text:
How should I feed and keep an ant queen?
I have captured wandering ant queen. I guess she was just fertilised and was looking for a place to start a hive.
I'd like to create my own ant hive in artificial environment.
I unfortunately only have a small clean chemical bottle (1.5 CM in radius) to keep her in. I was wondering how much space would she need to feel safe.
I'm also not sure what should I feed her. Every morning, I have dropped few sugar crystals in the bottle. She shows much more individuality than an ant, because she has immediately started to collect them. It seems that she ate almost everything. I have also dropped few tiny drops of water in the bottle. Although it's hot and she ate the dry sugar she doesn't seem to drink it at all.
So what does she need? (well, except of natural forest which I don't have in my room)

Why this was downvoted? is it not acceptable question or how it could be improved?

@ruffp Feel free to upvote, like I did (and always do). I agree, the question is entirely on-topic.

First you need to identify your ant, for Czech Ants: http://www.antweb.org/taxonomicPage.do?rank=species&project=czechants&images=true
How should I feed and keep an ant queen?
Home for Pet Ant, Ant Farm:
There are lots of things you can use, for example, a clean transparent glass or plastic jar, or a fish tank of a size which you will decide is best for the ants you're keeping in it. As long as the container provides enough space, and the addition of any air holes small enough to prevent the ants escaping (much easier said than done); and also so you can observe your ants going about their daily activities, then it should be fine! Worker ants like to forage, so your set up needs to allow for the ants to do a spot of hunting for their food.
It is possible to make your own type of "Ant Farm" by using lengths of wood or plastic which have 2 grooves cut into them, like the frame used in double glazing. As long as you can place the frame onto a sturdy base to prevent it from falling over; or you can use plaster and other materials such as aerated concrete blocks, better known as Ytong nests. Two panes of clear glass or plastic can be placed into the grooves and sealed. Use the silicone sealant that is used around baths or sold where you buy glass fish tanks, but do remember to let it set and dry out well, as this will allow any chemicals to disperse harmlessly into the air before you add any ants. Also make sure that you can safely access your ant home, so you can put food in etc. You can also check out this youtube video or Wikihow.

Always try to cover your ants when not observing them to exclude light, as for most of their lives ants live in underground nests or places well away from daylight. This does not mean that they won't tolerate light; but they prefer to be in total darkness if possible, and queens rarely come out from their nests in the wild.
Feed the ANT:
If you are using a  gel-filled ant farms, it  contains all the water and nutrients your ants need for survival. Make sure to keep your kit sealed so the gel does not dry out.

In sand-filled ant farms, you need to add a few drops of water and small bits of food every few days. Ants also love a special treat of water with sugar dissolved in it, but this can’t take the place of fresh water for drinking. You can provide them with a bit of honey at times, and they will probably drink some of that. A small section of meal-worm can help provide her with a protein boost. Again, feeding them until the first workers arrive is not necessary as they do not forage during this period naturally.

Moreover, Interesting Links:
http://askabiologist.asu.edu/collecting-queen-ants
http://ant-farm-stores-review.toptenreviews.com/what-you-need-to-know-about-ant-farms.html
www.tarheelants.com/
Also, try "Ants can be pets" group on Facebook.

Your PDF link is aimed to distinct ant workers, which might look differently than queens. It also only applies on species that live in united states and are considered harmful. You're also generally takling about making the colony - not very much about the queen herself. In an answer on another question, which you have deleted, you claimed she doesn't eat at all...

Sorry, you never gave your geographical region, I have removed that part. As for the last deleted question, I was trying to explain the general scenario. Queen ants doesn't eat after laying eggs as they fend of there flight muscle. It doesn't mean she doesn't eat if given provided to her, she even eat her eggs if she is hungry. There various links says the same thing: www.animals.howstuffworks.com/insects/ant-info3.htm
PS: I don't know why you have me so much. All the answer I gave are mostly liked, if not, I just remove them. I love Biology SO and I am not leaving here.


text:
Are common eye defects inherited?
If one parent is nearsighted and the other is farsighted.
One parent developed nearsightedness later in life, while the other was born farsighted and they are both the first ones in their family to have any sort of eye problems.
Is there a possibility of their children having a perfect vision since both their conditions are the result of a recessive gene and can the probability of inheriting one over the other be assessed?

Both Nearsightedness and farsightedness are inheritable.
According to Citizen Scientists Look into Nearsightedness, 23andme blog:

Nearsightedness, a condition in which far-away objects look blurry, is
  a problem of endemic proportions — approximately 30-40 percent of
  adults in the United States are nearsighted.  And, as computers and
  cellphones (which train our eyes to focus on short distances) play an
  ever-increasing role in our lives, we can only expect that this number
  will grow. One study in the United States highlights the rising rates
  of nearsightedness. These researchers found that in the early 1970’s,
  approximately 25 percent of Americans between the ages of 12 and 54
  were nearsighted, but thirty years later that number had skyrocketed
  to 42 percent. While it’s been clear that genetics play an important
  role in nearsightedness, until this month relatively little was known
  about which genes are involved. Two large studies on nearsightedness,
  however, have recently shed light on the subject. One of these studies
  was conducted by the 23andMe research team under the leadership of Amy
  Kiefer and Nick Eriksson.
Read more at
  http://blog.23andme.com/23andme-research/citizen-scientists-look-into-nearsightedness/#ijOHfuvePBSFOm4A.99

Which types of eye disease are inherited?
Genetic factors play a role in many kinds of eye disease, including those diseases that are the leading cause of blindness among infants, children and adults.
More than 60 percent of cases of blindness among infants are caused by inherited eye diseases such as congenital (present at birth) cataracts, congenital glaucoma, retinal degeneration, optic atrophy and eye malformations. Up to 40% of patients with certain types of strabismus (ocular misalignment) have a family history of the disease and efforts are currently under way to identify the responsible genes.
In adults, glaucoma and age-related macular degeneration are two of the leading causes of blindness, and both appear to be inherited in a large portion of cases. Researchers have mapped several genes for glaucoma and are starting to identify genes involved in macular degeneration. They also are making very significant progress in identifying the genes that cause retinitis pigmentosa, a degenerative disease of the retina that causes night blindness and gradual vision loss.
Can common vision problems be inherited?
Genetics also play a role in vision problems that occur in otherwise healthy eyes. Genetic ophthalmologic researchers now have evidence that the most common vision problems among children and adults are genetically determined. The list includes strabismus (cross-eyes), amblyopia (lazy eye) and refraction errors such as myopia (nearsightedness), hyperopia (farsightedness) and astigmatism.
Can inherited eye diseases be corrected if an early diagnosis is made?
YES
Source: http://my.clevelandclinic.org/disorders/inherited_eye_disease/default.aspx
This Table gives a better insight on Causes of Myopia:

So in conclusion there isn't a chance of our children having perfect vision, they will inherit one or the other. Whether they are going to be farsighted or nearsighted is completely unpredictable but if diagnosed early there is a chance to keep the severity in check. Am I correct?

No, actually there are chances of your children having perfect vision. Otherwise you are correct.

How? Both conditions are the result of a recessive gene.

There are SNPs and Environmental factors involved too.

@Giota B: Hope this solved your question, if so, mark this as answer?

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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The move from RNA to DNA and the necessity of reverse transcriptase
In this piece about giant viruses and the origin of life, in the context of the move from RNA world to DNA world, virologist Valerian Dolja states:

In order to move from RNA to DNA, you need an enzyme called reverse transcriptase

Is this true though? Don't many DNA polymerases work with both, ssDNA and ssRNA templates, i.e. they function as reverse transcriptases although they're not "true" reverse transcriptases. So, in order to move from RNA to DNA, a reverse transcriptase was not a necessity like ribonucleotide reductase was for RNA to Uracil-DNA and thymidylate synthase was for Uracil-DNA to DNA?

I don't know if this is helpful in the context of moving from RNA to DNA world, but I do know that certain mutations to T7 RNA polymerase will allow that enzyme to use 2' deoxy nucleotides in addition to the normal ribonucleotides. These mutations were discovered by humans engineering the enzyme, but it's feasible that some transitional enzyme could have utilized both types of nucleotide. Then, those individuals with more DNA were favored because the DNA backbone is more stable than RNA backbone, eventually selecting for the modern DNA to RNA to Protein model.
Here is an article: http://www.sciencedirect.com/science/article/pii/S0168165613002940

Yes, this is true. This flow of information is called the "Central dogma of Molecular Biology". It basically describes the flow of information from DNA to RNA to proteins. Since a virus needs to amplify its genetic information before it can take over the infected cell and make only viral proteins and its genetic information, it has two possible options.
DNA viruses can use the cells replication and transcription machinery to make copies and express proteins. RNA viruses either have to use a reverse transcriptase to make DNA from its RNA genome to go on like the DNA viruses. Or they have to have a special, RNA-dependent (works only on RNA templates) RNA-polymerase (our RNA polymerase are all DNA-dependent and work only on DNA templates) to make more copies of their genome. Our DNA polymerases are dependent on DNA, the same is true for our RNA polymerases. So if the virus is not encoding (and actually bringing a few molecules with it in the virus) of the RT-polymerase or the special RNA-dependent RNA polymerase it will not be able to spread.
Using ribonucleotide reductases would theoretically be possible, but it is not the way nature went. And since a cell contains huge amounts of RNA, I doubt this would be a feasible way, as the enzyme would reduce all RNA. And later on the new viruses also needs new (not reduced RNA) to be packaged into new viruses. This would also be problematic.

You're writing about protein synthesis while my question concerns the transformation from RNA World to DNA World.

Sorry, but this is absolute not clear from your question. Can you rephrase it?

