What is the mechanism by which seeds stay alive while in storage? I know folks who store seeds for months and sometimes a year before planting them. What is the mechanism by which they stay alive?
Also some associated questions:
How do the cells in the seed stay alive without resources for so long?
How long can the seeds stay alive in storage?
Does storing them long affect their growth?

Seeds are made from cells in an amorphous metastable superviscous state because the cell's cytoplasm becomes a solid matrix of hydrogenated oil and sugar. The fats also contain a lot of anti-oxidants, so that ambient oxygen that can affect the dormant cells is absorbed by buffer chemicals.
The sugars and oils in the cell cytoplasm (the inside of the cell) become hydrogenated, and change into margarine and then become solidified fat and solidified sugar. Then the consistency of the cell at that stage becomes glassy because it's so solid, which is what you can see if you try to crack a peanut or a lentil, it has a glassy surface. The cell fats can rapidly become liquid again if they absorb water and change their chemistry.
references and images
It's not very different from microbe dormancy, so it's like an ancient biological trick that cells have been doing for billions of years.
The cotyledon is the future baby leaves of the seedling, the radicle is the root and the plumule is the leaf shoots, they are all made of cells that are in a solidified dehydrated form made of fats and sugars and special chemicals that resist ambient water and oxygenation in a controlled way.


Can I control my dreams? Is it possible to completely realize that I am only dreaming and to completely manage my dream?

Thank you.

According to Psychoanalysis101.org, it is quite rare to be able to control dreams, though apparently it can happen 9according to the article.  Lucid dreaming is the term to describe when the person is aware that they are dreaming, further research and scepticism of lucid dreaming are outlined in this section of the article.


Are multi-chain proteins synthesized as one biological unit? Are multi-chain proteins (especially homo/hetero-dimers) synthesized together as one overall unit or are they separate monomers which bind together at some point after synthesis, and are there any relevant factors to know about this process?

Are multi-chain proteins synthesized as one biological unit?

Sometimes yes but mostly not.

Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See the figure below).

In other cases the chains are synthesized as different polypeptides which (with or without processing) subsequently associate with each other. In case of homo-multimeric proteins, the polypeptides are made by the same mRNA.


H3K36me3 role in RNA polymerase II elongation I found a paper describing the association of RNA polymerase II with the histone methyltransferase Set2 that methylates H3K36.

At the end they say:

  While our results strongly implicate K36 methylation as having a direct role in RNAPII elongation, the precise role is currently unclear. We propose three possibilities: (i) K36 methylation generates a chromatin structure that is more permissive for RNAPII passage. In this scenario, the loss of Set2/K36 methylation would result in a chromatin structure that is more difficult for RNAPII to pass, which might appear as an increase in RNAPII occupancy along the gene through increased pausing. (ii) K36 methylation generates chromatin structure that is less permissive for RNAPII passage. In this case, K36 methylation acts as a negative regulator of RNAPII elongation, and the loss of this “mark” permits increased RNAPII passage.

I am a bit confused about the (ii) point. If the loss of this mark permits increased RNAPII passage we would not see the H3K36me3 pattern in the active genes. Why is then H3K36me3 said to mark active genes?

We have a more recent study, Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin and they seem to suggest that in accordance with your '05 paper, H3K36me3 in part contributes to the formation of tightly packed, inaccessible chromatin. You'll see there's a lot of crosstalk, but you would also think that transcription in heterochromatin might be poor.

Looking at yeast studies, though, it would seem that RNA Pol II is capable of transcribing through heterochromatin anyways so long as specific cofactors are present (Acetylation of H3 K56 Is Required for RNA Polymerase II Transcript Elongation through Heterochromatin in Yeast)


Could an "overactive" brain increase the chances of Alzheimer's Disease? From  Raichle ME. 2010. Two views of brain function. Trends in cognitive sciences 14: 180–90:

  Alzheimer’s disease (AD) is the most common cause of progressive
  cognitive decline and dementia in adults. While the amyloid cascade
  hypothesis of AD posits an initiating role for the β-amyloid (Aβ)
  protein, there is limited understanding of why Aβ is deposited. A
  growing body of evidence based on in vitro, animal studies and human
  imaging work suggests that synaptic activity increases Aβ, which is
  deposited preferentially in multimodal brain regions that show
  continuous levels of heightened activation and plasticity across the
  lifespan. Imaging studies of people with genetic predispositions to AD
  are consistent with these findings, suggesting a mechanism whereby
  neural efficiency or cognitive reserve may diminish Aβ deposition. The
  aggregated findings unify observations from cellular and molecular
  studies with human cognitive neuroscience to reveal potential
  mechanisms of AD development.

I think the article that quoted(1) is different to what the link shows now(2). However, both the article quoted and the one in the link are relevant to the question.
Alzheimer's Disease : In a nutshell, AD is the most common form of dementia. Although the exact cause is still under investigation, several genes have been implicated in the development of AD. One of the things you see in the brain with disease progression is beta amyloid plaque deposition which disrupts brain activity.
Brain Activity : While the brain consumes around 20% of our body's energy at a baseline, an increase in brain activity only increases this consumption by around 5%. Hans Berger, the first to record an EEG stated that "mental work, as I explained elsewhere, adds only a small increment to the cortical work which is going on continuously and not only in the waking state".(2)
However, there are a few 'intrinsic' networks or regions that perform functions such as "information processing for interpreting, responding to and predicting environmental demands". One of the areas active in this state of the brain is referred to as the 'default mode network' (DMN). It's thought that DMN is the main target of the amyloid plaques responsible for Alzheimer's Disease.(2)
However, there are other multimodal regions of the brain that perform processing of various types of information. It's now suggested that "regions vulnerable to Ab deposition do not simply involve the DMN, but rather comprise multimodal brain regions that are highly interconnected, plastic, and capable of rapid ATP generation"(1).
So it's a variation of activity in these particular areas - not all - that are implicated with Alzheimer's Disease. When you are performing a task, activity in these areas diminish.
Why keep the brain intentionally active : The reason for the hypothesis that actively engaging in challenging activity may reduce the risk of AD is that individuals with a high cognitive reserve have been shown to cope with the pathological changes such as beta amyloid deposition better. Cognitive reserve has been linked to a bunch of factors including "education, occupation, socioeconomic status, social networks and lifelong participation in cognitive and physical activity" and reflects "lifelong patterns of behaviors, endogenous factors (including genetics) and exposure to environmental factors"(1).
Moreover, it's suggested that perhaps higher cognitive reserve increases neuronal efficiency which has been shown to reduce plaque deposition.(1).
So InquilineKea's question and jp89's answer aren't really contradictory.

August, et al. Lifespan brain activity, β-amyloid, and Alzheimer's disease.
Trends in Cognitive Sciences. 2011. 15(11):520-526.

Raiche. Two views of the brain.
Trends in Cognitive Sciences. 2010. 14(4):180-190.

Hafkemeijer, et al. Imaging the default mode network in aging and dementia.
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2012. 1822(3):431-441.

Harrison's Principles of Internal Medicine. 16th Ed. McGraw Hill.


Computer Virus that infects DNA? I have watched a talk by Mikko Hypponen (CEO of the security company F-Secure) called Silicon Plague. There, roughly at minute 51 of the talk, he mentions a computer code that is supposed to be able to infect DNA.

I was googling and found the corresponding article posted ~2.5 years, and some c++ codes. Let me cite:

 The computer code, written in C++, hosts the DNA sequence of M.mycoides
 JCVI-syn1.0. At runtime it acts as follows:

 1) Preparing the DNA sequence of M.mycoides JCVI-syn1.0 in the memory,
    (with slightly modified watermarks).
 2) Encoding own file-content in base32. The base32 code is then encoded in
    JCVI's DNA-encoded alphabet.
 3) This representation of its digital form is then copied to a
    watermark of the bacteria's genome in memory. With this, a fully
    functional bacterial DNA sequence including the digital code is
    generated.
 4) Next, it searches for FASTA-files on the computer, which are text-based
    representations of DNA sequences, commonly used by many DNA sequence
    libraries.
 5) For each FASTA-file, it replaces the original DNA with the bacterial
    DNA containing the digital form of the computer code.

 The code has a classical self-replication mechanism as well, to eventually
 end up on a computer in a microbiology-laboratory with the ability of
 creating DNA out of digital genomes (such as laboratories by the JCVI).

As far as I understand, the program tries to go into biology-lab computers with genome files, and modify the content with some content of itself. This sounds scary. Unfortunately, I'm not at the level yet where I would understand whether that could work (undergraduate student), so my question is: Does that idea work? Could there really be a computer virus that infects DNA?

As I understand from your post, the computer virus you are talking about is modifying database (FASTA files) in genetics. That would have a pretty bad impact on research in genetics and medicine.

If one uses such a database to synthesize/edit sequences and then introduce this DNA into a living organism, then yes the computer virus would have affected a living organism. If the sequence the computer virus has introduced is able to be transcribed into mRNA and go on infecting other cells, and eventually spread, then I guess one could say that the computer virus would have become an actual virus.

However, two things are to be considered. First, I very much doubt such a thing could go unnoticed. Second, anyone could have fun and create novel sequences. The only thing the virus does is corrupting files in a computer. The eventual existence of a man-made virus has no specific relationship with the computer virus and doing too much analogy here would stand little meaning.


PGC-1β Sod2 limiters/blockers I'd like to block a percentage of PGC-1β or Sod2 expression. According to the following paper's figure beta-blockers inhibit some expression of PGC-1α. Are there any medicines/chemicals which safely and temporarily block 50%-60% expression of PGC-1β or Sod2 in fully developed mice or humans?
Thank you

http://jap.physiology.org/content/107/1/8.full

Fig. 1.
Interactions of β-blockers and mitochondrial biogenesis. Aerobic exercise activates β2-adrenergic receptors (β-AR) on skeletal muscle and induces peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) transcription, a regulator of mitochondrial biogenesis. Selective and nonselective β-blockers can blunt β2-AR signaling, which restricts the expected PGC-1α response following exercise and can impair adaptations to mitochondria and aerobic capacity. V̇O2max, maximum oxygen consumption.

