cell membrane (i.e. exocytosis). Histamine causes constriction of the bronchioles via effects on smooth muscle, just like leukotrienes.


Why can't we see in low light if staring long enough?

For simplicity's sake, let's really reduce this to something like photography.

A camera's aperture can stay open indefinitely, allowing the plate (or whatever is receiving and recording light) to "collect and save the effect of photons" over time, if you want to phrase it that way. That allows a camera to make images that our eyes never can, for example, of "star trails".

The retina isn't like a photographic plate or a digital sensor's photosites (or pixels). It can't "collect and save" like a camera can. There is a "refresh rate", if you will, that disallows a collection and saving of light that doesn't apply to cameras, because cameras don't care if something in their vicinity is sneaking up on them and presenting a danger to their lives. Not being able to detect change rapidly is something that would be most inconvenient to survival.

  It is the time sampling with long exposures that really makes the magic of digital astrophotography possible. A digital sensor's true power comes from its ability to integrate, or collect, photons over much longer time periods than the eye. This is why we can record details in long exposures that are invisible to the eye, even through a large telescope.

How Digital Cameras Work


Why isn't the biological niche occupied by whales instead occupied by fishes?

The "niche" of whales comprises much more than just being big. I would actually argue that this is just a byproduct of the marine lifestyle, since endotherms need to maintain their body temperature which is easier when you're big (lower surface/volume ratio). Some reasons for whales being very successful are:

1) Higher oxygen use efficiency:
AMR already mentioned the advantages of the mammal metabolism in the terms of oxygen intake. This allows whales to forage in great depths. Note that no fish could withstand such rapid pressure changes, since they need to dynamically adapt their swim bladder.

2) Intelligence:
Mammals are much more intelligent and therefore have access to resources that are not available for most other marine animals. E.g. hunting in groups requires a fair amount of intelligence and is much more efficient than hunting alone.

3) Acces to cold environments:
In contrast to fish, mammals can maintain high activity regardless of the ambient temperature. This gives them almost exclusive access to highly productive ecosystems like the antarctic and southern oceans.

4) Echolocation:
Toothed whales including dolphins use echolocation to communicate and sense objects. This is a very powerful ability for locating and tracking prey.


What are the programming languages important to learn for a geneticist or bioinformatician?

Comparing some commonly used languages in bioinformatics

I think that indeed Perl is losing users but there are still quite a lot of people using it. Bash (or other shell) is essential. While one can replace Python with C or Java and eventually replace R by Python or Julia, I find Bash to be really necessary. To compare Python to R, Python is much faster. If you are a purist, you'll like Python much more than R. R is a weird language, I use it a lot but you always have to deal with very special kind of objects. The big advantage of R is its community; There are tons and tons of functions. Typically, for any task you you want to do and related to statistics or to phylogenetics, you'll find an already existing package that will do the job for you. C is nice and very popular. It is super fast but it is not super handy for most tasks. Moreover, C doesn't have an interpreter which is always kinda annoying when you're use to high level languages such as R typically. I know nobody who uses Ruby and I don't code in Ruby but it is an important language. Some may use it for bioinformatics and it is very much used in many other disciplines (unlike R, which only statisticians know).

What I personally use

Personally, I use mostly R, Python, C/C++ and Bash. Bash to organize stuff, modify files and manage processes on my machine and on remote machines. R for data analysis. Python when R is too slow (to analyze more data such as sequence data for example) and C/C++ to run individual based simulation. I happen to use some other languages for my work but not as often.

How to learn

Nobody excels at coding to start with. Actually, after my first class of programming I had in mind that programming was not meant for me. Now, I don't excel, I am just a biologist who codes a bit and not a computer scientist but I spend the majority of time coding and I love that. I learn a lot everyday but ever since I started to feel a bit confident, I found that I could do much with this knowledge. You'll probably realize after some time that few people are really good at coding and you can already do much with only a few days of training. Don't be afraid. I think that indeed one of the best way to learn a language is to use it for a project. Here are a bunch of things you could do:

Go on Dryad.com, get some data and analyze them. You can redo the analysis they did on the original paper for example. Or, better you could try to discover something by yourself by combining some existing data.
individual-based (OOP) simulations in population genetics

simulate genetic drift in populations. Try to estimate the probability of a new mutation to fix and the time it takes to get fixed.
Simulate the process of selective sweep with defining chromosomes.
You'd basically have to have a function that creates a list of objects of type individuals. Each individual has two objects called chromosomes. You have a function that simulate reproduction (without selection, recombination nor mutations to start with). And you need a function to print the statistics you need on a file. I think you could do a simple individual-based simulation in a few days only and then you'd feel more comfortable with the language and you would also have a better grasp on how one can numerically simulate a population through time.


For the media bottle, it is better to keep the cap a bit loose to avoid to pressure inside the bottle. A good way is to had autoclaving tape on the side so that it is clear that the bottle has been autoclaved. As Chris mentionned below once autoclaved, use gloves, and close the bottle firm after you open the autoclave and do not wait until it has cooled down completely.
It is not really important if it is slightly to tightly close. In fact you could have them on a tray or a bucket that would be fine to. One caveat is that it might depend on the equipment, the rules regarding the usage of the equipment etc. You would need to check these questions with a Senior person on the site.
The longer the better. If everyone operate at 35-40 min either there is a good reason to do so (often the case) or not. To be safe, I would suggest to be conservative there. Often what might happen is you want to make sure that you have the sample autoclaved at the highest temparature for at least 20 min. Because of leakages or other factors it might be best to leave it longer to make sure it is autoclaved at least 20 min.

Hope that helps!


Does thyroxine increase BMR or metabolic rate?

The definition of BMR from wiki is :

  Basal metabolic rate (BMR) is the rate of energy expenditure per unit time by endothermic animals at rest.

When BMR is calculated for a volunteer some conditions are taken into account:

complete physical rest
sitting upright
at a comfortable room temperature usually around 25 centigrade
at the post-absorptive phase of digestion

On the other hand metabolic rate may be calculated even when one is exercising, at high or low room temperatures, during digestion etc. So it is more generalised.

When you are talking about thyroxine or thyroid hormones, you must keep in mind what (factors) stimulates its secretion.
One such factor is coldness.

So that definitely indicates temperatures below the 25 centigrade mark at which BMR is usually calculated.

So in my opinion it was quite prudent of your teacher to advise you to use metabolic rate instead of basal metabolic rate for the thyroxine effect description.

REFERENCE BOOK:
Biochemistry by Debajyoti Das 14 th edition
Academic publishers P-677 to 680.


How do the chromosomes arrange themselves after fertilization in humans?

After fertilization the diploid cells divide by mitosis.  Chromosomes don’t need to pair with their partner during the eukaryotic cell cycle.  After S-phase each chromosome has been duplicated (so there are 46 + 46 = 92).  The two daughter chromosomes resulting from semi-conservative DNA replication are held together at one point: their centromeres. In M-phase two microtubules from opposite poles of the mitotic spindle will attach to the kinetochore that assembles at those centromeres.

Nowhere in this process is the maternal chr1 required to interact with the paternal chr1.

The pairing that you are refering to takes place much later after the new primordial germ cells haved developed into the germline, leading to meiosis.  The molecular details of homolog pairing during meiosis are best understood in the model organism C. elegans where each chromosome has specific cis-acting sequences that are recognized by different trans-acting factors that lead to recognition and then pairing, followed by synapsis, and eventually crossing over.


To answer your question multiple parameters which one should be taken into account.

There are two main sets of parameters: gene specific and cell line specific.

