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Starch vs Cellulose. What are the differences between Alpha and Beta glucose ring structure in them?
I'm studying "Campbell Biology, 10th Edition" and in chapter 5 page 71 there's a statement I can't understand. according to book:

In starch, all the glucose monomers are in the α configuration.

and then says:

In contrast, the glucose monomers of cellulose are all in the β
  configuration, making every glucose monomer “upside down” with respect
  to its neighbors.

My question is if all glucose monomers of cellulose are all in the β
configuration (according to figures) why each monomer in cellulose is “upside down” with respect to its neighbors and is not just all the same as in glucose monomers.

The reason the monomer units are shown as alternating orientation in the cellulose case and not for starch is due to the angles required for the bonds between the atoms involved.
Note that in α-glucose the OH groups of the #1 and #4 carbons are shown on the same side of the ring.  When these two groups are changed into a single O joining two α monomers into starch, they have to remain in the same position.  When a single O joins them together, that oxygen requires the angle between the bond be less than 180 degrees, so the two glucoses have to be on one side of the oxygen.  That's fine in the drawing because in α glucose both OH groups are pointing down.
On the other hand, in β-glucose the OH groups of carbons 1 and 4 are on opposite sides of the glucose ring. Joining two β monomers to make cellulose requires that these two OH groups point in the same direction so that when changed into bonds to the single O, the angle which the oxygen requires can be provided.  To get the two OH groups pointing the same way requires one of the two β-glucoses to flip relative to the other.  Hence you get the monomers of cellulose alternating in orientation.
Part of the problem may be trying to visualize these 3-D relationships from the 2-D diagrams.  On this α-/β- glucose webpage there are some rotatable images of the molecules which may help visualize the relationships.

I'm having trouble understanding the last part of your question: "why each monomer in cellulose is “upside down” with respect to its neighbors and is not just all the same as in glucose monomers."
I assume you want to know more about the beta configuration of cellulose. Cellulose is made of monomers of glucose linked together via B 1-4 glycosidic linkages. In contrast, "starch" more specifically amylose is made of monomers of glucose linked together via A 1-4 glycosidic linkages. Our bodies have glycosidases that can break down the alpha linkage but not the beta linkage.
This is the first time that I have seen cellulose polymers drawn that way. I am more accustomed to them being drawn like this: http://chemwiki.ucdavis.edu/Core/Biological_Chemistry/Carbohydrates/Polysaccharides/Cellulose


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what is the function of satellite in a chromosome?
What is the specific function of a satellite in a chromosome ? How are sat-chromosomes different from others ? On molecular basis, what are the functional advantages of it ?

There are at least 2 SAT chromosomes in each diploid nucleus. They
  play a vital role in the formation of the nucleolus after cell
  division is completed.
In humans, chromosomes number 13, 14, 15, 21 and 22 are examples of
  SAT chromosomes.

cuted from http://en.wikipedia.org/wiki/Satellite_chromosome

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

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

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

Deleterious side effects of pregnancy:

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

Other special cases:

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

An abnormal placenta position can lead to increased risk of heavy bleeding during placental delivery which further complicates the process by needing blood transfusion drugs. Anterior placental attachment is associated with increased risk of pregnancy induced hypertension , gestational diabetes mellitus due to dysfunction of lactogen hormone secreted by placenta, placental abruption, intra uterine retarded growth or fetal death.Rh factor incompatibility is a complication during the second delivery. Also, placenta encapsulation(conversion of placenta into capsules) has side effects on mother's health like pelvic girdle pain, constipation or diarrhea , PMS like emotional outbursts.
Placenta is an intimate connection between the fetus and mother but locational abnormalities can make placenta hostile to both fetus and mother. Also, the Rh factor incompatibility stays a major factor in being harmful.

Can you add some references to you answer?

This answer is unstructured, confused, and partially incorrect, and reveals a lack of understanding of the subject. The answerer has good points but mixes things up.

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Is it true that viruses cannot be seen with phase-contrast microscopy?
There appears to be a lot of material on the internet claiming that viruses can be only seen with electron microscopes, and not with light microscopes. To the contrary, for example this old paper published in Nature states that viruses can be seen using phase-contrast (light) microscopy. Who's correct? What is the smallest thing I can see using a phase-contrast microscope?

It is true for most viruses. They have a size of roughly 1/100 of bacteria (or smaller), so they are too small to be seen in light microscopy. According to Wikipedia the maximum limit with light microscopy is around 1500x magnification (or making structures, which are at least around 200nm in size visible).
A lot of viruses are smaller, for example the influenza A virus is around 80-120nm, the HIV virus around 120nm and the rhinovirus which causes the common cold around 30nm. They would only be visible in electon microscopy. The measles virus on the other hand has between 350 and 400nm and should be visible in light microscopy. However, since you are very close to the region where you reach the diffraction limit for visible light, it is usually not used very much.

What does diffraction limit has to do with with this thing?

It is true generally but it's not an absolutely truth.
There is a group of giant viruses which can be seen under the traditional light microscope - such as the pandoravirous - which its size is about 1000 nano-meters.
Sources:

An academical lecture of virologist (see here: 39:33, but I recommend you to start from 35:35) that answers directly your answer.
Live science-Largest Viruses Ever Revealed

Viruses are usually too small to be seen at the light microscope level. However: large virus conglomerates within cells can be seen under a light microscope. In that case they're called "inclusion bodies". These have diagnostic value. For example in the case of rabies, were those so-called "Negri-bodies" provide the beyond-any-doubt post mortem diagnosis of rabies.


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Vitamins located closely under the peel?
I came across an old saying (I would even call it a myth) that vitamins are concentrated under (or close under) the peel of apples or potatoes and
other fruit. This implies that they are more healthier when not pealed. My question is: Is this true? And does it make sense to concentrate important
substances there, where they might get lost when the peel is damaged?

There are some vitamins in the peel of some fruits/vegetables. The color of many fruits and vegetables is the result of high carotene concentration in the peel. $\beta$-carotene is converted by the human body into retinal, which is a form of vitamin A [1].
Another example is vitamin C. Guava and citrus category fruits contain high amounts of ascorbic acid in their peel and orange's peel contains greater amounts of vitamin C than its juice [2].
There are also other compounds in fruits peel like B vitamins and minerals [2].

This implies that they are more healthier when not pealed.

In most situations, yes. The peel can absorb insecticide sprays and can also contain high amounts of fibers which can cause indigestion [2]. The peel can contain allergens [3].

And does it make sense to concentrate important substances there, where they might get lost when the peel is damaged?

Yes. For example carotene plays a role in photosynthesis [1]. Fibers improve mechanical properties of the peel, thus protecting the fruit.

References:

Wikipedia contributors, "Carotene," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Carotene&oldid=625015773 (accessed September 14, 2014).
Umesh Rudrappa, www.nutrition-and-you.com. Fruit peel nutrition facts
Wikipedia contributors, "Peel (fruit)," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Peel_(fruit)&oldid=624708837 (accessed September 14, 2014).


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Can butterflies still fly after their wings are touched?
When I was a kid, I was told not to ever touch a butterflies wing, as it would lose its ability to fly. This was because of some dust which was supposed to be in place on the wings and when disturbed it had the described consequences. I doubt at least the story about the dust, which sounds a bit too much like "fairy dust", but am I right?
What damage will be done by touching a butterfly?

So basically the question could be rephrased as: Can butterflies still flight after being touched by humans? What kind of damages do human fingers usually cause to butterflies? Is it correct?

Yes, this would be a shorter version of my question. And probably more precise :-)

I've heard the same about moths which seem to be more "dusty"

Both the Forewing as well as the Hindwing of Butterflies are made of thin chitin structures which are pretty thin and sensitive. If you touch the wing with to much force, it may break.
Then the upper side of the butterfly wing is covered with small scales - what you called the "dust". This can be seen in this figure (from here):

and also in this electron microscopy image (from the Wikipedia):

The scales have a number of functions, they are responsible for the butterflies color and pattern (which are important for finding mating partners as well as for camouflage) and they also seem to play a role in insulation and thermo regulation (see here for more details).
The scales play also a role in making the wings stronger and help improving the flight characteristics. When flying upwards the get pressed to the wing and act aerodynamically, what the wings are in downward motion, they help stabilizing the flight. See here for more details: "Butterfly wing scales : pigmentation and structural properties".
Some of the scales get lost during flying and collecting nectar, so taken together, loss of a big number of them will influence the flight characteristics of a butterfly. However, I think it is much more likely that such a rude treatment will damage the wings, which is obviously more harmful. So light touches will not do harm, more severe will.

I happened to be watching a nat geo documentary last night about butterflies, and it claimed several times that the activity of the scales also helped to provide feedback to the animal while in flight.

Can they still fly beautifully if one of their wings is half cut?

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What is this woodlouse doing?
I picked an apple from the ground, it was wet with dew and a woodlouse was stuck to it, with its back against the apple. When it got loose, it started flexing its "tail" like this for a while. Why?

That's a really nice little video.

It was moistening its respiratory and osmoregulatory organs:
Woodlice as all other terrestrial arthropods face the major challenge of preserving water balance. In their case the two systems that immediately suffer from desiccation are osmoregulation itself and respiration. In woodlice these two functions are carried out mostly by the pleopods: modified leaf-like appendages on the ventral side of the hind body part ("tail") (see here and here some annotated photos and drawings of ventral side of woodlice).
To maintain these structures in moist state woodlice have a number of adaptations, one of them being the ability to "pick up water from external sources via uropodal dipping, with the water moving upwards by capillarity" (see here). Uropods are the tiny rod-like appendages on the tip of the "tail", and dipping of the uropods is exactly what you were observing.


