Can bacteria release free DNA into their environment? Natural transformation AKA natural competence involves the uptake of DNA into a competent bacterium (for horizontal gene transfer or as a food source). My question is about where this extracellular DNA can come from. Typically this "free" DNA originates from lysed bacterial cells. Are there instances where DNA is released without lysis that other bacteria can uptake via natural transformation?

Note: I am not interested in bacterial conjugation because I'm specifically interested in extracellular DNA that can be internalised by competent bacteria.

Natural Transformation
The process of Natural Transformation (Lorenz and Wackernagel 1994) has a very huge importance in evolution of prokaryotes. Definition quoting from (Stewart and Carlson 1986)

Natural transformation is part of the normal physiology of the cell.
It is the only form of bacterial genetic exchange whose functions are
encoded on the chromosome, and competence is a heritable trait,
subject to selective pressure.

This is almost similar to our daily use artificial transformation. You need some chemical like $CaCl_2$ to cell permiabalized, some chelating agents like EDTA and DNA material. You can imagine naturally occurring cell encountering such conditions, like decrease in temperature in presence of certain chemicals and proteins.
This concept of one cell externalising, and another internalising DNA got stronger when researchers observed free DNA in culture media (Catlin 1959, Sinha and Iyer 1971).
The Creation of eDNA
The release of eDNA (extracellular  DNA) can occur via spontaneous excretion or autolytic action.
There are known mechanisms for the release eDNA like formation of blebs (Dorward and Garon 1990). This extracellular DNA production is affected by many physiochemical factors than biotic (Paul and David 1989). There are many in detailed reports which shows such DNA can be passed through cell wall without any cell damage (Hara and Ueda 1981). Half life of such eDNA in various environment is reported in following table from (Lorenz and Wackernagel 1994)

Now there are even more novel ways of production of extracellular DNA like in Neisseria gonorrhoeae secretion of chromosomal DNA occure via new type IV secretion system (Hamilton et al 2005). Not just experiments, mathematical models also shows novel role of such process in gene-level selection (Draghi and Turner 2006). I haven't touched upon uptake of these DNA, which itself has lot of literature and unique mechanisms like this.


Why is coffee a laxative? How does caffeine (or any additional agents) act as a laxative when ingested? I'm interested in the metabolic/signaling pathway.

Coffee does have an effect on the peristaltic movement in the bowel.

  Coffee increases rectosigmoid motor activity within 4 min after ingestion in some people. Its effects on the colon are found to be comparable to those of a 1000 kCal meal. Since coffee contains no calories, and its effects on the gastrointestinal tract cannot be ascribed to its volume load, acidity or osmolality, it must have pharmacological effects. Caffeine cannot solely account for these gastrointestinal effects.

Effectively, decaf and regular coffee stimulate peristaltic movement in the colon as effectively as a meal does. Caffeine is not the active agent then, but some other compound in coffee.

Source: Boekema PJ, Samsom M, et al. Coffee and gastrointestinal function: facts and fiction. A review. Scand J Gastroenterol Suppl. 1999;230:35-9. PMID 10499460.


Are there any online resources one can use to access raw clinical trial data without having to contact those involved in the study? I want to do some statistical analysis and I have a preference for real data so I was wondering if there's somewhere I can get such data for free without a heap of bother in phoning those involved in the studies in question.

See these three sites:

ClinicalTrials.gov
NIDA
ClinicalStudyDataRequest

For clinical trials conducted by other agencies (in different countries), you may have to contact those authorities.


Survival of E. coli on agar plate at -20 degree C without glycerol stock If I kept E. coli transformed with plasmid at -20˚C without making glycerol stock, will it survive? Actually I have kept it this way for 18 hours. What will happen with it? Will it grow in fresh media?

Over time I suspect that ice crystals will form in the colonies from defrost cycles in the freezer and the moisture in the agar.  This will cause rupture of the bacteria membranes and over time may destroy the bulk of the bacteria cells.  The plates will also desiccate over time as well from the defrosting cycles of the freezer.  You may be able to leave them in the freezer for a while but I can't foresee them surviving indefinitely.

If the strains are really important I recommend just sucking it up and spending the small amount of time necessary to make the glycerol stock.  Glycerol is used in bacteria stocks as a cryoprotectant to prevent the crystallization of the stock.


Why is hunting big animals more dangerous for the species? I've heard in a lecture about protection of primates that one reason the classical population dynamics doesn't work is that the aboriginal hunters tend to hunt the big, strong and healthy individuals that have the best chance of becoming a successful parent.

Is this effect really so significant that it outweighs the fact that the hunters don't have to hunt so many of them in order to get the same amount of meat?

[Additional explanation]:

This question asks about the best strategy in protecting rare wild animal species against excessive hunting. We don't have to intervene when lions hunt zebras because less zebras means less food for lions - so the ratio of zebras and lions doesn't change much so there's no danger of any species getting extinct. Unlike the natural predators and prey, it has been found that the amount of meet hunted by people in forests isn't anyhow dependant on the number of animals living in the nature because humans use tools which give them a huge advantage over the "prey". Also, number of people living in a forest isn't  dependent on the sources in the wild, due to the rise of agriculture.

There was a research how much is the size of an animal connected to the probability a hunter will hunt specifically this animal and it has been found that the hunters tend to pick the physically biggest, strongest and healthiest individuals. This phenomenon has been marked as dangerous for the future preservation of wild species because (that's my guess) the most healthy and strong are the most likely to rear healthy offspring. I said to myself that from what I've learned about evolution, the difference between the physical fitness of an individual feed by a less strong parent (compared to the rest of the population) and an individual feed by a stronger parent can't be so big that it overweighs the fact that when a hunter hunts smaller animals, he's more likely to hunt more of them (That's something that has been studied) so the overall number of hunted animals is actually bigger. So my question is, wheter I'm correct or wheter the factor of the bigger number of animals you hunt when you hunt small animals actually isn't as important as the fact that healthy and strong parents will rear healthy and strong offspring.

I can see two different sides to this question.

On one side,

From Darwin's Theory of Evolution, the more adapted you are, the better chance at reproducing you will have, thus passing on your genes.

  "Survival of the fittest" is a phrase that originated from Darwinian
  evolutionary theory as a way of describing the mechanism of natural
  selection. The biological concept of fitness is defined as
  reproductive success.

In this case, you hunt the fittest, strongest animals that can procreate and protect their descendants, leaving the weakest alive. The weakest may not be able to continue the lineage because of their weakest gene pool and the species existence could be at stake.

On the other side,

A reputated Oxford Zoologist, Richard Dawkins wrote:

  We are survival machines – robot vehicles blindly programmed to
  preserve the selfish molecules known as genes

In this particular example, being strong, fit and healthy could be interpreted as being unfit for evolution, since it attracts predators (humans) to kill, as would not be the case for medium sized less meaty healthy individuals. The true adaptation that could make the specie survive in this case is via the weakest members that are not worth the effort to be hunted but still can survive other threats.

There is several more viewpoints that could be described knowing more details about exactly which animals, their environnement, the other predators and the exact contribution of the "healthy strongest" specimens you described as being hunted.

Nevertheless, hunting animals can always endanger the specie depending on the frequency of the hunt, frequency of the animal reproduction and several other factors, so can many other human behaviors.

Source: The selfish gene - Richard Dawkins (Book)


Can a neuron make a synapse onto itself? I was wondering if a neuron can make a synapse to itself? I suspect that it would be extremely unusual for a neuron to do this. Anyway, has anyone seen even a single instance of this?

Is the process by which a neuron 'knows' not to make a synapse onto itself is known?

A synapse from a neuron unto itself is called an Autapse. Not a whole lot is known about them. Tamas et al. (1) give a summary:

  Van der Loos and Glaser (1972)proposed the word “autapse” to describe
  a transmitter release site made by the axon of a neuron and its own
  somatodendritic domain. In addition to their original Golgi study in
  rabbit neocortex predicting the existence of autapses, possible
  autaptic contacts have been described in dog (Shkol’nik-Yarros, 1971)
  and rat (Peters and Proskauer, 1980; Preston et al., 1980) cerebral
  cortex, monkey neostriatum (DiFiglia et al., 1976), and cat spinal
  cord (Scheibel and Scheibel, 1971). (...)
  Although autapses formed in cell cultures have been used extensively
  to study the physiology of synaptic mechanisms (Segal, 1991; Pan et
  al., 1993;Shi and Rayport, 1994), few proposals have been made for the
  functional significance of inhibitory autaptic innervation in
  vivo(neostriatum, Park et al., 1980; Aplysia buccal ganglia,White and
  Gardner, 1981).


How does fluid pass through the glial limitans into the subarachnoid space? I have often heard that the cerebrospinal fluid (CSF) and interstitial fluid (ISF) are in free exchange. Because the CSF eventually drains (predominantly) into the dural venous sinuses, ISF's ability to access the subarachnoid space actually allows the brain to eliminate metabolic waste products that would otherwise remain the parenchyma. ISF presumably accesses the subarachnoid space, mixes with the CSF, and eventually, through arachnoid granulations, drains via the dural sinuses.

While that is fine and dandy...there are two layers that the ISF must first pass in order to access the subarachnoid space: the glial limitans and the pia mater.

How does ISF pass through the foot processes of astrocytes, which comprise the glial limitans? Does the H2O remain largely in the parenchyma while waste metabolites are selectively transported across the astrocytes and into the small spaces between the glial limitans and pia mater?

Excellent question. This is an active area of research.

The glia limitans defines the external most layer of brain parenchyma. Previously thought to primarily be a barrier against migration and growth of neural cells out of the brain parenchyma during development, recent work has characterized its involvement in regulating the immune environment of the CNS. A 2017 JCI paper demonstrated that the tight junctions of the glia limitans are inducible in mouse in response to inflammatory cues. You may find the associated editorial helpful. In addition to demonstrating a dynamic role for the barrier function, you can see that tight junctions are not the standard state, and the typical state allows passive diffusion as well as active transport of small molecules between the CSF and brain ISF, but the question is not fully resolved.

