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Length of dispersal flight of European spruce bark beetle?
I'm interested in length of dispersal flight of Ips typographus. I can barely find some information about dispersal distances, height of dispersal flight, but not at all information about how many days does it takes for one beetle to find suitable host in average? The only information I found is that it is highly variable (Forsse, E., & Solbreck, C. 1985. Migration in the bark beetle ips-typographus duration timing and height of flight. Z. Angew. Entomol. 100 (1). 47-57). I also know that it is weather dependent but this won't help me... thank you !!

You should check out this recent dissertation, which might contain useful information: Kärvemo. 2015. Outbreak dynamics of the spruce bark beetle Ips typographus in time and space.

thanks @fileunderwater! I didn't know about this one !

The number of days may still be unknown, and it is probably a large variation when they find a suitable host tree. The "pioneer males" might use "random-walks", when they try several trees before they chose the right one. Its also a large difference between endemic and epidemic periods regarding dispersals.
Anyhow, the flight distance of I.t. has been shown to be more than 8 km (see Botterweg, 1982), but during outbreaks when it can be pheromone sources everywhere most of them may disperse less than 500 m and maybe even less than 100 m. See:
Kautz. 2011. Quantifying spatio-temporal dispersion of bark beetle infestations in epidemic and non-epidemic conditions.
Whichmann and Ravn. 2001. The spread of Ips typographus (L.) (Coleoptera, Scolytidae) attacks following heavy windthrow in Denmark, analysed using GIS
and as mentioned above, the dissertation by Kärvemo and articles within.
I hope this helps.
cheers
Simon

Hi @SimonKärvemo, thank you very much for the answer and for the proposition of different papers. I hoped to obtain a type of answer as "10 days" or similar but I was sure that it will not be so simple... I am working with Kautz's paper but they simply establish that the flight  takes "several days". I also wanted to relate it to IT life cycle but this is highly variable too ( from 7 - 11 weeks - it is almost the double ! - to establish the threshold value). So, it still remains unknown... but I feel much more sure about this information now ! :)


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Model for calculating muscular activity from external measures
A physiologist wants to measure the intensity of the activity of a muscle or muscle group over a certain period of time. But the physiologist cannot measure what happens inside the the muscle itself (the strain on fibres, the blood flow and nutrient #Umsatz#, etc.), so the physiologist measures what the muscles do – the duration, force and frequency of contractions – and unifies these measures into a concept of "intensity of muscular activity" or "strain".
For example, think of an office worker clicking his or her mouse button. The physiologist conceptualizes the intensitiy of muscular activity as consisting of three partial aspects: the force with which the mouse button is pressed, the duration for which the mouse button is pressed, and the frequency of pressing the mouse button.
It is important to consider both frequency and duration, because there might be a difference between pressing a button for 30 seconds and then resting for 30 seconds, and pressing a button for one second, resting for one second, and then repeating the procedure for a minute. The same overall duration of muscular activity spread differently over the same period of time might "strain" the muscle differently.
So the physiologist measures these three aspects, and then calculates the latent construct "muscular activity" or "strain" from the three measures. But what formula would the physiologist use?
I'm pretty sure someone in sports, occupational or military medicine must have modelled this construct theoretically and/or validated it experimentally, but I cannot find anything in the literature.
Does anyone here know any models for calculating amount of muscular activity over time from external measures?

Electromyogram is one way to measure the electrical activity of the muscles.

@WYSIWYG Yes, and it gives duration, frequency and intensity of muscular activity, so how do I integrate all three aspects of the measurement into a unified scale?

@what Even with perfect EMG recordings, I think developing a general model is going to be a huge challenge. Every muscle (which will also vary somewhat person to person) has a different relative fiber type composition (different myosin isoforms) and different numbers of motor units which are recruited in different ways depending on the muscle/person/activity.

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What plant is it?
Do you know what plant is it? I found it in France

Why was this downvoted?

@MarchHo possibly because there is no mention of size/scale, what the overall plant looks like, where/when it was found (mountain, valley, seaside, plains, dry, wet, hot, cold, summer, winter, etc.).

That looks like a magnolia tree, those pods should bloom into an impressive white flower. https://en.wikipedia.org/wiki/Magnolia. While I can tell as much as that, I'm not familiar with identifying these any further.

I dont think it is a Magnolia tree because of the its size its huge!!!

That's a magnolia tree. They are grown around the world for ornament, wood, and foliage.
The seedpods are a bit further along than my nice, unripe one, but as they ripen and dry, all those "scales" (see the line up the middle of each one?) open up and let a ripe seed into the world.

Note the shiny, thick (evergreen) pointed oblong leaves with brown fuzzy undersides.

I would guess by the seedpod and the shape of the leaves that it's a Magnolia grandiflora. Magnolias are an ancient tree, like the Ginko.

Magnolia is one of the most ancient angiosperm (flowering plant) genera, with fossil specimens dated at 20 million years old, and fossils of plants belonging to the Magnoliaceae family dating to 95 million years ago. The genus appears to have evolved before bees appeared, so the floral structure developed to encourage pollination by beetles...
Eight species of Magnolia are native to the southeastern U.S., where they have become a popular symbol of southern culture, used in myriad place names and in literature, music (including magnolia-titled songs by the Grateful Dead, Beck, and JJ Cale), movies, and art. Magnolia is the state tree of Mississippi, and M. grandiflora (southern magnolia or sweet bay) is the state flower of both Mississippi and Louisiana.

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What is the name of the plant with the down-falling light purple leaves?
I've seen this flower in Scotland in August 2015:

What is the name of that flower?
To help people google it:
The plant has light purple leaves with some white spots. On those white spots are dark purple points. It is sometimes quite high (about 1.70m I guess). The bloom points downwards.

I'm asking this question because I would like to upload the photo on Wikipedia Commons. And for personal curiosity.

The common name in English is "foxglove". Note that they are poisonous.

Wow beautiful but do you telling that bright purple big things? they're NOT leaves. it is flower's corolla where petals fused and formed a bell-shaped structure. The 2-lipped 'personate' corolla with specialized abaxial surface ('throat') (here with dots and a tongue like shape) is a common characteristic of scrophulariaceae, or the snapdragon's family. It seems to be Digitalis sp of that family (however wikipedia shows now shifted to plantaginaceae)

It is a Digitalis purpurea
From the wikipedia page:


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What are those huge plants / fungi on trees called?
I've seen them in Scotland in August 2015:

The plants / fungi were quite high (over 2m) on the tree. They are almost circular if you view them from the top, I guess (except for the part where they are connected to the tree). I guess the diameter of them might be over 14cm.
What are they called?

I'm asking this question because I would like to upload the photo on Wikipedia Commons. And for personal curiosity.

From a basic google search they look like hoof fungi, but I could be totally wrong.

Are you asking for the species name or the general term for this type of fungi with "woody" fruit bodies? If you are asking for the general term, that is Polypore.

@fileunderwater The more exact you can say it, the better. But I'm already happy about "Polypore" :-)

It's a bit similar to the common Fomes fomentarius (which grows on birch), but I don't know the group well enough to say.

@fileunderwater That was my guess at first, but a quick check seemed to show their fruiting bodies look rather different.

Ok, it's now on Wikipedia: https://commons.wikimedia.org/wiki/File:Inverarnan-Tyndrum-2-Polypore.jpg

Well I will agree with fileunderwater, it is a Fomes fomentarious. For more info check this: Fomes fomentarius is a tough perennial polypore that usually becomes hoof-shaped with age; it is found on standing and fallen hardwoods. Its woody upper surface develops grayish zones, and its brown pore surface features tiny round pores. When sliced open (no easy task, given its toughness) it is usually composed more of vaguely layered tubes than flesh.
Along with Piptoporus betulinus, Fomes fomentarius is one of two mushrooms that the Tyrolean Iceman was carrying around 5000 years ago. He apparently used Fomes fomentarius as tinder.
Description:
Ecology: Parasitic and saprobic on the wood of hardwoods (especially birches and beech); causing a white rot; growing alone or gregariously; perennial; fairly widely distributed in northern and north-temperate North America
Cap: Up to about 20 cm across; shell-shaped to hoof-shaped; with a dull, woody upper surface that is zoned with gray and brownish gray.
Pore Surface: Brownish; 2-5 round pores per mm; tube layers indistinct, brown, becoming stuffed with whitish material.
Stem: Absent.
Flesh: Brownish, thin, hard.


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Colorado potato beetle diet
The Colorado potato beetle is best known for being a potato pest. However, I've just learned that it originates from Northern America and the potato itself comes from South America.
So the question is, what did potato beetles eat before they were introduced to potatoes?

Other Solanacae, in particular buffalo-bur — http://entomology.ifas.ufl.edu/creatures/veg/leaf/potato_beetles.htm#hosts — although the time period between discovery and potato was quite short.

I see, so the hosts were likely other members of the same family and not some completely different plant?

Basically, yeah.  This is a wolves-to-dogs thing, not a wolves-to-humans (bad analogy).

Please convert your first comment to answer

They ate other Solanaceae species.  This University of Florida info page gives an excellent overview of the species, including its hosts (emphasis mine):

Potatoes are the preferred host for the Colorado potato beetle, but it may feed and survive on a number of other plants in the family Solanacae, including belladonna, common nightshade, eggplant, ground cherry, henbane, horse-nettle, pepper (rarely), tobacco, thorn apple, tomato, and its first recorded host plant: buffalo-bur.

The naming history is a bit weird — being neither originally from Colorado or associated with potatoes — but hey, that's science.

That for the fun fact about the name :)


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Why Egg shell is not called a cell wall?
Egg is a single cell and has a outer hard covering outside inside which there is a cell membrane. Then why isn't the egg shell a cell wall?
Is it because no exchange of materials take place through it?