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Is this ladybird larva secreting a protective fluid?
I know that adult ladybird beetles can secrete a fluid to keep predators from eating them. Can the larvae do that too? Or are these yellow droplets something else?

Welcome to Biology Beta!!!

In larvae stage Ladybird beetles secretes yellow gooey alkaloids from its abdomen.
Ladybird beetles oozes hemolymph(in other word its blood), which is toxic and very smelly, when threatened. It's a mixture of various alkaloids and repulse the predators.
Good Job, There might be no picture more clearer than you provided

source:
[1]: Ladybird defence alkaloids: Structural, chemotaxonomic and biosynthetic aspects (Col.: Coccinellidae), Désiré Daloze, Jean-Claude Braekman, Jacques M. Pasteels
[2]: 10 Fascinating Facts About Ladybugs


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What are these two fruit flies doing?
When taking some pictures I accidentally captured two fruit flies doing this:

The photos are unfortunately blurry, but from what I can tell, one fly approaches the other from behind, and something is then retracted/pulled into the front fly's body. I'm guessing it has to do with reproduction, but it doesn't look like the fruit fly mating I've seen before.
Here are some stills from the sequence:

From what I can tell, the one that flies away is a male while the subject is a female correct? That also leads me to believe this has something to do with reproduction. My guess. Curious to see an answer.

I've been working on fruit flies now for 7-8 years, including a lot of large mating and courtship assays. I believe what you are seeing is the male (identifiable by the black end of the abdomen and different shape) approaching a female. Judging by the extension of the male's right wing in the second still image, he is making a brief courtship attempt, but its very difficult to be certain of that from these images. The female then extends her ovipositor.
I believe that this could be one of two things:

A mate rejection behaviour by females - she actively made the movement to stop the males advances
The female was simply preparing herself for oviposition - the male just happened to approach her

I've seen it happen enough times both with females subject to courtship and females not subject to courtship to think that either of those is plausible for what is happening in your clip. Given the possible courtship by the male and the following text & videos from a recent paper I would say it is option 1, a mate rejection.

"Recently mated females reject courting males through a variety of actions such as decamping, flicking their wings, kicking the approaching male, or extrusion of the ovipositor [8]. Thus, copulation switches female behavior from acceptance to rejection." - Kimura et al. 2015

and

"Under natural conditions, the recently mated female occasionally extends the ovipositor straight along her body axis (anterior-posterior axis) toward the courting male (Fig 1A, S1 Movie), who usually positions himself behind the female [21]. During the ovipositor extension, the female abdomen was width-compressed throughout its entire length. We refer to the ovipositor extension as mating-type extrusion when it was protruded horizontally along the female body axis. A mated female that has found a suitable site for oviposition will lower and bend her abdomen downward and insert the ovipositor into the substrate before performing movements to expel an egg that is inserted into the substrate (Fig 1B, S2 Movie) [9]. Unlike the extrusion for rejection, the female narrowed the abdomen only at its posterior part." - Kimura et al. 2015

In figures S1 and S2 you can see those two behaviours very clearly in videos.
Note, I came to my answer before finding this Kimura paper so that's two lines of independent evidence (my experience and their paper). I hope it answers your question.


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Identification of a Kakadu bird
This species of bird was spotted in Kakadu National Park, NT, Australia. It looks a bit like a lemon-bellied fly catcher, but I think my bird here is a tad bigger than the fly catcher, but I am unsure.
I was hoping one of the more ecologically proficient people here could help me out.

Note: This is the 3rd related question on this topic, so feel free to close-vote-for-whatever-reason, but I am generating a photo album with all the birds I have spotted there (heaps!), and a few of them I can't identify with the limited resources I have.

It is great bowerbird (Chlamydera nuchalis). It is much bigger than the mentioned flycatcher. I have seen both species and there is no room for confusion. Most of the pictures online are birds perched on the ground next to their "buildings", but I found a picture that should convince you.

Notice:
-Stout bill
-Patterned wing coverts
-Marks on the undertail coverts

Thanks!! Lovely :-) Could you add the link of the picture if possible? In my sources the bower bird looks brownish, whilst in my photo and your image above it looks yellowish - or is that a male/female difference perhaps?

Here is my resource - page 3, left column middle image - it looks brownish, not yellowish

@AliceD It was edited out I do not know why. (The picture is in the second page).  http://www.hbw.com/ibc/species/great-bowerbird-chlamydera-nuchalis        I think that the yellow is a picture effect, look at the color of the branch...that also look yellow.


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What causes inhalation during breathing?
I have read here that the two major inhalation muscles are the (1) diaphragm and the (2) external intercostals.
Additionally, inhalation can also be caused by (1) expansion of the abdominal cavity, or (2) movement of the pelvic floor.

I thought that inhalation was caused by muscles that essentially cause the intra-thoracic pressure to drop, thus causing air to flow into the lungs to fill the absence, like a straw. This is what I thought caused us to inhale.
MY QUESTION
If my understanding is correct, then do the muscles cause this drop in pressure? Which spaces within the trunk experience this drop in pressure? If not, how exactly do these muscles facilitate inhalation?

there are two main muscle groups. The diaphragm and the rib cage assists with breathing by using a pair of muscles located between each rib known as the internal intercostals and external intercostals. which are mostly unconcious and which change depending on hormones and air intake. The upper group is for high oxygen intake and it is very mysterious because it is a passive muscle group which allows the ribcage to become flexible and expand to a higher lung volume, try hyperventilating using only the diaphragm! The diaphragm is for rest and sleeping.

Other than the branching, gas filled spaces within the lungs themselves, there are no other spaces within the trunk and above the diaphragm that contain gas - for a normal healthy lung. All the other space is filled with either tissue or fluid that serve to extend any pressure applied by the muscles you mentioned to the pleural sac that surrounds the lungs - like a hydraulic device. It's only the gas space that expands in volume and this is what causes air to move into that space through the upper airway. Exhalation is caused by elastic recoil - the springing back of this compartment.

Either the diaphragm or the rib lifting muscles dependently or together can enlarge the lungs and cause a (partial) vacuum. The vacuum is caused by enlargement of the the chamber like for a bike pump.
The less known muscles raise and lower the ribs:

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

Here's a video of diaphragm movement:
https://www.youtube.com/watch?v=hp-gCvW8PRY

The best is to research the muscle groups on google images and check out graphs of them to see lists of studies.
The pressure drop is actually an expansion of the lung cavity, with the diaphragm being very good at drawing air in like a serynge and the expiration groups being stronger for exhaling, they can both expand, contract and compress for activities like swimming and coughing. You may want to check graphs and studies of air pressure, then it gets complicated with trans-thoracic and trans-pulmonary pressure:


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Are there differences in energy of glucose isomers?
There are many isomers of glucose, including galactose and fructose. Do they have different chemical energy levels, and why? What makes galactose and fructose useful compared to glucose, and would they be more or less energy efficient at storing energy?
Basically, can isomers have more or less chemical energy than others?

The common hexoses do not differ much in energy content (meaning Gibb's energy of formation, $\Delta_f G$). But they have different structures and chemical properties. Glucose and galactose are aldehydes when present in linear form (they are tautomers), while fructose is a ketone, which gives somewhat different properties. They are also used in different macromolecules and other metabolic products. For example, galactose is a component of hemicellulose in plants, while glucose is used for glycoproteins in humans.
Glucose has evolved to be the main blood sugar in vertebrate animals, and other sugars from the diet are quickly converted into glucose. This arrangement is useful as it provides a "common currency" of carbohydrates that can be exchanged between cells of the body, and reduces the number of enzymes needed in central metabolism. The conversion of fructose and galactose into glucose has a small biochemical cost, so in this sense, these sugars afford slightly less energy to human cells than glucose. But again this is not because of an inherent difference in energy content, but rather due to how the metabolic network is structured, with glucose as a "central", preferred metabolite.
In general, though, isomers of chemical compounds can have different energy levels, because some configuration are more energetically favorable than others. The classic example is the difference between the trioses glyceraldehyde/dihydroxyacetone and their isomer lactate, which differ enough in energy to support the synthesis of 2 ATP in lower glycolysis.


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Is there any mechanical digestion that occurs once food/chyme enters the small intestine?
Does mechanical digestion occur in small intestines and, if so, how does it occur? I found some sources that say digestion happens mechanically and chemically in the small bowel, and others that say it only happens chemically? Also, does chemical digestion only occur with acids (e.g. HCl) instead of enzymes, or does it occur with enzymes?

I believe in small intestine peristalsis is sometimes counted as mechanical digestion as the food is moved along the digestive tract. Chemical digestion occurs with enzymes secreted from the pancreas.
https://www.smartlivingnetwork.com/digestive/b/mechanical-and-chemical-digestion/ - source


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How can one measure the effect of a stem cell's matrix on the progeny of that stem cell?
A number of recent papers that have used hydrogels to alter the ECM of mesenchymal stem cells to quicken their development to cells used specifically for cartilage or really any other type of cell.
Here is an example of one of the articles
However, even after looking at the data sets from all of these experiments and research projects I still don't understand how this is done (i.e. what lab instruments, the actual procedure), for example of cartilage progenitors from stem cells.
I specifically want to know how this occurs in neuronal stem cells and how can we isolate those stem cells and test the effect of encapsulating them with a type of hydrogel to alter their fate? How could this be done?

I made some edits to your question for clarity - please check them out and alter if necessary. Thanks for your contribution!

