Why do people feel extreme cold at different temperatures compared to other people of same body structure? I have seen some people shivering in the room temperature of 18°C while others of similar body structure do not feel that much amount of cold.

Of course the clothing of both people is similar if not same.

What can be the cause of such different body reactions?

First of all, this observation is the norm across human perception. While humans react in roughly the same way to similar stimuli (e.g. both a cranberry and a tomato are seen as red, the destruction of tissue is felt as painful), the intensity tends to be different. Also, many stimuli elicit not just a knowledge of the state of the world or one's body, but also a reaction (e.g. shivering when cold, or emotions like fear when physical pain is felt), and these reactions differ between humans too. So, on a very general level, it can be answered with "Because that's how human perception works".

I know that this is a very unsatisfactory answer, so here are some factors off the top of my head. For any given case, one or more of them will cause the difference, and you cannot tell which ones from casual observation.

Your observation of "similar clothing" could have been incorrect. For example, an acrylic sweater can look exactly like a sheep wool sweater, but warms much less. Or, slightly shorter sleeves can cause much cooling if they leave the wrist exposed. Layering is also very important, and we generally only notice the uppermost clothing layer.
Your observation of "similar body structure" could have been not precise enough. People who have the same appearance can have different amounts and distributions of body fat. Maybe one person is simply better insulated than another one.
The state of their circulatory system was different. Vasoconstriction and vasodilation will change the skin temperature, which is sensed by peripheral thermoreceptors.
Estrogen is involved in thermal perception. The gender of the person and the current point in the menstrual cycle (or pregnancy) in women will make a difference.
The circadian cycle of the two people is probably not perfectly synchronised. Core body temperature varies during the cycle, and thermoperception depends on core body temperature too, not just skin temperature.
A different metabolism will cause one person to create more body heat than another
Other hormones (beyond estrogen and the ones ruling the circadian cycle and metabolism) probably have an effect on thermoperception, but I can't tell you details here. Temperature is regulated in the hypothalamic-pituitary-adrenal axis, so the hormones from it are likely to have an influence.
Normal variations in the two people's neural networks will change the intensity of signal perception. People are born with very unconnected neurons, and build unique connections depending on the environment they encounter while growing up. As a result, each person's brain functions slightly differently when given the same input.
Differences in neurotransmitter sensitivity can account for the difference in intensity of perception. People sometimes react differently to the same level of neurotransmitter, or also their brains secrete different amounts of neurotransmitter as a response to the same stimulus. These differences exist on an average level (e.g. glutamate can potentially "do" more for me than for you) but are also affected by drugs and illness.
Attention is a major part of perception. The CNS can suppress information from sensory organs at a very low level if the brain is focusing elsewhere.
Habit: people can intentionally or unintentionally learn to disregard or misinterpret their body sensations.
Psychological stress increases the core body temperature
The above reasons all assumed differences between a pair of healthy individuals. Some conditions, for example running a fever, but also neurological disorders anywhere along the complex pathways from sensors to cortex (and the other way round!) or diseases which for some reason alter thermoregulation, will all change the feeling of hot or cold.

This list is probably incomplete. Also, some of the factors I listed will overlap to some extent (e.g. vasodilation is frequently mediated through hormones, and ingrained habits are reflected in neural network connections). But the take away point is: Human perception is an active process, very far removed from simple "reporting" of the state of the environment. It is unrealistic to expect two individuals to have the same perception when exposed to the same stimuli.

For an in-depth description of how thermoperception and thermoregulation work physiologically, see this summarizing paper.


evolutionary reason behind sharing the same path for food and air? What is the evolutionary reason behind sharing the same path for food and air?

For example, we have a nose and lungs, yet they are linked by the pharynx, which is shared with the mouth and oesophagus.

Wouldn't it make more evolutionary sense for the nose + lungs to have their own "path", while the mouth and stomach have a separate system? This would prevent "choking", allow for breathing while eating/drinking, etc.

While it might make more logical sense to have separate passageways for air and food/water, this did not happen in evolutionary history due to the peculiarities of lung development. Vertebrate lungs develop as an outpouching of the gut tube, which itself has a very long evolutionary history (probably homologous among all deuterostomes).

In the image below, the trachea has budded off the esophagus. Further lung development will involve the differentiation of main, secondary, and tertiary bronchi as well as the alveoli, etc.

Additional images and description at http://www.uoguelph.ca/zoology/devobio/210labs/lung1.html

Air-filled organs like lungs and swim bladders actually have a broad distribution going way down into fishes. Human (and other mammalian) lungs are likely homologous with ancestral air-filled organs of fishes. We can't be certain, but there is no reason to think that mammalian lungs are a de novo evolutionary innovation. So our airway and food-ways are tied together developmentally and are constrained by evolutionary history.

As for breathing and eating (swallowing) at the same time, most mammals can do this, and baby humans can as well.

Like most anatomical systems that seem as though they could have evolved better, this system works most of the time and has worked well enough for hundreds of millions of years.


What are these strings used to describe animals? For example, what's a $dt^{sz}$ hamster? (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/).

What's a Rgs9-Cre/+;gtROSA/+ mouse? (http://www.sciencedirect.com/science/article/pii/S2212877813000719)

Those describe the genotype of an animal (or plant, virus etc.).

The nomenclature can be very varied and domain-specific, but for those two examples:

$dt^{sz}$ is a Syrian golden hamster model with a spontaneous mutation (i.e. occurred during breeding, without specific human intervention) which gives predisposition to seizures.
They are described in this paper:

Spontaneous seizures: a new mutation in Syrian golden hamsters. - Yoon et al. - J Hered 1976

  SPONTANEOUS motor seizures with tonic muscle spasms and severe paralytic states have been observed in inbred line BIO® 86.93 of Syrian hamsters
  (Mesocricetus auratus auratus). These animals had been inbred for 23 generations and maintained by Bio-Research Consultants. The seizures, which last from 2 to 5 hours, can be precipitated by mild stress, and occur in
  animals between the ages of 30 days and 60 days. Breeding tests have shown that the condition is transmitted as a simple recessive; accordingly, the gene symbol
  sz is proposed for this condition.

The lowercase indicates that the mutation is recessive that is, you need to have two copies of the mutation to see its effect (its phenotype).

dt comes from dystopia, another symptom of the mutation.

As for Rgs9-Cre/+;gtROSA/+ mouse, the genotype is a bit more complex.

Whenever you see /+ it means that the animal is heterozygous, that is, it only carries one copy of that specific gene.

For instance these are transgenic animals producing the bacterial protein Cre under the Rgs9 promoter. A promoter is a sequence of DNA that controls the expression of a certain gene. In this case the DNA sequence for the promoter of the gene Rgs9 was attached to the DNA sequence for Cre. This new construct was then inserted into the genome of the mouse.
The result is a mouse in which the cells that normally transcribe the Rgs9 gene also produce Cre.

This mouse line was then crossed with a reporter mouse line called gtROSA26, which expresses a certain protein called $\beta$-galactosidase in a Cre-dependent manner.

The gene for the galactosidase is present in all the cells, but only where Cre is present (in our case the Rgs9 positive cells) it will be transcribed.
Eventually the crossing leads to the expression of $\beta$-galactosidase in Rgs9 positive cells.
$\beta$-galactosidase has the nice property that it can change the colour of certain chemicals to blue, which allows to easily visualize the cells that produce it. This can help you answer questions like: "where is the Rgs9 gene transcribed?".

Wikipedia has a neat page on Gene nomenclature with lots of links to nomenclature guidelines.


Why sun rays don't burn our skin? Can you explain (or direct me to a link) the process by which a photon of $8.10^{14}$ Hz is absorbed by the skin without damage, whilst a slightly more energetic one (UVB) makes damage?

What area of skin is necessary to absorb one single photon? How many photons of visibile light per $\mathrm{cm^2}$ are required in order to produce burns to the skin?

The reason that UV light causes sunburn, while normal light does not, is not founded in the energy carried by single photon. As stated on wikipedia:

  Importantly, both sunburn and the increase in melanin production are triggered by direct DNA damage. When the skin cells' DNA is overly damaged by UV radiation, type I cell-death is triggered and the skin is replaced

The UV light can cause reactions in the DNA of the skin cells that directly damages the DNA. A low amount of this damage can usually be repaired by the cells, but a lot of DNA damage will lead the cells to die and cause inflammation reactions in the skin (the sum of which is then what we experience as sunburn).
[Here is a citation also explaining this, the paper is behind a paywall though].

  What area of skin is necessary to absorb one single photon? How many photons of visibile light per cm2 are required in order to produce burns to the skin?

A single UV photon has no measurable size and can therefore in principle be absorbed by any arbitrarily small patch of skin. In practice only those photons that interact with the DNA in your skin cells are relevant for sunburn (that will be a very small fraction of all UV photons). Additionally the melanin in your skin will also absorb photons and therefore protect the DNA from the UV radiation, which is why people with darker skin get sunburn less easily. This also means that the amount of radiation/skin area required to cause sunburn varies from person to person and can be influenced by the ability of your skin cells to repair the induced DNA damage.


Do humans have the hyaloid canal, after all? Most Google Images results for "eye anatomy" are pictures of eyes that don't have the hyaloid canal while some do (proof). Do humans have it, after all, or not? :)

Yes, humans do have the hyaloid canal.

Schematic diagram of the human eye (reference)

For function and other information, please refer to this journal article.


What is the advantage of not having cytokinesis after karyokinesis? In nature most of the cells are mononucleated, but in some cases like osteoclasts, umbrella cells of transitional epithelium, tapetal cells of another etc. are multinucleated. Wikipedia article about tapetum says that it is a strategy to increase the production of proteins. Why don't cells just up-regulate their genes for more production? What is the benefit of not having cytokinesis?

The absence of cytokinesis allows the two nuclei to remain in the same cell. If a cell has 2 nuclei instead of 1, it can transcribe DNA to mRNA at double the maximum speed, and so produce the desired proteins at double the rate. It's almost as if the cells become tetraploid, or hexaploid, and so on.

