text:
What are some characteristics of venules and arterioles?
I know that the vascular system of the human body is organized in the
two, "ever branching", structures of the veins and the arteries. These two
structures stem from their connections to the heart and stretch and
branch throughout the body.
The two structures are interconnected through capillary beds,
responsible for the interactions between the blood and the
extracellular liquid, surrounding the tissue cells of the body.
The capillary beds are connected to the arteries and the veins through
small vessels, venules, branching out from veins and arterioles,
branching out from the arteries.
The capillary beds consist of a web of capillaries, vessels small and
thin enough to allow exchange of nutrients and waste between the blood
in the vessels and the extracellular liquid surrounding the vessels as
well as the cells of the body.
Now, I realize that the capillary beds must be ubiquitous throughout
the body, sustaining every part of the body but the circulatory system
itself.
I am eager to find out more about the venules and arterioles. Looking
at the structure of veins and arteries, how prevalent are the smaller
blood vessels? Are the arteries and veins "fuzzy" with arteriole and venules or are the small vessels more sparse? Do they emanate from large vessels as well as smaller ones? How do their presence interfere with vascular interventions or
even drawing blood for blood tests?
I'd be happy for information in these matters.
Cheers
Mats

I think this question is a bit too broad to write a comprehensive answer to, and there will certainly be some variation between tissues.
However, here is one reference that might give you what you are looking for.
I used to make acrylic arterial casts, mostly of coronary arteries but also some dabbling in the pulmonary, renal, and hepatic systems. My experience with the coronary system is that most of the arterioles come off in a tree-like branching pattern from quite small arteries, but there are always exceptions. I think the "fuzziness" you refer to definitely depends on the scale of observation: the further away you are, the more "fuzzy" arterioles look: of course they will never be as "fuzzy" as capillaries, but certainly once you enter the muscles themselves there is a lot of branching, but that branching isn't necessarily uniform. That is, there may be larger branches running in one dimension, and smaller branches in another dimension.
In larger vessels you also have the vasa vasorum: arteries that feed the large arteries and veins themselves. Some of those vessels are certainly the same size as arterioles, and some branch directly off the main vessel, but I am not sure whether anatomists always consider those to be arterioles or if they are considered separate.
From the perspective of interventions such as surgery, etc, smaller arterioles aren't really any different from capillaries, and larger arterioles might need to be clamped off or cauterized, but there isn't really any way to avoid them if you are cutting into a vascularized tissue. One wouldn't avoid these vessels they way they might avoid larger vessels.

I would appreciate an explanation for the downvote, I am happy to make edits if suggested!

Thanks Bryan. Yes, I apologize for a poorly stated question. In spite of this, you helped me shed a little more light on the subject. I hope I am not responsible for any down vote. If I am please explain and I will rectify. I will accept this answer. It helped me. I will restate and ask a new, clearer question later on. Thanks again for your answer.


text:
Difference between imputing and typing in GWAS studies?
In genome-wide association studies (GWAS), what is the difference between imputing and typing? Are they the same?

'Typing' is an SNV-typing. It is an explicit SNV detection using Affymetrix GeneChip arrays, Illumina BeadArray.
'Imputing' is an imputation. It is a statistical inferring from existing genotype data using haplotype estimation. It is useful because different genotyping arrays genotype a slightly different set of SNVs and they can't detect all variants as whole genome sequencing is still pricey.

No, they are different altogether.
Typing in GWAS is genotyping individuals from a selected population to know say the genetic variation of SNP's (single nucleotide polymorphisms) among them via chips like Illumina Core-Exome etc.
Imputing is the statistical process of imputation of SNP's of an individual from a reference source like the HapMap reference panel. The process is a bit complex and typical tools like IMPUTE2/BEAGLE4/MINIMAC2 rely on HMM (Hidden Markov Models) to fill in the SNP's.
So, in essence within a GWAS study first, we genotype individuals (as it's cheaper than sequencing all SNP's) and get 300-500k SNP's via the chips as above, then impute the remaining variants using an established Human Genome Reference panel using the above software.
Edit:
An excellent resource for understanding imputation is Yun Li's 2009 paper.

Please add some references to your response.

I have added one here, but I usually don't see references in the answers from most of the people in this forum !!!

source: Stack Exchange

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

sort: votes


text:
What is the evolutionary advantage to a lifespan limit?
How/Why
Do Koi have a lifespan of hundreds of years?
Do humans have a lifespan of decades?
Do dogs have such a short lifespan?
Within these questions I pose further questions.  How does size relate to lifespan. Elephants?
If dogs were to evolve independent of humans (at this point) would they rule the world?

This question is far too broad, because you are asking too many questions. Please limit yourself to one focused question per post.

An interesting question and @Wesley has answered it quite nicely. Apart from this, I would like to direct you to a neat article published by Yaneer Bar-Yam in PRL last year on when does natural selection favour limited lifespans. A detailed explanation was given in Gizmodo website last year.

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


text:
Is the central axon of pseudounipolar neurons in dorsal root ganglia typically myelinated
As I understand, sensory nerve cells in the dorsal root ganglion are pseudounipolar neurons, with a sole protrusion from the soma branching into a central axon (or functional axon) and peripheral axon (or functional dendrite). Depending on the kind of nerve fiber, the peripheral axon may be myelinated to various degrees, and even not myelinated at all.
Now in an online lexicon (which is in German, unfortunately: http://flexikon.doccheck.com/de/Pseudounipolare_Nervenzelle), it is asserted, that while the peripheral axons (signalling from the periphery to the dorsal root) are usually myelinated, the central axon (signalling from the dorsal root to the posterior horn of the spinal cord) is usually NOT myelinated. The claim is unsourced. In spite of thorough research on the internet, I have not been able to find any notion whatsoever on the central axon being myelinated or not. So my question:
Is there any evidence that in dorsal root pseudounipolar neurons central axons are typically unmyelinated even when the peripheral axon is? Evidence on human neurons is preferred, but evidence on other species is welcome as well.


text:
Does the effect of light on melatonin release adapts to light level over long periods of time?
Or do you go to bed with low levels of melatonin when you stay behind a computer screen all day?

Melatonin influences sleepiness but isn't necessary for sleep: you can sleep even if you are in the light all day.

but how about the levels of melatonin under constant light? does the brain realize at some point it's not going to get dark somehow and starts producing melatonin, or will the brain simply not be able to produce it like it normally would do? @B

I think that would be a better question than the one you posted. I would try to avoid words like "realize" since even though we are talking about the brain we aren't really talking about cognitive control. What you seem to be wondering is whether the effect of light on melatonin release (it is release that is affected by light, I believe, not production) adapts to light level over long periods of time.

This paper, for example, shows that indeed, melatonin is suppressed more in the light after a week of dim light exposure compared to after a week of bright light exposure.
However, the authors note that although the result was statistically significant, the effects were fairly small compared to the overall variability in the data.


text:
What kind of fish did I see in waters off a tropical island in the Philippines?
Found this while diving in the southern Philippines.

The downvote was not by me however plz provide more information about its habitat , size and description. if possible provide clearer picture.

@AlwaysConfused you need not give an explanation for your votes (or for not voting).

This is a Blackspotted puffer, Arothron nigropunctatus a commonly found fish on coral reefs in the Philippines. Although this species has a large color variation, the photos provided show common coloration (white body with black spots, a large black area around the dorsal ray). The white strip above the mouth is also a commonly found characteristic of this species, along with a face and snout that resembles a dog.

CC- Attribution - Photo by John E. Randall


text:
What wavelengths of lights do plants need to grow?
So, I found a list of L.E.D.'s from Cree here (the company seems to be known for efficiency, they power most of the bicycle lights that I know of) is selling a line of lights designed for growing plants.  If you click on the data sheets, you'll find something like this:

Now, I know that plants reflect green preferentially because it is the least useful color to them (energetically speaking) so I assume that this matters.
I know the first few things about electronics, so I would really like to use one of these in something that I build.  However,the question becomes:
What kind of spectrum light and I looking for?  What is the difference between the "vertical farming" lights and the greenhouse lights?  (Viewing angle?
I kind of want to put some plants in a box coated internally with aluminum foil (it can reflect more than 90% of the energy), and hook one of these bad boys up for some inside growing.  Thanks alot.

A simple Google search using the title of your question will give you many resources. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure.

I'm voting to close this question as off-topic because it seems more suitable for Physics.SE

The main question is also unclear.

I think the question is on-topic but unclear and lacking in effort (exactly what do you want to grow and at what scale? what do you know from before, and what information are you missing?).


text:
What are the ploidy levels in major groups of organisms?
If total number of chromosome in the cell is x, then for-example;
Are all animals diploid (x= 2n) ?
Are all fungi haploid (x= n) ?
Are all plants diploid (x= 2n) ?
Are all Protists diploid (x= 2n) ?
Also, what is the ploidy of archaea and bacteria?
Thank you very much.

Is diploid = 2n your example for polyploidy in humans?

as a short hint, 1. yes ploidy means number of the chromosome set. (However, "basic-number of chromosome" and "haploid chromosome number" are 2 different thing). 2. Many protists are haploid. Many protists , all plants and some animals (like cnidarian eg jellyfish) show 'alternation of generation'. I. e. they have more than one life-forms in different  generations (eg. sporophytic generation and gametophytic generations of plants) that have difference in chromosome number (not possible to discuss in a comment). I'll write an elaborate ans later.

As well, though the question contains many short parts, still in my view this one question  seeks a single thing clear yet brief understanding about ploidy concept (all others are just examples from some discrete domains of life). so I think this question is not too-broad. However only 1 unclear thing is the variable x here is not explained, that could yet be improved.

@AlwaysConfused I think the OP is referring to total number of chromosome (not pairs) as x.

Could I request reopen so that I could post a more detailed answer? I think instead  yes/no, quite elaboration would be more useful. For example; many fungi show a "dikaryotic" (n+n) phase. In members with alternation of generation, we cannot use the term "this is a diploid species" or "this is a haploid species". Because unlike our eggs or sperms (n) which couldn't be considered as a "generation"; their meiotic products can stay & divide as a clear-cut "generation". (as well alternation of generation could be triphasic, too). If I get few day for library work I could try make better reference

Are all animals haploid (n=x) ?

