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How is olfactory acuity rated/measured?
Acuity of one's sight is rated on the 20/20 scale. An online search appeared to indicate there is no comparable 'standard' to rate olfactory acuity.
How is acuity of the olfactory system rated?

One olfactory acuity rating method that has found acceptance in some studies (despite the commercial-sounding name) is based on "Sniffin' Sticks,"
"a test of nasal chemosensory performance that is based on penlike odor-dispensing devices. It is comprised of three tests of olfactory function: tests for odor threshold, discrimination and identification. Previous work has already established its test-retest reliability and validity in comparison to established measures of olfactory sensitivity. The results of this test are presented as a composite TDI score--i.e., the sum of results obtained for threshold, discrimination and identification measures."
In the paper from which this abstract portion was taken$^1$, subjects were assigned a score based on their thresholds, ability to discriminate, etc., and the findings were said to be internally replicable (consistent from one test to the next).
This is probably not the only rating available but it has been used on other studies and seems to be taken seriously by M.D.s and others who measure such things.
There is no absolute measure of olfactory acuity. People are classed as 'anosmic' if they do poorly enough on the test but that doesn't mean they have no sense of smell (although that might be the case). Likewise people who get a high TDI score are--by definition--people who got the "Sniffin Sticks" right. They might be poor at discriminating a good coffee from a bad one based on smell.
The test seems to do what it was intended to do: quantify relative olfactory acuity in a replicable way.
An earlier study is somewhat reserved. From an abstract: "It is concluded that ‘Sniffin’ Sticks’ may be suited for the routine clinical assessment of olfactory performance."
$^1$ Eur. Arch. Otorhinolaryngol. (2000) 257(4):205-11. Multicenter investigation of 1,036 subjects using a standardized method for the assessment of olfactory function combining tests of odor identification, odor discrimination, and olfactory thresholds. Kobal et al.


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Are rods/cones rejuvenated periodically?
Pretty much what the title states.
Some cells/structures in the human body undergo rejuvenation periodically by flushing away older cells and growth of new ones.
E.g Skin, Blood
Does this (for want of a better word) 'rejuvenation' apply to Rods/Cones within the eye too? If so, how are the old cells flushed out - or do the old cells become part of the local humour?

The answer can be found in the excellent lecture from 1983 The Life History of Retinal Cells which also has gorgeous microscope fotos. The renewal time of rod outer membrane proteins is less than two weeks. Cells stay indefinitely, as I understand, but are periodically rebuilt in a logistical nightmare/wonder.

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Are all known germs benign in small enough quantities? i.e. Why do we wash our hands?
We know that we wash our hands because germs can get into our body through the nose, the mouth, the eyes, cuts, etc. But I doubt we can completely clean our hands of germs every time we wash them, down to the individual bacterium or virion, even if we use anti-septic soap. So chances are, even if we keep up with our hygiene, germs still get into our body, only in very very small quantities. So here are some questions:

In theory, is there a dividing line where we can say "ok, at this non-zero count of bacteria or virion, there is still (an arbitrary probability) that a normal healthy person won't get sick" for every germ known to man? If not, are there germs that are known to cause havoc in a healthy person even if he comes into contact with a single individual bacterium or virion?
Do we know a certain trend based on the classification of the germ?
How about the most commonly found germs (whichever they are)?
How about some of the most feared, but not so common, virii known to man, like HIV, ebola, SARS?

I think that without being able to answer some of these questions, especially #3, hygiene would be nothing but a ritual activity (because "it just works").

Kind of related: http://biology.stackexchange.com/questions/5395/how-much-weight-volume-do-microbes-occupy-within-the-human-body

the answer is closer to this - most of the disease causing germs continue to be around us all the time.  When conditions are healthy, the immune system and competition with other more benign organisms keep them from becoming a full blown disease.  Soap helps them from reaching critical numbers and does not affect the immune response much, helping to keep them in check.  Antibiotic chemicals do not because they create the conditions where antibiotic resistant strains appear.

Wouldn't soap create the conditions in which soap resistant strains appear?

There is a Wikipedia page  which gives some typical values for infectious doses of bacteria. I suspect that lot of these have been taken from this slideshow which confirms the values on the Wikipedia page, gives more interesting details of how they have been arrived at, and also mentions a few viruses.
It seems from the slideshow that infectious dose isn't estimated in the way that the OP envisages - "What is the probability of infection if I ingest one cell?".
What is clear is that the infectious doses for some bacteria can be less than 10 cells (e.g. Shigella flexneri, E. coli O157:H7). Conversely for many other pathogens such as other strains of E. coli the estimate is >106 cells, so standard hygiene precautions will always offer some protection.

I think that aside from the probability of illness if you ingest a few cells of bacteria XYZ, one important factor to consider is the probability of finding bacteria XYZ on your hands. While the first may probably be fairly high for, say, Yersinia pestis, usually the second should be very very low for that bacterium.

Washing your hands is an exercise in probability rather than absolute values. An important thing to keep in mind is that not only is it very hard to kill all the bacteria on your hands, it's also not something you actually want to do.  Most of the bacteria we encounter day to day are either benign or beneficial to personal health. We know that gnotobiotic mice (sterile mice) exhibit impaired development, especially in the immune system.  We want to come into moderate contact with bacteria.
Because it is a balancing act, I think hygiene needs to be reframed. For one things anti-septic soap should be reserved only for situations when it is absolutely necessary.  Anti-septic soap has a tendency to apply a selective pressure that encourages propagation of resistant strains.  Situations where it is worth using would include visiting an international transit center (airport), working in an Operating Room ward at a hospital, or going to a cafeteria during an epidemic.  In other situations, regular plain soap and water should be good enough to rub the majority of cells off your hands so that passive immunity has a good chance of eliminating any threats before they get to vulnerable parts of the body.  If you have the opportunity, paper towels are better for getting cells off your hands then blowers.

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Is there evidence that some non-human species perform sexual selection based primarily on intelligence? How do they do this?
I'm a biology amateur, but it seems like sexual selection is almost always performed based on physical characteristics, the outcome of physical contests, or some sort elaborate courtship. But do any non Homo-Sapiens perform sexual selection based on intelligence factors, like problem solving abilities? If so, how does the species accomplish this? I know natural selection as a whole would definitely favor intelligent individuals, but I'm curious if any species actually takes this into account when choosing mates.

Alas, selection based on intelligence is often absent in Homo Sapiens...

Super question.

Very intresting question. The problem is that animal intelligence is hard to measure not only for scientists, but probably also for the potential mate. Paradoxically, that is why selection for intelligence, if it occurred, may be very strong. One has to be smart in order to recognise smart behaviour, so preference and preferred feature are strongly connected. But that's only my opinion.
Boogert et al., 2011 1 reviews the current knowledge about animal preferences for cognition skills. They conclude that there is very little data on this subject. The given examples are:
1) Preference for elaborating birds songs (as songs are not inborn and have to be learned)
2) Spatial abilities:

In meadow voles (Microtus pennsylvanicus), males with better spatial learning and memory abilities were not only found to have larger home ranges and to locate more females in the field (Spritzer, Solomon, et al. 2005 2) but were also preferred by females in mate-choice tests, even though the females did not observe males’ performance on spatial tests (Spritzer, Meikle, et al. 2005 3).
In guppies (Poecilia reticulata), males that learned faster to swim through mazes to gain a food reward were found to be more attractive to females (Shohet and Watt 2009 4). However, females were not able to see the males’ performance in the mazes. Although male learning ability was weakly correlated with saturation of the orange patches on his body (a sexually selected trait (...)), orange saturation surprisingly did not correlate with female preferences. Thus, the cues leading female guppies to prefer faster learners are unknown.

It is possible, that females base their choose on some factors that correlates with cognitive skills or on total wellness, what may depend on intelligence.
3) bowerbird's abilities to build bowers (courtship constructions):

Comparative studies across bowerbird species have shown that relative brain size is larger in species that build bowers than in closely related nonbuilding species (Madden 2001 5). In addition, relative brain size increases with the species-typical complexity of the bower (Madden 2001 5), and a comparative study on the relative size of specific brain regions showed that species with more complex bowers have a relatively larger cerebellum (Day et al. 2005 6).

4) foraging performance

A recent experiment by Snowberg and Benkman (2009) 7 using red crossbills (Loxia curvirostra) showed that, after observing 2 males extracting seeds from conifer cones, females associated preferentially with the more efficient forager of the 2. The authors were able to exclude female choice for correlated traits by experimentally manipulating foraging efficiency, such that fewer seeds were available in the cones of one of the males. The males were also swapped between treatments (i.e., slow vs. fast forager) so that male identity could not explain the females’ preferences for the most efficient forager.

