What's up with all the vague protocols? I have lost count of how many protocols I've seen, including those supposed to be professionally written (such as manuals that come with kits from well known brands, or methods sections of papers in respected journals), that outright fail to give unambiguous instructions. Some common examples are:

Give centrifuge speed in RPM instead of RCF, and not say what rotor or centrifuge it is.
Say to spin a sample at "maximum speed".
Use subjective time periods, e.g. "incubate briefly" (is one minute brief enough or does it have to be five seconds?)
Subjective quantities, such as "get a good amount of cells" (!!!)
Give time ranges without explaining the consequences of the choice, such as "5-10 minutes" (is it 5 or 10? which one???).
Say "mix well", without specifying if vortexing is okay.
Say "mix well, don't vortex", and don't explain what mixing technique I'm supposed to use.
Give urgent-sounding warnings, such as "don't touch the pellet!", without explaining what happens if I do it or how to fix it (do I need to start over? will I just get 5% lower yield?).
Give urgent-sounding warning, without explaining how to actually heed the warning ("dry the pellet, but do not over-dry it!")

It is in fact extremely rare that I ever see a protocol that has none of these issues. It almost never happens.

It is extremely important that scientific results be reproducible, and it seems like you are opening yourself up to a lot of trouble with an ambiguous protocol. What if somebody fails to reproduce your results, not because your experiment wasn't legitimate, but simply because you left out some crucial detail from the protocol you gave them? You would look bad, and for no good reason.

So why is it so common for protocols to be ambiguous? Is there some nuance to this that escapes me, or do people just not care? How do you follow a protocol that left out crucial information so as to be impossible to follow? Or are you supposed to have amassed a sufficiently vast reservoir of practical knowledge that you can draw on it to "fill in the blanks" on the fly?

This is too long for a comment, so I post my thoughts about this here:

This falls into different important parts here: One is an insufficient understanding of the techniques on which the method is based. This makes it hard to decide which steps are important and which are not. One prominent example would be the use of EDTA in DNA gel running buffers. This recipe originated from RNA research (where you need the EDTA) which where then simply used for DNA as well. Since it worked somehow, it was never really changed.I have seen enough people in the lab clinging to old photocopies of protocols without knowing why they do certain steps.

And the other (connected) issue is that protocols are usually passed down through labs. Things are then done in a certain way because they have always done in this way (with some changes in the protocol probably not even documented) and are not changed. People are even told to use the exact routine, even if this makes absolutely no sense.

In publications there may also be another thing which comes into play: The fear that someone uses the own methods and will then be faster than the own group. At least some groups only publish incomplete and vague methods because of this reason. Then it's a thing of space: There are character limitations in publications and when you need to save a few hundred characters when the article is too long, it's much easier to shave the methods than the discussion.


How to do western analysis to lung tissue? I am working with lungs from mice, and I want to do a western blot analysis to my samples.
I am having trouble with this because my images turn out very "messy", with a high background.
Perhaps I should filter my samples following their homogenization?
Has anyone had this problem and knows how to avoid it?
What is the best method to homogenize the samples?

Doing westerns with primary tissue can be tough, especially because of the presence (sometimes at high levels) of extracellular matrix (ECM). This material can be quite resistant to homogenization and some lysis buffers. One method I have found to work is to snap-freeze the tissue in liquid nitrogen (not on dry ice or at -80°C) directly after removal from the animal, or after any sub-dissection you may wish to do. Then, when you are ready to prepare your sample, grind it thoroughly with a mortar and pestle in LN2, collect the dust and add a good lysis buffer like RIPA at 2-3X concentration, along with protease and phosphatase inhibitors, also at 2-3X. Then, instead of simply homogenizing, use a probe-tip sonicator (not a water bath one) and sonicate the lysate on ice with 8-10 pulses of perhaps 3-5 seconds each, ensuring that the lysate does not heat up too much, and making sure it does not froth up by getting the tip too close to the surface. Sonication sends very powerful shearing forces through liquid and is excellent at destroying membranes and breaking apart ECM. From here you can do your protein concentration assay (remember to use the same concentration of lysis buffer as your blank), aliquot the lysate and store at -80, or add SDS sample buffer and run your gel.

I routinely use sonication on all of my western samples, regardless of whether it's tissue or cell lines I'm dealing with, and I almost never get smeared lanes anymore. Sonication reduces the viscosity or "thickness" of the lysate, allowing you to pipette it much more easily and accurately. It is also useful when your sample "coagulates" after adding SDS sample buffer, and in this instance it doesn't matter if the sample gets hot, as you'll just be boiling it anyway.

I hope this helps, please let me know if you're still having problems. I used to do troubleshooting like this for a living :)


How do ants transport water? All living things need water to survive. Worker ants can drink directly from the source. But a queen ant would need help from the colony to get its daily supply of food and water. I have seen ants carrying tiny bits of food, but I have not really seen them carrying water. Do they use their hands like how they carry food? Do they use a receptacle like us humans? Or are there some other innovative ways?

The worker ants give water to the other ants in the nest. Also, they get most of their hydration out of the food anyway.
Here is a blogpost with some references and nice humour about it.


Mammary gland development and lactation I was reading on mammary gland development, and I found this (1):

As a girl approaches her teen years, the first visible signs of breast development begin. When the ovaries start to produce and release (secrete) estrogen, fat in the connective tissue starts to collect. This causes the breasts to enlarge. The duct system also starts to grow.

Wikipedia has an article about the duct system(2):

The development of the mammary gland occurs mainly after birth. During puberty, tubule formation is coupled with branching morphogenesis which establishes the basic arboreal network of ducts emanating from the nipple.

It goes on to say, developmentally, mammary gland epithelium is constantly produced and maintained by rare epithelial cells.

By the pubertal stage, the mammary ducts have invaded to the end of the mammary fat pad. At this point, the terminal end buds become less proliferative and decrease in size. Side branches form from the primary ducts and begin to fill the mammary fat pad.

In the end, I understood that the mammary alveoli (containing milk) are not formed during this. During pregnancy, the ductal systems undergo rapid proliferation and form alveolar structures within the branches to be used for milk production.
And from where is the milk produced? (Just for some more detail)

After delivery, lactation occurs within the mammary gland; lactation involves the secretion of milk by the luminal cells in the alveoli. Contraction of the myoepithelial cells surrounding the alveoli will cause the milk to be ejected through the ducts and into the nipple for the nursing infant.

Three questions:
An interesting case is one of neonatal milk.(3)

It is thought to be caused by a combination of the effects of maternal hormones before birth, prolactin, and growth hormone passed through breastfeeding and the postnatal pituitary and thyroid hormone surge in the infant.

The article doesn't mention anything about developement of mammary alveoli, though. How does that happen, then?

I know milk formation primary requires prolactin, oxytocin and indirectly, estrogen.(4) So does this process wait till pregnancy?(If yes, then the lobes and branches are devoid of any lumen, and they remain empty until pregnancy, which seems skeptical to me.)

Can lactation occur without alveoli formation?

1-
www.hopkinsmedicine.org/health/conditions-and-diseases/normal-breast-development-and-changes%3famp=true
2- https://en.m.wikipedia.org/wiki/Mammary_gland
3- https://en.m.wikipedia.org/wiki/Witch%27s_milk#:~:text=Breast%20milk%20production%20occurs%20in,not%20by%20prematurely%20born%20infants.
4- https://www.ncbi.nlm.nih.gov/books/NBK148970/#:~:text=Hormonal%20control%20of%20milk%20production,indirectly%20in%20lactation%20(2).

There is a comprehensive 2012 review of the development of the mammary gland by Macias and Hinck which covers the poster’s question(s). I shall try to summarize the points they make regarding the development of alveoli and their role in milk secretion, ‘borrowing’ two of their illustrations to do so.
Development of mammary gland and role of hormones

At birth there is a rudimentary system consisting of a few rudimentary ductal system.

Until puberty this system grows along with the rest of the organism, under the same hormonal influences that affect other tissues.

At puberty oestrogen — in concert with growth hormone and insulin-like growth factor — accelerates the growth of this ductal system, and its branching is subsequently stimulated by progesterone.

It is only in pregnancy that alveoli form, with a continued requirement for progesterone (perhaps partially indirect) and a specific requirement for a prolactin — which is secreted both from pituitary and — as a different molecule, placental lactogen — from the placenta. The alveoli express the genes for the synthesis of specific milk proteins such as casein, α-lactalbumin and β-lactoglobulin.

[Lactating Mammary Gland: Alveolar cells shown in pink (nuclei blue and milk droplets white) with surrounding adipose tissue yellow]
Oxytocin does not affect the development of the mammary gland (as is made clear in the reference cited by the poster). After parturition it is released from the pituitary in response to the nervous stimulus of suckling and causes the myoepithelial cells around the alveoli to contract causing ejection of the milk.
It should be mentioned that the alveolar cells apoptose on weaning, being replaced by adipocytes. However new alveolar can develop from undifferentiated epithelial cells during a subsequent pregnancy.
Regarding the poster’s specific questions
Q1 The article doesn’t mention anything about development of mammary alveoli, though. How does that happen, then?
A1 The development of the mammary alveoli occurs during pregnancy, under the influence of prolactin/placental lactogen and progesterone.
Q2 I know milk formation primary requires prolactin, oxytocin and indirectly, oestrogen.(4) So does this process wait till pregnancy?(If yes, then the lobes and branches are devoid of any lumen, and they remain empty until pregnancy, which seems skeptical to me.)
A2 The poster’s statements are not completely accurate. Milk formation does not require oestrogen, and oxytocin only affects it in so far as failure to remove milk causes involution. The ducts are indeed devoid of the alveolar lumen until pregnancy, and return to this state on weaning. It is not clear why you are sceptical that this is so. The mammary gland development after puberty prepares the ductal network, but alveolar cells only arise when they are required. Pregnancy is quite long enough for them to develop.
Q3 Can lactation occur without alveoli formation?
A3 I would think not, although the situation regarding neonatal milk secretion (witch’s milk) is unclear because of the obvious ethical barriers to its study in humans. The increase in breast nodule size is suggestive of development. So my opinion is primarily based on argument. The formation of milk requires cells with a specific pattern of gene expression, i.e. of milk proteins and metabolic enzymes that are required for fat formation. It also needs a structure and organization that allows the milk to be secreted into a duct. That is what an alveolus is. Therefore I would imagine that in these circumstances the rudimentary mammary ducts of a new-born infant develop alveoli under maternal hormonal influence.
Postscript
This is a topic I worked on for my doctorate, but have not had contact with for many, many years. It was interesting reading the review — how the technology has changed! I also find it curious that the review makes no mention of corticosterone, as one of the earliest systems for observing alveolar development in vitro was in explants of mammary gland from pregnant mice cultured in defined medium with insulin, prolactin and corticosterone. Perhaps the corticosterone was mimicking what is now known to be the effect of progesterone in vivo.