No

Are all fungi haploid (n=x) ?

No

Are all plants diploid (2n=x) ?

No

Are all Protists diploid (2n=x) ?

No

Also, what is the ploidy of archaea and bacteria?

Generally speaking, Bacteria and Archaea don't have chromosomes (but have circular DNA). As such the question of ploidy does not really apply to them.
You might want to read about Biological life cycle to understand the terms haplontic, diplontic, haplodiplontic (and other similar terms).
Ploidy level can easily varies among species of the same family (typically in plants for which hybridization is common). There is no reason to expect that a taxon as big as "fungi" (for example) would all have the same level of ploidy.
Note that your question that all animals are haploids is surprising as you just described that humans are diploids.

Just want to add that it's certainly possible to talk about bacterial ploidy -- in fact there's a huge amount of variation in how many copies of their chromosome they maintain.

@VictorChubukov Thanks. I don't know much about that. Do you know a good reference for further investigations?

In animal, reproductive cells are haploid for human
Male bees, wasps, and ants are haploid because of the way they develop: from unfertilized, haploid eggs
some fungi are also haploid

bhakti - can you add some references to your answer? we appreciate that very much on BiologySE and it will strengthen your answer greatly


text:
Do any RNAs directly inhibit transcription
In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can also complement DNA. So, do any regulatory RNAs directly bind to DNA (with a protein complex or alone)?
I am only interested in regulation, not modifying DNA (like CRISPR does). I assume that means I am asking if any regulatory RNAs persistently bind to DNA, blocking RNA polymerases?
This question is for either or both eukaryote and prokaryotes.

Yes there are reports of RNA directly inhibiting transcription.
RNA induced transcriptional silencing (RITS) is a well known pathway in Schizosaccharomyces pombe (fission yeast). Initial heterochromatinization is dependent on the RNA (as a DNA identfication module) that guides other functional proteins to the target (Also see Djupedal et al., 2009).
piRNA in higher eukaryotes are known to cause methylation of target DNA regions and thereby the repression of genes at these loci (Aravin and Bourc'his, 2008).
Some classes of small RNAs in C.elegans (such as 22G RNA) are also known to cause transcriptional silencing.
Many lncRNAs are known to inhibit transcription of their target genes. The most famous example would be that of XIST which causes epigenetic silencing of one of the X-chromosomes in the female.
On a purely biochemical note, RNAs can also form triplex with target DNA regions and impede transcription and replication (Bacolla et al., 2015).


text:
What is the name of the bond between phosphate and the sugar in a nucleotide?
I am slightly confused about what the name of the bond is between the phosphate and sugar within a nucleotide. All my research comes up with is a phosphodiester bond being the backbone of DNA. But within a single nucleotide, would we perhaps call it a phosphoester bond (all of my searches of phosphoester bond correct it to phosphodiester, so I don't think the term 'phosphoester' is in use...); or maybe it would be an O-glycosidic bond as it is a sugar molecule covalently bonded to another molecule via an O atom?

Please do not ask multiple questions.

@another 'Homo sapien' Glycosidic bonds certainly do not always involve an O atom (heard of N,C and S glycosidic bonds? Now THAT is something you can find out on Wikipedia). And I do not get your point- even if a glycosidic bond required an O atom, there is one between the sugar and the phosphate group.

@another'Homosapien' see above comment.

Phosophoester is a valid term. There are at least a 1000 peer-reviewed articles that use this term. IUPAC Goldbook defines nucleotides as:

Compounds formally obtained by esterification of the 3 or 5 hydroxy group of nucleosides with phosphoric acid. They are the monomers of nucleic acids and are formed from them by hydrolytic cleavage."

Phosphoester or phosphoric ester means an ester of phosphoric acid.

Expanding on WIYSIWG's correct answer:
Each nucleotide contains one phosphoester bond (between a phosphate O and sugar 5'-C). Additionally, two nucleotides are connected by one phosphoester bond (between a phosphate O and sugar 3'-C). So in a polymer of multiple nucleotides (DNA, RNA), the repeating monomer unit contains two phosphoester bonds, on "top" (5') and "below" (3') the sugar. Since the repeating unit contains two phosphoester bonds, and the phosphates alternate with the sugars in the sequence, we call this a sugar-phosphate backbone held together by phosphodiester bonds/linkages.
Schematic of single nucelotide  featuring vertical line as phosphoester bond (to 5' C):
$P \\
| \\
[sugar]-[base]\\
\\$
Two nucleotides, each with an internal phosphoester bond and with a new phosphoester bond connecting them (spanning 5' of one sugar to 3' of the next):
$P \\
| \\
[sugar]-[base]\\
|\\
P\\
| \\
[sugar]-[base]\\
\\$
Repeating unit in nucleotide polymer, with alternating sugar-phosphate backbone and one phosphodiester bond/linkage per unit/nucleotide residue (the ... ellipses indicate pattern continues for the entire nucleic acid polymer, with hydroxyls capping the very ends):
$...\\
P\\
| \\
[sugar]-[base]\\
|\\
...\\$

phosphomonoester is also a common term for the first case


text:
What is open complex in E.coli DNA replication?

The E.coli DnaB helicase is essential for replication initiation from the chromosomal origin of replication ( oriC ) and is present in vivo as a protein complex with six monomers of the DnaC ATPase protein and six ATP molecules (Wickner and Hurwitz, 1975; Lanka and Schuster, 1983). DNA replication initiation at oriC begins with binding of multiple molecules of the bacterial DnaA initiator protein to a 9 bp repeats (DnaA boxes). This binding promotes destabilization of nearby AT-rich sequences, resulting in unwinding of the DNA double helix and the formation of an open complex.

I looked up in DNA Replication by Arthur Kornberg, Tania A. Baker (the authors who probably coined this term), Google and Google.Scholar but didn't stumble upon any definition.
What is it actually?

The sentence itself is actually the definition of open complex: It is the structure that is created once the DNA double helix is unwinded due to the DnaA proteins.

This binding promotes destabilization of nearby AT-rich sequences,
  resulting in unwinding of the DNA double helix and the formation of an
  open complex.

I have also found a papera co-authored by Arthur Kornberg himself where the authors self-define "open complex" as well:

Three tandem repeats of a 13-mer in the AT-rich region are essential
  to the unique replication origin of E. coli and of remotely related
  Enterobacteriaceae. These iterated sequences are identified by
  deletion analysis and sensitivities to endonucleases as the site for
  initial duplex opening by the initiator dnaA protein. This “open
  complex” requires ATP and 38% for optimum formation and stability.

There are several papersb,c that use "open complex" in the same way.
References:
a David Bramhill, Arthur Kornberg, Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome, Cell, Volume 52, Issue 5, 1988, Pages 743-755, ISSN 0092-8674, http://dx.doi.org/10.1016/0092-8674(88)90412-6.
(http://www.sciencedirect.com/science/article/pii/0092867488904126)
b Ozaki, Shogo, et al. "A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin." Journal of Biological Chemistry 283.13 (2008): 8351-8362. (http://www.jbc.org/content/283/13/8351.full)
c Mukhopadhyay, Gauranga, et al. "Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication." The EMBO journal 12.12 (1993): 4547. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC413885/)

Thank you. Hope you don't mind if I take some time to respond to your entry.

An open complex is the complex of RNA polymerase and one DNA strand (antisense strand). Whereas closed strand means that RNA ploymerase is attached to both strands of the DNA.
Procedure: RNA Polymerase first creates the closed compex.
Then open complex is created when the double stranded DNA is separated to two strands.

I saw this term used in transcription too. But I'm interested in replication solely.


text:
Why do birches have a white bark?
Several species of the tree genres Betula have a white bark,especially when they are young. This is quite peculiar to trees - at least in central Europe; so I'm wondering if there is a ecological reason behind it.
The first idea I have is that they protection against the sun. But normally protection of nature against the sun is to make the opposite: put more pigments in the skin, so that the sun does not damage the underlying DNA.
If this is the explanation, how do other tree species protect against this?

They produce a rare pigment of white color, called betulin. Found the article about it: https://tmtml.blogspot.com/2017/12/why-birches-are-white.html

It is protection against rapid warming of the cambium layer. A lot of far northern timber has light colored bark which reflects sunlight. The rapid heating from very cold after sunrise can actually damage or even split the bark of dark colored species. This is called sunscalding.

Note that aspens, which grow at high elevations in the mountains, also have very light-colored bark.  But oddly enough, the conifers growing in dryer areas at the same elevations generally have dark brown to greyish bark.

conifers of course provide their own year long shade.

Not usually around sunrise, unless located in a dense stand.

@jamesqf thick, rough or rugose bark also aids in resisting it, conifers also experience less dramatic dormancy which helps resist the effects. Different solutions to the same problem.

The definitive study seems to be Karels, TJ & Boonstra, R "Reducing solar heat gain during winter: The role of white bark in northern deciduous trees" Artic vol 53 no 2 pg 168 (2003).

There is also a lot of other circumstantial evidence supporting this theory. The birch species that exhibit white bark, in N. America, B. papyriferia, B. populifolia, and B. cordifolia, are all pioneer species inhabiting barren, open habitats and thus exposed to more light. The more shade-tolerant, forest-dwelling birches, B. alleghaniensis and B. lenta, have darker bark, probably because their habitat has more tree trunks to absorb or block out the light so they didn't face the same selection pressure. Also what @jamesqf said about Aspens fits this pattern: they are also pioneer species.


text:
Common site for atherosclerosis
My book( textbook of anatomy abdomen and lower limb 2nd edition - by vishram Singh pg.no:286) says:

Acute arterial occlusion: It is mostly caused by embolism or thrombosis. It usually occurs in the femoral artery where it gives off the profunda femoris artery.

