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Are trees the only source of large amounts of oxygen?
Trees use carbon dioxide and produce oxygen in the presence of sunlight.
But is there any other source?
If yes, are trees the most important source of oxygen, or is there any other source which produce more than trees do?

Like I mentioned in your previous post— did you google something about it? Did you check about photosynthetic organisms other than land plants?

Yeah, I found that water molecules are split apart after being struck with ultraviolet radiation and oxygen called photolysis and many other chemical reactions which happens in earth atmosphere. I didn't mentioned as it will be quite off topic.

Why trees? They represent a very small part of the plant population of the planet. They just happen to be big.

@terdon - in terms of biomass trees do account for a lot of vegetation, and yes, because they are big. It's not about numbers, but mass.

@AliceD in terms of biomass, I'm pretty sure they represent a very small fraction when compared to photosynthesizing algae and phytoplankton as you point out in your answer. Let alone the grasses.  Individual trees are big, yes, but there are not that may of them. In any case, 1) I only mentioned the plant population, not biomass and 2) only a very small part of a tree's biomass is actually photosynthesizing so biomass is not really relevant anyway.

Unfortunately, this, as a relatively highly upvoted question, doesn't show research effort whatsoever. It seriously doesn't take more than a few Googlings to find out what 'aquatic' organisms can photosynthesize.

71% of the earth's surface is taken up by water. Not surprisingly therefore, the seas are an important source of oxygen. National Geographic claims that photosynthesis by phytoplankton (mostly single-celled phototrophs, such as cyanobacteria, green algae and diatoms) account for half of the earth's oxygen production. The other half, they claim, is produced on land by trees, shrubs, grasses, and other plants.
The Ecology Global Network takes it a step further and claims that all marine plants (including phytoplankton) together produce 70 to 80 percent of the oxygen in the atmosphere.
Based on these reports, hence, marine phototrophs account for 50 - 80% of the earth's oxygen production.
With regard to terrestrial oxygen production, NASA reports that 30% of the land is covered by trees, and as much as 45 percent of the carbon stored on land is tied up in forests. So on land, trees are definitely large contributors to oxygen production.

Not to mention that natural forests are going to be almost entirely oxygen-neutral on average; your typical natural forest will produce as much oxygen as it consumes (the dead trees will eventually decompose, consuming oxygen and releasing carbon dioxide among other things). To make them an oxygen-positive system, you need to prevent the decomposition - for example, in a bog (as in the trees we now mine as coal), or by cutting the trees down and making stuff out of the wood. So it's actually the industrial forests that consume more carbon dioxide on average than they produce. Now.

It's worth adding that trees are a very recent addition to the planet's oxygen budget. It was the evolution of cyanobacteria in the early oceans that produced all that oxygen in the first place!

I am not sure which class of organisms have the highest contribution in oxygen production but diatoms do have a significant contribution. The introduction in this paper says that diatoms account for 40% of marine photosynthesis which according to this site is "1/4 of the oxygen we breathe."

Trees are definitely not the only source of oxygen. First, all green plants do photosynthesis, not only trees. Moreover, about half of all photosynthesis on earth is done by microorganisms in the oceans known as phytoplankton.


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If eating 100% fat 2 times more worth the energy I spend during the day, will I store body fat?
So in theory, insulin hormone is the one that tells the body "eat more. don't burn body fat". Alongside with glucose blood level regulation and turning excessive glucose into liver (which later goes into muscles as glycogen or into fat cells). Fats are the only thing that do not provoke insulin secretion. 0 glycemic index.
So in theory, if I eat 2 or 3 times more worth the energy I spend during the day, I'll never store body fat because of 0 glycemic index?
Or will I still gain because such huge fat intake will make liver into making glucose from fats & proteins?
Surely u'll never find a sustainable product to eat that is 100% fat, but just a few examples are butter, lard, heavy cream. This is just a theoretical question, where the proteins/carbs intake is so low that it is not count.
Could you please clarify it since I got lost.

Interesting question! I would guess adipose fatty uptake and esterification would increase with higher fat ingestion, regardless of insulin levels, simply because there is more fat around. The body cannot make glucose from fat, so fat accumulation via glucose is not a possible. (Which is also a reason why such a diet would be lethal.)

@Roland how come it can't? It can. https://en.wikipedia.org/wiki/Gluconeogenesis

@Roland and also I can't consider "simply because there is more fat around" a legit argument. I am really curious about this and my local dietitians can't seem to satisfy my interest. Something has to tell the body to start storing the fat. If it's not insulin (that is significantly elevats due to carbs/protein intake), then what else can tell the body to store the fat? Btw what about "lethality" of this diet. I eat about 80% fat and 10% protein from calories. Other - from leafy greens. Also intake a lot of fiber and electrolytes. Not dead yet. Even more. I cycle 60k+ day at high speeds.

Gluconeogensis from fat doesn't work due to stoichiometric problems. With only acetyl-CoA from fatty acids, the TCA cycle cannot function, because oxaloacetate used for gluconeogenesis cannot be replenished. Organisms that can turn fat to sugar use something called the glyoxylate cycle, which doesn't exist in humans. See any major biochemistry textbook, like Stryer's.

I meant that there is likely a basal rate of fat uptake by adipose tissue even if you don't get a glucose-induced insulin peak. And adipose fat storage probably is faster at higher plasma fatty acid levels (I'm guessing). Also, note that in the presence of glucose, fatty acids do increase plasma insulin (see for example http://www.ncbi.nlm.nih.gov/pubmed/15929861), and animals and people on high fat diets are known to have higher insulin.

As for "lethality". 80% energy from fat (which sounds like a lot to me) corresponds to 65% fat in your diet (by weight). So you are still taking in 35% carbs and protein. Your hypothetical 100% fat diet would be more like drinking oil and eating nothing else.

"is the one that tells the body" sounds like a strange way to say it. The response to food is regulated by many more hormones and neurotransmitters. For example, gut cells secrete GLP-1 in response to both fat and carbohydrates. I don't know all pathways involved but I'd be very surprised if insulin is the only mechanism involved in telling the body to store fat. And then there is the theory that the trouble behind metabolic disorders doesn't come from storing too much fat, but  from storing too little fat - the overconsumed but unstored fat would wreak havoc in different tissues.

Agree with @Roland - any basic biochemistry textbook (i.e. Stryer) will tell you that you can't make sugar from fat. That is, you can't make glucose from fatty acids because the reaction catalyzed by pyruvate dehydrogenase is irreversible. When someone goes on a high fat diet (i.e. Atkins diet), they force themselves to become ketotic - which means the body begins making a significant amount of ketone bodies from the breakdown of fatty acids. The body is trying to 'hold on' to its glucose reserves by burning ketone bodies, which can cross the blood brain barrier for brain energy metabolism.

There are a couple of reasons why this approach doesn't work quite as well as you might hope.
First, insulin doesn't go away after a high-fat meal. This paper reports changes in serum insulin following pure-sugar and pure-fat meals. Although there is much less of an increase in insulin following the pure-fat versus the pure-sugar meal, you will notice in Figure 1 that the insulin levels following the pure-fat meals (panel A) are higher than the levels during a fast (panel B). So even if high insulin were the only signal for fat storage, your dream of eliminating insulin with a high-fat meal is not realistic.
Second, when a high-fat diet is designed for medical purposes, a good deal of care is required to avoid significant potential adverse effects. Adequate protein intake is still required, and amino acids from the protein can be converted to glucose. Furthermore, ketoacids are produced when fatty acids from ingested fat are in excess. (As noted in comments, humans do not convert fatty acids to glucose.) Although ketoacids can be excreted in the urine (admittedly, heading toward your goal of not storing all the calories you consume), the net metabolic effect on the body when you excrete ketoacids is increased acidification, which in turn can lead to difficulties with potassium regulation and thus, in severe cases, with heart function. In the extreme if this were continued for a long time, you may face a problem of life-threatening ketoacidosis as occurs in type-1 diabetics (low/no insulin) whose disease is not being managed.
That said, your basic idea is similar to the arguments for low-carbohydrate diets. How well they work and, if they do, through what mechanisms are still somewhat controversial, as I understand. Insofar as they work through excreting some of the ingested fat through urinary loss of ketoacids, however, the associated risks need to be considered.

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What makes a strong polyadenylation signal a strong signal?
I was wondering why is it that "AAUAAA" is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?

because enzymes, responsible for these reactions recognize strong signal more readily?...

Just expanding on aandreev's comment.

Polyadenylation is initiated by binding of CPSF (Cleavage and Polyadenylation specificity factor) after its binding to the AAUAAA motif.
From the introduction of this article:

CPSF (cleavage and polyadenylation specificityfactor) binds to the
  AAUAAA hexamer via its 160-kDa subunit and possibly its 30-kDa subunit
  (Keller et al., 1991; Murthy & Manley,1992; Jenny et al.,1994;
  Barabino et al.,1997). CstF (cleavage  stimulation  factor) binds to
  the U- or G/U-rich element downstream of the cleavage site, and
  stabilizes the binding of CPSF to the AAUAAA sequence of the pre-mRNA
  (reviewed in Colgan & Manley,1997; Wahle & Kuhn,1997).