Another way that intelligence may be favored by sexual selection is "cheating" during courtship. For example most frog species call to attract females. But this signal may also attract aggresive rivals or predators. Some males, especially the weaker ones, do not call  but stay near calling individual.  This allows them to avoid confrontation and wait for approaching females [8]. The successfulness of this strategy may depend on how "smart" the individual is (only my opinion).
[1] Boogert, N. J., Fawcett, T. W., & Lefebvre, L. (2011). Mate choice for cognitive traits: a review of the evidence in nonhuman vertebrates. Behavioral Ecology, 22(3), 447-459.
[2] Spritzer MD, Solomon NG, Meikle DB. 2005. Influence of scramble competition for mates upon the spatial ability of male meadow voles. Anim Behav. 69:375–386.
[3] Spritzer MD, Meikle DB, Solomon NG. 2005. Female choice based on male spatial ability and aggressiveness among meadow voles. Anim Behav. 69:1121–1130.
[4] Shohet AJ, Watt PJ. 2009. Female guppies Poecilia reticulata prefer males that can learn fast. J Fish Biol. 75:1323–1330.
[5] Madden J. 2001. Sex, bowers and brains. Proc R Soc Lond B Biol Sci. 268:833–838.
[6] Day LB, Westcott DA, Olster DH. 2005. Evolution of bower complexity and cerebellum size in bowerbirds. Brain Behav Evol. 66:62–72
[7] Snowberg LK, Benkman CW. 2009. Mate choice based on a key ecological performance trait. J Evol Biol. 22:762–769.
[8] Bateson P. 1985. Mate choice. Cambridge University Press. 181-210

I know nothing about biology however I did watch an amazing PBS documentary on cuttlefish that I think is fairly relevent.
From http://www.pbs.org/wgbh/nova/nature/kings-of-camouflage.html

NARRATOR: During mating, males outnumber the females, sometimes 10 to
  one. And they're all looking for the chance to pass on their genes.
  While a female lays eggs beneath a rock, a big male tries to
  monopolize her, staving off the other hopeful suitors.
Sometimes intimidation alone won't work, and the competitors hurl
  themselves into a violent and bizarre looking wrestling match.
Like an octopus, they'll squirt out an inky smokescreen when it's time
  for a hasty retreat.
But size and strength aren't the only ways to impress the ladies.
Thanks to the cuttlefish's skin morphing talents, the smaller males
  have a clever trick up their sleeve.
MARK NORMAN: The really interesting thing in this system is actually
  far less obvious, and when you first dive with them, you don't see it.
  It takes a while before you realize what's going on.
The small males, who have no chance in a contest with a big male, are
  actually doing something completely different. They're effectively
  cross-dressing. They're dressing up as a female, by pulling in their
  webs and putting on this mottled color pattern and gliding past these
  big, aggressive male, pretending to be a female, and will come in to
  the female underneath.
And what happens is, as another big male comes in and a potential
  conflict between these big guys starts up, the sneaker males start
  mating with her, successfully mate with the female, while the big guy
  isn't even aware of it.
NARRATOR: The cross-dressers' success is all the more impressive
  because the females often play hard to get, as Roger Hanlon has seen
  firsthand.
ROGER HANLON: These females are very picky. They reject 70 percent of
  approaches for mating. Yet they only reject 30 percent of the
  cross-dressing males. So this trick gets them in the door, so to
  speak, past the fighting male, and they're accepted by the female.

Sounds a lot like humans to me. Explain why females pick jerks rather than normal guy with money. If guys with money approach females, they got beaten up by stronger males with anti prostitution laws. Then some guy just seduce, and it works. Maybe it's how we are set up.

@JimThio I think Cracked has an answer for that here. http://www.cracked.com/article_18804_the-6-wrong-questions-men-love-to-ask-about-women.html


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Is there an enzyme for the transformation of the hydroxyl group?
I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme.
The substrate is aromatic hydroxyl group. Product should not have hydroxyl group.
How should these types of queries be searched for?

This question is not answerable without a lot more detail. Enzymes are often very specific about which substrates they accept, so you need to provide more detail about the substrates.

I will start querying for some dehydratase or dehydroxylase and look if some of them work on aromatic groups.

@MadScientist, I wish to have the enzymes which are non-specific, i mean which works on hydroxyl group rather than looking at the complete molecule.

if possible can i have some other functional group apart from replacing "OH" group with "H"

Does it have to be an enzyme?  There are plenty of organic reactions you can carry out on that group.

Sounds like any redox chemistry on the hydroxyl group would satisfy  the desired constraints. I would start there.

Can you give us some background? What is your aromatic compound? Why do you want to avoid having OH group on it? What do you want to use it for?

@Jonsca and Gergana Vandova, I am an organic chemist / synthetic chemist and would like to try with enzyme reactions. I had done the reactions using chemical route. The aromatic part is coumarin.

I'm beginning to like this question more and more. Try looking up "retro-biosynthetic design". Kristala Prather has done a lot of work in the type of question that you're specifically looking at.

@leonardo, as i have already mentioned, i would like to diversify my research towards biochemical reactions. Being an organic chemist, i have manipulated the functional groups and now i wish to manipulate using biochemical reactions.

It is possible to search for enzymes or a series of enzymes that will take similar reactants to similar products.
ReBIT allows you to query enzymes by your molecular structures of interest using their SMILES code. Unfortunately, a quick search using coumarin didn't produce any results but searches for phenol and phenolate gave some hits.
If you're seeking to do a more extensive search, I would suggest BRENDA. There you can search for reaction substrates and reaction products and even both. Both strategies may provide you with an enzyme that does the transformation chemistry that you're looking for.
Lastly there is always ENZYME, The Enzyme Data Bank. There you can search for chemical compounds. I did a search of coumarin and there are a few hits but they are for methyl-transferases and hydrolases. A more extensive search may give you a few leads.
Most of the concepts that I just suggested are explained in the following review: De novo biosynthetic pathways: rational design of microbial chemical factories.


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How is RNAse contamination in RNA based experiments prevented?
Does anyone have any suggestions to prevent RNAse contamination when working with RNA?
I tend to have issues with degradation regardless of whether I use DEPC treated / RNAse free water and filtered pipette tips.

Are you working with isolated RNA or with in vitro transcribed RNA?

@MadScientist: Isolated RNA with a Qiagen RNeasy Kit.

My answer is about avoiding RNAses while working with RNA, I'm not working with isolated RNA so there are probably additional steps you should take to avoid RNAses present during the isolation.

@MadScientist: I still think your answer is very relevant, I could be getting degradation during the down-stream experiments as well.  I was hoping that this question could be relatively general because I know a lot of different people have different processes to avoid RNAse contamination.

You need to be careful about everything that comes in contact with your samples. Every spatula, beaker and every magnetic stir bar need to be RNAse-free.
For metal- and glassware we usually put everything into a drying closet at 200-250 °C for a few hours. That should get rid of RNAses pretty efficiently.
The RNA chemicals should be seperated from other chemicals if not everyone in the lab is working with RNA. They shouldn't be weighed using spatulas, but just poured into an RNAse-free container to avoid contaminating the storage container.
Use disposable plastic wherever possible, you should be able to perform most stuff in falcons and Eppendorf tubes.
Be careful with performing e.g. a DNA-prep at the same bench as the RNA work. The first buffer for the DNA-prep contains RNAse.
Avoid keeping your Eppendorf tubes or falcons open for long, that should reduce the potential for contamination.
We've had pretty good experience with just using water from a Millipore system and autoclave it once, that seems to get rid of the RNAses. I know that this is not a sure thing as the RNAses can survive autoclaving, but it seems to work well enough.

Here are some tips from what I routinely do:

wipe all the surfaces (including pipettes and gloves) with RNAse Away or similar
do everything on ice
use a RNAse/DNAse free tubes. Use also commercial RNAse free water (it's worth the investment).
keep all your RNA reagents separate from your cell culture/animal work reagents. Autoclave all your buffers and don't let them sit forever. Just make fresh buffers every now and then.
don't talk over the tubes

If you keep having degradation following all the above, consider how you prepare your sample. Do you have enough RNAse inhibitors in there? Do you use a RNA-conserving solution? Is your tissue sitting for a long time before the lysis? If your extracting RNA from cells, try using trizol or a similar reagent to preserve the RNA right from the lysis. If your getting the RNA from tissue samples, try snap freezing them in liquid nitrogen.

Apart from tips already mentioned, change your gloves every now and then.
Also, in my experience (with the Qiagen kit), keeping samples on ice shouldn't make much of a difference.


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Has anyone tried Gibson Assembly Optimizations?
Has anyone tried the chew back-anneal in vitro DNA assembly method (known as Gibson Assembly) for difficult sequences, like GC-rich sequences? How big constructs could you efficiently assemble? Did you use the original protocol or some optimizations?

I've just joined the Gibthon team, so if you need any more specific help let me know.

I haven't tried Gibson Assembly myself, but I do know the Cambridge iGEM Team in 2010 and 2011 developed a web-based tool - Gibthon - for automatically generating primers for Gibson Assembly.
You could try running your difficult sequences through their tool to see what it suggests for primers.  It apparently gives you a "value for the Gibbs free energy of the worst case secondary structure of the primer."

Thanks. Yes, I have heard of the Gibthon software, haven't tried it yet. We have been using the IDT predictor of secondary structure of the primers. Might be worth comparing it to the Gibthon tool. It would have been nicer if some optimizations of the reaction conditions make the use of such predictors obsolete. Not to mention that their precision is questionable.

I also haven't tried it, but theoretically GC-rich sequences will interfere with Gibson assembly. Since unique homology between the ends is key to the assembly process, repetitive sequences which cause non-unique overhangs will increase the possibility of incorrectly ordered assembly. One solution would be to use alternative codons where possible to decrease repetitiveness.
I'm sure all the overlap design tools will try to avoid repetitive overlaps. Prof Jim Hasselhoff at Cambridge Plant Science is a big proponent of Gibson assembly, it was one of his students who wrote Gibthon. If you email him I'm sure he'll give you specific advice.


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What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?
In prokaryotic translation, how critical for efficient translation is the location of the ribosome binding site, relative to the start codon?
Ideally, it is supposed to be -7b away from the start. How about if it is -9 bases away or even more? Will this have an observable effect on translation?