Sorry about that, although I don't really see how it's possible to confuse the discussion of RNA to U-DNA and U-DNA to DNA transformations with protein synthesis. Anyway, I clarified the original post. For those not familiar with U-DNA, here's an article.. http://www.ncbi.nlm.nih.gov/pubmed/16164990

Could you give a reference for standard DNA polymerases using an RNA template?

@AlanBoyd Do you mean the original post by @5heikki?

@Chris yes, apologies for the ambiguity, OP asserts that standard DNA polymerase can use RNA template, but I would like to see the evidence for this.

@AlanBoyd Fine for me, I was just wondering. And yes, I would like to see evidence for it, too. Would be interesting.

Some top Google results for "DNA polymerase RNA template" (works even with Taq in vitro): https://norgenbiotek.com/display-resource.php?ID=82 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC389454/ http://www.pnas.org/content/71/4/1035.full.pdf From last paper: "It is clear from the results presented that E. coli DNA polymerase I is able to synthesize extensive, well-matched
complementary DNA copies from a variety of natural RNAs, provided that the molar ratio of enzyme to RNA template is above a critical level."

The PNAS paper is about the Rous Sarkoma Virus, which is a retro virus. I would expect a RNA dependent DNA polymerase (aka reverse transkriptase) there. The other ones are about DNA polymerase I from E.coli, which is interesting. However this paper (seems to be the original one on this topic) finds a much lower enzyme activity on RNA temples (between 0.1 - 0.4% of that on DNA templates) so the question is, how relevant this is. When there is DNA around this enzyme will most likely not use RNA as a template.

I imagine there wasn't much DNA around when RNA & protein to U-DNA & protein was happening (likely first in the viral realm) thanks to ribonucleotide reductase. The main point was that even present day DNA pols have at least some function in regard to polymerizing DNA from RNA templates and thus "true" reverse transcriptases were not a necessity to the transformation..

This argument seems to be very circular. In an RNA world there presumably wouldn't be any DNA polymerase at all - what we should be looking for is an enzyme that can make DNA using an RNA template - which is a reverse transcriptase. The key step in the evolution of such an enzyme would be switching from polymerising NTPs to polymerising dNTPs.

The fact that present day DNA pols can work with RNA templates in my opinion hints that their main substrate might have once been NTPs. However, then thanks to ribonucleotide reductase you got these fancy new dNTPs and it turned out that they worked as a substrate too. Maybe the higher affinity was there from the start or perhaps it was all about some other advantages (e.g. evading host defenses). So then, over the next 3.7 billion years or so DNA pols further evolved to make use of dNTPs more efficiently, losing their affinity to NTPs almost completely.

..I think "true" reverse transcriptases are a much later evolutionary invention that happened after dsDNA genomes were already a thing. RTs were a new way to avoid them host defenses. Do any contemporary RTs work with U-DNA? I know arcaheal DNA pols generally don't..

..As far as I know, no retroviral genome has ThyA or ThyX for de novo dTTP synthesis. Many dsDNA phages (Caudovirales) have such genes though and these branch near to the root of the relevant trees..

You may be interested in the paper here:
http://www.jbc.org/content/275/33/25523.full.pdf . The authors find that single mutations in an RNA-directed RNA polymerase can reduce selectivity for an NTP substrate to the point that there is no significant preference for NTPs over dNTPs. However this comes at the cost of very much reduced rate of polymerisation.

also, do you think the OP is asking why viruses would ever use RNA instead of DNA?

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Formation of peptide bond..?
Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by condensation in cytoplasm in the presence of water ?

The condensation is not done in water alone - the enzymatic function of the ribosome plays the essential part here. And in the active center of the ribosome where the formation of the peptide bond takes place, no water is present, only the growing peptide chain and the single amino acid (bound to the tRNA). See this schematic image from the Wikipedia:

If you make x-ray crystallography, this looks like this (from here). You can see that the tRNA with the unbound amino acid is actually inside the ribosome and protected from the outside:


text:
Significance of synthesis of D-glucose in plants..?
why plants can only synthesize D-glucose why not L-glucose along with D glucose. I know it very well that plants have only enzymes which can synthesize D-glucose but Why not they have enzymes which can also manufacture L-glucose. So that we could have mixture of L and D glucose molecules? What is the significance of synthesis of only D-glucose by the plants ?

You need only one set of enzymes to make and to metabolize glucose when you choose one isoform. This saves energy for making the enzymes.

@Chris has explained the advantage of using one isomer - why do you think that it would be advantageous to synthesise and use both?

Synthesis from chemicals in organisms is fundamentally different from laboratory synthesis of chemicals. In the latter, more than one chemical species or other unwanted byproducts are usually formed, whist living organisms use enzymes, that are often stereo-specific. This means that they usually can bind, in the case, produce, only one stereo-isomer.
To produce both forms they would need double sets of enzymes.
It makes sense for animals, bacteria, protozoa, etc. to digest whatever comes, so less specific enzyme, but since plants will only access the glucose they themselves formed use of a stereo-specific enzymatic pathway probably enables a more efficient metabolism.

D-Glucose and L-Glucose have similar names only because we humans decided that's how we should name sugars; they have as much in common as, for example, D-Glucose and D-Allose (one chiral bond is different).
So, in essence, organisms don't synthesize L-Glucose for the same reason they don't synthesize D-Allose: they have no use for it. Its similarity to Glucose is only coincidental, it is different enough that, biologically speaking, it's a totally different molecule.


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In chromatin, what are the differences among states, interactions, and structures?
I am new to the study of chromatin, and I am trying to understand what people mean when they write about chromatin states, chromatin interactions, and chromatin structures.
What are the difference among these?
Is there someone available to explain them to me clearly?
Are loops interactions or structures?

Chromatin state refers to the marks (i.e. methylated DNA, histone modifications, euchromatin v. heterochromatin) found at specific loci and is often referred to as open (readily bound by DNA binding proteins, like transcription factors) or closed (inaccessible to most factors).
Chromatin interactions can include the binding of transcription factors and other DNA binding proteins, but is usually used to describe local and long distance functional contacts between two or more regions of chromatin. These interactions are generated actively through protein-dependent chromatin organization and passively via polymer physics and the nuclear environment.
Chromatin structures can refer to the actual molecular shape and composition of the DNA or to the molecular modifications found at specific regions of chromatin (e.g. heterochromatin, DNA methylation). It can also refer to the ordered compaction of mitotic/meiotic chromosomes.
Chromatin loops are structures that may act in promoting regulatory interactions. Conversely, chromatin interactions may induce looping.
Cavalli and Misteli, Functional Implications of Genome Topology, Nature Structural and Molecular Biology 2013


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Currency metabolites vs. current metabolites: What's the right term?
I have seen the two terms currency metabolite and current metabolite used interchangeably. Is there a consensus on which is the right term?

Currency refers to anything that is used in any circumstances, as a medium of exchange [1]. That's why ATP and NAD are considered as currency metabolites [2]. So currency metabolite can be used for any metabolite that has multiple uses in different reactions/pathways.
Current refers to something that is prevalent at the present time [3]. So current metabolite is used to refer a metabolite that is already available for a specific reaction/pathway and doesn't need to undergo supplementary transformations to fit for that specific reaction.
The same metabolite can be simultaneously a currency metabolite and a current metabolite for a specific situation.

References:

Wikipedia contributors, "Currency," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Currency&oldid=611672968 (accessed July 12, 2014).
Gerlee P, Lizana L, Sneppen K. Pathway identification by network pruning in the metabolic network of Escherichia coli. Bioinformatics. 2009 Dec 15;25(24):3282-8. doi: 10.1093/bioinformatics/btp575. PubMed PMID: 19808881.
The Free Dictionary by Farlex. http://www.thefreedictionary.com/current

I wonder if 'current metabolite' is not simply a mistake? The second usage does not sound idiomatic.


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How big can cold-blooded animals get?
It seems impossible to have reptiles the size of dinosaurs, just because they are really big! Did they have different systems of maintaining body temperature or maybe they weren't the exact type of animals that we today call reptiles?

Wikipedia http://en.wikipedia.org/wiki/Physiology_of_dinosaurs#Metabolism looks like a good place to start.

You should have a look to the correct vocabulary and concepts in order to describe organism intern temperature. This post will help you

It seems that giant turtles are not so cold as we used to think. They are too big to quickly lose the warm from metabolism, so they may be thought of somewhat homeotermic. Perhaps that's what happened to dinosaurs.

Answer is quite simple as from @Alan Boyd link. They are cold blooded and thus, can go out for hunt in cold, they need to stay put till they get some prey.
So, it mainly depend on the temperature of the outside, I found this interesting paper on relation of body sizes and latitude.

