Does plasmolysis kill plant cells? I know when a plant cell becomes fully plasmolysed that the protoplast shrinks away and eventually is no longer joined to the cell wall.

Is this irrevocable damage? Can the cells survive it and continue to function if they are put back into a favourable solution.

If so how does the protoplast rejoin to the cell wall?

No. Cell-plasmolysis is not necessarily fatal for the cell. Plant cells normally recover from this condition when water is available. (But cell death can take place in excessive or prolonged lack of water).

It is an incomplete truth that during plasmolysis, plant cells get detached from the cell wall. Actually the plasmodesmatal connections remain there and a portion of the cortical (outermost)-layer of cytoplasm, mainly containing "cortical endoplasmic reticulum", a group of endoplasmic reticulum spanning close to the cell wall; remains there.

Now, when plasmolysis take place, the cell-membrane shifts apart from the cell wall; but at the place in-between, there forms fine cytoplasmic threads called Hechtian strands. So the connection is retained. (As well at some portion of cell-wall, the bulk protoplast remain touched there)

Here are photos showing hechtian strand; taken from the book Plant Cell Biology- structure and function, by Gunning and Steer, Jones and Bartlett publishers, Copyright 1996;

  Image-1 (Book image 16-C)

  Hechtian strands of stretched plasma membrane extended from the plasmolysed protoplast to the cell wall (K. Hecht , 1912, was the first to  study them in detail). This confocal micrograph shows strands in a 16 μm- deep zone. Some strands extend from plasmodesmata (arrows), where the membrane passes through the cell wall, butmany attached to other sites. in 1931 another early investigator J. Plowe, pushed plasmolysed protoplast along inside their cell walls, observing that existing strands stretched and broke, and that new strands could form. In today's terminology we would say that new strands arise when freebinding sites on the plasma membrane contact and bind their ligands in the cell wall.

Reference:

  Plant Cell Biology- structure and function, by Gunning and Steer, Jones and Bartlett publishers, Copyright 1996

Update: An interesting information; there is one method of plant protoplast isolation without enzymic digestion of wall; which uses plasmolysis. Since the protoplast(and cell membrane) get shifted from part of cell wall; it becomes easy to rupture the wall without rupturing the cell-membrane. (Discussed in this website). The protoplast remains alive after plasmolysis otherwise we won't be able to use this method for protoplast culture, cell fusion etc.


Can LSD in very small amounts increase mental ability? Can one take a small amount of LSD(acid) and not trip but still benefit from the intended purpose? It was said the military invented it for extra sensory abilities. It has also been said it could increase your hearing or sight?

The phenomenon you are referring to is called microdosing. It was brand-new in terms of research focus when you initially asked your question, and it is still a fairly novel and little-studied subject.

A lot of interest in this phenomenon stems from anecdotal evidence by microdosing users, who report beneficial effects. This is however not necessarily an indicator of neuroenhancing potential, since psychopharmacological agents are known to modulate subjective evaluations of performance more than constrained objective measures of it (compare tables 3 and 4 in this article, which does not discuss LSD or microdosing per se, but illustrates this psychopharmacological phenomenon).

Anecdotal findings regarding LSD are substantiated in an article, which found that microdosing LSD improved the self-reported mood of participants.
Additionally, this article showed an improvement of vigour (as per the POMS scale) at the highest dose.
This is, however, still not a behavioural effect, as POMS is a psychometric assessment method.
Still, this further substantiates the mood-enhancing effects beyond direct self-reporting.

Another article reported increases in creativity, focus, and well being, though again, it should be noted that all of these metrics were assessed using participant reporting, and not evaluated based on behaviour.

So to conclude, there is to date no convincing evidence that microdosing LSD improves “mental ability”.
There is however a growing amount of evidence that LSD microdosing improves mood, which in and of itself can be a desirable effect, and can further be argued to contribute to improved “ability” in more complex behaviours such as sustained deductive reasoning or social interaction.
Conjecturing from the first cited article on methylphenidate, modafinil, and caffeine, it is conceivable that a similar effect:

  In conjunction with results from neuropsychological testing we conclude that modifying effects of stimulants on complex cognitive tasks may in particular result from more reflective decision making processes. When not under time pressure, such effects may result in enhanced performance.

as the one seen with modafinil and methylphenidate could be present with LSD microdosing.
Appropriate data to address such complex evaluations is however very scant in general, and to date wholly absent for the emerging phenomenon of LSD microdosing.

TL;DR

No but maybe.


GWAS: marker map based on old genome assembly - can I use the new assembly to look for SNP positions? I have an old set of pig SNP data and the positions were mapped using v10.2 of the assembly.

I submitted a GWAS paper for review, and the reviewer wants to know if any of the significant SNPs that were located in previously unknown genes are now in known genes, with the release of the latest assembly last year.

I was under the impression that I had to use the assembly the marker map was based on to see where SNPs are located. Is this correct or can I use the new assembly?

Many thanks in advance!

Why haven't you tried using LiftOver to convert the coordinates?

https://genome.ucsc.edu/cgi-bin/hgLiftOver


What mechanisms tell temperate trees when to drop leaves? I've been looking around and cannot find a definite answer on what it is that tells trees to change their metabolism and drop leaves. I see that such activity is called Deciduous.

What interests me are the specific mechanisms by which a tree knows that it's time to drop leaves. Is it photoperiod shortening (day duration?) Is it temperature changing metabolism? Is it build up of some toxic compound?

Thank you for your input!

Here is a good USDA link:

http://www.usna.usda.gov/PhotoGallery/FallFoliage/ScienceFallColor.html

It would appear that the shortening days are a main trigger, and there are other factors. I did a basic search using Google for "what triggers leaf fall in deciduous trees?", since I always thought temperature and changing seasons were major triggers and wanted to double check.


How are oranges in the US or anywhere made seedless? How are oranges in the US or anywhere made seedless? Please explain the broad principles and not the technicalities.

Oranges and other fruits are generally not actively made seedless. Rather, seeds may fail to develop due to either lack of fertilization (pollination) or a natural tendency. The natural production of unfertilized and thus seedless fruit is called Parthenocarpy.

To quote the Scientific American article (3) mentioned by Oreotrephes:

  Fruit development normally begins when one or more egg cells in the
  ovular compartment of the flower are fertilized by sperm nuclei from
  pollen. In some plants, however, fruit develops without fertilization,
  a phenomenon known as parthenocarpy. Parthenocarpic fruit has
  advantages over seeded fruit: longer shelf life and greater consumer
  appeal.

  The most frequent reasons for lack of seed development are pollination
  failure, or nonfunctional eggs or sperm. In many plants,
  self-incompatibility genes limit successful fertilization to
  cross-pollination between genetically different male and female
  parents. This property is exploited by citrus farmers who grow
  seedless fruits, such as navel oranges and clementines. Because these
  cultivars are self-incompatible, they fail to set seed when they are
  planted in orchards of identical plants (clones). These plants have a
  high frequency of parthenocarpy, however, so they still produce fruit.

Parthenocarpic varieties may arise from a lack of pollinators. From the Wikipedia page on Parthenocarpy:

  Plants moved from one area of the world to another may not always be
  accompanied by their pollinating partner and the lack of pollinators
  has spurred human cultivation of parthenocarpic varieties. Some
  parthenocarpic varieties have been developed as genetically modified
  organisms.

To preserve the seedless trait, parthenocarpic trees can be propagated by grafting. It is possible that more kinds of seedless fruits will be engineered in the future (3):

  Plant biologists have learned that if the plant hormone auxin is
  produced early in ovule development, parthenocarpic fruit can grow on
  plants that do not usually exhibit this property. Thus, genetic
  engineering will most likely give consumers parthenocarpic fruit in
  many other species in the near future.


Oxidation means inflamation? All right, I was reading article on nutrition, that focussed on content analysis of pastry-like food product for kids. I have to say that I am not sure this article would pass the imaginary smell test, although it didn't raise any serious red flags, except one.
Among other things, this article said that oxidation means inflammation. It said this in connection with use of rapeseed oil in said product, saying rapeseed oil is less saturated and therefore more likely to oxidize. It then implied, that when this oxidation takes place in the human body, it leads to inflammation.
Now I am no biology, medicine, or nutrition specialist, but if something is still stuck in my head from high school biology, it is that inflammation is the physical manifestation of our immune system fighting off infection, no? Apart of some autoimmune reactions, I don't see how ingesting rapeseed oil could cause inflammation.

So my question is this: is it really possible to safely say: "oxidation = inflammation"? Or is it total nonsense? Or is there some theory that could support such claim and how reliable is this theory? Isn't it just one of those hypothesis disguised as theories?

Said article is in Czech, otherwise I would link it for you.

EDIT: Article link here, you can try it with Google translate :)

Oxidation does not mean inflammation. But oxidation can be a cause of inflammation.

Oxidation processes are part of normal cell metabolism (mostly in mithocondria). They lead to reactive oxygen species ($O_2^-$, $H_2O_2$ and $OH-$) which can trigger inflammation via activation of some transcription factors:

  NF-κB, AP-1, p53, HIF-1α, PPAR-γ, β-catenin/Wnt, and Nrf2 [1]

The metabolic processes also produce some  antioxidants to inactivate those reactive oxygen species. But the excess of oxidants leads to oxidative stress which seem to be linked with inflammation and even to cancer [1].

  rapeseed oil is less saturated and therefore more likely to oxidize

Being "less saturated" I guess it would be better, as studies have found that saturated fatty acid promote inflammation [2], while unsaturated fats decrease the production of inflammatory cytokines and reactive oxygen species [3].

  So my question is this: is it really possible to safely say: "oxidation = inflammation"?

NO. By definition, oxidation is a chemical reaction in which a molecule, atom or ion loses electrons [4]. On the other hand, inflammation is a very complex process, a biological response to harmful stimuli and requires cellular interaction [5].