Any alteration in the CPSF binding site will lead to reduced polyadenylation efficiency. Polyadenylation efficiency also depends on other factors such as secondary structure and presence of proximal CstF sites.

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What is the fate of micronucleus DNA?
Micronuclei are cellular structures that are formed as a by-product of, usually, defective mitosis. The piece of chromosome in a micronucleus may, or may not contain a centromere and the DNA is wrapped in a double lipid membrane.
I have tried to find information, but I failed to find out what the fate of these structures is within the cell once formed? And is the DNA within it lost for the cell?

Emergence of Micronuclei and Their Effects on the Fate of Cells under Replication Stress (2010) explores how micronuclei behave and determine cell fate. It found that micronuclei is pretty closely related to apoptosis. If the cells with micronuclei didn't go through apoptosis, there were instances where the micronuclei would literally just disappear. They were unable to determine if it was expelled by the cell or reabsorbed into the main nucleus. However, there were also cases where there would be an increase in the number of micronuclei.
They concluded that there is a number of ways for the cell to get rid of the micronuclei and they were unable to determine which is the most likely.
I was unable to find any more recent in-depth studies (that I could understand).

So, according to this paper there are several answers...

Case 1: It is reabsorbed into the nucleus and most likely the information within is saved.
Case 2: It is expelled from the cell and the information within is lost.
Case 3: The cell undergoes apoptosis and all information is lost.


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Mitochondrial inner membrane
I know that the cristae of the inner membrane can be tubular or vesicular but I would like to know what are the functions of each .

Can you add more details in your question? Anything that you searched for.

@WYSIWYG The answer to this question is unknown yet, however probably in 20 years we can come back to this question and answer something reliable. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219563/

There is a reasonable speculation. That is to get more areas where ATP synthases are localized in order to produce ATP. But this doesn't tell why the structure has to be the exactly that shape.
As the review Ilan show, the shape seems to be determined by ATP synthase dimerizetion. The shap may be just a consequence of ATP synthase dimerizetion, although it successfully enlarges the area where ATP synthase is localized.

The general morphology of cristae is dictated by ATP-synthase Complex dimers, which form rows along the edge of cristae, sort of pinching the inner mitochondrial membrane together (see http://www.pnas.org/content/108/34/14121.short). The angle at which the dimers form, which is different in various species, causes different cristae morphologies. In organisms that don't have ATP-synthase or in yeast strains that are devoid of key subunits required for dimer formation, the cristae of their mitochondria are much more irregular and have a less defined shape, often described as 'onion-like' in the literature (see http://www.jbc.org/content/279/39/40392.short).
Therefore, I guess you could argue that actually it's the form that is a product of the function, rather than the other way round i.e. different cristae morphologies having different functions. The purpose, or selective advantage, of mitochondria having cristae is most likely that they create a greater surface area that can facilitate a larger number of complexes of the electron transport chain, which would enable greater ATP production per organelle. This explains why in eukaryotes that don't produce ATP via the electron transport chain there is no selection to maintain cristae in their mitochondria, or homologous organelles such as hydrogenosomes and mitosomes, and so usually the cristae are lost altogether in such species.
Other protein complexes are also involved in cristae formation and general architecture. Search for MICOS and MIB complexes to find out more.


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How high into the air are spores of molds commonly occurring?
I understand so far that most of the air surrounding us contains mold spores so that given the right environment and a food source they start to grow. I assume this is true for air close to the earth. But how high mold spores are still common?
To clarify: I don't want to grow mold, I want to know how high into the air on earth mold spores are usually common.

You can grow molds in space if you give the right condition. You need to add details to your question; details about different parameters that you want to consider. Are you asking about natural distribution of fungi?

You can have a look at this article.

@WYSIWYG: Seems this article checks for the distribution of fungi growing at the ground in mountain-areas with higher altitude. I'm asking for the spores distributed through the air, to which altitude above ground they are still available.

Air currents can carry bacteria and mold spores into stratospheric altitudes.  Early balloon collections found bacteria and mold in air samples at a little above 71 thousand feet altitude.  There were only a few colonies, but we also know that our bacterial media often do not allow many microorganisms to grow.
More recent studies of the atmospheric microbiome have indicated that a wide variety of bacteria and fungi can routinely be found in the atmosphere thousands of feet up.  Modern measurements find about 10 million living microbes per cubic meter.
Sandstorms or jet streams are known to be able to move living bacteria long distances.  Spores are often of about the same size and I see no reason why we will not find that they do the same.

I remember reading in an HHMI bulletin about a rate infectious disease in babies. Apparently the pathogen is carried by seasonal air currents over very large distances. I am trying to remember more details.

Ohh yes. It is the Kawasaki disease but the hypothesis is still open as the causative agent is not yet identified.

Small addition: This article talks about Aspergillus spores being carried to Caribbean from Africa, by dust storms. However it also mentions that that dust free wind does not have spores. Perhaps you would like to add this in your answer.

Stratospheric altitudes sounds scary. Anyways, for all europeans like me: 71000 feet = 21640 meter.

thanks @Mnementh - i should convert everything to metric but I was lazy and just copied the reference

No problem, different countries have different units. This needed only a quick Google, Google puts that on the result-site. I added it in the comment for convenience.

forgot to say thanks for the additions @WYSIWYG - helpful as ususal!


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Why is cisplatin a very potent antineoplastic for testicular cancer, but not necessarily for other cancers?
Cisplatin (structure below) is a platinum-based chemotherapeutic agent which is very effective in the treatment of some cancers. Its introduction was responsible for improving the cure rate for testicular cancer from 10% to 85% according to the wikipedia page on cisplatin.
However, it is not very effective for other types of cancers; interestingly, ovarian cancer does not respond well to it (Siddick, 2003).
Does someone know why cisplatin is so specific to testicular cancer? I haven't found any sources explaining this.

From the Wikipedia article you cited: "Cisplatin combination chemotherapy is the cornerstone of treatment of many cancers".

I slightly edited the question to stress the sources of your claims. If you'd rather revert to your original question, please feel more than free to do so. It's just a suggested edit, mainly because of the wikipedia page providing quite deceptive data.

From the dedicated cisplatin website and Drugbank it appears its use is quite diverse and not confined to testicular cancers. Further, your linked (Siddick, 2003) paper mentions on the first line of its abstract that cisplatin has clinical activity against a wide variety of solid tumors.
Cisplatin.org mentions that cisplatin finds use as chemotherapy against a range of cancers:

Cisplatin is a chemotherapy drug which is used to treat cancers including: sarcoma, small cell lung cancer, germ cell tumors, lymphoma, and ovarian cancer. [I]t can be a valuable part of a combination chemotherapy regimen. Look at the regimens given to patients and you will often see cisplatin as one of the drugs.

Moreover, cisplatin is explicitly used to treat ovarian cancer:

Treatment of ovarian cancer involves putting the cisplatin into the peritoneal cavity rather than a blood vessel. The type and extent of a cancer determines the exact dose and schedule of administering the drug.

As to your comment that cisplatin has "magical powers" I can say that it does not. The article that your linked cisplatin wikipedia page refers to (Einhorn, 1990) is a review paper that describes the efficacy of  combination therapies with cisplatin. The high cure rate of 75% was reached when cisplatin was used in combination with etoposide plus bleomycin. The last 10% was theorized to be achievable with 'salvage chemotherapy'. Hence, it is not cisplatin on its own.
In general, it is common practice to use various chemotherapeutic agents in consort, preferably with differing modes of action to reduce the dose of each and hence lessening the side effects.
References
- Einhorn, JCO (1990); 8(11): 1777-81
- Siddick, Oncogene (2003); 22: 7265–79

This doesn't explain cisplatins nearly magical powers to treat testicular cancer (tc) specifically. When used for other tumors, it does benefit patients but not nearly as much as for tc.

@Daniel - Please check my added last two sections in my answer. Thanks for adding this notion.

Very interesting! Thanks for the addition! :)

This is an striking example why wikipedia without the primary literature as a reference can be deceiving. Thanks so much for asking this question. Excellent.

As a clinician, I can confirm that cisplatin has a very wide range of indication in cancer treatment.

Any apparently "magical" powers of cisplatin in testicular cancer have more to do with the disease than the drug.
Unlike the similarly male-specific prostate cancer, testicular cancer is generally seen in young men in their 20s or 30s (click on "number of new cases and deaths"). This paper suggests, as is generally thought to be the case for earlier-onset types of cancer, that the affected individuals thus had some predisposing mutation or change in gene regulation prior to 10 years of age. As a result, it takes fewer sporadic acquired mutations to lead to this early-onset cancer versus a late-onset type like prostate.
This difference in incidence pattern is important because a late-onset tumor has had more opportunity to develop a broad range of cancer cells having different mutations within the tumor. Such intra-tumor heterogeneity has been recognized for over 30 years as a reason for resistance of tumors to cell-killing therapy like chemotherapy. For example, a heterogeneous tumor might be more likely to have cells that have mutated in a way that happens to make them resistant to cisplatin.
Also, testicular cancers develop in an accessible part of the anatomy that typically receives a lot of attention from men of the ages of peak incidence, so they are much more likely to be caught at an early stage than are prostate, ovarian, or colon cancers within the abdomen.


