How is Open Reading Frame (ORF) chosen? I understand that AUG is the "start codon", and, because of this, most proteins begin with methionine as their first amino acid.
However, this ORF problem on Rosalind.info states that "AUGCUGAC... can be translated as ...AUGCUG..., ...UGCUGA..., and ...GCUGAC".  That is, something (the Ribosome?  The GTP cap mentioned here? Something else?) must cause the translation to be shifted by one or two nucleotides in the sequence.
My first question is :  What mechanism(s) cause(s) this shift in translation to another Open Reading Frame (ORF)?
Specifically, I want to know how the start codon, AUG, can have one ("A") or two ("AU") of its bases ignored in the Ribosome during translation.
My second question is : How often does this happen?  That is, what is the percentage of (known) proteins that start with methionine vs. the percentage that start with something else due to this "ignoring" of the bases of the start codon?
I am interested in the answers for both prokaryotes and eukaryotes.

Tl Dr: In the rosalind example they are showing the 3 reading frames that stem from the definition of a reading frame(non-overlapping triplets), not an example of open reading frames. Open reading frames are non-overlapping triplets between a start codon and a stop codon.
Its important to step back and understand what is meant by reading frame first.  It has been determined experimentally that translation occurs in non-overlapping triplets.  That is to say that if the ribosome starts reading at position n it will translate n, n+1, and n+2 into an amino acid, then it will start at the next non-overlapping position which is n+3.  For example, in the sequence: ABCABCABCABC if you start at A it will read ABC ABC ABC.... But if you start at B you will have an equally valid reading frame by the definition of a non-overlapping triplet and it will read BCA BCA BCA.  If you start at C it will read CAB CAB CAB.  What would happen if I start at the next A? ABC ABC ABC... See how you are back in the first reading frame?  No matter how long a given sequence it will only have 3 reading frames.
Why does that matter if they all start at an AUG?  You don't know which AUG translation starts at.  Not all AUGs are actually used as the first codon in translation, in fact, most are either internal to a translated protein or not translated at all.  An open reading frame is any sequence starting from an AUG to a stop codon.  An open reading frame can be within another open reading frame. E.g: AUGCTAUGGCGAUGUUAGAUGA. All of the valid open reading frames are:
    AUGCTAUGGCGAUGUUAGAUGACUAACUAA

    AUG CTA UGG CGA UGU UAG
         AUG GCG AUG GUU AGA UGA
               AUG UUA GAU GAC UAA
                      AUG ACU AAC UAA


What are the differences between cancer and tumour? What are the differences between cancer and tumour? I mean is it in the DNA or shape or something else... And how can a benign tumour turn into a malignant tumour? The body has a lot of tumours all the time, however not all of them become cancerous, why is this so?

So my main question is: What is so special about cancer cells that they can get out of control unlike an ordinary benign tumour?

A tumour is simply a space-occupying lesion (something that should not be there, that is; a "lump") caused by abnormal cell replication.

(In medicine, the word "tumour" literally means "swelling", and can sometimes refer to that instead, but that's a different story).

Cancer is a disease in which cell replication is totally out of control. What causes cancer is damage to the genes (DNA) which normally stop cell replication when it needs to be stopped.

There's no such thing as an "ordinary tumour"; all tumours are abnormal. However, what makes a benign (harmless) tumour different from a cancerous tumour is that there is still some mechanisms stopping the cells inside the tumour from replicating; they are doing it more than they should, but they are not totally out of control. When those last mechanisms are broken too, the tumour is cancerous.

(This is a simplified explanation; the actual explanation is a semester-long university course. It's mostly accurate for the layman, though)


Type I and Type II Topoisomerases Type I topoisomerase changes the linking number by ±1 by changing the number of twist present in a DNA, breaking only one strand.

Type II topoisomerase changes the linking number by ±2 by changing the configuration of the writhe,breaking both the strands.

Am I right?

The speculations are right.

Topoisomerase I changes the linking number by changing the number of twists and Topoisomerase II changes the linking the number by changing the writhe of DNA.

Confirmed by a college professor.


What happens to the precursor protein's signal sequence after it is cleaved? Where does this signal sequence "go" after it has been cleaved by signal peptidase and what is its next function?

After cleavage, the signal sequence is generally thought to be degraded by intramembrane proteases (since it is embedded in the endoplasmic reticulum membrane). For at least some proteins, the signal sequence is further processed and released into the cytoplasm or ER lumen.

Martoglio B. 2003. Intramembrane proteolysis and post-targeting functions of signal peptides. Biochem Soc Trans 31:1243-1247

  When translocation continues, the signal sequence’s c-region appears in the ER lumen and becomes accessible to signal peptidase, which cleaves the signal sequence from the pre-protein. The latter is further translocated into the ER lumen, while the liberated signal peptide is usually not detected in assay systems, implying rapid degradation. In a cell-free in vitro system with ER membranes from canine pancreas, we reported several years ago that after cleavage by signal peptidase, the liberated signal peptide is transiently embedded in the lipid bilayer and undergoes further processing to be released from the membrane.

The activity of released signal sequences is not entirely known and only partially characterized for some proteins. The following review discusses some functions of signal peptides after cleavage:

Martoglio B, Dobberstein B. 1998. Signal sequences: more than just greasy peptides. Trends Cell Bio 8(10):410-415

The signal peptide of bovine preprolactin and HIV gp160 can bind calmodulin.

