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Looking for a cancer drug target database to guide sequencing of patient tumor DNA
I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s tumors in order to guide treatment options. My job is to identify a list of all currently used anti-neoplastic drugs along with their known targets (i.e., specific genes and mutations) and accession numbers. I would like to put these data in a table in which each row corresponds to a different drug.
For example, a row in the table might read (column names are indicated in brackets): [disease] breast cancer, [drug] trastuzumab, [drug target] HER2/neu receptor, [gene] ERBB2, [location] chr17:37844393-37884915, [mutation type] amplification, [accession number] ENSG00000141736. The pathologists would then be able to use this database in order to select appropriate genes for sequencing whenever they receive a tumor specimen. If the patient’s tumor had an amplified ERBB2 gene, they could be given trastuzumab.
Currently our study is in pre-planning stages (i.e., we won’t actually be testing this on patients any time soon). I would appreciate it if anyone could give me on advice on how to go about creating such a database. I am aware of online databases including COSMIC, Sanger's Cancer Gene Census, and the Potential Drug Target Database (PDTD), but they don’t have everything that I’m looking for. I am familiar with R and could use it to combine data from multiple sources if necessary. If anyone else has comments or suggestions for further reading that would also be appreciated. Thanks!
Note: This question has also been posed on a Research Gate forum: http://www.researchgate.net/topic/Cancer_Biology/post/Looking_for_a_cancer_drug_target_database_to_guide_sequencing_of_patient_tumor_DNA

Would this question be better suited to healthcare-it?

Have you tried looking at the NCI-60? Here's a (dated) paper but might serve as a good starting point:
http://discover.nci.nih.gov/nature2000/paper/nature_v26_3_mar_2000.pdf

@RoryM I don't thinkg so, this is either our project or biostart.SE, rather the ours.

This ma be a good start http://www.pharmgkb.org/. I think biostar may be able to give you a good answer.

Is doing whole exome sequencing out of the question for your upcoming project? I feel like it'd crank up the chances of success for your project, and ... actually ... the exome isn't all that big, right?

Thanks for the comments everyone. We have purchased an Ion PGM sequencer, which is not capable of performing whole exome sequencing. The company says that the sequencer is "ideal for sequencing small genomes, sets of genes, or performing gene
expression profiling or ChIP-Seq." Researchers can interrogate "targeted genomic regions using up to 1,536 amplicons in a single tube, in a single day." Their website is www.iontorrent.com. For this reason we would like to design a panel of particular genes to sequence in each tumor type. I will check out the other websites that you all have suggested.

Although, upon further reading their website, it may be possible to upgrade the machine to do this in the future by changing the chip. We are getting the machine delivered to the lab this afternoon, so I haven't actually gotten to play with it yet. If anyone else has more comments or suggestions, please let me know! Thanks.

Am I right in understanding this, you're looking to aggregate data already available from other databases into your own custom database with a custom front end?  Assuming so a simple MySQL database could hold it with a couple BioPython scripts to fetch the data.  A PHP page would allow you to make it easily usable for your pathologists.  This is assuming it's all pretty straight forward, or did I miss the point?

Not sure if the exome sequencing is the way to go for this kind of tasks, especially if you have an idea of the mutations you might be looking for. Current arrays are pretty performant and are much more rapid and cheap.
For the data, you might consider having a look on The Cancer Genome Atlas. Otherwise Biological Networks might provide you the API for you if you aren't afraid of doing a little bit of Java to interface it with R.

There are no perfect resources for this information in the public domain quite yet. However, there are three that are making really good progress. The first is mycancergenome at Vanderbilt. They were one of the first resources to put this type of information on the web. They tend to be pretty stringent in the level of evidence and type of aberrations that go on the Web site. However, I am not sure if you can programmatically access there information. The second resource, is the https://pct.mdanderson.org developed at MD Anderson. This is really good resources however, it is only for a handful of genes, but albeit some of the most frequently mutated. I don't see a programmatic access to the information. The third resource and most promising for the community is the CIVIC database: https://civic.genome.wustl.edu/#/home. This is crowdsourcing resource that is set up to aggregate cancer associated mutation to drugs, phenotypes, and outcomes. I highly recommend this site and encourage not only consumption of data but also to engage in comments.
   As someone that has been doing drug to genome matching a couple pieces of advice. DNA based alterations are the best evidence to use for matching. If you do RNA be a little bit more cautious of matching based on 'is a target' mechanism. So rank DNA based changes above RNA. Additionally, just start with drug targets as place holders but try to acquire information on alteration as it relates to drug response. So alterations in a drug target could be (and often) are passengers and not drivers and in this case will not respond to drug. Frequency in other tumors and mutations in important domains are good guides for triaging variants like this. Also, the information on the disease and the mutations is important. If a drug variant mutation is observed in one disease there maybe mechanisms intrinsic to another tumor type that would preclude acting on drug to variant association in the different tumor type. Lastly, drug mechanism is something to take into account. Certain drugs that hit the same target do so but in different mechanisms that may preclude them being given in the context of particular mutations.
Good luck in your endeavors.


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What's the aim of genetically modifying of foods/organisms?
On news, articles etc. experts talking about Genetically Modified Foods and Organisms often mentions about their disadvantages like,

their potential to harm human health
allergies may become more intense, new allergy types may develop
possible damages to the environment

So I wonder, what's the aim of genetically modifying of foods/organisms? In other words, what are advantages of that?

GMO foods have a huge potential to make food cheaper to produce and more nutritious.
The most common GMO foods have at least one gene added to them - an enzyme that makes the plant resistant to RoundUp - an herbicide made by the same company (Monsanto).  this makes the farmers able to grow their crops with much less intensive labor to keep the plants healthy. It does cost some money and people wonder whether using so much roundUp is good.  I won't come down on the benefits of this, but you can see how it might be more economical way to grow crops.  roundUp is biodegradable and does break down in about 3 weeks, just FYI.
Other GMO foods can make the crops more resistant to drought, disease or insects. This might enable crops to be grown in areas and or with longer growing seasons - a big advantage for thirsy crops like tomatos or rice. Other GMO project may allow us to make the crops more nutritious.  A famous example of this is golden rice, which has been enhanced to produce pro-vitaminA, which will help malnutrition in millions of children who can die annually because of a lack of vitamins in their diet.
There is also an effort in nutriceuticals, where vaccines and common drugs maybe produced by edible plants for easily processing or even direct distribution of pharmaceuticals.
For people who can afford organic food and free range beef, I think its great that its available, but at for a hungry world, GMO foods can help solve some vital problems.

There's also a similarly modified cotton plant. While not nutritious, this cotton can be cheaper to produce. A GMO cotton could be engineered to require less treatment to make cloth, with lower environmental impact. I don't think the golden rice actually had very much bioactive vitamin A per serving.

In terms of crops, plants that are grown for food, one advantage is the targeted modification of a single gene. Classical plant breeding is slow, imprecise and carries many traits of negative benefit. For example, if you cross plant variety A with variety B for the purpose of obtaining one of B's traits (say oil content of the seed), the resulting progeny will have half of the B genome (which half? each offspring a different half of all possible alleles, and many of the hybrids may carry less desirable traits of B like altered germination and maturation times, which would be quite problematic for a farmer). Back-crosses to variety A are then necessary in order to make, in successive generations, offspring that are 75% A, then 87% A, then 93% A and so on. This takes time - to do those back-crosses and to test that the trait of interest remains. Knowing the gene for oil content, or a set of genes, can speed this process by modifying that gene alone while maintaining all the other advantageous traits of variety A.
This is but one example. If I think of others and find the time to describe those, I'll add such information here.

I'd like to add that most of the GMOs that might most dramatically improve human condition (ie via drought/salt resistance, greatly increased yield or nutritional value) are all unfortunately still under development (or not even that), partially because of the general public resistance to GMO in some regions of the world (like Europe; anyone remembers the tomatoes?) and organized campaigns against GMO (not really fact-based; ie Greenpeace & Co).
So yes, GMO can lead to development of crops with increased nutritional value, better resistance to environmental conditions or changes and/or increased yield, but we're not there (yet).
The above should not mean that what we have so far (insect resistant crops, disease-reducing GM insects or the golden rice) is not important, because it is, and it should not mean that the current legal/political context of GMO is fine, because it isn't.

I believe that there is a GMO potato now grown in Europe for paper production.

Imagine an apple which won't get brownish (oxidised) after being cut..

Imagine a tomato which will not get wrinkles and will not perish for a long time
Imagine a chicken and fish which gives more flesh in short incubation time

In endocrinology to get one unit of growth hormone one have to get 1000 pituitaries from cadavers.
Imagine a bacteria which produces growth hormone and other hormones like insulin for therapeutic and research purposes
Imagine a vaccine against flu in cow's milk and hepatitis in Banana. Eat it earn the protection
Imagine a iron rich rice ( fortified ) maize with complete nutrition without any amino-acid lag
Imagine glowing trees by the road side in night which prevent accidents
And there are much more and most advantages are coming out from GMO's.
The only problem is ethics i.e if we change our ecosystem to our wish it may collapse and either we may become extinct or else we may lead other species to it's extinction. But it's only a chance and it's a pointless fear. In the view of science logic is the prime and we can even bring the extinct alive. So we have got the power and we gotta use it and not waste it

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How many mice are on the Earth?
We are 7 billion human beings on the Earth. But how many mice are there? How would you estimate such a number?

Mark-recapture is the most frequently used method for small mammals. It's best when combined with uncertainty estimates and population dynamics models (e.g. projection matrix).
The fluctuations of small rodent populations have long fascinated scientists, and various models have been developed. Logistic regression models can be used to estimate likelihood of mice outbreak based on local rainfall data.
Estimates vary.
Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002.
The population of mice is often estimated per hectare - 0.25-60/ha in buildings and 1-200 in the field, over 1000/ha during outbreaks. 10^9-10^10 hectares of habitable land means
that populations of mice and men are, probably, of the same order of magnitude.

"Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002. " - why the reverse?

Can you try to extrapolate a very approximate world population from these numbers?

Good answer! Citations would be nice - eg. who's Davis?

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Neurons with thousands of connections: where are the extra connections coming from?
If every neuron has only one Axon but can can have thousands of (or let's say, even just ten) incoming Axon connections via its dendrites, where are the extra connections coming from?

It seems to me that since neurons dont act as initiators (that is, decide to initiate signals) but rather act more as repeaters (that is, sending incoming signals forward to the neuron that their axon is connect to), then for every neuron, there must be at least one neuron whose axon is connected to it, and at least one neuron that its axon connects to (because without those two things, the neuron does basically nothing, right?), but since each neuron can only have one axon, I'm confused about where all of these extra axons are coming from.
Based on that understanding: 1 billion neurons means exactly 1 billion axons and one billion required inputs (axon -> dendrite connections), eliminating the possibility of any one neuron having more than one dendrite connection, since there can only be one billion axons to connect to those dendrites (and each neuron would require at least one input to function, right?).
But regardless, I've been hearing people talk about neurons having thousands of connections. And based on my understood model, the brain would have to be just one long linear chain of neurons, which makes no sense at all.
So clearly I've got something wrong in my understanding of neural structure. What is it?

As you say, a neuron can have thousands of inputs via its thousands of dendrites.  Each of those dendrites can have a synaptic connection to the (axonic) output of a different neuron.  So the neuron can take inputs from thousands of different neurons, not just from one other neuron.
At the other end of the neuron, the output of the axon can form synaptic connections with many distinct neurons; that's what the branching at the end of the axon is for.
Also, it's misleading to say neurons don't "decide to initiate signals".  Neurons in the brain do "decide" when to initiate an output.  The decision is a complicated function of the arrival of pulses at dendrites from different neurons.  Only some combinations of incoming pulses will cause the neuron to fire a pulse on its output axon while other combinations will not.  The specific combinations can change over time; this forms the basis of learning.
So a brain neuron is in the middle of a very complicated network of synaptic connections from many neurons to many other neurons.

I guess the figure included in the question can be misleading in the sense that it seems to imply that an axon can connect to one neuron only. Therefore the OP's confusion.

The figure is an oversimplification in many ways. Some neurons project their axon trough different brain regions making synapses with many other neurons along the way. In other hand, the idea that neurons without inputs do nothing is wrong too. For example pacemaker neurons fires action potentials regularly even in the absence of any input.

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If my brain lost all of its activity for a moment, would my memory be gone too?
I can't remember which question it was, but in the past here, it was explained to me that memory is actively stored in the brain, rather than "physically". Meaning, memories are made up of the brain's activity, not its physical cell structure.
I'm not sure I have that right though. I mean, that, for one thing seem inefficient and overly complex. It seems like a vast amount of energy would be required to store so much information in the form of activity patterns. Maybe I misunderstood. So I'm asking. If my brain lost all of its energy (activity) for a moment (for example, one second), would my memory be gone too?

Summary
Working memory on a current task could be distorted, but I cannot find a reason to suggest sudden loss of electrical information would permanently alter short or long term memory.
Hopefully a neuroscientist can answer with a more electro-chemical oriented answer, but fundamentally I think the experts aren't sure what a memory actually is (there are only a handful of theories each that are understudied or flawed). This is also a fairly hypothetically question. Baring these points in mind, treat not only this, but all answers skeptically and take with a pinch of salt!
LTP
A recent review by Baudry et al covers the modern biochemical view on  long-term potentiation (LTP) of the hippocampus that is probably responsible for things like learning and memory. It is a complex protein formation involving BDNF, calpain, and synaptic modifications. If hypothetically you became 'brain dead' for a moment, this way of looking at memory probably wouldn't take a hit.
Engrams
Something I have less of a grasp on is Richard Semon's Engram, but was more heavily studied by Richard Thompson. Even the most modern studies describe this kind of brain mapping as chemical and cellular rather than electrical. So again perhaps nothing other than the unstored would be lost.
Working Memory loss
This rather technical article discusses primate prefrontal cortex neurone firing as a persistent stream needed for a "working memory". I am out of my depth here, but it seems like some "forming" memories may be lost if there was momentary activity loss, but I don't see why the underlying biochemical state that cause this effect would be lost, so very little information would be directly lost.
Memory loss. Diseases that cause memory loss involve tissue and protein changes along with other physiological changes. Memory loss induced by trauma is likely caused by swelling where the neurones are damaged by swelling or the trauma itself on a cellular level. It seems to be the case that the electrical information isn't the important factor to memory loss.
Note: I think memory would be lost indirectly, perhaps removed in a similar way as when you wake up from a dream or in cases of trauma. I am also ignoring that there would be a reasonable probability that this would induce seizure, stroke, or other bad health effects!

Memories are dynamic; that is not equivalent to "memories are evanescent". Cellular structure and composition controls memory, not just a continuous passage of signals. This point is already discussed in the comments.
Loss of energy (in the form of ATP) would cause memory deterioration and in some cases neuronal cell death too— strokes, which happen due to lack of blood supply to brain (and hence unavailability of nutrients and oxygen) can cause amnesia.
But one second will practically not affect anything.

I found the answer to my question here, however not linked to a duplicate question, so I'll quote:

Memories are represented in the brain as patterns of firing neurons.
  Let's say, for simplicity, that each neuron can either be on or off.
  Since there are 86 billion neurons in the brain, we can experience
  2^86bn possible brain states. That's a lot.
Of course there are a lot of simplifications here--most notably, there
  is a lot of structure to the brain, and so i'm not suggesting you can
  store 2^86bn memories--but the logic is the same. Even with only 1,000
  neurons, we can store a ridiculous amount of information (2^1000).
  - Jeff

And from the comments, I understand that this quote is not totally accurate, as a brain state is not a memory, and we just simply dont know enough about memory to do this kind of calculation, but the start of this quote is the key to the question:
Memories are represented in the brain as patterns of firing neurons.
Meaning yes, if the brain lost activity for a moment, its stored information would likely deteriorate tremendously, if not completely. That is, if my cited information (and interpretation of its effect)  is correct.

@Jeff I quoted you.

I cannot find any academic literature about memories being "firing neurones". Could you cite this please? I am quite interested!

@GoodGravy This is only information that I'm citing from another answer. It could be incorrect.

I found an article about persistent firing in the prefrontal cortex (responsible for conscious thought), and as a part of the study they found persistent firing, but this wasn't really to do with short or long term memory as far as I can deduce, but rather "working memory". As described in my answer, this firing is still the result of chemical cellular states, so might not take as big a hit as it would first seem.

There is no basis for this conclusion: "Meaning yes, if the brain lost activity for a moment, its stored information would likely deteriorate tremendously, if not completely. That is, if my cited information is correct." Since the neurons themselves are still extant and unchanged, as soon as they started firing again, the memories would all be there.

@anongoodnurse don't neural connections weaken when not active? Is that not a fast process?

You would have to define a time scale, its probably much much slower than axon firing.

@GoodGravy I edited the question to specify a period of one second.

@CuriousProgrammer - It takes longer than a second to disrupt neuronal pathways.

@anongoodnurse When you talk about disrupting neuronal pathways are you talking about altering synaptic connections, or how long it takes a voltage to be passed along the length of an axon?

@GoodGravy - altering synaptic connections.

@anongoodnurse Yes that would take time. I think what Curious is asking is that what if you removed the voltage from everywhere in the brain for a second. Would this change, or alter synaptic connections after a "reboot"?

@GoodGravy - Even though this is impossible to demonstrate, I'm pretty sure it would not have a significant effect.

@anongoodnurse I totally agree.

Let us continue this discussion in chat.


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How many transmissions does it normally take for a neuron to reach threshold for action potential?
This video illustrates and explains how the dendrite connections being activated causes the neuron to be polarized until it reaches "threshold", and firing. My question is how many times might a neuron's dendrites need to receive "fires" from other neurons in order to reach threshold. I think I understand that it isn't a binary matter, so I realize the answer isn't going to be 5 or 5,000 but a general range.
As a related question, how long does it take for polarization to wear off if additional transmissions don't come in, and if the polarization does wear off, is this wear-off mechanic important to the neural system? Is wearing off a significant aspect of the neural process, in other words?

To give a rough idea, according to my calculations it takes 153 inputs (individual action potentials) from CA3 pyramidal neurons to produce a depolarisation above threshold in the CA1 pyramidal neuron. This is of course a very simplistic division that does not consider spatial and temporal summation or any other complicating factor. Also note that each CA3 pyramidal neuron forms a variable number of synapses onto each CA1 pyramidal neuron (~5? according to the hippocampus book), and for each action potential only some of these synapses release a vesicle. Thus 153 inputs = xxx number of activated synapse (activated synapse = synapse receiving action potential).
So how did I arrive at 153?
According to this paper [1], a single action potential from a CA3 neuron produces an average depolarisation of 131 uV, presumably at the cell body, which we can also take, for simplicity, to be the depolarisation produced at the axon hillock. So assuming the threshold is 20mV (I'm not sure exactly but it should be in the 20-30mV range), the number of CA3 neuron each producing a depolarisation of 131 uV required to reach threshold is 20/0.131=153.
Again this is a simplistic division and may not be a good estimate once you take into account all the complicating factors in summation, but hopefully it gives some idea. Also bear in mind that synapses in different parts of the brain can have very different properties, so 153 might not be applicable to them.
[1] The time course and amplitude of EPSPs evoked at synapses between pairs of CA3/CA1 neurons in the hippocampal slice.
RJ Sayer, MJ Friedlander and SJ Redman.
Journal of Neuroscience 1 March 1990, 10 (3) 826-836

How many action potential are needed to cause an action potential in the postsynaptic neuron depends on the strength of the synapse(s) involved. It's not possible to answer this question in general.
It is not just the number of action potentials received but also the firing pattern in which they arrive and the location of the synapse(s) on the dendrites/soma (proximal/distal, on a spine or not, on which kind of spine,...) of the postsynaptic neuron.
However, for some neurons it is possible to trigger an action potential in a postsynaptic neuron with a single action potential. But in this case it is very probable that multiple synapses were involved between the two neurons (example paper).
To your second question: the time until polarization wears off is called the time constant tau of a neuron. It is a property that varies from neuron to neuron and is one of the things that can be measured when recording from a neuron. It is one of the many factors that affects how incoming action potentials are translated into a neuron's output firing.