I found an oldish paper on this topic (from 1994).  Here's a summary:
Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. by Chen, Bjerknes, Kumar, & Jay. Nucleic Acids Research. (1994)
Experiment
The authors constructed a series of synthetic RBS regions that varied the length separating a synthetic 5-nt Shine-Dalgarno sequence from the start codon.  The regions varied in size between 2 to 17 nt.  They assayed the activity of a downstream enzyme, chloramphenicol acetyltransferase.
Conclusion
The authors concluded that the optimal spacing between a consensus 5-nt Shine-Dalgarno sequence (5'-GAGGT-3') and the start site was 5 nt. Note: this synthetic SD was made of the last 5 nt of a 9 nt SD consensus sequence.  They also tested a synthetic SD made from the first 5 nt (5'-TAAGG-3')of the consensus SD.  In this case they found the optimal distance was 9 nt.
So the optimal distance depends on where your desired SD aligns with the consensus SD sequence, which optimally is 5 nt from the start.  Read on for more details.
Details

the RBS is considered to be large, extending 20bp on either side of a core Shine-Dalgarno (SD) sequence.  These days, I often hear of the RBS spoken of in sizes that are equivalent to the SD.  So in the parlance of the paper, you question is rephrased as "how does distance of the SD from the start codon effect translation?"
the canonical SD sequence referenced in the paper is 5'-UAAGGAGGU-3'.  It is 9 nucleotides long.  Distances between the SD and the start codon are defined as the number of nucleotides separate the 3' Uracil of the SD from the Adenine of the start AUG.
Example: the distance is 5 nt in the following mRNA
       5'.....UAAGGAGGUnnnnnAUG......3'

if the SD is not a complete 9 nt long, the distance is between the position of where the canonical Uracil would occur.  In the following example, the distance is still calculated as 5 nt:
       5'.....UAAGGAnnnnnnnnAUG......3'

the average distance between the SD sequence and the start codon varies considerably and on average is 7 nt. Other investigators have found "optimal" spacing (circa 1994) ranged from 5 to 13 nt.
the SD site complements with region on the 16s rRNA. The start codon complements to the anticodon of fMet-tRNA loaded into the ribosomal P-site.  So there are two distinct sites on the ribosome that contact the mRNA during translation initiation.

Also good to read

Designing Genes for Successful Protein Expression by Welch et al. Methods in Enzymology, Vol 498. (2011) (pdf)
Automated design of synthetic ribosome binding sites to control protein expression by Salis, Mirsky & Voigt. Nature Biotechnology. (2009). (pdf)

Note
I enjoyed researching this question because I found my own knowledge to be lacking solid empirical details. I do not have any direct experience besides this little lit review with this topic.

Thanks for your thorough answer. I guess I haven't realized that the RBS end is determined by this U base. Does this mean that it can be 100 bases away from ATG? I am actually asking this question, because I have a synthetic construct with RBS annotated on it and some of them are really far away from the start codon. Which could mean either wrong annotation of the following gene sequence, or that the distance doesn't matter that much. But on the other hand I thought that the ribosome should bind both the RBS and the start codon at the same time which I don't see possible with long sequences.

What I am also concerned about, are secondary structures formed between the RBS and the upsream or dowstream sequence. Any thoughts on that? Thanks again :-)

The main idea in the Chen paper I referenced was that the distance between the Shine-Dalgarno sequence / RBS and the start codon is limited by the physical distance between the complementary sites on the RBS. This distance seems to be about 5bp.  According to this old paper, the ribosome should not be able to bind effectively at all if the RBS is farther than say 20bp from the start site because the ribosome can't stretch out far enough to reach both sites at the same time.  New research may have more to say on this topic.

Secondary structure has significant effect on translation efficiency.  Many riboregulators have been observed and designed. For instance, one can design stem-loop secondary structure around the RBS region.  The region will self-complement in the absence of a particular aptamer or a strong complement.  In their presence, it unfolds and allows the ribosome access to the RBS and start site.  Engineered riboregulators enable post-transcriptional control of gene expression. Isaccs et al, Nature, 2004.

It was an interesting question to investigate and I enjoyed learning about it.  I hope more well-posed and provocative questions are asked here and that users react to them by actually going out and reading up on the primary literature.  Looks like that happens occasionally.  Cool.

Yeah, we will see where this site is going...I am also trying the RBS calculator :-)It would be nice if we chat more. Would you write me on gvandova@stanford.edu?


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What is causing my problem with very low yields when isolating a 42kb yeast plasmid?
I have to isolate a large plasmid from yeast and transform it in E. coli. After transformation, I often get no colonies. One reason for that is the yeast mini prep hasn't worked or the DNA concentration is too low. I tried two different isolation protocols:

Zymoprep I yeast plasmid prep kit
From the doc: "based on the old E.  coli alkaline lysis method with our Zymolyase added in the first  solution."
Phenol chloroform YAC isolation protocol
used by Dan Gibson et. al] for their huge constructs (>100kb)
They use an expensive Qiagen large-construct column at the end, in order to purify and visualize the yeast extract on a gel, but I skip that step because the Qiagen column cost $40 per yeast clone which doesn't scale if we do many of these.

How can I troubleshoot and optimize the above-mentioned protocols? Are there any other protocols that might be more suitable for a large plasmid and don't use too expensive materials?

A dependable protocol for yeast DNA extraction I used to use was broadly similar to the protocols you cite but included an ethanol precipitation before and after the P:C extractions. The only expensive material was time. The general outline was:

Alkaline lysis
Ethanol precipitation
RNase A treatment of resuspended DNA for 15 minutes
Phenol:chloroform extraction (x2)
Ethanol precipitation

You probably know that the ethanol precipitation lore is that the yield is better the longer and colder you do your ethanol precipitations. I only ever did reverse transcriptase reactions a few times, but the template DNA I prepared spent the night in ethanol at -80C to maximize yield. Another place to double-check is that your yeast cultures are sufficiently dense before starting.

What should be the OD of the culture? What is the volume of the culture?

I took 1.5mL of a "dense overnight culture" for this protocol. I don't remember being particularly careful about the OD for this (and the OD is relatively strain-dependent anyway). For us, "overnight" meant the culture was in a healthy stationary phase and that was easily gauged by eye. If you need to get a feel for the growth properties of your strain, start a culture in the morning and take periodic OD600 readings throughout the day. That should give you a clear picture of when you'll have the maximum number of healthy cells.

I've successfully used the Zymoprep kit, but only for smaller plasmids in 2-hybrid experiments. So their cell lysis enzyme/buffer system works well, but I'd guess that your 42kb plasmid is precipitating out with the genomic DNA.
The standard Qiagen midi columns are capable of capturing large constructs. This has worked wonders for me when I was purifying large BACmids from E. coli - and gets the cost down to $10/sample (it does require additional buffer, but that's a minor expense). It might be worth trying the Qiagen yeast DNA protocols for the midi kit and see if you can isolate your large plasmid?

And for what it's worth, the technical reps for Qiagen were very helpful on the phone. Unlike Invitrogen. I dread every call to Invitrogen technical service. >:[


text:
Effects of mRNA vaccines on human body processes
I would like to understand the effect of an mRNA vaccine on more complex processes in the human body.
To what extent does this "artificial", external addition of mRNA interfere with the body's processes? It seems naïve to me to think that it cannot set processes in motion that can be passed on - positively or negatively - to future generations.
Do I have a wrong idea about "artificiality" or the processes in the body?
As far as I know, there are (permanent) processes going on in the human body to modify the genetic information that will be passed on to future generations.
I also wonder to what extent this "reprogramming" of the immune system places a (too) strong focus on COVID-19 and whether this can weaken the immune response to other diseases. I have a naive idea of a "point system" where only a certain number of resources are available for different disease control.

I can address some of the points made in the post.
One point about the "artificiality": I think there's one fact that's often overlooked in the discussion of mRNA vaccines. SARS‑CoV‑2, for example, is a positive-sense single-stranded RNA (+ssRNA) virus. That means, the information that the virus uses to replicate itself and which describes the "blueprint" of its components, is stored as a single RNA. This RNA can more or less directly be translated into corresponding proteins by the ribosomes outside the nucleus, just like the mRNA used by mRNA vaccines. So, during a "natural" infection with such a virus, the virus's RNA also gets inside the cells and is translated into proteins, just like with the "artificial" mRNAs by vaccines! But the way this RNA enters the cell is somewhat different.
With viruses, they dock onto the cell and release their RNA into the cell. With mRNA vaccines like the one by BioNTech/Pfizer and by Moderna, this RNA is packaged into lipids (the stuff cell membranes are made of), which integrate more or less directly into the cell membrane and release the RNA. With vector vaccines like the Sputnik V or the Oxford–AstraZeneca vaccine, a different virus is used to carry the RNA load and infect cells (in the case of AstraZeneca, an adenovirus is used which usually infects chimpanzees and is normally harmless to humans). RNA in any case is degraded by the cells within a short time and leaves no traces.
Regarding the permanent modification of genetic information in humans: the genetic information in humans is stored as genomic DNA in the cell nucleus. DNA has a structure similar to RNA, but they do not work together, so RNA can't be simply integrated into the DNA. For DNA to form proteins, which make up most of the parts of a cell, it needs to be transcribed into RNA, which then is further processed into mRNA. This mRNA is tagged with a molecular export factor, which it needs to pass through the nuclear pore complexes, which are the highly specific transporters between the nucleus and the cytosol. After an mRNA has been exported from the nucleus, this tag is cleaved, so it can't return to the nucleus. Additionally, only if genetic information of egg or sperm cells is altered, this change is actually passed to the next generation.
So in summary: mRNA from vaccines behaves pretty much like the RNA inserted by RNA viruses into cells. And it can't find its way into the nucleus, where the genetic information is stored. And even if that happens by some way, it would first need to get "reversely transcribed" into DNA to be integrated. Some viruses can in fact do that, like HIV, which can also break into the nucleus in some instances (or wait for a cell division). Simple, "naked" mRNA of a vaccine however can't do that, only in extremely rare circumstances where the cell is already infected by another virus like HIV, I suppose.
But maybe you were talking about what is called "epigenetic modification", which is the molecular modification of the genomic DNA, where the actual stored sequence information is not altered, but the way it is read is modified. This process however is mediated for example by methylation of parts of the genome, for example, and does not intrinsically have anything to do with mRNAs in the cytosol. It should be noted that epigenetic modification is usually also reversible, not permanent, but it can be passed to the next generation, just like the genome itself.
What you said concerning the immune system focussing too much on another disease: I don't know a lot of immunology, but usually, building an immune protection against one pathogen also strengthens resistance against others. However, problems concerning the immune system most often arise when the immune system "overreacts" to an antigen and starts attacking parts of its own organism (autoimmune reaction). This can in fact be triggered by vaccines, even by only mRNA (and its protein products), as well as "natural infections", of course. Clinical studies are in place to analyze these occurrences.