  …the signal sequence of bovine preprolactin, which consists of 30 amino acid residues, is cleaved by signal peptidase and then further processed by an unknown signal peptide peptidase (SPPase; Fig. 4) … This signal peptide fragment resides initially in the membrane and, after a chase period, is released into the cytosol. Once in the cytosol, the signal peptide fragment binds to calmodulin in a Ca2+-dependent manner. A signal peptide fragment derived from HIV-1 gp160 also binds to calmodulin when it is released into the cytosol … With their n-regions having the potential to form a basic amphiphilic α-helix and their hydrophobic C-terminal region, they are similar to other calmodulin-binding domains. Calmodulin is a small, acidic protein involved in the regulation of many cellular processes controlled by Ca2+-dependent signalling pathways. It is possible that binding of signal peptide fragments to calmodulin influences Ca2+/calmodulin-dependent cellular signal-transduction pathways. Further studies are required to elucidate the physiological consequences of interactions between signal peptide fragments and calmodulin.

The signal peptides of MHC class I proteins are presented to NK cells by MHC-I (with HLA-E alpha chain). This allows monitoring of MHC-I expression, which is often disrupted in virally infected or cancerous cells.

  Peptides presented by classical MHC class I molecules represent the broad spectrum of peptides generated by the proteasome. In contrast to this general use of peptides, only a very specific signal peptide fragment is presented by so-called nonclassical MHC class I molecules (HLA-E in human). These molecules monitor the presence of classical MHC class I molecules by presenting a signal peptide fragment derived from HLA-A, -B or -C to natural killer (NK) cells (Fig. 5b). NK cells destroy cells unable to activate inhibitory receptors specific for MHC class I molecules.

This book section discusses the function of signal peptides in some viruses:

Kapp K, Schrempf S, Lemberg MK, Dobberstein B. 2009. Post-targeting functions of signal peptides. In: Protein Transport into the Endoplasmic Reticulum, Zimmermann R.


Do fake wasp nests actually fool wasps? I have seen fake wasp nests sold as a deterrent against wasps and similar insects. Do they really work? Is there some scientific evidence for it?

A related link: http://www.scienceworld.ca/do-fake-wasp-nests-fool-wasps

Wasps are extremely territorial creatures. They also have great sight. Wasp colonies will send out foragers and scouts to look for uninhabited areas with food in which they can build a nest. Because wasps are so fiercely territorial, a scout wasp will generally stay away from an area with another colony already in it.

Because of this fact fake wasps nest works!!

Source: http://www.environmentalsociety.ca/main/wp-content/uploads/2011/05/Fact-Sheet-Wasps.pdf


How does a spider's legs not get caught in silk when wrapping prey? When a spider catches a prey, it wraps it up in silk. It uses its legs to do this. So how does its own legs not get stuck on the silk?

Note: I'm not talking about walking around the web. There are non-sticky anchor strands of silk to walk on. I'm talking about when the spider actually wraps something up.

There are two parts to this answer.
Spider Legs
First, I would like to mention that spiders avoid sticking to their webs by more means than just non-sticky anchor strands to walk on.  To help keep the glue from sticking to their legs, an oily substance apparently covers spider legs.  Furthermore, the same study found that:

In addition, Eberhard and Briceno also noted that the spider’s gait seemed specially designed, such that it “reduced the area of contact between the sticky droplets and the setae [spiny leg hairs].” This, combined with the fact that the thread touched many (rather than only a few) branching hairs, made it very unlikely that any glue would slide all the way down the hairs to make contact with the main part of the leg – which would have made permanent adherence more likely.

Spider Wrapping Silk Fiber is Different
The main reason spiders do not get stuck to their silk when wrapping prey is because wrapping silks are different from silks used to make webbing.  There there are seven known types of silk that spiders can produce.  Aciniform, or wrapping silks are the strongest silk from a spider and specifically designed for wrapping.  This silk is typically dry, and does not contain the high amounts of N-acetylgalactosamine which give the distinctive quality of being sticky.   For a very detailed study on wrapping silk architecture, please see this recent study from 2015.


Can someone tell me what kind of reptile is this? It was found in El Paso Texas. It was very scared and weak when I found it. But I bought it a small aquarium and some food to make sure it’s ok before I let it go. It’s tail is broken off. It have blue and yellow dots on top of it and I think it’s a male. Can someone tell me about this lizard?

My guess is that you have in your a hand a lizard of the Genus Sceloporus , and perhaps Sceloporus occidentalis longipes.

Commonly called the Great Basin fence lizard is a subspecies of the western fence lizard . It is genrally found in the western part of North America

Here is  a link to a guide of small spiny lizards .


Merge several .ab1 sequence files into a single FASTA file? I have several .ab1 files generated from Chromas. I want to merge all of them into a single FASTA sequence file. How can I do this in an automated way?

Note that I don't have Chromas installed (the files were generated by someone else). I am using linux, so open-source, command line tools are preferred.

In general you should use a base calling algorithm to generate the sequences from the chromatogram and not directly convert it to fasta (Courtesy: Sven [SEQanswers] ). As mentioned in the link, phred and TraceTuner are popular base calling software that can generate a fasta output.

The software mentioned by The Nightman can be used for converting .ab1 to fasta. You can also try this BioPython module called abifpy. You can easily read each .ab1 file, using a python script, and write the sequences in fasta format as a single file.

Combining multiple fasta is quite trivial. You can use cat as mentioned by others.


Why does our visible range not include infrared or UV radiation? As the radiation peak of the sun is in the UV region and since at around room temperature materials emit radiation at IR, I wonder why our eyes are not capable of using these wavelengths.
I guess there is a reason why we exactly only see the region between these intensity peaks?

Usually we don't ask why in biology because the explanation is always the same, it was good enough for survival. But here are a couple of explanations.
The radiation peak from the sun is in the visible range of the spectrum, between 400nm-700nm with the highest point around 550nm as can be seen here or calculated from Wien's law and the sun temperature.
That's why photosynthetic pigments use the visible spectrum and following them the rest of the ecological system.
Our retina blocks most of the UV light and water absorbs the lower part of the IR, illustrated very nicely in this article, figure 1.
It is true that materials on earth emit more radiation in the IR than in the UV-visible spectrum due to their temperature but:

most objects have the same temperature approximately
the soil emits a lot of radiation
the radiation from the sun in the IR is high compared to the radiation of earth. This is the best graph I found, emphasizing the great difference between sun & earth intensities
in the IR range there isn't a lot of variance in the wavelength intensity and therefore it is less useful.
Notice how uniform the IR reflection is from this leaf spectral signature

To summarize:

UV light is dangerous so we filter it out and not use it
IR light is uniform and not useful
Visible light is the peak of sun emission and therefore the most efficient range to use


Can you identify this bird? Can somebody please identify this bird for me?

