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Parasites with both plant and animal hosts?
Are there animals (or plants) that are parasitic on both animals and plants?
Especially such that they rely on their plant host being eaten by their animal host?

haven't heard of a plant/animal like that... there are micro-organisms that wait to be ingested by animals to continue their life cycle though

My guess is that fungi would be the best candidate, without knowing about a particular answer/example to your question. I know that there are groups of parasitic fungi that have switched between animal and plant hosts (i.e. in relation to speciation events, not host switching/complex life cycles within the same species of fungi).

Plant to animal switching is known in e.g. rust fungi (from Pucciniomycetes), where you can also find complex life cycles with intermediate hosts (a Heteroecious life cycle).


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Relative microRNA comparison from from TCGA data?
I have a conceptual question that I was hoping someone could answer.
Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data?  Can I do this after normalizing the data?  Does it matter if I use RSEM or RPKM values.  It seems to me that it should be legitimate in any case since microRNAs are approximately the same length, but maybe I am overlooking something.
For example, I am following a paper published in Nature Communications entitled "Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif".  The authors download the data and collapse isoform reads to a single read count using the reads.  They say they used the reads per million microRNAs mapped, which establishes each microRNA read count as a fraction of the total microRNA population.  The authors then do upper quartile normalization which they say is important because a subset of microRNAs (miR-143 in particular) contributes so significantly to the total read count.  In the text, the authors appear to use the resulting values to do a direct comparison between microRNAs.
I definitely want the collapsed isoforms, and I think it makes sense to do the normalization.  However, I would like to say that a particular microRNA is expressed x-fold higher than another.  Can I do this from the collapsed and normalized data?
If this has already been answered, I apologize.  I could not find it.  Thanks.

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

Thanks Devon.  If there were no sequencing biases, do you think this with be a legitimate claim with isoform-collapsed and normalized data.  I have qPCR data on cell lines (though I used relative quantification and not absolute quantification), so I wanted to compare clinical data to that.  As an aside, I have been comparing the fold-change from microRNA A versus small RNA RNU6B to the fold-change from microRNA B versus small RNA RNU6B to determine fold change of microRNA to microRNA B.  I am wondering if your suggestion to use absolute quantification suggests that you don't think this is ok?

Small RNA sequencing is good for a preliminary screen because as with most high throughput experiments, the sample size is less and therefore inter-sample comparisons may not be accurate.
For miRNA expression calculation, I use mirdeep2's quantifier script with a slight modification. The script basically aligns the reads to known pre-miRNAs and finds if they are aligning to the annotated mature miRNA region (some window of partial mapping into non-mature region is allowed and can be set to zero as well). It uses bowtie for alignment.
What I generally do is, instead of running bowtie in the -v mode (as set in mirdeep), I run it in the -n alignment mode by making a small modification in the script. The -n mode lets you define a seed region, and number of mismatches in seed and non-seed regions. I set seed length to 10 with 0 seed mismatches and around 2 non-seed mismatches.
To calculate reads per million (RPM) I normalize it with number of unique mappings to genome, with same alignment parameters (except --norc). As per this study an RPM of 100 is biologically relevant.

Can I say that microRNA A is expressed x-fold greater than microRNA B?

Yes, if the read counts are clearly different. EM and other likelihood models calculate a confidence interval for read counts or RP(K)M and if two RNAs do not have overlapping intervals then they can be said to be expressed in different levels. I haven't used likelihood models for miRNAs though, but I guess it is fine because:

The search space is highly reduced.
Search is stringent.
Isoforms are collapsed.

This effectively eliminates the possibility of dubious reads. You can set an RPM difference of 100 to call two miRNAs as differentially expressed, as 100 is the lower limit of biological significance (as previously mentioned).
Most relevant miRNAs have comparable GC content; so there may not be such a great sequencing bias (moreover the read itself is quite small).

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Examples of how the presence or absence 2'-hydroxyl groups influence physicochemical properties of DNA and RNA
I know, for instance, that RNA is much more succetible to alkaline hydrolysis than DNA and this difference is determined by the presence of 2'-hydroxyl group in ribose.
I have also heard that "DNA is more stable" and thus was selected as the repository of genetic information. Though, I still haven't understood why the lack of just one hydroxyl would lead to more stability...

@Chris ok, I will actually delete the other because something similar has already been asked

My answer to this question may interest you, specifically the part about sugar pucker: http://biology.stackexchange.com/questions/19115/what-makes-dna-helical

From a chemical point of view, the phosphate can form a bond with the 2' hydroxyl, forming a cyclic structure and breaking the bond with the next nucleotide, thus breaking the RNA backbone.

As user137 said, the general base abstracts a proton from the 2'OH and subsequently the 2'O- renders a nucleophilic attack on the δ+ Phosphorous, leading to the hydrolysis of the phosphodiester bond. There can be slight variations in the mechanism and the intermediates; for details see this review.

After hydrolysis both 2'- and 3'- phosphates can form.
RNA is not thermodynamically unstable; apart from being unstable in the presence of a strong base RNA is biochemically unstable too. This is because there are several RNAses and most of them degrade RNA by a mechanism similar to alkaline hydrolysis (they cannot act on DNA). Also see this post.

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Why do most organisms have negative supercoiled DNA?
It has been observed that in nature most organisms have negative supercoiled DNA and that few organisms have positive supercoiled DNA. Some of the organisms that have the positive supercoiled DNA live in strong acidic environments but are very rare compared to negative supercoiled DNA. Why wouldn't all organisms have the same DNA supercoiling? Does it affect their survival in any way?

Very briefly, positive supercoiling can help prevent DNA denaturation. It's sometimes (often?) found in thermopiles since their DNA is prone to melting.

Negative supercoiling reduces the torsional energy. Positive supercoil is like a compressed spring.

@WYSIWYG It sounds like that could be an answer if its explained why that matters?

One important notion in DNA topology is the linking number ($Lk$) which is the sum of right-handed twisting # and left-handed writhing # ($Tw+Wr$). Say the $Lk = x$ for relaxed DNA. If $Lk<x$ then you have negative supercoiling while positive supercoiling happens when $Lk>x$.
The higher the $Lk$ value the higher the helical energy of the DNA and the harder it is to separate it meaning the DNA is now more stable. In so-called "extreme" conditions (e.g. high acidity or high T˚) the organism must protect his DNA from degradation. Therefore those organisms require a more stable form of their DNA which can be achieve by positive-supercoiling and/or high GC content.
Now why do the vast majority of the organisms have negatively-supercoiled DNAs? If you let the DNA by itself, it will adopt an $Lk=x$, i.e. it will be in his "relaxed"-form. Negative supercoiling arose because of the presence of Topoisomerases (type I and II), which are proteins that cleave the DNA and release the helical tensions and which cumulatively provokes the DNA to be slightly underwinded compared to it's relax-form. Is this good for the organism, if living in non aggressive conditions? Yes it is because a decrease of the $Lk$ will make the DNA easier to separate. This means replication and transcription can occur more easily or in proper terms, they now require less energy to perform their functions.
Here an excellent reference on this subject as well as a Youtube video that explains those concepts using strings. The latter is really helpful as those concepts are easier to understand visually than in writing.
I hope this helps.

in negative super coiling  number of the times the strands cross each other is LESS than positive super coiling making it easier to unwind it for the processes of replication,transcription....


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Using a Sphygmomanometer
If you were to use an older sphygmomanometer and a stethoscope to record blood pressure, why would you hear no sound when the cuff was inflated to 160mmHg

Welcome to Biology SE. Here at Biology we expect people to show at least some effort in answering the question when it comes to home work assignments. What did you try to solve this question? Any thoughts?

This happens with a new sphygmomanometer too.

The measured blood pressure is the radial pressure exerted by the blood column againt the arterial wall.
In a normal patient, this pressure varies between 120 mm of Hg and 80 mm of Hg.

click on the image to go to the source
When a cuff is inflated to 160 mm of Hg, the arteries collapse and circulation is temporarily suspended. As blood flow does not occur, no sound is audible.

The korotkoff sounds that are heard while measuring BP are due to disturbance in the streamlined flow of blood. When auscultating an artery without applying pressure no sounds should be heard in a normal person. Generally they are heard when blood flow occurs in spurts. This occurs when the cuff pressure is lesser than the systolic pressure but more than the diastolic pressure.


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Did baby bird hair and mammalian hair convergently evolve?
Chicks (baby of chickens) and ducklings seem to have fine hairs, at least something that look like hairs to me. Most mammals have hairs, but reptiles, fish, or other animal groups do not have hairs as far as I know.
I have looked up the tree of evolution, and it looks like this.

So, the tortoises, crocodiles (I do not know what lepidosauria means but I guess it is reptiles other than the aforementioned), and birds diverged after their common ancestor was split from the common ancestor of mammals.
Since none of the tortoises, lepidosauria, or crocodiles have hairs now, does this mean that the hair of birds and mammalian hair is an example of convergent evolution? Or did these other taxa lose hair during evolution?

Fledglings do not have hair, but "down" -- a very, very fine type of feather used to insulate the chicks (and convergent in purpose with mammalian hair there).

Is there any significant difference between hair and down?

I advice you to have a look into the commonalities (chemically, functionally and evolutionary) between feathers and hair and forget about feather-down. That should get you a lot closer to the bottom of things and will lead to a better question.

Hair, feathers, fish scales, shark armor - they're all skin cells.

Bird "baby hair" are modified feathers.  (Or perhaps feathers are modified "baby hair".  The ancestral state for feathers was probably closer to the chick's down in appearance, but I don't know whether chick down is unmodified original feather or whether it was feathers and then modified again.)
In any case, mammalian hair and dinosaur feathers (which includes bird feathers) are separately evolved from the same base structure, modified reptilian scales. They are therefore homologous, but evolved independently.