What is atrial fibrillation? I am wondering exactly what a-fib is (causes and symptoms).

I would really appreciate having a sample of an EKG with it (because in my limited research, I have found it nearly impossible to find just a sample piece of an EKG that has a-fib on it) with your answer, so I can actually get an idea of what it looks like. With the sample EKG, I would love to have a normal one beside it so I can kind of analyze the differences between the two.

Note: This is not and never was a homework question!

A human heart can be viewed as 2 hearts, the left and the right heart, each consisting of an atrium and a ventricle. The atrium's function is to fill the ventricle with as much blood as it can and the ventricle then pump the blood away. Also there is a system of valves to control blood flow on each side. Basically this is how our heart works.

Now, to make this system work we need to have a coordinated movement of atrium and ventricle, that is, first atrium is filled, then it pumps blood into ventricle, valve closes and then ventricle compresses.
The movement of heart muscle causes currents that can be measured (this is the ECG pronounced EKG). These currents are representative of the movements of atrium and ventricles are expressed respectively as p waves (for atria) and qrs (for ventricles).

It is the case that atria are not very important and sometimes they can stop working properly. They now longer have coherent movement and stop helping to pump blood into the ventricles, but they still move. This event is called atrial fibrillation.

From this explanation one can expect that no longer p waves will be identifiable in the ecg, but instead a random noise overlapping with "normal" qrs representing normal ventricular movement. The movement is actually not exactly normal, because the ventricular contraction due to atrial fibrillation now occurs at random times, that is qrs complexes occur with random spaces between them. The explanation for this is rather more complex: there are bundles of specialized cardiomyocites with different frequencies of depolarization. The fastest ones are on SAN and basically guide the whole heart rhythm through specialized bundles. When you have atrial fibrillation, the depolarization signals no longer come from these preferential bundles, but from any part of the atria at random. This causes the ventricles to initiate motion at irregularly spaced intervals.
I've included a photo of a normal rhythm and a atrial fibrillation side by side, but I hope you can use this explanation to find better ones by yourself in the web.

Note: don't confuse atrial fibrillation with atrial flutter. Flutter is a faster paced regular (therefore organized) atrial movement. It will appear as a saw-tooth shaped wave with regularly spaced qrs complexes.

Hope this helps.

Causes of atrial fibrillation are numerous, bur mainly high blood pressure, vascular disease, heart and lung disease among others. It can be asymptomatic in most cases or presenting with the symptoms of its underlying cause.

Please refer to http://www.webmd.com/heart-disease/atrial-fibrillation/heart-disease-atrial-fibrillation-basics for a quick overview.


eye myopia power changes with brightness Is there a condition where myopic power changes with ambient brightness. When I drive in the morning in bright sunlight my power is -4.0; however when I wear the same -4.0 glass in the evening (dusk time and night) I cant see properly. The images are blurred. I have to change to -5.0 glass. However the same situation does not happen in my right eye which has a constant -5.0 power in both daylight and night. I have observed this for many years (15+).

NIGHT MYOPIA -  is a tendency for eyes to become near-sighted in dim illumination.  There are multiple theories explaining the phenomenon, most of them are related to accommodation or chromatic shift in scotopic light conditions when to light is focused before the fovea thus worsening the existing myopia.

Citation:

  In dark adaptation the eye becomes more sensitive to shorter wave
  lengths (Purkinje shift- In the light-adapted eye the region of
  maximal brightness is in the yellow; in the dark adapted eye, the
  region of maximal brightness is in the green),and visual acuity
  depends on parafoveal blue cones. Shorter wavelengths come into focus
  in front of the retina, and this chromatic aberration accounts for
  some of the relative myopia that a normal eye experiences at night;
  much of the remainder is due to an increase in accommodative tone in
  the dark.  It is also called dark focus of accommodation, or tonic
  accommodation, or resting state of accommodation. Consequently, a
  measurement of the refraction (i.e. the determination of appropriate
  optical glasses to obtain good vision on these distant objects) gives
  the result that the eye is myopic. Night myopia can reach values of up
  to about - 4.0 D. Night myopia decreases with age31 and therefore it
  can be of special importance for young drivers at night. In one
  experiment with people aged 16 to 25 years, 38% had night myopia of -
  0.75 D or more, and 4% had – 2.50 D or more. Cause of Night Myopia:

  Spherical aberration (The optical effect of the larger pupil decreases
  the depth of focus) Chromatic aberration. Parkinje shift Ciliary spasm
  At low light levels there is a change of the biochemistry of imaging
  on the retina: in bright light the receptors in the retina are cones
  with higher image acuity, and imaging of colors, whereas in low light
  the receptors in the retina are rods with reduced image acuity, and
  imaging of black and white only. The transition between both states,
  i.e. to get maximum sensitivity when moving from the bright to the
  dark, doesn't happen immediately, but takes some minutes33. This is a
  problem e.g. when driving a car in sunlight and entering a tunnel. The
  low light imaging by rods in the retina can be further reduced by a
  lack of vitamin A and zinc Symptoms:
  1. Blur vision only in low luminance.
  2. Feeling discomfort while maintaining fixation in low illumination level.
  3. Difficulty in night driving.
  4. Hallows around light.


Why are skin moles (pigmented spots) circular in shape? I have never seen a rectangular or triangular shaped mole.
Is there any reason for why moles are roughly circular in shape?

Note: I am not stating that moles are in general circular in shape because there are no statistical studies to conclusively state so. This answer is mostly about default circular shape of cell colonies.

Moles (melanocytic naevi) are not strictly circular but generally have  have a rough circular shape. Moles can have irregular shapes too and you can easily check that by a simple google image search.

The exact causes and mechanisms of mole formation are not known but the somewhat circular shape can be explained by a simple spatiotemporal model of growth.

Moles are formed because of pigmented cells called melanocytes (which contain the dark pigment melanin). A mole would grow when a very small population of these pigmented cells divide and expand. In a 2D surface, cells would continue to divide and expand along both the axis at an equal rate, if there are no specific constraints. Since the expansion is same along both the axes, you get a roughly circular shape. For similar reasons, bacterial colonies (on petri plates) are also more or less circular. Note that there are stochastic factors that would contribute to irregularity.

Triangles and rectangles are very specific geometries. There need to be some constraints that would limit the cell growth to adopt these geometries. So the default shape would be mostly circular.


A question concerning the strength of synapses Synaptic strength can be defined

  »as the average amount of current or voltage excursion produced in the postsynaptic neuron by an action potential in the presynaptic neuron«

Synaptic strengths and their changes depend on many factors and mechanisms, from LTP and LTD to STDP and STF and STD. Possibly, also neuromodulators should belong to this list – but maybe they shouldn't.

Assuming that synaptic strength is a well-defined quantity even when the synapse is at rest, the strength of a synapse is a continuous or non-continuous function over time, that ideally can be plotted.

Now I wonder whether there have been recordings and/or simulations of the synaptic strength of a single synapse as such a function over time - and how the plot would look like at different time scales: long term trends superimposed by shorter and shorter fluctuations?

What you are describing is exactly how long-term potentiation/LTP (or depression/LTD, for that matter) is measured electrophysiologically.

Here's an example from a 1988 review by Nicoll et al:

Nicoll, R. A., Kauer, J. A., & Malenka, R. C. (1988). The current excitement in long term potentiation. Neuron, 1(2), 97-103.

The x-axis is time in minutes, the y-axis is a measure of synaptic strength: the slope of the local field potential response to simulation of a particular pathway. You could also measure an EPSP internally, measure voltage with a voltage-sensitive dye, etc.

At the point marked "tetanus", a long train of pulses is delivered that is known to cause LTP. Afterwards, you see an increase in synaptic strength that is maintained for many minutes.

It's also possible to perform these experiments over longer time scales, with different paradigms, in the presence of various drugs that influence LTP, etc. Different protocols will give different durations of LTP.

These sorts of plots are ubiquitous in the LTP/LTD research field, so if you read any papers in that area you are likely to come across many similar presentations.


Would the human body react faster to touch or sight I am currently working on an assignment for my physics class, but I believe my question is biology related.

For a two person lab, I am trying to time how long it takes a tennis ball to fall two meters, Using basic physics equations I was able to determine that the ball should take around 0.66 seconds to hit the ground but my results are generally very off.

Would I be able to react faster if I were to stop the timer when I felt the ball hit my other hand, or would I have a worse reaction time than if I were to use my current method of stopping the timer when I see/hear the ball hit the ground.

A "touch" or "haptic" sensation will be much faster due to several reasons:

Haptic feedback can be processed without the presence of any higher-order cognitive processing, therefore meaning that the signals are being processed via a monosynaptic route.
There are short reflex arcs between the spinal cord and the limb (meaning that you can react before you are consciously aware of it)

A visual sensation will be much slower:

The processing of the signal will require higher-order cognitive processing, and this takes time. I read that it takes between 50ms-200ms. (polysynaptic route)

Interesting article about this topic


What is this plant that spontaneously sprouted in my balcony? I have a big pot on my balcony that has inhabited many kinds of plants over the years. One spring I got to unexpected sprouts from seeds the size of an apple or orange seed. One survived and grew to what is depicted in the pictures here, but then unfortunately I got an infestation of spider mites that killed it.

I had previously rented out the apartment, and I suspect that this is the result of a couple of seeds that they intentionally or unintentionally put here. My best guess is that this is some kind of berry or something else edible that you buy in a grocery store.

You can also see some sun damage on some of the leaves in the picture. The plant in question is the most visible in the pictures, the others in the packground are passion fruit.