Learn more: http://www.nature.com/scitable/definition/cytokinesis-100

Why is it more desirable to have 1 cell with 2 nuclei than actually do cytokinesis and have 2 cells with 1 nucleus each (still 2 total)?

Because it is unfavorable to create two cells, which needs an extra investment in energy and nutrients to maintain, and is also harder to coordinate, and so it becomes more desirable to just have one single cell with the capacity of producing double the proteins.

Then why don't all cells adopt this strategy? What is the reason for such partiality?

First, because most cells don't need the extra transcription speed, as they don't produce a lot of proteins. Second, because of cell differentiation - to have cells doing different things they have to transcribe their genetic material differently, and so must be separate. Third, a lot of times it is desirable to have extra cells. For example, skin epithelial cells: their main purpose is to serve as a barrier or protection, and so there has to be a lot of them. That's why the basal cells are in constant mitosis.


What is the heritability of brain gyrification? Brains of mammals with a folded neocortex do not have identical patterns of folding in the same species.

Do two genetically identical individuals of a species have the same pattern of brain gyrification (i.e., folds/wrinkles)? Or are there other causes?

Short Answer:

Genetically identical individuals do not have identical brain structure.

Longer Answer:

The easiest way to answer your question is to look at "natural" clones: monozygotic (i.e. "identical") twins.

Brain morphology is of a lot of interest in neuroscience because differences in brain morphology are often confounding factors in human brain studies (for example those using MRI/fMRI).

I'll refer to a study by White et al., 2002. They studied volumetric and surface morphology measures in monozygotic twins. They found remarkably strong correlations in total volume (r values of .98-.99 for measures like total brain volume, cerebrum volume, cerebral gray matter/white matter, and cerebellum), and still strong correlations with different lobes of the cerebral cortex (r values from .69 to .97 for frontal/parietal/temporal/occipital gray and white matter).

However, surface measures: surface area, gyral and sulcal curvature, and surface complexity were more weakly correlated (r values of 0.49 to 0.69).

Of course, because these are monozygotic twins raised together, it's hard to know how much of the similarities are due to the shared environment as well as shared genetics. However, it is clear that brains of identical twins are not identical, and in particular their brains seem to differ more on measures of cortical surface structure rather than overall brain size. The authors write:

  Many different types of nongenetic influences may contribute to the plasticity of the cortical surface characteristics, such as educational experiences, physical activity or social interactions. Furthermore, probabilistic events during the complex process of neurodevelopment [e.g. connections between neurons (Muller et al., 1997)], differences in gene expression either by chance or modulated by early-immediate genes (Abraham et al., 1993; Worley et al., 1993), or variability in cell–cell interactions (Fletcher et al., 1991) may also contribute to variability between MZ twins.

References

White, T., Andreasen, N. C., & Nopoulos, P. (2002). Brain volumes and surface morphology in monozygotic twins. Cerebral cortex, 12(5), 486-493.


Which fishes produce alarm signals to warn other group members about in coming predators Atlantic Goliath Groupers are fishes which produce unique low frequency sounds to mate and when approached by predatory fish . The sounds produced when approached by a predator (or even a scuba diver) are different from those produced whilst mating.

The problem is this fish is found only in the Atlantic.  I'm specifically looking for fishes in the Indian ocean . Thank you for ur time :)

Here are some fishes produce alarm signals as sounds.

members of family Pamadasyidae-the grunts.

the family scaridae e.g.—Parrot fish.

sea catfish Galeichthyes felis

gafftopsail catfish

Indian loach

Trigger fish

Epinephelus striatus

For mor information see the link. http://www.fishfarmingtechniques.com/fish-structure/specialized-organs/sound-producing-organs/sound-producing-organs-in-fishes-specialized-organs-fisheries/13563


Do sodium channels keep renewing themselves with new subunits made by genes? genes make alpha beta gamma subunits (proteins) to be used in making sodium channels... If I understand correctly? And so, since the genes keep making those subunits, does that mean new sodium channels are continuously being made with those proteins till you die?
In other words, if those genes suddenly stop making the subunits in your 50's or something, your sodium channels will disappear or stop working? (Probably unrealistic, but theoretically...)

You are asking about two different processes: turnover (degradation) of mRNA and turnover of proteins.  In a typical mammalian cell the mRNA half-lives of stable messages approach the length of the cell cycle (e.g. 24 hr). One mRNA could be translated around the clock if needed. The resulting proteins will also have a measurable half-life, and that will vary with the protein and the cellular conditions. If a cell ran out of protein and its mRNA there is often a feedback loop that activates transcription of the structural gene back in the nucleus.


What's the difference between protein and DNA behaviour during agarose gel electrophoresis? I'm planning a science project about gel electrophoresis, and I'd like to know if there are any measurable, quantifiable (for example, things I could represent in a graph or chart) differences between the behavior of protein and DNA during agarose gel electrophoresis.
Detailed inputs and useful links are greatly appreciated.

There are two important properties that determine how a molecule will move during gel electrophoresis:

size and shape of the molecule
charge of the molecule

You're applying an electric field, and all molecules will move according to their charge. The gel itself hinders the movement of larger molecules. This means that small molecules will move further than large molecules.

Nucleic acids like RNA and DNA have a uniform negative charge from the phosphate backbone. This means that they will generally separate according to their size and shape (plasmids can be present in different forms like supercoiled, circular or linearized).

Proteins have different charges, some have a positive charge at the pH typically used for gel electrophoresis, some have a negative charge, and some have no charge at that pH. So if you would simply run proteins on a gel, some would move backwards, some forward and some not at all.

To make the proteins separate according to their size we use the detergent SDS to denature the proteins, and to give them a uniform charge (SDS is negatively charged). Proteins are also run on polyacrylamide gels and not agarose as the size of the pores in agarose is a bad fit for the typical sized of proteins.

While I've never seen anyone using agarose for proteins, it seems that it is possible and sometimes used for larger proteins. I found one paper describing a protocol, they used very high concentrations of agarose in the range of 4-5%. I suspect that they won't handle well, but you should try that out yourself. If the proteins you're examining are a bit larger, using agarose should be possible.


Osmosis vs protein-binding in preserving foods through salting I had assumed that the preservative function of covering foods with NaCl or brine was due to osmosis killing the microorganisms on the food by dehydration.  However, I am now wondering to what extent denaturing of bacterial protein through interaction with salt ions could be responsible for killing the microorganisms.  And what evidence suggests a dominant role for one or the other mechanism.  I hope someone can clarify this matter for me.  Thanks in advance.

In addition to killing microorganisms, the salt may provide a better environment for some 'beneficial' organisms, and a less beneficial environment for other 'problem' organisms. For instance, in production of kimchi and sauerkraut, salt encourages lactofermentation to the detriment of more harmful bacteria and fungi.


Converting fmri data to association matrix I am currently working on a new tool for the analysis of (large) weighted networks. Association matrices (correlation matrices) as obtained from fMRI data are perfect examples of the kind of data I am looking for. Unfortunately I am only able to locate raw fMRI data and the task of converting them is way outside my expertise.

Can anyone point me to a place where such converted data can be found, or where I can download software which automatically converts the data? Preferably a dataset divided into control/disease.

Thanks!

You can get raw FMRI data from https://openfmri.org/ on that website you'll also download your conditions files for the experimental design (you'll need this in creating your matrix). This is a link to an experiment(it's data) with "healthy" participants and participants diagnosed with schizophrenia: https://openfmri.org/dataset/ds000115

Raw image files from a scanner will be in .dcm format. You can use http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html to convert the multiple ".dcm" images of a scan into a 3 single 4D images for anatomicals, also known as T1 images. That converter will also convert the BOLD images into a single 4D image.

After conversion, the images you will want and need to load into whichever fmri data analysis software you're using will be in ".nii.gz".

Your question suggest that you don't need data analysis software but if you do,  I'm only familiar with FSL, you can find information on FSL from here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/

Hope this helps.


For fish, does a bony skeleton have any advantages over a cartilage skeleton? I have learned that two important lineages of fish are the bony fishes (Osteichthyes) and the cartilaginous fishes (Chondrichthyes). Many websites mention an advantage of the cartilaginous skeletons of sharks and other chondrichthyans: they're lighter than bony skeletons.

But it has been harder for me to find out if we know of any things bony skeletons do for fish that cartilage skeletons can't do, or don't do as well.

My research and hypotheses

I found an old Manual of Geology by Samuel Haughton (1865) that says

  [a bony] skeleton only affords an advantage over a cartilaginous skeleton by allowing a greater variety of points of attachment for the muscles of the Fish, and so admits of more powerful motions.

But maybe other people have discovered more things since this was written. Also, I'm curious if this is just a theoretical argument, or if we have actual evidence that bony fish are capable of using their muscles more effectively than cartilaginous fish.

I have three main hypotheses at present:

Haughton was right, and a bony skeleton is just more effective at serving as an attachment point for muscles.
Bony skeletons are more effective at protecting the fish.
There are no advantages to bony skeletons; bony fish just happened to evolve this way. (As far as I can tell, the early evolutionary history of fish has been a bit unclear and I haven't been able to determine if there is current consensus about whether bone or cartilage skeletons came first, and whether chondrichthyan cartilage skeletons are an inherited primitive feature or an innovation.)

As a fish morphologist, here's my best attempt. I really like the first reference I listed at the bottom, too.

