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What is the difficulty with cloning and genetic engineering in humans?
I asked this question many years ago and was told by my molecular biology professor that humans were (simply) more complicated than goats.
So, I didn't get a straight answer, but supposing he told the truth, what's the problem? Or are people really more complex than goats, from an engineering or genetic standpoint?

A molecular biology professor said "humans were (simply) more complicated than goats". Did (s)he really say that?! I know little about cloning but it sounds wrong to me. The main difference is likely to be a difference of ethics, not biology.

@Remi.b It's the truth. So, I also asked a related question on the philosophy SE: What is the ethical reason for avoiding genetic engineering in humans? Please chime in if you can shed light on that!

Please state your question clearly without reference to the title so it can be considered independently. We are not interested in your personal history, only what you are asking and what effort you have made to find an answer.

The question you are asking is an ethical problem rather than a biological one. This particular nature article highlights the problem I am speaking about.
In brief, children afflicted with SCID were subjected to what at the time was termed as a pioneering retroviral treatment. The idea being you replace the defective gene with the real one, in case of the quoted study, of 11 patients, 9 were cured and one of these babies developed leukemia due to the treatment. This was one of the first trials and it showed how these treatments can go awry.
Fast forward to today, last year you may have heard, something called the three parent babies garnered a lot of attention. This is basically mitochondrial donation, where a third-party provides mitochondria for IVFs for reasons where parents opting for IVFs may not be able to undergo successful IVFs due to mitochondrial mutations. This posed and still poses a serious ethical question, because what you are doing is mixing heritable DNA between lineages, please note that most geneticists will never cross this line, i.e. editing the genome such that the offspring carries the edited genome. Almost always the modified individuals are sterile (I know of no GMO crop which is not sterile)
But not to say, we have done nothing in terms of genetic engineering.
Scientists for the same reason (A human life is more important than any animal's) are wary of editing the human genome directly, so we now we also have something called siRNA treatment is just one example. And this is a list of siRNA based drugs which were in various stages of clinical trials in 2013. I know of a few which entered trial since then.
Lastly, this is just the tip of the iceberg, there's a whole lot which could be said on this topic, but it boils down to the same ethical problems.
Just so you know, since 2001, we have a lot of newer genome editing tools, such as TALENs and CRISPR-Cas. But remember, they still have the same problem as retroviruses from 2001, the issue about off-targets.
What if your tool targets a region which it isn't supposed to target?
Will another child develop a condition due to the treatment?
To avoid such an issue, we need to understand much better how the genome works, and sadly still we don't know enough. I cannot quote the study here because I have no idea where it is published, but at a recent conference I heard a talk from a lady about how retroviral integration works. The idea being, if retroviruses don't need specific integration sites, they should integrate at the first genomic region they encounter, that is not the case. I will not go into more detail. But I hope you have some food for thought.
UPDATE ON Genetic Engineering at a preconception stage

This is a link to the Nature article on Venter's minimal cell. There also exists an artificial Yeast genome page. The point I am trying to make is, we are really at the basic stages even now.
I will outline to you the behemoth scale problem we are facing.
2002: The first human genome draft is published. All the media is rife with stories about how we are going to unlock the secret to life.
Since then, DNA methylation and histone modifications have come to the foray as regulators of genome functionality.
We knew that DNA was transcribed into RNA and translated into protein. Noncoding RNAs came to the foray and messed up everything.
We thought that DNA functionality was governed by DNA methylation and Histone modifications, come 2009, we saw the first major article on Chromatin architecture. We understood that the genome has switches called Enhancers and promoters which regulated when and for how long RNA is transcribed. But sometimes these switches were so far away, we did not know how they switched on their target genes.
The problem can be summarized as this, making an artificial bacteria is easier than a human. In humans you have multiple layers of regulation, there's the DNA, where one part is silent (heterochromatin) and one part is active (Euchromatin), DNA methylation and histone modifications affect how genes are expressed, these modifications allow opening of the DNA so that genes can be expressed, The DNA is further compartmentalised (architecture) so that switches only affect nearby genes in 3D space. Non-coding RNAs act as messenger in such areas relaying proteins to their target DNA regions. So the cell is a mess!
Not to say that goat biology is simpler, just that a goat's life is cheaper than a human's. So we wouldn't feel a thing while "euthanising" goats for the advancement of mankind.

I had not heard about 3 parent babies... but I must be psychic or something because I was just thinking about it earlier today! Cool articles. But I would say that retroviral techniques are not really relevant with respect to what I mean. I understand the faulty tech- especially with multicellular organisms. I really meant engineering at preconception-stage.

Ahh...that needs a more detailed explanation.

Well, I think you did a good job pointing out the faults with the current progress with respect to later stages. But I would love it if you could add details regarding the technical problems at the single cell stage. Are there design or technical hurdles which make engineering more difficult for humans than other animals?

Well, I do feel bad for an animal that suffers. But + for calling my teacher a rotten liar (ha!)... but seriously he was a decent person.

There's a separate Stack Exchange for ethics, go there if you want to argue about that.
The first problem is how little is known about the functions of every gene. To properly roll out gene mods for humans, you have to know all the interactions of the original genes and their products and have an accurate computer model that predicts problems and other effects of the upgraded versions
Another problem: re-use of parts of the genome. In particular, some genes are used for several purposes, which means you could upgrade something and completely break something that would seem unrelated. It's similar to manually editing a compressed file's dictionary - changing 1 bit/base of compressed file content changes several in the output.
Then there's the problem of unexpected edits. What happens if your gene-editing framework misses and modifies something it shouldn't?
Assuming you ever get it working at a cost that people (or at least the military) will pay, you now have to figure out how to deliver the gene mods. Invasive or non-invasive? Retrovirus? Biocompatible DNA-producing chip? Update framework? Ability to roll back a bad update?
Cloning is even harder because you have to replicate the proper development conditions and there are all sorts of "gotchas" such as imprinting.
In short, humans might need to undergo an initial adaptation stage where these "gotchas" are gradually edited out and a synthetic programmable DNA editing and updating organ gets added - as a prerequisite for further upgrade.
With all of these difficulties, it's entirely possible that the best path to "Human 2.0" might be upgrade through machine parts maintained by microscale robots.


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Do Gametes contain mitochondria/chloroplasts from their parent cell?
It has now been established (according to the Cambridge A level text book) that

organisms form a symbiotic
  partnership, typically by one engulfing the other
  – a process known as endosymbiosis. Dramatic
  evolutionary changes result.
  The classic examples, now confirmed by later
  work, were the suggestions that mitochondria and
  chloroplasts were originally free-living bacteria
  (prokaryotes) which invaded the ancestors of modern
  eukaryotic cells (cells with nuclei).

It also states that

It was also discovered in the 1960s that mitochondria
  and chloroplasts contain small, circular DNA molecules,
  also like those found in bacteria

and lastly

The DNA and ribosomes of
  mitochondria and chloroplasts are still active and
  responsible for the coding and synthesis of certain vital
  proteins, but mitochondria and chloroplasts can no longer
  live independently.

So my question is:
Is this DNA found in the mitochondria and chloroplasts coded for in the host's (animal's or plant's) DNA.
If not are there fully formed mitochondria and/or chloroplasts in all gametes (obviously chloroplasts only in the plant gametes) which were transferred directly from the parent who had them transferred directly from their parent and so on?
If so are all the mitochondria and chloroplasts of one type identical in a organism? Are they almost identicle in families (of organisms not the classifictaion Family)?

Is this DNA found in the mitochondria and chloroplasts coded for in the host's (animal's or plant's) DNA.

No, the DNA contained in these organelles it not a subset of the nuclear genome. However, part of the original genome of the prokaryote has been moved to nuclear DNA. That is why, as you cited, they "can no longer live independently."

If not are there fully formed mitochondria and/or chloroplasts in all gametes (obviously chloroplasts only in the plant gametes) which were transferred directly from the parent who had them transferred directly from their parent and so on?

As the child organism would eventually need these organelles, and they can only be inherited, at least one of the gamete must contain them.
For the chloroplast, the general rule is that only one of the gamete provides it. For example, in gymnosperm it is the male gamete (pollen), in angiosperm, it is the female gamete (ovule). Either it is just not present in the other gamete, or a specific exclusion mechanism makes it mono-parentally inherited.
Mostly the same for the mitochondria, with the caveat that (motile) spermatozoa contain mitochondria for their metabolic functions (energy to move), but these are discarded when forming the zygote, and only the maternal mitochondria are inherited. (In plants, mostly maternal too with exceptions)
This does mean that there is a lineage of organelle on one of the parent's side, up to the most recent common ancestor (approximately, the first individual of the species). In humans, this translates to a presumed Mitochondrial Eve from which all human mitochondrial DNA descends from.

If so are all the mitochondria and chloroplasts of one type identical in a organism? Are they almost identicle in families (of organisms not the classifictaion Family)?

Every mitochondrion of an individual organism comes from the stock of mitochondria of the zygote, through replication. They are thus very similar, except for cell specialization (giving particular morphology to the organelles), and possible mutations. Same for the chloroplast.
Mitochondria (and chloroplasts) are basic components of the eukaryotic cell, providing essential functions  which are highly conserved in a species, let alone related individuals.
However, this does not means the DNA of these organelle is the same for every individual : different sequences may give the same protein, or mutation may affect non-coding segment of the genome. This is the basis for genetic genealogy, retracing family lineage though analysis of DNA, including mitochondrial DNA.

No to your first question. Mitochondrial DNA (m[t]DNA) is individual to the host's DNA- it has it's own DNAs in the organelles itself. The same goes for chloroplasts. The mitochondrial DNA is officially linked to the mother's X-chromosomes, and since the sperm's mitochondria is destroyed and only the maternal egg cell is left, the mother's mtDNA is remained to pass down.
Mitochondria grow, reproduce, and replicate mtDNA by their own - this is another proof that they used to be prokaryotes, not to mention their circular DNA, double-membrance structure, etc..
I am not so sure about the third question of their evolutionary relationships between each other, but you probably have to know that chloroplasts created food by fixing carbon dioxide, while mitochondria broke down sugars to release ATP.