There were no thorns, and the leaves felt a little bit hairy, kind of like a common nettle but shorter and a fussier feeling. The height in the pictures is about 30-40 cm and it was growing fast until the spider mite attack.

What could it be?

It looks like a raspberry, or some other kind of similar berry plant (blackberry etc.). The triple leaves and the habit of the plant are characteristic. Birds will often eat them and "deposit" the seeds randomly around the Earth.

https://plantvillage.psu.edu/topics/blackberry/infos

Berry plants usually have thorns or develop them as they grow. If no thorns are present, then perhaps it is another type of interloping plant. Other plants do look similar. In which case, your photos are insufficient for more further identification.


Do river sharks (genus Glyphis) have reduced rectal glands for salt removal? Do river sharks of the genus Glyphis have reduced or absent rectal glands for salt removal?

The rectal gland of marine sharks removes excess salts to maintain osmotic balance (Oguri 1964).  In freshwater stingrays (Potamotrygon spp.), the rectal glands are greatly reduced in size  (Thorson et al. 1978) but are apparently functionless (Goldstein and Forster 1971). This is not surprising because freshwater rays do not experience the regular influx of salt water.

I have been unable to determine whether such degeneracy or loss has been observed for the river sharks of Australia (genus Glyphis). Pillans et al. (2009) suggest that osmoregulation is probably similar to bull shark, which would not be surprising because they are in the same family. However, bull sharks that live in salt water but regularly enter fresh water have rectal glands that are normal size (Oguri 1964). River sharks are obligate freshwater species and thus have no need to maintain a large rectal gland for the same reason as the freshwater rays.  From an evolutionary perspective, I would predict reduction or loss of the rectal gland.

I contacted Richard Pillans, the primary author of the article linked to in the question. He told me that he did not know whether the rectal gland was reduced. Researchers are hesitant to capture and dissect the freshwater sharks because of their endangered status.

He did tell me that they have gathered much more data on the movement of the sharks since the 2009 paper was published.  Apparently, river shark is a bit misleading (my words, not Dr. Pillans). Glyphis does occur in freshwater (no salt) but tends to be found in the middle range of brackish water. Brackish water is considered to be anything that is not purely freshwater nor purely salt water, with typical values between 0.5 and 30 parts per thousand (ppt). Freshwater is 0 ppt and open ocean salt water is 35 ppt, the equivalent of 35 grams of salt in one liter of water.

If Glyphis is found primarily in the mid-range of brackish water, then I would expect the rectal gland not show signs of reduction. Pillans and Franklin (2004) showed that rectal gland mass of brackish water bullsharks (Carcharhinus leucas) in Australia did not differ significantly from either freshwater or saltwater individuals.  So, pending further evidence, I would conclude that Glyphis, which in the same family as bull sharks, probably does not show rectal gland reduction.

  Pillans, R.D. and C.E. Franklin, 2004.  Plasma osmolyte concentrations and rectal gland mass of bull sharks Carcharhinus leucas, captured along a salinity gradient.  Comparative Biochemistry and Physiology, Part A 138: 363-371.


What are the effects of buffer on genomic DNA shearing by sonication? Expt: I have isolated genomic DNA from LNCaP cells and would like to crosslink a small molecule (Chem-seq) to the DNA.  The small molecule is an alkylator so it will crosslink DNA on its own.  The buffer I am using for the crosslinking is TKMC (10 mM Tris-HCl [pH 7], 10 mM KCl, 10 mM MgCl2, 5 mM CaCl2).  After crosslinking I want to fragment the genome to 100 - 600 bp (300-400 bp average).  I am using a Bioruptor 300.

Question:  Should the TKMC buffer be sufficient for sonication?  Most references I have found use TE buffer (pH 7.5 - 8), and I can't find a reference using TKMC.

More info:  I tried a direct comparison between the two buffers (TKMC v TE pH8) and the TE buffer seems to fragment to smaller sizes compared to the TKMC buffer.

For example: Biorupter 300, Low setting, 1 cycle = 30/30 ON/OFF @ 3 C, 5 ng/uL DNA in 300 uL

average frag size @ 30 cycles: TE = 350bp, TKMC = 500bp

Any suggestions?  Using TE buffer for my alkylation crosslinking would not work due to presence of EDTA.  Should I play around with the cycle ON/OFF times?

Any help would be awesome!  Thanks.

UPDATE:

After running a comparison between TKMC, TKMC + 1mM EDTA, TKMC + 10 mM EDTA there was a slight tightening up of the fragment range as I added EDTA.  In addition, the fragment range (sizes) was smaller when EDTA was added (compared to TKMC w/o EDTA, after the same number of cycles).  The results were not drastic but there was indeed a noticeable effect on fragment size and range.  I will proceed with adding EDTA before sonication.  Thank you for your suggestions!

Could you use a spun column to exchange the buffer? Some sort of gel filtration column; equilibrate column in TE; add your DNA sample, spin through excluded DNA. TKMC components will be included in the column and thus retained.

Update
Have a look at this paper, and references therein. Apparently magnesium ions influence the flexibility of DNA. Clearly if the shape of your DNA in the two buffers is different this would impact upon the effects of shearing forces.


Is chromosomal DNA more likely to interfere with restriction mapping or PCR analysis in E. coli? We are characterizing YADH-1 in my biochemistry lab course. Over the course of the first weeks, we harvested E. coli cells, and isolated plasmid DNA via alkaline cell lysis. A previous exam for the course asked the following question concerning plasmid DNA and analysis:

"Is chromosomal DNA more likely to interfere with restriction mapping, with PCR analysis, or equally likely to interfere with both methods?"

Since we're using EcoRI and BamHI, my thought process is that while we can predict the cuts on a circular plasmid, we wouldn't be able to predict all of the cuts on high-molecular weight chromosomal DNA, and the resulting restriction map would be useless. However, PCR can work in a complex mixture of molecules, so even in chromosomal DNA, the primers should be able to find the target sequence. Is the answer therefore that chromosomal DNA is more likely to interfere with restriction mapping?

Welcome to Biology.SE!

I think you've come to a reasonable conclusion, but not for exactly the right reasons.

The genomes of several strains of Escherichia coli have been sequenced (e.g. https://www.ncbi.nlm.nih.gov/nuccore/U00096) so you could predict the sizes of the fragments you would expect from your digest.

The genome size of E. coli is about 4.6 million base pairs and six-cutters like EcoRI and BamHI cut on average about once every 4096 bp (you should be able to figure out how to come up with that number). From that what would you expect to see if you did a restriction digest on this bacteria's genomic DNA?

Does that help you improve your answer?

(If you have access to the appropriate software, I encourage you to download that sequence and check your conclusions.)

((Also note that the specificity of PCR is dependent on primer selection, so your answer is assuming that the primers were well designed!))


What will happen if a scorpion pierces itself? If a scorpion pierces itself, will it die or immune to its poison? If it produces the venom its blood should be immune to itself poison.

Scorpions are immune to their own venom (reference) as has been said in some studies as well (reference) But some other studies and eye witness accounts have referred to the contrary.

  in an experiment a scorpion, Bulteus australis, was killed by an
  injection of the same venom as its own (reference).

So, it should be safe to say that there is a very low chance for a scorpion to be affected by its own venom. It is said that

  Mutations in the scorpion’s own membrane protein genes make the
  arachnid immune to its own venom (reference).

A scorpion could die quickly if venom is injected into its brain (nerve ganglion). Larger species inject a higher amount of venom to overcome the smaller ones and should have specific neurotoxins if smaller scorpions are their prey to disable them (reference).


What kind of snakes are in this photo? What is the name of these snakes? I saw them in the street and I don't know if they are dangerous for people? Photo is taken near to Tbilisi, Georgia.

Based on the species description in Speybroeck et al. 2016 and pattern of stripes (one central stripe with stripes on each side), and the lack of a distinct neck, the specimen in the top left appears to be an Eastern slow worm (Anguis colchica). That species is known to occur in Tbilisi.
Based on the species description in Speybroeck et al. 2016 a smooth snake (Coronella austriaca), also known from Tbilisi. The reddish color, two rows of dark spots, and the markings on the head are typical of this species. Also it can be seen that the anal scales are divided, which is a characteristic of this species.
Cited
Speybroeck et al. 2016. Field Guide to the Amphibians and Reptiles of Britain and Europe. Bloomsbury Natural History (publ).


Sugar metabolism in preserved/cryopreserved livestock semen I wonder how can semen use di/tri-saccharide (e.g. sucrose, trehalose, raffinose) for spermatozoa metabolism in preservation/cryopreservation of livestock semen, since the semen itself never bring any enzyme to breakdown those sugars and the extender used also don't contain enzyme needed?

Is there any other way to breakdown sugar without enzyme, or is there any component in the extender which can substitute the enzyme function?

Thanks in advance.

The sugars that you mention are primarily used as a "cryoprotectant" and thus to reduce physical damage to the cells while frozen.  The sugars are not used to provide energy to the sperm as the enzymes will not function in the temperatures and conditions of a frozen environment. The addition of sugars is typically used with other types of cells/tissues in their cryopreservation as well.  The abstract in the link below summarized this.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/raq.12195


Why did evolution make people's skin dark? Why do people living in the equator have dark skin?
I know that Melanin acts as a protective biological shield against ultraviolet radiation.

But doesn't black absorb all light in a way making the body more heated than the surroundings ?

It didn't, the basal condition for humans is dark skin, all other pigmentation patterns evolved from it. Additionally Dark skin is not monophyletic/homologous in humans,
 that is some darks skinned humans evolved from light skinned humans who in turn evolved from ancestral dark skinned humans, (Evolution made skin lighter then made it darker again in other regions). Skin dark/lightness is also well correlated with latitude (which is correlated with UV levels).

First it helps if you remember skin is translucent so even very light skin absorbs a great deal of light. Additionally black also radiated heat better than white its is a double edged sword so to speak, it absorbs heat better but also sheds it better.

But the current hypothesis about why light skin evolved is due to vitamin D. The skin absorbs some UV radiation to manufacture vitamin D. Dark skin blocks more of this radiation reducing vitamin D levels. As humans migrated into higher latitudes with less UV radiation they needed lighter skin to harvest more of it. If your skin is too light you have issues with sunburn, skin cancer, and folic acid destruction darker skin protects from these. Now in modern humans clothing and diet completely swamps these effects, so studying it is difficult. the use of clothing in humans moving into colder climates may have exacerbated this effect. The later evolution of lactase persistence could further confuse the effect.