1) Ancestral Condition:: The cartilaginous skeleton of chondrichthyes (sharks, skates, rays, chimaeras) is almost certainly a derived feature--a synapomorphy-- defining the clade. There are a few lines of evidence for this. First, the cartilage in a shark skeleton is a very specialized form of calcified cartilage,  unique to the group. Second, in other gnathostome and pre-gnathostome ancestors (Osteostracans,  other armored jawless fishes) had big bony head shields. The groups most closely associated with sharks (Placoderms, paraphyletic acanthodians) has both bone and cartilage in their skeletons. Basically I guess my point is that, while cartilaginous skeletons were ancestral for gnathostomes, that cartilage was very different from chondrichthyan cartilage, and bone turned up in many stem fishes before chondrichthyan cartilage. So the ancestor for sharks and bony fishes probably had both cartilage and bone but not the specialized calcified cartilage of sharks

2) Bone as a Plesiomorphic (ancestral feature), but not the entire skeleton: If we take what I've said above, it certainly suggests that your point 3 is in the right direction w.r.t. split between chondrichthyes and osteichthyes. The chondrichthyan skeleton is light...But the osteichthyes definitely took endochondral bone and ran with it--which brings us back to your original question: why did they replace their entire skeleton with bone? Why is always a tricky question in evolution, but we can speculate:

3) Potential adaptive value of a bony skeleton:

bone is better at transmitting muscle force than cartilage, so in that sense, you are correct
when fish were coming into prominence and diversifying, there were a lot of big, terrifying, predatory arthropods. Many early fishes have big bony armor plates-- which may have served to project them from their chitonous predators
More evidence for that -- when big scary predators went extinct, fishes began to pare down their bony armor (most teleosts have highly reduced skeletons).

Without a time machine we can't be certain of these things, but I'm pretty sure what I've laid out is fairly close to the common consensus.

Relevant lit:

https://academic.oup.com/nsr/article/1/4/490/1512529
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237026/


Cell organels during cell reproduction When one studies cell division, usually the process is explained through what happens with the DNA of the cell, particularly, that in eukaryotes the nucleus dissolves. But what happens to the rest of the organelles? I read here what happens to the ER and Golgi complex, in particular I'm wondering what happens to the mitochondria, in which part does it reproduces? do they make a parallel process? or do they get dissolved?

$%---------
%I started wondering about this because I was reading Lynn Margulis' article _Bacterial Bedfellows_, and it baffles me that in such little time an organism can just coexist with an attacker and turn it in a _good relationship_, how ever it's not clear to me how cell reproduction might work in those cases.$

During mitosis the cellular organelles that have their own genetic information reproduce independently. Other organelles like the Golgi complex disintegrates and then form all over again in the daughter cells. Other organelles that are smaller and more numerous like ribosomes are divided between the two cells. Meiosis is the same thing only that there is crossing over in the nucleus of the cell.


Does H. pylori have paracellular activity? I know that it has transcellular activity i.e. it can pass through neighbouring cells.
However, I am not completely sure if it does not have paracellular activity, see this:

  H. pylori did not induce any modification of the paracellular pathway
  (R = 148 ± 10 versus 174 ± 16 Ω · cm2; JNa = 4.16 ± 0.44 versus 3.51 ±
  0.41 μEq/h · cm2; JMan = 0.081 ± 0.01 versus 0.058 ± 0.009 μmol/h · cm2), nor did it modify J3H-HRP (2,201 ± 255 versus 2,110 ± 210 ng/h ·
  cm2 for H. pylori-infected and control cells, respectively). However,
  in the presence of H. pylori, we observed a significant increase in
  JHRPi (520 ± 146 versus 171 ± 88 ng/h · cm2). This effect was not
  dependent of the cag status of the strain and was not reproduced by
  the sonicates or the culture supernatants.

Is there any evidence that Helicobacter pylori has paracellular activity?

I found no evidence for paracellular movement.

Some notes of mine

  Mucinase $\to$ lophotrichous flagella $\to$ Transcellular (actin fibrils, tails) movement
  ICF Vacuolating cytotoxin (VacA) $\to$ altered T-cell function $\to$
  damages epithelial cells, disrupts tight junctions and causes
  apoptosis.

I think the latter point makes transcellular momevment possible.
I see no way how paracellular movement would be possible.


How do afferent mechanoreceptors work on the finger pads? I'm having some difficulty understanding how the afferent signals are sensed in the finger pads. My understanding is that for mechanoreceptors, as the indenting force increases, their effective response also increases. Additionally, as contact area increases, so does the overall stimulus area and hence a larger response amplitude from the mechanoreceptor afferents should be found.

However, the results shown in this article in the Journal of Neuroscience that discusses this physiology shows contradicting results. In this article, the closer the dot spacing (1 mm or less) and the higher the contact area the lesser the receptors seem to fire, and stop firing altogether at about 1 mm dot spacing?

Why would this occur?

Short answer
Tactile grating stimuli with a higher line density (number of lines per surface area) and applied with an equal force result in a lower amount of pressure per unit of skin area under the grating, and hence smaller afferent responses.

Background
In the Discussion section of the linked article (Phillips et al, 1993) the authors explain on p. 838 (left column) that the reduction in the response of SA afferents (slowly adapting fibers) when grating density is increased is due to the higher proximity of neighboring areas of stimulation, i.e., the lines in the grating stimuli are more closely spaced. The authors reason that this leads to a reduction in the effective stimulus (i.e., compressive strain) at the receptor terminal due to the presence of adjacent stimulus elements that distributes, and hence reduces the skin loads per line.

Reference
- Phillips et al, J Neurosci; 12(3): 927-39


Which complexes physically pump protons in photosynthesis? The cytochrome b6f complex is often drawn as pumping protons, but then someone told me that actually there is no pumping, rather the Q cycle.

According to this view, what actually moves the protons is that a PQ takes up 2 H+ from the stroma as it is reduced and another two PQ release 2H+ into the lumen as they reduce PC and partially reduce the first PQ. The complex, therefore, does not physically pump the protons.

I now wonder if any of the photosynthetic complexes pump protons. For example, the PSII complex has PQ reduction with 2H+ removed from the stroma and its oxygen evolving complex releases O2 and 4H+ into the thylakoid lumen, so this could be its ‘pumping’ contribution.

General Approach

Although I am not an expert in this area, as an ex-chemist I find this topic one of the most fascinating and fundamental in chemical biology. I have constructed an answer starting from my copies of the 5th (available on line) and 6th editions of Berg et al. Biochemistry (2003 and 2007, respectively), and then searched the Protein Data Bank for structures of the cytochrome b6f complex, and worked from the papers associated with more recent entries.

Definitions

First, it is important to be clear on the following:

  What is meant by a proton pump (physical or otherwise)?

I think that the question — and the scientific community in general — probably assumes a pump to have some sort of channel or revolving door through which the protons are driven from one side of a membrane to the other. If one were able to tag an individual proton to follow it, one would find that it was physically translocated across the membrane. (A model for this might be the Na+/K+-ATPase. See also Berg et al. Biochemistry in Chapter 13 “Membrane Channels and Pumps” although this does not actually mention pumps in relation to either photosynthesis or oxidative respiration.)

This would be in contrast to the net translocation of protons across a membrane by chemical sleight of hand. A reaction at one side of the membrane would consume protons, and a reaction at the other side would emit protons. However no individual proton would pass through the membrane.

Both these processes would be working against a concentration gradient and require energy, in this case in the form of reducing power — not, of course, ATP.

This difference is illustrated in Berg et al. with respect to cytochrome c oxidase (Fig.18.21) in which both processes occur, where the authors refer to ‘pumped protons’ and ‘chemical protons’:

And the answer is…

That the situation in photosynthesis is similar to that for the oxidative electron transport chain:

  Net translocation of protons across the membrane is achieved both
  chemically (in photosystem II) and by ‘pumping’ (in cytochrome b6f).

So the ‘someone’ in the question was correct in saying that the chemical type of net translocation occurs in photosynthesis, but was incorrect in saying that this was at the cytochrome b6f stage.

Structural Evidence

The cartoons shown above (taken from Berg et al.) are based on a wealth of indirect experimental data. However some of us are never convinced until we have seen the stigmata. The structure of the cytochrome b6f complex was reported in Science in 2003 by William Cramer’s group, and in the diagram below (my modifications) there is a channel through which the passage of protons is indicated.

A more recent (2013) paper from the same group considers the proton transfer pathway in cytochrome b6f in more depth, and I reproduce below Fig. 1B from that paper to indicate the type of molecular detail.

Heavy reading, but wonderful stuff!


Where does the number 67 in the nuclear protein/antigen Ki-67 come from? Why not 66 or 68? I have read in in the original paper that in the year 1983 a research group in Kiel, Germany (that's where the Ki- in the name comes from) developed monoclonal mouse antibodies against Hodgkin lymphoma cells in multiple 24-well plates. If I understand correctly they were able to isolate antibodies from 63 wells and divided them into 493 microtiters into several 96-well microtitre plates. Of these 493 titres, 164 cell batches were chosen for further investigation and expanded. Somehow Ki-67 emerged from there, but why this number? Who gave it that name and why?

A teacher once told us in med school, the cells producing the antibodies were found in well 67, but I cannot find any source to back up that claim.

From Wikipedia: "The name is derived from the city of origin (Kiel, Germany) and the number of the original clone in the 96-well plate".


Is recognizing one's own mirror reflection a valid test of animal intelligence/self awareness? I've been looking at this Ted talk on interspecies internet, and it appears that they have selected a small number of species of animals (dolphin, elephant, and some ape(?)) and are intent on developing interfaces for these animals to be able to connect with other animals over the internet.

From the talk, it appeared as if one of the criteria for animal selection was whether or not an animal recognizes itself in the mirror. This got me thinking - there are many more cats that have access to technology like the internet or TV or cats that have been interacting with touch screen displays. Yet apparently cats cant recognize their own reflection as themselves.

What is so special about being able to recognize one's own reflection? Is it a true measure of self awareness? Does it only appear in animals with larger brains?

I think it is a necessary test of self-awareness. In order to make the connection that "I am the being in the mirror" and that every action I do will be reflected in the mirror (or, vice versa, every action I see the being in the mirror take is a reflection of my own action), one must first have a concept of self. One requires a constant present-tense (at least) story of oneself: "I am doing this. Now I am doing that. Oh look, I am doing this and that guy is doing the exact same thing." And then there's the ultimate realization, "Ah ha! That's me!". That realization would make no sense if the individual has no sense of "me"!