A nitpick - The Sputnik vaccine uses Human Adenoviruses (HAd26 and HAd5). The Astrazeneca/Oxford uses Chimpanzee Adenovirus (ChAdOx1, based on ChAd25).

The last point may be about the (effective) "memory capacity" of the immune system (a zero sum thought). This could maybe be addressed in the answer by stating (and comparing) the number of different pathogens (both new and already recognised) we are exposed to every single day. I don't know the number - in the thousands per year? Thus the "memory capacity" of the immune system must be at least on the order of 100 times that.

Thank you @bob1 for the correction, I fixed it!

Also thank you @peter-mortensen for fixing typos and adding Wikipedia links. I'm not sure if I'm qualified to comment on the "memory capacity" thing, maybe someone else could chime in to amend the post.

As @panda-byte writes in great detail, the mRNA processes in our cells are a one-way street and there is no conceivably relevant way for an externally introduced mRNA to modify your DNA.

Do I have a wrong idea about "artificiality" or the processes in the body?

Very likely, yes, if you (like me) do not have much more than general public knowledge, maybe as provided in a few short lessons in school if you were lucky.

I also wonder to what extent this "reprogramming" of the immune system places a (too) strong focus

The immune system is vastly complex and has many different layers and components. There is no way for a layperson (including myself) to have any luck in applying our intuition to these things - we must trust the scientists on this.
One of the best resources I know of which gives you a view of the insane complexity is the video How The Immune System ACTUALLY Works – IMMUNE from the excellent "Kurzgesagt" channel.  They provide the scientific sources as well if you wish to learn much more than appropriate for an answer here.

The information is passed to future generations mainly via egg cells and spermatozoa - as long as the genomes of these cells are not modified, there is no high risk (and, contrary to some antivax claims, mRNA vaccines do not modify any genomes). There may be some environmental effects on the immediate offspring, due to their contact with mother during pregnancy and breastfeeding, but these are also very limited.
On the other hand, the immune system of the vaccinated person develops new antibodies, which hypothetically might cause potential (over)reaction to other pathogens or manifest in new allergies.
Disclaimer: this is not an expert opinion, but a placeholder answer to motivate a deeper discussion. I will be happy to remove it as soon as the experts chime in.

The (unfounded) concern may be epigenetic changes (even if it wasn't directly mentioned in the question). Perhaps address that as well?

Re "new antibodies, which hypothetically might cause potential (over)reaction": Isn't the cytokine storm caused by something else than antibodies? (Not a rhetorical question.)

@PeterMortensen It might well be, but the cytokine storm is not the only concern. There are many kinds of autoimmune problems that include light harmless allergies and severe syndrommes.

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authors: Vladimir F Героям слава


text:
Can DNA produce ribozyme-like structures?
RNA is known to act as an enzyme via its ability to fold itself in specific ways.
Is DNA capable of such structures? Or is it some biochemical reason stopping the folding?
Have they been observed in nature?

There are no known natural DNA enzymes (deoxyribozymes), but there are various synthetic DNA enzymes. The first deoxyribozyme that has been reported (Breaker and Joyce, 1994) catalyzed the Pb2+-dependant cleavage of RNA.
Various deoxyribozymes have been synthesized, they can catalyze RNA cleavage, RNA ligation and many other reactions like DNA phosphorylation or Thymine dimer photoreversion, and even a Diels-Alder reaction (see Baum and Silverman, 2008 for a review).
DNA lacks the 2'-hydroxyl group that RNA posesses, but there is some evidence that this doesn't significantly decrease the potential of deoxyribozymes compared to ribozymes. In one experiment DNA and RNA enzymes that catalyze a Carbon-Carbon bond formation were compared and both achieved comparable catalytic rates (Chandra and Silverman, 2008).
For more information about DNA enzymes you can look at the publications from the Silverman lab, they're probably the most active research group in this field.

Baum, D. A. & Silverman, S. K. Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell. Mol. Life Sci. 65, 2156-2174 (2008).
Breaker, R. R. & Joyce, G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229 (1994).
Chandra, M. & Silverman, S. K. DNA and RNA Can Be Equally Efficient Catalysts for Carbon−Carbon Bond Formation. J. Am. Chem. Soc. 130, 2936-2937 (2008).

DNA has recently been designed to act as a targeted drug-delivery agent at George Church's lab.  This doesn't involve catalyzing a reaction between two substrates, but it does involve significant internal conformational changes based on binding to highly specific substrates.
http://www.sciencemag.org/content/335/6070/831.abstract

This isn't a ribozyme at all.

@bobthejoe It's not a ribozyme, but it does demonstrate a parallel flexibility of conformation and function to ribozymes.  Part of the question addresses whether there is a biochemical reason "stopping the folding".

In that regard, you should really cite Ned Seeman's work. The DNA in the box and the DNA origami work better reflect the conformational flexibility of higher ordered DNA structure. I would believe that the alternative discussion in http://biology.stackexchange.com/questions/287/what-implications-has-the-missing-2-oh-on-the-capability-of-dna-to-form-3d-stru better describes the limitations of DNA in achieving these non-canonical structures.


text:
Why are there nail growth differences  between humans and other mammals?
When a cat is growing, his nails are growing with him to some extent. A grown cat has a fixed nail length that is not extending.
By contrast, human finger nails just keep on growing, so we have to cut them to keep an aesthetically pleasing look.
Nature clearly has a mechanism to control nail growth.
What is the most probable reason as to why this is not implemented in humans?

Cat claws are growing all the time, like horse hooves, or human nails. However, cats and horses usually use their claws/hooves, so they get shortened through mechanical action.
An indoor cat may need their claws trimmed if it doesn't use them enough (that's why cats will want to scratch everywhere), or if has supernumerary toes that don't normally touch the ground. Similarly, cattle that doesn't get to move will suffer from hoof overgrowth, which appears to be very uncomfortable to the animal.
Consequently, if you were to use your fingernails more often for digging and scratching, you wouldn't have to trim them all the time.

Thank you Jonas for clarifying it for me. I guess the mechanism for limiting the growth when an optimal length is reached is non-existent, since there is no probing mechanism to know how long the nail actually is at a moment of time. The same may apply to hair.

Hair has a maximum length. A hair grows to full length, then sits idle, then falls out and is replaced by a new hair.

@Maxim Of course there are mechanisms for that. How else does a leg know when to stop growing? Or any other organ in the body. Most of the mechanisms behind that aren’t yet completely understood though.

@Konrad, well, the leg don't regenerate in case it's part is removed mechanically, whereas nails are in a constant growth state. Leg is a complex organ that has a feedback. It can tell the brain how long it is by the lenght of a neural connection network. Nail does not have it, so there may not be a mechanism to know how long it is.

@Jay, thank you. Good point. This proves that the hair provides an informational feedback to the brain about it's length also, unlike nails.

@Maxim Not in humans. But in plenty of other animals, and there doesn’t seem to be a fundamental reason why this couldn’t in principle work in humans.

@Konrad, sorry, I've lost you. Plenty of other animals have what?

@Maxim The ability to regenerate legs (or other parts).

@Jay, Maxim : I am not convinced hair has informational feedback. I think it's more that the skin provides the feedback e.g. heat retention information, or stress info due to the weight of the hair.

@JohnSmith I never suggested there is informational feedback. hairs grows for a certain length of time. Cutting the hair doesn't change the clock.


text:
How are whole Haplotypes for Sequencing isolated?
Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered irradiating sperm and attempting to create haploid females via gynogenesis, but I was wondering if there was a faster and easier method that could utilize gametes directly.

Are you limited to a particular species of fish? Or can you use one of the asexually-reproducing species?

If your aim is to isolate the two haplotypes (chromosomes) maybe you should try flow cytometry. You might read this paper http://www.ncbi.nlm.nih.gov/pubmed/21181533 by Dolezel which is leader in the field, at least for plant chromosomes. I'm pretty sure that the applicability of the method depends on the physical properties of the chromosomes you have (especially their size distribution).


text:
Why do people say that trans fatty acids are bad for your health?
I've heard from several sources that trans FAs are bad for you and their consumption will lead to cardiac problems, and that they are indigestible.
But I also learned from biochemistry that they are digestible. What is the reason for this, or is it true at all?