What would be a minimum number? The smallest number of transfers it can take? 2 or 3? In other words how big do the synapses get in terms of polarizing the neuron? 30%? 80%? 100%? Also is it proper to use the word "synapse" the way you did, to refer to the transfer rather than simply the location of the transfer? That's a topic of confusion for me.

The synapse is the structure that connects the presynaptic to the postsynaptic neuron. The effect on the postsynaptic neuron depends on the activity of the presynaptic neuron, but also on the strength of the synapse (see my answer to your other question: http://biology.stackexchange.com/questions/56402/how-are-neurons-synapses-biased/56477#56477)

Your question about how far in % a synapse can get in terms of depolarizing a neuron is misleading. It depends on so many other factors such as the location of the synapse (look up dendritic integration), the proteins expressed on the postsynaptic neuron and so on. You can't answer this question with a single number. It's more complex than that.

Let me change the question for the OP so that we can get a quantitative answer: In a CNS neuron, what is the threshold for action potential initiation at the axon hillock, what is the typical depolarisation produced by an activated synapse on the dendrite at the dendrite and what is the resulting depolarisation at the axon hillock. I know it varies with different neurons and with different distance of synapse from soma, but something like  ~20mV at the dendrite and ~1mV at the axon hillock will help us get some idea about how difficult it is to excite a neuron.


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How hot can a beverage get without burning the tongue?
What is the maximum temperature that a beverage can be without burning the tongue?
I suspect there's a maximum temperature that the surface tissue of a tongue can withstand without being damaged (causing the burning feeling that lasts even after the heat goes away). So let's say I want to setup a device to keep my coffee to the right temperature to drink without damaging my mouth - I'm interested to know the highest possible temperature that will not damage the surface tissue of the tongue in a way that will result in lingering pain after the heat is gone.

I think its about 45-50°C, but why don't you try yourself? ;-) By fever/hyperthermia: "Almost certainly death will occur; however, patients have been known to survive up to 46.5 °C" so I think it is over 46°C, it's over nein-nein-nein.

Afaik the tongue is not more heat tolerant than other parts of the body, so the minimum temperature to cause burn is about drinking a beverage having 45°C temperature for a long time (more than 5 minutes). The pain threshold of tongue is around 47°C, so you will feel when it really burns.
According to studies the hedonic value of coffee has a maximum by 60°C, and it is significantly lower by safe levels (45°C). Frequent burns of mouth increases the risk of oral cancer. So I think this will be a hard choice... ;-)

A burn is an injury which is caused by application of heat or chemical
  substances to the external or internal surfaces of the body, which
  causes destruction of tissues. The minimum temperature for producing a
  burn is about 44°C for an exposure of about 5-6 hours or about 65°C
  for two seconds are sufficient to produce burns.

Thermal injuries

I. With the object of producing standard low-temperature burns in
  animals, and of studying the area of tissue only partly damaged in a
  burn, a burning iron has been made capable of applying temperatures
  from 45°-80°C. to the skin; with this the amount of heat and
  temperature causing skin damage has been studied, and the macroscopic
  and microscopic damage due to graded temperatures have been
  delineated.

Graded temperatures of 45°-80°C. have been applied to the skin of shaved, anæsthetised guinea-pigs, and in some cases rats, for times
  varying from 10 sec. to 6 and 10 min. Observations have been made of
  the development of erythema, flare, blanching, blueing, heat fixation,
  incipient blister formation, œdema, and edge wheal, as also upon the
  later scab formation and rate of epithelium regeneration.
Applications of 47°C. up to 6 minutes produce no visible change.
At 50°-55°C. applied for 1 minute and over, there is a critical temperature for the development of permanent and irreversible damage;
  in animals good scab formation occurs after burning at this
  temperature.
After temperatures of 60°-65°C. the epidermis can be peeled off from the exposed area, leaving a punched-out exposed surface area
  somewhat like the exposed human blister.

1943 - EXPERIMENTAL THERMAL BURNS, ESPECIALLY THE MODERATE TEMPERATURE BURN
According to Green the pain threshold of tongue is around 46-48°C.
1985 - Heat pain thresholds in the oral-facial region

In all experiments, the chosen mean preferred temperature for drinking
  was around 60 °C (140 °F). Black coffee drinkers chose a slightly
  higher mean temperature than drinkers with added creamer, and they
  also chose a slightly lower mean temperature when the flavor was
  stronger. In all cases, consumers tended to choose, on average,
  temperatures for drinking coffee that were above the oral pain
  threshold and the burn damage threshold.

2006 - At What Temperatures Do Consumers Like to Drink Coffee?: Mixing Methods

Overall, the available results strongly suggest that high-temperature
  beverage drinking increases the risk of EC. Future studies will
  require standardized strategies that allow for combining data, and
  results should be reported by histological subtypes of EC.

High-temperature beverages and Foods and Esophageal Cancer Risk -- A Systematic Review

AFAIK TRPV channels open at ~45-50⁰C. This is not really a heat that can cause burn. I have bathed many times in water @ ~>=60⁰ and it just felt relaxing (my epidermis was alright :P). It takes higher temperatures to actually cause a burn.

@WYSIWYG "I have bathed many times in water @ ~>=60⁰ and it just felt relaxing" - I seriously doubt that. Our boiler is set to 60°C and the maximum I am capable to tolerate is half cold + half warm, so about 40°C.

@WYSIWYG https://www.youtube.com/watch?v=0WniZ1ly5Ik watch this.

@WYSIWYG Just to mention, long exposure to more than 37°C can cause hyperthermia. Afaik. humans cannot bear more than 50°C air (non-scientific source), because they would sweat more than they can drink. So putting aside the burn injuries you would still die because of hyperthermia if you would bath in 60°C water (which has about 4000 folds greater volumetric heat capacity than air).

Bath is not such a long process. Face is of course more sensitive but legs and torso can tolerate ~60⁰C (Not too sure about the temp but its usually higher than what other people prefer. I don't use hot water often though. I'll check the temperature next time :P ).

@WYSIWYG Okay. :-)

Just saw this answer, +1 for good answer as well as appropriate username.

This depends on a lot of factors, including how you take your first sip. If you sip with air, you are altering the temperature of the liquid as you sip, as well as decreasing the volume of hot liquid in your mouth, so that the increased surface area of your exposed tongue can quickly alter the temperature of a borderline scalding liquid into a non-scalding one.
So, there is part of the answer: it depends on volume, and time in contact with the tongue.
Most coffee pots keep coffee at about 170°F (77°C) - hot enough to scald your mouth.
This article, while not scientific, does discuss why people like foods at temperatures that cause scalding, and what better temperatures are. But the public wants what it wants.
Safety experts recommend that water heaters be set at 120°F (49°C) because you will not sustain a first-degree burn on contact, which is important if one has mobility problems. At 120°F (49°C), it takes 8 minutes of contact to acquire a second degree burn. At 155°F (68°C), it takes one second.
So, to guarantee no scald on contact with a small volume of coffee, I would think 145°F (63°C) would be about right. (At 140°F (60°C), liquid will scald in 3 seconds. If you don't chug your coffee, this seems safe enough. If you chug, it will scald.)

I took the liberty of clarifying your temperature units, since I assume that you aren't talking about superheated coffee ;)


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What are the structural characteristics of a protein-protein interaction network
I am an researcher in computer science. I am interesting in the alignment problem of PPI networks of difference species. I know a PPI network is a graph in its nature. I want to know whether there are any structural characteristics or constraints of a protein-protein interaction network (such as, a certain kind of protein can only have certain kinds of interactions with other proteins, a certain kind of protein can appears in a PPI network at most certain times, and any thing like this). If a PPI network does't satisfy these structural characteristics or constraints, then people can know that this PPI network is not a valid one.

I have changed the problem's description according to your comments. Thanks.


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How to determine whether changes of an allele's frequency are due to genetic drift or selection?
Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population:
Are there ways to determine whether a frequency shift for a specific gene/allele is due to genetic drift or selection? In other words: when we see an allele take over a population, is there a way to know whether it was selected or just 'got lucky'?
UPDATE: since apparently this issue is quite complex in experimental biology I want to clarify why I'm asking this and what I hope to learn.
I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift.
I'm applying a genetic algorithm to the optimisation of websites, where each gene determines an aspect of the user experience of that website. The question is whether the alleles I see emerging in the fittest solutions (= the best user experience, rated by visitors) got there by chance or actually contribute to the fitness of the candidate solution (= make a difference in shaping the user experience).

Is there a way to disentangle selection from drift
Yes, there are actually many ways...so many so different ways that it is impossible to correctly answer this question. Hopefully, below answer will give you some appreciation of why there is such a diversity of methods and wil give you sources to further your knowledge on the question.
It depends upon the data you have
The answer very much depends on the data you have in mind. Are you looking at a

panmictic population
a structured population
are you comparing a large number of lineages along a phylogeny
do you have information about a proxy for fitness in this population
can you perform an evolution experiment (depends a lot on the generation time)
do you have genetic data that are temporally separated
...

