Do's and Don't's of Undergraduate Research? I was fortunate enough to get a position as a researcher for the Mayo Clinic's SURF Program this year.  My PI's lab focus is on the the immune system's role in CNS axonal and neuronal injury, specifically through the lens of how innate and adaptive immune effectors interact w/ infected neurons.

Although I do research under a professor at my college and I volunteered for a state university lab during the previous summer, this is my first REU/SURF opportunity, and I REALLY want to make a good impression.  Here are my questions:

What are the do's and don't's in terms of being a skilled and efficient researcher?

Since I am still an undergrad, I know that I will be a less useful asset to the lab than a grad student or post-doc, but what can I do as an undergrad to not burden my colleagues and PI?

Thank you all for your help!  Wishing you all the very best!

Ask plenty of questions and write everything down. If you do not write notes when someone is explaining something to you, it will be embarrassing to go back and ask them a second time to explain it again. Before you get to the lab I would locate/Ask for review articles related to the project. Realize that you will likely shadowing a senior person while you are there, adapt to their schedule. Don't spend your incubation times face booking. Use this time to build relationships with others in the lab and on your floor and try to absorb as much information about the way the world of science works. Speaking from personal experience the small things you learn there may be insignificant but may come to be important to you in the future. If you have your own project, realize that it will probably be a small one attached to a bigger project another lab member is working on. Thats a good thing, because your time there is not long enough to get into something complicated. A simple, clear, and focused question will be key to your success.

What you should take away from the experience is not necessarily something that will amount to publication, but the actually experience in the actual process of designing experiments, performing them, and analyzing data. Assuming you are doing this to help prepare you to go on to work on a graduate degree in your favorite area of biology then remember that this is here to help you get to the next level. Programs like this allow you to demonstrate that you understand what it takes to perform graduate-level work, and potentially become a successful scientist one day.


Is there a limit to twinning? Can developing twins further divide and subdivide and become identical quadruplets or octuplets or...?
Can twinning be induced, either in utero or in vitro?
Might it be possible to just keep harvesting a few cells off the original clump indefinitely and making an unending stream of identical embryos for implantation in a surrogate uterus?

Sequentially:

Yes. Up to the limit of what the mother's body can tolerate.  Of course, if the cells never aggregate, that suggests some sort of fundamental problem with the embryo's developmental process, and you will probably not get a viable organism.

Sort of and yes.  In utero, fertility drugs can cause multiple eggs to be released per cycle, which can cause fraternal twins when each egg is fertilized.  IVF can do the same thing, but you can also manually subdivide a single embryo into two (smaller) viable embryos, provided you perform the division before any cell differentiation occurs.

Yes, but good luck getting an ethics review board to approve that :D


Do you know what plant it is? I saw this plant when I was on my trip to the Ukraine.

I wonder if those berries are edible.

It is of Phytolacca genus plant which could be toxic for mammals, DO NOT eat as is - it should be cooked properly to be usable/edible (the older, the more toxic leaves are).

Phytolacca acinosa:


How does an electrical impulse spread in a muscle fiber spread from the motor end plate? Does this impulse in skeletal muscle spread much in the same way it does in neurons, with an initial potential change that spreads to its immediate surroundings and is then re-amplified or is it the case that in muscle fibers, the initially produced end plate potential must be "enough" to depolarize the whole muscle fiber?

My issue is with this bit in a lecture about NMJs I took:

  Because the ACh-gated ion channels are localized to the end plate membrane, the End Plate Potential (EPP) is generated at and confined to the end plate region only and, therefore, the amplitude of EPP declines progressively with increasing distance from the end plate region.

I only found this site which talked about something similar, and there it talked about it in the context of a muscle fiber that's been blocked by a non-depolarizing neuromuscular blocker, i.e., no contraction occurs, it's just a measurement of how the EPP changes by itself, so perhaps the lecture was talking about something similar?

So, to put it simply, do electrical signals in skeletal muscles get re-amplified as they travel along the fiber, like they do with neuronal action potentials, or is the initial membrane potential sufficient and it just "spreads around"?

Skeletal muscle cells are excitable, like neurons. Enough summation of end-plate potentials causes the cell to reach threshold and fire an action potential (which then spreads throughout the cell membrane through positive feedback, just like a neuronal action potential).

There are some differences between skeletal muscle and typical neurons, like greater importance of chloride in setting resting potential in muscles, but otherwise their action potentials are driven by voltage-gated sodium channels, just like typical neurons.

You quote:

  the amplitude of EPP declines progressively with increasing distance from the end plate region.

which is true as long as the threshold potential isn't reached, and would also be true for subthreshold receptor potentials or post-synaptic potentials in neurons.

In the reference you link to, I assume you are referring to the mention of curare. Curare blocks the nicotinic acetylcholine receptor, so it is interfering with the end-plate potentials themselves, rather than the intrinsic excitability of the muscle.

See:

Philip M Hopkins, Skeletal muscle physiology, Continuing Education in Anaesthesia Critical Care & Pain, Volume 6, Issue 1, February 2006, Pages 1–6, https://doi.org/10.1093/bjaceaccp/mki062


How do paper wasp larvae not fall from their nest? There is now a paper wasp nest hanging from the eaves of my bedroom. Not very big, I supposed about a hundred chambers and about 7 to 10 adults in total. I observe it every now and then.

It just occurred to me that when the larvae first hatch, they are so small compared to the chamber diameter. So here are two questions:

How do they not fall off, being suspended and all?
Is there any known statistics of how often larvae fall off (for a particular species, let's say)?

Social wasp larvae hatch from an overhanging egg, and they grow up through a series of skin moults, typically 5 in number. The shed skins accumulate terminally behind their pointed anus, where the egg chorion peduncule remain. These wasps have a special body construction and skin texture (e.g. abdominal lobes, numerous spikes) that allows for pressing against the cell walls.

You can see these traits from high-resolution images shown in the larval descriptions:
Florida Entomologist, 95(4):890-899 (2012) https://doi.org/10.1653/024.095.0411
Sociobiology 63(3): 998-1004 (2016) http://dx.doi.org/10.13102/sociobiology.v63i3.988

Finally, it should be minded that gravity doesn't affect small insects in the same way it affect larger mammals like humans. This means it way takes less effort and sticky secretions for these bugs to hang onto walls than we typically imagine by common sense.

I don't know of any dedicated estimations on fallen larvae, but I guess the event isn't common, unless perhaps in abnormally structurally-challenged nests.


Is grip force a reflex? When we reach for an object, for example, a cup, is the force used to hold it a reflex? Which sensorial information is used to select the force to hold it?
Why I am interested in this question

With the development of robots with dexterity, it is necessary to develop a minimal amount of sensors so they can choose the strength to hold an object. Objects that look heavy and slippery need more force, while objects that are delicate need a lower force. Do we unconsciously use visual information to decide the force to hold an object? Can this be called a reflex?

When we reach for an object and it feels painful to hold it (it is too hot or too sharp) we immediately release it, is that a reflex?

In my search I found mostly results about the grip reflex of newborns. Is it Completely lost in adults?

(a personal reason) recently, I noticed that my grip force calculation is kind of “uncalibrated”. I am dropping cups, tools, my cellphone, more frequently than before. However this is not a problem of grip Force or shaking, I can hold myself on a bar with one hand and I have zero hand shaking on my hands. So, when I consciously choose to hold it, I have force, but when I am not thinking of which force to apply, I drop things. Note: this question is not for self diagnosis, this is just the initial observation that sparked my interest in the question.

holding an object is usually a task that requires visual and mechanical processing (i.e. what the object looks like (i.e. what material does it seem to be made of, what is your former experience with that material, how heavy does it feel) and muscle memory.
according to the physiological definition of a reflex:

Reflex, in biology, an action consisting of comparatively simple segments of behaviour that usually occur as direct and immediate responses to particular stimuli uniquely correlated with them.

according to this same source, innate reflexes such as walking, blinking and swallowing require skeletal muscles but are still considered reflexes despite the fact that for some of these tasks (such as walking and standing) we do not know from birth (meaning reflexes can be taught and unlearned/lost).
There are other reflexes such as intestinal smooth muscle contractions etc... that we are usually completely unaware of and are controlled by the central nervous system (CNS) unconsciously.
The response to pain is also a reflex; the thermal/mechanical neural sensors in your arm (for example) send the information to your spine which directly sends a signal to your muscles to contract in order to avoid/release the object.
the palmar grasp reflex is one of many reflexes babies have that they do not need to be taught. Adults usually unteach these reflexes as some of them are not as frequently necessary in later stages of life. Newborn apes for one use the palmar grasp reflex to hold on to their mothers (it is possible that is where that reflex came from from an evolutionary standpoint).
consider that all reflexes are caused by cues that your nervous system senses and responds to. Some of these reflexes can be controlled and others not and may vary depending on your environment. A famous example of this is the pavlov's dog experiment which proved that you could also be conditioned to respond to a certain stimulus. In your case, seeing or feeling the cup is supposed to provide a stimulus to your brain reminding you that you are holding an object that requires a specific mechanical maneuver which you have learnt over time.


What is the name of this graph/plot? What is the name of this graph/plot?

I think it is Chord Diagram. you can see this for more information.

  "A chord diagram is a graphical method of displaying the inter-relationships between data in a matrix. The data are arranged radially around a circle with the relationships between the data points typically drawn as arcs connecting the data." based on the Wikipedia


If ants have an antibiotic gland, how can they spread hospital infections? Wikipedia describes how antibiotics are produced in ants:

  "Metapleural glands ... are responsible for the production of an
  antibiotic fluid that then collects in a reservoir ... also referred
  to as the bulla ... From the bulla, ants can groom the secretion onto
  the surface of their exoskeleton. This helps to prevent the growth of
  bacteria and fungal spores on the ants and inside their nest."

So how are ants often cited as an important problem in hospitals, spreading infections from garbage and through the patients? Shouldn't their natural antibiotics prevent that?

