Meaning of units in ELISA based tests? For some ELISA based antibody tests (e.g. h-tTg antibody test), labs report units as RU/mL or U/mL. Also different labs have different cut off (normal range) values.

I understand that different kit manufacturers recommend different ranges because the units are not standardized (e.g. IU/mL) for enzyme activity concerned. But I didn't understand the difference between RU, U and AU

Question
Is there a difference between RU/mL, AU/mL and U/mL? Are the figures comparable across reports from different labs (which may be using different kits)?

The ELISA kits are calibrated to meet the requirements of
  internationally certified laboratories such as Center for Biologics
  Evaluation and Research (CBER) associated with FDA. In most cases, the
  presence and specific concentration of an antigen is the target for
  the measurements. Such measurements take place through the absorbance
  measurement. According to the Beer-Lambert law, concentration of a
  compound in a solution is proportional to the quantity of light
  absorbed at its specific wavelength and at a constant optical
  path-length. Following absorbance measurement, a simple calculation
  leads to the concentration of the analyte via equation below:

  A = εlc

  where A is absorbance of the solution at the particular wavelength, ε
  is the molar absorptivity, l is the path length or deepness of the
  solution (which for common spectrophotometers is 1 cm or less if a
  well plate reader is employed), and c is the concentration of the
  substrate in the reaction solution (M or mol/dm3). Majority
  of ELISA microplate readers correspond to this method for the
  calculation of the analyte concentration. Introducing standard
  solutions with known analyte concentrations can be the basis of such
  calculations for the instrument. Measurement unit are typically
  expressed in gram per liter (g/l), mol per liter (mol/l) and copies
  per milliliter (copies/ml) for nucleotides, plaque forming units per
  milliliter (pfu/ml) for infectious viruses, colony forming units per
  milliliter (cfu/ml) for cells and phages, as well as unit per
  milliliter (u/ml) for specific enzymes. These measurement units can be
  also reported over time (i.e. ng/ml/h). Relative units (RU/ml) or
  equivalent units (Eq/ml) are normally used if no international
  standard references exist for the conversion.

Source: Enzyme-linked Immunosorbent Assay (ELISA): From A to Z (SpringerBriefs in Applied Sciences and Technology) by Samira Hosseini, Patricia Vázquez-Villegas, et al. | Dec 31, 2017; ISBN-13: 978-9811067655; ISBN-10: 9811067651. Page 65.

Contrary, Units Per Millilitre (U/mL) are normally used when there are international standard references, agreed upon by scientists and doctors.

Please find the following information on Arbitrary Units (AU):

  The WHO Expert Committee on Biological Standardization (ECBS) is the
  scientific body that establishes WHO biological reference standards
  which serve to define an internationally agreed unit to allow
  comparison of biological measurements worldwide. WHO International
  Standards (IS) for biological substances are recognized as the highest
  order of reference materials for biological substances and they are
  assigned potencies in International Units (IU). International
  Standards are used to quantify the amount of biological activity
  present in a sample in terms of the IU, allowing comparisons between
  assays from different laboratories.  Calibration of assays using
  System of Units (SI)units is not appropriate given the variability of
  the specific activity of a biological material. Use of an arbitrary
  unit makes it possible to better define parameters such as the
  analytical sensitivity of tests or clinical parameters such as
  protective levels of antibody.

Usually, arbitrary units are defined within a particular study. For example:

  A human serum pool positive for anti-dsDNA IgG antibodies (DNAPo) was
  prepared by mixing equal parts of serum from 10 patients with SLE who
  had a positive CLIFT test ≥ 1:640. The DNAPo was arbitrarily designed
  as having 100 arbitrary antibody units (AU) per ml. Artificial serum
  standards containing different AU/ml were prepared by diluting the
  DNAPo with phosphate-buffered saline (PBS) containing 0.1% Tween 20
  (PBS-T). A human serum pool negative for anti-dsDNA IgG antibodies
  (DNANe) was prepared by mixing equal parts of serum from 10 healthy
  persons who had a negative CLIFT test and no clinical evidence of SLE.
  The DNAPo and DNANe pools were used as positive and negative controls
  in the ELISA and CLIFT reactions.

Thus, the U/mL figures are comparable, while RU/ml or AU/ml are not.


How do the flowers of Diphylleia grayi become transparent after rain? Known as the skeleton flower, its flowers turn transparent in rain. How does it do so? How can it gain transparency in rain when water is already present in flower? Or is it because other components present in the rain? Also is there any  advantage of this for the plant? I research using Google, but I couldn't find an answer.

YouTube

I have to hypthesise here:

the white colour you perceive is most likely near-to-full diffusion (or possibly better phrased: reflection with effectively undirected refraction due to multiple reflections) of light by structures on the surface of the petals and/or air space encapsulated in the petals. (This is true for most white flowers, by the way.)

Water fills the structures and/or the air space, which changes the refractive index of the petal surface.

In other words: the flower becomes like water, because the air is driven out.

Edit: seems I was right. SE asked me to add links to my answer, so I asked GoogleScholar about D. grayi and found this: "The inner part of the petal comprises numerous lacunae and intercellular spaces that are filled with air."
(source: Yong et al. (2015). Bioinspired transparent underwater superoleophobic and anti-oil surfaces. Journal of Materials Chemistry A, 3(18), 9379-9384.)


Definition of "Niche Complementarity" What does "Niche Complementarity" mean?

On this website they define "Niche Complementarity" as:

  The tendency for coexisting species which occupy a similar position along one niche dimension

I don't quite understand this definition. The tendency to do what?

Notes:

I know what is an ecological niche and therefore what is a niche dimension. There is no need to define this.
I am particularly interested in the use of this concept in speciation and adaptive radiation.

There is a really good discussion of this in Chesson & Kuang Nature 2008, they propose a way to measure niche complementarity accounting for competition and predation.


How does high-fidelity of DNA replication depend on the formation of hydrogen bonds? Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here?

Binding of the triphosphate group to the active site of DNA polymerase triggers a conformational change. Changing a conserved Tyr residue increases the error rate by 40 fold.

I don't quite understand the above two statements. Can anyone explain in detail to me? Thanks!

DNA polymerase must catalyse the addition of 4 different nucleotides to the growing strand. This means that it cannot directly determine which base to incorporate at a specific point (how would it 'know' which base to incorporate and how it would it change its specificity for different bases). This means that the specificity for which base pair to incorporate is dependent on the template DNA strand.

Correct Watson-Crick base pairing (that is, hydrogen bonding) between the template strand and the nucleotide to be incorporated triggers the closing of the finger domain of DNAP around the primer-template junction and positions the latter in the optimal position for catalysis (with the $\ce{\alpha-PO_4}$ of the incoming nucleotide near the $\ce{3'-OH}$ of the primer for a nucleophilic attack catalysed by two $\ce{Mg^{2+}}$ ions). This is where the conserved tyrosine residue you mentioned comes into play. An incorrectly paired nucleotide will not trigger this conformational change and will not be positioned optimally, thus catalysis is less likely.

Furthermore, the DNA polymerase makes contacts with the minor groove of the primer-template junction through hydrogen bonds. This interaction is not base-specific (all Watson-Crick base pairs have he same pattern of hydrogen-bond acceptors in the minor groove) but only occurs when the correct nucleotide is incorporated, thus stabilising the complex.

Finally, discrimination between ribonucleotides and deoxyribonucleotides is done by steric exclusion of the $\ce{2'-OH}$ by amino acid residues in the binding pocket.

These factors can be thought of as kinetic proofreading as they simply slow down the reaction rate and provide time for an incorrectly paired nucleotide to dissociate. However, they can still be incorporated and many DNA polymerases have a $\ce{3'->5'}$ proofreading exonuclease that can remove incorrectly paired nucleotides. This proofreading is again mediated by interactions between the DNAP and the primer-template junction (ie hydrogen bonding with the minor groove). A weakened interaction due to an incorrectly paired base reduces the affinity between DNA and the catalytic site and increases the affinity between DNA and the proofreading site (because it has a preference for cleaving ssDNA from the 3' end).


ID a marine creature found on a beach on the US east Coast While walking on a marshy beach, I found this creature. It has no eyes, no feet, no fin, no gills. The only thing I know is that the skin lightly contracts. I found at least three of these. It is basically carried around by water.

Found this on a Maryland beach, roughly 150 miles east of Washington D.C.

It's positively a sea anemone. It retracts the tentacles when disturbed and become quite rigid. It's hard to identify it in this condition, leave it for a whlie in a jar with sea water and you'll see.


Vine To Tree Root Grafting I am experimenting with grafting multiple heartleaf philodendrons(philodendron cordatum) to the root of an oak tree(quercus). If the grafting is successful, the next step is to cut the root from the trunk, cap it, and place it in a long rectangular potter. The experiment to follow this will be to sustain the tree root with the philodendrons, and symbiotically use the philodendrons to sustain the tree root. Does anyone have experience in this type of experimental research and advice to provide?

I don't think this will work. Grafting will usually work between the same species and sometimes between the same genus. You're talking about grafting Philodendron cordatum to Quercus robur. The former is a tree from Europe, the latter a flowering plant from Brazil. They aren't compatible in the slightest. The graft will never take.

One possible route you might want to consider that may be more successful, but a lot more difficult, is using agrobacterium tumefaciens to infect a mix of cells from the two species. If you have a homogeneous mix of individual cells in culture, infect it with A. tumefaciens, the resulting gall will contain cells from both (incompatible) species. How they grow from there is unknown.


Why are there "Old World" and "New World" families? I've been reading on biological classification of the animal kingdom and have come across the New World and Old World terms a few times when they are applied to ranks (family, as much as I could find). Some examples of what I mean:

Old World porcupine vs. New World porcupine.
Old World rats and mice vs. New World rats and mice.
Old World vulture vs. New World vulture.