The stem cells respond to the force they exert to the surface that they are plated on. Very soft matrices mimic the environment of the CNS resulting in neurons and hard matrices will result in cells like osteoblasts as this is more representative on the microenvironment of bone. The tensile force changes the expression patterns of the stem cells causing them to "choose" a particular fate. As for testing what is what, the way that I have seen is to do RNAseq on a sample of the cells and look at their expression patterns. Neural progenitors would be identified by expressing certain genes

Thank you, both of you. @AMR After looking into soft and hard matrices and how they actually affect a stem cell's fate, I found that it was indeed one of the ways you may motivate a stem cell to turn into a certain cell. I believe in my research I will be specifically searching for a way to chemically alter the surroundings of the stem cell to change it. But the advice about the RNAseq is great, and I will definitely be looking into that.


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In glycolysis, what is the source of the electron that makes NAD+ into NADH instead of NADH+?
I looked at the formula for the glycolysis reaction. The overall reaction seems balanced, however, I don't see anything on the left hand side of the equation that would provides the electron to convert NAD+ to NADH. Where does that electron come from?

This question would be much better if you included the reaction (then it would be considered your research) in the body of your question, the whole 'equation', including the enzyme(s). One reaction in detail would be sufficient. Otherwise, this reads like a homework question, even though it may not be.

If it were a proton transfer, it would be NADH2+ (You already had a plus charge on the NAD+ cation). What is another of a molecule picking up a hydrogen and an electron in exactly the same step?

@Hal I agree with anongoodnurse above - question as stated is vague... are you trying to balance the NAD+ and NADH?

@VanceLAlbaugh The question isn't vague, it is just that Hal is forgetting that there are ways other than proton transfer for a molecule to pick up a hydrogen.


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Why is beta actin commonly used as a control in Western blots?
It is about the western blot question. The paper:http://www.sciencedirect.com/science/article/pii/S1931312813001145.
In the western blot experiment in this paper, they use beta actin as control. And also I saw other research paper also use beta actin as control. So why is beta actin used, not other gene? is it because it expressed in all different kinds of cells?

Other genes can be and are used. Basically any gene which is expressed constitutively at high levels and is a different size than your protein of interest can be used as a loading control.

β-actin belongs to a class of genes called housekeeping genes. Their proteins typically perform functions that are required across essentially all cell types (for example, β-actin is part of the cytoskeleton's microfilaments), and are supposed * to be not affected by experimental conditions. In Western blotting, they are run as a "loading control" to show that very similar amounts of protein were loaded in each lane. This is absolutely essential in some experimental systems where it may not be possible to always collect the exact same number of cells for each sample, such as when working with primary cells, tissue samples, or systems where you may be altering protein synthesis, cell size/number, or apoptosis.
There are many different loading controls to choose from, and some may be dictated by the cell/tissue type you are examining — for example, when working with stem cells, you may want to show that your experimental conditions didn't induce differentiation in the cells, so a pluripotency marker like Oct-4A or Sox2 may be chosen. In other cases, you may be examining fractionated lysates (a membrane preparation, just the nuclei, mitochondria, only the soluble fraction, etc.) and so may choose Na/K ATPase, Histone H3, COX IV, or GAPDH, respectively.
The choice of loading control can also be influenced by the size(s) of the protein(s) you are analyzing, as investigators frequently either strip Western blots and reprobe them with the loading control, or run two different species and detect with different colored secondary antibodies when performing fluorescent Westerns. In either case, you want your loading control to be a different size than your original targets.
Finally, all of this is assuming that the researcher has already attempted to load equal amounts of total protein per lane by using any one of a variety of methods for quantitating protein concentration. These include Bradford, Lowry, and BCA type assays, which may or may not be detergent compatible, staining the membrane after transfer with dyes such as Ponceau S, SYPRO Ruby, or India ink, or staining the gel with Coomassie or other proprietary Western-compatible stains.
*In reality, some scientists are becoming more and more aware that many experiments actually do affect a number of "housekeeping" genes, but when most see variations by, for example, Western blot or qPCR, they often choose a different loading control to use.

Good answer. You might also add total protein as an option for a loading control, e.g. Comassie or Ponceau stains, or a Lowry/Bradford assay; this does not assume anything about a specific protein, but allows expressing the changes of protein X relative to total protein.

@Roland thanks for the comment. I had kind of assumed that the researcher would already have done a protein assay before loading the sample, but I can make that explicit.

I meant using total protein instead of housekeeping genes. (In my humble opinion the "housekeeping" gene concept is fundamentally flawed; typically such genes are in the end verified against total protein anyway, so why not use total protein in the first place.)

Beta-actin control provides assurance that effect you see in protein expression is not due to overall protein synthesis change.
For example, if you study some illness, it might cause change in metabolism, weight loss, loss of ability to synthesize different proteins or absorb amino acids from diet. You have to control for that, and something as universal as actin is one option.


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What is/are the molecular differences between HDL and LDL cholesterol?
Why exactly is HDL-cholesterol good for us and LDL-cholesterol bad for us. It has been well-established that LDL-cholesterol is associated with atherosclerosis and that HDL-cholesterol helps remove excess LDL-cholesterol from the circulation. From a biochemical view, however, what is the difference between the molecules that causes this difference?

First of all, we should specify that there is no such thing as "HDL-cholesterols" and "LDL-cholesterols". On the same note there is no such thing as "good cholesterol" and "bad cholesterol": cholesterol is just one molecule, with this chemical structure

What blood tests generally report is HDL-C and LDL-C, that is the amount of cholesterol in HDL or LDL respectively (again, cholesterol is always the same molecule, whether in an HDL or in an LDL).
HDL (high density lipoprotein) and LDL (low density lipoprotein) are lipoproteins, aggregates of proteins and lipids that can carry, amongst other things cholesterol.
There are 5 major types of lipoproteins, called chylomicrons, VLDL, IDL, LDL, and HDL and are distinguished by their size, density and the proteins they are composed of.
The main function of lipoproteins is that of carrying lipids (=fats) around the organism in the blood. The problem is that lipids are not soluble in water (try to pour some oil in a glass of water) and blood is mainly composed of water. Lipoproteins, on the other hand, have a hydrophilic (="water-loving") exterior and a lipophilic (="fat-loving") interior, like this:

In the picture, the "balls" represent proteins, called apoproteins, and the C represent cholesterol and T tryglicerids, which are both lipids.
As you can see, all the fats are inside the lipoprotein, but the exterior, being soluble in water can be easily dissolved in the blood.
The biochemistry of lipoproteins is quite involved and I will not go into details here (but please leave a comment if you want further explanations) but, to simplify things:

HDL bring lipids from the periphery back to the liver
LDL bring lipids from the liver to the periphery

It is very important, at this point, to note that lipids are a physiologically important part of our organisms. All the cells in our body contain lipids: the membrane of each cell in the body is made up of lipids (called phospholipids) and also contain cholesterol. In fact, cholesterol is extremely important for the correct functioning of the body as, for instance, it is used as the base to make many hormones (the so-called steroid hormones, such as estrogen, progesterone, cortisol, testosterone etc).
However, too high levels of lipids, particularly cholesterol, are not beneficial, as high cholesterol levels have been in fact linked to many cardiovascular diseases, which we hear a lot about these days.
So, because HDL tend to remove the lipids from the circulation and bring them back to the liver they can be considered as some sort of "cleaners", that remove excess cholesterol from circulation.

+1 for noting that there isn't a molecular difference.

Better answer than I could have ever hoped for!

Just to add that associations of high cholesterol with CVD are still not clearly established and probably never will be, as there is also good evidence against. This doesn't diminish that high fat diets (= probably more calories than you need) will lead to overweight with all associated risks.

@rwst: surely, I have simplified a lot the problem, I do not know the literature about CVD well enough to put appropriate refs., but if you do, please feel free to add another answer, I wasn't trying to be exaustive!!

I feel unsure about liver cells taking back LDL and/or IDL as well. In that sense LDL/IDL should be differentiated from "HDL tend"(ing) "to remove the lipids from the circulation and bring them back to the liver." If you ever get back to your answer  - I'd be interested in removal of LDL as/in the form of IDL or even VLDL by the liver.