Parameters related to your specific gene of interest :

Do you know the half-life of the RNA of your gene of interest? Most of the time it is not known but there are several tools and resources which can predict it based on a lot of different features such lengths and stability of 3'UTR, 5'UTR, number of exons introns, etc.
Another indication is if there are already people who have either perform a genetic perturbation (siRNA, CRISPR, etc) or a degradation assay. In this case you might be able to guess what is the relative half-life of the RNA or the protein.
Which leads us to the half-life of the protein of interest. Proteins which are soluble tends generally to have a smaller half-life than membrane proteins (not necessary true there are exceptions). For example doing a complete functional knockout of a transcription factor might be easier than a GPCR receptor. If it is a membrane protein, to which organelle does it localize? Is the organelle recycling the membrane a lot or is the cell dividing? In this case you might have chances that the viable proteins present before the genetic perturbation get diluted. In these examples, you might get ride of a soluble protein in less than 24-48 hours, whereas a very stable membrane protein might take 7-10 days.
The number of RNA copies is important as well as the number bound to ribosomes (less important) and their localization in the cell (less important)
The abundance of the protein in general.

Parameters related to your cell line of interest:

The lineage of the cell line you selected: different cell lines have different global transcription and translation rates.
The rate of division of the cell line (extremely important parameter): the faster the cell line will divide the faster  the mRNA copies which were not perturbed (wild-type) and the proteins present before the genetic perturbation will be diluted between daughter cells.
Number of copies in the cell line: if there are multiple copies of your gene of interest, you would need to make sure that each copy of the gene has been perturbed to lead to a functional KO.
Genomic stability of the cell line: some cells lines like HeLa are quite known for genomic instability where a lot of the genome can be rearranged can perturbed copies can be fix using viable copies

Last but not least, it depends technically how you do the CRISPR-Cas9 genetic perturbation: transfection of the gRNA, electroporation of the Cas9 with the gRNA, lentiviral mediated delivery etc. The time I have provided are after all the components have been delivered and are present in large amount in the nucleus.

I hope that helps!


Can a cleaved plasmid "close" without exact matching "sticky ends"?

The plasmid won't religate efficiently if the ends are not compatible.  However, it's possible that very rarely your plasmids may re-ligate, perhaps because of a tiny level of contamination with exonuclease that trims back the ends to be blunt.  Or there may be spontaneous blunt breaks or other strange events.  This may happen in a tiny fraction of the plasmids, one in millions, but since your transformation step selects for circularized plasmid very efficiently you may end up detecting it.

Note that these rescued plasmids are often aberrant since they are unpredictably trimmed at the ends or otherwise followed a non-designed path to circularize; this is not something you want to count on for your cloning, it's an annoying byproduct that you want to avoid.


Can untargeted metabolomics detect epigenomic changes such as methylation?

This is a fascinating question, and I spent a fair amount of time looking into it. From what I've been able to find regarding the relationship between metabolics and epigenetics, it seems that metabolites drive epigenetic changes, not the other way around.
This can be shown quite well by looking at cell differentiation and induced pluripotent stem cells. The epigenetic changes that happen in these processes happen due to the cell's environment.

However, epigenetic changes cause changes in transcription rates, so it can indirectly influence metabolics. The circadian clock uses this system (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3392647/).
Cell signaling appears to be the most significant cause of metabolic change, though. The aforementioned paper also says this:

  As most metabolites are not diffusible between mitochondria and
  cytosol/nucleus, accurate determination of the cytoplasmic pool size
  is critical to understand their effects on epigenetic signaling.
  Although attempts have been made, so far the technology to reliably
  measure metabolite concentrations in different cellular compartments
  is lacking.

Which, I'm sorry to say, leads me to believe that there are very few metabolic pathways that have known effects on epigenetic factors.
That said, there are several references in that paper which may put you on a good path forward.


What hydrolyses aspirin within the digestive tract and blood stream?

Acetylsalicylate deacetylase is the enzyme responsible for this reaction.

  Precisely, the present investigation reveals that the hydrolysis of aspirin in liver, kidney and probably other tissues of
  rats is catalyzed by two highly substrate specific microsomal
  esterases, ASA esterase I and II active at acidic and slightly
  alkaline pH, respectively. The findings that ASA esterases have
  distinct organ distribution pattern and display responses to
  various inhibitors/activators that are different in many respects
  from those exhibited by cholinesterase and nonspecific carboxylesterase suggest that the latter esterases probably do not play
  a significant role in the hydrolysis of aspirin.

  From:
  Ali B, Kaur S (1983) Mammalian tissue acetylsalicylic acid esterase(s): identification, distribution and discrimination from other esterases. J Pharmacol Exp Ther,226,589-594


Is my cell-culture contaminated with mold?

Most of the time you can find shards of plastic, defects in the plate and other non-cellular debris in brightfield that look suspicious. Even some cellular debris can look suspicious, like when your viability is really poor. That doesn't look like anything to me. You'd know if you had contamination because it would be in more than 1 field, you'd have more than 1-2 of them, and your culture would either change in color, turbidity or smell. If it's a plate defect, you probably wont see it move if you re-suspend the well, either.


Nocioception (pain perception) in subcutaneous tissue

"no nociceptors in subcutaneous fat"

Well nerves innervate tissue, but only the layers of skin above the hypodermis (Subcuteaneous fat layer).
You are correct.
If one was to burn below this layer they would not feel pain in that area due to having no nociceptors.
There is a great Kharn Academy video on this topic here.


How can you explain the origin of life out of nonliving matter (abiogenesis)?

Welcome to Biology.SE!

Your question has nothing to do with evolutionary biology

Evolutionary Theory does not explain the origin of life just like the Theory of Gravity does not explain the diffraction of light! In other words, explaining the origin of life is not within the scope of evolutionary biology. You should edit your title. But still, your question is within the scope of Biology so that your question is totally on-topic. This question would probably also be on topic on Chemistry.SE.

Some other posts may interest you

You may want to look at other posts on this site. This post for example explains what are our issues in order to select which of our hypotheses really explain the origin of life. This post, this one may eventually interest you as well.

Your question might be too broad. You may want to start with some introductory readings

Abiogenesis is not my field and I know very little about the origin of life. But at first sight, I am a bit afraid that your question is too broad and inaccurate and a good answer would ask for writing a lot. This post will give some good source of reading to further your knowledge. It may be good to start there and come back to this site with a more accurate question.

Hope I could help you a bit.


What sort of assay could be used to identify mutants with mutator phenotype?

There are a number of ways to screen for mutator genes. One straightforward approach in bacteria is to take an antibiotic sensitive non-mutator strain, grow it up, and expose to different antibiotics. Cells that survive in the presence of multiple antibiotics have acquired multiple de novo resistance mutations and thus are highly enriched for mutator alleles. Here is one example: Wiegand et al (2008) AAC.


Structure of RAP Antibodies (Specifically RAP-5)

The confusion that you're facing is because RAP-5 is actually known as RAB5C (GENEID). The ras superfamily (review) is divided into Ras, Rho, Rab, and Rap. But the Rap GTPases are divided only into two categories, RAP1 and RAP2. On the other hand, there are multiple Rab GTPases which include RAB5A and RAB5C.

There are a few crystal structures of both Rab5A and Rab5C in both human and murine forms.

Now, for RAP-5. RAP-5 is a monoclonal murine antibody which has no relationship to the RAP family of proteins. It's probably called RAP because Spandidos and Wilkie weren't thinking clearly when they named their antibodies RAP1-5. In this case, you're probably better off looking at the antibody Y13-259 which is probably called that since its the 259th antibody they tried.

To answer your questions, specifically, very few people have attempted to get a structure since it is an antibody and everyone knows what they look like. Secondly, the antibody is produced in a mouse and added to tissue. And yes, the RAP antibodies bind to different variants of Ras. Also, no one uses RAP-5 since anti-Ras EP1125Y seems to be more popular.