Dexamethasone can be used to regulate PGC-1β
http://www.ncbi.nlm.nih.gov/pubmed/20647557


In animals, birds, reptiles and fish, is a male sometimes unnecessary for a female to have/extend a male Apparently in the human (animal realm) there are females that are female in body but their DNA is (XY) male, apparently 7500 in U.S., but apparently not able to have children ( http://abcnews.go.com/Health/MedicalMysteries/story?id=5465752&page=1)

I understand species like female hammerhead sharks can make clones with no male necessary for their female offspring (clones).  However, can a female make/extend a male, without receiving male fertilization?

If you also happen to know about the insect or plant kingdom please comment there as well.

Rephrasing your question

The question is worded in a funny way. If I am not mistaken your question is

  Are there other means of reproduction than cloning that do not require mating with another individual? In particular, I am interested in such mean of reproduction that would allow an individual to create an offspring of another sex.

I will assume this is your question. I don't fully understand the point of the first paragraph though if this is your question.

Answer

Means of reproduction are much more diverse than we tend to think. So diverse that it is sometimes hard to really class each reproduction in non-arbitrary bucket.

Yes that exist! There are several modes of reproduction that may be of interest to you, the main one be selfing. Selfing is when an individual fertilizes itself. Now, by definition, such individuals need to be hermaphrodites, however it is not impossible that there are individuals that look males, others that look females and yet they (typically the females but not only) are able to self every so often.

Just to give a funny example to show how diverse system of reproduction might be. In social ants, the queen can either let the sperm of a male fertilize her eggs and produce a female worker (or a future queen depending on whether the larvae receive royal jelly) or chose to undergo normal meiosis but the gamete from the mother will directly develop into an individual without fertilization and make a male. This is not cloning because 1) only half of the genome is being transmitted and 2) recombination occur.

Related

What DNA does a self-fertile plant's seedling have?
Do males of all sexual species have Y chromosomes?


Are brassica oleracea cultivars the same species? I used to think Brassica oleracea cultivars (e.g., kale, cabbage) were different species originating from the same species Brassica oleracea.
But it seems I were wrong, right?

If so can we breed two different cultivars with each other, e.g., cabbage + cauliflower?

Cultivars are, per definition, the same species of plants. Animal breeds are the same species too, think of the bewildering phenotypical variety of dogs for example; they are still the same species, i.e., Canis lupus.

To your question - Yes, cabbage, broccoli, cauliflower, and Brussels sprouts are the same species.

Hybrids of these plants are called cultivars; broccoli and cauliflower yields broccoflower for example. However, I wasn't able to find evidence of a hybrid between cabbage and cauliflower - a cabbaflower?


Why does our hair turn white before we get old? White hairs are considered a sign of old age, but they often occur in young boys. I want to ask why my hair is turning white? And why black hair turns white?

Human hair color depends mostly on two pigments: eumelanin and pheomelanin. Eumelanin has brown and black variants, whereas pheomelanin is reddish/orange. Cells at the base of hair follicles produce those pigments and white hair is simply lack of those pigments. There may be many reasons why your hair is turning white at a young age:

melanocyte stem cell damage at the base of the follicles
vitamin B12 deficiency
problems with the thyroid
deficiency of catalase as in vitiligo (hydrogen peroxide would then accumulate and impair pigment production)

But most of the cases are purely genetic and you should not be worried if you are certain your B12 levels and thyroid are OK. Here's an article on that topic: https://www.ncbi.nlm.nih.gov/pubmed/23974581

There's also quite a bit of information on white hair on Wikipedia: https://en.wikipedia.org/wiki/Human_hair_color#cite_note-18
(sections Grey and white hair and Aging and achromotrichia)

Cheers!


Can a young voice have physical causes? I have noticed that some older adults (40+ range) can have voices that sound much younger than their actual age (i.e. an adult sounds like an adolescent).

My question is: could any physical aspects play a part? For instance the size of the throat, the tongue or something else? I am assuming that there are no external factors that are influencing this (smoking, exposure to chemicals, physical trauma, etc).

In general, a grown up man will have a voice with a lower pitch than when he was an adolescent (Cleveland Clinic). The pitch height basically depends on the length of the vocal cords. According to Wikipedia:

  Adult male voices are usually lower-pitched and have larger folds. The
  male vocal folds...are between 17 mm and 25 mm in length. The female
  vocal folds are between 12.5 mm and 17.5 mm in length.

So, the shorter the cords, the higher the pitch. There are other anatomical structures in the throat, mouth and nose that may contribute to more adolescent-like voice. To know what exactly is the cause in a particular man, an examination by an ear, nose and throat (ENT) specialist would be probably required. Additionally, a voice specialist could have a good insight even without physical examination.

There can be reasons associated with self-image that make one to consciously or subconsciously insist in speaking with a voice unusual for his age. Sometimes you can see this in singing competitions, when a young man introduces himself with a child-like voice but then sings as a grown-up man.


Which texts are good for beginners to understand evolution on the genetic scope? Are there good texts to study the evolution, how it works, and how mutations and changes lead to evolution of the organism ?

And how does the information increase through the long time using mutations and other mechanisms?

Can you recommend specific texts?

Books on my shelf right now (I'm an evolutionary genetics grad student)...

Entry level:

Evolution - Mark Ridley (not Matt Ridley)

A primer of ecological genetics - Connor & Hartl

Intermediate:

Elements of evolutionary genetics -  Charlesworth & Charlesworth

Advanced:

Principles of Population genetics - Hartl & Clark

Introduction to quantitative genetics - Falconer & Mackay

Further basic/popular-science books include R Dawkins' Selfish Gene/The Extended Phenotype/The Greatest Show on Earth and of course The Origin of Species by Darwin


What is the name of this plant with mango type leaves? Location: South India

Leaves: Mango Type

Indoor/Outdoor/Wild: Indoor

Month: May

This looks very much like a plant in the Ericaceae family, and specifically it looks to be some species of rhododendron.

Shrubby looking tree/shrub
Spirally arranged stiff (appears evergreen) leaves
Strong midrib on leaf
Large flower

With over 1000 species worldwide and more than 120 species known to occur in India, the picture likely doesn't have enough detail for someone without specific knowledge of Indian plant species to be able to ID to species. Even an expert might need the following details:

Exact leaf measurements, specific habitat details (elevation, distance to water, etc.) and closeups of leaf undersides, stem axils, bark and (opened) flower. A zoomed out picture showing the whole shrub/tree would also likely be helpful in IDing to species.

I would recommend reading Mao (2010) The genus Rhododendron in north-east India.

List of species and locations etc.

 Disclaimer: I am not very familiar with Indian flora, so I could be unaware of genera/species that might be a better fit. Please try using a flora with dichotomous key to ID.


Conservation Genetics - Book recommendations Can you please give me some advice for a book in (evolutionary) conservation genetics that offers an in-depth review of the mathematical formulations used in this field.

I read the book Evolutionary Conservation Biology (Ferrière and Dieckmann, 2009) and I really liked it. I'm seeking for another book of the same kind that goes further on the part A (Theory of Extinction) and especially on the concern of the importance of population structure and the genetic load. I am also interested in landscape genetics.

This book "A primer of conservation genetics" would suit quite well I think. In particular chapter five deals with "Genetics and Extinction" and is preceded by a lot of population genetics based theory. A beginner might also combine it with "A primer of ecological genetics" (Hartl & Conner) but you seem to have enough Pop gen knowledge to not need it!

The landscape genetics is perhaps a bit lacking from this book though. Maybe a better and more comprehensive solution, but slightly more advanced, is this book which does feature some aspects of landscape genetics in chapter 15 along with good population genetics type coverage of extinction.


Producing a genetically modified animal with cell walls I'm curious if there has been any genetic experiments transferring cell wall producing genes into the genome of a animal model organism such as the fruit fly (Drosophila melanogaster) or a larger animal such as a mouse (Mus musculus).

If there hasn't what do you think would happen, if anything at all?

Thanks!

Mammalian cells have a semi permeable membrane not a true cell wall like a plant cell. I could imagine that if the semi permeable membrane were replaced with a plant like cell wall then osmosis and other biochemical processes necessary to the organisms growth and survival could not occur correctly.


Why is thrombin time (TT) normal range longer than prothrombin time (PT)? Reference range for the TT is longer than that of the PT.

This is a great question.

I'm going to hypothesize here because I haven't had a chance to test my theory and I'm afraid that by the time I get around to it, I may forget about this question.

The real question is, what is the variable that makes the thrombin time act differently than what you would assume? I’d wager the answer is temperature.

Protimes are performed at 37 degrees in order to simulate the in vivo environment, but also because most coagulation factors aren't active at room temp, or at least they are very slow-acting at room temp. Heating the environment speeds this process up so the test doesn't take all day.

Now, we know if you take a tube of warm normal plasma and add calcium and thrombin to it, it clots right away, right? But this is a problem because the thrombin time is a quantitative assay and we need it to be sensitive, especially for those super old-school clinicians who use it to monitor heparin instead of a more modern test like the APTT or Xa inhibition. We need to be able to tell the difference between a patient that’s gotten a bolus of heparin and a direct thrombin inhibitor. So, if you remove the heat, you slow down the conversion of fibrinogen to fibrin, and in the process you stretch the calibration curve, effectively increasing the sensitivity of the test. But this also has the effect of slowing down the conversion to where it takes 14–18 seconds rather than one or two.

If you change your test setup to have the thrombin reagent heated, my hunch is that your analyzer will give an error because the sample will have clotted by the time the analyzer reaches minimum threshold time. Or better yet, try this experiment on a fibrometer. I don’t have access to one so I can’t try it out as I’d like to.

I’d be interested in discussing this with any other experts out there, especially those that have played around in the coag lab. I may have occasion to test this out in the coming weeks; I’ll try to do it and update my answer with my results.