I have worked in hospitals (US) most of my life, treating both community-acquired, and more pertinently to this question, nosocomial (hospital acquired) infections, and have read many articles on the subject.

I have never, ever seen ants mentioned anywhere.

People, flies, cockroaches and rats, yes.

Ants, no.

However, ants are vectors in a few foreign studies. The key word in these studies is potential.

As you stated,

  From the bulla, ants can groom the secretion onto the surface of their exoskeleton. This helps to prevent the growth of bacteria and fungal spores on the ants and inside their nest.

No antibiotic covers all organisms. Also, the secretions are to protect the ants against infection, not against the carrier state.

Pathogenic bacteria is cultured from ants themselves. The ant can be thought of as similar to a human: humans make antibodies to pathogens but are vectors of many diseases. Ants protect themselves via secretions, but are hosts to potential pathogens.

Part I: Review of Scientific Data Regarding Transmission of Infectious Agents in Healthcare Settings
Hospital hygiene and infection control
Ants associated with pathogenic microorganisms in brazilian
hospitals: attention to a silent vector
Ants in a hospital environment and their potential as mechanical bacterial vectors
Insect/Bacteria Association
and Nosocomial Infection


Inhibitory effect of GABA through GABA(A) receptors Over at Wikipedia, the following is written in the article about GABA(A) receptors:

"Upon activation, the GABA(A) receptor selectively conducts Cl− through its pore. Cl- will flow out of the cell if the internal voltage is less than resting potential and Cl- will flow in if it is more than resting potential. This causes an inhibitory effect on neurotransmission by diminishing the chance of a successful action potential occurring." (https://en.wikipedia.org/wiki/GABAA_receptor, Accessed: 22 May 2018)

Based on my understanding, if an action potential is to be inhibited, the internal voltage of the neuron needs to be decreased further away from the voltage at which the neuron's voltage-gated sodium channels open up.
With this in mind, I take issue with the statement Cl- will flow out of the cell if the internal voltage is less than resting potential.... If the internal voltage is less than the resting potential, and the Cl- flows out from the cell, then the internal voltage will increase, hence coming closer to the action potential.
This would increase the probability of reaching an action potential, not decrease it, wouldn't it?
My Question: Does Wikipedia have it wrong, or is there something I haven't understood?

Great question! This apparent contradiction has puzzled many neuroscience students before you.

Short Answer:

This is often called "shunting inhibition," in particular when excitatory and inhibitory conductances are out on dendrites.

Longer Answer:

The part that is wrong is this (emphasis mine):

  the internal voltage will increase, hence coming closer to the action potential. This would increase the probability of reaching an action potential, not decrease it, wouldn't it?

The idea that "hyperpolarization is inhibitory, depolarization is excitatory" is only partly true. It is very important to also consider what the spike threshold is, and to think in terms of reversal potential for a given ion channel (or more generically we can just call it a 'conductance'), and then you can revise the statement to say this:

  Conductances with reversal potential greater than spike threshold are excitatory, conductances with reversal potential less than spike threshold are inhibitory.

Most often, chloride-based channels fit into the second statement: their reversal potential is less than the spike threshold.

How Shunting Inhibition Works:

Any time you open a channel, you will shift the membrane potential towards the reversal potential for that channel. The amount of current that flows through a channel depends on the 'driving force': the difference in voltage from the reversal potential.

Let's consider a fairly typical textbook cell, with a spike threshold at -50mV, a resting potential of -65mV, and a chloride reversal at -60mV.

If the cell is at rest, and you open chloride channels (such as with GABA via GABA-A receptors), the resulting flow of current will tend to push the membrane potential towards -60mV, so the cell 'depolarizes'. However, no matter how big of a chloride conductance you open, you will never pass -60mV, so you will never reach spike threshold.

If, in that same cell, you instead opened AMPA channels, with a reversal of around 0mV, you also get depolarization, but in this case as you open more AMPA channels you can potentially depolarize the cell all the way to 0mV. Of course, unless you have blocked sodium channels you will get an action potential before you reach that point, but that's the key: you will cross threshold, therefore we call it excitatory.

Now let's consider a third case where we open both AMPA channels and GABA-A channels. As long as the membrane potential is <-60mV, both channels contribute to depolarization. However, as soon as the membrane potential is >-60mV, chloride ions will start flowing into the cell. We call this "shunting" inhibition because if you look at the sum current flow in the cell, it will look small, because you have chloride ions coming in at the same time as sodium ions, resulting in little change of the membrane potential despite lots of ions moving.

The result is that GABA-A channels, even if they can depolarize a cell that is at rest, will act to prevent the cell from depolarizing far enough to reach threshold. It's important to consider the dynamics of the membrane potential, rather than thinking of the membrane potential as something that is simply added or subtracted to instantaneously.

Important Caveats:

Ion concentrations matter! If chloride concentrations are not 'typical' or if the spike threshold is more negative than in a 'typical' textbook cell, then chloride conductances can indeed be excitatory! In fact, excitatory GABAergic transmission is important are certain stages of development. If cells have too much chloride in them, this can also cause GABAergic transmission to become excitatory (or at least limit the efficacy of the inhibition), and this can lead to epilepsy (see Cohen et al. 2002).

There can also be a time window where GABAergic transmission is excitatory even in a typical cell: this is the period where the GABA-A channels have closed, but the membrane remains slightly depolarized and has not returned to rest. Excitation that arrives during this time will sum with the residual depolarization, and there are no open GABA-A channels to 'shunt' the current.

Alger, B. E., & Nicoll, R. A. (1979). GABA-mediated biphasic inhibitory responses in hippocampus. Nature, 281(5729), 315.

Cohen, I., Navarro, V., Clemenceau, S., Baulac, M., & Miles, R. (2002). On the origin of interictal activity in human temporal lobe epilepsy in vitro. Science, 298(5597), 1418-1421.

Purves, D., Augustine, G. J., Fitzpatrick, D., Hall, W. C., LaMantia, A. S., McNamara, J. O., & White, L. E. (2014). Neuroscience, 2008. De Boeck, Sinauer, Sunderland, Mass.


What would cause E. coli to change from filamentous growth to normal growth? In my lab we've observed a phenomenon in which a culture of E. coli is found to shift from normal rod growth to filamentous growth and then back to normal rod growth again several times over the course of 400 hours. This was shown by an OD600 graph which oscillates from high values (~5) to low (~0.5) (the culture was also viewed directly).

The shift to filamentous growth is usually associated with an SOS response in E. coli and this makes sense (the media is M9 supplemented with 0.2% casamino acid and 0.1mM thiamine hydrochloride), however we don't know why it switches back from filamentous to normal growth.

Has anyone observed a similar phenomenon? Does anyone have any suggestions why this might be happening?

Expression of sfiA (sulA) causes filamentation during the SOS response, so presumably sfiA is induced, as part of SOS, in response to some sort of DNA damage. Once the DNA damage is repaired the SOS genes, including sfiA, will be repressed again and normal growth will resume.


Question about proto-oncogenes and oncogenes? My textbook says:

  Growth-promoting genes are called proto-oncogenes. Some can be changed into oncogenes by a point mutation that alters the ability of the proto-oncogene to be switched off. They remain permanently switched on. Oncogenes promote unregulated cell division. Such cell division leads to a tumour.

Does this mean that the change from proto-oncogene to oncogene is not a mutation in the exon, but rather in the intron?

I hope I used these terms correctly. Thank you for any help :)

I am going to add to @MattDMo 's answer a bit.

Proto-oncogenes Function, Developmental Program, and Regulation

Proto-oncogenes are normally functioning genes that are more often than not in the pathways that lead to mitosis and cellular replication. They have important roles in the development, growth, and maintenance of the organism. Proto-oncogene is an accurate description of the genes, but I unfortunately think that sometimes people think that the genes themselves are bad and that isn't the case.

Growth and development in multicellular organisms are highly regulated processes with many checks and balances. Certain cells need to grow in certain places at certain times, and then they need to go into and remain in interphase. If they don't, or they do things at the incorrect times, the multicellular organism will not develop properly or will develop conditions such as cancer.

It is often these points of regulation that become dysregulated when a proto-oncogene becomes oncogenic. If there are regions of allostery that are affected by a mutation in the coding sequence (exon) and a control molecule that represses the activity of the enzyme through conformation change can no longer bind, then that enzyme can remain active, always turned on.

You can also have a situation where you have transcriptional regulators of proto-oncogenes that can be effected making the gene product oncogenic. If there is a mutation in an enhancer (intronic) of the gene that affects the binding kinetics of enhancers leading to a great increase in transcription, this concentrational difference can lead to uncontrolled grown and tumor formation.

You could also have a situation like MattDMo talked about where you generate frameshifts and premature stop codons, though I would think this is more relevant in tumor suppressor gene mutations, as these types of mutations tend to kill the protein rather quickly, but it is possible that it can cause a problem.

RAS

There are however other types of mutations that can effect proto-oncogenes, making them oncogenic. One classic example is RAS. RAS is a G-protein that associates with G-Protein Coupled Receptors at the cell surface and transduce signals into the cell leading to the initiation of the cell cycle. In its inactive form, RAS is bound to GDP. When a signaling molecule binds to the plasma membrane receptor it is associated with the RAS molecule, a Guanosine-Exchange Factor removes the bound GDP, and because of concentration, GTP enters the binding pocket and activates RAS, which activates a phosphorylation cascade, leading to transcription of growth factors.

Normally RAS has GTPase activity and will quickly cleave the gamma phosphate of the GTP in its binding pocket, leading to GDP and inactivating itself. However if the mutation were to knock out this GTPase activity from RAS, then it would have no way to cleave the Gamma phosphate, and therefore it would remain activated and continue the signal transduction, even when it should not.