If you still want a crystal structure, I would hunt down the RAP5 patent and look up the peptide sequence. From there, you can look up similar structures in the IMGT database


When comparing oral infection v IV infection in mice, why would the CFU given be different volumes?

Intravenous delivery of pathogen produces infection more efficiently than transmucosal delivery.

10^7 is 2 orders of magnitude less than 10^9.  It is not the volume that is different (although it may be), it is CFUs or "colony forming units" which is a proxy for viable pathogens in the inoculum.  The oral dose is 100x that of the IV.

Getting germs directly into the bloodstream bypasses the built in protections that our mucosal surfaces have.  The GI and GU tract have a lot of defenses.   For example an experimental SIV infection produced intravenously in monkeys requires an order of magnitude less virus than an infection established rectally or vaginally.

I would suspect that the CFUs of a given pathogen via a given route is something established empirically as producing the desired outcome.  If you used the same CFUs for an IV route as were required for the oral route, you might have a fair number of mice that just died from septic shock from the huge number of bacteria suddenly in the blood.  Given the 2 order of magnitude difference of inoculum (IV vs PO) to produce infection you might conclude that the stomach kills 99% of any inoculum.


A more common terminology regarding 'intersensory associations' is multisensory or crossmodal integration. Crossmodal integration takes place in the association cortices in the brain (Fig. 1). An example is the coupling of auditory and visual input during lip reading, as mentioned in the comments. Lip reading can aid in acoustic speech understanding, especially so in the hearing impaired.

The association cortices include most of the cerebral surface of the human brain and are responsible for integrating the sensory input that arrives in the primary sensory cortices. The diverse functions of the association cortices are loosely referred to as “cognition,” which literally means the process by which we come to know the world. Cognition enables us to attend to external stimuli, to identify the significance of stimuli and to plan meaningful responses to them. The association cortices receive and integrate information from a variety of sources and in turn influence a range of cortical and subcortical targets (Purves et al., 2001).

Fig. 1. Association cortices. source: Brown, Physiology & Neuroscience websites

Reference
- Purves et al., Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates; 2001


How to reduce edge effects in cell-based high-throughput experiments?

Lundholt et al. describe a very simple trick: let the plates settle in air at room temperature for a couple of hours before placing it in the incubator. We tried it out, and although the color scales are different in the following plots, it is easy to see that it really does help:

(Thanks to Sigrun Gustafsdottir and Kate Madden for testing this.)

I have seen some people "pad" the plate by using only the 308 interior wells and filling the  76 edge wells with only liquid, but I have no data for how well that works.

Allison Tanner from Corning has collected a compendium of techniques to reduce the occurrence of irregular patterns of cell adhesion or “edge effect” in microplates. Brifly summarized:

Avoid bubble formation in the media when seeding cells.
Use cell harvesting methods that foster adequate mixing of the cells in the media and complete dissociation of the monolayer into single cells.
Seed cells at a density that will support attachment and growth.
Allow cell attachment to occur in media of the proper formulation for the particular cell type.
Dispense cells in an appropriate volume of media.
Follow strict aseptic techniques according to respected microbiological practices.
Cultures should be routinely monitored for mycoplasmal contamination.
Minimize entrance to incubators to help reduce fluctuations in the internal environment.
Allow cells to settle in the microplates while the microplates are on the benchtop.
Culture cells in an environment that reduces the formation of static electrical charges.


Pyruvate is negatively charged and quite polar, which makes it unfavourable to diffuse directly through any membrane. The outer mitochondrial membrane contains porins, which allow small molecules, like pyruvate, to passively diffuse through. Specifically, pyruvate uses voltage dependent anion channels. The inner mitochondrial membrane lacks such channels and depends on active transport by the long anticipated but only recently discovered mitochondrial pyruvate carrier (Herzig et al. and Bricker et al., 2012).


Lower affinity drugs longer time for pathways to rebound?

This article is a good starting point for this question.

It states:
"The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not."

The dissociation constant is explained fairly well by Wikipedia.
So, the higher the affinity of a drug with it's target, the stronger it binds.

I'm assuming that by "rebound" you mean that the pathway will regain its ability to function normally.

When someone takes a quantity of a drug, it disperses throughout the body. At any given time, at any given point in the body there is some concentration of the drug. If the affinity of the drug to it's target is very high, lots of molecules will bind to the target, whereas with a low affinity drug, fewer molecules will bind.

As time goes on, the body will filter out some of the molecules, and the remaining drug molecules will diffuse to fill the space where the filtered molecules were located. As this process continues, the concentration of the drug will decrease, lowering the dissociation constant of the drug-target equation, which means that fewer of the molecules will bind, and some of the bound molecules will be released to maintain equilibrium. The longer this process continues, the closer to "normal" the pathway will become, until the concentration of the drug is negligible.

Keep in mind that all of this is dependent on the rate at which the body eliminates the drug (and how quickly the drug degrades on it's own). See here for equations and such. While concentration of the drug is a large factor in it's effects, the half-life of the drug may be a better indicator of how long it takes for a pathway to rebound than affinity of the drug. For that matter, affinity is probably a factor in the length of a drug's half-life.


Do gene expression levels necessarily correspond to levels of protein activation?

It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. This paper on yeast and this paper on cancer both establish this, although using older techniques (SAGE and microarrays, respectively), while this more recent review discusses the topic in light of more recent technologies (e.g. RNA-seq).

Perhaps the difficulty with exploring the correlation between mRNA levels and levels of active, mature proteins is that we still know so little about so many proteins and and what makes them active and mature versus inactive, premature, etc. Not all proteins need post-translational modifications to be active, but some do. Currently, this is investigated on a very detailed protein-by-protein basis (as far as I know), so gathering enough data for a large-scale study could take a long time. On the other hand, there are a variety of (increasingly affordable) high-throughput methods for measuring the abundance of thousands of RNA species simultaneously. I think people are using mRNA levels to estimate expression not because it's the most biologically cogent course of action, but rather because it is much easier, more affordable, and more high-throughput (which is all the rage these days).


Do SSRIs downregulate or upregulate the 5-HT3 receptor?

There are five subunits to this receptor (5-HT3), which are encoded by the genes HTR3(A-D) and differentially expressed depending on cell location in the (human) body. In contrast to the information in the previous answer, my first source actually has shown HTR3A to be most highly expressed in the CNS. The others are almost exclusively found in cells of the gut.

My second source reveals that the 5-HT3A receptors are up-regulated (show increased expression) on the cell surface in the presence of agonists and antagonists to the receptor. So, if an agent was increasing the amount of 5-HT (serotonin, an agonist) outside the cell, as would an SSRI, the expression of the receptor subunit-encoding genes would be expected to increase.

Niesler, B., Frank, B., Kapeller, J. & Rappold, G. A. Cloning, physical mapping and expression analysis of the human 5-HT3 serotonin receptor-like genes HTR3C, HTR3D and HTR3E. Gene 310, 101–111 (2003).
Morton, R. A., Baptista-Hon, D. T., Hales, T. G. & Lovinger, D. M. Agonist- and antagonist-induced up-regulation of surface 5-HT3 A receptors. Br. J. Pharmacol. 172, 4066–4077 (2015).


what is the meaning of VIP-cre::LSL-TOM::SOMGFP(GIN) mice?

I think I can help explain all but your 3rd question.