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Trypsin and cell culture
I am doing an experiment where I have treat the cells with a drug and calculate their counts. I would like to know if is bad to trypsinize the cells in consecutive days i.e. twice within 48 hours. How much time do the cells need to attach again on the surface of the flask? I want to know if I can treat them with drug the same day I add trypsin for counting.
Thanks.

Your question was unclear and I edited it a bit. See if this is what you really wanted to ask.

Can you specify the cell strain? It really depends on it. I have done for example trypsinization on RPE1 cells (human fibroblasts) twice in 48h without troubles.

It would be stressful for cells to be trypsinized 24 hours after seeding. After cells are plated, there is a lag time to start growing. Perhaps, during the lag time, physiological state of cells is stabilized. They have to express proteins digested by trypsin and display on the surface etc. Then you could disturb the state again by trypsinizing cells again if you replate cells after 24 hours.
I would not deny some cells are not affected by trypsin much, but you should be carful.

if I can treat them with drug the same day I add trypsin for counting.

It is not preferable, but in some cases, such a way is taken actually. If you could, you might want to give us more information about which cells and drugs you are going to use.
PS
If you trypsinize cells to count and do not replate them, you do not need to worry about the cell condition, as WYSIWYG says.

It is not advisable to trypsinize the cells too often when you have to maintain them. However, in your case the situation is different.
Time required to attach depends on cell type. In any case while performing an experiment, your cells should not be already under stress. Therefore you should seed the flasks/culture plates with a smaller concentration of cells such that they reach around 60% confluence in 24 hours. 24 hours is generally considered to be enough for cells to recover from stress due to trypsinization. (You can have a look at this post for doubling times of some cell lines).
After doing the treatment you can count cells whenever you think it is fine; this actually depends on your experiment and you can treat the cells for the time that suits the drug's pharmacokinetcs. Trypsinizing is fine now because you won't be using these cells again.
However, there are methods to calculate cell numbers without trypsinizing. Assuming that your flask is homogeneous, you can choose a section of it and calculate cell numbers manually using microscope. You may also use software like ImageJ to make the task easier. GFP expressing cells will also make the task easier.

Might be considered "not answering the question" but:
Option 1:
Depending on the type of cells you are using, you can use milder methods to detach cells.  Example include Versene which is essentially PBS + EDTA.  Milder still is to just use PBS that has no Mg or Ca (no chelation).
Option 2:
Duplicate your setup - instead of two dishes - one with drug, one without, you make 4 dishes (dispensed from a common source - i.e. if your dish is a 6cm dish with 3ml media, you make 4.5x3mls of cells at the final dilution you want) each plate gets 3mls from the same source so you know they have the same number of cells.  Two dishes you add drugs, two you don't.  On the day you want to count, you take the replicate plates and count them.  This way, you get the count without touching the final dishes at all.
As a side experiment, if you put those trypsinized cells back on two dish (and replace the drug media in the drug treated replicate), and you count all plates on the last day of your experiment, provided cells are not at 100% confluency, any difference you see from your trypsinized vs untrypsinized can be viewed as potential error that you would have introduced if you went through your original methodology.


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Are there terrestrial plants that thrive on sea water?
Given the existence of coastal deserts such as in the picture below, I was wondering whether terrestrial plants can survive on sea water alone? If yes, why then do coastal deserts exist, instead of being grown over with belts of such plants along the shores?
If terrestrial plants thriving on sea water do not exist, then why? Especially given that there are marine plants like kelp and sea grass?

There are mangroves that live their lives immersed in salt water. Does that count as a terrestrial plant?

@Resonating Mangroves are considered terrestrial and they are not fully submerged. But I have seen mangroves only in backwaters and estuaries/deltas.

The University of California, LA mentions some genera and species of salt-loving plants (halophytes):
The genus Atriplex (Family Chenopodiaceae), saltbush, is found worldwide along saline shorelines. On the surfaces of the leaf are vesiculated trichomes (hairs). Each trichome has a stalk and a balloon-like tip, the bladder cell. The leaves use the bladder cells to excrete salt.

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

Cordgrass in the Chesapeake Bay. Source: Chesapeake Bay Program
Frankenia (Family Frankeniaceae) is a genus found both in coastal salt marsh and inland saline habitats. Saltcedar (Tamarix, Family Tamaricaceae) grows around the world in arid and semiarid regions. All of these taxa have salt glands, i.e., trichomes, in which salts are accumulated and excreted.
Several common mangroves secrete salts from leaves. So much crystalline salt can occur on the leaf of black mangrove, Avicennia germinans, that it appears whitish. Aegialitis annulata is a salt-excreting mangrove of Family Plumbaginaceae, a group in which other species are salt excreters in salt marsh and oceanside (Limonium and Armeria) or have chalk glands and live in dry, alkaline habitats.

Black Mangrove. Source: PlantDex.
Halophytic succulence is demonstrated in many genera of plants that inhabit saline environments, such as the mud flats of coastal salt marsh, but also is commonly observed on the leading edge of vegetation on coastal beaches, i.e., in strand vegetation. Common examples of succulence can be found in Family Chenopodiaceae: Allenrolfea, Arthrocnemum, Halimione, Nitrophila, Salicornia
Suaeda.
Succulence (fleshiness) also occurs in other famous and widespread species, such as Batis maritima, Sesuvium portulacastrum, Trianthema portulacastrum, and many Old World species of Zygophyllum. True succulents in the ice plant family, Aizoaceae, are also commonly found in saline habitats: Aizoon and Mesembryanthemum. By depositing salts in vacuoles, the toxicity is partitioned from the cytoplasm and organelles of the cells. As in Atriplex, salts are removed from the plant when the leaf of stem segment is shed.

Halophytic succulent Trianthema portulacastrum. Source: Altervista.
Among the halophytes, the seagrasses, which are submerged plants of shallow marine meadow, have salt tolerance, because the osmolality of cytoplasm is adjusted to match the osmolality of the seawater, so that desiccation of the plant does not occur. This contrasts the strategies of excluders and succulents, which are primarily salt avoiding mechanisms, attempts to reduce salt concentrations within the cytoplasm of photosynthetic cells.
As to why some shores may be devoid of plants, it may have to do with extreme temperatures, lack of nutrients, phytotoxic material etc.


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What is the genomic position of HLA-B*1502 variation?
I've searched the position and SNP ID of HLA-B*1502 variation. However, I couldn't find that where this variant exactly located on genome or HLA-B gene.

HLA-B*1502 is not a SNP ID but rather, a name of an allele of HLA-B. This allele is made up of multiple mutations which can be found here.


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Why a continuous supply of energy is needed to support a weight?
What motivates this question is the apparent discrepancy between the concept of Work in physics and in physiology.
Work in physics is defined as the dot product of the force applied to move a certain object by its displacement:
$W = \vec{F} \cdot \vec{d}$
$\text{ Work  =  (Force) $\cdot$ (Displacement)}$
Where $\vec{F}$ is the force vector, and $\vec{d}$ is the displacement vector.
Now if there is some weight lying on a table, it takes no Work at all to maintain its present configuration, since both $\vec{F}$ and $\vec{d}=0$, As a result $W=0$. In other words, this weight-table system does not need to be provided with energy at all, for the table to be able to support the weight, because it takes no energy to support it.
What about an identical case but with a human hand supporting a weight(at a constant height) at this time? Although according to the above reasoning one should expect that it does not need any energy to support the weight, this is not what we observe in everyday life, because when I hold the weight, it takes a tremendous amount of effort to support and maintain its position.
When I looked up the reason behind this, I found out that it has to do with the fact that the muscles of the arm are skeletal muscles not a smooth one.
If the arm were made out of smooth muscles, then it would take no effort or energy at all to support any weight at a fixed height.On the other hand, the muscle fibers that contract to support the weight in Skeletal muscles has to be continuously provided with energy to be able to support it, and hence although no mechanical work is applied on the weight so $W=0$, nevertheless energy is wasted in the form of heat in this process, and hence we get tired after holding an object for some time.
So what is the mechanism by which Skeletal muscles support certain weight? Why it needs continuous supply of energy while holding an object? How is this energy supplied( my guess is:some component of a cell breaking down molecules so as to transfer chemical energy to mechanical contraction of muscle fibers)?And how it differs from smooth muscles?

Welcome to Biology and thanks for your question. I think the big difference with a table and a human arm is the presence of joints. Even if holding a weight straight in the air, it is sill a balancing act that needs continuous muscle strain.

Do you have a reference for your statement about smooth muscle? It seems implausible to me.