Body sizes of poikilotherm vertebrates at different latitudes
Maximum sizes of 12,503 species of poikilotherm vertebrates were
  analyzed for latitudinal trends, using published data from 75 faunal
  studies. A general trend appears which may be summarized by the rule
  "among fish and amphibian faunas the proportion of species with large
  adult size tends to increase from the equator towards the poles". The
  rule holds for freshwater fish, deepsea fish, anurans, urodeles, and
  marine neritic fish arranged roughly in order of decreasing clarity of
  the trend). In general the rule applies not only within these groups
  of families but also within single families. In reptile groups, the
  rule holds weakly among snakes and not at all among lizards or
  non-marine turtles. Possible explanations include an association
  between small size and greater specialization in the tropics; the
  possibility in poikilo-therms of heat conservation or of some other
  physiological process related to surface/volume ratio; selection for
  larger size in regions subject to winter food shortages; and an
  association between large adult size and high reproductive potential
  in cold regions. Other suggestions can be advanced, but all are
  conjectural and few are subject to test. Global size - latitude trends
  should be looked for in other living groups.
Cite: Lindsey, C. C., 1966: Body sizes of poikilotherm vertebrates at
  different latitudes. Evolution: 456-465

Now lets compare some of the largest cold blooded Animals:

Reptiles
Amphibians
Fishes (Pisces)

Reptiles:
The smaller size of Reptiles give them more agility to hunt andsave them predators but some times when they are top of food chain they can grow as giants.
Anacondas (Eunectes), gigantic snakes from South America, are undoubtedly the largest living snakes.
The largest species, the green anaconda (E. murinus), likely only rarely exceeds 9 metres (30 feet) in length; nonetheless,
persistent but unsubstantiated reports have been made of anacondas that are 12 metres (40 feet) long.
The reticulated python (P. reticulatus) of Southeast Asia and the East Indies has been recorded at 10.1 metres (33.3 feet).
Others:

King Cobra(Ophiophagus hannah) 5.5 meters (18 feet)
Keeled rat snake (Ptyas carinatus), at about 3.7 metres (12 feet).
Nile crocodiles (Crocodylus niloticus) 6 metres (20 feet)
American crocodile (C.acutus) 4–5 metres (12–15 feet).
Marine leatherback sea turtle (D.coriacea) 2.7 metres (9 feet)
Galápagos tortoise (Geochelone nigra) 255 kg (560 pounds).
Komodo dragon (Varanus komodoensis) 3 metres (10 feet)
Green iguana (I. iguana) 2 metres (7 feet)

Green Anaconda http://www.wallshq.com/wp-content/uploads/main/2013_01/green_anaconda-wide.jpg
Green Anaconda

Amphibians:
According to Wikipedia:

"The Chinese giant salamander (Andrias davidianus) is the largest
  salamander and largest amphibian in the world, reaching a length of
  180 cm (5.9 ft), although it rarely—if ever—reaches that size today"

Others:

West African goliath frog, 30 cm (12 inches) 3.3 kg (7.3 pounds)
Caecilia thompsoni 1.5 metres (5 feet)
Axolotl(Ambystoma mexicanum) 30 cm (12 in)

Chinese giant salamander

African goliath frog

Axolotl (Small 12 inch)
Fish:

West Indian Ocean coelacanth, (Latimeria chalumnae), is 80 kg (176 lb), and they can reach up to 2 m (6.5 ft)
African lungfish (Protopterus aethiopicus), 2 m (6.6 ft) and may weigh as much as 50 kg (110 lb)
Ray-finned bony fish (Actinopterygii)
Ocean sunfish (Mola mola) 4.3 m (14 ft) from fin-to-fin, 3.1 m (10 ft) in length
and weighed about 2,300 kg (5,100 lb)
King of herrings or oarfish (Regalecus glesne) 6 m (20 ft)( The longest
known king of herrings, which was hit by a steamship, was measured as 13.7 m (45 ft) long)
Bowfin (Amia calva)  109 centimetres (43 in) in length, and weigh 9.75 kilograms (21.5 lb).
European conger (Conger conger) 3 m (10 ft) and a mass of 110 kg (240 lb)
Lancetfish (Alepisaurus ferox) 2.1 m (7 ft) long and can weigh up to 11 kg (24 lb)
Houndfish (Tylosurus crocodilus) 1.5 m (5 ft) and a weight of 6.35 kg (14.0 lb)
Giant Tigerfish (Hydrocynus goliath) 1.5 m (5 ft) and 50 kg (110 lb)
Golden Dorado (Salminus brasiliensis) 1 m (3.3 ft) in length and weigh 31.4 kg (69 lb)
Tambaqui (Colossoma macropomum) 1 m (3.3 ft) and 32.4 kg (71 lb)
Giant barb (Catlocarpio siamensis) 3 m (10 ft) and a weight of as much as 300 kg (660 lb)
Muskellunge (Esox masquinongy)  1.8 m (6.0 ft) and 45.4 kg (100 lb)
Atlantic tarpon (Megalops atlanticus) 161 kg (350 lb) and length is up to 2.5 m (8.2 ft).
The Atlantic cod (Gadus morhua) grows to 2 m (6.7 ft) long and 96 kg (212 lb)
milkfish (Chanos chanos) 22.7 kg (50 lb) and 1.84 m (6.1 ft) long
Electric eel (Electrophorus electricus) 2 m (6 ft 7 in) in length, and 20 kg (44 lb)
Opah (Lampris guttatus) 2 m (6.6 ft) in length and weigh up to 270 kg (600 lb)

Source: http://en.wikipedia.org/wiki/List_of_largest_fish
Source: Britannica.com

Mola mola

Oarfish

West Indian Ocean coelacanth

Bowfin

wow great answer bro really elaborate , to the point and deep answer

@Nick_Tsaftaridis: Can you mark as answer if it is correct?


text:
Why are neutral [sterile] female flowers present in inflorescences when they are reproductively incompatible?
In many compound and special inflorescences like spadix and hypanthodium there are sterile female flowers along with male and female fertile flowers and are often present in between male and female flowers, but what is their need in an inflorescence?

As far as I know inflorescences are meant for perpetuation of a plant's race by pollination of female flowers by the male gametes [pollen grains which bears vegetative and reproductive cells].
I know the infertile female flowers of the spadix inflorescence possess some surface area and this area would get some of the pollen grains which are coming in to the inflorescence, and eventually a sum of pollen grains might go in vain.
What is the need of sterile female flowers when fertile ones are present in it?

if not the answer can any one suggest me another site where i could find this answer

Sterile flowers enrich pollination quality by promoting pollen export and import, while limiting the mating costs of geitonogamy associated with large fertile displays.

You are actually looking for this paper: Link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523656/
Sterile flowers increase pollinator attraction and promote female success in the Mediterranean herb Leopoldia comosa

Key Results
The presence of sterile flowers almost tripled pollinator attraction,
  supplementing the positive effect of the number of fertile flowers on
  the number of bees approaching inflorescences. Although attracted bees
  visited more flowers on larger inflorescences, the number visited did
  not additionally depend on the presence of sterile flowers. The
  presence of sterile flowers improved all aspects of plant performance,
  the magnitude of plant benefit being context dependent. During weather
  favourable to pollinators, the presence of sterile flowers increased
  pollen deposition on stigmas of young flowers, but this difference was
  not evident in older flowers, probably because of autonomous
  self-pollination in poorly visited flowers. Total pollen receipt per
  stigma decreased with increasing fertile display size. In the
  population with more pollinators, the presence of sterile flowers
  increased fruit number but not seed set or mass, whereas in the other
  population sterile flowers enhanced seeds per fruit, but not fruit
  production. These contrasts are consistent with dissimilar
  cross-pollination and autonomous self-pollination, coupled with the
  strong predispersal inbreeding depression exhibited by L. comosa
  populations.


text:
What is the name of this plant?
This plant was found growing in Germany. I have never seen it before, reverse Google image search did not help either. Can you help me identify what type of plant this is?

Thanks, looks like it is something like this:
http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034
Related question:
https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610

Nice pictures! Thanks also for getting pictures of different plant parts.

Also see similar question on GL. (Highest voted three-word answer on the whole site.)

Shouldn't this question be moved to GL. As per this discussion on meta http://meta.biology.stackexchange.com/questions/151/plant-identification-questions

@PatrickB see this question: Is it a good idea to have an identical topic (plant identification) on both GL and Biology? I'm coming to the conclusion that plant identification questions can be asked on either site, but for different reasons.

technically these photos are very good.

This looks like some species of Phytolacca to me.
It's possibly Phytolacca americana, which is native to the US (in fact it's an enthusiastic 'volunteer' in my garden) but naturalized in Europe.
If you still have any in the ground, once they ripen, the berries are intensely purple and can be used as dye (or even eaten?)

Mark A. Nienaber & John W. Thieret. Phytolaccaceae.  In: Flora of North America Editorial Committee, eds.  1993+.  Flora of North America North of Mexico. New York and Oxford. (link goes to entry of P. americana)

Seems like it is an invasive species that can prevent others from growing.

It certainly grows very weedily here!

Oreotrephes You have a garden, therefore you should get over to GL now and then. =)

It is a Phytolacca, but not americana, because the flowers stand upright. P. americana has hanging flowers.

It is Phytolacca acinosa because the flowers grow upwards and the fruits are ribbed. Phytolacca americana has downward pointing flowers and smooth fruits.


text:
Is there any size limit to the amount of information a human (or other) brain can hold
Im not sure how this would ever be tested but is there a limit to how much the brain can 'hold' before it reaches capacity ?
I guess this could also be interpreted in terms of memory, as how well some one remember something before reaching capacity / forgetting 'old' memories to make way / space for new ones.

Yes. The brain has finite size. You can't keep an infinite amount of information in a finite space.

Yes, there is a limit:

Despite the impressive complexity and processing power of the human brain, it is severely capacity limited [1].

Human brain has 78.82– 95.40 billion neurons [2] and about $3.6 \cdot 10^{14}$ synapses in the cortex [3]. We shouldn't worry about running out of space, because neurons connect with each other to exponentially increase brain capacity to about 2.5 million gigabytes as Paul Reber, professor of psychology at Northwestern University claims for Scientific American [4]:

Each neuron forms about 1,000 connections to other neurons, amounting to more than a trillion connections. If each neuron could only help store a single memory, running out of space would be a problem. You might have only a few gigabytes of storage space, similar to the space in an iPod or a USB flash drive. Yet neurons combine so that each one helps with many memories at a time, exponentially increasing the brain’s memory storage capacity to something closer to around 2.5 petabytes (or a million gigabytes).