[speculation] On the other hand, perhaps it is too strict. It seems that it would unfairly favor social species, since it requires not only recognizing another member of the species (and being able to associate the anatomy of another member of the species with one's own anatomy), but it may also require the recognition of intent. That latter requirement is complicated by differentiating between intent and compulsion: at some point, one must realize that the being in the mirror isn't trying to copy but rather it always, inevitibly reflects one's motions. So, perhaps a cat is self-aware, in a sense that it has a constant story in its head of what it is doing and what it intends to do, but it cannot easily ascribe intent to other members of the species and thus cannot figure out that the cat in the mirror is automatically mirroring all of its movements. [/speculation]

Herein lies the rub: there is no perfect test for self-awareness; we can cast doubt on any outcome. The best would be if these animals could communicate with us by language. In lieu of that, we have to think of such tests that demonstrate with reasonable confidence that the species carries all of the characteristics that we attribute to self-awareness. I think another good test would be determining whether the species can plan individual actions in the future; in order to say, "first I will do this, then that; finally, that will allow me to do that", it seems like it would reasonably require an understanding of self and the consequences of one's actions. An example would be birds solving sequential puzzles.


Pedigree Analysis: Problem I'm struggling to arrive at the answer to the following question, which appeared on a pre-test of mine and which I am now using to study the material we've learned. According to this helpful video, I am assuming the possibilities for my question are also autosomal recessive, autosomal dominant, x-linked recessive, or x-linked dominant. I tried each approach as Mr. Douch did in the linked video, but I struggled to find a definitive answer. No matter which approach I picked, it seemed plausible that either the boy or the girl could have the trait, but it seems there's no guarantee that both the boy and the girl have to have the trait. During the pretest, I picked the first answer choice, both the boy and the girl, and got the answer correct by mere chance. But to say that the boy and girl are expected to have the trait would imply that there is a great deal of certainty that the trait will be passed on, right?

The pedigree below shows how a physical trait caused by a mitochondrial gene is passed from one generation to the next in a family.

Using this diagram, which children highlighted in yellow would you expect to have this trait?
(A) Both the son and the daughter -- correct, per answer key
(B) Neither the son nor the daughter
(C) The daughter only
(D) The son only

Please let me know what I am doing wrong or if I am not understanding the question wording correctly. Does it have to do with the fact that it's a mitochondrial gene? Thanks.

The key here is that it is a question about mitochondrial DNA. mtDNA in humans is inherited maternally (from the mother). Both sons and daughters inherit mtDNA, but only the daughters will pass it on to the next generation.

A child's mtDNA has to come from his or her mother, and all of a person's mitochondria are genetically identical. Therefore, children of an affected female will almost certainly have the abnormal trait, while children of an affected male will not.


Do "virgin" ant queens ever shed their wings? In species that reproduce sexually, if an ant queen goes on a nuptial flight and does not successfully mate, will she still shed her wings and try to found a colony (although she probably won't succeed because unfertilized eggs will result in drones only)?

Good question. I tried to find a few articles to validate my answer, but it would appear that very few professional studies have been done on the matter. One of my hobbies a few years back was ant keeping and I have had several colonies started from queens over the years, so I can share some of my personal experiences.

Anyway, back to your question. For the most part, no. An infertile queen will keep her wings and either find a safe place to lay eggs like a fertile queen or just walk aimlessly until she dies/is eaten. However, there are some rare instances where an infertile queen will shed her wings after the nuptial flight and find a safe place to nest and even in some occasions will lay eggs that are, of course, unfertilized and will therefore die or become male drones.

On the subject, the same is true vice versa. In rare instances, a fertile queen will NOT shed her wings, find a nesting place and even raise a colony all with wings on. Most of the time, however, her first workers to emerge promptly remove them.

I hope this answers your question.

CDB


What does "crude" mean in this context? Taken from Ian Freshney's Culture of Animal Cells:

  The enzymes used most frequently for tissue disaggregation are
  crude preparations of trypsin, collagenase, elastase, pronase, Dispase, DNase, and hyaluronidase...

What does crude mean in this context?

In this context crude means naturally occurring or unrefined.

Purified trypsin alone, for example, is usually ineffective for tissue dissociation since it shows little selectivity for extracellular proteins.

Source: Worthington Tissue Dissociation Guide


Measuring reverse transcription yield? Is there any measurement I could perform after RT that allows me to check the efficiency that the procedure had? Nanodrop cannot be used as remnants of RNA and poly T primers mask measure, or?

Nanodrop may be fine for the volumes but as you rightly guessed it is not so easy to distinguish DNA from RNA (and primers). Qubit (invitrogen) is a sensitive, dye based quantification assay. You can use that for estimating cDNA yield. The kit contains different dyes for DNA, RNA and protein estimation.


Structure of phosphates in nucleotides Nucleotides are made up of a heterocyclic nitrogenous base, a sugar (only ribose or deoxyribose), and a phosphate. In nucleotides, obviously the nitrogenous base matters as its variations dictate the production of certain amino acids, and the sugar can only be ribose (in RNA) or deoxyribose (in DNA), but does the type of phosphate matter? I've seen that a nucleoside describes the nitrogenous base and the sugar alone, and there are nucleoside monophosphates, nucleoside diphosphates and nucleoside triphosphates.

Do these three variations differentiate; when it dictating the production of amino acids; when looking at any sort physical variation; in any sort of way; or are all three just the same as each other??
Also, do all of the phosphates have to look like this?
(https://en.wikipedia.org/wiki/File:Phosphate-group.png). Or can they look like this (https://en.wikipedia.org/wiki/File:Phosphodiester-group.png). If they can look like the second image, then similarly to the question above, does it make any difference?

Well it turns out that when nucleotides are bonded together in a strand of DNA/RNA (nucleic acid) they ALWAYS HAVE only one phosphate group attached to their nucleoside (nucleoside = sugar + nitrogenous base (without phosphate)).

However, when they are by themselves, they are more often found with two or three phosphate groups as oppose to just the one. For this reason, the definition of a nucleotide is often misunderstood as it refers to containing one OR MORE phosphates, in reality, the official definition of a nucleotide states that only one phosphate group is present...

An example of a (so-called) "nucleotide" is ATP (adenosine triphosphate); it follows all of the rules that the misunderstood definition of a nucleotide states (these are; a nitrogenous base (adenine); a pentose sugar (ribose); and one "OR MORE" phosphate groups (triphosphate)). However, according to the official definition of a nucleotide, it is not, in fact, a nucleotide! It is instead considered a 'nucleoside triphosphate', since it is a nucleoside. with three phosphate groups (it is also a nucleotide with two additional phosphate groups, but I guess 'nucleotide-with-a-diphosphate' attachment doesn't roll off the tongue so well as nucleoside triphosphate).

Finally, as in nucleic acids and indeed anywhere else (according to the official definition of the nucleotide), there is only one phosphate group allowed to attached to each nucleoside (regular phosphate group) to form a nucleotide (officially). Therefore there is no variation allowed in the phosphate groups (since there's only one and they bond to other nucleotides, in the same way, every time (in nucleic acids)), furthermore in the pentose sugar the only variation allowed is whether it is a ribose (in RNA) or a deoxyribose (in DNA). So the phosphate-sugar backbone of the DNA strands and the RNA strands (nucleic acids) are consistent throughout the entire strand (and each strand of its type; differentiating only in the type of pentose sugar it consists of (ribose/deoxyribose)). Consequently, there is no phosphate-sugar backbone variation within DNA strands or RNA strands, for the phosphate or the pentose sugar to make any genetic difference to genetic material (those strands); only the nitrogenous bases and their sequences can make a difference to the genetic material...


What fruits will naturally ferment? If left unpicked after the fruit ripens, what fruits may ferment instead of just rotting? My perception is that most fruits just rot.

I know figs will ferment. I'm guessing that this is because the wasp that pollinates the fig carries yeast inside what will become the fruit.

Eating ferment figs got me thinking about how humans first discovered ethanol. I'd guess that they ate ferment fruit and fiddled around until they could reproduce the process.

First, before talking about fruits, let's remember that fermentation is an energetic metabolic process where there is no net oxidation of the substract. Bacteria, fungi, animals like you and me and even plants can use fermentation in different occasions. Plant cells, like fungal cells (and unlike bacteria and animal cells) perform alcoholic fermentation. So, there is no need of a fungal contamination to make a plant tissue producing ethanol.

But, of course, the presence of fermenting fungi, particularly yeasts, can make alcoholic fermentation much faster and noticeable. Several fruits contain what is called "ambient yeasts" (differing from "cultured yeasts", which we add to the fruits latter) covering them, and I believe the most famous example are grapes. Grapes are covered by several genera of Ascomycota (like Candida and Pichia), which can lead to alcoholic fermentation of the fruit. These species are different from Saccharomyces cerevisiae, the most common "cultured yeast" (and the one used in winemaking), but they can produce ethanol the same way.

This "natural fermentation" of grapes is known for a very long time, and it's probably one of the first cases of natural alcoholic fermentation known by civilized man.

EDIT: references for alcoholic fermentation in plant cells:

http://www.plantphysiol.org/content/149/2/1087.full

  Under oxygen-limiting conditions, pyruvate can either be converted into ethanol by pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) or to lactate by lactate dehydrogenase.

http://www.plantphysiol.org/content/100/1/1.full.pdf+html

  During the early hours of germination [...] seeds rapidly generate high respiratory quotients and exhibit increased ADH2 activities and active alcoholic fermentation.


Is there interphase between meiosis I and meiosis II? Is there interphase between meiosis I and meiosis II?
After 2 haploid cells are formed in meiosis I, do the cells go through a period of interphase (G1, S, G2) or do they go directly to meiosis II?

The technical name of this brief "interphase" between meiosis I and meiosis II is interkinesis.