These results reveal a new evolutionary scenario where hairs, feathers, and scales of extant species are homologous structures inherited, with modification, from their shared reptilian ancestor’s skin appendages already characterized by an anatomical placode and associated signaling molecules.

--The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes

iayork's answer is a good one, I will add one thing: Mammalian hair doesn't show up in the fossil record before the Late Permian; Feathers for their part have not yet been found outside of Dinosauria, a clade which started in the Triassic (which came after the Permian).
The common ancestor of Mammals and Dinosaurs however existed in the Carboniferous, around 312 million years ago, which is 12 million years before the beginning of the Permian and more like 50 million years or so before the earliest fossil fur found so far (I couldn't find a date more precise than "Late Permian" but the Permian ended 252 million years ago).
Add to this that the common ancestor of Mammals and Dinosaurs is also the common ancestor of basically all fossil tetrapods that weren't amphibians, and no fur or feathers have been found on any of those outside of a few Dinosaur groups and the Mammal lineage, that no feathers have been found in any ancestor of Mammals and no fur has been found in any ancestor of Birds... It is pretty clear that the common ancestor of Birds and Mammals had neither fur nor feathers, meaning those features evolved convergently.


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Why does high pH result in the denaturation of DNA?
In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample.
I find this counterintuitive since I expected that $\text{Na}^+$  cations would neutralize the negative charges of phosphate groups, hence stabilizing the double helix.

Both high and low pH can affect H-bonding especially in complexes formed by bases such as pyridine, quinoline, imidazole (ref). The bond is most stable when pH = pKa. I am not really sure if this is the case here. Perhaps alkaline denaturation is preferred because it won't cause hydrolysis. This question can be migrated to chemistry SE if no suitable answer is posted.

The pKas of (neutral) guanine and thymine are 9-10 (ref). At high pH (>~10), those bases will be deprotonated and exist as negatively charged conjugate bases. As the deprotonated species, part of the G/C and A/T hydrogen bonding networks are eliminated. In the figure below, green dotted lines represent the hydrogen bonds that explain the observed base pairing. Red dotted lines represent disrupted interactions.

I can add figures if that would help.

That would be great - it illustrates the answer better.

@jerepierre the figures you added were great. Thank you very much


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With humans, is being transgender innate, or caused by social factors?
In humans, is being transgender something that is innate, or is it caused (or made more likely) by social factors such as their political beliefs, their religious views or their social environment?

Something interesting  http://www.ncbi.nlm.nih.gov/m/pubmed/25667367

Transgender is a collective name for a wide variety of cases, the hormonal changes occurs in embryonic stage result in transgender case at birth time itself, for most other cases it is occurred in the puberty period.


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What is the difference between gene and CDS annotations?
I have a bunch of sequence files fetched from the EBI ENA and I'm trying to find the end of the 5' UTR for specific genes.
The UTR itself doesn't seem to be annotated in most sequence files I have. My original idea was to simply use the CDS annotations, as the start of those should clearly identify the end of the 5' UTR. But I also noticed gene annotations in many of the sequences, most of them starting and ending at exactly the same locations as the corresponding CDS annotation. But there are also cases where there are small differences between the gene and the CDS annotation.
So I'm wondering how exactly the gene annotation is defined (if there is actually an agreed definition) and how the gene and CDS annotations are used in practice.
Which annotation would be the most reliable to identify the end of the 5' UTR?

Realistically speaking, there's no guarantee that UTRs are in a given gene definition unless you're looking at a well annotated species (e.g., mouse or human). There are many species for which there is simply very little information on UTR sequences.

CDS is based on ORF prediction and unless the protein product is known it is classified as an mRNA for a hypothetical protein (Refseq id: XM_*).
As Devon Ryan said sometimes UTR ends are not accurately annotated. If you are interested in finding the 3' end of 5'UTR then the problem is basically to find the translation start site. You can have a look at ribosome profiling experiments or try doing eIF2 CLIP-RNAseq (I don't think it has been done); peptide sequences may not be of help because N-terminal region in many cases, gets clipped.
If you are interested in finding the 5' end of 5'UTR then the problem is relatively simple. You just need to do a 5'-RACE followed by Sanger sequencing (this would work in most cases or you can do a deep-RNAseq).
There are official GTF files that provide the most reliable annotations. For human I would recommend GENCODE.
In the annotations the term Gene denotes the entire DNA region that is responsible for all of its RNA products (splice variants, alternate start/termination etc). Other features include Transcript, Exon, CDS, UTR and in some cases translation start site is separately annotated. CDS comprises of just the protein coding region.
You should read more about the GTF/GFF annotation format.


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What is the protein with the highest affinity to lactose?
I was wondering: What is the protein with the highest affinity to lactose? Are there some databases with values for affinity?

About what kind of affinity are you thinking? Binding of the sugar? Or do you think about specificity of enzymes?

Galectins 1&3 perhaps

Did you make any attempt to find out the answer? If yes then please add that to the question. It is not appreciated that you ask others to do literature search for you.

Yes, I did some research. I found that galectin 1 & 3 had very high affinity but there were not specific to lactose. I found this website: http://www.bindingdb.org/bind/index.jsp


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Link between macro lncRNA and DNA looping
I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by the (macro) lncRNA transcript ?
Thanks

I didn't actually understand the phenomenon that you are describing. You mean a long RNA binds to different regions of DNA (in cis) causing them to come together?

It's more the act of transcription of a long RNA that may lead to bring distant chromosome regions closer by the act of 3D DNA conformation.

I don't think the act of transcription, per-se will bring DNA domains together. It would open up the chromatin. However the "act of transcription" has been said to precede recruitment of Polycomb/Trithorax complexes and these in turn can recruit chromatin remodellers/enhancers etc.

Thanks. Do you have in mind a recent paper talking about it ?

I haven't read a recent paper on this. I was doing a project on Polycomb in my UG and that is when I read this in an annualreviews article. It has been 7 years since then. I am sure more research must have been done on this. But in general this concept itself is quite dubious. I can only suggest you directions to look at. Another thing that you can look for is pervasive transcription.


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Are there anyother method under research for curing rabies?
Why is rabies incurable after onset of symptoms? Although we administer HRIG (lyssa virus antibody) to the patient, why doesn't it work after onset of symptoms? And are there any other successful treatments for rabies like that of Milwaukee protocol which are under research? I also want to know how successful  is Milwaukee protocol so far?

Antibody wont cross blood brain barrier. Rabies virus infects the hippocampus.


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What's the (or some of the) minimum(s) amount of atmospheric carbon dioxide needed by plants?
We currently have a problem of increasing $\ce{CO2}$ in the atmosphere.  But assuming we find a way to carbon sink it, what is the minimum $\ce{CO2}$ we need to leave in the atmosphere to provide a source for plants to photosynthesize?  I'm assuming this may vary per plant, and that we could choke plants so they're less productive - but at some point they will starve to death if we remove too much $\ce{CO2}$.
Where does this point lie?
Approximations, or a specific data point (say for one plant, or one type of plant) would be an adequate place to start.
Current atmosphere composition is $\pu{0.035\%}$ carbon dioxide.  In the past it has been higher (has it ever been lower?), which in theory has resulted in higher plant growth - but I've seen some contradictory statements about higher Carbon Dioxide.
(related: What is the effect of a pure-oxygen environment on a plant?)

The Carbon Fixation wiki page will interest you, especially the discussion about C3 and C4 carbon fixation.

In northern BC and Yukon with the increase in CO2 plant growth has accelerated over the last 40 years from my personal and others observations. The result in some values is thicker higher 'buck brush'.

The values provided in the other answer are actually related to the minimum values experienced by land plants in the past, not the theoretical minimum possible concentration of CO2 capable of maintaining plant life.
According to Gerhart and Ward (2010):

During the Last Glacial Maximum (LGM; 18 000–20 000 yr ago) and previous
  glacial periods, atmospheric [CO2] dropped to 180–190 ppm, which is among the
  lowest concentrations that occurred during the evolution of land plants.

Thus, what is the theoretical minimum possible concentration of CO2 capable of maintaining plant life?
According to the same paper (Gerhart and Ward, 2010), there has been several experimental studies focusing in low concentration of CO2:

In the mid-1990s, a later phase of technology was introduced at the Grassland, Soil, and Water Research Laboratory (USDA-Agricultural Research Service) that involves an outdoor tunnel system, whereby plants are grown across a continuum of modern to low [CO2] (Mayeux et al., 1993; Fig. 3b,c). During the day, air of known [CO2] is pumped into one end of the tunnel where plants experience relatively high [CO2]. Plants near the end of the tunnel, on the other hand, experience low [CO2] (similar to glacial values) as a result of photosynthetic removal of CO2 from air as it moves progressively through the tunnel. At night, airflow is reversed while plants are solely respiring, and this serves to equalize [CO2] throughout the tunnel.