Note that the cell wall in most species does allow exchange of materials. It is quite porous and unlike the cell membrane.

related: http://biology.stackexchange.com/questions/21675/why-are-hard-boiled-eggs-so-homogeneous

Egg shells are actually porous so that the organism inside can aquire oxygen and get rid of carbon dioxide as it develops (http://www.scientificamerican.com/article/bring-science-home-chick-breathe-inside-shell/).
Although gametes (eggs and sperm) are single cells, an egg shell (or "wall" if you like) is created by the mother (therefore external to the egg cell) and contains many compartments separated by protein membranes:

https://www.exploratorium.edu/cooking/eggs/eggcomposition.html
The initial egg cell is a tiny fraction of a size of the egg visualised here, so it would therefore be incorrect to call the egg shell a "cell wall" as it is a structure independent of the egg cell itself.

Also worth mentioning is that usually a cell produces its own cell wall but the fertilized egg doesn't produce the shell. It is produced by mineral deposition from the outside.

Referring to oviparous animals (given that you mention a hard shell), an egg isn't a single cell. It contains a single cell (called the zygote) for a little while, which has its own cell membrane, but that quickly develops into a multicellular organism.

Since when does a zygote contain a cell wall? Animals lack cell walls entirely.

Isn't the egg then more of an analog to an external Uterus and placenta?


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What is the evolutionary tradeoff against primates producing multiple offsprings (litter)?
If we evolved to have multiples all the time we would more likely have extended families living together in 1 house. This would be better than the spouses by themselves for multiple reasons including money.
And during prehistoric times it would have been better for several reasons including that 1 would be more likely to survive than if it was born without any siblings.
Most mammals have litters of at least 2. An extreme of this is the cheetah which has litters of up to 9 cubs. They evolved to have litters because they were in conditions where 1 is likely to starve. Lions evolved this for a different reason since lions are not likely to starve. They evolved it because of the fact that they live in prides.
So for primates including us wouldn't it be better if they had litters often instead of single babies?

No. Primate babies require a lot of care, as a significant amount of development occurs post-partum. Even though, say, a lion cub requires care and teaching, they are born mobile and with the ability to see and hear fairly well, if not very well. Human babies, on the other hand, are completely helpless. Please remember that money is an extremely recent invention in the span of human evolution, and plays no selective pressure whatsoever. Families choosing to have a limited number of children are also an incredibly recent phenomenon (really, in the last 100 years or so).

This is not a duplicate. The answer here is not simply "because not everything advantageous will evolve", this question involves the classic tradeoff between litter/offspring size and the energy expended to care for them. It would not actually be beneficial for primates to have larger litter sizes.

@terdon I am reopening this. If you have an answer for this question then please post it.

There is a tradeoff between having multiple progeny, with relatively low parental investment in each, and few progeny, with high investment in each.  This used to be called "r" and "K" selection respectively, though the terms are now used less.  Very simplistically speaking, long-lived species within a fairly stable environment tend to produce few offspring and invest large amounts of care in each; this description fits primates very well, and so it's not surprising that they follow this paradigm.  The bottom line is that because of primate life history, having small litters is a more successful evolutionary strategy.
The Wikipedia article on r/K selection theory is reasonably good and points to updates and some further reading on the subject.

But some big cats have long lives and large litters. Lions are a great example because lions live for up to 15 years in the wild and have litters of up to 6 cubs.  Likewise some animals with short lives have small litters. So the r/K selection theory isn't completely accurate.

The r/K selection theory is not completely accurate (as I noted, the terms are being used less; and the link I included points out the same thing), but lions are not a good counterexample.  For one thing, lions are often used as examples of K strategists -- the average litter size is closer to 2 than 6, and a typical interval between litters is closer to two years than one.  Three or four offspring every couple years is certainly K-strategy, since with r strategists we're often talking about thousands (or millions) of offspring per year. But as I said, and repeat, K/r is oversimplified.


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Troubleshooting PCR Steps
I am troubleshooting a PCR reaction that gives me no product, and there are a lot of different approaches that I can find in books and just in google searching (things like running a gradient, increasing cycle number, etc.). But it would be really nice if somebody could list out in order the steps they take to troubleshoot a PCR reaction. Thanks.

Did you observe a small band due to primer dimers but not your target? or you got nothing at all? For the first one, redesigning primers is a possible solution as well as modifying the annealing temp. For the later, try running a positive control PCR to make sure your reagents are working.

This question is broad. You can troubleshoot PCR in a thousand ways depending on what the problem is. Can you ask a specific question?

I think 30 cycle PCR is maximum to see bands by electrophoresis in most of cases, because under the ideal efficiency, one copy could be detectable by 34 cycles of PCR. However, if your expected products are longer than 1 kbp, you might extend several cycles.
I usually add DMSO 5% in any PCR reaction. In my experience, DMSO would not interfere PCR reaction--you can amplify your fragments without DMSO; you could get PCR products with DMSO. Betaine sometimes work better than DMSO, so I am shifting my default reaction mix from 5%DMSO to 5%DMSO and 0.5M betaine.
For annealing temp, you can not tell which is better, lower or higher than the first trial which showed nothing. When increasing the annealing temp, primers may be able to access your target sequence more and you could get efficient amplification. So you might want to try both. If you have a PCR machine set various temperatures at once by gradient. You could include lower and higher temp together.
Alternatively, I sometimes use the touch-down method. You do not need to determine the best annealing temp in this case. If you just want amplified products, this could be a quick solution.
Additionally, hot start is also my default condition, because this could not ruin PCR reaction without hot start.
Basically, I change annealing temp. If I do not get good amplification and specificity, I change PCR enzymes. Changing PCR enzymes could mean changing buffer conditions because companies try to give unique features for their products.

Generally I start with a temperature gradient running in 2 deg steps above and below the calculated Tm (which I calculate by the simple 2AT4GC method). If that fails, I might try something similar along with PCR "enhancers" - usually some variation on DMSO or betaine. Depending on the problem (detection/cloning from a reverse transcription reaction? Sequencable fragment from genomic DNA?) I might try redesigning the primers, changing the type of PCR polymerase, or improving the template in some way.


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Variance in reproductive success and effective population size
Background
The effective population size $N_e$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration.
The higher the variance in reproductive success among individuals, the lower is the effective population. Consider for example, a case where the variance in reproductive success is so high that only one individual reproduces (selfing for example) and contribute to the next generation. In such a case the variance in reproductive success is so high that the effective population size is reduced to 1.
During a meeting I have encountered the following relationship between the population size $N$, the effective population size $Ne$ and the variance in reproductive success $V$.
$$N_e = \frac{N}{V}$$
It makes intuitive sense to me. In the extreme case where $V≈0$, there is no drift and therefore no loss in diversity, everybody contribute as much to the next generation and therefore $N_e=\infty$. By definition, in a Wright-Fisher population $N=N_e$ and therefore $V=1$ should be correct.
Questions

Where does the equation $N_e = \frac{N}{V}$ comes from? How to derive it? Is it an approximation or an equality?
Is it true that $V=1$ in a Wright-Fisher population?

Here is a related post.

If you have a copy of Ewens' "Mathematical Population Genetics", check out chapter 3.7 -- he discusses this.

Yes, I have one. I'll check this out. THank you


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What is the last heavy atom of an amino acid?
I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it all atoms but hydrogen? Atoms heavier than carbon? And how do I know which is the last heavy atom?
The article: http://bioinformatics.oxfordjournals.org/content/early/2014/11/08/bioinformatics.btu746.full.pdf+html
It talks about the last heavy atom under Materials and Methods 2.1.1 Individual Representation and Population Initialization

Your description is not quite clear. Can you please give the complete reference for the article you're reading, and also the precise quote?

http://bioinformatics.oxfordjournals.org/content/early/2014/11/08/bioinformatics.btu746.full.pdf+html

It's under materials and methods on 2.1.1 Individual representation and population initialization

I haven't heard of this concept before, but it looks like the LHA is a reference atom at the "end" of the amino acid side chain. The precise definition appears to be empirical / heuristic, see http://www.cbi.cnptia.embrapa.br/SMS/STINGm/help/lha.html

As mentioned in the comments by Roland, this term is not common and is first used by the authors of the mentioned paper (also the package mentioned by Roland in comments - STING).
From this link you can find the definition of the Last Heavy Atom which is possibly the most distal non-hydrogen (N, C, O, S) atom in the amino-acid side chain.
$$\begin{array}{|c|c|c|c|}
\hline
Ala\ :\ C_\beta & Asp\ :\ O_{\delta^2}  &Trp\ :\ C_{\eta^2}  &Asn\ :\ N_{\delta^2} \\
\hline
Lys\ :\ N_\zeta & Glu\ :\ O_{\epsilon^2}  & Ser\ :\ O_\gamma  & Gln\ :\ N_{\epsilon^2} \\
\hline
Cys\ :\ S_\gamma  & His\ :\ N_{\epsilon^2}  & Tyr\ :\ O_\eta  & Val\ :\ C_{\gamma^2} \\
\hline
Gly\ :\ C_\alpha  & Leu\ :\ C_{\delta^2}  & Met\ :\ C_\epsilon  & Ile\ :\ C_{\delta^1} \\
\hline
Arg\ :\ N_{\eta^2} & Phe\ :\ C_\zeta  & Pro\ :\ C_\delta  & Thr\ :\ C_{\gamma^2} \\
\hline
\end{array}$$
They have mentioned in the same link that:

If in any of the PDB files (to be analyzed by the BLUE STAR STING components) that specific atom (LHA) is missing in the record, then our algorithms will search for the next closer atom in the side chain that would be considered as the LHA.

The exact location of some of the abovementioned atoms.
Some of the locations might be confusing. So I am just indicating what these are, for a few the amino acids (especially for the branched and cyclic side chains). [Images reproduced from here.]
Arginine

The terminal nitrogens $\eta^1$ and $\eta^2$ are symmetric and the atom that is actually (stereochemically) the most distal is considered the LHA, as inferred from the protein structure. The second choice, obviously is the $\eta^1$-Nitrogen.
Aspartic acid

The two terminal oxygens ($\delta^1$ and $\delta^2$) in the ionized form are equivalent (also otherwise because of resonance). The actual distal atom would be labelled as $\delta^2$
you can extrapolate the same for Glutamic acid
Histidine

$\epsilon^2$ refers to the pyrollic nitogen. .
Leucine

The last carbons ($\delta^1$ and $\delta^2$) are equivalent and the choice is based on the actual distance. Extrapolate for valine
Phenylalanine

$\zeta$ refers to the carbon in the para-position of the benzene ring. For tyrosine the LHA is the oxygen of the para-OH in the benzene ring.
Tryptophan

Proline

For Aspargine and Glutamine the LHA is the amide nitrogen of the side chain.