Your question is about the molecular differences between LDL and HDL.
The  way you formulate, asking about differences on the molecular level,  draws the attention to the surprising fact that the molecular structure is not that different as the big differences in physiological function may make you assume. Your question is valid, as textbooks list different contents of cholesterol, triglycerides and proteins, but do not elaborate on differences in structure of - for instance - "molecular markers of LDL". Similar to different classes of antibodies (IgM, IgG, IgA...) there seems to be a very similar structure to all transporter lipoproteins.
Conversely, to illustrate, the word "chylomicrons" may mislead to thinking of those as "micelles" or being very distinct from those  lipoproteins termed  HDL, LDL,IDL and VLDL. However, they also belong to the class of lipoproteins the function of which is transport of lipids, and they are more similar in molecular structure as labeling suggests.
Interestingly, a similar question on Stackexchange Chemics has been refered to your question. That might illustrate the above: any relevant differences do not relate either to the load of the lipoproteins or to their differences in coating or core proteins (that exist), but any difference is in biology that,ironically, very much corresponds to "labeling": which lipoprotein in contrast to the other derives from which organ, which one addresses and unloads at which kind of target cells.
To sum up: differences are neither differences in load nor coat but are differences in send and receive signalling which are differences, as it turns out, of apolipoproteins.
Thus, the ligand on LDL to
"LDL-receptor"
is key difference "literally",
which is remarkably reflected by the fact that the LDL-ligand on LDL-molecules is the biggest protein known, called
Apo B-100.
Anwswering your question: it is expression of Apo B-100 protein, that distinguishes LDL from HDL on the molecular level in respect of pathogenicity.
Conversely, the apoA-I protein may be considered distinguishing feature of HDL (see, for instance,  quote down below, Verghese et al.)
What's more, and may come to a surprise, is the fact that there is no one and the same HDL or LDL molecule, both terms denote classes of proteins; it seems that no single "LDL-cholsterol" is like any other "LDL-cholesterol". See, for instance, Kontush et al.,2014 Structure of HDL: Particle Subclasses and Molecular Components.
Relevant feature of those proteins are their receptor ligand proteins.
LDL-receptor downregulation is the key cause of  atherosclerosis (No known other detrimental effects of cholesterol).
From Nobelprize.org
"Brown and Goldstein have discovered that the underlying mechanism to the severe hereditary familial hypercholesterolemia is a complete, or partial, lack of functional LDL-receptors. In normal individuals the uptake of dietary cholesterol inhibits the cells own synthesis of cholesterol. As a consequence the number of LDL-receptors on the cell surface is reduced. This leads to increased levels of cholesterol in the blood which subsequently may accumulate in the wall of arteries causing atherosclerosis and eventually a heart attack or a stroke."
Note that hereditary disorder is not the only cause for LDL-R downregulation: "LDL receptors are downregulated by increased cellular cholesterol to prevent sterol engorgement, which is a characteristic of cells in atherosclerotic lesions." From: Biochemistry of Lipids, Lipoproteins and Membranes (Sixth Edition), 2016
The way you put your question draws attention to the fact that there is no corresponding downregulation of HDL-receptor.
Search on Wikipedia for "HDL-receptor" results in: "The page "HDL-receptor" does not exist." Presumably, no trivial knowledge that Nobel prize laureates Goldstein and Brown discovered  a whole family of so called "scavenger receptors".
What would happen if the HDL-receptors was downregulated (to  compare  with LDL downregulation)?
The "molecular difference" seems surprisingly unclear then: both HDL and LDL do carry cholesterol (It is  the very same molecule in both HDL and LDL). If too much LDL leads to depositon of cholesterol, same deposition might be made  by ("too much") HDL - your question is valid in that respect.  Downregulation of receptor distinguishes LDL from HDL.
There is one answer to a related question on Stackexchange that seems to exactly fit, in regard of the distinguishing role of Apo B100, quote: "Because LDL contains only the ApoB protein, it is less easily recognized. Thus, more LDL lingers in the blood.", with further reference about the pathological effects. If any  (distinguishing) molecular mechanism other than Apo-protein-signalling presumably protecting transported lipids from oxidation or degradation existed, it would had been mentioned.  Apo-B100 makes the difference.
The essential molecular feature of LDLs is the  LDL-receptor-ligand Apo B-100 which binds to LDL-receptors (on cells of adipose tissue) in contrast to HDL-receptor-ligand to HDL-receptor (on liver cells, surprisingly, however, not only on liver cells) - the latter known as "scavenger receptor class B type I"
which is  barely mentioned in  Wikipedia  (not having done intensive searching, admittingly:  there should  not be found in literature any discussion or even mentioning on  downregulation causing common disease, cp.Rigotti et al., 1997, A targeted mutation in the murine gene encoding the high density lipoprotein (HDL) receptor scavenger receptor class B type I reveals its key role in HDL metabolism: "(...) hepatic overexpression dramatically lowers plasma HDL." - wheras  only the  knock out experiment this paper is about is  cause for downregulation. Presumably, there is no downregulation of HDL receptor that would correspond to LDL-receptor downregulation.
On Apo B-100 as distinctive molecular marker see, for instance, Encyclopedia Britannica:
"LDL contains a single apoprotein and is the principal carrier of cholesterol to the peripheral tissue as both the free sterol and esters. The discharge of the lipid contents of this complex requires the recognition of the LDL B-100 apoprotein by a receptor located on the surface of recipient cells. When the protein is bound to the receptor, the receptor-LDL complex is engulfed by the cell in a process known as endocytosis. The endocytosed LDL discharges its contents within the cell, and B-100 is degraded to free amino acids that are used to synthesize new proteins or are metabolized as an energy source. The elucidation of the process of cellular uptake of LDL by Michael Brown and Joseph Goldstein earned them the Nobel Prize for Physiology or Medicine in 1985."
There is one more aspect to your question in the context of this answer.
The term "scavenger" (for HDL, not LDL) hints to the fact   that another difference between HDL and LDL lies in   LDL being degraded in lysosomes after uptake (by adipose tissue cells), whereas HDL is being recycled after  "touch down" on  HDL-receptor, i.e. not even uptaken by liver cells.  Please let me add this tentative thought: Thus, as there seems to be no "feedback" loop for LDL; the liver producing LDL (which start as so called VLDL, by the way) might not downregulate LDL-synthesis if target tissue downregulates LDL-receptors.
You may  skip the following further tentative thoughts of mine:
According to Voet et al, Biochemistry, the receiving of LDL via LDL-receptor by adipocytes leads to those "shedding" cholesterol (which seems to be picked up by "scavenging" HDL). See, for instance,   Verghese et al., 2007
"In the presence of HDL, composed of human apoA-I and phosphatidylcholine, adipocytes release cholesterol in a lipoprotein-dose and time dependent fashion."
This might be considered recycling of cholesterol (brought from liver to storing tissue by LDL and back again to liver on HDL, as delivery of fatty acids to storing tissue allows those to release cholesterol). In an evolutionary tentative concept, cholesterol as a molecule in itself  might once have been the very transport vehicle to transport lipids and fats from and to cells (see above: HDL is not even endocytosed, in very contrast to LDL-receptor-uptake, when it returns to liver cells, still cholesterol enters the liver cells. HDL leaves the receiving "scavenging receptor" as it is; it is some taxi; my analogy is to cholesterol). This idea leads to considering the sheer quantity of loaded  cholesterol as presumably distinctive: any quantity surmounting a level defined as upper limit for "taxi function" might be unloaded (or oxidized in scavenging funtion). This seems coherent with the existence of "remnants": there are LDL or VLDL-remnants and chylomicron remnants which the liver receives cholesterol  by. On a molecular level, there might be a difference in relative or absolute quantity of cholesterol, between LDL and HDL, reflecting that HDL as such "is" a remnant in the sense that it recyles cholesterol in "remnant quantity/thus quality". (There do exist LDL and chylomicron remnants, however, there is no such term or thing as  HDL remnant, to verify). By the way, counterintuitively, cholesterol is arguably considered "amphophilic", cp. source cited in comment to question and quote Encyclopedia Britannica above that mentions "sterols and esthers" as vehicles of cholesterol transport. Moreover, uptake of free fatty acids by adipose or muscle cells (that is the form derived from VLDL after lipase took on) seems not very well established in its mechanism. Cholesterol, then,  is known to be the distinguishing feature of animal cell walls in contrast to plant and procaryote cell walls. Cholesterol in cell walls might - by "softening" - enable heterotrophic cells to absorb free fatty acid (derived form autotrophic (plant cells, unsaturated fats)) without use of any - yet unknown - membrane transport canal or receptor mechanism. Please let me add one more argument that seems surprising: target cells of adipose tissue are made to "shed" cholesterol by LDL-receptor signalling. "On the other side" these target cells of LDL "take on in"  - and keep - cholesterol and lipids (from degration of LDL). There might be some feedback loop of receiving lipids and shedding free cholesterol that is - in evolution - still independent of APO-B100-LDL-receptor signalling, and downregulating the LDL-receptor  solely might interconnect both levels or regulating free "chole-sterols" in blood, or, if cholesterol is a former instrument of uptake as proposed, in interstitial fluid.   Thank you for having allowed this tentative thinking.
To sum up:
Lipoproteins resemble each other  in molecular structure and transported forms of fat/cholesterol more than the acronymes HDL/LDL may suggest.
The relevant difference lies in   their ligands, which address different target cells: ligand to "LDL-receptor" (which HDL does not seem to have or has to a much lesser extent)  is decisive in pathogenicity as there is "LDL receptor downregulation"; there is no physiological (in vivo) HDL downregulation.
Distinguishing molecular feature thus appears to be Apo-B100 molecule, which is the largest protein of the body.

Self-comment on   "... as delivery of fatty acids to storing tissue allows those to release cholesterol" - This leads to some other question: What is the role of  insuline on LDL-expression by adipocytes (and hepatocytes), as fatty acid delivery by VHDL should be enhanced by insuline (more LDL-Rs), and, because VHDL is precursor of LDL, any cholsterol  uptake via LDL is necessarily combined to fatty acid uptake via VHDL transport. In (diabetic) starvation less LDL-R, more release of cholesterol to HDL - and, question, more release of fatty acids by LDL-R-storage tissue.


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What is the effect of exendin on beta-cells?
Do you know if exendin, an analog of GLP-1 (glucagon like peptide-1), can be toxic for beta-cells? For example, what is the effect on INS1 or Min6 cells at a certain concentration or after 90 mins of incubation. And what is the impact on insulin secretion?

Old question, but new data: Protective effects of exendin-4 on ß cells incl. INS-1E lines (1)(2).

I recently tested exendin on INS1e cells in an Edu incorporation assay (similar to BrdU incorporation) to observe if this compound induces proliferation of the cells.  Compound incubation was for 24 hours.  I saw no incorporation of EdU with this compound over untreated levels.  In addition, during the assay I look at overall cell number with a DNA stain, but I did not see any effect on total cell number with exendin (ie, if it were toxic the total cell number should go down which I have observed with other compounds).


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Does having a total gastrectomy (removal of the stomach) cause individuals to be more prone to infections?
If a patient has a complete removal of his/her stomach (i.e. a total gastrectomy), then does that cause a person to be more prone to infections from eating unsanitary food?
I'm asking this question because the stomach plays a role in sterilizing food and, hence, without a stomach it would follow that one might be more prone to getting intestinal infections.