References:

Reuter S, Gupta SC, Chaturvedi MM, Aggarwal BB. Oxidative stress, inflammation, and cancer: how are they linked? Free Radic. Biol. Med. 2010 Dec 1;49(11):1603-16. doi: 10.1016/j.freeradbiomed.2010.09.006. PubMed PMID: 20840865.
Saturated Fatty Acids and Inflammation: Who Pays the Toll?
Alan Chait and Francis Kim
Arterioscler Thromb Vasc Biol. 2010;30:692-693, doi:10.1161/ATVBAHA.110.203984
Supplement: n–3 Fatty Acids: Recommendations for Therapeutics and Prevention:
Philip C Calder
n−3 Polyunsaturated fatty acids, inflammation, and inflammatory diseases
Am J Clin Nutr June 2006 83: 6 S1505-1519S
Wikipedia contributors, "Redox," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Redox&oldid=621442954 (accessed September 13, 2014).
Wikipedia contributors, "Inflammation," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Inflammation&oldid=625272396 (accessed September 13, 2014).


Can we change our dopamine baseline levels? Can we change our dopamine baseline levels? High dopamine levels improve alertness, problem solving, but may also cause anxiety and aggression.

I've read that smiling and laughing, eating certain foods, or having unexpected rewards can elevate dopamine levels in the brain. I also read that expecting a reward in the future (such as an upcoming vacation) elevates dopamine levels. Can these actions, if repeated over a prolonged period, increase baseline dopamine levels? Or will dopamine return to original levels once these actions are stopped?

Feelings of pleasure and reward are transient in nature. Similarly, the dopamine release in the reward centers (the limbic structures) is transient, namely in the order of seconds (Rebec et al., 1997).

One way to chronically elevate dopamine levels is by administering certain drugs. A notable/notorious example is methamphetamine, which elevates mood and generates euphoria for 8-12 hours. However, after chronic use, people may report a lack of motivation and anhedonia when they stop taking the drug. Anhedonia is an absence of pleasure in response to acts that had previously been pleasurable. Anhedonia may be reported as long as 2 years after the last use of methamphetamine in addicts. Chronic use of the drug overstimulates the dopamine neurons in the limbic system (and elsewhere), and destroys the dopamine receptors, explaining the anhedonia.

Hence, even with hard drugs like meth, the effects on dopamine levels are transient, just less transient as with physiological reward responses.

Reference
- Rebec et al., Brain Res (1997); 776(1–2): 61–7


Are the intestinal microbiota substantially different within a diverticulum of the colon? From the Wikipedia page for the vermiform appendix:

  This proposal is based on a new understanding of how the immune system supports the growth of beneficial intestinal bacteria, in combination with many well-known features of the appendix, including its architecture, its location just below the normal one-way flow of food and germs in the large intestine, and its association with copious amounts of immune tissue. Research...showed that individuals without an appendix were four times more likely to have a recurrence of Clostridium difficile.

This quote seems to be implying that the appendix can act as a breeding ground for certain gut flora that are slightly less common (like C. difficile) and not as ubiquitous as E. coli or Enterobacter sp. The appendix could be seen as an ideal spot for this growth of microbial populations in the gut.

Given that, to a first approximation, anatomically, the appendix and a common diverticulum of the colon are both outcroppings of the large intestine: to what extent would a diverticulum also be able to support less common or more diverse flora, and how likely is this to be due to a difference in extracellular environment (pH, ion concentration) and how likely is it simply due to shape?

The appendix is a type of true diverticulum of the colon, although it is one that is present in everyone (unless a surgeon has removed it). There are bacteria in the gut from the mouth all the way down to the anus, and the numbers and types of bacteria change along the length of the intestinal tract. A recent review from J. Ridlon published in the Journal of Lipid Research (2006) is available online and has documented these observations from a number of investigators. In that paper the bacterial species are described as changing as well as the relative abundances of bacteria which increases along the length of the intestinal tract. Figure 1 from that paper which is open access available from the link above is below.

I think its interesting that the wiki page you're citing states that individuals without an appendix were more likely to develop a recurrent C. diff infection. One could interpret that as they did on that site that somehow the appendix is repopulating the colon and making that individual more resistant to a repeat or "Recurrent" infection. However, I don't know of any studies that have directly tested that hypothesis.

In terms of whether or not the gut flora - aka "gut microbiota" - are significantly different in the appendix is possible, but I don't think anyone has identified that just yet. One of the problems with this would be that we don't routinely remove appendices unless they are infected/inflamed which intrinsically would alter the microbiome locally.

So, is it possible that the microbiome could be significantly different in the appendix itself compared to the cecum just a few centimeters away? The answer would be - potentially, but no one has been able to address that question to date.


Human sleep cycles and dream times, what influences the timing and intensity? Sleep history included I'm doing sleep and dreams research and have developed an iPhone application to help me track my bedtime, rise time, sleep onset and also mark dreams. The app also monitors overall activity overnight as an Actigraph, recording periods of elevated motion and inactivity.

I have a lot of sleep cycle data that I have trouble analyzing.

I know that circadian rhythm is at play with 90-110 minute sleep cycles ehxibited over the course of the night, each one is a progression of various sleep stages, from NREM to REM. REM is more likely to result in a dream reported if awakened during REM.

What I'm seeing is a bunch of orderly patterns, and a lot of chaotic behavior that I cannot explain. Particularly the times of going to sleep and awakening, while dreams exhibit more orderly behavior, with dreams reported at similar times on subsequent days.

I'm also interested in any insight as to what's causing me to wake up at certain times and report dreams. What could be involved in this kind of behavior? I saw research about deuretic hormones not being suppressed for the night, causing the urge to urinate to awaken the dreamer.

Right now I have 90 days of sleep onset and dream data that looks like this:

Complete 90 day sleep history

In this case, each black marker indicates the sleep onset time for
the night
The orange marker indicates the time of getting out of bed
The green markers are dreams that I report upon awakening from a
dream, so dreams occur prior to the marker's location.
Each green
    marker's brightness indicates more clear dream content remembered
    and    recorded.
Cyan markers are lucid dreams, where I was aware
    that I was    dreaming within a dream.
Cyan color of a marker
    indicates that I    could control the dream's content from within a
    dream.
Red markers    are periods of insomnia.
The cyan line is
    number of hours after    bedtime
The purple line is sleep cycle
    approximation (90 minutes).

The data is stacked with each row being a day of data. You will notice that your eyes start to automatically seek patterns within the vertical arrangement of markers. Because each marker is a dream reported upon awakening, they roughly trace the sleep cycles over the course of the night.

I'm interested in learning what influences the desire to go to bed at a particular time?
What influences the getting out of bed times?
is there some sort of analysis I can perform to understand the pattern within the sleep cycles as it evolves over multiple nights?

Any input is appreciated!

I'm interested in learning what influences the desire to go to bed at
  a particular time? What influences the getting out of bed times?

It is the circadian rhythm. Circadian rhythm is mediated by the suprachiasmatic nucleus of hypothalamus, which gets afferent nerves from optic nerve. So, the circadian rhythm is mediated by light. Initiation of the NREM Stage 1 sleep is controlled by the lateral preoptic nucleus, which is another area in the hypothalamus, so it is mainly the absence of light which starts sleep.

  I'm also interested in any insight as to what's causing me to wake up
  at certain times and report dreams.

Sleep is not equal to absence of consciousness, it is just an diminished state of consciousness. Sleep consist of mainly 4 stages, NREM-1, NREM-2, NREM-3 and REM. Every stage, the "depth" of sleep, or the level of the decrease in your consciousness changes. REM is the stage in which dreaming most frequently occurs, and also it is the sleep stage where your consciousness is highest, so you are more likely to awake because of the stimulus coming from the environment.


What kind of spider is this? This large white spider has made her home on our garage. We live in the upper peninsula of Michigan. I believe it's an orb spider but couldn't find any with the large black almost hourglass shape on the back

This is probably Araneus marmoreus var. pyramidatus.

Here is a better image for comparison:

Source: http://www.uksafari.com/marbled_orb_weavers.htm

PS: Despite A. marmoreus being found in US, this variety (pyramidatus) is  normally an European one. I don't know any observation of it in US. However, I'll leave this answer here until another ID is provided.


A non human adaptive behaviour with a spandrel Is there any adaptive behaviour in non humans which, when it is functioning as it was selected to do, creates a spandrel behaviour?

  In evolutionary biology, a spandrel is a phenotypic characteristic
  that is a byproduct of the evolution of some other characteristic,
  rather than a direct product of adaptive selection

One of the first example of spandrel that has been suggested by Gould was the genitalia of hyenas. At the time the term was created, behavioural consequences of having a big brain was a common example and of course, this does not concern only humans but many other animals.

The riddles on the knuckles is another example (that is not specific to humans only either). Those riddles are a by-product of the need the make movement with your fingers.

I am personally not a big fan of the term spandrel as used in evolutionary biology. This term easily leads to limit cases and it depends on how you define the phenotypic traits and the functions they serve.


Interpreting SNP-in-gene associations from GWAS studies For most SNPs identified in GWAS studies, is the underlying assumption that if it is indeed associated with a phenotype (and lets assume its associated because it affects protein function), that you don't need two knocked out copies of that gene for it to confer susceptibility risk to the individual?

In other words, is my assumption that GWAS is likely uncovering alleles that confer risk in single copy, correct?

In short, yes.

If a gwas study links a SNP to a particular phenotype then yes, it is an effect of a single copy. Bear in mind, however, that a SNP is not a knockout or even a knockdown. It can be, but it is not always the case.  SNPs can produce a change in the protein sequence or in the regulation of the production of that protein. Both types of variation can result in a phenotypical change.

In any case, SNP information is always about a single allele, I imagine that you can find cases where a cell is homozygous for a particular SNP but is is not necessarily, or even often as far as I know, the case.


What network motifs or other mechanisms can make the expression of a gene invariable to the environment? Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?

This phenomenon of being insensitive to certain fluctuations is called robustness. The fluctuations can be of two kinds for an input-output device such as a gene that is activated by a signal:

Fluctuations in the signal
Fluctuations in the intrinsic parameters

Signal fluctuations can be temporal but parameter fluctuations are not (parameters are supposed to be time invariant). Parameter fluctuation can exist in a genotypic space or a population of cells because of variation.

