Can difference in the expression potential of alleles lead to dominance? Several hour ago I was in thoughts what allele dominance really means on molecular level. As we know from basic genetics, if the organism had Aa type of some gene so trait is controlled by this gene would be equal to AA case. And we see it only when our organism is growing up. I'd like to know, how it works on molecular level, why Aa = AA in phenotype? I suggest, that expression level of A locus is greater than a locus and if so, why? Is that because of chemical structure of dominance allele that RNA polymerase interact with it more frequent?

Please, help me to understand. Thanks.

P.S. I don't consider different gene interactions as epistasis etc. just give you simplest example to describe what I want to know, but any useful considerations are appreciated.

Dominance is not commonly known to occur because of higher expression level, per se of one of the alleles. It can certainly be a factor but usually dominance is mostly known to arise because of a slight difference in function (or in other words activity) of the gene product (which may be a protein or an RNA).

Note that a change of function doesn't mean the alleles would have a totally different function. It just means that the alleles can be different in the way they function. For example two variants of an enzyme may have slightly different kinetic properties (such as Vmax Km and kcat). While change of activity may generally refer to Vmax (maximum enzyme activity), mutations can also change the other constants. Some mutations can make the enzyme sensitive to temperature by affecting the stability of the overall structure. The extreme would be a functional allele and a non-functional allele.

While concentration of the product does affect its activity, it does not change its specific activity, which may change in the presence of a mutation.

Moreover, even if one allele is actually has a higher expression than the other, the resultant trait can be differentiated from that of the aa homozygote only if the two alleles have slightly different functions or if the difference in expression level between of the gene product in Aa and aa is great enough to elicit different biological effects. In the second case there would be no change in the gene function and the effect of dominance is purely based on gene dosage. This review by Veitia and Birchler (2010) explores the possibility of stoichiometric alterations of macromolecular complexes or cellular networks being responsible for dominant phenotypes*.

Now, how can a mutation lead to a difference in expression level without changing the activity of the product?

There are three cases here:

The mutation is in the expressed region (exonic) but doesn't lead to change in activity (for e.g. synonymous mutations)
The mutation is in the transcribed region but in the intron.
The mutation is in the non-transcribed DNA regions such as promoter/enhancer etc. Exceptions: certain downstream promoter elements are actually transcribed.

Only mutations in the promoters/enhancers can affect transcription by affecting the recruitment of RNA-polymerase. However, you should note that mutations in the non-transcribed regions, especially in the distal regulatory elements are not considered a part of the gene in consideration. Since, such complex modes of regulation were unknown during the time of Mendel, the classical genetics does not explain these effects. Hence, these mutants would not be called alleles of the considered gene.

Mutations in the transcribed regions may affect the elongation rate of polymerase (especially if it leads to formation of stable DNA secondary structures). This is just a theoretical possibility and I have not come across any study that has reported something like this.

However, mutations in the untranslated regions of the mRNA can change the expression of the protein. These mutations may affect post-transcriptional regulation of the protein expression or even the RNA localization.

Synonymous mutations in the coding region can affect the rate of translation and hence the protein concentration.

*(quoted verbatim)


What was the evolutionary advantage of having seeds so large that they could only be dispersed by megafauna? I understand that fruits like the avocado and the osange orange are so large and unwieldy that their evolutionary "intent" was to be consumed whole by megafauna that are now extinct. What I don't understand is why there was selection pressure for such a relationship to develop. Wouldn't it be to the plant's advantage if its seeds could be dispersed by more types of animals? What advantage does the plant get by limiting seed dispersal to a small set of large animals?

There are a few advantages to megafauna:

they travel large distances and are hence are likely to be able to
spread your seeds widely.
They also eat large amounts, so can carry a lot of seeds and
distribute those around widely.
Large fruit capable of being eaten only by the largest fauna might have the seeds survive by not being eaten and destroyed by smaller animals
Large animals have large guts, so the more of the seeds might survive undamaged

Another significant factor is that a megafauna animal also produces mega-feces, literally a large pile of nice warm fertilizer for the new plants to grow in.


Do tRNAs that recognize multiple codons have any preference for one over another? What are the effects of the different binding strength/affinity between the synonymous codons corresponding to a single tRNA ?

There is an extensive literature on synonymous codons and their usage in different organisms. I shall assume that the question concerns relationship between strength of codon–anticodon interaction and the efficiency (speed in this case) of translation.

It is not disputed (I am aware of few experiments on this) that the strength of codon–anticodon interaction depends on the number of hydrogen bonds made.
It was predicted that for optimal rate of translation one needs a balance between association and dissociation of the codon–anticodon pair. Hence weak interactions (all AU) — which would disfavour association — or strong interactions (all GC)  — which would disfavour dissociation — would not allow a rate of protein synthesis as fast as that for intermediate interactions (mixed AU,GC).
This appeared to be borne out
in the codon usage patterns of rapidly growing organisms such as Escherichia coli, something subsequently confirmed by more extensive studies. To be precise, the more highly expressed proteins (e.g. ribosomal proteins) were encoded by mRNAs containing the intermediate  codon–anticodon interactions predicted to allow rapid translation. In contrast, poorly expressed proteins (e.g. repressors) were encoded my mRNAs predicted to produce slower translation.
One should be aware, however, that there are other factors that influence the codon usage in different organisms, and that these can overide the effect of codon–anticodon interaction strength.


Cellulose acetate membrane filters vs. glass microfiber filters At equivalent pore sizes and pressures, which exhibits faster flow rates, cellulose acetate membranes or glass microfiber filters?
I know cellulose acetate exhibits low protein binding, but what about glass microfibers? Would they be suitable when protein recovery is essential?

It would also depend on the pore densities and pressure resistance.
Silica is used for gel filtration chromatography to separate proteins. This can be achieved when proteins do not have affinity to silica, and most of proteins could be analyzed with silica gel. Silica and grass are similar materials. However, glass and silica have negative charges on the surface. Under low ionic strength condition, positive charged proteins or positive charged surface of proteins may bind to glass. Cellulose acetate does not have charge but it is hydrophilic.


Does current evidence support the use of resveratrol as an anti-ageing drug? A while back there was a lot of noise about resveratrol, a naturally occurring phenol which was touted as a potential anti-aging drug due to its role in regulating the SIRT 1 gene. A number of studies suggested that it could extend the lifespans of model organisms such as D. melanogaster and C. elegans.

Has there been any follow up on this? Have there been any human trials?

It's worth noting that earlier this month a large body of resveratrol research was retracted:

  The University of Connecticut, in what clearly seems like an attempt to get ahead of damaging news, has announced an “extensive”
  investigation into research misconduct involving one of its
  scientists, Dipak K. Das.

  According to a press release, the university has notified 11 journals
  that published Das’ work about the alleged fraud. One area of interest
  for Das, a government-funded professor of surgery and director of the
  Cardiovascular Research Center, has been resveratrol, a substance in
  red wine that has allegedly been linked to improved cardiac health.

Retraction Watch's coverage has been pretty thorough and includes comments and citations:

UConn resveratrol researcher Dipak Das fingered in sweeping
misconduct case
So how peripheral was Dipak Das’ resveratrol
work, really?
Resveratrol fraud case update: Dipak Das loses
editor’s chair, lawyer issues statement refuting all charges


Are the subordinate genes of a repressed operon really "turned off"? Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says:

  In addition to being physically close in the genome, these genes are regulated such that they are all turned on or off together. ... The ability to turn ... genes on or off as a group therefore provides an efficient way to quickly adapt to environmental changes. ... mutations affecting the promoter can prevent all of the operon's genes from being expressed, ...

The thing that confuses me is that I've also heard genetics aren't all or nothing, that genes can only be "down regulated" or "up regulated", not truly turned on and off.

Obviously, differing amounts of moderate levels of whatever effector is modulating the repressor could lead to different levels of downstream expression. But, what about situations where nothing is inactivating the repressors? Will the regulated genes be (for all intents and purposes) be turned off? Additionally (and relatedly), is it even a realistic scenario for an operator to always (or almost always) be bound to by such a repressor?

There are several mechanisms by which the expression of a gene can be completely turned off. Certain network architectures can ensure foolproof repression (for e.g. by using multiple repressors parallely or additional epigenetic silencing mechanisms). Bistable switches can also ensure robustness of expression in a way that small fluctuations in the transcription factor levels do not lead to expression of the gene. Sometimes the activator molecules need to co-operatively activate the expression. In such conditions the activation graph is sigmoidal with respect to activator concentration. All these mechanisms can prevent leaky expression.

Some genes do have a basal expression but it is not necessary for all cases. However, basal expression is absolutely necessary for proper functioning of the lac operon (see this post).

Having said this, there is always some non-zero probability of expression of a gene when it is actually turned off. This probability may be very low but it would not be zero. This small accidental expression may or may not have any significant downstream effects.


Are chromosomal and plasmid DNA in the nucleoid? I know plasmid DNA is not part of the chromosome, according to my textbook, but can you still class it as being part of the nucleoid?
Also is chromosomal DNA in the nucleoid?

"Nucleoid" (literally means nucleus-like), is a quite old term for "bacterial chromosome" (Better to write prokaryotic chromosome since in both type of prokaryotes i.e. Archaea (former archaebacteria) and bacteria (former eubacteria) the structure is similar).

Nucleoid structurally normally excludes the plasmid-DNA (the plasmid DNA is like additional or accessory). However sometimes a plasmid DNA could go through recombination with prokaryotic chromosome 's DNA (As seen in Hfr strain of Escherichia coli)

"Chromosome" in very brief means a structure made of DNA + Protein. In case of "bacterial-chromosome",  it contains both DNA and Protein; and if you take away the protein from bacterial chromosome; what you get, is the chromosomal DNA.