Despite those studies not focusing explicitly on what's the minimum possible concentration, we can still draw some conclusions based on them. For instance, in Fig.4 (ibidem):

As you can see, those vertical lines represent the minimum concentration experienced in the past. However, we still observe CO2 assimilation (photosynthesis) below those values. Unfortunately we cannot simply get the value where the line touches the x axis, because those values are intracellular CO2 concentration.
That being said, the answer depends on other concept: CO2 compensation point. For a C3 plant, carbon dioxide compensation point is around 50ppm (Tolbert, Benker and Beck, 1995).
Thus, we can say that, as a rough estimate, the value you want lies between 50ppm and 170ppm (probably closer to 170ppm than to 50ppm).
Of course, that minimum possible value depends on several factors, as the species of the plant, the type of photosynthesis (C3, C4, CAM), temperature, humidity etc.
Sources:

Gerhart, L. and Ward, J. (2010). Plant responses to low [CO2] of the past. New Phytologist, 188(3), pp.674-695.
Tolbert, N., Benker, C. and Beck, E. (1995). The oxygen and carbon dioxide compensation points of C3 plants: possible role in regulating atmospheric oxygen. Proceedings of the National Academy of Sciences, 92(24), pp.11230-11233.

There is no one answer of "how little".  Each terrestrial plant depending upon its type has some minimum below and a maximum above which it could not survive over a sustained time at that level. So it's not just "how little" but "what plant" and "for how long" until it dies, rather than just going dormant or simply not growing.  But the question doesn't involve carbon dioxide alone, there are other conditions (amount of sunlight, temperature, humidity,  annual rainfall, soil quality, air quality) impacting any lower and upper limits.  Deriving some answer for some plant in a closed system like a tube in a lab is one thing.  In nature, the conditions leading to some extreme carbon dioxide level (like either 50 ppmv or 5,000 ppmv) the conditions themselves just to get there likely would kill a plant before even reaching the level of carbon dioxide.
It's rather immaterial to the question this assumption that there is some problem in current atmospheric concentrations of carbon dioxide. Problem to what, how and why?   Yes, carbon dioxide levels rose in 2017 by about 2.48 ppmv, to 407.54 ppmv. https://www.esrl.noaa.gov/gmd/ccgg/trends/global.html  There's also a current 0.79°C anomaly to go along with that 408 ppmv level. https://www.ncdc.noaa.gov/cag/global/time-series/globe/land_ocean/12/3/1880-2018   Assuming some sort of a direct cause/effect relationship to the planetary average temperatures solely attributable to this rise in carbon dioxide levels, still asks the question, is that all a problem?  Trying to answer that is another issue entirely though, and also rather immaterial to the question of how little is too little, since it's going up not down.
We can scientifically - by observation and experimentation - establish  both that increasing atmospheric concentrations of carbon dioxide are happening, and that carbon dioxide absorbs and emits in the infrared.  We can also show the global average sampled near-surface temperature and trend are up.  However, like questions of what level of carbon dioxide is not enough for plants, what we can't observe or experiment upon - on the actual Earth's planetary weather systems - is maintaining everything else and seeing what occurs with a given amount of one or more greenhouse gases that is higher or lower than the current amount.   We can only experiment in non-Earth conditions or model scenarios on computers.  Simulation, given certain other assumptions.   This makes it difficult to do a lot of things, including calculating in the atmosphere when there's not enough carbon dioxide for plants.   In large part, this is because it's not possible to control most of the hydrosphere, or the sun, or the many other factors impacting plants and how well or badly they fare.
That said, there is only one period in Earth's history where the conditions are like they are now, and that is now.   In the existing conditions, it seems unlikely that - regardless of how much or little warming it causes - there is any way to reduce the amount of carbon dioxide in the atmosphere in any realistic timeframe to something lower than it was in 1880 (proxy, ice cores, 282.9 ppmv https://sealevel.info/co2_and_ch4.html)
A question like "at what level of carbon dioxide in the Earth's atmosphere do plants start to die" is a tricky one, because the conditions required to get to 250 (or 200 or 150 or 100 or 50 or 0) in the atmosphere would most likely require an atmosphere that would have lost much of the greenhouse effect to get there. Essentially plants (and just about every animal that would miss eating them) would be hit by extreme cold before they were hit by carbon dioxide starvation.
Although the best answer to these sorts of questions might be found in the ice core proxies, in that during the last million years or so, the atmosphere has not been lower than about 180 ppmv    https://carboncycle.princeton.edu/research/atmospheric
In a controllable laboratory environment, different plants have different levels of carbon dioxide at which they won't grow, go dormant, or die. These are created conditions though, artificial, unnatural.  On the Earth, in the system that actually exists, those levels of any of the greenhouse gases appear unreachable in a working biosphere anywhere near like the one we have. There are too many variables to just consider carbon dioxide, because it can only be experimented upon in a closed system that is unlike reality.

Your answer does not really address the original question. Can you please [edit] your answer to add points relevant to the question? Otherwise your answer may be deleted.

Minimum  concentration in PPM to support plant life varies from 185 ppm to 225 ppm. We are at 433 ppm at the moment. Prior to this Ice Age cycle that started about 3 1/2 million years ago the PPM Norm was between 900 and 1120 ppm. For reference if anybody is interested in knowing where we are at prior to man cause global warming we were at 240 to 250 ppm.  Yeah when I discovered with the plant life minimum was and then where we were at it scared the shit out of me too I.

Welcome to BiologySE! Can you list some references for those values? I'm not familiar with them, and we always appreciate references.

Actually we are only at 405ppm (Source: NOAA https://www.esrl.noaa.gov/gmd/ccgg/trends/global.html)

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why plants cannot use atmospheric nitrogen?
Earth's atmosphere constitutes 78% of Nitrogen, then why do plants need to absorb Nitrogen from the soil. Why couldn't it possible for them to absorb the atmospheric Nitrogen like they do in the case of CO2.
Most of the plants relies on other sources to fix their Nitrogen, why couldn't be there a single plant which can absorb atmospheric Nitrogen ?
Is there any ancient plant which is considered to be using atmospheric Nitrogen ?

I have done a simple research, I could only find that previously
  atmosphere is not so abundant with Nitrogen and plants developed
  mechanisms to use Nitrogen fixed in soil. So now they are following
  the same mechanism when Nitrogen is abundant in the atmosphere. Is
  this a valid answer ?

@anongoodnurse: I had seen that question while creating this thread.....but the answers are some what vague....I have came through some other answers but I cant find any reliable references in the answers given to that question.

Atmospheric nitrogen is inert and poorly soluble in water. It has to be converted to a soluble form before absorption.

@WYSIWYG: Can you please expand and add it as an answer

@Jay - the question (and the answer) is not "vague".

@anongoodnurse: I don't know the exact word for calling those answers which are having no references.

I agree with @anongoodnurse that the question is a duplicate. The answers there are, however, not satisfactory in that they do not give a clear cut answer. Hence, putting a bounty on that question would help. I understand 50 rep may seem a lot, but it would be the way to go here.


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Which organisms have their cell wall made of polysaccharides and amino acids?
I came across a question which somewhat goes like

In which of the following kingdom, most of the members have a cell wall made of polysaccharide and amino acids ? - Monera or Fungi.

To me it looks like both are correct answers because both are having hetero polymers of glucose and amine. Please enlighten me if I am wrong.

The correct answer is Monera.
It is so because their cell wall is made up of peptidoglycan.

Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid. Attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer.

Fungi is wrong because its cell wall is made of chitin which lacks amino acids.

Chitin $(C_8H_{13}O_5N)_n$ is a long-chain polymer of an N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world. It is a characteristic component of the cell walls of fungi, the exoskeletons of arthropods such as crustaceans (e.g., crabs, lobsters and shrimps) and insects, the radulae of molluscs, and the beaks and internal shells of cephalopods, including squid and octopuses and on the scales and other soft tissues of fish and lissamphibians.


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Strange Cordeyceps-looking Mushroom in Australia
In the past few weeks, after the rain started up I noticed these mushrooms around my local area. I'd never seen them previously out of the 20 years I've lived here (a town in Queensland, Australia).
Sometimes they have a net-like section, and they sometimes have 10+ flies around a mushroom cluster.
What are these mushrooms? Are they common in Australia?

Given the gumtree leaves this had to be down under :) I haven't seen them anywhere her in the ACT. Too dry, perhaps :)

You found a member of the stinkhorn family, The Phallales (in the family Phallacea), probably a Veiled Lady (Phallus indusiatus) or a Phallus multicolor (they have other names as well.) They are common in Asia, Africa, the Americas, and Australia. Don't eat them; they're attractive to dogs (lovely aroma!) and there have been dog deaths.

These fungi produce a spore slime which has an intense smell of rotting meat or sewage, which is why flies are attracted to them.
They are commonly found in rotted woody material.

The link also says " An edible mushroom featured as an ingredient in Chinese haute cuisine, it is used in stir-frys and chicken soups. The mushroom, grown commercially and commonly sold in Asian markets, is rich in protein, carbohydrates, and dietary fiber. The mushroom also contains various bioactive compounds, and has antioxidant and antimicrobial properties. Phallus indusiatus has a recorded history of use in Chinese medicine extending back to the 7th century AD, and features in Nigerian folklore."

@Jay - Yes, I saw that. The Japanese eat pufferfish, too. That doesn't mean it's not poisonous. That isn't the only site I checked. The reason I gave that caution is that there have been dog deaths. It might, on the other hand, be more toxic in dogs than humans.

According to the Wikipedia page that you took this image off, the image shows a P. multicolor instead.


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The human organism knows what we have to eat?
My mother has told that if your organism needs a vitamin, you want fruits include that vitamin. For example you have lack of C-vitamin you would like to eat lemon. Is there any explanation for it, or just it is a myth? The human organism knows that what we have to eat?

Probably organism not organisation

@ChrisStronks Please don't recommend Skeptics unless you explain the requirements of the site. Especially the notability rules, which otherwise tend to get most questions by new users closed.

@MadScientist - I have removed my comments. What are notability rules? And which requirements do you mean? those from Bio.SE or Skeptics.SE?