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Does plasmolysis kill plant cells?
I know when a plant cell becomes fully plasmolysed that the protoplast shrinks away and eventually is no longer joined to the cell wall.
Is this irrevocable damage? Can the cells survive it and continue to function if they are put back into a favourable solution.
If so how does the protoplast rejoin to the cell wall?

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Why is darker skin a better defense against sun than lighter skin?
We know from physics that the colour of something comes from the light it reflects.
Dark/Black objects absorb most light while light/white objects reflect most light.
Sunburn is the absorbance of too much light and is bad for your skin's health suggesting that absorbance of light is bad for you.
So why is darker skin better than lighter skin for high sun intesity living conditions? Logically darker skin should absorb more light (and so energy) while lighter skin should reflect most light (and energy).

I have realised there is a similiar question to my one already existing. Should I delete my question?


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Which enzyme is Nick Lane referring to?
In Life Ascending the author, Nick Lane, refers to an enzyme in his introduction:
'' It concerns an enzyme (a protein that catalyses a chemical reaction) that is so central to life that it is found in all living organisms, from bacteria to man. This enzyme has been compared in two different species of bacteria, one living in superhot hydrothermal vents, the other in the frozen Antarctic. The gene sequences that encode these enzymes are different; they have diverged to the point that they are now quite distinct. We know that they did diverge from a common ancestor, for we see a spectrum of intermediates in bacteria living in more temperate conditions. But from the gene sequences alone there is little more we can say. They diverged, surely because their living conditions are so different, but this is abstract theoretical knowledge, dry and two-dimensional.
But now look at the molecular structure of these two enzymes, pierced by an intense beam of X-rays and deciphered through the wonderful advances in crystallography. The two structures are superimposable, so similar to each other that each fold and crevice, each niche and protrusion, is faithfully replicated in the other, in all three dimensions. An untutored eye could not distinguish between them.....The building blocks bind tightly to each other, through internal bonds that work like cement, retaining the structure despite the buffeting of energy from the boiling vents..... In the ice, the picture is reversed. Now the building blocks are flexible, allowing movement despite the frost...... Compare their activity at 6°C, and the frosty enzyme is twenty-nine times as fast; but try at 100°C, and it falls to pieces.
The picture that emerges is colourful and three-dimensional. The changes in gene sequence now have meaning: they preserve the structure of the enzyme and its function, despite the need to operate under totally different conditions.''
Emphasis mine and .... indicates omitted text.
I would be very grateful if anyone could tell me what this enzyme is, and if possible point me to further information about it!
N. B. the enzyme is only mentioned in the introduction "... never found the opportunity for a mention in the book proper." There are no references for said introduction, only the chapters.
Thank you!

I'm not sure it'll be possible, since he doesn't provide any details in the book. There are a lot of enzymes with highly conserved structures, so it'll be hard to figure out which one he's specifically referring to here

This is conserved structure but totally distinct gene sequence, is that also so common? If so could you please give me a pointer to one of particular interest? I can probably read from there outwards till I have satisfied my curiosity.

@Mirte It doesn't say totally distinct, it says "they are now quite distinct"; "quite" is of course an imprecise word but I wouldn't say it means "totally", and the passage also refers to intermediates that would be intermediately distinct from each. It is not surprising that an enzyme would evolve similar structure to catalyze the same reaction at different temperatures, and that keeping this structure would require a different sequence of amino acids. As divibisan suggests, without further information from the author they could be referring to many enzymes.

Note the second snippet from the book link user1136 provided gives a revised version of the first sentence which OP quotes, to wit: It concerns a protein (a catalyst, or enzyme, called citrate synthase) that is so central to life that it is found in all living organisms, from bacteria to man.

@user1136 I'll vote for your answer if you write one :-)

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What is the attachment after this gene name, following the comma: SULF1,hCG18956?
What is this part mean: hCG18956? Is it an alternate naming convention for genes? I am trying to read in a list of gene names using R, but I don't have an extensive biology background.
There are some rows where gene names is not listed. Only something like this: hCG1809003. Does that mean there is no appropriate gene name?

Here, hCG stands for "human Celera Genome". hCG-prefixed protein and gene descriptors are used as a last resort for genes which are found only in Celera's database.
See for example http://www.ncbi.nlm.nih.gov/protein/119619226 , the gene you referred to as "hCG1809003". As the entry says, this was submitted by Celera in 2005 as a putative gene, after being found by "conceptual translation", that is, scanning the Genome Project data for start and stop codons. It is likely this gene has yet to be found as RNA or protein - because the only references for that gene are Celera's submission and the Genome Project paper. Nevertheless, Celera's sequencing (and microarray!) software and chips still look for it.
Your two example genes eventually made it to GenBank. The first example even has a proper name and function assigned - sulfatase 1. Many genes remain in hCG limbo.


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What is the gene corresponding to MIR382 RNA molecule?
Where can I find information such as this?

Did you try a Google search first before asking here? We ask that you thoroughly research your question and try to answer it yourself before asking here. Otherwise, the post may be downvoted and/or closed.

I did. Look at the comments in the answer, which I couldn't find from google search.

You find such information on ncbi gene (or ensembl gene)
http://www.ncbi.nlm.nih.gov/gene/494331
Note that Mir 382 still only is provisional.

So where's the gene?

The section on genomic context lists the physical location of the entrez gene 494331 which is the gene encoding Mir 382 in humans

Does it not give a specific name as to what gene it is?

The second line at the top has the entry for "Official Full Name". In this case the name of the gene is "microRNA 382" . For the human gene, this name comes from HGNC, which is the official naming committee of human genes. (see the entry on "provided by"). For additional non-standardized names you might also want to see the "also known as" and "Summary" fields at ncbi gene (which is basically one of the two major official resources for genes)


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If a promoter region of a gene is transcribed, can it get methylated?
Deletion of a transcription termination site can lead to a downstream gene's promoter region being transcribed. What if that portion of the mRNA acts like an siRNA methyltransferase recruiter?


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Would a complete lack of heterozygotes in a population indicate the presence of a recessive allele?
This doesn't instantly make sense to me.
Lets say you have 100 people from a subpopulation who were sequenced and aligned to a reference genome. For certain variants, people were either homozygous for the loss-of-function alternate allele, or homozygous for the reference allele.
This indicates consanguineous practices within the population. However, I'm told that this also indicates that the alternate allele is recessive and that if it were dominant, there would be very few heterozygotes due to selective pressure, and individuals would not reach a breeding age. This doesn't make sense to me. If it were recessive, there would be an excess of heterozygotes, and if it were dominant, there would be very few heterozygotes, but if there are no heterozygotes, that indicates that it's recessive?
I also fail to see how either condition can be determined in this case.


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Cloning a coding gene into a non-expression vector
Does it make any sense to clone a CODING gene into a NON-expression vector?
doing this will only give us multiple copies of the gene, while we could run  PCR instead (Let's say we know the gene sequence)

Welcome to SE Biology. Please take the tour and read how to ask a good question. You need to provide some context to your question as the reasons for cloning genes are numerous, and your quesition is in danger of being considered too wide. You should also indicate what efforts you have already made to answer the question for yourself. Tell us what you found and why it doesn't fulfill your requirements.

In principle, you can amplify any gene with PCR and then clone it into a vector of choice. However, it is often not as easy. Most things can be done with expression vectors, but sometimes it is easier to clone a sequence first and then subclone it.
Some sequences are hard to amplify, especially when they get long or very long. Amplifying 2,5kb can be tricky, digesting and subcloning such a piece might be easier. Additionally yields of PCR can be low, while you get a lot of DNA from a miniprep.
You might want to introduce additional restriction enzyme recognition sites (one can easily be done via PCR, but more again is tricky), linker or additional tags, which are not present in all expression vectors. Then it is easier to simply do a first cloning step into the non-expression vector and then take the complete insert into the expression vector.

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What does the MAF/MinorAlleleCount mean?
I'm not sure why reporting the second most frequent allele is helpful?
what is the Major allele?

Are you using a software that reports this? Where did you encounter this term? Please provide some context and explanation.

[W]hat is the Major allele [frequency]?

If the Minor Allele Frequency is $p$, then, for a bi-allelic locus, the major allele frequency is obviously $1-p$.

[W]hy reporting the second most frequent allele is helpful?

Most polymorphic loci of interest are bi-allelic. Hence, the MAF is an indication of genetic diversity. One could similarly report the expected heterozygosity instead ($2p(1-p)$).
It is common to consider only loci with a MAF greater than a certain value. There may be different reasons for that. Here are possible two reasons.
Sequencing errors
When sequencing your sample, errors are being made. Sure, error rate is pretty good (see this table from Molecular Ecology) but error still do exist. A polymorphic locus with a minor allele count of less than, says, 3 alleles might well just be caused by sequencing errors.
To avoid considering as polymorphic loci that are in reality not polymorphic, we often just disregard any data with MAF is below a given threshold.
$F_{ST}$
$F_{ST}$ is a measure of genetic differentiation among population. When computed on loci with low MAF, the statistic is biased (Beaumont and Nichols, 1996). Hence, it is usual to only consider loci with a MAF greater than an arbitrary threshold before computing $F_{ST}$


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Boys born in excess - how can the nature draw from non-natural distributions?
The probability of a newborn baby to be a boy is not exactly 50% but a bit more. I have been given the explanation that it is because boys act more self-destructive during the early ages and so the distribution evens out during time. But how can the nature know beforehand that boys should be made in excess?
It would make sense that the nature followed natural distributions in its choices like uniform, gaussian, exponential etc. but this seems not to be the case. What are the motivations and mechanisms to deviate from natural distributions? Can you come up with another examples of such "non-natural behaviour" in nature?