Yes.I think so as may of the bacteria are killed in our stomach

Yeah I think so too that's why I even asked the question -- to confirm what makes sense.

It would be nice to have empirical/epidemiological evidence to support this hypothesis.

I don't have time for a full right up, but here's a good starting point.


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How to increase the rate of absorption and assimilation of food?
i was reading this
and want to know
excerpt from the above linkThus, the time for food to travel from one end to the other probably ranges from about 20 to 30 hours
I believe it's 24 hours for a normal person going for poop every morning, But I was curoius if anybody could increase the rate of absorption making my digestive and defacaeting system better performing.

The rate of absorption is controlled by two essential physical factors:

Contact surface between intestinal content and intestinal mucosa.
Time of contact.

There are many other factors including intestinal peristalsis, gastric, pancreatic and bile secretions that stimulate/help absorption.
So increasing or accelerating intestinal passage of food won't do any good (see diarrhea). Water will not be absorbed into the blood flow thus leading to dehydration and hypovolemia. Also the alimentary principles, vitamins, essential aminoacids won't be absorbed.
On the other hand, slowing down the passage has negative effects. It allows bacterial saprophytic flora to multiply so much that those microorganisms become pathogenic by producing toxins. And increased contact time equals increased absorption both of toxins and food principles.

OOps! i was totally wrong


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ATP utilized in Glycolysis vs. Gluconeogenesis
In glycolysis, the conversion of glucose to pyruvate results in a net gain of 2 ATP molecules. In gluconeogenesis however, the conversion of pyruvate back to glucose requires 6 ATP molecules.  Why does there seem to be an apparent loss of energy?


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Why doesn't crossing over happen in mitosis?
If there was crossing over in mitosis, then there would various nature of somatic cells. May be that's the logic, but what is the mechanism? Why are there no crossover events during mitosis?

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

During mitosis both sister chromatids are identical si there would be no benefit to crossing over. During mieosis a person receives one chromosome from each parent which will encourage homologous recombination or crossing over to promote gebetic diversity.

during mitosis both sister chromatids are identical so no benifit of crossing over..During meiosis there are paternal and maternal chromosomes so crossing over promote genetid variability.

It can actually on very rare occasions however, it is also highly problematic and generally creates deleterious mutations and can inactivate genes. Depending on the location of the cell and the cross-over within the genome, it can also contribute to the formation of cancer. For instance, in the case of retinoblastoma, if there is one mutated copy of RAS on one chromosome and a normal copy on the other and mitotic crossing over occurs, then you can potentially remove the protective nonmutant copy of RAS from one of the daughter cells. This cell is then one step closer to becoming tumorgenic.
Thus, one reason this may not occur ordinarily is to reduce the chance of causing such a cancer. As for why it does occur on the rare times it does, I am not certain as of the time of writing this.
Reference: The Biology of Cancer, by Robert A. Weinberg

The mechanism is straightforward: in Metaphase I of Meiosis, chromosomes line up in two lines, with homologous across from each other, which allows them to interact by crossing over. In Metaphase of Mitosis, the chromosomes are all lined up single file, so the homologous chromosomes cannot interact.

This seems to contradict the possibility of mitotic crossover.

Yes, but mitotic crossover does not usually happen. It's more of a bug than a feature.


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When running gels what is the difference between constant volts or constant amps?
In general, you want to be consistent with running your gels either at constant volts or constant amps. However, it is very clear that during the progression of both PAGE and agarose gels, the free parameter changes due to the change in resistance of the gel.
While there are safety reasons why you run one vs. the other, I'm curious how these difference affect the migration of your gel.

I'll answer only for SDS-Page, which is the system I am most familiar with.
With a discontinuous buffer system, such as the well-known Laemmli system, resistance increases during electrophoresis, as (very mobile) chloride ions are replaced by glycinate (glycine ions).
From Ohms law:

Voltage (V) = Current (I)  x Resistance (R)

and the definition of power (Watts):

Watts (W) = Current (I) x Voltage (V) = I2 x R

At constant current electrophoresis will proceed at a uniform rate, however, as the resistance increases, so too will the voltage and the amount of heat generated.

In some discontinuous buffer systems, such as the Tricine/SDS system due to Schägger & von Jagow, this may be enough to crack the gel plates!
At constant voltage, the current will decrease during electrophoresis; as a result less heat will be generated than constant current electrophoresis, but the rate of migration of the sample will decrease with the decrease in current.

References
Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685. [PubMed]
Schägger, H. & von Jagow, G (1987).
Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166, 368-379.[PubMed]


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What causes the range of severity of neurological deficits in Down's syndrome?
It's known that the severity of symptoms caused by a trisomy 21 varies from individual to individual. Part of the explanation for this range of severity is the finding that 94% of Down's syndrome sufferers have a full trisomy, ie., all of the cells in their body have an extra copy of chromosome 21, while others have an underlying translocation (mostly a chunck of chromosome 21 being attached to 14). The last group has mosaic Down syndrome, where just a portion of cells is affected due to errors later in development.
However, this cannot be the only cause of the variation, as it would basically mean that 94% of all Down's syndrome patients should have similar complaints. Indeed, symptom variability is greater, as far as I am aware. I am specifically interested in the range of mental deficits caused by Down's syndrome:

The majority of children with Down syndrome function in the mild to moderate range of mental retardation. However, some children are not mentally retarded at all; they may function in the borderline to low average range; others may be severely mentally retarded.

What is the source of the variability in the neurological deficits? For the sake of answerability it may be best to narrow the scope down to the larger chunk of Down's syndrome sufferers with a full trisomy. Does any, or all of the variability in neurological deficits has to do with the stochastic process of X-inactivation?

Some useful sources I've read over, section 3 on pg 125 goes over some pathways implicated in intellectual impairment for DS, and more on the 21q22 region. Nothing conclusive yet.

As far as I know, a substantial proportion of the variance within neurological diseases are related to epigenetic marks on the genome. I wouldn't be surprised if this explains some (or perhaps most) of the variability in syndrome severities observed.

The symptoms of Down syndrome occur due to overexpression of genes present on the duplicated chromosome.
If possessing an extra chromosome meant an equivalent change in gene expression, one would expect to observe 50% more protein production for having 3 rather than 2 copies of a chromosome. However, due to complexities in regulation at the level of transcription, translation, and protein degradation, the actual expression levels vary substantially. These complexities can arise from alleles present on chromosome 21 or elsewhere on the genome. I will present some examples from three categories of variation that are known to contribute to the spectrum of symptoms in Down syndrome.
1. Complexity of chromosome duplication
Down syndrome is sometimes caused not by a complete, but rather a partial trisomy 21 (Antonarakis et al., 2004). These variations can also partly explain the severity of symptoms because some individuals do not possess a full duplication. You mention this in your question, but as you note, this is a fairly rare occurrence relative to full trisomy, so let us consider other contributions...
2. Variation of expression levels in normal individuals and those with trisomy 21
It turns out that among the genes expressed on chromosome 21, mRNA levels vary between normal individuals by as much as 40-fold! (Deutch, et al. 2005; Stranger, et al. 2005) This expression variability can explain the susceptibility of different individuals to trisomy 21, depending on the expression levels of the alleles they possess.
Among the different genes present on chromosome 21, some expression levels are consistently elevated in Down syndrome across individuals, some have overlapping but significantly different distributions (suggesting some Down syndrome patients have expression levels in the normal range and others do not), and others are indistinguishable between patients and controls (Prandini et al., 2007).
Presumably, genes in the first category contribute most to the shared phenotype of Down syndrome, and genes in the second category contribute most to the variation. Perhaps alleles that produce mRNA transcripts at the low end of normal for those genes are less susceptible to the effects of chromosome duplication.
A case study: Amyloid precursor protein
One protein of interest in particular is the amyloid precursor protein, APP, which is also associated with Alzheimer's disease (which shares some phenotypic characteristics with Down syndrome). APP expression varies widely among tissue types and individuals. Therefore, although APP mRNA levels are significantly elevated in Down syndrome individuals, the distributions between controls and Down syndrome are very overlapping; for example, see Figure 2B from the Antonarakis 2016 review.
3. Interactions with genes on other chromosomes
The third contributor to the variation of symptoms is the interaction of duplicated chromosome 21 genes with alleles located on other chromosomes. Just for an example where some of the genetic basis is understood, Down syndrome individuals are susceptible to certain leukemias, which are also associated with specific alleles on other chromosomes (Antonarakis, 2016). It seems that trisomy 21 affects histone modification in the areas of those alleles (Lane et al., 2014) and promotes proliferation of B-cells. Therefore, Down syndrome interacts with those other oncogenes to produce a greater combined risk. Individual with Down syndrome but not possessing the other alleles are less susceptible to the increased risk of leukemia
Similar interactions are likely with other systems that are influenced by Down syndrome, though the full molecular basis of all of those interactions are not fully understood. The Down Syndrome Genomes Project aims to, among other things, discover these other alleles outside of chromosome 21 that contribute to Down syndrome symptoms, which may also help understanding of the contribution of those alleles to other disorders (Antonarakis, 2016).