@Rolan the Feynman lectures on physics : "The smooth muscles work very slowly, but they can hold a “set”; that is to say, if the clam tries to close its shell in a certain position, it will hold that position, even if there is a very great force trying to change it. It will hold a position under load for hours and hours without getting tired because it is very much like a table holding up a weight, it “sets” into a certain position, and the molecules just lock there temporarily with no work being done, no effort being generated by the clam."

"Smooth muscle would be much more effective for holding up weights because you could just stand there and it would lock in; there would be no work involved and no energy would be required. However, it has the disadvantage that it is very slow-operating."

@OmarNagib You should note that even in pure mechanical examples, the energy consumed may not be equal to work done because some energy is also used up in countering the frictional force.

I think there are too many questions in here ! I answer on the most novel one (smooth muscles vs skeletal ones). For the basics of muscle contraction, I believe you can easily find answers online (look for myosin and ATP cycle)

For skeletal muscles, you'll find a discussion in the Physics SE: https://physics.stackexchange.com/questions/1984/why-does-holding-something-up-cost-energy-while-no-work-is-being-done
To make things short: while holding a position, muscles need to maintain a given length. However, internally, the muscle looks like a collapsible array of filaments, with myosin heads acting as crossbridges between them. Even when the muscle is not contracting, myosin heads unbind and rebind at some rate and would let the muscle relax -- unless you input more energy to compensate this with a further contraction.
For smooth muscle, according to this article, the rate of unbinding can be very slow:

Once the contraction has occurred, the cross bridge attachments need
  to be released in order that the muscle can relax. Although less is
  known about this phenomenon, it appears to be related to
  dephosphorylation of MLC20. In some situations, the dephosphory- lated
  MLC20 is very slow to allow detachment of the actin from the myosin
  cross bridge, resulting in a prolonged contraction. This has been
  referred to as a ‘latch-bridge’ (Hai and Murphy, 1988). This
  phenomenon may be of great value especially for tonically active SM
  beds as it would allow them to maintain basal tone through holding in
  an isometric state without a great energy cost.

So as the muscle is not relaxing, no input of energy is needed to adjust its length to the desired one. I assume a disadvantage of that is that the reaction time of the muscle is slower.

It would be nice if this answer could be expanded by adding an explanation of why binding and unbinding of myosin heads expends energy. Otherwise there is no final logical step connecting any of this to the question of energy expenditure.

@BenCrowell: well, in fact it is there. "myosin heads unbind and rebind at some rate and [would] let the muscle relax" : so in the absence of input, muscle yields to the load slightly, until "you input more energy to compensate this with a further contraction" : so at a small scale, you can picture it as cycles of yielding and bringing back load to previous position.

You should note that even in pure mechanical examples, the energy consumed may not be equal to work done because some energy is also used up in countering the frictional force.
In your example you consider an object kept on a wooden table and in this case the weight is balanced by the reaction force by the table. You have not considered the material properties of the table. The reaction force would be equal to weight only if the weight does not cause any distortion to the object that it is resting on. When distortion happens; for e.g. the if wooden plank bends, the resting object comes closer to ground with a reduction in its potential energy. Now the weight is balanced by the reaction force which is basically the force exerted on the plank to get back to its original position (analogous to the spring; $F=-kx$). Even in this case the material property of the wood is, more or less, invariant.
Getting back to biology. Muscles consume energy in order to maintain their material properties, even if they do not perform work. Muscles can be thought of as dynamic materials because their material properties can change.
When you are holding a dumbbell in your hand with your arm poised at an angle then your biceps need energy to keep maintaining that tension (a temporary material property). The energy is supplied in the form of ATP.
I won't discuss the case of smooth muscles. You should read more about what they exactly do.


text:
How to calculate biological half life of a drug that is dose dependent?
I would like to calculate the half-life of a biological drug.
This biological drug is said to have a biological half-life of:
3.33 days when a patient is receiving a dose of 0.04 mg/kg of body weight,
13.4 days when the dose is 0.2 mg/kg
and 14.9 when the dose is 1 mg/kg

How could I extrapolate this information to get biological half-life estimate for 2 mg/kg of body weight?
Could I also graph this? for example in R?

This sounds a lot like a homework question. I'm glad you got an answer though.

Maybe it does but I'm actually a doctor and I have a patient that has to switch from one clinical trial to another. He may go into the second clinical trial only after a wash-out period of 5 drug half-lifes. and the information I have given - is actually in the drug description.

I plotted your data using MATLAB and it looks like this:

Most degradation or clearance processes happen via first order kinetics. However when the clearance/degradation machinery gets saturated then degradation proceeds via a zeroth order kinetics i.e. it becomes independent of the concentration of the drug. The half life in first order reactions is independent of the initial state. Only in the case of the zeroth order reactions, the half life is directly proportional to initial state (See here). In this graph there is a huge gap in half life, between the first and the second points. We need more data points to say anything conclusively about this observation. However, I am assuming that the clearance reaction is already in the zeroth order kinetics as half life increases with concentration (though at different rates). For a rough calculation let us consider second point onwards. By calculating the slope between second and third points you can obtain the half life corresponding to dosage of 2mg/kg.
$$Slope=\frac{t_3 -t_2}{x_3-x_2}\\ t_4=x_2+slope\times2=17.15\ days$$
There can be other complicated explanations too, such as the drug inhibiting its own clearance etc. But for assuming such models we would require more information.

does it mean that more drug "clogs" kidney (for example) so that drug stays in blood stream longer? Is it real effect (observable in reality)?

@aandreev I haven't studied that with drugs but if you overexpress proteins beyond a limit then their degradation rates become zero order i.e. independent of concentration of the protein because proteosomes get "clogged". Same goes with drugs and if two drugs require same enzyme for their metabolism then taking them together may be harmful. I guess, that is why most drugs are metabolized slowly when someone has consumed alcohol.


text:
Why are the organs for reproduction and urinary excretion combined?
We eat food for getting energy to our body parts, and we excrete the wastes through urine, feces, and perspiration.
Why has nature combined the urinary tract with the genital system (urogenital system) in humans?

they really don't. Only overlap, i guess, is in urethra

I edited your question to remove textual ambiguities.

I think this is a question open for much debate, but part of the answer may be that sharing functions reduces anatomical complexity. In other words, adding functions to existing structures is one of the essences of evolution; complexity through parsimony.

@AliceD thanks for editing the question the right way and properly.

Actually it is there in all mammals (in fact most vertebrates), not just humans afaik. It is better to not limit the question to just humans. Related post.

It is surprising that "urogenital system evolution" is not giving any decent hit in google scholar!!!

@WYSIWYG Can't it be considered as nature's mistake
of combining truly liked and truly disliked
things (of most humans) together?

@AliceD  Can't it be considered as nature's mistake
of combining truly liked and truly disliked
things (of most humans) together?

@AliceD sir,I think no one will love to eat food in the toilet room

@sagar "nature" doesn't make mistakes, because there is no conscious thought involved. Evolution produces changes in DNA that accumulate over time and lead to new phenotypes. Those phenotypes either give a reproductive advantage, a disadvantage, or are neutral. These either allow a population to survive/flourish in a particular ecological niche, or not. Generally, traits that negatively impact a population's likelihood of survival are selected against, and tend to disappear over time. Since this combination you are interested in is widely spread across species, it likely confers an advantage.

Don't use terms like "nature's mistake" and all. I rolled back the title edit.

Developmentally, the urinary and genital systems (typically you will hear them referred to as "urogenital system") are derived from the same embryonic tissue, the intermediate mesoderm. The embryonic kidneys are drained by the mesonephric duct in both females and males. This embryonic tissue also gives rise to the ovaries and testes. The mesonephric duct degenerates in females, and becomes the ductus deferens in males. A second tube, the paramesonephric duct develops in both, but degenerates in males. The female paramesonephric duct becomes the uterine (Fallopian) tube.
Embryonically, the ureter, which drains the adult kidney is connected to the mesonephric duct. This connection is maintained in males, so that both urine and semen share a tube (urethra) for some of their exit pathway. In females, the paramesonephric duct and urethra are separate, so there are two openings.
In males, sphincter muscles and autonomic control prevent the simultaneous expulsion of urine and semen.

This system has worked acceptably well in mammals for at least about 200 million years (and in humans for the last 4 million or so), so I think it's not correct to call it a mistake. It's not how you would consciously design such a system, but evolution doesn't have a conscious designer.
Here are some slides that cover the embryology of the human urogenital system.

Excellent answer, well done!

Evolution has no conscious designer?? What about the great architect?

I would just modify the excellent previous by pointing out that the embryology describes a local maxima of fitness whose barrier to change is higher than any selective pressure.  The re-use of the "logic" of the intermediate mesoderm was either initially a bifurcation from one or the other, or, was of enough selective advantage to have the two developmental processes and the resultant physical systems folded together.

Can you please make your answer clearer? I don't understand what you try to say.

Any relatively stable developmental process has some selective advantage, but is not necessarily the best - like if you could only walk upward, and you had to pick a hill to climb.  You might not end up on the highest peak.
Embryonic processes are often "hijacked" for other purposes, through mutation and selection
It's possible that these two functions were at one time separate, separate "hills", but again through mutation and selection, merged embryonically.