Welcome to Biology.SE.
"Natural" vs "non-natural" Distribution
There is no such thing as a "natural probability distribution". Actually, biological system often produce distributions that does not match with commonly used distributions just because the assumptions yielding to these distribution are sometimes poorly met in nature. In other words, many biological variables meet more complicated distribution than the standard uniform, binomial, geometric, beta, exponential, and other distribution you know of.
Of course the gaussian distribution is kind of a special one that is often approximatively reproduced by biological system as a consequence of the central limit theorem.
Some distributions are more used than others but there exist an infinite number of definitions and anyone can construct one. Here is my distribution of the day. $P(x | y,z) =  C \frac{y^x - exp(-yz)}{x+z+y}$, where $C$ is a constant of integration to ensure $\int_{-\infty}^{\infty} C \frac{y^x - exp(-yz)}{x+z+y} = 1$. I will call this distribution the "remi.b distribution". I have no idea what kind or process it can model and nobody will probably ever use it but it is a legit distribution.
Developmental mechanism
You can read this post and that post about the developmental mechanism that yield to such bias sex-ratio at birth.
Evolutionary processes

how can the nature know beforehand that boys should be made in excess?

Organisms producing a bias sex-ratio are selected for as they increase the average fitness among their offspring. As such the population is selected toward creating such bias sex-ratio. Organism don't know, they just do.
In order to understand the evolution of sex-ratio a bit better, you should have a look at this post.


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New evidence about the beginning of life?
The cover story of the August Scientific American is about new evidence suggesting "volcanic pools" as the location for "first life" as opposed to deep sea smokers like "The Lost City".
I was under the impression that one of the strong arguments for the deep sea vents is that the DNA of the life there is some of the "oldest DNA" on the planet. I'm wondering how the authors would explain that. (Maybe life spread to every "nook and cranny" in a geological blink of an eye?)

Can you please give some reference to support your claims. You could add 1) the link to the article from the August Scientific American 2) a source that support your claim that strong arguments for the deep sea vents is that the DNA of the life there is some of the "oldest DNA" on the planet. especially so that the term "oldest DNA" is very unclear.

Really, if you want to know how the authors of an article explain something, ask them. The question is really not on topic here, given the wooliness of your statement about "the oldest DNA on the planet". This is a Q&A forum for precise answerable questions about biology.

It's an interesting question, but I agree with David that the idea of "the oldest DNA" is a bit strange. The parts of origin-of-life theories about geology are generally about how to create the basic molecules of life (bases, sugars, lipids, etc). These molecular parts don't have an 'age' - so I would not expect to be able to date DNA to any particular location on Earth.

Ah, reading the Sci. Am. article (https://www.scientificamerican.com/article/did-life-first-evolve-in-geothermal-pools/), I see it is about the chemical 'signature' (sodium, potassium, zinc) - that makes sense, as that's about the only way you could infer the geology of life's origins. Perhaps the question could be re-framed as "What do we know about the geological origins of life?" or similar.[ here is the paper, btw : http://www.pnas.org/content/109/14/E821.abstract ]

Okay, now that I've been wrung thru the wringer. I'm not sure what my original source was, but I probably worded my statement incorrectly. I think where i got the "oldest DNA" idea is from articles like this one http://www.pnas.org/content/110/27/11067.full.pdf supporting the idea that the "Last Universal Common Ancestor" came from a high temperature (ie. deep sea smoker) environment. I see upon further reading that this is still up for debate and I suppose "volcanic pools" were high temperature environments.


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What would happen if all magnesium was removed from a person's body?
Magnesium is essential to bodily functions. It enables ATP from which most energy is produced in cells. It regulates over 300 biochemical reactions in the body. It is important to the transfer of nutrients through cell walls. It stabilizes the structure of DNA and RNA.
What would happen to a person if some alien micro-organism totally depleted his/her body of magnesium? How quickly would they die? (Yes, there may be a sci-fi story being written here.)

well oxidative phosphorylation and glycolysis would both stop for a start, it is essential for several of the enzymes involved.


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The first species having circle of Willis (circulus arteriosus cerebri)?
I know mammals are not the only species that have this anatomical unit (i.e. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982101/).
But I was wondering what was the first species that had a similar structure in their brain (or brain-like organ). Do we know this?


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Pichia pastoris and ornithine
Can Pichia pastoris (species of yeast used for recombinant protein) produce the non-protein amino acid Ornithine? Or does it express ornithine at all?

is the pichia pastoris genome available from some sequence database? you could search for ornithine synthetic genes

yes, i can look for the pichia pastoris genome sequence on NCBI. do you suggest that i compare the genome sequence of pichia and ornithine and see if there is a match between them ?

Yes, it contains arginase. Thise enzyme converts arginine to ornithine and is probably part of the urea cycle.
You might notice the arginase is listed as coming from Komagataella phaffii GS115, but this is just another (new?) name for Pichia.


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Could trees be engineered to produce rainfall-nucleators?
Scientists are using genetic engineering to make trees produce more terpenes. Is it possible to genetically engineer trees to produce more hygroscopic volatile organic compounds? These trees could be used in drought areas to create more rain.

Welcome to Biology.SE! Don't forget to take the tour. Could you add a source for your terpenes claim? It would also help to give examples of hygroscopic volative organic compounds, although it's not essential.

Your question is just too broad (also opinion based). Please add details and avoid asking open ended questions.


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Constraint optimisation
I have been asked to talk about (constrained) optimisation like $$\max_{x,y} f(x,y)$$ $$\mbox{Constrained by } g(x,y) = 0$$
for high school students with applications to biology. However, I can not think of a single good example from biology that actually uses optimisation.
The existing application is proving what the optimal linear regression line is given by, but this is rather tedious to do and not really a fun exercise for high school students, which is why I hope you might have a great application that I can use.

Flux balance analysis involves constraint based optimisation and it is frequently used to study metabolic systems and drug effects. I think it's interesting but high school students may still find it tedious and interesting examples of it may be too complicated for them.

The most "naive" models of evolutionary biology are optimisation models. Otherwise, in bioinformatics, there is plentiful of optimization problems.

@Remi.b Would you by any chance have a link for those naive models for evolutionary biology?

The most famous are Hamilton's rule (original paper: Hamilton 1964 which is a bit hard to read because of a terrible notation) and Price's equation (wiki). I called them "naive" because they are simple in the sense that they don't make consideration of statistical genetics nor molecular genetics.

Are you looking of examples of usage of optimization models to model biological processes or of the usage of optimization algorithm for inference problems (or any)?

Nothing specific. I am going to present the topic of optimisation for biology interested high school students, so I need some examples that I can use to argue why it is relevant.


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What causes pinkish hue to some skins?
I know it is caused either by blood vessels beneath skin , or some pigment called "pheomelanin" . But what is it in fact?

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question.

The answer lies in hemoglobin, which is responsible for the transportation of oxygen throughout our bodies. It is the protein found in red blood cells, and thus it has a reddish hue to it. When an organism has lightly pigmented skin, the oxygenated hemoglobin causes the pinkish hue that you are describing.

then , this happens if the skin is not much pigmented, and if there are much melanin pigments , the hemoglobins in blood cant be visible, isn't it ?

Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted.


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How does action potential conduct across a branch in a neuron?
As the action potential travel in the dendrite towards the cell body, it will encounter many branches. What happens at the branch? What makes it go to the cell body instead of other dendrite?
Also, as the action potential travel from the axon to its branches, does it go to only one or all terminals? If it goes to only one terminal, how is it decided which terminal it has to go?

Awesome question!  Thanks for asking it and giving me the motivation to look back at the literature to increase my own understanding!
I do want to point out one issue of semantics before starting.  Just to avoid confusion, I'm going to follow the example of some of the well-known experts in this field and distinguish dendritic spikes from action potentials.  The main difference is that a voltage spike in a dendrite or dendritic spine will experience attenuation (essentially a weakening of the spike) as it propagates toward the cell body, and it is distinct from the all-or-none voltage response of an action potential.  It is generally accepted that action potentials are initiated in the axon (hillock) because that is where dendritic and somatic spikes will ultimately sum to fire the all-or-none voltage response.  I just want to clarify what I mean by dendritic spike when I use it during this explanation.
What happens at the branch? So, to answer your first question, you're absolutely correct that when a dendritic spike occurs, that spike will encounter multiple branch points along the dendrite as it proceeds toward the soma.  When a spike propagates to a branch point, the properties of the branches determine what happen to the spike.  One important property is referred to as the geometric ratio (GR).  This property was described Goldstein and Rall in 1974 (manuscript here for review https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334570/) and the gist of the equation is that spike attenuation is dependent upon the diameter of the branch the spike is coming from and the branch the spike is going into.  The concept behind this is called impedance mismatch, but that's complex and I won't get into it.  Just know that spike propagation is favorable from a large to a small branch, but is not favorable from a small branch to a large branch.  If you wish to read more about this concept, I'd recommend the Goldstein and Rall paper referenced earlier and chapter 14 of the textbook "Dendrites" by Spruston, Stuart, and Hausser.
Additionally, the presence of leak or voltage-gated channels in that branch can determine how well the spike will propagate or how much attenuation will occur.  This is an easier concept to grasp because the idea is essentially that more channels open when the spike passes through that branch, the more charge leaks across the membrane and causes attenuation of the spike.
All questions regarding preference of flow To sort of attempt to answer all your other questions at once, nothing really forces the spike toward the soma or a specific axon terminal.  There are dynamic changes in membrane potential that may prevent spike propagation down one branch or action potential propagation in a certain direction (like how action potentials aren't thought of as propagating from the axon to the soma because of the hyperpolarization and long inactivation of sodium channels at the area that just fired, preventing what is called backpropagation at that particular time).
I think a little reading on neuronal cable theory might be of some help with this question too.  This link is to a PDF that gives a pretty brief explanation of this concept https://nanohub.org/resources/20112/download/Lecture1_Passive_Conduction.pdf.  This is a pretty math-heavy field, so beware if math isn't your favorite subject!


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How much of a DNA difference is between Chicken of the Woods, and Hen of the Woods?
I've noticed that when a COW is touching the ground it turns a gray color, but when on a log/tree it's bright orange. Is there a correlation between the DNA, and where it grows?

I do not understand your question. What is changing color? The grass? The grass is going bright orange when you put a a tree log on it and grey when a cow step on it? Do you mean a change of color that takes a season to happen or is instantaneous? You ask Is there a correlation between the DNA, and where it grows? DNA of what? Are you talking about cows and trees, here? Is this question related to the claims about colors you made above? The title is talking about Chicken and hen but those are absent from your post!