Note that this hypothesis is controversial and only weakly supported because it is extremely difficult to test and the the multiple confounding factors.

http://evolution.berkeley.edu/evolibrary/news/140305_skincolor

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024016/

https://www.ncbi.nlm.nih.gov/pubmed/16766240

https://dl.dropboxusercontent.com/u/38568440/admixture/shriver01.pdf

https://en.wikipedia.org/wiki/Human_skin_color


How does new species come into existence? The only reason for the creation of new species that I found from the internet is geographical isolation. Are there any more reasons?

A paper from Müller et al. proposes a molecular marker called a CBC, differences in which can be used to call two different species, even when closely related: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950759/

  In this study we are looking for a molecular classifier that might indicate that two organisms belong to different species. We are interested in an indicator hypothesis that is easy to work upon and additionally yields a certain probability that two organisms belong to distinct species. Compensatory base changes (CBCs) in the internal transcribed spacer 2 region (ITS2) of the nuclear rRNA cistron have been suggested as such a classifier.

Some mutation event that creates sufficiently different CBCs in a viable offspring capable of further reproduction, i.e., survives natural selection, would therefore lead to speciation, by this measure.


What is the shortest mRNA the ribosome can read to produce a peptide? This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome.
In general, Glutathione has a "gamma" peptide bond, thus cannot be synthesized by the ribosome. However, is there an actual minimal length that ribosome can process?

I understand that the mRNA is more then just the codons, however, does it still require a minimum set of condos, e.g., say 18 nucleotides, to produce a peptide?

Reading the paper linked by @canadianer and its references was pretty illuminating. It's a straightforward paper except for its conclusions, and the most convincing part is the evidence of actual translation. There's some evidence that transcription start sites are used as a regulatory mechanism by displacing other things that might otherwise bind. An unknown fraction, but most(90%+), very short bioinformatically detected ORFs are not translated.

Some, however, are. See this table for the experimentally verified translated micropeptides. The shortest is a nearly unbelievable 6 peptides long.


What is the formal terminology for two species that are "close" to each other in a phylogenetic tree? Take for example the human and the chimpanzee, they are "closely related" species since they are "close" to each other in a phylogenetic tree. However, this terminology seems pretty informal, what would be the formal way to specify that two or more species are "closely related"?

Are you looking for something like "sister lineage" (or "sister taxon" or "sister group")

This term may be more specific than what you're looking for, and to use it correctly you'd want to be a little careful – I guess in this case you might have to say something like:

  "the lineage that includes chimpanzees and bonobos is sister to the
  lineage of which humans are the only extant species"

or

  "the lineage that includes chimpanzees and bonobos and the lineage of
  which humans are the only extant species are sister lineages"

both referring to this phylogeny.

It's also possible that explaining exactly what you mean by 'close', or what it entails, would be appropriate, be it Ilan's suggestion of % genetic similarity (or maybe genomic similarity?), # of nodes between your two taxa (again, this would have to be in reference to a specific phylogeny), or if you have a dated phylogeny you could refer to the time since divergence, as in "coding DNA divergencies ...place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago."(Wildman et al 2003).


Chickens roosting, is it sleep or torpor? At night when they roost, do chickens experience a state of sleep (meaning do they move from NREM1 to NREM2, NREM3 and REM) or are they in a state of torpor (reduced metabolic rate and decreased physiological activity)?

When birds sleep, they do experience NREM sleep [1]. Furthermore, Kavanau (2002) concluded that NREM has evolved in warm blooded animals [2].

  Birds provide a unique opportunity to evaluate current theories for the function of sleep. Like mammalian sleep, avian sleep is composed of two states, slow-wave sleep (SWS) and rapid eye-movement (REM) sleep that apparently evolved independently in mammals and birds. Despite this resemblance, however, it has been unclear whether avian SWS shows a compensatory response to sleep loss (i.e., homeostatic regulation), a fundamental aspect of mammalian sleep potentially linked to the function of SWS. Here, we prevented pigeons (Columba livia) from taking their normal naps during the last 8 h of the day. Although time spent in SWS did not change significantly following short-term sleep deprivation, electroencephalogram (EEG) slow-wave activity (SWA; i.e., 0.78-2.34 Hz power density) during SWS increased significantly during the first 3 h of the recovery night when compared with the undisturbed night, and progressively declined thereafter in a manner comparable to that observed in similarly sleep-deprived mammals. SWA was also elevated during REM sleep on the recovery night, a response that might reflect increased SWS pressure and the concomitant 'spill-over' of SWS-related EEG activity into short episodes of REM sleep. As in rodents, power density during SWS also increased in higher frequencies (9-25 Hz) in response to short-term sleep deprivation. Finally, time spent in REM sleep increased following sleep deprivation. The mammalian-like increase in EEG spectral power density across both low and high frequencies, and the increase in time spent in REM sleep following sleep deprivation suggest that some aspects of avian and mammalian sleep are regulated in a similar manner [3].

From the Abstract and reference [3] above, we see that EEGs have been taking on birds and show that birds enter REM and SWS similarly to mammals.

In response to Chris Stronks, researchers have also studied chickens see Evolution of Sleep: Phylogenetic and Functional Perspective by Patrick McNamara, Robert A. Barton, Charles L. Nunn. In the section for REM sleep in birds, the studies were conducted on pigeons and chickens see pages 204-205.


MHC restricted peptide What is an MHC restricted peptide?

I got this definition from wikipaedia, but cannot exactly extract what the phrase MHC restricted peptide means.

  MHC-restricted antigen recognition, or MHC restriction, refers to the fact that a given T cell will recognize a peptide antigen only when it is bound to a host body's own MHC molecule. Normally, as T cells are stimulated only in the presence of self-MHC molecules, antigen is recognized only as peptides bound to self-MHC molecules.

I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful.

First of all MHC stands for major histocompatibility complex. There are two types of MHC.

MHC type one is present on all of our cells with a nucleus. The purpose of these protein complexes is called antigen presentation. T-cells cannot recognize free antigens on their own, it has to be presented to them in the proper way. This is what these proteins do. In every cell there are lots and lots of proteins, that get digested to small polypeptides (short aminoacid sequences) by proteases during the natural recycling process. The cell takes a small portion of these polypeptides and presents them on its surface through MHC I complexes, that the immune system can read. This is like the cell saying to the immune syytem that "hey I got these proteins in me". Now if the cell is infected (by a virus most likely) then the "attacker's" proteins get digested and presented as well and its like saying " hey I'm infected and the attacker has these proteins".

MHC II serves similar function but it is only present on professional antigen presenting cells (APCs). These complexes present peptides derived from proteins consumed and digested through phagocytosis or receptor mediated endocytosis. It's like saying "hey we got a larger attacker and it has these proteins"

So, long story short T-cells cannot recognise antigens on their own it needs to be presented to them on MHC complexes and then and only then can they be activated.

Edit: A list of useful articles in the topic of antigen processing / presentation for further details:

January 14, 1998 14:59 Annual Reviews AR052-12
Annu. Rev. Immunol. 1998. 16:323–58
MECHANISMS OF MHC CLASS I–RESTRICTED ANTIGEN
PROCESSING Eric Pamer and Peter Cresswell

Cell, Vol. 76, 287-299, January 28, 1994.
MHC-Dependent Antigen Processing and Peptide Presentation: Providing
Ligands for T Lymphocyte Activation

Terry Y Nakagawa, Alexaiider Y Kudensky
The role of lysosomal proteinases in MHC class Il-mediated antigen processing
and presentation
This one may require subscription.

and the wiki page :)


How does a veggie-less diet affect the human body? I have some question, which I'm sure would fit better in the fitness section but proper answers should probably come from someone that knows biology.

My question is rather simple. How can a person that doesn't eat any vegetables at all be affected by such a diet? By no vegetables at all, I mean not eating any ever.

There is a list of several implications of not eating vegetables (references 1, 2, 3):

Weight gain (by eating fat-rich products);
Malnutrition (not reveiving enough vitamin A, C, D, K, etc);
Digestive problems (low fiber intake leads to digestion disorders, which could lead to health problems);
High risk of heart disease;
High risk of certain cancers.

I also pulled up the nutrition fact sheets for vegetables, fruits, and seafood created by the US Food and Drug Administration.

In order to obtain all the necessary vitamins, one can substitute vegetables for fruits. For example, to obtain 100% of the daily value of vitamin A, one should eat as little as one carrot a day. In order to get the same amount of vitamin A from fruits, one should eat 134g of cantaloupe, or 462g of grapefruit, or 50 large apples a day. Although this could be difficult but possible, the sugar content of the above-mentioned fruits should be taken into account.

Something else which needs to be considered is that vegetables are richer in minerals (iron, potassium, calcium), compared to fruits.

All this in mind, perhaps all minerals and vitamins could be acquired from a source other than vegetables.


Is iodised salt harmful to the lactofermentation process? I was discussing sauerkraut recipes with someone on IRC a minute ago, and they warned me not to use iodised salt in the process. My first (and so far, the only successful) batch is one I made with iodised salt - I think it's pretty much the default here. Searching the Internet shows roughly equal numbers of answers going either way, from "it doesn't matter" to "it discolours the vegetables" to "it kills the bacteria you want".

Clearly elemental iodine is nasty, as are any of the halogens. But is the iodide ion similarly harmful to the bacteria (and yeasts?) involved in lactofermentation, in the low quantities in which it's present in supermarket salt?

This study found no difference in the outcome of sauerkraut fermentation with or without iodized salt:

  There was no clear influence of iodized salt on microbial populations.
  Stable fermentations were achieved using iodized as well as non-iodized salt.


Is cancer caused by vitamin B17 deficiency? I have read in an article on the internet that cancer is caused due to deficiency of vitamin B17 which has been removed from our diets long ago in the western food. But some people say that vitamin B17 does not work. So, is it deficiency of vitamin B17 which causes cancer i.e. can this vitamin really be used to cure cancer?

Short Answer: No.