Old World X and New World X are usually not considered closely related. I assume this is because (at least partially) they evolved separately long enough to be distinct, if they were even related (at a non-trivial level) to begin with.

Is this naming scheme only thanks to convergent evolution? Researchers found families (or species etc.) in the new world that look like families in the old world and called them New World X, which prompted the other to be Old World X? I understand that a good deal of this classification was done in the 19th century when diagnosis tools were limited and conventions varied.

Yes, I think this is exactly right in the three cases you mention, convergent evolution noticed by the humans who were doing the naming. There are other cases (Remi.b mentions simians) where the "Old World" and "New World" versions are sister clades that became geographically isolated from each other.


How to combine gene set enrichment analysis with hierarchical clustering? I would like to find out how to combine gene set enrichment analysis with hierarchical clustering. The motivation for this combination is that potentially
too many gene-set symbols for leukemia may pass the p-value significance threshold. We are using an R-package for fast preranked gene set enrichment analysis (GSEA) with the URL, https://github.com/ctlab/fgsea.

Subsequent to the fast gene set enrichment analysis on a ranked list of gene symbols with different expression t-statistics, we specifically need to identify gene-set symbols belonging to a common functional group using the R language hclust function intended for supervised hierarchical clustering with a Euclidean distance between features in a timely manner, for example 15 or fewer minutes.

Quoting from Alan Moses 2017 book, "Statistical Modeling and Machine Learning for Molecular Biology" , "Clustering is meant for exploratory data analysis and therefore doesn't really have a strong framework for hypothesis testing".A new R package ClusterProfiler provides enrichment analysis of gene clusters as reported in this URL,  http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/

The fact that most quality measures found in the literature have been conceived to evaluate non-overlapping clusterings, even when most real-life problems are better modeled using overlapping clustering algorithms is analyzed
in detail in the following paper and University of Texas Ph.D thesis

Academic paper: CICE-BCubed: A New Evaluation Measure for Overlapping Clustering Algorithms. Available from: https://www.researchgate.net/publication/260421976_CICE-BCubed_A_New_Evaluation_Measure_for_Overlapping_Clustering_Algorithms [accessed Apr 16, 2017].

and

https://repositories.lib.utexas.edu/bitstream/handle/2152/ETD-UT-2010-08-2022/KRUMPELMAN-DISSERTATION.pdf?sequence=1&isAllowed=y

As I am a novice to this type of bioinformatics research, please correct any inaccuracies in my problem statement.

You can try Enrichr for enrichment analysis. On 'Results' page you can use Clustergram view.
Or you can upload your results to Clustergrammer itself.


Yeast contamination with fungus patch I am working on yeast mutant and I am observing their sporulation efficiency on agar plates. One of my plates got some dark green small fungus patches. I can't grow yeast again and dump this one with fungus because I am counting at a specific time interval to compare and it will take a lot of time to go through the entire process.

What should I do? Should I remove fungus from scalpel? And does this fungus going to affect the yeast growth?

Either you can cut out the fungus and get away with it, or the fungus will rapidly overgrow your plate regardless.  You might as well try to cut out the fungus.  If it overgrows your plate the experiment with that plate is done.

This is why you should have parallel plates for this sort of experiment.  There is a saying: don't put all of your eggs in one basket.  The reason is that if you sit on that basket all eggs are broken.  If you are counting on just one plate for your experiment and you sit on it, or it gets overgrown with fungus you must start over.

The other reason to have several parallel plates going is that you can average the spore count.  One plate might have more or less for some random reason, like fungus.  But if you have several and average them out you will reduce noise.


What is the difference between the Modern Synthesis and the Extended Synthesis? The NCBI talks about "Evolution beyond neo-Darwinism: a new conceptual framework." (source).

What is the difference between the Modern Synthesis and the Extended Synthesis?

The term Extended Synthesis has been invented very recently and the concept was defended in these two papers

Laland et al. 2014
Laland et al. 2015

I read each paper when it came out and haven't reread them since. Here is a short summary of what I remember.

Those who want to use term Extended Synthesis

In short, they are arguing new findings have extended our understanding of evolutionary biology so much so that we should rename our theory of evolution. The main findings they are talking about concern the field of evo-devo (merging Evolutionary biology and Developmental biology). The subjects that they consider having radically advanced our understanding of evolutionary biology include niche construction and inheritance of niche, developmental bias, plasticity, cultural evolution and epigenetics.

Those who do not want to use term Extended Synthesis

We have discussed both papers in groups in my department and in short, we pretty much all ended up saying that:

It is true that our understanding of evolutionary processes have advanced a lot since the time of Wright, Fisher, Muller, Kimura, and others. However...

There is no important enough rethinking that deserves a renaming of our Theory of Evolution
Most arguments are based on rephrasing of old concept without bringing anything new. This is especially obvious when reading the 2015 paper.
Do we really care about this debate anyway? It is just a name!

Reading

I recommend reading the 2014 paper as 1) offer both point of views and 2) is pretty short.

Note

I do not know your level of knowledge in evolutionary biology but it might be a pretty bad idea to start with complicated subjects such as evo-devo, niche construction, epigenetics, developmental bias, etc...


What is the ratio of head to waist and waist to floor of the human anatomy? I'm trying to find the ratio of upper body to lower body. That is, the ratio of the length of the waist to the head over the length of the waist to the floor.

It's been harder to track down a readable outline of the ratios of the human body than I expected.

The study of those measures is called anthropometry. Typing anthropometry on google image returned this

This is definitely not a peer-review source and might eventually be a good approximation only for white males (or whoever they considered to take these measurements on) but if we believe this image, then the ratio head-to-waist over waist-to-floor is $\frac{0.52}{0.485} = 1.072$.


Are all functions of a human cell known? Please bear with me as I'm intruding into your world from a computer science background.

In programming, once you have created a program, you know all functions of that program. Thus, 100% knowledge is achieved.

My question is, in the field of Biology, how much do we think we currently know about the human cell? Are all functions known (eg. 100%)? Are most functions known (60%)? Or do we know a miniscule proportion (1%~5%) of functions of a cell.

The reason I ask is I'm interested in the concept of simulating cells via computer. If we know about a given biological function of a cell, we could convert it into a mathematical function for use within a simulation. With simulations, you could simulate the cell's reactions to drugs, viruses, cell garbage cleanup, etc, based on it's defined functions. And the more functions we know about human cells, the better the simulation.

Thanks in advance.

As someone who has dabbled in both biology and programming, I assume you are referring to the theoritical ability  of functional programming to simulate organic behaviour from well defined input. From that point of view, our comprehension of the human cell behaviour is  currently near stone age level.
The astounding diversity of homeostatic and signaling parameters in our body makes a realistic simulation of human cell normal behaviour largely out of reach, so don't even think about patholgic states.

The more data we will acquire, the more precise our simulations will be. Currently, our data acquisition methods are too primitive, and clearly are not deterministic enough to base computed simulations upon them.

Of course, this answer reflects my own opinion, but I dare think that most of my colleagues will adhere to that view.


Why do genes, encoding the same proteins and in the same conditions, have different expression? Is it possible that two genes, which come from two different cell cultures and which encodes the same protein, produces different quantity of mRNA? If yes, why?
My question comes from the fact that I am doing statistical analysis of a microarray dataset for the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation. Microarray experiments measure relative quantities of mRNA in a cell. My file has values, for each gene of the genome, that are positive or negative since the scientists who performed the experiment made the log10 ratio between the fluorescence intensity of the sample that was irradiated and the reference sample (not irradiated). Indeed, in the microarray experiment we have two channels that typically are one for the "controls" and the other for the cells which are stimulated by an event (in this case the event is gamma irradiation), in order to make a comparison.
In my dataset there are two columns (that are indicated as "reference") that refer to the case in which they should have put the cell cultures not irradiated in both the two channels. I would expect that the values in the file corresponding to these two columns are 0 (since they are the log10 ratio between the intensities of the signals of the genes which encode the same protein and that are in the same conditions). Instead they are different from 0. Therefore I wonder what is the reason for which there is different quantity of mRNA produced from two equal genes?
I made a graph of relative mRNA produced (calculated as I explained before) vs time, in which you can notice that the relative mRNA produced of the reference  (I called them as "Ref" on the horizonal axis) is not 0.

Is it only due to some noise or are there biological reasons ? (the picture refers to a gene which encodes Ferritin-like proteins but it is the same story also for other genes).
Even though I think that my interpretation of the data is correct, I tell you that the dataset I am talking about is here, if you want to have a look.

If I understand your question and graph correctly, your Y-axis is log(x/REF), where REF is some external standard. Your "Ref" on the x-axis you expect to be the same as REF, so that log(Ref/REF) "should be" zero, but you find it is not.
However, it looks like the mean(log(Ref/REF)) is still approximately zero. This is what I would expect: values that deviate a bit from perfectly 0, but having an average around 0 (and this average should approach 0 the more samples you have per the law of large numbers). You don't expect to have zero variance in data like this, which is why you repeat the experiment a number of times. You'll notice you have variance in all of your categories.


Risks in bacterial phage therapy I just finished reading J. Craig Venter's book Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. The book is a little over a year old now, and Venter has an optimistic outlook that bacteriophage therapy will become an effective alternative to gene therapy and viral immunotherapy. He mentioned that the JCVI (J. Craig Venter Institute) is working on such projects. Are other companies also researching, and has progress been made? What are the expected risks? How can rogue, harmful phage mutations be controlled? Can this type of therapy be applied to cancers?

The Eliava Institute in Tiflis (Georgia (a country)) has been at it since the 1930`s. A US company sells a phageproduct for desinfection of meat.

The risk of Phagetherapy is there, if the phage is ill choosen or contaminated with other phage it could introduce pathogenic genes to the target or other bacteria.