Assuming you mean organism, not organisation, it's not entirely false that cravings can be driven by deficiencies. In the case of the eating disorder pica, where a person eats non-food items like dirt and clay, can be caused by iron deficiency (Source). However, that article also suggests the possibility that pica causes iron deficiency by causing the person to eat items that lower iron absorption. So, my answer to your question is, maybe.


text:
To which negatively charged components of the cell envelopes do the crystal violet complexes bind in gram staining?
The gram positive have negative components in the peptidoglycan layer in the form of teichoic acid phosphodiester bonds, and the gram negative have negative components in their outer membrane in the form of lipopolysaccharide. Is that where the crystal violet binds?

The gram staining relies on the differences in the bacterial membranes. The gram positive bacteria have a thick peptidoglycan layer on top of the cell membrane, the gram negative bacteria have a lipid layer on the outside followed by a thin peptidoglycan layer and then the cell membrane. See the image for clarification (from here):

Crytall violet dissociates into a positively charged dye molecule (CV+) and chloride (Cl-). The CV+ travels between the membrane layers (outer and inner membrane) and is trapped there by the addition of iodine. This is used to form large crytal violet-iodine complexes which are retained during the destaining process.
In the destaining process, the peptidoglycan layer of gram positive bacteria is dehydrated and therefore shrinks which prevents the staining from being washed out. In the gram negative bacteria, the outer lipid layer is removed and the peptidoglycan layer (which is much thinner) exposed which allows the removal of the stain. The teichoic acid is important for the rigidity of the membrane but not for the binding itself.
References:

Gram staining
The Gram Stain after More than a Century
Use of the Gram stain in microbiology


text:
Detailed mechanism of the cause of diabetes mellitus type 1?
I have read in some texts that diabetes mellitus type 1 is caused by degeneration of beta cells due to our body's own immune reaction.Is it true? Can you explain further how are such types of immune reactions are induced? And are there any other causative factors known?

It can be true of diabetes mellitus type I

Diabetes mellitus is divided into four  type 1, type 2, gestational diabetes, and specific type of diabetes. Type 1 diabetes is commonly called as Juvenile diabetes or Brittle diabetes.
It is also called as "Insulin-dependent diabetes mellitus (IDDM)". For our bad-luck the causes of Type 1 diabetes remains obscure, and scientists believes its mostly related to genetics and other environmental factors like mutations or virus attacks. I found some articles that may help.

But it
  is believed that genetic and environmental factors (possibly viruses)
  may be involved. The aetiology ('cause') of type 1 diabetes is
  unknown, but a good deal is known about its pathogenesis (the way in
  which it develops). As with other complex diseases, the outcome is
  determined by the interplay of multiple genes and (most likely)
  multiple environmental determinants, together with an element of
  happenstance. The risk of developing diabetes is strongly influenced
  by genes affecting immune function, particularly the HLA system,
  but other factors are involved. The best evidence for this comes from
  the study of identical twins: if one twin develops diabetes in
  childhood, the other (who has identical genes) has no more than a one
  in three chance of developing the disease. Prospective studies in
  human populations reveal that circulating auto antibodies directed
  against the islets typically appear in the first 5 years of life, and
  may be present for many years (sometimes 20 years or more) before the
  disease develops. A similar latent period is seen with coeliac
  disease, and implies that some sort of regulatory balance has been
  achieved within the immune system, and subsequently lost. This opens
  the door to the possibility of 're-education' of the immune system by
  various forms of immune intervention.
  Reference
The pathogenesis of Diabetes mellitus type 1 shows a strong tendency towards genetic related factors,

Reference


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How do genetic chimeras with different blood types not die?
If a person is a chimera and has two different blood types in his veins, how does he not die? Shouldn't the immune system attack one of the blood types?

In 1953 a human chimera was reported in the British Medical Journal. A
  woman was found to have blood containing two different blood types.
  Apparently this resulted from her twin brother's cells living in her
  body. More recently, a study found that such blood group chimerism
  is not rare.

Can you please give a reference for this happening?

This is particularly true for the marmoset. Recent research shows most marmosets are chimeras, sharing DNA with their fraternal twins.[5] 95% of Marmoset fraternal twins trade blood through chorionic fusions, making them hematopoietic chimeras.[6][7]

@Chris Taken from wiki page for chimerism

If they have both antigens from the beginning, they won't develop antibodies to them.

That's like people who have bloodgroup AB - if they have this from the beginning, they develop no antibodies.

Since these cells are there by the development of the immune system, the immune cells recognize them as self. By blood transfusion with incompatible blood type, the immune system recognizes the blood cells with different histocompatibility antigens (A,B,Rh etc...) as non-self, that's why it attacks them.


text:
What is the role pyruvate carboxylase in lipogenesis?
I just know that Acetyl-CoA is a positive allosteric modulator for pyruvate carboxylase, but I cannot find anything else.

Okay so pyruvate carboxylase is a ligase-class enzyme, meaning it forms covalent bonds. What we see is that pyruvate is carboxylated into oxaloacetate by pyruvate carboxylase, here's our proposed reaction,

What this does is replenish mitochondrial oxaloacetate levels, because when we switch into lipogenesis, TCA intermediates must be shuttled into the cytoplasm for forming triglycerides, like so,

Also here, page 2, they go into how the production of NADPH is coupled to acetyl group export and how PC must perform the aforementioned function to keep substantial flow maintained. Block quoted them for ease of access,

As shown in Scheme 1, the
  generation of NADPH is coupled to the transport of mitochondrial
  acetyl groups into the cytosol for fatty acid synthesis.
  Acetyl-CoA is generated in the mitochondria by the oxidative
  decarboxylation of pyruvate, and, after condensation with oxaloacetate,
  acetyl groups are transported to the cytoplasm as citrate,
  which undergoes ATP-dependent cleavage to yield acetyl-CoA
  and oxaloacetate. This pathway requires a continuous supply of
  oxaloacetate, which is produced by the activity of PC. AcetylCoA,
  a building block for the synthesis of long-chain fatty acids,
  is then converted into malonyl-CoA by acetyl-CoA carboxylase
  (ACC). Meanwhile, the oxaloacetate generated in the cytosol
  from citrate is reduced with NADH to malate, which in turn is
  oxidatively decarboxylated in a reaction catalysed by NADP+-
  dependent malate dehydrogenase (‘malic enzyme’; EC 1.1.1.40).
  The pyruvate thereby produced is taken up by the mitochondria
  and carboxylated to give oxaloacetate, while the NADPH
  generated is used in the pathway of fatty acid synthesis.


text:
Are bacteria necessary for an individual's life, or, how long could a person live without bacteria?
Bacteria are essential to life in that they are responsible for breakdown of organic substances, etc. but are bacteria necessary for an individual's life?
In other words, how long would a human survive if they took a super-antibiotic which killed all the bacteria in their body, with the current state of medical technology? If they died what would be the most likely cause of death?
Assume bacteria don't recolonize your body.
Background: I call bacteria the "Lords of the Earth" both to remind myself to be humble and (rather more) as a conversation-starter. I'd like to be able to underline their importance in the ensuing discussions.

I grant that the "Background" sentence is opinion-based but it was just intended as a light-hearted introduction. The "How long" sentence was my real question and is IMHO factual. In any case anongoodnurse has answered to my satisfaction (and surprise). Thanks!

Related: Do animal experiments really mean anything when it comes to extrapolating findings to humans?

You might need to demote your single-celled 'lords' to 'squires'. They're not essential to an individual's life. You wouldn't die (dispensing with the "how" right off the bat.) You'd be just fine if no bacteria reentered your body. Your fecal output would be greater; you would derive somewhat less nutrition from your food, you would need to take vitamin K, and there would be an adjustment period, but theoretically, you'd be just fine. You might even be healthier.
Your hypothetical is impossible, of course, because experimentation on humans is unethical. However, it might surprise you to learn that there are colonies of germ-free animals (also called gnotobiotic) used to study the effect of certain bacteria on animals.
The derivation of such subjects was initially fairly gruesome.

The process of engineering biology and machine began by removing intact uteruses from near- to full-term pregnant animals within a purpose-built germ-free "surgical isolator." The uterus was subsequently passed through various disinfection procedures, involving total immersion in germicide-filled "dunk tanks," before the progeny were surgically released and hand reared within a second microbially sterile isolator.

These animals are costly to keep, as you can imagine. The originals must be delivered by Cesarean section, and housed and raised in sterile conditions. But once you can do that, they can multiply.

To start a germ-free colony, one must remove a young animal from its mother’s womb through a careful surgical procedure to avoid exposing it to the microorganisms in the mother’s vagina and skin. Then, the animal is raised in a sterile cage and only exposed to food, water, and other equipment that has also been sterilized. On a weekly basis—or more often—a technician swabs cages and animal feces to ensure that no bacteria have contaminated the sterile housing. Once the colony has been created, it becomes easier to rear new germ-free animals; a germ-free mother can give birth naturally without exposing her newborns to any bacteria.

By the 1950s, researchers were rearing germ-free mice, rats, guinea pigs, and chicks inside sterile stainless steel (and later, plastic) housings. Germ-free animals are especially useful in researching, among other things, diabetes, auto-immune diseases, obesity, genetic engineering, cancer, immunology, nutrition, and the effects of normal intestinal flora on health.
Vitamin K must be added to their diets, and it is important to sterilize their food without destroying nutrients, but otherwise they do well in their environments. Their feces, of course, are sterile. Everything is microbe-free. They also have no "normal" antibodies.
Since generations of germ-free animals can exist and multiply, it is not only possible but quite likely that germ-free humans can exist as well.
Which is not to say that gut (and skin, etc.) microbiomes are unimportant. If you release a germ-free animal into a normal environment, it can die if it picks up pathogenic bacteria before more normal gut flora. To do this safely, a germ-free animal is first given a cocktail of bacteria to colonize the gut. After a while, they can be in a normal environment without problems. But your hypothetical human wouldn't even have this problem.
Germ-Free Mice
Gnotobiotics
Technology Highlights：ESTABLISHMENT OF THE FIRST GERMFREE MOUSE AND RAT COLONIES IN TAIWAN
"Life in a Germ-Free World":
Isolating Life from the Laboratory Animal to the Bubble Boy

I am rather confused how you cited the 4th source, but didn't use its case study of the bubble boy.