Sorry, title is talking about "chicken of the woods" and "Hen of the woods" (not chicken and hen). And COW is a priori short hand for Chicken of the Woods. So, I suspect you talk about the color of the mushroom. Is your question "Are there genetic predisposition to growing low or high on a tree for a chicken of the woods?" or maybe "Are hen of the woods more likely to grow at low height on trees than chicken of the woods?"?

Yes, I'm asking essentially if the COW is just a hen growing on the side of a tree or not.

I will assume from your comment that your question is

Is a chicken of the woods just a hen of the woods growing on the side of a tree?

, which is very similar to me to

Is a chicken of the woods and a hen of the woods the same species?

No, they are not the same species. Chicken of the woods is the common name of a number of species of the genus Laetiporus. Hen of the woods is the common name of the species Grifola frondosa. In fact, Grifola and Laetiporus don't even belong to the same family but only to the same order (order Polyporales).
According to the wikipedia links posted above, Grifola frondosa is indeed usually found at the base of the tree while Laetiporus is generally found in the wound of trees (mainly oak trees).


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Will omega 7 make it harder to produce high quality meat?
I heard from a medical show that Omega 7 makes it harder to gain weight, and was wondering if I would be be able to put on muscle better if I have sheep and pigs getting omega 7 through sea berry branches.

can you add some references/information sources? which medical show? is it published anywhere? etc etc

https://vimeo.com/107166478

No. The only sure thing about omega-7 is that the suppliers are making money.
There's no evidence that it's doing anything more than just being an unsaturated fat in humans. This make it extremely unlikely that it would do anything after you put it through a pig.

So if your trees are producing it, you will be making more money?


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Does the process of photosynthesis occur in insectivorous plants?
Does the process of photosynthesis occur in insectivorous plants?
Can you please give me a clear answer and explain to me how?
and also can you describe the environment in which they grow ?
Thank you

is this a homework question? you need to give a little more detail and effort when posting to this site... please see the help page where it discusses "how to ask a good question" - thanks!

@AlwaysConfused  if you know the answer then post it as an answer. Use comments only to request clarification and suggesting something.

"Carnivorous plants are plants that derive some or most of their nutrients (but not energy) from trapping and consuming animals or protozoans, typically insects and other arthropods. Carnivorous plants have adapted to grow in places with high light where the soil is thin or poor in nutrients, especially nitrogen, such as acidic bogs and rock outcroppings."
Source: https://en.m.wikipedia.org/wiki/Carnivorous_plant


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What kind of tree has this blossom?
I filmed this beautiful blossom on a tree, this past spring in Toronto, Ontario, Canada.

Is it a small tree? It's clearly in the rose family, but that includes apples, pears, quinces, apricots, plums, cherries, peaches, raspberries, blackberries, loquats, strawberries, roses (duh), hawthorns, almonds and more. Best guess? Some kind of plum, like (but not) Thundercloud Plum, because the leaves are out as well as the buds, and the leaves will be burgundy colored. It might also be a crabapple, likely Crabapple "Royalty", but the bark is off. It would help to have a better picture of the leaves and bark, Not an answer because I'm guessing.

Woah, just saw your other posts. You did this last year; you posted a bunch of photos you took in a botanical garden then asked for their names. It's one thing to be genuinely curious about a plant you've come across; it's another thing altogether to take a bunch of photos and ask someone else to identify them for you so that you can label them on your site (or whatever.) -1.

Hello, thanks for your guess and the intel anongoodnurse. It is a fairly large tree in my neighbourhood. Probably 25 feet high, 20 circumference.
Re. your other comment, I shoot stock footage so i'm really particular about describing what i have shot accurately. I am also genuinely curious about this beautiful world of ours that we live in! I also don't think it hurts to increase knowledge on stack exchange via these pics? For example, I posted a pic of a beetle a while back, which prompted a really great and interesting discussion that many people benefitted from, including me!

Maybe, maybe not. I think you're asking others to do work that you should have done yourself at the time you took the photos.


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Trying to identify the tree in this picture. Shot from the Nepenthe restaurant, Big Sur, California
I'm trying to identify the tree in this picture. This was shot from the Nepenthe restaurant, Big Sur, California.
Any help is appreciated!
Thanks,
Robert

It's difficult to make out the leaves in the photo, but the tree in the foreground appears to be a coast live oak (Quercus agrifolia).  The tree has hairy lichen growing on its branches.

Thank-you for the quick response. Much appreciated.


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Flower Identification: Pyrenees, France
I'm trying to identify the white flowers in this photo. Location is in the Pyrenees mountains near Luz-Saint-Saveur in France. The image was shot in early September of this year. Any help is greatly appreciated!
Robert


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Why do plants create enough energy for the entire ecosystem?
In my environmental class, we were recently learning about the $10\%$ law that basically says only $10\%$ of the energy goes from one trophic level to the next.
This got me thinking about why energy flows from one level to the next.  Specifically, why do plants create enough energy for the entire ecosystem?  Wouldn't they do fine without us, and wouldn't that save them the work of creating all that excess energy?

They don't create energy! They use the energy from high-energy photons from the sun and convert that into molecules with high energy chemical bonds. Many plant species have evolved to need animals to reproduce, but yes, as a whole, a plant-only biosphere would probably be stable.

As @AlwaysConfused points out, the assumption in the question is problematic, and this has resulted in vague answers that can't directly answer the question. I'm voting to close the question because it is unclear to me what the question is bearing in mind the assumption is false.

I agree that the question is problematic and a bit unclear. Generally, it invites confusion to phrase why questions in terms of taxonomic groups ("why do plants create...") - why-questions on evolutionary outcomes usually don't make much sense.

building upon @fileunderwater's comment, I've been taught and found it true that in the life sciences, "why" questions generally need to be rephrased as "how" questions to be answerable, leaving the remaining "why" essence of the question to philosophy. When we rephrase as "how" and learn lots from that, it can shed much light on potential answers to "why".

Plants collect energy for themselves via photosynthesis, not for others.
It is used for it's own growth and survival.
It's energy is then redistributed to other organisms when either the plant dies and decomposes or when it is consumed. Many organism cannot collect their energy like plants do, and thus must feed on organisms (like plants) that are able to collect and store energy. This is in many cases detrimental to the plant (it should be intuitive why being eaten might be bad), and many, many plants do have traits to discourage other organisms from eating them (plants with toxins, thorns, etc.).

Let's look at a very simple "ecosystem", cows and grass. Imagine there is 1000 kilograms of grass available. This can support about 100 kg of cow. There's your 10% figure, but mass here instead of energy.
When the cow eats the grass it must break down the food to get both matter and energy. Everytime energy is transfered, some of it is "lost" as heat. So as the energy in the bonds of the molecules of the grass are transferred into energy in the bonds of molecules making up the cow, much of that energy is wasted, radiated away from the cow as heat. The cow also has many tasks to perform that also use the energy in the grass. It has to walk around grazing, chew, make more cows, etc. By the time all this is accounted for, the cow has used 90% of the energy in the food to provide for its own energy needs as well as the waste.
In the process of breaking the grass down for energy, the cow transformed the food, from which it extracted the energy, into carbon dioxide and water. The carbon dioxide was breathed out into the atmosphere. Only 10% of the matter in the food remains to add mass to the cow. This is why the cow only put on 1 kg of weight for each 10 kg of grass.
So that cow, having only retained 10% of the matter that was in the food, only has 10% of the energy since energy is stored in the chemical bonds of the matter.
The 10% rule is an approximation. A number of my students were in FFA (Future Farmers of America) and raised animals. One of the tasks they were required to do is keep track of the weight of feed and compare it to the weight gain of the animal. Many that I spoke to did better than the 10% but much of that was probably due to the higher quality of the feed they used.

@AlwaysConfused FFA = Future Farmers of America. You must be a city boy! :) I edited that in above, should have done first time around. [this comment to be deleted]

" The cow also has many tasks [...], make more cows. "
The way this is said made me smile :)


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DNA extraction from plants and algae don't use phenol. Why?
I don't know if here is the correct place to make this question, but I've been noticing that protocols for the extraction of photosynthetic organisms DNA don't use phenol. Only CTAB / Chloroform.
Why?
Because bacterial or animal extraction are phenol:chloroform based.
Thank you

CTAB is for removing polyphenols and polysaccharides which are found in plant tissues. Animal cells/bacteria don't have these. You can do an additional phenol-chloroform extraction if you want.
See this protocol by Monsanto.

Weigh out 6g of processed tissue into a 50ml conical tube appropriate for centrifugation. Note: For unprocessed tissue, weighing
  m ay occur prior to processing as long as entire processed sample is
  transferred to the conical tube.
For each 6g sample add 25ml of a solution consisting of 24.25ml, pre-warmed (55°C) CTAB extraction buffer, 0.5ml 2-mercaptoethanol
  (2-ME), and 0.25 ml of 10mg/ml proteinase K for a final concentration
  of 2% (2-ME) and 100µg/ml (proteinase K).
Incubate the tube for 60 minutes at 55°C. Cool the tube briefly on bench (10 minutes)
Add 20ml of phenol:chloroform:isoamyl alcohol (PCI, 25:24:1).  Cap the tube and mix vigorously by vortex or inversion.
Centrifuge for 10 minutes at 13,000×g and 20-25°C to separate the aqueous and organic phases. Transfer the upper aqueous phase to a
  clean 50ml conical tube.
Repeat extraction two times for a total of three extractions (steps 4-5).
Transfer upper aqueous phase to a new tube and add approximately 2/3 volume of -20°C isopropanol and gently invert the tube several
  times to mix.
To precipitate the DNA place the tubes at -20°C for at least 30 minutes and up to three days.
To pellet the DNA centrifuge the tubes at approximately 13,000×g for 20 minutes at 4°C.
Redissolve the pellet in 4 ml of TE pH 8.0. Transfer to a 13ml Sarstedt tube and add approximately 40µl of 10mg/ml RNase, then
  incubate at 37°C for 30 minutes.
To extract the DNA add 4ml of chloroform:isoamyl alcohol (CIA, 24:1).  Centrifuge for 10 minutes at approximately 13,000×g at room
  temperature.  Transfer the upper aqueous phase to a clean Sarstedt
  tube.
Repeat step 11 then add half volume of 7.5M ammonium acetate, gently mix by inversion/pipette and add 2 volumes of 100% ethanol. Mix
  by inversion/pipette and place at -20°C for 30 minutes to overnight.
Centrifuge at 13,000×g for 20 minutes at 4°C to pellet the DNA.