If those risks are eliminated there is very little risk in phage therapy aside from the fact that it may not work at all. Phagetherapy is most useful in regions where bacteria are normally found, in other places the immunesystem will make short work of it.

The faster and cheaper sequencing gets the more effective phagetherapy will become. Since a "bad" bacteria can quickly be isolated and a proper "phage cocktail" can be prepared. If we get to the point that we can sequence the whole microbiom of a person then i bet that Phagetherapy will be a very normal thing.

To your cancer question, i think its rather hard to apply it to cancer therapy except if u are looking to combat the cancer with a Intracellular bacteria...but then again. How u get the phage to it.

A excellent read on this topic is the Book "the bacteriophages".


How can I accurately measure glucose concentration in culture media? I am trying to identify the best way to measure glucose concentration in culture media with E. coli. Now, I imagine I can use those glucose meters that diabetic people use, but unfortunately can't find any papers as background.
Any ideas would be appreciated.

The most common method of measuring glucose concentrations (in pretty much any sample) is an enzymatic assay based on the glucose oxidase enzyme. This method is reliable because the enzyme is known to be quite specific for glucose; it does not oxidize fructose, galactose, or any of the other common hexose sugars which can contaminate many other measurement methods. The enzyme can be coupled to other reactions so that the amount of glucose oxidized can be read out by a standard spectrophotometer. There are many kits commercially available based on this principle, like this one. A review of glucose oxidase from the glucose measurement perspective is found here.

Blood glucose analyzers are also based on glucose oxidase. Typically, they have disposable slips that contain glucose oxidase along with some electron-carrying chemicals that convert enzyme activity into an electrical current sensed by the device. It is possible to measure glucose in pretty much any solution with such insruments, but as mentioned in comments, you need to make a calibration curve for glucose in your solution of interest (culture medium, or whatever), as you cannot trust the readings from the instrument directly when measuring under different conditions. We have previously used this approach to measure glucose in mammalian cell culture medium, and it works fine in our hands.

It is also possible to quantify glucose by mass spectrometry or nucleic magnetic resonance methods, but unless you have such a facility and expert help, I guess that is not an option in this case.


Best method to cure cancer as of now? I am not talking about chemotherapy or radiotherapy. So, if it exists, what is the best biological technique to cure cancer as of now?

There is no general therapy for cancer - as there is no general cancer. Cancer is the umbrella term for a disease where you have body cells growing without control, leading eventually to death. But since there is a wide variety of cells in the body, there is also a very wide variety of different cancers.

To treat these, surgery is often the first line of therapy. For some cancers this is already sufficient to cure the patient, examples are skin cancers (not only melanoma but the other forms as well) where you can cure a very high potion of the patients. This only works for early forms of the cancers when there are no metatases present.

Besides this, additional therapies are used - as you said yourself chemotherapy in the different forms as well as radiation therapy. Chemotherapy is given systemically and targets fast growing cells (cancer cells have these properties) and causes mutations or other problems which let the cancer cells eventually die. Radiation works with the same principle, but is more focussed.

Relatively new therapies are the targeted therapies where the treatment uses the occurance of certain common mutations. An example would be the mutated BRAF kinase in melanoma (and also in a number of other cancers) which can be specifically inhibited with an inhibitor. This avoids a lot of problems general adverse effects of the drugs. Additionally immune therapies are also new which use antibodies against surface receptors of T cells to prevent their inactivation. These T cells then attack the tumor.

These are all non-biological treatments. More biological ones are modified oncolytic viruses. In this therapy you inject genetically modified viruses which preferrably infect the tumor and then destroy it. These are relatively new, but an interesting option. See references 1 and 2.

An old method is the usage of bacteria to treat tumors - the first obervations on this where done in the late 19th century, see reference 3 for more information and a lot of further references.

A number of the chemotherapeutic drugs used today are originated from nature, but are today synthesized and used in a pure form and not isolated from their origin anymore. Examples would be vincristine, irinotecan, etoposide, and paclitaxel. See references 4 and 5 for details.

Besides this, there are no effective "natural" cancer cures, despite the claims of several "alternative medicine people". These are either based on wrong assumptions of biology or wrong ideas like Homeopathy.

References:

Advertisement Oncolytic Viruses and Their Application to Cancer
Immunotherapy
Oncolytic viruses: a new class of immunotherapy drugs
Strategies using bacteria to target tumors
Anti-inflammatory and anticancer drugs from nature.
Drugs From Nature, Then and Now


How are chickens affected by light? When I was young, I was told never to put a fluorescent light in a hen house because it continuously turns on and off. Extra lighting is used, as far as I know, to 'extend' a chicken's day. Human eyes don't have the refresh frequency to notice that, but there are animals who have a frame-rate of up to 200 Hz (so they actually see the lights turn off and back on again). I was told chickens are among those animals and that they'd stop laying eggs when continuously exposed to interrupted lighting.

However, my neighbour has fluorescent lighting in his hen house. So either the above is bogus, or I have my facts mixed up. So, how (if at all) are chickens affected by light?

It seems like they are not affected by fluorescent light frequency. I did not find anything about their visual sampling rate. Their hearing is between 0-200Hz with an average of 86Hz so I guess the visual sampling rate is under this, but that's just a guess.

  We conclude that at the illumination levels used in this experiment,
  the hens did not perceive the flicker of low-frequency light or they
  perceived it but did not find it aversive. Low-frequency fluorescent
  light does not appear to adversely affect the welfare of hens.

1996 - Laying hens do not have a preference for high-frequency versus low-frequency compact fluorescent light sources

  It concludes that there is no evidence that fluorescent or high
  pressure sodium lighting, irrespective of intensity or spectral
  distribution, has any consistent detrimental effect on growth, food
  utilization, reproductive performance, mortality, behaviour or live
  bird quality in either domestic fowl or turkeys, nor in the egg
  production of geese.

1998 - Responses of domestic poultry to various light sources

A monochromatic (LED) light can be more beneficial according to this:

  A significant reduction in egg production was observed in all 880nm
  groups; no differences in egg production and quality were found in the
  other groups. Feed consumption was significantly lower by 7% in all
  0.01 W/m2 groups. We suggest that an important reduction in rearing costs of laying hens may be obtained by using this system.

1998 - New monochromatic light source for laying hens


Role of Melatonin in Circadian Rhythm Melatonin regulates the wake-sleep cycle by causing drowsiness and lowering body temperature, but which specific chemical pathways lead to this drowsiness?

This is a quite complicated question, as melatonin has quite a range of effects on the cells. First, melatonin binds to three different melatonin receptors, which are found in a wide variety of tissues or organs including brain and retina, cardiovascular system, liver and gallbladder, intestine, kidney, immune cells, adipocytes, prostate and breast epithelial cells, ovary/granulosa cells, myometrium, and skin.

Two of the receptors a G-protein coupled receptors (GPCR), the MT1 and MT2 receptors. The third is a quinone reductase called QR2.

For more details, see this papers:

Melatonin receptors in humans: biological role and clinical
relevance.
Melatonin receptors and their regulation: biochemical and structural
mechanisms.

The role of melatonin is pretty broad, see the figure (from this article:"Melatonin: Nature's most versatile biological signal?")

The receptors transport the outside chemical signal (the melatonin) to the inside and activate (or repress) a number of different signal transduction pathways. See the figure below (taken from Qiagen):

This includes MAP-Kinase pathways, proteinkinase C, IP3, adenyl cyclase and so on. This is quite complicated and I recommend reading some of the following articles if you are interested in a deeper insight. Finally these signals are transmitted into the nucleus and result in a changed gene regulation/expression.

Melatonin receptors, heterodimerization, signal transduction and
binding sites: what's new?
Physiological effects of melatonin: role of melatonin receptors and
signal transduction pathways.


Problem: What is this pattern of inheritance? The following question was on a pretest of mine, and I'm trying to figure out the answer using what we've learned about Mendelian and non-Mendelian patterns of inheritance. I'm struggling quite a lot with this question; I'm not sure if that's because of me or if the question itself is poor/confusing.

I don't know what the answer actually is, as there was no answer key to go along with the exam. My best guess is that the pattern of inheritance is Incomplete Dominance based on the Red x Yellow cross and the fact that neither allele was dominant over the other in the resulting progeny. But is it even possible to state this with full confidence? What about the other crosses?

  In a plant species, plants may produce red, yellow, or orange flowers. The table below shows the results of crosses between the plants that produce each flower color.

  Based on this information, which pattern of inheritance controls flower color in this plant species?

  (A) Codominance

  (B) Complete dominance

  (C) Incomplete dominance

  (D) Multiple alleles

The answer is incomplete dominance.

It can't be codominance, because codiminance involves both phenotypes being expressed in different parts of the organism: you would end up with red and yellow spotted flowers.

It obviously isn't complete dominance, because the red x yellow cross produces orange flowers.

Knowing that it has to be incomplete dominance or multiple alleles, we can examine what we would expect to see in either of these cases.

Multiple alleles

In the case of multiple alleles, each individual plant has two alleles out of a possible three. These alleles will also express some sort of dominance pattern over each other. Let's say, hypothetically, that the dominance pattern goes Red > Orange > Yellow.

In this case, all of the yellow flowers would have a genotype of yellow/yellow. The orange flowers could be orange/yellow or orange/orange. Red flowers can be red/orange, red/yellow, or red/red. When performing the crosses between red and yellow, you would then expect some mixture of offspring, probably mostly red. If the dominance pattern was different, you would still expect to see some mixture of offspring. But instead we see only orange offspring.

Incomplete dominance

In this scenario, homozygote red individuals have a red phenotype, homozygote yellow individuals have a yellow phenotype, and heterozygous individuals have the mixed orange phenotype.