How do changes in temperature affect body weight in humans? What would be effect on weight of individuals if we bring a fully adapted (to cold climate ) human individual and a fully adapted to very hot climate individual to a moderate climate region?

You would see moderate weight gain in both subjects.

Since humans thermoregulate and aren't terribly "adapted" to any extreme for either very hot or very cold climates, anything outside of short range of temperatures will cause us to either sweat or shiver.

Sweating or shivering will cost kcals ("Calories", "Joules"), and the extra energy expenditure will keep the subjects' weights lower than they would otherwise be.

Once the subjects enter an environment where they no longer need to sweat, shiver, or basically maintain a wide gap between the outside temperature and their body temperatures (which is the real driver here - the difference between the two), they will no longer expend as much energy maintaining human body temperature.

How much energy are they saving? Not much. I wish I could find the article again, but you're talking an extra 50kcal or so an hour saved - or a few pounds until the energy required to maintain the extra weight reaches equilibrium with the energy saved.

There are a few assumptions built into the above, which sees the question as more of a physics-oriented hypothetical than real-world example. In reality you have some large complications - getting anything done in cold temperatures is going to require a much larger energy expenditure, as you're usually carrying 30-50lbs of gear to not freeze to death, for example. A person used to wearing a dozen kilograms of animal furs during their weekly routine would gain a lot more weight than hypothesized above if they suddenly entered a mild climate with similar food intake, but without the constant load on their muscles.


Why do we age? or Do we have a theory of senescence? There seem to be a number of ideas about why we age. Hypotheses include the gradual accumulation of cell metabolic products affecting organism function and the reduction of telomere length during cell division.
My hand-wavey idea would be "wear and tear".

Are we anywhere near a consensus theory of senescence?

The 'wear and tear' argument is most likely true but it is also interesting to reason about ageing as inevitable from the evolutionary point of view.

To set up the argument, we need two things:
First, each individual has got a 'reproductive potential' which is realised throughout life. This means a deleterious mutation which has an effect in early life, will affect reproductive value more than a mutation which manifests itself in later life, after the individual has already had offspring. Thus selection will act strongly on genes which are expressed in early life than on those which are expressed later. For that reason, there's no strong selection against diseases such as diabetes or cancer. This argument can be applied not only to occurrence of disease but also to decay of ordinary functions of the body.

Secondly, cells in the body are constantly renewed and defects such as telomeric breaks are repaired. Mutations in the soma are taken care of by the immune system and can be in principle avoided. The fact that they tend to accumulate in later life can be explained by the first point: selection is weaker to oppose telomeric breaks and mutations in later life.

I was trying to be brief here, but there are more sides to the argument (e.g. Williams' antagonistic pleiotropy). Modular Evolution (Vinicius, CUP 2010) provides a good overview of the evolutionary aspect of theory of senescence (and many other interesting evolutionary arguments).


brain activity responsible for imagination Which part of brain is responsible for advance or unseen imagination
For example:ones brain can make a situation in mind which is impossible to happen ...which part of brain is hyper active?

Edit: Added two studies to better show how different types of imagination tasks use different parts of the brain.

Imagination is a complex process that can use many regions of the brain. Insights into how our brain imagines have been gained through a number of studies. There is not an "imagination" area of the brain. Instead, different areas, and often several at a time, may be used depending on the type of imagination. I'll highlight a few examples here.

Ogino et al. (2007) asked 10 male participants to imagine feeling pain while watching pictures suggesting either pain or fear. Both pain and fear tended to activate an area of the brain called the anterior cingulate cortex (ACC), which helps to regulate blood pressure and heart rate among other basic nervous functions. Imagining pain activated not only the ACC but also another four areas of the brain were especially active. In comparison, fear tended to activate the ACC and the hypothalamus, which regulates the "flight or fight" response. Both sides of the brain were activated at the same time.

Boly et al. (2007) studied 12 brain-injured patients who where not capable of communicating. They were not in a coma. They were asked to imaging tasks involving spatial skills or motor skills. The two most common areas of the brain that were activated were the supplementary motor area, which helps to control movement, and the dorsal premotor cortex, which may contribute to movement and spatial coordination. (Wikipedia information so interpret cautiously.)

A detailed study was recently provided in a study by Schlegel et al. 2013. (An alternate version is here; both versions are open access.) Summaries of their work written for the general public can be found in Popular Science and Science Daily.

The scientists identified what they called the "mental workspace" which is not a particular region of the brain but instead is several different regions of the brain (from both sides of the brain) interacting together.

The researchers asked the study participants (9 males and 6 females) to select from a set of abstract shapes to assemble a particular target shape.  The target shape (the one the participants had to create) was a 2x2 grid. Each abstract shape that to be selected would fit one of the grids. So, four abstract shapes had to be selected to assemble the target shape. They also tested the reverse: Given a target shape, could the participants identify the four abstract shapes needed to make the target shape.

During the task, the researchers used functional magnetic resonance imaging (fMRI) to monitor brain activity. After the analysis of the fMRI results, they identified 11 distinct regions of the brain were active during the task.  In nearly all cases, the regions were active in both sides of the brain. However, I noticed that one region, the medial frontal cortex, only appeared to be active in the left side of the brain. This region was identified as one important component of the mental workspace for certain tasks.

The researchers concluded that four of the 11 regions were most important. You can see the regions of the brain in any four of the links above (and the abstract shapes in all but the Science Daily article). They argue that the interaction among the four major and seven minor regions contribute to our process of imagination.

Each of the three studies I highlighted requires the participants to perform different types of imgination tasks. Each type of task showed that different regions of the brain were used. Each type of task also required that several areas of the brain were used simultaneously during the imagination process. Together, these results show that no single part of the brain is used for imagination. Instead, many different areas are used, depending on what the person is imagining.

Citations

Boly, M. et al. 2007. When thoughts become action: An fMRI paradigm to study volitional brain activity in non-communicative brain injured patients. NeuroImage 36: 979-992.

Ogino, Y. et al. 207. Inner experience of pain: Imagination of pain while viewing images showing painful events forms subjective pain representation in human brain. Cerebral Cortex 17: 1139-1146.

Schlegel et al. 2013.  Network structure and dynamics of the mental workspace.  Proceedings of the National Academy of Sciences USA 110: 16277-16282.


Do animals exist with an uneven total number of digits? I recently finished reading Contact by Carl Sagan. In the book they talk about a pattern in the transcendental number like pi or e, and comment that it is found in base 10 or however many fingers the race has to count with.

When in the end they find a pattern in pi it is in base 11, which I found a strange choice since I can't think of an animal that has an uneven total number of fingers, and I would think that most evolution would result in a somewhat symmetrical design.

Do any animal exist that has an uneven total number of fingers or equal lim, excluding polydactyly and oligodactyly?

Coscinasterias calamaria, the Eleven-Armed Sea Star! (Although I doubt it has much to do with pi)

Image from Wikimedia Commons


DNA methylation and the validity of the definition of epigenetics I am currently studying a textbook that presents the following definition of epigenetics:

  Epigenetics is defined as heritable changes in gene expression without changes in the DNA sequence.

The authors then claim the following:

  DNA methylation is a stable and inheritable epigenetic mark. This genetically programmed modification is almost exclusively found on the 5' position of the pyrimidine ring of cytosines (5mC) adjacent to a guanine.

Given these two excerpts, it seems somewhat contradictory to define epigenetics as heritable changes in gene expression without changes in the DNA sequence. After all, the DNA sequence is comprised of nucleotides, and it is these nucleotides that are modified during methylation (for instance, the addition of the methyl group on the 5' position of the pyrimidine ring of cytosines adjacent to a guanine), right? So, is it not technically true that the DNA sequence is changed? Or is what they're saying that, although the nucleotide is changed (such as in DNA methylation), the base pairs are unchanged (I'm unsure if this is true, just hypothesising)?

I would greatly appreciate it if people would please take the time to clarify this.

A methylated nucleotide is the same nucleotide, for the purposes of base-pairing events. The methylated base will be paired with its Watson-Crick opposite after replication, for instance (and methylation will even persist after replication).


Is blood pressure in the aorta and brachial artery the same or different? Does the blood pressure at the root of aorta equal the blood pressure in the brachial artery?

I've heard it does, but it doesn't quite seem to make sense as I'd think the blood pressure would be lowered the further it travels?

Blood pressure is mostly dependent on the height from the heart. Therefore, if it is below the heart it will have higher blood pressure and if it is above the heart it will have lower blood pressure.

Here you are asking from two parts of body that have same height as the heart,

so they will have approximately the same blood pressure.

For more see:
Netter's Anatomy Page 136 and Campbell Biology


EGFR, sialylation, and cancer progression EGFR (epidermal growth factor receptor) has been intensively studied in cancer and treatments have been developed to inhibit EGFR signaling.  Sialylation of EGFR is known to block dimerization  and down regulate signaling.  I just read this paper:

Liu et al. 2011. Sialylation and fucosylation of epidermal growth factor receptor suppress its dimerization and activation in lung cancer cells. PNAS 108: 11332–11337. (basically just read conclusion if you don't have time).

What I don't understand is that the authors seem to say that increasing sialylation might be a good thing to prevent cancer progression since it inhibits EGFR dimerization.  However, wouldn't this go against almost 50 or 60 years of research that suggest that increased levels of sialic acid are one of the well known hallmarks of cancer that aid in its progression and metastasis?  What could explain this apparent discrepancy?

Wikipedia claims (without reference) that

  Metastatic cancer cells often express a high density of sialic
  acid-rich glycoproteins. This overexpression of sialic acid on
  surfaces creates a negative charge on cell membranes. This creates
  repulsion between cells (cell opposition)[5] and helps these
  late-stage cancer cells enter the blood stream.

so I assume this is a summary of the "50 or 60 years of cancer research" that you mentioned. I don't doubt you, I've just never read up on this particular aspect of cancer. Be that as it may, there is a difference between a cell's expressing high levels of sialoglycoproteins overall, and inducing high sialylation of one protein in particular, in this case EGFR.

