What is the biological mechanism underlying caffeine intolerance? (CYP1A2 or other?) As far as I can tell, caffeine metabolism occurs primarily via the CYP1A2 enzyme. I am curious as to whether mutations in the CYP1A2 gene are associated with caffeine intolerance.  Some site that is not necessarily reputable suggested that caffeine intolerance is due to absence of the enzyme to metabolize caffeine. I am having difficulty finding evidence either supporting or contradicting this claim.

Does anyone know if there is evidence that suggests mutations in CYP1A2 (and therefore inability to properly metabolize caffeine) are associated with caffeine intolerance, or if there is another proposed mechanism for caffeine intolerance?

I have found that caffeine is mostly metabolized over CYP1A2 (as we know), but also over CYP1A1, CYP2E1 and CYP3A4. The question is how much the individual can cope with this alternate pathways if he is a CYP1A2 poor metabolizer. [1]

Secondly I found in my pharmaceutics textbook that CYP2A1 activity determination is indicated due to undesirable side effects to caffeine and theophyllin.[2]

UPDATE: 19.03.2013 12:30 GMT+1

@dd3: To clarify the second statement: I used the approach that theophyllin and caffeine are similar xanthin derivates. Since theophyllin is used as therapeutic drug in respiratory diseases (COPD etc.), I thought that scientific interest would be greater. And yes CYP1A2 plays an important role in both theophyllin tolerance and intollerance.

I found some new sources:

At first a study with CYP1A2 knock-out mice, which shows that the elimination of theophyllin takes 4-times longer in CYP1A2(-/-)mice. And they also assume that the same behaviour is also applicable to caffeine. [3]

Also there are two clinical studies by Japanese and Turkish scientists. The Japanese conclude, that theophyllin should be used with care in CYP1A2 poor metabolizer (even in haplotype poor metabolizer), since theophyllin has a narrow therapeutic range.[4] But the Turkish scientist assume that according to their findings, theophyllin is also metabolized over alternative pathways such as CYP2A13, CYP1A1, CYP2E1, CYP2D6 and CYP3A4. And according to this the genetic status of CYP1A2 is not as important as expected. [5]

Conclusion:
Assuming that theophyllin and caffeine are metabolized similarly, you can conclude that a mutation in CYP1A2 would lead to caffeine intolerance. In my experience people with caffeine intolerance describe severe nervousness after drinking a cup of coffee. Fatal cases I know were due to high consumption of energy drinks in children without or at least not known caffeine intolerance.

Sources

[1] http://informahealthcare.com/doi/abs/10.1081/DMR-120001392
[2] german source: http://www.medizinische-genetik.de/index.php?id=2642
[3] Derkenne S, Theophylline pharmacokinetics in mice: http://www.ncbi.nlm.nih.gov/pubmed/15970798
[4] Obase Y, Polymorphisms in the CYP1A2 gene and theophylline metabolism in patients with asthma. http://www.ncbi.nlm.nih.gov/pubmed/12732846
[5] Ahmet U, The effect of CYP1A2 gene polymorphisms on Theophylline metabolism and chronic obstructive pulmonary disease in Turkish patients http://www.jbmb.or.kr

Further Reading:

Xanthines as therapeutic drugs: http://web.carteret.edu/keoughp/LFreshwater/PHARM/NOTES/Xanthines.htm


Plant growing inside a fruit Today after cutting open a papaya , a plant was found in it:

How is it possible for a plant to grow in a fruit? How does it gets $CO_2$ and light for photosynthesis?

That is a papaya seed showing vivipary, or premature sprouting. The plant is getting all the sugar it needs from the nutrients stored in the seed so it does not photosynthesize. If it were to run out, the plant would die.


Are identical twins exactly the same? http://www.scientificamerican.com/article.cfm?id=identical-twins-genes-are-not-identical

According to this article some identical twins show differences with respect to their copy number variants. How is this possible? If mitosis of an egg can lead to this difference, why can't mitosis of any cell in our body?

If we assume that identical twins are exactly identical, then if we make a clone of a twin will all three be exactly identical?

Errors in division occur all the time and can show up in any dividing cell; this is, of course, important for cancer biology.  If one of my cells replicates oddly right now it likely won't matter since it's only one out of trillions, but if that happened at a very early age in development it could be present in many if not all of my cells.  Identical twins indeed come from the same egg-sperm fusion event but they develop separately from a very early state.  It's trivial to imagine a minor replication error in DNA at an early cell stage that results in different genotypes between so-called identical twins.  Besides, we've known for years that identical twins can have major epigenetic differences, so this isn't particularly ground-breaking.

  If we assume that identical twins are exactly identical, then if we make a clone of a twin, will all three be exactly identical?

Depends on your definition of "clone" but how identical is identical?  If you mean exact, then probably not; at the very least they will have different numbers of cells, for example, not to even mention CNV or epigenetics.  If you want some SciFi cloning thing then, well, join the club.


How the vaccine based on "non replicating viral vector" is produced? As I understand, this kind of vaccine is a virus that can infect the cell, start synthesis of  proteins encoded by its genome, but cannot finish the replication cycle till the proper end. It can have extra genes in its genome, encoding proteins that cause the wanted immunity to develop. Some important vaccines against COVID-19 are based on this approach.
The question is, how such an "incomplete virus" could be produced in large amounts? It would be logical to assume that it was replicating during the manufacturing process, but then why does it cannot any longer? The only hint I found is the usage of the "helper virus" that infects the same cell, so the "incomplete virus" can borrow some parts from the healthy "coworker". However this raises another question: the helper virus obviously replicates also itself, and how to discard it later without inactivating the "non replicating" one? It would just cause infection without any use if not discarded.
I have done some search over web and article databases but was not able to find a short and clear explanation of this method. The main focus of the works I found is always somewhere else. I understand that exact technology may be secret, but it is likely at least remotely based on some research work anyway.
How is a "non replicating vector" replicated to produce enough of it, for making a vaccine out of it?

Complementing cell line (or complementary cell line) is a cell line which has been genetically modified to produce proteins necesary for non-replicating virus replication. It is designed to express exactly the genes which had been deleted from virus to render it non-replicating. The non-replicating viral vector can replicate only in complementing cell line and not in other cells.


Do we actually get more sick (flu/cold) during winter? The word flu derives from the Italian phrase "influenza de freddo" meaning "influence of the cold".

Indeed it is that time of the year when my colleagues seem to have the flu/cold more often than not. I remember during university, winter lectures would be riddled with people coughing and sneezing - the so called "freshers flu"

Questions

Is there statistical evidence for this claim?
If so, what are the causes/factors involved?
Another post asks why our noses get runnier during cold whether, is this related?

The combination of these two reports from the CDC give information about the comparative prevalence of flu infection in the winter (September '12- May '13) and summer (May '13 - September '13). I'm going to assume that 2012-2013 was a fairly representative year as far as the level of detail of "do we get sick more in the winter" goes. Particularly striking are the graphs linked to in both documents of the number of flu-infected respiratory specimens per week:

Winter (infected specimens out of 311,000 tested):

Summer (infected specimens out of 52,000 tested):

Together these two figures cover data Sept '12 - Sept '13. Note the difference in scale on the vertical axis. Forgive me if I don't run any statistical tests, but I think you can spot the trend.

The sum of all the Winter cases represents 23% of the 311,333 specimens tested from Sept '12 to May '13, and the sum of all the bars in the Summer figure represents 3.9% of the 52,150 respiratory specimens tested from May '13-Sept '13.

Still left to answer: Why is this the case? In my preliminary research it seems like we still don't fully know the answer to this one; I'll leave someone else to speculate.

Edit: Some tentative answers to why is there a seasonal flu outbreak:

This review (1) does a nice job of laying out some of the current ideas about the cause of the seasonal flu. One interesting note is that seasonal flu is a phenomenon of temperate climates: in tropical regions flu outbreaks occur on a much less regular periodic schedule. Some possible causes mentioned by the authors (paraphrased from the article):

It takes time for virus to mutate enough to be infectious again to people who were already infected with it.
The efficacy of the immune system may vary seasonally, say, due to changes in daylight hours/vitamin D and melatonin levels (which have been shown to affect immune system function in hamsters)
Flu is transmitted better in more crowded conditions + in winter people are more crowded together. This is a popular explanation, but the authors claim that it has not been satisfactorily tested. It has been argued convincingly that the 1918 flu epidemic was exacerbated by the crowded condition of army barracks in WWI (see citation in paper).
Indoor heating encourages air recirculation, which allows virus to persist in the air around you longer.
Viruses survive/persist better in cold, dry conditions. This may allow them to spread in the atmosphere longer during the winter, and be more easily transmitted from person to person via "bioaerosols" (sneezes).

Ultimately, as I said before, we don't really know yet. Reading that list you can imagine several ways in which a few of those factors are not at all causal and are rather just strongly correlated with the "true" cause of flu seasonality.

(1): Lofgren et al. Influenza Seasonality: Underlying Causes and Modeling Theories. (2007). J. Virol. 81(11): 5429-5436. doi:10.1128/JVI.01680-06


How does pressure measured by sphygmomanometer translate directly to blood pressure? As per my understanding a sphygmomanometer when wrapped around the arm and inflated only measures the pressure of the air inside the cuff, doesn't it? How does that translate directly to the pressure value of blood flowing across the artery?

Korotkoff sounds!

The blood pressure measurement process is fairly cool, and goes like this.

Inflate the cuff to well over plausible blood pressures (250mmHg or so).
Slowly deflate the cuff while listening to the artery.
When you start to hear sounds, that's when the systolic blood pressure is higher than the cuff pressure and the heart can squeeze a little blood through the cuff, which makes a little squirty noise.
As cuff pressure continues to drop it stays between the systolic and diastolic blood pressures and therefore bloodflow stops and starts and creates audible turbulence.
When the artery stops making noise, the cuff pressure is below the diastolic blood pressure and the cuff has no effect on the artery, so it goes back to laminar flow that doesn't make noise.

Measuring the pressure of the cuff is just part of controlling the pressure of the cuff. You could conceivably measure blood pressure by submerging their arm in water(mercury would not require a conversion, but vats of mercury are unpopular in doctor's offices) and listening for Korotkoff sounds and measuring the depths where they start and stop.

