text:
In what range do humans generally interpret sound best?
I am currently working on a speech recognition frameworks. A generally used feature used in speech recognition are MFCC features, which uses the mel scale to extract features with.

The mel scale visualises how humans interpret different frequencies of sound compared to each. The graph shows that by linearly increasing the frequency from 0 -1000 will the sound/pitch be interpreted as linearly increasing. When the frequency is linearly increased beyond 1000 hz, is the sound not interpreted as linearly increasing but logarithmic increasing.
How MFCC make use of this:
When training the system, are audio files processed using band pass filters with center frequencies that are mel distant, meaning that they will be (somewhat) linearly increasing at the beginning and end up being logarithmic increasing.
How do I interpret this:
It seems to me that the human auditory system is very susceptible to sounds the range 0-1000 and not much above, but 1000 hz isn't much and I guess conversation must in somewhat higher range. So why are humans more susceptible to sounds in these ranges?

Well, I know in what range human interpret vocal sound best.... but not a range for all sounds, will that suffice your need?

Since you are working with a speech recognition framework.

I work on voice recognition too. Yes, very brilliant query about sound perception that I can clarify and not answer completely. Most of the text belongs to DSP SE forum, i.e. Voice rec, MFCC, filter, BP, audio processing. You may have confused the readers except for the image and the final paragraph.
I had to rephrase it to clarify it to myself:
Why are humans unable to hear pitches on a straight maths scale, they hear logarithmically? We hear according to a mystery ratio called MEL distribution, a well studied summary of many subjects perception of pitch, averaged to:

0.01% Humans have Perfect pitch, 95% are relative pitch, and 5% are tone deaf. MEL varies by the type of listener. Tone deafness is hereditary, ( info about biology and brain structurehere) and the rest of humans probably follow a gradual distribution of poor to good pitch differentiation, and they also hear amplitudes differently.
As you can see from the wiki page, there is no explanation for MEL theory, it's either neurological, a soundwave energy balance, or because of the ear anatomy.
To answer the title question, your graph shows humans have a continuous response to frequency spacings through all their perceived sound. However volume tests show amplitude sensitivity peaks at about 3kHz, which you can see on inaccurate amplitude perception and equal loudness contour graph.
MEL studies of Steinberg are stagnant since Volksmann, same as Donald D Greenwood suggested in 2009, they overgeneralize and the field needs to be developed a lot further under a different study name than MEL scale, which isn't english.
Why can they hear voice well under 1000Hz?
At least 1/2 of the sound energy of voice occurs below 1000Hz, same reason bass requires a lot of energy.

So humans can hear sub 1000Hz sounds from further away, but the more sound data you have the clearer the voice is, and computer should use nearly all of possible human voice frequencies to measure formants and N/M consonants to best accuracy. Sub 1000Hz may contain enough vowel subharmonic frequency bands at different spacings to represnt the vowels of sound basically, but it is less clear and realistic if the voice is filtered at 1000Hz, the subharmonics of AEIOU go multiple octaves above middle C male/female voicebox peak, near 440Hz.
The sub 1000Hz components are generated by the voice box, which changes tone at a slow rate, whereas the 2000-3000Hz sounds, i.e. Frictives, S,F, and N aspirated P, k, don't require very as complex sound processing to interpret (for digital sound filter processing)
The 625-1000Hz pivot component of the equation doesnt appear less straight under 1000Hz if the graph is from a parametric frequency view.
To resolve your query, Biologists would want to know:

1/Structure of the ear as a reason for sound perception imbalance
2/Child learning and adult learning of complex pitch tasks
3/Brain structures used in pitch recognition
4/Evolution of ears and psychoacoustics, reason for a hearing peak at 3k which is the same as rustling leaves
5/Physics energy and mathematical reason for MEL distribution (ask on DSP SE)

As a Voice rec researcher, you should think outside of the box. Computers don't hear like humans. Frictives like F and S have peaks around 3000-4000HZ, they are the highest and easiest to recognize and similar in all accents. Formants from vowels can peak from 400 to 500HZ roughly in men and women, at 700hz for children.
Vowels are vague and vary by accent are are the least precise element in voice-rec. That's why voice recognition hinges a lot on formants and accents which have energy peaks below 1000HZ, and timbral graphs which change wildly wether it's AEIOU sounds.
As a side not for voice-rec,
English is tougher to recognize than French because of the stress time, swingy nature and the 2-3-4 vowels per syllable, and perhaps that's why French have lost the wild traditional accents faster (I know I speak both since I was 0). Voice rec of French and other syllable time languages is easier.
I don't know why MEL is used at all in voice-rec filters. Perhaps because people use the same intonations as they hear from MEL, so the PC must know too, else because the programmers don't know enough about real sound physics, and have implemented it as a rough power-balancing graph for filter results? else some other physics reason. Other power-related filter shapes should work fine, as DSP SE if this has a known physical basis of if it uses human psychoacoustics for digital audio inaccurately:
mel-frequency cepstrum (MFC) is a representation of the short-term power spectrum of a sound, based on a linear cosine transform of a log power spectrum on a nonlinear mel.
Humans don't need perfect pitch for anything except music. Relative pitch, we nearly all have ok, and it makes sense because biologically relevant sounds, animal calls, physical signals of water, trees, voices, add together to make a continuous freqency spectrum that we have to measure all the frequencies by a similar rating of importance to interpret best. Voice contains lots of micro-expression subtones that represent clear psychological states that humans benefit to hear, and rustling leaves and other sounds all should biologically benefit from a high relative pitch clarity.

I need to know this too so i wrote a DSP version here https://dsp.stackexchange.com/questions/46092/mathematical-reason-for-mcpp-in-audio-recognition

So why are humans more susceptible to sounds in these ranges?
I can't find the references etc. As I'm on my phone, but the accepted wisdom when I was doing a PhD on inner hair cells was that there were more type I spiral ganglion neurons per hair cell in the mid frequency ranges for a given species than at the extreme ends of the frequency ranges. This was about 400-1200 Hz in humans and gerbils and 1000-4000 in mice.
Basically more sensory information is heading to the brain from the frequencies we listen to most.
I don't think it was known if it was genetic, or an acquired feature, but papers by Liebermann from the early 90s should point you in the right direction. I'll try and pull one up.
Edit: this review looks like it has the info: 'For instance, in mice and gerbils, the most heavily innervated hair cells correspond to sound frequencies with more acute thresholds of detection (Ehret, 1979; Meyer et al., 2009), in agreement with reports of dense innervation in the middle of the cochlea in other species (Dannhof and Bruns, 1993; Liberman et al., 1990; Meyer and Moser, 2010).'
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078955/


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In genomic DNA extraction, is it possible that too much CTAB hinders subsequent DNA precipitation with isopropanol?
I'm trying a genomic DNA extraction protocol that uses 4% CTAB, 3M NaCl, 2.5% PVP-40, 20mM EDTA (pH 8), 100mM Tris-HCl (pH 8) and 3% beta-mercaptoethanol as lysis buffer. I incubate at 65oC for 60 - 80 min. Then, precipitate complexed cell debris with chloroform:isoamylalcohol (24:1). Collect the upper fase and precipitate DNA with isopropanol.
I tried this procedure in 51 samples of cotton leaves. In most samples I obtain a nice DNA precipitate after adding isopropanol. However, in 12 of them, I obtain 2-phases, with no DNA precipitate at all. The lower phase looks yellowish and sometimes a bit dark. Why would this happen? Any thoughts?
Thanks!

I'm sorry to hear you had this issue, but relieved that I'm not alone in the unexpected seemingly random results. Did you ever figure it out? I'd love to know!

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Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?
Say pathogenic bacteriaA makes toxinA, which had D-amino acids instead of L-amino aids, does this difference in chirality cause a different conformational change in the receptor or enzyme, thus leading to either deactivation of the enzyme or signal transduction pathway or activation of a different pathway?
I understand what chirality is in the concept of organic chemistry — rotating plane polarized light, ingold-prelog system etc; however I never leaned what structural feature of chiral molecules changes the way they react inside a cell.
I do NOT understand HOW changes in chirality can be associated with cellular toxicity.
links:
https://www.ncbi.nlm.nih.gov/pubmed/24752840
http://www.jomb.org/uploadfile/2014/0113/20140113053743849.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960212/

There a few things you have to take care of with chirality in biological systems:
First note, that for amino acids we usually use L and D instead of r and s nomencalture.
In chemistry the difference between chiral enantionemeres is usually really just a difference in light polarisation like you described, otherwise they can be thought of as identical, since they have identical chemical properties. This way of thinking does not apply to biochemistry - the moment enzymes (large molecules with very defined 3D structures) are involved the structural difference between the two forms becomes very important for each and every biological reaction.
In the case of single amino acids this means that D amino acids are toxic to eukaryotic cells, because their similarity to the D form allows them to interact with some of the enzymes that usually bind it, but the binding is not a perfect match so the enzymes get inhibited, which makes the D form toxic. (This is already described in the second paper you linked:)

In animal studies, administration of D-amino acids to rats and chicks resulted in growth inhibition [18]. In addition, serious damages such as suppression of the synthesis of glutamate oxaloacetate transaminase, glutamic pyruvic transaminase, and lactate dehydrogenase resulted from D-amino acids accumulation in animal tissues [18].

Now in your question you are asking about the difference between a toxin made from the 'wrong' amino acid. The thing is, this change of the protein will most likely mean, that its not a toxin anymore. A protein toxin is toxic because it can interact with other proteins, based on its 3D structure. This structure is based on the chemical and structural properties of the amino acids building it. If you change the underlying structure of every amino acid it will fold differently and you will get completely different protein - and not a mirrored version of the original protein/toxin.

As Nicolai has mentioned in his answer, change of chirality (L and D) of amino acids will drastically change the way a protein folds. I searched online to find if a solved structure of D only form of any protein. However, there were none.
But, both right handed and left handed DNA are known. This difference does not happen because of the chirality difference of the DNA constituents but the way the bases are base paired. However, it exemplifies how the change in chirality can lead to non-trivial change in structure.