Importantly, this is mouse data, and mouse data in particular cannot fully resolve questions about human astrocytes.


Why would a bacterial population show initial growth when it is in unfavorable growth conditions? This figure shows the anaerobe E. faecalis grown in aerobic conditions, E. coli grown in restricted conditions that are not specified. Why do they show an increase in abundance initially? The black line is growth rate and to me I would think neither would grow at all.

E. faecalis is an aerotolerant anaerobe, while E. coli is a facultative anaerobe therefore if in a non-aerobic environment it can switch to anaerobic respiration. E.coli is also capable of fermentation.

Here is an article for on the various respiratory pathways of E.coli: http://www.sciencedirect.com/science/article/pii/S0005272897000340

One other reasons why cells may grow in a nutrient poor medium is that many types of bacteria have programmed cell death that ultimately is for the better of the entire bacterial population. When nutrients get low some cells commit "suicide" and release nutrients to surrounding bacteria. Just an extra thought.


What is the meaning of Dimer Catastrophe? What is the meaning of Dimer Catastrophe?  I still don't understand it even I've already read the paper about it.  Here's the link to the paper origin NCBI

A "plasmid dimer" is defined as a plasmid that has two origins of replication instead of the usual one origin of replication. This can happen if two copies of the same dimer undergo recombination resulting in one plasmid with two origins and one with zero. I hadn't seen this term before, but it seems to be the meaning with which it's used in this paper and a few others I saw.

The "dimer catastrophe" hypothesized in this paper refers to the idea that over time this would lead to a reduction in overall plasmid copy number (and thus an increased probability of plasmid loss), since dimers may be more likely to replicate than monomers (due to having more origins of replication).

For what it's worth, I also found the paper you linked a bit hard to understand, but I found this one more explanatory (your mileage may vary): Multicopy plasmid stability: Revisiting the dimer catastrophe.


Why are the sex chromosomes called X and Y? Is there a specific reason that the letter Y is used as the symbol for the male chromosome and X is used for the female chromosome?

Sex Chromosomes and Sex Determination by Ilona Miko

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

Wikipedia - Y Chromosome

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

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


Why do humans sneeze out mucus if it's a good thing? The Wikipedia article on mucus says that mucus acts as protection from bacteria and other microorganisms.

Given that mucus plays this positive role, why do humans sneeze out mucus?

Indeed, mucus is essential for in this case protecting the respiratory pathways, which includes the nasal cavity and the pharynx, against different threats, such as microbes. Sneezing, which is initiated by virtue of the activation of mechanoreceptors in the upper parts of the respiratory system, leads to a buildup of intrathoracic pressure, due to the contraction of expiratory muscles against a closed glottis. The pressure gradient, when the glottis opens, will then lead to the rapid flux of air from the lungs, through the respiratory tract and out through the mouth and the nose, whereas mucus containing the initial irritant will follow, merely due to the forces at play.

Note that the epithelia in the resp. tract normally transport the mucus containing everything from microbes which have been breathed in, and different particles, to the oropharynx, so as to allow you to swallow and take it to the GI tract instead.

For further reading, I recommend Boron Boulpaeps Medical Physiology chapter 32 on the "Control of Ventilation" (2012).


Is this a counter-example to Darwin's theory of evolution? Somewhere I read following paragraphs giving one counter-example to Darwin's theory of evolution.

(By the way, I am a physicist and not a biologist, but I am interested in this field.)

Do these paragraphs point to the reality? What is the current status of "theory of evolution of species" ?

  "Darwin cited the giraffe as an outstanding example of natural
  selection.  Supposedly, as a result of extended droughts, the supply
  of green leaves could be obtained only at the top of the trees, and
  therefore the shorter necked giraffe died off.  The giraffes which
  grew longer necks survived.  However, there is no evidence whatever in
  the fossil record or elsewhere that giraffes with short necks have
  ever existed.  And what would have happened to young giraffes with
  relatively short necks?

  Darwin failed to realize that body characteristics in offsprings are
  determined and programmed by DNA factors of the Genes or the Genetic
  material of the parents, and not by the stretching of the neck or any
  other bodily exercise."

Darwin cited the giraffe as an outstanding example of natural selection. Supposedly, as a result of extended droughts, the supply of green leaves could be obtained only at the top of the trees, and therefore the shorter necked giraffe died off.

The term outstanding is funny in its usage here but otherwise this text is quite right so far.

  However, there is no evidence whatever in the fossil record or elsewhere that giraffes with short necks have ever existed.

Actually there is. See this popular science article suggested by @James.

  And what would have happened to young giraffes with relatively short necks?

The answer in the text above. It rightly says the shorter necked giraffe died off.

  Darwin failed to realize that body characteristics in offsprings are determined and programmed by DNA factors of the Genes or the Genetic material of the parents [..]

This is an awfully phrased sentence making it very clear that the author has no idea about genetics.

  not by the stretching of the neck or any other bodily exercise

Sure. The concept that individuals stretch their necks, necks become longer and this characteristic is passed on to the offspring is wrong indeed. This is known as Lamarckism. It is funny because the above text describe natural selection and it then says that it is wrong by making a straw man, misrepresenting natural selection as a Lamarckist process.

  What is the current status of "theory of evolution of species" ?

You should have a look at the post Is evolution a fact?.

You should also have a look at an intro course to evolution. There are several online and free introductory ressource of information on evolutionary biology. Understanding Evolutionby UC Berkeley is probably one of the best. It is very short, very introductory and will already teach you a lot.


How is output of DNA assembler measured? I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs.
Many papers measure own algorithms and compare it against each other. There are basic metrics like:

N50, N70..,
number of contigs,
genom coverage,
error rate

I download tool QUAST and there I can see metric N50, L50, where is easy to develop own computation. But how I can measure error rate of my output contigs? Is there any tool which can do it?
I searched in many papers but I cannot find way how they do it. I would like to compare with some assemblers with some general way. I found only hints that it should be done by aligning contigs to reference genomes but I do not know how and if it is right way.

If you are interested on the topic of how to compare assemblers, have a look at assemblathon. That group has two papers and working on a third about comparing genome assembly algorithms.


Is a virus a poison? I've understood that a virus is not a living organism (like e.g. a bacterium). From Wikipedia I get that a poison is a substance that reacts physically or chemically with molecules in the human body. Since a virus is a protein that binds to certain cells in the body and alters the cell's function in a harmful way (resulting in the production of more viral matter), why is a virus not a type of poison? (Or is it?)
Additional info:
I'd like to understand the difference between them—if any—on a chemical and physical level, as well as the consequences for treatment. For example: we all know by now that viruses can only remain harmful/intact on surfaces for a certain amount of time. However, I would think that a poison on a surface does not have such a time limit (but I may very well be wrong). What's the difference, if there is one? Why is licking a banister with viral load older than 4 (or so) days not harmful, but is licking a banister with poison older than 4 days?

Although "Virus" literally means "Poison" in Latin, it would be a great over-simplification to regard a Virus as a Poison.
Now, most poisons are chemical compounds that interfere in some chemical pathway in our body. For example:

Carbon Monoxide: Binds with Haemoglobin, rendering it unable to transport oxygen
Sarin: Indirectly inhibits degradation of the  neurotransmitter "Acetylcholine"
at the synaptic cleft.   Mechanism of action of Sarin

Hence most poisons are quite "simple" in their actions. However, viruses can be considered as a complex machinery of functions that interfere with a multitude of processes in our body including cell transcription, receptor-mediated endocytosis, et.c
Hence, the best analogy would be to consider a virus as a tactical poison.
Now, as for last question, viruses are fragile assembled structures.  Viral Self-Assembly

Environmental factors like heat, uv-light, oxygen, etc may damage the assembled structure. Hence, viruses have a self life, and so do may poisons.
  Sarin (self life)
However, poisons tend to have a longer self life because chemical compounds are more stable than the capsid of viral proteins with weak hydrogen bonds.
As per David 's suggestion, poison is defined as "...substances that cause death, injury or harm to organs, usually by chemical reactions or other activity on the molecular scales, when an organism is exposed to a sufficient quantity."  Wikipedia
Viruses do work at molecular level, but not in the same sense as poisons do. Hence, viruses do fit into the description of poisons but not precisely.
Hope you find this helpful.


Color of the Fur coat of Polar bears Recently I was playing a quiz and a question was asked about the color of the fur coat of a polar bear. To my surprise the answer was black. I thought it was yellowish white or creamy. Why so ?

The fur coats of polar bears are in fact clear tubes - not white fur as is often believed. It is their skin that is black, to absorb the most warmth from the sun (and the clear tubes allow the majority of the light to pass through to the skin).

I recently watched the BBC's Frozen Planet TV series (with David Attenborough), where I heard the above answer. If you haven't already, I recommend watching it.


How does high-intensity aerobic exercise affect the brain? I have been reading articles claiming that serotonin, endorphins and BDNF are produced during exercise, but they never mention the intensity or duration of exercise for this to happen.

To not make this question too broad, I want to narrow it down to, lets say, a 4-5k run over 20 minutes. Also, I want to restrict it to the body's response during these 20 minutes.

How will this affect the brain? Which chemicals do the body produce/release into the blood stream that could have an effect on the brain? And, how much?

I am asking because I am always curious about the mechanisms underlying the effects of exercise on the brain and because it's always difficult to find information regarding results of exercise; Googling mostly results in content marketing articles (like this one for Buffer).

In this article The Effects of Acute Exercise on Mood, Cognition, Neurophysiology, and Neurochemical Pathways: A Review (Brain Plasticity, 2017), there's a comprehensive table The Time Course of Behavioral, Functional, Physiological, and Neurochemical Effects of Acute Exercise (scroll to Fig 1 and zoom it) that shows the duration and intensity of exercise needed for the effective release of cortisol, neurotrophins (BDNF, IGF-1), neurotransmitters (dopamine, norepinephrine, serotonin, acetylcholine, GABA and gltamate) and endogenous opioids.