@MarchHo - answered in Meta.

So finally, how long can humans live without bacteria? Is there any data on the longivity of such animals? Please include it in your answer. Do they live longer? Is the lifespan normal? Or is it short?

@CRags The life is definitely not NORMAL if normal means what is most common. Such a person may need to take a lot of dietary supplements. However, it is possible to keep that person alive as long as there are no other problems (independent of the said problem). It is same as: can a AIDS patient survive as long as their replica without AIDS -  yes, as long as they are kept in sterile environment

@WYSIWYG - their lives are "normal" compared to the controls, who also don't live a "normal" life. A better question is, What is the average lifespan of a patient with HIV on all the proper medications compared to one without HIV. Normal here applies to health, lifespan, etc., not activities in the wild.

Now it begins to sound as if bacteria-free humans would suffer from vitamin K deficiency (hemorrhaging?). After all, a question like "how long could you survive in a vacuum" would hardly be acceptably answered by "indefinitely, if you had an adequate spacesuit"

I am not asking about normalcy of life but lifespan. (That is the question?) Does the bacterial flora affect the lifespan? Many physiological processes are altered, due to sterile environment. So will this alteration increase / decrease or have no effect on lifespan? How do you relate HIV with this question? Patients with HIV have bacterial flora. And having HIV is not a part of normalcy.  HIV would actively work against host immunity, while absence of bacterial flora would result in a situation where no immunity reactions need occur. Please explain more @WYSIWYG. As the OP pointed out,

contd... let's say that all nutrients that are known as needed as of today are provided resulting in no deficiency of "known micro and macronutrients" for simplifying the answer.

@NL_Derek - Vitamin K is actually a group of compounds. The most important of these compounds appears to be vitamin K1 and vitamin K2. Vitamin K1 is obtained from leafy greens and some other vegetables. Vitamin K2 is a group of compounds largely obtained from meats, cheeses, and eggs, and synthesized by bacteria. No deficiency would necessarily occur.

@CRags I don't think loss of microflora would have any direct effect on lifespan. We don't even have enough cases to document the problems that may manifest because of living in sterile environment for a long time. Recent studies suggest the role of microflora on cancer (both positive and negative): this is mostly related to the biochemical reactions they carry out but we have insufficient data to say if their absence would make a great impact on the body except in case of nutrition. Low immunity on the other hand can also lead to cancer even in sterile environment


text:
What are pseudoknots?
I'm trying to get my head around what a pseudoknot is and how I can identify them given some RNA string. For example, suppose I have a string s = CGUUGUGUACACGAUAGUACAU. Suppose the two longest substring inversions are identified in bold CGUUGUGUACACGAUAGUACAU, which form the stack of the hairpin and everything after the first substring and before the start of the last substring make up the hairpin as illustrated below.
                                  U G U
                                G       A
                                 U     C
                                  C - A
                                  G - C
                                  U - G A U A G U A C A U

By definition, a pseudoknot is defined as a secondary structure formed by pairing between a loop and a region located outside of the stem flanking the loop. In this example, we would start the pairing using some substring of the outer tail and start matching bases around the hairpin. My question: is the pseduoknot the alignment of these base pairs, and what is the significance of this alignment?

is the pseduoknot the alignment of these base pairs

I'm not exactly sure what is meant by alignment, but if you mean base pairing from the flanking RNA to the loop of the hairpin you have depicted, then you would have an H-type pseudoknot.
Since you are interested in predicting these structures, it's important to note that a nucleic acid sequence capable of forming the necessary base-pairs for a pseudoknot structure does not imply that the sequence indeed forms a pseudoknot. It's likely that the sequence has a minimum free energy (MFE) structure that is not pseudoknotted. So the base-pairing capability is necessary but not sufficient for predicting these structures.
Take a look at the following (full-text) articles on pseudoknot prediction for additional information:

Computational Analysis of Noncoding RNAs
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
KnotSeeker: Heuristic pseudoknot detection in long RNA sequences

Are you aware of the requirements for predicting these structures? Thanks for the articles.

@ChrisD what do you mean by requirements; parameters?? You can read these papers for those.


text:
Procedure for doing western blot
I am writing a step by step guide for doing a western blot for a class.  It is intended for any  one with basic Biology lab skills.  I am hoping people will review my draft and give feedback on how to improve it.  Be as critical as you like about any aspect of it, I need it to be clear and concise as well as accurate.  Any tips appreciated.
https://docs.google.com/document/d/1Lpprwn4s127cb0D5TQezpurbjdF9hqJZQC0H7PIovE0/edit?usp=sharing

Welcome to Biology S.E.! If you need any assistance, please visit The Help Center.

You don't mention using a rocking platform in your blocking step. It's important or else all this particulate will sediment. Also this isn't really a question


text:
Common properties of herbs in creating anaphrodisiac effect?
Recently came across Wiki article about anaphrodisiac herbs and other products.

An anaphrodisiac (also antaphrodisiac or antiaphrodisiac) is something
that quells or blunts the libido. It is the opposite of an
aphrodisiac, something that enhances sexual appetite. The word
anaphrodisiac comes from the Greek privative prefix ἀν-, denoting
negation, and aphrodisiac, from the Greek goddess of love, Aphrodite.
Reference

The article mentioned some of the herbs and plant related putative anaphrodisiacs like,

Marjoram (Origanum majorana) (Family: Lamiaceae)
Humulus lupulus (Family: Cannabaceae)
Heracleum mantegazzianum  (Family: Apiaceae)
Morton Arboretum  (Family: Salicaceae)
Vitex agnus-castus (Family: Lamiaceae)
Ruta graveolens (Family: Rutaceae)
Coriandrum sativum (Family:  Apiaceae)
Tropaeolum tuberosum(Family:  Tropaeolaceae)

I am not sure that is there any relevance in these claims that these herbs triggers anaphrodisiac effect.
The question is,
Is there any common alkaloid, aromatic hydrocarbons or any other chemicals present in these herbs which triggers the anaphrodisiac effects ?

Why down vote ?

This might answer part of your question: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731873/

@skymninge:Which part ?

I did not read all of it, but it looked to me like it mentioned at least some of the herbs and the chemicals you were asking for.

@skymninge - that article deals with aphrodisiacs


text:
What is the role of Aspartate Transaminase in gluconeogenesis?
I know that oxaloacetate cannot cross the mitochondrial membrane, but can instead be converted to aspartate, shuttled out, and then re-converted back to oxaloacetate.  What does this have to do with gluconeogenesis?
The traditional route is to convert pyruvate to OAA to malate in the mitochondria, shuttle the malate out, and then convert malate back to OAA in the cytosol.  If lactate is the precursor, then the conversion of lactate to pyruvate in the cytosol can generate an NADH, making the conversion to malate in the mitochondria unnecessary.  Thus, OAA is converted directly to PEP in the mitochondria by mitochondrial PEPCK and shuttled out to the cytosol to begin gluconeogenesis.
If we have these two pathways, what is the point of using aspartate?

I think it is the other way round. Aspartate is pushed into the gluconeogesis pathway via OAA

I may have approached this problem from the wrong direction, so here's my attempt at an answer:
For gluconeogenesis to function, glycolysis needs to be shut off.  Glycolysis feeds the TCA cycle with Acetyl-CoA through the decarboxylation of pyruvate, and without glucose as a source, we need to look to other methods of generating OAA to make into PEP.  We can make OAA through Aspartate Transaminase by reacting Aspartate with α-ketoglutarate.

Here's an excerpt from Oregon State. See the section titled "Spatial separation of gluconeogenesis metabolites."

Now, the answer to "Why is aspartate pervasive in cellular metabolism?" That's a particularly hard to answer, and my speculation, in part, is that this was simply how the system evolved. We see aspartate participate and act as a precursor to many pathways, esp. in amino acid metabolsim, but not much data exists yet as to the "why" of it all.


text:
White/Gold vs Blue/Black dress
So I'm sure you've all seen the dress photo where people see the dress as either White and Gold or Blue and Black.
It has essentially 'split' the internet because some people see the dress and they think that it is coloured blue and black, whereas the other half think that it is white and gold. It is trending on most social media sites as people fight about what the colour difference is.
So my question is why do different peoples eyes perceive different colours in this picture specifically?
For reference the photo with a color breakdown can be found here

possible duplicate of How can you test what color different people perceive?

Sorry, I meant this as a specific question for this photo, not just in general. As far as I can tell, perceptive difference is totally random.

Whether you see it as blue/black or white/gold depends on how you interpret the spectrum of lighting in the room. I would guess that different interpret that differently based on the subtle cues available in the rest of the picture. But I don't have a solid explanation of what those differences might be or why people might cue on different aspects of the image.

U did put up the pic later so you can hardly blame me for closing it as a duplicate

True. Not blaming in the slightest, simply clarifying what I meant.

Please add more information about the background of the question otherwise it is likely to be closed as unclear

It's a possible duplicate of http://cogsci.stackexchange.com/questions/9405/what-color-is-this-dress-and-why on Cog Sci.SE and it has been quite neatly addressed there in an answer.