Original uploader was Richard Wheeler (Zephyris) at en.wikipedia - Originally from en.wikipedia; description page is/was here., GFDL, https://commons.wikimedia.org/w/index.php?curid=2117121
I will read some more on signal transduction and return to the question.

No.
One can make no generalization about the effect of the change in chirality in a ligand in the protein to which it normally binds. As the simple diagram below shows, as far as interaction with the ligand binding site is concerned there is no essential difference between a enantiomer of the normal ligand and a modified version of it:

Both may be able to interact with sites ‘a’ and ‘b’ on the protein, but whether this will be inhibitory or not cannot be predicted — it will depend on the energy of the interaction compared with that of the correct interaction (and the relative concentrations of substrate and inhibitor).
If it does bind it is most unlikely to cause a conformation change, and even less likely to trigger an alternative pathway. Most protein binding sites are tailored for a single response. In the event of disruption, inhibition is the most likely result.
As far as a bacterial toxin is concerned, the fact that it may employ D-amino acids is a red-herring. The overall structure of the toxin is what counts, and has evolved to act on a specific target. Each example is likely to be unique.
Any textbook of biochemistry will have sections on the substrate specificity of enzymes (e.g. Berg et al. online).

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Can nitrate be an electron acceptor for NADH generated in the citric acid cycle?
Is the citric acid cycle aerobic or anaerobic? I know that the oxygen is required to accept the NADH electrons so that NAD+ could be regenerated. Nevertheless, if other electron acceptors, as nitrate (NO3–), are present, could they also be used to regenerate the NAD+? I am asking this because I read a thesis claiming that “acetly-CoA enters the citric acid cycle and through anaerobic nitrate-respiration a multiple amount of ATP is generated.” If you have some literature that you can share with me I would be really grateful. Thanks.

I have changed your title because it is misleading. Strictly speaking the chemical reactions of the TCA cycle are anaerobic because oxygen is not involved in any of them. But that is not your question. Your question is about electron acceptors for NADH produced in the TCA cycle. I have kept the question in the body of the text for you to modify if you like.

Yes, many microbes can use electron acceptors other than oxygen.
https://en.wikipedia.org/wiki/Anaerobic_respiration
https://www.sciencedirect.com/science/article/pii/S0168165611000289

As it stands this is not the sort of answer this site encourages. See the Help especially the section "Provide context for links". Your answer would be improved by (1) Emphasising that the TCA is intrinsically anaerobic, it is the process of reoxidising NADH that can involve oxygen or not, (2) That for all organisms have a single electron acceptor, in most cases (and in all animals) oxygen. At the moment your answer could be interpreted as certain microbes having a choice of electron acceptor.

@David is that not true?

Not that I was aware. I thought they were highly specialized, but I may be wrong. The point is to address this important question clearly in your answer, citing an example if I am wrong.

The redox potential of other oxidizing pairs differs from that of oxygen and water and therefore a different set of reactions must be used to obtain energy (pump protons) from oxidizing NADH with them.I am not a microbiologist, but it appears from  this that, as I would have expected, most bacteria that employ other electron acceptors are obligate anaerobes and will not therefore operate alternative modes of respiration. But some facultative anaerobes appear able to do this.


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Appearance of Karyotypes in educational material
Most actual karyotypes online appear as single chromosomes (unreplicated). I was under the impression that a micrograph of the replicated chromosomes was taken during metaphase of mitosis and thus should show up as duplicated sister chromatids instead of single chromatids post anaphase.  Are the arms of the chromatids just so close to each other that they are hard to distinguish?

Many karyotype images, especially those used for introductory educational purposes, have been edited to show a regular human 2n. For example this image has been edited to depict a regular 2n (46) compliment of human chromosomes.

While this image is unedited and shows the replicated homologous pairs in metaphase:

So the first image you supplied does not show replicated chromosomes consisting of two chromatids for each of the chromsomes in the first pair?

Correct, the first image shows the normal 2n of 46 chromosomes arranged in 23 homologous pairs. The second image shows the replicated chromosomes at metaphase with the sister chromatid pairs arranged in tetrad with their homologues. If you look closely at the second image you can even see the centromere holding the sisters together.

This is incorrect; both images have been edited (to form pairs), and both are from cells in metaphase, which therefore have sister chromatids present.  (One is human and one is bird.) Both have chromosome images which clearly show the pinched waist caused by the centromere.  Some show the division between the chromatids, but the contrast in the second makes this easier to see.

I don't see the difference either

Can you add your sources to the figures?

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How is the effect of proof-reading on error frequency during DNA replication determined?
An article in Nature Scitable on DNA Replication and the causes of Mutation states that:

When an incorrect nucleotide is added to the growing strand, replication is stalled by the fact that the nucleotide's exposed 3′-OH group is in the "wrong" position… During proofreading, DNA polymerase enzymes recognize this and replace the incorrectly inserted nucleotide so that replication can continue. Proofreading fixes about 99% of these types of errors

I am interested to know how this value of 99% was determined, and this is not explained in the article.

hi @Johny, maybe you can be more expansive in your question. What is proofreading for example, you didn't even mention DNA replication. You have to make the distinction between Translation/ transcription and Replication...

Very sorry, I was unaware of the standards of asking questions on stackexchange. I have updated the question and if anymore information is needed please feel free to give me feedback.

I have edited your question in form that answers my criticism. Please note that the article and hence your question is about DNA replication — not transcription or translation. Consult a standard text book or Wikipedia if this is not clear to you. I have now recinded my negative vote and close vote as the question is reasonable and the answer not easy to find by an internet search.

It would be nice if Nature Scitable actually used citations. The most used technique in molecular biology to determine the function of something is actually to prevent it from functioning and observing the effects. I would venture a guess that, simply, replication error rates were determined with and without the proofreading activity. I’ll try and find some of the original papers that studied this, but they may be hard to dig up.


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Do mosquitos excrete blood?
Since insects like mosquitos ingest only blood, and insects generally excrete their solid and liquid waste at the same time as frass, I was wondering: is mosquito defecation more like iron pellets or droplets of blood?
I've never seen a mosquito defecate, so I have no evidence. Do they defecate during flight? If so, are tiny little droplets of digested-blood falling from the sky?

This could be related https://skeptics.stackexchange.com/questions/23072/do-mosquitoes-urinate-on-you-when-they-bite-you

When mosquitos feed on blood they release water droplets, this is so they can condense the amount of nutrients from the blood but dispose of the unnecessary water weight. This act of releasing excess water is often mistaken as 'pooping', a clearer view of the process here. Actual footage of fecal excretion however, is harder to come across.
Mosquito defecation is more like iron pellets, to maximize their meals they excrete water during or after feeding (in case they need to make a quick get away). Iron is toxic in high doses, so the mosquito excretes it after absorbing the nutrients in the blood, resulting in dark pellets, containing iron and uric acid.


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Identification of a beetle —Kerala

My daughter is studying biology and is interested in insect species. Please could you help her identify the species of this beetle found in Kerala (a tropical state in India).

For identification it is helpful to add information, where in the world and which habitat you found the animal/plant. Also the size could be useful. Could you please edit your question to add these information? And while your at it, maybe change the title to '... photo of a beetle'

And is your question about identifying this particular animal, or is this one just an example and you want to generally know, how to identify animals by yourself? Could you please clarify this?

And please reduce the size of your images before posting. On my browser the 0.3 Mb image (2000 px wide to fit a 600 px space) only shows in black. A quarter of the size is more than adequate.

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Difference between prions and amyloid proteins?
Amyloid and prions are misfolded proteins, but what, if any, is the difference between them?
Is amyloid a type of prion with a fibrillar structure?

Amyloids are protease resistant insoluble fibrils formed because of (mis)folding and aggregation of soluble proteins (Rambaran and Serpell, 2008, Sabate et al., 2015). The first definition of prion was given by Prusiner (1982):

Because the novel properties of the scrapie agent distinguish it from
  viruses, plasmids, and viroids, a new term "prion" is proposed to
  denote a small proteinaceous infectious particle which is resistant to
  inactivation by most procedures that modify nucleic acids.

Many prionic diseases are characterized by amyloid fibril formation and therefore some (if not many) researchers consider prions to be a subset of amyloids.

Prions are considered a subclass of amyloids in which protein
  aggregation becomes self-perpetuating and infectious.
(Sabate et al., 2015)

However, the amyloid structure formation is not essential either for the autopropagation or disease progression (Moore et al., 2014).

When wild-type C57BL/10 mice are infected intracranially with the RML
  mouse prion strain, PrPSc accumulates in diffuse nonamyloid deposits
  and brain pathology is distinguished by the hallmark gray matter
  spongiosis for which TSEs are named. Conversely, when transgenic mice
  homozygous for PrPC lacking the GPI anchor (Tg44 or “anchorless” mice)
  are infected with the same RML strain, the incubation time is longer
  and PrPSc accumulates in dense perivascular amyloid plaques with
  little or no gray matter spongiosis.9−11 Similar amyloid PrPSc
  deposition and disease resulting in death has been observed in humans
  with an aberrant stop codon in the C-terminal portion of the PrP
  sequence, resulting in the generation of PrP lacking the GPI anchoring
  group as well as some amino acid residues.13−16 Thus, GPI-anchoring of
  PrPC to the plasma membrane appears to be a primary factor determining
  the type of PrPSc deposition and the development of brain pathology.

You can say that the prion protein PrPC is amyloidogenic but it is not an amyloid.
There are non-pathogenic (and in fact useful prions) found in fungi. Many of these beneficial prions also form the amyloid (like) structure but they can be disaggregated by chaperones (Wickner et al., 2018). Now again, it is not essential for these beneficial prions to form an amyloid structure.