Edit: The actual question here is how does cuff pressure physically change the arterial surroundings, not how do we link the two clinically.

The body is mostly water, and water is incompressible. For small strains(amount of deformation) flesh isn't that springy and mostly "flows" like water. When you pressurize the cuff around the arm, the flesh of the arm equilibrates to the cuff pressure the way balloons equilibrate to the air pressure, only less dramatically because water is mostly incompressible. For small pressures and large cuffs, therefore, the cuff pressure is the pressure on the artery wall, and by listening for Korotkoff sounds while varying the cuff pressure the blood pressure can be roughly established.

The reason why you don't lose all blood flow to your extremities while diving underwater is because the systemic pressure on all of your body raises your internal blood pressure, making the net external pressure on any part of your body zero. (The cuff works by exerting a relative pressure difference on part of your body.) At high altitude the sphygmanometer is still accurate-ish because the cuff pressure relative to the atmosphere is still the same as the blood pressure, relative to the atmosphere. If you had air for blood(or any compressible fluid) your veins would collapse underwater. This is why your ears hurt while diving deeply if you don't equalize them: your ear is full of compressible air, and at depth the air attempts to shrink more than the flesh around it, pulling things out of place painfully.


Relative microRNA comparison from from TCGA data? I have a conceptual question that I was hoping someone could answer.

Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data?  Can I do this after normalizing the data?  Does it matter if I use RSEM or RPKM values.  It seems to me that it should be legitimate in any case since microRNAs are approximately the same length, but maybe I am overlooking something.

For example, I am following a paper published in Nature Communications entitled "Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif".  The authors download the data and collapse isoform reads to a single read count using the reads.  They say they used the reads per million microRNAs mapped, which establishes each microRNA read count as a fraction of the total microRNA population.  The authors then do upper quartile normalization which they say is important because a subset of microRNAs (miR-143 in particular) contributes so significantly to the total read count.  In the text, the authors appear to use the resulting values to do a direct comparison between microRNAs.

I definitely want the collapsed isoforms, and I think it makes sense to do the normalization.  However, I would like to say that a particular microRNA is expressed x-fold higher than another.  Can I do this from the collapsed and normalized data?

If this has already been answered, I apologize.  I could not find it.  Thanks.

I would be very careful in making such a claim from sequencing data. There are well known biases in sequencing due to things like GC composition and hexamer composition. Because of this, it's possible to compare relative levels of some species across treatments but tricky to do so within a given sample or samples. One way around this is to perform qPCR using absolute quantification on a few samples and then compare that to sequencing results. Granted, you're not going to have the same samples as TCGA or exactly identical library prep, but it'll be a reasonable starting point. You could then use that to calibrate how reliable the relative levels might be within the TCGA dataset.


Pyruvate as a final electron acceptor in the electron transport chain During anaerobic respiration, why are electrons carried by NADH not transferred to the electron transport chain (ETC)? What happens is that lactate dehydrogenase reduces pyruvate to lactate, while removing H+ from NADH to form NAD+.

Why doesn’t pyruvate simply take the place of O2 as the final electron acceptor in the ETC during oxidative phosphorylation? Electrons would still be able to flow through the ETC and allow for the regeneration of NAD+, wouldn't they?

Someone else may come along later with a definitive answer but I found this question intriguing so here are my thoughts:

The standard redox potentials of the mitochondrial ETC carriers are:

NAD⁺/NADH              -0.32 V
complex I (Fe-S)       -0.27 V
complex II (cyt b₅₆₀)  -0.08 V
complex III ((cyt c₁)  +0.23 V
complex IV (cyt a₃)    +0.38 V
O₂/H₂O                 +0.82 V

Note that electron transport is carried out from negative to positive.

Now, for pyruvate/lactate the standard redox potential is -0.19 V so on the basis of this pyruvate could in theory accept electrons from complex I, but not any further down the chain. However, complex I normally transfers electrons to coenzyme Q within the membrane. The standard redox potential of CoQ is +0.04 V which is already too positive to be able to then reduce pyruvate at the membrane surface. Thus there would have to be a novel way of transferring electrons from the final FeS centre of complex I, which is within the membrane, to pyruvate. Pyruvate is, of course, soluble and is generated by cytoplasmic glycolysis, so this transfer would have be at the membrane surface that faces the intermembrane space of the mitochondria.

If such a scheme had evolved then it might be possible to achieve some proton pumping through the novel version of complex I, which would be  energetically advantageous.

Another complication is – assuming that a complex I with pyruvate as electron acceptor had evolved – how would the cell/ mitochondrion regulate electron flow during aerobic respiration? Presumably the pyruvate-accepting version of complex I would have to be kept inactive somehow until needed.

Clearly it is much simpler to have a soluble lactate dehydrogenase to deal with the pyruvate and regenerate NAD⁺.


What is going on with these buccal epithelial cells? A pooled saliva sample from a 70 year old male. What is happening with these cells?

Are these cells undergoing normal apoptosis?

In the video, the cytoplasmic movement looks liquefied and jelly-like (A).

B looks more granular, with small vacuoles that seem to have bacterial activity in them (what could this be?).

Elsewhere in the sample were completely detached, intact nuclei.

Could this be indicative of diabetes? http://www.jdrntruhs.org/temp/JNTRUnivHealthSci1133-9277352_023437.pdf

The cell you've marked "B" is dead, as is common in cells in a saliva sample. The particular path to cell death is very hard to say with an unstained light micrograph, but the fact that you have a dead blebby cell in a saliva sample is not diagnostic or indicative of anything.


CDK3 1 simple coding mutation/missense mutations (S106N) glioma I found the below quotation in (Peyressatre, 2015)

  CDK3   1 simple coding mutation/missense mutations (S106N)   glioma
  [135]

The author has cited a database but not a paper. I want to find the paper that talks about the above mentioned type of mutation in CDK3

Good question, if you check COSMIC and search for S106N, you'll find no hit with CDK3. So it isn't there (anymore?). One possibility is that it was present in 2014, when the paper was written, and the mutation is removed in the mean time by curation.

However, if you look at genecards and look for the variants, on top of the table you'll find a link to expasy. here they cite to a paper in Nature, and in the supplementary data of this paper you'll find your CDK3 S106N mutation.


Does Rough ER (RER) produce phospholipids? I have found out that rough endoplasmic reticulum (RER) produces membranes. Therefore it has to produce phospholipids, but I thought that the smooth ER was where the synthesis of lipids occurs.

What specific part of the ER produce phospholipids?

The endoplasmic reticulum (ER) is one of the largest continuous membrane bound organelle of the cell.

The rough ER and smooth ER share the same membrane and some membrane proteins can diffuse between them. At the same time there are specific markers for ER sheets (rough ER) and ER tubules (smooth ER). The terminology of rough and smooth come from early electron microscopy and biochemical work where large amount of ribosomes (polyribosomes) were found on the rough endoplasmic reticulum membrane, and less on the smooth. These membranes can be biochemically separated one being more heavy (RER because of attached polyribosomes) than the other.

In general the ER has several functions: protein synthesis, calcium storage, entry of the secretory pathway and lipid synthesis. It can not only produce phospholipids but also a large array of precursors for steroids and neutral lipids.

This is a topic of research itself but it is general thought/accepted that the smooth ER is the one responsible for the synthesis of phospholipids.

In reality, there are multiple ways to produce phospholipids (from recycled membranes, from lipid droplet stores, etc) and there are multiple possible pathways for producing lipids and lipids precursors (de novo synthesis). This also implies that there are multiple enzymes involve in this process. Now these enzymes are often ER membrane proteins and they can but do not always specifically localize particularly to one part of the ER.


How likely is it that Earth has millions of different species? I know that the probability of life existing on a habitable planet is pretty slim. But, how likely is it that it hapenned millions of times in the same planet? Or was it only a few species that evolved into millions of other different species over time?

We can be reasonably certain that ALL species that exist today share a common ancestor, a common origin. Every single species we have even encountered, for example, uses a long chain of nucleotides (DNA or RNA1) to store its genetic information. If life had arisen through multiple independent sources, we would expect to find different solutions to the problem of passing genes to offspring.

To put it another way, all forms of life we have found can be placed in one of three main classes (superkingdoms): eukaryotes, prokaryotes and archea. All other types of life come under one of those three categories (viruses are special and not really considered alive2):

Now, any organism we have ever seen uses the same basic systems of storing its genetic information. In fact, there are even certain genes that are conserved (similar in sequence) across all domains of life (see my answer here for some examples). That is why this version of the tree has a common root. All lines start from a single original line (commonly known as the Last Universal Common Ancestor, LUCA).

In summary, all the evidence we have points to a single origin of life. There are too many shared features to assume multiple origins. Despite their enormous diversity, all organisms share certain very basic systems.

NOTES

As far as I know, only certain viruses use RNA instead of DNA, all truly living creatures use DNA. Even if I'm wrong about this, the differences between RNA and DNA at this level are small enough that the common origin still holds.
See here for more in why viruses are not alive.


Why are eggs "egg" shaped? Is there a reason as to why chickens lay "egg" shaped eggs, as opposed to spherically shaped eggs (or a random shape)?
For extra points:

why do plant seeds often come in this same "egg" shape (e.g. avocado
seeds), as opposed to a sphere?  Is it a coincidence that avocado
seeds and eggs are the same shape?

There is variance in egg shape; sea-birds often use a more pear or conical shaped egg to prevent it from rolling off the cliff (where they nest) if it is disturbed. Some reptiles lay very spherical eggs (some turtles) whereas some reptiles lay very elongated ones (see black pine snake eggs).
I imagine that we don't see square eggs because they would be difficult to shape and difficult to lay. Shape may also influence strength.
Google your question (like I did after writing the above) and it will come up with this article which pretty much says what I just did. Here are some of the author's key points...