From a search of Web of Science, it appears that LHA is a term that has been coined by informaticians and is not something that is used in Biochemistry or Organic Chemistry. There are only three articles that are under the topic "Last Heavy Atom," and all three are Informatics Journals. The abstract of this article gives a decent "definition" of the term. http://link.springer.com/article/10.1186/1758-2946-1-13

@AMR Yes it is not a standard term. There are quite some articles that use this term but I guess they are the ones using the abovementioned protein structural biochemistry package.

Seems a bit weird for the cyclic sidechains (except proline), given that they can rotate around the Calpha-Cbeta bond...


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How to convert FASTQ file format into GTF file format?
I have a plenty of FASTQ files (FASTQ is a standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer) and need to convert them to GTF format (gtf - file format used to hold information about gene structure which significant feature is that it is validatable: given a sequence and a GTF file, one can check that the format is correct. This significantly reduces problems with the interchange of data between groups).
I assume that (if those formats are popular files' standards) there must exist some software that easily converts information from FASTQ files to GTF file.
Did anyone hear about any such (is possible open-source) software? I am familiar with R statistical package and SAS and can learn Python on a fly.
Thanks for any help.

A quick Google search yields many hits, not to mention the feedback from below. Please [edit] your question and include more about what you have, what you don't have, what you're trying to do, what resources you have to work with, what your time constraints are, what your ultimate goals are, etc. There is absolutely no guarantee that anyone here will be able to answer it, or that it will be on-topic here, as "Too Broad" questions will get closed.

You should really read about both these file formats. As swbarnes mentioned, FASTQ and GTF hold different kind of information. GTF stores the annotation of a reference sequence. For example a GTF for a genome sequence will have the information about the locations of features such as genes, transcripts, exons, start codon etc.
FASTQ stores the sequence of a read obtained from sequencing along with the quality scores corresponding to each position.
As mentioned by others, asking for interconversion of these file formats, makes no sense.

I guess what you are asking for is "How to obtain novel annotations with a FASTQ file at hand?"
This also depends on what you want to annotate.
The sixth column in a GTF file refers to a score; you can assign expression values to different features. You can calculate expression using the read counts. If these are RNAseq reads then expression can be measured using packages like tophat-cufflinks, RNAstar or some others.
If you are doing ChIP-Seq then you can generate a GTF with a new feature called TFBS (transcription factor binding site) and annotate the locations. A popular package used for ChIP-Seq analysis is MACS, which takes your reads and outputs the TFBS in the form of a BED file which also stores co-ordinates. You can convert BED to GTF. You can also assign scores based on the read counts at different TFBS.
If you do not have a reference genome or if the annotation of the reference genome is incomplete, then you should first assemble your reads. If you have a reference genome then you can go for a reference guided assembly of the transcripts to obtain novel transcripts or splice variants; Cufflinks does this.
If you do not have a reference genome then you should go for de-novo assembly of your transcriptome and annotate the transcriptome for start codons or other features of processed transcripts. Velvet and Trinity are popular packages that do de-novo assembly.

A fastq contains sequences.  A gtf contains coordinates of where features like exons fall in a reference sequence.  You can't interconvert them, that makes no sense.

So it is impossible to create a gtf file when I have information only from fastq file?

If this is an novel organism, and you have a very nice large set of RNAseq reads, you could in theory align it to your reference, and make a gtf from that.  But in general, no, you want to download an appropriate gtf for your organism, not make your own.

No, I want to create my own file. I do have a very nice large set of RNAseq reads and the gtf file does not exist. That's the question :)

You can't just convert.  You have to align to your reference for starters, as Daniel says, making a gtf from scratch is a big project, to do it right will be a lot of work.  But if that's what you need to do, then that's what you need to do.

Your question is not very clear. What should the contents of your GTF file be? Typically, GTF files contain information about where exons are located in a set of DNA sequences. Determining the location and exon/intron structure of genes is no simple technical task (i.e. a "conversion" as stated in your question), but rather a large area of active research. Annotating genes involves the use of statistical modeling (ab initio gene predictors), aligning experimental evidence (ESTs, cDNAs, and potentially Illumina RNA-Seq reads), and in some cases manual refinement of computational predictions. If you're working with a model organism like human or mouse or fruit fly, reliable GTF files are readily available for download from public databases. If you're not working with a model organism, then you many have quite a lot of work cut out to annotate a genome from scratch.
Or perhaps you want to annotate new alternatively spliced isoforms for known genes?
Without more information, it will be difficult for us to help you understand how to process your raw data (Illumina reads in FASTQ format) into a GTF file that addresses some biological question you're interested in.

The Tuxedo Suite (Tophat, Bowtie and cufflinks) used to to process RNA_seq data, assuming that is the origin of your .fastq files, should work for you.
https://ccb.jhu.edu/software/tophat/index.shtml


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term for species that produces males only to mate with mother or sisters
In reading about unique reproductive strategies I've run into two closely related and comparatively unique mechanics.  Both involved a female who was born 'pregnant' with at least a male, but the male sole job was to impregnate the mother/sisters prior to immediate death, with the females never mating with a male other then their relative.  Thus, the outcome feels more similar to self fertilization of hermaphrodites then your traditional mutli-sex mating strategy.
I have heard of at least two species that did this.  One in which the son was born along with a batch of females that he immediately mated with, another where the son actually mated with his sisters while still in the womb, and the children would then eat their way out of the mothers corpse to be born (fun stuff!)
I also recall reading an article which said a mother would lay an egg to have a son who would mate with the mother to produce females and then immediately die.  However, this sounds so similar to the Haplodiploidy system that I wonder if the article I had been reading was simply misrepresenting a regular Haplodiploidy system by implying the males would never mate with other females (I read about it awhile ago so not sure, does anyone know if a species uses a haplodiplody system where the male never survive long enough to mate with other females?
I'm wondering if there is a name for this reproductive strategy.  Specifically for any strategy where a male is produced, but only as a means of providing DNA to mother or sisters; with no means to mate with non-familiar entities.

Dont bee's do this to some extent, via producing males for reproduction, and males for working? And if so, would that be considered Eusociality? Sorry if I am way off base, I am an undergrad. https://en.wikipedia.org/wiki/Eusociality

@RoSiv the first example I gave was one involving mites which do not have a eusocial (is that a word?) system.  Bees may do the same thing I described, but if so I think that's separate from eusociality.

@RoSiv - Bees aren't a good example of this as the drones of a hive leave as adults to find virgin queens to mate with. The queen of their hive mated with a drone outside of her birth hive to begin her own colony. She doesn't need to mate again.

The non-random mating of individuals within a population is called Assortative Mating. Mating specifically with individuals that share similar traits is called Positive Assortative Mating. However, sharing similar traits doesn't imply being closely related.
The reproduction by two closely related individuals is called inbreeding. The opposite of inbreeding is outbreeding (a.k.a. outcrossing).
To my knowledge, a mating system where all individuals inbreed doesn't have a special term. Searching google.scholar for mating system inbreeding will show you a lot of articles that talk about mating systems where all individuals inbreed without needing to use a specific term for it.


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gene duplicated on genome but is different
I've been looking at a miRNA cluster on a genome and I found it three times. The first two are right next to each other and look exactly the same, the third sequences is on a different scaffold of the genome and is both shorter and has a number of mismatches with the first two sequences.
Is there a particular name for this? The first two are most likely some sort of gene duplication, but I'm not too sure on what to call the third,
Thanks

That sounds line one of two things. Either a sequencing or assembly error (quite likely since you're talking about scaffolds so, presumably, not a completely assembled genome) or duplication and subsequent pseudogenization.
It is relatively common for genes to be duplicated and then to be rendered inactive by a mutation event. Such genes can still be detected in the genome and are called pseudogenes. The process of their creation is, unsurprisingly, called pseudogenization. You can think of such genes as fossils. They often have significant sequence similarity to the original and can even be transcribed.
A quick search brought up a couple of articles discussing the pseudogenization of specific genes:

Pseudogenization of CCL14 in the Ochotonidae (pika) family.
Pseudogenization of sopA and sopE2 is functionally linked and contributes to virulence of Salmonella enterica serovar Typhi.

That said, is also quite possible that what you describe is a simple duplicate that has diverged without becoming a pseudogene. The details will depend on the particular sequence. Are there in-frame STOP codons? Can the gene still be transcribed? Such duplication events give rise to paralogs (note that all three of the genes you mention would be paralogs of each other, it's just that one has diverged more than the others). You can read more about those here: What is the difference between orthologs, paralogs and homologs?


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What do Illumina HiSeq/MiSeq paired end reads look like?
My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this:
R1:
    AAAAAACCCCCC
R2:
    GGGGGGTTTTTT

Where the reads found in R2 are the reverse complement of those found in R1. This does not appear to be the case however, for my sequencing data. If it helps I have a read pair from one of my MiSeq runs below.
R1:
@M01814:86:000000000-A6MU9:1:1101:15397:1339 1:N:0:2
TACTCGCACCTATCCGGCACAGCAACACCATCTGGGGCTGAATCGCAATAGCATCTCTCACTTCCTCCATATCAGATTGCTCAAGGCAAGCACTACGCTGCAGTGCCCTCCACTCCCAATTCCCTGATGCTGGTCGTAACTTGCCACACCA
+
>>AA?BBBBBFFGGG2EEEGFBGHHHGA2FGHBGHF2EE?GHGHHFFEEHDGHEFGF5FEEFBGHGBCB5FHHH5F553@434FF31G11??233B1/1/?333B?3FB?/B24B2/2B2?44?3?23333B223<>@0CB22@2@F0/?/

R2:
@M01814:86:000000000-A6MU9:1:1101:15397:1339 2:N:0:2
TAAGGGGCCTAGAACAGGCACCATACATTCAATTGGCTGTGGCAAGTAACAACCAGCATCAGGGAATGTGGAGTGGAGGGCACTGCAGCGAATTGCTTGCCTTGAACAATCTTATATGGGGGAAGTAGACGAACCAATGTGGAGTCAGCCC
+
>AA>>>ADDAFFGGGGG4FGGGFHFHFHHHFHHHB3B32EFBGGE25FGHHHHACEGG533BAGFFF355331BG1@1>EF1E23F333/>//134B43?F34B3334B334444?443B?/<C/23333////<0/<11111/?01?G0?