Examples of effects of exercise on the cognitive function and mood:

Prefrontal-dependent cognitive function (learning, memory): 50 min exercise at 85% of age-predicted mean heart rate
Enhancement of positive mood: low to high intensity exercise 7-70 min
Decrease in negative mood: 60-120 min exercise at ~50% intensity

Cortisol:

  In humans, acute exercise stimulates the HPA axis in an
  intensity-dependent fashion, with increases in cortisol occurring
  after a threshold amount of exercise that equates to a duration of 10
  minutes or more at approximately 60% of VO2 max or greater...After
  exercise cessation, peripheral cortisol levels peak around 30 minutes
  and remain elevated for up to two hours.

  ...cortisol strongly influences learning and memory...The extent
  to which cortisol influences learning and memory processes depends on
  several factors including the intensity of cortisol elevation. For
  example, moderate increases in cortisol enhance working memory...Cortisol elevation over a certain threshold, however, serves to impair memory...

  acute exercise also helps mitigate the debilitating effects of stress.

Brain derived neurotrophic factor (BDNF):

Moderate exercise for 30 minutes can release BDNF.

  ...studies have shown a positive association between acute
  exercise-induced peripheral BDNF levels and short-term memory as
  well as motor skill memory.

But, this does not work in everyone and not in all circumstances...

Dopamine:

  Twelve, healthy, regular exercisers underwent PET scans after either
  rest or 30 minutes of treadmill running at 85% of age-predicted MHR.
  Surprisingly, dopamine was not found to increase after acute exercise
  in these humans.

Serotonin:

  Acute exercise significantly increased plasma serotonin, with a
  positive linear correlation found between serotonin concentration and
  exercise intensity.

  As serotonin regulates mood, emotion, sleep, and appetite, and
  dopamine regulates motivation memory, reward, and attention, the
  central fatigue hypothesis claims that the interaction between these
  two neurotransmitters contributes to exercise-induced fatigue, with a
  high serotonin to dopamine ratio supporting a low activity, exhausted state and a low ratio supporting a high activity, activated
  state.

The effects of exercise-induced increase of norepinephrine and acetylcholine on cognitive function are not well known.

Endogenous opioids (ß-endorphins, enkephalins and dynorphins) and endocannabinoids:

  Neuromodulators are involved in a variety of processes including pain
  modulation, reward, response to stress, and autonomic control.

  In humans, acute exercise causes significant increases in peripheral
  levels of endogenous opioids; this effect is intensity-dependent,
  corresponds to acute exercise-induced changes in HPA axis hormones,
  and is linked to improvements in mood.

  Though the endogenous opioids have received much attention in terms of
  their involvement in the “runner’s high”, scientists are beginning to
  understand that endocannabinoids may be equally or perhaps more
  involved.

Other sources:

Effects of physical exercise on anxiety, depression...(Clinical Psychology Review, 2001):

  Acutely, emotional effects of exercise remain confusing, both positive
  and negative effects being reported.

...or as Alex Corb, PhD says in Boosting Your Serotonin Activity (Psychology Today):

  Interestingly, if you try to do too much exercise, or feel forced into
  doing it, it may not have the right effect. Recognizing that you are
  choosing to exercise changes its neurochemical effect. That may be a
  result of your ancient instincts — the difference between running
  because you're hunting something, and running because it's hunting
  you.

How to increase serotonin in the human brain without drugs (Journal of Psychiatry & Neuroscience, 2007):

  Exercise improves mood in subclinical populations as well as in
  patients. The most consistent effect is seen when regular exercisers
  undertake aerobic exercise at a level with which they are familiar.


If DNA is the input, what is the output? How does cells use the DNA inside them? I am looking on DNA as a strip of tape of Turing machine, but with machines its easy. I can read the tape and calculate the behavior of that machine. With cells its different we don't really understand the language of DNA.

So instead of trying to understand the language I was wandering if there are any particular behaviors of cells that we can associate to different "outputs" of the DNA tape.

The central dogma of molecular biology states that DNA encodes the information for building proteins, the information is copied to messenger RNA through transcription, and messenger RNA is used to build proteins through translation. DNA is also copied through replication.

So while it's true that DNA contains the information needed to build a living organism, I don't think it can described as "turing tape" If I understand turing machines correctly, you have a string of 1s or 0s, and a machine reads this string. Based on rules provided by an instruction set the machine can set positions on the tape to 1 or 0. The analogy with DNA fails because DNA does not have a separate instruction set and cannot be written to. DNA produces RNA and DNA with the help of many many proteins and other molecules, all tightly regulated to coordinate replication of the genome and to produce the right amounts of RNA and protein at the right times. DNA can mutate when replication makes an error, but this is accidental, not comparable to turing machines.

If you're interested in how DNA might be used like a computer, there are several articles on DNA Computing, though you'll have to sort through those papers because many look like they just used a computer to analyze DNA.


Single copy housekeeping genes I am working on a tool for SNP calling in polyploid plants. To test my method, I need a list of housekeeping genes common in almost all plants. For my case, these genes must be single copy (ie each HK gene should have no paralogs).

Briefly I need a list of genes that are:

House keeping
Single copy
Common in almost all genomes, or genomes of a taxa

Any help is appreciated.

Just flying from the waist: filter approach:
If there is a data source that has the expression data for cells in multiple tissues for any organism i would use that to find the housekeeping genes by sorting which genes are expressed in the greatest number of cells (think excel or XML). Next, I would check which of those genes are also found in/similar to the respective gene (homolog I thin its called) in the plants (using genome browser, e.g., ensembl and blast or just look it and click on the button to bring you to the plant genome). If your model organism does not have sequenced genome... get primers and see if you can sequence it for yourself to see if its there. Then check to see if its a single copy. Hardest part is finding an expressome database spanning multiple tissues in an organism to find housekeeping genes - then hoping they are conserved to the plant. Alternatively, you can consult literature to find housekeeping genes.

You probly just wanted a listing of the genes... sorry.


Ripening bananas artificially: What is the biological theory behind? I am a resident of the tropical island of Sri Lanka, and we have a strange traditional method to ripen our banana harvest quickly.

What we do is this: We dig a pit in earth that is enough to put the whole banana cluster in. Then, after safely laying the bananas in the pit, we cover up the pit with a sheet such that only a small hole from a side remains: visualize a small 3-4 inch door to the pit.

After that, we light a fire with semi-dry leaves just outside the pit's door. (Semi-dry leaves are used to get as much smoke as possible. Dry leaves do not give that much smoke, because they completely oxidize quickly). And the smoke is sent through the door by blowing it with the aid of a bamboo.

This sends a good amount of smoke and warms the inside of the pit considerably. And by experience I can tell you that this makes the bananas to ripen really quickly. I have done a controlled experiment where half of the cluster was not put into the pit. Bananas in the pit ripen overnight and the control sample took days to ripen.

Can anybody explain what are the bio-mechanisms that are working here?

Ripening of bananas (and other fruits) is induced by acetylene and ethylene (Ethyne and Ethene) (see reference 1), which acts as a hormone and induces the ripening process. The incomplete combustion of the leaves produces ethylene, additionally the warmth of the process will help the enzymes as well. There is even a paper about this technique (although it is unfortunately not accessible), see reference 2 for more information. Smoking Chambers are routinely used in this process, see reference 3 and 4.

References:

Role of Ethylene in Fruit Ripening
Effects of smoking on some physiological changes in bananas.
Fruit Ripening
Technology for ripening fruits as important as marketing them


Advantages of gregarious vs solitary behaviour? I'm trying to explain why birds (specifically wildfowl) are gregarious during the winter and solitary during the summer.

I think that in winter, birds are gregarious to reduce the risk of predation and to share foraging information. But gregariousness also brings with it competition, and because birds have offspring to feed in the summer, they trade-off increased predation/loss of information with reduced competition.

Does this sound correct?

I will assume that you are talking about Mallards, although other wildfowl are likely to exhibit similar behaviors.

Mallards aren't actually solitary during the summer, instead they form breeding pairs.  They form groups (sords) in the winter to migrate and for protection while moulting.

https://sta.uwi.edu/fst/lifesciences/documents/Anas_platyrhynchos.pdf
http://thefarmatwalnutcreek.com/Ducks_Swans_Mallard-Duck.html


How are sound waves amplified while traveling within the cochlea? How are sound waves amplified while traveling from the basal membrane to apical membrane within the cochlea? Are they amplified by the movement of the stapes?

Short answer
Sound waves are, technically, not amplified in the cochlea. The answer to your question, however, is that outer hair cells amplify the acoustic signal in the cochlea.

Background
To answer your question what mechanisms exist that amplify sound within the cochlea - none.

What is amplified within the cochlea is the traveling wave that moves across the basilar membrane. The cochlear amplifier is mediated by the outer hair cells. These outer hair cells are thought to be able to contract and extend when the basilar membrane moves and thereby amplifying the traveling wave (Fig. 1).

The middle ear ossicles as you say do amplify the acoustic sound, but they are situated in the middle ear, as is the tympanic membrane, which also amplifies sound by funneling a large contact surface onto the small stapes footplate.This is not the answer to your question, as they are all middle ear structures.

Fig. 1. Inner ear structures (Fettiplace et al., 2001)

Reference
- Fettiplace et al., 24, Trends Neurosci (2001); 3: 169-75


Negative role of Placenta How can a placenta turn hostile to the mother or fetus ?
What are the abnormalities found during placental delivery ?

The placenta does not turn "hostile" to the mother or fetus. Placentation abnormalities can result in harmful situations, but these are a secondary result.