So my question what makes this site more susceptible for atherosclerosis?
In general what are factors that make some sites more susceptible to atherosclerosis?

Homework questions are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy. "Homework" is interpreted to mean any academic or other assignment, test preparation, or task given in relation to a class, educational setting, or self-learning. There is plenty of information on atherosclerosis available easily online, starting with Wikipedia.

I can give you some facts about atherosclerosis, but I should warn you that--judging by your question--you may be making a false equivalence between atherosclerosis thrombus/embolism. The two are often very interrelated, but there are times when an atherosclerotic plaque is significant without causing an embolism (e.g. stable angina) and there are times when a thromboembolism forms without the presence of a significant atherosclerotic plaque (e.g. atrial fibrillation). The likelihood of thrombus formation is dictated by Virchow's Triad: Endothelial Dysfunction, Blood stasis/turbulence, inherent coagulability of the blood (factor problems mostly).
Now to get to your main question: atherosclerosis. The current theory is called The Response to Injury Theory. The general idea is that whenever there is damage to endothelial cells they will release inflammatory cytokines, and these will lead to a thickening of the wall. There are a lot of different things that can lead to this endothelial damage. There chemical factors: exogenous sources like cigarette smoke and endogenous sources like elevated levels of homocysteine. However the two most important factors that lead to endothelial damage are high cholesterol and hemodynamic factors (Robbins, 494). That second point hints at why atherosclerotic plaques are more common at branch points. As blood is going past a branch point it becomes more turbulent which makes it more likely to cause damage. This is especially true when blood is flowing more forcefully, as in the case of hypertension (another risk factor for the development of atherosclerotic plaques).
There are many other factors that play into the development of atherosclerotic plaques. For example, the abdominal aorta distal to the renal arteries has no vasa vasorum, which makes it more susceptible plaque formation(5). This is just a small sample though. There are a plethora of factors that go into plaque formation: literally textbooks full of information about he disease. If you're really interested in the topic and want to dive in, I'd suggest taking a look at Inflammatory Atherosclerosis.

Evolution of arterial wall changes in the response to injury hypothesis. 1, Normal. 2, Endothelial injury with monocyte and platelet adhesion. 3, Monocyte and smooth muscle cell migration into the intima, with macrophage activation. 4, Macrophage and smooth muscle cell uptake of modified lipids, with further activation and recruitment of T cells. 5, Intimal smooth muscle cell proliferation with extracellular matrix production, forming a well-developed plaque. (Kumar 495)
Kumar, Vinay, Abul Abbas, Jon Aster. Robbins & Cotran Pathologic Basis of Disease,  9th Edition. Saunders, 062414. VitalBook file.


text:
What placement of plasmid parts makes the most sense?
If you want to express the largest amount of a certain or a few proteins using a plasmid, does it make sense for the antibiotic resistance gene to come after genes for proteins you intend to synthesize?  So that the promoter and RBS/origin of replication would specifically come before the proteins intended to be synthesized and the bacterium would put less resources into its antibiotic resistance?  But would that be canceled out by bacteria not surviving as much as if the antibiotic resistance gene is downstream of the other proteins?  Or is it roughly the same in either order because they're both being synthesized anyway?

The relative placement of genes on a plasmid should not affect their expression.
Both will be expressed and to what extent is dependent on the strength of the promoters and a few other factors like codon availability.
However where you ultimately plan to express these genes can be an important consideration in plasmid design. For example, if you are designing a binary vector for agrobacterium mediated transformation of plants then positioning the plant resistance cassette next to the left border is a sensible move.

Placement can alter protein expression. You could for example make a synthetic operon, and proteins located closer to the promotor will usually be expressed more. You could include your resistance marker in this, and probably get some interesting effects.
However, the resistance marker is usually not such a high metabolic burden that it makes any difference. Increasing expression would be needless. Decreasing expression would free up some resources, but it's extremely likely that your expression is already limited in some other way. Probably promotor strength, plasmid copy number, protein solubility or toxicity.


text:
Beginner question about growing E. coli
I have bought a hobbyist kit which involves growing E. coli. The steps said to grow the E. coli on an LB agar Petri dish overnight. No incubation devices were included in the kit.
I let the E. coli grow overnight at room temperature (65-75°F), but there's pretty minimal growth, if any. I found this question which seems to imply that it's hard to grow E. coli without having temperatures near 37°C, which is much warmer than I can reasonably make my house.
Is it possible for me to do this experiment without purchasing an incubator of some sort? If so, does the lack of growth indicate that I've made a mistake somewhere?

You can always put the plates close to the heating source for your house - forced hot air vents, baseboard electric or hot water heaters, radiators, etc. (I'm assuming you're in the Northern hemisphere and you have the heat turned on). It will be several to many degrees warmer there than in the rest of the room. Make sure you place a good thermometer at exactly the distance away from the heat source that you'll be putting the plate(s) so you don't cook them accidentally - steam radiators, for example, get really hot.

The higher the temperature the faster E. coli will grow, with a maximum growth rate around 37 Celsius.
If you grow E coli at lower temperature, the ecoli will grow slower.
At 37°C you will see colonies overnight (16hr).
At 30°C you will see colonies in about 1 and a half days.
At 25°C you will see colonies in about 3-4 days.
You can do experiments at room temperature, but you will be waiting for days for what you will normally see after a 37°C overnight incubation.
As for satellite colonies.. yes ampicilin does break down with time and water. You can solve that problem by increasing the amount of Amp you are using from 25ug/ml to 100ug/ml. Or use 75ug/ml Carbenicilin. Or change your selection markers and use a more stable antibiotic like Chloroamphenicol.

Pedantic stuff: Overnight is typically 8-9 hours and the colony growth rate also depends on the concentration of the inoculum.

@WYSIWYG Your overnight is 8-9 hours? What are your lab hours? Mine is at least 16h.

@MattDMo 16h is your lab hours?!! I guess not, unless you are a robot :D I guess you meant "overnight". My lab hours are variable (as less as 3h to max 15h) :P Recently I was doing only computational; so I could fire commands from anywhere. When I was doing experimental then lab hours were on an average ~10h; 10 AM to 8 PM. All my "overnight" inoculations are done at ~9 PM (but later the better) and I harvest the cells in the morning ASAP. For maxipreps I inoculate late and harvest in 9-10h. Overgrown cells give bad preps.

@WYSIWYG sorry, I meant my "overnight" is about 16-ish hours. I work in industry, so 9AM-5PM is the norm :) It's been a few years since I've done plasmid preps, but I can't recall having any issues with the longer incubation time. YMMV, of course.

@MattDMo There are no big issues but the cell lysis doesn't happen properly when the cells are overgrown. The lysate is very sticky and viscous. The yield goes down.

@WYSIWYG If we're being pedantic, then 8-9h as an overnight incubation definitely isn't "typical" :P that's overday if anything.


text:
What is the difference between intials cells and meristems cells?
Generally plant tissues:

meristems tissue: meristems cells, apilal meristems, lateral meristems
Non meristem tissue: dermal tissue, vascular tissue, ground tissue

my question:
What is the difference between intials cells  and meristems cells? Are intials cells the same as meristems cells?

To contrast with meristem tissue; instead "non-meristem" tissue,  you may use the term "permanent tissue" (that is unable to divide normally untill de-differentiate at special conditions)

Meristems are undifferentiated plant cells. There are two types:

apical mesistem that occurs at tips or branches and roots as well as buds which produces elongation, and
lateral meristem or cambium that produces lateral growth (stem thickening).

As cambium cells divide, cells toward the inside differentiate into xylem (wood) - these cells are 'xylem initials'. Cells toward the outside that eventually differentiate into phloem tissues (inner bark) and are 'phloem initials'.
One could similarly label apical meristem cells that are in the postion and/or process differentiating into leaves or flower organs as x-initials.

can you add some external/citable references to help back up your answer? We appreciate references so that others can read more and better understand the question/answer on BiologySE. Thanks for your efforts


text:
meaning of abbreviations h and m in Na channels
In a voltage-gated sodium channel, there are two gates, one for activation and one for inactivation. They are also known as h- and m- gate. What are these letters standing for?

Are the gates referred to h- and m- in a diagram or as text. I looked up online and nothing seems to mention the gates as those two letters. A citation or picture reference would be great.

Those initials were proposed by Hodgkin and Huxley in their original paper modeling the action potential in nerve cells: https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model
They are not names for subunits, domains or motifs in the sodium channel, as your question may imply. Instead,

n, m, and h are dimensionless quantities between 0 and 1 that are associated with potassium channel activation, sodium channel activation, and sodium channel inactivation, respectively.

However, there is no indication of what those initials mean (if anything), apparently being just letters they chose to name the variables in their equations.

It's unusual for algebra notations to use non-consecutive numbers, such as x, y, z, or p, q, r, but you seem to be right. The H&H article indeed states "m then represents the proportion of activating molecules on the inside and 1-m the proportion on the outside; h is the proportion of inactivating molecules on the outside and 1-h the proportion on the inside." Again, very unusual.

@NickSandor If this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered. If you have >= 15 reputation points, you may also upvote the answer if you wish. There is no obligation to do either.

My point was that I am not sure that there is no better answer. I will accept Gerardo's answer if after a few days, nothing better comes up.

@NickSandor think m and n were chosen purposely as being in sequence and both referring to activation, while h was another variable letter distinct from m and n to separate it as an "inactivation" - I'd also note that there are a lot of other variable names in the Hodgkin and Huxley paper: they use alpha and beta for rate constants so it's nice to avoid a & b as variable names to avoid confusion; g and V are standard for conductance and voltage, "p" might be confused with probability; q and r are typically used with p, and xyz are typically used for coordinates or more arbitrary variables.