Background: First of all, there is no such thing as vitamin B17. The compound, amygdalin or laetrile, which is referred to by this term, is not a vitamin1. Amygdalin is indeed a cyanogenic glycoside (like glucosinolates, see this answer) which is poisonous to organisms including humans, because it forms cyanide which is toxic2. See this image for its structure:

The notion that amygdalin is a vitamin started when Ernest Krebs Jr., inventor of 'laetrile' (a modified form of amygdalin), rebranded it as a vitamin to get around the new FDA drug regulations and get it approved as nutrient supplement instead of pharmaceutical3. Ernest Krebs Sr., in 1920s, formulated a theory that amygdalin could kill cancer cells4 and the notion was carried forward by his son, though Ernest Krebs Sr. himself considered amygdalin as too toxic for human consumption. This view received a huge uplift when, in 1973, a public relations officer at Sloan Kettering Hospital, which was given the task by the NIH of performing a series of laetrile trials, alleged a cover up of, and leaked, data that claimed potential for laetrile as an anti-cancer agent5, though nobody else was able to reproduce the same test results in a series of followups. Yet, perhaps the most prominent force which still keeps this myth alive is the book World Without Cancer: The Story of Vitamin B17 by G. E. Griffith (interestingly, reviewed by 'Dr.' Ernest Krebs Jr.). According to all these reports, laetrile might work in following ways6:

malignant cells have higher levels of $\beta$-glucuronidase and lesser levels of rhodanase, because of which they are more susceptible to effects of laetrile.
malignant cells have higher levels of $\beta$-glucosidase (different from $\beta$-glucuronidase) and lesser levels of rhodanase, because of which they are more susceptible to effects of laetrile.
cancer is due to deficiency of vitamin B17 (laetrile) and vitamin B17 is required by cells to restore health (though there is no evidence for this).
cyanide released by laetrile has a toxic effect beyond its interference with oxygen utilization by cells. According to this theory, cyanide increases the acid content of tumors and leads to the destruction of lysosomes. The injured lysosomes release their contents, thereby killing the cancer cells and arresting tumor growth.

Laetrile is even supposed to raise the red count in blood, be of value in treating sickle cell anemia, treat parasitic diseases, help regulate intestinal flora, cause lowering of blood pressure in cancer victims and provide relief from arthritis3.

However, all clinical tests have concluded that laetrile is poisonous to humans (and other organisms) due to cyanide poisoning and thus, its effect in cancer treatment is unambiguously negative6,7,8. In fact, use of laetrile has even led to a number of deaths9.

In reality, when amygdalin is ingested, the enzymes  $\beta$-glucosidase, emulsin and amygdalase hydrolyze it into gentiobiose and L-mandelonitrile. Gentiobiose is further hydrolyzed to glucose, whereas L-mandelonitrile is converted into benzaldehyde and hydrogen cyanide, which causes cyanide poisoning2. The concerned process looks like10:

If the quantity of cyanide generated is under the acceptable daily intake limit (0.05 mg/kg body weight)11, then it can be handled easily by enzymes, like rhodanase which converts toxic CN- to non-toxic SCN- ion12. But this quantity is often beyond the limit; a single apricot seed contains about 0.5 mg cyanide13. Hence, it results in cyanide poisoning.

Thus, the so-called vitamin B17 cannot cure cancer.

References:

 1. Lerner IJ (1981). "Laetrile: a lesson in cancer quackery". CA Cancer J Clin. 31 (2): 91–5

 2. Wikipedia contributors. "Amygdalin." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 10 Mar. 2017. Web. 11 Apr. 2017.

 3. United States, Food and Drug Administration. “Laetrile, the Commissioner’s decision” 1978

 4. (1991), Unproven methods of cancer management: Laetrile. CA: A Cancer Journal for Clinicians, 41: 187–192. doi:10.3322/canjclin.41.3.187

 5. WADE, NICHOLAS (1977). Laetrile at Sloan-Kettering: A Question of Ambiguity. Science, 198, 1231-1234.

 6. Ellison NM, et al. “Special report on Laetrile: the NCI Laetrile Review. Results of the National Cancer Institute’s retrospective Laetrile analysis.” N Engl J Med. 7 September 1978.

 7. Milazzo S, Horneber M. Laetrile treatment for cancer. Cochrane Database of Systematic Reviews 2015, Issue 4. Art. No.: CD005476. DOI: 10.1002/14651858.CD005476.pub4.

 8. Milazzo S, Ernst E, Lejeune S, Boehm K, Horneber M (2011). "Laetrile treatment for cancer". Cochrane Database Syst Rev (Systematic review) (11): CD005476. doi:10.1002/14651858.CD005476.pub3. PMID 22071824.

 9. Editors of Consumer Reports Books (1980). "Laetrile: the Political Success of a Scientific Failure". Health Quackery. Vernon, New York: Consumers Union. pp. 16–40. ISBN 0-89043-014-4

 10. Amygdalin - TradMPD

 11. FAO Meeting Report No. PL/1965/10/2;
    WHO/Food Add/28.65;
    Evaluation of the hazards to Consumers resulting from the use of
    Fumigants in the protection of foods

 12. Cipollone R, Ascenzi P, Tomao P, Imperi F, Visca P (2008). "Enzymatic detoxification of cyanide: clues from Pseudomonas aeruginosa Rhodanese". J. Mol. Microbiol. Biotechnol. 15 (2-3): 199–211.

 13. S Krashen. Are Apricot Kernels Toxic?. The Internet Journal of Health. 2008 Volume 9 Number 2.


What is this spider, and what is this object that emerged from its rear end? I was observing this spider (caught in a Petri dish) under my microscope, when I noticed that a small, round object emerged from its rear end. It appeared to be black and white in appearance. I am guessing that it is an egg, but I am not sure whether it is one or not. The diameter of the object is approximately 300µm.

The spider seems to resemble Hasarius adansoni from photos:

The scale bars in the image are 5mm in length. The spider and the object are imaged together in the frame for scale.

Can anyone conclusively identify the spider and the object? The photo was taken in Singapore in November (although the seasons don't really matter in Singapore).

I do not know what species of spider this is, but I think the white ball is actually spider poop.  Unfortunately a quick search did not return many references, but here is a picture for comparison.

Spiders produce uric acid, which is a near-solid and excreted out white.  This is done to minimize water loss. These malpighian tubules drain into an pouch attached to the digestive tract, or stercoral pocket.  The uric acid waste from the is combined and eliminated together with solid waste from the digestive tract.  In your spiders case, this would be undigested insect parts (black) mixed with the uric acid (white).


Diploid cells and number of chromosomes I'm struggling to get a hang on this. I'm getting confused by this sentence from one of my tests:

Each human diploid cell has two sex chromosomes and _____ autosomes.

I'm guessing they're meaning 46, but can someone tell me this in another way? Like in a really easy way, so that I can understand it?

By definition, an autosome is a chromosome that is not a sex chromosome. Therefore, as a human diploid cell has a total of 46 chromosomes, including two sex chromosomes, I guess the answer to your question should be 44. I hope it's clear enough for you. :)


Oral Administration of Immunizations Small children and people in developing countries may take oral dosage forms of vaccines. Antigens passing through the GI tract will come into contact with Peyer's patches and be absorbed by microfold cells into lymphoid tissue, evoking an immune response.

Some of these vaccines are attenuated and can colonize in the small intestine, mimicking a natural infection. I am wondering why vomiting and diarrhea, which are common symptoms in many natural infections, aren't more prevalent.

To be even more specific: Serotonin is released in response to a cytokine release by immune cells. Serotonin activates 5-HT3 receptor to induce vomiting. Why is this response not provoked by an attenuated infection, which mimics an actual infection.

First, ongoing inflammatory process/immune reaction in the gastrointestinal tract is not necessary associated with vomiting or diarrhoea. As an example we can consider infection with Helicobacter Pyroli, which may last for many years unnoticed.

Second, exposition to foreign antigens obtained form food or microflora and subsequent antigen presentation to the immune cells (which is indeed partially driven by locally released cytokines) occur in the GI tract all the time and again, is not usually manifested by vomiting or diarrhoea.

But moving to vaccines, attenuated oral vaccines (like Polio Sabin or Rotavirus) are developed in order to diminish the risk of pathological symptoms. Attenuation weaks the pathogen that is usually no longer able to proliferate and invade, but still poses antigens that may be presented to the immune cells and induce long-term immunological memory. Moreover, immune response (antigen presentation, production of the local IgA, B-cells affinity maturation) triggered by attenuated vaccines is the closest to the one induced by full infection (in comparison to inactivated/toxoid vaccines), but significantly weaker and localised. This we mean by "mimicking a natural infection".

Also, see: https://www.sciencedirect.com/science/article/pii/S0042682215001725


Yeast absorption of different spectra of light I'd like to monitor the growth of a yeast population by shining light through it and monitoring the change in light that gets through as it grows. I'm not sure if I should use IR, or any particular colour of light.

Are there any charts that show the light absorption of brewers yeast to different spectra of light?

Most of the loss of light being transmitted through individual cells is not absorbed, rather it is scattered (redirected from its original direction to a new one without loss of energy).  There is actually not very much in cells that can absorb visible light, and virtually nothing at all that can absorb many red or near-infrared wavelengths.

Scattering does depend on wavelength, but the relationship is very complex.  For scattering from small cellular components (mitochondria for example), Rayleigh scattering dominates, which will decrease with the 4th power of wavelength, so that green light will scatter much more strongly than red.  For larger components that are comparable or larger than a wavelength (nuclei or whole cells), scattering will increase much more slowly.  The relationship between the direction of scattering and the size/wavelength is even more complex, but is very useful in applications like label-free cytometry where cells can be sorted based on scattered light.

600-800 nm light is a reasonable choice because it will not damage the cells unless the power level is very high, although using shorter wavelengths may give you more sensitive measurements.


Insects emerging from vertical tube I found a vertical mud tube about the thickness of a pencil in my garden with a series of metallic green insects coming out of it. They came out when I pulled a weed but stopped when I stopped, as if the vibrations were scaring them out. I think they were bees, wasps, or flies. They were 1/2" long or a little longer and thin. Head, thorax, and abdomen were all shiny green, wings transparent. What are they?

I live near Philadelphia and it was in the upper 60s F today.

Mud tube, metallic green, bee-like - sounds like a mason bee to me.