Prions (defined as “infectious proteins”) need not be amyloids. The
  vacuolar protease B (Prb1p) of Saccharomyces cerevisiae is made as an
  inactive precursor that is normally cleaved and so activated by the
  action of protease A (Pep4p) [32]. However, in the absence of Pep4p,
  mature active Prb1p can activate its own precursor [33]. This
  self-activation can propagate and pass from cell to cell in an
  infectious manner, acting like a prion, and named [BETA] [34]. In the
  absence of Pep4p, [BETA] is necessary for meiosis and spore formation
  and for survival in stationary phase [34]. It is thus a functional
  prion.

[SMAUG+] is another example of a non-amyloid yeast prion which has beneficial effects (Chakravarthy et al., 2019 and Itakura et al., 2019; Jarosz group). Unlike Prb1p, [SMAUG+] actually forms self-propagating aggregates.
My summary
Many known prions are amyloidogenic and can switch to amyloid form. However, as per the definition, prions are "infectious" or in other words, self-propagating proteins.
What qualifies as a prion depends on our definition. Mode of action of most known prions is catalyzing a change in the protein fold. Wickner et al (as quoted above) reason that the original definition does not explicitly include the mode of action and hence proteins that activate themselves via proteolysis should also be considered prions. Jarosz's group has shown an example of a non-amyloid prion that forms self-propagating aggregates. It quite likely that more such proteins will be discovered in near future.
In any case, "amyloid" is a structural property whereas "prion" is a functional property and they cannot be considered a sub/superset of one another, even if they happen to be correlated.
The bottomline is:
Amyloid is a form of supramolecular protein structure which is often formed by many prionic proteins. However, not all amyloid forming proteins are prionic and not all prions necessarily form amyloids.


text:
How do cone cells underneath capillaries receive light?
Came across this image of retina's cross section:
1) How do the cone cells directly underneath the blood vessel ('demarcated in the picture') receive a spectrally correct representation of the incident light? Wouldn't the blood absorb most of the spectrum, leaving only red behind. Is it because the blood vessel is too thin?
2) The fovea region seems to be void of any such capillaries, how do the cells then receive nutrition and oxygen?

1) The photoreceptors in fact don't receive all the light because some of it is absorbed by the blod vessels and nerve cells above the photoreceptors. The Wikipedia article on the retina states:

Although the overlying tissue is partly transparent, and the accompanying glial cells have been shown to act as fibre-optic channels to transport photons directly to the photoreceptors, light scattering does occur.

Here is the direct link to the article describing the fiber-optic effects.
The red blood cells in the capillaries do absorb some light but the brain corrects for the color distortion. The most notable effect of the capillaries is that you can actually see white blood cells moving across your retina when looking into the skye:

The white blood cells in the capillaries in front of the photoreceptors can be perceived as tiny bright moving dots when looking into blue light. This is known as the blue field entoptic phenomenon (or Scheerer's phenomenon).

However, our eyes are still extremely sensitive:

A rod cell is sensitive enough to respond to a single photon of light.

Furthermore, the inverted retina actually protects the light sensitive cells from overexposure and damage by UV light.
Interestingly, cephalopods (e.g. squid, octopus, nautilus) have their photoreceptors on top of the retina, making their eyes more sensitive and better adapted to the low light conditions of the deep sea.
2) While blood circulation is necessary to maintain nutrient concentrations in large tissues, small distances can be covered pretty well by diffusion of the nutrients through the tissue. The fovea is only 5.5 mm in diameter which is small enough for diffusive nutrient supply.


text:
Approximately how thick is a single strand of cat (domestic housecat) hair?
I did a little research to lead me to finding the general range of width for human hair, which is anywhere from around 30µm to 180µm... approximately.
I'm trying to compare this to the width of cat hair, since I have been told (and it does seem a bit evident) that cat hair is much thinner than human hair in general.
I can't seem to find any information on this.  Does anybody have any answers?
Note:  I apologize if this isn't the right Stack Exchange forum for this question.  I wasn't sure where to put it, so I did an SE site search for 'cat' and this one seemed to be the most appropriate.

Off hand I don't know, but I actually do know a few books that might have it in it (unfortunately I couldn't find open copies).  But if you really want to find out the answer of say your cat, you could do this experiment and let us know.  I will post an answer if I find one.

Google  cat hair diameter gives this as top hit (30 micrometers).

Oh Google algorithms.  That's the third hit on mine.

Thank you.  Hmmm... I didn't see that when I searched earlier...

There are a few different types of hair on a cat.  But I think you are referring to the down hair on the cat.  It will also vary on the breed of domestic cat.  As a general statement, you can find a lot of quirky characteristics of mammals by looking at early genetics papers where people where trying to find genetic elements to obvious phenotypes.
For the down hairs, you can see "The ‘rex’ type of coat in the domestic cat."
Journal of Genetics [0022-1333] Searle, A G and Jude, A C yr:1956 vol:54 iss:3 pg:506
Table 3. Thickness in µ of normal and rex down-hairs

[Type of Cat][Diameter in um][SE of Mean]

Normal          25.8;   1·32;

English rex     16·2;   0·54;

German rex      17·0;   0·50;

Ooh that's pretty.  Thanks for the edit, I now know how to make tables.

You're welcome. It's not really a proper table, but the code formatting does make it look nicer.


text:
Why would decreased temperature be associated with increased cell size, in deep-sea crustaceans (or in general?)
I was reading Wikipedia regarding deep-sea gigantism -- the fact that deep-sea species are often much larger than their shallow-dwelling counterparts. The article said,

Decreasing temperature is thought to result in increased cell size and
increased life span... both of which lead to an increase in maximum
body size.

The citation is:
S F Timofeev Izv Akad Nauk Ser Biol. 2001 Nov-Dec:(6):764-8.
[Bergmann's principle and deep-water gigantism in marine crustaceans]
I haven't tried to retrieve that article because I can't read Russian. Following up on "Bergmann's principle" doesn't help; it's just identifying ecographic patterns in gigantism.
From a surface area to volume ratio perspective, I can see how smaller cells are adaptive to cold temperatures. A huge amount of cellular processes are diffusion-driven. All of them, except for some potential electron or proton tunnelling processes, all mediated with thermal movements.
So let's say the transport of glucose into a given cell is driven by the concentration gradient (diffusion). At lower temperatures the diffusion rate is lower, so a cell of a given volume gets a reduced import of glucose. So it seems that increased surface-to-volume ratio (a smaller volume) would allow for a cell to compensate, and to accomplish the same rate of import as the warmer cell. This would also apply to some intracellular processes.
So assuming my thinking about diffusion processes is irrelevant to the real-life biology, as it predicts for colder temperatures that smaller cells are adaptive, is the point that metabolic processes are slower at lower temperatures? Then, a reduced rate of transport is not necessarily the limiting factor. Maybe the cellular volume can be scaled up until the total metabolic flux is comparable to the warmer-living cell? If there's more dissolved oxygen at lower temperatures, and if oxygen equilibrates well-enough, maybe no other nutrient or signalling diffusion is relevant?
This thinking does not at all seem consonant with this story by Curtis Deutsch and coworkers: Impact of warming on aquatic body sizes explained by metabolic scaling from microbes to macrofauna.

The model reproduces three key aspects of the observed patterns of
intergenerational size reductions measured in laboratory warming
experiments of diverse aquatic ectotherms (i.e., the "temperature-size
rule" [TSR]). First, the interspecific mean and variability of the TSR
is predicted from species' temperature sensitivities of hypoxia
tolerance, whose nonlinearity with temperature also explains the
second TSR pattern-its amplification as temperatures rise. Third, as
body size increases across the tree of life, the impact of growth on
O2 demand declines while its benefit to O2 supply rises, decreasing
the size dependence of hypoxia tolerance and requiring larger animals
to contract by a larger fraction to compensate for a thermally driven
rise in metabolism. Together our results support O2 limitation as the
mechanism underlying the TSR, and they provide a physiological basis
for projecting ectotherm body size responses to climate change from
microbes to macrofauna.

are there any deep sea animals limited by a skeleton or exoskeloton? that wouldn't be related to cell size.  another consideration is whether the cell size difference is average or median.  I know there are a few single celled organisms that are like the size of the basketball that live on the sea floor. most of the sea floor is deep, so if you have a few species down there like that, they could dramatically increase the "average" cell size without affecting the median. then again, maybe Caulerpa taxifolia is proof that actually the largest average cell size is actually not in the deep sea.

I didn't know about how large the cells can be in C. taxifolia. That does seem to place tensions on any theory that emphasizes deep sea conditions and doesn't include oxygen availability as a factor. Since photosynthesizers generate their own local oxygen, they would be able to flaunt any biophysical constraints on cell size for ectotherms mentioned below in @Eonema's answer.

Woods (1999) proposed an explanation for the negative effect of temperature on ectotherm cell size based on the rates of transport and metabolism of oxygen - both of which you considered in your question. The diffusion of oxygen decreases with increasing temperature. However, this effect is small compared to how much the consumption of oxygen increases with increasing temperature. Therefore, in a warmer environment, despite having greater oxygen supply, a cell is still more oxygen-limited because of the relatively greater increase in the oxygen demand. In a colder environment, a cell can be larger because it is less oxygen-limited and can afford to have a lower surface area:volume ratio. As Woods puts it:

The critical observation is that oxygen supply (determined jointly by [the surface concentration and diffusion coefficient]) rises slowly with temperature, but that oxygen consumption rises rapidly with temperature. Thus, at higher temperatures, the oxygen gradient within a metabolizing sphere will be steeper, and the radius at which the oxygen concentration at the center falls to zero will be smaller.