Also, what type of selection are you thinking of?

balancing selection
Are you trying to find epistasis for selection
Are you looking at some form of balancing selection
Local selection
...

Also depends upon whether you have data about potentially correlated variables such as

phenotypic data
ecological data

There are tens (or even hundreds of methods esp. when having data about related lineages) under each bullet point above, so your question is definitely quite broad.
Source of information
Statistical tests that test to the null that there is no selection are often called "test of selective neutrality". You might want to read Nielsen 2001  and Nielsen 2005 to get an overview of tests of selective neutrality in panmictic populations.
You might want to have a look at this answer, this answer and especially this answer.
What does it take to understand the methods for disentangling selection from drift?
Understanding the tests of selective neutrality can be a bit demanding as it requires having good knowledge in classical statistics, bayesian statistics, MCMC, Approximate Bayesian Computation and even machine learning algorithms. It also requires good knowledge in population genetics (typically incl. coalescent theory) and statistical phylogenetic.
A specific example
Unfortunately, I can't think of any specific example of a test which is really easy to grasp without a priori knowledge. A classical, not too hard and historically example test for neutrality in panmictic population is the used of Tajima's D (which derivation require basic knowledge in branching processes). You might want to learn about it to have a specific example. I recommend Gillespie's book Population Genetics: A Concise Guide to learn about this test. More book recommendation can be found here.

I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift. I'm applying this to the behaviour I see in applying a genetic algorithm where each gene determines an aspect of the user experience of a website. The question is whether the alleles I see emerging in the fittest solutions got there by chance or actually contribute to the fitness of the candidate solution. I probably should have clarified this in my question but didn't because I didn't realise the complexity of this issue.

I would suggest that you open a new post for this more specific question. Don't forget to clearly define your algorithm model. A priori, if I were you, as a first step, I would examine the site frequency spectrum and perform a Tajima's D test.


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Bug Identification: what type of bug is this small ant-like bug?
It's not an ant; do you know what it's called? Found some in the building different times.

Edit: Size is 4mm (length) x 1mm (height)

It looks like a ground beetle (family Carabidae)

Thanks for the quick identification! looked up ground beetle sizes and found: ground beetles are from 1/8inch (3.1 mm) to 1/2inch (12.7 mm); though I haven't seen any quite as long (12.7 mm); perhaps these are baby ground beetles then.

Baby beetles are not small versions of adult beetles as beetles undergo complete matemorphosis (more info there). There are about 40,000 species of ground beetles. If you only see individuals that are relatively small it just mean that the species that you often see is a relatively small species of ground beetle.

This isn't a ground beetle; the lack of focus makes any identification uncertain, but my best guess is one of the grain beetles (family Silvanidae); if any have been seen since this question was asked, you probably should try to get rid of them -- they're after stuff in your pantry.

Are Silvanidae differentiated from Carabidae by having clubbed antenna tips rather than straight? If so I tend to agree.


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Which agricultural crops attract rodents?
Are there any data on rodent populations per acre of different types of agricultural crops?

"Which agricultural crops attract rodents?" - I guess which they can eat :D corn, wheat, oat, etc... with high starch (and so energy) content. but almost everything I think.


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Polar bodies in females
What is the fate of first and second polar bodies formed during the menstrual cycle in human females?
Do they degenerate?
Does any other mammal also produce polar bodies?

According to this article polar bodies sometimes apoptose but sometimes are "capable of developing into complex, highly organized structures, or even enabling parthenogenesis". Despite their fate being far less than the oocyte.
It also states they're present not only in other animals, but also some plants.
"In other animals and some plants, polar bodies give rise to vital tissues that protect and nourish the embryo. These apparent “oddities” reveal the diverse mechanisms used during reproductive development and may even allude to the origins of meiotic strategies."
It looks like polar bodies are very important in humans, but not other organisms:
"Polar bodies may, however, give rise to human embryoids if fertilized and twins may even result when one spermatozoa fertilizes the ovum and a second sperm fertilizes its sister polar body (Bieber et al., 1981). No twin pairs resulting from fertilization of the second (haploid) polar body have been reported (Machin, 2009), but clearly polar bodies have cellular and developmental potentials beyond apoptosis, even in humans."
"But in many other organisms, polar bodies are not dispensable. They are not simply waste bins for three-quarters of the genetic material produced during oogenesis, and they do not disappear following meiosis."

So the second sperm fertilises the first polar body? But wouldn't that require two sperms entering the ovum? Is it practically possible?

The first polar body is separate from the ovum, so the second sperm would fertilize the first polar body as if it were an egg. Two sperm can enter one ovum though, but the majority don't survive. When they do, the egg needs to split. If it doesn't, it results in something called a mole pregnancy; the offspring will eventually miscarriage unless aborted.


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Does TSH and Growth hormone have any role in menstruation?
Actually, I came across this on a mcq (multiple choice question) exam:
Name the hormone which has no role in menstruation:
A. LH
B. FSH
C. GH
D. TSH
(only 1 correct option)
Both FSH and LH have direct roles in the menstrual cycle, they're responsible for the follicular phase and ovulation, respectively. Menstruation takes place due to the decreased levels of progesterone. Does GH and TSH have any role in the process? If so what is that role?

I don't think they have a direct role but can affect menstruation indirectly by influencing metabolism.

TSH has an effect slightly similar to that of FSH and LH. This is found to be problematic in thyroid diorders. For example, in hypothyroidism the TSH overflow causes children to become fertile at an earlier stage, compared to the norm [1].
[1] Ann N Y Acad Sci. 1997 Jun 17;816:280-4. PMID: 9238278. http://www.ncbi.nlm.nih.gov/pubmed/9238278

If hypothyroidism or hyperthyroidism resulted in menstrual disorders, then can't we say that thyroxine(secreted by thyroid) has a role in the proper functioning of the menstrual cycle, rather than TSH?

Not necessarily, correlation doesn't equal causation. While Thyroxine is the main hormone secreted by the thyroid, it doesn't directly mimic FSH and LH like TSH.


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If the half life of Caffeine is ~6 hours, why do people consider it ineffective after its half-life?
Caffeine has a half-life of ~ 6 hours in the body.
So assuming you take 200mg of caffeine, after 6 hours there should still be 100mg of caffeine in your body.
Then why is it generally said that after 6 hours caffeines effect should wear off? Shouldn't it only be diminished since there is still 100mg of caffeine in your body?

You need to consider what concentration of caffeine within the body will have biological effects. That is, you could have 1 picogram of caffeine on your body but you may be well below the threshold needed to have a biologic effect.

@VanceLAlbaugh Yeah, but it's generally stated that after 6 hours regardless of dosage that caffeine "wears off", so technically my 200mg original dose becomes ineffective even though after its half life I'd still have 100mg (which is definitely enough to have biological effects?)

where are you reading that - what source?


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What is the median concentration of spike antigen in COVID positive patients?
I am searching for the plasma spike concentration in COVID patients. The closest possible reference I found claims that spike was only detectable in 5 of 64 COVID-19 positive patients.
However, their spike assay is relatively insensitive with a LOD (limit of detection) of 70 pg spike protein/ml; multiple vaccine-related studies detected a spike concentration of around 1 pg/ml.
Are there better sources?

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


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Why a cell contains all DNA when it only needs a few genes?
Is that what they called junk? Why does a simple cell have the DNA code for everything else when it just needs a few codes to function? Wouldn't that be a wasteful?

Why does a cell contain all DNA when it only needs a few genes ?

I interpret this question to mean "why does every cell contain the whole human genome even though it doesn't use it all, i.e. why does a liver cell contain the genes for eye color?"
If that is what you meant, then we can easily answer the first question in your actual text:

Is that what they called junk?

No, that is not what is called "junk DNA". "Junk DNA" can refer to many concepts, but generally it refers to parts of DNA that serve no function in the body: they are not transcribed into proteins, they don't serve to regulate other genes, and if you remove them or change their sequence this will have no effect on the overall organism. This means it refers to parts of DNA that are used nowhere in the body, not parts that are used in one place but not in others.
How much DNA is "junk", how useless it actually is, and why we have it are complex questions that don't all have known answers, but it is completely different from your headline question.
I don't have the time to look up a detailed answer to your first question so I will leave that to others, but here are some elements that might help:
1) I think cells use more genes than you realize. I don't know the proportion of genes that are used for the cell to live as a cell vs those that are used for the specific tasks this cell needs to do beyond maintaining itself and reproducing, but I'm pretty certain there is no cell in the body that "only needs a few genes". I would even guess all cells in the body use most of the genes they contain.
2) not all cells contain an unmodified copy of the whole genome. Some cells lose their nucleus, i.e. their DNA entirely (red blood cells); others multiply some genes that they use a lot.
3) having said all that, I would guess that liver cells indeed don't need the genes for eye color, yet they might have them. Consider that cells reproduce by copying themselves, and copying their whole genome. Is it more of a waste to keep the copy as it is, or to go around before or after the copying cutting out all the bits this specific cell won't use? Do I go around editing the code of my text editor and recompiling it to get rid of all the functionalities I don't use? I might save some space on my hard drive but it is very obviously not worth my time to do that either. If the extra DNA doesn't do enough harm, there is no reason it would be taken out; indeed the wasteful thing would be to do so.