However, the problem does not need to be with RAS to drive RAS to oncogenesis. If RAS GEF becomes hyperactive and starts to exchange GDP for GTP constitutively, whether or not there is a signal, then RAS will constantly be activated, even if it is still able to cleave the Gamma phosphate and inactivate itself. So there can be Cis-acting drivers of oncogenesis and Trans-acting drivers as well.

I am providing you a link to Scitable's page on Proto-oncogenes to Oncogenes to Cancer. It gives the following summary which is a helpful summary:

  Point mutations, deletions, or insertions that lead to a hyperactive
  gene product
  Point mutations, deletions, or insertions in the promoter region of a proto-oncogene that lead to increased transcription
  Gene amplification events leading to extra chromosomal copies of a proto-oncogene
  Chromosomal translocation events that relocate a proto-oncogene to a new chromosomal site that leads to higher expression
  Chromosomal translocations that lead to a fusion between a proto-oncogene and a second gene, which produces a fusion protein with oncogenic activity


Optimization of annealing temperature I am trying to optimize annealing temperature for some primer pairs. I have tried optimization using cDNA, genomic DNA, Taq polymerase, phusion polymerase etc., but every time I am either getting non-specific amplification, a band of larger size than expected or no amplification. Every time I am getting a primer-dimer. Can anybody help me optimize the annealing temperature?

I'm going to give this question a blind attempt, assuming you are talking about PCR (since you are talking about genomic DNA and cDNA) and not RT-PCR or qPCR, since I know very little about them. This answer is not necessarily optimisation for annealing but checking some basics and potential solutions. In my work I had to do a lot of site directed mutagenesis and genotyping and there are some important rules you have to follow in your primer design. First try to keep your primer length between 25-30 for sequencing (at least thats what I do) and for site-directed mutagenesis between 25-45 since anything above 45 bases increases the likelihood of secondary structure formation. Primer melting temperature (Tm) should be >=78 oC (Tm= 81.5 + 0.41(%GC)-675/N [with N being primer length in bases]). Also primers should have a minimum CG content of 40% and should ideally start and end with a C or G. So check your primer CG% since if its too high then it will make a few problems including increased Tm and possibility of primer-dimer formation due to CG triple hydrogen binding. This document has some nice information (http://www.genomics.agilent.com/files/Manual/210518.pdf)

In my opinion if all else fails and you are still struggling with your primers, then re-design a new primer set, if possible. Now getting back to the annealing temperature issue, in my experience for cDNA, annealing temp of 50 oC works best and for genomic DNA, annealing temp of 55 oC works best, which is about the range most people work with and I have so far had no problems. I'm more than happy to share my genomic DNA PCR cycle information with you if you wish through an edit.

Hope this helps!


What is the meaning of "E-value" in the BLAST search? After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that?

https://en.wikipedia.org/wiki/BLAST
This expectation or expect value "E" (often called an E score or E-value or e-value) assessing the significance of the HSP score for un-gapped local alignment is reported in the BLAST results.

If a lower E value means closer results to the query sequence, what is its difference to "Sequence Identity Cutoff"? http://www.rcsb.org/pdb/search/advSearch.do?search=new

You can find the definition here:

  the number of hits one can "expect" to see by chance when searching a
  database of a particular size.

Also read some of the background information given to understand the meaning:

  It decreases exponentially as the Score
  (S) of the match increases. Essentially, the E value describes the
  random background noise. For example, an E value of 1 assigned to a
  hit can be interpreted as meaning that in a database of the current
  size one might expect to see 1 match with a similar score simply by
  chance. The lower the E-value, or the closer it is to zero, the more
  "significant" the match is. However, keep in mind that virtually
  identical short alignments have relatively high E values. This is
  because the calculation of the E value takes into account the length
  of the query sequence. These high E values make sense because shorter
  sequences have a higher probability of occurring in the database
  purely by chance. For more details please see the calculations in the
  BLAST Course. The Expect value can also be used as a convenient way to
  create a significance threshold for reporting results. You can change
  the Expect value threshold on most BLAST search pages. When the Expect
  value is increased from the default value of 10, a larger list with
  more low-scoring hits can be reported.

If you want to understand the calculation I would highly recommend to read the BLAST course

Update
Identity is not the same as the E value
I would try to explain this as easy as possible so let's suppose a sequence:

query sequence: ATGCCGTGC

When you BLAST this (of course your sequence is much longer), you can get the sequence ATGCCGTGC, which will result in 100% identity (NOTE most of the time when you have 100% identity, you have the right sequence but I just picked 100% to make the difference clear. When you have lower percentages of identity the E value is much more important. So when you have 70% identity in different matches e.g. it is important to look a the E value to decide which match is the "right" one for your purpose), now you probably would think that's nice that's the sequence I was looking for. However this would be a mistake! Maybe this sequence is present many times in the database and this is just a random match, this is the point were the E value comes in. Looking at the E value this would be pretty high because you have a short sequence and the chance of matching this in a big database is really high so you can get an E value of let's say: 10. What this means is that you have a chance of finding 10 matches by chance when searching a database of a the current size in other words this match would probably be random! So it's much better to conclude if a match is "significant" based on the E value cut-off than on the identity. Further the choice of the E value is completely yours as said by WYSIWYG♦ as answer to a cut-off question:

  E-value refers to the expected number of random hits for a given
  alignment score. Smaller it is more reliable is your match. There is
  no hard and fast rule for e-value cutoff. You can keep whatever you
  want depending on the level of stringency that you require. But you
  should note that for smaller sequences (< 30nt) there is always a
  higher likelihood of random matches. In such cases it is practical to
  relax the e-value cutoff.

Short simple example

Both of these sequences got the same identity but a different E value. What does this mean? Both of the sequences match the same amount(57%) of the amino acids however based on the E value you can say just as you said that the first match is less likely to be a false positive. I want to note one thing: Always take a look at the biological significance of your result. E.g. you extract proteins from a red blood cell and find proteins with a high E value for red blood cell proteins and a low E value for proteins from nerve cells. It's clear that despite the high E value the red blood cells are probably more biologically significant.


Spider Identification (UK) I found this spider (~10 mm body length) indoors on a wall (South-East England) and I was wondering what species it was.

My first guess is false black widow, but I can't be sure.

I'd be grateful if anyone could help me out.

Yes, it's Steatoda, probably nobilis, the False Widow.  The white band curving around the front of the abdomen is a good Steatoda diagnostic, and the light-colored abdominal pattern is pretty variable in this species - only hints of it here, but the pointy front end and the bits of a skeletal 'shield' pattern are there.
The spider is pretty harmless, although it is supposed to sometimes give a bite that's like a very mild Widow bite.  Not at all dangerous, but a little more potent than the usual harmless spider bite.

Below are a couple of pictures of nobilis, showing a range of markings:

Here is a citation describing the effects of S. nobilis bites that's not a fear-mongering tabloid story:

https://www.researchgate.net/publication/320623444_Envenomation_by_the_noble_false_widow_spider_Steatoda_nobilis_Thorell_1875_-_five_new_cases_of_steatodism_from_Ireland_and_Great_Britain

The images were taken from a random survey of Steatoda nobilis images from the internet, as a broad selection was desired.  However, this note (below) discusses some of the features I mention, along with photographs that support my comments.

https://cisr.ucr.edu/european_spider.html


What's a replicate line? The methods section inside a paper I'm reading make mention of replicate lines.
Example: "We founded 10 replicate lines from a single clone". This is in the context of experimental evolution and artificial selection of Chlamydomonas in a laboratory.

Can you please explain to me what a replicate line is?

Here's a reference to the paper:
Collins, S., Sültemeyer, D., & Bell, G. (2006). Rewinding the tape: selection of algae adapted to high $CO_2$ at current and Pleistocene levels of $CO_2$. Evolution 60, 7, 1392-401. DOI: 10.1111/j.0014-3820.2006.tb01218.x

In the context of experimental evolution, replicate lines are simply separate experimental (or control) lines the are established from the founder population at the beginning of the experiment. In this paper, the authors must have established 10 separate experimental lines that then evolved in different carbon dioxide levels. For example, 10 separate aliquots of algae are drawn from the same source population and then separately subjected to the agent of selection. These replicate lines should remain separate and not be mixed or crossed.

Replicate lines are useful in experimental evolution for a few reasons. Because you are studying a population that is experiencing a selection pressure, you expect that genetic changes are in response to that pressure. However, changes can also occur due to drift. Replicate lines (and a consistent response to selection among them) is important to ensure that changes are a response to selection rather than to some other force (drift, mutation). Some drift is bound to happen when the lines are founded, because you are selecting a subset of the population, which is actually a good thing. Each line gets a random subset of genes which then evolve together. This potentially allows discovery of different genetic pathways to the same adaptive response.

The background and lots of examples are in Garland and Rose, Experimental Evolution (UC Press, 2009).


Why do the deoxyribonucleotides use T and ribonucleotides use U? We all know deoxyribonucleotides form DNA while ribonucleotides form RNA, DNA is double stranded while RNA is single stranded, and RNA can transcribe from DNA. We also know that DNA use A, G, C, T, while RNA use A, G, C, U and that it's the DNA that stores genetics information, not RNA.

My question is: how does the lost oxygen atom on deoxyribonucleotides 2' site of the sugar (turning it into a ribonucleotide), make such a large difference in function? It just an oxygen atom. Why don't they just all use U or all use T?

Why deoxyribose for DNA and ribose for RNA?
This answer may solve the question why is DNA double strand, RNA single strand, but it doesnt explain why does RNA uses U instead of T.

For the switch from thymine (T) to uracil (U), it actually doesn't have anything to do with the sugar backbone of the nucleotides. This article on Science Daily explains that U is more cost efficient to produce than T because it can be easily gotten from a chemical degradation of cytosine (C). Since RNA has a short life span and because the cell needs a lot of RNA it uses U. DNA, on the other hand, undergoes a lot of checks and repairs. If it were to use U, it wouldn't know if the U was really a U or if it was a C that got damaged. Since it is important to keep the number of mutations to a minimum, DNA uses the more costly T to ensure fidelity.