Some motifs are robust to signal perturbations whereas some are robust to parameter fluctuations.

Negative feedbacks and incoherent feed-forward can confer robustness by correcting the output fluctuations because of fluctuations in the input.

When an all or none sort of (binary: one state need not be smaller in magnitude than the other) behaviour is important, then positive feedbacks confer robustness to such systems because of their property of bistability.

I cannot recall any particular motif that is robust to parameters. There are certain cases though (I am still working on that!! :P).

In any case environment can be thought of as an input.  For your question "what mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another":

There can be a heterogeneous population of cells which can arise because of bistability or even otherwise, due to stochastic effects. If the gene that is in one of the two states (expression levels) in these two sub-population of cells, and this gene is responsible for the expression control (the controller gene in feedback), then one sub-population will be sensitive to the environment while the other will not be.

For more information on biological robustness read this review.


How is minimum infectious dose defined? I'm a bit confused by the concept of a minimum infectious dose (MID). It seems from what my research so far has turned up, that while any dose greater than 0 could potentially cause an infection, for most pathogens the likelihood of this occurring is low enough to be dismissed.

What I'm now trying to figure out is, what metric is used to define the MID? Is it the amount of the pathogen which is expected to cause an infection in 50% of those exposed (similar to an LD50?) Is there some other value used instead?

Secondly, is there a specified relationship between the received dose, as a multiple of the MID, and the likelihood of infection (for example if the MID caused an infection in 50% of people, then perhaps 2 MIDs would cause infection in 75% and 3 MIDs would cause infection in 87.5%).

Note, I am not asking about how the MID is empirically measured, but rather about the conceptual underpinnings of the concept itself. Also, any links you can provide to additional resources would be most appreciated. Google is useless these days now that the search results are flooded with nothing but SARS-CoV-2 specific articles.

Minimum infective dose is the minimum number of infectious particles that causes infection/illness in 50% of those given that dose.

Practically this is only really measurable in a controlled laboratory setting, but one can estimate it for real world circumstances as well.

It isn't easy to know how exactly the probability will vary around the MID - there are too many factors related both to the individual and the pathogen to make simplistic assumptions (like assuming each individual infectious particle has an independent probability of leading to infection). It is typical that higher initial exposure (particularly for foodborne illness, but seems to be an issue with SARS-CoV-2 and other respiratory viruses as well) leads to more severe illness, however.


Cause of short sightedness/ far sightedness I recently had gone for an eye test. The doctor told that short sightedness/ far sightedness is caused due to shrinking or expanding of the eye.
One thing i forgot o ask him was what causes that shrinking/expanding.
Can anyone explain it to me?

The physical shape of the eye and lens are as @RoryM points out, the reason we become near/farsighted.

The most common cause of farsightedness is pretty well known.  The lens of the eye allows us to focus as a ring of muscles pulls outward and flattens the lens, allowing it to focus on closer objects.  As we get older the lens of the eye becomes stiffer and inflexible, which means that the muscles that pull on the lens can't flatten it as easily and focusing on nearby objects becomes difficult or impossible.  This is why we need to get bifocals or reading glasses as we are older.

The reasons for nearsightedness are 'natural changes in the shape of the eye'.

Mentioned briefly in the WebMD link above is that close work (e.g. reading, web surfing, phone videos, reading and reading, etc) tends to cause nearsightedness.

25% of adults in the US and 40% of adults in Asia are myopic and it does look as if there is a strong genetic component to myopia.  If neither parents have myopia, the incidence is only about 7%.

I'm probably going to get ding-ed for this, but I am going to offer alternative explanation, which makes good scientific sense to me, so hear me out.

This seems like a poor adaptive phenotype for humans who are otherwise so optimized for survival.  Why would we naturally lose our ability so young (often before the fifth grade)?  So many people who have myopia are so impaired that they can't find their way around their own house (or legally drive) without glasses/contacts/corrective surgery.

This is supported by studies which show that non industrial societies have almost no natural myopia compared to industrialized ones.  This is just one example reference, not a survey of all evidence.

Physiologically the explanation for myopia is this: in the relaxed state, the eye is focused at the horizon (infinity).  If one habitually focuses on a book or screen within 1-2 feet from your face, the muscles might well adapt to a set point that is closer than infinity.  This would make myopia an adaptive response to modern life.

Eye exercises are proposed as a way to correct myopia.  This is a bit controversial - some say they help, others say they do not. I would not be surprised that myopia developed in youth (8-15 y.o.) when the eye and body are developing can't be overcome by eye exercises when you are 25-30, but the jury is still out.

There are enough free descriptions of eye exercises out there that you don't really need to pay for them.  Getting young students outside to look around once in a while doesn't sound like a bad idea either, given this.

If you are going to down vote or complain, I would appreciate it if you please cite counter reasoning other than 'this is not a popular explanation'.


Why does the face turn pale in dangerous situations? I know what the effects are of a dangerous situation on the brain, i.e., an activation of the hypothalamic-pituitary-adrenal (HPA) axis which eventually results in an increased heart rate and elevated blood pressure. However, I do not understand why enhanced blood circulation would result in a paling of the skin? Do red blood cells actively change direction?

Red blood cells are not equipped with a motor system to propel them through the blood stream. Instead, they are passively transported through the vasculature by the the pumping action of the heart. The effects of dangerous situations on the skin have to do with hormonal effects on the blood vasculature, and not with direct effects on red blood cells.

Dangerous situations trigger the fight-fright-flight response, and is a direct result of adrenaline being released into the bloodstream. Adrenaline prepares the body to fight for its life.

Adrenaline has a variety of effects including enhancing perspiration (or diaphoresis, which prepares the body for the increase in temperature associated with fleeing/fighting), dilation of the pupils (which increases light sensitivity, but reduces acuity), dry mouth (gastric juices and saliva production decreases because blood flow to the digestive system is decreased), enhanced smell and hearing, and a cool, pale skin.

The cool and pale skin is caused by a reduced blood flow to the surface of the body, while blood flow to the arms, legs, shoulders, brain, eyes, ears and nose can be increased. Besides getting ready to run and fight, the body is preparing to think quickly and be aware of threats by hearing, seeing and smelling things better. Pulling blood away from the skin also helps decrease bleeding from cuts and scrapes (Source: Army, Navy & Air Force Australia).

Adrenaline stimulates alpha-adrenoreceptors in blood vessels, which causes the smooth muscles around the vessels to constrict (Bolli et al., 1984)

Adrenaline (epinephrine) released from the bloodstream dilates vessels in the skeletal muscle via beta-receptors, and constricts them in the digestive system and the skin through alpha-adrenergic receptors. Source: Marian University College, Indiana.

Reference
- Bolli et al., J Hypertens (1984); 2(3): S115-8


On which strand does the promoter sit? My book keeps giving different indicators as to whether the promoters are on the coding or template strand.

It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that the -10 and -35 regions are binding sites for RNA polymerase.
It also says that CAAT and GC, unlike -35 in prokaryotes, can also be on the template strand. Which implies that they are still most common on the coding strand. And then it shows me a figure, where a promoter sequence is shown in the template strand, with the transcription complex attached.

All the sequences are written 5'-TATAAA-3' (for example). This also implies they are on the coding strand, since the template strand will then be 3'->5' which is the direction that transcription happens in.

Obviously I'm confused, and hope someone can clarify this. In which strand can I find the promoters? Does stuff act on the promoter sequence itself, or its complementary sequence? If the promoter can also be on the other strand, should it be reversed?

The answer to this question depends upon the definition of the word 'promoter'.

In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the σ factor recognises the core promoter elements directing the polymerase to bind to the DNA to form the closed complex. The next step is the switch to the open complex involving separation of the DNA strands.

Articles describing investigating the interaction of the σ factor with the DNA (e.g. here) refer to the protein making contacts with base pairs. I conclude therefore that the original question doesn't make sense - a promoter is a dsDNA entity even though we might describe it in terms of the sequence on one or other of those strands. So, for example, in a promoter the consensus -35 sequence - 5'-TTGACA -  would be present on the coding strand (upstream of the coding sequence), but the promoter property of the sequence is due to the presence of this sequence and its complement on the other strand.


Are genetic crosses between asexual organisms possible? To my knowledge (Please correct me if I am wrong), genetic basis is the key in defining species. When we encounter an unknown species, we can sequence it's genome and compare the genome with other known organisms from the genome data bank and see if there is a significant similarity. If no significance were found then we can call it a newly discovered organism. Also careful study of genetic crosses between species pairs and partially isolated sub species to identify general patterns in the genetics and origin of reproductive isolation helps to answer the question of speciation. Then how would we cross asexual organisms like many bacteria or protists? Is it possible to cross asexual organisms? If not, how do scientists study their genetics and define species of asexual organisms?

When it comes to viruses and bacteria, genetic cross is just as a vaguely defined concept as species. The latter is often defined on the percentage of the sequence similarity (for viruses) or the percentage of common genes (for bacteria).
If we speak about simply mixing genomes of different organisms, there are many possibilities, how this could happen. Just to give a couple of examples:

Some viruses integrate their genome into the host genome. In some cases these integrated genomes cease being functional viruses, and may evolve to be functional genes of the host. This is truly a genetic cross. See here, for example.
Bacteria and viruses routinely undergo horisontal gene transfer in which genes from one bacteria are integrated into the genome of the other one. A typical bacterial species has a few hundred core genes, and thousands of genes that are present only in some specimen or borrowed from other species, which significantly vary from one bacteria to another. Thus, every individual bacteria or bacterial community can be thought of as a genetic cross.


Energy metabolism in Cancer cells The TCA cycle intermediate Isocitrate dehydrogenase commonly undergoes point mutations in cancers. This allows IDH to reduce a-Ketogluterate to 2Hydoxygluterate, causing a reduction in pVHLs ability to hydroxylate HIF-1a, and a subsequent accumulation of HIF-1a. This leads to angiogenesis via VEGF. If the cancer cell is converting its a-KG away form the TCA cycle, how does the cell make up for the loss of TCA function, and subsequent ETC function for energy production? Why would the cancer cell prefer to lose high yield energy production in exchange for low yield energy production?