Note that while this hypothesis makes theoretical sense, it's not clear that the effect of temperature on cell size actually drives differences in body size or even occurs in nature. The study on temperature and cell size (Van Voorhies, 1996) that was cited by the Timofeev (2001) paper was solidly refuted by Partridge and Coyne (1996) for looking at genetically identical individuals and failing to consider latitudinal genetic variation, along with other sources of faulty inference. There are a number of plausible competing hypotheses to explain deep-sea gigantism and Bergmann's rule, not all relating to cell size.
Nevertheless, this same process proposed by Woods could also apply to organisms as a whole, rather than individual cells. Deutsch et al. (2022) consider the same mechanism as Woods, except they considered whole organisms. Therefore, their equations are somewhat abstracted from the biophysical processes that Woods deals with, but it's basically the same mechanism.

Bergmann's Rule is ecographic, but that's because higher latitudes tend to have lower temperatures. "The rule derives from the relationship between size in linear dimensions meaning that both height and volume will increase in colder environments" from the wiki article.

First, some corrections to assumptions in your question. As I pointed out in my comment; Bergmann's Rule is ecographic, but that's because higher latitudes tend to have lower temperatures. "The rule derives from the relationship between size in linear dimensions meaning that both height and volume will increase in colder environments."
Also a careful reading shows that rather than contradicting you, Deutsch and his collaborators’ article fully supports your hypothesis; “Maybe the cellular volume can be scaled up until the total metabolic flux is comparable to the warmer-living cell?” Not only that but increasing temperature increases the metabolic rate, further exacerbating the problem of oxygen uptake for the warmer cell.  From the Woods article quoted by Eonema: “rates of reaction are more sensitive to temperature than are physical processes such as diffusion and electrical conductivity.” And Eonema correctly states that in larger cells this increased rate of metabolism prevents the diffusion of sufficient oxygen to the center of such cells.
From the Deutsch article; “Among aquatic ectotherms, the TSR has been ascribed to limitation by dissolved O2. According to this hypothesis, a thermally driven increase in O2 demand outpaces any rise in O2 supply, a balance that can be restored by confining growth to a smaller size, resulting in a larger ratio of respiratory surface area to body volume.”
And from your excerpt:
“Third, as body size increases across the tree of life, the impact of growth on O2 demand declines while its benefit to O2 supply rises, decreasing the size dependence of hypoxia tolerance and requiring larger animals to contract by a larger fraction to compensate for a thermally driven rise in metabolism.”
The Deutsch full article shows that it is the oxygen concentration decreasing with increasing temperature, rather than the temperature increase itself,  that is the real driver of TSR.
The paper introduces several different models and experimental results to compare the effects of increasing temperature and decreasing oxygen concentration across a wide range of fauna, from bacteria on up.

This relates resting oxygen demand rate to size.
Whilst the Deutsch paper does not directly address increasing cell size, it does show the same effect in bacteria and other microbes, indicating that this probably applies to individual cells in larger ectotherms.
So, in conclusion, it is the decreased metabolic rate, coupled with the higher oxygen concentration in cold water that enables and encourages larger cell and animal sizes.
This answer has not addressed the possibility of longer lifetimes on increased size.

Besides the assumption that my considerations of temperature-dependent metabolism were different from the model of Deutsch and others (thanks for explaining how my picture is closer to theirs than I thought), what assumptions needed correction? I wasn't saying anything about Bergmann's Rule (other than correctly labelling it as ecographic). My question is focusing entirely on deep sea gigantism and the role of low temperatures in supporting it on a cellular level.

It was just that you said " Following up on "Bergmann's principle" doesn't help; it's just identifying ecographic patterns in gigantism." I was only pointing out that Timofeev's paper refers to Bergmann's principle as related to temperature rather than location.  "An increase in the geographic latitude and depth of crustaceans habitat (correlating mainly with lower temperatures) leads to an increased cell size"


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What are the disadvantages of forbidding flights to and from the African Ebola region?
After looking through the available Stack Exchange sites, this one seems to come closest to the appropriate place to ask...
Popular opinion, including my own, is that banning flights to and from the Ebola-ridden portion of Africa would protect us overall. I understand it would increase pressure on that region, making it more chaotic and less conducive to tracking people, so that eventually it could "explode uncontrollably" out of that region in a year or whatever time frame. Sanjay Gupta explains this briefly in Jon Stewart's (at points hysterical) report.
The disadvantage of allowing free travel to and from these regions, as I see it, is that the disease spreads much much faster, and to many many more disparate locations. This is because of the variety of places where each passenger comes from. And also the flight crew and plane itself, which affects all future passengers.
I'd appreciate more educated opinions. I'm far from it, regarding these issues, as are many Americans.

The main disadvantage is that you will not get aid into the region which is extremely urgent.

I suspect that the main issue is the balance between containment (might favour closing borders) and control of people that enter the country (might favour allowing controlled airtravel). It has been argued that banning flights will lead to more people entering the country illegaly, which means that they cannot be screened for the disease in the same way as airtravellers. However, much of this also deals with politics, trade etc. From a biological viewpoint the issues should mainly be routes/vectors of dispersal and identification/containment of infected individuals.

The question is if this would help. I doubt it, since people which are infected, but have not yet developed symptoms (meaning they are not contagious), can travel via land across borders. This will probably slow the spreading down but it will not prevent it completely.

Well, it seems prudent to at least have flights from these locations limited to highly-prepared sections of the airport. It would also make sense to permit them to land only at specific airports. In the dead center of JFK is probably not a good idea.

Having them separated at the airport only gives you better options in separating out passengers that started showing symptoms while on board. Infected passengers without symptoms could still change to another plane afterwards, that will not be tracked as it did not depart directly from the Ebola region.

:)  https://uk.news.yahoo.com/ebola-us-restricts-air-travel-africa-160416055.html

I think the disadvantages are mostly economical in that region and so they has nothing to do with epidemiology. Possibly a long term effect can be, that the economy of the region turns from bad to worse, which can affect the healthcare too, but that's just speculation.
The advantages are obvious, ebola is quarantined at some level, so these measures prevent or at least slow down its spread around the world.


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What are these bugs skittering about the kitchen sink?
I found a bunch of these around a kitchen sink in an apartment building in Toronto, Canada, in late October, 2019.
The bugs vary in size, but are all very tiny, less than one millimeter (the photos were taken with a macro lens, and still barely captured them).
They move very fast when they detect light changes, and hide in the crevices around the sink.
They die very easily when squashed.
Edit: Managed to shoot a larger, more photogenic specimen.

Thankfully they are not cockroaches or bedbugs, but I cannot tell what they are from the pictures.

@KarlKjer Thanks for ruling those two out! I posted some better pictures, do they help narrow it down?

Yes, they define them.

Those are springtails, order Collembola. Looks like they are in the family Entomobryidae. They are completely harmless. They don't bite, or spread disease. They often find their way into potted plants in people's homes. I'm not surprised that they are in your sink. Their small size makes them subject to desiccation.
https://en.wikipedia.org/wiki/Springtail https://en.wikipedia.org/wiki/Entomobryidae


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What's the name of this Heteroptera bug from Toronto, Canada?
My friend already identified it as belonging to the Heteroptera order, but I was wondering if anyone knows the name of the species.
Found in Toronto, Ontario, Canada, on July 21 2017, in a residential bathroom.

@BernardoRamos Yes, thank you, I forgot to add it, here it is.


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What's the name of this beetle?
I found him in a kitchen located in Toronto, Ontario, Canada.


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Bug on wall identification request
I've been finding a few of these on the same wall of my apartment the path month. Size is maybe 3-5 mm.
I live in an apartment in Toronto Canada.
Thanks in advance!

Without clearer photos it is pretty hard to say, however, I think it is likely to be one of the Dermestidae family of beetles.
These include a bunch of common pests in the household, including "carpet beetles" (Anthrenus sp.), and the larder beetle (Dermestes lardarius).
I think this is most likely to be a carpet beetle, given the light/dark mottled pattern on the shell.


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Why is hydrogen sulphide being generated on Caribbean beaches?
Once again, there has been a massive influx of Sargassum weed in the Caribbean. It is coming ashore on Atlantic facing beaches and forming piles up to 3m deep. As it dries and decays, hydrogen sulphide is being emitted. Why?

It would seem from a quick perusal of the literature that this is caused by sulphate-reducing micro-organisms. To quote from the eponymous Wikipedia article:

Sulfate occurs widely in seawater, sediment, or water rich in decaying organic material. Sulfate-reducing microorganisms are common in anaerobic environments where they aid in the degradation of organic materials.

which is consistent with the situation described.
In biochemical terms, these anaerobic bacteria are using sulphate rather than oxygen as the final electron acceptor (oxidizing agent) in the elctron transport chain which generates ATP through the chemiosmotic mechanism. The reaction for the reduction of the sulphate to hydrogen sulphide (dissimilatory sulphate reduction), according to the Wikipedia article already quoted, is:

A simple way of thinking about this is that in both aerobic and anaerobic respiration the oxidizing agent itself becomes reduced. Whereas oxygen is reduced to H2O, sulphate is reduced to H2S.

Thanks. I think you’re right. That suggests that agitation might stop formation of the gas.

Decomposing plants in fresh water also generate H2S. Anaerobic bacteria in deep underground strata generate H2S. , Also, sometimes in home water wells pumping water from shallow strata. The darn bacteria are everywhere.

What’s the best way to stop the process? Add oxygen (air)?

@Dave No, remove the rotting stuff.

@Dave — I personally wouldn’t know, but if you could arrange to fly me out to the Caribbean I would do my best to help. ;-)

It piles up to 2m deep at the high water mark and forms in a mat over 100m out to sea. The dogs can walk on it! If you clear a section of beach it refills at the next tide.


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How to integrate transcriptomics data with kinetic metabolic models?
I have created a convenience kinetics† model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have read some publications related to this work but can’t get a satisfactory idea of how to do it properly.
Details
I've got a pancreatic model for the study on type 2 diabetic patients. It has a few compartments and the reaction pathways; the species are metabolites. All the reactions are convenience kinetics based. Enzyme is a constant factor, so its production and regulation is not considered. From my model, I'll get the Vm values for all the reactions and then I'm supposed to get the Vm (Vmax of Michaelis-Menten kinetics) values for the type 2 diabetic patients by somehow integrating the transcriptomics data with it. I was asked to use the fold change values but I couldn't find any relevant publication on this topic (my PI has suggested me these but hasn't worked in this area before).
Any leads or references will be highly appreciated.