I spotted this in July 2012 while birding in Ranganthittu Bird Sanctuary.

This is a Cattle Egret (Bubulcus ibis), which is a heron in its breeding plumage. When not breeding, the bird is white. See the images for comparision:

Breeding cattle egret with colored feathers.

Nonbreeding cattle egret, completely white.


Are probabilities of mutations symmetric? For the premise of this quiestion let's assume that there is an allele A and an allele B. The allele A has a probability P to mutate into the allele B in the given timeframe.
Is it also true that the allele B has the probability P to mutate into the allele A?

The short answer is no, there is heterogeneity in the rate at which different nucleotides mutate into one another. This is generally a property of their differing chemistries (although I'm not an expert on this). Therefore, it doesn't really make sense to talk of alleles being $p$ or  $q$ like we do in most of population genetics, because the actual nucleotide (whether it's A, C, G or T does make a difference).
This is important in fields like phylogenetics, where people construct substitution matrices which describes the rate at which one base in a sequence changes to another nucleotide. Currently, it's possible to estimate the matrix parameters from empirically data relatively easily.
For example, in one of the earliest and most simple models, Kimura (1980) introduced a matrix which had two parameters - one for the mutation rate of transition substitutions (A/C -> G/T, more likely) and one for the rate of transversions (A/G -> T/C, less likely). Later methods got progressively more complex, which account for e.g. the different amino/keto properties of different nucleotides. Felsenstein's model (1981) accounted for the equilibrium frequency of the target nucleotide. These substitution values are also allowed to vary across time as well within a phylogenetic tree (e.g. Yang 1994).

References

Kimura, Motoo. "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences." Journal of molecular evolution 16.2 (1980): 111-120.
Felsenstein, Joseph. "Evolutionary trees from DNA sequences: a maximum likelihood approach." Journal of molecular evolution 17.6 (1981): 368-376.
APA
Yang, Ziheng. "Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods." Journal of Molecular evolution 39.3 (1994): 306-314.


Is sugar absorbed into the bloodstream through the walls of the mouth? If you let a piece of candy melt in your mouth, but did not swallow it, would the sugar be absorbed through the walls of your mouth?

Simple sugars such as glucose, fructose and galactose will be absorbed.

They are most probably transported by a common carrier, which is why if you present both glucose and galactose, the presence of one will inhibit the absorption rate of the other.
Uptake rate also seems to partly depend on the concentration of sodium ions in the buccal cavity. This was identified and explored subsequently.
It seems that at the cellular level, absorption is not the quickest but there is a lot of vascularization which allows it to enter the bloodstream quickly, regardless.

Here's a back-of-the-envelope calculation: about 10mg is absorbed in 5 minutes when you hold a solution of 3.6g/l in your mouth. A normal gulp volume is around 10ml. That's 36mg of sugar in a mouthful. Result: you can absorb 10mg of sugar from a theoretical maximum of 36mg. In other words, within 5 minutes, you absorb ~30% of all available sugar. That's pretty good, given that a sugar solution is not a more concentrated, solid sugary food!

Worthy to note that most complex sugars will not be absorbed. Note that many complex sugars actually won't be uptaken even in rest of the GI tract, like cellulose.

See other posts already here on the topic.


How can calcium be a kept as a local signal in the cytoplasm? We went through this in my class last week and it doesn't make sense to me at all.

It's small and it diffuses in and out so easily so wouldn't it diffuse out quickly and thus not be a local signal? Or where it's stored in the RER does that change things?

As @BryanKrause says in his comment, net flux of calcium would not ever be from inside the cell to outside the cell. There is a large gradient the other direction. Per Berg, the cytosolic concentration of calcium in a resting cell is on the order of 100nM, while extracellular concentration is in the mM range.

Signalling occurs when channels open up and allow $Ca^{2+}$ to diffuse down that very steep electrochemical gradient (from extracellular or topologically similar sources, e.g., the endoplasmic reticulum).

At least part of your question seems to involve a concern that the signal would not be very long lived. Though your concern about it diffusing out of the cell isn't warranted, the question about the time dynamics of calcium signalling is interesting. Calcium signals are, in fact, often very brief (though in other cases they last much longer). This is actually a benefit, and is one reason these signals can have very localized, very brief effects. For localized membrane fusion events, e.g., exocytosis, the signal lasts on the order of microseconds. The control of the time and position of a calcium signal involves a large number of players, including sequestering proteins, various compartments and stores, and tight control of the balance between calcium on and calcium off signals. It is discussed in this nature review, and summarized in this simplified figure:

You might also be interested in looking at some videos of calcium signalling. There are a number on youtube. This is one example


Are some people more 'attractive' to mosquitos? If so, is that a hereditary trait? Mosquitos clearly love me-- but I have been told I am just more reactive to mosquito bites. Are some people more 'attractive' to mosquitos (get bit more)? Or is it just that they are more reactive? If it is an 'attractive' trait-- is this hereditary?

There is a genetic component to mosquito's attraction to humans.

  Female mosquitoes display preferences for certain individuals over others, which is determined by differences in volatile chemicals produced by the human body and detected by mosquitoes. ... Overall, there was a strong narrow-sense heritability of 0.62 (SE 0.124) for relative attraction and 0.67 (0.354) for flight activity based on the average of ten measurements. The results demonstrate an underlying genetic component detectable by mosquitoes through olfaction.