Two things...

Rapidly proliferating tissues (esp tumours) rewire their energy metabolism anyway to aerobic glycolysis where you have energy being produced by lactic acid fermentation even if oxygen is present. This is called the Warburg effect.Here's the thing about "low yield" though - glycolysis chucks out less ATP per reaction at the end, but you can crunch through a lot more ATP by just having more of it going on.

Secondly, hypoxia in a tumour is generally rate limiting, and therefore the shunting away of alpha-KG with the consequence of increased angiogenesis is good for the tumour.


Is a part of the spinal cord from the mesoderm? The caudalmost part of the neural tube is formed by the caudal eminence. Isn't this mesodermal? So does it mean that, a part of the spinal cord is mesodermal in origin?

Does it have any significance apart from being something just academic?

The caudalmost part of the neural tube is formed by the caudal eminence. Isn't this mesodermal?

No,the neural tube is not mesodermal at caudal end.

According to Gray's Anatomy:

  At the time of caudal neuropore closure, the caudal midline cells are generically termed the caudal eminence (O’Rahilly and Müller 2004). A specific population of mesenchymal cells, the caudoneural hinge or junction, shares the same molecular markers as the primitive node. These cells aggregate at the midline and undergo mesenchymal/ epithelial transformation, producing a cellular cylinder that is contiguous with the caudal end of the neural tube. Further elongation of the caudal neural tube involves cavitation of the neural cylinder.

So, the cells in the caudal eminence form a solid cylinder(medullary cord) which is made hollow by elongation of neural tube. Therefore, mesodermal cells of caudal eminence are not forming the caudal end of neural tube.

Let's see the process of neural tube elongation from the citation given in the Gray's textbook:

Abbreviation used can be seen here

Schematic diagram can be seen here


Colormetric assay for a phenol product? I am working on an assay for phenol products created by a colony of bacteria. I have searched up a paper that involves gibbs reageant but the protocol is kind of unclear.

Does any of you know where I can look for a detailed protocol for a gibbs reagent colormetric assay (preferably one that uses cell medium)

Thanks

I have not used the assay myself, but Bhuiya and Liu "A cost-effective colorimetric assay for phenolic O-methyltransferases and characterization of caffeate 3-O-methyltransferases from Populus trichocarpa." Anal Biochem. 2009 384(1):151-8 [link] seems to have a relatively straightforward protocol.

Roughly, you make a 0.4% (w/v) solution of Gibbs reagent in ethanol, and then add one fifth volume of that to your enzymatic reaction mix. You then observe the solution spectrophotometrically.

The biggest issue I see is that it looks like each phenolic compound has its own absorption maximum, and widely varying extinction coefficients. In their protocol it seems they look at full range scans, rather than single wavelength measurements. You'll definitely need a standard curve for your particular phenolics in order to get quantitative results. (Also, any background phenolics or medium absorption in the 400-600 nm range may throw off measurements - use appropriate blanks.)


Receptors for red and far-red light in plants: Shade avoidance Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading.

My question is: which receptor is stimulated by the red and which receptor is stimulated by the far-red?

In his paragraph on Phytochromes (3rd page, right column), K. Franklin seems to say that PhyB is responsible for measuring this ratio but I am not sure.

As far as I know there are 5 receptors for far-red and red light which are the phytochroms(phyA-phyE) Its all about the ratio between red and far-red light.

Each phytochrom has an inactive(PR) and an active(PFr) conformation. phyA is the only phytochrom which is activated by far-red light, so its active state is PR. (Only if the ratio between red and far-red light is low.) The other phytochroms, are activated by red light (high ratio between red and far-red).

An active phytochrom blocks the COP1/SPA complex. This complex is a E3 ubiquitin ligase which ubiquinates transcription factors for the light answer like HY5 or HFR1.

Example:
Under normal light conditions, phyB-phyE is active. They block the COP1/SPA complex so the transcription factors for the light answer are not getting ubiquinated. The plant can get a light phenotyp.
In the case that a plant grows under another plant, it gets less red light because the higher growing plant uses it for its photosynthesis. phyB-phyE become inactive. COP1/SPA can ubiquinate the transcriptions factors. The plant gets an low light phenotyp by trying to grow out of the shadow.

The function of phyA is to produce a light phenotyp if there is a lot of far-red light but almost no red light. Than it is getting activated and blocks the COP1/SPA complex. Under red light phyA is not only inactivated it also gets degraded.

I just found a paper for further reading: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828699/


Can below-threshold potential changes of neurons convey information? In neuroscience we learn that when the membrane potential of a neuron reaches a threshold (typically around -55mV) it "spikes": That is, it actively propagates a signal. I have two related questions with this respect:

The spike initiation zone is typically (e.g. for mammals) at the axon hillock - from there the action potential is actively (opening of ion channels..) propagated through the axon. But what happens then at and after the (chemical) synapse? Is the propagation after the synapse to the postsynaptic cell passive?

Newer imaging techniques (e.g. calcium imaging) can capture sub-threshold changes in the membrane potential. How are these sub-threshold potentials relevant for information processing? Are they propagated to postsynaptic cells, albeit again only in a passive manner?

Electrical synapses (Gap junctions) can generate current to other cells without the emission of a spike. This sub-threshold interaction is proven to have functional implications in neural activity (eg. Retina).


Why don't antiseptic agents kill 100% germs? I've seen innumerable antiseptic, mouthwash, handwash advertisements that claim to be able to eliminate as much as 99.9% of all germs over a surface...but why not the remaining 0.1% (i.e- why can't they eliminate all germs)?

Clarifications:

What they mean by "germs":

Being a student of Biology, I can tell that the term "germs" is crudely defined. I would prefer to use "pathogens" (less ambiguous), and I suppose the guys that market these products have (roughly) the same idea in mind. Pathogens normally include bacteria (monerans), protozoans, fungi and viruses... so I guess these are the "germs" they're talking about.

What I'm looking for in an answer:

Why is it that these (commercial) products can't eliminate 100% of all pathogens? Is this due to the inability of antiseptics to act on a particular (class of) organisms? If so, what's the problem there? Or is it because, the guys who market stuff like this assume an arbitrary amount (0.1%) of the pathogens present on a surface (say, the human hand) is located in microscopic niches that are inaccessible to the antiseptic solution? (If it isn't possible to provide a blanket statement in this regard, use of Listerine as an example will suffice)

In other words:

Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?

Also,

Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?

This is actually an interesting question! Let me answer both the parts separately, taking the example of Listerine® mouthwash.

  Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?

In most of the cases, this is due to the physical factors. Clearly, your mouth is not a flat surface. It has many depressions and elevations. And these irregularities are the perfect hotels for all kinds of pathogens. Also, it is difficult for most chemicals to reach those spots and stay there for long enough so that they can act on the pathogens. Thus, most of these chemicals would be unable to kill 100% pathogens because of their inability to reach all of them. Also, in rare cases, it might also be due to chemical factors(!) Yes, I'm talking about antibiotic resistance. And in that case, it would be practically impossible to kill 100% pathogens, no matter whether they're hidden or exposed.

  Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?

For that, lets first see what Listerine® contains. As given on its website, its main ingredients are (I'm simply copying what they write on their page, followed by checking whether its true):

Eucalyptol – with antibacterial properties, this eucalyptus-derived essential oil works as an anti-fungal agent within the mouth.
Methol – this natural oil as germ-killing abilities to help halt the growth of bacteria.
Thymol – this powerful oil is derived from the ajowan herb, and helps decrease the risk of gum disease.
Methyl Salicylate – for minty freshness from morning til night, the flavouring agent in this essential oil is, well… essential!

We just need to know whether these ingredients really work or not (why? We'll talk about this later on) and I'll skip methyl salicylate for this (they don't even claim that it is antimicrobial). Beginning with eucalyptol, it has been shown that oil of Eucalyptus globulus (of which eucalyptol is a component) has antimicrobial properties against Escherichia coli and Staphylococcus aureus (see Bachir et al, 2012). It has also been shown to possess antifungal properties (Safaei-Ghomi et al, 2010). Coming to methol, it has also been shown to have antibacterial properties against various Staphylococcus and Lactobacillus species (Freires et al, 2015). Finally, there have been lots of studies about the antimicrobial properties of thymol. You can check out the Wikipedia page for information.

So, where is the percentage? The point is, the exact percentage depends on a lot of factors. When an enterprise, such as Listerine®, claims that their product has been shown to be 99.9% (or any number) efficient against bacteria, they need to cite the particular study through which they claim this number. But they can not, in any case, be definite that their product will be 99.9% effective everytime. How effective a product is also depends on the conditions under which it is tested. Mostly, these tests are performed on a petri dish in a laboratory, something very different from your mouth. Thus, although they can claim that their product is scientifically proven to be 99.9% effective, they cannot claim it to be 99.9% effective when you use it. Again, they cannot claim 100% effectiveness because this makes them liable (saying our product has been shown to be 100% effective requires them to show that even a single microbe did not survive on the petri dish they used for experiment). Also, this gives them a way to escape in case anybody complaints about their product not being effective (since they caught infection even after using their product). In such situation, they can easily say that their product is not 100% efficient!


Minimum size for a peptide/protein to be immunogenic in human? What is the minimum size for an (injected) peptide/protein to cause immunogenic response in human?
A reference is very helpful, as well.

Thanks in advance

There's a few limiting factors including how proteins are presented that constrains the actual size needed to get peptide presentation. These depend largely on the MHC molecules (HLA in humans). The binding groove in MHC-I actually limits the size of peptides it can load to 8-10 amino acids, 9 being the most common. This is because "pockets" at either end of the binding groove are said to actually grasp the peptide, and it doesn't allow for much longer sequences. MHC-II lacks these grasping pockets, and so it can bind much longer sequences (Figure 1). MHC-II typically binds sequences of 13-25 amino acids.

Figure 1. Difference between the MHC-I and II binding groove.

There are also a given number of requisite anchor residues that complement the binding pocket of the MHC binding groove that mostly display a particular character at the given position (normally polar at a given position, etc.) (Figure 2).