Two popular articles on this: http://www.dogonews.com/2015/3/6/white-and-gold-or-blue-and-black-the-great-dress-debate and http://www.wired.com/2015/02/science-one-agrees-color-dress/


text:
What is the chemical makeup of mealworm frass?
We have been raising mealworms for some time and while mealworm frass has proven very useful as a plant fertilizer, I started wondering about other potential uses of this leftover waste.
Can someone please explain what kind of compounds make up the frass from mealworms as percentages of overall makeup?
In particular I would like to understand how mealworm waste compares to other commonly used animal wastes used as fertilizer.
Bonus points if you can suggest other applications (than just fertilizer) for mealworm frass!


text:
Survival of streptococcus after my scarlet fever
I'm currently sick because of scarlet fever but I got treated with antibiotics. I know that after 1.5 day using antibiotics the streptococci I release at home are dangerous anymore. But my question is, what about the streptococci I've spread before? I've read that Streptococcus pyogenes can survive 3 days to 6.5 months outside the host, does that mean, I have to disinfect the whole house? And if so, with what should I desinfect? I worked heavily on the laptop, how do I desinfect that? Thank you.

Seeing that the OP is enquiring about the survivability of a virus outside a host, I don't consider this a medical question.

@TheLastWord .... "does that mean, I have to desinfect the whole house? And if so, with what should I desinfect?": This is a health advice

I'm sorry, I didn't find any medical/health stackexchange, and my question is about the survival of a bacteria, why is that not related to biology and bacteriology? I highly doubt that many physician that know. I just want to know, how long they survive and how big the danger of infection is, implying whether I have to desinfect some thing or not.

Please see here to understand how health advice works:http://meta.biology.stackexchange.com/questions/2885/what-is-health-advice?noredirect=1#comment2709_2885

If you can remove the data about the personal sickness and recovery, your question won't be considered health advice anymore.

It is hard to answer this question. There is an http://en.wikipedia.org/wiki/Infectious_dose by every disease, so you might don't need to disinfect the whole house. (I don't know the exact number by S. pyogenes, it probably depends on host.) You can reduce the risk by cleaning the tools you touch most frequently. You should find something which does not damage the plastic your laptop is made of.
@TheLastWord S. pyogenes is a bacteria and not a virus. Btw. I don't think this is a medical question either, it is about disinfection and not about how to cure the disease.

@inf3rno This was the answer I've been looking for. I'm not sick anymore, so it's not a health advice question but a general question about the bacteria itself.

@AndSchu Be aware that you are more (but not completely) resistant to further infection, than people around you who never got the disease.

"Note: Septic sore throat, scarlet fever and other pyogenic and septicemic syndromes are also infrequently acquired from ingestion (low infectious dose of <1000 organisms) of contaminated food (onset after 1-3 days)" http://www.life.umd.edu/classroom/bsci424/PathogenDescriptions/Streptococcus.htm So I think you don't need many of them to get infected. If somebody has your S. pyogenes strain in they flora, then they probably need a much higher dose to become ill. Btw. this is just my opinion, I don't want to look for articles, so I won't post an answer.

@anongoodnurse Fine, I was hasty and put that comment up doesn't mean you be all sarcastic about it.

@TheLastWord - It was unkind, maybe, but not sarcastic. Haste makes spilled milk.

The Streptococci are a part of the normal human flora.

The streptococci are widely distributed in nature and frequently form part of the normal human flora (seeTable 29-1). Approximately 5-15% of humans carry S pyogenes or S agalactiae in the nasopharynx.

Please see:http://www.ncbi.nlm.nih.gov/books/NBK7611/#!po=51.4706 for more details on epidemiology of streptococci.
As 5-15% humans have it in their nasopharynx, it is not really possible to maintain streptococci free environment. It will get repopulated quickly.
Usually the reason you get infected is because of some alteration in your normal flora.

S pneumoniae and, to a lesser extent, S pyogenes are part of the normal human nasopharyngeal flora. Their numbers are usually limited by competition from the nasopharyngeal microbial ecosystem and by nonspecific host defense mechanisms, but failure of these mechanisms can result in disease. More often disease results from the acquisition of a new strain following alteration of the normal flora. (From the same article, under pathogenesis)

So basically disinfecting wont help much as humans have the streptococci as a part of their normal flora. And it is very likely that the people you live with or come in contact with regularly have the streptococci already in their flora (either they got it from you or they originally had it themselves).

If something is wrong please tell it in the comments along with down voting so that the OP can get the correct view!

If someone simply downvotes for the sake of downvoting then I don't mind! Have fun :)

I don't think this is true. There are many strains of S. pyogenes, and s/he is probably infected with a new one.

I pointed it out in the second quote, that a new strain (a change in flora) can cause it @inf3rno

With this logic we can call every infection as "change in the flora"...

That is what the paper said. I did not tell anything on my own. Well, if you choose to disagree, I can't help it. @inf3rno

I think the wording of the article is not the best, there are lot of opportunistic pathogens which work the way they described, e.g. by C. difficile we use to talk about infection and rarely about the change of normal flora. Every pathogen has an infectious dose, so by disinfecting the house or the tools they frequently used, they can reduce the risk of somebody else gets infected. I think this is independent of whether somebody already got the new strain. (That probably increases the infectious dose, but does not make you totally protected.)

The fact remains that the host may get infected with normal flora strains too due to some alteration in the host and or the flora. Are you telling this mechanism is wrong? @inf3rno

Pathogen which gets outside the body has to compete with the normal flora which is already there outside the body. The advantages it enjoyed inside the body due to its increased virulence (thus ablity to penetrate host defence) won't help it outside the host where it has to compete with other micro-organisms against which it has no special supressing effect. So its replication and survival is not a surety

"The fact remains that the host may get infected with normal flora strains too due to some alteration in the host and or the flora." - Ofc. this is true. If we are talking about a new strain, then we cannot say that it was originally part of the host's flora, so we call it infection. By S. pyogenes, getting infected with a new strain typically causes disease (which in rare cases can lead to death). After that the host's immune system and other microbes in the flora learn to deal with the new strain.

It will probably die outside of the host after a while, but it is better to make this faster with disinfection, so you will protect those who are not infected. I don't know the exact data about how S. pyogenes survives outside the body, so that's all I can say currently. gn8! :-)

Good night! Have a good sleep!


text:
How do I use BEAST for divergence time estimation in this case?
I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ago. That is all the information I have. Is it possible for me to do a divergence analysis using BEAST and set an informative prior based on the information I have ?

Doesn't BEAST require molecular sequences for it to do its work?


text:
What (open) software there are for simulating behaviour of human (cortical) neurons?
Is there any reliable open-source software for simulating the behaviour of human cortical neurons? I am looking for serious software, so let's assume I have access to a computer with more than 10,000 computing cores.
What I would like to do is to scan a subject's brain with MRI, record EEG during a simple task (e.g. listening to tone pips), project the EEG data to the cortical surface calculated from the MRI (solve the so-called electromagnetic inverse problem), and once that is done try to simulate the behavior of the cortical neurons at the "active" regions.
This simulation part is new to me, the rest I know quite well. All hints and ideas are welcome!

I just know NEST, but how would you get the map of the connections ?

The answer by Memming is a bit misleading. People do source-modeling with EEG and MRI all the time in neuroscience, though, as stated, the accuracy is not that great (> 1cm). There's a great variety of algorithms for that, such as dSPM, sLORETA, .. Please mods make this a comment :)

Thanks for the feedback! Yes, of course you can do source localization, assuming there are a few dipoles (or under other simplifying assumptions), but it's difficult to connect to the neuronal level simulation as the OP wants to do. (Sorry. I don't know how to turn your answer into a comment.)

Perhaps I misread OP's question. Upon re-reading, OP only says "simulating the behaviour of human cortical neurons", I guess it could be larger scale model. I'm editing my answer.

There are a number of neural simulation programs available: Neuron, NCS, Genesis come to mind.  However, none of them have anywhere near the computing power to do even a halfway realistic simulation of a human brain.  You're looking at roughly 86 billion neurons, with something like 10K synapses each.

One can also use a distributed model, e.g. minimum norm estimates (when there's thousands of dipoles distributed along the cortex). This can be done using e.g. FreeSurfer+MNE.

Anyway, you are correct that is is an ill-posed problem. It is an inverse problem, having many (indefinitely) different possible solutions. The nice thing about the distributed models is that they use the shape of the individual's cortex for constraining the dipole locations and orientations. The answer then becomes unique..

Sure, you can regularize your solution, and put extra constraints to get a better solution, but do you really recover the behavior of the cortical neurons with a thousand dipole model? Are dipoles the right representation for neural computation? We don't know the answer, but I'm betting they are insufficient.

No, not in the neuronal level. Because IMHO this is an ill-posed problem.

EEG combined with MRI won't have the resolution to do solve the inverse problem of neuronal network simulation. There are at least hundreds of thousands of neurons that would be involved in your specific behavioral task, and you have at most a few hundred electrodes. You'll have to make grossly simplifying assumptions about how the brain works to start any inference. You might learn something, but the claim would be somewhat weak.
Personally, I wouldn't work with EEG if you are interested in the mechanistic details of the brain. It is a very useful signal for some cognitive investigations (especially for humans), but the current technology lacks the spatial resolution.