Reference:

Microbiology / Pelczar, Chan and Noel/ Edition-5;

Part 2: Bactria,

Chapter 5 (Morphology and fine structure of bacteria)

  "Because it is not discrete nucleus, this nebulous structure has been designated by such terms as the nucleoid , the chromatin body, the nuclear equivalent, even the bacterial chromosome"

General Microbiology / Hans G. Schlegel / Edition-7:

Chapter-2 ; The cell and its structure:

2.2 The prokaryotic cell (protocyte) -> 2.2.1: The bacterial 'nucleus'

  " Plasmids : In addition to chromosomal DNA, many bacteria contain extrachromosomal DNA in closed, circular, double stranded form. These autonomously replicating DNA elements are called plasmids. Linear plasmids have been found in some bacteria"


Recombination-based vs. Sequence-based genetic mapping Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?

I think that in the past recombination-based genetic maps were used as blueprints for sequencing projects. But since now the entire genome can be sequenced pretty cheaply both in time and money, what is the unique value of recombination-based genetic mapping?

One thing that comes to mind but I am not very sure. It might be suitable for mapping novel phenotypic markers e.g., unmapped diseases.

A couple of months ago I listened to a plant physiologist who strongly recommended recombination-based mapping over sequencing based mapping. The main reason he gave was the error-rate of 2nd generation sequencing. The error rate on Illumina platforms are about 1 % if I recall. In a small genome like that of Arabidopsis thaliana (157 Mbp) that accounts for over 1 million sequencing errors. That can of course be reduced having a proper sequencing depth and using the consensus sequence. But it can still cause problems if you're tracking a phenotype caused by an SNV. In plants like A. thaliana where back crossing can be used to create homozygous plants, recombination-based techniques can be particularily effective.

But he was talking from a plant physiologist's view when working with A. thaliana as a model organism. When working with humans which always are heterozygous, can't be back-crossed, don't have a generation time of six weeks and where samples sizes will probably be small I imagine that the situation is different. The classic geneticists' working with human diseases that I have talked have expressed fear that their work will soon be obsolete due to falling sequencing prices and growing sequence data collections.


How exactly are petri dishes used (e.g. in medicine)? I know that petri dishes with a growth medium are used to grow micro organisms. I guess this works as follows:

The petri dish has to be kept sterile. To make it easier, I guess one could cool it.
The microorganisms are somehow put on the petri dish.
The petri dish is put in an incubator (e.g. 37 °C if one wants to simulate the human body).
After some time (how long?) one can look at the colonies.

Does one only look at them with the naked eye or is there a way to make more detailed studies?

For example, when I have an illness, can the doctor (for some illnesses) simply use this petri dish / naked eye technique to confirm a hypothesis what kind of illness I have?

I think the petri dishes you are referring to are also called agar plates. Agar is a 'growth medium' for microorganisms. It provides the nutrients that the microorganisms need to survive. It can also contain main other 'things', such as antibiotics or pH color change indicators. There are many types of agar, for example, tryptic soy agar is used to grow E. coli. I think the oven you are referring to is called an incubator. Incubators provide the atmosphere, particularly temperature, needed for the organisms to grow. There are many types of incubators. Some microorganisms actually cannot grow in oxygen rich environments, and some only grow at specific temperatures. These organisms must be incubated under their preferred conditions in order for them to grow.

And yes, a lot can be learned from simply looking at the agar with the organisms on it. What exactly can be learned depends on the growth medium (agar or other medium).

To summarize, petri-dishes are just the plastic dishes that contain growth medium. And incubators are usually refrigerator looking things that provide the proper temperature for the organisms to grow. The goal is generally to mimic the natural environment of the organism, but as I stated, scientists often add many other things to the environment for experimental and diagnostic purposes.

Here is a list of common agars used in bacteriology http://learn.chm.msu.edu/vibl/content/differential/


Absorption of pentoses in intestine Why pentoses are absorbed by facilitated diffusion in intestine? Wouldn't it be futile because , when the pentose concentration is lower in intestine, the pentoses would diffuse back to the intestinal lumen? So does our body looses them? If not then what is preventing this backflow?

First, pentoses aren't a major source of nutrition, at least for humans. That said, pentose absorption works the same way a lot of nutrient absorption works: the "magic" of metabolism, with respect to diffusion.

Pentoses leave the intestinal lumen, entering the intestinal cells, where their concentration is lower. From there, they again travel via facilitated diffusion into the bloodstream, again because their concentration is lower in the bloodstream.

From there, we can expect one of two outcomes: either an equilibrium will eventually be reached(i.e., lumen==intestine==blood), or the bloodstream pentoses need to be metabolized into something else. Indeed, certain pentoses (specifically D-ribose; I'm not sure if others can end up in this pathway as well but it is a very common pentose) can be metabolized in the pentose phosphate pathway for anabolic purposes. Others may end up in proteoglycans.

Regardless of the metabolic pathway, the effect on the process you are wondering about is the same: the metabolites no longer "count" in terms of concentrations for diffusion. Because membranes are not permeable to everything, if they are not permeable to the products of metabolism there is no way for those products to "diffuse backwards."


How do viruses or bacteria survive outside the body long enough to spread? Say I cough on my table, then someone else touches it and picks up something I've got... how is it that these things can live outside the body, how long can they manage it, and how long is generally 'safe' to consider something no longer carrying these germs?

It depends entirely on the environment the virus or bacterium is in and also the size of it.

Virus

With regards to viruses, the most important thing is typically whether or not the virus has an outer membrane or envelope.

Non-enveloped viruses such as rhinoviruses, noroviruses and adenoviruses can in fact survive for long periods outside the host (up to several days) whereas viruses with membranes such as HIV, influenza and the herpes viruses which do well in the host survive for shorter time periods.

Experiments with rhinoviruses and influenza viruses have shown potential survival times ranging from a few minutes to 48 hours or more.  They remain active longer on stainless steel, plastic and similar hard surfaces than on fabric and other soft surfaces.

This is because many enveloped viruses rely on the proteins on the surface of the membrane to attach to the host cell, this envelope is generally sensitive to degradation to sunlight and normal cleaning procedures.

Outbreaks associated with the non-enveloped viruses can continue for many months due to their relative stability in the environment, think of winter vomiting outbreaks, hand foot and mouth in animals as good examples of this phenomenon.

Bacteria

Because bacteria can undergo metabolism, synthesise proteins etc. for themselves, their life span is usually longer. If we split them into gram positive and gram negative its easier to discuss. Gram positive bacteria have a protein coat that prevents drying allowing them to survive longer. An example is the bacteria Staphylococcus aureus, which is responsible for toxic shock syndrome, food poisoning, and wound infections. With its protein coat it can withstand temperature and humidity extremes. The spore may survive for weeks on dry clothing using sloughed skin cells for food. The Bacillus anthracis, the anthrax bacteria, can also form spores and survive tens to hundreds of years. This is in comparison to gram negative which need humidity. An infamous example is Escherichia coli which survives typically only a few hours at best.


Are there evolutionary advantages for the bee sting to kill the bee? The question title says it all: are there advantages for the sting of a bee to kill the bee? It seems to me getting rid of this would have only advantages, and might've been selected for if a mutation like that occurred.

Fitness of the colony vs fitness of a single worker

Bees have a division of reproductive labour (they are eusocial). Only a queen reproduce (and the males called drones) while the workers dedicate their existence to ensure the survival of the colony. If committing suicide will be of any help to the colony then one would expect a bee to do so. What I just said is an oversimplification of the structure and mating systems of bee colonies.

You should have a look at the field of social evolution to have a better understanding of what's going on with bees!

What is the cost?

Above I argued why nobody really cares much if a single worker dies. This being said, if the bee survived to stinging, then it could eventually keep protecting the colony as it was doing before stinging. So why does it has to die? Clearly, there must have a cost to not die. It seems very plausible to me (but cannot offer an evidence for it) that there would be a strong physiological cost to create a stung that that would not kill its carrier. Such physiological cost (even if mild) can by large outweigh the cost of losing a single worker for the colony.


Do our belly buttons consist of scar tissue? I read an interesting post on Facebook the other day saying that we all have a visible scar since birth - our belly button. This got me thinking (and research for me only found results regarding belly button piercing) is the belly button made up of scar tissue?

I seem to recall that there are some stem cells still within the umbilical cord (which is why doctors tell you to spend the money to have it saved (I think)) so I was wondering if scar tissue closed the hole left by our cut umbilical cord, or if the stem cells divided to produce normal skin tissue.

The place where the cord was cut do not stay with us - it falls in a week +- after the birth, while the umbilicus is the only visible natural scar formed by natural processes, not by gynecologists:

Multiple sources say the umbilicus has a scar tissue in it.

  After birth the umbilicus is the only naturally formed visible scar on
  the body.

Br J Plast Surg. 1998 Oct;51(7):538-41. Umbilicosculpture: a concept revisited.

  Umbilicus is a scar, which is the place of the previous merger of the
  fetus with the umbilical cord.


How can we decide at which level does natural selection apply? Here is a passage from The Selfish Gene

  If selection goes on between groups within species, and between species, why should it not also go on between larger groupings? Species are grouped into genera, genera into orders and orders into classes. Lions and antelopes are both members of class Mammalia, as are we. Should we then not expect lions to refrain from killing antelopes, 'for the good of the mammals'? Surely they should hunt birds or reptiles instead, in order to prevent the extinction of the class. But then, what of the need to perpetuate the whole phylum of vertebrates?

So shouldn't it eat the other animals? Also in the next line, it says about vertebrates that since reptiles and birds are vertebrates, the lion should go for invertebrates.

It sounds illogical, but what stops lion from eating his "relatives", or from sparing a deer? And till what extent is the term "relatives" valid?

Is the question is too broad, please give a source where I can get an answer.