I have used phenol:chloroform many times for algal DNA and RNA extractions. These protocols needed only minor tweaks to adapt it to a particular species (some cell walls can be extremely though). The general principle behind phenol chloroform works on almost any sample once you have lysed/pulverised the cells. The only major issues occur when tissues are extremely fatty or full of carbohydrates.
I have also used CTAB but it seems to be less universally applicable to algal samples.


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What does 'half life' of a protein mean?
Why do we use the term 'half life' for proteins?
Here is a link to some information regarding this question, but I am unable to infer it.

"Half-life time" is a general term. This is a time after which the amount of substance X decreases by 50%.
If you take a bulk of something (say, 100 protein molecules), if this protein has half-life time of 1 hr, then 1 hr later you'll have 50 molecules left.
In cellular biology it usually means that 50% of protein got recycled/degraded in given half-life time

why is not the term "life time" used?

@souravthampan comparing to https://en.wikipedia.org/wiki/Fluorescence-lifetime_imaging_microscopy I think main difference is that "lifetime" is a characteristic of process, which can be measured by "half life" time.


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How does noradrenaline result in rise of systolic blood pressure even when the cardiac output is decreasing?
Systolic blood pressure[SBP] depends on the cardiac output. When Nor adrenaline is given there is vasoconstriction due to alpha-1 action on blood vessel, vasoconstriction results in increased total peripheral resistance and thus increases the diastolic blood pressure. The beta-1 action [increase in cardiac output] on heart by Nor adrenaline is counteracted by the reflex bradycardia  resulting in decreased cardiac output. Given the fact that SBP depends on cardiac output and the cardiac output is decreasing, why is there a rise in SBP on administering nor adrenaline?

Vascoconstriction, research it maybe?

Your question involves comparing an observed response to administration of noradrenaline/norepinephrine, which causes vasoconstriction thereby increasing the BP (during both systole & diastole,) to the hemodynamic/pharmacodynamic response of the cardiovascular system as a whole, which is decreased cardiac output & decreased cardiac work.  This is similar to asking why opening a finite water tank eventually slows down even though the pressure increases when you turn on the faucet.

Welcome to Biology.SE! This might be a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion and very difficult to verify by a non-expert. This is a good example of how to format references. ——— Please take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!


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Can severe vasoconstriction increase systolic blood pressure?
I know that, vasoconstriction results in increased total peripheral resistance which is responsible for the rise in diastolic blood pressure. Also, cardiac output is responsible for the systolic blood pressure. But there are conditions, as in administering nor adrenaline, where there is severe vasoconstriction and a fall in cardiac output but a rise in both systolic and diastolic blood pressure. In this case, I understand that the rise in diastolic blood pressure is due to vasoconstriction produced by nor adrenaline. I am not able to account for   the rise in systolic blood pressure in the setting of falling cardiac output. Can severe vasoconstriction also influence the systolic blood pressure?

Yes. Imagine you're blowing into a balloon. Your airflow into the balloon represents 'cardiac output'. As the balloon gets larger and larger, the pressure inside the balloon (the 'peripheral resistance') rises, and the amount of air you can blow in ('cardiac output') falls. Your systolic and diastolic BP both rise. Does that make sense?

Yes I understand, I had come to a similar conclusion. Thank you for confirming it.

'Total peripheral resistance determines diastolic pressure, cardiac output determines systolic pressure'—what is the source of this statement? In what context was it made?

Highest pressure measured in an arterial pulse pressure trace, systolic blood pressure, is during the systole of the heart, so it is the cardiac output responsible for this whereas the lowest pressure in an arterial pulse pressure trace, diastolic blood pressure, is maintained by the tone of the blood vessel (total peripheral resistance). This is my understanding.

@souravthampan Hmm, that does not look like a very sound argument. Nor is this statement supported by any experimental evidence (as far as I know).

I think the heuristic 'total peripheral resistance determines diastolic pressure, cardiac output determines systolic pressure' is not a good one after all. E.g., it does not explain the effects of norepinephrine. Nor does it explain the phenomenon of age-related change in blood pressure: see https://www.ahajournals.org/doi/full/10.1161/01.cir.96.1.308. Part of the reason is, it does not take into account vascular compliance, which has a major role in determining pulse pressure.


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why is erythrocyte sedimentation rate higher in females?
erythocyte sedimentation rate should be independent of the sex.
what is the reason behind this sex bias and why does it increase during pregnancy and how does age influence it.

Why would you think ESR should be independent of sex? Do you understand what the test is and what it indicates? What have you done to try to find out why it's not independent of sex?


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flying insect the size of a bird
On my farm a few weeks ago I started to see a large insect(?) I never, in my 76 years, seen before.
It is bright yellow, about the size of a man's hand, flies not like a bird but more like a butterfly and its large long legs hang down in flight. Observations are from 75 yards away.
The encounters are too brief to get a picture or even a magnified view without stationing myself in position all day.

It could be a hornet, try to film it, maybe it's easier to recocnise it then.

The hand of a man; 6 or 7 inches. See them (4) morning and afternoon. The legs are long and hang down in flight. Wish I could get closer or maybe snap a picture. It's one of those things, like a movie, you wait for an hour, see none, then when you turn and walk away, they appear.

@AlwaysConfused: Your hands are 1m long?

@Edwin: Please edit your question.

Without seeing it my guess would be a Hummingbird moth or Clearwing.. Look it up


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Transport mechanism in absorption of monosaccharides in small intestine
In the cell membrane of the intestinal cells, there is a mobile carrier protein called Sodium  Dependent Glucose Transporter(SGLT1).It transports glucose and galactose to inside the cell using energy.The energy is derived from sodium-potassium pump (Primary Active Transport).How it is possible cause we need energy in Na-K pump too ?

From my initial reading on this, the SGLT1 does not itself directly use energy in the form of ATP. https://en.wikipedia.org/wiki/Sodium-glucose_transport_proteins It appears the uptake of the sugars by this protein are achieved by cotransport. In this case, they "hitch a ride" into intestinal epithelium by following the flow of sodium ions back into the epithelial cells. The reason the Na+ ions flow into the epithelial cells is because of their higher concentration outside the cells. This concentration gradient is created and maintained by the Na-K Pump. So, ATP is used to create a chemical gradient, higher [Na+] outside compared to inside. Then the natural flow of Na+ down its gradient "drags in" the sugars.

I still dont get the point . Na-K pump uses the ATP to keep the concentration gradient stable. How the ATP is generated by this pump to be source of energy for SGLT1 mechanism ?

The pump uses the energy in ATP to create the gradient. The gradient itself is another form of energy. It is the energy in the gradient that brings in the sugars. Forming a gradient is like blowing up a ballon. Once that balloon is full of air, the compressed air inside wants to rush out. As it does, we can get it to do various chores for us. In this case the higher concentration of Na+ outside the cells is allowed to flow in through the SGLT1. As it does, sugars ride in with the ions. The Na-K Pump keeps pumping Na+ out to keep the process going.


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How can some residues in the active site of enzymes be protonated with a pKa < 7?
It is reported in many papers, that some residues in the active site of enzymes need to be protonated to get functional enzyme, where these residues have a low pKa (for let us say 5).
How can that happen in the physiological conditions (with pH=~7.4)?
It is mentioned that a raise in the pKa value is happening during the catalytic activity to get that protonation state. But how is that happening?
Here is a publication where this protonation and pKa raising is described.
https://www.ncbi.nlm.nih.gov/pubmed/7306491

This conclusion is confirmed by the result that a group with a pK value of 6.7 must be protonated for the binding of methotrexate. It is proposed that the binding involves the formation with N-5 of dihydrofolate or N-1 of methotrexate of a hydrogen bond which has considerable ionic character and which lies within a hydrophobic environment. Further, it is suggested that the same hydrogen acts as an auxiliary catalyst which facilitates hydride transfer from NADPH to dihydrofolate for its conversion to tetrahydrofolate. Evidence to support this suggestion comes from the finding that the V profile is similar to the V/K profile except that the pK of the group which must be protonated for maximum enzyme activity is shifted upward by about 2 pH units. Such an increase in a pK value is consistent with the formation of a hydrogen ionic bond in the ternary enzyme-NADPH-dihydrofolate complex. The results of inactivation experiments with trinitrobenzenesulfonate appear to indicate that a lysine residue is necessary to maintain the enzyme in its active conformation.