Interkinesis is normally short (it may not even happen) and it's not divided in G1, S or G2, mainly because there is no DNA duplication, which defines the S (Synthesis) phase.

Source: A Glossary of Genetics and Cytogenetics: Classical and Molecular


Is there a biological or technical reason for a 40 Ct cutoff in nucleic acid detection assay? I have developed and validated a modified a nucleic acid test (NAT) for SARS-COV-2 detection using real-time RT-PCR (aka rRT-PCR, aka RT-qPCR). My assay is not for diagnostic use, but for donor screening (which are similar, but different enough to require independent validations). The PCR step is sensitive enough to detect a roughly a single gene copy per reaction, but not always with a sub 40 Ct (which may or may not be an issue).
You see, the protocol is built around the primer/probe sets first published by the US CDC, so I initially adopted the criteria in the CDC EUA protocol, which stipulate a Ct value < 40.00 to classify a target as positive. This means is that amplification with a Ct value of 39.99 is classified as positive, while a nearly identical amplification curve with a Ct of 40.01 is classified as negative. Looking at similar NATs for in vitro diagnostics, most use this same cutoff. It seems fairly common with tests for other pathogens too.
For a little background, using a cutoff like this reduces the potential for subjective classification errors between users by providing a qualitative, binary interpretation for an ostensibly quantitative data readout. The trade-off is that an improperly assigned cutoff can result in systematic classification errors that are universal among all users. Anyone who has used one of the protocols based on the CDC probes has noticed that the two primer/probes sets targeting the SARS-CoV-2 viral genome do not perform equally well. It's common for test results to be classified as "inconclusive" when one viral target is positive, but the other is "negative" because of a Ct value just above the 40Ct cutoff. (I've already tweaked my protocol to reduce this kind of error, but could not eliminate it completely).
As I am writing this up for publication, I'm wondering if it would be better (more honest) to recommend a Ct cutoff that reflects the empirical range of Ct values in my validation studies, as opposed to keeping it at some seemingly arbitrary round number (even if it is almost universal among similar tests). Doing so would not change any of the major findings I report (sensitivity, specificity, etc.), but would change some of the numeric values. More importantly, I think it could help prevent misclassification of late-amplifying samples as negative.
Does anyone know of a biological or technical reason why this cutoff should not exceed a Ct of 40? Maybe this is just some convention that is blindly carried forward; or maybe there's some quirk of TaqMan chemistry to justify this value that I'm just not aware of.

This is done because at some point you start amplifying nonsense and not get a meaningful signal. If (and this is most often not the case) you have the ideal doubling of you DNA template in each cycle, you can calculate how little DNA you start with to detect it only around cycle 40 - or the other way round: What you will amplify and see as a "signal" by then.
If you have templates which always really come this late, I would use more DNA (and probably more RNA to start the rtPCR) until this comes at least 2-3 cycles earlier and then do serial dilutions of your template to see if this signal is real or not. If so, you should see a relation between Ct and dilution.
For doing this you need a negative control which stays really negative until your sample signal shows up - which is tricky on its own because at some point you will see some kind of primer self-amplification. If this occurs in the same range as your sample, your signal cannot be used. If no other primers can be used for technical reasons, sometimes nested PCR has to be considered.
And last but not least all your reagents degrade over time by cycling them 40 times through the PCR program (also the polymerase), which affects the efficiency of the reaction.


How much of my ancestry comes from each grandparent? Three of my grandparents were Eastern European, back at least several generations. I recently discovered that I am less than 25% Eastern European, the rest being Western European and other. How likely is this?

On average, 25%, because you have 4 grandparents, and all of your genetic material came from them as a collective. Of course it's possible to be more genetically similar to a particular grandparent by random assortment of chromosomes, but the average will be 25%.

Genetic tests can't tell you what your ancestry is (companies implying this are probably misleading you on purpose). At best, they can tell you how correlated certain features of your genome are with people from a certain geography. Even people who are currently live in Eastern Europe will not test as "100% Eastern European." There is far too much mobility and breeding of populations across geography and far too much variation within populations.


What does saying a phylogenetic tree is 'well resolved' mean? I'm not sure what 'resolution' means in the context of phylogenies.

It means incomplete separation or a failure to split into two groups unambiguously.

There are multiple ways to estimate the resolution of a phylogenetic tree; involving an index to measure the likelihood of observing the phylogenetic tree that you derive relative to those produced by drawing species at random, for instance, or permuting species to produce a null distribution.

A badly resolved tree should show up in sets of randomly generated trees far more often than well resolved ones.

See http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00196.x/abstract


If during exercise the affinity of oxygen for haemoglobin is decreased, what are the general consequences for tissues? During exercise more respiration occurs, and hence more oxygen is required.

So the oxygen dissocation curve is shifted to the right.

So at a given Oxygen partial pressure, the haemoglobin is less saturated with oxygen, i.e. haemoglobin has less affinity for oxygen.

What is confusing me is that the role of haemoglobin is to move oxygen around the body, so if it has a lower affinity for oxygen, won’t it compromise this function? Even though more oxygen is released, doesn't the haemoglobin have to carry it to all the tissues in the body? So how is this change in affinity of benefit if it reduces the oxygen subsequently available for other tissues?

It may help to consider the diagram below which shows the percentage saturation of haemoglobin with oxygen (and hence how much it takes up or releases) at the different partial pressures in different tissues. (The actual pattern — and values — depends, of course, on the blood flow to different tissues.)

In general, the curves show that at the high oxygen pressure of the lungs haemoglobin is near saturated with oxygen — Hb takes O2 up —, whereas at the lower oxygen pressure in the peripheral tissues the saturation is less — Hb releases some O2. So in normal circumstances oxygen will be gradually released to tissues as it circulates through the body. The oxygen pressure in the tissues is acting as the control valve for release.

In cases where there is a vastly increased demand for oxygen, this normal control is insufficient. The hydrogen ions in the acids produced by respiration (carbon dioxide and perhaps lactate) act as an additional control as they cause the oxygen dissociation curve of haemoglobin to change e.g. from 1 to 2 in the diagram. (The molecular mechanism of this is understood, but that is not the question.) Hence at the same oxygen pressure, more oxygen is released (cf. the percentage saturation at 1 and 2).

Does this harm tissues other than the ones producing the acid? They obviously have lower priority, but you can see there is still oxygen left at 2, and physiological mechanisms (faster heart beat etc.) will increase the blood flow in general. So it is wrong to think of this as ‘all or nothing’, but as part as a general response which alters the balance towards the tissues in greatest need.


What are the Gateway clonase enzymes? The Gateway cloning system utilizes what Life Technologies refers to as "Clonase enzyme mix" to catalyze the BP and LR reactions.

What is in this enzyme mix? Is there a sequence for them?

The prototypes for these proteins are:

the bacteriophage λ proteins Int and Xis, required for, respectively the integration and excision of prophages. They are, as mentioned by @WYSIWYG, recombinases.

Genetic map of bacteriophage λ (source of image)

the original Ihf (integrative/integration host factor) was identified as an E. coli protein required for prophage integration.

As you might expect Int and Xis proteins occur in many phage genomes, and in integrated prophages in bacterial genomes, and Ihf, because it is involved in bacterial DNA replication, is ubiquitous. I imagine the actual source of the proteins used by Life Technologies could be a trade secret.


Why is the ribonucleoside derived from thymine, 5-Methyluridine, abbreviated m5U and not T? The wikipedia article about Nucleosides presents a table in which there are three columns — Base, Ribonucleoside and Deoxyribonucleoside — and structures, names and abbreviations for the nucleosides corresponding to the five bases, adenine, guanine, thymine, uracil and cytosine.

The abbreviation pattern for the deoxyribonucleosides is quite regular — they are all termed dN, where N is the first letter of the name of the base and ‘d’ indicates ‘deoxy’ (i.e. dA, dG, dT, dU, dC).

In the case of ribonucleosides, apart from one exception, the pattern is similar — they are all termed N, where N is the first letter of the name of the base (i.e. A, G, U, C). The exception is the ribonucleoside related to the base, thymine, which is not abbreviated T — as one might expect, but as m5U, from its name 5-methyluridine.

What is the reason for this? Why does the abbreviation for ribonucleoside derived from thymine deviate from that for the other bases?
Do people distinguish between m5U and U when referring to RNA, or is the letter U used for both?

From the standpoint of modern molecular biology, one can say that the table in the Wikipedia article would be better if — in the first instance at least — it left blank the entries for the ribonucleoside corresponding to the base thymine and the deoxyribonucleotide corresponding to the base uracil. This is because the thymine ribonucleoside is not a normal constituent of RNA, and the uracil deoxyribonucleoside is not a constituent of DNA.

It would also be more honest if the article explained that the abbreviations used in DNA and RNA databases employ the single letter to represent a deoxyribonucleoside monophosphate residue or a ribonucleoside monophosphate residue, as the case may be, and that only the chemist or student of nucleotide metabolism is likely to be concerned with the abbreviations presented.

It is in metabolism (for which these were named) that the abbreviations make sense. ATP is adenosine triphosphate, so the ‘A’ has to represent the nucleoside, adenosine, and dTTP, deoxy-thymidine triphosphate, is the metabolite that is a DNA precursor used by DNA polymerase. The reason that dU justifies inclusion is that dUMP exists in cells — as a precursor of dTMP (which is then converted to dTTP).

So finally to your Q1 about 5-methyluridine. The answer is that, as far as I am aware, this does not occur in cells as the free nucleoside or the free related base or nucleotide. It can only be considered as occuring at a particular positions in certain transfer RNAs (and ribosomal RNAs) where it is produced by the enzymic modification of the uracil ring by a 5-methyluridine methyltransferase. So in the metabolic era, before the detailed chemical analysis of minor bases in structural RNAs, there was never any reason for biochemists to refer to 5-methyluridine and consider its abbreviation.