I would also like to point out @AMR's comment. It isn't just an oxygen atom. An oxygen atom is the difference between the air we breath and ozone that can kill you. It's the difference between water and highly flammable hydrogen gas.


Are there any examples of information compression in nature? As the title suggests, I am looking for any examples of naturally occurring information compression. Initially, I thought protein synthesis was such a form of compression, creating larger entities (proteins) from a small subset of chemicals (A,C,G,T(U) in DNA) via ribosomal translation. However, I was quickly disillusioned as the amount of information contained in DNA is not increased within proteins after their formation.

So are there any natural processes, whether in animal, plant or otherwise that exhibit information compression?

Preliminary Remarks

Many of the posts to this list about biological information (usually equated to DNA) from mathematical and informatics scientists start from what I regard as false premises, especially that the genome is similar to that man-made artefact, the computer. This post does not explicitly make that assumption, but I think it important to address the difference between computer systems and biological systems before considering possible examples of what is requested.

Do biological systems need to compress information?

Although one can argue that not all biological information resides in DNA (or RNA, in the case of organisms with an RNA genome) I suspect the poster was thinking of that, and that is what I shall restrict myself to — i.e. to genetic information. (Other answers may quite validly address other types of information.)

The point, at least historically, of compressing digital information on computers is space limitation. Lossless compression involves re-coding the information in a more compact form. For example, instructions in the PostScript language can substitute ‘d’ for draw, ‘s’ for stroke. Gif or tiff image compression can substitute 20x(256,0,0) for repeating (256,0,0) — a red pixel — twenty times. Such compressed information must generally be decompressed when it is used (e.g. when the gif file is displayed in a web browser).

I find it difficult to think of any compression/decompression of this type in biological systems, and I would point out that genome ‘space’ is generally (but see below) not a limiting consideration in biological systems. One example of this is the fact that many organisms (especially plants) are polyploid — that is they have multiple (apparently unnecessary) copies of the complete genome. Another example is that the genomes of mammals contain at least some DNA that can be regarded as unnecessary. Although there are arguments about ‘junk’ DNA having a function, it is difficult to argue that processed pseudogenes and SINES and LINES are necessary. However genome ‘space’ has not eliminated them.

Where space or size is a problem, there Nature often uses other solutions than compression. For example the genomes of RNA viruses are thought to be restricted in size because of the occurrence of slow non-enzymic alkaline hydrolysis of RNA. Influenza virus, for example, has a genome consisting of several shorter (less vulnerable) RNA segments, which may be considered as a solution to this problem.

However, here are a couple of possible examples, although not with the sort of compression used in computers.

Possible example 1: Antibody Genes

To put it in simple terms, the genome has the potential for expressing millions of different antibodies, but the immune system requires that antibody-producing cells only produce one type. Instead of having millions of antibody-producing genes, only one of which is expressed, there is a much smaller number of segments of the genes, from which each of the two antibody chains are combined in a process called recombination. This is illustrated below for the heavy-chain genes where combination of one of 250 V-regions with one  of 20 D-regions with one of 4 J-regions, giving 20,000 possibilities. The resulting heavy chain can combine with one of 1000 different light chains, giving twenty million possibilities. (The diagram and data are old, but the principle holds. See, e.g. the Wikipedia entry.)

Of course, there is an alternative, and converse, way of thinking about this. Rather than the existence of 500–600 genes being a way to compress 20 million, one can regard the existence of 500–600 being a wasteful way to encode only protein.

Possible Example 2: Alternative splicing of pre-mRNA

This is similar in principle to the first example, although the mechanism is different. Most of the protein-coding genes of higher eukaryotes are built up of two components — exons, which encode sections of the protein product — separated by introns, which do not. Both these components are present in the initial RNA transcript, but the introns are removed from this (spliced out) to produce the mature mRNA, which is translated into protein. An advantage of this arrangement is that there are alternative ways for the splicing to occur, involving removing some of the exons (as well as the introns). This can lead to different protein products, in some cases just two, in others dozens.

So one could regard this similarly as a compression mechanism — or alternatively as an example of wasted space in the genome occupied by the introns.

Possible Example 3: Read-through and frame shift proteins

Certain mature mRNAs have the potential to encode more than one codon by the processes of read-through or frame shift. In brief, a protein of 100 amino acids will have a mRNA with a stop-codon 300 nucleotides after the signal for the start of translation. However in a few cases (and most notably with small bacterial RNA viruses) the structure of the mRNA near the stop codon is such that in a certain percentage of cases a tRNA will misread the stop-codon, resulting in continued translation, producing a longer protein of different function.

Similarly, certain mRNAs have a structure at a certain point that encourages the tRNAs to continue reading in the wrong phase (missing a base or starting a base too early — I forget) so that the continuation of the protein has a completely different amino acid sequence.

There is an old review of this topic in Current Opinion in Cell Biology.

Although this is technically a way of compressing two proteins into one, its rarity makes it difficult to regard its biological rationale as being compression.

&c.

No doubt there are more examples. I had toyed with considering Wobble as a way of saving space for tRNA genes, but have probably written enough.


What is the origin of the name "λ phage"? The lambda bacteriophage which infects E. coli was first discovered by Esther Lederberg  in 1950.

However, in the earliest paper on the lambda phage that I could find, I was unable to find the reason behind why the phage was named after the Greek letter λ.

Is there a source (by Lederberg or previous scientists) that mentions the etymology of this phage?

The original paper from Lederberg from January 1953 (see reference 1) indeed doesn't mention the origin of the name, but the paper in reference 2 does. It says:

  The isolation of λ was first reported in 1951 by Esther Lederberg
  (119), then a Ph.D. student at the University of Wisconsin, and later
  was described, in greater detail, in a 1953 Genetics paper by Esther
  and Joshua Lederberg (120). The discovery was accidental, when a
  λ-sensitive strain of Escherichia coli K-12 (W518, obtained after UV
  irradiation) was crossed with its parent. The mixture yielded plaques,
  and the source of the virus was the K-12 parent. W518 cells that
  survived infection became stable lysogens which, like the K-12 parent,
  were immune to superinfection and which released unaltered phage.
  Although the Lederbergs were initially opposed to the notion, crosses
  between lysogens and sensitive cells led them to suggest that λ
  prophage was chromosomal and linked to gal. Joshua Lederberg recalls
  that he was convinced, from earlier work of Burnet and Lush (21), that
  lysogeny was a real phenomenon but that he “fully expected lambda to
  be a [plasmid]—in fact the term lambda was modeled after Sonneborn's
  kappa [in Paramecium; see reference 156 for a recent review], so it
  was quite a shock to discover the contrary.” (In fact, years later
  Hideo Ikeda and Jun-ichi Tomizawa [98] showed that prophage P1, unlike
  λ, is a plasmid and not part of the host chromosome!)

The mentioned kappa particle in Paramecium is an inheritable cytoplasmatic symbiont and the Lederbergs thought of something similar for their discovery. My assumption here is that lambda was the next greek letter, hence the name. The publication in which Sonneborn describes Kappa can be found in reference 3, a short historical overview on the discovery of Kappa in the review in reference 4.

References:

Genetic Studies of Lysogenicity in Escherichia Coli.
Little lambda, who made thee?
Mating Types in Paramecium Aurelia: Diverse Conditions for Mating in
Different Stocks; Occurrence, Number and Interrelations of the Types
R-body-producing bacteria.


Why must bacteria outrun diffusion? In 'E.coil in Motion' Howard Berg says that

  'If it [a cell] is to go far enough to find out whether life is
  getting better or worse, it must outrun diffusion.'

I am confused about the exact meaning of this expression and can't seem to find an explanation. What is meant by 'life is getting better or worse' and why can't a cell just wait for things to come to it by diffusion?

Because then it wouldn't be going anywhere, and the first part of the sentence is specifically about traveling.

Without more context that might make me wrong, I think the statement is intentionally tautological and is just meant to set up a problem to solve.

By "better or worse" I think the author means to generalize about conditions that an organism may prefer: nutrient concentrations, temperatures, etc.

Restated, I think the author is roughly saying "For cells to spend more time where conditions are best for them, they have to move on their own power."


Why are stem cell therapies more preferred (theoretically) over current measures? i understand that when stem cells are used to treat injuries using induced pluripotent stem cells (IPS), they can prevent the risk of having any tissue rejection and thus, there isn't a need for use of immunosuppressant drugs.

However, based on the researches using animal models thus far, I note that surgeries are still the main mode of delivery of such stem cell-regenerated organs/organoids. Meaning, to transplant a part of a organ or a tissue into the animal model, a surgery still needs to be done - how is this different from current measures?

Specifically, how are stem cells going to aid or further research into areas such as curing heart or lung diseases and I wonder how are these methods going to be better than current ones.

Stem cell therapy was never going to replace surgery, and it isn't supposed to. We just don't have the tools to move stuff around inside the patient without breaking the skin.

Stem cells therapies offer replacement parts for organs that can't regenerate themselves. For example, after a heart attack the heart often forms a scar where heart tissue has been injured or died. The scar often doesn't conduct electrical signals properly or doesn't beat at all, both of which are a problem for a heart. The scar can't be surgically removed, because there's nothing to replace it with. Stem cell therapy would provide new heart muscle to replace the damaged tissue.

There are of course exceptions, some stem cell therapies are injected and left to 'settle' in the right tissues. That kind of therapy generally doesn't replace a surgery either, because that kind of problem can't be fixed with surgery at all.


Is there any biosafety level scale for plant pathogens? Biosafety levels commonly defined on basis of human/animal pathogens, but what would be the biosafety levels for plant pathogens?