Figure 2. Just a sampling of possibilities across HLA isoforms.

All information and figures courtesy of Parham "The Immune System," 4th ED.

If the presented peptide has met the prerequisities and has been identified by a leukocyte, in theory it should produce an immune response. I think these are some good considerations to make when you're thinking about how small can a peptide be. I'm assuming here that MHC-II would be handling your injected protein through an extracellular pathway (I can't know for sure), and so the smallest literature MHC-II peptide range I've ever seen is 11 amino acids on the low side. There are a number of computational studies out there that attempt to predict MHC affinity, but it's problematic due to the range of sizes MHC-II may bind and there is variability among the binding cores that contain the anchor amino acids.


Fab fragments of antibodies to fight viral infections I was reading about Fab fragment and about using them to fight of viral infections. It seems that the Fab attaches to the viral receptors, which stops the viruses from attacking the cells. It seems that it has been done before. I was wondering, since Fab fragments can't activate immune response, what happens to the Fab-virus complex in the blood?

There are three pathways by which soluble antibodies (which is what the Fab fragments arise from) can inactivate viruses (from Janeway's Immunobiology):

What you describe with the Fab binding to the viral receptors is a type of neutralization. Janeway claims that the type of naturally occurring antibody primarily responsibly for neutralization, IgA, is mostly exported to mucous secretions, so presumably it gets digested/excreted along with the rest of the mucous proteins.


What is a flux control coefficient? In metabolic control analysis, a number of coefficients are defined, including the flux control coefficients. How is this coefficient defined and what does it measure?

The flux control coefficient measures the relative change in the steady state pathway flux in response to a relative change in enzyme activity. Mathematically it is defined according to:
$C^J_{e_i} = \frac{dJ}{de_i} \frac{e_i}{J}$
Because enzyme activity is proportional to enzyme concentration, the flux control coefficient is often define with respect to the enzyme concentration, $e_i$.
This can be also expressed in log form:
$C^J_{e_i} = \frac{d\ln J}{d\ln e_i}$
It can also be expressed approximately as a ratio of percentage changes:
$C^J_{e_i}  = \frac{J\%}{e_i\%} $
This definition makes it easy to measure. For example, if the activity of a given enzyme is changed by a factor of 1.5 which results in a 1.25 fold change in the steady-state flux, then the value of the flux control coefficient is approximately 1.25/1.5 = 0.83. Because flux control coefficients are measured using relative changes, the coefficients are dimensionless.
Flux control coefficients are useful to gauge how much a given enzymatic reaction influences the flux in a pathway.
For further information I recommend the following paper:
Kacser, Henrik, James A. Burns, H. Kacser, and D. A. Fell. "The control of flux." (1995): 341-366.


Confusion over role of current/potential in Nervous system? I am taking a course on the nervous system and I am do not have any physics background. Therefore, I would like to know, what are we precisely talking about when we talk about current in the nervous system?

At the same time what are we talking about when we talk about potential (i.e membrane potential or action potential.

I once heard an analogy about waterfall and water comparing current and potential (voltage), can someone elaborate on that for me.

Also, I know that electrical activity is the flow of electrons. Therefore does that mean that passive current in an axon/nerve is a flow of electrons? And is it also a flow of electrons when we have action potential.

Thank you in advance for all the help.

Current flow is the movement of charged particles (ions in this case). The membrane potential is the charge difference across the cell membrane. Usually there is more negative charge inside the cell than out, so the membrane potential is said to be negative. When ion channels open, typically positive ions (Na+, K+) will flow into the cell as they are flowing from a medium that is approximately uncharged (extracellular space) into an environment that is highly negatively charged. By analogy, the positive ions can be viewed as water flowing down a gradient (waterfall). Electrical activity is not a flow of electrons per definition, especially not so in nervous tissue where it is ions that move (it is indeed electrons in electric circuits and the likes). During an action potential, therefore, it is not electrons that are moving across the cell membrane, but ions, most notably Na+ and K+, but also Ca+, Cl- among other charged particles.


Is it unusual for a child to be diagnosed with diabetes? Recently, I came to know that a boy in my town who is 6 years old is diabetic and many people were shocked from this news.

Short Answer

Type 1 diabetes is commonly diagnosed in children; type 2 diabetes is more common overall and is much less likely to be diagnosed in children, though possible.

Longer Answer

Type 1 diabetes is caused by damage to the pancreas and depends on environmental and genetic causes, most often leading to autoimmune loss of the insulin-producing beta cells in the pancreas. Type 1 diabetes occurs because insulin levels themselves are low. It commonly begins in childhood, and is also sometimes referred to as "juvenile diabetes" although it lasts life-long. Type 1 diabetics often take insulin to replace the insulin they are not producing.

Type 2 diabetes, by contrast, is caused by reduced insulin sensitivity and develops over time (lack of insulin can also eventually occur). Obesity and other lifestyle factors are strong influences on the development of type 2 diabetes, though genetics can also play a role. Type 2 diabetes is most often diagnosed in adults (and is also referred to as adult-onset diabetes, though it is also possible to occur in children), increases with age, and is overall more prevalent than type 1 diabetes, so this is likely where your community's surprise comes from.


Help me identify this animal from Bangladesh I have come across this animal in a facebook group. After one group member identified it as Asian palm civet, I looked at some google images, I am not convinced. Judging from google images, this animal doesn't look like any of the common civet species found in Bangladesh.
Location: Noakhali, Bangladesh

Looks like the Large Indian civet. Notice the size and the fur coloration pattern on the neck.

From wikipedia:

  The large Indian civet ranges from Nepal, northeast India, Bhutan,
  Bangladesh to Myanmar, Thailand, the Malay peninsula and Singapore to
  Cambodia, Laos, Vietnam and China.[1]

Looks like it is found in eastern parts of Bangladesh including Noakhali district – the place where the picture was taken.


Identify This Glowing Insect When I was walking in my garden at night I saw this small glowing insect, can you identify what is this insect?

Location: Middle-East Palestine

Size: Length about 1 CM

This image in the dark (see the light of the insect)

These images taken by flash.

Appears to be a larviform female firefly (order Coleoptera; family Lampiridae).

I cannot find a good source for listing/IDing Palestinian fireflies, so I unfortunately cannot give you a definitive answer. I do want to provide some of an answer and an example specimen to get you going on the path of accurately IDing your specimen.

To get you started, your specimen appears similar to Photinus bromleyi (seen here) and below:

Photinus are a group of North American fireflies, so not likely your species.
According to firefly.org, the subfamily Luciolinae is found throughout Eurasia, while the genus Lampyris is a "wastebin taxon" used as a "catch all" for misfit fireflies that is found throughout the world. So I'd start looking in those groups.

I'll dig around for a more Palestinian-oriented bug guide. Again, this is not meant to be an exact answer but just a starting point for you or another user who might have access to Palestinian resources. I'll update if I find something definitive.


Is NADPH salt still usable after an hour at room temperature? I accidentally left a delivery of NADPH Tetrasodium Salt (Santa Cruz Biotechnology) at room temperature for a little over half an hour.

In addition, when I opened up the package, I briefly held the bottle by the body instead of the cap (which would have prevented body heat from contacting it).

It was packed with airbags, but no ice packs, which is why I am asking this: is the powder still stable and usable?

In my experience, half an hour at room temperature will make absolutely no difference.  Boehringer Mannheim (now part of Roche), who at one time supplied the best NADPH, used to recommend storage at 4o C.

By A340 callibration, NAD(P)H is typically about 85% 'pure' based on dry weight measurements, and Sigma will try to tell you that the remainder is mainly water.  That is, if you calculate a concentration based on the dry weight, the A340 will be about 85% what you expect.

Even if some water is absorbed from the atmosphere, this will make little difference as you are probably going to calculate the concentration based on
the A340.

As User 243 has pointed out, if you are concerned that the NAD(P)H is degraded or oxidized, then an A340
measurement will probably set things right.

If you are concerned that all the A340  absorbing material is not NAD(P)H, or that a significant proportion is in the α-form (Oppenheimer & Kaplan, 1975) or is otherwise enzymically inactive, the best thing is an enzymic calibration.

This is done by adding limiting amounts of NAD(P)H to an assay system containing excess substrate and calibrating enzyme, and measuring the total decrease in absorbance (Racker, 1957).

A popular calibrating enzyme for NADH is aldehyde dehydrogenase (EC 1.2.1.3), as the reaction is practically irreversible, and it makes it easy to 'drive' the calibrating reaction to completing (and you don't have to worry about equilibria).

As I said in a previous post, NAD(P)H is UNSTABLE IN ACID (Oppenheimer and Kaplan, 1974). To put it crudely, 'the head (nicotinamide moiety) falls off', causing a bleaching of the absorbance at 340nm.  Making 100mM acetate, pH 5, 100 micromolar in NAD(P)H produces a very significant decrease in A340 absorbance with time (which may be very easily monitored in a spectrophotometer).

Just because all the A340 material is due to NAD(P)H, this does not necessarily mean that the commercial preparation is pure.  In fact, far from it.  Dalziel (1963) showed that commercial preparations of NADH then available contained a competitive inhibitor of many dehydrogenases, most probably adenosine diphosphate ribose.

Accepting Dalziel's value of 17 600 M-1cm-1 for the extinction coefficient for NADH at 260nm, and assuming that NADPH has an identical value, then highly purified samples of NAD(P)H should have an A260/A340 ratio of about 2.83, and values higher than this may indicate the presence of impurities that absorb at 260nm, but not at 340nm. ADP-ribose is a prime example, but NAD(P)+ is another possibility.

I notice that in one of the links given by AliceD, Sigma quote a A260/A340 ratio of 2.32. So is the higher value due to the presence of residual NAD(P)+, or something else (a breakdown product?), or both?

You may need to use chromatography, typically on an anion-exchange resin, to obtain NAD(P)H free of impurities.