Whether there is junk DNA

The common view of a gene is a sequence of DNA which, upon transcription, which I assume in your understanding is a process by which DNA is read by a RNA polymerase to produce mRNA, and upon translation, produces a functional protein to regulate cellular metabolism (sum of all chemical reactions in a cell). It is not until the discipline of epigenetics emerged that we discover that most of other non-protein-coding sequences have important regulatory functions on the protein-coding sequences. Without them, the cell simply has no clue as to when it should produce more of a protein and when it should produce less, or whether the protein should be produced at all. And of course, DNA also encodes information about rRNA, which is an integral component of ribosome, which you know, is imperative for protein synthesis. Thus, the ‘functions’ of the DNA cannot be limited to protein synthesis, and after extension of the concept of functions, the parts of DNA we can dispense with are incredibly small.
Then let it be argued that those small parts of DNA which really serve no functions are the junk DNA. In fact, even this view is untenable because the ‘functionless’ DNA may be situated between the important sequences that can subtly affect the chemical properties of the protein interactions during an important biochemical process. Specifically, consider NtrC, a bacterial transcription regulator that activates transcription by directly contacting the RNA polymerase. Note that the regulatory sequence (the part of DNA the protein binds to) is very distant from the promoter of the gene(the part of the gene that RNA polymerase binds to). To directly contact it, DNA looping must occur. It is a phenomenon in which an otherwise linear DNA macromolecule is looped out(imagine bending a wire so that two extreme end of the wire touches each other) to allow for the contacts between molecules. Since the protein has such biochemical properties that allow it to contact another protein at a distance, we do not know what will happen if the ‘junk DNA’ the DNA spacing the promoter and the regulatory sequence is deleted. It is well possible that the two proteins will not make contacts anymore. And DNA looping is also ubiquitously found in transcription regulation of eukaryotes.

Why a cell needs to contain all the DNA when it only needs a few genes to function

Once the notion of junk DNA is found to be elusive. This question’s premises no longer hold. But let’s assume there are really genes that when deleted have no observable effects on the phenotypes of the cells or their health, why does not nature delete them during differentiation of stem cells? To explain it in evolutionary terms, there are two main mechanisms nature can design to keep the ‘functionless’ genes at bay during differentiation of stem cells. One is to silence them by wrapping them in a compacted nucleosomal structure, or to delete them once and for all. We do not know if nature has once experimented with deletion, if it has then this design must have endowed less fitness then the wrapping model. What reasons then can we speculate about the failure of the deletion model? To delete the useless sequences, there is a widespread effects on the length of the DNA, the resultant secondary structure (topology of the chromatin). And a protein must be designed to specifically recognise what genes to delete, together with the cooperation of nucleases. This is analogous to writing a computer code that contains information that specifies some of the codes to be deleted while not influencing the instructions of the code that follow, all while being consistent in the process. This is logically possible, and we can never say this design is entirely prohibited. But computationally this is not as elegant a solution than just genes in the DNA that code for a repressor protein for the ‘useless’ code when the right time has come, or by just using proteins to wrap around the sequences to render them unreadable.

Whether ‘non-functional ‘ DNA constitutes a waste

Not at all.

I expect you were downvoted because it's not the consensus that little to no DNA has no function. It isn't just about how non-coding DNA might have other functions; for example, looking at which parts of the genome show evidence of selection and which don't can serve as a proxy for them having a function or not, and by that metric most human DNA is indeed "junk". I also don't think it has been shown that most non-coding DNA has a regulatory function. Some yes, most no. Highest number I find is 40% here, and even that's a hypothetical. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431477/


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Is it a coincidence that the sensory systems for smell, vision, taste, and hearing are all near each other in the head?
I was wondering if it's an evolutionary advantage to have many sensory systems in a small place of the body, the head. This applies to mammals, reptiles, synapsid, dinosaurs... and many more.
My theories:

The distance to the brain is short and thus smaller time delay to
respond faster to the outside world,have more reflexes, hunt faster
prey and fight more accurately.
The short distance makes the "wire" (signal carrying) shorter and
thus less vulnerable to be cut from a injury, because for a organism
losing an eye reduces possibilities of survival dramatically.
In humans at least the head is the upper part, then vision organs
see more with less obstacles such as vegetation or terrain irregularities, or anything that obstacles vision, normally higher
means seeing more things. This I'm not sure applies so strongly to
smell. To taste, certainly not. To hearing, possibly a little,
thought nor much as vision.

We evolved from a common ancestor that was like that but that doesn't explain why it's not common to get out of that coincidence.

The existence of a common ancestor is part of the answer to the question of why the layout of vertebrate sensory systems are so consistent (it's included in both answers). The identity of the common ancestor is a separate question and I think it's off-topic for your main question so it would be best posed as a separate question may with a link to this one.

It's called "design"

@BenPiper Who or what designed what? Do someone designed the organs to be all in the head, that's what you are saying?

No it's not a coincidence that eyes, nose, mouth, and ears are all near each other in the head. As you note the layout is inherited from an ancestor, that's your answer.

A study of vertebrate head sensory systems shows that the

The olfactory, vestibular auditory, and lateral line sensory organs displayed a strong link with the urochordate-vertebrate ancestor.

So this paper highlights that these structures go back earlier than the animals in your list. The development of vertebrates is very complicated so major departures from this developmental program which are successful are going to be rare events. This is reflected by blind cave dwelling animals that have vestigial non-functional eyes. The lack of selection pressure means the eyes don't work but they are still there because building an eye is part of a deep developmental programme. The image below shows (in orange) the key drivers of differentiation for various cell types. It makes it obvious that the program that produces olfaction also produces vision (otic) so modifications to the developmental program will have wide-ranging effects.

The theories that you've listed are interesting and there is work going into developing new senses. Udo Wachter wore a belt that vibrated to north 24/7, "north" became part of his dreams, he always knew where home was, and he mourned the loss of the the sense. So proximity to the brain is not a critical factor for the senses.


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fastq-dump using mkfifo to stream data
So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk.
I'm curious whether it would be possible to use fastq-dump to write to a named pipe (using mkfifo) and feed that into another program, for example Trinity, to run an assembly on the FASTQ file without ever having to write all that data to disk. For large datasets, this could actually save quite a bit of time in aggregate.
Has anyone done something similar? I am going to try and experiment with the technique soon, but I a) don't know much about the mkfifo process to begin with and b) am unsure of how this procedure would work for paired-end data where fastq-dump is splitting the SRA file as it goes. How would one specify which output would go to which pipe?
EDIT: A (hypothetical) example:

mkfifo fileStream
fastq-dump SRR123456 > fileStream
Trinity --single fileStream misc_args

That should take the fastq-dump data and stream it into the named pipe "fileStream", which can then be used to stream data into Trinity. I don't know enough about all of the commands, however, to know if this makes any sense.
I would welcome any thoughts from more experienced users!
EDIT: Added update as an answer below.

Can you give an example of the kind of piping you are trying to do? Frequently I just try something like bin1 infile | bin2 - and see what happens.

I you don't get an answer here you should try asking at http://stackoverflow.com/ or http://unix.stackexchange.com/, since this deals a lot with tools and piping in Bash.

I agree with @fileunderwater ... this should be migrated to stack overflow (I just don't have the power to do so!)

@fileunderwater, @T Abraham: I am not super familiar with the culture on here, and I am fine with having this question go wherever. It's possible, however, that with the updates this post might prove useful to someone else in bioinformatics using Trinity.

@glarue You should post the last update as an answer instead, since that is what it is. It is perfectly fine to post answers to your own questions, and then the community can decide (by voting) on which answer is the best.
And for the record, with regards to my suggestion to move/crosspost; I don't think the question is off-topic here, since it clearly deals with methods in bioinformatics.

fastq-dump can write to stdout ; the -Z option allows you to do that. This, you can pipe to any downstream process. [An example]. Also see the SRA-toolkit manual.
I guess someone asked this question in biostar too.

As WYSIWYG pointed out, fastq-dump can output to STDOUT, so if you want to combine it with named pipes, you'd do:
mkfifo mydata.fifo
fastq-dump -Z mydata.sra > mydata.fifo &
cat mydata.fifo # or whatever
rm mydata.fifo

If you try to catch the output from fastq-dump without -Z it fails with the Illegal seek(29) error:
mkfifo mydata.fastq
fastq-dump mydata.sra &

By the way, be careful with your downstream analyses: if the input is to be read more than once, respective program will fail to re-read from your pipe. For single-end data and Trinity that's probably not the case, but I suspect that for paired-end data Trinity will attempt to read the input files at more than one step.

Thanks for the additional info. I am now much more familiar with the commands and have gotten it working. I also appreciate the note on PE data; I believe for Trinity however it's not a problem because the first thing Trinity does is write the data to FASTA files (which it later concatenates). The trick with PE is to deal with the convolved data such that it gets properly split into separate streams for feeding into Trinity. I will update post with a working example soon.

Okay, so just for others who might stumble upon this, here is a brief description of one implementation of this technique to run with paired-end RNA-seq data:
fastq-dump SRA_file --split-files -I -Z | tee >(grep '@.*\.1\s' -A3 --no-group-separator > namedPipe_1) >(grep '@.*\.2\s' -A3 --no-group-separator > namedPipe_2) >/dev/null

This first requires the creation of two named pipes using mkfifo. For paired-end data, the -Z flag becomes problematic because it forces the data into a single stream. There are many ways to regain the two pairs, but the way I've elected to do it is to use --split-files to break up the stream beforehand, -I to append either ".1" or ".2" to the end of each header, and then use tee to duplicate the stream plus grep with a regex to parse the info from each pair back out into separate pipes for downstream use.
I have tested this with Trinity, running on each named pipe just as I would with a FASTQ file, and it seems to be working fine. While I am not 100% sure that Trinity won't try and go back to the original FASTQ files, the first thing Trinity does is take those FASTQ files and parse them into FASTA format, which it later concatenates into "both.fa", and so I'm pretty confident that this will work.
UPDATE: This implementation will not work (at least, not as far as I can tell) with the Trimmomatic plugin for Trinity. Something seems to get screwed up because of the way Trimmomatic pulls from the streams - just a cautionary note, I haven't figured out the cause.