Plant pathogens are not a health hazard to the experimenters. However, they can pose health hazards to plants and cause damage to ecosystem. There are plant biosafety levels: BL1-P up to BL4-P (also sometimes abbreviated as BSL-1P and so on). The four levels have an increasing order of stringency of containment. Containment of plant pathogens (also seeds and pollen) is the primary concern, not exposure to them.

From NIH guidelines:

  For research involving plants, four biosafety levels (BL1-P through
  BL4-P) are described in Appendix L, Physical and Biological
  Containment for Recombinant or Synthetic Nucleic Acid Molecule
  Research Involving Plants.  BL1-P is designed to provide a moderate
  level of containment for experiments for which there is convincing
  biological evidence that precludes the possibility of survival,
  transfer, or dissemination of recombinant or synthetic nucleic acid
  molecules into the environment, or in which there is no recognizable
  and predictable risk to the environment in the event of accidental
  release.  BL2-P is designed to provide a greater level of containment
  for experiments involving plants and certain associated organisms in
  which there is a recognized possibility of survival, transmission, or
  dissemination of recombinant or synthetic nucleic acid molecule
  containing organisms, but the consequence of such an inadvertent
  release has a predictably minimal biological impact.  BL3-P and BL4-P
  describe additional containment conditions for research with plants
  and certain pathogens and other organisms that require special
  containment because of their recognized potential for significant
  detrimental impact on managed or natural ecosystems.  BL1-P relies
  upon accepted scientific practices for conducting research in most
  ordinary greenhouse or growth chamber facilities and incorporates
  accepted procedures for good pest control and cultural practices.
  BL1-P facilities and procedures provide a modified and protected
  environment for the propagation of plants and microorganisms
  associated with the plants and a degree of containment that adequately
  controls the potential for release of biologically viable plants,
  plant parts, and microorganisms associated with them.  BL2-P and BL3-P
  rely upon accepted scientific practices for conducting research in
  greenhouses with organisms infecting or infesting plants in a manner
  that minimizes or prevents inadvertent contamination of plants within
  or surrounding the greenhouse.  BL4-P describes facilities and
  practices known to provide containment of certain exotic plant
  pathogens

  Section III-D-5-a. BL3-P (Plants) or BL2-P + biological containment is recommended for
  experiments involving most exotic (see Section V-M†, Footnotes and
  References of Sections I-IV) infectious agents with recognized
  potential for serious detrimental impact on managed or natural
  ecosystems when recombinant or synthetic nucleic acid molecule
  techniques are associated with whole plants.

  †Section V-M.  In accordance with accepted scientific and regulatory practices of the discipline of plant pathology, an exotic plant pathogen (e.g., virus, bacteria, or fungus) is one that is unknown to occur within the U.S. (see Section V-G, Footnotes and References of Sections I-IV).  Determination of whether a pathogen has a potential for serious detrimental impact on managed (agricultural, forest, grassland) or natural ecosystems should be made by the Principal Investigator and the Institutional Biosafety Committee, in consultation with scientists knowledgeable of plant diseases, crops, and ecosystems in the geographic area of the research.

These descriptions refer to plant experiments in greenhouses. When working with plant pathogens in a lab (in vitro culture or on whole plants in incubators), similar guidelines should be followed.


Why do we see colours when we close our eyes and press our hands against them? Whenever we close our eyes and press our hands against them we either see some colours or sometimes some weird patterns(similar to hypnotic patterns).
What is the cause of this phenomenon?
Also, is this the right place to ask this question? Does this question have more to do with biology than physics?

Yes, this is a biological phenomenon, not a physical one, because the phenomenon depends on a cellular response. Pressing your eyeballs (mechanically stimulating them) causes you to see phosphenes.

  What is the cause of this phenomenon?

The increased pressure in the eye causes activation and inhibition of cells in your retina (retinal ganglion cells). These cells are intermediates between the light-sensitive sensory neurons and the brain which interprets information into an image.

Quoting a well known study from 1989:

  Eyeball deformation [pressing] in total darkness led to an activation of the
  on-center ganglion cells, while the off-center ganglion cells were
  inhibited. The latency and strength of this activation or inhibition
  varied considerably between different neurons, but were fairly
  constant in the same neuron when the eyeball indentation was repeated
  after a pause of 1-3 min. The latency and strength of neuronal
  activation or inhibition seemed to be dependent mainly upon the neuron
  location relative to the point of eyeball indentation. Some on-center
  neurons also exhibited a short activation at "deformation off". [...] We assume that the activation of on-center and inhibition of off-center ganglion cells by eyeball deformation are caused by retinal stretching, which also leads to horizontal cell stretch. Stretching the horizontal cell membrane probably generates an increase in membrane sodium conductivity and a depolarization of the membrane potential [neuron firing]. This depolarization of the horizontal cell membrane potential is transmitted either directly or indirectly (via receptor synapses) from the horizontal to the bipolar cells.

This is a phenomenon at the retina (periphery), i.e. not in the brain region associated with vision processing (occipital lobe). You can achieve the same visual effect by vigorously sneezing or blowing your nose, stimulating the same cells electrically (by injecting current with electrodes) or magnetically (with coils that generates a local magnetic flux, whereby currents are locally induced). It is also possible to duplicate the effect by stimulating only the visual cortex, but it is likely due to the fact you are simply approximately replicating the retinal firing patterns coming to the brain via the visual nerve.


Science experiments at home with Minimal Cost What is a good recipe for making agar at home for a minimal cost? Are there materials that could be found in the kitchen cabinet?

Instructions
1
Place a coffee filter in a strainer and hang the strainer over the opening of the clear bowl.

2
Slowly pour the broth into the filter, making sure that the broth doesn't overflow from the sides of the filter. If the filter becomes clogged with particles, remove the used filter, replace with a clean filter and continue pouring the broth.

3
Remove the strainer and filter from the top of the bowl and observe whether the broth appears clear (i.e., there are no suspended particles in the liquid). If particles are floating in the liquid, repeat Steps 1 and 2 using a second clear bowl and a fresh coffee filter.

4
Place the pot on the stove and pour the clear broth into the pot.

5
Add 16 ounces of distilled water to the pot containing the broth.

6
Turn on the stove and adjust the heat to medium-low. Heat the broth to a simmer (i.e., small bubbles appear near the side of the pot).

7
Add 1 teaspoon of the agar-agar powder to the simmering broth (approximately 2.5 grams) and stir the mixture until the powder is dissolved. Make sure to stir the powder to dissolve and prevent the gelatin from sinking to the bottom of the pot (where it can burn).

8
Repeat Step 7 until all agar-agar powder has been dissolved in the broth.

9
Continue stirring the broth for about 1 minute to ensure that all powder is completely dissolved.

10
Turn off the stove, place the lid on the pot and let the liquid cool for at least 15 minutes.

11
Arrange the sterile petri dishes in a row for easy assembly, but do not remove the lids.If desired, place a trivet to hold the warm pot. If you're using lidded custard cups instead of petri dishes, sterilize the custard cups by placing the cups and lids inverted (upside down) on a foil-covered cookie sheet and bake in the oven for at least one hour at 375 degrees Fahrenheit. Make sure the sterilized cups and lids are completely cooled before use.

12
Carefully touch the outside of the pot to check that it is warm to the touch and place the pot on the trivet. If the pot is too hot to touch, wait at least 10 minutes to let the pot cool.

13
Remove the lid and set aside. Place the ladle in the pot.

14
Remove the lid from one petri dish and dispense nutrient broth to fill the dish halfway. Cover the dish immediately with its cover.

15
Repeat Step 14 for each of the petri dishes.

16
Allow the nutrient broth to solidify in the petri dishes for at least 1 hour, undisturbed.

17
Gently shake the petri dishes side to side to check that the nutrient broth has completely solidified. If the broth is not completely gelled, wait another 20 minutes before checking again.

18
Cover a table or flat surface with a roll of paper towels to create a sterile work area. Tear off a sheet of paper towel and fold it four times to create a thick, rectangular wad. Set this wad on one end of the work area.

19
Transfer one petri dish to the sterile work area and remove the lid. Carefully turn the dish over and place one end on the side of the folded wad, so that it lies inverted and slightly angled (with a slight gap by the paper towel wad).

20
Turn the lid over and place it above the petri dish on the sterile work surface. If water droplets appear on the lid, gently shake this moisture off before placing on the covered surface, but do not touch the inside of the lid.

21
Repeat Steps 19 and 20 for each petri dish, positioning one side of the inverted dish on the side of the previous dish rather than the paper towel wad. The dishes will appear as a staggered set, with gaps on one side so that excess moisture can evaporate.

22
Look at the inverted petri dishes to check whether the moisture on the sides of the plates evaporated. Once all moisture has cleared, turn the plates right-side up and immediately cover with the lids for use.

23
Inoculate the nutrient agar on the plate by wiping a swab containing the desired culture on the nutrient agar surface before covering with the lid. Turn the petri dish over so that the solid is on top. Store the inoculated petri dish with the solid on top for culturing and the lid on the bottom to catch any moisture, loose particles or growth.


Are original x-ray diffraction data available Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these data may be downloaded?

In many cases they are available.  One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors.

If the question is 'why are they giving only the structure factors and not the original data they took' - such a task would require a lot of curation effort for very little scientific benefit.   Scaling the individual sets of data from the detector used to be a bear of a task.  The original myoglobin structure would entail scanned films in an ancient format from the 50s.  Nobody would be able to use that now without hacking the image format, if it wasn't on paper tape or cards.  In fact in that case the structure factors are not available.  Scaling many or several data collections together was often done with custom tweaks into the 70s and then in the 90s data collection became more routine, but several generations of x-ray detectors became popular and then faded from the market.  Each had its own eccentricities and requirements for combining data sets from multiple reads.

The purpose of having structure factors available is to allow anyone to reconstruct the electron density and evaluate the interpretive act which is tracing a peptide through electron density.  Since that format is mainly independent of the detector and has been fairly consistent over the years, it delivers a significant amount of scientific bang for the buck.