† You can call convenience kinetics rate laws as approximate rate laws or you might have heard about "modular rate laws", they are more or less the same. We use this approximate rate law approach in cases where we don't have the experimental data for all the true rate law parameters.

Anyway, I have come across people who have been trying to incorporate transcriptomics data in flux balance models. I'm not sure how much that improved the accuracy of the predictions. There are problems at multiple levels. I don't know much about what are the parameters that can be incorporated in FBA but I am a bit familiar with kinetic models. If you can present a minimal model with the details on how you are planning to write the equations and so on, I may be able to give some suggestions.

I've added that information in the question now. Can you please tell me about those researchers/labs who have worked on their integration? Maybe provide me with the links to their webpages or the publications that you're referring to. It'd be of great help.
Regarding the approach, I myself have no idea and have been stuck here from the past week, and have been asking around people at different labs. So, any kind of lead will be appreciated. @WYSIWYG

I am assuming that in your model, the reactants and products (species) are metabolites and each reaction denotes conversion of one metabolite to another.
From transcriptomics, you will get the relative expression levels of different genes.
When you have two samples from different conditions you can calculate the differential expression.
A model can be as complex as you can make it but we can start with simple assumptions. As you said, enzymes are assumed to be constant with respect to metabolites and are not dynamically changing. I also guess that you are not considering genes other than enzymes to be affecting the metabolic reactions (you might actually want to consider the solute transporters). Also, you are assuming Michaelis-Menten kinetics for all reactions.
In that case your Vmax (i.e. maximum rate of a reaction) would be kcat × E0 where kcat is the turnover number and E0 is the total amount of enzyme.
E0 can be approximated using the transcriptomics data. However, transcriptomics data is relative and not absolute. If you need absolute quantification, you must have at least one reference whose absolute mRNA copy number is known. Another issue is that the ratio of protein and mRNA expression would not be the same for all genes and it is basically the amount of active protein you need to know. So proteomics would be one step closer.
When you are comparing two conditions, you can use the differential expression (fold change values) to adjust the parameters between the two conditions. For e.g. if you know that phosphofructokinase is 2 fold downregulated in diabetes (compared to healthy case) then you can reduce the Vmax of the corresponding reaction by 2 fold in your diabetes model. However, it all would make sense only if the parameters of your "healthy" model are reasonably close to the biological reality.
Moreover, you still need to know kcat. It cannot be obtained from high throughput studies. You may have to either make some guesses or check out papers/databases. Also, your rate is not always Vmax. To estimate the dynamic rate you must know KM too (when the substrate is in excess you can ignore KM). BRENDA may have some information about these constants for different enzymes.
At a very crude level, you can remove the reactions whose corresponding enzymes have zero expression.

These are some articles on integration of transcriptomics data with FBA (not kinetic models):

Blazier and Papin (2012)
Machado and Herrgård (2014)
Guo and Feng (2016)

Machado and Herrgård actually claim that integration of transcriptomics data does not improve their model predictions:

Also, it is observed that for many conditions, the predictions
  obtained by simple flux balance analysis using growth maximization and
  parsimony criteria are as good or better than those obtained using
  methods that incorporate transcriptomic data.

Another alternative is to model Transcription data as very sharp hill function with some fitting parameter. This will essentially mimic Boolean Model and have used successfully in generating regulatory networks. Lot of Eric Davidson's reviews have explained this. For example, Bolouri and Davidson 2002


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How many different colors can a normal human distinguish?
I am not talking about asking a person to sit for 10 hours to separate one color. I want to know is the normal person in a normal life.  How many different colors can a normal human separate?

What do you mean by "separate"? Do you mean "distinguish"? If so what has sitting for 10 hours to do with it. Please clarify your question, indicate its relevance to biology and why you wish to know something like this. See the Help on "How to ask a good question".

Right. Distinguish. From biological point of view, each human can classify 10 millions of color. However, that is not usual. People may need to take very long to classify between two very close color. That situation is not a normal situation.

What do you mean by "normal human" and "separate"?  A lot of it is simply training: If you include say interior decorators as normal humans, they can separate and give names to perhaps dozens of shades lke bone, eggshell, cream, ivory, linen and ecru, that most of us just call off-white.

For example, a jpg image use RGB with 256 color intensity. A total of 16.78 millions of combination.  Note, those are color intensity not color depth. But this gives us the general idea of human can separate will be less than color depth X light intensity = 16.78 million combination, because computer monitor are normally used. I want to know about the color depth of human vision in normal use!!

Values like this are determined via careful psychophysical experiments in the lab. You're asking about 'everyday life' or something? You need to carefully define what you are after then. This question is unclear, open to debate and as a consequence opinion-based and therefore offtopic in its current format.

I remember trying to find research on this subject some years ago, and the best data I could find said the range of human color vision was about 10,000,000 colors. Unfortunately, the article (which I cannot now find) didn't say how this number was reached, but I believe it was based on the response curves of the cones and didn't take into consideration whether or not the brain combines input from the cones as well as the rods to determine colors, which I believe it does. If anyone finds some definitive research, I'd find it very interesting. And I do not think this question is off-topic.

Just to correct a comment from the poster. The 16.8 million colours that can be represented in an 8-bit RGB image tell you nothing about human colour perception. (And colour intensity — whatever its relevance here — is the extent of difference from grey.) The jpeg algorithm reduces image size by reducing the number of colour on the basis that the human eye cannot distinguish (or does not notice) the difference between very similar RGB values. Although the basis of the answer to your question will be biological, your question isn't really biology in terms of SE Biology.

@David It is a biology question. I think that you do not live in USA because your colour has an 'u'. What is the traffic light color in your country? Almost all traffic light in the world have red color, it is because red trigger warning signal in the brain. My 2 hours ago comment was to use an approach to explain to people a possible direction of thinking. We could have different angle to analyze a problem.

Interestingly the answer appears to vary by culture, A lot like sounds it appears it is partially effected by what colors people are taught to distinguish between. http://imbs.uci.edu/~kjameson/ECST/Kay_Cook_WorldColorSurvey.pdf

I may not be in the US, but I live in the country where traffic lights were first introduced. My point is that you could ask the average speed of a cheeta and get an answer, but the question isn't really what we are after on SE Biology. That would be a question of the type, "Why is a cheeta faster than a horse?", where a useful answer would be in terms of body structure, musculator or whatever. Likewise, the question of how we discriminate millions of colours is much more pertinent than whether it is 1 million or 10 million.

@ Giordano Fearghas: The use of 8-bit color depth in JPEG & mainstream computer displays isn't really linked to how many colors a human can distinguish, but on hardware considerations.  8 bits fit in a byte, 3 color bytes plus an alpha (transparency) channel in a 32-bit word.  Increase color depth, and you double the amount of memory & bandwidth needed. making your system uncompetitive except for special purposes.  (Especially in the past, when memory &c was much more expensive.)  Nowadays greater depth is sometimes used: many digital cameras can do HDR (High Dynamic Range) photographs.


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Providing small molecules to cells on a filter plate
Lets imagine that I have mammalian cells that I've immobilized on a filter. Now I want to keep providing small molecules to these immobilized cells without resolubilizing the cells.
The caveat is that I would like to do so without fixing the cells or waiting for them to adhere to the filter. The small molecules are small enough to diffuse through the filter.

perhaps you can dip the filter plate in a medium containing the small molecules.. and then keep changing the bath after few days.. btw you want a batch or continuous system??

@WYSIWYG, Batch should be fine. The question is what would be the setup to do so. Would it be as simple as reversing a 96 well lid over and placing the filter plate on top? What about the wetting?

I am not very sure but you may try the plates used for growing ES cells over feeder layers separated by a membrane

Perhaps you're looking for these hanging inserts, for example: "Millicells"

Can you elaborate a bit more on why this meets the OP's requirements?

The original poster would like to feed his immobilized cells small molecules, without fixing or waiting for adherence. The inserts contain a membrane, which forms a permeable barrier, to allow diffusion of small molecules, and site for attachment. The insert itself is free to move and hang in different culture media/wells, so no need to trypsinize or resolubilize them, and provides containment of the non-attached cells.


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Under what circumstances and why is terrific broth preferred to LB broth for E.coli growth?
Terrific Broth will result in a greater density of cells compared to LB but I have certainly seen it isn't as effective for the protein production of certain proteins compared to LB or defined media. I was curious what other limits and constraints exist with TB.
Migrated and derived from Quora http://www.quora.com/Under-what-circumstances-and-why-is-terrific-broth-preferred-to-LB-broth-for-E-coli-growth

I have used terrific broth to grow up transformed E. coli so they grow faster.  Often people will conduct a transformation, screen the cells, and grow them up in broth for plasmid extraction.  This growth would be for 12-16 hours.  Instead a person could use terrific broth to grow up the cells and it would take may 6-8 hours for adequate cell density for plasmid extraction.  If you are trying to express a protein then I would go with LB.
Also, I learned recently that terrific broth is also preferred over LB when needing to express proteins after transformation.


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Confused about plant phyla
My kids and I are doing a fun project collecting pictures of life in parks and national parks around us. We are trying to classify what we find down to genus and species.
However, I'm confused about what the plant phyla are. With animals, it is pretty clear (e.g. arthropods, chordates), but I don't understand what they are for plants. I see informal groupings and divisions, but not what phyla.