"If eggs were rectangular little boxes, they would be very strong on the corners, but very weak in the middle of the straight walls."
"The strongest shape of all is a ball, or sphere. But if you were to push or gently nudge a spherical egg, it would roll away downhill, never to be seen again."
"So one reason that eggs have an asymmetric tapered oval shape is that if you nudge them, they'll come back to you. They'll sweep out a circle around the pointed end, and come to a stop with the pointed end facing uphill. In fact, the eggs of birds that have their nests on cliffs are more oval than the eggs of birds that nest on the ground. This means the 'more-oval' eggs of these cliff-nesting birds will roll in a very tight little circle, and be less likely to roll out of the nest — and off the cliff."
"Another reason for eggs to be egg-shaped is that they fit together quite snugly in the nest, with only small air spaces between them. "
"Yet another reason that eggs are tapered is so that they can get pushed out of the hen."


Is there a scientific proof that smoking spoils face skin? I saw that cigarettes-smokers (more than 3 cigarettes per day) often have the skin of the face which is a little bit spoiled.

Is there any scientific proof that cigarette smoke (or the nicotine inside it) is a damaging fator for face skin?

Or it is just due to the skin-smoke interaction casued by the smoke that the person breaths out from the mouth?

This page is pretty complete with examples and references.

In summary a lot of the evidence is empirical - you look at smokers and the quality of their skin and compare to non-smokers and the differences are statistically significant and reproducible.  It seems as if this is old work, dating from the 1970s.

So in many cases these are only observed correlations.  But they are pretty strongly agreed upon by medical people.  Given the fact that we still don't know exactly what causes cancer, I think this is not an unusual level of explanation for medical conditions.

As you can see some theories would include direct effects of the smoke and some indirect effects.

  It is not certain exactly how smoking causes early ageing of the facial skin. Theories include:

  Heat from the cigarette directly burning the skin
  Changes in the elastic fibres of the skin
  Narrowing of blood vessels (vasoconstriction), which reduces blood supply to the skin and can cause changes in skin elastic fibres and
  loss of collagen
  Reducing Vitamin A levels and moisture of the skin


How are subspecies defined, in contrast to species? When should a taxon be considered to be a subspecies of a certain species, and when as a different species? Are there some general guidelines how to assign a specific taxonomic status to a taxon?

Generally speaking, different species can't interbreed. For example, a giraffe can't mate with a gorilla.

Occasionally, very closely related species do interbreed - e.g. lions and tigers breeding in zoos. But the offspring are generally infertile.

Subspecies can interbreed, but they seldom do simply because they're separated from each other.

For example, consider the brown bear and the wolf, each of which have vast ranges embracing a wide variety of habitats. A subspecies adapted to a montane environment isn't likely to breed with a subspecies adapted to a desert environment. Of course, it would have been virtually impossible for a Eurasian wolf subspecies to interbreed with the wolf subspecies that lived in Newfoundland prior to its eradication.

The separation doesn't have to be geographic. Subspecies can sometimes evolve physical or behavioral differences that inhibit them from breeding with other subspecies.


Blood draw from the elderly or those with tiny veins A lot of people have very small veins making it next to impossible to draw blood.

Would a nitroglycerin tablet (or some other vasodilator) before drawing blood help to enlarge veins?

When we need to collect blood from patients we typically draw blood from peripheral veins that are superficial. These are the veins that you can see in some individuals hands and forearms. There are superficial leg veins that are visible. Drugs like nitroglycerin or other vasodilators do not have significant effects on the superficial veins that you'd be trying to withdrawal blood from in the extremities (i.e. arms and legs).

If you wanted to really engorge someone's veins, you'd likely have to load them up with intravenous fluids. However, this would not be safe in patients needing routine blood draws; especially elderly people who might become fluid-overloaded to the point at which the develop congestive heart failure. Younger patients might temporarily have minimal increases in their circulating blood volume, but their kidneys would very quickly eliminate the excess fluid as urine.


Details of Needleman–Wunsch algorithm I try to understand details of the Needleman–Wunsch algorithm and use an example from the book [Nello Cristianini, Matthew W. Hahn. Introduction to Computational Genomics. A Case Studies Approach, www.computational-genomics.net].

To my opinion, the algorithm is described not very neatly, so the question arises.

Consider two sequences:

I: VIVALASVEGAS

II: VIVADAVIS

The first step is clear:

Also, the calculation of the score for diagonal neighbor is also clear,

because this is an alignment without a gap:

I: V

II: V

Unclear moment is the alignment for left (or above) neighbor. Say, the left  neighbor

corresponds to this

I: V

II: -

or this

I: -

II: V

alignment?

This is a classic application of dynamic programming in bioinformatics, and is one of the first dynamic programs that I was exposed to in university! Let's begin..

Overview of algorithm

Step 1. Conceive of a scoring system.
 Step 2. Create a table using the two character sequences.
 Step 3. Iteratively fill in each cell, row by row, left to right. This is achieved by selecting the maximum (most positive) value coming from either:

(1) the cell that's located diagonally (top-left) to the current cell, plus the "cost" to align the two characters in consideration (cost value is obtained from scoring system).

(2) the cell to left of the current cell, plus the gap penalty (score issued for insertion/deletion mutation); looking at your example, the gap penalty is -1.

(3) the cell just above the current cell, plus the gap penalty.

Again, the greatest (most positive) of these three [sum] values will be placed in the current cell.

..

If you want the recurrence relation for this, then, if $T$ is the table being filling in, and $T(i, \ j) \equiv T(row, \ column)$, then

$$T(i, \ j) \ = maximum \begin{pmatrix}
T (i-1, \ j-1) + [alignment \ cost],\\
T (i, \ j-1) \ + [gap \ penalty],\\
T (i-1, \ j) + [gap \ penalty]
\end{pmatrix}$$

Scoring system

For simplicity sake, and to remain true to your example, I'll define and use the following:

Character match score: 0
Character mismatch score: -1
Gap penalty: -1

The character scores are potential alignment costs, and which to use is determined by if the two characters in consideration (row vs. column) are the same or not.

Now, to fill in table $T$..

Let sequence 1 run along the rows of $T$, and sequence 2 run along the columns, as you already have. If $T$ is initialized with a value of zero at location (0, 0), then, in order to fill in the first row [going from cell (0, 1) to (0, 9)], since there are no diagonal cells that exist yet, nor is there yet a row above the current row, for all cells in the first row we will use the second option that was mentioned above to obtain each cell value. So then, with the gap penalty being defined as -1, the first row will range from 0 to -9.

Make sure to keep track of which adjacent cell was used to obtain the value for each cell. This descriptive will later be used to trace $T$ once it's completely filled out, in order to obtain the optimal solution. If you're writing this on paper, people usually just draw arrows (from current to adjacent cell), however, if it's on a computer, an adjacency matrix is created & filled in.

In cases where more than one adjacent cell yields the greatest value, draw an arrow to each one. This is to say that there can be more than one optimal solution.

Next, we start with the first cell of the second row. Since a left & diagonal cell doesn't exist, that omits options 1 & 2, and leaves only option 3, which yields a value of -1 (only gap penalty). And, as you maybe have noticed by now, this behavior will always be true for the first row, and for the first column, and so, this is why you're able to so immediately fill out the table as you already have.

Continuing, to compute cell (1, 1), we now have to compare all three potential values and choose the maximum. For options 2 & 3, they both yield a value of $-1 + (-1) = -2$, however, option 1 yields $0 + [alignment \ cost]$, and, since both characters are the same (V and V), cell (1, 1) will have a value of $0 + (0) = 0$.

If we're to then fast forward a little and calculate cell (2, 1) ...

Considering option 1, we have $-1 + (-1) = -2$, since the characters being compared are I and V (and are a mismatch). Option 2 yields a value of $-2 + (-1) = -3$, and option 3 gives $0 + (-1) = -1$, hence, cell (2, 1) = -1.

Continue doing this for all cells until $T$ is filled.

Obtaining an optimal solution..

As mentioned, multiple optimal solutions may exist. In order to obtain an optimal solution, you must trace $T$, using the arrows you've been drawing (or the adjacency matrix), as a guide.

To obtain the path for best alignment, simply begin with the bottom-right most cell of $T$, i.e. the most recent/last computed cell, and trace your arrows to create a path back to the first cell (the top-left most).

To then construct the alignment, you will traverse this alignment path, beginning with the top-left most cell, and going to the bottom-right most cell, and, when considering the orientation of each arrow when going from cell to cell (diagonal, horizontal, vertical), you will do one of the following:

Diagonal arrow

For the first alignment sequence (top), simply add the character that's in the column of the cell you just moved to; for the second alignment sequence (bottom), use the character that's in that row. So then, when considering your example, and for both sequences, the first characters of an optimal solution when going from cell (0, 0) = 0 to cell (1, 1) would be:

V

V

Vertical arrow

When this happens, it means that there is a gap in the [initial] sequence that runs along the columns, since there are two rows for one column. Because of this, for the first alignment sequence, you will use a - to denote a gap. For alignment sequence two, use the character that's in the row.

Within the context of your sequences, for the optimal solution, a gap isn't encountered until the 7th character, at which point, the partial optimal solution will look like:

V I V A D A -

V I V A L A S

Horizontal arrow

This is the same concept as the vertical arrow rule, except it implies there is a gap in the row-oriented sequence, and so, a - will be placed in the second alignment sequence; the first alignment sequence will use the character in that column.

After all is said and done, your optimal solution is:

V I V A D A - V I - - S

V I V A L A S V E G A S

An interactive version of this algorithm can be found here.


Are carbohydrates an essential component of human diet? Are people able to satisfy all the needs of a healthy diet without consuming carbohydrates?

My question includes the assumption that a person has no health condition that would prevent them from meeting their caloric needs with only fat and protein.

I'm also not asking about the practicality of eliminating all carbohydrates.  If a person could consume no carbohydrates whatsoever, this other question would clearly matter a lot, but I'm not asking it.

If there are essential dietary components that happen to be carbohydrates, but are not converted into glucose, I'll say up front that it wouldn't satisfy what I"m asking.  However, it would be interesting footnote on an otherwise correct answer.

From a theoretical perspective this is a very interesting question, mostly because it is difficult to completely abstain from carbohydrate intake on a normal diet. Even the popular low carb diets of the late 1990s and early 2000s (e.g. Atkins Diet, South Beach Diet) were just that, they were Low Carb, Not No Carb.