Natural selection favors genotypes that produce phenotypes that survive to reproduce.  To the extent that natural selection drives the instincts that drive predation, the (essentially tautological) answer is that, "It has proven selectively beneficial for that particular genotype to eat whatever it's eating."

Indeed, nature has shown us a variety of solutions to these selective pressures.  Cannibalism is not hard to find.  In the extreme case, mothers from diverse species are known to kill and eat their own offspring, which at first glance may seem like the height of failure when it comes to propagating one's genes.  And yet we can hypothesize a number of selective advantages of that behavior.  (E.g., the mother can produce large litters when food is plentiful, and then adjust for shortages to shore up a smaller litter when food is scarce.)

We also know that there are selective pressures against eating similar animals.  For example, pathogens that kill an animal are likely to afflict its genetic relatives, and so that could drive the aversion of some carnivores (including humans) to eating close relatives.

There are plenty of examples of evolved symbiotic organisms.  Alligators don't eat plovers, and sharks don't eat remoras.

But it is hard to imagine selective pressure for altruistic behaviors that don't benefit a particular genotype.  E.g., if there are mammals to be eaten, the lions that eat them will survive and the ones that don't will die.  If the entire class Mammalia is under pressure, population dynamics trump evolved behavior: If prey become scarce, predators will become scarce.  But if any predators survive, it will be the greedy ones.


fastq-dump using mkfifo to stream data So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk.

I'm curious whether it would be possible to use fastq-dump to write to a named pipe (using mkfifo) and feed that into another program, for example Trinity, to run an assembly on the FASTQ file without ever having to write all that data to disk. For large datasets, this could actually save quite a bit of time in aggregate.

Has anyone done something similar? I am going to try and experiment with the technique soon, but I a) don't know much about the mkfifo process to begin with and b) am unsure of how this procedure would work for paired-end data where fastq-dump is splitting the SRA file as it goes. How would one specify which output would go to which pipe?

EDIT: A (hypothetical) example:

  mkfifo fileStream

  fastq-dump SRR123456 > fileStream

  Trinity --single fileStream misc_args

That should take the fastq-dump data and stream it into the named pipe "fileStream", which can then be used to stream data into Trinity. I don't know enough about all of the commands, however, to know if this makes any sense.

I would welcome any thoughts from more experienced users!

EDIT: Added update as an answer below.

fastq-dump can write to stdout ; the -Z option allows you to do that. This, you can pipe to any downstream process. [An example]. Also see the SRA-toolkit manual.

I guess someone asked this question in biostar too.


Is there a tool to find the action of an enzyme in a metabolic pathway? Is there any tool to search the biochemical action of a particular enzyme in a metabolic pathway of an organism? In other words, how can I find if enzyme "E"  is involved in the metabolic pathway for organism "X".

I think the KEGG pathway database may be of some use to you.

Link is here: http://www.genome.jp/kegg/pathway.html

This a database of manually drawn pathway maps, I have used the site myself and it is very useful in determining if your enzyme is in a pathway and where it lies in it. This is assuming though, your enzyme is in the database and has been mapped.


Coniferous trees in temperare rain forests In temperate rainforest, the dominant plant form is often coniferous trees (source). However, coniferous trees are also the dominant plant form in a very different climate and form a different biome (boreal forest). Why are broad leaved evergreen trees not so adapted in temperate rain forests as in tropical rainforests? What is the advantage of needle-shaped leaves in the climate with temperate rainforest?

The largest area of temperate rain forest in the world is on the west coast of North America, which has a summer dry season. In other words, at precisely what would be the best time for plants to grow (based on temperature), there's a shortage of water. (Summer vacation visitors to the rain forests on the Olympic Peninsula are often wondering "where's the rain?")

Conifers have small, waxy, and (generally, with a few exceptions) evergreen leaves. All the conifers in the rain forests of western North America are evergreen; that allows them to grow in the cooler months of the year, when there can occasionally be hard frosts (and when deciduous trees are dormant). The waxy, small leaves help them conserve water in the dry summers. A double advantage.

North of about central BC, there's no longer the summer dry season, but by that point the growing season is getting short enough that conifers have an advantage despite the perhumid climate (Prince Rupert, BC is further north than Edmonton, Alberta).

I'll add that this is not the only non-boreal climate where conifers are abundant: consider for example the piñon-juniper woodlands of the American Southwest or the Piney Woods of the Deep South.


Why all particles have same influence on osmosis When people talk about osmosis, they say that when we add a mole of NaCl, then each its molecule gets dissolved into 2 separate particles and therefore we have 2osM/L solution.

But both Na & Cl are attached to molecules of water which means that those water molecules are not water anymore and they can't penetrate the membrane. Thus not only the presence of Na & Cl itself changes the concentration of water in solution, but also the number of water molecules taken by those particles.

Therefore if we put 1 particle that binds to 1 water molecule and 1 particle that binds to 5 water molecules - they change the water concentration differently.

Please somebody tell me where I'm wrong.

When you dissolve something in water, you build a solvation shell around this - so each ion (in the case of salts) gets surrounded by a number of water molecules. For more details read this Wikipedia article.
The concentration change in free water molecules is usually not taken into account since it can be neglected due to the vast number of "unbound" molecules. So if you have one litre of water, it contains approximately 56 moles of water molecules. If you dissolve 1 mole of sodium chloride in this water, and take in account that this takes quite some water to get solvated, there is ways more water available. So the water concentration is almost constant (especially when you work at physiological osmosis condition).


How many species can have the same scientific name? For my science homework, a question came up asking how many species can have the same scientific name. I'm pretty sure that each species has a different scientific name, but just to be sure...

The scientific name (better known as latin name or binomial name) of a species is unique to this species. No two species can have the same latin name. Also, a single species cannot have two different latin names. But of course, mistakes happen and we don't seem to bother too much about them (esp. when the two species are very unrelated; see What instances are there in which two species share the same binomial name? (thanks @fileunderwater and @HRA).

Of course, the above is true as long as there is agreement in the limits of the definition of a species. In absence of such general agreement, there can be some issues. Consider for example, Homo neanderthalis who is often called Homo sapiens neanderthalis. See the post How could humans have interbred with Neanderthals if we're a different species? for more information about the definition and delimitations of species.

Have a look at wikipedia > Binomial nomenclature for more information.


When do the spindle fibers attach to the chromosome At what phase does this occur in mitosis (or even meiosis); some text books say prophase while others say metaphase.

Your confusion comes from the inconsistent terminology in the literature. The attachement of the spindles to the chromosomes happens in the Prometaphase [1, 2]. The name already suggests that this is not one of the classical phases is cell division, but lies somewhere between Pro- and metaphase. Wikipedia states:

  Prometaphase is sometimes simply included as part of the end of prophase and early metaphase.

If you really need to stick to the classical scheme of pro-, meta-, ana- and telophase, I would personally suggest to treat the attachement (not the formation!) of spindles as a part of the metaphase.


Could biofilms float and survive in the sulfuric acid clouds of Venus? The atmosphere of Venus is composed of 96.5% carbon dioxide, 3.5% nitrogen, and traces of other gases, most notably sulfur dioxide.
The main cloud deck is located in the 48-70 km altitude range and is composed mainly (75-96%) of sulfuric acid droplets, with a temperature of 27$⁰$C and a pressure of 0.53 atm at 55 km.
But to put the acidity into perspective, the mass loading of the droplets is 10 mg/m$³$, while the density of CO$_2$ at that altitude is about 950 g/m$³$.

Despite these harsh conditions for life, could biofilms float and survive there when certain bacteria species producing hydrogen could live within them ?

Nostoc commune for instance,is a  colonial species of cyanobacterium which forms a gelatinous mass for protection and can withstand acidic exposure and other extreme conditions like desiccation and high and low temperatures.
In addition the cells contain pigments that absorb ultraviolet radiation, which enables it to survive high levels of it, and in some cells nitrogen-fixing occurs.

There are also bacteria, like Enterobacter aerogenis, which produce hydrogen, and when it could live inside the gelatinous mass it could provide  the necessary buoyancy to float within the clouds of Venus.

Assuming the biofilms could be provided with the necessary trace elements, could they be airtight to some degree, to even float in the air with gas vesicles for buoyancy ?

I have pondered life on Venus.  I think the biggest problem would be lack of free water.  The atmosphere is thick and under high pressure, and polar CO2 and H2SO4 like to bind with water.  There is no water there.  Mass action would pull water out of any concentration of water (like a Nostoc blob) and into the waterless density of the adjacent atmosphere.  It would be like putting a Nostoc in a tub of salt grains.

Dessication would be the biggest problem.  The other problem related to lack of water is its requirement for photosynthesis.  If you had a photosynthetic organism there would be CO2 in abundance, but green algae type  photosynthesis also requires water as a raw material:  CO2+H2O+ light -> O2 + CHO (carbohydrate).  If you have only the water you brought with to Venus, with no prospects of replenishing it, you will run out quick.

You would need an organism that is not only durable, but had the metabolic chops to either pry H2O off of H2SO4 or use sulfur as its reducing agent instead of water.  Purple sulfur bacteria can do sulfur chemistry like this but they like starting with reduced sulfur, not H2SO4.  Purple sulfur bacteria need water as a solvent inside the cells just like we do.  But maybe something that can handle H2SO4 can make water out of it also?


PDB id to protein environment ph How can one find the information of a protein environment ph from its PDB id?
Can one assume the ph to be the same as its cellular location?

I know that ENSEMBL, PDB and the Human Atlas give known locations for many proteins at different levels of certainty, but such data is far from complete. Also experimental indication of a proteins localization does not prove the absence at other locations. Dependent on your scientific questions it might still be valid to theoretically look into specific scenarios of a proteins localization and to assume a certain pH of that sub-cellular context. SO to answer your question: Higher pH-resolution than the hypothesized cellular sub-localization is unrealistic, and the justification of the assumption of localization depends on your specific plan.