In this scenario, you would expect red x red to produce only red offspring, and the same goes for yellow x yellow, because both parents have to be homozygous. Orange x orange would produce offspring in a genotype ratio of 1:2:1, as is the case when you self-cross heterozygous organisms. Orange x red and orange x yellow will produce offspring in a 1:1 genotype ratio, as is the case when you cross a heterozygote with a homozygote. These are exactly the patterns we see, so we can conclude that the answer is incomplete dominance.


What is the gas inside a Capsicum pepper, and how does it get there? Every time I make fajitas, I cut into bell and chili peppers and notice how hollow they are.  I always think to myself: what is the gas inside this pepper, and how does it get there?

Perhaps Capsicum peppers are porous.  I did a little kitchen experiment to try to find out.  (I'm afraid I don't know much about biology, so this "experiment" is likely to be flawed in at least one basic way, but I figured I should at least try to figure it out myself before asking.)  Here's what I did:

I filled a small container with water and submerged an uncut Anaheim pepper.  It was quite buoyant!  I put the lid on the container so it would stay submerged.  It didn't seem to become any less buoyant, and its interior didn't seem to fill up with water.  No bubbles emerged from the pepper, as least as far as I could tell.

So air doesn't seem to easily pass in or out of the pepper.  And of course they don't grow around air, so how does the gas get in?

Here are my guesses:

The fruit is porous to air, but the holes are small enough that, in my experiment, they were sealed by the surface tension of the water.
The fully isn't porous to air when fully grown, but it is porous to air while it's still developing.
The fruit does some amount of photosynthesis, and the air is waste oxygen.

To answer your question of what the gas is, how about the glowing splint test for oxygen! I guess it might work with a recently snuffed out match too. Cut a plug in the the pepper but leave it in place until you have the glowing match ready, then quickly open the plug and hold the match into the opening. It should relight if it is oxygen and you may hear a popping noise.

As for whether the surface tension is preventing the flow of air, you could try adding some detergent (washing up liquid or soap) to the water to break the tension and see what happens.

However, I have found an article suggesting the environment is, compared to the standard atmospheric concentration anyway, low in O2 and high in CO2 in two different pepper cultivars.1

  Samples withdrawn from the fruit locule over time show that CO2 ranges between 0.5% and 3% (5000–30,000μmol·mol–1) (Fig. 2, top) while O2 ranges between 18% and 20% (Fig. 2, center), compared to the composition of standard atmosphere (400μmol·mol–1CO2; 21% O2)

1 Blasiak, J., Kuang, A., Farhangi, C.S., and Musgrave, M.E. Roles of Intra-fruit Oxygen and Carbon Dioxide in Controlling Pepper (Capsicum annuum L.) Seed Development and Storage Reserve Deposition. J. AMER. SOC. HORT. SCI. (2006) 131(1):164–173.


Does the Peptide bond produce water in our organism? According to Wikipedia http://en.wikipedia.org/wiki/Peptide_bond , when a peptide bond is made a water molecule is released as a secondary product.

So, my question is simple (perhaps silly). Considering that proteins are being made every time in our organisms and this water molecule is being released in every peptide bond, why our bodies are not flooded of water?

Thanks!

The simple answer is that there are literally thousands of chemical reactions (mediated by enzymes) going on in the cell. Some produce H2O, others consume it. For example, when proteins are broken down into their individual amino acids as part of normal turnover in the cell, a water molecule is necessary to break the peptide bond. Therefore, the overall balance of water produced vs. water consumed is fairly equal, especially when you take into consideration the consumption of water and its excretion via urine and sweat.


Correlation between morphology of neurons and neurotransmitters Are there known significant (positive or negative) statistical correlations between the morphology type of neurons and the neurotransmitters that they use (presynaptic, i.e. transmitters that are released, and postsynaptic, i.e. transmitters that are received)?

This question assumes, that a definite set of morphology types has been defined. The answer depends on this definition, of course.

Yes, at least for the neurotransmitters that a given cell releases.

As far as the neurotransmitters a cell responds to, you are really better off thinking in terms of receptor expression. Most neurons will express receptors for many different neurotransmitters. It's far too broad to go into them all in an answer here.

As far as the transmitters that cells release, morphological types of neurons are very often associated with release of particular neurotransmitters. In the cortex, for example, pyramidal cells principally release glutamate while there are potentially dozens of morphological types (again, depending on how you define them) that release GABA; in the cerebellum, Purkinje neurons release GABA whereas granule cells release glutamate.

However, be careful: some terms like "granule cell" don't really refer to a special morphological type. They are really just describing "small cells in close proximity": these can be completely different types in different brain regions. It really makes no sense to ask these types of questions for the brain as a whole, you have to study individual brain regions, each of which is organized quite differently from the others.


PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart? I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors.  I do this by predicting the location of Hydrogens on residues and then calculating how far these Hydrogens are from aromatic rings.  If a certain Hydrogen is <7.0 Angstroms from a certain aromatic ring, then I take it under consideration: I form the N-H vector, which is the vector created by the Hydrogen under question and the Nitrogen in the backbone of the residue that the Hydrogen belongs to.  I test that this N-H vector is pointing toward the plane of the aromatic ring, and I also test that the point of intersection between the plane of the aromatic and the N-H vector is within 6 Angstroms of the center of the aromatic ring.

If all of these conditions are met, then I consider it a Hydrogen bond between the Hydrogen and the aromatic ring.  However, my data must be incorrect, because I am seeing situations where a Hydrogen is < 1.0 Angstrom from the plane of the aromatic.  Atoms should not be getting that close to each other.

I thoroughly tested my method by hand using an example situation where my code identified one of the sidechain Hydrogens on an ASN is 0.3 Angstroms from the plane of the aromatic of a TRP.  Unfortunately, I could not find any bugs.  You can find a PDF of this verification here.

Any suggestions on how my method might be flawed would be greatly appreciated.

if you are using NMR structures you might be making the mistake of using several superimposed structures - it would be nice to develop with x-ray structures at less than 2.0 A resolution for starters.

Some of the models at low resolution can be sloppy, but submitted after 1994 or so will not have any center to center distances as that's when the x-ray structures used molecular models rather than just electron density rigorously and wierd steric violations in the structure should be rare.

Still, this might not be wrong - the hydrogen might be pointing right into the aromatic ring's center.  This has been observed quite a bit.  In such a case, the atom to ring plane distance might be very small.

You only need to worry if the center to center distance between atoms is less than the vanderWaals radius.   I would filter for atom center to center distance and see if you see violations.


When is an anatomic entity named "laterale" vs. "lateralis"? I'm trying to learn the latin names of anatomical entities and I have a hard time remembering whether it's "Os cuneiforme laterale" or "Os cuneiforme lateralis".

In that case it's "laterale". But in a case like "Nervus cutaneus antebrachii lateralis" it's "lateralis". What's the logic here? How do I remember the right one?

This is actually much more of a lesson in Latin linguistics/grammar.
The root, Lateral, comes ultimately from latus meaning “side" or "flank” in Latin. [Source].

By adding one of these suffixes we instead create an adjective meaning "of the side."

However, the suffixes differ in their inflection (specifically their gender):
Laterale has the neutral, singular suffix of the nominative 3rd declension.
Lateralis has the masculine, singular suffix of the nominative 3rd declension.

 Source: Wiktionary

The difference between the gender-assignment of these suffixes is due to Agreement.

[Agreement] happens when a word changes form depending on the other words to which it relates. It is an instance of inflection, and usually involves making the value of some grammatical category (such as gender or person) "agree" between varied words or parts of the sentence.

More specifically, adjectives must agree with the nouns they modify in case, number, and gender.

Let's break down each of these anatomical structures to understand the agreement-induced inflections [Source]:
os cuneiforme laterale - each of these words is neutral/singular:

os = noun, declension 3, nominative, neutral, singular
cuneiforme = adjective, declension 3, neutral, singular
laterale = adjective, declension 3, nominative, neutral, singular

nervus cutaneus antebrachii lateralis - the 2 adjectives match the  masculine/singular noun they describe:

nervus = noun, declension 2, nominative, masculine, singular
cutaneus = adjective, declension 2, nominative, masculine, singular
antebrachii = noun, declension 2, genitive, singular
lateralis = adjective, declension 3, nominative, masculine, singular

 Note: you see a shift to the genitive case for antebrachii because in this instance this phrase means "Lateral cutaneous nerve of the forearm."

Latin Linguistics  For Dummies:

Declension = category of nouns in Latin and Greek with broadly similar case formation (i.e., they are inflected/conjugated similarly).

Inflection = the modification of a word to express different grammatical categories such as tense, case, voice, aspect, person, number, gender, and mood.

Nominative = The case used to indicate the subject of a finite verb.

Genitive = The case used to express some relationship such as possession or origin. It corresponds roughly to the English preposition "of."


Can parents' learned traits be transmitted genetically? I am wondering whether a behavioral trait (e.g. fear or stress experienced in the lifetime of the parent) can be transmitted genetically to its offspring?

I understand that a behavioral tendency for stress acquired through evolutionary time can be transmitted from parent to child, but I'm wondering whether a trait not present before can be transmitted between 2 generations.

For example many studies claim that offsprings of holocaust survivors inherit psychopathological disorders. I'm wondering how this inheritance could occur genetically given such a short time period?

Strictly speaking no. There are ideas about cultural inheritance though that seem relevant here: see http://www.ncbi.nlm.nih.gov/pubmed/11425279.  Cultural inheritance theory uses the plasticity of the human brain as the evidence for the underlying genetics of culture.  I.e. we aren't born with the ability to speak English because our parents learned it but we have an the underlying brain structure that is controlled by genetics to learn cultural traits.  It seems far more likely that the phenomenon you describe with holocaust survivors is more related to some environmental effects (from their parents) than anything genetic.  In the comments stress hormones in pregnant mothers were mentioned.  Any impact these have on the offspring are not truly "genetic", they're termed "maternal effects" in the evolution literature.  In fact most selection studies go to great lengths to control for them or eliminate them.  They aren't truly genetic because these traits would never get passed down to the grandoffspring of the original mother.