There are several metallic green mason bees (Osmia spp.). As Wikipedia explains:

  Mason bees are named for their habit of using mud or other “masonry”
  products in constructing their nests, which are made in naturally
  occurring gaps such as between cracks in stones or other small dark
  cavities; when available some species preferentially use hollow stems
  or holes in wood made by wood-boring insects.

One example here:

Photos at http://www.laspilitas.com/insects/megachilidae/osmia-mason-bee.html


Can an argument be made that humans are 90% bacterial? On the blog, All about Scientist in Microword: Microbiology, I read the post We are 90% bacteria, actually, which says that humans are 90% bacterial cells.

If this is the case, then why don't we behave like them and why isn't the bacteria genetic material more dominant?

As bacteria helps us in making many enzymes for us, can we say that we are symbiotic creatures?

I am not sure what you read as you have not supplied any references, but humans are not 90% bacterial cells. (OP subsequently provided; see Edit 2)

Humans are 100% human cells, however for every one human cell, approximately 10 single celled organisms (Bacteria or Fungi) live in (colloquially) or on the human body. This is referred to as the microbiome. You can find more information in the link I provided or in the answers to the following questions on Biology SE.

Do intestinal flora have the same DNA as their host?
How many diseases can be linked to disruption in the microbiome of a human?
What is the function of E-coli bacteria in our stomach?
How heavy are all foreign microorganisms in and on the human body?

Think of it this way; just because the human body provides these organisms with a home does not mean that it is composed of them, that would be like saying an apartment building is made up of x percent of humans or pets or mice or insects just because that is where they live.

You may also find some interesting information at The Secret World Inside You from the American Museum of Natural History.

Edit

  As bacteria helps us in making many enzymes for us, can we say that we are symbiotic creatures?

The definition of symbiosis is:

  The interaction between two different organisms living in close physical association, typically to the advantage of both.

Given that definition, and given the fact that there are some bacteria in our microbiome that are able to produce metabolites that our cells cannot, and we provide them with a "home" with the necessary nutrients for their propagation, then you can say that this is in fact a symbiotic relationship.

The more technical description that is often used for the microbiome is that these organisms that populate the human body are commensal.

Commensalism is defined as:

  An association between two organisms in which one benefits and the other derives neither benefit nor harm.

In this respect, the majority of our microbiome are commensals, they live on us, but give us nothing in return, and for the most part do us no harm.

Some of the organisms can be opportunistic pathogens in the sense that if they are able to gain access to normally sterile areas of our body, such as in peritonitis arising when the intestines are perforated, then they can be harmful, but in their general niche, they are just there.

As we learn more about the microbiome, we are beginning to see that there is a far more complex relationship between host and microbe than we anticipated, so over time, the views on the microbiome are likely to change from the understanding that we have today.

Edit 2

To address the source that you added All about Scientist in Microword: Microbiology, I would say that the blogger is guilty of hyperbole. While Steven Gill, the molecular biologist that the blogger quoted, may not have chosen his words carefully, he was not implying that humans are 90% bacteria, as the blogger then posits.

Gill makes the mistake of using the word "in" when he states "There are some estimates that say 90% of the cells in our body are actually bacteria...." The microbiome exists on the surfaces of our body not in it.

We forget that the gastrointestinal tract, urogenital tract, and respiratory tract are lined with epithelial cells and are thus external surfaces, just as our skin is an external surface. So the microbiome lives on our body, and not in it or as a part of it.

No place in our body do we have organs or tissue that is a homogenate of human cells and bacterial cells functioning together normally. And while there are bacteria that are able to infiltrate cells and live within vesicles or the cytoplasm, this is a pathogenic condition and not what we would normally expect to see in a healthy human.

We know that this is the case, because developmentally all of our body cells and germ cells arise for the fertilized egg. It isn't until much later in development or at the moment of birth (there are some reports that microbiome begins to cross the placenta prior to birth) that we acquire our microbiome. If it were the case that humans, or any eukaryotic organism for that matter, were 90% bacteria, then we would not develop in the sterile environment of the amniotic sac. The lack of bacteria during development would be fatal.


What would cause crows to be attracted to a human body? On another SE site, there was a comment that told me something  about biology that I already know:

"A man left murdered in the fields would soon have a flock of crows mobbing his fragrant corpse."

But I don't quite understand why. Is it the "death" part,the fact that someone was injured/bleeding or just the fact the he was immobilized,that would attract the crows?

That is suppose you tied up someone and left him on the field. Would that attract the crows?
Suppose this person fell down, was bleeding, and immobile, but not seriously injured? Or is it the death part?

I think the key is "his fragrant corpse." When an animal dies and begins to rot, a number of quite smelly chemicals are given off, including putrescine and cadaverine. Crows and other carrion birds like vultures are probably very sensitive to these compounds, rather like sharks are to the smell of blood.


meaning of abbreviations h and m in Na channels In a voltage-gated sodium channel, there are two gates, one for activation and one for inactivation. They are also known as h- and m- gate. What are these letters standing for?

Those initials were proposed by Hodgkin and Huxley in their original paper modeling the action potential in nerve cells: https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model

They are not names for subunits, domains or motifs in the sodium channel, as your question may imply. Instead,

  n, m, and h are dimensionless quantities between 0 and 1 that are associated with potassium channel activation, sodium channel activation, and sodium channel inactivation, respectively.

However, there is no indication of what those initials mean (if anything), apparently being just letters they chose to name the variables in their equations.


Do lysogenic viruses only infect bacteria? In the video sent by my teacher on viruses, the example he used for lysogenic viruses was a bacteriophage infecting a bacteria. When he was describing how the genetic material was incorporated into the host cell's genetic material, he said something along the lines of:

  Now the genetic material is incorporated into the cell's chromosome.

My question is, did he describe it as one main chromosome because that was the example being used? Or do lysogenic viruses only infect bacteria?

I guess a better way of phrasing this would be, are bacteriophages the only type of lysogenic viruses?

Thanks!

evamvid

Bacteriophages are the only viruses where this phenomenon is called lytic and lysogenic cycle. There is a similiar phenomenon in humans (and other mammals as well) which is called "endogenous retrovirus" and is pretty common.
For humans, there are estimations that something between 5 and 8% of the human genome are made of endogeneous retroviruses. See these two references:

Long-term reinfection of the human genome by endogenous retroviruses.
Endogenous Retroviruses and Human Evolution

Otherwise I can recommend reading the article on "Endogeneous retroviruses" in the Wikipedia, it is pretty extensive and has a lot of references.


Function of human kidneys Why are the kidneys called metanephric? What does the term metanephric actually mean? I tried to search that on Google but couldn't find the exact meaning.

There are metanephric diseases, which refer to the location of pathologic tissue relative to the main kidney mass, but unless someone with more expertise wants to weigh in, I don't think that kidneys themselves are called metanephric.

There is also a developmental stage of the kidneys, in which they are referred to as metanephros. Perhaps you're thinking of that?


Are serotonin levels in humans affected by light? I'm reading this Wikipedia article on light therapy  and noticed a peculiar statement:

  The production of the hormone melatonin, a sleep regulator, is
  inhibited by light and permitted by darkness as registered by
  photosensitive ganglion cells in the retina. To some degree, the
  reverse is true for serotonin, which has been linked to mood
  disorders.

If I read this correctly, when melatonin is suppressed, serotonin is released? This makes some sense. I'm interested if there is any scientific backing to serotonin being affected by light levels.

I'm not sure about humans, but this is true of many vertebrate's retinas. There is experimental evidence showing light-inhibited production of serotonin. This article reviews how serotonin is regulated in response to day lenght (as well as fasting/feeding cycles). The authors suggest a mechanism in which serotonin and ghrelin integrate signals from fasting/feeding and night/day together.

Nowak JZ, Z Urawska E, Zawilska J. Melatonin and its generating system in vertebrate retina: circadian rhythm, effect of environmental lighting and interaction with dopamine. Neurochem Int. 1989;14(4):397-406.
Kirsz K, Zieba DA. A review on the effect of the photoperiod and melatonin on interactions between ghrelin and serotonin. Gen Comp Endocrinol. 2012 Nov 1;179(2):248-53. doi: 10.1016/j.ygcen.2012.08.025. Epub 2012 Sep 5.


Quantifying DNA in a band on gel electrophoresis I am a first year science undergraduate and I am just asking this as a more theoretical question rather than for carrying out a protocol, so I would appreciate if answers do not involve lots of complicated chemical names.

I was wondering how one would go about quantifying the amount of DNA in a given band on a gel electrophoresis. Some ideas I have had so far are:

Cut out the DNA band and extract the DNA. Quantify using some known method such as measuring the absorbance at 260nm of the DNA in solution to find the concentration.
When the DNA is stained with ethidium bromide, clearly there will generally be more stain uptaken in a band region if it has more DNA so it will fluoresce with greater intensity when illuminated with UV light. However I would have reservations to using this method because I would think that the amount of stain uptaken would depend also on the state of the DNA (i.e. if it is supercoiled or not), but then again I do not know how much of an impact this could have on how much stain is uptaken. Of course, if you know that all of your DNA is in the same state then there shouldn't be a problem with this method I think. Although here you would have to be aware that the concentration of ethidium bromide in a certain band depends on the concentration of nucleotides there, which depends both on the number of the DNA fragments and their size (which is known from the position of the band). Compare this with the final method...
Finally, if one is making the DNA for example using dideoxy chain termination/Sanger sequencing in PCR, then you can use a radioactively labelled primer. The intensity of the image on the radioautograph would then directly tell you the number of molceules of that DNA fragment present in the band.

I was wondering which of these are viable options to use in the lab, and why/why not.

All three methods could be used to measure the amount of DNA. However in practice, method 2 (estimation by dye brightness) typically works best in a normal workflow. It really depends on what you plan to do as your downstream application.

Problems with method 1:

Yield from gel purification methods is sometimes finicky and prone to loss.
Absorbance of remaining agarose can influence the results. DNA cleanup is a must.