@GerardoFurtado While you are somewhat correct that the "h-gate" "m-gate" etc terminology doesn't refer to particular domains in the channel, they do refer to the motifs that Hodgkin and Huxley proposed to exist, and that terminology is still used in reference to their hypotheses, which although imperfect have largely been proven true, so OP is not incorrect to refer to the "h-gate" and "m-gate" when talking about HH equations or sodium channels, the translation would be "h-gate" = "domains of the voltage-gated Na channel that contribute to inactivation"


text:
Oral Administration of Immunizations
Small children and people in developing countries may take oral dosage forms of vaccines. Antigens passing through the GI tract will come into contact with Peyer's patches and be absorbed by microfold cells into lymphoid tissue, evoking an immune response.
Some of these vaccines are attenuated and can colonize in the small intestine, mimicking a natural infection. I am wondering why vomiting and diarrhea, which are common symptoms in many natural infections, aren't more prevalent.
To be even more specific: Serotonin is released in response to a cytokine release by immune cells. Serotonin activates 5-HT3 receptor to induce vomiting. Why is this response not provoked by an attenuated infection, which mimics an actual infection.

It should be noted that only some vaccines are recommended to be delivered orally, while others require an injection (typically intra-muscular) for optimal efficacy.

First, ongoing inflammatory process/immune reaction in the gastrointestinal tract is not necessary associated with vomiting or diarrhoea. As an example we can consider infection with Helicobacter Pyroli, which may last for many years unnoticed.
Second, exposition to foreign antigens obtained form food or microflora and subsequent antigen presentation to the immune cells (which is indeed partially driven by locally released cytokines) occur in the GI tract all the time and again, is not usually manifested by vomiting or diarrhoea.
But moving to vaccines, attenuated oral vaccines (like Polio Sabin or Rotavirus) are developed in order to diminish the risk of pathological symptoms. Attenuation weaks the pathogen that is usually no longer able to proliferate and invade, but still poses antigens that may be presented to the immune cells and induce long-term immunological memory. Moreover, immune response (antigen presentation, production of the local IgA, B-cells affinity maturation) triggered by attenuated vaccines is the closest to the one induced by full infection (in comparison to inactivated/toxoid vaccines), but significantly weaker and localised. This we mean by "mimicking a natural infection".
Also, see: https://www.sciencedirect.com/science/article/pii/S0042682215001725

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


text:
Significant presence/absence of plant species
I have approximately 300 cluster of 200 different plant species and a presence absence matrix of all species versus clusters (since some species don't have clusters so they are checked if they are present or absent in other clusters). Now I want to find out if there is significant presences or absences of this plants in their clusters. At the same time I need to know which clusters have this significant presences. I want to know that if there is spesific software can do this or do I have to write code?
edit: it is not clear what i mean with significant presence and absence as i understand. by significant presence i mean "species being in the same clusters all the time. not one of them being in another cluster without the other." by significant absence i mean that "if leys say Y species never tooks place in clusters of which X species exist."

Exactly what do you mean by "significant presences or absences"?

significant presence means: two (or more) species being in always together in clusters. significant absence means: lets say X species never tooks place in a cluster if Y species exist in it.

Are you with "clusters" referring to plant presences at different sites (i.e. a species co-occurrence matrix) or something else? When you say "clusters" I mostly think about groups created by some sort of algorithm (i.e. clusters) to find patterns in data.

I am not quite sure what you mean by "significant presence". If you observe any non-zero number of plants of a given species in a cluster, then the rate at which this plant occur in this cluster is different from zero. No stats required to infer such thing. You should clarify your post.
Logistic Regression
It sounds like you would like to do a logistic regression with presence / absence as response and the nominal variable cluster as solo explanatory variable. In R you could for example do something like
# Dummy data
d = data.frame(
 presence = sample(0:1, 120, replace=TRUE),
 cluster =  rep(LETTERS[1:4], 30)
)

# Logistic Regression
m = glm(data= d, formula = presence ~ cluster, family = binomial(link="logit"))
summary(m)

You can find here another example of logistic regression in R
Phylogenetic signal and pseudoreplication
You might want to make sure to decorrelate your variable from the phylogeny to avoid pseudoreplication. There, the solution you might end up going with will depend on your genetic data. If you have a genetic PCA, you could go with using the first 2 axes as simple covariates in a type I sum of squares kind of model (which is probably the default of the logistic regression I performed above). If you have a kinship matrix you could use it with lmekin or MCMCglmm (see here for adding a kinship matrix). There would have many different statistical tools for such decorrelation depending on your data.

By "significant presence in clusters" the probability of lets say 3 species being together in one cluster is not due to chance. They are being together in every cluster, inot one of them present in another cluster.

It phrasing "Is a probability due to chance?" makes no sense. You can only ask the probability of something to happen under a specific model. The expression "significant presence in clusters" is still unclear. You might want to follow an intro course to statistics to understand the logic and context of probabilities and statistical testing.

i think it is pretty clear what i am asking. i have clusters of plants. IF ONE SPECIES IS ALWAYS WITH OTHER SPECIES IN ALL CLUSTERS, it means significant presence. It means that one of the species can not exist without the other. i really don't understand which part of this unclear.

Or, one species can not be together with one other spesific species, it means significasnt absence. It means they can not live together, and that's why they are never located in the same clusters.

Well this sounds very different from what you said before. It just mean that you want to compute interaction (probably all two-way interactions only) in a logistic regression.


text:
Number of serotonergic neurons in mouse/rat DRN
What is the (approximate) number of serotonergic neurons in the dorsal raphe nucleus (DRN) of mice and rats?

The mouse and rat dorsal raphe nuclei contain about 9000 and about 11.500 serotonergic neurons, respectively. It turns out the corresponding 1988 and 1982 references are widely cited - directly as well as indirectly. I could not find any newer data/evaluations.


text:
How well can humans detect vitamin-richness?
Humans do prefer fatty, sweet/starchy and salty. And fatty foods are rich in vitamins. How well can humans detect vitamin content apart from fattiness of food? Can humans choose the vitamin-richer of otherwise identical peanut butter, cheese or chicken leg?

Do you have a source for your claim that "fatty foods are rich in vitamins"? Have you looked at the nutrition information on a bag of potato chips recently?

Based on what I could search I guess that humans (and other organisms) usually do not have strong sensory mechanisms for micronutrients (Miyamoto et al, 2013).
There are some reports on sensing of metal ions, especially zinc and copper, by some organisms, including mammals (Bird, 2015; Ballou and Wilson, 2016). However, I haven't come across any study that talks about vitamin sensing.

From wikipedia

A vitamin is an organic compound and a vital nutrient that an organism requires in limited amounts. An organic chemical compound (or related set of compounds) is called a vitamin when the organism cannot synthesize the compound in sufficient quantities, and it must be obtained through the diet; thus, the term "vitamin" is conditional upon the circumstances and the particular organism

A vitamin is therefore not defined by its structure but by its availability. There is therefore no taste associated to vitamins in general. So, no we are not able to sense vitamins generally speaking just because there is no natural objective category of substances that one can call vitamin.

Note by the way, that the health effect of vitamins supplmentation (for most people) is debated. For example, you might want to have a look at the following two skeptics posts

Do vitamins improve memory abilities?
Do vitamin supplements have any health benefits?

One of the most important scientist of the 20th century, Linus Pauling advocated for the health benefits of vitamin C. Due to his strong influence, the reputation of vitamin C quickly grew but his work remained controversial and there are still very little evidence that supplement of vitamin C does any good.

That wikipedia article seems human-centric and lists 13 vitamins. If we limit our definition of vitamin to those, is your "no we are not able to sense vitamins" still true?

Yes, very likely. You can have a look at the diversity of food source in which those vitamins are found and imagine a single taste would be common to them all.

"Note by the way, that the health effect of vitamins is debated." That's just wrong. The health effect of vitamin supplementation - at least for people without deficiencies - is debated. If you do not provide enough vitamins in your diet you will most definitely have adverse health effects.

That was more a typo than a misunderstanding from me as this point was made clear in the last paragraph. Thanks for the comment, I edited the post accordingly.

This sounds wrong to me. There are certainly structures associated with the recognized human vitamins. There are no taste receptors for them, but humans also have hundreds of olfactory receptors, and for most of them the ligands are still unknown. Also, we might detect vitamins "by proxy", for example recognizing the smell of citrus fruits as "healthy", even if there is no direct receptor for ascorbate (vitamin C). I don't think we know enough about olfaction to be able to answer this question in the negative.


text:
Mechanism of RNA synthesis by RNA polymerase
I want to study the mechanism involved in RNA polymerase's catalysis in E.coli. Things like:

How does it bind to the promoter?
How does it unwind the DNA?
How does each component of the enzyme contribute to this synthesis?

I have looked into books like, Berg, Snustard Simmons, Lehninger, Alberts, Lodish and Google.Scholar, found information like:

After σ binds to the core the holoenzyme binds to duplex DNA and moves along the double helix in search of a promoter, forming transient hydrogen bonds with exposed hydrogen-donor and -acceptor groups on the base pairs. (Without σ the core enzyme can bind to DNA but unspecifically.)
After the RNA polymerase binds tightly to the promoter DNA in this way, it opens up the double helix to expose a short stretch of nucleotides on each strand . Unlike a DNA helicase reaction , this limited opening of the helix does not require the energy of ATP hydrolysis. Instead, the polymerase and DNA both undergo reversible structural changes that result in a more energetically favorable state.
Interaction of the σ subunit with a promoter signals the polymerase to initiate transcription at a specific sequence in template DNA.
The β and β′ subunits polymerize ribonucleoside triphosphates (NTPs) as directed by the template strand.
The α subunits interact with regulatory proteins and, in some cases, with DNA to control how frequently RNA polymerase initiates transcription from a specific promoter.

But that's all that I have found. Where can I find a full length explanation about this with proper diagrams(if possible)?
P.S. Has the mechanism not been fully discovered?

Almost everything in this world has something additional to be known. For what you are asking you have to go through different papers. I don't think there is a book dedicated to the mechanics of RNA-polymerase. You may find some extensive reviews but the likelihood of finding a recent one, despite its importance, is low. Considering all this, your question appears to be too broad.