Does pH affect Michaelis constant? I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in the 21.5. According to this paper, Fig. 2C, the normalized specific activity of the enzyme is about 70% at pH 6.3 and about 47% at pH 7. If I divide 34 mM at pH 6.3 by 0.7 (which should get me the optimum Km at the optimum pH of 5.5) and then multiply by 0.48, then I get 23 mM. However, the paper says Km is between 30 - 38 mM, so if I divide 30 and 38 separately by 0.7 and multiply by 0.47, I get 20 and 25.6 mM respectively. Because my value falls within this range, this then must mean that I have the right enzyme and the same result as the paper.

So my questions are:

When the paper says Km is "34 +/- 4 mM", can I assume that means the Km can be anywhere between 30 - 38 mM? I'm surprised to see how wide the range is. I assumed Km is usually just one value with a deviation of at most 0.1.
Do pH change Km values? I understand that pH changes the shape(s) of the enzyme and/or substrate. Therefore that must affect how much it wants to bind to the substrate. If the enzyme's desire to bind to a substrate decreases due to increase in pH, for example, that would mean more substrates are needed to surround the enzyme, thus increasing Km.
If pH does change Km, is this how I determine the Km value of a different pH value if the Km value at another pH is already known? I know that specific activity and Michaelis constant are different, but how much product can be converted per minute depends on how much the enzyme likes to bind to a substrate, which is represented by the Michaelis constant. Did my reasoning and calculation arrive at the right conclusion? If not, how is the calculation done?

From the derivation of Michaelis-Menten kinetics you can see that:

$$K_m=\frac{k_f + k_{cat}}{k_r}$$

Where $k_f$ and $k_r$ are binding and unbinding rate constants (for Enzyme-Substrate binding), respectively, and $k_{cat}$ is the turnover number. This is for the Quasi-Steady-State approximation (QSSA). For the equilibrium approximation:

$$K_m=\frac{k_f}{k_r}$$ which is same as the association constant.

In both the cases pH can affect the rate of binding and unbinding by affecting the affinity between the enzyme and the substrate. For example lets assume that the substrate binding site is negatively charged. Low pH would increase the electrostatic potential of the substrate binding site towards zero by affecting the ionization of the functional groups.

pH can also have indirect effects on the substrate binding site because it can modify the overall structure of the protein.

Many enzyme catalysed reactions involve acid-base catalysis i.e. there is a transfer of proton. In reactions like these, pH can affect $k_{cat}$.

  If pH does change Km, is this how I determine the Km value of a
  different pH value if the Km value at another pH is already known?

You can do that by making a Lineweaver-Burk plot for the changed pH.


blue/white screening - results are opposite as expected We inserted GFP-gene into plasmid Bluescript SK+, transformed E. coli with this construct, and then plated on an agar plate with Ampicillin and X-gal to do a blue/white screening. We got blue colonies and white colonies, and normally the white colonies are considered positive for the insert and the blue ones are negative for the insert.
The problem is that the results we got are actually the opposite. If we look at the plate under UV-light, we see that ALL the blue colonies are fluorescent, which means they actually produce the GFP, and ALL the white ones are not!! How would you explain this??
Thank you

Edit: i thought that maybe the insert could be in frame with lacz', so we get fusion proteins. However this doesn't explain why we got white colonies which are not fluorescent

Given the fact that the negative control uncut plasmids are producing white colonies, it seems that there have been significant mutations within the lacZ gene in the plasmid, causing the uncut plasmids to become white due to inactivation of the gene.

I would suggest purchasing a new batch of pBluescript, or if that is not possible for whatever reason, perform a miniprep on one of the blue colonies and sequence its multiple cloning site to verify that the MCS is present and not mutated before continuing. If you are not going to buy a new batch of plasmids, it would also be prudent to verify the plasmid's length using gel electrophoresis.

The most likely explanation is that the plasmids are mutated, and therefore you are getting bad results in the blue/white screen.


Why are there no multicellular prokaryotes Why don't complex multicellular prokaryotes exist and also what makes eukaryotes multicellular?

Why are there no multicellular prokaryotes?

From a Molecular Cell Biology introduction course web resource from the University of Illinios, which explains the general sentiment in microbiology over this question:

There are lots of unicellular eukaryotes, including amoebas, paramecium, yeast, and so on. As to whether there are multicellular prokaryotes, the standard answer is No, but there is a lot of evidence that some bacterial species can aggregate together and divide labor so that the "colony" is working more efficiently. This is characteristic of any traditional multicellular organism, but there's still a lot of resistance to the idea of calling these prokaryotes "multicellular."

Here's a Scientific American article on the subject, which is good for the layman and will add to your understanding. Note that the most complex 'multicellular prokaryotes' known do not form comparably large or complicated structures when contrasted with eukaryotes. Even though prokaryotes have more biochemical tools available to them, their largest multicellular specimen pales in comparison to our small multicellular eukaryotes, let alone out large eukaryotes like the Armillaria ostoyae fungus in Oregon (nicknamed "the largest organism on Earth"), giant sequoia trees, the dinosaurs, or blue whales. But I digress! Total organism size is not a requisite for multicellularity, which is why some bacteria can be termed so.

Here is a paper I found in the literature on the first reported 'true' multicellular prokaryote, from 2004. Similar organisms have been observed since. See Pubmed link.

The same question has also been answered extensively by specialists on Quora and on ResearchGate.

  What made eukaryotes to become multicellular?

Your question implies external influence. Biological evolution does not proceed teleologically, with an end goal in mind. Instead, traits gradually accumulate if they are not detrimental to the replication of the genes. The evolution of multicellularity is a complex and active field of research but there is no reason behind this major switch in cellularity other than that it works as a strategy for the replicating organism and its genes. Multicellular organisms survive. That's all.


After fat is burned from one part of the body, is fat moved around the body? If you go running, for example, and burn fat from your legs, does your body send fat from other parts of the body to that area? If so, why would it do this?

Fat burning is a generalized procedure so there is no such a thing that some part of body loses fat and other part gains it.

Targeted Fat Loss still is a myth.


Cell life: division for immortality or reproduction with aging Are the two cells that are derived from one cell, ‘twin sisters’ or a ‘mother and a daughter’?  In other words, can a cell really be divided to live an "immortal" life or is cell reproduction the reality of cell life that accounts cell age difference between two successive generations, cell aging-associated senescence in cell reproduction, and cell line survival after the death of old cells.

First of all, in eukaryotes (as far as I'm aware), older cells can be distinguished from younger cells due to telomere shortening, so there is an ageing process. HeLa cells mentioned by @Gary Chou have a more active telomerase which mitigates telomere shortening, allowing cells to continue to divide indefinitely. I think it's a very interesting question whether this immortality eliminates any sense of "older" and "younger" cells from in HeLa cell culture. I suspect not, but I am not sure on the specifics.

In general this question will depend on how an organism divides (we're going to talk single-celled organisms from now on). For example, the yeast Saccharomyces cerevisiae is a budding yeast, which means that it divides by budding a smaller cell off of the larger cell. This clearly allows for an interpretation of "mother cells" and smaller "daughter cells." Indeed, as lots of research on ageing in S. cerevisiae has shown, beyond being larger, the mother cell undergoes replicative ageing: over time the mother cell is less capable of growth and division--she gets old!

Perhaps the most interesting case of all (and maybe the one you had in mind) is when the organism divides symmetrically, like the bacteria, which undergo binary fission. For decades, as far as scientists could tell, the two cells that were the product of one bacterium dividing looked identical, and all measurements seemed to indicate that the cells were "sisters," i.e. exactly the same, both newborn. So if in the right conditions bacteria could continue to divide indefinitely, it seemed that bacteria were immortal, since each division reset the ageing clock for each bacterium.

However, a seminal study in 2005 (1) changed this view. The researchers took time-lapse microscope movies of a colony of Escherichia coli from a single cell. E. coli is rod-shaped, so when it divides it has to synthesize two new ends or poles, one for each cell, so just after division each cell has a "new pole" that was made in the process of that division and an "old pole" which had originated before. In this study Stewart et al. kept track of the old poles in the growing colony, and they defined the age of a cell as the age of its old pole. They found that older cells (i.e. cells with older poles) displayed replicative ageing, just like yeast! They grew more slowly and were less capable of dividing. This was examined rigorously by Wang et al. (2) in a "mother machine" in which bacteria were able to grow in constant nutrient conditions (by flowing fresh media across them) in dead-end channels. The cell at the dead-end of the channel always inherited the old pole, and so was a "mother" to all future cells. They found that, while a cell line was able to grow for very long periods of time completely stably, after hundreds of generations there was an increased likelihood for the cells to display signs of stress. They attributed to the accumulation of toxic factors in the mother cell over time. So even in cells dividing by binary fission, there appears to be some difference between the two cells arising from the division, depending on how old the pole that they inherit is.

These effects in bacteria are small, and require watching many generations to reveal. Even in light of these results many researchers will still call the "mother" cell the cell about to divide and the "daughter cells" the cells that result from division, implying that there is no difference between "daughters." Stewart et al. claim that on the basis of their work this conception of bacterial division must be revised, and that instead of division producing two identical daughters,

  the old pole cell should be considered an aging parent repeatedly producing rejuvenated offspring.

Furthermore, they add a nice philosophical touch to their findings:

  These results suggest that no life strategy is immune to the effects of aging, and therefore immortality may be either too costly or mechanistically impossible in natural organisms.

(1): Stewart EJ et al. (2005) Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division. PLoS Biol. 3(2): e45

(2): Wang P et al. (2010) Robust Growth of Escherichia coli. Curr. Biol. 20(12): 1099-1103.