References:

Marois R, Ivanoff J. Capacity limits of information processing in the brain. Trends Cogn. Sci. (Regul. Ed.). 2005 Jun;9(6):296-305. doi: 10.1016/j.tics.2005.04.010. PubMed PMID: 15925809. Full text available on http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf
Azevedo FA, Carvalho LR, Grinberg LT, Farfel JM, Ferretti RE, Leite RE, Jacob Filho W, Lent R, Herculano-Houzel S. Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. J Comp Neurol. 2009 Apr 10 513(5):532-41. p.535 right column top sentence. Via Bionumbers http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106322&ver=4
Roth G, Dicke U. Evolution of the brain and intelligence. Trends Cogn Sci. 2005 May9(5):250-7. p.253 right column 1st paragraph. Via Bionumbers http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106138&ver=2
Paul Reber. What Is the Memory Capacity of the Human Brain? Scientific American. Apr 2010. Available from http://www.scientificamerican.com/article/what-is-the-memory-capacity/. Accessed 12.07.2014

amazing answer thank you


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What happens once a brain is full?
I just read the answer to this question, and it got me thinking...
If the human brain (or any other brain) has a finite amount of storage, what would happen once the brain has taken in its maximum amount of information?
This is, or course, assuming that the individual can live long enough to acquire that much information.
I would take a guess that just like how we forget things all the time, the new memories would "override" some older ones.
Has there been any research or hypotheses on a brain's behavior once the its storage has maxed out?

It's very likely that memory is "lossy" and holographic, such that you can keep adding more information indefinitely, but retain it with less and less accuracy.
Memory isn't a digital storage system with X gigabytes of capacity, and the inputs to memory aren't neat little packets. What we remember are a web of associations and patterns. Vastly oversimplified, we group similar memories together into a baseline, and remember the deviations from that.
If you walk the same route to work every day, you take in a huge amount of information the first few days: stretches of residential buildings, cars parked on the street, portions of curb painted red, trash in the gutters. In successive days different cars will come and go, front yards will get overgrown and trimmed, etc, but these details get mixed in with what you saw the first few days into a blurrier and blurrier sort of average. Trillions of impressions from hundreds of days take up very little more capacity than the first day did, and still tell you what you need to know about the route.
Imagine that there's a particular green car of common make and model, that was parked in front of a certain house about 3/4 of the time for the first hundred days you walked the route. Your memory reduces this to something like "green car usually along here somewhere". If the green car stops parking there, you'll probably notice "green car not there today" because that's a contrast to the common case that you've memorized. But if a week goes by with no sightings of the green car, it's very hard to remember which day you last saw it, because you don't remember individual sightings. (I actually had this happen to me with my own car; I discovered it stolen on a Wednesday and could not for the life of me recall whether I'd seen it on Monday or Tuesday even though I'd walked past the spot it should have been parked both days.)
As you remember more things, you remember them in less and less detail; you can't remember if you've been to New Orleans once or twice; you can't remember which memories were from your first trip to Las Vegas or your second, etc. So the brain never becomes full, it just becomes fuzzy.

Three possible mechanisms are mentioned in the first referenced article [1]:

Attentional blink - the failure to detect a (visual) stimulus [2].
Visual short-term memory - non-permanent storage of visual information over an extended period of time [3].
Psychological refractory period - the period of time during which the response to a second stimulus is significantly slowed because a first stimulus is still being processed [4, 5].

References:

Marois R, Ivanoff J. Capacity limits of information processing in the brain. Trends Cogn. Sci. (Regul. Ed.). 2005 Jun;9(6):296-305. doi: 10.1016/j.tics.2005.04.010. PubMed PMID: 15925809. Full text available on http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf
Wikipedia contributors, "Attentional blink," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Attentional_blink&oldid=615277943 (accessed July 12, 2014).
Wikipedia contributors, "Visual short-term memory," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Visual_short-term_memory&oldid=508372290 (accessed July 12, 2014).
Pashler H. Dual-task interference in simple tasks: data and theory. Psychol Bull. 1994 Sep;116(2):220-44. PubMed PMID: 7972591.
Wikipedia contributors, "Psychological refractory period," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Psychological_refractory_period&oldid=603184270 (accessed July 12, 2014).

I'm not sure this actually answers the question. It was about storage capacity, not processing capacity.

This answer only talks about short-term aspects, while the original question is about long-term perspectives, I think.

I realize that this answer doesn't really answer the question I had. The sources seem to be talking about an overflow of information at a single time rather than taking in over the long run. However, I may just need more explanation.


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Is there a correlation between total neurons and intelligence?
Thanks for looking.
First off, I am not a biologist, just a curious layman, so I apologize in advance if this isn't a "good" question.  Please don't downvote me into oblivion.
I read today that the human brain has about 100 billion neurons and that got me wondering: is that number pretty standard for everyone or does someone like say,
Einstein, have many more neurons than this daft poster.
Question
Is there a correlation between total neuron count and intelligence, or does intelligence depend more on the way neurons are used--or some other factor like previous experience--rather than their total count?
Can this question be answered?
There are two very valid points-of-view posted as answers below, but it sounds like we simply don't have a solid answer to this question at this point in time, so I hesitate to select a "correct" answer.

See this too: http://skeptics.stackexchange.com/q/2948/19552

@Cornelius--Thanks.  I wasn't aware of that subdomain of SE.  Although, is it really the same question?  It seems like more neurons would equal more brain mass.  I truly don't know--not trying to be sarcastic or anything.  Thanks again.

@Cornelius--One other thought--if what the OP says on that post is true, it would seem that mass has no correlation to intelligence and, by extension, maybe neuron count doesn't either.  Wonder if that means we all have the capacity to be an Einstein?

somewhat related what is an effective metric for the complexity of a neural net / [cogsci.se]

we can't measure no of neurons precisely 2) we don't know exactly what "intelligence" is 3) walking is more difficult for brain than solving riddles (https://en.wikipedia.org/wiki/Moravec%27s_paradox)

Totally agree with point 2 of @Mithoron comment.

There are an estimated 100 billion neurons within the human brain. In general a minor variation in the number of neurons should not effect individuals too much, however when there is a more significant loss, such as brain injury or in some forms of dementia cognitive abilities do decline. So in this sense yes the number of neurons does relate to intelligence. However this variation is not what accounts for general variation of intelligence in the population.

I know of no correlation between number of neurons in cortex and intelligence. This question is fraught with controversy because there has been very little work on it but much speculation. Some have suggested that the connectivity between neurons is what is important rather than the number which is logically possible but remains to be supported by definitive evidence.

Unlike a computer, the speed at which any brain can perform a computation is related to the number of synapses it goes through. This means fewer synapses in series correlate with decreased reaction time.
An example of fewer neurons correlating with a decrease in reaction time is exemplified in sensory neurons. All sensory nerve cell bodies are all located in the dorsal ganglia of the spine. Only projections from single nerve cells here reach our tissues. Furthermore, it's only in ganglia, nuclei, and the cortex that we see additional nerve cells. This is because each nerve cell in series introduces latency.
Latency in our sensory and motor circuits is very important to survival. Our intelligence is limited by a pressure to have a desirable reaction time. Reaction time does correlate intelligence. This is why tests of the sort are timed.
There is another factor in intelligence relating to number of neurons: An increase in grey matter means an increase in white matter. There has been some speculation that humans have nearly reached the limit of our cognitive ability, as our ability to store white matter has been reached.
We seem to be occupying the intelligence Goldilocks zone where reaction time, energy consumption, white matter are all in near optimal balance. It's the balance of these things, the sophistication of the circuits themselves that determine intelligence, not neuron count.
Here's a news link about running out of room for white matter
Here's a study which correlates perception time with reaction time

There is perhaps a trade-off between speed and functional complexity, since synapses are the sites of 'learning' and signal processing, by combining or subtracting, or applying conditional logic to different inputs to the next neuron in a pathway. We have many different neural pathways whose form suits their 'job', carrying out very different tasks - the anatomy of a reflex pathways looks nothing like a visual info-motor control network.
The nervous system is fascinating and curious!

there is no question there is a rough correlation between neuron count and intelligence capability in a general way from looking at the biological species "spectrum" outside of humans. see wikipedia list of animals by number of neurons. eg in wide differences such as comparing insects vs primates etcetera. there is also a rough correlation of neuron count with body mass and total cell count in animals. however within a single species, small variations in neuron count probably do not have much effect on overall intelligence. also it is known that homo neanderthalensis, the ~30k yr precursor to [homo sapiens] had a larger brain cavity and therefore presumably more neurons but apparently less intellectual capacity than homo sapiens, possibly one factor in its extinction due to competitive evolutionary pressures. even various gorilla species have larger brain mass and conceivably correspondingly larger amounts of neurons (under a rough assumption that neuron density per mass would not vary strongly).
it is also thought that brain size has been affected by evolutionary pressure wrt smaller skull size which has to comfortably fit through the birth canal as a constraint. another aspect to study is the enteric nervous system in the human which has a large number of neurons but does not seem to exhibit a large measurable "intelligence" in the classic sense of guiding the animal behavior, but conceivably uses significant processing to manage gastrointestinal control.
another aspect of the question to consider: programmed cell death in the developing nervous system. large numbers of neurons die during normal natal development in "critical windows" and this seems to show that biologically, total number of neurons is apparently not a key measure or controller of intelligence (otherwise evolutionary pressures would tend to decrease this). the nervous system appears to grow "extra" neurons more than "necessary" for smooth functioning of the human organism.

Homo neanderthalensis was not an ancestor of Homo sapiens. It is discussed, if H.n. is a sideline of the H.sapiens line. They lived around the same time. See here for some details.

ok good pt; however this all still applies even if neanderthalensis was a relative. quoting the start of your article "There is some debate as to whether they were a distinct species of the Homo genus (Homo neanderthalensis) or a subspecies of Homo sapiens." another funky point from "how has our brain evolved": "With some evolutionary irony, the past 10,000 years of human existence actually shrank our brains." thought to be due to decreased nutrition.