--Heritability of Attractiveness to Mosquitoes

  However, analysis of a comparative rating variable "compared with your twin, who is bitten by mosquitoes more often?" indicated a strong genetic influence on frequency of being bitten by mosquitoes, with no significant differences observed between males and females.

--Twin study of adolescent genetic susceptibility to mosquito bites using ordinal and comparative rating data.

There are many other influences on how attractive people are to mosquitos, including diet, alcohol consumption, and various disease conditions.


How difficult is to renature a protein? I know of Anfinsen's experiments and I'm aware that some denatured enzymes may regain their lost activity through the removal of the denaturant agent. What I'm unaware of is how rare is it for a protein to be able to renature? Can all proteins do that? If not all of them can do it then how rare or common is it to find a protein which can be renatured?

P.S. To avoid answers like "depend on your denaturation process" let us assume that a protein can be renatured if it has been shown to renature in at least one experimental setup.

The answer is more like "It depends on the protein, and the renaturation (or refolding) process." There are a lot of factors that contribute to an individual protein's ability to refold, including size, sequence, secondary structure, amount and type of inter-amino acid links like disulfide bonds, number of subunits, the presence of chaperones/heat shock proteins, and, yes, how it was denatured in the first place (sorry, I couldn't resist). Smaller proteins will refold more easily than larger ones. Hydrophilic proteins tend to refold better than more hydrophobic ones, especially membrane-bound proteins. Multi-subunit proteins/complexes tend to need some help to properly reassemble. Adding in chaperones/heat shock proteins will almost certainly help the process along for all but the smallest and hardiest samples, and will give you better results than just dialyzing all the salts/detergents/chaotropic agents away into PBS. Finally, if you denature by boiling in Laemmli buffer, you're going to have a very difficult time refolding most things, while going from Guanidine HCl to PBS isn't always that bad, depending on what you're looking at.

So, unfortunately the answer is "it depends." You have to remember that the intracellular environment is very complex, and is designed to correctly fold proteins after they're made, and break down misfolded proteins before they can aggregate or cause other damage. There are hundreds of thousands of proteins just in humans, so it is rather difficult to make blanket statements, but for the sake of resistance to damage, many smaller, single-subunit proteins can likely be at least partly to mostly refolded and regain some or all of their original activity. As complexity grows, however, the likelihood of successfully regaining function decreases.


Can animals make their own unsaturated fatty acids? I know that animals can't make poly-unsaturated fatty acids (PUFA) and so require them from dietary sources. For eg.Omega -3 and Omega 6 fatty acids.

My questions : Can animals synthesize other unsaturated fatty acids from scratch? If not, does the unsaturated fatty acids in the phospholipids of plasma membrane of animals come only from dietary sources?

Yes, animals can make their own unsaturated fatty acids.

Mammalian fatty acyl desaturases can introduce double bonds at the Δ5, Δ6 and Δ9 positions (i.e. numbering from the functional group). As shown in the diagram below, this means that we cannot introduce double bonds at the ω3 or ω6 positions (i.e. numbering from the methyl end of the molecule) in fatty acids of a reasonable length (see any Biochemistry textbook for confirmation).

I've illustrated the impossibility of us making α-linolenic acid as an example.


Why is mammal coloration so dull? I have seen species of birds, insects and fishes with splendid colours. But when it comes to mammals (including us humans), they almost always appear in shades of brown, grey, orange, or in black and white. I don't recall seeing any pink, green and purple. Why is that so?

I don't think, there is a precise answer about the evolutionary mechanisms, but "mechanically":

mammals have principally just two types of pigments: eumelanin and pheomelanin, both of which have their color variants, but within a known range. Bird pigments, besides melanins, include carotenoids and porphyrins. Arthropods generally have carotenoids, melanins and ommochromes [and other pigments?]. E.g. carotenoids and ommochromes alone can create rather "exotic" coloration from a mammal point of view (green, pink, violet).
both birds and insects actively utilize iridescence. With fur it seems to be technically much more difficult to achieve than with feather or scales.
many (most?) mammals do not differentiate colors. Birds have much better vision abilities in this respect. From a selectionist point of view this cuts out a considerable part of selection acting upon coloration, which could otherwise produce broader spectrum of phenotypes.


Are “tremors” and “ tetanic contractions” the same thing? Do these two expressions have the same meaning?
1- Tetanic contractions in the skeletal muscles
2- Rythmic shaking of the hands
(These two expressions are supposed to be two symptoms of Parkinson’s disease ,however I am told that this is repetition)

Tetanic contractions and tremor are different phenomena.
Tetanic contraction (or tetanus) refers to sustained contraction of a muscle subjected to high-frequency stimulation. With this high frequency, a new contraction begins before the previous one has ended. Thus the contractions get 'summed up'. You could see this interesting video for a demonstration.
Tremor is an involuntary shivering movement which is caused by alternating contractions of opposing muscle groups. The causes are many, ranging from physiologic tremor to degenerative disorders of the nervous system (such as Parkinson disease).
Note that tetanic contractions are not a symptom of Parkinson disease. In fact they are not a symptom of anything at all, inasmuch as they are a physiological property of isolated muscle. Tremor, on the other hand, is a phenomenon seen in muscle groups, and is one of the core symptoms of Parkinson disease.


Why aren't there any competing biologies on Earth? Why aren't there any competing biologies on Earth? I read sci-books about life based on silicon and I've read an article that said that other structures than DNA can encode genetic information.
So does physics allow for many competing biologies? What makes DNA-based biology the dominant biology on earth according to known laws of physics?