Structural anomalies of placentation:

placenta accreta/percreta: means that the placenta took hold not only in the uterine mucosa, which is the normal state, but through it up to the myometrium (muscle layer, in placenta accreta), or even up to the serosa (outermost uterine layer, in placenta percreta). These anomalies will convey a much higher chance of massive haemorrage at delivery, and therefore are dangerous to the mother.
placenta praevia: placental insertion covers the entrance to the uterine cervical canal, partially or totally. Therefore, the way of the fetus for natural delivery is blocked, and the placenta will tear during labor, causing massive haemorrage.
marginal implantation of placental vessels: vessels linking the placenta to the fetus (the umbilical cord) are implanted on the periphery of the placenta. This causes structural fragility, and a greater risk of bleeding for both the mother and fetus.
retroplacental hematoma: in such cases, the placenta partially or totally loses its hold on the mucosa, and blood fills the space left behind. This is an immediate threat to both the fetus and mother because of the potential for massive haemorrhage and interruption of oxygen delivery to the fetus.

Deleterious side effects of pregnancy:

preeclampsia/eclampsia: misunderstood biological syndrome that causes the classical signs of arterial hypertension, peripheral edema, hepatic cytolysis, and thrombocytopenia in the mother. Eclampsia is all that plus added seizures (in which case maternal mortality is high). This is not due to placentation abnormalities, even if it is true that delivery is the only cure, and can justify a premature artificially induced delivery in extreme cases.
fetal/maternal rhesus factor incompatibility: During labor and delivery, a small amount of fetal blood will come into contact with the mother's organism. If the mother is Rh neg, and the baby Rh pos, the mother can develop antibodies against the rhesus factor. This can cause haemolysis in the newborn, and in grave cases, kernicterus (toxicity of degraded red blood cell metabolites to the baby). While this may threaten the baby to be born, problems are much more common for subsequent Rh pos pregnancies. We check for antibody presence in the mother with the Kleihauer test and give preventive injections of rhesus antibodies to Rh neg mother with a Rh pos pregnancy to decrease the chance that the mother develops her own antibodies.

Other special cases:

molar pregnancy/choriocarcinoma: A structural genetic accident happening on fecundation that can cause the embryo to behave as a type of cancer.
ingesting placental extracts: this is mentioned is another answer here. This has nothing to do with the placenta, but the deleterious secondary effects are due to direct toxicity of the hormones contained in those extracts ingested in an inadapted situation. This is not to say that one should take them while pregnant, because hormonal deregulation would also be toxic in a normal pregnancy.


Are there terrestrial plants that thrive on sea water? Given the existence of coastal deserts such as in the picture below, I was wondering whether terrestrial plants can survive on sea water alone? If yes, why then do coastal deserts exist, instead of being grown over with belts of such plants along the shores?

If terrestrial plants thriving on sea water do not exist, then why? Especially given that there are marine plants like kelp and sea grass?

The University of California, LA mentions some genera and species of salt-loving plants (halophytes):

The genus Atriplex (Family Chenopodiaceae), saltbush, is found worldwide along saline shorelines. On the surfaces of the leaf are vesiculated trichomes (hairs). Each trichome has a stalk and a balloon-like tip, the bladder cell. The leaves use the bladder cells to excrete salt.

Coastal saltbush. Source: Enviro Active Australia.

Excreting salt glands occur in numerous unrelated plant groups, including grasses that live in alkali sink and salt pans and in warm temperate to tropical salt marshes (Sporoboleae, Chlorideae, and Aeluroideae (Family Poaceae)). These include such well-known tidal saltmarsh plants as the cordgrasses (Spartina alterniflora, S. patens), alkali grass (Puccinellia phryganodes), saltgrass (Distichlis spicata), and shoregrass (Monanthochloe littoralis). Short, two-celled trichomes have evolved as collecting chambers for salts, from which salts are excreted through tiny pores.

Cordgrass in the Chesapeake Bay. Source: Chesapeake Bay Program

Frankenia (Family Frankeniaceae) is a genus found both in coastal salt marsh and inland saline habitats. Saltcedar (Tamarix, Family Tamaricaceae) grows around the world in arid and semiarid regions. All of these taxa have salt glands, i.e., trichomes, in which salts are accumulated and excreted.

Several common mangroves secrete salts from leaves. So much crystalline salt can occur on the leaf of black mangrove, Avicennia germinans, that it appears whitish. Aegialitis annulata is a salt-excreting mangrove of Family Plumbaginaceae, a group in which other species are salt excreters in salt marsh and oceanside (Limonium and Armeria) or have chalk glands and live in dry, alkaline habitats.

Black Mangrove. Source: PlantDex.

Halophytic succulence is demonstrated in many genera of plants that inhabit saline environments, such as the mud flats of coastal salt marsh, but also is commonly observed on the leading edge of vegetation on coastal beaches, i.e., in strand vegetation. Common examples of succulence can be found in Family Chenopodiaceae: Allenrolfea, Arthrocnemum, Halimione, Nitrophila, Salicornia
Suaeda.

Succulence (fleshiness) also occurs in other famous and widespread species, such as Batis maritima, Sesuvium portulacastrum, Trianthema portulacastrum, and many Old World species of Zygophyllum. True succulents in the ice plant family, Aizoaceae, are also commonly found in saline habitats: Aizoon and Mesembryanthemum. By depositing salts in vacuoles, the toxicity is partitioned from the cytoplasm and organelles of the cells. As in Atriplex, salts are removed from the plant when the leaf of stem segment is shed.

Halophytic succulent Trianthema portulacastrum. Source: Altervista.

Among the halophytes, the seagrasses, which are submerged plants of shallow marine meadow, have salt tolerance, because the osmolality of cytoplasm is adjusted to match the osmolality of the seawater, so that desiccation of the plant does not occur. This contrasts the strategies of excluders and succulents, which are primarily salt avoiding mechanisms, attempts to reduce salt concentrations within the cytoplasm of photosynthetic cells.

As to why some shores may be devoid of plants, it may have to do with extreme temperatures, lack of nutrients, phytotoxic material etc.


Synthetic biology using existing cells I was watching the video at this link:
http://www.bbc.co.uk/news/science-environment-17436365

The speaker says that a cell is taken and its original DNA content is stripped out and replaced with synthetic DNA.

Does this mean scientists are not able to create a synthetic cell yet? Is this why they use existing cells, stripping them out and replacing the DNA?

The J. Craig Venter Institute recently has indeed created a synthetic, self-replicating cell (see the press release). So it's definitely not impossible to create completely synthetic cells for use in synthetic biology, but that doesn't mean it makes much sense to do so. E. coli in particular have been used as bench tools for decades: lots of protocols exist for using them in the lab, their genome has been extensively sequenced and is well studied, and they're cheap. I'm not a bench biologist anymore, but I'm guessing these are the reasons they stripped living bacteria and replaced their DNA rather than trying to build a completely synthetic microbe from scratch.


Can a macrophage differentiate back into a monocyte? I know that monocytes differentiate into macrophages when they enter the tissues, but do macrophages stay in those same tissues for the remainder of their lifespan, or do they differentiate back into monocytes and re-enter the bloodstream at some point?

No, macrophages can not turn back into monocytes, usually once a monocyte travels around the bloodstream for 1-3 days, it then leaves the bloodstream and travel to a tissue where it will differentiate to a macrophage or dendritic cell. It undergoes a conformational change, this usually happens during inflammation as the macrophages travel over a chemical gradient, macrophages can still enter the bloodstream, however, they won't re-differentiate to a monocyte. So to answer your question directly, macrophages don't stay in the same tissue forever as their life span is pretty long(1-2 months) so most likely an inflammation will occur and force the macrophages to diffuse across the chemical gradient, but they usually patrol around the tissue area where they differentiated.

source: http://www.histology.leeds.ac.uk/blood/blood_wbc.php


what is the active ingredient in cymbopogon citratus that repels mosquitoes? We are doing a project about mosquito repellants using lemongrass, cymbopogon citratus. But, based on our researches online, it stated that it was all a hoax and a better alternative is its cousin cymbopogon nardus.So, is the hoax actually true??? And please tell about the active mosquito-repelling ingredient.

I think the problem isn't a hoax; it's just that people are overly excited about 'natural' as opposed to synthetic remedies.

C. citratus might be hazardous - the active ingredient is citral α-pinene.

C. nardus might be hazardous, too - the active ingredient is citronellal or citronella. [There's confusion, in the article, about whether citronella has other plant chemicals in addition to citronellal.]

They're both partially effective as insect repellents.

"It is commonly assumed that plant-based repellents are safer than DEET because they are natural. However, some natural repellents are safer than others, and it cannot be assumed that natural equates to safe."

This info all comes from a 2011 scientific article about plant-based insect repellents:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059459/

Here's a link to a table with the results, summarized below:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059459/table/T1/?report=objectonly

And a table with possible toxicities:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059459/table/T2/?report=objectonly

Citronella has found its way into many commercial preparations through its familiarity, rather than its efficacy. Citronella was originally extracted for use in perfumery,..."

C.nardus is at least somewhat effective in 3 lab studies; citronellal    is the active ingredient.

C. citratus - the active ingredient is citral α-pinene.  Again, it's at least partially effective in 3-4 studies, e.g., "74% protection against An. darlingi for 2.5h"

Here's a scientific article from 2011 about the scientific basis for the therapeutic use of Cymbopogon citratus, stapf (Lemon grass):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217679/

But it doesn't mention 'insect repellent' among its possible uses!:

"Studies indicate that Cymbopogon citratus possesses various pharmacological activities such as anti-amoebic, antibacterial, antidiarrheal, antifilarial, antifungal and anti-inflammatory properties. Various other effects like antimalarial, antimutagenicity, antimycobacterial, antioxidants, hypoglycemic and neurobehaviorial have also been studied."


Why did humans evolved the scratch reflex? I've been wondering about this for some time, and I can't come to an answer...