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Is it dangerous to eat a mutated eggplant descended from a radioactive ancestor?
What is the risk, if any, associated with eating a 100th-generation mutated eggplant derived from a radioactive ancestor?
In another word, is that possible that organic toxin will be produced by the mutated plant and is it a good idea to plant it in America? These plant seems very beautiful to me! Ha Ha
Note: The descendant eggplant is not radioactive.
Motivation: There are many mutated eggplants around Japanese power plants.

If it is not radioactive, why should it be dangerous? Mutations are occuring always and we also introduce changes in plants by selective breeding. Assuming that no toxins are produced, I would say there is no risk about these plants.

What mutations happened?

@Chris non-radioactive plants can be dangerous for many reasons. Toxins, pharmacology, for example. Without more information about the plants, we can't really answer this question.

@Articuno That's why I wrote "assuming no toxins are produced"...

That doesn't add any info though. That's like saying "assuming there is no risk about these plants, I would say there is no risk about these plants." I was answering your question about "if it is not radioactive. .."

@Articuno - But people complaining about genetically engineered food already, i will be surprised if that anything is not much severe than the normal genetic modified plant...

@Chris - REad the above comment

@user5479 You mean about genetically engineered food? Actually all our main food plants are modified since we settled some 8000 years ago. Until very recently this was done by selecting and breeding but essentially this modified the plants, too. So I don't see a reason to panic about genetic modifications when they are tested and safe.

@Chris - I mean terrorist could modify our food possibly

@user5479 Of course this would be possible, but how likely is that? That would first need the expertise to make the changes, than they need to propagate the plants to cause widespread poisoning. And when it is detected, the counter measure is rather easy: Discard all plants which might be contaminated. Packing a car with explosives is more easy and brings more fear, I would say.

While it's always possible that a mutated eggplant will produce a new toxin, this is very unlikely. I don't know how much higher the mutation rate is near Fukushima than in general but the difference can't be huge. Even if it's, say, 5 or 10 times higher than normal (I'm making up these numbers), the risk is still tiny. Actually, plant breeders sometimes use radiation to produce more variety to work with and we don't worry about that.


text:
Book recommendation on mammal (or just primate) behaviour, especially in relation to child-rearing
I have a growing frustration with the lows 'new-age' parenting is reaching, along with asininity of so much of our public schools' (and summer camps') philosophies and policies in relation to our kids. Whatever the implications, this has continually lead me to the thought of

what the natural precedent is for how primates (or other mammals) raise their young, collectively or otherwise -- how they're guided, rewarded, chastised, and conditioned.

May someone please recommend a book that delves in to some of this? (Humans don't necessarily have to enter the picture, but something that does compare and contrast with the human condition would be a bonus.) (Preferably not a text book, but, by all means, please recommend those too.)

Please don't fall into the other new age fallacy that states that natural == good. Rape is perfectly natural for example (just look at cats) as is incest (most mammals) and war (chimps for example). That something is 'natural' or the way it is done by a different primate in the wild is no indication that is is a good approach for raising the young of our species. It might be, just not always.

Suggested Reads:
Evolutionary Psychology
By Lance Workman, Will Reader
Evolution of Human Behavior: Primate Models
edited by Warren G. Kinzey
Social Behaviour of Children: A Cross Cultural Assessment
By Ralph E. S. Tanner


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Regarding signalling pathways
Do all signalling pathways have something that can inhibit them? If the signal pathway is benefitial  and it is inhibited would the inhibitor be caused by a biological problem?  Are all inhibitors controlled by some subcellular  mechanism?

Do you think about "artificial" inhibition or an inhibition that occurs naturally in the cell?

There are some inhibitors in the cell, which have specific effects on signal transduction. These are mostly second messengers (like cAMP, cGMP, calcium ions,  inositol 1,4,5-trisphosphate and others), which are then able to diffuse relative fast to other proteins. There they can either amplify a signal or cause inhibiting processes to start which then terminate the activation of the signal transduction cascade.
The problem is that these inhibitors that they work unspecific in their inhibition and termination. Signal transduction is tightly controlled as they directly influence the expression of various genes.
A lot of the proteins in these cascades are kinases which are activated upon phosphorylation and then carry on by phosphorylating the next step of the cascade. The activity is stopped by phosphatases which remove the phosphorylations from the kinases and thus inactivate them until the next signal is passed down the cascade. It works like in this figure (from here):

Specific inhibitors for single proteins in the signalling cascades are available as drugs against cancer. Since these signalling cascades regulate gene expression including cell cycle control, they are important targets for dysregulation in cancer. A numer of kinases in the MAP kinase pathway for example are mutated there and constantly active. The so called small molecule inhibitors bind to the protein and inhibit the kinase activity, preventing a permanent signal. See this article for more information:

Targeting cancer with small molecule kinase inhibitors

"There are no inhibitors of signal transduction occuring in cells." Are you talking about small molecules? There are plenty of specific inhibitors of signal transduction, they just happen to be proteins for the most part, and not all of them are phosphatases. Each signaling pathway is very tightly regulated by a variety of mechanisms, including second messangers (which are technically small molecules).

Ok, that's right. I was thinking about molecules like the small molecule inhibitors (like all the kinase inhibitors in clinical trials or already licensed like vermurafenib) which specifically inhibit one kinase. And there is no analogon to these in the cell to my knowledge. I will make my answer more precise.

Could a cell be considered like an EXTREMELY complicated subcellular and intracellular signal processing 'machine'? Where any signal pathways are tightly regulated..

If you like this, why not? A cell is a extremely complicated mechanism...


text:
Regarding apoptosis and inhibitors
If there is an apoptosis shut-off mechanism of any kind, one could call it a null-apoptosis mechanism.
If this is possible, could there be a null-apoptosis inhibitor? Something that inhibits an apoptosis inhibitor?

Apoptosis is very tightly controlled for obvious reasons. Setting it off without proper control would result in the uncontrolled loss of cells. Apoptosis is one of the major pathways which are either mutated or shut-off in cancers, preventing the body from eliminating malingnant cells. These two papers are interesting in this context:

Apoptosis: A Review of Programmed Cell Death
The role of apoptosis in cancer development and treatment response

In this context it makes no sense to have a shut-off mechanism once the apoptosis cascade has started. It is only set off when there is a real reason (and is well controlled), so I don't think there a "null-apoptosis" mechanism. It would of course still be possible to artificially make substances, that inhibit parts of the activation cascade. But besides for apoptosis research I don't see any use for it. There is actually some research going on to find out how to activate apoptosis again in cancers.

What about 'something' that could inhibit some pathways or mechanism that is about to shut down or turn off the apoptosis mechanisms? An Apoptosis Inhibitor Inhibitor ( if you could call it that)..

There are mutations or dysregulation occuring in cancer which actively shut down apoptosis. You could of course think about designing molecules which could do the same. But to my knowledge they are not occurring naturally.

Could DNA-polymerase or something like this correct any genetic mutations or genetic 'mis-configurations' in a cell that may be causing the apoptosis mechanisms to be shut off?

I don't think the DNA polymerase could do that, as this enzyme is only directed to promoters which are active. When apoptosis is shut of due to epigenitic silencing or mutations, that is usually not reversible by the cell. There is research being done if this can be reversed in cancer cells to promote apoptosis there and get rid of the cells.

If a cell has had its apoptosis mechanism shut down and it then reproduces or is 'forced' to reproduce would its daughter cells develop in a way where their apoptosis mechanisms malfunction? If this is so would this develop a cancerous group of cells?

This is exactly what happens in cancer. To be able to grow and metastasize the tumor needs to overcome apoptosis. Have a look at this and this article.


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Do ants feel acceleration?
The organ we have to provide us with current acceleration information is quite complicated. Because an ant queen didn't seem to notice when I picked up the bottle she was in, I have a suspicion that ants don't really care about acceleration and therefore can't tell where it's up and where it's down.
Am I right? If not, how do they sense acceleration?

can you explain what you mean by The organ we have to provide us with current acceleration information is quite complicated? its confusing sentence.

The organ is complicated. - talking about human organ that detects acceleration.

If you snorkel with weights on you find that the buoyant force of water nearly matches the pulls of gravity. It's easy to become disoriented even though we are quite sensitive to the acceleration of gravity. Ants may have a similar issue because their mass is very small and the acceleration of gravity is unlikely to cause them injury. But an insect which carries large loads and walks probably has an acute sense of gravitational acceleration, even if it's tuned in a different way.

Sorry, I misinterpreted your question. I have removed my answer, which is now available in two different question.  http://biology.stackexchange.com/a/19678/8186 and http://biology.stackexchange.com/q/19677/8186

According to Clinical Neurophysiology of the Vestibular System
 By Robert William Baloh, Vicente Honrubia, page 8, the vestibular system (animals' "accelerometer") is as old as 600 million years and is present in invertebrates.
I assume (without a precise source) that this is especially important for flying insects (after all, accelerometers were engineered for flying machines in the first place!) and that the ant didn't respond because the acceleration to which you submitted it was not deemed harmful.

I hope somebody will find a research which proves that. Thanks for your input.

You can find a lot of data searching for "flight control" for insects. Concerning the decision whether to react or not to an acceleration input, it is probably to be found in cognitive science publications. Maybe you should ask another question about it, as it is not linked with ''feeling'' acceleration but to cognitive decision-making.


text:
Upon drinking water for the first time in a long time, why do I sweat?
If I don't drink water for a long period of time (e.g. 10 hours), as during fasting, and then I break the fast by drinking water, I start sweating. Why is this?