We know there are essential dietary nutrients for humans, like essential fatty acids and essential amino acids. The reason that these must be obtained in the diet is because humans do not have the enzymes to synthesize these nutrients de novo (aka, "From Scratch").

From a biochemical perspective we know that fatty acids and acetyl-CoA cannot be converted back into glucose or other carbohydrate intermediates. This is because of the irreversible biochemical reaction catalyzed by pyruvate dehydrogenase, which converts pyruvate to acetyl-CoA. Thus, fatty acids (lipids) can be oxidized to acetyl-CoA (for the TCA/Krebs Cycle) but cannot be further converted to glucose within the body.

In terms of protein, however, amino acids are either glucogenic, ketogenic, or both. If amino acids are ketogenic, then this means they can be converted into acetyl-CoA for the Krebs Cycle. If amino acids are glucogenic, then it means that they can be broken down into glucose. The breakdown of amino acids can be used to synthesize glucose or for anapleurotic reactions of the Krebs Cycle.

As stated in the editorial noted in the comments of this question (From the American Journal of Clinical Nutrition), there are daily "requirements" for carbohydrates. However, it does not appear that any diseases are unmasked by very low to zero carbohydrate absorption (which is most closely occurs in the Inuit populations whose diet is entirely fat and protein).

So, if you ask the question "are carbohydrates essential components of a human diet?" the answer would be probably not. However, as mentioned above, carbohydrates are ubiquitous and it is impossible to abstain from all carbohydrate intake.

Below is a picture freely available online from this website (from Lehninger Principles of Biochemistry, 5th Edition) of the glucogenic and ketogenic amino acids and the metabolic intermediates to which they can be converted. This is how Krebs Cycle intermediates can be generated from amino acids and are not dependent on dietary carbohydrates.


How does blood reach skin cells and other closely packed cells? When I see diagrams of cellular structures such as the layers of the skin, these diagrams show the cells as being closely packed together. For example here is a typical such diagram:

So, it shows the capillaries of the vascular system going only to the bottom of the many layers of tightly packed cells. So, I assume that all the cells need oxygen, so they all need to be in contact with the blood cells that bear oxygen, so how does this happen? Obviously each individual cell can't have its own personal capillary. If blood were to be released just loosely around the cells that would not work either because the blood would have no way to get back. All the blood has to be in vessels of some kind so it can circulate. But these vessels are not shown as reaching the upper skin cells in any way, so how are those cells getting oxygen?

The skin is highly vascularized up to the epidermis, with dense vessels right at the top of the dermis (your picture omits these, but you will find them in better diagrams like this one). The epidermis itself gets substantial oxygenation from the outside air (see Stücker et al, for example), though the very outermost layers are not metabolically active ("dead") and do not require oxygen.
As a gas, oxygen moves quite well through tissue, and cells can get sufficient oxygen from sources up to a few hundred micrometers away. No need to be in direct contact with blood cells (and typically no tissues of the body are in direct contact, besides vascular endothelial cells that line all blood vessels). Many small animals have no need for a circulatory system because their entire body is close enough to the outside for gas diffusion.

Stücker, M., Struk, A., Altmeyer, P., Herde, M., Baumgärtl, H., & Lübbers, D. W. (2002). The cutaneous uptake of atmospheric oxygen contributes significantly to the oxygen supply of human dermis and epidermis. The Journal of physiology, 538(3), 985-994.


Career advice for a bachelor of biology with russian STEM diploma I'm from Russia. I majored in biology(genetics), wrote a bachelor's diploma in the field of psychogenetics, and graduated with mean grade of roughly 4 out of 5. Back then some circumstances arose that prevented me from an academic career (including lack of biotech companies in my area), so I had to make do with an entry-level job. Biotech companies in Russia can afford to be picky and hire only experienced staff even for an entry-level position such as lab technicians. With a lot of people in the field looking for a job, and a few biotech companies, I don't have a lot of chances there.

I've heard that Russian diplomas in STEM fields are valued abroad, probably more than they are in Russia; that brings me here. What are my chances of finding positions as a junior lab member, lab technician, etc. in a biology-related field overseas with my higher education diploma and practical experience (achieved during two years of lab work in the university)? What skills/qualifications do I need to get to improve my chances? What direction would you suggest to start my research on possible employers? Could you give me any further tips on career track?

You have so many questions, and it seems like you have no idea what to do next. So you better ask Russian guys who are really into this as

Good FAQ with a lot of cases from real life:
https://vk.com/career_in_biology
More like Career in Biology 101:
https://vk.com/science_career (also they have a chat in Telegram)
Career adviсe and pretty decent list of positions: https://blastim.ru/
Winter biotech school (in my opinion you have good chances to get there as they do it for people just like you): https://vk.com/futurebiotech
Completeish list of biological summer schools where you can get hands-on experience: https://vk.com/coolresearch


centiMorgan distribution among human chromosomes Using the rough estimate of 7,000 centiMorgans in a human... Is there an estimate that breaks down this total by chromosome (including the sex chromosomes)?  E.g., in the human karyotype, do chromosome pair 1a and 1b have n1 cM, 2a and 2b have n2 cM, etc. so that n1 + n2 +...+ n22 + sex chromosomes = 7,000?

If you understand what I'm getting at and can re-phrase my question to clarify it, please do so.

The short answer is "yes". Here is an early example: https://science.sciencemag.org/content/265/5181/2049.abstract

I am sure that with some searching around you can find the most recent version. I was able to find somewhat more recent maps here. The data has to be in the UCSC genome browser somewhere. Most likely you should find your 7000 cM estimate source and figure out which map that estimate comes from if you like that source.

These data structures are called "genetic maps" or "linkage maps". Each chromosome has positions that are defined by cM, and you could use that for your purpose I believe by just taking the largest cM value marker for each chromosome.

(Note that the two copies of a chromosome do not have independent genetic maps- after all, the map is defined by recombination between the two homologs. e.g. for chromosome 1 there is usually just one map, and therefore one maximum cM value- the map is an average across the human chromosomes sampled.)

Edit
The question seems to be related to a genealogical heuristic for identifying relatedness in cM values. I'm still not 100% sure how they measure this exactly.

The source shares expected values for relatedness here: https://secureservercdn.net/184.168.47.225/35b.ded.myftpupload.com/wp-content/uploads/2018/12/Relationship_Chart_FINAL_August_2017.jpg


Are there any DNA sequences shared by all/most Viruses? Is there any one DNA sequence shared by all or most viruses?

I highly doubt there is mainly because of how different all of them are, but it's still worth a try.

Thanks

No, virus are polyphyletic and there are no genes that are common to all viruses. There may be similarities in capsid structure due to convergent evolution, but these are not universal. See Moreira and López-García (2009) for further detail.


Can we identify an individual from their palm lines Can we identify an individual from their palm lines. Is there any uniqueness for palm lines among family members ?

It was tricky searching for this through the morass of palmistry sites.  But, in the field of biometrics, I found the article "Palm Print Recognition", which states that (bolding mine):

  Because fingerprints and palms have both uniqueness and permanence..

it has been used for identification the same as fingerprints. The only reason it is not as widespread as fingerprints is largely due to logistics such as computer processing.


Which mushroom species is this? Which type of mushroom is this? Hope the image has enough quality to allow answering the question.

Following community rules...

Images: please find below
Location: West-Northern Germany
Size - about 7 cm height, 5 width
Prior research: very hard to undestand which species is this, therefore asking here. Maybe this could be a Gymnopus peronatus - but here the stem is darker.
Specific characteristic: hollow stem

You are probably right that it is a Gymnopus, It's difficult to know which one. There's also Gymnopus Fusipes. For a difficult ID, it's best to have a cross section, a description of the scent, compare the color under the youngest specimens, as the gills often change from very light to very dark with age.


What kind of spider has colonised my timber framework? I'm in the south east UK. I have a site I'm doing intermittent timber work on, that's been left idle for much of the summer. When I came back it has huge webs strung from walls to beams and across the open spaces, everywhere, with the spiders in this picture sitting in them.

At a a guess they are about 30 - 40mm across (maybe 25 when 'sitting' with legs curled at rest close to body?). They sit in the middle of the webs, not hidden at the edges. The webs are quite strong and look like they are durable, as webs go.

Any ideas?

You've encountered a very common spider, found all over holarctic.
Common names: European garden spider, diadem spider or cross spider
Scientific name: Araneus diadematus
link to wiki:
https://en.wikipedia.org/wiki/Araneus_diadematus

They can bite, but are hard to provoke.
If bitten it will feel similar to a wasp sting.
So nothing to worry about, unless you are allergic.

picture from underneath:

source: http://c8.alamy.com/comp/H45CTY/spinning-network-garden-spider-araneus-diadematus-bottom-side-animal-H45CTY.jpg

picture from above:

source: enter link description here


HELP hepes preparation I need help: I would like to prepare an HEPES solution, without using the powder. It is possible? I remember that I did it once, but maybe I'm wrong...does someone know a protocol for HEPES preparation without using a powder? thanks!!

I need It for morpholino dilutions. 5mM, ph 7.6.

HEPES is a particular chemical, not a mixture of chemicals so unless you have the ability to synthesise your own chemicals you cannot produce it without having the dry chemical preparation.


Transmitted electrons in TEM When some electrons of the electron beam pass through the specimen, what exactly happens after that in order to produce the black white image? What I understand is that electrons transmitted collide with a film and make that part of it black on the image, and those that don't collide make their part white. But why is it said that electrons that pass readily make the area brighter or more electron lucent and vice versa for scattered electrons?

The pixels in a TEM image are whiter or blacker based on the dose of electrons that impact that pixel in the whatever detector is being used to form the image, be that photographic film, a scintillation screen, or a direct detector camera.

As for how the image that reaches the detector is formed by the specimen being imaged, there are two different mechanisms.
Amplitude Contrast is relatively simple - denser parts of the specimen scatter electrons strongly enough that some electrons do not make it to the detector at all, so pixels below these parts of the specimen will receive a lower dose than pixels below less dense parts of the specimen.
Phase Contrast is more complex, and is responsible for most of the contrast in high-resolution cryo-TEM. Briefly, the specimen is illuminated by a parallel beam of electrons and every "pixel" of the specimen scatters some electrons but lets most of them pass straight through without interaction. The scattered electrons go off in a different direction than the main beam but are focused back by the lenses to the same point on the detector as the unscattered electrons. Because the scattered beam took a different path from the unscattered beam, and because electrons are waves as well as particles, there is a phase difference between the two beams which causes them to interfere. Typically, areas of the specimen that scatter electrons more will cause destructive interference, so darker pixels. If there is no scattering, then there is no interference, so brighter pixels. There are many resources explaining the technical details of this mechanism (1, 2, 3), but these tend to focus on crystalline specimens.