This site is a good start, https://pdb101.rcsb.org/motm/40 as is this one http://mol-biol4masters.masters.grkraj.org/html/Gene_Expression_I2-RNA_Polymerases.htm

I have found an article which describes all the major steps of the mechanism of working of RNA polymerase II. Since the article is too long, I'd rather put the main points here. You can read the complete article here. Since putting the whole answer under blockquote would be inappropriate, I am just putting the main points with the reference at the bottom. Remember, this is not the complete article, this is just the summary for the ones who can't read the full article from NCBI or who don't have time or access to do so.
THE RNA POL II TRANSCRIPTION CYCLE
Pol II transcription typically begins with the binding of gene-specific regulatory factors near the site of transcription initiation. The core promoter serves to position Pol II in a state termed the Preinitiation Complex (PIC) analogous to the bacterial Closed Complex. In this state, Pol II and the general factors are all bound to the promoter but are not in an active conformation to begin transcription. Next, a dramatic conformational change occurs in which 11–15 base pairs of DNA surrounding the transcription start site are melted and the template strand of the promoter is positioned within the active site cleft of Pol to form the Open Complex. After synthesis of about 30 bases of RNA, Pol is thought to release its contacts with the core promoter and the rest of the transcription machinery and enter the stage of transcription elongation. Factors that promote productive RNA chain synthesis, RNA processing, RNA export, and chromatin modification can all be recruited to elongating Pol II.

PROMOTER RECOGNITION USING MULTIPLE LOW AFFINITY INTERACTIONS
Sequence elements found in core promoters include the TATA element (TBP binding site), BRE (TFIIB recognition element), Inr (initiator element), and DPE (downstream promoter element). The core domain of TBP consists of two imperfect repeats forming a saddle shaped molecule that binds the widened minor groove of an 8-bp TATA element, unwinding about a third of a helical turn and bending the DNA about 80 degrees toward the major groove. Biochemical studies elegantly showed that TBP does not bind to TATA elements with high orientation specificity, leading to the finding that other promoter elements in combination with TATA determine the orientation of transcription machinery assembly at a promoter. The other two core promoter elements with proven function, Inr and DPE likely serve as binding sites for the TAF (TBP Associated Factor) subunits of the general factor TFIID.
The role of TBP at TATA-less promoters: From biochemical studies of the yeast HIS4 promoter, mutation of the TATA to a GC-rich sequence allowed recruitment of the transcription machinery to a promoter at a reduced level, but transcription initiation was completely abolished. These results demonstrate that at one class of promoter, assembly of the transcription machinery into a productive complex requires that TBP bind the TATA element as seen in the crystal structure. Although TBP has tremendous flexibility in the ability to bind variants of the TATA sequence, not all sequences are compatible with TBP binding.
GENERAL FACTORS INTERACTING DIRECTLY WITH TBP
TFIIA and TFIIB are the two general factors that interact specifically and independently with TBP. TFIIA stabilizes TBP-DNA binding and strongly promotes binding of TFIID to DNA through an anti repression mechanism by competing with the TAF1 N-terminal domain (TAND) that occludes the DNA binding surface of TBP when TFIID is not bound to DNA. TFIIA can also compete with the negative regulatory factors Mot1 and NC2 to promote TBP binding in vitro.
TAFS ARE SHARED SUBUNITS OF TWO LARGE COMPLEXES
The TAFs function in promoter recognition as well as in positive and negative regulation of transcription. A subset of TAFs has DNA binding activity and at least one TAF has the ability to bind acetylated nucleosomes, protein acetylase, and ubiquitylation activity. A core of 5 TAFs are found in both TFIID and the acetylase/coactivator complexes.
POL II THE CENTER OF ATTENTION
Pol II subunits can be classified into three overlapping categories: subunits of the core domain having homologous counterparts in bacterial Pol (Rpb1, 2, 3, and 11), subunits shared between all three nuclear polymerases (Rpb5, 6, 8, 10, and 12), and subunits specific to Pol II but not essential for transcription elongation (rpb4, 7, and 9).
Pol II structure: Pol II is composed of four mobile elements termed Core, Clamp, Shelf, and Jaw Lobe that move relative to each other. The Core element  accounts for about half the mass of Pol II and is comprised mainly of subunits common to all cellular Pols. At the center of the enzyme is a deep cleft where incoming DNA enters from one side and the active site is buried at the base. This cleft is formed by all four mobile elements and has been observed in both closed and open conformations in the 10 subunit enzyme. The Shelf and Jaw Lobe elements move relatively little and can rotate parallel to the active site cleft. The Clamp element, connected to the Core through a set of flexible switches, moves with a large swinging motion of up to 30 Å to open and close the cleft.

The Pol II CTD molds itself to a binding partner: Pol II undergoes regulatory phosphorylation and dephosphorylation as part of the transcription cycle with the Rpb1 C-terminal domain (CTD) the target of this modification. The CTD, which is unique to Pol II, contains 25–52 repeats of the tandemly repeated heptad sequence YSPTSPS, with both Ser2 and Ser5 the sites of phosphorylation. The CTD acts as a platform for assembly of factors that regulate transcription initiation, elongation, termination, and mRNA processing. New structures of CTD interactions with two different binding partners have revealed that the CTD appears to mold itself to its binding partner, adopting different conformations. In one study, a complex of a single copy of the CTD with Ser2, 5-P bound to the Pin1 peptidylproline isomerase was solved.
ASSEMBLY OF POL II WITH THE TRANSCRIPTION MACHINERY
These studies showed that the transcription machinery makes extensive interactions with promoter DNA between positions −43 and +24 with respect to the transcription start site. Two RNA Pol II subunits (Rpb1 and 2) make extensive DNA interactions over 60 bp. TFIIB and the small subunit of TFIIF (TFIIF$\beta$) both interact with DNA on either side of the TATA and the large TFIIF subunit interacts with DNA downstream of TATA. TFIIE interacts with promoter DNA just upstream of the transcription start site while the TFIIH helicase subunit interacts downstream and possibly upstream of the transcription start.
Pol II and TFIIF interact over an extended surface: TFIIF binds Pol II as a heteromer and contains two subunits that are conserved among human, insects and yeast, termed Tfg1 and Tfg2 in yeast (Rap74 and Rap30 in humans). The N-termini of both conserved subunits form a dimerization domain and the C-termini of both subunits are winged helix domains. The structure of Pol II with the Tfg2 subunit alone implicated Tfg2 binding to the extended clamp region and Tfg1 binding to Rpb4/7.
OPEN COMPLEX FORMATION AND THE TRANSCRIPTION START SITE
Transcription start site selection: At TATA-containing promoters in vertebrates and Drosophila, the transcription start site is located about 30 bp downstream from the beginning of the TATA sequence. A model to explain the transcription initiation site in higher eukaryotes would be that TFIIB binding to both Pol II and promoter DNA sets the distance needed for the DNA to travel from the TFIIB binding site on Pol II to the active site of the enzyme.
REFERENCE
Structure and mechanism of the RNA Polymerase II transcription machinery: Steven Hahn, 2005 Aug 24

@SanjuktaGhosh maybe you don't need a book after reading this :)

@SanjuktaGhosh if you are focused at only the initiation phase, then this might be helpful. If you want, I can post it as a separate answer.

No, it's alright. I'll follow the link.


text:
Movement in microvilli
My textbook( COMPREHENSIVE TEXTBOOK OF PHYSIOLOGY VOL-1 by GK PAL) says:

Microfilaments project into microvilli present on the epithelial surface such as on the intestinal mucosa, and extend up to the tip of microvilli. They help in microvilli movement.

How far is the second sentence correct? When I searched on Wikipedia( in a page about microvilli) I found following:

As mentioned, microvilli are formed as cell extensions from the plasma membrane surface.Actin filaments, present in the cytosol, are most abundant near the cell surface. These filaments are thought to determine the shape and movement of the plasma membrane.

So does these two imply that there is some sort of movement (due to actin) in microvilli?

Just the presence of actin filaments does not mean a cellular structure that contains it would be dynamic. Moreover there are different types of actin filaments (filopodia, lamellipodia etc) and they have different dynamics.
Microvilli closely resemble filopodia; both these structures also share some regulatory and structural proteins (other than actin). However, there are some differences which makes filopodia highly dynamic in comparison to microvilli (Sebé-Pedrós et al., 2013; Sauvanet et al., 2016).
Microvilli, though not as dynamic as filopodia, are not static structures. They can grow and retract and there are regulatory mechanisms that govern these processes (Sauvanet et al., 2016).

REGULATION AND DYNAMICS OF MICROVILLI AND MICROVILLAR COMPONENTS
Microvilli on cultured cells are dynamic structures with three phases
  in their life cycle: (a) the generation of microvilli growing at 5
  nm/s, (b) a steady state of ∼5 min, and (c) a retraction phase with a
  rate of 1.2 nm/s (Gorelik et al. 2003). This leads to an average life
  cycle of 12.1 ± 5.6 min. The turnover of microvillar proteins has been
  recognized for a long time (Stidwill et al. 1984). The F-actin core in
  the microvilli of Caco-2 cells at steady state treadmills, with a rate
  of monomer addition at the barbed end of approximately 1.5–3.0
  s−1 (Loomis et al. 2003, Tyska & Mooseker 2002),
  corresponding to approximately 0.2 μm/min. The protocadherin
  intermicrovillar link stabilizes microvilli of intestinal epithelial
  cells, resulting in a prolonged steady state (Crawley et al. 2014).
  The actin filaments in the core of stereocilia treadmill more slowly,
  at 0.002–0.04 subunits s−1 (Rzadzinska et al. 2004) or
  hardly at all (Zhang et al. 2012).

so does the movement implies growth and retraction?

@JM97 yes. It is pretty much evident from the quoted text. For more details you can check out the article.


text:
Could there be any effects from low powered infrared being used to track eye movements long term?
Basically,  looking  into infrared LED's and a camera with an infrared bandpass filter for tracking eye movements; my concerns are whether there would be any potential negative long term effects from constantly illuminating the eye with low power infrared?
TIA
A

Most likely not. We are exposed to IR light every time we step out into the sunlight, so a very small amount from an electronic device designed to follow the eyes is not going to matter much at all.