What (open) software there are for simulating behaviour of human (cortical) neurons? Is there any reliable open-source software for simulating the behaviour of human cortical neurons? I am looking for serious software, so let's assume I have access to a computer with more than 10,000 computing cores.

What I would like to do is to scan a subject's brain with MRI, record EEG during a simple task (e.g. listening to tone pips), project the EEG data to the cortical surface calculated from the MRI (solve the so-called electromagnetic inverse problem), and once that is done try to simulate the behavior of the cortical neurons at the "active" regions.

This simulation part is new to me, the rest I know quite well. All hints and ideas are welcome!

No, not in the neuronal level. Because IMHO this is an ill-posed problem.

EEG combined with MRI won't have the resolution to do solve the inverse problem of neuronal network simulation. There are at least hundreds of thousands of neurons that would be involved in your specific behavioral task, and you have at most a few hundred electrodes. You'll have to make grossly simplifying assumptions about how the brain works to start any inference. You might learn something, but the claim would be somewhat weak.

Personally, I wouldn't work with EEG if you are interested in the mechanistic details of the brain. It is a very useful signal for some cognitive investigations (especially for humans), but the current technology lacks the spatial resolution.

Yes, in the coarse scale network level. (response to @sets' feedback)

If you don't care about micro-scale dynamics of the neural network, and want to model some population-wide activation that changes EEG, as @sets commented, there are various source localization & dynamical system models that you can use. I am not an expert on this, so see @sets' answer, or hopefully someone else will answer in detail.


How long does foreign DNA stay intact in human blood? How aggressively is foreign DNA in blood targeted and degraded by the human body?
I am asking because we have a metagenomics project where we want to detect parasite DNA in the human blood. The process from DNA extraction to sequencing to bioinformatic analysis is not a problem for us. But the question is if we can expect some signal in the data.

The De Vlaminck Lab has extensively studied the origins of circulating cell-free DNA (cfDNA) in human plasma and its utility in detecting infections and organ injury.1,2  Concerning your question of parasite DNA detection and parsing signal from noise, I don't think you'll find a better resource than their 2020 publication in Microbiome.3
If the (uncited) claims on their website are to be believed, cfDNA from all sources is cleared within one hour after release into the blood.

Our research pursues technologies and applications of cell-free DNA in infectious and immune-related disease. The great promise of cfDNA in diagnostic medicine derives from i) its abundance: 10-100 billion molecules of cell-free DNA can be isolated from just 1 mL of plasma. The combined DNA sequence of these molecules is sufficient to cover the human genome 1,000 to 10,000 fold. ii) Its origin: cell-free DNA is derived from dead cells and comprises rich information about cells in the blood and any vascularized tissue that can be accessed noninvasively. iii) Its short lifetime: cell-free DNA is cleared from the blood within 60 minutes. Cell-free DNA therefore provides a very dynamic window into health.

References

Burnham P, Kim MS, Agbor-Enoh S, Luikart H, Valantine HA, Khush KK, De Vlaminck I. Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma. Sci Rep. 2016 Jun 14;6:27859.
Cheng AP, Burnham P, Lee JR, Cheng MP, Suthanthiran M, Dadhania D, De Vlaminck I. A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection. Proc Natl Acad Sci U S A. 2019 Sep 10;116(37):18738-18744.
Burnham P, Gomez-Lopez N, Heyang M, Cheng AP, Lenz JS, Dadhania DM, Lee JR, Suthanthiran M, Romero R, De Vlaminck I. Separating the signal from the noise in metagenomic cell-free DNA sequencing. Microbiome. 2020 Feb 11;8(1):18.


Would a plant survive if it was watered using hard-water? Hard water is water with high mineral/salt content. I'm told that a potted plant watered with a salt solution dries out sooner or later. Is this true?

If so, would a plant survive if watered using hard-water?

It would depend on the content of the hard-water. If the water contained heavier metals like lead or radioactive elements like tritium (Hydrogen-3), the plant would most likely die. Most land plants cannot survive when watered with massive amounts of salt water as the salt would absorb the water from the leaves.


How many systemic reactions in inflammation? I have this sentence in my notes

  Inflammation consists of two local reactions and one systemic reactions.

which is difficult for me to accept.
Two local reactions are vascular and cellular.
I think there are two systemic reactions too:

White blood cell response
Acute-phase response

How many systemic reactions there are in the inflammation?

There are two systemic reactions in inflammation too: mediated by leucocytes and acute-phase response (proteins).


Why sister chromatids and daughter cells but not brother chromatids and son cells? In biology, why do we have terminologies in terms of female relatoinships such as daughter cells and sister chromatids and not in terms of male relationships. When did this custom started and is there a reason for it ?

During the days when philosophers used to debate, they tended to regard  reproduction as a feminine trait. So naturally organisms/cells capable of producing offspring are also given a feminine trait. The parent cell is often called the mother cell, and the daughter cells are so named because they eventually become mother cell themselves.

I presume there exists a similar argument for sister chromatids, in that they are identical. When they separate, they are usually termed as undivided chromosomes.


Secondary structure and function in mRNA and single-stranded virus RNA Although some mRNAs and the RNA of single-stranded RNA viruses do have some secondary structure, this is much less than in rRNA, tRNA etc.

Why is this so? What prevents their folding to the extent of the RNAs mentioned?

And surely mRNA cannot have very much secondary structure. It enters the ribosome in a linear fashion, so if it bound to itself, wouldn’t that stop translation?

Summary

Both mRNA and the RNA of ssRNA viruses can have secondary structure, which is often important in regulating translation
The extent of secondary structure of RNAs depends on the base composition and sequence, so that RNAs of various degrees of folding are possible.
Weak RNA–RNA hydrogen bonding can be competed for by weak RNA–protein interactions, so that a dynamic situation is possible — secondary structure in some circumstances which is unwound in others.

Evidence for Secondary Structure in mRNA and viral RNAs

Work in the late 1960s and early 1970s on the translation of the polycistronic single-stranded virus RNAs (MS2, R17,Qβ etc.) provided evidence for their secondary structure. The extent of masking of the ribosome binding sites (Shine and Dalgarno regions) of different cistrons affected their translation, and treatments and mutations that destroyed the secondary structure stimulated translation. This 1980 paper by Iserentant and Fiers and this 1982 paper by Hall et al. provide entries to that literature.

Eukaryotic mRNAs do not normally have ribosome binding sites, although those of certain RNA viruses like polio do, and these have distinctive secondary structure (ribosome landing pad) — see e.g. this paper from Sonenberg’s group. However the majority of eukaryotic mRNAs have extensive secondary structure at their 5'-ends, which requires a specific helicase — initiation factor eIF4A — in conjunction with eIF4B and eIF4H to unwind — see e.g. Svitkin et al., RNA (2001).

Secondary Structure varies with Sequence

A little reflection is enough to convince oneself that the extent of self-folding of a single-stranded RNA depends on its nucleotide sequence. The extent of hydrogen bonding of, for example, an (AG)n polymer (A does not base-pair with G in a Watson–Crick helix) would be expected to be much less than that of an (AU)n polymer where A–U base pairing can occur. Likewise, continuous stretches of complementary bases are likely to result in extra stabilization by base stacking, and hence in a more stable secondary structure than the same number of interspersed base pairs. The fact that the secondary structure of a mRNA can be altered by changing the nucleotide sequence without changing the amino acid sequence of the protein product is illustrated by the algorithm described in this paper by Gaspar et al., Nucleic Acids Research, (2013).

Competition by Proteins

It has already been mentioned that proteins (eIF4A and other initiation factors) are involved in unwinding eukaryotic mRNA, and there are numerous examples of the interaction of proteins with specific nucleic acid structures (including the ribosomal landing pad (aka internal ribosome entry site — IRES), previously mentioned above and shown below).

[IRES for Hepatitis C virus RNA, showing areas of interaction with various proteins. From Hellen and Sarnow, Genes and Development (2001)]

The general concern that mRNA secondary structure would impede secondary structure has some basis, but the movement of the ribosome can disrupt secondary structure, as the initial RNA phage experiments indicated. One should remember that after each peptide bond is formed, the ribosome causes the translocation of the mRNA by three nucleotides with respect to the A and P sites, so that it is continuously applying a motive force to the mRNA.

Turning to viruses, tobacco mosaic virus (TMV) — a positive single-stranded RNA virus — was the first virus the structure of which was determined by X-ray crystallography. There is, therefore, a wealth of detail as to the organization of RNA and protein in its virion — this PDB ‘Molecule of the Month’ article (illustrated below with the RNA in red) is quite accessible (in both senses). (A schematic of the virion of a different virus — vesicular stomatitis virus — VSV — is also shown.)

The assembly of the TMV virion involves initial protein self-assembly followed by the looped RNA (secondary structure) being fed in and winding round the inner core. The secondary structure origin of assembly of the TMV RNA is shown below.


Source for 'EVERY living organism uses ATP as energy carrier', and can we make a synthetic one that doesn't? I have read it repeatedly that 'all living organisms use ATP as an energy currency etc' and 'some use GTP in addition'. However I am yet to find a reliable resource, rather than just quora/reddit/researchgate posts, that states this.

Also, would it be possible to create a synthetic organism which does not use ATP? Or GTP? What might be the best energy currency to use then?

Well your request for a source is rather like asking who first reported that 2+2=4. Not quite, but that should give the idea to someone who has not studied biochemistry. I doubt that you will find a source, but the following from Jacques Monod — the Nobel laureate — is worth quoting:

  “Anything found to be true of E. coli must also be true of elephants.”

In fact, this turns out not to be true for anything, but it is true of the role of ATP.