As you may be aware, EGFR dimerization induced by multiple methods, including EGF binding, overexpression, mutation, chemical or antibody crosslinking, etc. activates tyrosine kinase domains in its intracellular region to auto-phosphorylate specific Tyr residues in its tail, which then recruit adapter and scaffolding proteins which support downstream signal transduction.

The paper you read shows how increasing sialylation of EGFR reduces its trans-affinity for itself and inhibits dimerization, and hence the downstream signaling cascade. This is a good thing in certain types of cancer which are driven by aberrant EGFR signaling, whether through overexpression of EGF and/or EGFR, mutations in the kinase domains, mutations in the dimerization domains, or otherwise.

This paper is also a great example of an apparent bad thing turning out to be good, when properly targeted and controlled. Excess sialylation of a cell may be bad, but specific over-sialylation of EGFR could turn out to be very useful, if we can learn how to modulate and target it. Another common example of this phenomenon is radiation therapy. Normally, high levels of radiation are bad for your body, and can actually cause cancer, among a range of other illnesses. But, there are many different ways of specifically targeting radiation to a tumor to kill it while sparing (to varying degrees) the surrounding tissue and the rest of the body.


What material is permeable for plant roots, but "impermeable" for fungi & bacteria? I'm designing an experiment where the roots of the plant will grow in a sterile environment while the shoot will grow in a non-sterile grow room. For this reason the environments of the shoot and the root should have some form of physical separation.
Is there any material that allows roots to grow through it but will stop fungi and bacteria?

I might have found a solution! Kuijken et al. (2015) first germinate seeds in a sterile eppendorf filled with agar and nutrients. They then cut off the bottom of the eppendorf and stick it through the lid of a sterile plastic jar and pad it with sterile cotton. So I guess they are using the agar as a material that is permeable to the roots and "impermeable" to bacteria and fungi.
Kuijken, R. C., Snel, J. F., Heddes, M. M., Bouwmeester, H. J., & Marcelis, L. F. (2015). The importance of a sterile rhizosphere when phenotyping for root exudation. Plant and Soil, 387(1-2), 131-142.


Different kind of M13 primer I m looking for universal primers M13. I found different version. For instance :

M13 (-21) Forward TGTAAAACGACGGCCAGT
M13 (-40) GTTTTCCCAGTCACGAC

What's the meaning of (-21) and (-40 )

This dates back to the 1980's when these M13 primers were first cloned.

Heidecker G, Messing J, Gronenborn B. 1980. A versatile primer for DNA sequencing in the M13mp2 cloning system. Gene 10(1):69-73.

In this paper, they discuss the construction of a primer for sequencing of the M13mp2 phage vector. An EcoRI/AluI digest releases a 92 bp fragment from a portion of the lac operon. This fragment contains what are now called the M13 forward -21 and -40 primers. I do not know who first named these primers but, counting from the centre of the EcoRI palindrome, I think it's clear where these names came from:


What's the difference between tumor cells and host cells? When you talk about cancer, is there a difference between tumor cells and host cells ? What is the role of immune cells ? in a nutshell ?

This question is a bit broad but I'll try to narrow it to be specific in the terms of "tumor" vs "normal" cells.

 (Source)

Basically a tumor contains cells which have a part of the cell cycle regulation broken (very broad way of saying this). There are literally thousands of things that can cause this. Broad groups of things that cause this could be knockdown of a protein (of which many are involved in replication), mutation of a gene (most likely), etc etc. Basically any type of DNA damage can lead to cancer.

 (Source)

So what creates damaged DNA? Well here is a small list:

UV light (Can cause DSBs)
Carcinogenic chemicals (eg: Ethidium Bromide)
Replication proteins getting stuck or loosing function

 (Source)

Well how does that compare to a "normal" cell. Normal cells have a proper cell cycle with all the "checkpoints" working normally to essentially throw away any cells that detract from the cycle in any way. They also have mechanisms to fix DNA that has been damaged before it gets replicated. If none of that works they have mechanisms to basically commit suicide so they never replicated. When all of that fails you get cancer.

In summary, a cell becomes cancerous when the following things happen:

DNA is damaged by one of the above methods
The DNA damage repair mechanisms fail to fix the damage, or cause further problems by attempting to repair (NHEJ is a repair mechanism for DSBs that is implicated in causing cancer)
The DNA damage causes abnormalities in the cell cycle (replication)
The body fails to recognize the particular cell with abnormalities in order to kill it
The abnormal cell is allowed to replicate without hindrance from the body's checkpoint mechanism
You now have cancer

As for the role of immune cells that question is too broad as there are many different types of immune cells. Their "general" role is to clean the body of foreign agents but there are differences even in that role. There are many different types of them.

 (Source)

While I love teaching this stuff I do feel like you could find A LOT of this by doing google searches. Please try that next time.

EDIT: Updated with plenty of sources.


What does Δcys mean after a gene name? I am reading a paper and I have come across the following statement:

"Plasmids encoding full-length NCAM140 and NCAM140Δcys, intracellular
domain of NCAM140, and the NCAM140ID729–750 fragment were as
described".

I know that NCAM140 is an isoform of the NCAM protein with a molecular weight of 140kDa. However, I am not sure what Δcys means in NCAM140Δcys. Any insights are appreciated.

When describing mutations, $\Delta$ usually stands for deleted sequences. In this case it means the exchange of 4 cysteine residues in the NCAM protein by serines to disable palmitoylation and the association of the protein to lipid rafts. If you search for this specific mutation, you will find the paper from Niethammer et al., 2003, which describes the mutation. Figure 2a (below) shows a schematic view of the locus and is described as following in the caption:

Mutation of NCAM140 palmitoylation sites abolishes NCAM140 raft association.
(A) Schematic diagram of the structure of NCAM140 and
NCAM140Δ. The plasma membrane is indicated by the pair of vertical
lines. The semicircles represent the five Ig-like domains. The two
fibronectin type III–like domains are shown as black boxes. The
expanded segment shows the NH2-terminal sequence of the cytoplasmic
domain and the four cysteines that were mutated to serines in the
NCAM140Δ construct to remove all sites for palmitoylation.


How can Valonia ventricosa cells get so big? Valonia ventricosa are single-celled algae that range between one and few centimetres. In rare cases, they can reach sizes exceeding 5cm. They range from grass-green to dark green, and some are even a blackish colour.

Weirdly, a lot of the literature covering these organisms seems to be pre-1950. This X-ray crystallography project in 1937 identified key structures in the cell wall of V. ventricosa:

It is found to consist of layers in which the cellulose chains in any
one layer are inclined to those in the preceding and subsequent layers
at an angle which is on the average rather less than a right angle.
The two sets of striations on the layers of the wall correspond closely to the
meridian and spiral directions of cellulose chains, while the
extinction directions, being defined both by the directions and by the
relative proportions of the two sets of cellulose chains, lie in
variable positions between. The development of the rhizoids has been
investigated and found to be associated with regions of the wall
adjacent to the poles of the spiral.

Although the authors hesitate to speculate on their function, has any progress in the field suggested the fibres identified in this 1948 Nature paper be involved in sustaining such a massive cell (Figure below)?

So it seems like the cell wall structure has been categorised long ago. But what allows these single-celled organisms to get so big? Is it the plant-like cell wall, or something else? I was under the impression that cells would burst or collapse well before reaching this size.

Ventricaria ventricosa (previously called Valonia ventricosa) is not exactly a single cell. It has a coenocytic structure with multiple nuclei and chloroplasts. As Jasand Pruski correctly guessed the organism possesses a large central vacuole which is multilobular in structure (lobules radiating from a central spheroid region).

The entire cell contains several "cytoplasmic domains" with each domain having a nucleus and a few chloroplasts (See the figure below). Cytoplasmic domains are interconnected by cytoplasmic "bridges" that are supported by microtubules (like in axons). The peripheral cytoplasm (whose membrane is overlaid by the cell wall), is only about 40nm thick.

  Fluorescent confocal micrograph of a cytoplasmic domain. From Shepherd et al. (2004) Protoplasma 223: 79–91. Here, n is nucleus c is chloroplast and v is vacuole.

So these are not huge cellular balloons that can burst easily. Nonetheless a huge structure like this is susceptible to injuries by shearing forces of water currents and by other organisms like fish which may try to feed on them. These organisms have some mechanisms other than the cytoplasmic organization that allows them to cope up with injuries:

When the outer membrane ruptures, then the cytoplasm contracts with the help of actin filaments that are attached to the former. Subsequently the membrane fuses, protoplasts form and then cell wall is regenerated. This movement is likely to be triggered by extracellular calcium.
A single cytoplasmic domain with nucleus and other essential organelles can regenerate an entire organism.
A muclilagenous layer made up of sulphated polysaccharides coats both the vacuolar and extracellular surfaces. During injury it impedes the movement of water and ions (by retaining them in the form of a gel) and therefore acts like a plug.

Other organisms like this (siphonous algae) also have similar mechanisms. Some even employ calcium carbonate to maintain rigidity.

REFERENCES:

Shepherd et al. (2004) Protoplasma 223: 79–91
Menzel (1988) Protoplasma 144: 73-91


Ribosomal Turing Machines, DNA/RNA computation I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if you could design a synthetic ribosome that acts as a Turing Machine on strings of RNA? (you could do similar things with DNA enzymes)

The immediate applications could be stuff like correcting mutations in RNA to cure genetic diseases, which is a relatively simple computation:

Check if a string is bad.
If so, fix bad letter.

Another could be "shredding" DNA/RNA of viruses:

Check if a string is a virus.
If so, shred it.

I'm not sure the status of the literature on this is, or synthetic biology's ability to create something like that. Do you think it is a good idea to pursue this idea or not?

I realize this is a soft question. Perhaps a better one would be, is this possible?