So I may cite from Wikipedia:

The term phylum was coined in 1866 by Ernst Haeckel from the Greek phylon (φῦλον, "race, stock"), related to phyle (φυλή, "tribe, clan").[4] In plant taxonomy, August W. Eichler (1883) classified plants into five groups named divisions, a term that remains in use today for groups of plants, algae and fungi.[1][5] The definitions of zoological phyla have changed from their origins in the six Linnaean classes and the four embranchements of Georges Cuvier.[6]
Informally, phyla can be thought of as groupings of organisms based on general specialization of body plan.[7] At its most basic, a phylum can be defined in two ways: as a group of organisms with a certain degree of morphological or developmental similarity (the phenetic definition), or a group of organisms with a certain degree of evolutionary relatedness (the phylogenetic definition).[8] Attempting to define a level of the Linnean hierarchy without referring to (evolutionary) relatedness is unsatisfactory, but a phenetic definition is useful when addressing questions of a morphological nature—such as how successful different body plans were.

I recommend reading the full article... It is really well-written

Phyta means plant... The different 'phytae' mark different levels in the taxonomy...
Example:
Streptophyta from the Greek strepto, for twisted, i.e., the morphology of the sperm of some members and phyta (plant), a group including land plants and some algae
Embryophyta - land plants
Tracheophyta - vascular plants (from Ancient Greek τραχεῖα (trakheîa, “windpipe”) + -ophyta)
To answer your question... Phyta is a part of many plant taxonomy levels... It is not one type of plant but it marks the membership of a group to the kingdom of plants.

What I was really wanting to know was what the plant phylums (or phyla) are. My confused brain thought phyta = phyla. So your answer was perfect--it was just that I was asking the wrong question and didn't realize it. I've updated my question to ask what I was really asking.


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Why does the side of the mebrane of a neuron with a high concentration of positive ions become electrically negative?
I am having a real hard time understanding why the side with a high concentration of positive ions becomes the negative side of the membrane (in a neuron). This website http://www.st-andrews.ac.uk/~wjh/neurotut/mempot.html says its because "...the positive ions flow away from the high concentration side". But I still don't get it. Wouldn't it make more sense to then say that the high concentration site (more positive ions) has more positive voltage?

Q. “Wouldn’t it make more sense to then say that the high concentration site (more positive ions) has more positive voltage?”
A. No.
I know little about electrophysiology, but looking at the graphics and explanation that precede the screen from which the sentence you quote is taken the statement is justified. Where are you going wrong?
Your argument implies that the side with the high concentration should be positive because it has more positive (K+) ions. But it has (initially) an equal number of negative ions (Cl–) so it is initially electrically neutral. (The graphic indicates this by having no charge on the K — not a very satisfactory idea in my opinion.)
The important thing to note is the premise — that the membrane is permeable to K+ ions, but not to Cl– ions. So, even though there is a concentration gradient, only the K+ ions can move across the membrane (the graphic shows those moving with a +ve charge). As they do so each leaves its ‘partner’ Cl– ion behind, so a negative charge builds up at the high concentration side. At equilibrium there may be a high concentration of K+ ions at the ‘left’ of the diagram, but there is an even higher concentration of Cl– ions!
Good luck with your further reading of these pages! It looks as if it gets much more complex as it goes on.

David's answer is good.
I would also add that the resting membrane potential is not strictly because of moving K+ ions - if you were "teleporting" ions out of the cell, you would need to move a lot more ions to get a potential of ~-70mV. Instead, the resting potential is essentially given by "how much electrical force would I need to put on this membrane to get those potassium ions to disobey their tendency to flow down their concentration gradient." You should always be thinking about the Goldman equation and the relationship between concentration gradients and permeabilities, or neurophysiology will be very confusing.


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How do T-cells determine which cells they've already inspected?
From what I understand, T-cells are constantly traveling in the body, inspecting cells by looking for antigens. If they're self antigens, then the T-cell doesn't attack, whereas if they're non-self, they attack. My question is how does a T-cell know when it just inspected a cell? Does the T-cell leave something behind on the cell to mark it as checked or does the cell itself present something on its surface to indicate that it has just been checked? If there is no such system, then what prevents the T-cells from being stuck in a loop, and just inspecting the same cell over and over?

As answered on Reddit, where you asked the identical question, it's because there's extensive movement even in the relatively calm environment of the lymph nodes, so that once the T cell disengages from its target the natural movement makes it unlikely to bump into the same cell.  See the references and videos on Reddit.

Here is the Reddit link for anyone who's interested.

I've edited your title and removed anthropomorphic 'know'.

Your question spans two activities of T-cells that are related to each other: migration and activation. T-cells that usually stay in lymphoid organs migrate to non-lymphoid organs with different mechanisms for each T-cell subtype. When migrated to non-lymphoid organ, the T-cells move through the organ looking for infected cells.
Migration
As you can see in the image below, there are many mechanisms for moving T-cells across the endothelial layer.

The main idea for all three mechanisms is that the tethering of the T-cell to the endothelial layer is weak. Because of the weak interaction, the blood flow causes the T-cell to move across the endothelial layer while still being attached to the endothelial layer. This is known as rolling. Other stimuli (usually chemokines) such as CCL21, CCL25, or ICAM 1 are needed to induce T-cell to migrate across the endothelial layer. This is important because these chemokines are expressed where there is inflammation. For example, there is a correlation between CCL25 level in the gut and inflammation in the area.
T-cells express α4β7 integrin or CCR7 that bind T-cell to the endothelial layer. Central memory T-cells and naive T-cells express CCR7 and CD62L and thus reside preferentially within the secondary lymphoid organs. Effector memory T-cells bind to gut endothelium with α4β7 integrin, CCR9, and LFA-1.
CCL21 is expressed by both stromal cells of lymph node paracortex and endothelium of lymphatic vessels to assist migration of activated dendritic cells and naive and central memory T-cells to lymph node respectively. Dendritic cells are professional antigen-presenting cells (APCs) that migrate to lymph node where it can interact with T-cells more efficiently.
T-cell activation
One important concept to take away from T-cell activation is that there needs to be direct contact between MHC complex and T-cell receptor (TCR).
T-cells that have moved into the lymph node interact with dendritic cells, which have high MHC complex concentration on their cell surface. This leads to subsequent activation of the T-cell leading to release of cytokines such as IL-2 leading to proliferation of activated T-cells.
The activated T-cells now are able to freely move across the endothelial layer of non-lymphoid organs to infiltrate and look for infected sites. (Naive T-cells enter endothelial layer of non-lymphoid organs as well but this is chemokine independent nad thus not a reaction to inflammation).
Sources:
Difference between naive T-cells and memory T-cells: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782715/
Dendritic cell's role in immune response: http://lab.rockefeller.edu/steinman/dendritic_intro/immuneResponse
Memory vs naive T-cell migration:
http://www.nature.com/icb/journal/v86/n3/full/7100132a.html
Dendritic cell and role of CCL21:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078419/
Naive T-cell non-lymphoid organ infiltration: http://onlinelibrary.wiley.com/doi/10.1002/eji.200535539/full
CCL25 and inflammation relation:
http://www.sciencedirect.com/science/article/pii/S0896841116300014

Please add a citation to your answer (like the process of a T-cell inspecting a cell, there are no such markers ever discovered, etc.)

Sorry, I meant there's no marker that is well known to have that function. Several literature searches yielded no results, so I simply have written "none commonly known".

Its all right. You should just have a back-up claim if someone asks you about the correctness of your answer.

@John It was hard to find in other literatures whether T cell bind to MHC or antigen first. However, that doesn't matter in this case because you cannot have one without the other! MHC and antigen go together. If the cell wasn't antigen presenting cell, it wouldn't have MHC to bind in the first place!

The more effector T cells respond to antigen, the more inhibitory receptors it starts expressing that lead to death of that particular T cell. At that, the longer it takes for the T cell to die, it starts to enter progressively more severe stages of exhaustion. So really the T cells regulate their own persistence (in part). It would be useful to cover this as well.

@CMosychuk I believe the question was about the affinity of T-cell to APCs and duration of binding between the two cells. The concept you mention is interesting, but outside the scope of the question. Which means to not be hypocritical I should take out the "Unrelated" last paragraph.

Down voted, because this answer is wrong.  T cells do bind to APC that don't have non-self antigen, although it's a transient interaction unless the appropriate antigen is present.

Building on @iayork's comment - T cells bind to endothelial APCs (not professional APCs necessarily, just regular endothelial cells) in the blood vessel walls via weak interactions between molecules on the T cell surface and on the APC. This produces a "rolling" phenotype, where the T cells "sample" the surface of the APCs In the absence of pro-inflammatory cytokines or activating chemokines from the surrounding tissue, the weak interactions break under the force of blood flow and the T cell moves on. (...)

(...) If there is inflammation nearby, the cytokines and chemokines will very quickly induce the surface expression of other adhesion molecules, allowing the T cell to come to a stop and begin the extravasation process. This is a good image from the Nature journal Immunology and Cell Biology.

@iayork Thank you for your inputs. I changed the answer to fit your statements. Yes, T-cells bind to endothelial cells lining the blood vessel. Also, please feel free to give input to the answer (the edit answer button).

@MattDMo Thank you for your inputs. I changed the answer to fit your statements. Yes, T-cells bind to endothelial cells lining the blood vessel. Also, please feel free to give input to the answer (the edit answer button).

T-cell does not inspect any cell until the cell shows a piece of the "non-self" antigen on it by the MHC.
The helper T-cell connects with the antigen which is on the cell's surface. The T-cell sorts the cytokines that activate the cytotoxic T-cell to divide and form a colony of cytotoxic cells. The colony of cytotoxic cells then attack the "non-self" antigen expressing cell.

It'd be a lot better if you give some more explanation and a reference too.

I'm confused, although maybe I'm just confusing terminology. Please see here (http://sepa.duq.edu/regmed/immune/SpecifAntigen.html) and here (http://sepa.duq.edu/regmed/immune/SpecifAntigen.html). As this site seems to be saying, T-cells attach(bind) themselves to cells regardless of the antigens on its surface and then after its attached, sees if it has  a matching non-self antigen, which binds it further. Am I reading this incorrectly?

Sorry, the other link is (http://sepa.duq.edu/regmed/immune/SpecifMHC.html).