There are indeed almost certainly other potential alternatives to DNA-based biology and the RNA-based biology that may have predated it, which could be used to form viable organisms.
Many of them likely have some energetic disadvantage relative to DNA and RNA (e.g., requiring a higher bond formation energy, having a less flexible backbone) and those would naturally be expected to be outcompeted. But some probably aren't so different from DNA and could indeed have formed a viable alternative---if nothing else, the opposite chirality molecules are certainly candidates. Why aren't alternatives still around?
Surprisingly, it turns out that when time scales are long enough, we should expect a natural loss in the number of different independent lineages. Another more recent example of this is the fact that all modern humans are descended from Mitochondrial Eve and Y-chromosome Adam, despite the fact that these two individuals were members of thriving human populations at entirely unrelated times. Biodiversity is constantly being gained through divergence of existing lines and lost through lines that fail to reproduce. Over many generations of reproduction, this produces a random walk pattern that converges toward elimination of all but a single lineage in a given population even if all lineages are equally fit.
Now back to the origin of DNA-based life.  If abiogenesis is a rare and difficult event, then we would expect only one or a small number of life models to have emerged billions of years ago. Random fluctuations over all that time will tend to drive all but one toward extinction. With evolution at play as well, any lineage that randomly gains an advantage will be even more likely to outcompete the others.
And once there is life of any sort around? Well, potential alternatives to DNA are still nutrients, and therefore will simply be eaten by existing life forms before they have the chance to evolve into something new and interesting.


Genetic pros or consequences of children born to parents of mixed nationalities? I've gleaned a potentially flawed impression over time that a more diverse gene pool should, in theory, result in healthier progeny. Something about dominant genes promoted over recessive genes..

As a result of the above, I always assumed I should favor a mate from another region if I want to have children, thus hopefully ensuring the children have a diverse mix of DNA bits to assemble out of.

I'm an American male (almost 38), and by a curious chance I find myself dating a Russian female (almost 29) who is in a US PhD program. We've been together a little over a year, and we've discussed marriage/children. So far so good.

However there's an observational wrinkle.. She sometimes associates with a local group of Russians and I tag along. Not long ago at a gathering with several young families, of which I think many are mixed-national (Russian and American), I was discouraged to observe what I thought was a disproportionate number of children with various disorders. If memory serves, there were 2 or 3 autistic and one down syndrome child out of about 11 or 12 kids of the same age.

[It might be worth noting that this is a church group. Church might provide a kind of social safe-haven that allows these families, particularly the children, to socialize with fewer concerns. As such it might make sense to see them in greater numbers.]

Anyway, suddenly I'm doubting my prevailing assumption about genetic diversity and wondering if there is a correlation between autism and the children of parents of mixed nationalities.

In this article, I read:

  In the studies conducted in Nordic countries, a statistically
  significant 58% increased risk of autism was observed among the
  offspring of mothers born abroad.

So I find myself vexed. Is there a propensity for genetic challenges in children born to parents of mixed nationalities?

(FWIW I realize our ages dip into another risk factor, but I'm specifically asking about regional genetics.)

Did you read the rest of that article? The authors suggest many alternative possibilities for the effects they observe:

  Several hypotheses have been postulated, including the idea that fathers with social disability potentially due to a genetic mechanism associated with autism may be less able to find a spouse from their own country and may therefore find a wife from a foreign country with whom to have children91. More likely, Gillberg et al.91 suggested that women born in another country may not be immunized against the common infectious agents in the country in which she gives birth and may therefore be more susceptible to relatively innocuous infections which may increase the risk for autism. Other possible explanations include a potential role of maternal stress due to the demands of residing in a new country, particularly with limited social support, or stress resulting from the experience of emigrating, perhaps due to economic or social factors. These hypotheses do not explain the relationship with maternal place of birth seen in a cohort study of children born in California between 1989-199416, which showed a 40% decreased risk of autism among the children of women born in Mexico as compared to California. The association between maternal immigration and autism risk requires further examination in other areas of the world to examine whether the relationship can truly be generalized.
  Gardener et al., 2009

(emphasis mine)

In addition to these factors, note that p-value for that trend was only .06, and although there are a lot of problems with basing conclusions on fairly arbitrary p-values, a p-value of .06 suggests that differences of the magnitudes observed would often occur by chance. I'd say it's an area of open study, but it is quite a leap to jump to a conclusion that mixed nationalities result in higher incidences of things like autism from 1) the observation of a very small cohort of 12 children and 2) this other study which suggests many alternative possibilities for what is a small and possibly insignificant effect.

There are two main benefits for populations to avoid becoming inbred. The first is that there may be many deleterious alleles with low-incidence across a whole population, but you have a very high likelihood of producing a homozygous recessive offspring with a close relative. The second is overall maintenance of genetic diversity across a population, which could be important if suddenly exposed to a new disease, for example.

However, it is also possible for outbreeding depression to occur, which is a reduction in fitness after mating genetically distant individuals. However, outbreeding depression usually occurs either when fitness of some variable is low at intermediate values: for example, high fitness for small or large animals, but not for medium-sized animals, perhaps due to slightly different niches within the same species. Outbreeding depression can also occur when there is sufficient genetic separation between two individuals such that their whole protein milieu has evolved on a different background, such that alleles that cause no problems in either population alone are incompatible with alleles in the other population.

This previous answer here on Biology.SE talks about the lack of evidence for outbreeding depression in humans and a bit about why. Briefly, there is simply not the type of disparity in fitness conditions or sufficient genetic variability within humans for either of those situations to occur.


Does the brain process sound in "clips" or "frames"? I've always been under the impression that our brains process images (relayed to it via the eyes) at a particular frequency or "framerate"; this is supported by lots of sources, such as this one.

I'm wondering how close this compares to the way our brains process sounds:

Do we sample "snippets"/clips of sound? If so, is there any evidence as to how long (duration-wise) these "clips" are? Do we "sample" at the millisecond level? Microsecond?; or...
Do we actually sample "sound frames" (much like we do with visual images)? If so, how does our brain process a "frame" that contains multiple noises occurring at the same time (say a dog is barking at the same time the television is on)? After all, a frame is all the input for an instantaneous point in time, versus a clip, which is all the input over a period of time.