Insect ID, found in shower, northeast USA I want to know if this is the kind of critter that will lay eggs in the drain and then have larvae emerge from there. We had that a few years ago and it was nasty...

That is a silverfish (Order, Zygentoma). The most common species of household silverfish is Lepisma saccharina. Details can be found here. https://en.wikipedia.org/wiki/Silverfish
They are relatively harmless.


What's the difference between CREs and DHSs? I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene expression.

Cis-regulatory elements are simply DNA regions upstream or downstream of a gene that can affect its expression (basically they have to be in the same chromosome).

DNAse-I hypersensitive sites (DHS) are regions of chromatin that get digested during the DNAse treatment because they are exposed i.e. not protected by a protein (complex). The protein complex can either be a nucleosome or a transcription factor. It should be noted that a DNA region can be DNAse insensitive also because of its conformation.

Usually the cis-regulatory elements exert their effects by serving as a binding site for a transcription factors (or chromatin remodellers). If the proteins bind at these sites then these regions would be protected from DNAse digestion thereby making them not-DHS. However, it is known that DNA elements can act in trans as well (see papers on 3C- chromosome conformation capture, and its variants). Moreover, whether a site is protected from DNAse or not does not tell anything about its function.


Why cytotoxic T cells don't kill dendritic cells when they present antigen? When a cytotoxic T cell (CTL) recognizes a peptide presented in the MHC-1 of a dendritic cell (APC), why it doesn't kill this cell?

I know that initially, in the lymph node, the T cell is inactivated. But eventually it becomes activated and travels to the tissue, where it again finds APCs presenting the offending antigen. So why doesn't the CTL kill the APC at this point?

Moreover, not all MHC-1's of the dendritic cell present antigens from phagocytized cells. Some MHC-1's present peptides coming from the dendritic cell itself, so that if the dendritic cell itself becomes infected with virus or bacteria, it can be killed by a CTL that recognizes the peptide. So in this case, the CTL does indeed kill the dendritic cell.

So my question is, when exactly does the CTL kill the APC? How does the CTL knows that should or shouldn't kill the APC?

The presentation of antigens on the cell surface is done by two different molecule complexes: The MHCI and the MHCII complexes. These are coupled to different pathways and are recognized by different T cell populations.

The MHCI molecule presents all proteins which are present in the cell on the surface. To do so, peptides coming from the proteasome (where long proteins are digested) are transported in the the endoplasmatic reticulum (ER) by a special transporter called Transporter associated with Antigen Processing (TAP). By doing so, a profile of all proteins expressed in the cell is presented on its surface, including proteins which arise due to an infection of the cell. MHCI is recognized by cytotoxic (or CD8 positive) T cells which subsequently kill all cells which show foreign antigens on their surface (since this is a sign for an infection).

The MHCII complex only presents proteins on its surface which have been taken up by phagocytosis (so here only external proteins are presented). To prevent binding of cellular proteins in the ER (like for MHCI), the binding pocket of the receptor is blocked by the invariant chain. This chain dissociates only when the MHCII complex enter the phagolysosome with its acidic conditions. This makes sure that only proteins which have been taken up by phagocytosis are presented. MHCII complexes are recognized by helper (or CD4 positive) T cells, which in turn can activate B cells to raise a proper immune response.

In theory this should prevent all problems. In the practical life this is different for dendritic cells in a mechanism called "cross presentation". In this mechanism antigens which are taken up by phagocytosis are exported from the phagolysosme and imported into the ER. This pathway also involves the TAP protein. By choosing this way, APC can activate naive CTL which will kill all cells which present this antigen. See references 1 and 2 for more details.

This pathway is important for the immune response to a number of viruses as well as tumors which evade the MHCII mediated immune response by suppressing the MHCII antigen presentation. See references 3 and 4.

It is also important for the stability of the self-tolerance by the deletion of auto-reactive CTL. See reference 5 for details.

References:

Outside looking in: the inner workings of the crosspresentation
pathway within dendritic cells
Cross-talk between the endocytic pathway and the endoplasmic
reticulum in cross-presentation by MHC class I molecules
Role of bone marrow-derived cells in presenting MHC class I-restricted tumor antigens.
Cytotoxic T-cell immunity to virus-infected non-haematopoietic cells
requires presentation of exogenous antigen.
Exogenous class I-restricted cross-presentation of self antigens can
lead to deletion of autoreactive CD8+ T cells.


Algae and greenhouse effect Just a thought: the CO2 concentration is increasing . Due to a different but possible related phenomenon, the algal blooms are on the rise. We humans want to control both. But algae are the major source of O2. Could the rise of algal blooms in the rising concentration of be related CO2 ? I wanted to know if this would eventually be advantageous to the environment, even though algal blooms may be detrimental to some species and directly or indirectly to humans too?

In most situations the lack of sufficient CO2 is not what is limiting algal growth. In general the limits to growth are set by the availability of nutrients such as iron, nitrogen and silica. They actually touch on that in the paper. For example removing iron limitation has a much more dramatic impact on algal growth or blooms than increasing CO2 by a few percentage points (see here). This also explains why there are more algal blooms, the increase of fertilizer use results in more food for the algae to grow on and all round bad things (see here).

Perhaps some algae will benefit since they will not have to invest much energy/nitrogen in creating carbon concentrating mechanisms. However several species of algae use calcium for their cell walls and these would actually suffer by increased CO2 concentrations as this leads to ocean acidification (e.g. coccolithophores). Taking into account that these are heavy sinking algae that take a lot of carbon with them to the ocean floor and you see that ocean acidification is not likely to be a good thing.


Does caffeine increase the speed at which sperm travels? I'm not even sure if this claim is true, but...

This source states that

  Caffeine gives both types of sperm a boost, but the Y-sperm would get a little more of a boost.

This article reinforces the quote. In fact, this "tip" can be seen all over the internet to preferentially conceive a male rather than a female.

My question is how. What is happening at the molecular to increase the overall mobility of sperm? It clearly wouldn't work as a neurotransmitter (as it "normally" works).

The cell response for caffeine, is at the molecular level of RyR (Ryanodine receptor), and the main effect could be a temporal rise in Ca+2 cytosolic concentration, so it can change the electrical behavior for the whole cell, and then affect their mobility. But the main area for RyR research is at spermatogenesis, there are a lot of papers like this one, for that topic


I found a bug on my bedroom floor. Is this a bedbug? I found this insect on my bedroom floor. I'm worried. I hope this is not a bed bug.

Size: 3-4 mm

To answer your question this is very likely NOT a bedbug.

See this answer for a positive ID of (and more info for) a bedbug.

However, based on the size and body shape of your specimen, it appears you've found another blood sucking paristic pest: a flea.

 Sources: Here, here and here.

 General Info:

Fleas are small flightless parasitic insects (order Siphonaptera) that consume the blood of mammals (including humans) and birds.
Over 2,500 species of fleas have been described worldwide.
Adults are 1.5-3.3mm long, narrower than wide and brown (or reddish brown). [1,2]
Flea larvae are worm-like (vermiform) in shape with a sparse covering of bristles.  They rarely live on the body of their host.  Instead, they are usually found in its nest or bedding where they feed as scavengers on organic debris (including adult feces).

 Likely Species:

I'm assuming you have a pet (cat or dog perhaps). If that is the case, you're likely looking at a cat flea or dog flea (depending on your locaiton). From UF IFAS:

  The most common [American] flea is the cat flea, Ctenocephalides felis  (Bouché). The adult cat flea, unlike many other fleas, remains on the host. Adults require a fresh blood meal in order to reproduce.

  The dog flea, Ctenocephalides canis (Curtis), appears similar to the cat flea, but is rarely found in the United States. Cat fleas are commonly found on both cats and dogs in North America, while dog fleas are found in Europe.

  The two species are distinguished by a slight morphological difference which is detectable only under high magnification.

 Cat flea (Ctenocephalides felis) from University of florida IFAS

Note: both species will parasitize multiple species (including both cats and dogs as well as humans), and their distinction (as mentioned above) is more dictated by geographic location. However, both can be found worldwide.

Linardi & Santos (2012)1 have an excellent publication for correctly identifying between the dog and cat flea.

For More General Information See:

  Wikipedia
 - Terminix
 - Orkin
 - Univ. of Evansville
 - Purdue University
 - UFL IFAS (cat fleas or dog fleas)

 Fleas vs. Bed Bugs

See this Terminix page for "What is the difference between bed bugs and fleas?"

Your specimen is almost certainly a flea because:

The body of the insect in your picture is thin but vertically "tall" (or "laterally flattened"). In other words, it appears to be narrow like a flea.

A bed bug, on the other hand, is wide and vertically very flat.

Though, an engorged adult can appear to be more narrowly long when engorged on blood. See here.

Fleas are narrow so that they can easily maneuver through a host's fur/hair/feathers; while a bedbug is flat to be able to effectively hide in crevices.

The size (3-4 mm) is more appropriate for a flea.

Although some larval stages of bed bugs can range between 2.5 - 4 mm, these larval stages still retain the relatively flat appearance of the adult (except when engorged).

Notice the reflection toward the posterior end of the specimen in your photo. This is not present on bed bugs. This light is reflecting off the flea's pygidium (or sensilium).

Some fleas have bristles on the posterior end of their body. Bed bugs do not. The insect in your picture has these posterior "hairs."
Fleas have powerful hind legs for jumping that stay relatively close to the body, while bed bugs have very skinny legs that spread laterally from the body.