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basic programming and bioinformatics
As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work with RNA-Seq data, compare and interpret them?
Thanks!

I think that you should try to be more specific with your question. Right now it is too broad (you can do an entire degree in bioinformatics). What do you do now? What do you want to be able to do?

I know its too broad and thats why I am asking actually. Now I am a masters student in neurosciences and will continue with a PhD in the same area. A post-doc from my lab was saying to me that I need to be able to understand basic stuff about programming and bioinformatics. Lets say I am going to compare RNA-seq results and interpret them.

Then the question might be better suited for academia.SE or biostars. I think you're going to get too many discussion-type answers here.

The coursera classes are a good introduction - one is starting next week!  the focus on python a lot I think...

Thanks! Is it the one that you mentioned?: https://www.coursera.org/course/pkubioinfo

I was thinking of this one, https://www.coursera.org/course/bioinfomethods2 but that one looks good too.  If you are a PhD student you should learn computation closely related to your research - that will motivate you. either R or better yet python as tools.

Indeed the question is broad and quite hard to answer I think. I'll give a try. I very welcome editing to improve this answer.
The field of bioinformatics is a big field. Bioinformaticians need basic knowledge in

biology
molecular genetics
Population genetics
programming
statistics

You may find courses on statistics applied to bioinformatics here (R-language) and here (I haven't watched these sources).
How to start programming? - Python
You seem to be mostly interested in is programming. I think that Python is a very good start to get in touch with programming. Programming might look a bit scary when you don't really know what it is about but you can easily, in a few days, acquire basic knowledge in this field and already solve some pretty neat problems. Many people actually have lots of fun learning how to program. And you'll probably be amazed by all the power this tool will offer to you. I personally really enjoyed learning to programming in Python. I did it (I was mostly interested in object-oriented programming, you'll learn what it means) in a day or two with a very good source but unfortunately, this source is not available in English. But there are tons of introductory documents, you'll have no difficulty to find a good one. I'd counsel you to directly download Python and to look at online courses on khan academy or EdX (I haven't watched them).
Data analysis - R
While Python is very popular, I think that, as a biologist, it is very important that you know about R. R is a programming language which is slow (compare to Python, C, Java, …) but it is very useful for statistical analysis and visual display of data. Also, many people use R in bioinformatics (for phylogenetic analysis typically). I think that acquiring basic knowledge in R takes more time than in Python because we tend to use R because of its huge amount of already existing functions and therefore, we have to learn many of these functions before understanding that R can indeed be much more useful than Python for some tasks.
Command line - Shell script
Shell script (BASH for example) is a very specific and very important language too. Very useful for manipulating, transferring files, managing processes or pretty much anything that is happening on your computer.
Other
C and C++ are very fast and very much used as well. Perl is commonly used for genomic sequence analysis (although Perl is slowly losing users to the advantage of Python).
Usefulness of programming
You also ask about the usefulness of programming. Well, it is used in pretty much all areas of biology. It is used for analyzing empirical data, computer simulations in population genetics, graph theory, annotating DNA sequences, … I guess that 98% of biologists have at least some basic knowledge in programming. The main point about programming is that it performs calculation much faster than anything you could ever realize with your calculator. Typically, in bioinformatics, analysis of DNA sequences often asks for very intense calculation and asks for big computation power. Processes such as constructing phylogenetic trees, determining a goodness of fit of evolutionary models, annotating DNA, aligning DNA sequences, analyzing microarray and many other things are all sorts of tasks that require programming.

This is the answer I was looking for actually. Thanks a lot!

I'm not at all sure that R is slower than python. Both are interpreted scripting languages. C and Java are completely different.

What you need to remember is that R is more of a domain-specific language (statistics and related fields like visualization), while Python is more of a "generic" programming language like the C superfamily, Java, Ruby, etc. What sets Python apart is its comparative ease of learning and use, the "batteries included" philosophy of the standard library, and the huge number of 3rd-party modules available for everything from bioinformatics (Biopython, etc.) to visualization (matplotlib) to numerical analysis (numpy/scipy) to web frameworks to natural language analysis and more...

Python also has interfaces to other languages (R, C/C++, Fortran, Java, etc.) so you can do domain-specific work in the best language for that project, and use Python as the "glue" to piece it all together.

@terdon R is definitely slower than Python, though not dramatically.

Why are you making a trivial edit to a question that was closed almost two years ago?

I did not realize it was closed when I edited it. I often improve my past posts. Why are you asking?

...because it comes back to the view of everybody and waste your time probably....mmhh ok. Well sorry about that.


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Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?
I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks:

Isotopes
  If the mass spectrometer you are working with has sufficient resolution look at the isotopes, a singly charged ion will show isotopic peaks that differ by 1 mass unit, a doubly charged ion will show peaks that differ by 0.5 mass units and so on. This is another way to deduce the charge state of a peak and thus the mass.

So let's suppose the spectrometer has a sufficient resolution to look at the different isotopes. It's not really clear for me at which peak I have to start. So to summarize my questions realted to this topic:

Which peak do I have to look at when determining the charge based on the isotope distribution?
Why would the peaks differ 0.5 mass units (see above)?

update

source: http://mascot.proteomix.org/help/mass_accuracy_help.html

When looking at the above graph, there is a difference of 1 amu between the different peaks.

What do the isotopes have to do with the charge?
What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?

It's not clear whether your second quote is talking about mass, charge, time of flight (which is not measured in all MS systems, only TOF ones), or a ratio of two of those parameters. Also, is this single or tandem MS?

The source says it's about ESI @MattDMo, I'm not really into this subject so I can't clearify it that much...

I happen to work with a bunch of people using nanospray LC-MS/MS for protein sequencing and analysis of post-translational modifications, so I'll forward this question on to them and see what they think.

Would be great! @MattDMo

@RickBeeloo; the first article is referring directly to TOF analysers in your quote. It is irrelevant to your question and should be removed.

If you have an ion of mass 100 and charge 2, the m/z ratio (let's exclude the root) will be 100/2=50. If you have isotopes, then you expect to find several peaks for a given fragment. For example, the masses of different isotopes of the same molecule could be like: 100, 102, 105 and 107. In this case the spectrometer will detect four peaks, instead of one, for the same molecule (will look something like this): 100/2, 102/2, 105/2 and 107/2. The charge of all that peaks is the same.. it's only the mass that differs.
The page you linked simply makes an example, "singly charged ion will show isotopic peaks that differ by 1" example m=10 z=1 m/z =10, for the isotope m=11 z=1 m/z=11 (difference of 1). If you have a doubly charged ion m=10 z=2 m/z=5 and for the isotope will be 11/2=5.5 (difference of 0.5).
So, if you take the spectra of a compound and you see the isotopic peaks having a distance of 0.5 among each other, you are looking at a doubly charged ion, if the distance is 1, it's a singly charged ion.
What do the isotopes have to do with the charge?
Given that the isotopes peaks are around 1 units far from each other, you can conclude that the ion you are looking at has 1 charge.
The last question is not clear to me.

That's exactly what I thought until I read the givin citation that isotopes can be used to determine the charge of ions in the spectrum @alec_djinn

Do you have a spectrum example of this to clarify what you are suggesting? alec_djinn

Here you see the spectra of a molecule having 2 positive charges, the zoom-in picture on the right shows how the peaks of that specific compound are 0.5 units distant from each other.

If the ion has only one charge, m/z=m , since there are no "half masses", the isotopes can differ only by full units of mass (+1, +2, +3 ...). To explain a difference of 0.5 units in an m/z chart, z must be 2! It's not the mass that is 0.5.

Thankyou for your effort! Can you please answer the questions beneath my update. If I get those two questions clear I think I'm done and can mark your answer. (answer them in your answer please) @alec_djinn

I've changed the order of your questions so that the answers follow from one another.

What do the isotopes have to do with the charge?

The presence of isotopes has no effect on the charge of the molecule. The physiochemical properties of the molecule and how the MS has been setup dictate how molecules acquire charges.
This is important as methods which utilise isotopic labelling rely on the presence of isotopes in molecules having no effect on their physiochemical properties. Secondarily, life would become untenable if the incorporation of isotopes altered the properties of proteins (see below).

Which peak do I have to look at when determining the charge based on the isotope distribution?

The m/z of the isotope peaks provides information about charge so you use the spacing between isotope peaks. It is important to use the most accurate measurements, which will be the strongest peaks, to calculate the mass difference. There is no need to use the monoisotopic (M) peak which in some cases will not be present.
~ 1.1% of the carbon on the planet is C13 so on average in biological molecules 1.1 out of every 100 carbons will be the C13 isotope. Therefore, as biological molecules get larger C13 will be incorporated more frequently and the chances of measuring the monoisotopic peak reduces.

What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?

Lets assume the m/z difference between the monoisotopic peak (M) and the isotope peak with 1 isotope per molecule (M+1) is; 1086.55 - 1085.55 = 1
We know that the mass for the isotope is ~1 so z must equal 1 when the isotope peaks have a difference of 1 m/z.

Why would the peaks differ 0.5 mass units(see above)?

Let's assume we're working with the same molecule as above (M = 1084.543) but it is  doubly charged. In this instance it will have an m/z = 543.778 and the first isotope peak (M+1) will be measured at 544.278 m/z.
We know that m = 1 when a single isotope is present so the difference of 0.5 m/z => 1/0.5 = 2. The charge (z) is 2.
Note that every charge adds a proton at 1.007276 mass units to the monoisotopic mass of the charged molecule. However, when we talk about the monoisotopic mass of the molecule we don't want to include protons. That is why M = 1084.543 rather than the 1085.55 m/z (and mass) of the singly-charged molecule that was shown in the image above.