A transgenic mouse will typically have the genetic construct in all cells. Unless you get a chimeric animal, which is screened for during the making of the mouse.
VIP::Cre means that the promoter of VIP was used in front of the region of DNA that encodes for Cre recombinase.  Note, the animal still has the endogenous VIP gene that makes VIP. This is an additional construct. The intent of this kind of system is to limit the expression of Cre recombinase to only the cells that would also be expressing VIP.
LSL stands for Lox-Stop-Lox cassette. LSL:TOM is the gene that encodes for tomato red protein with a premature stop in the transcript such that it never makes a correct protein (and no red).
If Cre is expressed in a cell with the LSL-TOM construct, it will recombine the LSL and remove the stop codon, thus enabling the creation of functional tomato red transcript and fluorophore (protein). Again, this construct is in the DNA of ALL cells, but the recombination event (and subsequent expression of function TOM) will only happen in the cells that are also expressing Cre recombinase. And for a VIP::CRE mouse this only happens in VIP expressing cells.

Your questions:

1) Actually every cell in the animal has a VIP::Cre (excepting blood of course or sex cells that got the non transgene allele during meiosis. This is because usually the cre genes are kept at Hets during mouse mating).

2) All neurons (and all cells; see answer 1) will contain the genetic construct VIP::CRE.  The intent is in the VIP::CRE mouse, only cells that would express VIP would express Cre recombinase.  This means that other tissues in the body that express VIP should also fluoresce red in a VIP::CRE/LSL-TOM mouse.  As an aside, all cells that normally make SOM should also be making GFP in the SOM::GFP mouse, but every cell will have the DNA transgene.

3) This question is outside my breadth of knowledge. I've done lots of work with transgenic mice, but other than looking up that that viral construct has something to do with calcium and imaging in neurons, I am not sure.

Per Bryan Krause: "...the expectation is that it will infect most if not all cells, not even just neurons, but it is using the 'synapsin' promotor which is neuron-specific (but would be expressed in both VIP and SOM cells, as well as other neuron types). Presumably the authors are using calcium imaging to detect activity across a whole mixed population but then using tdTomato to identify one subpopulation or the other, depending on which animal is used."

4) For VIP-cre::LSL-TOM::SOM-GFP(GIN).   As written, this would imply the expression of Cre is necessary to activate transcription and encoding of tomato red in VIP expressing cells. But that GFP is already active in SOM expressing cells from day one of development.

Some uses of Cre-Lox systems are illustrated here. This picture from that website demonstrates graphically what is going on with a LSL construct.

Your system has tomato red instead of lacz and is using VIP expressing cells as a targeted system.


I would speculate that there is no direct advantage imparted by the deuterostomic development process over that of protostomes with regards to the evolution of more complex species. Instead, I would guess that sometime after that split, a series of novel alleles arose in various genes which were eventually fixed and laid the groundwork for future increased complexity. Given the trait in question (increased organismal complexity), I would be certain that these alleles were in mostly unrelated genes and were selected for some other function (in other words, there is no gene encoding a protein that imparts organismal complexity; that trait is, by definition, a complex one!). Perhaps the genes involved in the deuterostome/protostome split were part of this groundwork, given their activity at the base of development, however it would be very difficult to know at this point.

I don't know why I didn't think about this before, but the more likely explanation for the difference in complexity between deuterostomes and protostomes is actually unrelated to that difference. Most of the complex deuterostomes that you're probably thinking of are vertebrates. Vertebrates went through a couple of rounds of genome doublings (tetraploidizations) during their early divergence. The extra copies of all the genes provided fertile ground for evolutionary novelties that seems to have led to some wonderfully complex creatures. It's still possible that the tissue groundwork laid out by the deuterostome developmental process somehow contributes to that complexity, but it would be rather indirect, I think.


Yes, this is possible (and I have done it uncounted number of times) - the method is called "Freeze and squeeze". What you basically do is to run the gel, cut out the band of interest (be careful with the UV light, it causes damage to your DNA and also sunburns, so wear appropriate shielding for your face), dissolve it in a buffer, then freeze it in liquid nitrogen (or the -70°C, doesn't matter) and centrifuge it at room temperature for 10 minutes. During this time the ice melts and the agarose pellets at the bottom. Take the supernatant, do a ethanol precipitation (with glycogen when you only have little DNA) and you have nice and clean DNA. No need for expensive kits and is done approximately in 2 hours.

You can find a very nice and detailed protocol here: "Elution of DNA from Agarose Gels" (The rest of the handbook is also very useful).


What is the impact of sertraline on white blood cells?

Short answer
While sertraline may theoretically affect the immune system, there is no evidence, as far as I know, that it negatively impacts immune status.

Background
In the article (Atkin-Smith et al., 2015) sertraline (a.k.a. Zoloft, an antidepressant) is shown to block the formation of ‘beads-on-a-string’ protrusions and apoptotic bodies after from dying white blood cells.

Generally, when cells die physiologically, they do not just disintegrate, they undergo programmed cell death called apoptosis.

Beads-on-a-string from a apoptotic monocyte. Source: (Atkin-Smith et al., 2015).

The authors hypothesize that these beads-on-a-string and apoptotic bodies may boost immune responses by containing antigenic material, or that they may contain a warning signal for other immune cells that a pathogen is on the loose.

These claims, however, are hypotheses.

There are many reported side effects of sertaline, but immune suppressant effects are not evident. The only side effects reported touching on it are, e.g., a fever and a sore throat. However, such general symptoms can be caused by a variety of causes and were not reported frequently.

Indeed, in a small study in HIV patients, sertraline showed no adverse effects on the immune system (Rabkin et al., 1994).

References
- Atkin-Smith et a. Nat Comm (2015); 6: 7439
- Rabkin et al. J Clin Psychiatry (1994); 55(10):433-9


What is the difference between gene expression and protein synthesis?

According to the homonymous article of Wikipedia

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product.
These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.

As shown by this picture, gene expression consist of genetic transcription, that results in a mRNA, maturation of the mRNA (splicing, incorporation of a poly(A) tail, capping, ...) and finally protein synthesis by means of translation of the mature mRNA.
Again, the homonymous Wikipedia article tells us what is protein synthesis:

Protein synthesis is the process whereby biological cells generate new proteins [...]. Translation, the assembly of amino acids by ribosomes, is an essential part of the biosynthetic pathway, along with generation of messenger RNA (mRNA), aminoacylation of transfer RNA (tRNA), co-translational transport, and post-translational modification.

The following picture describes the process of mRNA translation by ribosomes that results in a polypeptide.

Once folded in its proper 3D structure, the polypeptide becomes a functional protein.
In order to work properly, some proteins need post-translational modifications, which is (citing Wikipedia again) the covalent modification of proteins following protein biosynthesis and goes beyond the scope of this answer.


Identify this dragonfly with orange body and orange wings?

These seem to both be Neurothemis taiwanensis.
On iNaturalist, if you search for dragonflies in Taiwan, it finds 104 species observed and submitted, and this Neurothemis taiwanensis is the most popularly-submitted species.
Browsing the gallery of photos in their database shows both red and orange varieties. If we filter the sex on just males, we see mainly deep-red ones:

...and filtering on just females yields mainly orange ones but also some red ones:
https://inaturalist.ca/taxa/503081-Neurothemis-taiwanensis/browse_photos?term_id=9&term_value_id=10&place_id=7887


When life first formed in earth's ocean, was it salty yet?

Current estimates suggest that last universal common ancestor of life on earth lived in hydrothermal vents 3.8–3.5 billion years ago.1  Petrologic examination of quartz formed near these vents during that time suggests that seawater had a higher salinity compared to current oceans 2 --

Our data are in agreement with six other data sets—from the 3.75 Ga Isua Greenstone Belt (W. Greenland), the 3.24 Ga Pilbara region (W. Australia), the ∼3.2 Ga Barberton Greenstone Belt (South Africa; 2), the ∼2.7 Ga Matagami area (Abitibi Greenstone Belt, Canada), and the Proterozoic (∼2.2 Ga) Ongeluk Formation (South Africa). The consistency of fluid inclusion data suggests that Archean and early Proterozoic seawater may have been more saline, and potentially stratified, compared to modern seawater.