References

Dalziel, K. (1963). The purification of nicotinamide adenine dinucleotide and the kinetic effects of nucleotide impurities.  J. Biol. Chem. 238, 1538 - 1543.  [pdf]

Oppenheimer, N. J. & Kaplan, N. O. (1974). Structure of the primary acid rearrangement product of reduced nicotinamide adenine dinucleotide (NADH). Biochemistry 13, 4675 - 4685.[pubmed]

Oppenheimer, N. J. & Kaplan, N. O. (1975). The alpha, beta-epimerization of reduced nicotinamide adenine dinucleotide.  Arch. Biochem. Biophys.166,  526 - 535.

Racker, E. (1949). Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme.  J. Biol. Chem. 177, 883 - 892. [pdf]

Racker, E. (1957). Spectrophotometric enzymatic methods for the determination of aldehydes and ketoaldehydes.  Methods Enzymol. III, 293 - 296.

Other References

Ciotti, M. M. & Kaplan, N. O. (1957). Procedures for determination of pyridine nucleotides.  Methods Enzymol. III, 890 - 899

Horecker, B. L. & Kornberg, A. (1948). The extinction coefficients of the reduced band of pyridine nucleotides.  J. Biol. Chem. 175, 385 - 390. [The definitive determination of the extinction coefficient at 340nm] [pdf]

Kornberg, A. & Pricer, W. E. (1950). On the structure of triphosphopyridine nucleotide.  J. Biol. Chem. 186, 557 - 567.
[This paper shows that the 'extra' phosphate in NADP(H) is attached to the  2' position of a ribose.  In Coenzyme A, of course, the phosphate attached to the ribose is on the 3' position. [pdf]

Pullman, M. E., San Pietro, A. & Colowick, S. P. (1954). On the structure of reduced diphosphopyridine nucleotide.  J. Biol. Chem. 206, 129 - 141 [pdf]


What does hemozoin do? My bio book refers to HEMOZOIN that is responsible for the shiver during malaria. How does hemozoin work to raise the body heat?

That is correct. When plasmodium infects red blood cells, it consumes the hemoglobin in the cell, leaving the heme behind, which they can not metabolize (heme is a heterocyclic porphyrine ring with an iron atom coordinated in the center). Since the heme (or $\alpha$-hematin) causes the production of reactive oxygen species and thus oxidative stress, it has to be removed from the cell. This is done by the conversion into the insoluble and inactive hemozoin (or $\beta$-hematin). This crystalizes in the cell and is not causing any harm to the parasite. See here for more details.

When the parasite finishes this development step, the cells burst and set their interior free into the blood stream. Among the substances released in this step are hemozoin and also glucose phosphate isomerase which stimulate macrophages to secrete cytokines and other factors which then cause the fever and the shivering observed in malaria.

See here for more details:

Hemozoin Induces Macrophage Chemokine Expression through Oxidative
Stress-Dependent and -Independent Mechanisms
Malarial pigment hemozoin and the innate inflammatory response.
Effect of malaria components on blood mononuclear cells involved in
immune response.


What is meant by genomic imprinting being reversible? I'm not trying to understand the underlying molecular processes, rather understand it conceptually.
This is what it says in my coursebook:

"The imprint, obtained during gametogenesis, is reversible: an allele
with paternal imprint will, after transmission through the female
germline, be changed into an allele with maternal imprint.
In other
words:
Paternal imprinting means that some gene obtained from your
father is 'silenced'. These 'silenced tags' remain during your whole
life, but are reset during the formation of egg-cells or sperm-cells.
Some genes are always silenced in egg-cells, others in sperm-cells.
There is a continuous activation and deactivation in function of the
parent who transmits the gene"

I don't understand how the first paragraph and the last paragraph can both be correct.
If the paternal imprint changes into a maternal imprint after passing through the germline, this implies that the gene is just deactivated in the chromosome that is passed on and we call is paternal or maternal depending on who passes it on.
On the other hand, the last paragraph (and the middle one) imply that, if you receive a gene with maternal imprint from your mother as a man, your body resets the 'silencing' during gametogenesis, realizes a sperm cell is being made and decides not to silence it since it will now be passed on from a father. Only this can explain why it would lead to continuous activation/deactivation or reversibility.
Which of the two is correct?

Only during the formation of egg-cells or sperm-cells one can leave the maternal or paternal imprint, respectively. So for example a man, will leave its paternal imprint on an allele (during spermatogenesis) that was given by his mother (while the allele was maternally imprinted in the rest of his body).


How are 6 "fixed" CO2 molecules joined toegther as glucose? When we study calvin cycle, we study it with 6 molecules so as to form 1 glucose in a single cycle as:

6 RuBP + 6 CO2 => 12 3-PGAL => 1 Glucose + 6 RuMP

But if we look deep, then we know that the molecules are synthesized one-by-one & 6 cycles give 1 glucose, but:

1 RuBP + 1 CO2 => ... => 1/6 Glucose + 1 RuMP

My question: What is actually this 1/6 glucose (organic carbon fixed from inorganic carbon and how are such 6 molecules joined together?

It's not really possible to break it down this way. The CO2 fixated by the RUBISCO enzyme generates two phosphoglycerate (2 x 3C) molecules from one ribulose bisphophate molecule (5C), while the rest of the Calvin cycle serves to regenerate 3 ribulose bisphophate from 5 phosphoglycerate. Hence, one 3-carbon sugar (glyceraldehyde phosphate or dihydroxyacetone phosphate) can exit the cycle for every 3 CO3 captured. The regeneration of ribulose bisphosphate involves several enzymes, and the stoichiometry is rather complicated; it would take an entire essay to describe it all. I suggest you look the calvin cycle in the metacyc database, it's a nice interactive resource where you can explore all the details of the reactions. Wikipedia also provides some details on these reactions.

The glyceraldehyde phosphate produced by the Calvin cycle is then converted to glucose and other sugars by the enzymes of gluconeogenesis. The key enzyme is fructose diphosphate aldolase (or simply "aldolase") which condenses glyceraldehyde phosphate and dihydroxyacetone phosphate to one fructose-1,6-diphosphate. A chart of the pathway leading to other sugars is found here.


can you tell me what kind of animal this is? I found this skull over 2 years ago and i have been unable to find another like it or even come across someone who knows what it is. i live in south mississippi and the animal it came from looked like a deer, or even a dog, it was almost completely decomposed. I have been curious for 2 years now and have posted this before on other sites with no luck. someone help please .

Looks rather like a boar skull, which would make sense in Mississippi (especially Southern Mississippi), where their population has been growing for decades.


Functioning of BRCA2 I know that BRCA2 interacts with RAD51 to repair DNA damage.

But how exactly does it function ? What are the other proteins that interact with it ?

I'm just skimming through it now, but this 2011 review in Nature Reviews Cancer looks like it has everything you could possibly want to know about the BRCA1/BRCA2 pathway. If you don't have access to the journal, the first page of this Google search should have a PDF link to Researchgate down near the bottom, or you can try this direct link.

I apologize for the "link-only" answer, but there is a ton of info in the paper, and it would be rather difficult to summarize it in just a few paragraphs. This is a rather broad question, so perhaps you could read through the review and references, and if you still have specific questions about the pathways or interactions you can ask another question.


Turning publicly available genome data into proteins I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller steps.

First, I downloaded a complete human genome from http://hgdownload.cse.ucsc.edu/downloads.html#human  There is a FASTA file for each chromosome.

Then, I wrote a java program which can convert FASTA DNA sequences into the appropriate amino acid chain.

Next, I made my program look for the "start" code (ATG) and "stop" codes (TAA, TAG, TGA).

So, now I have sequences of amino acids which might theoretically end up folding into proteins. But, before I start diving into protein folding, I wanted to try to verify that the steps I took so far were done correctly. I looked up some important human genes in an online database and found their amino acid sequences. I then searched through my program's data for those sequences and confirmed that they were there. However, the gene was in a different base-pair location than the database said that it should be in.

This led me to some questions, which, so far I have been unable to answer and hopefully people here will be able to help shed some light.

I know there are a lot of different publicly available genomes. Maybe the UCSC one that I downloaded is different from the one used by the gene database. How much does each genome vary from each other genome and in what ways do they vary?
In attempting to answer that first question, I was going to download a bunch of genomes from the 1000genomes website and do some comparisons, but I wasn't sure which files to download. Each of the files begins with either ERR or SRR and I'm not sure what that means. This is the folder I'm currently looking in ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/
Lets say I'm trying to model a white blood cell. How do I know which parts of the genome get turned into proteins for that type of cell?

Sorry if anything I said doesn't make sense. As I said, my expertise lies in programming, not biology/genetics.

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are:

Genes (eukaryotic genes anyway) are spliced to produce mRNA, a process that removes introns and leaves only the exons. If you just translate the entire chromosome file you will get noise.
Splicing also changes the frame a gene is read in, you don't mention frames at all in your question but you can't work with sequences unless you deal with them.
Many genes (most even, in some species) are alternatively spliced. One gene can give rise to multiple protein sequences. Which one is produced at any one time can depend on a multitude of factors ranging from pure chance, through environmental conditions to the cell type where the gene is expressed.
Genes can be present on both strands of DNA and a gene on the + strand can overlap with a gene on the - strand. In some cases they can even overlap on the same strand (nested genes). You need to check both strands for coding sequences.
You're assuming that all coding sequences start with ATG (most do, not all) and you seem to be assuming that an ATG always starts a coding sequence. A given gene can have dozens or hundreds of ATG codons, how can you know which one is used as a START codon?

The process of identifying the parts of the genome that get translated into protein is not trivial. It is the subject of countless PhD theses, mine for example. There are many programs (gene predictors) that are designed specifically to detect genes in genomic sequences. Having spent many years working with them I can assure you that they're not something you can just whip up one afternoon. They tend to involve very complex models of coding vs. non-coding sequences and are way more sophisticated than simply looking for START and STOP codons. Trying to write one without knowing a lot more about biology than you seem to is just a waste of time.