How do primers anneal to ssDNA? In a PCR type protocol, the high temperature stage of the cycle will cause dsDNA to denature, as well as any annealed primers. At the lower temperature the denatured dsDNA will remain denatured. As far as I understand, though, the primers are re-annealed.

My question is this: are there any enzymes that catalyses this re-annealing, or does this happen by chance?

No enzyme is involved in base-pairing (annealing).

This does happens by chance, but the chances are governed by stoichiometric considerations.

The main such consideration is that the (low molecular weight) primers are added at a high concentration (greater than that of the DNA) and therefore have a greater chance of encountering the appropriate region of the DNA than its complementary strand does. (Reannealing of the denatured DNA strands can occur, but not over the time period of PCR.)


Who creates first nitrogen compounds in the food supply chain As I understand the food supply chain, organic compounds have to be created from a unlimited source (air, water...).

For instance, I figure that plants transform CO2 from air to organic carbon compounds, mainly carbohydrates, which are then the main source for most other life forms.

But I never heard about a plant turning atmospheric N2 to nitrogen compounds.

Where nitrogen compounds come from, and from which source ?

There are nitrogen fixing bacteria who turn N2 into NH3.  Some are free-living in soil, others live symbiotically with plants.

https://en.wikipedia.org/wiki/Nitrogen_fixation


PBST vs. TBST buffer in western blotting What is the advantages and disadvantages of using either PBST or TBST in western blotting, or while working with proteins in general? Are there other buffers which are also used for western blotting, or washing steps while working with proteins?

I used to work for a company well-known for its modification state-specific antibodies, including phospho-specific ones, and they actually performed extensive in-house testing of PBST vs. TBST in Western blotting. Part of the reason the company chose to recommend the use of Tris-buffered saline over phosphate-buffered saline based buffers was the clearly-demonstrated fact that some phospho-specific antibodies just didn't work as well in PBST as they did in TBST, for whatever reason. As I recall (it's been quite a while since the testing was performed), some of the antibodies tested gave weaker signals, with more background, and one in particular just didn't work at all in PBST - no signal whatsoever. For that reason, the company chose to standardize its recommended Western blotting protocol with TBST, and it's been that way ever since.

That being said, I'm sure that the majority of antibodies out there would work just fine in either buffer. However, to be on the safe side, if a company states one buffer or other in their protocol, it would be best to use the recommended one.


Type of Tree With Somewhat Squarish Fruit I live in the SF Bay Area and am trying to identify a tree on my street. It's the fruit that is confusing me -- does anyone know what this fruit is?
It's not a rare tree -- there are at least several more on the surrounding streets.

Mature leaves are about 6" long and greater.

That looks like a persimmon — your first image is of immature fruit.

Compare with:

UC Davis — Fruit and Nut Education

Google Image link


Why are bacterial cultures necessary? I notice that in a lot of bacteria testing procedures the sample has to be cultured. You place the sample in agar or another growth medium and wait for the bacteria to proliferate before examining them.

Why is this necessary? If the bacteria are present in the sample, can't you just examine the sample directly with a microscope to find them? Is it a needle in a haystack problem?

For example, a listeria bacteria is about 1 micrometer in size and has a positive gram stain. So, at 1000x magnification the organism would be 1mm in size in the objective which is highly visible. Even at 100x magnification you should still be able to see a tiny dot and be able to zoom in on the dot.

With only a microscope, you might be able to find the bacteria, but how do you know what kind of bacterium it is?

Taking Listeria, under a microscope, it looks like a small rod. Well, so do lots of other bacteria. If you only see that one bacterium, you can't take it and do any further tests with it, you can only see it.

So we do cultures, where bacteria multiply and form colonies. Whether they even grow under these conditions already tells you a lot - a lot of bacterial species won't grow colonies on The type of colony is another factor in determining what bacterium we are looking at - does it have fuzzy or clear edges, what color is it, is it "shiny"?

And then, with that culture, further tests can be done, like what chemicals the bacterium in this colony can break down, what they produce, whether they can be stained with certain dyes, etc. Many times this is needed because bacteria look very much alike (round or rods).

For Listeria specifically, there are special plates used as a growth medium that has certain chemicals added that makes their colonies appear red-violet. Other bacterial species won't show this color even if they do grow on the plates.


What Goes on in Photosystems at the Molecular/Atomic Level? In light-harvesting complexes, how is the energy of a photon transferred from one pigment molecule to another? And in reaction-center complexes, how does the primary electron acceptor capture an electron from the chlorophyll a? It’d be best if any of you could explain this to me in terms of what’s happening at the molecular or atomic level, say with electrons.

The energy transfer is achieved by a process called "resonance energy transfer". It needs the positioning of the donor and the acceptor in very close proximity to each other - the light harvesting complexes are optimized for this. This allows the collection of small amounts of light energy and still enables photosynthesis. The figure shows how this works schematically:

The figure is from this webpage, which gives a good introduction.


Recommendation for book about soil and their food webs Are there any de facto books for studying soil biology; specifically with details in the context of food webs? I am trying to teach myself about the subject and would like a good introductory book, although I will take any recommendations. Thanks

A very good resource can be found here:

http://esdac.jrc.ec.europa.eu/content/global-soil-biodiversity-atlas

If you focus on soil analysis this resource could be helpful:

http://www.geokniga.org/bookfiles/geokniga-handbook-soil-analysis.pdf

I could also recommend the book
http://www.springer.com/gp/book/9783642309410
with which I worked extensively. It covers the soil chemistry very well.


Purpose of K+ channels in action potential I understand that they serve to repolarize the neuron after the Na+  influx. What I don't understand is why this is important.

Meaning, let's say all the K+  channels disappeared. So now the potential is up near +50 mV about. It doesn't go back down quickly, because the K+  channels aren't there. Instead, we have to wait until the Na+/K+  pump can restore the proper intra-/extra- cellular balance between them. And then the neuron can fire again.

I can see that it will take longer for the potential to be restored. But don't we have to wait until the Na+  concentration is restored before we can fire again anyway? If we don't wait, wouldn't that interfere with maintaining sufficient/proper extracellular Na+ concentrations (which I would assume would have other effects)? And the same amount of time will be needed for the Na+ balance to be restored.

So what do we really gain by having a way to restore the charge differential?

Great question! However, your question is based on some misconceptions about what polarization means and how ion movement is involved, as well as the difference between equilibrium and the time it takes to get there. That's okay - it's a mistake that many many people learning about neurophysiology make, including instructors.

Na+/K+ concentrations actually change very very little during an action potential. The Na+/K+  pump establishes the concentration gradient, not the resting membrane potential. The resting membrane potential is caused by the concentration gradient plus the relative permeability of different ions via the Goldman equation: specifically, that permeability to K+ is much much higher than Na+.

When you open voltage-gated Na+ channels during an action potential, the relative permeability to sodium increases dramatically, so the new "equilibrium potential" is closer to the reversal potential for sodium (again, use the Goldman equation). There will be a net flow of ions (mostly Na+ coming in) until that new equilibrium potential is reached.

However, voltage-gated Na+ channels inactivate quickly, so that equilibrium isn't really reached. Instead, as the Na+ channels close, the new equilibrium potential is back near the original resting potential (for a third time, use the Goldman equation), because the primary permeability is to K+ through leak channels, and therefore the net current flow direction changes.

Okay, so what's the need for the voltage-gated potassium channels in all this? Well, the rising phase (sodium phase) of the action potential is fast because there is a really high conductance to Na+ so lots of Na+ can flow quickly in. In comparison, there is a lot less conductance of K+ through the leak channels. If all you have are leak channels, it takes a long time to return to rest. Equilibrium potential is just that: the equilibrium. It takes time to get to equilibrium. Voltage-gated K+ channels speed up that return to rest.

What if you had no K+  conductance, including no K+ leak channels? Well, then it doesn't matter at all what the relative concentration of K+ is inside and outside the cell: check the Goldman equation! You can't really have no conductance to anything at all, but if there is no dominant ion then the membrane potential will be something around zero. In that condition, the charge imbalance of the Na+/K+ pump process can contribute a couple mV, but nothing more than that.

All that said, to address your specific questions:

  I understand that they serve to repolarize the neuron after the Na+ influx. What I don't understand is why this is important.

It's important for speed and for the minimum refractory period between action potentials. Nervous system activity would slow way way down if action potentials could only occur every 100 ms.

  Instead, we have to wait until the Na+/K+ pump can restore the proper intra-/extra- cellular balance between them. And then the neuron can fire again.

  But don't we have to wait until the Na+ concentration is restored before we can fire again anyway?

Na+/K+ pump is only needed to maintain ion balance over a very long term. On the time course of a single action potential, the concentrations of Na+ and K+ do not change appreciably. That's not what repolarization is.

  So what do we really gain by having a way to restore the charge differential?

Speed!

You can also see my answers on some related questions:

Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?

Why does K+ moves out of the cell?


How can I fetch nucleotide sequences based on ENA accession numbers and positions? I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that manually.

Is there any existing tool or script that can fetch all those entries from a database and extract the correct subset of the sequence?

From ENA

  To retrieve results by a single identifier for all records other than
  Taxon and Project please, use the following URL syntax:

  http://www.ebi.ac.uk/ena/data/view/

  For example, the following URL returns the EMBL-Bank entry with
  accession number A00145 in HTML format:
  http://www.ebi.ac.uk/ena/data/view/A00145

Check this.

If you use a *nix system (such as Linux, Unix, or OSX) then you can do this:

[ if list.txt contains all your ids ]

for i in `cat list.txt`; do wget -q -O $i".fa" "http://www.ebi.ac.uk/ena/data/view/"$i"&display=fasta"; done

OR ELSE

Download the entire database and pick up sequences based on your identifiers, offline. You can use your favourite programming language to retrieve sequences. [I prefer awk but python is also good]


Question about contents of small bowel I know, or at least I think I do, that the contents of the stomach are called chyme and that it is acidic.  What are the contents of the small bowel called and is it acidic?