If you want raw image data or detector-proprietary data before multiple data sets from different crystals before they were combined you will have to contact the authors, who would probably have to sift through a sea of DVDs to get to it.  In older cases it might be tapes.

So as far as Structure factors, which are essentially the square root value of the combined and scaled Intensity data, they are available and a part of every submission to the pdb:

Look on any X-ray Structure Page at RCSB.  For example this one.

There is a box called "Experimental Details" and you can download the structure factors there by clicking a link.

If you are looking for more than one at a time, there are bulk downloads available through their download page.  Check the "Structure Factors" box.  Raw intensity data should be available if you look around for it as well.

Further Suggestion:  I was thinking that if you look at the scaling software that comes with the X-ray detectors you might find some tutorials with unscaled raw data.  I found one example at Marresearch - hen egg white lysozyme.


Could mating/recombination be responsible for evolution of entirely novel features? The diploid chromosomal architecture is rather interesting. For example, because of diploidy we Humans have to mate. Of course in that sense, because diploid organisms often have mate, this has led to emergence of sexual organs as novel features etc.

But, what I am interested in, is the prospect of recombination and mating being able to lead to drastically novel evolutionary traits.

For example, if a remote tribesman from the Pygmy peoples of Central Africa were to mate with an urban dweller, one theoretical example of a novel feature could emerge in the offspring are new inter-gene/protein interactions between these "never met before" sets of alleles. Recombination would then "seal the deal" by shuffling these allele sets between the maternal/paternal chromosomes, such an individual's offspring would now become a mosaic of their hybrid parent. Just imagine cross-over events occurring between two very divergent promoters of the same loci.

Questions:

Could the unison of such divergent sets of alleles theoretically lead to unique phenotype and features that bear little resemblance to any features belonging to the parents?
Are there any real examples of morphological/physiological features such as that I have tried to describe?

Could the unison of such divergent sets of alleles theoretically lead
  to unique phenotype and features that bear little resemblance to any
  features belonging to the parents?

Though it is possible that some unique characteristics may emerge but it is very less likely that the offspring will bear no resemblance to the parents. You start with an example of humans. In this case it is, in my opinion, very unlikely because there is not so much of genomic diversity yet that may lead to such an outcome as you ask about.

Some examples exist, such as the liger (offspring of a male lion and female tiger) that is bigger than both the species. This happens because of improper growth regulation because of interspecies differences. This could happen because the divergence between lion and tiger is much more than the intraspecific variations.

Just a speculation : perhaps the offspring of H.sapiens and H.neanderthalis could have had such a feature but it seems unlikely for the current population of H.sapiens


Do green algae form obligate symbioses with fungi? I understand that obligate symbioses means that the two organisms cannot live without each other and are in a symbiotic relationship, but do green algae from this with fungi?

Yes, Lichen are composite organisms of green algae (or cyanobacteria) living togther with fungi.

In most cases the fungi-part is completely dependent on that symbioses and is completely dependent on the symbiosis. For the algae it seems that some species can survive on their own, but not necessarily in the same enviroment as the lichen, while other species may again be completely depedent on the symbiosis (see also the comments).


Why do some cuts leave scars, while others do not? Last year I got a moderately-deep cut on my finger, and it left a scar. Six months later, the scar is still there. On the other hand, I've had lots of other cuts on my fingers, though none have left scars. Why is this? Is scarring related to the severity of the cut, or something else?

This depends on a number of factors. Here are the first two that come to mind:

1) Is the cut deep enough to reach the dermis (this is the layer below the epidermis) where scar tissue will form?

2) What is your general state of health, and was there an infection at the site of the cut, which would have altered the normal healing process.

Basically, not all cuts are created equal, especially if some are deeper than others and become infected.

This article studied scratch depth
http://www.ncbi.nlm.nih.gov/pubmed/17440346


Value of mathematical models in biology Sorry if this is too much of a soft question or if it is too broad for this site.

As a person who has much more experience with math than biology, I've always been really interested in the mathematical side of biology. As I study math in biology, however, I am left with the question of "how is this actually useful?"

What kind of unique insight can mathematical models give us about biological systems that we couldn't just find experimentally?

This question is broad.

There are plenty of uses of mathematical modelling in biology.

Wikipedia

You may want to read the wikipedia article: Mathematical and Theoretical Biology.

Books

There are tons of books on theoretical biology. I am personally working in the field of population genetics, a field where much of the theory has been expressed mathematically. Here are book recommendations for this particular field.

On Biology.SE

We have a tag for mathematical-models (you used it in your post). You may want to see what kind of posts are tagged for mathematical-models.

To repeat @fileunderwater's comment, What physics knowledge can be applied to biology of organisms and ecosystems and When are population dynamics models useful? are examples of posts you may want to read.

What prevents predator overpopulation? will give you an example of an easy and classical mathematical model to describe population dynamics of predators and preys.

Personal historical/philosophical note: At some point physicists have started to describe the laws of nature with mathematical expressions and at that time many physicists didn't quite like the idea that physics could be described by math. Biology has gone through the same phase but much later. Early mathematical biologists developed the modern science of statistics (Francis Galton, Karl Pearson, Ronald Fisher). Biologists used existing mathematical tools such as diffusion processes (Kimura). Note that part of the work in the field of diffusion equations have been done by physicist (Einstein solved the 2D equations for diffusion processes). Note also that the dynamic of diffusion processes called brownian motion have been named after a biologist. Today, biology produces massive amount of data that require good computational skills to treat. The time when biologists had only to know how to recognize species is over, now there are few biologists left that aren't able to code in at least one programming language.


Why are there so few multicellular anaerobes? There are a few documented cases of multicellular anaerobic organisms, but I can't see a reason for it to not be more common. On the contrary, it seems pretty useful to be able to create energy even when deep inside tissues, yet the Loricifera are the only ones I've found documented. Given how often multicellularity has arisen, is there something that's fundamentally difficult about being anaerobic while multicellular?

One thought that might inspire others- multicellular organisms certainly tend to be bigger than unicellular ones, and in an oxygenated world larger organisms are more likely to run into oxygen than unicellular ones. However, there still exist an abundance of anaerobic niches for large organisms- the deep sea, for example.

I'm also drawing a distinction between facultative anaerobes and obligate anaerobes- there are plenty of facultative multicellular anaerobes, and I'm not as curious about that.

Useful sites that I came across while searching:

Journal article announcing the first anaerobic metazoa

Anaerobic fungi, presumed to be unicellular?

I did a bit of reading myself, and it seems as if Loricifera are the only multicellular obligate anaerobes.

I see your point with niches for anaerobic organisms in deep water. Many organisms near the hydro-thermal vents use anaerobic cellular respiration.
From my understanding of Loricifera, it seems as if they would utilize chemosynthesis as their method of obtaining energy.

  Loriciferans are found exclusively in marine habitats, and live in the spaces between sand grains or in the mud at the bottom of the deep sea. The nanaloricids prefer sand with low levels of detritus (material derived from the decomposition of once-living organisms) or clean shell gravel, whereas the pliciloricids are often found in such deep-sea sediments as the white abyssal Globigerina ooze and the red deep-sea clay from the hadal zone (below 20,000 ft; 6,100 m).

--From Encyclopedia website: Loricifera (Girdle Wearers).

Lociferans live in a rather oxygen-less environment.

So you're right about niches in the deep sea.

But typically the deep sea has extremely high levels of pressure that few multicellular organisms are built to handle.

Additionally, I was able to find a few other obligate anaerobic Eukaryotes, but those were Protozoa, so thereby not unicellular.

About it fundamentally being difficult to be exclusively anaerobic while multicellular, with multiple cells, there is more upkeep and more energy is required to run the "system". Aerobic processes tend to be a lot more efficient, producing more ATP for usage.

Only 1 ATP (from my understanding) is produced from this, whereas with aerobic respiration:

Aerobic ATP sum

Much more ATP is produced from aerobic processes.

In the end, the majority of obligatorily aerobic organisms are unicellular, or are extremely small.

  Their sizes range from 100 µm to ca. 1 mm.

So... that's why multicellular organisms are typically carry out aerobic cellular respiration.

Also, about the fungi you mentioned, it goes through Horizontal gene transfer, which unicellular organisms typically use:

  Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring. HGT is an important factor in the evolution of many organisms....
  Most thinking in genetics has focused upon vertical transfer, but horizontal gene transfer is important, and among single-celled organisms is perhaps the dominant form of genetic transfer.

--From Horizontal Gene Transfer Wikipedia page

So yes, it seems as if the fungi that you mentioned and other similar types of fungi would be strictly unicellular, such as yeast (thought yeast is a facultative anaerobe).


Approximately how long do bacteria live for? I would like to know how many days or years do the bacteria live approximately.

They're effectively immortal, albeit in a Phoenix-rising-from-the-ashes sort of way.

In general, a bacterial cell will divide as soon as it's biochemically able to do so, leaving behind two daughter cells. Neither daughter cell is actually the same as the mother cell, so in one sense the mother cell will have "died". On the other hand, the daughter cells are genetically identical to the mother cell and all of the physical material present in each of the daughter cells at the moment right after they split came from the mother cell.


Does any animal species have two sexes and more genders? Are there any animal species that have two sexes and a kind of different internal diversification in two genders or more? I don't mean something like different-task-based diversity, but something biological?
For example let's imagine a species with:

2 sexes (male and female)
2 gender (A and B)

and individuals can match iff they are not only of different sex but also of different gender.
So you can only have Ma-Fb, Mb-Fa.

Many organisms have multiple sexes. For instance, here is one which apparently has 7 (and each sex, or "mating type" can only mate with the others). The "gotcha" is that, mostly, they're unicellular organisms where mating in itself is weird to begin with. I haven't ever heard of a metazoan which truly has more than one sex (there may be variation within the males or females, but I think the sperms or eggs are always interchangeable).