The better question, I think, is not what the source of such a quotation is, but what is the evidence for such an opinion. The evidence that has accumulated over the last 80 years or so is from examining the metabolic pathways present in different organisms, and, more recently, sequencing their genomes to identify the genes for various enzymes. What has been observed is a core of common pathways, involving a core mechanism of energy metabolism involving ATP. This is consistent with the idea that this arose early in evolution and was fixed in the last common ancestor of living things.

If you want a more recent source to the ideas above, I suggest another SE Biology question, Immortal genes common to all organisms, may provide a starting point.


Is DNA actually like source code repository? So after reading articles like "People Use Just 8.2% of Their DNA" etc., and thinking a bit... I got this idea:

What if DNA is actually like a software source code repository? You know, it has "master" branch - which is most stable and up-to-date version of program but also it has other branches, experimental ones and of course it has huge amount of "junk" - i.e. backed up version of files from previous changes to code that is not used in any way in actual program.

So what if first primitive single-cellar organisms had super primitive and very short DNA, then it got improved, but original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

Theoretically, the more primitive organism is, the shorter DNA it should have. For example, some very old sharks that still survive from Mesozoic era should have shorter DNA than modern sharks... Is this confirmed by actual experiments?

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

Also this explains why human embryo come though all this steps of been single cell, multi-cell, fish, amphibian, mammal etc.

I'm no expert in biology by any means, and I suspect that this idea was around for long time, but I'm not sure... What do you think?

I think this analogy is not actually that bad, but you are making some incorrect conclusions from it especially regarding 'junk' DNA and which parts of a repository DNA holds (which shows the limits of analogy!). Think instead of the DNA of an organism as a single local copy of a particular commit.

There is no remote to compare to and no list of historical changes, each organism just has its own local copy of the most recent source that can sometimes be merged with other local copies via sexual reproduction or horizontal gene transfer.

What you need to drop from the analogy

Get rid of any thought of a master branch or ideas that the repository contains backups of previous versions. These thoughts will only mislead you.

This statement:

  original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

makes little to no sense in biology. There is no backup, except in that each organism is a branch of it's parent(s) source.

Where the analogy could work

Genomes of different species are all branches from some original source code. Therefore, you find a lot of commonality when you compare even very distantly related life, especially in the most key libraries that are involved. There is a ton of conserved sequence in the basic machinery for replicating DNA and producing proteins, for example.

This is why your statement:

  This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

is mostly correct.

Length of source

Your analogy has gotten some criticism for your conclusion:

  Theoretically, the more primitive organism is, the shorter DNA it should have.

but I would argue this is actually a way in which your analogy works, yet your conclusion from it does not. Software development involves both adding new code and deleting obsolete code. Lines of code is a poor measure of how primitive some code is. Biology shows this well: all life is equally primitive in terms of years of existence, and single-celled organisms are much more advanced in terms of numbers of generations. If organisms contained some log of all the past changes (which they do not), the repository would be way way bigger in bacteria than in animals because of that large number of generations.

Summary

In summary, analogy can be helpful to wrap your head around some information, but be careful in taking it too far. Sometimes analogy is good for generating new hypotheses and for guiding your learning, but you need to verify those hypotheses in the actual biology (see Richland and Simms 2015 for one take on the usefulness of analogy as an educational tool).

I disagree strongly with the comment by @SPr stating "The analogy between the genome and source code repository is unhelpful and poor": even the imperfection in an analogy can be very helpful in that they help you build a relational map of the world by finding where analogies work and where they conflict.

Richland, L. E., & Simms, N. (2015). Analogy, higher order thinking, and education. Wiley Interdisciplinary Reviews: Cognitive Science, 6(2), 177-192.


Is local equilibrium a reasonable assumption for evolutionary processes? Whenever I look at discussions of fitness landscapes (in particular, Kauffman's NK model) the questions tend to resemble:

  The population is at a local equilibrium, but another equilibrium of higher fitness exists, how will the population cross the fitness valley between these equilibria?

These sort of statements assume that the population has reached a local equilibrium. Although, the local equilibria must exist, why do the people working in this field believe that they can be found before environmental (or other external events) change the fitness function? Are the timescales required to go from a random initial population to one that is at a local equilibrium compatible with the typical time-scales on which a fixed fitness landscape is an appropriate approximation?

If we switch to the polar opposite model of complete frequency-dependent selection (say replicator dynamics in evolutionary game theory) then limit-cycles (think rock-paper scissors game) and chaotic-attractors are common and it is possible for the population genetics to be constantly changing and never at equilibrium.

In an experimental setting, it also seems like although beneficial point-mutations are much more rare than deleterious, they do exist. This would suggest that experimentally, organisms are not at a local equilibrium. Do model organisms tend to be at local fitness equilibria?

In general, is the local equilibrium assumption in fitness landscapes research a reasonable assumption?

Nothing is at a genome-wide local equilibrium. Graham Bell wrote fairly extensively on this (IIRC).

Some loci

will be at what are likely global optimums (e.g. Cytochrome oxidase)
will be at local but not global optimums (e.g. low-fitness malaria resistance vs. high fitness malaria resistance: for the extremely cool story check out this page)
will not be at any optima because the environment shifts too quickly (e.g. loci clearly under frequency-dependent selection, such as MHC).

So, in general, it depends what you are trying to model. If you want to model a specific kind of evolutionary change, then model that kind of evolutionary change. If you want to model a different kind of change, then model that kind of evolutionary change. Natural populations will likely follow any model some of the time, but will probably never follow any model all of the time.


Will bark-beetles infest the Methow Valley? What is the Methow Valley (esp. Winthrop, WA) area's susceptibility to bark beetles?  Did the 2014 Carlton Complex wildfires increase the vulnerability due to the large numbers of dead, dying, and stressed pine and fir species in the area.  Are there ways I can reduce the vulnerability of my property, which is already in open, park-like stands?

I had trouble finding any academic or governmental references for rates of spread of Scolytids (bark beetles) in your region, but the answer to this would require speculation (i.e. prediction). Many factors, including the 'health' of the trees surrounding your home, and the connectivity of your trees to invaded areas, would aid in bark predicting whether these beetles will eventually make their way onto your property.

If your property is large, consider cost-share programs for management/prevention in your area.

See the bottom of this .gov webpage for more references. Good luck.


Is the missing "life-ingredient" in today's Earth's existence the reason why we cannot recreate life? As far as I know, there was no report of "life" popping up in a lab or in nature so far.

Everything that we know is only some copy with similarity to previous life-forms.

We certainly can mix some amino acids and stuff, and even some of the chemicals can retain some structure for a certain time and even form some proto-RNA-like structure (not sure how they called it in one document I have seen), but it's very very far from a living organism.

Does it mean that life cannot be "sparked" in today's Earth like conditions or, was it not even sparked here to begin with? I have read, as many others have done, this article: New research supports an idea that the Red Planet was a better place to kick-start biology billions of years ago than the early Earth was. They argue that you need molybdenum to create life-like structures and that it's not common in the right form on Earth.

What do you as biologists think about the statement that life cannot evolve on Earth because the conditions in the beginning of the Earth were not good for life to develop.

Three important concepts about abiogenesis
Let's start with three important concepts
Definition of life
You'll need to give a good definition of life, because biologists actually don't have one (it is a matter of philosophy to define life, not biology).
Time it took for life to emerge
Life as we know it emerged only after a huge period of time (hundreds of millions of years), which we obviously cannot reproduce in a lab.
Current competition
Even if some kind of protolife would appear at some point, it would still have to face the competition with its veteran partners. Hypothetical protocells would be eaten by some microbe with no doubt.
Panspermia
The idea of panspermia (the hypothesis that the life may have appeard in outer space or in another planets, and then "contaminate" the Earth) has been on the scene in many forms for quite a long time. Regularly we hear of some study which proposes that life, or at least some key biomolecule, may have formed in asteroids, comets, in Mars or somewhere else. They're quite interesting, mainly because they suggest more than one way that life may have appeared.
Molybdenum
While molybdenum is rare in the Earth, it still exists and so the study doesn't deny the posibility that life may have formed in the Earth. Nowadays, molybdenum is used by many organisms as part of the core of some key enzymes, such as nitrogenase (the enzyme complex that catalyzes the conversion of molecular nitrogen into nitrate). Molybdenum has very interesting catalytic qualities and may have been a key factor for the origin of life.
Phosphorus on Mars
However, those studies say that Mars has higher concentration of phosphorus, which is one of the main components of life, and that was pretty rare in the early Earth. The hypothesis is interesting but, without experimental data, it is only that. The authors suggest that nowadays those phenomena may happen in Mars, so the hypothesis may be confirmed in a few years as the exploration of the Red Planet continues.


What kind of beetle is this (2cm long, brown, "V-shaped" body)? I've seen this brown beetle, which was about 2cm-3cm long (I guess) near Loch Lomond (Scottland) a few days ago.

What kind of beetle is it?

Honestly, that looks like a stink bug, family Pentatomidae.

You can see some slightly different coloured ones here on Insects of Scotland

Here is a photo of the one that I used to see in the States (From Master Gardening):


Is there a known or quantifiable correlation between capsaicin and its effect on the body's metabolism? I've often heard that spicy foods can speed up your metabolism, I presume, due to the capsaicin.  Though I'm sure this is a minor effect - I doubt eating a pound of jalapenos a day will help me lose weight - has the medical/nutrition community quantified how various levels of capcaicin affect the body's metabolism?