During the time when you are not drinking water, you still lose some water to sweating and urine. Especially in hot climates, sweating is an important function of the body to maintain the body temperature in the desired range. If this water is not replaced, the body gets dehydrated. This induces a reaction which reduces the activity of the "body thermostat", in order to tolerate a higher body temperature without excessive sweating. This, in turn, helps to maintain the fluid balance of the body.
When you start drinking again after this the dehydration period, the body starts sweating to regulate the body temperature again, since the loss of water is no longer critical. For a detailed discussion, including further references, please see:

The effect of water temperature and voluntary drinking on the post
rehydration sweating

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


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How to recognize a conserved motifs of the protein
I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids sequence of this protein. But if I know this protein from another organism and the structure of this protein is known, then I can compare both of the sequences and conclude something, right? what I mean, is that there is no specific sequence corresponding to, for example, helix-two- turn-helix motif, and that I can take this sequence, check if my protein has it and say that there is helix-two- turn-helix motif or not. I can do this only by comparison to the protein which structure is already known, right?

Yes. You have to know a sequence motif (another example for that would be transcription factor binding motifs) and then you can do sequence comparisons. They will give you a clue, what structures might be present, but you will still have to do some crystallography to make a definite proof. But it will give you a direction. The other possibility would be to look at homologous proteins from other species where more is known about the structure if possible. Sequence comparisons will give you here a more accurate picture.

Thank you. 'You have to know a sequence motif' -- do you mean that, for example helix-two- turn-helix motif has the specific  the same for every protein sequence? or that I need to identified that motif in homologous protein and then check if I have the same sequence in my protein?

I have done this for helix-loop-helix motifs. Here we aligned one known protein to a number of different species. And we were able to identify some motifs that were conserved between species while other regions were not conserved. I think homologous proteins would be better, but you can also try with other helix-turn-helix proteins.

It seems to me that you're asking about homology modelling. In that case, yes you need to compare your protein of interest to a protein (or proteins) of known structure. Homology modelling in a nutshell includes three (four?) steps: template identification/template alignment, modelling, quality assessment.
You start with finding a template for your modelling. This is usually done by sequence alignment, for instance BLASTing. Preferably you use multiple sequence alignment which more sensitively aligns conserved regions. You then want a template with as high sequence identity as possible (above 50 % usually produces models with about 1 Å RMSE [1] in main chain atoms. Avoid less than 30 % where modelling errors rapidly increase.)
There are then a number of different modelling strategies (wikipedia). But basically, they all aim to predict the structure of the conserved protein core as well as possible (which usually is what you're really interested in). Peripheral amino acids are more dynamic and more prone to evolution and are therefore more difficult to predict. Then, most importantly, you assess the quality of your model. This can be done by calculating violations of statistical potentials or physics based conformational energies (or using more advanced methods like multivariate regression methods). As in all modelling, this really is a most crucial step because prediction with a poor model is misleading and utterly useless.
If you don't find any template you could resort to the exciting field of De novo protein structure prediction, where the aim is to predict the structure from the amino acid sequence alone. I am not very familiar with their methods, but de novo prediction is hard (!). I don't remember any exact numbers but the number of conformations in a normal sized protein is astronomically large, which leads to great algorithmic and computational challenges. Additionally, without any reference sequence the model assumptions are greater than those of homology modelling. Although, I have heard that the field has been making great progress the last few years.

Edit:
It struck me that you might be asking about protein fold recognition as well. There exists a large number of different tools and methods for recognizing and locating protein domains using the amino acid sequence as input. Many of them are available as web servers. For instance phyre which uses the amino acid profile and predicted secondary structures to search structure libraries. Threading based methods like MUSTER. A number based on Hidden Markov Models (HMMs) also exist. For instance FISH which uses structure anchored HMMs.


text:
How to know if your breathing is normal?
Is it possible for a device to measure how much air we breathe in and out over the entire day and at what rate? I think if we have access to this data we can compare it across people.

it is certainly possible to make. might be clumsy to wear though.

What you are looking for is a spirometer. There are different types of spirometers serving different purposes like the Incentive spirometer and the peak flow meter. I would suggest that you go through the wikipedia page on it to get more info.

thanks, but then the most advanced spirometer seems to measure breathing only temporarily and not on-the-go i.e. complete day analysis when doing routine tasks. so i guess the state-of-the-art has not reached that level.

@user13107 Might be in development if the need arose but I am unaware of it.

Another possibility is K4 device and K4 device. Beyond spirometry it can measure other variables such as:

Pulmonary Gas Exchange (VO2, VCO2)
Breath by Breath Technology
Telemetry Data Transmission up to 1000m
Indirect Calorimetry
Integrated GPS System
Integrated Oxygen Saturation (SpO2)
Integrated 12-lead Stress Testing ECG


text:
To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)
I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y?
I searched of course Google and BLAST. There is no data supporting that this specific bacteria ever produced this protein sequence.
However, my thesis supervisor wants me to go deeper[1], but I don't know how to do it in silico in a way to offer a proper answer.
What I'm thinking of doing with the data at hand is to create a DB on localhost with all the versions of the protein listed in BLAST (I'm using ruby, not sure how can I fetch all this data in FASTA format yet, but I'll figure it out), and all the strains of the bacteria listed in BLAST and perform a fuzzy string matching.
That's like brute-forcing. After I have a possible score I can get the closest score of them all, study it a bit and then submit my answer.
Is there any other way to attack this problem in order to submit a proper, at least partially polished answer?
NOTE: I don't have access to any lab, any experiment must be performed in silico.
[1] My supervisor believes that IF this bacteria needed this protein it WOULD be able to to produce it at will without undergoing mutations. And since his level of dedication and knowledge revolving molecular biology is scary, it's kind of hard to believe that he is wrong.

I am coming from the wet lab - and my experience is that you can clone practically every gene into a fitting vector and express is in bacteria. You need the right regulatory sequences (promotors and so on), but it is possible. The question, if this protein is produced in big amount and if it soluble is something different. Also many proteins are modified posttranslationally which is something bacteria cannot do.

Hello Chris. I'm not interested in to cloning anything but thanks for the info.

I understood that. I simply wanted to add some comment on the practical side of this problem, this might help you as well?

Of course @Chris, I will mention to my paper that it's possible to achieve the wanted result with cloning. Without your comment I wouldn't had that extra paragraph, which will make my paper better anyway :-) ... So thank you again!

To be clear: You want an algorithm to match if the given fasta can be produced by the bacteria genome?

@DevashishDas No, I already have a gem with a list of fuzzy matching algorithms. I'd like to know if there's any other approach worth pursuing except that. NOTE: Any comment on the algorithms would be good also: Hamming, Jaro, JaroWinkler, Levenshtein, LongestSubsequence, LongestSubstring, PairDistance, Sellers. These are the ones supported by the library I'm going to use.

Are you talking about whether the Bacterium naturally produces a protein or whether it could express a particular protein?

@JackAidley Whether if needed it could express a particular protein (at any quantity).

you can predict an ORF from DNA/RNA sequence but you cannot be sure if the protein is produced. You can either do LC-MS to see if signature peptides are produced or use molecular bio experiments as Chris suggested. You can also tag your sequence with GFP and see if it expresses.

you can download proteomics data (if available) for your bacteria and search for the signature peptides that your protein-x is likely to produce.

If you're just looking at whether a protein can be expressed, you might be misunderstanding your supervisor. The set of proteins needed by a given bacteria is a tiny, tiny subset of the set of proteins that bacteria is capable of producing, provided the gene coding for the protein is provided to the bacteria. If instead you're curious about whether a bacteria can express a given protein without any changes to its genome, there are plenty of proteins that are coded for in the genome but only expressed under specific circumstances. I'd look into promoters if I were you for more info on that

Your problem will finally boil down to searching your sequence in the Blast databases. Performing Blast seems to be probably the best way to find out if your bacteria has that specific protein expressed or not. If you could not find it in the nearest species using Blast, then try running PSI-BLAST, which would return you distant homologs, by which you can see if your protein is expressed in the other bacterial species.

I'm on to something using blast (I dropped out the idea of writing my own script to do this as soon as I played around with BLAST). I know that E. Coli can produce my protein (it's documented) at protein level. I couldn't find a perfect match thought, I've found a 74% positive match. Then searched about Desulfovibrio and found a 75% positive match (for a specific strain). I think it's enough, I can't take the risk to answer the question in a definitive way but, it's enough data to give some food for thought and possible direction. Comments are more than welcomed! Ty!


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How does someone with red-green colorblindness see yellow on a monitor/television?
I recently watched the video This Is Not Yellow explaining how red, green, and blue pixels can be used to create images of all other colors. Since yellow is created with red and green pixels, how is a person with red-green colorblindness (me, for instance) able to perceive yellow on a monitor?

Below is a summary of the information found here and from how Enchroma glasses work (although, I've tried the glasses and the effect is too subtle for me to wear them regularly).
Human color vision works because there are three different color-sensitive receptors called cones that detect short-wavelength light (bluish), medium-wavelength light (greenish), and long-wavelength light (reddish). The charts below show the sensitivity of these receptors in people with different genetics.