When bedbugs become engorged and appear more like the insect in the question picture (i.e., not flat), their abdomen grows posteriorly but their legs do not extend very far back.
Notice when I brighten the OP's picture from the question you can see the light reflecting on the wide posterior femur that is both close to the body and extends relatively posteriorly as compared to the overall abdomen:

Location & Behavior: Although both fleas and bedbugs are generally nocturnal, both can be found during the day. However, they would generally be found in different places:

Bed bugs are likely to be digesting meals on the piping of your mattress, in and around the bed frame or box spring, along the baseboards and creeping around in other well-hidden cracks and crevices
Fleas, however, (like your specimen) are more likely to be found making themselves at home in animal sleeping areas or lurking around in your upholstery or carpeting, waiting to hop on for a bite. [Source]

Should You Still be Concerned?

Some fleas are well known to transmit diseases (e.g., plague, murine typhus, etc., and a host of issues for your pets) unlike bedbugs. So really, fleas could potentially be more harmful.

Unlike bedbugs, however, vacuuming goes a long way for managing fleas on bedding, carpets, and furniture.
However, one flea can lay between 150 and 300 eggs every week, so do not wait!

 Works Cited:

1  Linardi, P.M. and Santos, J.L.C., 2012. Ctenocephalides felis felis vs. Ctenocephalides canis (Siphonaptera: Pulicidae): some issues in correctly identify these species. Revista brasileira de parasitologia veterinária, 21(4), pp.345-354.


Why do pink rain lilies flower only after rains, and not from being watered? We have pink rain lilies (Zephyranthes carinata) in the garden. In my personal experience, I've found that they always flower, without exception, shortly after rains. However, there are roughly ten totally dry months each year. During this time, even though I water them regularly with well-water, they never flower. I've tried copious amounts of water, and frequent watering, but to no avail. They seem to depend on rain.

The rains here come at different times each year. We just had a totally unexpected rainstorm in May, causing them to flower. We are inland in southern India. It's very hot here, and the climate is quite dry in the periods when it's not raining.

How can this be? What's going on inside the plant, biologically speaking? How can it "know" whether it's getting rain water or well water? I'm looking for a description of the biological processes inside the plant which cause these different responses to rains versus watering.

Also, (minor, secondary point) is there any evolutionary reason why a plant would develop this trait?

I prefer answers that cite their sources for the information.

Edit: A user added some quite relevant personal observations in the form of an answer. I'm adding it here, as the observations are quite relevant to the question.

  I live in central India which is marked by a heavy rainy season from mid June to September and almost dry rest of the year. This behavior of rain lilies has been a mystery to all of us for generations.

  No matter what season, what temperature, the lily bush will give you
  at least one bloom even if rains for a mere few minutes. Rest of the
  time, any amount of watering does not help. I've seen the plant bloom
  with just a bit of drizzling in summers when temps cross 40 degrees
  celsius.

  Whereas, a friend is growing them in a pot in a water lily pond.
  Basically, in shallow water where the rain lilies are just dipping
  their feet in water all the time. So basically, for a large portion of
  the year, the plant is meeting the low temperature, high water criterion.
  It doesn't work. The plants bloom only and only when it showers.

  By the way, the behavior is not limited to pink rain lilies. It's the same with yellow and white lilies.

It looks like sustained or consistent moisture might be (at least part of) the phenological cue for flowering:

The wikipedia article mentions that consistent humidity will induce flowering in at least some species and cites Fernández-Alonso & Groenendijk (2004), which says:

  It generally flowers after the rainy periods, but in humid pastures and under cultivation conditions, colonies show staggered flowering during the whole year.

There's a reference in Lange et al. 2013 to Zephyranthes flowering after "watering of at least 10 h[ours]", but I'm not able to find the original citation in the google books preview (which is given at "Nitsch 1965").

Edit: I tracked down Nitsch 1965, who cites 2 sources on the topic. He reports Kerling 1949 as showing that Zephyranthes rosea after a certain period of development goes into dormancy, which is broken when two conditions are met: low temperature and high water, which must be extended over at least 10 hrs. He adds that Holdsworth (1961) presents evidence showing that Zephyranthes citrina and Z. tubispatha are primarily triggered by soil moisture.

Fernández-Alonso, J. L. & J. P. Groenendijk (2004). A new species of Zephyranthes Herb. s. l. (Amaryllidaceae, Hippeastreae), with notes on the genus in Colombia. Rev. Acad. Colomb. Cienc. 28: 177-186

Holdsworth, M. (1961) The flowering of rain flowers. Journal of the West African Science Association 7︰28-36.

Kerling, L.C.P (1949) The gregarious flowering of Zephyranthes rosea Lindl. Annals of the Botanic. Gardens. Buitenzorg 51: 1-41

Nitsch, J. P. (1965). Physiology of flower and fruit development. pp 1537-1647 in Encyclopedia of Plant Physiology Vol XV Part 1, W. Ruhland (ed.)

O. L. Lange, P. S. Nobel, C. B. Osmond, H. Ziegler (2013). Physiological Plant Ecology III: Responses to the Chemical and Biological Environment. Springer.


What plant is this, seen at the Allan Gardens? I tried a couple of apps on my phone, but I could not identify this flower and plant species.  These are at the
Allen Gardens Conservatory, at the beginning of Spring in Toronto.

This is a Schizanthus "orchid" (actually not a real orchid) called Schizanthus pinnatus ("butterfly orchid" or "poor man's orchid").

  It is native to Chile but the plants are also cultivated as ornamentals. It is commonly known as the "small butterfly" ("mariposita") or "small, white butterfly" ("mariposita blanca").

Description

Annual plant of 20-50 cm in height
Stem: Glandulous-pubescent
Leaves: 2.5-3 cm long; pinnatisect (divided into 6-8 pairs in oblong-linear segments, entire or separated).
Flowers: white, pink or violet, 2-3 cm diameter, arranged in panniculate inflorescences, sometimes dichotomous.


How does drug-induced photosensitivity work? Some drugs (tetracyclines, for instance) can cause photosensitivity reactions—that is, some patients become extremely sensitive to the sun, developing rashes or inflammation after spending time in bright sunlight. Sources I've read describe this as an immune reaction similar to an allergy, but I've also heard that antihistamines are generally ineffective at treating such reactions.

So my question is, what are the biological processes behind this reaction, and how does it differ from a normal skin allergy that could be treated by antihistamines?

Drug induced photosensitivity (DIP) refers to the development of a cutaneous disease in response to the drug chemical in combination with light. Only the drug or light alone cannot cause the reaction and both are required to be present together. The underlying pathophysiology is important clinically to identify the type of cutaneous manifestation the drug-light combo has caused. There are majorly two types of reactions, phototoxic and photoallergic reactions.

Also, the kind of light required depends on the kind of drug and the the wavelength at which it gets photoexcited. Although UV-B is a mojor cause of sunburn, the wavelength required for DIP for most drugs falls in the UV-A part of the spectrum.

Phototoxic reaction

Phototoxic damage refers to the direct damage the photoactivated drug can cause to the tissue. Light leads to excitation of electrons and as they return, they can lead to formation of reactive oxygen species which damage the cell membranes and DNA. This tissue damage leads to activation of proinflammatory cell signal transduction pathways and leads to inflammation in the area. Clinically, it looks like an exaggerated sun burn.

Photoallergic reaction

This is similar to the same old hapten story. A drug which is otherwise non-antigenic turns antigenic after a photoreaction. Most probably, the reaction should have caused the modified drug to bind to cutaneous proteins leading to cell mediated immune reaction. This T-cell mediated inflammatory response usually has an eczematous morphology if the photoallergen is applied topically or the characteristics of a drug eruption if the photoallergen is administered systemically

It is important to differentiate the kind of reaction, a drug would cause.For example, the tetracyclines that you mention are phototoxic but not photoallergic. Photoallergic reactions have far lesser incidence than phototoxic ones.

Coming to the other part of your question, on the treatment, most important is to educate your patient for appropriate photoprotection. If severe, the drug could be withdrawn and switched to a safer one. Treatment includes topical corticosteroids to bring down the inflammation in either reactions. Oral antihistaminics are reported to have limited advantage. Why this is so,I'm afraid, I do not know. Hence your question remains partly answered.

Reference: http://emedicine.medscape.com/article/1049648-treatment


If only dicots have pith, what is the foam in the middle of cornstalks? I've heard that the only plants that have pith are dicots, because of the shape of their vascular bundle. If that is true, what is the foam inside of the corn plants, which are monocots?

Monocots do have pith in their stems. The link even has an image of a maize stem:


DNA quantification in a high school bio lab I'm working on a project in a high school bio lab (so limited resources), and I need a way to quantify the concentration of DNA in a PCR product. I can't use spectrophotometry (cheap spectrophotometers at school can't measure absorbance at 260nm), and any fluorescent dyes are out of the question as we don't have a transilluminator. Right now I'm looking at measuring absorbance change in a visible-light dye like crystal violet or methylene blue, but there isn't enough data on quantification using these dyes. Can anyone suggest anything?

Thanks.

Within some linear range, the intensity of stained DNA bands in a gel is directly proportional to their mass. By making a standard curve from bands of known mass, the mass of unknown bands can be estimated. This process is called densitometry. I wrote briefly about its use in quantifying protein bands after SDS-PAGE in this answer, but I'll go into more detail on how this is done using the following ethidium bromide stained gel:

On the right is a molecular weight marker (BstEII digest of λ DNA) with bands of known mass. On the left are two bands of unknown mass (actually a double-cut plasmid).

I use a free program called ImageJ to estimate band intensities. They have a tutorial on measuring band intensity here. You can also get ImageJ packaged with Java (and bunch of other stuff) in the software Fiji.

Open the image in ImageJ and use the Rectangle tool to draw a box around the marker, then select Analyze > Gels > Select First Lane (or shortcut Ctrl+1). Next, drag the box over to surround the other lane and select Analyze > Gels > Select Next Lane (Ctrl+2). Now select Analyze > Gels > Plot Lanes (Ctrl+3) to plot image intensity as a function of position on the gel:

The area under each peak (minus the background noise) represents the some total of intensity for each band. To measure this area, use the line (Straight) tool to draw bounds on the base of each peak:

I've done it somewhat haphazardly here, but you get the idea. Now, using the wand tool, click inside each peak and ImageJ will tabulate the integrated intensity of each. Shown below are the intensities of the marker bands (with the top band being Band 1) as well as their masses (which are known):

          Mass (ng)    Intensity
Band 1    45           5319.891
Band 2    28           3816.234
Band 3    24           3256.406
Band 4    16           2298.749
Band 5    15           2074.749
Band 6    8            1084.991

Take this data into Excel (or similar) and plot intensity as a function of mass. Band 1 looks like it is outside the linear range and is underestimating the mass. This was actually expected since, if you look closely at the band in the gel image, there are red pixels indicating that it is oversaturated. Ignore this band and perform a linear regression on the rest.