I would have said that IR is safe, but some studies have suggested otherwise.
This is a vague study on rabbit eyes:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116568/
https://academic.oup.com/annweh/article-abstract/35/1/1/170395
So there may be a dosimetric exposure limit of some kind that you have to aim for. LED's are very controllable. I'm amazed that they talk about cataracts with a chemically soft, non -ionizing wavelength like IR, because we get IR all day from the sun. If you control the levels to be less than a sunny day, you may find that you can use equivalent of 1hr of sun exposure to run many hours of eye tracking. the figures are a matter of research.

Heat waves are probably infra-red waves. We have these all around us (with great intensity) all the time. A small intensity Infra-red from an LED shall not cause any problem at all even in long terms. Our eyes are evolved to withstand far greater(i.e. around temperature of 45°C)  intensities. So, no need to worry.
But since, water is lost from heat waves, do allow subject to blink his eyes frequently.

LEDs are near IR, while low temperature radiant heat is far IR. Near IR behaves much more like visible light. Like others have said near IR is significantly present in the solar spectrum, so to a degree effects are bounded by what we observe with sunlight exposure.

@Real sorry, what do you mean, i don't understand ? Is there any clarification you need?


text:
Can only fully matured sperm fertilize an egg?
Are only mature sperm able to fertilize an egg? If so, is there typically a reserve of mature sperm that are saved after an ejaculation or does a male need to wait for new sperm to mature before trying to fertilize an egg again? In humans it seems that the the shortest maturity period for sperm is around 42 days (New Findings on Sperm Life Cycle Could Impact Fertility Treatments). Do the new immature sperm serve any purpose after ejaculation?

Do you mean naturally?

@WYSIWYG, yes, not IVF.

There seems to be the misconception that sperm maturation period starts over after each ejaculation. It is a continuous process : at any given time, there will be populations of cells at various stage in the process; for instance, sperms that are at day 36 will be mature in 6 days, regardless of intervening ejaculations that could expend mature sperms.

As far as I know, sperm cells undergo maturation in the epididymis, where they become motile. As Eliane pointed out, this is a continuous process, so the male does not have to "wait", because there is continuously a batch of sperm cells that will shortly become mature. Furthermore, maternal factors are required for the process of capacitation in which the sperm cell becomes capable of fertilization and undergoes motility increase.

An immature sperm cell is simply non-motile and even if present in the ejaculate, it will not be able to travel towards the fallopian tube to fertilize the oocyte. A sperm cell which did not go capacitation will also have no ability to fertilize an egg (that's why prior to IVF it's important to capacitate sperm).
My sources:

https://kjcscientific.wordpress.com/project-excalibur/
Gilbert's Developmental Biology (2009)


text:
Why does RNA synthesis in E.coli begin with a Purine?
From Berg's Biochemistry:

Most newly synthesized RNA chains carry a highly distinctive tag on the 5′ end: the first base at that end is either pppG or pppA.

Is there a reason why the synthesis initiates with a purine?

From this paper, which is the 2nd result of a Google search for rna synthesis begin with purine, the abstract ends with this sentence: "Our results suggest that the purine-rich sequences at the 5' ends of the nascent transcripts of many genes act to stabilize the early ternary complex." You can read the papers citing this one to learn more if you wish.

I didn't find any suitable result with the keywords I was using. Anyways thank you. @MattDMo

Purine-rich sequences at the 5' ends of the nascent transcripts of many genes act to stabilize the early ternary(elongation) complex.

P.S.Source: MattDMo's comment.


text:
Valve-like layers example in nature?
I am searching for an example in the nature, where a layer of something (skin, coat, film etc) can allow fluid to flow trough (not absorb) from one direction and prevent/repel from other direction. I am not talking about vein valves, prefer more like a nano-structure of valves as a layer on/around something.
Update:
I found something similar what i am searching for, but its not clear:

Gap Junctions (animals)
Directly connects the cytoplasm of two cells, allowing various ions
  and molecules to pass freely between the cells.

And there is a reason why this channel is hydrophilic, someone can explain this?
About me I have no deep knowledge about biology, please be patient and help me to understand things on basic level. Thank You!

I think an answer that explains this question at your level of understanding might be too broad. The things you want to understand are cell membranes, concentration gradients, osmosis, channels for water and other ions, transporters for ions, etc. Someone might find a special example, but typically in biology, besides bulk transport, water is never moved by itself: instead, osmotic gradients pull water into particular spaces. Many plants, for example, collect water by pumping potassium into their roots: water follows this osmotic gradients.

Gap junctions don't have any "direction" to them: they are basically just open "holes" between cells that allow for diffusion depending on concentration/electrical gradients.

You've correctly found connexons at gap-junctions work as gated-channels. There are many such of names that doesnot contain its 'categories', for say the term 'trypsin'  does not end with 'ase' though it is enzyme. But that is an unrelated issue. You may use the chat because commenting is not considered for extended discussion.

I don't know any-such continuous-membrane-material that can do so. But yes certain membrane-transport-proteins can do so.
Carrier proteins are normally highly specific about in which-direction to transport which molecule; and in general,  they are classified as uniporters, symporters and antiporters.  *

So an uniporter would be an accurate example of situation you are asking about.
Carrier proteins those utilize ATP for pumping (those shows "primary active transport"), are also normally highly specific to direction. For example the Na+-K+pump and the H+ pump.
Channel proteins too, sometimes show directionality, for example certain K+ channels ** such as inward-rectifying potassium channel

A potassium channel diagram showing the selectivity filter (diagram from The cell/ Cooper **, slightly edited: Na+ filter-out not shown, and the term 'selectivity filter' is labelled in image ).

KcsA potassium channel diagram from wikipedia. In its open-conformation out of the following;

i.e. the third one, can conduct the K+ ion in a specific direction, because the pore-region is very specific- it allows K+ ion only to enter in the cell.

Reference:

* Plant biochemistry by Hans Walter Heldt, 3rd edition, Academic Press-Elsevier, Paperback edition.
** The Cell, a molecular approach/ Cooper/ Sinauer and ASM press.
Harper's illustrated Biochemistry/ Murray, Bender, Botham, Rodwell, Well/ Lange and McGraw Hill.
Wikipedia.

Clear demonstration, thank you! But i can't transpose this method to able to control fluids. But helped me to go further, check the Update of my question.


text:
In induced pluripotency experiments, what happens to the cells that do not become pluripotent?
I am new to this topic, so forgive me if my question is naïve. In an induced pluripotency experiment a few transcription factors are overexpressed in somatic cells and as a result a small portion of the cells become pluripotent (fully or partially), but the vast majority of the cells do not. My question is this: what does happen to these cells (the ones that do not become pluripotent) in terms of gene expression levels? Do gene expression profiles of these cells remain unchanged (the same before and after overexpression of the pluripotency factors)? Or do they change and become something that is different from both pluripotent cells and the original somatic cells?


text:
Does a software exist to automatically design antibodies that target a given protein or antigen?
I'm looking for software to automatically design antibodies that target a given protein or antigen.

No, there does not. It is possible to do in silico tweaking of sequences to do some affinity maturation, for example, but I've never heard of a method for de novo CDR design. Nature is much better at doing that for us. Also, even if such software existed, the computing power required would be enormous - much much more than an individual computer.

Much easier said than done!
If I had sufficient funds and time to pursue your goal what I would do is comb the Protein Data Bank for all the PDB files of interest. Surely you have some protein that interest you. Might consider doing the following:

Figure out what family your protein belongs in, considering it's number and presence of motifs: coils, helices, beta sheets, etc...
Do a literature review of any protein that has already been studied belonging to this family. So when a protein in this family catalyzes a reaction what are its flexible and restrained regions?
Use a program like Autodock to dock your protein to a protein that its protein family might interact with.
Calculate the interaction energies using Gromacs, NAMD, or Gaussian. You can do a zero time calculation of initial states or pursue a molecular dynamics approach as the proteins move randomly to their most stable configurations, or even a molecular mechanics approach. Which systems are most favorable?
You got this far. Now what? But then none of these steps creates your candidates. It just gives you an idea of the physics involved in already structurally identified compounds. Yes, you can make point mutations in VMD and Pymol. But, if you want to add a new motif to an existing protein structure it will not work because more than 20 amino acids in a peptide do not fold properly.

To do some of the biological statistics, the research collaboratory of structural bioinformatics is right here: http://www.rcsb.org/pdb/home/home.do
You can parse through their folders with wget or curl in bash scripting
at http://files.rcsb.org/
But then assuming you do figure out a candidate protein that doesn't exist yet. How are you going to make it in the lab? It appears that it would be better to do microbial studies. Maybe you can screen for a match with micro-array plates.


text:
How does rho-dependent termination occur?
Rho-dependent termination is not fully understood but there’s a brief description in almost every concerned book about it.
In Snustard and Instant notes-Molecular Biology it is written that, the rho protein binds a stretch of 72 nucleotides at the 3' end of the nascent RNA, which could be a recognition site and then moves along 5' -> 3' direction separating the DNA-RNA hybrid.
But how's it possible, rho binding to 3' end (which is not free) and moving in 5'-> 3' (if so it is sure to fall off!)?
Diagram from Berg showing something opposite, i.e. it has attached to the 5' end and is moving in 5' -> 3' direction.

What is the right thing?

There is no dichotomy in the two sources you have described. The text book you linked to says, exactly (emphasis added):

Rho appears to bind to a stretch of 72 nucleotides near the 3'-end of the nascent RNA...

It doesn't say at the 3'-end, which is obviously impossible since the 3'-end forms a double-stranded hybrid within the transcription bubble.
Rho is not loaded at the 5'-end of RNA, either, but rather binds internally at cytidine-rich Rho utilization (rut) sites, which will be somewhere 5' of the actual point of transcription termination. As you mentioned, there is a lot of uncertainty in the process and, while a lot is known about rut sites, as far as I can tell there is no consensus sequence, thus making it difficult to systematically identify rut sites throughout the genome. I have found papers which identify rut sites in the 5'-UTR (1) as well as within the 3'-UTR, intercistronic regions and coding sequences (2, 3, 4).