References:
Antonarakis, S. E. (2016). Down syndrome and the complexity of genome dosage imbalance. Nature Reviews Genetics.
Antonarakis, S. E., Lyle, R., Dermitzakis, E. T., Reymond, A., & Deutsch, S. (2004). Chromosome 21 and down syndrome: from genomics to pathophysiology. Nature reviews genetics, 5(10), 725-738.
Deutsch, S., Lyle, R., Dermitzakis, E. T., Attar, H., Subrahmanyan, L., Gehrig, C., ... & Antonarakis, S. E. (2005). Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Human molecular genetics, 14(23), 3741-3749.
Lane, A. A., Chapuy, B., Lin, C. Y., Tivey, T., Li, H., Townsend, E. C., ... & Yoda, A. (2014). Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation. Nature genetics, 46(6), 618-623.
Prandini, P., Deutsch, S., Lyle, R., Gagnebin, M., Vivier, C. D., Delorenzi, M., ... & Baldo, C. (2007). Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance. The American Journal of Human Genetics, 81(2), 252-263.
Stranger, B. E., Forrest, M. S., Clark, A. G., Minichiello, M. J., Deutsch, S., Lyle, R., ... & Deloukas, P. (2005). Genome-wide associations of gene expression variation in humans. PLoS Genet, 1(6), e78.
(note: the two references I have linked here: Antonarakis 2016 and Prandini et al 2007, are, respectively, a nearly direct answer to the posed question that establishes the current state of knowledge about symptom variability, and an original research paper that provides much more detailed genetic analysis of the variability of expression of many relevant genes than would be appropriate for an answer here; I highly recommend them both for further reading on the subject)

This is really a magnificent and exemplar-styled answer. I'll refrain from either accepting and giving you a well earned bounty until the bounty expires, because I think there may be more to it. This is more of a nature approach and I think the nurture approach may also be an important lead, just as with other mental disorders like schizophrenia and depression. Who knows? Apart from all that, many thanks for this interesting answer. +1

@AliceD Styled after your own answers, no doubt. I believe that "early intervention" strategies can improve the functioning and quality of life of affected individuals, but I am more familiar with similar strategies in ASD so I will have to do some reading. I also expect that all of the factors that influence cognition broadly would have an influence on Down syndrome individuals: things like socioeconomic status, and connected with that nutrition and parental care. I'm not sure what empirical research exists but I will check and may update my answer.

@AliceD (...continued:) I think Parkinsons and Alzheimers might be better analogies than schizophrenia and depression (though all have relevance): both Parkinsons and Alzheimers give some evidence that there can be a fair amount of resilience in the brain, such that symptoms arise not when damage begins, but after damage has accumulated to a sufficient degree. Therefore, I would expect symptoms of Down syndrome to be worse whenever there are other accompanying factors that negatively impact cognitive ability (and vice-versa) and influence the cognitive "ceiling" for that individual.

please do not feel pushed into doing more reading. This answer is great. I was more of hoping another user may step in and give another answer. But then, of course you're more than welcome to add info but that was not the intention of that comment (-: I really haven't the faintest clue whether nurture is involved

@AliceD I don't feel pushed at all, I am quite curious myself. :) I am confident that there is a role for nuture to play, though for the types of "nurture" I have in mind there could certainly be a semantic argument about whether it really reflects the severity of the neurological deficits or rather helps compensate for some of the symptoms to improve quality of life (i.e., does "improved vocabulary" mean the severity is lessened, or just mean a DS patient can communicate better despite the challenge they face?).

The extra genetic material present in DS results in overexpression of a portion of the 310 genes located on chromosome 21. This over expression has been estimated at around 50%. Some research has suggested the Down syndrome critical region is located at bands 21q22.1–q22.3, with this area including genes for amyloid, superoxide dismutase, and likely the ETS2 proto oncogene. Other research, however, has not confirmed these findings. microRNAs is also proposed to be involved.
The dementia which occurs in Down syndrome is due to an excess of amyloid beta peptide produced in the brain and is similar to Alzheimer's disease.This peptide is processed from amyloid precursor protein, the gene for which is located on chromosome 21. Senile plaques andneurofibrillary tangles are present in nearly all by 35 years of age, though dementia may not be present.
Epigenetics
Down syndrome is associated with an increased risk of many chronic diseases that are typically associated with older age such as Alzheimer's disease. The accelerated aging suggest that trisomy 21 increases the biological age of tissues, but molecular evidence for this hypothesis is sparse. According to a biomarker of tissue age known asepigenetic clock, trisomy 21 increases the age of blood and brain tissue (on average by 6.6 years).
Ref-wikipedia.

An interesting read, thanks for that. But it doesn't really target the question - why the range in severity of symptoms?


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Beetle identification - Kakadu NP, NT, Australia
I am trying to ID this beetle;

Size: not too big - approximately 2 cm (3/4 inch)
Where: Litchfield National Park, Northern Territory, Australia;
When: Southern hemisphere's spring, early September; the end of the dry season;
Time of day: night.

To my untrained eye, it looks like a cockschafer, but from the linked wiki page I understand they are a species confined to Europe. I tried a reverse Google image search and sifted through the site of Parks Australia and related pages, but to no avail.

After a hint from @fileunderwater I also think now that it is much more likely that this beetle belongs to the family of the Scarabaeidae which contains some 30.000 species worldwide. Scarabaeidae and Trogidae (what I thought was right before) are part of the same superfamily, the Scarabaeoidea.
The way the antennas are shaped as well as the body shape and the way the legs are ordered looks pretty much like this, even better than for the Trogidae. Have a look at this poster which shows a lot of different varieties (from here):

Some more information and real images can be found here and here.

Wow thanks Chris. Yes, the shape of the antennae is indeed an outstanding feature and reminded me of a May bug. I'll look into this!

I will have a further look tomorrow, when I have my experiment measuring and have idle time in front of the computer. :-)

Looks like belonging to the Genus: Anoplognathus

What makes you say Trogidae instead of Scarabaeidae (both belong to Scarabaeoidea)? The clubbed antenna with flat lamellae is typical for both families, as are the strong legs with spurs. Also, Trogidae usually have "bumpy" elytra, and there appear relatively smooth. I think it belongs to Scarabaeidae.

@Chris - You are not really trying to tell me in a lot of scientific words that my beautiful May bug is a cockroach do you ;-)


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What is the energy source for adipocytes?
Since adipocytes export fatty acids and glycerol and don't use them as an energy source, what is the main source of energy for adipocytes?

Adipocytes use glucose as an energy source. They express the insulin-responsive glucose transporter GLUT4 just like muscle cells so that when blood glucose levels rise they are primed to take the glucose up for fatty acid biosynthesis, but they also use glucose as a fuel molecule.

Thank you! And in the fasting state, which fuel they use? Glucose too?

In the fasting state blood glucose levels will be maintained by the liver via gluconeogenesis, so yes. During fasting the main function of the adipocytes is fat mobilisation and release of fatty acids (and glycerol, used by the liver as a substrate for gluconeogenesis).

But if adipocyte's GLUT4 recepetors are not being stimulated by insulin in the fasting state, how can they uptake glucose? Does hydrolysis of the ester link between a fatty acid and the glycerol releases energy?

@AlanBoyd, this is an interesting question, do you have any reference for the statement that glucose is the main energy source of (white) adipocytes? They are capable of fatty acid oxidation too (see for example http://www.jlr.org/content/17/5/516.short) but I have not seen any data on the relative importance of glucose vs fatty acids.

@AlanBoyd, also, to my knowledge, human adipose tissue does not synthesize (much) fatty acids from glucose. See for example http://www.ncbi.nlm.nih.gov/pubmed/1113680


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Can the kidneys utilize ketone bodies for energy?
Ketone bodies are water-soluble and should pose no problem to the kidneys because of solubility. If the kidneys are able to utilize ketone bodies for energy, then they must express the enzyme 3-ketoacyl-CoA transferase, correct?
Do the kidneys express the enzyme 3-ketoacyl-CoA transferase?
Can kidneys use ketone bodies as fuel?

This article's abstract says that 3-ketoacid-CoA transferase was found in the kidney: http://www.nature.com/pr/journal/v42/n4/abs/pr19972518a.html

Alexandria's answer:
This article's abstract says that 3-ketoacid-CoA transferase was found in the kidney: nature.com/pr/journal/v42/n4/abs/pr19972518a.html


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Why do some drugs require you to take them in an "upright position"?
A friend of mine was taking the supplement Metamucil and on the container it says to take in an "upright position." Why would this be necessary? Doesn't your digestive system push food/liquid downwards anyways?

Maybe you digest poorly when lying down, as compared to when upright. Is that not why "they" say to walk around a bit after eating a large meal and suffering from indigestion?

Metamucil is taken as a drink. You're more likely to aspirate versus swallow when drinking supine if you're ill with impaired swallowing reflexes.
It's also recommended that you take bisphophonates standing up so that gravity, and a glass of water, make sure the drug passes into the stomach. It can be highly corrosive if it gets stuck in the esophagus.


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Would short term increases in oxygen lead to beneficial effects?
After some thinking, I am wondering if having a 30% atmospheric oxygen concentration (or some other concentration) for a short time would increase the regeneration of energy in a body? It seems like it does have some mental effects, but I haven't found any other positive effects on the body.

what positive effects have you found? can you add those sources to the question?

You can't really go by simple percentages.  It's generally the partial pressure that matters, so for instance the FAA requires pilots of non-pressurized aircraft to use supplemental oxygen above IIRC 14,000 ft.  (And no whining about non-metric: the FAA regulation says feet :-))  OTOH, using normal air for deep diving can cause oxygen toxicity - though nitrogen narcosis generally happens before that's a problem.

Humans are pretty well suited to a 21% oxygen atmosphere (at STP). It's what our lungs are used to dealing with, and it's what brings the appropriate amount of oxygen to our brain (in particular, most organs are more forgiving, although not a lot more).
A lower concentration grows quickly and strictly deleterious, leading in short order to hypoxia, subsequently death. A higher concentration is also deleterious, leading initially to an oxygen high (as seen with Oxygen Bars), but also causing vision problems, seizures and death.
Oxygen is also highly reactive, and increased concentrations for even short bursts could, if frequent, lead to cancers, especially lung cancer. (The primary cause of lung cancer prior to asbestos and smoking? Breathing.).
There are cases in which increased oxygen concentration can be beneficial, but they are rare and specialised.