The regression gives the equation $I = 134.74M + 53.988$ with $R^2 = 0.9975$. Rearranging for mass, we have $M = \frac{I - 53.988}{134.74}$. Get the intensity of the unknown bands as described above and calculate their mass with the preceding equation:

          Mass (ng)    Intensity
Band 1    27           3736.991
Band 2    15           2125.284


Why are fatty acids synthesized in two carbon units? Why does long-chain fatty acid synthesis involve the two-carbon precursor, malonyl CoA, rather than the one-carbon acetyl CoA (or even a three-carbon precursor).
Is this because fatty acids with an even number of carbons are somehow ‘better’ than those with an odd number, or does it reflect some aspect of the chemistry involved?

The answer to this question lies in the chemistry of fatty acid synthesis — specifically the chemical energetics of the reactions. For those new to the biochemistry there is a basic concept that must be understood: that a reaction can occur spontaneously only if it involves a negative change in Gibbs Free Energy. This is discussed, among other places, in my answer to another question.
As regards long-chain fatty acid synthesis, the answer can be found in Section 22.4 of Berg et al. Biochemistry some of which I summarize here.
The reactants in fatty acid synthesis are linked to a protein during the cycle of reactions — acyl-carrier protein, ACP:
malonyl CoA + ACP ⇌ malonyl ACP + CoA
The first condensation reaction of a malonyl constituent in the elongation cycle of reactions is shown below.

The key point to note is that in this step the malonyl carboxylic acid
group is released as carbon dioxide with a substantial decrease in
free energy that makes the reaction favourable. Without it the
reaction would not proceed, which is why the synthesis of acetoacetyl
ACP from two molecules of acetyl ACP does not occur.

It is worth adding that this free energy is ultimately derived from ATP, which is needed to drive the reaction in which malonyl CoA is formed from acetyl CoA and carbon dioxide.


What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way? First post here, so bare with me if I violate any etiquette or formatting rules.

Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm very interested in.  I see a highly homologous (~85% AA identity) protein in plants, and it's widely conserved.  I'm interested in eliciting the same activity of this protein in plants.  Only problem is that there's no native plant-produced ncRNA to interact with my protein of interest in the same way.  So I had an idea:

What if I introduce a transcript to plants that addresses this problem?  If the plant version of this protein interacts with this (introduced) RNA in the same way it will be really cool.  I'd like to test this hypothesis with some synthesized constructs.  But before I plunk down thousands of dollars on a few constructs, I'd like to explore any predictive or analytical tools to strengthen the case.  I'm aware the odds are against me.

Thanks!

The ncRNA sequence from human may bind to the plant protein in the plant cells, but so what? You may be able to say the plant protein works as RNA binding protein, but no more than that.
Another concern is that the plant protein may not recognize the same RNA sequence to the human protein.

There are several ways to find RNA partners of RNA binding proteins.

SELEX

This method is used to find consensus sequences that your protein recognizes in vitro. Once you find consensus sequences, you can search ncRNAs from the plant.

CLIP

This is similar to Chip assay. You could find real targets of your RNA binding proteins


What is the difference between "hamstring tendon" and "common hamstring tendon"? What is the difference between "hamstring tendon" and "common hamstring tendon"?  I have seen both terms being used but I don't know whether they referred to the same tendon.

For example,
Johnson, Anthony E., Robert R. Granville, and Thomas M. DeBerardino. "Avulsion of the common hamstring tendon origin in an active duty airman." Military medicine 168, no. 1 (2003): 40-42. (https://doi.org/10.1093/milmed/168.1.40) uses the term "common hamstring tendon" but I don't see any difference with the "hamstring tendon" when reading the article.

Since there are more than one hamstring tendons, I would have guessed that  "common hamstring tendon" specifies which hamstring tendon is being referred to, but I haven't seen the term of any anatomy diagram yet.

The hamstring tendons that I am aware of are:

Lateral hamstring tendon of the biceps femoris (long head) (2 tendons: distal+proximal)
Lateral hamstring tendon of the biceps femoris (short head) (2 tendons: distal+proximal)
Medial hamstring tendon of the semitendinosus (2 tendons: distal+proximal)
Medial hamstring tendon of the semimembranosus (2 tendons: distal+proximal)

(image source)

(image source)

In the paper you cite, they are talking about the tendon on the other side from the ones you've listed, at the "origin from the ischial tuberosity" (quoted from the abstract).

In this case, the word "common" is used in the dictionary sense of "same" rather than "ordinary": it's "common" because it's the same origin for the different muscles that make up the hamstrings. This terminology is used elsewhere in anatomy, too, for example the common carotid artery splits into the internal carotid and external carotid; the "common" portion is the larger proximal vessel.


Why re-label the strand ends in 3' DNA labelling? I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works.
I took a diagram from my lesson and tried to understand with it; this is what I understood.
If I’m wrong, please tell me and correct me.

We take a restriction enzyme which will cut both strands. The bottom strand will be a 5’ end. So, the top strand is shorter than the bottom strand.
We will add a Klenow fragment which, with its polymerase activity, polymerizes in the 5’->3’ direction the missing part of the top strand, with dNTP α 32P (labelled by a radioactive phosphate in the alpha position).
We get two strands which have the same size, of which one will be strongly labelled.
We finish with a terminal transferase which will catalyse the addition of dNTP α 32P on the 3’OH ends of both DNA strands (in order to label these ends).

But, if I’m right, could you explain the necessity of the last step; why label both ends since we have already labelled the top strand?

There are many ways to label nucleic acids for probes (Summary of Methods).

While there are cases where Klenow fragment-mediated fill-in should sufficiently label both strands of your probe, there are many others where this would not be enough.  Here are two illustrative, although somewhat contrived, examples:

  Example 1: Double digest with 5' and 3' overhangs
  Imagine you did a double digest with BamHI and KpnI to release your probe sequence from the plasmid in which you propagate the sequence.  BamHI will give you a 5' overhang, but KpnI gives a 3' overhang.

Resulting BamHI & KpnI double digest fragment:
  5'-    GATCCNNNNNNNG      - 3'
             |||||||||
  3'-        GNNNNNNNCCATG  - 5'

  Subsequent treatment with the Klenow fragment + $\alpha$P32-dATP + cold dNTPs will both fill-in the 5'-overhang (Klenow's 5'->3' polymerase activity) and remove the 3' overhang (Klenow's 3'->5' exonuclease activity).

Post-Klenow reaction (bold = new bases, * = radio-labeled nucleotide):
  5'-    GATCCNNNNNNNG      - 3'
         |||||||||||||
  3'-    CTAGGNNNNNNNC      - 5'
           *

  At this point only one strand is radio-labeled so the terminal transferase step is needed to add a label to the top strand.

When using $\alpha$P32-dNTPs, you often pick only one base to be radioactive (eg dATP as above).  Sometimes you also just spike the reaction with radioactive dNTP leaving a population of cold dNTPs to be used most of the time.  In either case you now have the chance of not incorporating only non-radioactive bases.

  Example 2: Fill-in reaction that fails to incorporate $\alpha$P32-dATP:

  Imagine a digest with PspI and want to fill-in the 5' overhangs using $\alpha$P32-dATP + cold dNTPs.  PspI recognizes CCWGG sequences where W is either A or T so that some fill-ins will incorporate the $\alpha$P32-dATP, but others will not.

Possible digests and fill-in reactions:
   5'-  CCTGGNNNNNNNNNNCCTGG - 3'
        ||||||||||||||||||||
   3'-  GGACCNNNNNNNNNNGGACC - 5'
                 |
         Digest with PspI
                 |
                 V
   5'-  CCTGGNNNNNNNNNN      - 3'
             ||||||||||
   3'-       NNNNNNNNNNGGACC - 5'
                 |
        Fill-in with Klenow + hot dATP + cold dNTPs
                 |
                 V
   5'-  CCTGGNNNNNNNNNNCCTGG - 3'
        ||||||||||||||||||||
   3'-  GGACCNNNNNNNNNNGGACC - 5'
          *

  Again you are left with only one strand being labeled (or no strand labeling if the sequence was 5'- CCAGGNNNNNCCTGG - 3') and a need for the terminal transferase step.


Is the quality of sleep dependent on sleep duration? I've been facing this lately, where I will wake up in the middle of the night after sleeping for perhaps 2-3 hours and be wide awake, but when I go back to sleep, I wake up more tired than before.

Can anyone shed some light on this?

Sleep duration certainly affects the quality of sleep, but it is nowhere near a simple correlation. It is just one of many factors, and these factors don't work in isolation. Statistically speaking, it's a multivariate model - and one which includes a differential equation, because the way sleep duration affects your sleep today depends on the sleep quality (and also the sleep duration) from yesterday. For example, if you go several day with too little sleep, but keeping firm going-to-bed and waking-up times, the ratio of your sleep phases changes significantly, giving you much more deep sleep. This is what compression therapy is based on.

And beyond that, the way you feel upon waking is also dependent on sleep quality in very complicated ways, and other factors (for example the synchronisation of the time at which you woke with your circadian cycle) play a much larger role than the sleep quality you got. Also, there are some unexpected effects, where getting too little sleep making you feel good - it's a kind of lightheaded, giddy state, somewhat comparable to having had a small glass of champagne.

So yes, there is a dependence, but you cannot expect that having had lots of sleep will make you feel good in the morning.


Neural signals amplitude Can anyone explain me if there is a difference in amplitude of signals between extracellular recording and intracellular recording. I know that the amplitude of neural signals when an action potential occurs is from -70mV to 45mV for intracellular recording. The same results are for extracellular recording?Can someone help me?