I'm no expert at this but I don't think you need a Turing machine to achieve this, at least for DNA, since in conventional sense (not including carcinogenic factors such as UV) the most probable stage in which a DNA mutation can happen is during DNA replication so DNA polymerase engages in proofread to ensure accurate DNA replication, and then the DNA can get back into being heterochromatic (eventually). This will be more difficult for RNA as they are single stranded although they do fold onto themselves.

Also there many many strands of RNA that are produced through alternative splicing, VDJ recombination and RAG imprecise rearrangements for antibody production, which can give rise to infinite possible RNA productions. So how would you know what is "good" and what is "bad" in terms of RNA and its production. Half the time we don't even know what they do and what their roles are and the only reason we call something as a "bad" or "faulty" RNA is because it is having a negative effect not because we understand the precise role of the sequence, which means a theoretical table would be useless.

So in short, a turing style protein machinery is neither possible (due to almost infinite potential number of RNA produced) nor feasible (since the number of proteins that would have to check each RNA sequence would in turn have to be almost infinite). And none of these takes into account SNPs i.e. individual variations, which can produce proteins with different sequence but identical structure/function, since obviously any lethal variations would be selected against but thats a whole different argument.


Can one die from pain? Is it possible that a human or any other creature can die from pain?

I googled and found different answers. Some articles say Yes while others say No.

I very much doubt it. You may however die from whatever's causing the pain. The reason you feel pain is so you stop doing whatever is causing the pain. Hence someone knows not to touch a hot fire because it is painful. But the pain itself is not actually the danger - it's the fire burning away skin. So pain is actually a good thing, a survival mechanism. So for something that is meant to prevent death it's hard to imagine it doing the opposite.

Perhaps if you were in SO much pain you may be unable to breath and paralysed - but even then I still think you'd go unconscious before that would happen, and you'd start breathing again, etc.

The only other thing I can imagine is having a cardiac event, and the heart stopping. Again, this would be because of stress. Other than that - you may commit suicide on account of insufferable pain, however it's a different situation.

However pain never comes on its own for no reason, just like smoke needs a fire. In this case it's the fire - not the smoke, that will kill you!

People who've ever been in a desperate or life threatening situation like a car accident, have often walked on a broken leg for example - feeling no pain. In this case the body was giving them a chance to escape what might have been a lion, etc.

In short, no - I don't think you can. However I cannot give a 100% correct answer. It would take just one example to prove that however!


Why does high-voltage mostly shock a person, and even small current kill? This may be the wrong forum to ask.

For instance several people are known to have survived a direct lightning strike; albeit the number of fatalities are probably far larger. Anyway, I found myself wondering why high-voltage may shock a person and throw them off whereas high-current even small current is, purportedly, a killer.

These statements are not true, simply speaking. Currents as little as few microampers can kill a person if, for example, applied directly next to the heart. A few seconds of 220V can kill a person even if the current is in miliamper range (Biksom, cited below, mentions 4s at 120mA). However, it is true that it is not the voltage alone that kills, that there are other factors (most importantly, the effective current, which, however, normally increases with voltage).

Look, Ohms law states that R = V / I (resistance equals to voltage divided by current). Given a constant resistance, a higher voltage produces also a higher current, full stop. Given a voltage of, say, 24 V, and the resistance of our bodies being 1000 - 4000 Ohm, the current will not exceed 6 - 24 mA. Note that in case of 220V this largest current would be less than ten times these values, so well below 1A! Yet, this is sufficient to kill an adult.

What's more, extremely high voltage can actually break the skin and effectively lower the skin resistance, which results in an even higher current (see formula above).

So where does this popular knowledge come from? Well, we know that things like electric sparks can have very high voltage, but are harmless. They are harmless not because the current is low, but because the duration and the total energy is low, since the total energy is given by power (in watts) times seconds, and power P = V * I (voltage times current).

Also, it comes from anecdotical evidence, since being shocked by thousands of Volts and survive can make you famous... precisely because it is extremely rare to get into contact with a high voltage line which can supply a steady flow of the current and survive.

Another reason became apparent in the comments: confusion between the factual current of the jolt one is getting and the nominal amps on the fuse. The former is given by the resistance and voltage; the higher the voltage, the higher the current. However, an 1A fuse is likely to blow quicker than a 10A fuse, thus cutting the line before the current penetrates our body to reach the heart and bring it into fibrillation.

It is a similar story with lightnings: duration is extremely short, but more importantly, in most of the cases the lightning did not run through the person who survived -- because if it did, they would be dead (also, see this fascinating bit). It either run over the skin, seeking the path of the lowest resistance, or through a material nearby.

Also, high frequency currents are less likely to penetrate the skin.

Literature links:

Biksom, "A review of hazards associated with exposure to low voltages"


Is the transcription starting site located before or after the promoter? It's maybe a stupid question, but I really want to know the answer.

The definition of Promoter (From Wikipedia):

  In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes

And the definition of the transcription start site (From Wikiversity):

  The transcription start site "is the location where transcription starts at the 5'-end of a gene sequence.

I also Found this image (The source):

I'm asking this question because as far as I know, the RNA Polymerase binds to the TSS, and a friend of mine told me that's it binds to the Promoter.

PS : I'm interested in bacteria.

Just in addition to David's answer, there are examples of internal promoters (those which have elements 3' of the transcription start site). As an example, internal promoter elements of tRNA genes direct binding of and transcription by eukaryotic RNAP III:

White RJ. 2011. Transcription by RNA polymerase III: more complex than we thought. Nature Rev Genet 12:459-463.

Many class I retrotransposons also contain internal promoters which allows them to be transposed along with the other elements:

LINE - internal RNAP II promoter
SINE - internal RNAP III promoter


How can a continuous RNA be transcribed in the lac operon? The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if there is a stop codon in between?

RNA Pol doesn't worry about stop codons.  Transcription termination can occur through the formation of a hairpin in the new RNA sequence, or through the action of Rho proteins.  A lot of the time prokaryotes have polycistronic mRNAs, that is, mRNAs with multiple protein coding regions.  The stop codons are detected during translation, so you will often have all three lac proteins being translated at once off of the same mRNA.

Here's a nice section on transcription termination, or look up Rho-independent or Rho-dependent transcription termination for more info.


Where happens MHCII coordination to a self-peptide, and what happens if the bond would be irreversible? MHC-II proteins are presenting antigens on the surface of cells with lysosomal activities where they eventually might get transported off by some T-cell receptor-anti-gens, as far as I understand (pls apologise and correct me if I am wrong). I would be interested in two questions regarding this specific immuno-cascade reaction.

It appears that in cases self-pepties are bound to the MHC-II proteins (say HLA-DP2) when they are at the surface already. Where do such self-peptides come from? Do they come from inside the endosomal active cell or could they also come from "outside" from where the T-cell comes?
What would happen if (for some reason)
a) the self-peptide binds "irreversibly" to the MHC-II?
b) the self peptide binds irreversibly to the MHC-II and at the same time is structurally significantly distorted (e.g. if there is something, like a heavy metal bound in-between the MHC-II and the self-peptide)?

(I apologise for the case I got some terminology wrong or some basic concepts, I am no specialist in bio-chemistry.)

It appears that in cases self-pepties are bound to the MHC-II proteins (say HLA-DP2) when they are at the surface already. Where do such self-peptides come from?

Class II MHC molecules are capable of presenting any peptide of appropriate length, regardless of where it came from. Contents in a phagolysosome will contain both self and non-self peptides.

  Do they come from inside the endosomal active cell

Some do, yes. While many proteins are degraded by the proteosome, some are actively imported into a lysosome and degraded there. This is termed chaperone-mediated autophagy. Full organelles may also be brought into the lysosome through "regular" autophagy.

  or could they also come from "outside" from where the T-cell comes?

This is the case as well. Any ingested material from the outside could contain cellular debris, protein agglutinations, or foreign organisms. Peptides from all of these sources can be presented at the cell surface.

  What would happen if (for some reason) a) the self-peptide binds "irreversibly" to the MHC-II?

According to this study, MHC II molecules are recycled, and their turnover is carefully regulated. There is no need for the bound peptide to dissociate during antigen presentation, so likely problems would occur when MHC II turnover is disrupted.

  the self peptide binds irreversibly to the MHC-II and at the same time is structurally significantly distorted (e.g. if there is something, like a heavy metal bound in-between the MHC-II and the self-peptide)?

If the MHC itself is structurally distorted, it will not be recognized by any other cells. Remember that, during T cell selection, the cells must be able to recognize the MHC itself with a low affinity. T cells which bind strongly to the MHC itself undergo death by negative selection, whereas those which do not recognize the MHC at all undergo death by neglect. As a significant structural change would result in either an excessive affinity, or no affinity, no T cells capable of recognizing the complex would be present.


Gene and Protein isoform What is the relationship between term "Gene isoform" and "Protein isoform"?

Say a gene can make 3 isoforms, will it produce only (maximum) 3 isoform protein?

The term isoform has become a little ambiguous over the years (see http://blogs.cornell.edu/collinslab/2012/05/30/protein-isoform/)... still some things are consistent:

In some genetics literature 'isoform' has been used in the place of allele when talking about the allele states at a locus for a gene
Typically a gene isoform is equivalent an alternate transcript. The gene isoforms are the set of mRNAs that can be produced by a gene.
Protein isoform commonly refers to the set of proteins produced by a gene, this can include variations produced by alternative splicing and post-translational modification. Note that in some contexts the set of products from closely related gene duplications can also be included.

Note that databases will typically have a specific definition in mind for their use of isoform in their annotation, check their documentation for details (e.g. in UniProt see What is the canonical sequence? Are all isoforms described in one entry?)


Why does DNA need to be pure for restriction enzymes to act on it? My textbook states: “In order to cut the DNA with restriction enzymes, it needs to be in pure form, free from other macromolecules. Therefore DNA isolated from other chemicals of the protoplasm like carbohydrates, lipids and proteins via techniques of DNA isolation.”
My question is, why does DNA need to be alone? Won’t restriction enzymes work if there were a DNA molecule in a sugar solution? I understand that the DNA has to be freed from cell membranes and walls for restriction enzymes reach the DNA but how does the presence of other macromolecules hinder DNA’s digestion of a restriction enzyme?