You may or may not be aware that there are many minor bases of this type in different tRNAs, all produced by enzymic modification of the four bases occuring in an initial RNA transcript synthesised by RNA polymerase. There are over half a dozen different modifications of uracil, so it was far more meaningful for the scientists working on them to distinguish them with abbreviations that indicated their chemistry, rather than assigning arbitrary single letters to them. The fact that one could logically employ T as an abbreviation for 5-methyluridine would have been of no practical use, and, because of the association of thymine with DNA, could well have led to confusion. Hence, the committee standardizing nomenclature would have been faced with a fait accompli. In such circumstances realism prevails over idealism. (And in any case the names of the bases are a mess — how many students have been confused by adenine/adenosine but cytosine/cytidine.)

Regarding your second question: people don’t talk very much about m5U and U, but when they do they naturally distinguish between them because they are different molecules. Specifically, the databases for tRNA structures will distinguish clearly the different modified bases.


Why is there a mass limit on biological powered flight? So, this is a thing I never fully understood. There are a lot of reasons for a flying creature to be limited in mass (though I'm unsure if I'm familiar with all of them), from energy consumption to material strength. However, there seems to be an argument that goes along the lines that over a certain mass, no matter what, they can't generate enough power to counteract gravity.

What limitation could they exactly mean with that?

One of the physical limits to biological flight is muscle physiology.

Muscle force output is proportional to muscle physiological cross sectional area (PCSA) multiplied by its specific tension (Gans, 1982):

$$F = \text{PCSA} \times \text{Specific Tension}$$

PCSA is basically just the cross-sectional area of a muscle adjusted for its architecture. Pennate muscles have higher PCSA than parallel fibered muscles, because more fibers are packed into the area (at the cost of shorter functional distances). Specific tension is the force output per unit area. For a single species, specific tension is essentially constant.

So the way to make more force is to make more PCSA. But muscles don't scale only in area, they scale in volume as well. Increased volume increases mass as a cubic power, but muscle area only scales as a square power. So any increase in area that requires a volume increase (which is inevitable), will quickly outstrip any gains in force output.

Note that this doesn't mean that very large flying vertebrates were not possible: the largest pterosaurs (e.g., Quetzalcoatlus) had ~15 m wingspan and perhaps weighed 200 kg and the largest birds (e.g., Argentavis) had ~7 m wingspan with a mass over 50 kg. Both, however, were likely gliders.

Gans C. 1982. Fiber architecture and muscle function. Exerc Sport Sci Rev 10:160–207.


Can hunting of large specimens of a species make the size and weight of the species tend to be smaller? Siberian tigers in the wild don't grow as much as they used to be in past (in the 1900s).
Their average weight was measured 176 kg in 2005 study. But it was also said that those tigers observed in study were sick and in conflict to humans.
I think their smaller size is because of low prey density because at that time, hunting of animals that come as tigers' prey was high.
Could it also be because all the large specimens were shot?

I don't know of any research about this on tigers or any other terrestrial predators, but this is a well-known phenomenon in "trophy" animals1 (i.e. big game hunted for sport) and wild-caught fish1-4.
1: Allendorf, F. W., & Hard, J. J. (2009). Human-induced evolution caused by unnatural selection through harvest of wild animals. Proceedings of the National Academy of Sciences, 106(Supplement 1), 9987-9994.
2: Heino, M., Pauli, B. D., & Dieckmann, U. (2015). Fisheries-induced evolution. Annual review of ecology, evolution, and systematics, 46.
3: Monk, C. T., Bekkevold, D., Klefoth, T., Pagel, T., Palmer, M., & Arlinghaus, R. (2021). The battle between harvest and natural selection creates small and shy fish. Proceedings of the National Academy of Sciences, 118(9).
4: Bowles, E., Marin, K., Mogensen, S., MacLeod, P., & Fraser, D. J. (2020). Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest?. Evolutionary applications, 13(6), 1128-1144.


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

Tissue plasminogen activator is a serine protease consisting of approximately  530 amino acids and about 13% carbohydrate.

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

(Image Source: https://www.researchgate.net/figure/Structure-and-functions-of-tissue-type-Plasminogen-Activator-tPA-A-Structure-of_fig1_284797342)

Plasminogen is the precursor for synthesis of protease plasmin. Plasminogen is converted to plasmin by cleaving Arg561 and Val562. The  activated plasmin is formed by making disulfide-linkage between these two polypeptide chains.

The heavy chain  is at the N-terminal and light chain is at C-terminal.  The activation takes place by removing the signal peptide and activation peptide  by autolytic cleavage. This activation peptide is released from the N-terminal  to convert Glu-plasmin to  Lys-Plasmin. The active site which plays role in binding with fibrin is situated on the light chain.

(Image Source:  https://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/plasmin.html)

So, this proteolysis only produces one working peptide sequence, as the peptide bond cleaved and then amino acids are again joined by disulfide bond. And this peptide bond between arginine and valine is at 561/562 instead of 560/561 according to various sources.


How to distinguish those flowers in outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)? How to distinguish those flowers of the forest outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?

I am not asking about concrete species it should be extremely hard since they have hundreds forms, but what are observable differences between genus?

I have read wikis articles but still not sure that I could distinct those flowers in the field right way.

http://en.wikipedia.org/wiki/Leontodon
http://en.wikipedia.org/wiki/Hieracium
http://en.wikipedia.org/wiki/Crepis

It's quite hard to answer this question and the best would be to follow a flora, which I'll not just copy informations from to past here.
So following are general observations subject to numerous exceptions.

Hieracium generally have lanceolate to oval leaves, not or little toothed, most hairy.

Crepis and Leontodon have generally Taraxacum-like leaves, that means, dentate to lobed.

Some Crepis have leafy stems (but some don't), while Leontodon always have their leaves concentrated to the base, forming a rosette.

[edit on 2014, october 2]

Be aware that there is another genus of the Asteraceae family which may be mistaken with the Crepis/Leontodon/Hieracium group, although it's easier to distinguish. It's the Hypochaeris genus.

Hypochaeris have few but not so homogenous species as there are within the other genera.
Hypochaeris radicata (which may be the most common species in France and wester Europe) have all its leaves basal, forming a rosette and sticking to the ground (never erected). These leaves are always lobed (neither entire, nor toothed), with erected hard hairs covering there upper faces.
Hypochaeris maculata may be mistaken with some Hieracium : it have hairy smooth entire leaves wich are (all or mostly?) basal forming a rosette.

[Addition on August, the 5, 2014]

Also Leontodon and Hypochaeris have hollow stem just below the capitulum(1). When you press the stem just below the capitulum, you fell it flattens under your finger, and if you use the nail to make an incision in the stem, you will see it is hollow like a pipe.

  NB : Taraxacum also have hollow stems but they are fully hollow (from the base up to the capitulum), while Leontodon just have the upper part of the stem which is hollow.

Leontodon are almost always monocephal, that means, the stems are not branched : they have only one capitulum per stem, while Crepis and Hieracium and Hypochaeris mostly (if not always) have branched stems carrying several capitula.

(1) the capitulum is the type of inflorescence in the Asteraceae family. It's also called "head" (and actually, "capitulum" is the latin word for head).

You may like to have a look at this page [in french] presenting some common yellow and ligulate weeds from the Asteraceae family to get some illustrations of what I explained here.


Why add hydrogens in molecular dynamics simulations? In my molecular dynamics lecture, our prof said, that we always have to add hydrogen atoms to titratable groups, before we start the force field simulations, and that it is especially important for Histidine.
But why is that? Why do we always have to add the hydrogen atoms? And do we only have to do that for titratable groups, or for all?

The RCSB Protein Data Bank (PDB) presently has 137,917 structures deposited in it, of which less than 10% have been solved by nuclear magnetic resonance (NMR). Most techniques in structural biology simply cannot resolve the positions of hydrogens in macromolecular structures; only NMR and neutron diffraction provide the positions of hydrogens "by default." Therefore, all-atom molecular dynamics force fields, the most notable of which are the OPLS, CHARMM, and AMBER series, require that the positions of hydrogens be deduced from the starting macromolecular structures and geometric criteria and patterns, that hydrogen bonds are known to generally follow, if the starting structure doesn't have hydrogens. "Generally" is an important word to point out here, as there often is no unique, unambiguous way to place the hydrogens in a structure. This is especially true of histidine, where the local environment of residues and/or cofactors may perturb its pKa in often unexpected ways. Simulating histidine in the wrong protonation state, when that histidine is an active site and crucial to the mechanism and process under study, may lead to spurious, misleading, and/or potentially nonsensical results. Hydrogens are required for a faithful, (relatively) realistic description of macromolecular structure, simply because they are always present in macromolecules and are crucial for macromolecular structure and functioning - recall that hydrogen bonds stabilize the secondary structure of proteins, the DNA double helix, etc., moreover, they often mediate intermacromolecular recognition and function. Thus, an explicit representation of hydrogens is required. The so-called coarse grained force fields, the most popular of which I believe are the various versions of MARTINI, group hydrogens along with heavier atoms to achieve an increase in the simulation time step and to reduce the number of particles in the system, but these force fields are a very poor choice when modeling specific recognition and interactions.

The ambiguities of protonation are not a matter of opinion, I'm afraid. One can go through all the structures in the PDB, only to find that the majority of  them have no hydrogens at all. One can explore the link to the PDB I've provided; one will find that out of the 131,917 structures in the PDB, 123,461 have been resolved by X-ray crystallography, of which only 10,749 have a resolution below 1.5 Å. To resolve hydrogens, a resolution below 1 Å is required. Indeed, high resolution crystal structures, NMR structures, and neutron diffraction structures (only 60 in the entire PDB!) are less than 20% of the entire structural archive. Techniques like electron microscopy have resolutions between 4 and 10 Å; in such cases, people are unsure about the positions of the heavy atoms; they don't even dare think about the hydrogens. So, it's not just the titratable groups that are problematic, in most structures one can't see ANY hydrogens. Of course, for backbones and alanine side chains, one probably has a pretty good guess where the hydrogens are, given the positions of the heavy atoms. But to answer the question - in MD, most often one needs to add hydrogens everywhere, not just in the titratable groups, because the starting PDB structure doesn't have any hydrogens. In fact, often times structures from the PDB have missing heavy backbone or side chain atoms, because those couldn't be resolved; sometimes termini are missing, sometimes large stretches of protein; these often need to be modeled-in.