Capsaicin do affect your metabolism. It affects your Capsacin receptors ( scientifically TRPV1 receptors). These receptor starts calcium influx into various types of tissues. In endothelial cells because of this it mimics stress response (McCarty et al 2015). Quoting from McCarty et al,

  Clinically, ingestion of capsaicin-or its less stable non-pungent analogue capsiate-has been shown to boost metabolic rate modestly. opical application of capsaicin via patch was found to increase exercise time to ischaemic threshold in patients with angina

Coming to your question, there are scientific studies which suggest that capsaicin helps in maintaining weight by limiting weight regain after weight loss. Not just this, capsaicin has also shown potential in treatment of obesity. However you should remember that it will required specific amount of dose (you can check details in papers I cited ) to help maintaining your weight. Do not eat pound of jalapenos a day :P


Bad Eyesight and Evolution Why do many humans have bad eyesight, such as near-sightedness, which hampers performance in a wide variety of tasks? Shouldn't there be evolutionary pressure towards better eyesight?

Remi.b and Potterbond007 have put forward excellent answers. Would like to add something..

One of the reasons that Myopia (near sightedness) happens is because of use of eye in work like reading, which requires working with close objects. I don't think there was much working with close objects in the past. So very few people with myopia might have been present (and of course, they may have had disadvantages in catching prey.)

Other common disease is hypermetropia which generally occurs during old age, past the reproductive prime, so it could not have much evolutionary impact.


Can the psychology of a person alter his immune system and health? Can the psychology of a moderate aged person alter his immune health? because I have read many a times about the different types of linkages between nervous system and immune system.

Can someone outline the general facts about what is understood in this relationship from which i would gain some knowledge?

I'm not sure what you mean by psychology exactly, but assuming you are referring to a persons mental state there is a known link between stress and immunity. This link occurs through neuro-endocrine pathways. The central nervous system and endocrine (hormonal) systems are linked through the hypothalamus, a key controller of hormone release in the central nervous system. In a state of stress our central nervous system reacts by increasing the release of hormones such as the steroid cortisol and catacholamines such as adrenaline (a.k.a epinephrine in USA).

We know that steroids have an effect of dampening down the immune system (in fact steroids are often used for this intentionally in the case of autoimmune conditions for example). Thus based on this we have a scenario where stress can lead to increase in cortisol (and other hormones) which in turn can have an effect on your immunity. The effect to which this impacts on your life is then further dependent on your psychology and social support.

More generally, the links between illness and psychology are integrated together in what is called the biopsychosocial model of illness. I suggest you look this up to gain a more in depth understanding of this complicated issue.


About artificially induced processes that would normally cause a cell to self-destruct Are there certain biochemical processes that would normally cause a cell to self-destruct but if the cell being tested has apoptosis mechanisms that have malfunctioned or been 'turned off' the cell will not 'malfunction' because of the induced process ? Are there such biochemical processes that could indirectly indicate which cells have no functioning apoptosis mechanisms? If so would this be a possible test for cancerous cells?

In some cases yes — when there is a mutation in apoptotic regulators such as Bcl2 family of proteins. In other cases it is difficult to identify and only identification is that those cells are growing rapidly; in other words failure to undergo apoptosis is not the cause but the effect of the cancerous transformation (as in case of p53, Ras, Myc mutations etc).


Is glutamate always involved in the deamination and amination of the other amino acids? For example, are there pathways for the deamination of phenylalanine that simply produce ammonia or pathways for it to be synthesized from phenylpyruvate with ammonia being utilized to form the amine group?

Preferably, I want to know how it is with human metabolism mainly.

For most amino acids, the removal of the α-amino group involves α-ketoglutarate and glutamate. The amino group is first transferred to a-ketoglutarate by transaminases, and the resulting glutamate is then deaminated (via glutamate dehydrogenase) to yield ammonia.

The same is true for amination. Glutamate and glutamine are the two major amino group-donors. Most ketoacids are converted to their respective amino acids by transamination involving glutamate or glutamine. Glutamine can be synthesized by amination of glutamate with ammonia without transamination (via a synthetase enzyme) and glutamate can be aminated with ammonia too.

Exceptions do exist, of course. For example, Not all transaminations involve glutamate/glutamine (as this user has replied), and serine and threonine can be directly deaminated (via dehydratase enzymes, as opposed to the dehydrogenase used for glutamate).


Are there any types of cancer that cause neurons to divide? After birth neurons generally do not divide. But is there any specific type of rare cancer or tumour where neurons divide? And if there is such a cancer, then how is it possible for a neuron to regain the division power?

I think that most mature cells do not divide in all tissues. If an organism needs to repair tissues, it uses tissue cell precursors -- stem cells.

In case of neurons, these are neuroblasts. Neuroblasts can divide and can repair brains under some circumstances (I don't know under which).

There is a cancer grown from neuroblasts, called neuroblastoma.

I think it is very improbable to have tumor from neurons, because division genes are turned off in mature cells. Can't state it is not occurring in practice.


What are the minimum conditions required for "open-ended evolution"? According to a paper about artificial life systems, the following four conditions have to be fulfilled for "open-ended evolution":

  Condition 1: A rule should be enforced that individuals must meet some minimal criterion (MC) before they can reproduce, and that
  criterion must be nontrivial
  Condition 2: The evolution of new individuals should create novel opportunities for satisfying the MC
  Condition 3: Decisions about how and where individuals interact with the world should be made by the individuals themselves
  Condition 4: The potential size and complexity of the individuals’ phenotypes should be (in principle) unbounded

My question
Must these conditions be met for open-ended evolution to occur? If so, do we have evidence that all of these conditions fulfilled in nature? If not, could you give examples where one or more conditions are violated?

In principle open-ended evolution can occur with condition one violated. Because evolution is simply a change from one generation to the next (see answers here, here, and here), the is no requisite for a "non-trivial minimal criterion". Such a minimal criterion (e.g. survival to sexual maturuity) would imply that evolution is occurring by drift or selection, because being non-trivial implies that some members of the evolving population will fail to reproduce. However, evolution also occurs by mutation (and migration).

For example, we can have a population at generation $1$, and each individual within that population produces one offspring, present in the next generation. This means no variation in reproduction exists. If generation $2$, the offspring of generation $1$, carry new mutations then the characteristics of generation $1$ and $2$ can differ, and the descendant generation has evolved from the ancestral state. This can be seen in mutation accumulation lines as an example:

  "In a typical mutation accumulation experiment a single inbred and
  highly homozygous line is replicated.  Each of the replicated lines is
  maintained at a very small population size (usually brother sister
  mating, or in plants, selfing).  These lines are maintained for many
  generations.  During that time mutations accumulate, and the lines
  generally decline in fitness, and the variance among lines increases." - UVM Blog

So the answer to your question, these conditions are not necessarily met in nature. However, that doesn't mean evolution can't be open ended - the conditions outlined in the paper are flawed when trying to compare to nature. Evolution can occur when the "minimal criterion" is trivial (when all individuals are capable of meeting the criteria). The existence of a non-trivial MC only implies drift (e.g. some don't reach survival to sexual maturity by bad luck) or selection (e.g. some don't reach sexual maturity because they carry a genetic disease which kills them first). A trivial MC says that there is no drift or selection, but says nothing of mutation. I have since spoken with one of the authors who describes a non-trivial MC as the same thing:

  "Regarding nontriviality, it should at least be possible that some
  individuals do not meet the MC"

Note: I have only focussed on condition 1, because this condition is not necessarily met in nature, thus your question is answered (are all conditions satisfied in nature)


Why is only one primer used for DNA sequencing instead of two? I understand that PCR uses two primers that anneal to the two ssDNA's in order to exponentially amplify a DNA and that Sanger sequencing uses only one primer because a sequence can be determined with only using one primer and one single-strand with ddNTPs. However I've read this:

"Sequencing uses one primer, while PCR utilizes two. If we try to sequence with two primers present, you'll get the two sequences back, superimposed on each other and completely unreadable."

I'm struggling to visualize why using two would be an issue though, how will that make the DNA unreadable?

Thanks in advance!

The reaction for the Sanger sequencing reacting contains beneath the normal dNTP (which are needed to make most of the DNA) the dideoxynucleotides, which lack the 3'-OH-Group and which are labelled with a fluorescent dye. Once one of this nucleotides is incorporated, the chain reaction stops here, leading to a product with a specific length and a known (by the fluorescent dye) end base.

In theory this leads to products of a length primer + 1 ddNTP base, primer + 1 base + 1 ddNTP base, primer + 2 bases + 1 ddNTP base and so on. The sequencer seperates these bases by sizes and the sequentially reads out the fluorescent dye and translates this into a sequence of bases. See the image from the Wikipedia for illustration:

If you now add two primers (and of course have a double stranded DNA), this reaction will start from both ends of the DNA (always in 5'--> 3' direction) leading to two sets of marked DNA of the same size (so again the base + 1 ddNTP, base + 1 base + 1 ddNTP and so on). Since these are equal in size, you will always read out two bases at the same time and you will not be able to tell, which signal belongs to which strand. This looks like this (from here):


What happens to human dopaminergic reward system once a teenager becomes adult? I've recently heard a podcast which explained teenage impulsivity and novelty seeking in part by

"Lowering the baseline dopamine activity in the reward system"
"Increase in dopaminergic reward in response to novelty"

I assume that by reward system the author means mesolimbic and mesocortical dompaminergic pathways in the brain.

Here's an article that seems to state similar findings:

  Starting in early adolescence and peaking midway through, this
  enhanced dopamine release causes adolescents to gravitate toward
  thrilling experiences and exhilarating sensations. Research even
  suggests that the baseline level of dopamine is lower—but its release
  in response to experience is higher—which can explain why teens may
  report a feeling of being “bored” unless they are engaging in some
  stimulating and novel activities.

The dopamine system here is being compared to the child's dopamine system. I'm interested in what happens to the dopaminergic system once a teenager/adolescent becomes an adult at around the age of 24-25?

I'm looking for insight along these lines - does the reward system of an adult "settle down" and no longer respond to novelty as strongly? Is the baseline dopamine level higher?