Some other macromolecules or other solutes may be present that could interfere with the affinity of the restriction enzyme. For example, there could be salts that denature or modify the conformation of the enzyme or inhibitors present that may interfere with the enzyme. Hope this helps.


Preferred Aspect Ratio for Human Eyes Our eyes are spherical, our retina is circular, but still our eyes can see more in the horizontal direction than in vertical direction. Why is it so, why is the preferred aspect ratio not square?

I found the explanation given below here (my emphasis). It may not be authoritative, but it makes sense to me.

You can determine the approximate shape of your visual field by looking straight ahead, and holding a hand out to each side and noticing where you can no longer see them. Do the same for above and below, and you'll see that your peripheral vision probably extends to about 180 degrees (or a little less) left and right, and about 100 degrees up and down. Your brow, nose, and cheeks narrow the vertical angle.
So your visual field has a ratio of about 1 to 1.8.
Interestingly, and not entirely coincidentally, ordinary films and wide-screen TVs have a ratio of 1.78 (16:9).

Another way to see this effect is to look at someone's head in profile and from directly above. In the former  case you have a clear view of their eyes, in the latter you don't. (Tested on a small sample - one 3 year old male, playing with an iPad).


Meaning of "U" in "Viral Protein U" What does U mean in Viral protein U?

  Viral protein U (Vpu) is a unique gene product of human immunodeficiency virus (HIV) type 1 (HIV-1) with two well-described functions...

So does U in this case mean unique?

Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC114397/

So does U there mean unique?

No. The name of the Viral Protein U comes from the names of the Open Read Frames (ORFs) of the Visna lentivirus, termed by Sonigo et al (1985).

According to the paper that actually named the Vpu (Strebel, Klimkait and Martin, 1988):

  In this study, we show that another small (81 codons) HIV-1 ORF, designated vpu ["U", see (2)] encodes a 16-kD protein that is expressed in vitro and in vivo. Mutagenesis of vpu in an infectious molecular clone of HIV-1 results in the synthesis of particles with altered replicative capacity.

If you look at that reference number 2, you will find a paper named Nucleotide Sequence of the Visna Lentivirus: Relationship to the AIDS Virus, from Sonigo et al. (1985).

In that paper you will find several ORFs, named F, Q, R, U3, U5 etc. Why are they named like that is another question, but it seems to me that they are just letters of the alphabet, with no meaning. Vpu was named because of U3. By the way, HIV also has a Vpr, because of the ORF R.

Sources:

Strebel, K., Klimkait, T. and Martin, M. (1988). A novel gene of HIV-1, vpu, and its 16-kilodalton product. Science, 241(4870), pp.1221-1223.
SONIGO, P., ALIZON, M., STASKUS, K., KLATZMANN, D., COLE, S., DANOS, O., RETZEL, E., TIOLLAIS, P., HAASE, A. and WAINHOBSON, S. (1985). Nucleotide sequence of the visna lentivirus: relationship to the AIDS virus. Cell, 42(1), pp.369-382.


What is the difficulty with cloning and genetic engineering in humans? I asked this question many years ago and was told by my molecular biology professor that humans were (simply) more complicated than goats.

So, I didn't get a straight answer, but supposing he told the truth, what's the problem? Or are people really more complex than goats, from an engineering or genetic standpoint?

The question you are asking is an ethical problem rather than a biological one. This particular nature article highlights the problem I am speaking about.
In brief, children afflicted with SCID were subjected to what at the time was termed as a pioneering retroviral treatment. The idea being you replace the defective gene with the real one, in case of the quoted study, of 11 patients, 9 were cured and one of these babies developed leukemia due to the treatment. This was one of the first trials and it showed how these treatments can go awry.

Fast forward to today, last year you may have heard, something called the three parent babies garnered a lot of attention. This is basically mitochondrial donation, where a third-party provides mitochondria for IVFs for reasons where parents opting for IVFs may not be able to undergo successful IVFs due to mitochondrial mutations. This posed and still poses a serious ethical question, because what you are doing is mixing heritable DNA between lineages, please note that most geneticists will never cross this line, i.e. editing the genome such that the offspring carries the edited genome. Almost always the modified individuals are sterile (I know of no GMO crop which is not sterile)

But not to say, we have done nothing in terms of genetic engineering.

Scientists for the same reason (A human life is more important than any animal's) are wary of editing the human genome directly, so we now we also have something called siRNA treatment is just one example. And this is a list of siRNA based drugs which were in various stages of clinical trials in 2013. I know of a few which entered trial since then.

Lastly, this is just the tip of the iceberg, there's a whole lot which could be said on this topic, but it boils down to the same ethical problems.

Just so you know, since 2001, we have a lot of newer genome editing tools, such as TALENs and CRISPR-Cas. But remember, they still have the same problem as retroviruses from 2001, the issue about off-targets.

What if your tool targets a region which it isn't supposed to target?

Will another child develop a condition due to the treatment?

To avoid such an issue, we need to understand much better how the genome works, and sadly still we don't know enough. I cannot quote the study here because I have no idea where it is published, but at a recent conference I heard a talk from a lady about how retroviral integration works. The idea being, if retroviruses don't need specific integration sites, they should integrate at the first genomic region they encounter, that is not the case. I will not go into more detail. But I hope you have some food for thought.

UPDATE ON Genetic Engineering at a preconception stage

This is a link to the Nature article on Venter's minimal cell. There also exists an artificial Yeast genome page. The point I am trying to make is, we are really at the basic stages even now.

I will outline to you the behemoth scale problem we are facing.

2002: The first human genome draft is published. All the media is rife with stories about how we are going to unlock the secret to life.

Since then, DNA methylation and histone modifications have come to the foray as regulators of genome functionality.

We knew that DNA was transcribed into RNA and translated into protein. Noncoding RNAs came to the foray and messed up everything.

We thought that DNA functionality was governed by DNA methylation and Histone modifications, come 2009, we saw the first major article on Chromatin architecture. We understood that the genome has switches called Enhancers and promoters which regulated when and for how long RNA is transcribed. But sometimes these switches were so far away, we did not know how they switched on their target genes.

The problem can be summarized as this, making an artificial bacteria is easier than a human. In humans you have multiple layers of regulation, there's the DNA, where one part is silent (heterochromatin) and one part is active (Euchromatin), DNA methylation and histone modifications affect how genes are expressed, these modifications allow opening of the DNA so that genes can be expressed, The DNA is further compartmentalised (architecture) so that switches only affect nearby genes in 3D space. Non-coding RNAs act as messenger in such areas relaying proteins to their target DNA regions. So the cell is a mess!

Not to say that goat biology is simpler, just that a goat's life is cheaper than a human's. So we wouldn't feel a thing while "euthanising" goats for the advancement of mankind.


In CRISPR bacteria, how does viral genomes get integrated into the spacers of CRISPR? Also, in its use, where does Cas9 cut the DNA? I've been out of Biology for about a year polishing my programming skills. I know CRISPR/Cas9 allows targeted 'cutting' of DNA via RNA-guidance. Few questions regarding this.

Regarding to its natural phenomenon, when a virus infects a microbe with CRISPR capabilities, how does the genome get integrated into the 'spacers' of CRISPR region versus elsewhere of the prokaryote genome so that when transcribed, the Cas enzymes know that it's a foreign DNA element to be targeted? My understanding of virus infections is a little cloudy too; I'm thinking random transpositions.
I'm looking into it now, so I may figure this out before someone answers, but when the target DNA is located via the guiding RNA, where does the Cas9 enzyme decide to 'cut' -- rendering it useless -- the DNA, and how does it identify the location?

-EDIT- Ah. The target sequence must also include a 'PAM' sequence downstream (Protospacer Adjacent Motif), which allows binding of the riboprotein complex(guiding RNA + Cas9), and biochemistry magic cuts it ~3-4 bases upstream of the PAM). citation: https://www.addgene.org/CRISPR/guide/

Just thought of another question, if the DNA is cut at the seemingly specific spot, is the DNA repair that ensues downstream totally random? I feel like it would be in the organism's best interest (anthropomorphogenic, oops), and evolution generally says it usually does, to have a mechanism to repair it to its original state.

This paper should clear up a lot more than anyone on here truly can about the CRISPR system.

CRISPR/Cas9 is very unique, even compared to other proteins purified from bacteria like Taq Poly.

The reason is due to how complex it is actually induce this protein. Essentially you are transfecting a plasmid with the Cas9 protein and its guide RNA (gRNA) on the vector. Transfecting itself is not easy, not to mention you are essentially adding a mechanism to a cell trying to knockout genes and you've got a handful. In fact doing that for one cell line, and noting the effects of what you knocked out, would be enough to produce a paper in a pretty impactful journal. (Image from: https://www.systembio.com/)

Also some recent advancements in CRISPR include:

Light-induced CRIPSR/Cas9 (easier regulation of enzymatic activity)

Basically these researchers were trying to deduce a method allowing for more control of the CRISPR technique, since CRISPR has had issues with off-target effects. While it isn't a change in how CRISPR works, or even where, the change is how much you can control the reaction. Simply put they devised a way that allows you to turn CRISPR on/off using light allowing more precise control of its activity. Surely it will be helpful to reduce off target effects.

"This was accomplished by fusing the light-inducible heterodimerizing proteins CRY2 and CIB1 to a transactivation domain and the catalytically inactive dCas9, respectively." (Lauren R Polstein & Charles A Gersbach)

Cpf1 to replace Cas9 as cutting protein (more percise activity)

This one is a bit more interesting in that it is a direct change to the CRISPR system itself. Cas9 has been the standard cutting protein used for the CRISPR system although it has had controversy due to its somewhat imprecise cutting. Cpf1 has been shown to be more precise (so their data says) and it is now being implemented by some to see if this is truly the case. Combined with the above "light-induced" system this brings CRISPR down to safer levels when talking about off-target effects.