@Abram You can just edit your answer to include more information.

kmm gives what is likely the best possible answer, as it is argued from causality rather than teleology. As my ninth grade biology teacher used to say, "there is no 'why' in biology, only 'how'".
On the other hand, it is fun to speculate! Here's my two cents in the form of a Bad ad hoc Hypothesis:

Holes going into the body are an expensive and risky prospect at best for any animal. In order to maintain homeostasis they need to keep any holes constantly supplied with fresh mucus and a ton of antibodies. Total orifice count tends to be kept to a highly conserved minimum along evolutionary lineages. Thus, the reason why urinary and genital systems are merged along a single urogential tract is so that they can both efficiently share the same hole. As evidence for this view, consider the reptile: they manage to use their holes even more efficiently than we do, mating and excreting both liquid and solid waste out of their single cloaca.

I think the orifice count reduction that led to eating and talking at the same time out of the same hole was a mistake.

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


text:
What is the mass of a pigeon tail feather?
There is question at Space.SE If I drop a feather from orbit, would it burn up or “hit” the ground? there is an attempt to answer the question, but the mass of pigeon tail feather and possibly the drag coefficient is required to complete the answer.
I have looked around on the web and if there is an answer it is not jumping out at me.
What is the mass & drag coefficient of a pigeon tail feather?

An African or European pigeon?

@terdon - oddly enough, the same question was asked in a comment in the question that gave rise to this one.

I just weighed a pigeon tail feather (~10 cm) long. The mass was 0.05 g. Although all tail feathers are not equal in length (and all pigeons are not equal in size), this is probably a good approximation.
Measuring the drag coefficient is going to be very challenging, because it will vary with the orientation of the oncoming airflow. A feather falling with its broad surface (in this feather ~1.2 cm in chord width) perpendicular to the flow will have a much high drag coefficient than a feather falling with the broad surface parallel to flow.

Heh, nothing like the old fashioned empirical approach. I would expect the feather to orient itself with the pointy bit downwards though, it should be relatively standard.

@terdon such alignment, however, will only happen after the feather hits the atmosphere and survives the initial onslaught of unsuspecting air molecules. The orientation is uniformly arbitrary before the feather touches the atmosphere.

@JanDvorak yes, but we only care about the orientation after it hits the atmosphere. Obviously, there will be no drag coefficient in vacuum. I am guessing that as soon as it hits the atmosphere, the drag will orient it thusly.

Dropping most feathers (certainly primaries and body coverts, anything else should be in between) actually leads to them falling in a fluttering motion, rather than pointy-end first.  Pointy-end first is unstable (c.f. rocketry etc., or ask at physics.se)  Try it and see, it's also great for entertaining a cat.  A sheet of paper will often do the same.

@ChrisH I think (no idea really) that pigeon feathers, being relatively large (I'm thinking of entire plumes here, not tiny fluffy ones) would orient themselves pointy end down because of the extra weight of the plume. I may well be wrong though.

@terdon, in my experience it's not guaranteed even with the larger, stiffer feathers.  If you drop them shaft first they may keep going that way but dropped on any other angle they flutter and fall slowly.  The thing is that there isn't much extra weight because it's hollow.

@terdon I think it will flutter regardless, seeing as it is curved slightly.


text:
What is the optimum length of abstinence for maximum ejaculation volume in humans?
There have been papers discussing this, and whether the abstinence period should be 1 week, 2 weeks or other [1, 2]. Some think the time to maximum ejaculation volume is even longer than this.

doi: 10.1530/jrf.0.0570391
PMID: 7114956

This value is going to be species-specific (cf. mouse vs. elephant), so in its current version your question is too broad.

There don't appear to be many robust studies on this, but this study by De Longe et al in 2004 suggests that, whilst the volume of the ejaculate is increased after 5-days of abstinence (in most participants), for many this did not increase further after 8-days [1].
Here are the 11 participant included (along the x-axis), and for each participant there are four coloured boxes:  dark blue, day 1 (corresponds to 24 hours' abstinence); red, day 3 (corresponds to 3 days' abstinence); yellow, day 5 (corresponds to 5 days' abstinence); light blue, day 8 (corresponds to 8 days' abstinence).

This study has a very small sample size, and really shows how the variability between people is massive. There could be many other factors affecting individuals, from smoking and drinking behaviours, to exercise and stress.
What seems much clearer is that sperm concentration increases with abstinence [2]. This study included 27 men and did not specifically ask them to remain abstinent for periods of time, but asked them how long. The average abstinence is about 2-days.

I could not find any study which investigated abstinence for longer periods - but there are undoubtedly more that I did not see.

De Longe, at al. 2004. Influence of the abstinence period on human sperm quality. Fertility and Sterility (http://dx.doi.org/10.1016/j.fertnstert.2004.03.014)
Carlsen, et al, 2004. Effects of ejaculatory frequency and season on variations in semen quality. Fertility and Sterility (http://dx.doi.org/10.1016/j.fertnstert.2004.01.039)

Very interesting findings.


text:
How can a ligand be an integral membrane protein?
My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am reading a review of EGF signaling (Epidermal growth factor receptor targeting in cancer: A review of trends and strategies by Chetan Yewale, et. al.), and it states that "Various ligands can activate EGFR ... These ligands are expressed as integral membrane proteins." This statement makes absolutely no sense to me, and makes me question my understanding of signal transduction. I think of ligands as freely floating molecules that may eventually come into contact with the cell membrane and attach to some receptor. But a ligand expressed as an integral membrane protein? This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells). Integral membrane protein ligands would only be useful for autocrine signaling, which I don't think is true of EGF.

Can you please link the review?

Membrane-bound ligands are also used in cell-cell signaling. This is especially (but not exclusively) true in the immune system, where circulating immune cells "scan" other cells for signs of, say, viral infections, which will induce the expression of certain proteins on the infected cell's surface, which are in turn ligands for receptors on the immune cell's surface.

You're thinking of hormones. Ligand is a much broader category of thing that includes everything that can be bound by some biomolecule.

Wow, I must say this is my first ever post to biology stack exchange, and I'm very impressed with the quality (and even quantity of answers!!)
The article I was describing is http://www.sciencedirect.com/science/article/pii/S0142961213009289

These kind of ligands act via juxtacrine signalling because they cannot diffuse. Ephrin is another example.

@WYSIWYG I think you should make that an answer since it seems to address the crux of the question.

@canadianer Actually Poka Nandor has almost said it. I'll either suggest him this point or add this to his answer as an edit.

In biology ligand is a very broad term. Everything is called a ligand that has a receptor for it, regardless whether it is free or membrane-bound. There is very much sense in membrane bound ligands, because many cells in our body are capable of actively moving around (for example T-cells). Cells can use signal transduction by direct cell-to-cell contact - like in activation of T-cells, or cytotoxic T-cell killing. This wiki page covers the basics quite well.
Also, a quite thorough wiki page on ligands.
From the comments under the question by @WYSIWYG:

These kind of ligands act via juxtacrine signalling because they
  cannot diffuse. Ephrin is another example.

I am beginning to see now how a ligand can be a transmembrane protein. I think I am still confused, however, because my understanding is that growth factors (such as EGF or TGF-beta) are secreted by cells during migration, and I always assumed secretion meant the release of a soluble thing that is able to diffuse to other areas of the cell population (maybe I should mention, I'm considering this during an in vitro experiment in a well plate). It doesn't seem to me that a membrane-bound ligand would be useful during migration, as the movement of cells and signal propagation may be opposite.

You can add that these kind of ligands act via juxtacrine signalling because they cannot diffuse. Ephrin and Notch are other examples. Sometimes diffusible signalling may not be. preferred.

Ah, so EGF acts via juxtracrine signaling, and is not some sort of diffusible ligand released by cells? I think this would answer my question if my understanding is correct!

@NaiveHalmos EGF/EGFR do not act via juxtacrine signaling. EGF is soluble, and EGFR is transmembrane. The juxtacrine signaling being referred to by WYSIWYG is the interaction between an immune cell like a T cell and, for example, an activating cell like a dendritic cell.

OK, I'm sorry for continuing this thread far longer than it needed to be, but then was the review I read possibly incorrect about "Various ligands can activate EGFR ... These ligands are expressed as integral membrane proteins." If we consider the main ligand for EGFR to be EGF?

A perfectly reasonable definition of a ligand from Wikipedia:

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose.

A ligand can be anything, so long as it binds to a biomolecule. Often, the ligand is a small molecule or peptide, and the thing that it binds to is a protein. On the other hand, both ligand and binding partner can certainly be proteins (or one could be a Mg$^{2+}$ ion and the other an RNA molecule, etc.). Ligand is a very broad term, and is often used in other biochemical areas aside from signaling. For example, the things that an enzyme binds to (substrates, allosteric regulators, etc) can be called its ligands.
Also, the things you describe in your post:

This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells).

are hormones, which is a much more specific category of thing than is ligand.
Edit
There seem to be some 'ahem'... doubters as to the broadness of the definition of ligand, so, time for some examples from the literature:
From the biochemistry textbook Berg, 7e (emphasis added):

The final step is affinity chromatography with the use of a ligand specific for the target enzyme.