Bacteria as predators Why do some bacteria kill each other? And how do they do that?
It's really a mind-blowing thing if you think about it. Please give me a simple answer.

They do that because a bacterium contains all the molecules required for life, that is they are a source of amino acids, lipids, glucids and nucleic acids. This is the same reason why we eat in the first place: we need a source of these molecules to survive or, in other words, to allow our cells to carry out their tasks such as replicating the DNA or producing proteins.

Bacteria can kill other bacteria by a kind of infection: the predator bacterium enters a bigger prey and then start consuming the prey's molecules. By the same token, Mycobacterium tuberculosis enters the macrophages and used them for its own biochemistry, for instance.

Interestingly, this process of bacterial predation is under scrutiny for the development of a new breed of antiseptics in the age of antibiotic resistance (see https://phys.org/news/2017-03-predatory-bacteria-antibiotic.html).


What is the state of actin-myosin in my biceps after I have flexed my arm? When I'm starting to flex my arm, the myosin and actin slide over each other in a ratchet like mechanism. When I've totally flexed my arm, are the actinomyosin left in this contracted state? Since there is a visible decrease in length of the muscle, muscle fibres should have contracted.

So do they remain in this contracted state? Does the myosin head attach to the actin all this time? If it leave the actin, does the myosin snap back to its original position and relieve the tension/comeback to original length? Does it require any energy expenditure? Because I can keep my arm flexed throughout the day without getting fatigued. Also, What is the state of the actinomyosin if left in a half flexed state?

By state, I mean, the stage of the cross-bridge cycle

When I've totally flexed my arm, are the actinomyosin left in this contracted state?

Yes, the sum of the length of all sarcomeres in series determine the length of the muscle.

So do they remain in this contracted state? Does the myosin head attach to the actin all this time?

Yes, it stays attached.

If it leave the actin, does the myosin snap back to its original position and relieve the tension/comeback to original length?

It doesn't really 'snap' back, it 'walks' back over the actin.

Does it require any energy expenditure?

Yes, the myosin heads require ATP to 'walk' back as well. If ATP is depleted cannot walk back, as is the case with rigor mortis (https://en.wikipedia.org/wiki/Rigor_mortis).

What is the state of the actinomyosin if left in a half flexed state? By state, I mean, the stage of the cross-bridge cycle

Myosin will partly overlap with the actin, but not completely. But this has nothing to do with the cross-bridge cycle. The myosin heads need to complete several cross-bridge cycles to fully contract the sarcomere.

For further reading, the Wikipedia page on the sliding filament model is a good start: https://en.wikipedia.org/wiki/Sliding_filament_theory


Movement of stem cells from mother to fetus Recent results from J Lee Nelson and colleagues (Sci Am. 2008 Feb;298(2):64-71; available as full text through Google) show that cells from the mother were found in a person aged 46. Logically, these cells should be stem cells, as any other cells would die in such a long period of time.
So, what stem cells could be transferred from mother to fetus?
Why doesn't the immune system reject those cells?

Since the maternal cells can be found in a number of tissues including

  In second trimester fetuses the thymus, lung, heart, pancreas, liver, spleen, kidney, adrenal gland, ovary, testis and brain had maternal Mc (microchimerism)

it's clear that these are stem or stem like cells that are being incorporated into fetal tissue.

Since these cells arrive while the immune system is developing, they are considered as self and not foreign. But a breakdown of that immune tolerance is thought to be involved in a number of autoimmune diseases, especially systemic sclerosis which resembles a host vs graft disease where the patient's immune system attacks tissues holding the maternal cells.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516290/


Spruce growing high up in a maple trunk: Can a partially rotted trunk completely sustain another tree? I've come across a spruce tree that is growing 15ft up in the crotch of a sugar maple tree:

According to Google StreetView, the spruce has been there since before 2007 (over 10 years ago!).

I've seen other trees growing out of rotted stumps or in trunks near ground level before, but I've always just assumed that the roots of those trees reached down to soil -- in one way or another -- to get the nutrients they need for survival.

But with the subject tree, it's so high up that I would assume that that the roots do not have access to any soil. It's my guess that the spruce is getting all of its nutrients from decomposed wood in some rotten portion of the trunk.

I didn't know biology worked like this. I wouldn't have guessed that a live, partially decomposed trunk could contain 100% of the nutrients that a tree needs to survive for 10+ years. I know soil is made, in part, from decomposed wood, but it's my understanding that there are a lot more ingredients too.

Can the decomposed wood in a partially rotted trunk completely sustain a tree?

Note  This answer makes the presumption that the crotch in the maple's trunk is indeed a breach through its bark, and does reach the inner woody tissues.

The heartwood of most trees consists of the dead connective tissues, xylem, which surrounded the cells that once formed the living layer of phloem under the protective bark.  That connective tissue itself mostly cellulose, and is a polymeric chain of glucose i.e. sugar molecules bonded and linked in such a way as to make them indigestible to most lifeforms.
Certain bacteria and fungi, among others, are able to do so, and they are among the first responders in the decomposition scene.  When these microbes, often present in the gut of various insects, are able to break down the woody fibers into forms that permit their re-use by other plants, the detritus is comprised mostly of carbohydrates, alcohols, carbonic acid, and water.  Phosphates and various other trace elements which were present in the cells of the woody tissues are released also.
Later, visiting birds and mosses will further augment the ecosystem, adding nitrates and various salts — potassium, sodium, chlorides, and the like.

Another thing that needs to be considered is the drainage.  Where does the excess water go?  Pressure on the capillaries inside the xylem of the maple should be able to channel some water downwards, but not much will exit through the roots.  I've never heard of such a thing.  The hole in the maple will widen and exacerbate, deepening the rotted area, but it will be acidic and somewhat saline due to the lack of drainage.

Can it completely sustain another tree?  As the ecosystem flourishes, probably; unless the new tree has special requirements for the pH or salinity of its soil which are not maintained by the rotten wood, then it should be able to gain enough nutrition in the form of nitrates, phosphates, and water, but not all of that will come from the other tree directly.

The branches of a tree will only grow so large as can be sustained by their root system, of course.  The limited space in which this little sapling has taken root will result in the less than maximal form that you see in the photographs.

So, in conclusion, that spruce will probably not thrive by any means, but it will manage to survive.  Spruces do favor more acidic soils — lower pH — than many other trees, so it has that going in its favor.
That much is obvious, I suppose:  ten years, and it no larger than a four–year shrub.

There is a problem if all this occurs inside a tree which has not fallen, however.  Usually, the outer bark of a tree protects it from such decompositional actions, because the inner woody tissues of most trees do not contain adequate chemicals to deter insects and fungi from chomping or ‘mycelizing’ their way through the heartwood.
Eventually, the maple will either need to be cut down or will be weakened enough that it will collapse.


Can anybody recognize this cardiac waveform? Is this an artifact or an arrhythmia?

To be conclusive, another couple of leads recorded at the same time as this event would be helpful though the fact that you do have a recognisable QRS complex and a T wave and that the QRS happens before you would expect it to based on the prior rhythm and the P wave, if that is one, prior to it is to close to the QRS complex to have caused it would suggest a premature supraventricular arrhythmia.  There are many technical texts to consult to refine this further, if this is a small animal ECG, I recommend Larry Tilley's textbook entitled ECG for the small animal practitioner.


What does substrate mean? I have been reading some literature on measurements related to biofilms.

In some articles the word "substrate" seems to stand for the material on which a biofilm is growing. In other articles, it seems to stand for the nutrients that are freely floating in (say water) where the biofilm is growing, and which then diffuse into the biofilm and which it uses to grow.

Have I misunderstood something or are both of these meanings in active use? Is there a disciplinary or some other difference that determines who uses which term?

The review article [1] uses substrate to mean freely floating nutrietnts. Also, searching for "substrate loading" or "substrate loading rate" or such (on Google scholar) gives examples of substrate as something that is fed to the biofilm.
For example Wikipedia uses the other meaning of substrate: https://en.wikipedia.org/wiki/Substrate . Scientific literature with this meaning can be related to how easily biofilms detach from a given material in the presence of shear forces.

[1] Harald Horn and Susanne Lackner. Modeling of biofilm systems: A review. In Kai Muffler and Roland Ulber, editors, Productive Biofilms, pages 53–76. Springer International Publishing, Cham, 2014.

A substrate is an underlying substance or layer, or less strictly, the medium within or upon which an organism grows. For instance, you can have a filamentous fungus grow on a solid medium (e.g. on an agar plate) or in liquid medium (e.g. in a shaken flask containing a solution) and its substrate would be the contents of the agar or solution. It's nothing more fancy than that.

For instance, you could design 4 growth conditions for a strain of fungus.

Case in point, a hypothetical table could look like this:

                        *Substrate*

                Wheat straw     Sugar beet pulp
                             |
          Liquid         1   |   2
                             |
*Medium*             -----------------
                             |
           Agar          3   |   4

Simple!


Which part of human body sustains most pressure when standing up straight? Let's suppose a healthy fit barefoot young adult standing comfortably on a flat solid surface.

A reasonable guess is somewhere around the foot.
But is it the ankle, the heel, or the Metatarsus?

It is logically clear that the ankle could only partly be analyzed in the group of joints that are below its height. There is no direct way to measure the pressure on ankle joint (on talus bone), but from the logic it is clear that it should be the point of highest pressure in the group of points lister in the question, however the pressure is distributed through the other joints of the foot.

Below are the graphs of pressure distribution according to surfaces (not joints). From the graph we can conclude that part of the pressure experienced by ankle joint distributed tangentially to metatarsal region and other surfaces.