Here are some good online seminars to get you started:

CRISPR/Cas9 from start to finish
Improve CRISPR-Cas9 experiments with rationally designed guide RNAs

These seminars I can't really comment directly on because they explain everything so well on their own. Anything I say really will only detract from what they are teaching since I am by no means an expert with CRISPR but simply someone who is looking into possibly using it for my lab. Right now there is a lot of guide material on how to properly format your CRISPR experiments but my personal opinion is to give the technique maybe a year or two more when it is more standard for research.

That is unless you want to directly research the method and improve it in your own way.

Let me know if this answers your questions sufficiently.

Sorry that I cannot do much more in terms of explaining the links. The studies are not ones I can easily access unless I am at work since I usually access them through the university.

As far as the repair mechanism goes (your #3 question) I can't really answer that for sure but I have recently received a pamphlet that describes how to ensure the cells uses HJ rather than NHEJ.


How can carnitine enter the mitochondrial matrix without OCTN2? Some people have defects on the gene SLC22A5, giving them problems with their OCTN2 transport protein (Organic cation transport).

OCTN2 transports carnitine into the mitochondial matrix where it can be used to create cellular energy.

Treatment indications for individuals with the defect on SLC22A5 includes oral or intravenous carnitine supplementation.

But one piece is missing...

If their OCTN2 is defective, then how does supplementing carnitine solve the problem? If they are deficient or lacking in OCTN2, how does carnitine even enter the mitochondrial matrix? (with no functional OCTN2 to transport it through?)

But the condition of these patients often improves with supplementation. So the carnitine is getting in there somehow.

Is there another route via which carnitine enters into the mitochondrial matrix?

Short answer -- looks like the image in my question might be flawed, and OCTN2 probably isn't even involved in inner mitochondrial transport. Lesson: don't believe everything you find on google image search!

Longer answer - So I went back to the page where I originally found the image and saw that Dr. Ikumi Tamai was featured as one of the researchers who originally described OCTN2 back in the late 90s.

So I contacted Dr. Tamai via email-- and he responded to me a few hours later!

In his response, Dr. Tamai stated that while OCTN2 is expressed in various places in the body -- it is mostly active in the kidney -- and works there to conserve blood carnitine by re-capturing it from urine and returning it to the blood.

He added that jvm mice (which have defects in OCTN2 that cause carnitine deficiency) respond favorably to carnitine supplementation because the defect mostly just lowers blood carnitine levels, and simply raising those levels improves the condition of the mice.

This seems to suggest that OCTN2 does NOT play any role in transporting carnitine within the mitochondria.

Dr. Tamai noted that the image, which seems to depict OCTN2 sitting on the inner mitochondrial membrane, might have been designed by someone who did not fully understand the science of OCTN2, and that different transporters are likely responsible for the transporting of carnitine into and out of cellular and mitochondrial membranes (not OCTN2!).

In short -- it seems like that little pink blob in the image above should NOT be OCTN2 (even though it is labeled as such) and should probably be another transporter altogether.


Can two different species in the same genus generally succeed in the same habitat? This plant-care website writes

  In the context of plant care, usually most plants within the same genus need the same environmental conditions suitable for plant growth. If the genus of a plant is known, the information can be used to apply the appropriate levels of plant care.

I'm wondering if this is true in general. A more general question would be, if I know that two species are in the same genus, what phenotypical similarities will they have?

So far I've only found that genus classification is based on genetic similarity, but that doesn't say anything about what phenotypical similarities there may be between different species in the same genus.

It is not correct to say that genera are based on genetic similarity. Different lineages diverge genetically at highly variable rates, and there is no set cut-off for what defines a genus. Instead, genera are based on publications, which could be over 100 years old. Genera are not a biologically real category the way species are, so one genus may hold hundreds of species, while another, only one. Most of these genera were defined before molecular data was possible. There are no set phenotypic criteria for the definition of a genus, except that a well-described genus should have at least one fixed character that defines it. So in answer to your question, yes, two species in the same genus (congeners) will often exist in the same habitat. There would be selective pressures to separate them in terms of the niche that they occupy. The publication you referred to is simply a best guess: if you don't have information on the habitat requirements of a species, it would most likely share many similarities with its close relatives. Phylogeny is predictive, but different species in the same genus need not be identical in terms of their ecological requirements.


Inheriting Modified DNA after CRISPR editing If CRISPR is used to modify the DNA sequence to cure a disease - say MS in a woman - will the RNA guides also modify the sequence in her eggs so her children could be born without MS inherited from her.

First off, CRISPR can't be used to cure diseases in an adult human or, more generally, for any adult vertebrate at present.

As you can see in this paper, a major problem with CRISPR is it has to target specific cell types in tissues. As long as the targets are somatic and not germline, the edits made by CRISPR will not be heritable.


What exactly is the time constant of an ion channel gating? Let's take a channel that does not get inactivated, but is only in open and closed states. I understand what m (activation variable) represents. It's the fraction of the gates open.

But what does $\tau$ (tau) , the time constant represent? Does it mean the time taken to open the gate? If tau is higher then it mean more time taken to open the gate?

I'm slightly confused.

Although the membrane time constant is very important in neuroscience, the time constant described in the original question is about ion channel gating rather than the rate of change of membrane voltage.

The "tau" when referring to ion channel gating is indeed referring to how long it takes to open/close.

When the membrane voltage changes, there is a new equilibrium value for the probability of the channel to be open versus closed (note: there can be other states for channels too, but for this explanation I will stick to open/closed). The rate at which this equilibrium is approached from the previous open probability is described by an exponential function, with "tau" as the time constant of that approach. A small value of tau means that the new equilibrium is reached very quickly. This site has a good explanation of the terminology and gating process, as do many others.

Time constants are involved in any system described by an exponential (these are called "linear time invariant" processes), whether decay or increase, and it is equal to the time it takes to progress approximately 63.2% of the way to the equilibrium. The cool thing about time constants (and linear time invariant processes in general) is that it doesn't matter what your starting point is or how far into the process you are, the time constant stays constant and every time "tau" passes you are now 63.2% closer to equilibrium than you were at time t-tau.


What is the instructional language of DNA? DNA carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses (Wikipedia).

Is it already know how ATCG's sequences create theses instructions? Or equivalently, what is the instructional language of DNA? My interest in this question is to know if we already understand how ATCG's sequences can create, for example, human epidermis with an excess of a determined mineral or change cell's shape for more fundamental geometrical ones (triangles, rectangles, diamonds, etc.).

Please, forgive me for this foolish question: I'm not a biologist.

This language is called the genetic code. But before talking about this specific code, it is important to talk about how the code is read. Please note that the below answer is a simplification of the reality.

Mechanism by which the code is read

To make things easier (reality is a little more complicated), DNA is "formatted" into RNA which is then "formatted" into proteins. When "formatting" occurs, we do not lose the previous format but we only copied the information into a new format. The formatting from DNA to RNA is called transcription and the formatting from RNA to proteins is called translation.

Proteins are the active units that affect cell activities. The activity of the proteins is a function of their sequence. As a consequence the language/code we must understand is the relationship between DNA and proteins.

Numeral systems of DNA

DNA, as you said, is written in quaternary (=numeric system at base 4). The four letters are called A, T, C and G which stands for Adenine, Thymine, Cytosine and Guanine (4 nucleotides).

Numeral systems of proteins

Proteins, on the other hand, are coded in a system at base 21 (21 amino acids).

Redundancy

Because $4^2=16<21$, we need to use (at least) 3 letters in DNA to code for 1 amino acid. Because $4^3=64>21$, we necessarily have several codes of 3 nucleotides that match to the same amino acid. We talk about redundancy. In computer science, a byte is a series of 8 bits. In biology, a codon is a series of 3 nucleotides.

Code

Below is the code:

, where Phe, Leu, Ser, etc... are an abbreviation for specific amino acids. Phe for example is the phenylallanine.

As you can see in the above table, most of the redundancy is caused by changes in the third letter of the codon. More information on why it is the case on this post.

There are 4 special codons.

AUG: Is the start codon. It is an indication of where translation should start.
UAG, UAA and UGA are stop codons. They are an indication of where translation should stop.

Possible confusions

Central Dogma of Molecular Biology

The unidirectional relationship between DNA, RNA and proteins has been called Central Dogma of Molecular Biology. Of course, there is no place for dogma in science and the term is very improperly used. Interestingly enough, the Central Dogma of Molecular Biology is partially wrong because this relationship between DNA, RNA and proteins is not necessarily unidirectional. The reverse transcriptase is an enzyme that reformats DNA from RNA.

Genetic code

If you google "genetic code", most hits will display the letter U instead of the letter T. The reason is that the code is often presented for the relationship between RNA and DNA and the only difference in the code between RNA and DNA is that T (Thymine) is replaced by U (Uracile).

mRNA vs RNA

Not all RNA are meant to be translated into proteins. Only mRNA (m stands for "messenger") are. For example, the process of translation is itself catalyzed by RNA (called rRNA, where "r" stands for "ribosomial")

Note also that DNA is first transcribed into pre-mRNA which is then modified into mRNA before being translated.

Is all of DNA transcribed?

No. In eukaryotes (which include pretty much all the living things you may think of to the exception of bacteria and viruses), most of the DNA is not transcribed. The rest is used for regulatory purposes or might not be used at all. The regions (called locus/loci) of the DNA that is being transcribed are called genes


Termination of translation What dissociates first - the last tRNA, mRNA and release factors or the subunits of ribosomes?

I tried searching this from Lehninger but couldn't get a clean answer.

Shigeta's got a point: the ribosome is latched onto the mRNA so those two are intrinsically linked.  You're really asking whether the ribosome comes off first or whether the tRNA does, but it's actually the new polypeptide, which makes sense:

  The stop codon is recognized by a protein, the polypeptide chain release factor (RF), which triggers the hydrolytic release of the nascent polypeptide chain from the P-site-bound peptidyl-tRNA.