Note: Ga (for gigaannum) – a unit of time equal to 109 years.

Weiss, M., Sousa, F., Mrnjavac, N. et al. The physiology and habitat of the last universal common ancestor. Nat Microbiol 1, 16116 (2016).
Weiershäuser, L., Spooner, E.T.C. Seafloor hydrothermal fluids, Ben Nevis area, Abitibi Greenstone Belt: Implications for Archean (∼2.7Ga) seawater properties. Precambrian Research, Volume 138, Issues 1–2, 2005, Pages 89-123.


Regarding snake venoms, they tested 28 snake venoms at 100'C: 19/28 of the venoms were still very dangerous after 5 minutes at 100'C.

"Heating all venoms led to the denaturation and loss of some proteins; however, most of the venoms retained a significant number of proteins. Seventeen venoms contained more than seven proteins after heating, whereas five venoms contained only one to three proteins. All but nine of the heated venoms had substantial hemorrhagic activity, and Agkistrodon piscivorus piscivorus venom had very high activity, almost four times that of the second most hemorrhagic venom from Crotalus viridis lutosus."

There is a good chance that land animals have higher heat tolerance spiders and snakes can experience a lot higher heat than marine organisms.

study of marine venoms and hot water says:
Sting ray venom is especially fast to denaturize in heat, and most fish spine venoms are. HWI hot wat immersion is recommended for fish spine stings by some organizations. They did tests to find that box jellyfish, sting rays and other sea creatures stings react significantly to HWI.

They tested that 122/138 marine envenomations were improved by HWI from a variety of surveys.

there are 50,000 marine stings a year from 2000 species and
about 5 million snake bites, 2mn envonomings and 20-125,000 deaths by snakes every year from 400 species out of 3000 species of snakes which are dangerous to humans.

Dangerous snake and spider bites are generally treated in hospital, and the only wise thing to do is not to not make your blood go around your body very fast by being active after a bite, stay calm and alert.


Usually,blood moves through the body by force from the contraction of ventricles, the contraction on muscles, gravity, or other forces. At death, the only force left is gravity, which is why we see lividity (or livor mortis -pooling of blood in dependent positions) after death. This continues for ~8-12 hours (depending in part on temperature).

The blood in the arterial system at the moment of death is still under pressure because arterial wall musculature has not relaxed yet. (I don't know how long this takes, to be honest.) If an artery is pierced (say, a bronchial artery, e.g. by a knife), blood will flow from a high pressure area to a lower one (e.g. into non-inflated lung tissue, the abdominal cavity, or the outside or the body) So post-mortem hemorrhage can occur until the arterial musculature has completely relaxed. After this relaxation, stabbing a corpse will produce a small amount of oozing at most, unless pressure is applied somehow, e.g. during CPR. CPR may make small petechiae larger.

Livor mortis can occur in the lungs post death as well.

  as the blood accumulates in the dependent areas, the pressure of the settling blood can rupture small vesslels, with development of minute hemorrhages (petechiae)... This usually takes 18-24 hours... and is more common in (asphyxia).

Hanging is death by asphyxia, and is known to be associated with lung hemorrhages, but very small ones.

Forensic Pathology, Second Edition By Dominick DiMaio, Vincent J.M. DiMaio, M.D., pp.22-25


How do CO₂ and carbonic acid (H₂CO₃) work in buffering the blood?

What do you mean by "there's a net zero change in $\ce{H+}$ thus no buffering action took place"? The property of a buffer system IS to prevent drastic change in pH.

Buffer capacity, a measure of how much a buffer system can sustain a change in $\ce{[H+]}$ (aka. pH), (mostly) depends on two parameters -- the concentration of that buffer, and how close the desired pH is to its pKa. $\ce{H2CO3}$ has pKa's of 6.4 and 10.3. Given that the pH of blood is about 7.4 and better to stay that way, the base/acid pair, $\ce{[HCO3_^{-}]/[H2CO3]}$ (pKa=6.4) (plus a whole bunch of various proteins such as albumins in blood, all of which has its own pKa) does provide a good buffer capacity around that pH.

True, $\ce{CO2}$ is constantly removed through respiration, but it is also constantly generated by cellular respiration, making $\ce{H2CO3<=>CO2 + H2O}$ a "volatile equilibrium" and keeping both $\ce{HCO3_^{-}}$ and $\ce{H2CO3}$ in high enough concentration to sustain its buffer capacity.

HCl has a pKa of about -7 so it would make a good buffer around pH of -7. In an aqueous environment, all HCl molecules will 100% dissociate, and no $\ce{H+}$ will ever bind to $\ce{Cl-}$ because water itself will first "hijack" the proton as  $\ce{H3O+}$ (pKa=-1.74) before $\ce{Cl-}$ by about five order of magnitude.

---EDIT---

You may be thinking that when cells release $\ce{CO2}$ to the blood, $\ce{H2CO3}$ would be the first product, and in order for $\ce{H2CO3}$'s conjugate base to work as a base to absorb any extra $\ce{H+}$, first it must release a $\ce{H+}$, resulting in no net change in free $\ce{H+}$ and hence no capacity in balancing extra or insufficient $\ce{H+}$ to maintain the pH. Indeed, if $\ce{H2CO3}$ is the ONLY chemical species in the blood when it would not be a buffer. A buffer requires at least two species -- a potential proton donor and a potential proton acceptor, both of which in high and comparable concentration. pH is a measure of external free $\ce{H+}$, a result of final proton balance of all the acid and base in the blood, dictated by the Henderson–Hasselbalch equation. Thus when $\ce{H2CO3}$ is released in the blood, the blood's basic pH will causes most of $\ce{H2CO3}$ to become $\ce{HCO3_^{-}}$, releasing free proton. Again IF that's all the $\ce{HCO3_^{-}}$ in the blood after being made from $\ce{H2CO3}$, the blood's pH will drop, but there is already abundant amount of $\ce{HCO3_^{-}}$ in the blood, helping the system to reach new equilibrium. Of course, the buffer capacity of blood is not infinite. If there is so much metabolic acid being produced that it shifts the ratio of $\ce{[HCO3_^{-}]/[H2CO3]}$ toward excessive acid, acidosis would occur.


A human heart can be viewed as 2 hearts, the left and the right heart, each consisting of an atrium and a ventricle. The atrium's function is to fill the ventricle with as much blood as it can and the ventricle then pump the blood away. Also there is a system of valves to control blood flow on each side. Basically this is how our heart works.

Now, to make this system work we need to have a coordinated movement of atrium and ventricle, that is, first atrium is filled, then it pumps blood into ventricle, valve closes and then ventricle compresses.
The movement of heart muscle causes currents that can be measured (this is the ECG pronounced EKG). These currents are representative of the movements of atrium and ventricles are expressed respectively as p waves (for atria) and qrs (for ventricles).

It is the case that atria are not very important and sometimes they can stop working properly. They now longer have coherent movement and stop helping to pump blood into the ventricles, but they still move. This event is called atrial fibrillation.