Everybody keeps telling me that scratching one's own skin is bad. It damages the epidermis, creates the hazard of malicious bacteria getting past the skin barrier, and creates the vicious circle of scratching increasing the itching, and itching increasing the scratching (I think I recall reading that this vicious circle also happens even without any special skin diseases, like atopic dermatitis - I might be mistaken here, however)

So, it seems there are hardly any benefits for the body from the scratch reflex. However, if this was true, then "grandma Evolution" wouldn't have given this to us!

What are the benefits of scratching? Are there any benefits of it from the evolutionary point of view? I can come up with just one such benefit, namely fending off insects such as ticks, mosquitoes, fleas or lice. Would this be the evolutionary benefit of scratching?

With about 20 square feet of skin constantly exposed to potential irritation, itching must serve an important protective/defensive function.

The "scratch reflex" (I'm not sure I would call it that) is necessary to life and limb. Itch is a major somatic sensation, along with (and different from) pain, temperature, and touch. Itch can be an acute sensation, e.g. a mosquito bite, or a chronic condition (peripheral or internal disease).

Research on itch signaling is still at its infancy, and basic mechanisms by which the itch sensation is transmitted and regulated have yet to be fully understood. It is meant to give us information about how we are interacting with our environment. Loss of such fine sensation, such as occurs with Hansen's Disease - aka leprosy, where patches of skin become painless and do not itch, so are ignored by the patient - leads to festering wounds and resultant problems.

As @MattDMo stated in a comment, sensation allows us to respond appropriately to irritants which, if ignored, might lead to festering wounds: thorns and other foreign bodies, sucking or biting insects (parasites or other, which can act as disease vectors as well), etc. It allows us to learn how to avoid and treat such irritants.

Various types of itch can be classified by the origin of the itch, which could be skin-related, neuropathic, systemic, or psychogenic. The most common cause of itching is dry skin; tiny cracks in the skin cause an inflammatory response, which (within reason) is not a problem in and of itself. The response to the itch, though, can be beneficial or damaging. One can treat dry skin, wash off irritants, treat infections, avoid causes, etc.

Scratching can be benign if done sensibly, or it can injure the skin, allowing infection, etc. However, the benefit of having such sensation under normal circumstances certainly outweighs the inconvenience.

That is not to say that pathological conditions that cause itching are not problematic. They are, and one might reasonably curse the sensation under those circumstances.

Edited to add: Itching, or pruritus, is defined as an unpleasant cutaneous sensation that serves as a physiological self-protective mechanism to prevent the body from being hurt by harmful external agents. (Nature, 2007)

Scratching is simply a reasonable response to itching from any source and is not necessarily harmful. It's not a reflex per se. You can avoid scratching. Some animals must actively seek out a way to scratch. This takes it well outside of the terminology of reflex as neurologically understood.

Itch Signaling in the Nervous System
Pruritus
When you have an itch, what is happening under your skin?


How common is bacterial mediated transformation? In plants? In animal cells? The most common method to transform plants is by soaking plant tissue in cultures of agrobacteria (this is not their current classification) which transfer DNA into the plants.

Is lateral gene transfer ability like this found a lot in nature?  Is agrobacterium tumificans especially good at this or is its use in plant genetics only because this strain is well studied?

Is a method like this used for animal cells at all?

In animal cells the process is called transfection, to differentiate from transformation which is the process by which cells become immortalized (cancerous). I'm mainly familiar with mammalian cells, and in these systems some reaction is required to open pores of some sort in the cell membrane to allow the genetic material to enter. Viruses can mediate cellular entry on their own, but I am unaware of any method that uses live bacteria (although this doesn't mean that some specialized method doesn't exist).


What could account for an apparent loss of mass at death? An interesting tidbit floating around the internet these days is that Dr. Duncan MacDougall apparently weighed people shortly before and after death, and found an average of a 21 gram discrepancy, to which he attributed to be the soul departing. As we all know, this certainly can't be the right explanation.

Putting aside likely extreme bias and instrumental/experimental error, is there any bodily process at death that could potentially explain a small decrease in observed mass?

Snopes.com gives a discussion of possible issues with the original experiment.  Evaporation or bowel or body movements for instance.  I think the biggest complaint about the experiment is that it has not been reproducible and that the original experiment was flawed.  MacDougall only took six measurements and he threw two of them out in his original work.  The Wikipedia link you give cites a paper where sheep were found to gain weight at least for a time after death.  Dogs are found to have no weight change.

MacDougall and his contemporaries were inclined to interpret their results such that animals simply do not have souls, or have different sorts of souls.  But if you look at an average of all experiments cited, it could also be said that the average weight loss up on death averages to zero.  3/4 of an ounce of a human being (or a sheep) over the course of something like a death is not an easy measurement.  You can't give them a drink of water, you worry that they are breathing too much and losing water.  Its not an easy experiment, at least for human beings where you can't control the circumstances of death so well.

In any case this really needs to be measured better.  In 90 years it doesn't seem that there's been a real rush to do it.

I just stumbled across this blog post that talks about an effort to measure a change in blood flow to the brain when in intense mental activity popularized in the late 19th century.  The investigator Mosso claimed he measured a difference, but the result is disputed today.  It could not have been more than a few grams. In any case a description of how difficult this measurement can be.


Opening coverslip package I feel pretty silly for asking this but I don't want to damage these coverslips.

I just ordered a 100ct box of coverslips and see no way to open them without destroying the container they are in. How are these little boxes typically opened? It seems smooth and sealed on all sides.

Looking at the container from the side, it's probably a situation like this:

There might be some clear plastic wrap around the entire thing as well that you would need to cut/break.


Is there such thing as "meters per calorie" for living organisms? I'm interested in learning if there's some way of quantifying the organism's metabolic efficiency associated with movement.

It seems to me that some organisms would be more efficient than others at using energy. For mechanical systems, there are clear metrics of efficiency, for example "miles per gallon" or "liters per 100km". Is there a similar metric that converts calories into how far an organism can go?

Thank you for your input!

Halsey & White (2012) Comparative energetics of mammalian locomotion: Humans are not different. Journal of Human Evolution 63:718–722

This paper presents a comparison of the metabolic cost of walking and running in humans, Australopithecus and other mammals.  They use a parameter NCOT (net cost of transport), whose units are ml O2 consumed m-1. The inverse of this parameter would be related to your metres per calorie.

The authors quote an NCOT of 12.77 ml O2 m-1 for a walking human. Using a value of 4 kcal g-1 for glucose, I calculate that this NCOT is equivalent to 14.6 m kcal-1.

Here I found an energy consumption value of 5.8 kcal min-1 (for a 73 kg man) walking at 6.4 km h-1, which translates to 18.5 m kcal-1.

Incidentally, according to the authors of the paper:

  The predicted net cost of transport (NCOT, ml O2 m−1) of mammals is related to mass (M, kg) according to 0.54M0.70.


Why hasn't there been a serious effort to develop an anti-inflammatory that blocks the responsible genes? After numerous years of reading about how to disable inflammation and related treatments, it appears that the common existing approaches are fundamentally wrong.

The most popular over-the-counter treatments target cyclooxegenase (COX) - see:
https://en.wikipedia.org/wiki/Paracetamol#Mechanism_of_action
https://en.wikipedia.org/wiki/Aspirin#Mechanism_of_action
https://en.wikipedia.org/wiki/Ibuprofen#Mechanism_of_action

COX inhibitors have been known to have a wide range of side effects (with even more recently reported, I forget what specifically). They are generally weak and only decrease rather than eliminate inflammation completely at the recommended dose.

The common prescription approach is largely topical steroid creams such as hydrocortisone - another crude and bad approach due to increased risk of infection among other side effects

The most recent and promising novel approach appears to be peptide chains that manipulate the immune system:
https://en.wikipedia.org/wiki/Immune-selective_anti-inflammatory_derivative

The main question: Why hasn't there been visible progress on a gene-blocking approach? There are all sorts of ways to block them - find all the proteins and other products that promote or cause inflammation, then consider all sorts of options to stop them. Options including blocking transcription, blocking translation, stopping the protein/product from exiting its cell, blocking its receptor, blocking intermediates.

Future "last resort" treatment for chronic debilitating inflammatory diseases could include "nonsense mutation" gene edits that permanently disable inflammation in specific cell types.

The end result would be a new generation of anti-inflammatory treatment guaranteed to block known mechanisms of inflammation at the source, instead of the largely ineffective and side-effect ridden standard approaches.

The cost might be prohibitive with today's technology although it would almost certainly become feasible with biochemical 3D printing.

Your question is very complex, so for now I'll focus on a few points and answer these first:

  Why hasn't there been visible progress on a gene-blocking approach? There are all sorts of ways to block them - find all the proteins and other products that promote or cause inflammation, then consider all sorts of options to stop them. Options including blocking transcription, blocking translation, stopping the protein/product from exiting its cell, blocking its receptor, blocking intermediates.

You are right that all of these options to block genes exist for laboratory or research purposes. Using them on humans as medicine is a lot more complex in a lot of ways though. One main factor I'm not going to discuss much is the cost of all these techniques - which generally a lot more compared to making a simple chemical drug.

Blocking translation
This is a almost a standard experiment for research labs and can usually be done quite specifically (without side effect on most other genes). In oder to achieve a transient (short lasing) effect you usually use RNA knockdown: The introduction of small RNAs, that specifically target the mRNA of the gene you want to knock down, into a given cell with stop transcription in that cells. There are two problems with using this in patients: 1) transformation efficiency: you need to bring RNA into to the cells, which is not a very efficient process. You'll need even higher doses of the stuff to get a strong enough effect in the immune cells you want to target, since it's very hard to specifically target them. 2) The transformation process itself requires either potentially toxic chemicals or viruses to get the RNA into cells, both of which a costly to make and no one wants to take them unless they have to. Taken together this makes RNA knockdown a very bad drug / treatment strategy.