For reference, this is the reverse complement of R2:
GGGCTGACTCCACATTGGTTCGTCTACTTCCCCCATATAAGATTGTTCAAGGCAAGCAATTCGCTGCAGTGCCCTCCACTCCACATTCCCTGATGCTGGTTGTTACTTGCCACAGCCAATTGAATGTATGGTGCCTGTTCTAGGCCCCTTA

This is the alignment (with BLAST; alignment shown only for the HSP):

                                                           60                                                                                148
                                                           |                                                                                |
TACTCGCACCTATCCGGCACAGCAACACCATCTGGGGCTGAATCGCAATAGCATCTCTCACTTCCTCCATATCAGATTGCTCAAGGCAAGCACTACGCTGCAGTGCCCTCCACTCCCAATTCCCTGATGCTGGTCGTAACTTGCCACACCA
                                                           |||||| |||||| |||||| |||||||||||| | |||||||||||||||||||||  |||||||||||||||| || ||||||||||
                                  GGGCTGACTCCACATTGGTTCGTCTACTTCCCCCATATAAGATTGTTCAAGGCAAGCAATTCGCTGCAGTGCCCTCCACTCCACATTCCCTGATGCTGGTTGTTACTTGCCACAGCCAATTGAATGTATGGTGCCTGTTCTAGGCCCCTTA
                                                           |                                                                                |
                                                           126                                                                                38

What was the size of the library and what is the read length?

MiSeq chemistry is 150 cycles and fragment size is exactly 150bp.

Are you sure the fragment size is exactly 150bp? Usually you have a distribution of fragment size.

How many such reads are there; did you remove the adapter sequences?

I am sure of the fragment size and the adapter sequences are removed, but thanks for blasting this, that is more of an overlap that I have been able to force. Maybe I just need to allow for many more mismatches than previously thought.

Where the reads found in R2 are the reverse complement of those found
  in R1.

This statement seems incorrect.
Paired-end reads comes from opposite ends of a fragment (you could learn the reason it happens from Illumina's video). If insert size is 150bp, read length usually is ~60bp as quality score after 60th bp is unacceptably low. In this case, R1 length is ~60bp, and it is 5'3', R2 length is ~60bp, and it is 3'5'. When a number of reads are enough to cover the gap, they form a contig.
Here's an illustration from Illumina's website:

There is a little wobble in the lengths of your fragments, that's why the reads don't exactly overlap.  Is there a reason that you are spending the time and money to do the second read when the first read gives you almost the exact same sequence information?

There is no wobble in these fragment lengths (this is not just fragmented DNA). And yes paired end reads are likely to be necessary.


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What is the use of crystallized Photosystems from cyanobacteria?
I read a lot of articles about techniques for the crystallization of Photosystem I and II from cyanobacteria. My question is what is the reason for that and what can you do with Photosystem crystals?

The main purpose of crystallizing a molecule or molecular complex like a  Photosystem is usually to provide a crystal for X-ray crystallography.  A crystal has its molecular components arranged in a structured systematic repeating pattern, and this repeated pattern allows the X-rays to reveal the 3-dimensional shape of one of the components.  Knowing the shape is of biological interest as it suggests how the molecules perform their function.


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Are there emotions that motivate pattern completion? If so, where in the brain are they located?
I have been studying musical "tension." Musical tension essentially refers to the "expectations" one builds up in a melody that are then "released" when a stimulus matching the expectation occurs. For example, if you play the white notes on a piano in order CDEFGAB, you have a "tension" that motivates you to finish the scale and play C to complete the pattern.
I am aware pattern completion occurs in the brain and have seen a few biological models of this. For example, with attractor network models of human memory. So I am not surprised obviously that pattern completion occurs. But this example with musical tension highlights how there is an emotion (aka drive or motivation) that compels me to complete the pattern. When I hear the sequence CDEFGAB, I am compelled to finish the sequence.
My Question
Can someone provide me of examples of canonical models of emotions influence on pattern completion? I would like to learn example mechanisms as to how, on a circuit level, emotion would influence pattern completion.  I am particularly interested in examples relating to common forms of human creativity like visual art, problem-solving, etc., but any examples will do.

This question should also be suitable for http://cogsci.stackexchange.com/, and users there might be able to offer a different perspective.

This "tension" is actually called anticipation in neurobiology and related fields. Whole purpose of this is to get higher reward. This is generally happens because of dopamine release. Many musicians have utilized this 'anticipation' technique in their compositions. Famous example is Led Zeppelin's stairways to heaven in which audience is 'anticipating' third part of song where Page's guitar in high tempo. Anatomically distinct dopamine release happens during anticipation and one will experience of peak emotion to music. You can read this paper for experiments related to this. This paper's introduction has given reference to many of such research papers. Go through it's references.


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How does Cro protein expressed by lambda phage kill its host?
I read that the DNA segment of lambda phage integrated in host DNA could switch between lysogenic state where cI represses the expression of Cro and lytic state where Cro expression takes over and self produces more.

But how exactly does the high production of Cro kill its host?
The virus has a DNA segment shielded with a protein coat. While entering host it gets attached to host membrane and releases DNA inside without damaging host. Then how does host get killed when virus goes outside it which happens during lytic phase and doesn't happen when it got inside?
And if the virus has to go outside host, it needs protein coating. How is that produced? Is it produced only during lytic phase or also during lysogenic phase?

Have a look at the wikipedia page on lambda-phage (it is nicely illustrated and referenced).
See this map of the lambda-phage genome (Source).

Cro (Controller of Repressor's Operator) does not kill the host. It is a transcription factor that represses cI. cI, in turn, represses Cro and other pro-lytic genes (expressed from the PL promoter), thereby forming a positive feedback loop with Cro (some people also use the term "double-negative" feedback loop which in my opinion is incorrect).
During infection the virus just injects its linear DNA into the host via a porin protein (a sort of membrane channel). But at the peak of the lytic cycle many virus particles are formed inside the host cell (not just DNA but fully packed viruses). The viral proteins R and S cause breakdown of the cell membrane and the cell wall, which facilitates cell lysis.
As mentioned in the previous point, the virus is fully packaged while inside the host. This happens only during the lytic phase. During lysogeny, the viral DNA gets integrated with the host genome and remains dormant until triggered by some kind of stress such as UV (which actually leads to activation of SOS response protein RecA which by degrading cI tilts the balance towards the lytic cycle).

I thought that a positive feedback loop is when a gene product either directly, or indirectly, stimulates its own activity, essentially an amplification mechanism.  I don't understand how cI and cro together form a positive feedback loop; doesn't each one shut down the other one?

@mdperry the sign of the loop is the product of all the individual interactions (or edges). So negative times negative is positive. By repressing its repressor Cro is indirectly activating its own synthesis (same for cI ).

The viral replication happens only due to the host reproduction, so one cell divides into two, each of the cells have only one viral dna segment integrated in their dna. At any time one host has only viral dna. Then even in the lytic phase only one virus will get out of host which should not burst it. Am I right or does virus replicate in a single host into many copies of itself? If so, how does it perform?

@Pavan No viral replication is not dependent on the host. See this section of the wikipedia article.

The second illustration is awesome, detailed, and answers too many questions.  but the link (source) is dead. Could you update the link when possible?

@AlwaysConfused Yes. The link doesn't seem to work. I don't know the original source of this image. Unfortunately, I am not able to find a better (easy to understand but yet descriptive) replacement for this image.

After infection of the bacterial host, but before initiation of DNA replication of the viral genome, the phage has to decide between two mutually exclusive fates:

A lytic infection that will lead to the death of the host by lysis, and a simultaneous burst of phage growth.

OR,

A lysogenic infection where the viral genome integrates into the host's chromosome, and remains dormant, like a parasitic passenger.

Upon entering the host cell both the lambda repressor cI protein AND the cro protein are synthesized from viral transcripts. Essentially, whichever one "wins" will throw that switch. If cro levels are high enough they will shut off transcription of the cI repressor, leading (eventually) to cell lysis. If cI levels are high enough they will shut off transcription of the cro gene leading to integration and lysogeny.
This explanation is a bit simplified; there are other players that influence how the switch gets "thrown."
In a lysogen, just about the only phage protein being made is the cI repressor, and it keeps all the early genes shut off.
In the general viral life-cycle, early genes are transcribed before DNA replication of the viral genome, and late genes are transcribed after DNA replication of the viral genome.  So typical early gene products are regulators, and DNA replication and recombination proteins.  Once there are many, many copies of the viral DNA typical late gene products are the structural proteins that make up the viruses protein capsids, and enzymes required for packaging the DNA into the phage pro-heads.


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Root etiology of non-pituitary low T4 and low TSH
Please note: I'd like to preface this question by stating that this is neither homework nor me seeking medical advice. I am simply trying to understand the biological, physiological root etiology behind various thyroid-related structures.
This question shows research and is not a duplicate.

My undertanding of the pituitary gland is that it will produce TSH when it senses total T4 (not free T4) is low. So if both total T4 and TSH are low, this implies two things:

There is some underlying reason why T4 is low; but moreover...
There is some other (or related) reason as to why TSH is low

In all the literature I can find, the main antagonist in this scenario is a malfunctioning pituitary gland.
So I ask: if the pituitary gland is deemed functional and non-diseased, are there any other root causes for both a low total T4 and a low TSH? Biologicaly/physiologically, how do they work to produce this low level of hormone production?

Are you sure such a condition exists? Can you link to it? Also, are you sure about your total T4 statement?