I think its still called Chyme:

  After hours of mechanical and chemical digestion, food has been
  reduced into chyme. As particles of food become small enough, they are
  passed out of the stomach at regular intervals into the small
  intestine, which stimulates the pancreas to release fluid containing a
  high concentration of bicarbonate. This fluid neutralizes the gastric
  juices, which can damage the lining of the intestine, resulting in
  duodenal ulcer. Other secretions from the pancreas, gallbladder,
  liver, and glands in the intestinal wall help in digestion.

  When food particles are sufficiently reduced in size and composition,
  they are absorbed by the intestinal wall and transported to the
  bloodstream. Some food material is passed from the small intestine to
  the large intestine. In the large intestine, bacteria break down
  proteins and starches in chyme that were not digested fully in the
  small intestine.

http://en.wikipedia.org/wiki/Chyme


Online repositories of scanning electron microscope photographs? I have looked at every single Wikimedia commons photo in the category 'scanning electron microscope'. Unfortunately, I could not find any other repositories of such photos, but I would readily look at every single photograph there as well. It strikes me that such repositories are also bound to be useful to biologists and biology students. A simple Google search did not yield much. Can anyone help out?

First off I'd like to reccomend the University of Dartmouth's publicly available collection located here.  They have both SEM and TEM images of a wide range of organisms and cells from algae to see urchins through everything from cholera to mammalian cells.  Images are high quality, fully captioned and properly attributed.

I'm a little confused as to the problem you're having with google - see my original comment on your question.  However I have looked at the photos of Wikimedia Commons in the SEM category and see that they are either images taken with, images of SEM Microscopes or technical drawings regarding their function.  I assume that you're looking for the images taken with SEM.

I was able to find a great number of similar images to those in the commons with a Google Image search - I read above that you were having problems with this approach so perhaps try the search term "SEM images" in image search (or this search to avoid duplications from images you have already seen on Wiki Commons)?

Examples found on just the first page:


Why do human females have permanently prominent breasts? Humans seem to be the only animal whose females have breasts that permanently have a "full" appearance, ie a prominent amount of tissue even when not lactating, whereas other species' breasts seem to almost totally "deflate" when not longer lactating.

Why is that?

This feature has costs to the organism; significant biomass is dedicated and perhaps mobility is impacted. Given there are costs, for the feature to have come into existence, evolution/adaptation principles suggest there must have been some advantage.

Is there some biological advantage?
Are they vestiges of an adaptation that gave a significant advantage to some prior species or in some specific (presumably cold) prior environmental conditions?
Is there any credible research to support certain reasons?

My suspicion is that although genders can be distinguished easily enough, even from a distance, using other secondary characteristics, the answer may have an anthropological/social answer, rather than a biological one.

You may be interested in Breast asymmetry, sexual selection, and human reproductive success.

Abstract:

  Breasts of human females are large compared to those of closely related primate species,
  and they can thus be hypothesized recently or currently to have been subject to directional
  sexual selection. Here we show that (1) large breasts have higher levels of fluctuating
  asymmetry than small breasts, (2) breast fluctuating asymmetry is higher in women without
  children than in women with at least one child, (3) breast fluctuating symmetry is
  a reliable predictor of age-independent fecundity, and (4) breast fluctuating symmetry
  appears to be associated with sexual selection. These conclusions were similar in studies
  from two cultures differing in fecundity and brenstfeeding traditions (Spain; New Mexico,
  U.S.A.). Choosy males that prefer females with symmetrical breasts may experience a
  direct fitness benefit in terms of increased fecundity and an indirect benefit in terms of
  attractive or fecund daughters.

Some quotes from the text:

  The size of breasts in human females is large compared to that of other primate
  species, and there has thus been a recent evolutionary change in breast size.
  Human breasts are characterized by their large size and rapid development prior
  to and during puberty, when growth of other body parts also reaches a high level.
  They can thus be considered costly structures in terms of energy use. …
  Heavy investment in breast development during puberty may seem puzzling
  because the functional significance of breasts is far from obvious. There is no
  or little relationship between breast size and production and composition of milk
  in current industrial societies (reviews in Anderson 1983; Cant 1981; Low et al.
  1987), and breasts have therefore been hypothesized to constitute a deceptive signal
  used by women to attract preferred mates (Low et al. 1987). In prehistoric
  human populations, conditions may have been different, when mother's milk
  was the sole source of nutrition for young children and when resources often
  may have been more limited than in present industrial societies. In this study
  we show that large breasts tend to be more asymmetric than small breasts. In
  prehistoric societies, where resources were likely to be less available or more unevenly
  distributed among women, breast asymmetries are likely to have been much
  larger than in present industrial societies with relatively easy access to resources. …

  If the relationship between breast size and fluctuating
  asymmetry is robust, we hypothesize that a directional preference for large, symmetrical
  breasts, as apparently found in some cultures (Ellis 1954), can be maintained
  in the population because selection for large breasts will be balanced by
  selection against asymmetrical breasts

  We also show that breast symmetry is a reliable predictor of age-independent
  fecundity, and that choosy males that use breast symmetry as a cue in their mate
  choice will experience an advantage in terms of reproductive success. Breast symmetry
  can thus be considered a reliable signal used in intersexual communication.


How does RNA transcription determine which half of the DNA to use? I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?

I'll keep this short and simple. The direction of transcription (which determines which strand is used as the template) is controlled by the promoter, which is a region of specific DNA motifs at the 5' end of a gene. RNA polymerase binds to the promoter, which orients it on the correct strand and in the correct direction, after which it can proceed to transcribe the gene.

That great little animation is from this website.


Can Thraustochytrids such as Schizochytrium do photosynthesis? I know they belong to the phylum of heterokonts and that they are being heterotrophically grown on an industrial scale but I can't seem to find any reference to them being grown photoautotrophically. People call them marine algae yet there is no mention of photosynthesis.

I did find this paper which says they have several carotenoids so I assume they have those because of their LHC's and photoprotection. It would be great if anyone had some more detailed information (papers) regarding their properties.

I think not.

from Kingdoms and Domains: An Illustrated Guide to the Phyla of Life on Earth By Lynn Margulis, Michael J Chapman. as found on google books

You will see there are no chloroplasts depicted.  These are eukaryotes and so to do photosynthesis they would need chloroplasts which should be evident.


How do I perform recurring pattern mining or regular expressions of nucleotide sequences? I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?

I'm no expert in MATLAB but I know that it is possible to do regular expressions in MATLAB with the general rules explained here. However there are alternative approaches and softwares you could use to achieve this with softwares that are freely available and quite powerful in performing such functions. Although I'm aware that perl and python are the programs of choice for regular expression analysis; however I would urge you to consider the R language. R allows you to construct your mining results in a format of a table, which each column containing the data you are interested! there are many packages in R that allows you to process many data types. I would say R is worth the investment to learn for any future data analysis. I use the RStudio to interact with the R language software.

The best place to get help for MATLAB or R is the http://stackoverflow.com which you can sign on with you current account. In fact I have asked a few questions there on regular expressions and the community is very helpful however ensure that you show your attempt at the problem and where you are stuck in order to get a constructive responses!


Why do teeth decay of sugar? Sugars is a common component in diet of mammals. Why then their teeth did not develop resistence to sugar decay?

The reason for the decay are ever evolving bacteria, which happen to be very hard to overcome, even nowdays. There is a lot of research centered towards protein interactions, even mapping whole interactomes, which would help us get rid of decay, yet naturally our system wasn't able to evolve as fast as technological advances, but bacteria did.


Optimal pH of protein buffer? Basic principles to adjust buffers according method and analysis Protein buffers such as PBST, which is used in western blotting, are normally adjusted to pH 7.4. When I try to find why, I find some information about optimal pKa for protein stability. Im not sure I really understand this, because it seems as through regardless of protein - most laboratories just use PBST with a pH of 7.4.

I am a bit curious about this, and have a few questions

Why is pH 7.4 set as the standard for western blotting?
For an optimal western blots, should the pH always be above the pI of the protein?(since 7.4 seems a bit high)
Should the pH of a buffer be at the pI of a protein for extractions before SDS-pAGE, and while washing NC-membranes after blotting?
How should one calculate the optimal pH, or evaluate/think about this when working with a protein?

The correct pH depends on the properties of the proteins that you are trying to exploit. These are a good deal different between extracting proteins from tissue and performing Western blots.

Extracting proteins means keeping them soluble in aqueous solution. Working at the pI of the protein might be the worst choice as the protein then has no net charge, typically reducing its water solubility. An extreme case would be the highly basic histone proteins with very high pI values but best extracted at low pH.

After proteins have been run on a denaturing gel and transferred to a membrane for Western blotting, they are already denatured and bound strongly to the membrane through hydrophobic interactions little affected by pH except perhaps at extremes. For the blotting, you want to exploit the interaction of epitopes on the protein with the antibodies against them. During antibody production, the interactions between the epitopes and the antibody-specific receptors on the antibody-producing cells occur at normal extracellular body pH, 7.4. Using that pH for the blotting best recapitulates the charge state of both the epitopes and of the antibodies as they existed when cells producing the best antibodies were selected.


Are all/most/any membranes comprised of lipids from the smooth ER? I'm attending an introductory high school course to cell biology. Based on my understanding, lipids – the building blocks of membranes – are formed in the smooth ER. Are all/most/any membranes comprised of lipids that are formed in the smooth ER? If not, where do the lipids of membranes come from?