Generally speaking, even though physiological pH is generally ~7.4, this is not necessarily the pH inside the enzyme active site. The enzyme's catalytic machinery may experience a completely different pH for one of two reasons: 1) because the enzyme is located in a place where the pH is simply not 7.4, and 2) The enzyme's amino acid composition shifts either the pH in the active site or the pKa of the active site residues relative to the surrounding environment such that the effective local pH in the catalytic site is lower or higher than 7.4.
For example, there are places in humans, such as the stomach or around muscle cells during anaerobic respiration where the pH is actually acidic relative to the standard physiological pH of 7.4, due to the presence of HCl or lactic acid respectively. Additionally, certain subcellular organelles, such as lysosomes, also are relatively acidic, since they are a site for breaking down proteins into amino acids.
However, the case presented in this paper seems to be an example of the second situation, where an enzyme that is in a pH neutral environment relies on one or more protonated amino acids to perform catalysis. This is relatively common. Basically, the enzyme's active site has an amino acid composition that when folded correctly, alters the local pH around the catalytic residues to favor catalysis. For example, in the enzyme acetylcholinesterase, the active site serine is rendered nucleophilic by being positioned next to a glutamate and a histidine, in an arrangement referred to as a catalytic triad. The glutamate is an acidic residue, and its close proximity to the histidine means that it will stabilize the protonated form of the histidine. Energetically, this makes protonation of the histidine very favorable. This causes the histidine to take a proton from the active site serine. Now that serine's oxygen is deprotonated, it can act as a strong nucleophile. After the serine forms a covalent interaction with the substrate, the histidine will facilitate a similar nucleophilic attack by a water molecule, regenerating the enzyme and completing the catalytic cycle.
Something similar is seen with the beta-lactamase TEM-1. In this case, TEM-1 uses a lysine (pKa ~11) instead of histidine (pKa ~6), so multiple acidic residues are in the active site to facilitate the deprotonation of the lysine during the catalytic cycle. In effect, the amino acid composition of the active site allows for the shuffling of protons needed for catalysis.
So to summarize, while physiological pH is widely regarded to be 7.4, an enzyme's catalytic machinery may experience a very different pH through either the cellular/physiological localization, or through the amino acid composition of the active site. In the latter case, the presence of acidic or basic residues can alter the protonation state of other acidic or basic residues, meaning the effective pKa of these residues or the effective pH around them is higher or lower than 7.4.

It seems incorrect to say that the enzymes are altering the pH of their active sites. Rather they are altering the pKa of the active site residues. I would also add that pKa is a measure of equilibrium and thus even if, for example, the pKa of a moiety is below the pH, this does not mean it is completely deprotonated.

Martin - Thanks, I totally forgot to mention that; it is an important point.

Canadianer - Thanks! Your second point is important and I didn't to mention it. Concerning your first point, while I agree that it is generally more useful to think about residue pKa rather than pH of the active site changing, and that this is probably the more important factor, I would think (I may be wrong)  that both are changing. If a pocket in a protein has many acidic or basic residues, the solvent in the pocket will likely have more or less hydrogen ions per unit volume than the solvent outside the pocket. Since pH is a measure of [H+], this would differ between the two environments.


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How can ionized amino acid form be important for the catalytic activity?
I can imagine that protonated amino acid form, particularly at the active site, is important for the catalytic activity so hydrogen bonds can be created between the substrate and the enzyme. However, I cannot imagine how the ionized form can be important for the activity?
Both forms are important for the activity as stated in this study:
https://www.ncbi.nlm.nih.gov/pubmed/7306491

The pH dependence of log V/K for dihydrofolate showed that a group with a pK value of 4.7 must be ionized and that a group with a pK value of 6.6 must be protonated for activity

I cannot understand how the ionized form is important for the activity, could some one help me to understand that?

Without seeing a crystal structure it's hard to tell. But the abstract suggests 2 carboxyl groups, on a glutamate and aspartate. The abstract also mentions a lysine is necessary to maintain active conformation. Could the negative carboxyl group form an ionic bond with a postively charged lysine?

@user137, I am not sure, but isn't the ionic bond too strong for enzyme-substrate complex?

Although the answer provided by @MartinKlvana is correct, I would like to clarify the question of the strengths of non-covalent interactions in proteins, as this seems to be the basis of the poster’s problem. As I would put it:

Life is dynamic. So the chemistry of life depends on weak interactions that can be made and broken.

Ionic interactions are similar in energy to other non-covalent interactions
According to Berg et al. and the Wikipedia article typical ranges for non-covalent interactions are:

Ionic interaction: 1.4 kcal/mol (3Å in water — depends on distance and dielectric constant)
Hydrogen bond: 1–3 kcal/mol (depends on distance and angle)
Van der Walls interaction: 0.5–1.0 kcal/mol (depends on distance)

This is in contrast to, say the covalent C–C bond with an energy of about 100 kcal/mol according to this site. Thus, the ionic bond is clearly a relatively weak bond.
The charged state of a residue involved in enzyme mechanisms is often partial and dynamic
As the reader will know, the percentage ionization of a residue depends on its pKa and that of the medium. In neutral solution a histidine side chain (pKa 6.0) would be only 10% protonated. At the active site of a protein things may be different however. In a hydrophobic environment the acidic side chains of aspartic or glutamic acid may have far less tendency to ionize, and thus have an effective pKa much higher than that in water (4.1). The proximity of other residues may also influence the ionization or protonation by accepting or donating a hydrogen ion.

The point of this is that the residues involved in catalysis are often effectively less charged than a fully charged residue in solution, and
  this allows the ionization or protonation to be reversed at the end of
  the reaction, returning the enzyme catalyst to its original state.

Some examples
Although the functional role of Asp-27 (the presumed pKa 4.7 group) in tetrahydrofolate reductase would appear to be to donate a proton to the substrate, the details of this reaction are not completely clear. So it is easier to illustrate this point with two classic enzymes.
Serine Proteases (Trypsin etc)
More details of this can be found on the web and in any biochemical text, but the following illustration taken from Berg et al. illustrates the key point I wish to make.

This is that during the reaction the histidine is able to alternate between being protonated and unprotonated, receiving a proton from the adjacent serine.
Lysozyme
Here the mechanism of action involves two acidic groups, one charged (Asp-52) and one (Glu-35) uncharged. This difference is because the latter is in a hydrophobic environment. During the course of the reaction however it is able to ionize, but returns to its protonated form when the reaction is complete. This is shown in the illustration below, taken from a Nature Structural Biology review article by A.J. Kirby.


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The effect of 3D structure and solubility of the binding site of enzyme on its affinity Km and maximum activity Vmax?
Could some one provide me with some resources or papers where I can read more about the following:
1- How can the 3D structure of an enzyme affect its Km and Vmax? (some papers, books or articles will be very neat).
2- How can the solubility of the amino acids of the binding site of an enzyme affect its Km and Vmax? (again some paper, books or articles will be very helpful).
Or maybe some description about that with some references? I spent some time in searching but unfortunately with no attractive results.
I just resay that I am inneed for some resources or papers about the two points in addition to some word explanation.
Thanks in advance!

Probably the big reason you were unsuccessful in your previous searches is that nobody quite knows exactly how enzymes' 3D structures lead to particular kinetic parameters.
It's wrapped up in the concept of "how the heck do enzymes work, anyway?" -- surprisingly, it's a question we don't really have a good answer to. The leading concept currently - influenced in large part by catalytic antibodies - is the transition state stabilization theory. That is, enzymes work by preferentially stabilizing the transition state, reducing the activation energy of the reaction. (A good overview of the theory can be found in Structure and Mechanism in Protein Science by Alan Fersht, one of the must-reads for anyone interested in enzymes.)
But that's probably not all of how enzymes work, or at the very least "bind the transition state well" is a rather coarse overview of the process. There's thoughts that the precise arrangement of active site sidechains are involved in a quantum mechanical interaction with the transition state. This is the "theozyme" concept put forth by Kendall Houk and colleagues.
The role of enzyme flexibility in catalysis is a highly disputed topic currently. The dynamics of proteins are an important concept for the understanding of the full reaction pathway, but there are some people who think that an important contribution of the protein is funneling vibrational energy into the appropriate bond motions for catalyssi. Nobel prize winner Arieh Warshel is (vocally) against it, though, favoring an electrostatic view of catalysis. (That is, enzymes work by stabilizing the charge distributions found in the catalytic pathways.)
So the long and the short of it is that we really don't understand how enzymes work, so we're rather far from being able to predict how the 3D structure changes the catalytic parameters. There are a number of efforts (particular from David Baker's lab) trying to use computational modeling of 3D enzyme structures to design enzymes, but the results have been rather modest. While such enzymes have been designed, their activities have been modest, and nowhere near the activity of native enzymes.
Doing the reverse - trying to predict the catalytic activity from 3D structures - is difficult, given the lack of knowledge. That's not to say people haven't tried. For example, there's been some efforts to use machine learning to predict catalytic constants from different mutants in a series. The problem with machine learning-type approaches is that the results tend to be only applicable for the particular system they've been trained on, and there's only limited interpretability of the results.


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How does BH2 reduction to BH4 need only one NADPH molecule?
Dihydrofolate reductase (DHFR) reduces dihydrobiopterin (BH2) to tetrahydrobiopterin (BH4). Someone told me that this reaction needs only one NADPH molecule (I am not sure if this is correct), namely, NADPH provides one hydride atom and becomes NADP+.
Could someone explain to me how is this possible? How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?

Information, such as standard biochemical reactions is readily available on the web. Please check this before posting and provide a link for those who may not be familiar with the reaction (and /or post an image). This is a courtesy to the site and you will see that it is explicitly expected of posters if you read the help on asking questions.

@xusr, David is right, your comments belongs to an answer. Please rewrite them in an answer, I do not want that someone deletes them.

@xusr, I did not request to delete them, I just said that they would be more organized in an answer. There were valuable info in them, it would be great to rewrite them in an answer please. Additionally, I would be able to vote you up and accept the answer if it really answers me.

@86BCP2432T, you are absolutely right, I was searching yesterday and found the same what you explained. However, does the H.OH becomes only OH-?, or does it bind to the NADP+ and becomes NADPOH?

@xusr, may I ask you to repost you comments? they had very interesting information.

The short answer is that in reduction of BH2 to BH4 by dihydofolate reductase not only is a hydride ion (a proton plus an electron) transferred from NADPH to BH2, but the product also picks up a proton from the solvent: N5 of BH4 is protonated.
$$\ce{BH2 + 2e- + 2H+ <=> BH4\tag{1}}$$
Enzymically (see EC 1.5.1.34):
$$\ce{NADPH + BH2 + H+ <=> BH4 + NADP+\tag{2}}$$
Thus the reduction of BH2 to BH4 involves 2 electrons and 2 protons. NADPH donates 2 electrons and 1 proton (as a hydride), forming a new carbon-hydrogen bond. The solvent accounts for the other proton. The situation is very similar to the alcohol dehydrogenase reaction (discussed below).
The reduction of biopterin all the way to tetrahydrobiopterin by dihydrofolate reductase is a 4-electron reduction, and requires 2 NAD(P)H.
Background
There a couple of points about NADP-linked enzymic oxido-reduction, and about oxido-reduction in general, that possibly need clarification.