From the paper Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations, Wade et al (emphasis added):

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it.

From the paper Geometries of functional group interactions in enzyme-ligand
complexes: Guides for receptor modelling, Tintelnot et al (emphasis added):

There are many more examples of arginine-carboxyl interactions that appear to have key functional
roles in enzymes, including some in which an arginine-like structure in the ligand interacts
with a carboxyl group from the binding site (i.e., the reverse of that described above).

It is true that the one particular compound that natively binds to an enzyme's active site is often called a substrate, in part to differentiate it from allosteric regulators and other ligands that can also bind to the enzyme. Thus, the set of all of an enzyme's substrates can be thought of as a subset of the enzyme's ligands. Again, ligand is an extremely broad concept that simply refers to something which binds.
Edit 2
Fun fact! The modern word ligand comes from the latin verb ligāre, meaning "to bind". More specifically, ligand derives from the gerundive form of ligāre, ligandus, which translates to something like "(that which is) to be bound".
Not that this has much bearing on how it's used in the modern scientific literature. I just thought it was cool.

Umm as far as I know "the things that an enzyme binds to" are called substrates rather than ligands...

@Nandor Whelp, you're partially right, but mostly you're wrong. An enzyme's substrates are a subset of its ligands. See the edit for more details.

Ligands are not "usually a small molecule." A ligand is something that binds to a receptor. It can be a neurotransmitter, hormone, peptide, protein, bacterial/viral/parasite component, or a higher-order complex made up of multiple species of any of the above. I would suggest completely removing that from your answer, as it's just factually wrong (probably based on the bias of the person that wrote that phrase in WP).

@MattDMo That's legit. I can appreciate your point. If you feel strongly that this is wrong, edit the Wikipedia page and I'll update my quote to match.

OK I now see that ligands can include integral membrane proteins (IMP), however, I thought a hormone has to be secreted by a cell and transported through the circulatory system to another area? If we're working in an in vitro experiment (in a well plate), this clearly cannot happen. So I guess my real question is, if we are considering EGF in a well plate (during a cell migration experiment), is its ligand really an IMP? a soluble factor that diffuses makes much more sense to me, as cell movement and signal propagation may be acting in opposite directions.

@user3521072 First, EGF is not a hormone, it's a protein. Second, there's no rule that says that a hormone "has to be secreted [...] and transported [...] to another area". You can very easily grow cells in a 96-well plate and treat them with insulin or estrogen or whatever hormone you feel like. EGF's receptor is EGFR, which is an IMP, to use your abbreviation. I'm not very clear on why you're thinking that its binding partner (here called a receptor, since EGF is the soluble ligand) should be soluble as well - if it was, how would the target cell receive the signal? (...)

(...) I'm also not sure what you mean by "cell movement and signal propagation may be acting in opposite directions." Cells move one way or another, signaling cascades generally move from receptor to nucleus (to affect gene transcription), or in this case, from receptor to cytoskeleton (to move the cell).

@tel I'm on my phone now, but I'll edit the article as soon as I can tomorrow.

@MattDMo You imply that proteins cannot be hormones but then mention insulin (a protein hormone). See also human growth hormone and follicle stimulating hormone, to name a few.

@MattDMo Actually I believe I misinterpreted your comment. In any event, proteins can be hormones but, as you say, EGF isn't necessarily one.

@canadianer yes, there are several classes of hormones, including peptide-based (insulin, oxytocin, etc.) and protein hormones like human growth hormone. Perhaps my wording was slightly off, I probably should have said "EGF is not a hormone, it's a protein growth factor."

@tel I have corrected the Ligand (biochemistry) wikipedia page to remove the emphasis on small molecules.

@MattDMo I didn't think EGFR was soluble -- I am having a bit of trouble understanding how the EGF ligand can be both soluble and an IMP. But seeing that EGF uses juxtacrine signaling, am I right in thinking that EGF is not soluble, but is an IMP and thus spreads through a population via cell-cell contact? This would clear up my confusion from yesterday. (And you can ignore my statement about cell migration and signal propagation moving in opposite directions -- I was thinking about a very specific, unrelated study)

@MattDMo I changed the quote to match the new one on the Wiki and updated the wording in my answer a little bit to deemphasize small molecules

@NaiveHalmos see my other comment. I think you were getting confused with comments about entirely different things. Just to put it plainly here: EGF is soluble. EGFR is a transmembrane receptor. Plain typical paracrine signaling here, with maybe a bit of autocrine thrown in just for fun in certain cases, like cancer. I don't believe EGF even has a transmembrane domain in its gene sequence, so juxtacrine signaling isn't even possible. Some cytokines and other proteins have both soluble and transmembrane domains, and can be cleaved, so they can signal via both juxtacrine  and paracrine means.

Most ligands are synthesized as the same way as receptors integrated in membrane: synthesized on rough-ER, pulled into the lumen of ER. If proteins synthesized on rough-ER have a hydrophobic amino acid sequence, the hydrophobic region could stay in membrane because inside of membrane is hydrophobic and has affinity to hydrophobic amino acid sequences. Soluble ligands do not have such a region in the sequences, but membrane integrated ligands have it.
As I mentioned above there are ligands integrated on membrane: Fas, TNF, Notch ligand family, etc. As you mention in the question, they are not soluble so that ligand-receptor signaling occurs by cell to cell contact.
You can see various types of membrane integrated ligands from the URLs below.
http://www.nature.com/onc/journal/v27/n38/full/onc2008229a.html
http://www.sanfordburnham.org/talent/Pages/CarlWare.aspx
http://www.sci-online.org/article/view/3946/4855
http://www.bio.davidson.edu/courses/immunology/students/spring2003/swails/fas.html

I don't understand how this answers the question...


text:
Different names in paired-end sequence files
I am aligning paired end sequence reads using bwa mem and I get an error saying that paired reads have different names: "M01814:86:000000000-A6MU9:1:1101:15545:1335", "M01814:86:000000000-A6MU9:1:1101:16059:1338" So it looks like the locations for some of the reads don't quite match up. Is there a way to ignore these reads? Or to use them but not treat them as pairs?

are those Illumina reads?

Yes from the MiSeq

Ok, just wanted to confirm. Will look into it.

Do you have equal number of reads in your files (I assume you have separate files for the two ends).

Yep exact same number in each file.

According to this document : http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm the position of your reads on the sequencing tile don't match, but I think you've figured that out if i'm not mistaken by " it looks like the locations for some of the reads don't quite match up" You could delete these reads to solve the problem. I have no other suggestion without knowing more of your setup.

Yeah I did already figure that out. And deleting the reads would be less than ideal, but may be the route I need to go. Thanks anyway for the help.

I assumed that you've figured this, but wanted to make sure, so that I don't make mistakes while trying to help you. I found some links that might help you resync your files : https://www.biostars.org/p/6925/#6928
https://www.biostars.org/p/12576/#12578 http://seqanswers.com/forums/showpost.php?p=141460&postcount=45
originally from here:http://seqanswers.com/forums/showthread.php?t=46538

Let us continue this discussion in chat.

Paired reads do not have different headers. Most likely these are singletons. You can provide an option to your aligner to not align singletons.

@TheNightman How many singletons do you have? Just parse and see.

I'm not sure how to see how many singletons I have. Do you know how to do this?


text:
Do we have evidence of heritable personality traits in chimpanzees?
I have read that chimpanizees have distinct personalities. Do we have evidence of heritable personality traits in them?

you should add some details such as what all do you include in personality traits. I am not sure if personalities are heritable in humans. Personality has a very large environmental component

Can you add some more background? Where did you read this?

@WYSIWYG the Big Five are considered to have up to 50% heritability in humans, so I don't see a problem with the premise. I don't know if there is sufficient research on personality traits in apes (or how researchers would deal with the distortion which being lab-reared will introduce to a twin study), but I find the question quite interesting.

There has been some research in order to explore this direction, for instance, see this reference:
A. Weiss et al. - "The Heritability of Personality Factors in Chimpanzees", Behavior Genetics, Vol. 30, No. 3, 2000.,
in which the authors study five human-like factors - Surgency,
Dependability, Emotional Stability, Agreeableness, and Openness.
Quoting verbatim their findings:

Only Dominance ... was significantly heritable. Dependability showed evidence that it might be heritable, but the parameter estimates were not statistically significant ... Two other personality traits, Agreeableness and Emotional Stability, showed positive heritability estimates but the parameter
  estimates were nonsignificant and small. Openness and Surgency showed no evidence of heritability.