I'll try to get to a formal response later. In the meantime, fatty acids are not bad or unhealthy for humans if taken in moderation. We need fat and cholesterol in our diets, but too much raises the risk of poorer health. Some fatty acids are more beneficial than others.

Trans fatty acids are digestible, but they cause an increase in LDL and a decrease in HDL, which is the leading mechanism for atherosclerosis. So, they increase the risk of a cardiac infarct.
LDL means Low Density Lipoprotein, it's one of the 5 major lipoprotein groups. Lipoproteins carries the fatty acids and cholesterol which were absorbed from intestines (because lipids are hydrophobic and cannot be carried within the blood directly like glucose or proteins.)
So, LDL mainly carries cholesterol and fatty acids from intestines to tissues. (fatty acids and cholesterol are essential for cells.) But in excess levels, they tend to accumulate in vessel walls, which also starts and inflammatory response and makes the situation worse. (mainly includes macrophages and T cells) This is the main mechanism for atherosclerosis.
In the other hand, HDLs serve as a reverse cholesterol transport system, which carries the cholesterol back, mostly to the liver (for bile secretion) or steroidogenic organs such as adrenals, ovary, and testes by direct and indirect pathways. So a high HDL reduces the atherosclerotic process.

Thanks, nice response, but could you give me some resources on why transFAs raise the LDL level more than any other fatty acids? If they don't than this is just an argument against consuming excessive amounts of fat.

No, it's not an argument just against consuming excessive amounts of fat. Trans fatty acids increase LDL more than cis unsaturated fatty acids, even equal to saturated fatty acids. http://www.ajcn.org/content/59/4/861.full.pdf+html You can check the discussion section.

Thanks, I'll read it more in depth on the weekend. Anyway, I'm still a bit skeptic about the topic. Do  you (or anybody) have some texts on the physiological background of the phenomenon?

When you say they are digestible, do you mean that the GI tract can cut off the glycerol and make trans-fatty acids, or do you mean that cells can process trans-fatty acid into other molecules? I thought the problem was lack of enzymes that can handle the trans double bond.

Studies have been done in which saturated fats and cis-unsaturated fats in the diet were replaced with trans-fatty acids. In all cases there were increases in LDL cholesterol, blood triglycerides and Lp(a) lipoprotien, and decreases in HDL cholesterol and particle size of LDl cholesterol. All of these changes result in an increase in the risk of cardiovascular disease. Beyond that the incidence of CHD in prospective studies looking at trans fatty acid consumption has been greater than what would be predicted from the changes in blood lipid profiles. Over the past decades it has become clear that trans fatty acids increase the risk of CHD more than do saturated fats. In addition, they have been shown to increase systemic inflammation and decrease endothelial cell function. The FDA suggests that consumption of trans fats should be kept at 2 gms/ day or lower.


text:
How does Halosulfuron-methyl kill nutsedge, while leaving lawn grass and most weeds undamaged?
I use Halosulfuron-methyl to control yellow and purple nutsedge in lawns. This chemical acts by interfering with the acetolactate synthase enzyme, which quickly slows cell division, and growth at all points.

How does this work without also interfering with enzymes in the lawn grass?

http://hortsci.ashspublications.org/content/30/2/285.full.pdf

@DevashishDas The paper does not seem to be relevant in answering this question.

Halosulfuron-methyl is a member of the family of sulfonylurea herbicides. Brown (2006) mentions in his abstract the following, and I quote:

This class of herbicides acts through inhibition of acetolactate synthase [...], thereby blocking the biosynthesis of the branched-chain amino acids valine, leucine and isoleucine. This inhibition leads to the rapid cessation of plant cell division and growth. [...] Crop selectivity results from rapid metabolic inactivation of the herbicide in the tolerant crop. Under growth-room conditions, metabolic half-lives in tolerant crop plants range from 1–5 h, while sensitive plant species metabolize these herbicides much more slowly, with half-lives > 20 h. Pathways by which sulfonylurea herbicides are inactivated among these plants include aryl and aliphatic hydroxylation followed by glucose conjugation, sulfonylurea bridge hydrolysis and sulfonamide bond cleavage, oxidative O-demethylation and direct conjugation with (homo)glutathione.

Hence, metabolic inactivation activity differs between susceptible and insusceptible species. To get to your question: this means that the enzymes in lawn grass are also inhibited, but to a lesser extent, as the herbicide is metabolized and inactivated more rapidly in grasses.
Reference
Brown, Pesticide Science 2006;29:241–378


text:
Is it possible to genetically modify a plant at home?
Would I be able to genetically modify a plant at home? What equipment will be necessary? I think it might be a fun change from the 'norm' of regular hybridisation, to try some inter-family gene insertion, instead of staying within a genus. Are some plants easier to modify than others?

You might also have to consider any regulations that might exist in your country. In some countries genetic modified organisms can only be handled in designated laboratories.

@MadScientist Do you know of any such regulations in Pennsylvania, United States?

The USA regulates the product of genetic engineering, not the process, so there are no federal regulations (some state/county laws may be different) to prohibit you. Most likely you cannot just release the plant into the wild though as it may require USDA approval (depending on the genes inserted and method of inserting them).

This q. is a follow-up to the the above problem....can't it be simply done by creating a hybrid??...I mean that too is a genetic mix-up & will show features diff. from the parents..

@souvik But you cannot add genes from out of the genus this way, so not the same. I've hybridized plenty of plants in my time, including some quite nice roses.

Oh...I get it...so try something like this- http://biohaxlab.site90.com/lib/Gene%20Expressing/Luciferase%20Gene%20in%20Plant%20Cells.pdf ...it's cool..

Well, that depends on your home. ;) I think it is not an easy process.
There are two main methods that are used to genetically modify plants:
Using the bacterium, Agrobacterium tumifaciens, as a vector for the DNA. Agrobacterium has the ability to infect plants and insert DNA into a plant's genome. It causes crown gall tumours in natural infections. This method has mainly been used to modify broad leaved plants, such as sugar beet and oilseed rape, but is now also being applied to monocot species, such as maize and rice
Particle bombardment or biolistics where the DNA to be inserted is coated on minute gold particles and fired into plants cells. This approach is used for monocot plants such as maize and rice
Here I found simple step by step article, but lil bit old. may be there are new methods for this process.
How To Genetically Modify a Seed, Step By Step

What equipment might I need?

With agrobacterium, a usual practice is to dip the flowers in the bacterial suspension (Floral dip). You would need the bacteria, culture media and your gene inserted in the agrobacterium Ti-plasmid.

Yes it is. The easiest plant to transform would be Arabidopsis, which can be transformed by agrobacterium using the floral dip method. The process would be as follows:
1. Design a gene sequence you wish to insert into the plant
2. Synthesize (or otherwise acquire the DNA)
3. Insert the DNA into your agrobacterium, at home you would use a cold snap transformation process described here: https://www.youtube.com/watch?v=PvkfIECvyqs This can be done at home using a dry ice bath.
4. Then use the floral dip method to insert the dna into the plant. This involves growing a plant to just the right age when it is flowering and dipping the Arabidopsis flowers into a solution of the agrobacterium.
5. Then grow the flowers to seed and grow the seeds on a suitable select able marker (which you designed into your DNA plasmid).
The specific experimental conditions needed to do all this are too long for this answer, but you can look them up online as all the procedures are standard.
Plants which result from this process would not be legal to release into the wild due to USDA regulations.
Engineering other plants, depending on the species, can be more complex but could possibly also done at home. There are even designs online for an open source gene gun if you didn't want to use agrobacterium.

genetic modification can be done with mutations. A mutation is a permanent change in the sequence of DNA. In order to obtain an observable effect, mutations must occur in gene exons, or regulatory elements. Changes in the non-coding regions of DNA (introns and junk DNA) generally do not affect function.
Mutations can be caused by:

external (exogenous) factors, such as chemicals and radiation

or

endogenous (native) factors

Mutations can be advantageous and lead to an evolutionary advantage of a certain genotype..this will be a solution for your plant modification..
A mutagen is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level.
chemical mutagens:

Bromine
Sodium azide
Psoralen
Benzene

long term treatment plant with mutagens caused mutations some might be advantage
then select advantage ..
 As many mutations cause cancer, mutagens are therefore also likely to be carcinogens!

Yes, It is.
An Indian Company IndieBB can help you get one.
IndieBB: a DNA system designed to help you and your friends to explore genetic engineering and synthetic biology by making fluorescent bacteria at home.

That's pretty cool! How about plants?

I haven't watched the youtube video completely, but I think they are pretty good.

Do you mind expanding to the other points I asked about?

How fresh do the hair follicles have to be?

@J.Musser: I haven't tried it myself. but I think it had to be fresh. PS; I don't know how you will get it with follicles??

That's a Mimosa pudica, or "touch-me-not". This won't work.

@DevashishDas Thank you for removing the reference to the hoax video, however this refers to bacteria, not plants, and links to a defunct indiegogo campaign.

@user137 I can't delete the answer till it is unselected as the correct answer.

Not to forget that simple cross breeding your plants the Mendelian way also modifies their genetic make up, as @souvik bhattacharya indicates in his comment. No equipment necessary, no chemicals, no ethical issues.

But you cannot add genes from out of the genus this way, so not the same. I've hybridized plenty of plants in my time, including some quite nice roses.