Any ideas?

In your question, you ask about processing and sampling. I'd like to make a distinction between sampling, which in my view does not have a framerate, and perception which there is some evidence that there is sort of a framerate (though not as concrete as the framerate of a video display, for example). Processing is everything in between, and as such, whether it shows "framerate-like" behavior depends on the stage of processing.

Does vision really have a framerate?

The "framerate" depicted in those sources for vision is sort of a special case, talking about perception of a particular stimulus. There are no real "frames" in your vision, only temporal averaging (because phototransduction is quite slow on the timescale of neural processing in general). The article you link makes a mistake in logic in concluding that humans have a frame rate: the research they cite is about discriminating between separate flashes, which is an issue of temporal averaging rather than framerate. There is a separate issue, which is whether perception correlates with particular oscillatory frequencies; I'll get to this later in my answer.

If you flash a very bright 1 ms light, and record it with a video camera, you will often miss the light entirely (or it may appear only in part of the image, depending on the scanning pattern of the camera). With vision, though, you will always see the light, and for very brief flashes you will perceive changes in duration as changes in intensity.

The other contributor is the "magic" of perception: effectively, what you perceive is not directly the signals that come in through your eyes but rather the model your brain makes for the world based on that information. This process is the origin of all perceptual illusions; the appearance of "backward" images like with a spinning wheel is one example.

Our current model for how processing of sensory stimuli works in the brain is that there is a functional hierarchy with significant abstraction at higher levels of the hierarchy. As you get to higher order levels of processing, you will cease to see the "pixel information" and simple edge/feature detection, and begin to see more abstract representations like detection of particular visual objects or encoding of object velocity.

Okay but the question is about auditory stuff..

It's easiest to start with vision simply because, for better or worse, it is best studied historically. For auditory processing, there are a lot of similarities with vision even though the input stimuli start very different. At low levels of processing, auditory neurons are well described by spectro-temporal receptive fields. At higher levels of processing, you will instead see representations of whole features in sounds, such as phonemes.

Object segmentation is a very difficult problem in both vision and hearing (and a difficult task for computer/AI-based versions of those senses, as well). This is definitely an active field of research, but there is good evidence that some segmentation is present throughout the cortical hierarchy (for example, see here). There are no concrete answers for 'how' exactly segmentation works, just that it does, some evidence for where it might be happening, and some understanding of factors that make it harder to segment different sources. Sound localization is certainly one of the key factors, though segmentation can occur even when there are no localization cues. For example, if you have multiple speakers on the radio, or multiple musical instruments playing, there are some shared spectral characteristics of the speakers or instruments

Discrete signals in cortex

All that said, this does not mean that the brain is free from any discrete elements of processing (like "frames"), although it probably doesn't make sense to think of a frame rate but rather a type of "threading". There is recent strong evidence that activity in the neocortex can be organized into packets of activity that contain sensory or other information. So even though the auditory stream is sampled continuously, that continuous sample is most likely distilled into discrete auditory objects that reflect both the content and source of those stimuli.


If life is discovered on another planet, will it likely be classified using the current domain/kingdom/phylum system? This may be a stupid question showing my lack of understanding of taxonomy, but I was wondering if the current classification system we use contains broad enough categories to include new life forms, if they are discovered on other planets?  Would this depend on whether or not the new organisms could be shown to be evolutionarily related (eg have DNA), or are the highest levels of organization independent of relatedness and more dependent on physical similarity?

Background

There are basically three highest taxonomic levels: bacteria, archaea and eukaryotes. Many sources distinguish only prokaryotes and eukaryotes, subdividing prokaryotes into bacteria and archaea. Other sources posit archaea as a third domain on the highest level. That's a long debate though and fortunately not the topic here.

By appearance, the dual-domain system makes more sense because archaea and bacteria look very much alike under a microscope, and can both be clearly distinguished from eukaryotes (which have membrane bound nuclei). At the same time, comparing genetic structure and the protein machinery that interacts with DNA, eukaryotes and archaea are very similar and bacteria are clearly different from both of them. This demonstrates how appearance and molecular organisation have been typical criteria for distinction between branches of the evolutionary tree.

There are, however, many features that even those three most basic branches of life share, and they are in no way simple or few in number. For example, all extant life uses DNA to store genetic information and proteins for almost all processes governing the various reactions going on at any time in a cell. However, RNA for example is able to perform both the information storing function of DNA as well as the catalytic functions of protein. This just shows how the principles behind life are not unique to the molecules in use now, and extraterrestrial "life" may work by the same principles on an entirely different molecular basis.

Extraterrestrial life

If you want to know whether life found on another planet could be fit into our current classification system, the answer would be: No, most likely it will not be classified using the current domain/kingdom/phylum system. This is because our system describes evolutionary descendency, so unless this newly found life shares some common ancestor with an organism on earth, it would have to be classified in an entirely new system. (Of course this is subjective as you may find it more likely that it does share a common ancestor [Panspermia], while I personally find it more likely that life would have evolved entirely separated on this other planet seeing as we haven't heard of any life within reasonable distance.)

However, it is possible that this new life will follow the same evolutionary rules such as natural selection, and similar evolutionary pressures may drive to evolve similar properties. It may then be possible to draw parallels to characteristics of the current classification system, especially based on molecular function, and possibly appearance (micro- and macroscopically).


Saliva test for Toxoplasma gondii? I am trying to find some reliable gene kit by which you can rapidly test Toxoplasma gondii.
I am not sure if it exists.
I have an intuition that some tests done during 90s-00s on this species had high false negatives.

Which genes should you detect to find Toxoplasma gondii in a gene kit?