Thanks @anongoodnurse (+1) - here is an article showing that a low TSH and a low/normal T4 are attributed to pituitary disorder. I can provide other links as well.

Yes, I'm sure it can happen with a pituitary condition, but you stipulated in your scenario that the pituitary was healthy. I'm asking you if you know that condition to exist, and can you link to it?

Thanks again for verifying @anongoodnurse (+1) - if you scroll to the bottom of that link, you'll see a table where it shows that low TSH and low T4 can be caused by two categories of conditions: (1) "rare pituitary (secondary) hypothyroidism" (which like you understand, we're assuming to not be the case here as the pituitary is healthy), and (2) "Non-thyroidal illness".

When you ask a question, it's much easier to summarize the part you have a question about rather than make a user read the whole paper just to understand what you question.  That's why I asked for more information in my first comment.


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What is this plant?
It was found in Eastern Pennsylvania (in the United States) in a deeply wooded area.

Those are the fruit clusters of a common "wildflower" that often grow in wet areas, called Eastern Skunk Cabbage or Symplocarpus foetidus.  Initially (early Spring), it's not bad looking (and some species - such as the western skunk flower - are even pretty):

But after a while, the spathe (sheath) dries up while the seeds grow in the spadix (the fleshy thing in the middle with the little 'flowers') grow, leaving the swollen spadix (fruit):

The tip off, though, is the characteristic new growth, very skunk-cabbagey, so I would guess those fruits are from the previous year (?).

Eastern skunk cabbage is notable for its ability to generate temperatures of up to 15–35 °C (27–63 °F) above air temperature by cyanide resistant cellular respiration in order to melt its way through frozen ground, placing it among a small group of plants exhibiting thermogenesis.

This allows it to flower through melted ice or snow. Also:

It's a member of the arum family.
It depends for fertilization on bugs that like carrion.
It's virtually impossible to dig up a well-established plant because the roots pull the plant down deeper into the soil every year (it has contractile roots).
It was widely used medicinally.

Skunk Cabbage (Symplocarpus foetidus)

Some types can also be mistaken by the uninitiated for rhubarb, which it definitely is not :)

@MattDMo - Eeeeewww! The smell should be a tip off, no? I mean, they produce chemicals like "putrescine" and "cadaverine". I'll take rhubarb! (Now that I think about it, I can see a tiny resemblance maybe.)

it was a long time ago; I was young and innocent :) I'm not even sure if it was "true" skunk cabbage, but that's what someone else called it after I tried nibbling on a leaf stem and almost threw up. This was in central Pennsylvania, not far from where the OP found the specimens in the question.

@anongoodnurse Putrescine and cadaverine to attract flies? I have also noticed that flies get attracted to spermine/spermidine. I just left a solution (with some sugar) in an open bottle to see and in some days it had maggots. Tried this twice (not enough replicates :P).


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What's the name of this bug from Toronto, Canada?

It's about 3 millimetres in length. Found on September 10, 2015.

It's a moth fly. They're cute fuzzy little things. Most people consider them pests.

An annoying and troublesome pest that concerns numerous homeowners is the moth fly, also commonly known as the drain fly, filter fly, or sewage fly. Moth flies are frequently found indoors on windows, sinks and walls.

They're often found around sink drains because the eggs and larvae survive on the biofilm in your, well, drains.

This IS a Moth Fly (Family Psychodidae), but the heavily-patterned wings and their posture at rest argue against the genus Psychoda; the pale spots at the wing margins suggest Clogmia albipunctata (Williston, 1893) which has been extending its northern range limits (half a century ago, this species and Toronto mentioned in the same sentence would have been considered a likely misidentification; this diptera.info thread discusses two localities for that species that are even further north -- Clallam and Grant Counties in Washington).


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Amplification technique for proteins similar to PCR for DNA?
I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up the protein but simply making more of the original sample.

You can't amplify proteins. You just have to express more and/or purify better.

You can use in-vitro translation kits but they require mRNA as a template and the amplification is not exponential as in PCR. There is no biological mechanism to synthesize proteins using themselves as a template. This is unlike the DNA and RNA.

PCR takes advantage of the polymerase mechanism, which can build more nucleic acid from a template of nucleic acid. There's no such mechanism by which protein can be produced from a read of protein, as it's really the ribosome which produces protein from a nucleic acid template, right? As canadianer notes, you can only hope to express more, and purify it nicely!

Pull down the gene, make a cDNA and clone it into a high copy inducible expression vector. Transform bacteria or yeast and grow a culture under selection. Let them grow to 10^10 or more, then induce expression. Purify lots and lots of protein. If you can't get the gene, then you could undertake the very difficult task of sequencing the entire protein. Then you make a synthetic cDNA from the sequence and use that in your expression vector. You cannot get around the Central Dogma; DNA<->RNA->Protein

There isn't any technique with one exception. PCR generates DNA from DNA so you can establish cycles. For protein synthesis, an mRNA is a template to produce proteins. Most likely proteins you are interested in would not synthesize mRNAs, so that you can not establish cycles.
The exception I said earlier is Protein Misfolding Cyclic Amplification (PMCA). Some disease associated misfold proteins can induce misfolding of the same polypeptide which is not misfolded. So you can establish cycles of misfolding reaction.
PS:
There are technique to synthesize proteins from DNAs or RNAs, but they are not chain reactions.
https://www.promega.com/products/protein-expression/eukaryotic-cell-free-protein-expression/
https://www.neb.com/products/e6800-purexpress-invitro-protein-synthesis-kit

It is impossible to amplify protein like PCR. DNA and RNA can undergo PCR because basepairs are complementary: A-T C-G A-U. But amino acids are not complementary; can you find an amino acid that matches glycine? Besides, proteins are not only a single polypeptide chain like DNA, proteins need to be folded after polypeptide chain are synthesized. Usually a protein molecule need more than one polypeptide chain to combine together to form a protein molecule. It can not happen that it works as PCR.

I would say impossible is a stretch. An inventive biochemist could create molecules that are "complimentary" to each amino acid similar to a Dna polymerase. Then a protein would be needed to both detect and translate this similarity into protein elongation. Unlikely, hell yes, impossible, no.

-1. There is literally no known mechanism through which this can be carried out. Designing functional proteins de novo is way out of reach of modern biochemistry.

Even if you succeed in that process, the protein is still linear or worse.

there multiple mechanisms for testing this methodology. Why would anyone initiate this process de novo? Evolution both in nature and the lab starts from a pre existing template. And all proteins are linear to begin with.


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Interpretation of faint band for Linear Array HPV Genotyping Test
After having used the test for research it would appear as if it is very specific. What is one to make of bands that are there but faint? Or what if there are two bands and one is big and bold and the other is faint? Intuitively, I would believe that the starting concentration of the type represented by the bold band is way higher than the type represented by the faint band. Is my intuition correct? Any insights into what that means? Are both HPV types driving the disease process (eg papillomas) or is it just the bold one? Any data? Any intuitions? Any references?

Could you add some example images of bands of the type you are describing?

I received this answer privately and was given permission (in fact asked) to share it without attribution.
The package insert for the Linear Array assay defines any visible band as a positive band, so a faint band counts as a positive.
The difference in band intensity could be related to viral type abundance but really depends on which bands are being compared.  Because this is an end-point assay, it's possible that some virus types amplify with better efficiency than others when found in a mixed infection and it is also likely that overall sensitivity or detection limits may be different for each type.  Additionally the probe for HPV52 is cross-reactive with types 33, 35, 58 and in the presence of any of those additional types, it may increase its intensity.
The driver of the disease process is the virus with the most oncogenic potential (but I assume that is only when we are talking about cancer or dysplasia, perhaps not when referring to recurrent respiratory papillomatosis or genital warts), which does not change in the presence or absence of other viruses (and regardless of the band intensity).  Additionally, it's important to remember that the resulting disease is clonally derived, originating with a single-type infection (ie. each lesion will be linked to only one HPV type).  When multiple viral types are found within an exfoliated sample it signifies multiple different infection sites (and not multiple virus types within single cells).  Not all of these will progress to high-grade disease, but rather, the lesions caused by genotypes with the highest associated risk are the most likely.


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What is the radius of the Ora Serrata and lens in rabbits?
I'm interesting in estimating the surface area of the hyaloid membrane connecting the vitreous and aqueous chambers. This is a crude estimate however i'm struggling to find parameter values for rabbits.
I have estimated in humans the radius of the Ora Serrata, measured from the
centre of the lens, to be 1 cm. The radius of the lens to be 0.5 cm, giving the surface area of the region between the two to be roughly 2.36cm^2.


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Recombination fraction( frequency) in Homozygotes
I have a question about the recombination frequency I hope you have time to answer.
Background: If we look at homozygous individual A/A B/B which has been formed from the gametes AB and AB, this individual will in turn have the gametes AB, AB, AB, AB. These are the same as the gametes that were used to form the individual.
My question: Is the recombination frequency 0? Or should we consider the A's and B's as different, i.e like A$_1$, A$_2$, B$_1$, B$_2$. Then we get the possible gametes A$_1$B$_1$ (parental), A$_1$B$_2$ (recombinant),A$_2$B$_2$ (par), A$_2$B$_1$ (recomb). We then get that the recombination frequency is 50 percent (which it should be according to the source given at the bottom). Which interpretation is correct?
Definitions used in my question:
"Meiotic recombination is any meiotic process that generates a haploid product with new combinations of the alleles carried by the haploid genotypes that united to form the meiocyte." (Griffiths et. al, Introduction to Genetic Analysis, tenth edition, International Edition, p. 95)
Recombinants: "Recombinants are meiotic output different from meiotic input." (same book).
Recombination fraction: "Recombination fraction (also called recombination frequency) between two loci
is defined as the ratio of the number of recombined gametes to the total number
of gametes produced." (Shizhong Xu, Principles of Statistical Genomics, Springer, Chapter 2, page 11, 2013).
Furthermore: "When genes are unlinked, they have a recombination frequency of 0.5, which means 50 percent of offspring are recombinants and the other 50 percent are parental types." (Source: Boundless. “Genetic Linkage and Distances.” Boundless Biology. Boundless, 21 Jul. 2015. Retrieved 11 Sep. 2015 from https://www.boundless.com/biology/textbooks/boundless-biology-textbook/modern-understandings-of-inheritance-13/chromosomal-theory-and-genetic-linkage-97/genetic-linkage-and-distances-427-11654/)

Welcome to Biology.SE
Your question stems from the confusion between measuring a recombination rate and the actual recombination rate.
In the A/A, B/B individuals you describe, recombinations still occur. Those recombination just don't affect linkage disequilibrium between the Aa and the Bb loci as there is no variance at those loci in the individuals you considered. There is therefore, no way to tell whether or a recombination event occurred in a specific case. You need genetic variance at both loci in order to have a linkage disequilibrium which can be affected by recombination. But it is not because you can't measure the recombination rate that recombinations does not occur.