@J.Musser: you're right, but across-species gene insertion is not mentioned in the question anywhere - I'm just answering the question

My bad, I edited my question to clarify.


text:
Why doesn't the herbicide 2,4-D damage lawn grass?
I sometimes use 2,4-Dichlorophenoxyacetic acid to control broadleaved weeds in lawns. It is selective, and quickly kills the dicot weeds, while other plants are unharmed.

2,4-D is a synthetic auxin, a class of plant hormones. It is gets taken in through the stomata on the leaves, and is transported to the meristems of the plant. This causes uncontrolled, unsustainable growth, and the plant wilts, and dies.
Why doesn't this affect most monocotyledons?

According to this link from Purdue, the seed of the answer is this:

The herbicide is used to kill broadleaf weeds, which are dicots, while monocot grasses, such as sorghum and corn, are more resistant. That's because grasses inactivate 2,4-D inside the plant, while broadleaf dicots do not.

But on the other hand, Song 2014 has this to say about 2,4-D:

However, the underlying molecular mechanism of how auxinic herbicides selectively kill
  dicots and spare monocots is not
  understood yet (Grossmann 2000; Kelley
  and Riechers 2007; McSteen 2010). The mechanisms of auxin biosynthesis, transport,
  and signal transduction
  are conserved in monocots and dicots make this question more complex (McSteen 2010). Early research has
  proposed that the selectivity of auxinic herbicide is because of
  either limited translocation or rapid degradation
  of exogenous auxin, altered vascular anatomy, or altered perception of auxin in monocots (Monaco et al. 2002;
  Kelley and Riechers 2007). Auxin transport is influenced by plant vascular
  systems (Mattsson et al. 1999;
  Scarpella et al. 2006). The difference in vascular tissue structure between dicots
  and monocots may contribute
  to the selectivity of auxinic herbicides. In monocot
  stems, the vascular tissues (the phloem and xylem) are
  scattered in bundles, and lack a vascular
  cambium; in dicot stems, the vascular tissues are form
  ed in rings and
  possess a cambium.

So in other words, we don't know yet. It seems to be very strongly tied to auxin transport, but we do not have the full mechanism of action; since auxin is such an important plant hormone, and the pathway is therefore highly conserved (that is, the genes tend to be nearly identical on the parts of the sequence that affect the phenotype), the general conclusion is that the pathway itself is not affected, but an accessory pathway clears up auxin in levels excess of any normal amount in monocots.
Edit: Whoops, got the author's first/last names mixed up.

The specificity of 2,4 D may be due to either limited translocation or rapid degradation ,altered vascular anatomy or altered perception of auxin in monocot

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text:
Determining if a specific proline is cis or trans in the protein?
While peptide bonds usually adopt the trans conformation, peptide bonds to proline can exist in either cis or trans conformation. The isomerization between cis and trans is slow, and has been shown to be the rate-limiting step in folding of certain proteins.
What methods can be used to determine the conformation of a specific proline in a protein?

Sarkar et al.(2007) Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein. Molecular Cell 25, 413–426 (DOI 10.1016/j.molcel.2007.01.004), available here.

The authors report on the interactions between two SH3 domains of the Crk adaptor protein. Basically they find that the linker which tethers these two domains contains a proline which interconverts between the cis and trans conformations, and that this interconversion determines the interaction between the two domains. They follow isomerisation by using NMR.
Cis-trans peptidyl-prolyl isomerization is a subtle change, and I don't think that you will find a way of following it in a specific protein that is simpler than this, unfortunately.

i'd agree - the most common method is to determine the structure


text:
What is the title of Darwin's paper on cellular structure?
I read somewhere that Darwin wrote a paper that dealt with cellular structure, but I've been unable to find the title or contents of the paper because Darwin wrote such a volume of material. What is the title of this paper or papers?
A google search does not turn up any helpful results, and a similar search in google scholar yields equally ambiguous results (at least to me, since I do not have a background in biology).

Darwin had written lots of papers which dealt with fertilization (which involves single cells), as he primarily dealt with the reproduction, continuation and thus evolution of a species, but these did not deal with cell biology specifically.
After a closer look at the complete list of all his publications, I found that he did have two cell-related publishings, specifically about the size of cells, one entitled Bees in Jamaica increase the size and substance of their cells, and the other, Bee-cells in Jamaica not larger than in England, in which he retracts the statement he had made in the previous article.
Ultimately, to answer your question, it seems as though none of his works dealt with cellular structures.

References

Charles Darwin. "Bees in Jamaica increase the size and substance of their cells". Journal of Horticulture (15 July): 305.
Charles Darwin. "Bee-cells in Jamaica not larger than in England." Journal of Horticulture (22 July): 323.


text:
Which hormones can cross the blood brain barrier?
Can hormones such as testosterone, aldosterone and estrogen cross the blood brain barrier?
I looked on Wikipedia and there no mention of it in the testosterone article. Through Googling around I also didn't find a list of which hormones can cross the barrier.

Yes, both steroid and peptidic hormones can enter the brain, the obvious proof being that the brain responds to changing blood concentration of hormones.
The situation is different for steroid hormones (such as estrogen, testosterone, cortisol etc) which are small and lipophilic, and peptidic hormones (such as insulin, ghrelin, prolactin etc) which are big and hydrophilic.
The blood-brain barrier (BBB) is selectively permeable to steroid hormones: some of them (such as the gonadal steroids) can readily pass the BBB, while others (such as corticosteroids) pass only in small concentrations. This may however be modulated by hormone carrier proteins in the plasma.
See: Transport of Steroid Hormones through the Rat Blood-Brain Barrier - Pardridge et al., JCI, 1979

When speaking of peptidic hormones, the classic hypothesis is that hormones pass through the areas where the BBB is "leaky", i.e. where capillaries are fenestrated.
These include circumventricular organs such as the median eminence (where the terminals of many neuroendocrine neurons are located), or the organum vasculosum of the lamina terminalis (OVLT), important for reproduction and osmoregulation. The chorioid plexus is also often mentioned as a site for hormone entrance and/or sensing.
However, how exactly hormones enter the brain is still very unclear.
Our lab published a paper on this topic recently:
Rapid sensing of circulating ghrelin by hypothalamic appetite-modifying neurons - Schaeffer et al., PNAS, 2013

Yeah indeed they can.  The obvious proof is puberty and development, but a more involved look into how that is achieved can be found in this free article from last year.  In particular,

Nearly every mechanism by which a substance can cross or interact with the BBB is used by one hormone or the other. In general, steroid hormones cross the BBB by transmembrane diffusion whereas thyroid hormones, peptide hormones, and regulatory proteins cross by saturable systems.

In particular, I like figure 1:


text:
What do we know about the Last Universal Common Ancestor (LUCA)?
All life on Earth (bacteria, archaea, eukarya) is thought to have evolved from a common ancestor, or last universal common ancestor (LUCA). What do we know about the characteristics of LUCA based upon extant life?

Wikipedia's article does a pretty fair job of summarizing the likely nature of the LUCA.

Seems rather broad at the moment. Perhaps one should constrain the question?

Carl Woese has much to say on this subject, including:

“The ancestor cannot have been a particular organism, a single
  organismal lineage. It was communal, a loosely knit, diverse
  conglomeration of primitive cells that evolved as a unit, and it
  eventually developed to a stage where it broke into several distinct
  communities, which in their turn become the three primary lines of
  descent [bacteria, archaea and eukaryotes].”

There is a 2000 Scientific American article by W.F. Doolittle that discusses much of Woese's (and others') work understanding this question.
Also, see a couple of Woese articles here and here.

LUCA already had the following - the genetic code - all 20 aminoacids and their codons, the ribosome (which was essentially modern and complete), tRNA etc. Basically it had the entire RNA-to-protein translation system, and it also had DNA.
Now, to add something about its metabolism - there is a paper which suggests that LUCA was an autotrophic, thermophilic organism that fixed CO₂ with H₂ via the ancient acetyl–CoA pathway, harnessed energy through thioesters and natural proton gradients at alkaline hydrothermal vents in a sulfur-rich environment.

I will quote the relevant paragraphs from https://pmc.ncbi.nlm.nih.gov/articles/PMC6095482/:

LUCA lived from gasses. For carbon assimilation, LUCA used the
simplest and most ancient of the six known pathways of CO2 fixation,
called the acetyl–CoA (or Wood–Ljungdahl) pathway [95–97], which is
increasingly central for our concepts on early evolution because of
its chemical simplicity [97,98] and exergonic nature [99–101]. In the
acetyl–CoA pathway, CO2 is reduced with hydrogen (H2) to a methyl
group and CO. The methyl group is synthesized by the methyl branch of
the pathway, which employs different one-carbon (C1) carriers in
bacteria (tetrahydrofolate) and archaea (tetrahydromethanopterin),
cofactors that are synthesized by unrelated biosynthetic pathways
[96]. Carbon monoxide (CO) is synthesized by carbon monoxide
dehydrogenase (CODH), the archaeal and bacterial versions of which are
distinct but related [96]. The methyl and carbonyl moieties are
condensed to an enzyme-bound acetyl group that is removed from a metal
cluster in acetyl–CoA synthase (ACS) as an energy rich thioester.
Thioesters harbor chemically reactive bonds [102] that play a crucial
role in energy metabolism [101] and in metabolism in general, both
modern and ancient [101,103,104]. Although CODH/ACS clearly does trace
to LUCA [78,96], this is not true for the methyl synthesis branch,
which consists of unrelated enzymes in bacteria and archaea [78,96].
Life is about harnessing energy [44]. Thioesters are chemically
reactive—they forge direct links between carbon metabolism and energy
metabolism (ATP synthesis) as they give rise to acetyl phosphate, the
possible precursor of ATP in evolution as a currency of high-energy
bonds [111]. Relics of ATP synthesis via acetyl phosphate were found
in LUCA's genes [78], as were subunits of the rotor–stator ATP
synthase itself. The ATP synthase might appear to present a paradox
because no proteins of the proton-pumping machinery that cells use to
generate the ion gradient that drives the ATP synthase traced to LUCA
[78]. Yet some theories have it that the first cells arose at alkaline
hydrothermal vents [91,96,111], meaning that the inside of the vent is
more alkaline than the ocean outside. Such naturally existing pH
gradients could have been harnessed by LUCA to synthesize ATP (Fig 3).
Ancestral ATPases might have harnessed either proton gradients or
sodium gradients generated by proton/sodium (H+/Na+) dependent
antiporters [112], or they might have even been promiscuous for both
kinds of ions, similar to the ATPase of modern microbes that live near
the thermodynamic limits of life [113].
LUCA's environment was rich in sulfur; thioesters, SAM, proteins rich
in FeS and iron–nickel–sulfur (FeNiS) clusters, sulfurtransferases,
and thioredoxins were part of its repertoire, as were hydrogenases
that could channel electrons from environmental H2 to reduced
ferredoxin, which is the main currency of reducing power (electrons)
in anaerobes [114]. A recent report provided phylogenetic evidence
that archaea are ancestrally H2-dependent methanogens [62], compatible
with an autotrophic, H2-dependent lifestyle of LUCA.
LUCA had a reverse gyrase, an enzyme typical of thermophiles,
suggesting that LUCA liked it hot. But independent of the reverse
gyrase, simple chemical kinetics provide strong evidence in favor of a
thermophilic origin for the first cells [115,116]. The reason is that
only uncatalysed or inorganically catalysed reactions existed before
there were enzymes. Their rates of reaction were lower than the
enzymatically catalyzed reactions. Between 0°C and 120°C (the
biologically relevant temperature range), organic chemical reaction
rates generally increase with temperature [115,116]. Before there were
enzymes, high-temperature environments were more conducive to organic
chemical reactions than low-temperature environments [115,116]. Taken
together, LUCA's requirement for gasses (CO2, H2, CO, nitrogen [N2]),
the prevalence of sulfide, its affinity to high temperature and
metals, plus an ability to use but not generate ion gradients all
point to the same environment: alkaline hydrothermal vents.


text:
How do you design a drug to be delivered to the CNS?
I have just started reading up on structure-based methods for drug design (this is completely not my field so apologies for stupid questions that will be coming along!)
Clearly, some drugs are designed to target the central nervous system. However, I understand that the extracellular fluid of the central nervous system is separated from the blood by the "blood-brain barrier" which restricts the passage of large molecules between the two systems.
My question is : how do you design a drug to be delivered to the CNS?

You can read up on the design of opioid drugs (morphine, codeine, etc...). These provide a classic example of rational drug design in relation to the blood brain barrier.

In a nutshell: in order to pass through the blood-brain barrier (BBB) the substance has to mimick soee properties of the substances that are allowed to pass through.
There are different types of "transporters" -- integral proteins going through the cell membranes and accounting for the active transport of the substances they can actively bind to. Smaller molecules of drugs can use solute carrier transporter (SLC), whereas bigger molecules (oligo- and polymeres) would use the receptor-mediated transporter (RMT).
There is a nice article on this topic published by ScienceDaily.
Here is the quote:

One technology for enabling active transport of small molecule drugs
  across the BBB involves targeting endogenous nutrient transporters.
  These transporters are members of the solute carrier (SLC) transporter
  superfamily. Transport of small molecules across the BBB by these
  membrane proteins is known as carrier-mediated transport (CMT).
In order to design drugs that utilize CMT to cross the BBB,
  researchers modify their chemical structures so that they resemble
  nutrients that are transported across the BBB by specific SLCs. The
  prototypical drug that uses this strategy (which was developed long
  before mechanisms of CMT were known) is L-DOPA, the major current drug
  for Parkinson's disease. L-DOPA is used to replace dopamine that is
  lost due to degeneration of dopaminergic neurons in the substantia
  nigra of the brain.
Another major system that is used in normal mammalian physiology to
  enable needed molecules to cross the BBB is receptor-mediated
  transport (RMT). The brain uses RMT to transport proteins, peptides,
  and lipoproteins that are needed for brain function across the BBB.
  Examples of biomolecules that are transported into the brain via RMT
  include insulin, insulin-like growth factor (IGF), leptin,
  transferrin, and low-density lipoprotein (LDL).
In RMT, molecules in the circulation may bind to specific receptors on
  the luminal surface of brain capillaries (i.e., the surface that
  interfaces with the bloodstream). Upon binding, the receptor-ligand
  complex is internalized into the endothelial cell by a process called
  receptor-mediated endocytosis. The ligand may then be transported
  across the abluminal membrane of the endothelial cell (i.e., the
  membrane that interfaces with brain tissue) into the brain. This whole
  process is called receptor-mediated transcytosis.


text:
Effect of steroid hormone on specific cells?
As steroid hormones can pass through the plasma membrane by simple diffusion because they are lipid derived hormones, it means that they are capable of passing through every cell of our body, BUT why are only specific cells responsive against steroid hormones?
For example, all of our body cells almost contains the genes for the development of secondary sexual characters but why do only specific cells show a response against these steroid hormones because the development of secondary sexual characters occur only in specific region of our body, that is, beard formation occur only in a specific region of the face, etc.
IN SUMMARY: When steroid hormones can pass through every cell of our body then why do they show only a localized response?

Unlike other types of hormones, steroid hormones do not have to bind to plasma membrane receptors. Instead, they can interact with intracellular receptors that are themselves transcription activators. Steroid hormones too hydrophobic to dissolve readily in the blood  travel on speciﬁc carrier proteins from their point of release to their target tissues. In the target tissue, the hormone passes through the plasma membrane by simple diffusion and binds to its speciﬁc receptor protein in the cytoplasm. The receptor-hormone complex then translocates into the nucleus where it acts by binding to highly speciﬁc DNA sequences called hormone response elements (HREs), thereby altering gene expression.
Hormone binding triggers changes in the conformation of the receptor proteins so that they be- come capable of interacting with additional transcription factors. The bound hormone-receptor complex can either enhance or suppress the expression of adjacent genes.
The DNA sequences (HREs) to which hormone- receptor complexes bind are similar in length and arrangement, but differ in sequence, for the various steroid hormones. Each receptor has a consensus HRE sequence  to which the hormone-receptor complex binds well, with each consensus consisting of two six-nucleotide sequences, either contiguous or separated by three nucleotides,
The ability of a given hormone to act through the hormone-receptor complex to alter the expression of a speciﬁc gene depends on the exact sequence of the HRE, its position relative to the gene, and the number of HREs associated with the gene.

The quick answer is that only certain cell types express the required steroid hormone receptors that are necessary to induce signaling and gene regulation when bound to their target steroid hormones, like estrogen, testosterone, cortisol, etc. If no receptor is present, the steroid doesn't effect any change.
The second part of the answer involves the particular signaling pathways induced by the ligation of certain receptors by certain classes of hormones. Testosterone, for example, has numerous effects across the body, from promoting the growth of hair to building muscle mass to effects on mental well-being. Testosterone and its primary metabolite 5α-dihydrotestosterone bind primarily to the cytoplasmic androgen receptor, which then translocates to the nucleus, binds DNA at hormone response elements, and alters the transcriptional activity of genes (either increasing or decreasing, depending on the gene and the cell type). Testosterone can also be metabolized to estradiol and bind estrogen receptors, which function similarly to the androgen receptor (although it can have DNA-independent effects as well).
So, depending on the cell type, receptor expression levels, other DNA regulatory elements, the presence or absence of various testosterone-metabolizing enzymes, and other factors like age, gender, etc., a single steroid hormone can have a multitude of effects throughout the body.


text:
What is immunopanning (vs. immunoprecipitation and FACS)?
I had never heard the term before today. From what I can tell, it's using antibodies to purify a cell population of interest. I would appreciate more details, especially in how it differs from "immunoprecipitation" of cells via cell surface markers, and FACS.

Immunopanning is essentially an immunoprecipitation (IP) of cells using an antibody immobilized to a solid surface, like a cell culture plate. Conventionally, an IP is performed using small agarose or magnetic beads (~50 to 150μm in size) conjugated to an antibody or Protein A/G, and can pull down individual proteins, protein complexes, and/or nucleic acid complexes.
Cells are much larger than protein complexes, obviously, and for the most part much smaller than beads, but they can be damaged during a traditional IP, so immunopanning utilizes a single solid surface coated with the specific antibody or cell-surface protein ligand of choice. In this article (free PDF here), retrograde axonal transport was used to selectively label specific populations of neuronal cells with the extracellular portion of cholera toxin β (CTB) adsorbed to fluorescent beads, then the cells were purified using an immobilized anti-CTB antibody.
Fluorescence-Activated Cell Sorting or FACS is another way to purify cell populations. Cells are labeled with a fluorescent marker (either conjugated to an antibody specific to an extra-cellular epitope, via absorption as in the example above, or by expression of a fluorescent transgene like GFP), then scanned in a flow cytometer. Cells which match certain parameters or "gates" in the machine's software are then diverted into a separate collection chamber, allowing for the generation of a quite pure cell population.
However, as the authors point out in their paper above, FACS requires an expensive piece of equipment (can be over US$100,000), can be harsh on the cells, and is dependent on the availability of an antibody to a cell surface marker specific to the desired population of cells. Immunopanning is much less expensive, is more gentle on the cells, and in the authors' case was really the only choice for purifying their cell population of interest, as no specific biomarkers were available. It certainly won't replace FACS in the long run, but is another tool for investigators to use when studying specific cell types.