Your specific questions are basically irrelevant because of the points mentioned above. Nevertheless, the answers are:

They vary but not much. For well annotated genomes like the human one, the differences will be negligible. That is not why you have strange results though as I explained above.
All public FTP sites tend to have a README file that explains what the files provided are. You should read the relevant README from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/
Answering that question will get you a Nobel prize. There simply is no way of predicting what genes will be activated in a particular cell. We're not even close to that level of understanding of how a cell works but I can tell you that it will not depend on the sequence, you will never be able to predict whether a gene is active in a particular cell based on its DNA sequence. It will depend on various things including the gene's methylation state and is largely an emergent quality of the cell's complexity (think of various proteins interacting with one another, leading to the activation of a gene).  The best you can do is get a list of genes that are known to be active from the literature.

In summary, if you want to do something as complex as modelling a cell I suggest you first take the time and study some basic biology so you can understand the system you are trying to model a bit better. The cell is not only an extremely complex system that we don't fully understand yet, it is also not wholly deterministic and contains a lot of stochasticity that you seem to be ignoring completely.


Difference between thylakoids and lamellae in a chloroplast? I'm slightly confused as to the difference between thylakoids and lamellae. My understanding was that thylakoids are 'discs' that are stacked into grana and there is a membrane between the grana called the integranal lamellae. However in my text book it says that 'the inner membrane is folded into lamellae, which are stacked up like piles of pennies. Each stack of lamallae is called a granum.' This sounds to me like the description of thylakoids.
It later says 'grana are stacks of flattened membrane compartments, called thylakoids'...

Could someone clarify this?

Thank you in advance :)

The answer above goes in depth so I will try go off that.
Firstly, lamella is the word used to describe plate-like structures. A thylakoid therefore, being a flattened vesicle, would fit this description, so a thylakoid is a type of lamella.
As mentioned earlier, a lamellar system consists of uniform thylakoids, the thylakoids being the individual lamella.

I have the same textbook as you, OCR A2 Biology, and I must admit I had the same confusion. What this textbook fails to mention is the fact that thylakoids are just one type of lamellae.

The textbook also states that the inner membrane of the chloroplast is "folded into lamellae (thin plates)". There are two types of lamellae in the chloroplast, thylakoids and intergranal lamellae, both are stacked, however only thylakoids appear as "piles of pennies" as it states. Intergranal lamellae look nothing like pennies, which is why the textbook is strongly misleading, they are big flattened bits of membrane that connect together different grana (stacks of thylakoids).

Note: my answer comes in 3 years late (I'm currently doing my A2), and the textbook in question will see its last use this year as the current A2 level syllabus is updated, I hope my answer still helps to clear up any confusion should OCR mess up again on this one


Safe level of chlorine in water Chlorine is usually mixed in water to make it safe for consumption. What is a safe quantity of chlorine that can be consumed? What are the side effects of chlorine and does this include hair loss? What are some common chemicals utilized for water purification? Thank you.

Chlorine is a reactive substance and an oxidizing agent. It can cause damage to surfaces exposed to it such as eyes, skin etc but it cannot penetrate deeper. Chlorine can damage your hair by oxidation — hair becomes rough and brittle. This is not same as hair loss — chlorine doesn't cause hair to fall out because it cannot penetrate to the follicles. See here

EPA has set maximum residual disinfectant level for chlorine (as Cl2 and other chlorinating agents such as chloramine [NH2Cl] and chlorine dioxide [Cl2O]) beyond which it is considered unsafe.

Chloramine       :  4.0 mg/L or 4 ppm
Chlorine         :  4.0 mg/L or 4 ppm
Chlorine Dioxide :  0.8 mg/L or 800 ppb


Do RuBisCo and Haemoglobin have any similarity? In RuBisCo and haemoglobin both can bind to CO2 as well as O2. Do these proteins have any structural similarity?

Try reading about these proteins. Apart from wikipedia, you can check out pfam which classifies proteins into families. Globins and RuBisCO are very different protein families. Perhaps the only similarity is that both these are made up of amino acids!


What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem? For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match.
Does the optimum alignment of the three DNA sequences

AAATTT

AAAGGG

GGGAAC

equal to:

AAATTT---

AAAGGG---

---GGGAAC

with the total score S =  294 + 294 - 6 = 586? In this case I sum the alignment score for each of the three pairs.

Or does it equal to:

---AAATTT

---AAAGGG

GGGAAC---

with the score 200 - 7 = 193? In this case I am rewarding only the matches that occured across all three sequences at the same time.

Which of the two scores are the common Multiple Sequence Alignment algorithms trying to optimise for? Or if both are valid, then which optimal alignment (i.e. with respect to which definition) is preferred if realistic reward/penalise values were used?

In your case both answers are equally valid.

The scoring matrix, for example DNAFULL (http://rosalind.info/glossary/dnafull/) usually contains various penalties for wrong alignments.

Also the introduce gap score should NEVER be set at 0 as it will cause the aligned sequences to be filled with artificial gaps!

The only thing the algoritms try to optimise towards is the score, therefore you need sane values for calculating the score and those you propose does not result in usefull alignments.


Why do dogs try to cover their poop? It may seem obvious to us humans to hide our excreta, but this is not quite normal behavior for animals.

Interestingly, dogs have the habit to pee all over the place. It's know that they do so to mark their territory. So when they want to mark their territory, why do they cover up their poop?

I found an old web article where someone asks the same question, without getting a credible answer. He quotes a Yahoo Answers answer making the following claim:

  This behavior is natural in dogs. They cover up their "waste" so that
  an enemy does not find them, from the scent of the poop or pee. It is
  an instinct handed down from wolves, who hid their scent by covering
  up their feces in leaves, sticks, soil, or other nearby natural
  materials. They also rolled in animal carcasses to hide the scent of
  them. Your dog is just using her natural instinct to protect herself
  from predators.

  Another things that dogs do, called marking, is when the dog pees in a
  certain area. They do not cover it up, as it is marking a territory as
  their own. Male dogs usually do this on trees, wooden posts,
  furniture, and other things. Female dogs do this in heat. Dogs do not
  poop to mark something, only pee. When you dog pees or poops and then
  covers it up, this does not mean she is marking her territory. Just
  wanted to add it so you don't get confused. :)

I find it hard to believe these two opposite claims. One time dogs want to mark their territory and the other time it's scared from predators. I know many dogs that do not cover their pee, but do cover their poop, sometimes even within the same walk (and so the same territory).

If this is true, why do dogs do both in the same walk?

On Wiki Answers I found this answer:

  The animals are not actually covering up the pee or pooh but spreading
  their scent. This often happens with animals that are dominant (for
  instance show dogs).

It's so that dogs never actually cover their poop anymore, they only perform some random scratches, throwing a little sand on the turd, sometimes even nothing. That fact makes this answer quite more likely than the previous one.

Another take that's similar to the previous one is this one from Dogster:

  So, why do dogs scratch with their hind legs after defecating? You
  might think the dog is trying to cover up his poop like a cat does,
  but it’s actually a way to mark territory, with the scratch marks in
  the ground pointing to the scent the dog has left.

I also found an eHow article on this subject. It seems to agree with the previous two explanations, but is more detailed.

  It is normal for dogs of both sexes to vigorously kick the ground with
  their hind legs after defecating. This is called scraping or peeling
  out. Some dogs will also do it after urinating. Dogs are descended
  from wolves, which also perform this behavior. It is not a bad habit,
  but a vital part of a dog leaving a visual message and scent message
  to any other dogs that happen to pass by.

They also say that the specific reason why they spread scent with their paws is because paws just contain a lot of scent.

  Dog paws contain scent glands. There are also glands in between the
  toes. The action of scraping the paws against the ground helps release
  the scent inside of the glands. Dogs scrape the ground in order to
  increase their scent on the area near the feces pile, according to
  veterinarian Dr. Justine Lee. Before domestication, dogs wandered in
  large territories. One vital way to communicate with other wandering
  dogs is through scent marking. This instinct has not been bred out of
  the domestic dog.

So, which theory is the most valid? I tent to go for the scent one. Any additions?

I cannot find any definite articles on why there would be a reason for this behaviour other than the same ones that you have mentioned in your article. It could be because it wants to mark its territory or the dog wants to hide its scent.

One point that I would also like to add is force of habit. As Charles Darwin (the father of evolutionary biology) had said in his book titled "The expression of emotion in man and animals"

  ‘Certain complex actions are of direct or indirect service under
  certain states of the mind, in order to relieve or gratify certain
  sensations, desires, etc.; and whenever the same state of mind is
  induced, however feebly, there is a tendency through the force of
  habit and association for the same movements to be performed, though
  they may not then be of the least use’ (reference 1 and reference 2).

It is more of a guess that we make when we see them hide their faeces but in the end, there may not be a reason at all but a habit that do not serve much purpose passed on through evolution. It is left upto our own liberty as to guess what the exact reason is.


Medium preparation, using calcium hydroxide instead of potassium hydroxide As the question states, I am interested in growing alkaliphile bacteria. I have seen many media use KOH, mainly to neutralize, and was wondering if it is possible to change this to Ca(OH)2?
Is there a reason KOH is used instead of any other alkali solution to neutralize media?

As @Chris said, $\ce{K+}$ salts are soluble in water whereas plenty of $\ce{Ca^{+2}}$ salts such as $\ce{CaSO4}$ and $\ce{Ca3(PO4)2}$ are insoluble in the aqueous medium. Therefore it leads to the precipitation of phosphate-containing proteins and sulfate-containing metabolites. In addition, $\ce{Ca^{+2}}$ forms coordination complexes with calcium-binding proteins which participate in discrete signaling pathways. Interfering with this system could lead to subtle and irreproducible results. $\ce{K+}$ ion mostly participates in creating a voltage gradient across the membrane, nothing more.
Moreover, ionic strengths should be considered. $\ce{Ca^{+2}}$ is a divalent cation. A solution of $\ce{KOH}$ and a solution of $\ce{Ca(OH)2}$ with the same pH would definitely have different ionic strengths. Therefore despite achieving the same pH of the medium, ionic strengths vary depending on the salt used. Abnormal ionic strengths affect the structure of proteins in many ways. In general, it has been proven that changes in $\ce{K+}$ concentration lead to less severe outcomes compared to $\ce{Ca^{+2}}$.
EDIT: $\ce{Ca(OH)2}$ forms precipitates in an aqueous solution because it is barely soluble in water ($K_{sp}$ $\pu{=5.5 \times 10^{-6}}$). The pH of a saturated solution of $\ce{Ca(OH)2}$ is 12.347. To achieve other pHs one must add strong acid or base (a standard $\ce{KOH}$ solution perhaps) or use dilution; so as you can see, introducing $\ce{Ca(OH)2}$ just leads to unnecessary complexity, best to be avoided. Also, $\ce{Ca(OH)2}$ leads to the formation of $\ce{CaCO3}$ in the presence of atmospheric $\ce{CO2}$, making it even a less appropriate material for the preparation of the medium. Calculations using $K_{sp}$ shows a saturated $\ce{Ca(OH)2}$ solution has pH = 12.347 and [$\ce{Ca^{+2}}$] =  0.01111


Moth that resembles a leaf. What species is this? Location: Urban area near the Western Ghats, Kerala, South India

Date: Sometime in September, 2016

Climatic Conditions: Humid, frequent rains.