Blocking transcription
The only way to block transcription of a gene permanently is gene editing - which you really don't want to as a short term treatment against inflammation. To make it work transiently you'd have to bring proteins into the cell that bind to and block the genes you want to suppress - inactive transcription factors would do the trick. One (almost minor) problem is that they wouldn't be very specific, so you'd get lots of side effects. The bigger problem is that it's very hard the get a lot of proteins into cells. You'd need large scale transformation and there are many problems with that, which I discussed above.

Stopping the protein/product from exiting its cell
This is an interesting idea, which might actually work - given a few additional years of research. It's probably not possible to this specifically, so you'd generally block the release of proteins from cells. However if you find a drug that only lasts for a few hours it might work. One important caveat is, that the same (or at least a very similar) mechanism is used, when synapses release neurotransmitters - which you definitely do not want to mess with.

There seems to be active research in this area

Blocking its receptor / blocking intermediates

This strategy is very viable in the immune system, where many soluble factors like cytokines with respective receptors are important. Blocking of receptors or soluble proteins can be done by antibodies and there are many people working on this, some antibodies are already licensed by the FDA as drugs for humans. In most cases these are however intended for use in cancer or other more severe diseases, as all of these are immensely expensive.

  Future "last resort" treatment for chronic debilitating inflammatory diseases could include "nonsense mutation" gene edits that permanently disable inflammation in specific cell types.

You do not want to this. Inflammation is an important process that keeps your body healthy and permanently disabling it would basically make you immune deficient, which is not a good thing.

  The cost might be prohibitive with today's technology although it would almost certainly become feasible with biochemical 3D printing.

Biochemical 3D printing will likely never be a thing. It's possible to print e.g. organs with cells, but printing proteins requires molecular construction and it's unlikely we're ever ging to find a system that's better than what nature came up with during a few million years of evolution.
In general though technological advancements should decrease the cost of all these strategies.


Can anyone identify this spider? (greater Poland region) This is in Poland, in the Greater Poland area, found a few days ago by a garage in the city.
I didn't have any coins on me to give a sense of scale, but the body is roughly 1.5cm long. It was dead when I found it.
I'm curious because I haven't seen any spider like this one during my stay here, they're all tiny specimens normally and this one really stuck out.

That looks like a Funnelweb Weaver (family Agelenidae), specifically Tegenaria atrica,  based on the patterning of the abdomen and thorax.

Female Tegenaria atrica, picture by Jørgen Lissner

Their range includes Poland:

Range: Andorra, Austria, Belgium, Bulgaria, Croatia, Czech Republic, Denmark, Faroe Islands (introduced), Finland, France (Corsica), France (Mainland), Germany, Great Britain (Channel Islands), Great Britain (Mainland), Great Britain (Northern Ireland), Greece (Crete), Greece (Dodecanese Islands), Greece (Mainland), Ireland, Italy (Mainland), Latvia, Liechtenstein, Lithuania, Macedonia, Netherlands, Norway (Mainland), Poland, Portugal (Mainland), Romania, Slovakia, Spain (Mainland), Sweden, Switzerland, Ukraine, Yugoslavia (van Helsdingen 2009.1).

Source: http://www.jorgenlissner.dk/families.aspx


Where can I find a transcriptome of a normal uveal melanocyte? I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?

I can't find any transcriptome data, but I did find miRNAome data from GEO at NCBI and Array Express at EMBL.


Is transition more common than transversion during the evolution of duplicated genes? Transitions are base mutations of purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T). Transversions are purine to pyrimidine or vice versa (A <-> C, A <-> T, G <-> C, G <-> T). And it is well-known that transitions are more common than transversions in the populations.

So what is the condition in the evolution of duplicated genes? Suppose a gene A is duplicated with two copies A1 and A2 in the same genome (not two alleles in different sets of chromosomes, or the same gene in two different cells/organisms). At first A1 and A2 had the same sequence, but then they went through an evolution process and each got some mutations. Now let's check the sequence of A1 and A2 again, are the differences between A1 and A2 mainly transitions instead of transversions?

Although I think it would not be surprising to find that transitions are more common in this condition, I've searched some papers focusing on the evolution of duplicated genes to look for some support. However, they mainly discuss what happened to their functions instead of sequences.

If we consider that the biochemical impact of transitions vs transversions is constant across the two scenarios, then the only discrepancy can be due to the level of purifying selection, or the level of positive diversifying selection, or both, between the two duplicates.

By far the most common fate to one duplicate copy is for purifying selection to be relaxed, leading to accruing deleterious mutations and eventually loss. This means that fixation of non-synonymous mutations are more common, and as transversions are more likely to be non-synonymous, this implies that the rate of fixation for transversions would increase.

Similarly, one might expect functional change leading to positive diversifying selection, which implies a greater rate of fixation of non-synonymous mutations and, following the same logic as above, a greater rate of transversions.

Whether or not this contributing increase to the rate of fixation of transversions mean that transversions actually outnumber transitions, or instead merely decreases the ratio of transition:transversion, will be dependent on the particular gene and selective scenario.

As a final note, while the first cause I identified (biochemical)  actually changes the rate of mutation, the selection-specific factors are changes to rate of fixation, which is a population-level process. So while the relative rates of transition and transversion may stay the same, the fixation rates of these two categories of mutation between the two duplicate copies are the important difference.


Does pre-operational exercise affect recovery from surgery? Statistical Analysis https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210

I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on Table III in the article linked above. I am evaluating the WOMAC scores. My first question is can effect size confidence intervals cross zero and still be valid? My second question is about the negative and positive values of the Hedges'g. The first study scores the WOMAC in a way where the higher the score, the better the outcome. The second two studies score the WOMAC in a way where the lower the score, the better the outcome. Does this mean that in the first study a positive Hedges'g indicate larger effect for the treatment group and a negative Hedges' g for the other two studies indicate larger effect for the treatment group?

Regarding your first question, the effect size is not invalid if the confidence interval (CI) crosses 0. The effect size is a point estimate. When the CI -a range estimate of the coverage probability- includes 0, the probability that the range of the effect size can include 0 cannot be rejected at the $1-\alpha$ level of confidence.

Regarding your second question, from the definition of Hedge's g:

$$g = \frac{\bar{x_1} - \bar{x_2}}{sd_{pooled}}$$

we can see that if $\bar{x_2}$ is larger than $\bar{x_1}$ then $g$ will be negative. So, the sign only determines which of the estimates is larger and that will depend on which estimate is considered as the reference.


Where can I find a global life expectancy table? I've found good information on specific countries and demographics, but I can't seem to find global numbers.  I know that the world life expectancy is around 71.0, but I'm trying to get a percentile breakdown in the form of something like an actuarial life table.

Not surprisingly, the WHO has a lot of data, I think especially interesting for you is this interactive figure, which you can find here:

Other data on this topic can be found on the WHO website here, in the Wikipedia or from the Worldbank.


What determines the spiral direction of plants? Some plants and vines spiral clockwise as they go along (right direction) and some spiral anticlockwise (left direction). What determines which direction they spiral along? At first, I believed it to be determined by which hemisphere you are in (influenced by the Coriolis Effect), and this result could be tested by finding spirals in both northern and southern hemispheres and comparing their directions. However, the very first spiral I found seemed to cripple that idea.

The spiral I found spirals first in the right direction, then suddenly decides to spiral in the left direction, and then further along in the right direction again. Since the Earth does not arbitrarily change its rotational direction, this phenomenon must be explained by some other explanation. The change in rotational direction seems to be abrupt, almost like a catastrophic event. A few that I thought of:

1: Arbitrary. The spiral seeks merely to latch onto something, and will try both directions to see if either work out.

2: The spiral is somehow influenced by the night day cycles. Since the spiral switches from right to left back to right having been subjected to two sudden changes, the only large changes I can think of is the day night cycle.

-I live in Australia by the way

First of all, you assumption seems to be incorrect. Plants in same part of the world can twine in opposite directions.

Little seems to be known exactly. Gravity has nothing to do with plant's chirality (or "handedness") or spiraling:

  How plants do this is still unknown. Darwin proposed that it was "autonomously induced." This came to be known as the internal oscillator theory. In the 1960's the gravitropic overshoot theory explained mathematically how circumnutation could spontaneously occur as a result of forces related to gravity and growth. Recent experiments on the Space Shuttle have demonstrated that gravity is not necessary for circumnutation.

Here is another link to a blog, but it does contain reference to original paper on observation of chirality. Main conclusion, taken from the abstract, is:

  The predominance of right-handed helical growth in climbing plants cannot be explained by hypotheses attempting to link plant growth behaviour and global location. One alternative hypothesis for our findings is that the widespread phenomenon of anticlockwise twining arises as a function of microtubule orientation operating at a subcellular level.

To elaborate a little on that, remember that actin filaments as well as microtubules are all chiral polymers. That is, they form spiral structures with defined orientation. Even more, microtubules all start roughly from the nucleus away to membrane, so this might suggest cellular mechanism for preference toward twining chirality. However, this does not address your observation that given plant changes direction of growth twice.


How can a two genera share a latin name? Recently, someone asked if species could share a latin name. In his answer, Remi.b said the latin name is unique to the species, and I think he is right.
However, this made me remember that I once stumbled upon a latin name that is shared between a genus of birds, and a genus of plants: oenanthe.

https://en.m.wikipedia.org/wiki/Wheatear

https://en.m.wikipedia.org/wiki/Water_dropwort

My question is: how come? Is it allowed for genera to share a name (not likely)? And why did Linnaeus, who named both, choose to do so? Error?

No, not an error. Plants, Animals and Bacteria each have their own independent nomenclatural codes. So while it is not advised, it is not forbidden by the code to have the same genera. It would be forbidden to have the same genus within one of the three codes. As a side issue, don't forget that the species ALWAYS includes the genus. Species are always binomens. The species epithet is the second word in the species binomen. Thus our species is Homo sapiens, not sapiens.