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Why do fungi and bacteria have macroscopically distinct patterns of colonies?
Why do microbes, when incubated on an agar plate forms a distinct kind of appearance i.e., d shape of colony.
 Its kind of less unique in case of bacteria.
Bacterial colony
http://image.shutterstock.com/z/stock-photo-colonies-of-bacteria-from-sea-water-on-a-petri-dish-agar-plate-isolated-on-black-background-300465722.jpg
Fungal colony
http://textbookofbacteriology.net/penicillium_colonies.jpg
. But if we  consider fungi, an amazing kind of pattern is seen as compared to bacteria.
So, on a broad spectrum if we speak, what is the real or basic motive behind forming these specific shapes.
Does it serve any purpose in protection or any such particular reason why do they do so?
Even plant leaves do the same. I mean to say every leaf is different from eachother making itself unique..
Why is this particular pattern seen in d universe and what it has to do with the colony of microbes.

can you give some examples of what you're talking about in the question... for example... "an amazing kind of pattern is seen compared to bacteria" - what exactly do you mean? Can you attach a photo, etc?

So sorry, its pattern*.

Fungi have more variable range of colonies as compared to bacteria..tats all i wanted to say in tat particular sentence

If i directly come to the point, i would ask, why do these microbes possess different kind of colony shapes. What is the primary purpose?

Plz check the post again i've attached links with respect to the question

Well the more simplified form of this question would be this:- If we incubate different types of organism on specific medium we see different colonies or patterns for ex- fungi appears different from bacterial colonies in terms of patterns.
Even plants leaves have different symmetrical shapes. So my question is why do different living organism acquire different shape. Do these shape helps in protection  or any other  reason.


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How much of the jejunum is bypassed during gastric bypass?
There is both long and short limb gastric bypass surgeries (along with several other variations on intestinal bypass procedures). How much of the jejunum is bypassed with a long-limb and short-limb gastric bypass?

One of the most used surgical technique is Roux en-Y where the small intestine is divided approximately 40-50 cm below the lower stomach outlet and is re-arranged into a Y-configuration.
The portion of intestine (jejunum) from the upper stomach is called the "Roux limb". It has a total length of 80 - 150 cm.
So the Roux en-Y technique "bypasses" only the duodenum and a small portion of jejunum - no more than 50 cm, that's about 7-10% of total length of small intestine.
"Total gastrectomy with Roux-en-Y" by ignis - Own work. licensed CC BY-SA 3.0 via Wikimedia Commons.
Reference: Wikipedia contributors, "Gastric bypass surgery," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Gastric_bypass_surgery&oldid=606081291 (accessed June 27, 2014).


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How is the enzyme glycogen synthase regulated?
How is the enzyme glycogen synthase regulated in regards to glycogen synthesis? I think I understand that phosphorylation decreases its activity (through glycogen synthase kinase?), but what role do molecules like insulin, glucagon (or epinephrine), protein kinase A, and Protein phosphatase 1 (PP1) play? Do they activate or inhibit glycogen synthesis, and how so?

The answer to this question can easily be found in standard biochemistry texts, e.g. one available online (albeit an old edition): http://www.ncbi.nlm.nih.gov/books/NBK22444/. Presumably this is why this question has not been answered previously. However I think it worth providing a summary answer in order to stress something that I feel perhaps does not receive enough emphasis in texts, and is ignored in the question.
This is that the regulation of glycogen metabolism (and indeed other aspects of carbohydrate metabolism) differs in different tissues because of the different situations in which its synthesis and breakdown is appropriate in relation to the integrated metabolism of the organism. If we just consider skeletal muscle and liver, the muscle stores glycogen to use itself when it needs to generate ATP to power contraction, whereas the liver stores glycogen so that it can provide other tissues with glucose when they require it either for work (e.g. the skeletal muscle) or in starvation (e.g. erythrocytes and brain).
The appropriate integration is provided in the first instance by the hormones mentioned (so-called first messengers), and the presence or absence of receptors in the tissues so that they will respond to these hormones or be refractory towards them, as appropriate.
Both liver and skeletal muscle have receptors for epinephrine (adrenaline) which is secreted as a stress response. This results in the breakdown of glycogen — used internally by the skeletal muscle and released as glucose by the liver, as already mentioned.
Liver also has receptors for glucagon, the hormone which is secreted in starvation or fasting, and also causes the breakdown of glycogen. The skeletal muscle does not have glucagon receptors because the nutritional state is irrelevant to its energy requirements.
Both liver and skeletal muscle have receptors for insulin, the hormone of the fed state, and respond to this by increasing the synthesis of glycogen to build up supplies to be available when needed.
How do these hormones work?
Glucagon and epinephrine (adrenaline) both work by activating adenyl cyclase (a so-called second messenger) in a G-protein-coupled manner to generate cyclic-AMP. This acts by a phosphorylation cascade to activate glycogen phosphorylase and inhibit glycogen synthase as described in any standard text. (Protein phosphatase 1 is also involved.) Glycogen breakdown is this enhanced.
Insulin acts differently. Binding to its receptor activates the protein's intrinsic tyrosine kinase, and there is a chain of subsequent protein self-phosphorylations culminating in the phosphorylation of protein phosphatase 1. This causes it to dephosphorylate both glycogen synthase and glycogen phosphorylase leading to the activation of the former and the inactivation of the latter. Glycogen synthesis is thus enhanced.
It is important to understand the molecular mechanisms of metabolic control, but it is also important to see them in the context of integrated tissue metabolism. So I will end with a question for the reader. The brain (which is absolutely dependent on glucose for part of its metabolism) stores a small amount of glycogen. How would you expect the brain to respond to the three hormones mentioned, and what would you expect to be the fate of the product of glycogen breakdown? If you have understood the principles above for liver and muscle you should be able to make rational predictions for brain (even should the facts turn out to be more complex).


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Why is a urea solution hypotonic relative to RBC?
If I place a RBC in 0.5M urea we see haemolysis.
My textbook says that "the solution is hypotonic. Urea enters the RBC down it's concentration gradient. Water follows the movement of urea by osmosis. This influx of water causes lysis".
I am very confused by this, for a number of reasons.

I thought tonicity only applies to non-penetrating solutes (i.e. a solution is hypertonic relative to a cell if the solution has a greater concentration of non-penetrating solutes then the intracellular fluid). If urea can penetrate the membrane, then why is the solution hypotonic? As a penetrating solute isn't it not factored into tonicity.
If urea is a penetrating solute, then won't it just come to an equilibrium across the cell membrane, and hence there will be no net osmosis since the concentration inside the cell will the same as that outside the cell.

I feel like I have a conceptual failing here, but the more I google the more confused I get.

It would be helpful if you could quote the entire scenario from your text book.

I think you have the conceptual understanding down, but my guess is that the textbook is not representing the situation quite correctly.  Based on the phrasing of the statement, I can imagine they are describing one of two situations:

Imagine a dropping a cell in to a solution of 0.5 M urea with no other solutes.  Urea will diffuse across RBC membranes due to facilitated diffusion.  It won't really factor in to this situation much.  So, the RBC contains proteins and other solutes that cause water to flow in to the cell and the cell lyses.  I don't think this is what the textbook means.
Now, imagine a situation in which you precisely calculated the water potential of a RBC.  You mixed up an isotonic solution of urea and some non-penetrating solutes.  This solution is perfectly isotonic at first, but as the urea diffuses in to the cell, it alters the water potential of the cell and the outer solution leading to osmosis.  I think this is the situation the textbook is trying to describe.

Imagine a third situation now in which a RBC is at equilibrium with a solution.  If you just added urea to the solution, it would not affect osmolarity in the long term for the reason you describe.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Pitch perception - why is the missing fundamental not directly detected in the cochlea?
I'm learning about pitch perception, and learned about the case of the missing fundamental.
In the main image in that wikipedia page, it seems like the bottom graph, with the fundamental frequency and its second harmonic removed, that the wave is still very periodic at 100 Hz. Since the Organ of Corti has some area which should be excited when there's a sound wave of frequency 100 Hz, why does this sound wave, which seems periodic at 100 Hz, not directly excite that region of the organ?
Can someone explain the workings of the inner ear and detail on why the missing fundamental does not activate the cochlea? Reversely, how can 100 Hz be heard when the cochlea is not even activated at that frequency?

Also tried asking on the DSP community.

I just saw you cross-posted. That's strongly discouraged at SE. I changed the pitch of your question (pun unintended) to make the questions sufficiently different. It's a good question.

The basilar membrane in the inner ear (cochlea) is a place-dependent Fourier transformer (Fig. 1). This means that there is an orderly tonotopic map projected on the basilar membrane (BM). Traveling waves imposed on the BM via the ossicle chain and the oval window start of at the base and travel all the way to the apex. Along the way the resonance frequency of the BM gradually decreases, as the BM gets wider and more flexible (like piano strings).
Now, if a certain frequency is missing, the BM is not moving at that frequency location, and hence the hair cells do not become activated, and the neurons with that specific characteristic are not activated either. How on earth can you still hear that frequency?
It is the harmonic structure that determines our perception of pitch, rather than the lowest harmonic alone. Our brains are sensitive to the frequency difference from one harmonic to the next and base the "real" pitch of the tone on that difference. This is referred to as the "difference tone". When you hear two pure tones, the ear and brain subtract one frequency from the other, and you "hear" a tone with a frequency of this difference (source: National Taiwan University).