This may shed light on why the teenagers response to dopamine changes. Quote from reuniting website

  There's much still to learn, but it looks like a number of reward
  circuitry events occur after climax that have the potential to
  desensitize us for a time. First, androgen receptors decline after
  ejaculation, and take up to seven days to normalize. (That means the
  effects of testosterone on the reward circuitry are probably blunted
  for a while, quite possibly affecting outlook.) In addition, opioids
  released during copulation hang around for a while, apparently causing
  lingering declines in oxytocin, which hamper sexual responsiveness. As
  noted above, there is also likely a drop in responsiveness to a
  neurochemical vital to our sense of well-being: dopamine. In effect,
  the brain has changed. It now requires more stimulation to get the
  same pleasure response as before, and sometimes no amount of
  stimulation will truly satisfy—until it recovers. Anecdotal evidence
  suggests that such changes affect both sexes.

The author further suggests that orgasm and ejaculation increase prolactin levels for up to 14 days, during which the brain is less responsive to pleasure and requires novel entertainment or partners to produce pleasure.

From the info on that site, it seems that the 14 day dopamine-affecting cycle following orgasm continues for as long as a person is sexually active (with orgasms). With this in mind, it appears that the adult response to dopamine release is the same as teenagers who are sexually active.


White flower with spikes around base? What type of flower is this?
Location : India

This does in fact look like the flower to the cactus species Selenicereus grandiflorus.

 Source: Wikimedia

According to "Indigenous Cactus biodiversity: A viable genetic resource to fulfill multiform needs under rainfed ecosystems"1, this plant is found in India:

  Different varieties of the cactus are found in India which has immense ethnomedicinal value (Table 1). Selenicereus grandiflorus (with large sweet-scented night flowering flowers) and the Opuntia stricta are found in the wasteland as hedge plants

See here for a good image, and see here for a cool gif of one of these flowers blooming!

1. Rai, M., Singh, R.K., Sharma, P.C. and Singh, L.K., 2011. Indigenous Cactus biodiversity: A viable genetic resource to fulfill multiform needs under rainfed ecosystems.


Which one is true about sunflowers, "follow the sun across the sky" or "always face east"? Which one is true :

Sunflowers follow the sun across the sky.

Or...

Sunflowers always face east.

Or are there 2 kinds of sunflowers with different behaviours?

Both are correct.

The issue here is the developmental stage of the flower, that is, if it is a immature or a mature flower (actually, not a flower but an inflorescence instead).

Immature or young flowerheads do display heliotropism. However, as the flower matures, it stops showing heliotropism and becomes "fixed", always facing east.

This is a photo of the sunset. If the mature flowers (or inflorescences) still displayed heliotropism, they would be facing the sun (at the west). However, they face the opposite side (east):

Also, to be honest with the sources, the first link (Science ABC) you provided does make that clear. You can read next to the end:

  Mature sunflowers finally stop displaying heliotropism.

So, there is no contradictory information here.

A good source of information, with videos, can be found at this page of Berkeley University, which says:

  As the sunflower matures and the flower opens up, overall growth slows down and the plants stop moving during the day and settle down facing east. This seems to be because, as overall growth slows down, the circadian clock ensures that the plant reacts more strongly to light early in the morning that in the afternoon or evening, so it gradually stops moving westwards during the day.

Source: https://nature.berkeley.edu/news/2016/08/sunflowers-move-clock


Calculation of water potential For a mesophyte growing in a moist soil, water potential of its root sap is -3 atm, then how to find the water potential of moist soil and leaf respectively?

I don't know if we can calculate the exact values. The only thing I can say is that the potential of the soil will be less negative than -3 while that of the leaf will be more negative.

You know that water travels from higher potential to lower potential. So, it will travel from a region of less negative water potential to a region of more negative water potential.


Where can I find mutation datasets for cancer? My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by checking how they hold up against other cancer datasets.

I know that one resource we can use is the International Cancer Genome Consortium but I'm wondering if members of this forum can suggest a few other places we can get both clinical and somatic mutations data for cohorts of cancer patients.

As I'm sure you're aware, there is no complete centralised database for cancer gene mutations. The most comprehensive database is the TGCA as you've already mentioned. That doesn't mean that other data isn't out there.

A broad option that might fit your needs is to query OMIM hosted by NCBI. You can search "cancer" or something more specific and then select the dbSNP tab and it will return a list of gene locations of mutations that match the query.

For a more specific search, COSMIC hosted by SANGER allows downloads of the "cancer genes" in fasta format, and various other downloads with other information are available. It's manually curated which is always a bonus, however this does mean that it's limited to just a few genes. There is also BIC. This is specifically focussed on genes related to breast cancer and is hosted by NHGRI. Again, an account is required for the download and it is limited to genes affecting breast cancers.


Does sympathetic nervous system acts bilaterally for pupil dilation or other two sided organs? The question might seem weird. Does sympathetic nervous system acts 'bilaterally' meaning if you shout to a person's left ear a loud noise (e.g. by headphones), will it activate sympathetic system just on the left or on the both sides. For example it will only dilate left pupil or dilate both ?

Yes, they do. At least in the case of pupils. In fact, the absense of simultaneous regulation of the diameter of the pupil is used as a medical test for the evaluation of brain damage.


Why are my calculations for O2 requirements of daily metabolism so far off? When I attempt to calculate the O2 necessary for a day of metabolism at rest (for an imaginary average human) and compare it with the expected O2 consumed per day my results differ by a factor of 3. I don't expect it to be 1 to 1, but a factor of 3 makes me think that I am missing a fundamental concept.

For our fictional human, I'm starting with the values for 1 MET. Specifically:

RMR (kcal / kg / hr) = 1
VO2 (mL / kg / min) = 3.5

I then define the weight of my human:

weight (kg) = 70
RMR (kcal / hr) = 70
VO2 (mL / min) = 245

And convert to more useful units:

RMR (kcal / day) = 70 * 24 = 1680
VO2 (L / day) = 245 * 60 * 24 / 1000 = 352.8

At this point, my understanding is that consuming 352.8 L of oxygen should produce somewhere in the ballpark of 1680 kcal at rest. My next assumption is going to be that aerobic respiration of glucose is accounting for all of the energy throughout this day of rest. I'm aware this isn't reality, but I wouldn't expect it to be 3x off. I'd guess that either this assumption is wrong or I'm misunderstanding something in the following math.

Let's start with some more constants regarding cellular respiration.

ATP creates 7.3 kcal / mol
An average of 30 ATP are generated per glucose (glycolysis, krebs, etc)
6 O2 are required to aerobically metabolize 1 glucose

Given the energy to ATP ratio, we can compute the ATP necessary per day. I should note that the result here is about twice as high as reference numbers I've seen so I am suspicious.

ATP (mol / day) = 1680 / 7.3 = 230.1369863
Glucose (mol / day ) = 230.1369863 / 30 = 7.671232877
O2 (mol / day) = 7.671232877 * 6 = 46.02739726

To convert the O2 requirements for our ATP from moles to liters, we use Avogadro's law at standard pressure (100 kPa) to conclude there are 22.712 liters per mole in a gas.

O2 (L / day) = 46.02739726 * 22.712 = 1045.374247

And finally, we can see that my calculation says that you need 1045.37 liters of oxygen to produce 1680 kcal of energy through aerobic respiration, but earlier I computed that you should only need 352.8 liters using 1 MET as my basis. There were assumptions made in there, but these results make me think that I am still misunderstanding a fundamental concept.

The math was correct, but there was a misunderstanding in what some of the numbers represent. The energy expenditures listed for RMR include resting dietary thermogenesis in addition to the actual ATP energy used for work. You can see that the same is done for reporting Calories in food (e.g. 4 per carb) at http://www.fao.org/docrep/006/Y5022E/y5022e04.htm

When this is taken into account, we use 686 kcal/mole of glucose to get similar oxygen numbers. This includes the energy for the ATP and the energy from heat.


Why do people say that trans fatty acids are bad for your health? I've heard from several sources that trans FAs are bad for you and their consumption will lead to cardiac problems, and that they are indigestible.
But I also learned from biochemistry that they are digestible. What is the reason for this, or is it true at all?

Trans fatty acids are digestible, but they cause an increase in LDL and a decrease in HDL, which is the leading mechanism for atherosclerosis. So, they increase the risk of a cardiac infarct.

LDL means Low Density Lipoprotein, it's one of the 5 major lipoprotein groups. Lipoproteins carries the fatty acids and cholesterol which were absorbed from intestines (because lipids are hydrophobic and cannot be carried within the blood directly like glucose or proteins.)

So, LDL mainly carries cholesterol and fatty acids from intestines to tissues. (fatty acids and cholesterol are essential for cells.) But in excess levels, they tend to accumulate in vessel walls, which also starts and inflammatory response and makes the situation worse. (mainly includes macrophages and T cells) This is the main mechanism for atherosclerosis.

In the other hand, HDLs serve as a reverse cholesterol transport system, which carries the cholesterol back, mostly to the liver (for bile secretion) or steroidogenic organs such as adrenals, ovary, and testes by direct and indirect pathways. So a high HDL reduces the atherosclerotic process.


Identify this insect, found in Central Vietnam, with long antennae, black wings, and red body Last year this insect landed on my hand when visiting the My Son city ruins in Central Vietnam.
I've been trying to identify the insect, but until now without result.

Can you help me? Or do you know who could?

This is a male scale insect, which are Hemipterans from the superfamily Coccoidea.

The one in your photo is probably from the Genus Drosicha. Here is the Wikipedia page for Drosicha corpulenta.

Here is an image, for comparison:

Here is another one, with black antennae, like yours:

There is no doubt that your specimen is a male because sexual dimorphism in Coccoidea is huge. Have a look at the females of Drosicha:

In conclusion, determining the exact species here is very difficult. However, we can be sure that the Genus of your insect is Drosicha.