Gender, I think, is more of a social term relevant to human behavior. Especially nowadays, so much of the literature and understanding of what is referred to as "gender" is closely linked to things such as gender identity, sexuality, gender roles and personality that is difficult to see how you could meaningfully speak about the "gender" of (non-human) animals.

It's analogous to the idea of "animal language" - certainly some animals may be said to behave in stereotypical ways which influence their mating behavior. Does that mean that what is written about human gender applies? I suspect precious little of it would. I would be quite skeptical of someone discussing gender (in the modern sense) for even uncivilized humans, let alone non-human animals.


Why is herpes virus neurotropic? A neurotropic virus is a virus which capable of infecting nerve cells.

Herpes simplex virus (HSV) has low neuroinvasivesess and high neurovirulence. HSV is transmitted in vesicle fluid, saliva and vaginal secretions. So the site of infection determines the disease - "mixing and matching of mucous membranes".

Source: Murray 2013, Medical Microbiology.

Why is herpes virus neurotropic?

Simply because it has neurotropic receptors. Why did acquiring these receptors seem evolutionarily advantageous? Well the immune system doesn't target nerve cells for destruction as well. There are few if any white blood cells in the CSF within which the neurones are bathed. The immune system is about protecting against damage, it doesn't care as much if a virus doesn't cause damage as it isn't geared to respond as well if that's the case.


Reliable recipe to make DIY yeast slants Does anyone have any good ideas on a reliable way to activate basic grocery store yeast?
I realize this is a total beginner's question.  I've built a small yeast ranch at home with my kid, and we're trying to learn how to innoculate agar'd petri dishes with home grown samples we're trying to make from basic grocery store yeast.  Eventually, want to do more advanced experiments, but for now...we're just looking for some growth.
So far, our best attempts at using grocery store yeast packets have yielded no results (i.e. no visible growth).  My best attempts to find a good recipe have lead nowhere.  I see lots of good advice on how to follow sterile procedure on making agar'd dishes and how to innoculate from an existing slant; but we thought it'd be easy to just start with grocery store yeast instead of buying a slant.
FYI -- there's obviously some kind of growth happening on the petri dishes.  When we break from sterile procedure and invite contamination; then it's clear something (not yeast) is happily growing on the plates.
My mistakes that could've lead to zero growth on the petri dishes include:
(A) Perhaps adding the dehydrated yeast to water that's way too hot?
(B) Perhaps I did not add enough wort or sugar for the yeast to feed on?
(C) Maybe i should've let the dissolved yeast ferment for a while before innoculation?
Would very much appreciate any help from someone more experienced on this.
best wishes...

Yeast grows very well in liquid. The initial innoculum from the store will visible grow (“prove”) in warm water with a little sugar.


Photolysis of Water? In chemistry, I studied the decomposition of water as being $2H_2O_{(l)} \rightarrow 2H_{2(g)} + O_{2(g)}$. However, when water is split, the equation is $2H_2O_{(l)} \rightarrow 4H^+ + 4e^- +O_{2(g)}$. Why is that? How does $H_2$ just ionize?

Moreover, what is the mechanism for photolysis? I would have thought that splitting water molecules requires a ton of energy; yet it can be accomplished simply with light energy during photosynthesis?

Water is split in chloroplasts in the light reaction of photosynthesis. Chlorophyll, acting as a photopigment, captures sunlight and transfers that energy to an electron pair of a water molecule. Under the influence of a water-splitting enzyme (George et al, 1989) it is separated into 2 protons, molecular oxygen and a free electron pair.

Reference
George et al. Science 1989; 243(4892): 789-91


Online multiple sequence alignment with constraints This is probably a naive question.

I have accesssed the Clustal Omega online multiple sequence alignment tool at http://www.ebi.ac.uk/Tools/msa/clustalo/ for the first time, but I think I need to provide more input to get it to do what I want, by specifying more constraints.

Edited to clarify constraints:

The original sequence P sequence has four symbols, say A,B,C,D.

The algorithm has access to 4 derived sequences.

P1: all occurrences of A,B deleted, no other change

P2: all occurrences of A,D deleted, no other change

P3: all occurrences of C,D deleted, no other change

P4: all occurrences of B,C deleted, no other change

Goal: given P1,P2,P3,P4, recover P

Example

P:
ABACCADDACBBC

P1
CCDDCC

P2
BCCCBBC

P3
ABAAABB

P4
AAADDA

Note that I have removed the under bars by which I had tried to indicate deleted symbols but since the deletion processes for the Pi are deterministic they can be supplied to Clustal or whichever tool is appropriate.

End of edit

Toy madeup example illustrating my input, the output, and the problem.

The actual sequence from which these sequences came after deletions, followed by the resulting sequences is as below:

p  ABACBAC

p1 A_AC_A_

p2 _BA__AC

p3 __ACBA_

so I input

>p1
AACA
>p2
BAAC
>p3
ACBA

and got the output

p1 _AACA_
p2 BAAC__
p3 __ACBA
      **

Which is entirely reasonable, but I have constraints.

I want to align with the constraints that

for certain symbols matches between certain sequence pairs should be maximized, and
for certain symbols mismatches between certain sequence pairs are allowed

In fact given p1,p2,p3,p4, which all arose from p after deletions, there are the pairwise constraints

A should be a match between p3 and p4 (it never appears in p1 or p2)
B should be a match between p2 and p3 (it never appears in p1 or p4)
C should be a match between p1 and p2 (it never appears in p3 or p4)
D should be a match between p1 and p4 (it never appears in p2 or p3)

This means that p1 has only C,D; p2 has only B,C; p3 has only A,B; and p4 has only A,D characters after deletion.

I want to obtain the most likely alignment or a few most likely alignments of p1,p2,p3,p4 under these constraints.

I have looked to see if I could figure out how to input the constraints but no luck.

Should I have used another tool? In general I will have much longer sequences, typically 4 of them, with pairwise agree/disagree constraints, as stated above.

Answer

You can't. Clustal doesn't provide the options of setting the sort of restraints you would like. Multiple Sequence Alignment (MSA) is difficult to program and the authors of Clustal have been refining their algorithm for years. If it were perfect and completely robust they might be in a position to add more user tweaking, but at the moment you're stuck with those provided.

Comparison matrices and forcing alignments

It may be worth while to mention how one can force particular correspondences in simpler pairwise alignments. This involves manipulation of the comparison matrix used to score the comparison. DNA comparison matrices may be very simple, scoring, say, 1 for a perfect AA, TT, GG, CC match and 0 for any mismatch. Protein comparison matrices are more complex, with the values for perfect matches dependent on rarity and unique function (e.g. In the PAM250 substitution matrix WW scores 17, whereas GG scores only 5) and the values for mismatches also varying markedly (e.g. ED scores 4, compared with 5 for EE; but EW scores –7). There are various matrices available, so implementations of the Smith Waterman and Needleman and Wunsch pairwise comparison algorithms generally allow you to specify your own.

Suppose you have biological information (not intrinsic in the algorithm) that makes you wish to force an alignment. For example, AAATAA sequences near the polyA tail of two mRNA 3'UTRs should align, but sometimes do not because other stretches of As give better scores. What you can do is replace the AAATAA by AAAZAA in each case, and then modify the scoring matrix so that ZZ scores very highly (e.g. 20) compared with AA. This will force the alignment, after which you can change the Zs back to Ts.

Multiple Sequence Alignments tend to to use position-specific dynamic scoring matrices. As the overall sequences align, the original scoring system is adjusted to reflect the frequency found at a particular position. (For example if a position is skewed to E in 90% if cases, EE will score more than at a position in which E is found only in 20% of cases).

I'm not saying it would not be possible to change the initial Clustal matrix with Zs at a particular position, but I don't think this possibility is provided. (Anyway your situation is more complex.) Glancing at the Clustal Omega paper, I see that they allow, indeed encourage, you to build up alignments from previous profiles. If you managed to force the alignments of a few sequences and input the profile derived from that, you might get what you want. But I imagine that requires the command-line program from Dublin, rather than the EBI online version.


Development and function of spindle neurons In his book How to Create a Mind author Ray Kurzweil makes some claims about spindle neurons that he provides no source for.

Concretely he states that spindle cells:

Are Involved in handling emotion and moral judgement;
Are believed to first have occurred in the last common ancestor of chimpanzees and humans;
Are non-existing in newborns, but appear around the age of four months, and increase significantly in number from ages one to three.

Is there a scientific consensus backing these claims?

The spindle-shaped brain cells you refer to are called von Economo neurons —named after the man who first described them  (source: Smithsonian).

In humans, von Economo neurons reside only in the anterior cingulate cortex (ACC) and the frontal insula (FI) (Allman et al., 2011). These two regions are particularly active when people experience emotion and they are reportedly important for "self-monitoring," such as noticing bodily sensations of pain and hunger, or recognizing that one has made a mistake. The ACC seems broadly involved in nearly every mental or physical effort (Smithsonian). By contrast, the FI may play a more specific role in generating social emotions such as empathy, social awareness, and self-control (Allman et al., 2011), but also trust, guilt, embarrassment, love, and even the sense of humor Smithsonian).
Humans and the great apes (chimps, bonobos, gorillas and orangutans) have von Economo cells. Lesser primates, such as macaques, lemurs and tarsiers, do not. That means the neurons evolved in a common ancestor of all the great apes about 13 million years ago, after they diverged from other primates but well before the human and chimp lineages diverged about six million years ago (Smithsonian). However, elephants and whales have them too, possibly explaining their complex social behavior (Allman et al., 2011).
I couldn't find literature on the development of these cells in children. Note, however, that, as far as I know, the presence of these cells can be only detected using microscopic techniques, i.e., on coupes of post mortem tissue (e.g., Santos et al., 2010)). This will make research in infants and children difficult.