Fig. 1. Frequency tuning in the cochlea. source: New York University


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How are isovolumetric contraction and afterload related in the cardiac cycle?
In the cardiac cycle isovolumetric contraction occurs and causes a pressure gradient. The "afterload" is the pressure exerted on the ventricle from the artery.
Is the afterload the cause of isovolumetric contraction, or what is the exact relationship between them?

The important thing to remember is that the "afterload" on the heart is the diastolic blood pressure in the aorta. In other words, the pressure in the aorta that the heart must overcome to open the aortic valve and create a pressure gradient to force blood into the aorta and generate flow. The isovolumetric part of the contraction is the generation of pressure up to the afterload 'pressure'. Once the pressure in the heart is higher than the pressure in the aorta a pressure gradient is generated and the aortic valves open and blood flows out of the heart into the aorta. During this movement of blood the heart is contracting again and changing volume (i.e. not isovolumetric anymore).
If the afterload is higher (i.e. higher blood pressure or hypertension) it increases the work on the heart because it has to generate an even higher pressure within the heart to open the aortic valve to generate the pressure gradient and flow.
If the afterload is lower (i.e. low blood pressure or hypotension) the work on the heart (with all other factors remaining constant) would decrease because the pressure to open the aortic valves and create flow is lower. The diagram below is available online at this link. This is a very common picture/diagram that can be found in any cardiovascular physiology textbook.
Note: In the picture below the isovolumetric contraction is only the time between the two vertical lines as indicated. During that isovolumetric contraction you can see that the volume (i.e. the red line) stays the SAME, but the pressure in the ventricle significantly increases up to the point of aortic pressure.


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Whole gene sequence analysis to determine source infection
Is it possible to use whole gene sequence analysis to distinguish between a common source infection and a person-person disease transmission?

Is this a question out of general curiosity or is it part of a homework or research project?  I ask because while genome sequencing of pathogens can be used to distinguish routes of transmission, it is not usually necessary.  Usually just sequencing specific regions is sufficient.

Thanks for this. A guest lecturer referred to this practice while giving a talk. I cannot understand the process or understand how it would work. Many thanks.

Are you able to comment any further  please?

Sure, the idea is pretty straight forward.  Suppose you have a single source of an infection: each new infection should be fairly similar to that original source.  However if the infection transmits person to person, each new copy should be similar to the original copy, so errors will be more likely to accumulate.


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How many, and how severe, are known single gene polymorphisms for obesity?
A fairly recent meta-analysis of studies examining the association between adult obesity and polymorphisms of the FTO gene (Peng et al., 2011). The paper looked at 59 studies and concluded that, "FTO may represent a low-penetrance susceptible gene for obesity risk", although the association was weaker (or non-existent) for some ethnic groups.
Are other polymorphic genes which are currently known to be more strongly associated with obesity risk than the FTO gene?

I was always wondering whether detecting such SNPs links to diseases (risk) is of significance. Sometimes, I think biology is so complex, even for diagnosis SNPs don't help very much. I am just chattering.

I think there are some statistical issues with this - such as multiple testing and family-wise error, but most of the studies in the meta-analysis I linked to seem to be quite solid and found odds ratios with confidence intervals comfortably above 1. Clearly it is well known that obesity etiology is multi-factorial and genetics plays a relatively smaller part (compared to the environment), but the evidence does seem clear that there are some genetic components, and gene-environment interactions are also likely.

MC4R, TMEM18, GNPDA2, KCTD15, NEGR1, BDNF, ETV5, MTCH2, and SH2B1 have also been identified as being associated with adult onset obesity risk, however FTO currently appears to be the one with the strongest evidence. For example see Thorleifsson et al. (2009), Elks et al. (2010) and Willer (2009)

Yes, FTO is the strongest thus far in the populations thus far tested. If Asians or African populations were to be tested as deeply, as often as European populations, other genes certainly may be added to the list.


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I'm trying to identify a tree i saw in Taormina, Sicily, Italy. Can anyone help?
What is the identity of this tree? These pictures were taken in Taormina, Sicily.

Was an obviously planted tree or did it look like a native species of the region?

It was on farmland..so I would have guessed a native species, but it seems not; Thanks to RHA for explaining that its native only to eastern Australia. Greatly appreciated!

It looks like the Silky oak, Grevillea robusta, which is btw not related to our indigenous oaks (quercus).
It's native only to eastern Australia, so planted in Sicily.
https://pommepal.wordpress.com/tag/silky-oak/

This looks spot on.


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Can a non-disjunction event occur in meiosis II (in the paternal gametes) to result in an XXY male?
My professor stated that non-disjunction in meiosis II of the father cannot produce an XXY male. However, a disjunction event in meiosis II of the mother can. I'm not understanding why this is (?)

The reason maternal non-disjunction during meiosis II can produce XXY offspring.

In this case, meiosis I occurs as normal so that after the first division the replicated homologous chromosomes, each consisting of two chromatids connected at a centromere, have separated. If a non-disjunction occurs at this point, haploid cells will not be formed. Instead, the sister chromatids of a replicated chromosome will not be separated and a gamete containing two X chromosomes will be formed. When this gamete combines with a sperm containing a Y chromosome, the offspring has the XXY genotype.

The reason paternal non-disjunction during meisosis II cannot produce XXY offspring.

This is similar to the maternal case except that after meiosis I, in one cell will be two YY chromosomes while the other cell will be two XX chromosomes. When non-disjunction occurs (assuming it occurs in both divisions), these chromosome arrangements remain the same and two cells are formed. One with two XX chromosomes and one with two YY chromosomes. If either of these gametes combines with a female X gamete, either XYY or XXX will be formed but never XXY.

Wikipedia discusses nondisjunction occurring in males or females, and both can result in the karyotypic condition (XXY) called Klinefelter Syndrome that often results in a male phenotype.


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What are the effects of non-ultraviolet light radiation on DNA?
I am trying better understand the effects of varying the frequency of light on DNA, however, most of what comes up is "UV light" and how it is damaging to DNA (presumably by ionization). Have there been any studies on radiation on DNA at lower frequencies of light?

have you tried googling?

yes that's why i'm here. everything i get keeps going back to uv light on dna.

Visible light aids DNA reparation after UV exposure (in prokaryotes at least) by activating the machinery. High-energy radiation (x-ray, gamma) causes double-strand DNA breakage (i.e. tears DNA into pieces).

@EliKorvigo any reference?

@aaaaaa Sure, this is for the visible light part, this is for the double-strand breaks

@EliKorvigo I think this is a good answer to OP if you format it as such

@EliKorvigo I'm unable to look at the full article, but I want to know what spectrum of light they used, and what sort of dependence on the frequency is observed in terms of the repairs that take place. Is this the only study that has been done or is there a broader field of study that this topic heads under?


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Doesn't the sarcomere contract during isometric contraction?
During muscle contraction, the lenght of the sarcomere changes, length of myocyte changes and so does the length of muscle. However, if the length of muscle is not changing length as in isometric contraction does it mean that the sarcomeres are not contracting?

Yes, sarcomeres do contract during isometric contraction, they just don't change the overall length of the muscle. This is due to the tension being transferred to elastic filaments within the muscle that maintain the same muscle length but increase the muscle tension. Thus, this is how sarcomeres can contract while the muscle does not have an overall change in length. (See this link for a paper discussing these elastic elements within the muscle itself; also, this is discussed at this wikipedia link as well).
In an isometric contraction the sarcomere is increasing the tension in the muscle, but without an overall change in length. (Isometric Contraction = No change in length, but INCREASE in tension)
Once a muscle overcomes the tension needed to lift a weight/load, then the tension ceases to increase but the sarcomeres begin to shorten which moves/lifts the load. When the length of the sarcomeres change and the tension remains the same, that is called isotonic contraction. (Isotonic Contraction = No change in tension, but DECREASE in length)

The picture below is from a website discussing these muscle physiology principles and is freely available on the web.

I vaguely recall having studied that even though there is sarcomeric contraction, there is no reduction in length in isometric exercise due to equal compensatory relaxation of sarcomeres elsewhere.. is this true? If not how is the length maintained despite contraction?

so, contraction (in the sarcomere context, not the muscle) need not mean decrease in sarcomere length right?

I learned something new... looks like the sarcomeres can contract during an isometric contraction, though this doesn't mean the muscle contracts. What appears to happen is that the sarcomere contracts but the tension is transferred to elastic filaments in the muscle which maintain the same muscle length but increase the tension - this is how sarcomeres can contract while the muscle does not (see http://jcb.rupress.org/content/105/5/2217.full.pdf+html for more info) - I will add this to my answer


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How does gene editing in one cell affect other cells?
I have read about gene editing and I have some questions concerning this technology:

With gene editing, are we correcting the genes in all the cells or a single cell?
If the gene editing is done for only one cell, then how (or can) it affect other genes in other cells?

Gene editing is not done on a single cell but a bunch of cells. However, it still does not affect all the cells. Gene editing/therapy for the entire organism works in these cases:

Stem cells are edited, which give rise to many other somatic cells. Usually done in case of gene therapy in which the stem cells are obtained from the patient, edited and re-implanted.
Some embryonic cells are edited and reimplanted in the developing embryo which gives rise to what is known as a chimeric organism (some cells in the body carry the edit while others don't). Now some of the edited cells will give rise to germ cells which in turn give rise to gametes. In the next round of breeding the chimeric parents would give rise to a fully transgenic (with edited gene) organism.
For unicellular organisms, it is pretty obvious: you just use a selection marker or extensive screening to select for the cells carrying the edited gene.