Yes, in the coarse scale network level. (response to @sets' feedback)

If you don't care about micro-scale dynamics of the neural network, and want to model some population-wide activation that changes EEG, as @sets commented, there are various source localization & dynamical system models that you can use. I am not an expert on this, so see @sets' answer, or hopefully someone else will answer in detail.


text:
How can TMS induce enough depolarization to cause an action potential?
Creating an action potential needs at least tens of mV potential difference across the membrane to occur.
But the membrane is really thin, surely less then 0.01µm (some reference give 25A).
Then the potential gradient, that is to say the electric field E, must be very strong :
The order of magnitude of the needed electric field is much greater than 10mV/0.01µm = $10^{6}$ V/m
But TMS produces E of the order of 200 V/m on the scalp, which is even less inside the brain. Then how can TMS induces neurons depolarization ?

Do you have a reference for those TMS numbers? I found here that computed field is even less, on the order of 1 V/m

http://cntrics.ucdavis.edu/c2meeting1/talks/Lisanby.pdf

my guess is that TMS is used to depolarize myelinated axons (white matter). They are thicker (up to 20um) so that required field is on order of 100s $V/m$, not $10^6V/m$. And here TMS fields are noted at 500V/m level

That would make sense

And by "depolarize" I mean that you don't explicitly cause action potential to fire (like cortical electrodes do), but rather increase excitability of the region. Does that make sense?

No I wanted to say depolarize enough to provoke an action potential

In fact I'm not sure the myelin explanation can work since an action potential can only be created at Ranvier nodes

I think my mistake was to believe that the electric field has to be somewhat perpendicular to the membrane, so that it can directly apply a voltage difference across the membrane, and that the resistance inside and outside the axon was the same, so that a tangential field was useless.
In fact these are false : depolarization and action potential creation happen where the axon is parallel to the electric field and where the gradient of the tangent field is the bigger.
Here you have a complete explanation but I think we can make a simplified one :
http://stbb.nichd.nih.gov/pdf/Nerve_Fiber_Stimulation_Model.pdf
Let's look at a membrane model (Hodgkin-Huxley) :

As we said if we try to apply an electric field $\vec{E}$ along $\vec{y}$ , it should be incredibly strong to produce a trans-membrane potential $V$ strong enough to create an action potential.
In between the inside an the outside of the membrane you have all the channels and the capacitance of the membrane. but I think the crux of the matter here are the resistances inside and outside : the small surface of a section of axon limits the conductivity, whereas the outside is supposed to be bigger so that its resistance is negligible.
As a result if you apply a gradient $\frac{dE_{x}}{dx}$ you can create trans-membrane current and potential:
because of the gradient, the fields $E_{1} = E(x)$ and $E_{2} = E(x+\Delta x)$ are different : $E_{2} = E_{1} + \frac{dE_{x}}{dx}\Delta x$.
Then using electricity laws :
$$i_{m} = I_{1} - I_{2}$$
$$i_{1} = -\frac{ E_{1} \Delta x}{R}$$
$$i_{2} = -\frac{ E_{2} \Delta x}{R}$$
then :
$$i_{m} = \frac{\Delta x}{R} (E_{2}-E_{1}) = \frac{\Delta^{2} x}{R} \frac{dE_{x}}{dx}$$
This trans-membrane current will produce a potential across the membrane which will be proportional to $\frac{dE_{x}}{dx}$, electromagnetic stimulations shows that TMS can easily produce gradients strong enough to create actions potential.


text:
Biochemical coupling between two enzymatic reactions - Enzymes physically associated?
I am wondering what the exact definition of biochemical coupling between two enzymatic reactions is. I know that these two enzymatic reactions have to

share the same intermediate(s)
one is thermodynamically favorable and the other is not.

So  the thermodynamically unfavorable reaction can happen when it coupled with the  thermodynamically favorable reaction. I just want to confirm that : Do these two enzymes have to be physically associated with each other? Since I do not have any evidence to support the physically interactions between these two enzymes, can I still use the term "biochemical coupling"?
Many thanks.

The enzymes don't need physical interactions to couple reactions. Some enzymes do share subunits which are physically associated, but this is a special case. The following review gives a sort of general example during glycolysis,

For example, in the biochemical pathway that breaks down glucose for energy, two enzymes work one after the other to create a high-energy ATP molecule:

We can also look at the peptidyltransferase reaction during the elongation step in translation. Earlier, an aminoacyl tRNA synthetase catalyzed the covalent addition of an amino acid to it's associated tRNA. The energy from breaking this bond in the ribosome provides energy for the peptidyltransferase to link the two amino acids together. This isn't assuming the ATP/GTP needed by elongation factors, etc.

In any coupled system the activity of one component is dependent on the other. For example translation and transcription are coupled; here translation is dependent on transcription but not vice versa. Coupling need not be bidirectional.
There is no question of unfavourable thermodynamics.
For coupled biochemical reactions:

One of the reactions should be dependent on the other. In multicomponent systems there should be at least a pairwise unidirectional dependency (A→B, B→C, C→D). In other words there should be a pathway that connects all the components.
There need not be any physical interaction


text:
How are 23 chromosomes in human sperm chosen?
I'm not biologist and I have just a basic knowledge. I've been thinking for a long time about the following question: How does the body choose which 23 chromosomes should be active in human sperm and female eggs?
Thanks in advance for helping me with this!
Edit:
Each egg cell or sperm contains 23 chromosome whereas a normal cell has 46 chromosomes. So How is it that those specific 23 chromosomes are the chosen ones. Are a random collection of chromosomes selected at the end of meiosis or is it more specific than that?

What do you mean by "decides, which chromosomes to choose to be active in human sperm and female egg"? The human body has either sperm or egg, not both. Or do you mean the developing embryo?

@chris I think that this question means the OP doesn't know of diploidy and assumes that a more or less random half of the chromosomes present in a normal cell end up in a gamete.

Amir, welcome to the site! Your question is very basic, and we have trouble finding out what exactly is unclear to you. Please edit the question to explain which situation you mean exactly (when are they "chosen"? Do you know that human chromosomes are paired? etc.) I will vote to put the question on hold until you have done so, else you will get the wildest guesses as answers, and they won't be very helpful. You can also try reading http://en.wikipedia.org/wiki/Ploidy, but I admit the language will be hard for somebody who is not a native speaker of English and does not know much biology.

This should clear up some of your confusion: Wikipedia: meiosis. Meiosis is the process that halves the genetic content and produce haploid eggs and sperm.

I understand your question, without you having to rephrase it. I found a helpful link for me. Maybe it helps you too. http://sciencelearn.org.nz/Contexts/Uniquely-Me/Science-Ideas-and-Concepts/Meiosis-inheritance-and-variation

They are not chosen, they represent an even half, a complete set of chromosomes.
The entirity of a cells genes (found on the chromosomes) is called a genome.
Somatic cells are the cells in our bodies that exclude sperm and egg. Sperm and egg are called germline cells.
The billions of somatic cells in a homo sapien have the same 46 chromosomes. 23 ( half) of them came from dad and 23 from mom. Thus we say somatic cells have two copies of each chromosome and it is abbreviated 2n. The germline cells are 1n or just n.
So your sperm has 23 chromosomes and after sexy time one of them can combine with an egg (which also has 23) to produce a cell(called a zygote) that has an entire complete genome (46). Then that zygote splits, and splits and splits.... And each time before it splits, all 46 chromosomes are copied (the copies are called sisters, or sister chromatids, respective to each other). The cells split into two new cells called  daughter cell and each daughter has an entire genome. This form of cell splitting is called mitosis.
Probably the most important event in the cell cycle is the duplication of every DNA stand. This is called a Synthesis (S) phase. This is not a component of mitosis! It's a required event that happens before mitosis. So all 46 chromosomes get copied and then during mitosis each copy (an identical copy) is attached to each other at a region called the kinetachor. A kinetachor attaches sister chromatids (each sister is a copy of each other).
At the beginning of mitosis a web forms in the cell and you can think of the strands that make the web as sliding chains that can pull stuff from the center of the cell to 1 of two perimeter locations (poles) of the cell.
The chain like web attaches to the kinetachor and it rips apart the pair of chromosomes, rips apart the sisters. So that one sister goes to one side of the cell and the other sister chromosome goes to the other side of the cell. So now at opposite sides of the cell you have a complete genome (which will become the new daughter cells).
An identical process occurs in meiosis (specifically meiosis II) which is part of the  process that forms the sperm and the egg. During meiosis however there's additional separation (separation of homologs which occurs in meiosis I) that occurs but it's really not pertinent to your question.

In biological terms, I believe the original question is asking if the separation of homologous chromosomes is random or not. Perhaps you could touch on that briefly.

Good point @canadianer

Thanks @rhill45 for your answer. I know the steps of the process, I just wondered, how are those initial 23 chromosomes chosen (@canadianer - separation of homologous chromosomes). So the answer is random as I deducted from your reply? Thanks! :)

@ememem It is random, and of course it would have to be: don't forget every person has hundreds of eggs or millions of sperm! The fact the assortment is random means every egg and sperm within a same person has a different combination of half of that person's chromosomes. If that weren't the case then brothers and sisters of same parents would be identical!

How specifically is this randomness achieved? Computers e.g. often have problems generating random numbers, how does the body achieve it?


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Are there cats with black skin?
Some mammals can have a black, pink or spotted skin, depending on race - see for example humans or pigs. But I recently learned that this is not the case with mice. Even black furred mice have pink skin, and there is a rare mutation which produces black skinned mice.
I was talking with a friend about cats and we got to wonder if (domestic) cats are the type of animal which can have dark skin, like pigs, or the type which doesn't, like mice. The tons of cat related sites on the Internet seem to all talk about black furred cats only, or about diseases presenting with skin discoloration, but they don't mention the skin color. So, which type of animal are cats?