Problems with method 2:

Quantification is difficult as you must estimate the band brightness against a known standard (add a known quantity of your ladder and use that for estimation).
Supercoiling of plasmids causes multiple bands to appear, so the estimation must be performed multiple times and then added (now it's less of an estimation and more a guess)

Problems with method 3:

Working with radioactivity adds a significant amount of safety protocols into a simple procedure
All products from radiolabeling must also be handled as radioactive material
Using an image has the same issue as method 2 where you're estimating instead of actually quantifying.
You could get more quantitative results from a scintillation counter, but then the products become more difficult to use because of purification from the scintillation fluid (maybe this is possible but I never tried it).
You're limited to procedures which would incorporate the radiolabeled nucleotides
If you do something like dA-tailing, then you're not quantifying the amount of DNA, but the amount of copies of a transcript.


Can oncogenesis happen without apoptosis pathway being affected? Has there ever been incidences of one or more cancerous cells having all it's cell-death pathways and apoptosis mechanisms intact and functional?

Usually the cell death mechanisms are overridden and therefore oncogenesis. The pathway components themselves are not mutated. One classical case I can cite is that of Ras-oncogene. See this article for details. Usually the survival/growth signals (MAP-kinase) are activated with simultaneous inactivation of apoptotic regulators (Akt-pathway). A mutation of MAP-kinase component ERK can also cause cancer but apoptosis is nonetheless supressed because of the interconnections of these tow pathways in the gene regulatory network.

Whereas in the case of tumor suppressors, the cause of cancer is genomic instability and failure to initiate apoptosis.


Is it necessary to calculate lane normalisation factor when doing western blot data analysis? I have recently done my first western blot and I am doing data analysis to quantify my blot. I have labelled my membrane against inactive GSK3 and active GSK3 which are phosphoproteins so I am using total GSK3 as an internal loading control. I have read some guides and handbooks  about western blot data analysis and I have seen that some of them calculate a lane normalisation factor to account for variations in signal intensities of the loading control. For all loading control bands in each lane, they divide by the loading control band with highest intensity to get the lane normalisation factor. Then for each band of the target protein of interest they divide by the lane normalisation factor to get the normalised intensity.
I was wondering in general with western blots is it good practice to calculate the lane normalisation factor when doing the data analysis? Any insights are appreciated.

Generally speaking, the proper way to quantify a western blot is to normalize to a loading control such as Actin or GAPDH. In this case it would be (pGSK3/Actin)/(GSK3/Actin) as total GSK3 is not a loading control. A loading control is to protein that is accepted as unvarying in concentration across multiple samples if the same protein amoun is used, and to my knowledge GSK3 would show more biological variability than accepted loading controls. This would be considered the best practice to compare protein concentrations across samples.
That being said, if all you care about is the ratio of active to total, pGSK3/Total GSK3 is probably sufficient to assess if your manipulation changed active/inactive:total ratios. For example, in autophagy assays you can measure autophagic flux by measuring LC3-I to LC3-II, and I've never seen them normalized to a loading control since its a ratiometric readout contained within a single sample.


Binocular microscope use, diaphragm? I am try to review my scope work, since my proffesor asked me to calibrate all the scopes for an intro class in biology, and it has been awhile since I used one. I googled "Binocular microscope use" and saw a powerpoint as my first link.

On page 21 it stated:

  The diaphragm should be opened just enough to allow the objective lens
  to collect all of the light that comes through the sample. Opening the
  diaphragm too wide, allows some of the light to escape collection by
  the objective lens. Closing the diaphragm too much, causes aberrations
  of the image.

But if the diaphragm controls the amount of light passed through, why is "light escaping" a bad thing? Why cant I keep the light as wide as possible?

As an aside, if anyone has any suggestions for review on binoc. compound microscope use, I would appreciate it.

The escaping light causes unnecessary illumination, thus reducing the contrast.
This webpage has a couple of photos that demonstrate different microscope setups.


Biosphere that simulates sun and moon shifts Is there an enclosed biosphere that artificially simulates the movement of the sun and moon at increased intervals?

It is known that the sun and moon alter plant movements therefore I was wondering how far experimentation has gone.  Ideally I am wondering if they have experimented with different speeds of the moon and sun rotation and how it effects plant(and possibly other animal behavior ideas) growth.

Sun and moon-faking devices exist. Not sure about 'biosphere'. I have personally observed one for honeybees, but that one was fairly crude(bees are dumb). It was just a big room with a hive stand in the middle and a series of fluorescent lights on the ceiling that turned on one after the other. The goal was to mess with bee circadian rhythms and see which genes became more or less expressed in their brains.

There's a slightly more sophisticated thing called a 'grow cabinet'. It has expensive lights to produce sun-spectrum light at direct sunlight intensity and humidity and temperature controls. Scientists use them for crop research when the weather is too random and unpredictable and absolute control is required.

I believe advanced versions simulate moonlight and angle of insolation, but that sort of thing is expensive.

I don't know of any full-sized biodomes with fake celestial objects. The cost of such a biodome would be prohibitive, and the experiments it enabled might be easier(certainly cheaper) to do in a smaller container.


How do I measure bacterial growth in agar dishes (either by cell mass or by cell count)? I am doing an experiment in which I am growing S. mutans in agar dishes, and I am not sure how I would measure the growth of the S. mutans. I am also not sure if I would do this by measuring cell mass or by cell count. Any ideas?

The most simple way is seeding the plates with a suspension of bacteria ensuring that you spread the solution properly. Then you can count the number of colonies, wich would be equal to the number of single cells.

If you want to mesure the growth speed, usually it's simpler to just measure the diameter of the colonies, always ensuring you inoculate the plates with the same amount of inoculum.

Lastly, it's even easier to estimate the growth if your culture is un liquid media and you measure the optic density with an spectophotometer.


What is an "end-to-end fusion" in the context of telomerase? Telomerase is said to prevent "end-to-end fusion" of chromosomes.

My question is threefold:

What is an "end-to-end fusion"?
How does Telomerase prevent end-to-end fusions?
Why do end-to-end fusions cause problems in cells?

An end-to-end fusion is the result of two chromosome ends fused together. This happens when telomeres (repeated sequences at the ends of chromosomes) lose their protective telomere-binding proteins. In mammalian cells, loss of TRF2 (telomere repeat-binding factor 2) leads to chromosome fusions.

Here is an example of how it looks with metaphasic chromosomes (the DNA is stained in blue and the telomeres are stained in pink; picture from Rai et al, 2016). The left panel shows normal chromosomes, the right panel shows end fusions upon depletion of TRF2.

What causes chromosome fusions in such situations is the DNA double-strand break (DSB) repair machinery, which is normally repressed by telomere proteins (mainly by TRF2; see van Steensel et al, 1998). In mammalian cells, telomere-binding proteins are collectively called the shelterin complex (they literally shelter chromosome ends; see de Lange, 2005).

Telomerase doesn't repress the DSB repair machinery directly. Because of the structure of telomeres (a single-stranded 3' overhang) and of the way replication is primed, linear chromosomes cannot be fully replicated and will gradually shorten at each replication. When telomeres become critically short, they don't recruit enough telomere-binding proteins and therefore fail to repress the DSB repair machinery. Telomerase, when expressed and activated, maintains the length of telomeres in replicating cells at each replication (by adding repeated sequences complementary of the RNA template that is a component of the telomerase holoenzyme), providing binding sites for telomere-binding proteins, and thus indirectly contributes to the repression of the DSB repair machinery.

End-to-end fusions cause problems in cells in part because fused chromosomes will likely not segregate properly during mitosis and meiosis. The resulting daughter cells end up with altered ploidies that can be severe enough to prevent cell viability.

de Lange T (2005) Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev. 19: 2100–2110 https://doi.org/10.1101/gad.1346005

Rai R, Chen Y, Lei M & Chang S (2016) TRF2-RAP1 is required to protect telomeres from engaging in homologous recombination-mediated deletions and fusions. Nat Commun 7: 10881 https://doi.org/10.1038/ncomms10881

van Steensel B, Smogorzewska A & de Lange T (1998) TRF2 protects human telomeres from end-to-end fusions. Cell 92: 401–413 https://doi.org/10.1016/S0092-8674(00)80932-0


How does Line Integrate work on a laser scanning confocal microscope? Most microscope software provides options for line average or line integrate as a function that helps the signal to noise ratio when taking an image. The math behind line average seems straight forward, but not so much for line integrate.

Line average takes X number of scans per pixel and averages the scans into a final pixel intensity. The same principal of multiple scans for a single pixel is taken for line integrate, but the math involved in the integration of the intensity is not clear to me. I assume it involves summing pixel intensity and operating on that somehow, but it simultaneously is able to reduce noise in the system so I am not sure what else it is doing.

Most microscope software provides options for line average or line integrate as a function that helps the signal to noise ratio when taking an image.

Averaging sums the lines and then divides by the average number. Integration sums the lines without dividing.  They're functionally the same thing just with different scales.

  I assume it involves summing pixel intensity and operating on that somehow, but it simultaneously is able to reduce noise in the system so I am not sure what else it is doing.

In terms of shot noise, both have an equal reduction.  If you are averaging over extremely dim signals at low gain (particularly those averaging less than 1 DN per pixel), integration can save you signal from being rounded down to zero.


Do antagonist-receptor complexes get absorbed into the cell? My understanding is that normally, a neurotransmitter binds to a receptor and then that ligand-receptor complex gets absorbed into the cell and either degraded or recycled. So does the same thing happen when the ligand is not the endogenous neurotransmitter, but instead an "artificial" antagonist -- like, say, bupropion bound to a nicotinic receptor?

When a neurotransmitter, like serotonin, binds to it's specific receptor, the ligand-receptor complex is not phagocytosed.  Picture the human cell membrane and think of the serotonin receptor like a long piece of rope that has been wound up, but is embedded inside the cell membrane forever.  After the serotonin binds, the structure of the receptor changes, causing lots of steps to start (like a domino effect) where molecules are released from the inner aspect of the receptor, thus carrying the message into the nucleus.


Are there any mammals in which polyspermy produces viable zygotes? Are there any mammals in which polyspermy produces viable zygotes? In the wikipedia page it is mentioned that there is a delicate equilibrium between female defenses against many sperms, which ocassionally results in low fertility rates (which in not all cases might be an evolutionary disadvantage, but i disgress)

My question is if there are cases where a ovum can be fertilized by several sperms, and the zygote somehow manages to select fairly between a subset of all chromosomes, avoiding polyploidy and producing a viable embryo.

The short answer appears to be "no".