How is green fluorescent protein distributed while inside an organism? I would like to know a relatively simple thing, but something I wasn't finding the answer to.  When fluorescent protein is used in a relatively large, non-transparent animal, like a mouse, or theoretically a dog or a human, how is the protein generally incorporated into the tissue?  I suppose that it would bind to elastin and otherwise it could be transfected into different cells in and throughout tissue, both around the skin and deeper.  However, wouldn't it only be useful near to the skin, since ultraviolet light and visible light would penetrate a limited distance through tissue?  Then again, a relatively bright light source could possibly produce light from deeper in tissue.  I'm not quite sure.  It's a relatively simple question, but I appreciate it.

(Edit): I may have been a little vague with the question, a more specific version of the question I asked would be; given the brightness of a fluorescent light source that is directed at fluorescent protein filled tissue (with UV assumed to be close to the visible spectrum) and the portion of that light which is converted to visible light, approximately how could you calculate the relative brightness of the protein at a certain depth in the tissue.  Of course it probably is very difficult to get accuracy with that because that would depend on the portion of fat, muscle, collagen, etc in the tissue.  But if there's something rough and general, like the depth of the protein would reduce its relative brightness proportionally to the natural log per millimeter or something, that would be fine.

Distribution of GFP

When used as a reporter usually GFP is expressed by the cells themselves or attached to an antibody and injected. It ends up everywhere, is what I mean.

Localization of GFP

There are three solutions to the hidden-behind-tissue problem for fluorescence.

Use a functionally 2D sample (nematodes, mouse limbs, etc)
Sacrifice the organism(if it's not dead already) and use optical clearing
Cleverness

Of these cleverness is the most interesting. Types of cleverness include time-resolution imaging(Light scatters instantly but most fluorescent proteins take a few nanoseconds to relax) to separate fluorescence from backscatter. Excite a slice of the sample and look at it from a slight angle 3 ns later, and you should see a depth-map. Repeat.

You could also use optical tomography to essentially use computers and many cameras instead of time-delay imaging to solve for the 3d distribution of signal. Computed tomography is much cheaper, mostly because you don't need a nanosecond-scale laser + capture system(those are expensive).


How does a garlic clove thrive inside a closed refrigerator? A garlic clove has been growing very well inside a closed refrigerator.

It has developed beautiful green stalks, which I think are the equivalent of leafs.  Since they are green, I assume they contain chlorophyll.

Without any source of sunlight (for photosynthesis) or soil (for nutrients), how can such a plant thrive so well?

Is it simply growing off the internal stored energy of the clove itself?

Will it continue to grow without sunlight and soil?

Your garlic was likely purchased as a bulb, not seed, and stored in the fridge.  The garlic 'clove' is not frozen, so your fridge readily mimics underground conditions in the temperate late winter or spring season. The bulb is generally buried underground, and the subsequent initiation of plant development and growth uses the stored energy. In a garden, the garlic would, however, begin photosynthesizing soon thereafter. Bad news: in your fridge, the plant is certain to become etiolated, because the lack of light, and yes, eventually run out of the stored resources--and die. Good news: you can eat or transplant it.


What are the benefits of elucidating the crystal structure of a protein? I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we potentially learn from the structure in terms of biological significance?

Are there examples of drugs, or treatments that have only been made possible because of a known crystal structure?

Generally speaking, why do people spend all the money on synchrotrons, laboratories, robots and so on, for a crystal structure?

Protein structures, which can be obtained from protein crystals or from concentrated solutions of pure protein via NMR, are arguably the primary source of knowledge that we have about how genes perform their function on the molecular level.

I've added a link to RCSB.org above - they write up a story on an important protein structure monthly(?) - its a great way to pick up some fascinating stories.

The precise atomic positions from a protein structure are indispensible for several reasons.  Since biological processes are all fundamentally chemical ones.  The specific positions of the atoms reveal how proteins, nucleotides, lipids, drugs and other biological molecules specifically interact.

Examples:

Protein structures broke the ground in biological inheritance (Watson / Crick / Franklin's DNA structure)
Protein structures of lysozyme and proteases were the first to show exactly how proteins bind their substrates and enzymatically catalyze chemical reactions.
Protein structure of hemoglobin in both oxy- and deoxy- forms (i.e. with and without oxygen bound). showed that proteins change their spatial arrangement to modulate their function.

This list goes on to more recent breakthroughs in how signals and molecules interact with the cell through the membrane.  There is literally no topic in cellular biology which has not substantially benefitted from having a protein structure revealed.

The advantages of working with protein crystals are that they can be larger proteins and certain kinds of difference experiments an be more easily performed when a protein crystal is obtained.  For instance if you have a crystal of a 100 kDa (~900 amino acid) protein, you can often find the binding pocket of the enzyme without a tremendous amount of work.

The disadvantage of working with protein crystals, as you probably know well is that getting crystals is often a quixotic effort soaking up months or years, often with little or no results.  Pretty demoralizing until you hit the target.

If you're astounded to think that proteins, which are often hundreds or thousands of times larger than a salt or mineral you usually find in crystals...you are dead on.  The crystals are often very tiny - a decent sized crystal measures about a millimeter on one side, but often are only a fraction of that size.  That's why protein crystals often are taken to synchrotrons, linear accellerators or other free electron X-ray sources which are millions (?) of times more intense than a dental x-ray. I would guess that most protein crystal structures are obtained using special beamlines created especially for biological crystallography.

That sort of tells you the funding priority science is willing to put into x-ray protein crystal structures.  Simply the idea that protein crystals might be easier to grow in microgravity (along with the low weight of the experiment) justified over a decade of protein crystal growth experiments on the shuttle and ISS.

Interesting note: The Guardian (which is based in the UK where crystallography, protein or otherwise started out) has posted a short video outlining highlights of crystallography's contributions over the past 100 years.  If you watch assiduously you will see protein crystallography cropping up with a litany of nobel prizes.

New thoughts:
There are signs that crystal structures are coming to an end.  Using an electron micrograph to simply take a picture of many thousands of individual proteins laying about can be digitally averaged to create low resolution structures they are gradually becoming higher resolution and are a lot less work than preparing and making a protein crystal - and it works well on larger proteins and protein complexes!


Exact definition of single nucleotide polymorphism (SNP) So, I know on a higher level what an SNP is but I'm a bit confused about the details.

Firstly, our professor said that an SNP has to have at least a prevalence of 1% in the general population to be considered an SNP and not just a mutation. Wikipedia says the prevalence needs to be 0.5%. Is this actually a strictly followed cutoff? And which of the two values is correct?

Secondly, he said that SNPs never cause a disease but can only predispose you to one. However, the wikipedia article mentions thier role in diseases that are clearly caused by single mutations (cystic fibrosis, sickel cell anemia, and beta thalassemia). So, can SNPs cause a disease or not?

In genetics, a SNP (Single Nucleotide Polymporphism) is the substitution of a nucleotide with a different one.
A SNP can have phenotypic effects or not.

A mutation, in genetics, is any kind of inherited change in DNA. Mutation types are: SNPs, indels, structural variants, translocations and so on.

Sometimes researchers (especially in the field of medical genetics) call "mutation" (meaning "pathogenic mutation") a SNP which is responsible of a disease (especially in case of a Mendelian disease). Since mutations causing severe Mendelian diseases are usually rare, several people use the arbitrary threshold of 1% to discriminate between a "SNP" and a "mutation".

So, probably your professor is stating that SNPs cannot cause a Mendelian disease because he uses the last definition I gave. However, while this definition may be useful for medical genetics purposes (i.e. I also agree that a very common variant is unlikely to be causing a rare Mendelian disease), it is arbitrary, if not wrong.


How can I avoid digesting protein-bound DNA? I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion.

When digesting protein-bound DNA, is all of the unbound DNA digested? Is there a way to maximize the amount of unbound DNA that is digested?

Well, it depends if you just want to sequence your protein bound fragments.
If that is the case, I suppose you could go for a FAIRE-seq.
Basically, you perform several iterative phenol/chlo extractions, thus separating the bound and unbound fragments.
Then you sequence the unbound fragments that are present in the aqueous phase, and after the mapping, you can deduce the regions that were actually bound to proteins.

I don't know if it is possible to treat your bound fragments (that you isolate after a phenol/chlo extraction in the organic phase) with proteinase K, then perform another phenol/chlo extraction to purify your formerly bound fragments and sequence them.
Could be worth trying.


How can I get brighter DNA bands? I amplified my DNA with real time PCR. The amplification curve shows good amplification but not a single band is observed in my gel after gel electrophoresis. What would be the possible reasons?

I am attaching a photograph of my gel below. My ladder opened correctly but not a single band can be observed:

As you can see from the bottom of the gel, the brightness of the bands have reduced even for the DNA ladder/marker. The main reason for this is that when you are running an agarose gel containing EtBr, due to the positive charge of the EtBr, the stain runs to the negative chamber, against the direction of the DNA migration as @Chris has pointed out! Although some of the DNA will stain but the rest of the EtBr will migrate towards the top of the gel (where the DNA is loaded).

A quick remedy for this is once you ran your gel is to soak your gel in a separate container containing your stain and running buffer such as TAE. I do this for one hour and that makes a huge difference!! Also make sure you regularly change the buffer in your agarose gel running apparatus and don't use the same buffer for a long time since again as @Chris has correctly pointed out there is a reduced conductivity in the older buffers when they heat up so migration does not work as well! Obviously this response assumes that you have a good degree (amount) of DNA in your gel bands, which can be calculated by nanodrop once you extracted the DNA using an extraction kit, or whatever method you normally use. I hope this helps!

This answer is more suited to the title of the question since after reading the main question a bit more carefully I'm slightly confused! So do you see anything at all or your product is far too faint? could you tell us where on the gel, relative to the ladder you expect to see this band? are they the ones at the button of the gel, below the loading buffer?