Indeed the highest pressure in standing person in on feets. The term you are asking about is foot pressure distribution (FPD).

In we assess the FPD dynamically, in younger persons the FPD is nearly equivalent between calcaneus region and metatarsal region, while in older persons the FDT in calcaneus region is higher than metatarsal pressure.

During stance:

Foot pressure distribution. A. Maximum pressure distribution on all sensors during stance for one subject. B. The nine anatomical masks superimposed on the insole (MC = medial calcaneus, LC = lateral calcaneus, MA = medial arch, LA = lateral arch, MT1 = first metatarse, 3 = second and third metatarse, 4 = fourth and fifth metatarse, H = hallux, and T = toes).

Pressure distribution by anatomical region. Normalized maximum pressure distribution for the young (white bar) and elderly (black bar) group for each anatomical region (medial calcalneus mask p = 0.0001, lateral calcaneus mask p = 0.03):

source article, you can find much more using FPD as a keyword.


Mean and standard deviation of human bone density? Are the human bones about equal in density? Or is there any published data on the mean + s.d. density for a given bone available?

Interesting question that I'd not considered before.

Bone density is commonly measured by assessing the bone mineral density (BMD) using dual-energy x-ray absorptiometry (DMA), literally the g/cm2 of minerals in the bone.

Having had a search I can only find values for a small number of bones commonly measured when testing for osteoporosis (characterised by reduced BMD). Unsurprisingly the age and sex of the individual has a large effect on BMD; after puberty males have higher BMD (1) and during ageing this then declines, sometimes dramatically (2).

These values are from a Vietnamese study (3) show that the hip and the spine are different.

Men [ mean (SD) ]

Femoral neck: 0.85 (0.13)
Total hip: 1.00 (0.13)
Lumbar spine: 1.05 (0.12)

Women  [ mean (SD) ]

Femoral neck: 0.80 (0.11)
Total hip: 0.95 (0.12)
Lumbar spine: 0.96 (0.11)

There must be other reference values for other bones in different populations but I don't have time to look them up now! Good luck in your own research.

I found this website by the US National Institute of Health and this PDF by the World Health Organisation immeasurably enlightening.

Bonjour JP, Rizzoli R. Bone acquisition in adolescence. In: Marcus R, Feldman D, Kelsey J, eds. Osteoporosis. San Diego, CA, Academic Press, 1996:465–476
Cummings SR, Kelsey JL, Nevitt MC, O’Dowd KJ (1985) Epidemiology of osteoporosis and osteoporotic fractures. Epidemiol Rev 7:178–208
Ho-Pham, et al. (2011) Reference Ranges for Bone Mineral Density and Prevalence of Osteoporosis in Vietnamese Men and Women. BMC Musculoskeletal Disorders, 12:182  doi:10.1186/1471-2474-12-182


How exactly can dsRNA be introduced to a cell? Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?

Besides viral infections there are different pathways for cells to take up dsRNA. Inside the cells these dsRNA are processed by Dicer which processes these RNAs into small interfering RNA, which play an important role in the regulation of gene activity.

These pathways have mostly been researched in Drosophila and C. elegans, I am indicating where evidence for them in humans is available. The different possibilities for the uptake are:

Uptake via transmembrane proteins: In C. elegans two different transmembrane proteins have been discovered which passively transport
dsRNA into the cells. They are called SID-1 and SID-2 (systemic RNA-interference defective protein), at least for
SID-1 a homologue exists in humans as well. These receptors are important for the uptake of systemic (produced by the own organism) dsRNA. See references 1-3 for
details.
Uptake via Endocytosis: In drosophila cells active transport happens through the scavenger receptors SR-CI and Eater. They bind
the dsRNA and are then internalized. Knockdown of these genes
inhibited the import of dsRNA and inhibited the endocytosis mediated
knockdown of genes. This process seems to be evolutionary conserved,
as knockdown of the orthologous genes in C. elegans led to similar
results. This mechanism seems to be more important for the uptake of environmental dsRNA. See references 4 and 5 for more details.
Uptake via Phagocytosis: At least for drosophila, there is evidence for a phagocytosis mediated uptake mechanism, which is
independent of endocytosis. See reference 6 for details.

References

SID-1 is a dsRNA-selective dsRNA-gated channel.
Uptake of extracellular double-stranded RNA by SID-2
RNA interference: a mammalian SID-1 homologue enhances siRNA uptake
and gene silencing efficacy in human cells.
The endocytic pathway mediates cell entry of dsRNA to induce RNAi
silencing.
Double-stranded RNA Is Internalized by Scavenger Receptor-mediated
Endocytosis in Drosophila S2 Cells
A phagocytic route for uptake of double-stranded RNA in RNAi


What happens if you intake pure magnesium? We know that body needs a certain amount of magnesium. Why are magnesium supplements in the form of magnesium oxide, magnesium citrate, etc?

Because like a lot of material we need the ion not the pure form. Pure sodium is explosive metal and pure chlorine is horribly toxic gas but change them into their ionic form and they are essential nutrients, sodium chloride, table salt.

In the case of magnesium however the problems one of reactivity and absorption. If you swallowed a solid lump of magnesium, not much will happen, the molarity of stomach acid is fairly low, it reacts too slowly to get significant amount of magnesium (or hydrogen) out of it before it passes. Your body just is not equipped to break down solid magnesium since it does not occur naturally often. We can only absorb it in it's ionized state.

More importantly we take in some ion combinations better than others, this is called bio-availability and is influenced by a number of factors. Magnesium oxide for instance has very low absorption rates and basically just passes through without doing much, while magnesium glycinate has a fantastic absorption rate, some combinations can actually be mildly toxic like magnesium sulfate. This is a reoccurring issue with dietary supplements many do not contain bioavailable forms of the mineral they list, which is how people can end up with deficiencies even while taking supplements for that mineral.


Decreasing Solubility as Solvent Moves Higher in Paper Chromatography In paper chromatography, as the mobile phase (I used 1:9 acetone/petroleum ether) climbs higher and higher, will the solubility of the solutes decrease as the solvent moves higher? I speak mostly about the beginning, when the solvent just begins to climb up the paper. Will the solutes travel right at the solvent front at the beginning, and then start to lag behind (and separate) as the solvent front moves higher?

The solubility of the solutes is the same at all points in the chromatography process. The solutes are clustered together at the beginning (at the solvent front) because none of them has moved very far yet. The reason for the separation of the solutes isn't that they become less soluble, it's that the solutes are moving at different speeds, like cars in an auto race:

  _______
 /____/SF\___
 |_,._____,._)
---`'-----`'--
  _______
 /____/S1\___
 |_,._____,._)
---`'-----`'--
  _______
 /____/S2\___
 |_,._____,._)
---`'-----`'--

At the beginning, both cars (solutes) S1 and S2 are even with the solute front car (SF) because the race (chromatography) has just begun. However, over time, the SF car outpaces S1 and S2 because it is moving faster.

                     _______
                    /____/SF\___
                    |_,._____,._)
                   ---`'-----`'--
         _______
        /____/S1\___
        |_,._____,._)
       ---`'-----`'--
              _______
             /____/S2\___
             |_,._____,._)
             ---`'-----`'--

And at the end, you get great separation:

                                                                _______
                                                               /____/SF\___
                                                               |_,._____,._)
                                                              ---`'-----`'--
                        _______
                       /____/S1\___
                       |_,._____,._)
                      ---`'-----`'--
                                           _______
                                          /____/S2\___
                                          |_,._____,._)
                                         ---`'-----`'--

(Thanks to retrojunkies.com for the ASCII car)


How many cells are there in the apical meristematic tissue? How many cells are there in the apical meristematic tissue?

Looking at this picture...

, I would tend to think that there are few hundreds cells in the meristem tissue. But I guess this is a picture of a root tip and the answer will be much different if we look at big branches and big trunks of roots. Also, the answer will probably differ between monocots and eudicots.

Roughly speaking, how many cells are there in different apical meristematic tissues (root, branches, trunk, different species)?

Meristem size is a very controled, highly genetic feature. It doesn't change between big or small branch/root (The SAM and RAM are obviously different).
There are very levels of potency in the meristematic tissue, so you should explain more which section of the meristem is of interest.
SAM (shoot apical meristem)
In *Arabidopsis thaliana* there are 9 long-lived meristematic cells, 3 in each lineage (L1, L2, L3) (https://www.sciencedirect.com/science/article/pii/S0012160609013840)
But the whole meristem is somewhat larger. If you consider the organizing center and cells that react to wushell by creating CLV1, CLV3 you get a few dozens.
If you consider cells that express miR156, miR172 or AP2-like genes you can get a few hundereds.
The scale is similar between species but the number and genes used to asses it vary.
RAM (root apical meristem)
I know less about the RAM but we can consider there the Quiescent center and also the Intial cells togheter called the promeristem.
THe Quiescent center consists of 10-20 cells and there is one (sometimes more) initial per file of cells in the root giving 20-30 cells in the promeristem.
The meristematic zone is somewhat bigger than the promeristem but the cells are pluripotent with relative small mobility.
 Roughly speaking
The most meristematic zone of each meristeme has no more than 50 cells.
The full area considered a meristeme can have a few hundered cells, depending on the research goal.


Is there a specific word for bacterial death? What do you call it when a bacterium dies? Cellular death is apoptosis, necrosis, and bacterial is ...? I don't simply want to write in a paper that it - well dies!

Death is appropriate. Using this word to describe both unicellular and multicellular organisms places them in the same hierarchy. This hierarchy is the domain of life.

Both prokaryotes and eukaryotes have unicellular and multicellular species.

If you choose another word for death I would suggest not using it exclusively for bacteria. If a reader finds the idea of bacterial death esoteric, they may be inspired to dig deeper into the subject. Encouraging an informed reader would seem to be an effective device in a paper for communicating scientific information.

You could qualify the word 'death' to be more precise. Senescence is the natural process of deterioration of life with age.

Google has a great tool for tracking word popularity. Here's a Google graph for 'senescence'.