In fact, the statistical correlation between dominance and heritability makes a strong sense.  Here's what I make out of this - this was a correlation based study, or kind of an experiment, hence the stress on statistical significance. But the question it raises is - is there a causal relationship between the two, i.e. does there exist any proper mechanism for the inheritance of "dominance". Finding such a mechanism was clearly beyond the scope of this study, but I believe the requisite answer for your question is if one stumbles on to such mechanisms, and not statistical correlations, which are mere pointers.
But on the basis of the study at least, all that one can safely conclude is - statistical correlations suggest that inheritance of "dominance" appears plausible, but the exact mechanism of how this implements out in practice, is beyond the scope of this study.


text:
Bacterial capsule vs. slime wall
I've read that the bacterial capsule protects the bacterium from phagocytes and prevents water (and nutrients, possibly?) leakage from the bacterium.
A less organized and less dense version is called a slime layer. It seems that the slime layer has similar functions, according to Wikipedia.
What are the differences between the effects a capsule and a slime layer bring to a bacterium?
I thought about the followings:

The capsule covers most part of the bacterium, so adhesion proteins and transport proteins on the plasma membrane do not work effectively, whereäs with a slime layer, more proteins on the plasma membrane are exposed to the exterior, making them work more effectively.
Maintenance of the capsule takes more energy than that of the slime layer simply because there are more glycoproteins in the capsule.
Bacteria with capsules are less likely to lyse than those with slime layers.

Is there anything else significant that goes on this list? Or are there any points I made that are not true?

According to the Wikipedia section on bacterial capsules, they're made of the same thing:

When the amorphous viscid secretion (that makes up the capsule) diffuses into the surrounding medium and remains as a loose undemarcated secretion, it is known as slime layer.

Todar's Online Textbook of Bacteriology synonymizes "slime layer" and "biofilm":

A true capsule is a discrete detectable layer of polysaccharides deposited outside the cell wall. A less discrete structure or matrix which embeds the cells is a called a slime layer or a biofilm.

This makes sense with what I remember learning about slime walls--the main difference I saw was that the capsule was directly associated with/only protects a single bacterial cell, whereas the slime layer is associated with/protects multiple bacteria. I'm not sure that I'd call it a biofilm though, as those are notoriously difficult to remove; their removal in hospital and food processing sysyems is a current research topic.
Regarding your three points above, I might instead argue that the slime layer provides another layer of protection in addition to the bacterial capsule.

So the slime layer protects multiple bacteria attached to each other due to the polar polysaccharides? If so, is this protection weaker than that of the capsule? Also, I don't understand how the polysaccharides can "diffuse into the surrounding medium". I thought the capsule / slime layer is the network formed by the polysaccharide parts of plasma membrane glycoproteins. How do these polysaccharides detach from their protein parts and diffuse into the surroundings? Or is it just that the polysaccharides have polar attractions with water (and possibly other polar substances)?

From Wikipedia: "The capsule... is a polysaccharide layer that lies outside the cell envelope of bacteria... which can be found in both Gram-negative bacteria and Gram-positive bacteria should not be confused with the second lipid membrane (or bacterial outer membrane), which contains lipopolysaccharides and lipoproteins and is found only in Gram-negative bacteria.

So the capsule is not a network of polysaccharides of membrane glycoproteins but simply a network of polysaccharides.


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What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?
This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different from each other.
So What is the difference between SNPs, Mutations and Structural Variations?

it is always good idea to start with googling and present some results in the question. then move to asking for clarifications,m instead of asking for definitions.

Lets state what a Mutation is first.
Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/GrCH38 from 2013, which are the most current genome assembly).
Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have been validated to be present in more than 1% of the population with the help of Genome-wide Association Studies.
Structural Variations: These are any mutations which cause a change in the organism's chromosome structure, such as Insertions, deletions, copy number variations, duplications, inversions and translocation.
For more please read Wiki Link here.

Thanks to WYSIWYG for his interesting question regarding SNPs.
This piqued my interest a bit, and to my surprise I found that the same actually applies to all other species for example chickens; This paper from way back in 2002 describes how EST mining was sometimes used to generate potential SNPs but also notes the possible false positives due to the possibility of RNA-Editing.
This paper describes the usage of SNPs to allocate bovine individuals to their source population. As does this paper which highlights the economic importance that SNPs may hold for identifying pure breeds and crossbreeds.
Apparently there are also SNP chips available for other animals as highlighted by this particular paper

Is this definition applicable to all species (esp regarding SNP. Can you add some info with references on that) ?

I hope the new edits answer your question

Yes, these terms are well established terms for describing mutations in genetic data. SNV is the more general term for SNP (without restriction of > 1% in popn). You will also hear the terms indel (insertion + deletion) and mnp (multi nucleotide polymorphisms). It should be noted that SNP is often used synonymously with SNV. All these things (SV, SNP, SNV, indel, MNP) are types of genetic mutations.

Nice. Just a minor comment, you don't need to do an association study to establish that an allele frequency is > 1%. Just genotyping.


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Introductory book in genetics?
I am working in the field of neuroscience with a background in computer science. I try to find new ways of analyzing brain imaging data (mostly MRI, EEG, MEG, fMRI) with modern machine learning methods.
I would like to take a step up by adding genetics to the data arsenal. My work this far has found connections between some X and Y but not really shed insight to why things should be like that. I hope I could get a partial answer from biology.
To get started, I would need some good material to read. It does not matter if the content would be difficult in mathematical/statistical/technical aspects, but it should be approachable with limited knowledge in biology and/or chemistry and physics.
Suggestions?

What type of genetics?

You should clarify what you really require in detail. Else this would count as duplicate of the abovementioned post.

GENETICS: Analysis and Principles, 4th edition, Robert J. Booker
This book is used in my school's ( NYU Poly) undergraduate genetics class.

MIT Open Course Ware has a course on genetics, which uses the following text:
"An Introduction to Genetic Analysis", Griffiths, Anthony J. F., Jeffrey H. Miller, David T. Suzuki, Richard C. Lewontin, and William M. Gelbart, 7th ed. New York: W. H. Freeman, 2000.


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Cause of Crease in Drupe Fruit
What causes the crease through the pericarp of a drupe fruit (peach, nectarine, olive)?  It may just be in exocarp as @Ilan pointed out, but I assumed (perhaps wrongly), that the division continued through the pericarp.  I'm also not sure if this true generically for drupe fruit, so I'm not sure which phylogenetic step down to take.  Olives for example have a divot that seems to extend from the stem down, but it stops well before the midline of the fruit in most cases.
I assume the crease has something to the initial genesis of the fruit tissue, but I haven't found any arguments on it's formation.  A more technical term might be "cleavage," but that was after some searching and not coming up with more certain term.
Botany is not my strong suite, but I recently entered into a collaboration where we will be making some recombinant alpha viruses (which is within my strong suite) that will infect drupe tissue.  Finding good pathology papers has been difficult, and they tend to be specific (not trying to imply that's bad).  Can anyone point towards a reference text/article on the genius of drupe fruit if the cause of the "crease" is not clear?  Disruption of the crease seems to be a particular phenotype of infection for some strains, and I'm searching for the correct terminology and mechanisms that might be effected.
If I can get permission I will include photos of an infected vs control peach.  In the mean time to clarify what I mean, the line that seems to transverse from one poll to the other of the fruit:
Peach:

Nectarine:

On the sea mango it is pronounced, but on most other mango it seems like just a slight marking along the exocarp:

Even the coconut seems to have at least one:

What do you mean "crease" - a part of a normal state, or abnormal sign?

@Ilan Part of the normal state.  The outside of the fruit tends to have one line/partition/crease going down it from the outside.  I'm uncertain if there is a technical name, which is where I could be failing in my lit review.  I suppose I could put up a picture and circle what I mean.

I think you should change pericarp to exocarp (pericarp is all-out-of-stone term)

@Ilan I actually don't know if this just on the surface at the fruit or if it extends down to the stone.  That may vary based on species even.  I'm not sure on how many species will be tested, but distorting the line in peaches seems to be an unexpected phenotype.

The structure you are relating to is a seam (suture). This seam is formed during development of a carpel.
The indentation of the seam varies and depends on the climate and environment: for example, water stress will give a very deep suture -

Know any proteins related (screen via Western) or genes (q-PCR)?  We could grab samples in various stages during carpel development (though this particular set of trees might not make it to next year).

@AtlLED check this one out - http://www.ncbi.nlm.nih.gov/pubmed/19264761


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What is a selectively neutral genotypic change?
I am reading the paper "Neutral evolution of mutational robustness". Because I am new to neutral evolution, I have a few questions.

Firstly, from my understanding, genotypic neutrality means the genotype is not responsible for an increase in fitness. What else can we say about genotypic neutrality? Does it have something to do with the population being randomly selected?
Secondly, how to understand a neutral network exactly? Another article says "by linking every pair of genotypes that are mutually accessible through mutations, genotypes organize themselves into neutral networks", so what means "mutually accessible through mutations"?
Thirdly, the neutral network is like an assumed black box we know nothing about, is it right? That is why in the original article with title "neutral evolution of mutational robustness", the authors mentioned that "one can infer important structural information about neutral networks from data on evolving populations."

Thank you for editing @AliceD. I didn't even tried to read the post the first time!