This minireview puts forth a model (see below) where, in E. coli at least, the 50S ribosome subunit is then dissociated from the mRNA/30S subunit/tRNA complex, following which the final tRNA is removed.  An in-depth review from a few years later gives more context.


Osmotic Pressure Clarification My textbook states that the higher concentration of solutes, the greater the osmotic pressure will be and the greater the pull of water in will be. However, osmotic pressure is defined "as the pressure that would have to be applied to a pure solvent to prevent it from passing into a given solution by osmosis." Therefore wouldn't a high osmotic pressure PREVENT water from passing, not pull water in? Can someone please clarify this for me so it makes sense? Thank you!

I think you've got the solutions the wrong way round and that you should be applying the pressure on the non-pure solution, not the pure solution. Pure water is drawn in through the membrane so you have to put pressure on the non-pure solution to keep it out. Which textbook are you using? See the following quote from Voet et al. 5th ed. p. 30 and figure from Lehninger. Principles of Biochemistry p. 57.

  The osmotic pressure of a solution is the pressure that must be applied to
  the solution to equalize the flow of water across the membrane in both directions
  (the added pressure forces more water from the solution through the membrane);
  it is proportional to the concentration of the solute.


Any idea what this red plant is? I live in South central Indiana, US, and these have just started appearing in the grass in my yard. I just bought this house last fall so I've never seen them. Anyone know what they are? Are they harmful to dogs?

We called those "Indian strawberries". They are also known as Mock Strawberry (Duchesnea indica). Survivalists are pretty familiar with this plant.

They are a lot like strawberries in appearance, but the berry is rounder, not pointed, and held upright (they point up) on the stem, not pending. Though the berries are edible, they don't have much flavor at all. The leaves are also similar, and the flower is yellow, not white. The fruit's seeds are the same color as the fruit. They flower late spring and throughout summer. Your specimen looks like it was nibbled on at some point. The inside of this berry is white and kind of spongy and dry (especially compared to the real thing, i.e. wild strawberries.) The stalk it's on is hairy (as it should be) but damaged, and only one part of the leaflet is visible in your photograph.

They're in the Rose family, but there's some discussion about what genus they really belong to; may be more similar to Potentilla.

See also http://www.sierrapotomac.org/W_Needham/IndianStrawberry_080617.htm


Difference between prions and amyloid proteins? Amyloid and prions are misfolded proteins, but what, if any, is the difference between them?

Is amyloid a type of prion with a fibrillar structure?

Amyloids are protease resistant insoluble fibrils formed because of (mis)folding and aggregation of soluble proteins (Rambaran and Serpell, 2008, Sabate et al., 2015). The first definition of prion was given by Prusiner (1982):

  Because the novel properties of the scrapie agent distinguish it from
  viruses, plasmids, and viroids, a new term "prion" is proposed to
  denote a small proteinaceous infectious particle which is resistant to
  inactivation by most procedures that modify nucleic acids.

Many prionic diseases are characterized by amyloid fibril formation and therefore some (if not many) researchers consider prions to be a subset of amyloids.

  Prions are considered a subclass of amyloids in which protein
  aggregation becomes self-perpetuating and infectious.
  (Sabate et al., 2015)

However, the amyloid structure formation is not essential either for the autopropagation or disease progression (Moore et al., 2014).

  When wild-type C57BL/10 mice are infected intracranially with the RML
  mouse prion strain, PrPSc accumulates in diffuse nonamyloid deposits
  and brain pathology is distinguished by the hallmark gray matter
  spongiosis for which TSEs are named. Conversely, when transgenic mice
  homozygous for PrPC lacking the GPI anchor (Tg44 or “anchorless” mice)
  are infected with the same RML strain, the incubation time is longer
  and PrPSc accumulates in dense perivascular amyloid plaques with
  little or no gray matter spongiosis.9−11 Similar amyloid PrPSc
  deposition and disease resulting in death has been observed in humans
  with an aberrant stop codon in the C-terminal portion of the PrP
  sequence, resulting in the generation of PrP lacking the GPI anchoring
  group as well as some amino acid residues.13−16 Thus, GPI-anchoring of
  PrPC to the plasma membrane appears to be a primary factor determining
  the type of PrPSc deposition and the development of brain pathology.

You can say that the prion protein PrPC is amyloidogenic but it is not an amyloid.

There are non-pathogenic (and in fact useful prions) found in fungi. Many of these beneficial prions also form the amyloid (like) structure but they can be disaggregated by chaperones (Wickner et al., 2018). Now again, it is not essential for these beneficial prions to form an amyloid structure.

  Prions (defined as “infectious proteins”) need not be amyloids. The
  vacuolar protease B (Prb1p) of Saccharomyces cerevisiae is made as an
  inactive precursor that is normally cleaved and so activated by the
  action of protease A (Pep4p) [32]. However, in the absence of Pep4p,
  mature active Prb1p can activate its own precursor [33]. This
  self-activation can propagate and pass from cell to cell in an
  infectious manner, acting like a prion, and named [BETA] [34]. In the
  absence of Pep4p, [BETA] is necessary for meiosis and spore formation
  and for survival in stationary phase [34]. It is thus a functional
  prion.

[SMAUG+] is another example of a non-amyloid yeast prion which has beneficial effects (Chakravarthy et al., 2019 and Itakura et al., 2019; Jarosz group). Unlike Prb1p, [SMAUG+] actually forms self-propagating aggregates.

My summary

Many known prions are amyloidogenic and can switch to amyloid form. However, as per the definition, prions are "infectious" or in other words, self-propagating proteins.
What qualifies as a prion depends on our definition. Mode of action of most known prions is catalyzing a change in the protein fold. Wickner et al (as quoted above) reason that the original definition does not explicitly include the mode of action and hence proteins that activate themselves via proteolysis should also be considered prions. Jarosz's group has shown an example of a non-amyloid prion that forms self-propagating aggregates. It quite likely that more such proteins will be discovered in near future.

In any case, "amyloid" is a structural property whereas "prion" is a functional property and they cannot be considered a sub/superset of one another, even if they happen to be correlated.

The bottomline is:
Amyloid is a form of supramolecular protein structure which is often formed by many prionic proteins. However, not all amyloid forming proteins are prionic and not all prions necessarily form amyloids.


How does Golgi's neural histological stain work? What is known about the targets of Golgi staining of neurons? Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?

The current wikipedia article says the mechanism is still not fully understood. What is preventing us from using the advanced molecular biology techniques to understand the process?

Some background information.

First of all one should notice, that Golgi staining belongs to so-called morphological types of stainings in neuroscience, where the actual anatomy of different neurons is revealed (compared to other techniques, like Ca-imaging or potential imaging).

Second, Golgi staining is a type of silver staining, there the sedimentation of silver or its salts (here: silver chromate) reveals the morphological traits of the cels.

And, third, Golgi staining is applied to fixed preparation. This means that the tissue (normally a brain slice) is pre-treated (here: with formol) to kill all cells and arrest every biological process.

What is known about the targets.

The common description of the target is quoted as "a limited number of cells at random in their entirety". This is the essence of Golgi staining:

Only single cells are stained, therefore there is no impediment from adjacent cell staining while deriving the morphological structure of the cells (very important for light microscopy where you have integrated input from different depths).
The cells are stained randomly, there is no known preference among neuronal cells for Golgi staining and I haven't seen any other types of cells in CNS stained with Golgi, therefore it is quite specific for neuronal cells (and leaving macro- and microglia, astrocytes etc. intact).
The cells are stained in their entirety, meaning that the complete cell is stained very nicely, showing detailed arborisation of dendritic tree, that was very important in studying of Purkinje cells in cerebellum.

Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?

Golgi staining is used mostly for brain slices (I have never seen or heard its application for other tissues). Traditionally one of the biggest cells here are pyramid neurons (NA, ACh-ergic) and one of the smallest are interneurons (often GABA-ergic) -- both are amenable to Golgi staining (reference) and there is no seemingly clusterization of stained cells by their size or transmitter type.

What is preventing us from using the advanced molecular biology techniques to understand the process?

I can name several reasons for this:

Since Golgi staining is applied to fixed preparation the tissue is already "damaged" (formol leads to dessication of cells and shrumping), therefore it is difficult to use some fine mollecular biology methods to investigate these tissues.
There is no way to tell which cells get stained beforehand. And as long as  the microcrystallisation of silver chromate is started it can't be (easily) stopped and reversed. Therefore it is difficult to look at what caused the staining afterwards, then the whole cell is impregnated with silver.
I think there were no real attempts to crack the mistery of this staining: how intersting it might be, this seems to be an interdisciplinary question on the brink between biology and chemistry. So, maybe one day somebody will look into it and explain everything.


Best colour for a dog to track an object against green background As dogs have limited colour perception, what colour would appear with most contrast against a green background for a dog? I understand that red and green are very close in a dog's colour perception, so would blue offer better contrast?

Dogs are a dichromatic species, featuring only a long wavelength (L) and a short wavelength (S) cone (source: Smithsonian). As such, they are thought to perceive mainly blues and yellowish hues (Fig. 1). This is unlike trichromatic species like humans, who are able to distinguish red and greens as well (Fig. 2). Whether dogs perceive greens or yellows is hard to say, but either way, they see those longer wavelengths (red, green, yellow) as one hue (say, yellowish).

Hence, in dogs, green hues are basically seen as yellow (or vice versa) and indeed blue (short wavelengths) are best to create a good color contrast.

Of course, brightness contrast will work fine too (white and black).

Fig.1. Dichromatic (dog) color spectrum. source: Dog Vision

Fig. 2. Trichromatic (human) color spectrum. source: Dog Vision


What type of guatemala beetle is this? it was in Guatemala
it was really big like 4 inches
sorry I don't have a better photo

This click beetle belongs to the species Chalcolepidius rugatus.

According to the original description, this species is clothed, dorsally with white pubescence, with the sides of pronotum and elytra marginated by yellow, and ventrally, with brown pubescence. source

source

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Distribution

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