From this explanation one can expect that no longer p waves will be identifiable in the ecg, but instead a random noise overlapping with "normal" qrs representing normal ventricular movement. The movement is actually not exactly normal, because the ventricular contraction due to atrial fibrillation now occurs at random times, that is qrs complexes occur with random spaces between them. The explanation for this is rather more complex: there are bundles of specialized cardiomyocites with different frequencies of depolarization. The fastest ones are on SAN and basically guide the whole heart rhythm through specialized bundles. When you have atrial fibrillation, the depolarization signals no longer come from these preferential bundles, but from any part of the atria at random. This causes the ventricles to initiate motion at irregularly spaced intervals.
I've included a photo of a normal rhythm and a atrial fibrillation side by side, but I hope you can use this explanation to find better ones by yourself in the web.

Note: don't confuse atrial fibrillation with atrial flutter. Flutter is a faster paced regular (therefore organized) atrial movement. It will appear as a saw-tooth shaped wave with regularly spaced qrs complexes.

Hope this helps.

Causes of atrial fibrillation are numerous, bur mainly high blood pressure, vascular disease, heart and lung disease among others. It can be asymptomatic in most cases or presenting with the symptoms of its underlying cause.

Please refer to http://www.webmd.com/heart-disease/atrial-fibrillation/heart-disease-atrial-fibrillation-basics for a quick overview.


Total amount of CO₂ / Oxygen in Bloodstream in Humans

Your calculation for O2 is along the right direction, but missing a factor I think.

Each red blood cell holds millions of molecules of hemoglobin, each hemoglobin molecule, when saturated (at the lung), holds four O2 molecules.  So this is off by a factor of millions at least.  Wikipedia estimates that hemoglobin makes up about 35% of the total weight of blood.  We can use this figure and an average of 4.5 l of blood for a human being ( numbers vary, but it will be within 30%).

4.5l blood * 1.060 g/ml density of blood * 1000 ml/l water * 35% = 1667 g hemoglobin

4 molecules O2/molecule hemoglobin * 1667 g hemoglobin / (64000 g/mol molecular weight of hemoglobin)  = 0.104 moles O2

so I get:

0.104 moles O2 * 30 g/mol for O2 = 3.12 g O2 in the blood at a time.

In the muscle and tissues it gradually depletes so that all four molecules will usually end up somewhere in your tissue.  So this is all assuming that counting all the hemoglobin bound O2 will approximate the count of O2 in the body.

We know this is a crude estimate as myoglobin in mammal muscle will store O2 for use later, and the average hemoglobin is not in the lungs and will have given up some of its O2.  It also doesn't count the O2 which diffuses into the blood and is carried by the water.  This is about 0.035 g / l, which is why we need hemoglobin - total blood saturation would carry about 1.15 g of O2.  Hemoglobin multiplies the oxygen carrying capacity of blood by 100 fold.

CO2 is much more soluble in water (blood/tissue) than O2 is- about 1g/l.  There is I think only 2 CO2 binding sites for hemoglobin, which means it carries out only half the CO2 oxygen that it carries  in.  Hemoglobin is is only considered to account for 10% of the total CO2 carrying capacity of humans.  So calculating CO2 respiration by hemoglobin is not a good way to estimate blood CO2.


Which cell organelle is more important in giving colour to petals?

When I read your question (headline), my first thought was: "Vacuoles!"

After reading in more detail about your problem, I agree with you that there is some controversy with this question. The problem is in my opinion that the question is not well formulated. The term "more important" is not really scientific, because what decides importance? Do they mean with importance that it plays a role in more flower species? Or do they mean that the color palette is larger with vacuoles compared to chromoplasts?

I do agree with the answer though, the pigments in the vacuoles are responsible for more colors in petals, and probably also in more species. However, there might be some plants in which the petal colors are dominated by the chromoplast colors. So the question is not well phrased, "more important" is too vague for exact science.


What is the biological/evolutionary advantage to baldness?

Baldness would appear to be a trait on display. That being said, hair loss can be selected against the opposite condition (full head of hair), or selected by way of precise pattern deemed attractive. So, male pattern baldness evolution for mate selection purposes is probably a factor in play. But, either way, hair loss appears to have both its advantages and disadvantages as far as both fitness and mate selection is concerned.

Similarly, in terms of fitness, the advantage/disadvantage you state is the immediate positive advantage of hair as a protectant.  The immediate advantages of hair diminish as one grows older, making age apparent. Old age is disadvantageous in itself (older can mean less fit). Hence, the immediate advantage for a protection against the elements decreases and becomes less relevant to survival as one grows older. Please see the references below.

https://en.wikipedia.org/wiki/Mate_choice

https://en.wikipedia.org/wiki/Evolution_of_ageing


Optimal agriculture: maximum yield with minimum environmental impact

Publications by the Food and Agriculture Organization http://www.fao.org/documents/card/en/c/ca9692en of the United Nations would be a good place to start as they are freely accessible. There are plenty of articles looking at crop yield of different production methods and different management techniques. You may consider subscribing to a journal, like Agronomy https://www.agronomy-journal.org/, or CAB Abstracts https://www.cabi.org/publishing-products/cab-abstracts/ as those would contain most of the subject material you're looking for. Those would also contain information on optimizing food production under resource constraints. Happy researching!


Why does spraying water on plants help them survive in case of frost?

The question has already been asked in Physics.

According to the information there and here the sprinkling must continue throughout the period when temperatures are below freezing, and is only effective for temperatures down to around -5 °C.

Explanations invoke three interrelated effects: when water freezes heat is released so there is a warming effect; the temperature of an ice-water mixture is 0 °C; and an ice layer will insulate the leaf. As long as the temperature of the leaf stays above freezing there will be no frost damage.


Think about what gametes the father could have given the child. If the mother contributed an "A", then the father gave two "C"s, if the mother contributed a "C" then the father contributed an "A" and a "C".

In meiosis I, the father's chromosomes duplicate, so he has AA and CC - normally, at the end of meiosis I, these would be pulled into separate cells, so one of the resulting cells would be AA (and then in meiosis II, split into two further cells both with one "A") and CC (which in meiosis II splits into two further cells both with one "C"). The final result would be four gametes (sperm cells), two with "A"s and two with "C"s.

Since this is tagged "homework" I'm not going to give the final answer - but think about what phase of meiosis would have to go wrong to create an "AC" sperm, and what phase of meiosis would have to go wrong to create a "CC" sperm.


I disagree with GForce's explanation; the meaning is not that growth of prey populations causes instability in predator species.

The sentence is merely saying that without predation, prey population growth is more likely to be at a level which leads to ecosystem instability. The term "but for predation" means "if it wasn't for the effects of predation". In other words:

  "Ecosystem instability can occur when population growth of some species goes unchecked by predation."

See here for more explanation, where this example comes from in which it says that running a red light caused a crash:

  "but for running the red light, the collision would not have occurred"

Biologically this makes sense in the sentence you show; without predators a species is limited by its supply of resources, and it can use these resources at an unsustainable level, whereas if you add predators to the mix there is additional extrinsic effects on population size, not determined by ecosystem properties such as space or nutrients.


Nice question - this terminology isn't referring to a special type of cell or anything, but to a peculiarity of the technique they are using.

They are labeling a subset of cells with rabies virus; rabies then travels in retrograde fashion to presynaptic cells, and labels those as well.

The "starter cells" are those initially infected cells, where the tracing "starts." This reference more explicitly states this terminology, and talks about the technique extensively, I would strongly recommend it for helping to understand the paper you are reading.


Is it possible to do chip-seq on a specfic region?

If the question here is to perform an assay that only sequences from a specific set of segments of the genome, you probably could, but it would be a lot of work and you'd need a good reason to want to go through that trouble.

Not sure how you would limit the nucleotides you get back to a specific region of the genome say.  The entire point of a CHP-Seq experiment is to get as unbiased a set of nucleotides read and so using specific primers designed against only a specific set of the genome would be hard.