Can you add a link to the two papers and indicate where the citation come from in the papers? I never heard the term of genotypic neutrality but saying the genotype is not responsible for an increase in fitness sounds like there is some semantic issue in your mind. I don't know either the concept of neutral networks. So the papers would help a lot. You should always restrict your post to only one question.

I'd suggest to divide the current post into two and ask for explanation about the meaning of one particular sentence.

Mutations in DNA or RNA sequences do not necessarily result in significant changes in the functions of the proteins they encode (or in the case of RNA ribozymes, ribozyme function ). This is because, for a variety of reasons, the change in DNA/RNA sequence may not significantly alter the structure and function of the ribozyme/protein (the function that contributes to the fitness of the organism). If two alleles of a gene with different sequence have equivalent function (again with regard to the function of the gene that provides fitness) the differences between them are selectively neutral.
The neutral network consists of every variation in the sequence of the gene that can be reached from another sequence (of equivalent fitness) by a single base pair mutation (these aren't the only type of mutation, possible, but they are common and more likely to be neutral than more drastic changes). So for example (using an unrealistically short sequence), if I had a gene with the sequence  0 AACAATGCTGACTGA, and alleles 1 AACAATGCTGACTAA, 2 AACAATGCTGACAGA, 3 AACAATGCTGACTGG with equivalent function, 1, 2, and 3 would be directly linked to 0 in the neutral network as they all differ from 0 by a single base pair. The sequence 4 GACAATGCTGACTAA if of equivalent function would also be in the network as it differs by one base pair from sequence 1.
Each gene in the network being mutually accessible through mutations means that I could start out with any of the above sequences and reach any of the others through a series of single base pair mutations that traverse the network (i.e. I could mutate 0 into 4 by first mutating to 1, another network member, then to 4).
The genotypic space includes the sequences of all extant alleles of the gene. This paper suggests that there is a tendency for these sequences to form these networks and especially to evolve towards highly interconnected networks. This is the structural information the author refers to. It should be easy to imagine how this might confer robustness to deleterious mutation. Let's think about our sequences from above, imagine if every sequence was only linked to two other selectively neutral sequences forming a long chain. The sequence AACAATGCTGACTGA is 15 base pairs long with 45 possible single mutations, if only two of those are selectively neutral, the chance of mutating to a neutral network member is low, and even if you do hit on a neutral mutation, your chance of hitting another neutral mutation next time (reverting back or moving on down the chain) is still only 2/45. Now imagine that the neutral network is highly interconnected, with sequence 0 linked to sequences 1, 2, 3 and several other neutral 1 base pair changes, imagine those sequences are linked through each other by other neutral intermediates (being 2 base pair mutations away from 0). Not only is the chance of a single mutation being neutral higher, but subsequent mutations (remember that these include reversions from prior mutations) are more likely to stay within the network (you're more likely to come back around to 0.
Would you have more long-term success walking around a fitness plateau or walking across a fitness rope suspended over the abyss?

Oh this is what a neutral network is +1! I never heard of this term before. The concept is closely related to the concepts of adaptive landscape and quasi-species. Can you please add a reference that uses the term neutral network as you defined it? Is this term most often used in the  genetic algorithm literature? You talk about the authors. I am not sure which authors you are talking about.

Ah, the original question before the edit sounded as if it was referencing this paper or related literature: http://www.pnas.org/content/96/17/9716.full.pdf
I don't know the body of the literature well enough to comment on how broadly the term is used. I would

Thnks. I edited the post to add the reference. Feel free to roll back and place the reference elsewhere if you prefer.

Great explanation. Two questions. (1): In the last sentence of the forth paragraph, you said "not only is the chance of a single mutation being neutral higher, but subsequent mutations...", I can not see the reason that the chance of a single mutation being neutral get higher. (2): In your last paragraph, long-term success means being more firness? This is an interesting question.

(1) At any given node in the network (a given genotype) the chance of the next mutational event being neutral is higher if that node is connected to many others (assuming the event is random the chance of a neutral event is (possible neutral mutations)/(all possible mutations)). If the new node also has many connections, the chance of a neutral mutation is likewise higher, and so on. Therefore a network in which most nodes have many connections to other nodes (a highly interconnected network) will be more robust to mutation than a network in which most nodes are not linked to many other nodes.

That makes sense to me now. So, mutational robustness means the insensitivity of the phenotypes to mutations, right? In a highly interconnected neutral network, the phenotypes would be more insensitive to mutations, because the fractions of neutral mutations are higher. --


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Can you Transfer Cancer Between People via Saliva or other Bodily Fluids?
This may sound like a strange question. But could a Cancerous cell be transferred from one person to another from Oral contact e.g. Through Saliva, or other exchange of bodily fluids?
I know that other diseases from Bacteria / Viral can be transferred in this way, but does the same apply to Cancerous cells? - or would the recipient's body just breakdown and destroy the cancerous cells?

have you done any research on the topic on your own? simple googling might give an answer

Possible only if they share the exactly same HLA types. In other words, it is almost impossible.  It is taboo that researchers culture cells from their own tissues and experimentally transform the cells to get cancer phenotype. Such transformed cells could grow when the researchers accidentally contact them because rejection would not occur. But, I think oral contact would be safer than wounds.

Although transmissible cancer has been found in some species, such as Tasmanian Devils and clams, it is quite rare in most species. Certain viral and bacterial agents that cause cancer, however, can be transmitted. One example is HPV, which can cause cervical cancer

Cancer is successful at killing it's victims because it is genetically still very similar to the host.  The immune system does not respond to it sufficiently to eradicate the mutated cells and this allows it to grow out of control.
When dealing with any kind of transmittal this would be close to an organ donation.  Without a very close match, and Immunosuppressants the body will "reject" any cancer cells, and wipe them out.  Saying this here have been freak incidents where in an organ transplant scenario, cancer was transmitted.


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Can all animals of the same species crossbreed?
For example, take Canis lupus, the species of dog and wolf. Within their species, can all dog and wolf types crossbreed? We can forget the logistics and assume this is all done through artificial insemination or in vitro methods (let's assume that the in vitro methods would be feasible).
If yes to the main question, does cross-breeding stop at the species class, or does cross-breeding extend across other taxonomic classes? From what I gathered, the taxonomic classes seem somewhat loose in their definitions. Perhaps I should ask, is there a rule "in general" to cross-breeding?
Let me know if this question ought to be refined in any way.

To clarify; you are mainly asking if all individuals within the same species can interbreed?

Whether dogs (Canis familliaris or Canis lupus familliaris) and wolves (Canis lupus) are the same species is debatable. I believe the modern consensus tends towards considering them different subspecies of the same species but as far as I know, the details are not entirely clear. Remember that the line between species is blurry at best.

@fileunderwater Yes, for the most part. The choice of species was a bit arbitrary. I'm wondering if there is a general rule as to what individuals can interbreed with others. Within a species just makes the question a bit more specific.

Can and do is a big difference a lot of things we consider different species can breed if we force them.

Species definitions are a somewhat contentious part of biology. There are no hard boundaries in nature that mean "this group here is one species, this group here is another species". Some people don't even believe that species truly exist and there are only gradations of relatedness. That being said, the Biological Species Concept is one of the more popular species definitions.
From the linked website: "The biological species concept defines a species as members of populations that actually or potentially interbreed in nature". Thus, by definition, all animals of the same species can and do interbreed in nature. If two individuals breed in nature, they are considered the same species (under this definition).
Of course, you can already see some problems with this definition. Under the BSC, are a dog and a wolf the same species? Do dogs and wolves breed "in nature"? Of course, fertile half-dog half-wolf animals exist, but does it even make sense to ask whether a domestic species breeds "in nature". I suppose you can say they can "potentially" breed in nature. But how do you define "potentially" breeding? Asking questions about species can lead to many exciting debates.

breed and give rise to fertile offspring will be more precise definition?

@aaaaaa Yes, that is correct

I'd say it's "in nature" if the male wolf or coyote comes from the wild to your domestic bitch who happens to be in heat.

even this definition runs into problems things like ring species A can breed with B and B with C but A can't breed with C,, it is also completely useless for asexual organisms or extinct organisms. that is why there are more than a dozen working definitions of species.

Even under the Biological Species Concept, there is no requirement for universality of interbreeding. It is a population level definition, not an individual ones. Genetic incompatibilities that prevent successful reproduction are extremely common.

No, definitely not. Even under the Biological Species Concept (BSC) the requirement for interbreeding applies at the population level not at the individual level.
The most common example of how the mechanism breaks down are Ring Species. In the simplest case there are three populations - call them A, B, and C - where A can breed with B, B can breed with C, but A and C cannot directly breed. Because there continues to be genetic flow across the whole collective they are considered to be a single species under the BSC. Two real world examples of ring species are Larus gulls and the Greenish Warbler.
However, the biggest example is simply the majority of species which are asexual and thus cannot cross-breed at all. This, and a host of other problems, are why many biologists reject the BSC as a functional definition of the species concept.

Try breeding a Chihuahua female with a Great Dane male. Both are dogs.