A minor data point for you: look at the skin on the pads of the paws - our black and white cat has some black pads and some pink.  You might also look for pictures of cats that have been shaved for operations (e.g. spaying).

I have a black cat with white skin, so it doesn’t go hand in hand.

Easy: look at images of hairless cats. You will see they can be not only all black, but also grey, spotted, pink, and a few other rarer colors.

Also, take an average cat - and shave for surgery:

Note pigmented skin matching dark stripes.

This source seems to suggest that cats' skin colour is determined by their fur colour, as the same genes expressed in the fur which produce the colours (melanins) are also expressed in the skin.

The density of melanin can vary from one part of the body to another, down to patterns within individual hairs or gradients across skin, thus accounting for a wide variety of cat colors. Cats' skin appears strongly tied to fur pigmentation.
A cat who has darker fur probably has darker skin and vice versa on account of the melanin content of his skin and fur. Tortoiseshell cats and their white-stricken siblings, calico cats, have patches of both dark and light skin.

The color of mammals is determined by the pigment melanin. More specifically it is the mixture of the dark brown to black Eumelanin and the red to yellow Pheomelanin. These pigments are made a specialized cell type called melanocytes, which are located in the hair follicles (when they pigment the hairs) and in the skin.
Some animals (like mice) almost completely lack melanocytes in their skin (except for their ears, nose, parts of their feet and sometimes the tip of the tail), so they can only be pigmented when their fur is pigmented. For cats there is only very little data available and more, I haven't really found a good scientific article yet. From the descriptions (like here) I would say that the skin of cats is pigmented. Additionally they can get cutaneous melanoma which have their origin in skin melanocytes which would be possible if they weren't be there (this is the reason why mice cannot get cutaneous melanoma if they are not engineered).


text:
if the load is removed from an eccentrically contracting muscle, will it start contracting concentrically?
Geometrically speaking, a muscle contraction should exert a force between the two attachment sites. However, the actual effect of the force on the overall geometry of the body near the point of attachment may not match the direction the force pulls. For example, although the bicep contraction in principle would pull the forearm closer to the humerus, instead during eccentric lengthening the arm is actually extending due to how the rest of the system is configured. This is an example of where the direction of force exerted by the muscle doesn't coincide with the movement of the
My Question:
Can a muscle's net effect on the geometry of the system it acts on change mid-way through contraction?
For example, if my arm is eccentrically extending due to too heavy a weight in my hand and suddenly I drop the weight and now the bicep can contract. That's a simple example but I'm wondering how common it is for a the effect of a muscle's action to change midway through.

A muscle's action is one way, and not two-way as you seem to imply if I understand the question correctly. The biceps bends the arm by contracting. Upon bending the triceps relaxes. The reverse happens when the arm is flexed, i.e. the triceps contracts and biceps relaxes. Biceps and triceps are known as antagonists. Many striated (skeletal) muscles work this way, i.e., with antagonistically paired muscles.

These folks would seem to disagree: http://biology.stackexchange.com/questions/29655/do-both-ends-of-a-muscle-contract

They don't disagree with me and I not with them as far as I can see, it's kind of a huge post. Be specific in who disagrees with what and why.

It is not clear to me what you are asking.

The question in the title and the body are asking two different things.

I don't think this question is unclear. If I understand correctly, it's asking that if the load is removed from an eccentrically contracting muscle, will it start contracting concentrically.

Yes, that's exactly what I am asking. I just didn't phrase it that well. Maybe I should adjust the title

"This is an example of where the direction of force exerted by the muscle doesn't coincide with the movement of the"..... something missing here

Yes, because net force is the only thing that matters. To address @Chris's comment, in an eccentric contraction and a concentric contraction, the muscle is applying force in the same direction. However, in an eccentric contraction, the muscle is not applying enough force to actually lift the load. A biceps curl is a good model:

SportScience
In the second image, the muscle is contracting but not exerting enough force to lift the weight--the net force causes a slow lowering of the weight.

Rather than working to pull a joint in the direction of the muscle contraction, the muscle acts to decelerate the joint at the end of a movement or otherwise control the repositioning of a load. - Muscle contraction (Wikipedia)

It may be clearer with an actual force diagram:

University of Guelph
The only factor influencing which way the lever (your arm) moves is the net force. So yes, if you change the load (force F in the above image), the muscle could begin pulling your arm in the opposite direction. The muscle isn't really "changing action", it's exerting the same force, but now there's less force resisting it and the overall movement changes direction.
The question in the title and in the body are not really the same question, but the force is still exerted in the same direction as the muscle. You don't "see" movement in that direction because the forearm on which the force is being exerted is fixed at the elbow joint.

Yes.
You can confirm this by yourself easily. Put your right hand in front of your shoulder and use your left hand to push it out in front of you and downwards (keep the left upper arm in place). Resist the movement, so that your left biceps contracts eccentrically. Now snap your right hand away and you'll notice that your left hand snaps upwards (contracting concentrically).
This also works for isometric contraction (unless you're contracting at the end of the range of motion, because then the muscle cannot lengthen anymore for further concentric contraction). Do the same setup, but equalize the push forces the hands exert upon one another.
You can fonfirm this with another person exerting and releasing the force, if you're suspicious that you might be tricking yourself.


text:
Protein-Bound Drugs in Kwashiorkor
Kwashiorkor is characterised by decreased serum protein (including serum albumin) due to poor dietary protein intake.
What is the effect of this lowered serum protein on highly-protein-bound drugs? Is it substantial enough that administering such drugs (such as warfarin, though it's hard to imagine a situation in which a patient with kwashiorkor would need anticoagulant therapy) is potentially dangerous, and if so, can this be compensated for?


text:
how food moves in horizontal coils of small intestines
This is a very very basic question, and I am looking at it more from point of view of physics. The small intestine is a highly coiled structure, which means it has horizontal coils as well. I can understand the vertical downward movement of food (when the person is in standing position) due to gravity, but how come the food can move in horizontal direction?
Any insights will be highly appreciated.
Thanks

Food moves thanks to Peristalsis through whole gastrointestinal system

@Mithoron closely related (and the answer is the same), but not a dup--this question asks specifically about the small intestine, whereas the other asks about swallowing

Food moved against gravity too, thanks to peristalsis.

@Luigi if another post has the same answer then this can be considered a duplicate. Note that duplicate doesn't mean a bad question; It just reduces redundancy of posts.


text:
interpreting enhancer and promoter regions of a target gene
I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor binding sites.
The paper says

Sequence data were taken mainly from the international nucleotide
  sequence database. Accession numbers and approximate locations of the
  MEF2 site centers are as follows: human adolase A, X06351 and
  1985/1986, rat adolase A, X04260 and 450/451...

Now, I looked up accession number X06351 but I find no evidence of a enhancer region on that page.
Can someone explain to me how I should be looking for these sites?
The paper is available for free and can be found here: Link to paper
My interest is in the first and third paragraphs of Materials and Methods where the first paragraphs gives a general description of the MEF2 sites and the third paragraphs gives specific accession numbers.

Can you provide a link to that paper?

The NCBI nucleotide page will not have information on regulatory regions. Check out UCSC browser for that gene and allow the display of tracks for regulatory regions. If the annotations are there in the records then it will display that region.
The paper mentions the center of the enhancer site, look for the 1895th position in the sequence.

I've added the paper in question. I'll check out the UCSC browser and see what  I can find there.

So what information are you looking for exactly?

Well basically like you said, the annotation. I want to look at the specific bases at site 1985/1986 and some sort of validation that this is indeed a MEF2 binding site. But I don't know how to use that accession number and put it in the genome browser.

just put the gene name in the browser.

Searching for aldolase A shows me many different forms (with the same name but different coordinates). Is there an easier to way to go from accession number to genome browser?

Hm, correct me if I am wrong but the link I provided (for the accession number) only talks about CERTAIN features of the gene right? It's like a little summary based on a study. The actual gene may be much bigger than this and may have OTHER features also not covered in this accession number. Am I correct?

Aldolase-A has six variants arising from the same position. Click on any of that and you can see the genomic locus. If I am not wrong they all have same 5'UTR (which is what the linked sequence is).

The NCBI nucleotide page does not have information on regulatory regions.
UCSC browser also displays regulatory regions mostly based on the ENCODE ChIP-Seq data. ENCODE project has MEF2 ChIP-Seq experiment for human cell lines. You can have a look at that. There is a MEF2 ChIP-seq experiment for mouse too.
You can analyse these data for a more detailed information.

I am relatively new to this. So basically, if I look at the peaks of MEF2 Chip-Seq data from ENCODE I should see a peak where my original paper is saying there exists a binding site?

@masfenix Yes you would see a peak there. You can also get the sequence of MEF2 binding site.


text:
Two heterozygote mice for skin color are reproduced. Find the probability that in 3 children 2 will be dark and one white
Two heterozygote mice for skin color are reproduced. Black is dominant to white color. Find the probability that in 3 children 2 will be dark and one white. How did you do the ordering. Well I found it that in F1: 1/4 are AA, 1/2 Aa, 1/4 aa or 3/4 black and 1/4 white.Now nI think I should multiply the chances: 3/4*1/4*3/4, but it would be according to an order. What should I do? Is my answer correct?

You are on the right track, but you have to keep in mind there are multiple ways to have two dark and one child in a group of three. You have to add the probabilities of each unique outcome that results in two dark and one light child. So, the probability is (1/4) x (3/4) x (3/4) PLUS (3/4) x (1/4) x (3/4) PLUS (3/4) x (3/4) x (1/4)

Alternatively, multiply one outcome by 3P1.