Chart taken from Color Art and Science, edited by  Trevor Lamb and Janine Bourriau
The bottom chart, marked (c), shows the sensitivities of eyes of people with normal color vision. Short-wavelength (blueish) cones detect a distinct patch of light while the medium- (greenish) and long- (reddish) wavelength cones overlap, but are still separated enough to reliably distinguish between the two color ranges.
The middle chart, marked (b), shows mild protananomaly or deutananomaly color blindness in which the color regions that medium (greenish) and long (reddish) cones react to are more overlapped than in people with normal vision. This can lead to trouble distinguishing these colors since the overlap causes both receptors to light up for more colors.
The top chart, marked (a), shows complete protanopia or deutanopia, where the long (reddish) and medium (greenish) receptors completely overlap in their sensitivity ranges. This can also happen if one receptor is entirely missing from the retina.
I was under the impression that all red-green color blindness was of the protanopia/deutanopia type, meaning that the yellow generated on a computer screen should look red because the green light wouldn't be activating any of the non-functional medium (greenish) cones. In actuality, I only have a mild protananomaly/deutananomaly, so my eyes are still sensitive to the differences between red and green light, just less so than normal people. The yellow I see may be subtly different than other people, but I can still differentiate.
Enchroma glasses work for mild colorblindness by filtering out light in the overlap region of medium (greenish) and long (reddish) cones. This creates more separation in the detection region of those cones, thus making some colors more distinct at the cost of blocking some light.

Normal people see color due to the bellow mentioned combination of red, green and blue:

But due to genetic factors, The graph Distorts:

Now,If consider the normal Color code for yellow:
Yellow = R(255) + G(255) + B(0)
Or in other words
Max. Red + Max. Green + no Blue = Yellow
That means even if you can see a little of Red and Green, you can still a little deeper or lighter shade of yellow.
So Summing it up in the images:

Normal

Red ColorBlind

Green ColorBlind

Blue ColorBlind
Source:
Coblis — Color Blindness Simulator
A quick introduction to colorblindness

What is the effect of having mutated green cones? Are they non-functional, of reduced sensitivity, or something else?

@MarkH: Can you ask it as a separate question?

@MarkH: Hey, hope my answer solved you query, if so, please mark this as answer.

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


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Which phylum appeared most recently
I'm aware that our earliest records of many major animal and plant phyla come from the Cambrian or Precambrian periods, and I'm also vaguely aware of some of the objections raised with general concept of phyla. With this in mind, I'm curious which of widely accepted biological phyla appeared most recently, and what evidence do we have of their relatively recent appearance?
I'm most interested in animals, but I'd also welcome any information about other organisms.

In my view, we simply don't have good enough data to answer this question. The fossil evidence is too sparse prior to the Cambrian and the evidence that we do have suggests that the phyla were already too separated. Meanwhile, the depth of time and the different lifecycles and circumstances of the species involved mean that any "genetic clocks" we might use are likely to be too poor at keeping time and, indeed, different attempts have delivered different estimates of the time of divergence.

Can you give an example of a widely accepted phylum which is itself a member another phylum (according to phylogenetic analysis)?

Actually, I've decided I was wrong about most phyla being clearly paraphyletic. I think it's true, but we don't have the direct evidence needed for many phyla. The Echiura and Spinuncula group inside the Annelida.

As far as I know there is no phylum which appeared after the Cambrian. Every discussion beyond that is close to speculation, as the divergence estimates of different studies vary significantly.
You might want to look into one of the resources mentioned below:

http://www.timetree.org/index.php
http://www.onezoom.org/

I didn't mean for my question to be exclude the Cambrian from consideration. If it's true that all phyla appeared during or before the Cambrian, I'd still like to know which phylum appears latest in the Cambrian.


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Turning publicly available genome data into proteins
I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller steps.
First, I downloaded a complete human genome from http://hgdownload.cse.ucsc.edu/downloads.html#human  There is a FASTA file for each chromosome.
Then, I wrote a java program which can convert FASTA DNA sequences into the appropriate amino acid chain.
Next, I made my program look for the "start" code (ATG) and "stop" codes (TAA, TAG, TGA).
So, now I have sequences of amino acids which might theoretically end up folding into proteins. But, before I start diving into protein folding, I wanted to try to verify that the steps I took so far were done correctly. I looked up some important human genes in an online database and found their amino acid sequences. I then searched through my program's data for those sequences and confirmed that they were there. However, the gene was in a different base-pair location than the database said that it should be in.
This led me to some questions, which, so far I have been unable to answer and hopefully people here will be able to help shed some light.

I know there are a lot of different publicly available genomes. Maybe the UCSC one that I downloaded is different from the one used by the gene database. How much does each genome vary from each other genome and in what ways do they vary?
In attempting to answer that first question, I was going to download a bunch of genomes from the 1000genomes website and do some comparisons, but I wasn't sure which files to download. Each of the files begins with either ERR or SRR and I'm not sure what that means. This is the folder I'm currently looking in ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/
Lets say I'm trying to model a white blood cell. How do I know which parts of the genome get turned into proteins for that type of cell?

Sorry if anything I said doesn't make sense. As I said, my expertise lies in programming, not biology/genetics.

I think that you need to be more specific than "I downloaded a complete human genome". Was this an entire genome sequence, or a set of FASTA sequences corresponding to predicted proteins?

An entire genome sequence. There is a FASTA file for each chromosome.

A comment on your third question: Which genes are expressed depends on the state of the cell, and this is especially complicated for immune cells. These can go through different state of activation which are all different. You can try to find data from gene expression experiments in such cells and use this data. Datasets are available in the "Gene expression omnibus".

You completely ignored Central Dogma of Life.
You haven't considered the RNA.

Devashish, I have a mapping from DNA codon to amino acid. I don't think I need to do anything with the RNA.  For instance, whenever I see the TGC codon, I map that to cysteine

Have you considered introns? Also, not every start/stop codon is transcribed.

As a general note, please don't ask multiple questions on a single post. In future, please split each question into it's own post instead. I have answered all three here since in this particular case, your questions are basically irrelevant since the main problem is a huge underestimation of the complexity of the task you are attempting. Good luck though!

which organism are you studying?

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are:

Genes (eukaryotic genes anyway) are spliced to produce mRNA, a process that removes introns and leaves only the exons. If you just translate the entire chromosome file you will get noise.

Splicing also changes the frame a gene is read in, you don't mention frames at all in your question but you can't work with sequences unless you deal with them.

Many genes (most even, in some species) are alternatively spliced. One gene can give rise to multiple protein sequences. Which one is produced at any one time can depend on a multitude of factors ranging from pure chance, through environmental conditions to the cell type where the gene is expressed.

Genes can be present on both strands of DNA and a gene on the + strand can overlap with a gene on the - strand. In some cases they can even overlap on the same strand (nested genes). You need to check both strands for coding sequences.

You're assuming that all coding sequences start with ATG (most do, not all) and you seem to be assuming that an ATG always starts a coding sequence. A given gene can have dozens or hundreds of ATG codons, how can you know which one is used as a START codon?

The process of identifying the parts of the genome that get translated into protein is not trivial. It is the subject of countless PhD theses, mine for example. There are many programs (gene predictors) that are designed specifically to detect genes in genomic sequences. Having spent many years working with them I can assure you that they're not something you can just whip up one afternoon. They tend to involve very complex models of coding vs. non-coding sequences and are way more sophisticated than simply looking for START and STOP codons. Trying to write one without knowing a lot more about biology than you seem to is just a waste of time.
Your specific questions are basically irrelevant because of the points mentioned above. Nevertheless, the answers are:

They vary but not much. For well annotated genomes like the human one, the differences will be negligible. That is not why you have strange results though as I explained above.

All public FTP sites tend to have a README file that explains what the files provided are. You should read the relevant README from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/

Answering that question will get you a Nobel prize. There simply is no way of predicting what genes will be activated in a particular cell. We're not even close to that level of understanding of how a cell works but I can tell you that it will not depend on the sequence, you will never be able to predict whether a gene is active in a particular cell based on its DNA sequence alone. It will depend on various things including the gene's methylation state and is largely an emergent quality of the cell's complexity (think of various proteins interacting with one another, leading to the activation of a gene).  The best you can do is get a list of genes that are known to be active from the literature.

In summary, if you want to do something as complex as modelling a cell I suggest you first take the time and study some basic biology so you can understand the system you are trying to model a bit better. The cell is not only an extremely complex system that we don't fully understand yet, it is also not wholly deterministic and contains a lot of stochasticity that you seem to be ignoring completely.

Thanks for the detailed post. I'm going to use this as a reference going forward and look into the topics you've mentioned.

@nether you're welcome and sorry to piss on your parade and all. I really recommend you find a biologist to collaborate with. You are greatly underestimating the complexity of the task you want to attempt. First of all, it is simply impossible with the knowledge available today. Even if it were possible though, you are looking at several years work from a team of highly qualified experts. You may be a brilliant programmer but that is not enough here. Also, you are reinventing the wheel, there are already many programs that do what you have written (identify genes and translate sequences).

Because there's an xkcd for everything...http://xkcd.com/793/

@terdon I was expecting the piss-on-parade / what-your-doing-is-impossible type post, but I'm happy that yours also contained useful information in addition. People told me things were impossible when I was trying to make software for the financial sector. Now my software is used by banks all over the world. It's not like I sat down in a room and made it by myself -- many experts in the financial world helped make it possible. I plan to do the same thing here which is why I've been reaching out to experts in computational biology and already have some meetings set up :)  Collaboration is key

@nether ah, good, I'm glad to hear that. There is actually a lot of work being done in the subject. What is impossible (today) is to create a full working model of a cell. Impossible not because you're not good enough but because we simply don't understand the cell well enough. That could change in the future, what will never change is that the DNA sequence will never be enough for this. The sequence is only a subset of the information necessary to model a cell. By the way, you might want to look up BioPerl or BioPython if you're going to be working with this type of data.