Usually CHP experiments focus the readout they are getting by only focusing on a specific transcription factor for instance.  The number of variants of short binding sequences that usually come out will easily be read by a sequencing lane.  You'd have to have a strong reason not to take all the data genome wide.  Generally the results for many such pulldown sequences are pretty short and frequently can't be found uniquely on the genome, esp if there are lots of binding sites for the protein to be found.

I could speculate that you might synthesize labelled primers from random segments of a cut up library coming from a chromosomal segment you cloned somehow.  That again that seems like a lot of work to cut back on the data you get from the experiment without a big reason for doing this.

Using a CHP-CHP experiment that only has specific regions tiled can make do something like this - this makes the chip itself more economical, making the experiment more accessible.

Hope this helps...


What is this small black spider found in NY?

It resembles a juvenile Phidippus audax, of the family Salticidae.

Image Source: SpiderZule

According to Wikipedia >>

  They are typically black with a pattern of spots and stripes on their
  abdomen and legs. Often these spots are orange-tinted in juveniles,
  turning white as the spider matures.

Phidippus audax is a common jumping spider in North America and definitely not an invasive species.


Where does the first oxaloacetate comes form in the citric acid cycle?

There's not just one molecule of acetyl-CoA that's going through the TCA cycle. Every intermediate compound is present at a certain concentration, so there will be many oxaloacetate molecules per cell.

When the cell divides, it's split in two and the contents are also divided. So a new cell will also have many oxaloacetate molecules in it. This way the daughter cell can just keep running.

For the "first" oxaloacetate molecule we have to go back billions of years, and this would be a very complex question to answer. My guess would be that the first oxaloacetate molecule was produced by a non-TCA pathway, and the TCA cycle evolved later.


Can skin be removed and replaced so that it maintains its original cellular structure?

As pertains to skin, no. As pertains to your other fears, that's a different question.

Every cut that extends into the dermis significantly (and to remove skin, it must include the dermis) will leave a scar behind.

Cuts that extend only very superficially into the dermis may hit some capillaries and bleed, but these will usually not bleed much, and can heal "seamlessly". But anything that extends deeper will bleed more. Those are the cuts that often get stitches if they are long enough, won't stop bleeding, etc.

Lifting and replacing a piece of skin would necessitate the damage of many cells and the destruction of a lot of fine blood vessels, but even with the best microsurgical techniques, a scar will form. The best techniques combined with the best pre- and post-surgical care will only minimize scar formation; it can't be eliminated.

  In skin, the process of wound repair can be generalized into three cascading phases each with characteristic cellular events: 1) inflammation; 2) fibroplasia or proliferative phase; and 3) scar formation.

Wound Healing in Development


There are metabolic processes in which ATP is synthesised without the involvement of ATP synthase. The best examples are, in fact, two steps in the glycolytic pathway, catalysed by phosphoglycerate kinase and pyruvate kinase. This is why, in the absence of any aerobic metabolism, many organisms (like yeast for example) can grow quite happily, producing two molecules of ATP for each molecule of glucose that is metabolised.

Presumably this process is what enabled ATP to gain its central role in energy metabolism without any need for an ATP synthase.


Suggestions for self-studying experimental techniques

I cannot more highly recommend Molecular Cloning 4 ed.. It is a really comprehensive text which covers numerous molecular biology experimental techniques including different types of PCR.

EDIT: Also, there are some great suggestions for other books and websites that also cover molecular biology techniques in the answers to this question: Short, concise, practical manual for doing experimental biology


Why are the sex chromosomes called X and Y?

Sex Chromosomes and Sex Determination by Ilona Miko

  The first inkling that sex chromosomes were unique from all other chromosomes came from experiments conducted by German biologist Hermann Henking in 1891… Henking saw that some wasp sperm cells had 12 chromosomes, while others had only 11. Moreover, while observing the stages of meiosis that formed these sperm cells, Henking noticed that the mysterious twelfth chromosome looked different from all the others. He thus named this chromosome the "X element," to represent its unknown nature.

Wikipedia - Y Chromosome

  The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens … during a study of the mealworm Tenebrio molitor … Stevens proposed that chromosomes always existed in pairs and that the Y chromosome was the pair of the X chromosome discovered in 1890 by Hermann Henking … Stevens named the chromosome "Y" simply to follow on from Henking's "X" alphabetically.

I know that this is not the most reputable source, but it does cite a couple of books. Take it as it is. Keep in mind that all human chromosomes, even the Y chromosome, appear as X shaped when replicated and condensed. The Y chromosome is quite acrocentric and so the short arms may appear to be one, but they're not.


Now I have the answer, and if you are reading this soon after eating the fruit you should probably seek medical attention.

Looks like Cascabela theviata which is in the Apocynaceae and the Wikipedia article makes clear that the fruit is also poisonous.


What are some examples of genes that code for multiple proteins?

There are a large number of ways a protein variant can be produced by post translational modification.  The question may seem obvious, but its really quite broad.

I can start this out.  I doubt I know all the ways a single transcript can produce variant proteins.   A detailed description might be more like a review article than an answer here.

First, there are very rare cases of eukaryotic polycistronic mRNA: mRNA which code for more than one protein.  In this case, after translation, the mRNA are processed to make multiple monocistronic RNA.

Then there are proteins with molecules added by covalent bonding to the protein.  Glycoproteins are notoriously variable. Many other small molecules can be bonded to a protein to make a variant of this sort: ubiquitinization, N-acetylation, SUMO domains, lysine methylation are just a few of the more common covalent modifications of proteins.

There are RNA editing which removes some of the coding RNA to make alternative splice RNA.

The list goes on and on. So does any of this come close to what you wanted to know?


Is most of the human genome functionless “junk DNA”?

What is junk DNA?

The term junk DNA is not used that often in the scientific literature and when it is it is often used very generally, often early in the introduction. It generally refers to any non-coding DNA.

In humans, about 25% of the non-coding DNA is introns and regulatory sequences. These sequences are highly essential for the working of the organism. There are many cases of adaptation from these regulatory sequences (see this answer).

The term junk DNA is very loaded and may make it feel to people that this DNA is not important for the organism survival but this is not quite what was first meant by the term junk DNA. It is true though that repeated DNA such as those in  transposable elements are thought to have little impact on the organism phenotype. Transposable elements can however have important role on the evolution of a lineage.

IMO, the claim is false and insulting

By saying things like They do this because they gave no idea what it does and, from their version of reality, it appears to serve no function., it feels to me that David Icke is using the loaded side of the term junk DNA to insult all geneticist in general.

D. Icke is 1) doing a strawman by suggesting that geneticists think that regulatory sequences are of no use and 2) he is suggesting that geneticists are biased and will invent whatever theory in order to match with a pre-conceived opinion of the reality.

About David Icke

I don't mean to make an intentional fallacy but I would like to note that David Icke is a famous conspiracy theorist who has been illogical and obviously opinion based many times. For example David Icke claims that the moon is actually a spaceship and not a natural satellite (see here). He has made many other fantastic claims of the kind. Scroll down the wikipedia article to enjoy some non-sense!


Is it safe to publish a person's genome?

It is as safe as to publish your fingerprints. Right now, there is little that anyone can do with your genetic information but in the future, this will change.

One of the feared consequences it concerns what companies may do with that information. Can it be used against you? In some cases, it may.

For example, if you have a predisposition for a genetic disease, then an insurance company may find a way to refuse to insure you. As far I know, right now this is illegal, but you never know.


Are Whales More Intelligent Than Humans?

The "wiring" of the brain is more important than the actual size. If only size would matter that basically humans would be rather unintelligent beings ( many many animals have larger head and brain than us). Intelligence is more related to the complexity of the brain (number and size of different brain components) and the number of connections between neurons. We humans are intelligent because we have high complexity compared to our brain size, our brain has more grooves therefore higher surface than a whale brain. So even though whales are quite smart they're not as smart as us.