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Why I obtain larger bands than expected after minipreparation?
guys!
I made a "home made" minipreparation to obtain my plasmid+insert (totalizing approximately 6Kb). But, when I run a agarose gel, I saw a unique band with 10Kb. Why?

Maybe it was open circular DNA.

Can you please add a gel image?

Have you done this same miniprep with a commercial kit? It may not be related to your homemade procedure. It might also be helpful to know how you were doing your ligation and your homemade miniprep protocol.

If the DNA got damaged in handling it could relax or linearize. That's to say, you have a 6kb vector but it's running about as slowly as the 10kb band in your ladder. You can maximize the supercoiled form by working quickly and gently with the prep.


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How often does parthenogenesis in mammals happen?
Probably everyone knows that mammals can't produce viable offspring by parthenogenesis.
But there are reports of human chimeras (see: a human parthenogenetic chimaera) and it's known for mice to quite often develop parthenogenetic embryos that will not survive past the 10th day of gestation (see: birth of parthenogenetic mice that can develop to adulthood).
So, how often does parthenogenesis happen in mammals and how long do parthenogenetic embryos survive? I have heard an estimate that 0.01% of human blastocystes are parthenogenetic with gestations always ending in miscarriage before the 3rd month, but I couldn't find any source for this claim.


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Most painless method for killing insects
I'm planning on having a small farm of crickets or grasshoppers.
I would like to cause them as little suffering as possible, so I'm wondering what is the most painless way to kill them?
So far, the plan is to put them into the fridge (+4C) to slowly chill them (that way they will not notice it as much), and then to freeze them in the freezer (once they are chilled and are either unconscious or barely so).
EDIT: It is important to note that I am planning on eating them.

They have a wikipedia page for euthanising insects, to my surprise. I'm far from experienced here, though.

I think the freezing method makes sense, since that is how they do it with lobsters. And lobsters are just underwater large bugs really. You could try decapitating them?

4⁰C won't kill them.. see here.. You can freeze them in a deep freezer, if you have one..

As far as I'm aware, there really isn't conclusive evidence that insects can actually feel pain in the same sense that we do, as their nervous systems just aren't that complex. So, I really wouldn't get too hung up on this.

I commend you for a) growing your own and eating insects (so 21st century; not a joke), b) caring that they not suffer. An uplifting question!

I doubt if it is possible for such small nervous system to produce any sentience. Human finger probably contains more neurons than grasshopper.

The faster you kill them, the lesser they can "feel". So the best way should be shock freezing and or throwing them into boiling water.

@AstronAUT at what temperature do they die? Boiling, I would say is a pretty bad way to go, unless it's a second or less.

Thats true. You only need to exceed the temperature, which leads to denaturation of their body proteins. That could be already at >41 °C.

The terrestrial invertebrate taxon advisory group of the Association of Zoos and Aquariums recommends anesthetizing the insects with carbon dioxide and then placing them in a freezer to euthanize them.

Can you post a link to this information? It sounds correct, as CO2 is used by Drosophila labs, but it is always a good idea to source your answers with a link.

Hi and welcome to Biology StackExchange!  Do you have any links to reference your answer?  I see that group mentioned on Wikipedia but usually in reference to freezing.

Using CO2 doesn't feel very practical to do at home though, if the purpose is to grow them for on a large scale for food.

@fileunderwater well, you could always breathe at them. :P


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Why do doctors still advise HIV+ couples to wear a condom during sex?
HIV infected people already have HIV, but why do doctors still advise condom use for HIV+ couples?

Doctors would recommend the use of barrier protection for couples where both partners are HIV+ because the virus can mutate. Mutated forms of the virus can become resistant to Highly Active Antiretroviral Therapy (HAART) treatments, rendering them ineffective.
The use of barrier protection reduces the risk that a resistant mutant strain of HIV is transferred into the population.
Also a child conceived by a couple that is HIV+ is at high risk of being born with the infection.
This link explains some of the risks and ways to attempt to prevent mother to child transmission of HIV.
Edit
In retrospect, I have been thinking about the answer I gave, and while I still think that what I said above is relevant, I feel that I left out an import aspect of why a medical doctor would recommend the use of barrier protection during sexual activity, even if both partners are HIV+.
One thing that we should remember is that a person with HIV, even when the virus is suppressed by HAART is immunocompromised to some extent and they will likely be more susceptible to secondary pathogens and cancers initiated by oncogenic viruses.
An HIV+ person will be more vulnerable to sexually transmitted diseases such as human papilloma virus, herpes, hepatitis, chlamydia, gonorrhea , or simply opportunistic pathogens such as C. albicans than they would have been had they not been HIV+. Cells that mediate innate immune response are affected by HIV as well as cells of the adaptive immune system, so any dysregulation of the immune system creates an opportunity that a pathogen would not normally have.
Not only will these diseases have an easier time infecting an immunocompromised patient, but these infections will also be more difficult to cure once they have taken hold, as the person's immune system will likely not be able to mount as robust a response as it would have if the person was not HIV+. So barrier protection provides a means to help protect a person from secondary infections as well as for the reasons given previously.
Use of barrier protection during sexual activity to prevent the transmission of sexually transmitted diseases is just as relevant for people who have HIV as for those whose HIV status is negative.


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Question about flux and changes in net flux of molecules across a membrane
I've been reading a book called Principles of Human Physiology by Stanfield 5th edition, and was reading a chapter on membrane transport when I came across a figure question which will be posted below.
It says "As time passes, does the one-way flux from side 2 to side 1 increase, decrease, or stay the same?"
I have unfortunately been unable to comprehend why and how the answer is "Increase". I would suppose it stays the same, correct? There is no possible way that a flux would occur, unless by individual molecules (regularly) passing through each side on a equal basis.
It was a topic on Simple diffusion.
P.S. This book, as i've noticed hasnt been quite explaining some things in a clear-cut way to understand as a beginner, and also it has had some mistake within it.

Does it help to emphasize that the question is asking about flux from side 2 to side 1? It's not asking about flux from side 1 to side 2 or net flux.

Keep in mind that diffusion is just the random movement of particles. Over time, the solute will randomly distribute throughout the entire available volume. Under initial conditions, there is no solute in side 2 and so it cannot move to side 1 (thus flux from side 2 to side 1 is 0). At equilibrium, the net flux is 0 but there is still flux from side 1 to 2 and from side 2 to 1 (which is equal and opposite) due to the random motion of the solute. So, flux from side 2 to 1 goes from 0 at initial conditions to some non-zero value at equilibrium (ie it increases).

@canadianer You can post that as an answer. However this is a physical chemistry question and off-topic.

Diffusion is just the random movement of particles. Over time, the solute will randomly distribute throughout the entire available volume. Under initial conditions, there is no solute in side 2 and so it cannot move to side 1 (thus flux from side 2 to side 1 is 0). At equilibrium, the net flux is 0 but there is still flux from side 1 to 2 and from side 2 to 1 (which is equal and opposite) due to the random motion of the solute. So, flux from side 2 to 1 goes from 0 at initial conditions to some non-zero value at equilibrium (ie it increases).

This is also what is refered to as steady-state. Or dynamical equilibrium. Overall, the net flux is zero, but still there's constantly flux from side 2 to side 1, even more so when more solutes are in side 2.


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white and brown mushrooms. same species but...?
On Cooking SE and Wikipedia we wonder if someone can claify:
Are white vs brown immature fruiting bodies of Agaricus bisporus different stages of development like many kinds of fruit change color as they ripen? Or are they different cultivars or are they due to different environmental conditions when forming?
Bonus: what isnthe brown pigmentation? Is the difference in taste due to that or meerly correlated with it but due to some other difference?


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Algae and greenhouse effect
Just a thought: the CO2 concentration is increasing . Due to a different but possible related phenomenon, the algal blooms are on the rise. We humans want to control both. But algae are the major source of O2. Could the rise of algal blooms in the rising concentration of be related CO2 ? I wanted to know if this would eventually be advantageous to the environment, even though algal blooms may be detrimental to some species and directly or indirectly to humans too?

It also may be related to how many trees we cut down too... Just a thought, I have no evidence.

"Rising CO2 levels will intensify algal blooms across the globe" (from http://phys.org), based on this paper in PLOS one.

In most situations the lack of sufficient CO2 is not what is limiting algal growth. In general the limits to growth are set by the availability of nutrients such as iron, nitrogen and silica. They actually touch on that in the paper. For example removing iron limitation has a much more dramatic impact on algal growth or blooms than increasing CO2 by a few percentage points (see here). This also explains why there are more algal blooms, the increase of fertilizer use results in more food for the algae to grow on and all round bad things (see here).
Perhaps some algae will benefit since they will not have to invest much energy/nitrogen in creating carbon concentrating mechanisms. However several species of algae use calcium for their cell walls and these would actually suffer by increased CO2 concentrations as this leads to ocean acidification (e.g. coccolithophores). Taking into account that these are heavy sinking algae that take a lot of carbon with them to the ocean floor and you see that ocean acidification is not likely to be a good thing.