Also, I have read a paper that refers:

  Neural signals from extracellular recording are very weak (typically between 10 μV and 500 μV). As a result, amplification is needed before such signals can be processed further."

So my question is why neural signals are so weak (maybe author when he says 10μV refers to amplitude) when we know that an action potential has amplitude approximately 75mV(-70mV to 45mV)?

Those voltages refer to the difference between the inside and outside of the cell (i.e., -70mV means the cell is 70mV more negative than the outside).

You can't possibly measure that potential difference from outside of a cell. When you do extracellular recording, you are measuring spatial differences in ion concentrations that occur due to ions flowing in and out of cells. For example, when a cell fires an action potential, lots of positive ions flow into the cell; this makes the area just around the cell slightly more negative than an area further away. The magnitude of this potential as measured depends greatly on your recording configuration, the type of signal you are recording (i.e., population activity or just a single cell; synaptic currents versus action potentials), how close your electrode is to the signal you are recording, and where your ground is (or position of both of your electrodes if you are doing a bipolar recording).

Although it varies, in most cases the signals you record extracellularly are on the order of microvolts to a couple of millivolts.


Identify tropical flower Can anyone identify this tropical flower? It was found on a vine(?) in a garden adjacent to a rainforest in tropical north east Australia, however it may not be indigenous.

Some sort of passionflower (genus Passiflora). They have very distinctive flowers.

Could possibly be Passiflora miniata.


Circular mRNA to produce long proteins Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I assume they can bind long enough before disassociating)
However after doing some search on this topic, it seems that I am able to find only about 2 related papers. One of them seems to be from 1998, while the other one is more recent.

These articles suggest that it's doable. If this works, we'll be able to produce biopolymers with the sequence exactly as we designed, there would be massive applications, but I'm curious why it's not getting much attention, or why aren't there more papers related to this area?

In vitro translation is not as efficient as other chemical polymer reactions. For example, when proteins are synthesized using in vitro translation systems, many researchers have been using radio-labeling to see the products because the yield is too low to detect them by other methods, although few small proteins have been successfully produced at a microgram level. It should be noted that it is also difficult to produce exogenous long peptides at sizes more than 100kDa in E coli in vivo expression system.


Do leaves grow larger by adding cells at the centre or at the edge? I'm writing a paper on wrinkling of plant leaves. For biological and physical background information, I would like to know whether leaves grow by adding cells at the edge, at the center or in a completely different way. Since I need to confirm any information I get, please do not write opinions or guesses. It would be great if someone could find a reliable source with link since all my researches didn't lead to a good answer to this question.
Thanks in advance!

Plant leaves develop from leaf primordium or meristem tissue (this tissue has special properties that allow it to continue dividing to make more more cells, i.e. stem cells - not stem cells like cells in the stem but the technical term 'stem cells). Because of the hormone balances to maintain this division property the meristem tissue will remain close to the stem or branch of the plant at the base of the leaf whilst the new cells added to the leaf slowly move outwards.
https://www.sciencedirect.com/science/article/pii/S1369526616300929


Why is a solution of cesium chloride used in Meselson & Stahl's DNA replication experiment? Centrifugation involves separating particles of different sizes, masses, density and etc.
In the experiment, the DNA macromolecules are suspended in a solution of cesium chloride gradient and then centrifuged.
Why is cesium chloride needed? Considering the possible DNA produced in the experiment will be the same size but of different mass resulting in different density, DNA will be separated based on their density by virtue (without the need for cesium chloride) under the influence of a centrifugal force.
I noticed someone asked the same question on Khanacademy but there was no answer for it. Other websites I found doesn't seem to offer a valid answer e.g. here which says " the DNA comes to equilibrium in the gradient where its density equals the density of the surrounding CsCl" which I think doesn't really matter when considering the argument I proposed above in the third paragraph.
Here is a diagram of the experiment for reference. Thanks in advance.

In saline solution all the DNA ends up at the very bottom.
Under centrifugation, the Caesium Chloride solution forms a density gradient, each DNA rises or sinks to the equivalent density.
The same procedure is used with Sucrose solutions for other separations.


Is this a bed bug? I found it crawling on me in hotel bed Is this a bed bag? It doesn't have the stripes that I saw in other pictures. I'm traveling and for 5 days I was sleeping in different hotel rooms. What should I do if it is. I searched the bed and found no more.

As already stated in the comments the animal you found is a tick (Wikipedia).

Since they are known to carry diseases you should make sure you have not been bitten or even still have one sucking your blood. So search your body. If you happen to find one still attached, do NOT squeeze it as this may stimulate fluids to flow from the tick into your body (bad). Instead get it out asap using tweezers or even better specialized tools. If you can't do it yourself ask another person preferably a doctor.

If you have been bitten watch for symtoms of an infection such as a red circle. If in doubt always see a doctor since you might require antibiotic treatment.

NOTE: usually nothing happens so don't worry too much but be alert for changes in skin around bites (if bitten that is).

EDIT: since hotel beds are not a typycal habitat of ticks you probably carried it there yourself.


List of genes across species (or just for humans) Wondering if there is a place that has a list/table/database of all the genes in the human genome, and/or all the known genes in all the species we've studied so far. Something that contains any of this would be great.

I found this but not sure yet if that is just for humans and just for one chromosome. But I'd like something along those lines across species, or the closest thing to that that exists.

In principle there are a LOT of these databases and depending on your specific questions you may want to look into different ones. Like already mentioned NCBI hosts basically all of the available information, however it's not always easy to find the bits you care about.

The database I personally use the most is biomart (hosted by the ensembl consortium). It doesn't just contain all known for genes for pretty much all organisms, but is also able to link this to a ot of different information sources.
I usually access the database directly via the biomaRt R package, so I can't really say how good the actual website this. However, this link should allow you to download a table of all human genes with names, (unique) identifies & descriptions (I selected these from the 'Attributes' section).


Why cooking make foods , e.g rice, vegetable etc, soft? My initial guess was it is due to absorption of water during cooking (role of heat is probably to accelerate this process). So to verify this I have left uncooked rice  in water for two days but so far it hasn't softened noticably. May be for sufficient absorption of water for softening I have to leave it longer. Or may be my initial hypothesis is wrong altogether.

Short answer Hydrolysis

Cooking shortens many molecules, particularly carbohydrates and proteins although almost anything long is affected. By heating them in a aqueous environment (many foods supply their own water) we are inducing billions of hydrolysis reactions. This chops up long polymers into shorter ones.For proteins heat also causes them to unwind which makes them easier to digest.  In effect we are outsourcing a major portion of the digestion. This is why cooking is believed to have evolved as a behavior in the first place – it greatly increases the nutrient availability of the food by putting it in a much more easily digested state. Without heat the number of hydrolysis reactions is negligible, although a few things like extreme PH or infusion of enzymes can be substituted for heat.

For most edible molecules shortening them also makes them softer (most macronutrients are polymers, after all) which is an additional benefit. This is also why there is a balance in cooking, cook too long or at too high a temprature and you start to get lots of other kinds of reactions that produce new indigestible molecules. Cook too short or too low a temp and you get few hydrolysis reactions and it essentially does nothing. Hydrolysis is one of the reasons cooking will also dry out foods, since water is being used up in hydrolysis.


Extremely rare occurence of Heart cancer? The occurrence of Heart cancer (similar, but not the same as Rhabdomyosarcoma) is extremely rare, about 1 per year according to MayoClinic. The reason for this rarity is explained to be the post-mitotic nature of cardiac muscles. Since they stop dividing early in the life cycle of humans and grow only by increasing in volume, they are very less prone to oncogenic activation events caused due to mutation as a result of an error in DNA replication (since they do not replicate their DNA as they do not divide).

Although I am not an expert in tumours and cancers, I think that malignant tumours in nervous tissue, i.e. brain tumours are fairly common, at least more common than heart cancer by several orders of magnitude. But neurons constituting these tissues are also permanently in interphase and hence do not divide.
 Moreover, secondary malignancies in Brain and nervous tissue is also much more common than secondaries in heart (rare) though metastatic secondary tumours, I believe, do not require oncogenic transformations in the host tissue. A metastatic fragment of a primary malignancy transported by blood is enough to cause secondary tumours.

How then these tumours (primary and metastatic-secondary) are more common in nervous tissue than heart, though both are post mitotic, i.e. permanently in interphase?

Here and here are a few links which give some basics of cardiac malignancies, though they don't address the question quite directly. The study here provides possible explanation of lack of cancer due to high oxygen content.

This is a specific version of the great cancer question: "Why are some cancers more common than others?" The answer is either "Some have more common causes", and (or) "Some are cured spontaneously more often". So now all you are asking is "What causes cancer?" and "How do we cure it?"

Given that, I don't expect a general definitive answer will be forthcoming. A specific answer might be possible, but I doubt there will be any existing experiments that address this. With the obvious caveat that only experimental or statistical results can really answer your question, here are a couple of off-the-cuff hypothesis for consideration:

1 - Differences in stem cell populations.

Apparently, differentiation can actually be targeted as part of a treatment in some neuroblastoma cases - see the section on "Differentiation therapy" in this page from Sloan-Kettering. Cardiac stem cells seem to exist, but a difference in relative population and turnover rates between brain and heart might be related to the relative frequencies of these types of cancers. @WYSYWIG referred to neural progenitors in his comment above.

2 - A filtering effect due to a more extreme selection pressure in the uniformly stressful environment of the a beating heart.

Although there is a relation between elevated levels of oxidative stress and cancer causing mutations, it could be that this only matters in a punctuated stress environment, where cells have down time to recover. A sustained stress environment might actually helps prevent cancer. The path from normal to cancer cell requires multiple mutations, and I would not expect most pre-cancerous cells to be more fit than correctly wired ones. The extra stress of the cardiac environment might produce an elevated mutation rate, but also produce an even higher rate of apoptosis in early "sick" cells before they accumulate enough mistakes to become become cancerous, resulting in a net decrease in the rate of cancer.

Both of these ideas fit with heart cancer being less common and with metastasis from elsewhere being more common in heart than primary cancer, but unfortunately, a higher rate of clearing of sick cells would necessitate a higher rate of replacement from stem cells, so these two hypotheses partially cancel each other. Again, hypotheses without experiments are not really answers.