Mechanism of internal Rho loading:

Koslover DJ, Fazal FM, Mooney RA, Landick R, Block SM. 2012. Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level. J Mol Biol 423:664-676

Your diagram is correct. Rho protein binds at the 5' end and "chases" RNA Polymerase. It's not possible for Rho protein to bind at the 3' end, as this hasn't been transcribed by RNA Polymerase yet.

can you add some references to your answer?


text:
Wouldn't a non-poisonous variety of a mutant plant be at selective advantage?
I don't know much of evolutionary biology, but when someone asked, this seemed very much plausible to me.
Say there's a mutant plant, that produces much lesser toxin than its usual counterparts (same species). Then, wouldn't this plant be at a selective advantage over the others, since the predators (here, herbivores) wouldn't consume it assuming it to be poisonous. But sowly, as these mutants increase in number, the herbivores too realize and start feasting on them. Again selecting out ones with more toxin. Ultimately reaching some kind of equilibrium (?)
Is this phenomenon(?) called something? Is it similar to the selection that occurs in the  sickle cell trait? Are there real examples with plants with toxins showing this?

By "sickle cell thing", do you mean sickle-cell anemia?

@Harris Weinstein yup. Will edit it to be a bit more formal there.

Your question is very sensible; we would indeed expect this kind of negative frequency-dependent selection: i.e., if toxin-producing plants are common, non-toxin-producing plants should gain an advantage because they don't pay the costs of producing toxins but they do (or may) gain an advantage from herbivore deterrence. (Conversely, if toxin-producing plants are rare, they could gain an individual-level benefit by being the only ones in the population to deter herbivores.)
As of 2007, however, it seems that the empirical evidence for this phenomenon was pretty weak. In the following, "resistant genotypes" means genotypes that have some kind of anti-herbivore trait (typically production of secondary compounds that deter herbivory) [emphasis added]:

... Only a few studies have examined the role of frequency-dependent selection on plant defenses against herbivory (i.e., Berenbaum & Zangerl 1998, Roy 1998, Siemens & Roy 2005). ...  No study has manipulated the frequency of resistant/tolerant host genotypes explicitly to examine if the evolution of plant defensive strategies is subject to frequency-dependent selection. However, some studies tested some of the predictions of the frequency-dependence selection hypothesis (Berenbaum & Zangerl 1998, Roy 1998).
The study by Berenbaum and Zangerl (1998) found that in Pastinaca sativa, the range of variation in the level of a resistance component (coumarin) against its consumer Depressaria pastinacella did not change from 1873 to present, suggesting a cyclical dynamic promoted by frequency-dependent selection. In a reciprocal transplant experiment Roy (1998) did not find evidence that common hosts are eaten more and have lower fitness than rare hosts.  In a recent paper, Siemens and Roy (2005) evaluated the following: (a) if the amount of damage experienced by the most common host genotype was higher than that expected by its frequency, and the amount of damage experienced by the most rare host genotypes was lower than that expected by its frequency (assortative damage hypothesis); (b) if the most common host
genotype had higher levels of damage and lower average fitness compared with the more rare host genotypes; and (c) if the amount of damage correlated positively with the frequency of the most common host genotype. ... Unfortunately, their results provide little support for the hypothesis of frequency-dependent selection acting on plant defenses against herbivory.
... Although two studies have explored the potential for
frequency-dependent selection on plant resistance, no study has yet
examined this possibility on plant tolerance. Before
frequency-dependent selection can be put aside as an explanation of
the maintenance of variation on tolerance and resistance, explicit
experimental tests of the hypothesis are required.

(I haven't followed up the more recent literature to see if there is more recent evidence ...)
There is a related phenomenon that's much better documented: toxin-producing bacteria produce antibiotics to kill other bacteria of their own and other species, to minimize competition for resources. In "rock-paper-scissors" systems (2), cheaters (bacteria that are resistant to toxin but don't produce it themselves) invade toxin producers; then non-resistant bacteria invade the cheaters (because there's no toxin being produced any more); then toxin producers reinvade (because nobody's resistant any more, so there is once again an advantage to producing toxin).
I would say that the connection between this type of frequency-dependent selection and the selection that maintains polymorphism for the sickle-cell allele is loose. Sickle-cell is usually cited as an example of heterozygote advantage. It is loosely speaking a form of negative frequency-dependent selection at the level of alleles rather than genotypes; a gamete carrying a sickle-cell allele is more likely to end up in a heterozygote (and thus gain an advantage via malaria resistance) when it's rare and more likely to end up in a homozygote (and lose fitness due to sickle-cell disease) when it's common. It's also theoretically possible (although I haven't seen it discussed, and I would guess that it's not very important in practice) that increasing frequency of sickle-cell heterozygotes could also feed back at the population level to reduce the incidence of malaria, lower the advantage of resistance, and hence generate a more analogous form of negative frequency dependent selection.

Núñez-Farfán et al. "The Evolution of Resistance and Tolerance to Herbivores", Annual Review of Ecology, Evolution, and Systematics, Vol. 38 (2007), pp. 541-566 http://www.jstor.org/stable/30033871
Kirkup and Riley, "Antibiotic-mediated antagonism leads to a bacterial game of rock–paper–scissors in vivo", Nature 428, 412-414 (25 March 2004) .

This is called mimicry:

In evolutionary biology, mimicry is a similarity of one organism, usually an animal, to another that has evolved because the resemblance is selectively favoured by the behaviour of a shared signal receiver that can respond to both.

and yes, plants can do it, in multiple ways.

In evolutionary biology, mimicry in plants are several forms of mimicry, such as Bakerian mimicry, Dodsonian mimicry and Vavilovian mimicry, of other organisms by plants, most commonly flowers.

I don't have any particular knowledge of the equilibrium cycle you mentioned, though it seems hypothetically possible (no comment on the likelihood of it). If the cost saved from not producing the toxin is more advantageous than having the toxin itself, the new strain might have an advantage.

But isnt mimicry with two different species?

Ah, I missed the part about it being one species. Conceptually, I wouldn't say it's a huge distinction, though, since it's one organism deceiving others into thinking it's a more dangerous organism. I'll look into if there's a more specific term for the same-species case, though.


text:
Ancient DNA of ancestors or existing species?
Ancient DNA appears to be at most "several hundred thousand years" old.
Do we have an aDNA sample which we can reasonably confidently attribute to a species which has at least two modern descendants?
PS. This question is much less interesting than I originally thought: there are modern species which are proven ancestors of other multiple modern species (lake Victoria Cichlids).

The question seems to me a bit fuzzy. why not? according to this source, "Cats have 90% of homologous genes with humans, 82% with dogs, 80% with cows, 79% with chimpanzees, 69% with rats and 67% with mice" ; so why not with an ancient ancestor of them we would not find the genetic similarity?

@AlwaysConfused: the problem is that we do not have DNA sample of the common ancestor.

That-is-why ancient-DNA helps us. Did you mean, do we have an "ancient-DNA sample that is evidence for 1 branching point"  ? however even-if the sample is not of an exact branching point; DNA similarity with near groups would exist. So the condition in OP doesn't mean to me a branching point

@AlwaysConfused: yes.

Thanks then it is an interesting question because in my books and notes on the DNA-based phylogenies, all the fossil-taxa-DNA has been put at the termini of the phylogenetic trees. No-one show any further line-extension.

Assuming you mean by "modern descendants" "two different species that are also different from the ancient DNA", then to the best of my knowledge, no; the large vertebrates (bear, horse, humans, mammoths) that have been focused on for the most ancient DNA samples have common ancestors that are outside the range of ancient DNA isolation. I'm not very familiar with plant ancient DNA; maize DNA from a few thousand years ago is the oldest I'm aware of, but I might easily have missed some.
However, it's important to point out that the way this question is phrased makes it merely trivia, with no scientific significance.
Assuming (from the poster's other questions) that he believes this is somehow relevant to questions about speciation, I would point to modern genomes from ongoing speciation.  For example, Heliconius butterflies are speciating, and there's some work looking at the genomic components of that speciation:

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies.
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing.
Divergence with gene flow across a speciation continuum of Heliconius butterflies

Stickleback fish also show a number of examples of incipient evolution, and again genome studies have been done:

(Genomic landscape of early ecological speciation initiated by selection on nuptial colour.](http://onlinelibrary.wiley.com/doi/10.1111/mec.13774/abstract;jsessionid=DB86FB85259118805B95C1C52138D3EA.f03t03)
Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback.

Since, as I say, the question as phrased is simply asking for scientifically unimportant trivia, I'll leave it that as far as guessing as to what the actual point is.

DNA is "lego-like" structure from "lego"-blocks
ancient DNA is just a name of more or less long lego DNA sequence
let's say someone in the future finds a box of lego block but does not find any of lego-blocks built toys of our times
or finds sequences only of a few blocks
what would it mean?
another thing - lego blocks are made from a pretty sturdy material (actually like DNA). However, DNA is not the only molecule that can be a template for the protein assembly - RNA can do similar job. However, RNA is extremely fragile and degrades in minutes, and therefore cannot be found in fossils. Have you seen a cake made from lego blocks made from dough and cream?  How long such cake will last?
If you don't find a dough lego, can you say that it never existed?
ps
i agree with these words from the first answer
"However, it's important to point out that the way this question is phrased makes it merely trivia, with no scientific significance."

Please add some references and, if possible, some more scientific points to your answer.


text:
What does it mean to protect RNA polymerase?
From this paper

However, based on the strong interaction between NusA and RNAP, we propose that the chaperone activity of NusA could provide more direct and concentrated protection for RNAP under stress, i.e., NusA could simultaneously act as a latent protector of RNAP during transcription elongation and termination.