The longer answer seems to be dependent on what you mean by "viable". Triploid humans do exist that apparently arise from dispermy, but most such fetuses die shortly after birth. Those that do not die soon after birth have a variety of health issues such as intellectual disability; "The few [triploid] infants that do survive to term have multiple severe birth defects." They're almost certainly sterile, though that source doesn't say anything about it.

The existence of elaborate physiological mechanisms for blocking polyspermy in sexual organisms generally, and further mechanical means for limiting sperm number in mammals, argue that polyspermy is something that we spend a lot of effort because it's bad. Here is a recent review of polyspermy in mammals; it has a lot more information about both mechanisms and statistics on the outcomes of dispermy.


Range map atlas for insects? I often use BONAP's North American Plant Atlas, for researching plant taxa ranges.

  BONAP maintains relatively complete phytogeographic and related botanical databases for all free-living vascular plants found in North America (north of Mexico). For over four decades, we have worked collaboratively with many federal and state government agencies, private groups and individuals across the continent to produce and edit our databases

It generates incredibly useful range maps, and I can search by higher taxa (i.e., genus) to investigate many species based on their ranges at once. For example, Fagus:

However, I have so far been unable to find a similar online atlas (or any range-map query tool) for insects.

Does anyone know of any similar range-map resources for insects?

I'm most interested in maps for the US, but global maps would be incredibly awesome :)

I think the Global Biodiversity Information Facility (GBIF) may be what you are looking for https://www.gbif.org. It is not limited to plants and insects.


Which proteins are part of the most different protein complexes? Let n be the number of different protein complexes (as defined here) that a protein may be a stable part of for a considerable amount of time (and not only transiently). Which proteins have the largest n?

An answer should include the number of different protein complexes  the protein is part of.

Or where should I start doing my own research? I have no clue.

This answer does not address the number of complexes that a protein participates in, but rather a related question -- With how many proteins does a protein interact?
I acknowledge this  is a fundamentally different question, though I think it's a good starting point on which other people can build a better answer.

Taking the data from STRING v11 for all protein-protein interactions (PPIs) in Escherichia coli str. K-12 substr. MG1655, we can subset these PPIs to include only those of action type "binding".  This database provides PPI scores between 0 and 1 based upon experiments (co-purification, co-crystallization, Y2H), textmining, co-occurence, co-expression, and co-localization of coding genes across genomes.
If we set no cutoff for the confidence in these binding interactions, we see that 2585 proteins have ≥1 binding partner, and one protein has an astonishing 273 binding partners (pfo, a putative pyruvate-flavodoxin oxidoreductase).  Also, this database states this E. coli strain has 4127 distinct protein-coding genes, so approximately 63% (2585/4127) of genes encode a protein that interacts with at least one other distinct protein.
If we limit the interactions to those with a "high confidence" score (≥0.900), only 656 proteins (~16%) are seen to have ≥1 binding partner, with a maximum of 55 binding partners seen for 4 proteins.  Unsurprisingly, and consistent with the comment from Maximilian Press, these proteins are all associated with the ribosome (sra, rpsP, rpsI, and rpsR).  The spike in the graph below at 54 interacting partners for the high-confidence PPIs is a group of of ribosomal proteins, most of which are annotated as co-interactors.

Two important notes on interpretation of interactions in this database:

splice variants and post-transcriptionally modified proteins are collapsed into single nodes in the interaction network, so all gene product variants are represented by one coding sequence
self-interactions (e.g. dimerization) are not counted, which are a valid type of protein complex per the question


Blood become denser when you are dying of deshidration? Blood become denser when you are dying of deshidration? I mean, when you are dying of deshidration does your body extract water from blood to survie more time?

Yes blood becomes denser on dehydration (water dilutes the blood, if there's no water in blood it becomes dense). No, body does not draw water from the blood. When you are dehydrated, blood is the first source to be depleted. Then blood pulls water from cells (there are various hormones acting on kidneys and blood vessels trying to preserve the remaining amount of water by increased reabsorption, decreased excretion and vasoconstriction to comparitively useless parts of the body) and on continued dehydration, heart is not getting enough blood to pump as liver is sacrificing all its blood to the brain and cells are being depleted of water and are dried up. So blood is dense and there is not enough amount to reach the brain and brain cells don't get enough glucose (ischemia) and build up of urea and BUN in blood on the other side. Brain Cells switch the metabolism as they try to keep the cells alive only to produce radical oxygen species as by-products which in turn destroys the cells. And hence. Death. Eventually.


Is it possible for human body to convert carbohydrates to protein? Is it possible for human body to convert carbohydrates to protein to build muscle for example?

EDIT: I read in many articles that you should eat more than 1.5 gram protein for each 1 kg weight of your body to gain muscle, but I see some bodybuilders that I know they don't eat that much of protein but gain muscle and have muscular body. So it was interesting to me to ask this question here!

Essential amino acids cannot be synthesized from carbs, but non-essential amino acids can be synthesized. Intermediates from the citric acid cycle or pyruvate can be used to synthesize at least 11 kinds of non-essential amino acids. They will be incorporated into muscle, but you need all the essential amino acids available in order to produce complete proteins that will build muscle tissue. Proteins are made from the entire repertoire of amino acids, and I don't think there exist any (perhaps very, very few, none to my knowledge, *I've checked the literature) that are made from only non-essential acids.


Are there any situations in which phenylephrine is preferred to pseudoephedrine? In the mid 2000s in the US, due to issues of drug enforcement, pseudoephedrine containing medications were brought behind the pharmacy counter and in most cases require ID, and phenylephrine was substituted in most over-the-counter products.

Pseudoephedrine increases the amount of endogenous norepinephrine, whereas phenylephrine works on α1-adrenergic receptors directly.

There are numerous cases where experts have spoken out about the effectiveness of phenylephrine, so it likely is a less effective substitute for pseudoephedrine in its main role as a decongestant.

What I'm curious about is whether there are clinical indications for which the phenylephrine is actually preferred (so situations where the α1-agonist nature without the increase of endogenous NE is sought after)?

Yes, in all clinical situations where you need pure vasoconstriction without heart rate acceleration (mostly valid for iv administration route).

The classical example would be in the operative setting. If the patient is in a hypotensive state due to hypnotic drugs, opiates, etc. and has atherosclerosis, you will prefer a drug that will reverse the hypotension without an increase in heart rate, i.e phenylephrine. The reason is that an increase in heart rate will shorten the duration of diastole, which will therefore shorten the time interval where the coronary arteries are perfused. Moreover, an increase in heart rate also means an increase in heart oxygen consumption. The end result will be an imbalance between oxygen input and requirement, i.e ischemia and potential heart infarction.

Conversely, if you have a patient with aortic valve insufficiency (regurgitation), you will prefer ephedrine (or any drug with beta 1 activity), because you will be aiming at shortening the available time for regurgitation to occur.


Author statements (Readers) in biological nomenclature I know that a binomial name may be followed by the name of the reader who has been the first to identify the species and to give it that binomial name.

It is not completely clear to me what the same of a botanist, zoologist etc. means if it is placed between parentheses, as in Blysmus compressus (L.) Panzer. Does it mean that Panzer gave that species the binomial name Blysmus compressus but it was Linnaeus that identified it as a species? I cannot find precise information on line, nor in my books...

Moreover, the pattern may get more complicated if we introduce the subspecies, for example another Cyperacea: Carex ferruginea Scop. subsp. macrostachys (Bertol.) Arcang.. It seems quite trivial to me that Scopoli (Scop.) identified and gave the species the name Carex ferruginea; as to the subspecies,  did Arcangeli (Arcang.) named it macrostachys after that Bertoloni (Bertol.) had identified it as a subspecies?

I thank any answerer very much.

As @C_Z_ mentions, the double author citation is due to a naming revision. In your case, 'Panzer' has revised the name given by 'L' (Linneus). It can for instance be due to an assignment to a new genus or a change in rank status (e.g. going from subspecies to species).

Note that author citations differ between botany and zoology, where changes in authorship are usually not recognized in zoology (as long as there is a proper and complete species description in the first place), while the botanical code allows for multiple author citations. From Wikipedia: Author citation (botany):

  ... in contrast to the situation in zoology, where no authorship change is recognized within family-group, genus-group, and species-group names, thus a change from subspecies to species, or subgenus to genus, is not associated with any change in cited authorship

So under the Zoological code, the old author name is kept when a species is reassinged to a new genus, e.g. when Seriola gracilis (Lowe, 1843) --> Cubiceps gracilis (Lowe, 1843). On the other hand, the Botanical code allows for multiple and sequential revisions, so you can have situations as "Dummy species (L.) Thom. emend. Müll.".


How much vanilla will kill a person? I received a gift that is a jug of Pure Mexican Vanilla. Having never dealt with large quantities of vanilla, it made me curious as to what would happen if a person had too much vanilla.

I understand that the alcohol has a higher toxicity rate and is probably more fatal than the actual vanilla itself, but I'm curious as to what ratio of mass of pure vanilla to mass of the human would be considered fatal.

Also, what is the physiological effect of a vanilla overdose as it pertains to inhibiting critical bodily functions? That is -- specifically what about a vanilla overdose would cause fatality?

Vanillin is the chemical that gives vanilla its flavour and smell [1].

  Vanillin is pharmacologically active, causing depressed blood pressure, increased respiratory rate & death due to cardiovascular collapse [3].

  Non-Human Toxicity Values [4]

  LD50 Rat oral 1580 mg/kg
  LD50 Rat ip 1160 mg/kg
  LD50 Rat sc 1500 mg/kg
  LD50 Mouse ip 475 mg/kg
  LD50 Guinea pig oral 1400 mg/kg
  LD50 Guinea pig ip 1190 mg/kg
  LD50 Rat oral 2.8 g/kg
  LD50 Guinea pig oral 1.40 g/kg
  LD50 Mouse ip 0.78 g/kg
  LD50 Rat sc 1.8 g/kg
  LD50 Dog iv 1.32 g/kg slow in fusion.

References:

Wikipedia contributors, "Vanillin," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Vanillin&oldid=613429267 (accessed June 26, 2014).
PATTY F. A. 1963. Industrial Hygiene and Toxicology. Volume II Toxicity, page 1696 (referenced from TOXNET, Vanillin - Human Toxicity Excerpts)
TOXNET. Vanillin