NAD(P)-linked enzymes, almost invariably (and perhaps always), catalyze the direct, stereospecific transfer of a  hydride ion (a proton plus two electrons) as a single entity between the nicotinamide cofactor and acceptor.

This statement probably needs some explaining.  The fact that NADP-linked oxidoreductase reactions are consistent with the transfer of a hydride ion is one of the great contributions of Westheimer to enzymology (see here). In many cases, this results in the formation of a carbon-hydrogen bond.
Secondly, hydride transfer is stereospecific. Amazingly, NADP-linked oxido-reductases distinguish between the two hydrogens at C4 of NAD(P)H.  This is an example of prochirality (the Ogston effect in the Krebs cycle is another).
For simplicity, the two hydrogens at C4 are called the HA and HB.  The work of Westheimer,  Vennesland and co-workers showed that NAD(P)-linked enzymes can be divided into two classes: those that transfer HA from cofactor to substrate (A-sterospecific dehydrogenases) and those that transfer HB (B-stereospecific dehydrogenases).
It is now known that sterespecificity of hydride transfer is one of the most evolutionary conserved traits of NAD(P)-linked oxido-reductases. Enzymes that may be shown to be descended from a common ancestor by amino acid sequence analysis invariably display the same stereospecificity of hydride transfer (Yeast and horse liver alcohol dehydrogenase is an example) 1†.
In addition hydride transfer displays apparent absolute stereochemistry fidelity: the 'wrong' hyride is never transferred.  Transfer of HB by lactate dehydrogenase, which is A-stereospecific, could not be detected experimentally, for example (see here).
A great review of this aspect of dehydrogenase biochemistry has been published by You (1985), available as a a pdf from here. (An earlier review may be found here)
Finally, a brief word on oxido-reduction in general. Oxidation is the loss of electrons, reduction is the gain of electrons.  An ionization is neither an oxidation or a reduction, and neither is hydration/dehydration. This, of course, is 'basic stuff', but seems to sometimes cause confusion.  When dealing with oxido-redution reactions we can add in as many protons as we like, or take out as many protons as we like, and this may be important stoichiometrically, but  ionization does not change the oxidation state of a molecule.
An Illustrative Example - Alcohol dehydrogenase
Alcohol dehydrogenase (EC 1.1.1.1) catalyzes the following reaction, the 2-electron reduction of acetaldehyde to ethanol with NADH as hydride donor:
$$\ce{Ethanol + NAD+ <=> Acetaldehyde + NADH + H+ \tag{3}}$$
This very nice diagram, taken from Cornforth's nobel lecture, Asymmetry and Enzyme Action, illustrates all the points made above.

The hydrogen labelled with the asterisk it HA. Stereospecific transfer of hydride to acetaldehyde results in the formation of a new carbon-hydrogen bond.  If the asterisk represents deuterium or tritium, the result is deuterated or radiolabelled ethanol.

If, instead, HB is deuterated or tritiated, the result is deuterated or tritiated NAD+, with no transfer of label to product.

Formation of the alcohol involves 'picking up a proton' (from the solvent).

Transfer of hydride acetaldehyde is also stereospecific. The hydride is stereospecifically transferred to one of the faces of the planar carbonyl group.  I am ignoring this aspect here (but see Cornforth's lecture) 2†.

To be very pedantic, HA is more correctly called the pro-4R hydrogen, and  HB is the pro-4S hydrogen.

(In Cornforth's original diagram the H+ was left out).
The Specific Question Posed by the OP

How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?

As stated above, BH4 (tetrahydrobiopterin) contains one more pair of electrons than does BH2 (dihydobiopterin), but (like the alcohol dehydrogenase reaction) there are two protons involved. The fact that reduction involves hydride transfer accounts for one. The other is picked up from the solvent.
This is illustrated in the diagram below, where the key point is that the carbon atom at C6 now has a new carbon-hydrogen bond.  This bond accounts for 2 electrons plus 1 proton. But the nitrogen atom at C5 has also picked up a proton.
(We must be very careful when dealing with reduction of the pteridine ring because of the quininoid form (see here).  This is why I first picked  alcohol dehydrogenase as an illustrative example, and I am ignoring such complications here).

The OP chooses an interesting substrate for DHFR, an unconjugated  pteridine. The 'more usual' substrate, of course, is the conjugated pteridine, dihydrofolate (FH2). Although DHFR does catalyze the transformation of BH2 to BH4 , the enzyme usually associated with this transformation is dihydropteridine reductase (EC 1.5.1.34).
One final point.  Both chromosomal and plasmid dihydrofolate reductase, although unrelated from an evolutionary point of view, are both A-stereospecific with respect to hydride transfer from NAD(P)H.
(The above diagram was modified from one found on the internet. The original may be found here)
Four-Electron Oxidoreductases
Most NAD(P)-linked oxidoreductases catalyze a two-electron reduction that involves just one molecule of nicotinamide cofactor.
A few, such as dihydrofolate reductase can catalyze two sequential 2-electron reductions, where the  first 2-electron product is released into solution before it is reduced to the final product by a second encounter with enzyme. (In the case of DHFR,  the reduction of folate to dihydrofolate is a two-electron reduction, and the reduction of dihydrofolate to tetrahydrofolate is another 2-electron reduction).
Some oxido-reductases, however, catalyze a four-electron oxido-reduction where the intermediate product is not necessarily released into solution. Such enzymes are called four-electron oxido-reductases, and are very rare.  They have been reviewed by Feingold & Franzen, (1982).
One example is histidinol dehydrogenase (EC 1.1.1.23), that catalyzes the reduction of an alcohol to an acid (the aldehyde being the intermediate 2-electron reduction product).
$$\ce{L-histidinol + 2 NAD+ + H2O = L-histidine + 2 NADH + 3 H+ \tag{4}}$$
Another example is HMG-CoA reductase (EC 1.1.1.34), a key enzyme of cholesterol metabolism (that is inhibited by statins).  In this case, the enzme reduces a substrate formally at the oxidation level of a carboxylic acid (but 'activated' by thiol ester linkage to coenzyme A) all the way to the alcohol.
$$\ce{Mevalonate + CoA + 2 NADP+ = 3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ \tag{5}}$$
A third example is UDP-D-glucose 6-dehydrogenase (EC 1.1.1.22), which catalyzes the reduction of the C6 alcohol group of UDP-glucose all the way to the acid.
$$\ce{UDP-D-glucose + 2 NAD+ + H2O = UDP-D-glucuronate + 2 NADH + 2 H+}$$
So, a four electron NAD(P)-linked oxido-reduction is possible.  But such reactions are relatively rare. The key to the biochemistry of the NAD(P)-linked enzymes, IMO, is to realize that a hydride is transferred as a single entity (and that hydride transfer is stereospecific).
Footnotes

Alcohol dehydrogenase from Drosophila is unrelated to the yeast and horse liver enzymes from a evolutionary perspective, and is B-stereospecific.
The same Cornforth that reputedly said that if the β-lactam structure of penicillin was correct he would give up chemistry and grow mushrooms (see here).


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Is it possible to build a hive for bumblebee or hornet
People commonly build hives for honey bees and it works . Is it also possible to build a hive for a bumblebees or hornets ? Should it have any special shape or form or is it just impossible ?

Yes, it is very common practice and there are many instructions and plans for beehives/nests available online, there are some for wasps


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What is RNA Engineering
I've been hearing the term passed around, and my own research has led me to some very high-level papers which propose new tools for accomplishing RNA engineering.
From the abstract of one of the above linked papers:

These methods advance our ability to develop broadly applicable genetic tools and to elucidate the underlying sequence-structure-function relationships that empower rational design of complex biomolecules.

It seems as though we are edging close to designing fine-tuned lifeforms. It's easy to jump to exorbitant conclusions, so I'd like to make sure I understand what this is all about.
My questions are:

What exactly is RNA engineering and what can it accomplish (in plain english)
What are the implications of the advent of RNA engineering tools


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Gaps in FASTA formatted genome?
I'm just getting interested in genetic structure and I decided to find a FASTA formatted genome (human) and I found one here. However, I'm confused. I know that A can only match up to T and C to G but it appears as though T is matching up to T, A to A, C to A, and etc. How is this possible? Can there be gaps where T,A ,C ,or G is connected to nothing? Small part of genome: ATTTAGAAATGACTAACAATTATGTAGGTTTATTTCTCTCAGTATAGAATGTTCATATAGAATT

Your question is based on a misunderstanding. You have a single strand, lets assume it's the red sequence in the image. The linear sequence along this strand is not limited by base-pairing rules.
The base-pairing rules (A-T, G-C) apply to the complimentary strand, given in blue in the image.

It's convention to only give the sequence for one strand because the base-pairing rules allow us to infer the complimentary sequence.

If I got your question correctly, then you are referring to the base pairing of the genome. Here you have been misled as to how base pairing is presented. ATTT does not refer to a base pair between A,T and T,T but rather the sequence of letters in the sense strand of the human genome. What you see here are more stacking interactions than base pairing between bases. Whenever navigating databases please remember that whatever genome you are viewing, you will always be presented with the sense strand of that genome. To get the base paired strand or anti-sense strand of that particular genome, you need to a reverse complement that particular sequence of letters.


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Lethal gene and population genetics
In the European population, about 1 in 2500 people suffers from Cystic Fibrosis, a genetically determined (descared), autosomal disease. Healthy parents have a child suffering from Cystic Fibrosis. The woman remarries a healthy man. What is the chance of a child from this second marriage suffering from Cystic Fibrosis ?
My attempt
http://i.imgur.com/4mhU3Qh.jpg
But the answer given is 1/100

Welcome to Biology.SE! Images are not searchable and are problematic for people with visual impairment. Please, always type everything when asking a question on a SE site.