By "protection" the authors mean that in the presence of NusA, some proteins are less prone to aggregation after heat shock. "Protection", in general, could also refer to stabilization i.e. reduction in the degradation rates of the protein.

To detect the influence of NusA on heat-induced aggregation, we used
lactate dehydrogenase (LDH). LDH was incubated at 48°C in the absence
or presence of NusA. As shown in Fig. 2b, LDH slowly aggregated at
48°C without the protection of NusA. However, when this experiment was
performed in the presence of NusA, aggregation was visibly reduced.
These results suggest that NusA also protects unfolded proteins from
irreversible aggregation during thermal stress.
...
...
In E. coli, RpoA and RpoB, the major components of RNAP, are prone to
aggregation under heat stress in vivo. They were reported to interact
with GroEL and DnaK, mainly for the protection from aggregation or
refolding into a nonnative state48,49. However, based on the strong
interaction between NusA and RNAP, we propose that the chaperone
activity of NusA could provide more direct and concentrated protection
for RNAP under stress, i.e., NusA could simultaneously act as a latent
protector of RNAP during transcription elongation and termination.


text:
Transcription by RNA polymerase in absence of inducer and activator
Does the presence of activator(CAP-cAMP complex) and inducer(lactose) only increase the likelihood that a particular gene(here operon) gets transcribed, i.e increases the rate of transcription of that gene?And transcription of some(assumption) genes always happen?
Because as I know basal level transcription is something that happens always,even without an inducer.

Some genes have basal transcriptional activity whereas some may not at all. Are you asking whether all genes have some basal activity in the absence of an activator?

@WYSIWYG No. I'm asking what is the role of inducer and activator for e.g in lac operon. Do they solely increase the rate of transcription of the operon increases? Is it same for all genes (It mustn't be because you said that not all genes have basal level transcription)? For some set of genes then transcription factors (activators) and inducers solely switch on the gene.


text:
Is there a list with common mistakes in database entries?
I am a university student at the department of Biology. As part of my assignment for the subject Bioinformatics, I was asked to refer to common mistakes in biological database (e.g. Uniprot). For instance, "dehydrofolate reductase". Is there any list with such common mistakes? Otherwise, in your own experience, could you mention some examples of similar mistakes that you meet regularly?

"dehydrofolate reductase" does not meet my definition of common. It is used in 14 out of 71 000 000 trEMBL entries in Uniprot. trEMBL is comprised of computationally annotated entries which are explicitly awaiting curation. Is there an error? Dehydrofolate reductase type I (Q4QZB8) has a meaningless name, but plenty of proteins or genes suffer from that fate. The gene ontologies and domain annotations correctly indicate the presence of dihydrofolate reductase.

If there were such lists (maintained by the databases) then why would the errors be still present? This is a manual curation assignment. You have to go through them one by one.

Microsoft Excel has a nasty habit of thinking it knows your data better than you do, and when it sees gene names like Mar3 and Sept7, it tries to be helpful and convert them to dates.
So anytime someone puts a long gene list in to Excel and takes it back out again, you see those genes and their relatives converted to dates.
This has been known for years, but you still see it in lots and lots of published papers.
According to http://dx.doi.org/10.1186/s13059-016-1044-7, almost 20% of article supplementary material gene lists made with Excel contain such errors.

Sequencing artifacts in the type A influenza databases and attempts to correct them. is a paper that describes errors in one biological database. There are several other papers that similarly address errors in influenza genome databases, but I particularly liked this one because of its unique approach:

As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate.

Kudos to the lead investigator, David Suarez, for combining a genuinely useful project with cool outreach.

Interesting though this is, it isn't the kind of textual mistake that the poster is referring to.

"could you mention some examples of similar mistakes that you meet regularly" - I think the paper covers this part of his question pretty well

Strictly speaking I should just vote to close this question as homework or too broad, or repeat WYSWYG’s comment as an answer. However if one changes the question to how one should go about this problem as a bioinformatician, it becomes more interesting.
For a Biology student with no programming skills, it seems something of a distortion to call it bioinformatics. One aspect of bioinformatics is to use programming techniques that automate repetition and if/else decision-making to avoid laborious manual operations. So can one think of possible non-programming approaches? Here are a couple of suggestions to which others might wish to add.

Make up a list of terms like nitrate, phosphate, citrate, sulphate/sulfate, which all end in -ate. In German these are generally similar but end in -at (without the e). Even if you have no German you can use an on-line translator. In my experience some entries in the PDB have mis-spellings arising from such linguistic similarities, so you could search for the German spellings. You might even search for German or French abbreviations for RNA and DNA (RNS, DNS, ARN, ADN). Still a manual approach, but it would have some logic behind it.
If it is possible to find all the key words in your database of interest, can you find how many times each occurs. I could do this with a program, but perhaps Excel has some facility for doing this. You could Google to see. Then you could make the assumption that mis-spellings would only occur a relatively small number of times. You could then work through the terms with the lowest frequency of occurrence, looking for mis-spellings.

If you had some programming ability you could modify approach 2 by looking for words that differ by a single letter, on the assumption that some of these differences would be spelling mistakes. (Presumably a language such as Perl that is designed for use with regular expressions would be most appropriate.)

If you find any such errors in curated databases such as UniProt, please let the database curators know.
In the expert-curated, reviewed section UniProtKB/Swiss-Prot, we'll be happy to fix typos and other errors. As far as the unreviewed UniProtKB/TrEMBL records are concerned, this is slightly more complex as Michael_A states above. However, in many cases, the nucleotide sequence databases (EMBL-Bank/GenBank/DDBJ) can be asked to correct the underlying source, and the corrected names can then be updated in/reimported into UniProtKB/TrEMBL.


text:
A question about a succession study by Chapin et al. (1994)
The succession study in Glacier Bay, Alaska (Chapin et al., 1994) is an example that is used in almost all introductory texts on ecological succession. In the study, the effect of each succession stage on the germination and development of spruce seedling was examined, and complex results were found (see Figure 4b in here). For example, In Dryas stage (one of successional stages), spruce seedlings had weak germination and survival rates due to increase in seed predators. Likewise, the results show the effect of each successional stage on the various attributes of seedling germination and survival.
My question here is what is the control/reference of this study? For example, Dryas stage decreased the survival of seedlings compared to what condition? The results show "increase" and "decrease", but the reference is not clear. Is the control same for all successional stages?


text:
BLAST protein sequences from 2 different bacterial species
I am interested in finding a consensus sequence of a protein found in e.coli, in Pseudomonas aeruginosa. I am using pseudomonas.com to BLAST p the amino acid sequence of the protein that i have found with help of PDB. However i have seen that people do the BLAST N first and then BLAST P if they are interested to check whether they can find similarity of the protein sequence. Also in PDB the aa sequences are strange since they are not that specific.
Any advise on this issue or reliable links to databases when i can search and align sequences for similarities?
thanks


text:
How do I score differential activity of cellular pathways in microarray data (not enrichment)?
I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset. The goal is to use the average pathway activity for machine learning (sample classification), not to identify pathways enriched in differentially expressed genes (i.e. not performing a classical gene set enrichment analysis).

How do I score differential activity of cellular pathways in microarray data (not enrichment)?

You would look at downstream genes, which are selective for individual pathways - or genes which have binding sites for transcription factors that sit at the end of your pathway. Depending on the existing literature, and your experiment, and the specific pathway, this can include genes, which are themselves part of the pathway (if feedback). For interpretability you would prefer genes, which have previously been established as makers of a pathway in preceding literature.

I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset.

This might be tricky, since the taking the average introduces several assumptions such as: little impact of technical background (expression of most genes of pathway above background), average being representative of the KEGG pathway of interest (and not only of the most abundant pathway members), and enforcing a somewhat arbitrary decision of whether to average log-transformed data (which is justified for many genes, but not genes that don't scale multiplicatively, such as many stress genes), or not log-transforming.

The goal is to use the average pathway activity for machine learning (sample classification),

You can use this to your advantage, and create multiple features per pathway (e.g.: median, mean, variance, non/log-transformed etc..., manually -curated signature genes of pathways), and then having machine learning choose the best features for your classification (e.g.: as would happen if using Random Forest Classifiers)

You can use the PathVar software available here: www.pathvar.embl.de
See also the corresponding publication:
http://bioinformatics.oxfordjournals.org/content/28/3/446.long

use the GSVA R package to collapse gene expression data to pathway activity scores. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7


text:
What is known about the coding sequence of Factor H in the human genome?
Factor H is a protein coded in 20 domains.
My question is whether these domains form some kind of repeat cluster in the human genome. Basically, I'm interested in the coding sequence from an assembly point of view: Is the coding region fully resolved? Apparently there is only one copy of the gene per haplotype, but are coding domains maybe similar to each other or repetitive in themselves?

As clearly stated in the WP article:

The molecule is made up of 20 complement control protein (CCP) modules (also referred to as Short Consensus Repeats or sushi domains) connected to one another by short linkers (of between three and eight amino acid residues) and arranged in an extended head to tail fashion.

So in your terminology yes, it is a repeat cluster. Each of those 20 domains will be similar to the others, although not identical.

The ensembl entry, which was easy to get to from the Wikipeda page, shows that the protein is one gene with 20 domains
http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000000971;r=1:196651878-196747504;t=ENST00000367429

I don't see how this answer adds anything to what I already mention in the question. The question is whether those domains form a repeat cluster in the genome and whether the full sequence has been resolved in the human genome.

@BlindKungFuMaster your question said "a molecule made up of 20 proteins"; the answer says "one gene with 20 domains". Those are enormously different things.  If Factor H is a single protein and not 20 proteins, then obviously it forms a cluster (called a gene).  What makes you think it is formed by 20 proteins (a claim that isn't substantiated by your wikipedia link)?

The key word in my question is "repeat". Yes, it is one big protein and yes its domains are clustered. If you read my question carefully, you'll see that I mention that it is coded by a single gene. My question is whether these coding domains are "similar to each other or repetitive in themselves". Whether you'll call the parts proteins or not is not substantial to the question, but I'll change it just in case.