@terdon BioJava for me ;)    And what about this?  http://www.cell.com/abstract/S0092-8674(12)00776-3

@nether that's exactly what I'm talking about. Note that i) they used M. genitalium, the simplest organism known to man, which is orders of magnitude simpler than a "white blood cell" (there's no such thing by the way, there are dozens of cell types called that) ii) they used a hell of a lot more information than the DNA sequence and iii) despite all this, the model is extremely limited. It can predict certain behaviors but cannot be considered a "true" representation of the living cell. My main point is that expecting to model a cell by using its DNA sequence is impossible.

I'll just explain a bit on why it is impossible. You can predict a protein sequence from a DNA sequence. It is very hard to predict the protein structure from its sequence. More difficult it is to predict what the folded protein will interact with. and so on...

Why bother predicting proteins badly from DNA sequence when you could have just as well downloaded the manually curated human proteome?
As to your questions:

Are you asking about human genomes or genomes in general? The vast majority of the variance in human genomes is in non-coding sequence. As to genomes in general, they vary in pretty much every imaginable way.
I think those files are quality filtered Illumina reads. SRA = Sequence Read Achieve. SRR = SRA RUN accession. ERA = EMBL SRA. ERR = ERA RUN accession.
You should look into transcriptomics data. Predicting such stuff in silico is currently pretty much undoable.

I think the OP meant differences between different assemblies of the same genome. For example, differences in gene coordinates between UCSC and EnsEMBL.


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What is the mechanism of monofunctional glycosylases?
I am learning about the base excision repair mechanism. I understand generally how glycosylases work, but I am trying to understand this with much more detail. I found a paper where they write:

Monofunctional glycosylases catalyze the single-step displacement of damaged base via attack of an activated water molecule on c1' of the substrate.

I am not sure what an activated water molecule is and how, for example, an aspartate residue is making a water molecule 'activated'. Furthermore, how is this activated water molecule hydrolyzing the N-glycosyl bond to remove the damaged base. Thank you for any help.

The article referred to in the question is Fromme et al. (2004). I was able to find several proposed mechanisms for the monofunctional uracil-DNA glycosylase but I'll discuss two that seem most relevant in the context of your question.

The first I'll mention was outline by Parikh et al. (2000) who studied recombinant human mitochondrial uracil-DNA glycosylase. They report a mechanism where the glycosidic bond cleavage is not induced by a nucleophilic attack by water but rather by valence electron rearrangement, induced by conformational changes of the substrate by the enzyme, leading to a resonance stabilized oxocarbenium intermediate. This figure shows an electron pushing representation as well as the various stabilizing effects produced by orbital overlaps which favours cleavage of the C-N bond:

Original caption: Structure-based reaction mechanism that resolves the apparent orthogonal paradox for electron transpositions by altering the substrate stereochemistry. (A) A simplified valence-bond representation of the glycosylic bond dissociation hides the paradox that the three electron pairs to be transposed are involved in orthogonal orbitals. (B) In the normal anti-conformation of deoxyuridine, the σ*-orbital involved in the anomeric effect and the π-orbital of the C2⩵O bond are orthogonal to one another, thus preventing orbital overlap. (C) Severe distortions of the deoxyribose and the glycosylic bond in the strained conformation of deoxyuridine enforced by the UDG active center align the pairs of atomic orbitals participating in each electron transposition, thereby electronically coupling the anomeric and σ-πArom effects to promote bond cleavage.

They also go on to say (emphasis added):

A water is tightly positioned 3.54 Å below the deoxyribose C1′ by four hydrogen bonds (Fig. 3B) but is likely a poor nucleophile. Instead, the UDG–DNA substrate structure suggests this water is well positioned to become the 1′-α-OH after dissociation of the incipient deoxyribose oxocarbenium ion from the uracil ring.

Here is Fig. 3B from the article, where the water molecule is the red sphere at the bottom of the image coordinated by four hydrogen bonds:

The next mechanism involves a nucleophilic attach by an activated water molecule and was outlined by Drohat et al. (1999) studying Escherichia coli uracil-DNA glycosylase. Here is the first step of the mechanism:

From the Wikipedia article on uracil-DNA glycosylase (accessed 15 Jul 2014)

Drohat et al. (1999) describe this:

UDG apparently follows a [...] mechanism by deprotonating the incoming water nucleophile using the completely conserved residue Asp64 as the general base. Site-directed mutagenesis studies of the human enzyme support the structural evidence that His187 and Asp64 act as a general acid and base, respectively, because conversion of these groups to leucine and asparagine resulted in 300- and 2500-fold losses in activity (11). However, structural and mutagenesis data alone cannot establish the catalytic roles and ionization states of active site groups; thus other complementary approaches must be utilized to establish a chemical mechanism.

To answer your question, the water molecule is considered activated because it is a better nucleophile due to proton abstraction by the aspartate residue side chain. Thus the electrons used in in the original O-H bond in water (which are polarized towards the electronegative oxygen) are free to attack the partial positive 1' carbon of the deoxyribose. Although it is a concerted mechanism, you could perhaps think of the nucleophile being the hydroxide anion, which is much stronger than water.

So which mechanism is correct you might ask. Well, I don't know, but I refer you to a paragraph from Parikh et al. (2000):

Despite the importance of UDG and the many proposed mechanisms for its catalysis of glycosylic bond cleavage, the structural chemistry underlying efficient catalysis by UDG has remained elusive. Two groups, including our own, have proposed a traditional acid-base catalysis carried out by a cationic His-268 and an absolutely conserved Asp-145 (13, 26). Two proposals (27, 28) invoke only general base catalysis via the same catalytic aspartate and a neutral histidine. Another proposal (29), based on a computationally simulated uncleaved-substrate complex, predicts that Asp-145 is fully solvated in the substrate complex so that it cannot act as a general-base catalyst. These proposed mechanisms are inconsistent with each other and with the uncleaved-substrate crystal structure presented here. Moreover, they are problematic in that they rely entirely on functional group chemistry and thus do not adequately explain UDG's efficiency or the activity of mutants that alter evidently key functional groups (13, 27). UDG mutations that remove apparently key active site functional groups are actually faster enzymes than several wild-type DNA glycosylases (30). Thus, without knowledge of a substrate complex structure, the characterization of UDG mechanism is severely hindered. Here, we present the structures of UDG bound to both uncleaved-substrate analog at 1.8-Å resolution and cleaved-product DNA oligonucleotides at 2.0-Å resolution. These high-resolution cocrystal structures suggest how UDG applies part of the DNA-binding energy to glycosylic bond cleavage by conformationally altering its deoxyuridine substrate to take advantage of stereoelectronic and strain effects in what is then an apparently dissociative process.

References:
Drohat AC, Jagadeesh J, Ferguson E, Stivers JT. 1999. Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase. Biochemistry-US. 38(37):11866-11875.
Fromme JC, Banerjee A, Verdine GL. 2004. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol. 14(1):43-49.
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA. 2000. Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. P Natl Acad Sci USA. 97(10):5083-5088.

To answer your question in brief: an "activated water molecule" is one which is partially deprotonated (in this case... in other cases, partially protonated or metallated). Here, the bond between the water oxygen and one of the hydrogen atoms is partially broken, having been elongated (HO-----H). This is accomplished by a protein residue, which is often a carboxylate-containing residue, such as Asp or Glu in glycosylases. The negatively-charged carboxylate residue acts like a base (called a "general base"), removing the proton from water, thus leaving behind hydroxide ion (OH-). Now, why do all of this? Because water is a poor nucleophile and hydroxide a strong nucleophile. Here, the nucleophile is intended to attack the deoxyribose at C1' after the glycosylase has cleaved the sugar/base - or "N-glycosidic" - bond. This "quenches" the carbocation that forms after losing the base (the "oxocarbenium ion")... because having a strong electrophile hanging around the vicinity of DNA would be bad! Hope that helps!

You should add some references to your answer (Wikipedia articles are sufficient for basic claims) to (i) ensure that what you are saying is scientifically valid (ii) allow others to read up/deeper on the problem.


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What is the formal terminology for two species that are "close" to each other in a phylogenetic tree?
Take for example the human and the chimpanzee, they are "closely related" species since they are "close" to each other in a phylogenetic tree. However, this terminology seems pretty informal, what would be the formal way to specify that two or more species are "closely related"?

What do you mean by "formal"?

The way that you would find it written in a scientific journal.

Are you looking for something like "sister lineage" (or "sister taxon" or "sister group")
This term may be more specific than what you're looking for, and to use it correctly you'd want to be a little careful – I guess in this case you might have to say something like:

"the lineage that includes chimpanzees and bonobos is sister to the
  lineage of which humans are the only extant species"

or

"the lineage that includes chimpanzees and bonobos and the lineage of
  which humans are the only extant species are sister lineages"

both referring to this phylogeny.

It's also possible that explaining exactly what you mean by 'close', or what it entails, would be appropriate, be it Ilan's suggestion of % genetic similarity (or maybe genomic similarity?), # of nodes between your two taxa (again, this would have to be in reference to a specific phylogeny), or if you have a dated phylogeny you could refer to the time since divergence, as in "coding DNA divergencies ...place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago."(Wildman et al 2003).

Sister lineages would have been my suggestion..

But of course it depends about context, I mean, e.g. fungi and animals are sister lineages just as much as bonobos and chimps..

Good point 5heikki. It's one of those terms like 'endemic' that is pretty meaningless without context.

As genus comes above species I'd consider using this term for the species which are close genetically ("these two species are from the same genus"). Above genus comes family etc...
On the other hand, the proximity or similarity of species could be probably "measured" by degree of biodiversity, and especially genetic diversity considering two close species having low biodiversity and very different species as having higher biodiversity.
Thirdly, and I feel that this is the most strong term to use, you can "express" the genetic closeness of species as being "genetically similar":
"Some monkeys and humans have 98% genetic similarity" or "are up to 98% genetically similar" or "... DNA similar"...