EDIT: After getting a few comments I felt I need to clarify my answer, so here it comes: as pointed out by user137 humans have much higher brain-to-body size ration than whales and this is very important. What I was trying to explain (yet failed for the first time it seems), that mere physical size / volume is not that important. The level of development and complexity is that matters the most. Many parts of the human brain is found in lower order animals as shown in the image below:  (taken from http://en.wikipedia.org/wiki/Brain

The surface to volume ratio matters because the higher ratio implies a more complex brain structure. So while whales have a higher surface in absolute value (approx 2-3 times) yet their brain is larger by approx 5-6 times ( lots of comparison data here), thus we have higher surface/volume ratio (i left the ratio part out on my original answer). In the accepted answer on the question linked by Bez it is said that more grey matter in frontal lobe correlates with IQ. Now since grey matter is made of neuron bodies and (fewer)axons, this is quite straightfoward --> more neurons = more connections = higher complexity. But all that comparison was made between humans. So brain size differences between different individuals of the same species may contribute to individual qualities. Comparing mere physical brain sizes of different species is not straightforward because of different brain development levels and brain structure.


Visibility of a cell membrane under microscopic Imaging

The membrane(and associated proteins) isn't actually opaque, it is just "more opaque" or "less translucent" than the cytosol: when you look through the microscope, you are utilizing this contrast to detect the edges.

In the center of the cell you observe, you see the membrane straight-on, and light is only affected by 1-2 layers of membrane. On the edge, you are viewing through the membrane somewhat "sideways" , so there is effectively more "thickness" of membrane. Maybe not an exact replica of the situation, but one that might be easier to visualize, is earth's atmosphere viewed from space. You can see the "blueness" of the atmosphere at the edges, but when you look straight down at the ground you see clouds, oceans, landmasses not tinted as blue.


What's the difference between diuretic veggies and alcohol that make the latter bad?

Firstly I would suggest if you have concerns about suffering from symptoms fluid overload you should consult your doctor. Self diagnosis and self treatment is not a good option.

In terms of alcohol being used as a diuretic, you have to bear in mind that there are many deleterious effects of excess alcohol. By consuming alcohol as a diuretic you would most likely cause more health problems than you solve.


Type of plant cell that builds a secondary wall in between two primary walls?

Secondary cell walls are found in many plant cells especially ones used in for structural functions, such as the lignified cell walls in xylem such as in wood. This occurs in a mature plant cell, where the cell constructs a second wall between the primary cell wall and the plasma cell membrane, which is made up of strong cross-linked cellulose microfibrils, which are then lignified.

The secondary cell wall adds additional support to the cell, enabling it to carry out effective structural functions in the plant such as transportation of water and mineral ions in xylem from the roots to the leaves.

Occasionally, there is a tertiary cell wall located on the inner side of the secondary cell wall adjacent to the plasma cell membrane. This is usually very thin and is made up mainly of xylan with a small ratio of cellulose (unlike the primary and secondary cell walls which are mainly cellulose). It can be found in the xylem tracheids (usually found in the wood) of gymnosperms (e.g. conifers, ginkos). As for purpose, again, it strengthens the cell even more and sometimes contains nutrients ready to pass through the membrane into the cell.


Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I quickly aligned your sequences, and as far as I can tell, the answer is that your "consensus" sequence is a poor match for the 3 other sequences:
CLUSTAL format alignment by MAFFT L-INS-i (v7.310)

Consensus_cepa_ gaaagccaaccaccacatccgccatccctcacagtatgccaacgagcagctgaatgactc
MV_A_SP6_izreza aaaaatcaatctccacatccgccatcactcacagtatatttac-agtagataaataa-tt
MV_C_SP6_izreza aaaaatcaatctccacatccgccatcactcacagtatatttac-agtaaataaataa-tt
MV_B_SP6_izreza aaaaatcaatctccacatccgccatcactcacagtatatttac-agtagataaataa-tt
                .***..***.* ************** **********... ** **.*. *.***.* *.

Consensus_cepa_ cgaacaacgcaaagcatgacgcccaaaccgacgaacacccaaccgaaaggccacaagcgc
MV_A_SP6_izreza aaaataacgcaaaacataacgcccaaacagacgtactctcaacctaataacctcgaacgc
MV_C_SP6_izreza aaaataacgcaaaacatgacacccaaacagacatactctcaacctaataacctcgaacgc
MV_B_SP6_izreza aaaatgacgcaaaacataacgcccaaacagacgtactctcaacctaatgaccttgaacgc
                 .**..*******.***.**.******* ***. ** *.***** ** ..** ..*.***

Consensus_cepa_ aacgtgcattccaaaaccccatgaaccaccgaatcctgcaatgcacaccacgctcgacgc
MV_A_SP6_izreza aacttacattcaaaaactcgataattcacgaaattctgcaattcacaccaaatattgcat
MV_C_SP6_izreza aacttacattcaaaaactcgataattcacggaattctgcaattcacaccaaatatcgcat
MV_B_SP6_izreza aacttacattcaaaaactcgatgattcacggaattctgcaattcacaccaaatatcacat
                *** *.***** *****.* **.* .*** .***.******* ******* .. . .*..

Consensus_cepa_ cattcgctacagaccacatcgacacgagcgccaagccatccatcacccgaagccatccac
MV_A_SP6_izreza --ttcgctacgttcttcatcgacacgaaaaccaaaatatccattgccaaaaatcattcag
MV_C_SP6_izreza --ttcgctacgttcttcatcgacacgagaaccaaaatatccattgccagaaatcattcag
MV_B_SP6_izreza --ttcgctacgttcttcatcaacacgaaaaccaaaatatccattaccagaaatcattcag
                  ********.  *. ****.******. .****. .******..** .**..***.**

Consensus_cepa_ ccactcacaaacataccacgaagcacagcaaatatgaagacaaaccctc
MV_A_SP6_izreza acgctcactgaaataacacaaaacacatcaaa-ataataacaaactttc
MV_C_SP6_izreza acgctcactgaaataacacaaaacacatcaaa-ataataacaaactttc
MV_B_SP6_izreza acgctcactgaaataacacaaaacacatcaaa-ataataacaaactttc
                 *.***** .* *** ***.**.**** **** **.* .******..**

I would suggest trying to come up with a different, more appropriate consensus/reference sequence. This one does not appear to be appropriate.
Granted, I have no idea how you came up with this consensus sequence (it certainly is not a consensus of the other sequences you show), and possibly there is something else going on that I am not understanding.
This does not seem to have anything to do with the bisulfite conversion, as the data also include changes that cannot be attributable to bisulfite, gaps, etc.
Knowing more about the whole workflow would help.
UPDATE
Also, while I'm not familiar with the workflow, could such gaps not be related to methylation on the opposite strand? E.g. CGTA-->TACG.
Is there a particular methylation context that you are looking at? CpGs only?
In some cases there is support for weird variants (e.g. consensus is not an outgroup).
If it's sanger data, it's always a good idea to directly inspect traces.


Does endo- and (or) exocytosis require energy? Do they belong to active / passive transport?

Wikipedia is your friend:

  Exocytosis... is the durable, energy-consuming process by which a cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space.

and

  Endocytosis is an energy-using process by which cells absorb molecules (such as proteins) by engulfing them.

Emphasis mine.  Here's a nifty paper which gave some evidence a few decades ago for some basic intracellular thresholds for budding and fusion, and this paper shows that endocytosis definitely requires ATP, using a novel assay.  Check the sources, too, some of them are excellent.