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How did scientists establish the reactions that occur in metabolism?
How did scientists establish that macromolecules like proteins, carbohydrates and lipids are synthesized from other molecules with intermediate products by living cells. Did they observe this under microscope. I want to know this because I am studying bioenergetics and while studying photosynthesis and cellular respiration I have doubt that whether this all stuff is correct or not. I hope that you will help me to clear this doubt.

Welcome to Biology.SE. The way your question is currently written, it is hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. Please also take the [tour] and read through the [help] to learn more about the site, including what is on-topic and what is not, and how to ask a good question.

What exactly do you have a question about? The fields of metabolism and bioenergetics are huge, much too broad to be covered in a single question here. Is there something in specific you are unsure about?

In addition to biochemical methods, a lot of this was figured out using radioactive tracers. Cells would be fed a radioactive substrate and as they convert the substrate to other molecules through metabolic reactions, the radioactivity can be detected in the products and intermediates.
Calvin's 1940s-50s experiments to establish carbon flow during photosynthesis (i.e. the Calvin-Benson Cycle) using $^{14}CO_2$ remain some of the most elegant work along these lines. You can actually read some of his reports here, though maybe someone else has a good link to a less technical overview.
Similar methods are still used today, though stable isotopes instead of radioactive ones are more commonly used.

The short answer is no, you do not study metabolism under the microscope. (Modern high resolution microscopes can visualize macromolecular processes like transcription and translation, but that is not how they were studied originally.)
In brief, biochemical pathways were studied in broken cells by studying individual reactions or in whole tissues or animals studying chains of reactions. In broken cells chemical methods (often colorimetric, but historically by measuring the evolution of gases) were used to identify products of reactions when particular chemicals are added, and enzymes purified from tissues to find out what reactions they catalyse. Centrifugation methods were used to different organelles from cells (mitochondria, nuclei, ribosomes). In whole cells radioactive precursors are added and one separates and identifies the compounds in the cell to find out which compounds have acquired radioactivity, i.e. what the original compound has been converted to.
In bioenergetics the methods are/were more specialized using spectrometry to identify the oxygenation state of different cytochromes, and the oxygen electrode to measure the utilization of oxygen. In animal cells isolated mitochondria were often used.
This is a very wide area, although because it is not currently very active it is difficult to find an internet source to recommend you. Perhaps someone else knows of one.


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How does having an empty stomach affect absorption of compounds?
From personal experience, compounds such as nicotine, caffeine and alchohol appear to absorb much quicker into the blood on an 'empty' stomach', or after extended periods of fasting. If this is the case, why would that occur?
Does time play a significant role in absorption in an average 'healthy' individual? Are there any srudies published on this phenomenon?

Welcome to BiologySE... have you looked anywhere in particular for the answer to this question? You may want to google drug absorption without or  with food. Different nutrients can affect the rate of gastric emptying (i.e. prolonged gastric emptying with fatty foods), though if you are strictly talking absorption from the stomach that may not matter (or could if you're taking about a highly lipophilic drug). Can you clarify if you are talking specifically about gastric specifically or overall GI absorption? Are you talking about "food compounds" or "drug compounds" or both?


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Meaning of phrase with term, "intelligent design"
I am am mathematician, kindly correct me, If I am wrong somewhere.
I am reading a book titled "Sapiens " by Noah Harari.
He says

Organism are increasingly shaped by intelligent design rather than natural selection

I am not able to understand what he is trying to say.
What does he mean by "intelligent design".
What I know is that natural selection is the main process that brings evolution. Is he trying to say that natural selection is no longer the driving force ?

Any reason for downvotes, Please explain. I want to know what went wrong.

-1, Intelligent design is a common term. An internet search will provide a definition, does that definition fit with what the author means? If that doesn't make sense then more context is required. Also, it appears to be a misquote as it isn't grammatically correct.

@Sri You used the right format for quotes before and you changed it. I changed it back but don't hesitate to let us know if there is any reason you prefer not using the quote format.

downvoted - based on the good research by @tomd

I've changed your title as nobody reading a list of titles would know what the question was about with "this phrase". Try to do better in future.

Welcome to Biology.SE! You have seen some criticism about your question here, but some of that might not have been very useful for you. Please consider taking the tour and look at our guidelines for good questions. Enjoy! :)

Please first note that Noah Harari is not a scientist but a historian.
What does he mean by "intelligent design"?
Intelligent design is a set of fallacies invented by christian extremists to try to contradict a set of evidences that they have a hard time to include into their faith. Intelligent design has nothing to do with science. It is therefore impossible to state anything about this sentence except that it does not mean much.
However, from this quotation alone, one can't be sure that Noah Harari chose the term "Intelligent design" in reference to the commonly referred concept of intelligent design. He might have meant something else and might have tried to use some term that sounds sensational and poetic as talking about this book some have said that the attractive features of the book are overwhelmed by carelessness, exaggeration and sensationalism. (see theguardian.com). My first feeling is that you could try to ask him (contact information are there)!
@tomd found this source which clarifies the author intention.

Not all people accept this idea. Religious fundamentalists insist that intelligent design rather than natural selection has shaped life on earth. They argue that the intelligent designs of a great god sculpted the long necks of giraffes, the colorful tails of peacocks, and the jumbo brains of humans. To the best of our scientific understanding, these religious zealots are completely mistaken. The past history of life owes nothing to divine intelligence. Ironically, however, the zealots may well be right about the future. Very soon, the four-billion-year-old regime of natural selection may be overthrown, and life in the universe will increasingly be shaped by the intelligent designs of divine beings. For in the medium future, we humans are likely to turn ourselves into godlike beings, possessing divine abilities of creation by design.

What I know is that natural selection is the main process that brings evolution.
Natural selection is one process yielding to evolution. There are other processes such as genetic drift. Stating natural selection is the main process that brings evolution all depend upon what statistic of evolution you would like to consider. For example, you might want to know that most fixed genetic variation among species is due to neutral mutations (and therefore genetic drift) and not due to natural selection.
You might want to have a look at Understanding Evolution by UC Berkeley for a short introduction to evolutionary biology

+1 for quoting the review. Hopefully the question gets update with a little more context.


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Release of Nor-Epinephrine by presynaptic beta receptors
Presynaptic alpha-2 receptors on stimulation decrease the release of nor-epinephrine by certain mechanisms where as activation  of beta presynaptic receptors increase or facilitates the nor epinephrine an effect which is opposite to the alpha receptors
How does this facilitation of nor-epinephrine occur by the pre-synaptic beta receptors

This a very interesting question! I'm assuming the "presumptive" is a typo for presynaptic. I don't know what you mean by 'hetero tropic interaction' in this context (I thought that was for enzymes) but still, the alpha2 presynaptic acts by coupling with the Gi, thereby reducing Ca+2 and reducing vesicle release. How the beta presynaptic acts, I couldn't find out.. But increasing the calcium doesn't seem to be probable because beta receptrors couple with Gs and hence increase cAMP. Whether cAMP can induce vesicular fusion, that I don't know

@polisetty  I looked heterotrpoic interaction to find that the alpha-2 receptors located presynaptically for the cholinergic neuron but postsynaptically to the sympathetic neuron inhibit the release of acetylcholine by binding to the gi specifically in the intestine where there is close proximity of the sympathetic and cholinergic neurons. Though the term hetertropic interaction might just be an interaction and not a mechanism for inhibition of neurotransmitter release.


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Ripening bananas artificially: What is the biological theory behind?
I am a resident of the tropical island of Sri Lanka, and we have a strange traditional method to ripen our banana harvest quickly.
What we do is this: We dig a pit in earth that is enough to put the whole banana cluster in. Then, after safely laying the bananas in the pit, we cover up the pit with a sheet such that only a small hole from a side remains: visualize a small 3-4 inch door to the pit.
After that, we light a fire with semi-dry leaves just outside the pit's door. (Semi-dry leaves are used to get as much smoke as possible. Dry leaves do not give that much smoke, because they completely oxidize quickly). And the smoke is sent through the door by blowing it with the aid of a bamboo.

This sends a good amount of smoke and warms the inside of the pit considerably. And by experience I can tell you that this makes the bananas to ripen really quickly. I have done a controlled experiment where half of the cluster was not put into the pit. Bananas in the pit ripen overnight and the control sample took days to ripen.
Can anybody explain what are the bio-mechanisms that are working here?

Nice illustration :P

Ripening of bananas (and other fruits) is induced by acetylene and ethylene (Ethyne and Ethene) (see reference 1), which acts as a hormone and induces the ripening process. The incomplete combustion of the leaves produces ethylene, additionally the warmth of the process will help the enzymes as well. There is even a paper about this technique (although it is unfortunately not accessible), see reference 2 for more information. Smoking Chambers are routinely used in this process, see reference 3 and 4.
References:

Role of Ethylene in Fruit Ripening
Effects of smoking on some physiological changes in bananas.
Fruit Ripening
Technology for ripening fruits as important as marketing them

This is also why you can ripen bananas (or other fruits) by placing apples (or pears) next to them - apples emit ethylene as they ripen, thereby speeding up the ripening process in the banas.

Yup, that would be a natural way to do this at home.

As the ethylene acts as chemical messager between different organisms (different banana trees) the word pheromone would be better than hormone (though hormone is also valid as the plant emitting the ethylene is also affected by its own ethylene). Other than that, a perfect answer.

+1, I often have to explain to folks who bought their potted plant at the grocery store why it is seeming to die for no reason. They are often on a stand near fruit, and ethylene is toxic to many growing plants.