Brief description:

Head isn't prominent from the dorsal view. Wings outstretched even when at rest. Antennae largely concealed under the fore wings. Also it...um...does a pretty good impression of a leaf.

It resembles Pelagodes antiquadraria, which belongs to the moth genus Pelagodes in the family Geometridae.

Image Source: FlickRiver


How to get taxonomic tree data I am looking for taxonomy data of individual species and their classes something like the following format:

{
  "type": "family",
  "parentType": "order",
  "parentScientificName": "hymenoptera",
  "commonName": "ant",
  "scientificName": "formicidae"
}

{
  "type": "species",
  "parentType": "genus",
  "parentScientificName": "...",
  "commonName": "black ant",
  "scientificName": "lasius niger"
}

Basically, from this, you can construct the full taxonomic tree. When looking at the pubmed taxonomy data I don't see how to reconstruct the tree. Please show me how.

I can't leave a comment at the time of writing this (since I don't have enough reputation right now), so I'll leave this as an answer.

Your question is a bit confusing. It's titled "How to get taxonomic data", but at the end of the post, you mention "Basically, from this, you can construct the full taxonomic tree. When looking at the pubmed taxonomy data I don't see how to reconstruct the tree. Please show me how."

I'll try to address both your questions here.

Acquiring the lineage data:

Are you perhaps looking for something like this?

NCBI taxonomy itself is also accessible programmatically via E-Utilities.

Constructing an evolutionary tree:

You could perhaps use something like the data.tree R package to construct your tree using the lineage data.

Your question is a bit too vague, so I apologize if my answer is of no assistance here.


Herbal vs Chemical Insecticides Well, insecticides are used to kill insects.
I have always wondered why are herbal / natural insecticides more effective in killing insects than chemical ones. I have read this at many places but havent found a reason for it.
Also why don't insects develop resistance to herbal insecticides while they do for chemical ones?

I think you probably mean insect and pest control from plant extracts.

I have seen posters where extracts from herbs were pretty effective in killing insects.  Really common herbs - rosemary, basi.   It makes sense that plants (and animals) would evolve chemical defenses against insects.

For instance, a quick search under google scholar talks gives you an idea of the research going on (mostly not in the US) here.  Pestoban, an Indian herbal preparation is quite effective against some pests while less effective (~50% effective) in removing fleas from treated livestock.

It also stands to reason that the compounds found in edible herbs and plants would tend to be selectively effective against insects found in the environment local to the plants.

Another related topic is the search for antibiotics in herbs and spices.  Tumeric is a common topic of research, which explains one of the possible reasons its used in cooking. Garlic components show interesting medical properties too.

While this may seem suspect to some, the research is done in the West too, but it is usually spun a different way. In general if you are looking for bioactive compounds that are not completely toxic (like heavy metals or cyanide for instance), you would want to look at compounds which are made by living things.  Nearly all pharmaceutical designs come from or are derived from plant or microbial / fungal extracts.   This is in fact the field of Natural Products Chemistry which is still a big thing in chemistry and biochemistry.  Few if any of the hot targets of organic synthesis are not some fancy compound found in a plant, fungus or sponge extract.  E.g. the surreally complex Palytoxin, the miracle breast cancer drug Taxol, and the venerable cholesterol control drugs, the Statins.


How are vaccines and inoculations different? If so are vaccinations more safe? If so how? And how is the vaccine a magical invention?

If you became infected before the advent of vaccination, you would either live or die. You would also probably die with really good odds. Being said, someone who lived a disease developed immunologic tolerance to the causative agent, that much you could begin to understand. To expose someone to smallpox was to really endanger their lives, so they found that a similar virus known as Vaccinia, which would normally cause cowpox, could be administered to a patient and they would catch cowpox, but now they were resistant to catching smallpox. You can read about all this on the wiki page for vaccination.

Inoculation generally differs because in the case of inoculaton, you could hope for a less virulent strain of a pathogen but you weren't guaranteed it. You ended up with vaccination methods that increased the safety of the process: On one hand, you could infect someone with related pathogen that causes a milder disease for protection from a more dangerous, related pathogen. On the other, you could find a way to disable the agents pathogenicity, such as heat-killing.

Modern vaccinations are much more refined in that we know so much more. Attenuated strains, for example, you take a virus that grows well in human cells and infect monkey cells just as an example. After many generations the virus grows well in the monkey cells, but no longer the human cells. The strain should still retain it's antigens, however, so when you inject a human now, the virus doesn't cause a disease but you produce antibodies to the virus.

In short, you can protect a population from a disease that would normally devastate it with a dramatically improved efficacy.


How does shortage of oxygen halt the NADH dehydrogenase complex? I understand that in the absence of oxygen the functioning of cytochrome c oxidase stops because it is its substrate. However I don’t understand how stopping cytochrome c oxidase also stops the previous complex (the NADH dehydrogenase complex).

At a basic level this is quite straightforward if you look at an old-fashioned simplified diagram of the electron transport chain, such as the one below that I filched from the web.

If oxygen is absent then there will be a build up of the reduced forms of each cytochrome. Starting from the bottom, in the absence of oxygen cytochrome a is not reoxidized; if there is no oxidized cytochrome a then reduced cytochrome c cannot be reoxidized, and if there is no oxidized cytochrome c then cytochrome b cannot be reoxidized. The latter is the substrate of the NADH dehydrogenase complex — NADH-Coenzyme Q reductase in the figure — so this reaction stops for want of oxidised cytochrome b.

(Years ago I demonstrated on a standard undergraduate laboratory class using rat liver (or perhaps beef liver) mitochondria, where you inhibited different stages and detected the reduced forms by their colours in the visible spectrum.)


What is the difference between a bacterial artificial chromosome (BAC) and a plasmid? Is it just that a BAC is generally larger and artificially constructed? Or are there any other differences?

BACs are a special kind of plasmid, based on E. coli's F-plasmid:

The BAC is based on a plasmid in Escherichia coli that is termed the F (for fertility) plasmid. The F plasmid (or F factor) contains information that makes possible the process called conjugation . In conjugation, two Escherichia coli bacteria can physically connect and an exchange of DNA can occur.
A BAC contains the conjugation promoting genetic information as well as stretch of DNA that is destined for incorporation into the bacterium.

Source
It isn't necessarily larger than a plasmid.


How are the vitreous humour and aqueous humour of the eye, connected? My question is regarding the biological nature of the separation between the vitreous humour and aqueous humour of the human (or mammal) eye. What connects the two in terms of the passive transport of proteins between the two? Is there a single membrane?

If so what is the name of this membrane and is it the only thing separating the aqueous from the vitreous? What is the anatomical difference between the aqueous and the vitreous?

Apologies, I am far from a biologist.

Specifically what sort of transport is arrow 9 in the figure below representing? And is backward transport (from the aqueous to the vitreous) possible?

Any links to papers detailing this mechanism would be highly appreciated, I can only find references to experimental readings of concentrations, but nothing about the transport process itself.

Don't be confused by the word "humour": the vitreous body is presented in birth and has very low "exchange" rate of its components, while aqueous is in constant turnover.

Secondly, the vitreous is an organ-like structure and is separated from other eye structures by its membrane, while aqueous is fluid produced by ciliary body processes into the posterior chamber and moves  anteriorly throughout the pupil. Aqueous can move posteriorly in a case of trauma, operations and other non-physiologic states.

ADD (after attachment of the image)

I'd correct some things in the scheme - call Vitreous as Vitreous, not Vitreous humour, change arrow pointing at the ciliary body as on the following image, depict the vitreous body membrane as I did.

In addition learn two terms: Cloquet canal and Berger's space.

Number 9 shows a vitreo-aqueous route which will follow blood, drugs injected to the vitreous (not an only route), etc.


Citing species in a biology article My question concern the abbreviation of the genus of a species.

I talk about two species: Amphiprion clarkii and Amphiprion perideraion.

Question 1

Let's assume I haven't said a word about these species in my article yet. Should I say:

Amphiprion perideraion is a small fish and Amphiprion clarkii is a big fish

or

Amphiprion perideraion is a small fish and A. clarkii is a big fish

Question 2

If I talk about these two species in the abstract, should I use the abreviation the first time I cite them in the introduction or not?

To avoid confusion all species names should be written in full at first, and can then be abbreviated. In this particular example it would probably not be a problem to use the second, shorter version. But what if you had four species divided into three genera with all names starting with 'A'? As for question 2, the full name usually only needs to be used in the title (if relevant) and once in the body text (which includes the abstract), so you can abbreviate after the abstract. However, this is really only a space issue, and you can use the full name at all instances (you may abbreviate, but don't have to), unless of course journal style prohibits this. I find it useful to write the name in full both in the abstract and once in the main text.

See The International Code of Zoological Nomenclature (Appendix B: General Recommendations) for a reference. To be picky, technically, authorship and year of species names should also be included at least once in each paper (e.g. Amphiprion clarkii Bennett, 1830), to clarify exactly what definition of a name you are using. However, this is often not done in practice (in fields outside taxonomy/systematics). What you often see is that people refer to a authoritative source, e.g. "... all species names used in the study follow Doe et al. (2008)."