All research on saliva tests I've found involve antibody detection which, as you suspected, can produce false negatives depending on the disease process or the presence of immune disfunction (such as due to AIDS). Thus, if you can isolate T. gondii gDNA from the saliva, a genetic assay may be more sensitive. However, Amato Neto et al. report:

  In 26 patients with AIDS, including six with tomographical evidence suggesting cerebral abscess caused by Toxoplasma gondii, no parasites were found in the saliva by the use of the mouse inoculation model. This trial [suggests] that the search for Toxoplasma gondii in the saliva is not an alternative method for the diagnosis of toxoplasmosis in patients with AIDS.

So perhaps the most difficult aspect of generating a gene based saliva test is actually isolating the parasite from the saliva. I was unable to find other isolation attempts, but my research was very brief.

As for which genes to detect, studies involving human blood samples have found that PCR amplification of B1 paralogs provides a sensitive and selective method for detecting T. gondii. Burg et al found that there are about 35 copies of the B1 gene in T. gondii and also state that:

  Because of its repetitive nature, the B1 gene is an attractive target for detecting T. gondii parasites through amplification of B1-specific DNA.

They were able to amplify and detect the gene from crude cell lysate as well as from purified DNA samples containing a 1:10 000 ratio of parasite to leukocyte. Furthermore, they could not detect the gene when assaying other organisms. Ho-Yen et al. later attempted PCR amplification of the same genes in human blood from patients with suspected toxoplasmosis and found that:

  PCR can be reliably used on human blood samples. For a reference laboratory, this is a valuable addition to its array of diagnostic tests, and provides a more rapid assay than animal culture.

Jones et al. compared detection of the B1 genes with P30 and 18S rRNA genes in aqueous humour. They were able to detect 50 fg of gDNA using the B1 assay, which is equivalent to a single parasite. They concluded that:

  The B1 PCR protocol appears to be the most sensitive protocol in the detection of T. gondii DNA and has been successful in identification of T. gondii DNA in ocular fluids and retinal sections.


What are the minimal chemical requirements for a food which we all can eat? I've been puzzled by the following though experiment for the past few days:

I want to make my own food from scratch, but I do not know where to start from.
I want to be 100% sure that what I eat will never contains something that can damage my body. For example: If you buy something from the local market you can not be 100% sure that it's safe to eat. (99.9 % maybe... but that's not 100%)

I want to ask you to tell me, how can I make a food that I can eat, or should I say - live on it, for the rest of my life, that's 100% safe, I can control every aspect of it's creation and has many combinations of taste because I love diversity.

Thank you for your time : )

Edit:
Because I realized my question is very broad and indeed is a little... too much scientific I want to close it. But before I do so, here's what I had in mind:
I wanted to take some chemical elements, put them in a jar, run some electricity, heat, whatever through it, filter it, do some additional processing and eat it.
 I wanted to know if the stomach can take it, because I was going to eat food that's not hard to digest.

Considering the three basic biomolecules used by the body are carbohydrates, lipids, and proteins, you would need to consume these three molecules only. Now we can choose three substances.

Glucose, one of the most basic carbohydrates, is needed for ATP production, so that would be a food choice there.
Any oil or butter will provide lipids.
Protein comes from a variety of sources. Meat is typically though of as the best, but nuts are a pretty good source too.

Since nuts satisfy proteins and lipids, I'd say honey roasted peanuts are the most basic food you could live off of, if you replace pure glucose for the honey.


Mendelian dominant trait involved with Hypodontia If the absence of teeth is a dominant trait, then why is it not seen in generations? My teacher taught that absence of teeth is a mendelian dominant trait, but why don't we see this trait if it is dominant?

Hypodontia isn't a single gene phenotype, but a poli-genic mechanism involved with epistatic phenomenons and environmental scenarios.

The trasmission isn't clear till now, but when you're talking about a poli-gene phenotype isn't so easy to describe the way in which the trasmission is performed. You could find every info about this disease here, in a meta-review study:


How to find Exons in mRNA Computationally I'm having trouble finding a method to find exons in the original DNA sequence used to create the mRNA, even given the sequence of the mRNA, as I cannot find a way to reliably identify the beginning and end of introns and exons. Is there an algorithm or method that I can use to do this? What information am I missing to be able to find the beginning and end of exons and introns?

Thanks in advance for answers.

The only information you are missing is a way to identify the splice sites. There are many ways of doing what you need. The simplest, assuming you are sure of the origins of the mRNA, is to use a BLAST flavor, either plain BLASTn or, even better, BLAT, to compare your mRNA sequence to the genome of interest. BLAT really should be all you need if the mRNA comes from the genome you are aligning it to.

BLAT however, has no knowledge of splice sites and will simply cut your mRNA so as to maximize local alignment scores. If you need something more sophisticated than BLAT, use a specialized aligner as @SteveLianoglou suggested. These programs include a model of splice sites (both canonical and non) and will align exons correctly. My personal favorite is exonerate.

Assuming you are using Linux (which you should be if you are planning on doing a lot of this type of analyses), you can install it on a Debian based distribution (such as Ubuntu and its variants) with this command:

sudo apt-get install exonerate

Then, to align the mRNA to its gene do:

exonerate -m est2genome -n 1 mrna.txt dna.txt > out.txt

-m is the model that exonerate will use to align your two sequences. Since the important thing in your case is to correctly model splice sites, you should use either est2genome or, if you are comparing different species, coding2genome, or if you have a full length cDNA including UTRs, cdna2genome.
-n 1 means find the best match only. Assuming you are aligning an mRNA to its coding gene, this is all you are interested in.


Is this a venomous (poisonous) spider? Today I found a spider in my home that I have never seen before.
I live in Karachi, Pakistan.

I want to know which spider is this and if it is venomous and danger for me or my family ?? Is this spider commonly found in homes. I have seen many home spiders but they were never like that.