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Meaning of "non-homologous virus"
From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:

More recently, concerns have been raised that HGT from genetically modified organisms (GMOs) could have adverse effects (Pontiroli et al., 2007). HGT of an introduced gene in a GMO may confer a novel trait in another organism, which could be a source of potential harm to the health of people or the environment. For example, the transfer of antibiotic resistance genes to a pathogen has the potential to compromise human or animal therapy (Bennett et al., 2004), transfer of a viral gene to a non-homologous virus may result in an emerging disease (Falk and Bruening, 1994) or gene transfer to humans has been controversially proposed as a potential trigger for oncogenesis (Ho et al., 2000).

What is a "non-homologous virus"? A virus whose species is the same but the strain is different from the virus taken as the donor for the GMO? Or just any virus (including viruses from different species) whose DNA or RNA sequence is different from the GMO donor virus?
Excuse me if the question seems too simple.

It is not a standard term. What it means is unrelated viruses.

It simply means a two dissimilar viruses. If you read the paper Falk and Bruening, they are worried that if you place a viral gene in a plant (here we call that the transgenic gene), then natural viruses may "mix" it's genes with the transgenic genes and create a superior virus. The thought is, you are speeding up the evolution of the virus by taking a beneficial gene from a non related (non homologous virus), something that would probably take a long time.

Thank you! And this wild\natural non-homologous virus could be of the same species with the donor virus, the difference being only that it lacks this 'beneficial' gene sequence that was introduced into the GM plant?


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How do muscle cells synthesize glycogen?
Hexokinase enzyme is present in all cells (including muscle cells) and can be suppressed by excessive G-6-P product. So that's why in the liver, glucokinase can act on glucose without inhibition of it despite excessive G-6-P product; that's why it can generate glycogen and not let excessive glucose flow back in bloodstream. My question is then: why muscle cells can generate glycogen despite having HK instead of GK? Because as i said above, HK activity is dependent on intracellular glucose level, and cannot phosphorylate glucose to hold it inside the cell. So glucose enters back to bloodstream and prevents the synthesis of glycogen?

@user4147 I reworded your question. If you don't like it, you can change it back.

@user4147 - can you please clarify your question above? You mentioned that hexokinase kinase activity is dependent on intracellular glucose level and cannot phosphorylate glucose glucose to hold it inside the cell – but that's exactly what happens (?) – Can you clarify your above text because it doesn't make any sense – thanks!

the HK enzyme activity is suppressed by excessive product (G-6-P) that is why when the cell is well fed (having enough ATP) it wil not consume unwanted glucose therefore not phosphorylating it and thus it can go back to bloodstream to maintain glucose level.my question was on muscle cells that then why they make glycogen when they have only HK enzyme

"...back to bloodstream to maintain glucose level" this is done by liver. "when the cell is well fed (having enough ATP) it will not consume unwanted glucose therefore not phosphorylating it..." and thus it will convert glucose to glycogen for storage. I think you should have a look at cori's cycle (https://en.wikipedia.org/wiki/Cori_cycle) and @sunboyharry's answer.

The answer to the question is that under conditions favouring glycogen synthesis (e.g. the fed state) G6P only accumulates in skeletal muscle cells when the capacity of those cells for storing glycogen has been reached. Until then the G6P is immediately converted to G1P and on to glycogen, in the reactions in sunboyharry's answer.
The question suggests a misunderstanding of the role of glucokinase in liver, which can be better considered if we first make clear the role of liver and skeletal muscle in glucose metabolism. The role of the liver is to deal with excess glucose after a meal by trapping it in the cell as G6P. Although initially the G6P may be converted to G1P and hence to glycogen, this is not the only fate of G6P. Subsequently it may be directed to glycolysis and to the pentose phosphate shunt to provide the acetyl units and reducing power (NADPH) needed for fatty acid synthesis. (The fatty acids are converted to triglycerides and exported to the adipose tissue.) When the blood glucose falls the role of the liver is to release glucose into the blood to supply those tissues that depend on it (brain and erythrocytes in starvation, skeletal muscle if the fall is due to muscle exercise). The skeletal muscle, in contrast, is only concerned with storing glucose as glycogen when it is available, and converting it to G6P for glycolysis when it needs ATP to power muscle contraction.
Glucokinase has a key role in the regulation of blood glucose concentration by the liver. To paraphrase (and edit slightly) Cornish-Bowden and Cardenas: "Mammals have two types of enzymes to catalyse the formation of G6P from glucose. Glucokinase [hexokinase D in their nomenclature] differs significantly from the other type [generally just referred to as hexokinase]. Its abundance varies markedly with hormonal status; it requires much higher glucose concentrations (about 10 mM) for half saturation, and is insensitive to physiological concentrations of G6P. It is thus well adapted to respond to variations in blood-glucose concentrations."
To clarify, 10mM is in the region of the blood glucose concentration (ca. 5mM) so the glucokinase reaction will be affected by the relative concentrations of blood glucose and intracellular G6P in a standard mass action manner, which will determine whether the liver takes up glucose or releases it into the blood. If glucokinase were inhibited allosterically by G6P like hexokinase, this couldn't work.
Now let's turn to G6P and hexokinase in skeletal muscle. Hexokinase has a much higher affinity for glucose than hexokinase and will convert it efficiently to G6P. As long as G6P is then converted to G1P for glycogen synthesis, G6P will not build up. However when glycogen synthesis stops because the capacity of the muscle to store glycogen is reached, the concentration of G6P will increase and turn hexokinase off. This, in turn, will cause a build up of intracellular glucose and prevent glucose transport into the muscle. This makes sense, because with full glycogen stores, and in the absence of need for contraction, glucose will not be metabolized by the muscle; it will be left in the blood for the liver to handle.
Thus, the key point about G6P inhibition of hexokinase, and the apparent source of confusion in the question, is that it only occurs at concentrations that are reached when the G6P is not being metabolized within the cell.
Reference and Footnote
Ref for citation: Cornish-Bowden, A and Cardenas, M.. (1991) Trends in Biochemical Sciences 16, pp281-2. (This article also makes the point that the kinetics of glucokinase are sigmoidal and not hyperbolic as stated in most texts, and that the enzyme is not specific for glucose. Neither of these points affect the argument here. The former does indicate that my reference to glucose control of glucokinase operating in "a standard mass action manner" is a simplification. It does respond to changes in glucose concentration in the blood range, but in a more sophisticated manner than an enzyme with simple Michaelis-Menten kinetics.)

Hexokinase catalyze glucose to form G-6-P is only the first step of the glycogen synthesis, and then the G-6-P will continue to processing a series reaction and finally become glycogen. So once the G-6-P forms, it will keep reacting, which will not inhibit the activity of hexokinase.

You should add a reference to the source where you obtained the reaction pathway scan.


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Why a repeat wasp sting cause an anaphylaxis shock?
I understand that an anaphylaxis shock caused by a huge dose of histamine. But why the first sting does not cause an anaphylaxis shock like the second sting? As i think there may be a relevant between antibody and histamine because the victim already have antibody presence in the second sting, is that right and what is it?

It probably has to do with the amount of toxin. It isn't alway a gradient, it can be like walking up a hill (mild response) until you get to the top and jump off the cliff (anaphylactic shock) on the other side.

The reason is the way anaphylactic shock is caused by massive release of certain cytokins as well as inflammatory mediators such as histamine by two types of white blood cells: mast cells and basophils. This release is triggered by the binding of immunoglobulin E (IgE) to the antigen (the foreign substance provoking the allergic reaction). Antigen-bound IgE then activates so-called FcεRI receptors on the mast cells and basophils. IgE molecules specific to the allergen provoking the allergy are not present in the blood in sufficiently large quantities until after the first (several) exposures to this foreign material. Initial exposure triggers IgE production by specific B-lymphocytes. Only once one or more exposures to the antigen have occurred will there be sufficient quantities of the relevant IgE to trigger this excessive mast cell and basophil reaction.


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A trivial question on the meaning of "relatives" in an article on horizontal gene transfer
Am I right in suggesting that by close relatives the author meant closely related species, or did he have individual organisms in mind?

DETECTION OF HORIZONTAL GENE TRANSFER
There are several approaches to identify genetic changes due to HGT,
  including:
(1) experimental evidence, whereby a genetic marker is monitored for
  gene transfer to a recipient organism;
(2) phylogenetic analysisof gene sequences to identify topological
  inconsistencies between different gene families;
(3) nucleotide compositional analysis to identify any gene that has a
  nucleotide pattern that differs significantly from the overall genome;
  and
(4) evolutionary scenarios to explain the patchy appearance of a
  genetic signature, sequence or function that is not shared by close
relatives.

(From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese)

You are correct.
From the author's point of view there is not much difference, however. Phylogenetically speaking 'species' are kind of artificial distinctions that exist only as sets of individuals and don't usually convey information, so it makes sense to forget that species exist when talking about HGT. Hopefully that helps provide context for why such imprecise wording is so common.


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How will changing the concentration of a Tris buffer affect amylase enzyme activity?
For instance if you increase the amount of Tris but pH still does not change then will the enzyme activity still proceed normally?  If it does change the pH will it change enzyme structure and why?

I am a novice at biology, but googling "amylase ph" resulted in a recommended pH of 7.0 for "Human pancreatic alpha-amylase" . So wouldn't it depend on the pH of the Tris, which I forgot, since there are alot of different kinds of tris buffer preps? Googling "Tris" resulted in a wikipedia page with the pH being 8.0. So given that information, wouldn't it have less functionality?

Would increasing the amount Tris but no change in pH do anything significant?

To be honest, I wouldn't know. But increasing the amount of the Tris would cause a change in pH would it not? Unless you mean to balance it with something basic or acidic? And then in that case i still would not know. I always thought TRIS was just used to obtain the optimal pH for enzymes and the like and the pH was its reason for being used.

Assuming the Tris is chemically inert to the reaction, a higher amount of Tris will increase the buffering capacity (i.e. the pH changes less).