Are intestinal and pancreatic lipases different? For explaining the action pancreatic lipase, my book wrote this equation:-
$$fat\space particles + lipase\rightarrow fatty\space acid + glycerol + lipase$$
But for intestinal lipase, my book has a different equation:-
$$fat\space particles + lipase\rightarrow monoglyceride + fatty\space acid$$
So, did my book make a mistake or are intestinal and pancreatic lipases different?

Pancreatic lipase and intestinal lipase are almost same in their functions. In the intestine, the name of the lipase is a triacylglycerol acyl hydrolase it also called colipase dependent lipase or Pancreatic lipase,  Free fatty acids, and 2-monoacylglycerol are the primary products of lipid digestion in the jejunum. and Pancreatic Lipase also produces Free fatty acids and 2- monoacylglycerol.
so we can say that both enzymes are almost same and produce the same products.
Sources Lippincott's Illustrated Reviews Biochemistry 5th edition Chapter 15


Will the climate change help the trees to grow? I've heard several contradictory views and I'm not sure which factor do climatologists count with. Counting with all the effects of the current climate change (including changes of biotopes on places such as Siberia, as well as the higher percent of CO2 in the atmosphere), will the conditions help make better conditions for growing trees (I know the effect on biosphere is usually claimed to be synergic, e.i. for example coral reefs will have less CaCO3 to work with so they will make the global warming appear faster. So please consider just the average effect on trees)

I don't think anyone knows for sure. It will certainly depend on which spatial location, and which tree species, you're thinking of: while "global average effect on growth (e.g. measured by change in net ecosystem exchange of forested ecosystems) of all tree species" is at least well-defined, it will be an average across an enormously variable set of communities, and species within communities. Some of the relevant factors:

if you count the direct effects of increased CO$_2$, this will generally increase growth rates, although it will be highly variable across ontogeny (life stage, i.e. seedling vs sapling vs adult) and species. In general changes in growth rate will be higher for seedlings and for early-successional/fast-growing species, which may in turn change community structure: see Bolker et al. 1995 for one synthetic study of this.
increased temperature would be expected on average to increase growth rates
decreased moisture availability (potential evapotranspiration) would be expected on average to decrease growth rates
increased microbial activity (e.g., due to increased temperature and/or moisture availability) would be expected to lead on average to increased nutrient availability, increasing growth rates
if you're just measuring "net biomass accrual to trees", then changes in large-scale disturbance (wildfire, windstorms, pest and pathogen outbreaks ...) will tend to decrease standing biomass (although it may also lead to temporary pulses of increased carbon accrual as forests re-grow after disturbance)
note that almost all of these driving factors (temperature, precipitation, water availability, frequency of disturbance) will themselves vary a lot in space.

For a summary, you could start by looking at Purves and Pacala 2008 for some of the ways in which people are trying to put these pieces together.


When did birds and mammals diverge? Which was the most recent common ancestor between mammals and birds?

Form a rapid google research I could not find good answers. This site seems to imply it was at least 250 milions of years ago. This scientific article mentions 600 milion years but the sentence is a little unclear.

The Most Recent Common Ancestor (MRCA) of birds and mammals was the first amniotes.

Fossil record

The latest known fossil of amniotes are 312 million years old (Bentou and Donoghue, 2007).

Genetic data

From EOL, using data from The Paleobiology Database, the first amniote is in between 314.6 and 323.2 million years old. Those results are a little bit older than the latest known fossil which very much makes sense.

The (apparent) contradiction in the sources you found

  This site seems to imply it was at least 250 milions of years ago.

They actually say 250 to 320 millions years. This broad estimates match the above studies and data.

  This scientific article mentions 600 milion years but the sentence is a little unclear.

It is actually a news feature published by a science writer (former neuroscientist according to her twitter account), not a researcher. She indeed made the claim (Even so, 600 million years of evolution and radically different brain architectures separate birds from humans.). There is no reference for the claim and based on above evidences, it appears at first to be a mistake. It is not impossible though that she considered the evolutionary time in both branches in her statement but that would be very unusual If two lineages diverged $t$ years ago, then they both evolved for $t$ years and it could arguably be said that they are separate by $2 t$ years of evolution. If this is what she meant, then the claim is correct but quite misleading.


Cell-type specific methylation profiles: original reference finding? This is a general question, and a specific question. I'm looking for the original reference that first talked about how DNA methylation profiles are cell-type specific.  This is specific, because I care about this specific reference paper, but it is general because I don't know how to go about finding original reference papers to begin with.

Any help would be super appreciated!

Note: This is not my field, and only the result from a quick  database search

Doing a quick search in the Web of Knowledge, I found the paper Ehrlich et al (1982), Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells, which is relatively well-cited. This in turn mentions that:

  Recent studies indicate that for many genes associated with vertebrate development, there are tissue- or cell-specific differences in the extent of DNA methylation.

The oldest studies referenced in this paper that seem to refer to tissue-specific methylation are Vanyushin et al (1970), Rare Bases in Animal DNA, Nature and Vanyushin et al (1973), The content of 5-methylcytosine in animal DNA: The species and tissue specificity, Biochimica et Biophysica Acta. The 1973 paper is also one of the earliest papers cited in another well-cited paper from 1983 (Gama-Sosa et al, 1983)), so it might be the best bet. However, Gama-Sosa et al also mentions Kappler (1971), The 5-methylcytosine content of DNA: Tissue specificity, which is clearly relevant. In total, Gama-Sosa et al has references to 13 early papers on DNa methylation, so you might want to check them all out, and backtrack from there. Also, Vanyushin seems to have published in smaller, more obscure journals around the same time (e.g. DOKLADY AKADEMII NAUK SSSR), so there might be earlier papers that express the same ideas. The earlier papers seems to deal with bacterial DNA methylation though.

A couple of other references are:

Van der Ploeg & Flavell (1980), DNA methylation in the human gamma delta beta-globin locus in erythroid and nonerythroid tissues,
Mandel & Chambon (1981) DNA methylation: organ specific variations in the methylation pattern within and around ovalbumin and other chicken genes
McGhee & Ginder (1981), Specific DNA methylation sites in the vicinity of the chicken beta-globin genes


Are there biological reasons why life expectancy is lower for men in most countries of the world? I've been checking life expectancy figures for men versus women in many countries of the world and the figures for men sometimes are terrifying. Countries like Russia have a 12 years gap in disfavor of men. Developed countries have usually a 4-5 years gap in disfavor of men. My country Argentina has a 7 years gap. African countries and middle east countries where supposedly women have a harder life because of religion have usually a 3 years gap in disfavor of men. So far I haven't found a single country where men lives more than women.

Now I know there are more men than women who dies in homicides, suicides, work accidents, wars, etc. men are more likely to get addictions because of depression, etc. but aside of all that, is there any biological reason why men lives less than women everywhere?

There are both biological and  social factor for that:
Biological

Females have two X chromosomes. When mutations in genes of the X chromosome occur, females have a second X to compensate. Males, on the other hand gave just one chromosome X and all genes its genes express themselves, even those lethal or deleterious.
Females have better resistance to biological aging and hormones and the role of women in reproduction are known to be associated to greater longevity (e.g. estrogen offers some protection against heart disease because it facilitates elimination of bad cholesterol while testosterone has been linked to violence and risk taking).
The female body evolved to accommodate the needs of pregnancy and breast feeding hence deals better with making reservation. This ability has been linked to a female's better ability to cope with overeating and eliminating excess food

Social
This "advantage" women seem to have was once nullified by the status and life conditions they had back then, as the risks and the burden of pregnancy and the lack of attention to health and rights women had in a way more misogynist world.
Given the economic, social and political changes that the world experienced, a general progress in female life conditions took place and women have not only regained their biological advantage, but have gone beyond it, achieving higher life expectation. Social and comportamental factor are involved in this higher longevity:

Women tend to engage in fewer risky and bad for health behaviors than men do, e.g. men have more problems than women with alcoholism, smoking and road accidents.
The world is still very sexist and the gender roles to be played would expose men to higher risks. Regarding to work, for instance, although women nowadays participate in the work force, their professional activities remain different and are less prejudicial to their health (on average).
Also regarding to  very sexist gender roles, men are expected to be strong and manly and powerful and women are expected to be gracious young and beautiful. As a result of that, women are more attentive to their body and health, engage themselves in more healthy activities and benefit more from medicine and science. Men on the other hand submit their bodies to challenges from early ages and tend to neglect their bodies needs.

You can have access to detailed statistics (male/female, country by country, life expectancy and other health data) here:
http://www.who.int/gho/publications/world_health_statistics/2016/Annex_B/en/
And also, read more about the issue here:
https://www.scientificamerican.com/article/why-is-life-expectancy-lo/
http://www.who.int/mediacentre/news/releases/2016/health-inequalities-persist/en/
https://en.wikipedia.org/wiki/List_of_countries_by_life_expectancy#cite_note-10


Why would you mix polymerases in PCR? I was reading a manual for kit that requires you to amplify DNA by PCR before analyzing it in the kit. The manual suggests mixing proofreading and non-proofreading polymerases:

  For
  PCR
  products
  >2500
  bp
  in
  length,
  use
  a
  DNA
  polymerase
  blend
  containing
  Taq
  DNA
  polymerase
  supplemented
  with
  a
  proofreading
  DNA
  polymerase

How would this improve the amplification of long products? It suggests using only a proofreading polymerase for fragments below 2500 bases. Does the addition of a non-proofreading polymerase improve speed? I have TAQ and PFU Ultra, but both instructions say to use an extension time of 1 minute per kb.

The Taq polymerase is a rather fast enzyme (the synthesis rate is around 1 kb/min), but the backdraw is that it has no 3'- 5'exonuclease activity which would enable to proofread the newly synthesized DNA. This leads to the introduction of errors and the chance of getting these is higher the longer the DNA you want to synthesize is.