It sounds like we're mainly interested in phospholipids here, as they're the main component of cell membranes. Since your question didn't specify, we'll talk about Bacteria/Archaea and Eukarya separately

Bacteria/Archaea

Here, the answer is fairly intuitive. Bacteria and Archaea don't have endoplasmic reticulum, so they can't synthesize phospholipids in it. In this case, it seems like they create fatty acids directly from enzymes in the midst of the cytosol.

Eukarya

Here, the answer is a bit more complex. Fortunately, there are some good reviews about the topic that answer the question. Here, they talk about the entire phospholipid biosynthesis pathway and only mention the ER as an organelle, although it's worth noting that there are several sub-locations within the ER where specific groups are added. However, they fail to distinguish between rough and smooth. In another source, they mention not only the ER but also the mitochondria as having some ability to synthesize phospholipids. That's pretty cool, in my opinion.

TL;DR:

Bacteria and Archaea certainly don't rely on the smooth ER for lipid synthesis. In eukaryotes, there are several areas where lipids can be made but the smooth ER does seem to be the main source.


Why can we breathe only oxygen? Plants has the capacity to take in both CO2 and oxygen, that's during day CO2 and at night oxygen. Why don't humans have such a capability?

You should have a look biological processes which are:

cellular respiration
photosynthesis

Loosly speaking, these two processes are just the opposite but deal with the same chemical compunds.

$C_6H_{12}O_6 + 6O_2 \xrightleftharpoons\  6CO_2 + 6H_2O (+ Energy)$

or in words...

glucose + Oxygen $\xrightleftharpoons\ $ Carbon Dioxide + Water (+ Energy)

From left to right is the process of respiration and from right to left is the process of photosynthesis.

Respiration releases energy from glucose (sugar). Therefore, animals, plants, fungi respire in order to get their energy from their food. More information on the chemical pathways on  Krebs cycle (or citric acid cycle). The main organelle involved in celullar respiration is the mitochondrion. Note: (Loosely speaking) the glucose is the end product of the digestion
photosynthesis allows organisms to create its own tissues from water and $CO_2$. But this cost energy. This is why plants use capture the energy form the sun with their leaves. More information on the chemical pathways on Calvin Cycle. The main organelle involved in photosynthesis is the chloroplast.

Note: In our lungs comes air which is a mixture of different gases (just like coke (Coca-Cola) is a mixture of different compounds). The two main compounds of air are Nitrogen (~78%) and Oxygen (~21%). We use only Oxygen. More info on the air composition here


Example of a virus becoming symbiotic with an organism The human gut has an indispensably beneficial ecosystem of bacteria. What are the examples of a virus that becomes symbiotic with an organism, or even incorporates beneficially into the genome of the organism?

In humans, endogenous retroviruses (HERVs) comprise a substantial fraction of the genome, as much as 8%.  While many historical viral incorporation events into the primate genome were likely neutral or detrimental (and therefore selected against), some were co-opted and are now functional elements in humans.  An example: human syncytin is the envelope gene of a defective HERV, and the protein has been co-opted for fusion during human placentation.  More HERV resources here.  The Feschotte Lab at Cornell studies the evolution of HERVs and other mobile elements in mammalian genomes, and their lab site provides more resources.

In bacteria, prophage (integrated bacteriophage) can be co-opted by their hosts for niche-specific transcriptional control.  A cool example is the pathogen Listeria monocytogenes, which utilizes prophage excision during intracellular growth to activate its Com system and escape from phagosomes.


If gene differs between chromosome pair does individual get a mixture of protein shapes? Do diploids such as humans end up with a mixture of two different shaped proteins where the appropriate gene is expressed differently in the two halves of a chromosome pair or is there some governing factor that dictates that only one of the alleles is ever used to direct protein synthesis?

Yes, that mixture of shapes can happen.  Differences in the nucleotide base sequences between the two alleles of a gene can lead to differences in amino acid sequence, which in some cases large differences in protein shape.  One example would be if one allele changed a cystine codon to any other codon, leading to loss of a disulfide bond needed to stabilize the tertiary structure of a protein.  For an extreme example, consider a mutation causing sickle-cell anemia; in this case, the disease-causing allele leads to altered shape of the entire red blood cell.

If a heterozygote carries a healthy allele and a disease-causing recessive allele, the protein produced by the healthy allele provides enough activity to mask the lack of activity of the "broken" protein provided by the recessive allele.  If, instead of being a true recessive, the disease-causing allele is partially penetrant, then the heterozygote would suffer from the reduced level of the active protein (only one allele is providing the good stuff).


Why can't our eyes smoothly transition from side to side without focusing on a moving object? Why are we not able to slowly and smoothly look from side to side, or up and down in a single and smooth transition, given that we are able to do this if our eyes are focused on a moving object?

Short answer
Smooth pursuit is driven by retinal slip, which is determined by external input registered peripherally in the retina.
Background
The smooth pursuit system is a system designed to minimize retinal slip, i.e., the movement of an image across the retina. Saccades are rapid eye movements meant to fixate quickly on a new target (Purves et al., 2001).
Both movements are readily apparent when sitting in a train and staring outside; the eyes focus on a distant object and pursue that object. Once it exits the field of view, the eyes target a new object via a saccade and smooth pursuit is again initiated (the train window phenomenon).
Saccades can be triggered both involuntary (due to a sudden, unexpected stimulus) and voluntarily (Walker et al., 2000).
The smooth pursuit system cannot be voluntarily controlled, barred in some highly trained observers (Purves et al., 2001). Instead, it is guided by eye movements dependent on the movement (slip) of the fixated target on the fovea (Thier & Uwe, 2005). Hence, this system is controlled by external stimuli, not by internal ones. Retinal slip can of course be voluntarily manipulated by moving the eyes away from the target, for example by moving the head. The smooth pursuit system detects this by registering retinal slip, and keeps the eyes fixated on the target, through smooth pursuit which is involuntary.
References
- Purves et al., Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates (2001)
- Thier & Uwe, Curr Opinion Neurobiol (2005); 15: 645–52
- Walker et al., Exp Brain Res (2000); 130: 540–4


Can "red" cone cells actually see much red light? In electronics, the most common color scheme is the "red-green-blue" (RGB) scheme.  This choice is often justified by claiming that the long-  (L), medium-  (M), and short- (S) type cones in the human eye are most sensitive to red, green, and blue light respectively.  But this seems clearly wrong if you look at the actual normalized frequency receptivity spectra for the three types of cone cells:

It's clear that the L-type cones are actually most sensitive to yellow-green light and are actually relatively insensitive to red light. (Presumably the brain distinguishes between yellow, orange, and red light by the rapidly decreasing ratios of M-type to L-type signal.)

My question is threefold:
(1) The L-type cones are usually called "red" cones.  Is this simply incorrect, or is there some justification for this name that I can't see from the receptivity spectra?
(2) Does the RGB color scheme give a better color range than, say, a "yellow-green-blue" scheme (which would more closely correspond to the actual cone sensitivities) simply because red is at one end of the visible spectrum, so you can more easily get a wide color range?
(3) If this is the case, do we not use a "red-green-violet" color scheme (which would give an even wider color range) simply because the human eye is so much more sensitive to blue than to violet light?

This is a good question. The first  thing to note is that human colour vision is very complex and still poorly understood. If you visit the wikipedia page on RGB,  you will find that this correctly mentions that the S, M and L cones are most responsive to violet, green and yellow wavelengths respectively (which answers your first question - calling the cones red, green and blue is primarily for historical reasons, because there aren't any real wavelengths that only activate a single cone, it's hard to say what colour a cone 'is'). So why do we use red, green and blue phosphors? A practical answer can be found by looking at the CIE 1931 colour space: this was essentially an attempt to find how one could add together different amounts of a small number of wavelengths to make the result indistinguishable from any desired wavelength (read the linked page if you want more information, also have a look here). The result found was that the colour matching functions should look like the following graph (what this is showing is how much of a red, green and blue light are required to simulate a wavelength):

You can see that this is similar to the responses of the cones except for the peak in the red (which corresponds to violet looking like red-blue):

To answer the question in your title, red cells do see the most red light of any cone, but that is not where they see the most light. Here is an example set of spectra of the red, green and blue phosphors in a CRT:

To answer your question about why we use red, green and blue in the first place (rather than yellow-green-blue or red-green-violet), it's good to understand why the CIE 1931 functions are that shape in the first place. The wikipedia RGB page mentions that:

  ...good primaries are stimuli that maximize the difference between the responses of the cone cells of the human retina to light of different wavelengths, and that thereby make a large color triangle.

This gets at the fundamental reason, which is that it is generally believed that we do not perceive colours in terms of the activities of each cone, but in terms of the differences between those signals (as it says here), an opponent process. The following image illustrates a simplified version of how the opponent signals in colour vision processing are thought to function, so that the resulting signals are a black-white, a yellow-blue and a red-green axis:

This image shows the theorized shapes of the response curves of these opponent functions (see here for an interesting historical paper on this theory and here for more details and some predictions of the theory):

It is possibly apparent from the last graph why the CIE 1931 colour graph is the shape that it is, since we see red as a bimodal distribution with a distribution of green in between, and a large distribution of blue at short wavelengths and yellow is red + green. (Incidentally this also explains why we also perceive yellow as a primary colour - see the 4 highlighted points R, Y, G and B where one curve passes through 0). Additional information on the neurological and psychological correlates of colour vision can be found here and here and more technical theoretical details here.

The upshot of all of this is that red, green and blue are the best 3 colours to use as the basis for additive colour mixing, but not because they are what L, M and S cones are most sensitive to. Rather it is because it has been shown that these particular colours fall where there is maximal difference between the cone signals and because they can accurately represent all of the colours in our colour space as illustrated by CIE 1931 (due to being widely spaced and all perceived easily as you have mentioned in points 2 and 3 of your question). Effectively, the reasons are complicated and to do with the neurological processing of the colour signals and the differences between the signals rather than the straightforward signals themselves.