Thankyou great explanation! I still have a question, let's assume I need to anlyse a spectrum by hand. I first have to look at the charges of the ions (thus peaks) to determine the molecular mass right? but how can I determine the charge of a peak? I know I can look at the spec and see if there are peaks with half the mass so I know they are doubly charged, but are there other methods? @Michal_A

No worries. The question(s) about MS/MS should probably go in a new question. The details depend on how the fragments were produced and the detector that was used. Mascot provides good details about fragmentation.

Thankyou I appriciate your help! I posted a question which is related to spectra analysis http://biology.stackexchange.com/questions/52034/mass-spectrum-analysis maybe you are interested answering this one @Michael_A. Feel free to edit this question because as I said earlier I'm not really into this topic but really want to understand it.

OK, I've edited your question to exclude references to calculating "t" as it was based on a misunderstanding of the original paper. I think the question is clearer/better without it.


text:
Kinetic Vs Potential Energy in Biochemical Contexts
This question is causing great confusion in my head.
Which of the following is an example of potential rather than kinetic energy?
A) the muscle contractions of a person mowing grass
B) water rushing over Niagara Falls
C) light flashes emitted by a firefly
D) a molecule of glucose
E) the flight of an insect foraging for food
Answer:  D
A) Muscle contractions is caused by the use of potential energy in ATP used by actin and myosin.
B) This is a classic example of what potential energy means.
C) Bioluminescence is a process caused by the use of chemical (potential) energy.
D) Yes, the molecule of glucose does contain potential energy. BUT, it is not potential energy itself...
E) Flight is kinetic energy. However, you can still boil this down to ATP in actin and myosin.
How do I approach this problem? My teacher said this is the type of problem she would give us. But this is so ambiguous. Am I lost?

If you find one of the answers solving your problem accept it. Doesn't matter which!

I think you are right and many examples are ambiguous.  Even D) is ambiguous as a molecule is always in motion due to entropy except, perhaps, at absolute zero (0 Kelvin). But normally, it does contain kinetic energy.
However, as you already identified the ambiguity, look at the best, or in this case least incorrect answer; The only option without any physical movement explicitly mentioned in the question description is D). All the others mention 'emit', 'flight', 'rushing down', etc.
Also ask your teacher :)

Is emitting really a form of kinetic energy? Maybe they were referring to "light energy" and not the potential energy that was used to make the light.

A moving photon has, however small, kinetic energy

Going by the answer, the key to interpret this question seems to be the absence of kinetic energy.
Total Energy (mechanical) = Potential + Kinetic (let's ignore the pressure component as this question does not involve it).
So the key to answer this question would be a system where the full energy is represented by the Potential energy.
In a contracting muscle - let's consider gross dynamics - the muscle is in motion (the myofibrils are moving) ~ Kinetic Energy
Water moving in a falls - Definitely kinetic energy (In fact this system is one where the potential energy is constantly decreasing while the kinetic energy is increasing constantly)
Bioluminescence - Light Energy which is neither kinetic nor potential (as I understand physics, so correct me if I am wrong)
Glucose as a source of energy - In its unutilised state (only during which it is called glucose) is purely potential energy. When glucose is talked in terms of potential energy, the movement of glucose inside a medium is not what is being talked about.

Yes, well broken down answer +1

You'll find the answer glucose best fits the definition of potential energy, as in it's standard state the glucose has all of it's energy stored in it's bonds (1). Every other answer is some sort of expenditure of energy (ATP in the case of firefly luciferase reaction, see (2)).

authors: илиян арабаджиев


text:
What are these little creatures on the fish?
I'm not a fisherman, but I just caught a cod fish (my first one) and found a lot of strange little creatures all over the fish:

What are those? Are they harmful to the fish, or to the human?
Edit: it's caught on Faroe Islands

For identification questions please: 1) upload an image, and 2) include the location (e.g. country and region — the more specific the better). ——— The location can be an essential clue for identification and links are discouraged since 1) if they break they render this post and any answers worthless, and 2) they can be used to link to malicious websites. Thanks!

Though it's hard to say exactly what you're talking about based on the image, that cod appears to have several sea lice on it:
https://en.wikipedia.org/wiki/Sea_louse
Sea lice are common parasites of fish.


text:
How long does it take for a cell to synthesize an enzyme?
Where can I find data regarding the times distinct cells take to synthesize distinct enzymes?

on an average it takes ~10 hours to reach steady state.. this is called the response time- not synthesis time.

In human cells it takes about 20 s to make a 20,000 dalton enzyme.
Assuming that the cells concerned are already making mRNA for the enzyme, there will be two main factors:
(1) The time taken to synthesize the polypeptide
(2) Any time taken to fold the protein
(If the enzyme is secreted from the cell there will also be the time taken for the protein to traverse the secretory pathway - perhaps you want to include this time - if so it could be 10's of minutes.)
Here I will focus on (1). What is the rate of polypeptide elongation?
For bacteria:

Young & Bremer (1976) Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate Biochem. J. 160: 185-194

They quote values of:
17 s-1 for fast-growing cells
and 12 s-1 for slower-growing cells.
For yeast:

Bonven & Gullov (1979) Peptide chain elongation rate and ribosomal activity in Saccharomyces cerevisiae as a function of the growth rate. Mol. Gen. Genet. 170: 225-230

minimal glucose 9.3 s-1
minimal acetate 5.5 s-1
In human cells:

Ramabhadran & Thach (1981) Translational elongation rate changes in encephalomyocarditis virus-infected and interferon-treated cells. J. Virol. 39: 573-583

They measure a control value of 9.4 s-1 and quote (with citations) values of 9-10 s-1 in reticulocytes and CHO cells.
Let's use 9 s-1, and assume 110 daltons per amino acid
Then e.g. a 20.000 dalton enzyme (= 182 amino acids) requires 20 seconds.


text:
Does the body lose energy or gain energy relatively when drinking or eating hot things?
Does the body lose or gain energy when drinking or eating hot things compared to more neutral temperature things?
On the one hand,
The body could somehow convert the heat energy into human usable energy,
And on the other hand,
The body heats up and needs to be cooled down, and this way it loses energy.

Depends on the definition of "energy". Energy in physics does not correspond to colloquial word "energy"...

Gains heat; humans are not particularly well-adapted to make use of heat as an energy source.  In a simple matter, if something you eat is hot when it goes in then the average temperature of the body has increased.  More relevantly (and to get this more on-topic for biology), eating anything will generally increase your body temperature, as in order to digest the food your rate of metabolism will rise.  Metabolism produces a lot of heat, and that's what you feel after eating, especially a big meal.
Something like cold water, however, that doesn't require a whole lot of metabolism, will cool you down.  In fact, even drinking hot water might cool you down.  The paper cited there claims that drinking a hot drink on a hot day will disproportionally increase your sweat response such that you actually cool down.


text:
What is a good Microbiology atlas for Bacteriology as online version?
I am looking for a online atlas for Bacteriology, the cost does not matter.
I have been searching SpringerLink, and Amazon but no good online version found.
What is a good atlas for Bacteriology as a online version?

Not sure what you are exactly looking for? If you change the question or comment I can update my answer...
NCBI's taxonomy site has a listing of bacteria.  Encyclopedia of life is also great.
Then there's UCSC's microbial genome browser.
Biocyc is  great reference for bacterial genes.  to get into E coli, which is the model bacterium there's Port Eco featuring 130 E coli genomes.
Am Soc Micro has an excellent E coli/ Salmonella site based on their classic reference - you have to pay for access though.

Thank you very much! The http://eol.org/ is outstanding resource for the basic course of Microbiology.

Ah glad I could help you find what you wanted! :)


text:
Blood circulation and blood pressure in different tissues
The volume of blood coursing the blood circulation is approximately five litres. A typical vein will stretch about eight times as much as corresponding artery. Because veins have high capacitance, large changes in blood volume have little effect on arterial blood pressure.
If the volume rise or falls, the elastic walls stretch or recoil, changing the volume of blood thus blood pressure in the nervous system.
What else tissues can we consider?
I am interested in blood circulation and blood pressures in different tissues.

I don't understand what you're asking. Please clarify

I'm not sure I understand your question very well-maybe try and rephrase it? As another example, low blood pressure in the kidneys is sensed by the juxtaglomerular apparatus which secretes renin into the circulation. Renin converts angiotensinogen (released by the liver) into angiotensin I. Angiotensin I is then converted into angiotensin II by angiotensin converting enzyme (this is the target of anti-hypertensives called ACE inhibitors) secreted by the lungs. Angiotensin II is a potent vasoconstrictor which directly increases the blood pressure (and hence glomerular filtration rate).  Angiotensin II also causes the release of aldosterone which acts on the kidneys to re-absorb salt and water again all facilitating an increase in blood pressure. I hope I've answered your question, if not please edit the question so it very clear.

I think you are correct. I got the exercise as is in the title. I discussed in the exam about Centers in Brain and Receptors. Basoreceptors and vasomotor center, for instance. Should I include neural regulation of blood circulation to the exercise in the title? I think now no.

The diameter of the blood vessel affects the speed of the flow of blood. Blood flow slows down as it moves from arteries to arterioles and subsequently to the capillaries because the cross-sectional area in the capillary beds is much bigger than the arteries or any part of the circulatory system. Use this drug awareness forum to know more about this.

Although the question isn't very clear, I'm not sure that this answers it and does rather read like an advert.


text:
Do Yersinia genus spp have anything movement factors?
It can spread in blood (Type III secretion system -> apoptosis).
I am interested if there is any others ways to move.
Do Yersinia spp have anything virulence factors to move?