Polymerases which are able to proofread (which have the exonuclease activity) like Pfu have a much lower error rate, but are on the other hand also much slower, typically around 0,5 kb/min. Pfu is also more expensive than the Taq polymerase. See table 1 from reference 1 below:

To combine the advantages of both polymerases, you typically use a blend of Taq and Pfu. Then you get the high processivity of the Taq combined with the proofreading capacity of the Pfu and get good yields of DNA with a low amount of mutations. See also reference 2 for details on this system.

References:

Error Rate Comparison during Polymerase Chain Reaction by DNA
Polymerase
Effective amplification of long targets from cloned inserts and
human genomic DNA.


Can a woman possessing 1 mutated allele show attenuated color-vision deficiency? Women possess two X chromosomes. However, during development, when the embryo has about 32 - 64 cells, one of these chromosomes is randomly inactivated (in each cell) by an lncRNA named Xist. As a consequence, females are mosaics.

I was interested if this might affect phenotypes of X-linked genetic diseases, for example...

1) Is it possible for a woman who is heterozygote to color vision deficiency be "partially" color blind, considering that some of her cones will only possess the mutated allele?

2) Is it possible that a heterozygote female who carries a dominant allele for a X-linked disease be asymptomatic?

Any references on these issues are welcome.

Short answer
Skewed X-inactivation may lead to phenotypic manifestation of X-linked color blindness.

Background
What an interesting question!

In a study by Jorgensen et al. (1992) two female identical twins that were heterozygotes for X-linked deuteranomaly were investigated. Phenotypically, deuteranomaly refers to anomalous trichromacy, i.e., reduced perception of a color. Note that deuteranopes are totally color blind. Deuteronomaly in the twins was associated with a defective gene derived from their father. Interestingly, while monozygotic twins are genetically identical, one of the twins was phenotypically deuteranomalous, while the other had normal color vision.

Analysis of skin cells of the color vision-defective twin revealed that almost all skin cells had the paternal abnormal X chromosome active, explaining her color-vision defect. In contrast, skin cells from her sister with normal color vision had predominantly the maternal X chromosome active. Hence, deuteranomaly in one of the twins could be explained by an extremely skewed X inactivation.

As pointed out by @mdperry, extreme skewed X-inactivation is rare, and most heterzygous females for color blindness (carriers) are indeed asymptomatic (Jordan & Mollon, 1993). Regarding your second question, all gene mutations leading to color blindness are recessive (NIH).

References
- Jordan & Mollon, Vis Res (1993); 33(1): 1495-1508
- Jorgensen et al. Am J Hum Genet (1992); 51: 291-8


How is the mRNA transported out of the endoplasmic reticulum? In eukaryotes the nuclear envelope is continuous with the ER, so what helps it out of that?

The proteins mediating the transport of mRNA out of the nucleus (nucleoplasm/karyoplasm) are called "karyopherins" and belong to the nuclear pore complex family.

Prior the creation of the final form of mRNA, various proteins are attached to the so called pre-mRNA and a mRNA-protein-complex is built (co-transcriptional). Some of these proteins carry factors for splicing and processing, later RNA-binding proteins are added. (RNA binding proteins such as $Npl3p$, $Gbp2p$ and $Hrb1p$ (serine/arginine-rich proteins) accompany mRNA out of the nucleus. )

After mRNA processing mRNA export is initiated by dephosphorylation of $Npl3p$, leading to binding of $Mex67$ (Saccharomyces c.), forming a complex that interacts with the nuclear pore complex.

That is the way mRNA is able to leave the nucleus.


Ideal low-protein binding membranes I'm looking through the literature on the topic. It seems like hydrophilic PVDF membranes are ideal for low-protein binding but it also sounds like Regenerated Cellulose is an appropriate substitution.

Looking at one resource (http://www.zellnet.com/elispotplatescolumn/)

  When PVDF filter plates were introduced, some investigators chose to use PVDF plates and some continued to use NC.  The reasons for choosing one plate (membrane) over the other are highly varied and won’t be addressed in detail here.  The fact that some laboratories and individual researchers feel strongly that one membrane is superior to the other runs contrary to the large body of Western blotting experience:  Despite some clear-cut differences in how each of the membranes can be used, there is essentially no reported difference in terms of detection sensitivity or signal to noise on NC versus PVDF in the Western Blotting application.  This having been said, it is clear is that the two membranes and their properties are quite different.

The assay that I am looking at in particular is protein/nanoparticle binding to mammalian cells. I am looking for a balance that will enable me to remove free protein without fouling the membrane and/or killing my cells.

Apparently poly(ethylene oxide) is a biologically interesting polymer, with minimal protein interactions.

The apparently means that I haven't tried it myself, but my polymer teacher told us so.

http://www.sigmaaldrich.com/materials-science/material-science-products.html?TablePage=20204110

http://en.wikipedia.org/wiki/Polyethylene_glycol

Nomenclature seems to favour poly(ethylene glycol). I prefer poly(ethylene oxide), because then I know from what monomer the polymer was synthesized.


Gel Electrophoresis - loading dye and more I'm a student new to molecular biology coming in from an eco-evo background looking for tips from you molecular pros! It seems that I'm running quite a few gels. The loading dye I'm using is Gel Loading Dye, blue (6X). The supporting document calls for 5uL:25uL reaction and 10uL dye:50uL reaction. Here's the problem: I'm trying to get my PCR to work and so I'm doing a lot of 'just checking' trials where I only load 2uL of reaction to each well from different 20uL PCR reactions. What volume of Gel Loading Dye, blue (6X) should I use when running only 2uL of PCR product

My goal now is to learn to do a DIG in situ hybridization to localize the distribution of mRNA of a gene I'm interested in so any tricks and tips would be greatly appreciated!

The loading buffer you add to your samples for gel electrophoresis has a few different purposes, but the exact amount does not really matter. The purpose of the loading buffer is

to make the sample heavier so it is easy to get into the pocket and stays there
to visualize how far the gel has run
to denature the sample (only for denaturing gels)

Sample buffers for agarose gels usually use something heavier than water like glycerol or sucrose together with a tiny amount of a dye like bromophenol blue.

So in general there is no issue with using too much dye, but using not enough could lead to the sample being not heavy enough and problematic to pipet, or the sample not being properly denatured. I'd either use 1 ul of the sample buffer (smaller amounts can be annoying to pipett) for your sample, or dilute the sample to 5-10 ul and use the regular amount.


Halophiles' food habit We know that some halophiles are heterotrophic, but in those highly saline environment what do these organisms eat as there might be very little chance of survival of any other organism?

When we look at the definition, Halophiles are just archaebacteria that require salt in their environment to live. Wikipedia states that they live in salt concentrations of 0.3 to 0.8 M (1.7 to 4.8% — seawater is 0.6 M or 3.5%).

According to The Saltwater Wetland bacteria in estuaries will get their food from dissolved organic mater in the water. An estuary can have a salt concentration of 0.5 to 35 ppt (according to google). This would be 0.05 - 3.5% salinity depending on the estuary, so obviously there are some estuaries would not be able to host Halophiles, but the concept is still the same. They would get their food from dissolved organic matter in the water.


metabolism preference by the body What I know about metabolism is that,during exercise body uses carbohydrate first then fats and then protein,so my question is why does body prefer glucose first as fuel for energy and what makes glucose biochemically preferred molecule to be metabolized first

None of them can be directly use for energy. We all talk about aerobic oxidation, which is the major process for metabolism.

They all need to go into the tricarboxylic acid cycle (TCA cycle) and oxidation phosphorylation to produce ATP, which is the energy used in organism.

For glucose, they can break down into two pyruvate and enter the TCA cycle. That is the fastest pathway organism use to produce energy.

For fat, since they have long carbon skeleton chain, they cut off 2 carbon compounds from the fatty acid every time. And under a series of process, it become pyruvate and go into the TCA cycle. So it really takes long time and complicated pathway to oxidate the whole fatty acid molecules.

For protein, it is much more complicated. Since protein is not energy store form, it need to become a energy store form first. First it need to be degraded into amino acid, and different amino acids takes different procedure to go into the TCA cycle. Here is the picture I found on the book  by John L. Tymoczko, Jeremy M. Berg and Lubert Stryer.

In sum, glucose is the fastest energy form that body can use to take metabolism, oxidate fatty acid or proteins take much more complicated pathway.


What's the purpose of colorful mushrooms' caps? What's the purpose for many mushrooms to have colorful caps? Is not it is in their interest to hide as well as possible? Or there are mushrooms that propagate by being eaten, like fruits?

Why not all the mushrooms are poisonous?

Mushroom is actually the reproductive organ of the actual fungal body beneath the surface. It have a high surface area to disperse or spread the spores.

If the eating predators are low or dispersing is not an option, then it will need other organisms to attract to that they can be spread, so they are not toxic. Analogous to fruits, they uses different colors which are non-toxic to attract.$^1$

Whereas brightly colored mushrooms are less toxic, whereas, most toxic ones are either brown or white.$^2$

Edible Mushrooms

Toxic Mushrooms:

Source:

Why do mushrooms come in so many shapes and colors?
Mushroom poisoning

Image Source:

https://www.etsy.com/listing/93680839/antique-1900-edible-fungi-print


What is the fluid clearance rate inside the retina? I'm attempting to model the chemical concentration between several compartments of the eye, including the retina. Does anyone have any idea what the rate of fluid removal is in the retina, or could direct me to a study of this?

EDIT: It appears that Müller cells play a crucial role in this, dehydrating the retinal tissue. I am attempting to find the rate at which they achieve this. (see link)
http://retinatoday.com/2008/11/1108_07.php/

As I mentioned in a comment, the RPE (retinal pigment epithelium) is in charge of absorbing the "water" from the retina and beneath it.

  Water is eliminated from subretinal space by active transport by the
  RPE. The transportation rate was estimated to range from 1.4 to 11 µl
  x cm-2 x h-1.