So immunopanning is "gentler" than immunoprecipitation because a flat surface is used rather than beads (and thus, there is no centrifugation step to isolate the beads)?

@dd3 - right. Also, you don't have the beads physically interacting with each other in the tube, potentially crushing or tearing cells. A cell could easily be tightly bound to two beads, one on either side, and possibly ripped apart when they separate. It's also much easier to remove cells bound to a plate than it is to separate the cells from the beads after the wash steps.

Thanks.  I've never done any of these before (just read about them being used in papers), so all of your links were very helpful.

@dd3 - no problem at all, I'm here to help. Thanks for checking it answered!


text:
How does inorganic phosphate inhibit alkaline phosphatase?
I want to know how is inorganic phosphate able to inhibit alkaline phosphatase.

When alkaline phosphatase dephosphorylates a substrate one of the intermediates in the reaction pathway is a phosphorylated form of the enzyme in which the phosphate from the substrate has been transferred to the enzyme. This phosphate is subsequently lost by hydrolysis. Under certain conditions alkaline phosphatase will actually catalyse a reverse reaction - the addition of inorganic phosphate on to alcohol substrates, and this also proceeds via the phospho-enzyme intermediate, but proceeds in the opposite direction.
This means that phosphate will inhibit the enzyme as a phosphatase via the formation of the phospho-enzyme, thus blocking the active site to substrates for dephosphorylation.

Reaction mechanism of alkaline phosphatase based on crystal structures: Two-metal ion catalysis
  Kim, EE &  Harold W. Wyckoff, HW 1991 Reaction mechanism of alkaline phosphatase based on crystal structures: Two-metal ion catalysis. J Mol Biol. 218: 449-464

So does that mean that inorganic phosphate actually can act as a competitive inhibitor and bind to the active site of the enzyme and interfere with its activity? Can it also act as a mixed inhibitor and bind to the Enzyme-Substrate complex as well or just the enzyme?

Yes it can bind to the active site. According to this abstract the kinetics are consistent with primarily competitive inhibition.


text:
Excretion and metabolic waste?
I know there is a difference between digestive and metabolic waste, but which one is called excretion? And what's the other one called? Thanks!

Egestion is the expulsion of undigested food which occurs typically via the anus. Although, interestingly or maybe just gross, flatworms must use their mouth has they have no anus. This is the non-metabolised material.
Excretion is the transfer of any metabolised material to the environment, including urine or carbon dioxide.


text:
Can a human smell through the ears?
The title does, prima facie, appear absurd.
Performing a swallowing action whilst pinching the nostrils shut gives the impression of listening through a bucket filled with water around the head; audible sound levels are perceptibly reduced. Some humans may encounter a similar sensation blowing their nose - hard.
This makes sense give the ears connect to the mouth/nose through the eustachian tubes. Can an odour make its way to the olfactory sensors through the ears?

do you mean "are there olfactory receptors in the ears" or "can smelly things make their way through our ears to the nose". Cause in the second case, the eardrum is in the way.

@Shep: The latter; sometimes when i put drops in me ears, i get this weird taste too ...

@Everyone - It doesn't take a high concentration of aromatic compounds in the air to actually stimulate a smell (or taste) response. I'd bet that enough of the drops vaporize in your local head-space that you end up tasting the stuff. Happens with me and menthol all the time.

A quick diagram to point out to people who may not know what Eustachian tubes are (#2).

In order for the aromatic molecule to reach the olfactory bulb, it would first have to get through the Tympanic Membrane (#22) [a.k.a. - Eardrum]. The Tympanic Membrane is water/airtight unless pierced.
So, while it's plausible that an aromatic molecule could travel through the Eustachian tubes and enter the pharynx areas, there isn't any way to get into the middle-ear in the first place unless the Tympanic Membrane has been compromised.
In a healthy and intact individual, the answer should be No.

TY, clear, and to the point.
p.s. I'm doomed )+:

Modified 6 Dec 2012: One approach to this question is to perform a sequence similarity search for genes encoding genes with a functioning in sensing external stimuli, be they
olfactory receptor, taste receptor or other such genes that are expressed in cDNAs or RNA-Seq data from library preparations of the appropriate ear tissue. While there is not likely at this point in time to be much data available in RNA-Seq format, one might find cDNA libraries from cochlea or neighboring tissue.
A "hit," meaning there is evidence that, for example, an olfactory receptor gene is expressed in cochlea, eg, only means that there is potential to smell through the ears. Taste receptors are expressed throughout the alimentary canal in humans, but tasting the contents - food or other - is not readily perceived as de facto taste outside the oral cavity. Nonetheless, there is no reason not to expect such sensors are expressed to relay information to the brain as to what is or is not present. "Smelling" in/by the ear for the purpose of detecting the presence of a given entity or molecule could serve a similar function.

You jumped the gun a bit. You're addressing the literal interpretation of the title, instead of the hypothetical situation addressed in the question. ;-)

And in any case, I am afraid that your data would not support your conclusion. The expression of an olfactory receptor gene in cochlea only means that an olfactory receptor gene is expressed in cochlea. It does not necessarily follow that the gene's product has the same function there as it does in the nasal canal.

@terdon I wrote that expression of a olfactory receptor means there is the potential for that function and not an absolute, defined function.

I know, but I am a horrible pedant and have recently been working on ways of predicting protein function and this is one of my pet peeves :). To my great annoyance I cannot use expression data to infer function.


text:
Neuromediator, Neuromodulator, Neurotransmitter?
Of these three words, perhaps Neurotransmitter is the most obvious. I took a look at Wikipedia page for Neuromodulation and found that this is pretty similar to Neurotransmitter too. I guess Neuromediator is somewhat more broad. Could someone clarify these nomenclature for me?

Neurotransmitters were classically the most specific in terms of demands on experimental demonstration (thus, the so-called "classical neurotransmitter") but the chief role of neurotransmitter is direct neuron-to-neuron communication via the synaptic cleft in which the post-synaptic neuron has channels that readily engage the neurotransmitter.  Classical neurotransmitters also require inactivation and are stored in vesicles in the presynaptic terminal (while under the modern definition, these last two requirements aren't as strict, allowing peptides and gasses like NO to be considered a neurotransmitter).
Neuromodulators, are more of an extra-synaptic application... a bath in the extracellular medium that modulates the excitability of a population of cells.  In this regard,neurotransmitters can be considered neuromodulators when their action is on channels outside of the synaptic cleft.
I have never heard the term neuromediator before, but looking at the results on Google suggest that it is the result of translation from Easterm European languages (Polish and Romanian) and seems to be synonymous with neurotransmitter.


text:
Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction
Presently I am working on metagenomics of coal biomethenation by bacterial consortium.
I have got the sequence result (Illumina). The sequence is huge and I can't predict anything from the sequence.
I have gone through different database like Metacyc, Biocyc etc.
Please help me that how can I draw an inference towards the metabolic enzyme that are involved in biomethenation of coal.

The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you unclear on ligands in many cases. So, the final step is to clarify the function with biochemical lab methods.
So, if you are stuck with a huge sequence, first try to find the genes in it.
http://en.wikipedia.org/wiki/Gene_prediction
For subsequent annotation/classification, I recommend InterPro and PROSITE.
http://www.ebi.ac.uk/Tools/pfa/iprscan/
http://prosite.expasy.org/scanprosite/

Well first off, we don't know how you sequenced the data. What did you actually sequence? Did you look at transcriptional activity using RNA-seq or did you do a full genome sequencing. Were there any paired-end reads? How did you create your library? Did you enrich the bacterial consortium for biomethanation activity?
Where do you reads map? The consortium complicates things but you will likely need to build a quality contig library before you do anything else. Without a doubt, much of your library will not map to anything interesting but you should still annotate the library by seeing where the reads map up. Identifying ORFs will be useful.
Likely, you will have a set of genes that will be involved with biomethanation. You should BLAST the bejesus out of your contig library for hits. Do they match any of your ORFs? Going the otherway, do your ORFs match any of the genes in EcoCyc or BioCyc. Do you need to use a larger database?


text:
Can frequent ultrasound diagnostics be harmful?
Are there any short or long term effects apparent in tissues if a zone (or the whole) of human body is scanned with ultrasonic waves often?

Medical advice questions are off-topic here, I think if you edit the last portion out and make the first question more general to the science behind it, it will be okay.

You might want to see this question though

@RoryM Thanks for editing and reopening my question. Your hat covers your eyes btw °<|)

Ultrasound is considered a safe procedure (reference) which is accepted by the WHO as well (reference). There have been studies however, that show the link of ultrasound treatment to some undesirable traits.
Ultrasound could be possibly linked to a decrease in body weight on birth of infants (reference).
Frequent use of ultrasound may influence babies scanned to grow up left handed (reference)
A significant migration of neurons (change of neurons from their rightful area) has been observed in mice on exposing them to ultrasound at the prenatal stage. (reference).
A study has found detrimental affects to the brains of mice on exposure to ultrasound in the fetal stage (reference).
So based on these papers, I wouldn't call them a 100% safe but these tests all relate to repeated usage of ultrasound imaging. Ultrasound usage sparingly and on valid medical indication should not be a matter of concern.