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How do marine mammals control buoyancy?
Presumably, as a whale or seal dives, its lungs get compressed by the increasing water pressure, and it gets less buoyant.
Under this model, for a given amount of air taken in at the surface, the animal has a very specific depth D at which it is neutrally buoyant. Any deeper, and the lungs shrink, making it negatively buoyant. Any shallower, and the lungs expand, making it positively buoyant.
In other words, until it reaches depth D, the animal is positively buoyant. To get to depth D, the animal would have to do a lot of work swimming down, fighting against its own floatiness.
The amount of air that keeps you neutrally buoyant at 10 meters will inflate to twice the volume once you surface, keeping you pinned there. Speaking as a scuba diver, I can say that it would take a lot of work to dive back down to 10 meters. (We deflate our air vests at the surface and re-inflate at depth from our incompressible tanks, something animals don't have.)
For very deep divers like sperm whales, swimming down against positive buoyancy seems like a huge energy waste, the kind that one might expect wouldn't be tolerated long by evolution.
So do marine mammals do anything to compensate for the effect of fluctuating lung size on their buoyancy? One guess is that they actually exhale fully before diving, thus making lung buoyancy a small player in the overall body buoyancy. Another guess is that they compress the air with their chest muscles at the surface in order to sink. These are just guesses; I'd love to hear the real story.

related: http://biology.stackexchange.com/questions/20400/what-are-the-buoyancy-control-mechanisms-of-chambered-nautilus

Nautilus falls under mollusks....this Q is about mammals...totally diff. mechanism...so can't be related..

@souvikbhattacharya I wrote related (not duplicate) as in related topic, not taxon.

From what I can tell, marine mammals can't dynamically control buoyancy during a dive. They ease the beginning of the dive by starting with a small lung volume to reduce buoyancy.
Pinnipeds like seals do this by exhaling half their breath before diving.
Deep-diving whales actually breathe in before diving, but their lungs are small relative to body size to begin with. This makes their surface buoyancy weak enough to swim against without great difficulty (unlike humans).
As they dive their lungs compress rapidly with depth:
V = Vs / (1 + D/10)

V is lung volume, Vs is lung volume at surface, and D is depth in meters.
At 90m, the lungs are already at 10% original volume. Pretty soon they've shrunk enough that their effect on buoyancy is negligible compared to the density of the incompressible tissues. Presumably, these are close to neutrally buoyant (though the fact that dead whales sink suggests that they're slightly negatively buoyant).
Thanks to @souvik-bhattacharya for the ucsc.edu link.

This  scenario is called neutral buoyancy, and it's what marine mammals have, so it doesn't take energy for them to stay still in the water, and it's not particularly hard for them to go up or down when they want to either.
Imagine an animal that is as dense as a rock trying to swim up for air, or one that has low density, like a balloon, trying to dive down to find food; it would take a lot more energy to counteract that net buoyancy-weight force (up or down) than it would if that net buoyancy-weight force was 0. So by having neutral buoyancy, marine mammals save energy.
And how do they achieve neutral buoyancy?
They have more fat in their bodies (fat is less dense than water), It also helps that saltwater is a little more dense than pure water, so the buoyant force is a little stronger.
So...as you predicted...neutral buoyancy helps them, but not by inhaling specific amount of air...instead one can say that's their inherent property...

Neutral buoyancy is not an "inherent property" of any soft body that contains a compressible fluid (air).

@SuperElectric , what I meant is that they don't need the help of any external component like air to maintain their neutral buoyancy....also if I go by technical details...during a dive the body of a mammal virtually becomes incompressible with Air cavities, lined with venous plexuses, filling at depth,along with lungs, thus obliterating the air space.

Lungs with a volume Vs at the surface will have volume V = Vs/(0.1 D) at depth, where D is the depth in meters. Buoyancy force B is proportional to V. Therefore it's true that buoyancy becomes less sensitive to depth the deeper you get (lim D->inf dB/dD = 0). So for the operating depths of, say, sperm whales it may not matter as much... but only once they've achieved that depth. If they wish to achieve neutral buoyancy at 1000 meters, they will be extremely buoyant at 0 meters, making it quite a chore to swim down to that depth. This seems like a wasteful aerobic excercise.

One workaround would be to exhale as much as possible before diving, so that lung volume V is a small component of overall buoyancy of the body to begin with. This means relying only on the oxygen reserves dissolved in the blood, which won't compress. That's just one guess, though, and I'd appreciate more expert opinion.

Your guess is correct & for expert opinion go through this research article of University of California...http://bio.classes.ucsc.edu/bio131/Thometz%20Website/Ponganis%202011%20Diving%20Mammal%20Review.pdf ........hope this helps...

The only relevant passage seems to be "Cetaceans appear to dive on inspiration, while pinnipeds usually dive on expiration", which doesn't really answer the question of how whales are able to dive with lungs full of air.

Ok, figured it out. Whale lungs are small to begin with: http://www.catalyststudent.org.uk/dl/14429127b24f101e437528772fcc3a94b4508002/272-catalyst_22_2_500.pdf Thanks for the link; will use it in the answer.


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Why doesn’t p53 cause the repair of cellular DNA that has been altered experimentally?
When scientists mutate bacteria or even embryos of lambs and other animals, why doesn't the p53 reverse whatever mutation the scientists cause? I know that the p53 stops the DNA from mutating and since the restriction enzymes essentially mutate the DNA, why doesn't the p53 stop it? Does the p53 gene have to be temporarily turned off?

You seem confused. Explain why you would expect p53 to do this from what you know about it. Then we can address your misconception.

@David Is this better?

Yes. Anyone who knows about p53 (not me) will be able to focus on your concern.

I have altered your title, which was misleading in its mention of restriction enzymes, and hope that this has made it clearer and more likely to attract answers other than my own.

I am no expert in this area, and this answer is only based on a reading of the Wikipedia article on p53, which you should perhaps have read carefully. I welcome edits or correction by persons more knowledgeable than me on this topic.
First, although the Wikipedia article neglects to mention it, you can forget about bacteria as the protein is only found in eukaryotes.
Second, one needs to consider what exactly p53 does in relation to protection of DNA from mutation, how it is activated to do this, and hence whether this would occur in the circumstances of the introduction of mutated DNA into a eukaryotic genome.
From the article it appears that “It (p53) can activate DNA repair proteins when DNA has sustained damage”, and that “p53 becomes activated in response to… stressors, including… DNA damage (induced by either UV, IR, or chemical agents such as hydrogen peroxide)…”
The manipulation of animal DNA will be performed outside of the target organism, and the modified DNA re-introduced into the genome by one of several mechanisms that are unlikely to evoke the stress signals that are evoked by agents that damage DNA ‘naturally’. Hence there is no reason to expect the activation and action of p53 in response to this type of experiment.


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Analyzing Messy Data Files
I was writing some code scripts to analyze some plasmodium spp. using this database. However the names assigned to the various epitopes and other items on the list is very very very disorganized. In some places there are acronyms and other places the full name. Sometimes hyphens replace the spaces for the same epitope name. So I was trying to collect lists of all the different names that are actually synonyms of each other. However there were some words that were added on sometimes that I wasn't sure would count as synonyms:

"xxx" and "xxx, putative" synonyms?
"xxx" and "xxx like antigen" synonyms? (this one made little sense to me as both are epitopes
"xxx" and "xxx 1" synonyms?
"xxx" and "xxx partial" close enough to    be synonyms for sake of
grouping?

I'm rather new at analyzing these sorts of databases. I'm sure I'll find other such messy naming issues and was wondering how to approach such a problem and solve such discrepancies.

The answer of David explains most of the common/general problems you encountered and how to tackle them. In case you don't have anyone more experienced to consult, I'll try to give suggestions for the specific cases you mentioned.

"xxx" and "xxx, putative"
These might synonyms, but the 'putative' indicates that the authors of the entry weren't sure themselves. If you want robust results don't group these together (or exclude the putative ones). If you need more samples, group them but maybe test how much difference it makes.
"xxx" and "xxx like antigen"
I think it's quite likely that many of these will not be synonyms. Many genes and proteins are named after similar known ones ('xxx' - known; 'xxx like' - new gene), but that doesn't mean they have related functions.
"xxx" and "xxx 1"
These could be synonyms. I don't know any examples where two different genes/proteins named like this exist. To be save you should check this on a case by case basis and look up both versions on uniprot or NCBI.
"xxx" and "xxx partial"
You can group these together. You're dealing with peptide  antigens, so fragments of proteins. Therefore partial proteins are not a problem.

Thanks! This answer helped a lot! Both of your answers did! :)

It’s not the fault of the database, it’s the fault of the individual scientists that described the epitopes. O.K. in a perfect world the curators would have gone through the entries and tried to standardize the descriptions. But they probably lack the time or expertise. I sympathize with them.
So what can you do? You have to use your own expertise or that of experimental scientists you are working with and make your own decisions, some of which will be incorrect.
This is a general problem with databases compiled from papers or individual submissions, and is a headache for data mining: misspellings, spaces or no spaces, hyphenated or not, different names for the same entity. Unfortunately there’s no fairy with a magic wand to solve the problem for you.

Thanks! I wish there were some kind of dictionary at least that kind of outlined some of the basic terminology(like when to use and when not to). I guess I've been spoiled by IUPAC in orgochem.


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Identity and similarity for Multiple Sequence Alignment (MSA) of proteins
I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am using T-Coffee to do the alignment. I would like to have some numerical descriptors of the different sequences and I have been told to include the percentage of similarity and identity. How can I compute them? Is there an on-line tools to do this? Thank you.

I've never used T-Coffee but it looks like the web-server version gives you a total score as well as a score for each individual sequence; do you know if those numbers are related to the numerical descriptors you need?
A good place to start would be to read the documentation. Another good place to look would be the Google Groups page for T-Coffee.

Thanks you for the reply. I just finished reading the documentation. I found out that I can use Chimera to see the percentage of identity, so one problem is solved. The main problem is of a different nature: let's say that I have the MSA from residue 1 to 100 of the query. I would like to have a tool that automatically computes the number of insertions, deletions etc... Some numerical quantities that I can use to see if the alignment is good and how much. Thank you.

It would appear that this answer solved the user's question. His comment includes an additional question which is not relevant. I have therefore upvoted it in response to the Cummunity homepage bump.