Yersinia enterocolitica does express flagella at a temperature around 25°C, but not at 37°C. Kapatral et al.
Besides that it can rely on peristaltic movement in the intestines.
Yersinia pestis is as far as I know nonmotile in the host, but motile if isolated Medical Microbiology.
As there are some other Yersinia species, including Y. pseudotuberculosis of course, I think you cannot totally generalize the answer for Yersinia spp., but searching for the Yersinia of interest with "flagella", "motility", "movement" or similar keywords on Pubmed might help.


text:
Pathogenesis of Chronic Venous Congestion in Lungs?
I am thinking how CVC in lungs lead to the left-sided heart failure.

I think CVC lead to Pulmonary congestion and edema.
They produce heavy, wet lungs.
Pulmonary changes include

perivascular and interstitial edema, particularly in the interlobular septa;
progessive edematous widening of alveolar septa; and
accumulation of edema fluid in alveolar spaces which contain Hemosiderin and microhemorrhages

Now, the progression of the disease to heart should be discussed.
I am not sure if hemosiderin can go directly from lungs to heart or if it has to travel through circulation and then to left-side of lung.


text:
Can you approximate Cardiac Output by Ohm's law?
I found this sentence from my notes which I cannot understand
PR < CO, CO $\uparrow$, PR > CO $\downarrow$

where
\item CO = AP / PR, Cardiac Output = Arterial P / Peripheral Resistance

I cannot understand the first sentence.
I cannot understand how you can deduce by Ohm's law the relationship.
What is the point of the first sentence?

I don't get the first sentence either, since PR and CO in your notation are in fundamentally different units. It's like saying '4 Celsius < 5 meters.' You will have to think about what you are implicitly holding constant and ignoring in that relationship to make it meaningful. I suspect the first sentence is just emphasizing the inverse relationship between CO and PR (PR goes up, CO goes down, etc).
As for Ohm's law, absolutely! You have it written right there. I assume Cardiac output is the flow rate of fluid in a blood vessel, and AP is arterial pressure, and PR is peripheral resistance. Stated another way,
$\textrm{Flow} = \frac{\textrm{Pressure}}{\textrm{Resistance}}$,
which is exactly Ohm's law. Frequently electrical current is described with a Hydraulic analogy, with pressure$\rightarrow$voltage, fluid flow$\rightarrow$current, and flow resistance$\rightarrow$electrical resistance. It makes a lot of sense, since electric current is literally flow of electrons. Poiseuille's Law that makes this analogy rigorous, deriving an Ohmic relationship between those variables. Interestingly enough, Poiseuille derived the law in the context of blood flow, making it particularly applicable.


text:
Is there any format for official Physiological/Medicine answers?
Assume you have an exam which has 5 extensive questions and 60 minutes.
You do not have time to cover most if you write everything in essay format.
If you start to write essays, you do not really have time to cover all mechanisms and so on.
I just heard that one student did the exam with by list format, for instance

sitting -> venous return down & skeletal muscles not working correctly -> trombus.

and then describing relevant mechanisms similarly and combining the their roles shortly.
Another morphology of H. pylori

Curved (spiral shape), Gram-negative, 2-4 micrometer long, coccoid forms in older cultures,

Is there any official standard or unofficial accepted way how to answer questions in Physiology/Medicine?

Given the highly variable nature of such processes and systems, it's unlikely that a common standard is feasible or sensible. In medical questions, a bottom-up order like in your example usually makes sense, starting with the most specific known cause and deriving from there until you arrive at the symptoms. Treatments can branch off or into the order at the point where they apply logically.
If your exam instructions ask for flow text, your question is alreay unnecessary - but if you believe you have the choice, use a note format that is appropriate by common sense. You are essentially creating a diagram, and like any diagram you have to ensure that it is self-contained and comprehensive.
You can shorten the amount of time it takes to write sentences by reducing the literary quality. Of course a well-written text is more pleasing to read and mark, but the main emphasis in your grading will usually be content, meaning that you can afford to form sentences of repetitive structures or lacking logical connection if it is difficult to figure out quickly whether there is one or how to express it etc.

I usually answer in a extensive and descriptive way, and I try to put as much information as possible. If it's a process I usually add a little diagram. If there are lot of attributes to add sometimes I do lists, but usually teachers don't like them an it's easier to find errors or lacks in lists.
There is no standard answer model at least in my University.

I completely agree with figures about the anatomical structures. They help a lot and help you to think what to answer.


text:
What makes something food?
From my (limited) understanding, animals get energy from food by breaking chemical bonds between molecules.
There's a lot of water here [citation needed], so it seems like natural selection would favor any organism that could live off it. Why, in the history of life on earth, hasn't an organism appeared that eats water?
Same applies to dirt, rocks -- (although maybe lichen eat rocks? I'm fuzzy on lichen.)
Or air?
Why are humans and other animals like us only equipped to eat certain types of molecules, when others are so much more plentiful?

Because breaking H2O into H2 and O2 is an endothermic reaction: that is, it takes energy to break the bonds.  Food has molecules that can be broken down, or combined with other molecules such as oxygen, in exothermic (that is, energy producing) reactions.

Food has two purposes: providing energy and providing raw material for growth. Water can only be broken down into hydrogen and oxygen which requires energy input, and water isn't by itself a raw material for anything other than ice. It is however important to life on Earth as a solvent (non-polar and electrolytic), and component of some structural chemicals (hydrates).

You don't get energy from breaking chemical bonds, you only get energy from making chemical bonds, while breaking chemical bonds requires the input of energy.  However, in practice chemical bonds are always broken as others are formed, and the net number of bonds is generally constant.  Otherwise you would end up with free radicals, which are highly reactive and looking to form a chemical bond with the next thing it touches.
For example, the burning of glucose in respiration involves the breaking of C-C, C-H, C-O and O-H bonds in glucose and O=O bonds in oxygen, with the simultaneous formation of C=O bonds in CO2 and O-H bonds in water.  But the C=O bonds in CO2 and O-H bonds in water contain much less energy than the bonds we break within in glucose.  So the key is that the bonds formed contain less energy than the bonds broken, and energy is released overall.
And actually it's a bit more complicated than that, because you also have to consider entropy, which is how disordered the system is.  Generally the more molecules in a system, the more entropy, so breaking a few big molecules down into lots of small molecules tends to release energy by increasing entropy.
So to answer your question, "food" is what we can draw useful energy from in the process of turning it into something else as we make and break chemical bonds.  We can't do this with water, or indeed with rocks, because their chemical bonds would require more energy to break than the energy we'd get back out by forming alternative bonds with anything else.

Oh, that's really clear! So to attempt to parrot it back to you: animals that eat food are turning high-energy bonds into low-energy bonds, and using the energy that results. The low-energy bonds that get created in this process are in things like water and CO2, which get turned into high-energy bonds again by plants (they get the extra energy from sunlight).

So if something is "food" to an animal, it's probably because it has a lot of high-energy bonds.

Yes, that pretty much sums it up.  Ultimately, food stores energy in high energy bonds, and we extract the energy by breaking them and replacing them with low energy bonds in CO2 and water.  In fact most organic compounds contain high energy bonds, which is why they burn in air to give out energy (the heat and light of a flame), although we haven't evolved the enzymes to use them all as food.

So we're talking about bonds that have a lot of potential energy. Are these always bonds that are easy to break, or do the two categories just have some overlap but are unrelated?

The energy of a bond and whether it is easy to break are not directly linked as it depends on the energy of the transition state, but generally the more energy stored in the bond, the easier it is to break and the less energy required to break it via the transition state.  However most enzymes work by reducing the energy of the transition state so that bonds break and form more easily, and thus they speed up the reaction.

PS. A good example to illustrate this, is that gasoline does not spontaneosly combust in air, you need an initial spark to pass through the transition state, then the energy released allows the rest of the reaction to proceed via the transition state.  Similarly, glucose does not spontaneously combust in air and you need enzymes to reduce the energy of the transition state so that the reaction goes at body temperature.

Plants use both water and air as food using photosynthesis where water is split and recombined with carbon dioxide from air to make glucose.

Overall, the chemical reaction of photosynthesis is as follows:

Light energy + plant enzymes
6CO2 + 12H2O ------------------------------------------------> C6H12O6 + 6O2 + 6H2O
...which means that it takes
six molecules of carbon dioxide plus
12 molecules of water

in the presence of light and the proper enzymes in the cell, to make
one molecule of glucose
6 molecules of oxygen
6 molecules of water

Energy is released when glucose is burnt

about 16 enzymatic rxns
  C6H12O6 + 6O2 + 6H2O ------------------------------------> 6CO2 + 12H2O + ENERGY

...which means that
one molecule of glucose in the presence of
six molecules of oxygen and
six molecules of water

can be "burned" to release stored energy as well as the "waste" products of
6 molecules of carbon dioxide and
12 molecules of water

http://www.bio.miami.edu/dana/dox/photosynthesis.html

"Plants use both water and air as food using photosynthesis ... to make glucose." - No, glucose itself is the "food" that is burned with oxygen in respiration, while CO2 and water are used by plants to make the glucose food by photosynthesis with the sun's energy.  Water and air could never be described as "food".  Food is what you get energy from by oxidation (burning it with oxygen).

The Cambridge dictionary disagrees with you.

I'm just saying it is more accurate to say that plants make their own food by photosynthesis, and that food is glucose, not "air and water", because there is no energy to extract from air and water: you have to put energy in to get the glucose (food), from which you can then get energy out.

There's a quote from Richard Feynman floating around in which he says that trees "eat air" to get sustenance. Over 95% of the trees mass is obtained from atmospheric Co2 and water.

One could also say that houses "eat bricks" to get sustenance, but that doesn't make it food.  Food is a source of both energy and building blocks.  Glucose provides both, but air and water provide no energy.

PS. If you don't believe me, check how many calories of energy are advertised on a bottle of water (or air for that matter). ;-)