Genetics of Cystic fibrosis
Cystic fibrosis is caused by an autosomal recessive allele. We therefore know that the frequency of the homozygote recessive allele is $P_{aa} = \frac{1}{2500}$, where $a$ denotes the recessive allele and $A$ will denote the dominant allele.
Solving the problem
The probability of the second child (from a second husband) has cystic fibrosis is the probability that a second husband is heterozygous ($P_{aA}$) times the probability that this father will transmit the recessive allele $a$ ($\frac{1}{2}$) times the probability that the mother transits the recessive allele $a$ ($\frac{1}{2}$, note that we know the mother is heterozygous as she is healthy but already had a child that suffers from cystic fibrosis).
So the answer is $p_{Aa} \frac{1}{2} \frac{1}{2} = p_{Aa} \frac{1}{4}$, we only need to calculate $p_{Aa}$. Let $x$ denote the frequency of the recessive $a$ allele, then $P_{Aa} = 2 x (1-x)$ at Hardy Weinberg equilibrium. As we know $p_{aa}=\frac{1}{2500}=x^2$, it results that $x=\sqrt{\frac{1}{2500}} = \frac{1}{50}=0.02$. Therefore, $p_{Aa}=2 x (1-x) = 0.0392$. The final answer is  $p_{Aa} \frac{1}{4} = \frac{0.0392}{4} = 0.0098 ≈ \frac{1}{100}$.
What you did wrong
You were pretty close to the right answer. In your calculations you multiplied the frequency of the recessive allele $a$ (which I called $x$) by $\frac{1}{4}$ but you should have multiplied the frequency of heterozygote genotypes (which I called $p_{Aa}=2 x (1-x)$) by $\frac{1}{4}$.

@Rajdeepdhingra Thanks for letting me know if it answered your question. If you think the question is answered, you can check the answer (top-left of the answer).


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What is this large brown bug with pincers?
What is this large, brown insect with pincers? Seen in Waltham, Massachusetts.

You probably have a specimen of a stag beetle.
In Europe we have a very big one: Lucanus Cervus
but it seems to be absent in US.
Then I found an interesting web-site referring to the different stag beetle and mentioning the link to the European one.
In this above site, they mention you have to look into the antenna and as they are not very visible on your picture I think it would be difficult to define precisely what is the exact taxon of the one you found.
For specifically Massachussets region, I found this interesting link.
and they refers to Lucanus Cepreolus, but I would not be 100% sure it is this one as the antennas are not present on your picture.
References

http://beneficialbugs.org/bugs/Ground_Beetles/stag_beetles.htm
http://bugguide.net/node/view/3104/bgpage
http://www.insectidentification.org/insects-by-type-and-region.asp?


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What is this plant with purple berries?
This plant was seen by a friend of mine in Virginia. What is it?

It looks to me like beautyberry. Here is a link to a species page to judge for yourself. It's a very common cultivar and I've heard of people using it to control garden pests.
http://uswildflowers.com/detail.php?SName=Callicarpa%20americana
Here is an image of American Beautyberry from gardenknowhow.

It is often confused with Japanese Beautyberry which has smaller berries on stalks.


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Is this an eastern hemlock (Tsuga canadensis) seedling?
I recently planted a few seeds gathered from a Tsuga canadensis cone in soil gathered from a garden full of weeds. I can't tell if what I have growing is a hemlock seedling or just another weed. See photo:

This is not a Hemlock seedling but a young specimen of the family Amaranthaceae, almost certainly an Atriplex, known in English as Saltbush or Orache.
You can tell by the shape of the opposite leaves and the 'frosty' look (not sure if frosty is the correct English word)
This specimen looks quite similar to yours.

Taken from here
As North America is very rich in species, I don't think anyone can be more exact than Atriplex.
Atriplex grows in salty soils such as deserts and seashores, but also in moist environments. Most species prefer bare soil, so are also well adapted to grow between crops, so yes, this might be called a weed.

No, this is not a Tsuga canadensis seedling.
A hemlock seedling should look something like this:

http://www.uky.edu/hort/propagation-canadian-hemlock


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How do you sequence a tree genome?
I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a conspecific?

how is that different from sequencing animal genome?

I don’t know. Is it different?

Are you trying to sequence the entire genome or just portions of it? This review paper may help you get started, specifically the portion titled "how do we sequence" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456863/

it seems like you haven't done studying on your own, which is the first step usually. Genome sequencing is pretty common these days, and a lot of information is available. Maybe start with simple googling "how to sequence genome". Also, as grant writing goes, if you include work that you don't know how to do maybe you should seek collaboration with genomics people

I agree with aaaaaa - if for a grant, the level of this question indicates you need to do way more reading of the literature than you apparently have been. (Otherwise you're just wasting the grant committee's time.) For example, a quick search finds a list of sequenced plant genomes - you can start from the references there to see how they did it. -- That said, you're probably looking for "genotyping" rather than "whole genome sequencing". Doing a web search for "genotyping trees" pops up a number of papers you can start from.

In journal articles, they are doing many studies every year describing the state of the art tools and procedures for sequencing plant genomes.
by researching 5 minutes you have results of this kind:
http://www.pnas.org/content/95/16/9693.full

Protocols involved commercially available kits (e.g., Qiagen’s RNeasy Plant Minikit), non-commercial RNA extraction lab protocols (e.g., CTAB, acid phenol) and hybrid methods that combined components of both commercial kits and lab protocols. The detailed protocols used for all isolations are available online in Appendix S1.
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050226
Tissue and organ samples for Northern blot analysis of gene expression patterns were taken during the growing season and frozen in liquid nitrogen, then stored at −80°C. Shoot-tip samples are the terminal 1–2 cm of succulent stem tissue from elongating branches and terminal leaders. Immature xylem was harvested with a vegetable peeler from the surface of woody stems after removal of the bark, and includes cells with primary cell walls derived from the cambial zone through the zone of radial cell expansion. Compression wood and side wood immature xylem RNAs were those used for preparation of the libraries, whereas vertical immature xylem denotes samples taken from stems of control trees growing vertically. The tissue described as “phloem” was collected from the inner surface of the bark of vertical stems and actually includes periderm and other tissues as well as active phloem. Planings were collected from the surface of vertical woody stems with a wood plane after immature xylem was harvested and includes cells that have formed secondary cell walls strong enough to resist harvesting by the vegetable peeler. Needle samples were partially expanded juvenile needles.

here are some more texts for you to check
http://www.pnas.org/content/106/31/12794.full
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214
From_field_to_film_Rapid_sequencing_methods_for_field-collected_plant_species
It took me 5 minutes to find these informations by searching articles for

plant sequencing methods


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Are there laws in ecology?
Are there clearly defined ecological laws, as in the science of physics? If not, why is this the case?

first rule of biology: there is an exception to every rule, including this one.  But seriously this article may help you. http://www.ecology.info/laws-population-ecology.htm

I think this is really more of a question of philosophy rather than science. You can read a bit about the meaning of a scientific law on Wikipedia: https://en.wikipedia.org/wiki/Laws_of_science My personal opinion is that the reason people don't talk about laws as much in biology is because laws are too small/specific to be the most interesting answer to a biological question. In physics, a law is something that you are able to reduce a broad phenomena to. In biology, it's rare outside of mathematics to be able to reduce to one statement that describes an entire phenomenon.

What is law and what is ecology?
I always find the definition of "law" a little hard to grasp but maybe only because I am a mediocre philosopher. To me, I don't quite understand the difference between a theory (a theory is not a hypothesis in science) and a law.
It is also hard to know what exactly you would consider being part of ecology and what you would be considered part of evolutionary biology, agriculture or paleoecology / paleogeology and those disciplines are very much related. Here are a few concepts that I don't if they would qualify for an answer

General latitudinal diversity gradient
The concept that symbiosis is more a rule than an exception (it also comes with the discovery that mitochondria are/were endosymbionts).
Theory of natural selection
Positive and negative feedbacks in glacial period
Geographical area law/hypothesis
Parental effects
Adaptive radiation
r/K selection theory
Theory of island biogeography
...

Are there science that create more laws than others?
I am really not qualified to answer this question but I would tend to think that in ecology, there is a lot of important discoveries that lead to a conceptual rephrase or to a reconsideration of the relative importance of different concept or to the realization of a single fact, more than to the phrasing of a law per say.
Laws in ecology
Here are a few concepts in ecology that are often being called law.

Liebig law of the minimum
Ten percent law
Allee effect law
Square-cube law, allometric scaling and the metabolic theory of ecology
Ecological systems theory

as well as all the laws regarding population growth such as

Malthusian, Verhulst and Lotka-Voltera laws.


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Is it possible to graft plants from different families?
For example, I have some Eastern Hemlock rootstock (Pinaceae), and want to graft a scion from Dawn Redwood (Cupressaceae) onto it. Is this possible? Is anything like this possible?

Not knowledgeable in this area, but I note the Dawn Redwood is deciduous and the Hemlock, like most conifers, is not.  Since deciduous plants commonly store reserves over the winter in their roots, an evergreen rootstock may not be compatible with a Dawn Redwood scion.

It makes me think of a french artisan who sells trees with 20-40 individual heirloom grafts on a single tree, which all flower and fruit throughout the summer. all apples, apricots, compatible trees. i found fig on mulberry, both moracea family.

No. Exceptions are always possible, but it would be a noteworthy.
I just find this notes in: https://courses.cit.cornell.edu/hort494/mg/specific.grafting/compatibility.html

Interfamilial
Although there are a few reports of short-term graft union formation between distantly related (interfamilial) herbaceous species, there are no confirmed reports of interfamilial grafts between woody perennials.
One extremely curious report of natural interfamilial graft compatibility which must be considered unconfirmed, and even unlikely, was the observation of La Rue (1934) [...]


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Is sperm (spermatozoa) a bacteria?
Is spermatozoa (ie human) technically considered bacteria? I've been told it is and I've been told it isn't. Would it meet the definition? If not what is sperm considered?

A sperm is not a bacterium - a sperm cell is an eukaryotic cell with a haploid set of chromosomes.

Complement: it's not even a real being: it can't reproduce, it's almost not functioning (I'm not even sure than his DNA material is in a transcriptible form. Basically, it's a dedicated half-cell of a multicellular organism, frozen genetic packed content + a flagellum + mitochondria + enough energy to make it beat for a short duration.
As such, we might even find it to share common things with the definition of virus :-)