I realize I'm 4 years late, but wanted to give an answer to this. It appears that tris often has inhibitory effects on amylase activity. Adding more Tris will lead to competitive inhibition with the substrate and will skew the results.
Binding of Tris to Bacillus licheniformis alpha-amylase can affect its starch hydrolysis activity
https://www.ncbi.nlm.nih.gov/pubmed/18289113

After 4 years of working in enzymology I've got say tris is really tricky first of all when you use more tris to keep pH at the same as before you will need to re adjust the pH as tris is about 9 but most enzymes work around 6to7.5 (for alpha amylase it's 5.8) if you don't then your enzyme wont work properly ,it needs very low or high pH grade to destroy 3D structure of enzyme ,so we can simply say it will lost it's functionality , if you adjust the pH high concentration can cause some problem such as surrounding substract here amylase and not letting it to connect to enzyme in some cases acid you use to adjust pH has toxic effects on enzyme chlorine in this case but pretty sure the best way is optimization to understand the reaction.
Best regards .

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


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Do Red blood cells(mammals) really have no organelles?
I have read that mammal mature Red blood cells lack most organelles, including mitochondria, golgi apparatus and an ER. ( https://en.wikipedia.org/wiki/Red_blood_cell#Mammalian_erythrocytes ) This makes sense since there purpose is to transport oxygen via hemoglobin, and according to the wiki, they make any energy needed via glycolysis. But are there really no more organelles in a mature red blood cells? A simple google search did not help me.

Yes. This is true. During the final stages of red blood cell formation in the bone marrow, the nucleus and several other organelles are broken down and/or expelled from the cells. In the process they decrease markedly in size, from about 24 to about 7-9 micrometer. Presumably this makes them small enough to pass through the smallest capillaries. Lacking those organelles also limits their life expectancy to approximately 120 days.


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In this illustration about CRISPR function, what do these objects mean (image provided)?
In the paper on CRISPRs, the following figure is shown:

I added the light-green boxes.
What do the red arrows and the line with a filled circle on the far left mean?
What does the arrow in the middle mean (also just infront of cas9)?
Is the purple square to be understood as the RNA section in the B plot (blue arrow)?
Taken from here.
The caption is (cited):

The type II-A system from S. pyogenes is shown as an example. (A) The
  cas gene operon with tracrRNA and the CRISPR array. (B) The natural
  pathway of antiviral defense involves association of Cas9 with the
  antirepeat-repeat RNA (tracrRNA:crRNA) duplexes, RNA co-processing by
  ribonuclease III, further trimming, R-loop formation, and target DNA
  cleavage. (C) Details of the natural DNA cleavage with the duplex
  tracrRNA:crRNA.

The arrow direction denote transcription direction and its location denotes the transcription start site. The circle is probably the transcription terminator (I cannot access this article at the moment, but this is what it should mean).
The purple boxes refer to the protospacers which are derived from foreign DNA. These elements help in recognizing and cleaving foreign DNA. These are transcribed as RNA which in turn guide the Cas complex to the target DNA. In a way, these protospacers provide some kind of immunological memory to the bacteria. See the below figure (From Nuñez et al. 2015 ):

"They are the protospacers": What exactly do you mean by "they"?

@TMOTTM the purple boxes.. I'll edit the answer


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Can any enzyme be produced?
After reading about how recombinant insulin is produced, the following question occured to me. Does the current level of technology allow any enzyme to be produced in a similar way?
As I see, producing amino acid sequences is not an issue. A possible difficulty I can think of is modifying the amino acid chains. In the case of insulin the problem has been solved. Are there some generally applicable solutions available to this problem, or do they have to be researched on a case-by-case basis?
Are there any other limitations to producing enzymes?
EDIT: As pointed out by P. Jay, the question might seem to suggests that insulin is an enzyme which it is not.

Anything can be produced, the problems lie in producing large amounts with high quality.

No, not all enzymes (or other proteins for that matter) can be obtained in functional form by recombinant expression with today's methods. As you suspect, problems arise when complex post-translational modifications are necessary to obtain the correct function.
Direct modifications to peptide is one potential problem. Some of these can be resolved by expression the recombinant protein in the right cell type: for example, expression in a bacteria may not provide the right modification, but expression in yeast or a mammalian cell might. CHO cells are a common mammalian cell type used in such cases; antibody production in hybridomas is another well-known example. But there are plenty of posttranslational modifications that are poorly understood, and most likely there are still many completely unknown types; new ones are still being discovered.
Another posttranslational event is association with cell membranes. Membrane proteins (including membrane-embedded enzymes, for example in lipid metabolism) can be very difficult to express properly, as not only the peptide but some surround membrane structure must be reproduced in the expression system to obtain correct function. This is also a major hurdle in obtaining structures for membrane proteins, notably many cell surface receptors. This article is a summary of the current challenges and unsolved problems in this area. And you can imagine the problems with proteins that need to form large superstructures to be functional --- large protein polymers, respiratory chain complexes, ribosomes, DNA replication forks ...
So there is no universal method; all proteins are different, some are easy to express, some are extremely hard.

If you are talking about the possibility, the answer is yes. However, you might have some difficulties in producing some proteins. In some cases, the reasons could be obvious--sugar modification and phosphorylation which can not happen in E. coli. Although phosphorylation is involved, if you do not know if your protein is phosphorylated, you would never find the reason why you can not get the active protein.
Polypeptide folds in the correct way or incorrect way in E Coli. Sometimes, it is difficult to fold proteins correctly in E coli expression systems. In addition, if your proteins has multiple polypeptide chains, it could be more difficult.
There are mammalian, yeast, insect expression systems, and these systems could be better if you have problems in producing proteins in E coli. But it is not always that these systems work.

Yes enzymes can be produced and even be optimized like restriction enzymes which are now mostly recombinant thou to low efficiency or biosafety level of source bacteria leaving that behind ,the greatest problem here is the size of protein and it's gene as when you produce artificial bio products you've got a prokaryote host to do that in cases which they do it out of cells then it's completely different but for sure possible the greatest problem is efficiency of production....and by the way insulin is not an enzyme


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If a human is stranded with beer but no water, should they drink it?
TL;DR: At what percent (if any) will alcohol dehydrate you more/faster than drinking nothing?
Let's contrive a situation for dramatic effect...
A human goes out on a boat for a nice sail in the sea. But oh, the sea was angry that day, my friends. The weather turns, and the sailboat is tossed asunder. Luckily, our survivor grabs hold of some debris and is washed onto a deserted island.
Lo and behold, the debris that floated with the survivor to the island is a cooler, and it is filled with beer! There are no other food or water sources on the island. What should our survivor do in regards to the beer to stay alive for as long as possible?
The crux of the situation and my question: will drinking the beer help hydrate the human, keeping them alive longer? Or would the effect of the alcohol as a diuretic actually dehydrate them, causing an earlier demise?
Details and follow up questions:
Let's assume this is an average beer ~4% alcohol. However, I know there must be a breaking point. Some kombucha or ginger beer with .5% alcohol should surely be imbibed. But should this beer still be drunk? What if instead it was a 7% IPA? Or a 14% quadruple IPA like I have in my fridge? What about wine, whiskey, or gin?
How would the situation change for a caffeinated beverage like coffee? Or what if the cooler was filled with energy drinks?
I look forward to your answers!
EDIT: The linked question, while similar, does not answer my question. It links to one 1996 study that talks about the effect of alcohol on rehydration, but not the specifics of yes, probably ok to drink at about this percent ABV, and no don't drink at above this percent. It also doesn't discuss rate of intake, changes based on body weight, etc. which are all things I would surmise have an impact on this. I understand there isn't going to be a hard and fast STOP percent level, but I would like to understand more about the underlying mechanisms and factors that change things.

This is way too many questions. Focus on one or two beverages, please, or just alcohol, plain and simple.

There is one main question, at what percent alcohol is drinking nothing better than drinking the alcohol for survival. A possible follow up would expand this to caffeine.

If you read The Ghost Map, you will find that the people who survived a particular cholera epidemic that erupted around them in London, were workers in a brewery who were paid in part with the fruits of their labor, and drank beer and not the water from the local pump.

Let's hope the beer is chilled ;)

There is quite a lot of misunderstanding about alcohol (and caffeine) as a diuretic. It's not nearly as cut and dry as you're presenting.
There is no answer to your question. Sodium and water are very tightly regulated, and a lot has to go wrong before they fail. If alcohol could easily derail water regulation, there would be far, far fewer alcoholics in the world.
Alcohol is primarily a toxin, not primarily a diuretic. The diuretic effect of alcohol depends partly on your hydration status. If you're fully hydrated, you'll produce slightly more urine on drinking an alcoholic (>2%) beverage than when you drink water. If you're dehydrated, your body will conserve the water more. The more alcohol in the drink, the less value it has as a rehydrating solution.
You won't find good studies because it's not a scenario truly worth studying. The toxic effects of alcohol are already known and bad enough. It would be unkind to conduct a study where higher concentrations of alcohol were the sole fluid available and length of survival on animals, let alone humans.
N.B. There have been lots of studies with acute alcohol intoxication and diuresis because that is a scenario that occurs, and which can be mitigated.
Effects of a moderate intake of beer on markers of hydration after exercise in the heat: a crossover study
Hydration Status and the Diuretic Action of a Small Dose of Alcohol

Why do you say that alcohol is a toxin? It is common metabolite in many species and unlike methanol, ethanol is not considered toxic.

@WYSIWYG Alcohol is most definitely a toxin. Your assertion is absurd.

Can you cite a valid reference where alcohol is classified as a "toxin"? By your logic even oxygen would be primarily a toxin.

@WYSIWYG - by your logic, tetrodotoxin (made naturally by puffer fish), though it does get someone high, is not toxic. Enough.

Please refrain from making unprofessional expressions. If I do not understand what you are saying then I have the right to ask. Alcohol is an end product of fermentation and is not a product specially synthesized to cause harm to other species. It is like lactic acid (which can also cause metabolic acidosis at high concentration). Comparing TTX with alcohol is too far fetched.

@WYSIWYG- as I said, I'm done with this. Surely you can look it up yourself. You didn't so much ask a question as make an absurd statement.

I can look it up. But being a member of the community I have the right to ask for a referenced answer. Your claim can mislead others. And I do not really understand the "absurdity" in my comment. Would you please care to enlighten me?

Ethanol poisoning https://www.cdc.gov/niosh/idlh/64175.html