References
- Allman et al., Ann N Y Acad Sci (2011); 1225: 59–71
- Santos et al., Brain Res (2011); 1380: 206 – 17


In centrioles, what type of fibers connect the triplet microtubules? In a centriole, each "arm" (a triplet microtubule) is attached from its A-tubule to the C-tubule of the adjacent arm. What is the type of fiber that connects each arm ("connecting fibrils" in the image below)?

Winey M, O'Toole E. 2014. Centriole structure. Phil Trans R Soc B 369:20130457

  Cross-sectional images of centrioles and basal bodies show a linker between the A- and C-tubules in many different organisms... Surprisingly, candidate molecules serving as constituents of these linkers have not yet been identified.

That's as of 2014. I don't have the time right now, but I'll try at some point to find if there are more recent developments.


Why can white hairs get dark again? I have learned (probably in high school?) that hairs turning white is caused by the part of the folicle which produces the pigment dying and being replaced by an air bubble. This sounds very irreversible.

I have long dark brown hair, and since I turned 25, I have had a few white hairs here and there. It is not unusual to find hairs which have a dark tip but are white at the root, which fits the above theory.

But I also have hairs which are the opposite: the lower ten centimeters are pure white, but at some point, there is an abrupt transition to dark brown, and the hair is dark again up to the root. This is all a natural phenomenon, I haven't used dyes or bleaches.

So what makes white hair white, if it can turn back to dark? Why would a single hair turn back?

The pigmentation of hairs is achieved by the follicular melanocytes (specialized pigment cells) at the base of the hair shaft. These cells produce the pigment which is subsequently transported into the cells which produce the hair and integrated into the hair matrix.

Besides genetic reasons, there are two major ways of losing this pigmentation. First, as a part of the normal hair cycle, the hair grows for a while until it falls out and the hair follicle regresses. In this process the cells in the hair follicle die, including those which made the hair as well as of the melanocytes. In this step of the hair cycle the hair follicle changes its morphology. When a new hair cycle starts, the pigment cells in the hair follicle are replenished from a stem cell population called melanocyte stem cells. These cells are located in the hair bulge (marked in red in the figure below). The cells then start to proliferate to multiply their number. A few of these cells stay stem cells (to be able to repopulate the pigment cells after the next hair cycle.) Others differentiate into melanocytes which subsequently migrate towards the bottom of the hair bulb (shown in green in the figure).

Over time, the number of stem cells gets lower, and at some point there are none left. This leads to a situation where the pigment cells are not replenished at the beginning of a new hair cycle and the hair stays unpigmented. As this is a continuous process, the pigmentation gets weaker before it is completely lost. As far as this process is understood to date, this depigmentation is irreversible.

There are two very interesting papers about this topic:

Melanocyte Stem Cell Maintenance and Hair Graying
Melanocyte stem cells: biology and current aspects.

The other reason for losing pigmentation (temporarily or permanent) is the generation of so called "reactive oxygen species" (Hydrogenperoxide) in the cells of the hair follicle, which then destroy the pigment. This is basically the same reaction which is used to bleach hairs, but in this instance from inside. This reaction can have numerous causes, among them are vitiligo and stress. The reason for the build-up of the hydrogenperoxides is that enzymes, which usually break them down before they can cause harm are either mutated or downregulated. If the level of these enzymes (the catalases) goes back to normal, pigmentation is also getting back to normal. This has been tested experimentally with people who suffer from the pigmentation disease vitiligo.

Oxidative Stress in Ageing of Hair
Basic evidence for epidermal H2O2/ONOO−-mediated oxidation/nitration
in segmental vitiligo is supported by repigmentation of skin and
eyelashes after reduction of epidermal H2O2 with topical
NB-UVB-activated pseudocatalase PC-KUS


The genetic code and the effect of point mutations on proteins I was asked a question, "Considering degenerate and non ambiguous nature of genetic code, Why is that certain mutations don't disturb the protein synthesis leading to synthesis of functional proteins where as certain mutations cause synthesis of non functional proteins or diseased proteins?"

My argument was that according to Wobble hypothesis, the tRNA carries anticodons that have A,U,G,C,I where I is inosine (sugar phosphate with hypoxanthine) that can bind with A,C,U of the codon and also G binding with U and vice versa is possible. Then, I gave the example of serine -AGU- whose anticodon is -UCI- for instance and after mutation say, -AGU- becomes -AGC-, it still codes for serine and -UCI- stills agrees to bind with -AGC- giving us serine as before and hence no disturbance is brought up leading to synthesis of functional protein. But suppose -AGU- got mutated to -CGU- , then the anticodon -UCI- no longer can bind with the codon and hence another tRNA molecule with anticodon of that of arginine gets attached and hence leading to interruption in the amino acid sequence which ultimately leads to non functional protein.

But my professor disagrees with my argument and says I am not clear with the concept. Can anyone please help with where I am going wrong ?

Nonambiguity refers to the fact that codon X will always code for the same amino acid.

Degeneracy refers to the fact that an amino acid can be coded for by many codons.

I rephrase the question to get to the gist of things:

  Why do certain mutations cause no difference for protein synthesis, while others make a big difference?

Certain mutations can change the codon but still code for the same amino acid, so the resulting peptide sequence is unaltered (synthesis of a functionally identical protein). This is due to degeneracy, explained above. Certain other mutations change the codon in a way that produces a completely different amino acid, and these result in the synthesis of a different, distinct peptide that may be dysfunctional. This due to nonambiguity of the code. Simple!

It's best to refer to our translation guide, the codon table. If you know your codon table, you might have noticed that within a codon frame, changing the 3rd nucleotide often has no effect on the translated amino acid (see outer ring, below). Changing the 1st and 2nd nucleotide produces a more drastic effect in the translation of the codon.

That means that the position of a nucleotide mutation within the reading frame is key to the effect of the mutation on protein synthesis.

  Where I am going wrong?

You are complicating the picture needlessly. You fail to explain that the resulting amino acid depends on its codon, and that the effect of changing the codon in different places (position 1, 2 or 3) has different outcomes. You also have to think about different kinds of mutations; we are discussing substitutions, but you must also consider what deletions and insertions of nucleotides do to the translation of the peptide! You may also get bonus points for discussing the start and stop codons... they are special cases.


How do snakes determine the direction of prey from their thermal infrared sensing pit organs? This answer to How does the “heat vision” of some snakes work? explains the basic idea and there are several linked sources within that go into greater detail on the sensing mechanisms on a physical and a molecular level.
But searching these sources for terms like "spatial" or "angular" in an attempt to understand how they get direction information (specifically for striking a  pray) turned up nothing.
Some snakes have multiple pit organs that point in somewhat different directions, and I suppose it's possible that the heat-sensitive nerves across the pit membrane could have spatial resolution and the whole thing act like a pinhole camera, but so far I've found no actual explanation of how they obtain direction information from their pit organs.
Question: How do snakes determine the direction of prey from their thermal infrared sensing pit organs?

From Wikipedia:

The facial pit actually visualizes thermal radiation using the same optical principles as a pinhole camera, wherein the location of a source of thermal radiation is determined by the location of the radiation on the membrane of the heat pit. However, studies that have visualized the thermal images seen by the facial pit using computer analysis have suggested that the resolution is extremely poor

Individual pit organs act like pinhole cameras because they are arranged, well, like a pinhole camera: there is an invagination of tissue surrounded by heat-sensitive cells with a smaller hole to the outside world. From Sichert et al 2006 it looks like this:

The dashed lines here indicate heat originating from some distant point source. That point source covers some fraction of the heat-sensitive membrane. Points at different distances and directions will be picked up on different parts of the heat-sensitive membrane. For example, because this source is coming from below, only the top of the pit is illuminated; for a source coming from above, only the bottom of the pit would be illuminated, etc.
If you have access to the Sichert paper, they go into more detail about the mathematics that the pit organ geometry creates. In summary, for any cell you can map a receptive field of places in the world that can project to that spot, and through a summation of these receptive fields across the whole pit organ you can reconstruct a map of where heat is originating. At that point, the principles are no different from visual organs like the retina. The authors show that even with each individual detector having imprecise resolution, the combined activity can be decoded to form a clear image from a simple linear combination of the receptive fields.
Other studies like Chen et al 2012 show that vipers integrate retinal vision with their pit organ senses, because occluding a pit on one side and an eye on the other is worse for prey targeting success than occluding both on the same side. Neuronal evidence of this integration has been observed for quite some time, see for example Newman & Hartline, 1981.
Bothe et al 2019 is a more recent paper investigating some of the neural circuitry behind the processing of pit organ information and integration with vision.

Bothe, M. S., Luksch, H., Straka, H., & Kohl, T. (2019). Neuronal substrates for infrared contrast enhancement and motion detection in rattlesnakes. Current Biology, 29(11), 1827-1832.
Chen, Q., Deng, H., Brauth, S. E., Ding, L., & Tang, Y. (2012). Reduced performance of prey targeting in pit vipers with contralaterally occluded infrared and visual senses. PLoS One, 7(5), e34989.
Newman, E. A., & Hartline, P. H. (1981). Integration of visual and infrared information in bimodal neurons in the rattlesnake optic tectum. Science, 213(4509), 789-791.
Sichert, A. B., Friedel, P., & van Hemmen, J. L. (2006). Snake’s perspective on heat: reconstruction of input using an imperfect detection system. Physical review letters, 97(6), 068105.


What determines whether the maternal or paternal allele is expressed? I am taking cell biology and have this question:

During the process of gene expression, it is possible to express either the maternal allele or the paternal allele.

When and how is the determination made to express one allele over the other?

Except in the case of X inactivation in females, and genes on the Y chromosome in males, generally speaking both alleles are expressed in cells.

A good example is the ABO blood type marker system. If the mother is type AA, she will pass on an A allele, which codes for the A antigen. If the father is type BB, he will pass on a B allele, coding for the B antigen. Therefore, any children will be type AB, as the maternal chromosome 9 will express the A form, and the paternal chromosome 9 will express B.