The spider is around 2cm long (front legs to back legs span as shown in 1st image)

This looks like either a young or rather hungry Theridiid spider.  I am not particularly experienced with Eurasian spiders, but as far as I know, the only Widows you're likely to come across in Karachi are either the Redback (Latrodectus hasselti) or the relatively non-problematic Brown Widow (Latrodectus geometricus).  This does not appear to be either of these - the front pair of legs is nice and long, but the abdomen is too plain and the bands at the leg joints are not particularly dark brown and contrasting.

Young female Brown Widow from Bug Guide:

Male Widows, both Black and Brown, tend to have small, rather stripy abdomens, and as adults, will have enlarged ball-like structures at the end of the face-mounted pedipalps.

Male Black Widow from Bug Guide:

That just leaves one of the medically unimportant Theridiids as the most likely candidate, and that's where I unfortunately cannot help any further.  Still, the rule of thumb is that unless you identify it as a problem biter, it's not worth worrying about.  The trick is to look at its underside.  If it shows a red hourglass, it's a problem - if not, no worries.
Judging by the photos, I'd go with "no worries", unless you can come up with a clear image of something troublesome.

I include references to support my claims regarding the distribution of Widows in Pakistan:

https://pdfs.semanticscholar.org/f7c7/3ec7c79da6b3b685e4f05649069c4717803e.pdf

http://eprints.iisc.ac.in/15097/1/First_report_of_the_brown_widow_spider%2C.pdf


Heterochromatin v Euchromatin. Which is more abundant? So I was just reading that whether heterochromatin or euchromatin is more abundant in a particular human cell depends on how active that cell is. But considering that most of the 25,000 or so genes in the human genome are transcriptionally inactive in any given cell, how is it possible for cellular activity to affect the chromatin structure to a degree that significantly alters how a nucleus looks on microscopic images? Since, after all, whether the cell is active or not will only affect little of the chromatin.

And since most of the genome is inactive, shouldn't it be in a heterochromatic form, and thus most of the chromatin in any given cell will be heterochromatin?

(I know this is not true, but I was wondering why)

Percentage of euchromatin varies between cell types and organisms. It has been shown that upto 88% of the human genome is transcribed; a phenomenon called pervasive transcription [1]. Highly specialized cells may have a lower percentage of transcribed regions and in females one entire X-chromosome is silenced (some regions in the silenced-X do show transcriptional activity).

Euchromatic regions not only constitute the geneic regions but also regulatory intergenic regions such as enhancers, locus control regions (LCR), silencers etc. It has been found that ~97% of these elements fall in the DNAse hypersensitve (DHS) region of the chromatin [2].

DNAse hypersensitivity is directly proportional to the chromatin state such that open/accessible regions are more prone to DNAse-I digestion. You may call these regions as euchromatin.

Though the total DHS density is not reported in the paper [2] or supplementary data, the ENCODE project that the paper concerns, will have all the detailed information. You can can find these datasets here, from which you can calculate DHS density distribution for different cell types. However, most of these cells are actually cell lines and not from primary tissues.


de novo assembly applications Hey I hope this question supposed to be in this forum.

I'm not from the biology community, I'm from the data security community so im not familiar with the words you might use for answers

I need to use an algorithm that very similar to the de novo assembly algorithm.
I'll try to explain myself better I've some sequences of '1' and '0' all of them are pieces of one big sequence.

I've seen some applications that work with this algorithm such as SPAdes tadpole and Geneious but i couldn't make any of them to work for me except the Geneious because it was the simplest.

Geneious is not good for me because i need something that i can use by command line in the terminal
what application do you recommand me to use that i give input the sequences and the output will be the big sequence.

BTW, in the Geneious I've used a FASTA file for my sequence where my '0' and '1' translated to 'C' and 'D'

Thank you very much wait for your answers :))

You can try Velvet, but you'll likely end up with thousands of contigs unless your expected reference genome is pretty simple. This question hits many of the difficulties with de novo assembly. I'm also not sure what you mean by this:

  BTW, in the Geneious I've used a FASTA file for my sequence where my '0' and '1' translated to 'C' and 'D'

Are you trying to use this for a purpose other than actual genome assembly? You say you're from the data security field, so it's unclear what's your end goal. If you only have a binary sequence, you better have a really long read length and hope there aren't too many repeats or you'll really have issues finding a consensus sequence.


What biological processes can affect the temperature of the shadow a tree casts? Assuming two trees have similar shape and leaf coverage, could differences in the biological processes among them lead to differences in the temperature of the shadow they cast?

What biological processes occurring in plants could affect this? I was thinking that transpiration will cause heat loss, and photosynthesis also absorbs energy, so these would contribute. What other processes that occur in a tree could affect the dissipation of heat causing cooler shade?

Has there been any studies specific to rates of transpiration and photosynthesis, and the effect on shade temperature?

The short answer is NO. A shadow is strictly due to the blocking of sunlight, so the shadow of 2 equally non-transparent (i.e., same density of leaves, both have similar trunk diameter, etc.) trees on the same hillside in the same weather conditions would not have different temperature shadows.

A plant's metabolism can and will affect the temperature surrounding the tree, but this affect is lost almost immediately as you move away from a tree. For example, in a study I did a few years ago measuring spruce tree temperatures (unpublished), we found that even within 5-10cm from the tree, the rise in ambient temperature was no longer measurable.

You're correct that the leaves of plants will absorb sunlight and as a result will increase in temperature. Walter Loomis's (1965) paper, Absorption of radiant energy by leaves (found here), suggests that leaf temperatures can raise to 30 $^\circ$C or more. However, he notes that their study found that even wind speeds of 5mph instantly cooled the leaves via conductive heat transfer. Our study with spruce trees also found this to be true. Transpiration will further help the tree rid itself of that increased temperature fairly quickly. Regardless of these facts, radiant energy from leaves in the canopy will not be felt how-ever many meters below within its shadow.

Finally, yes, transpiration can affect local climate, but this is only on the scale of whole forests. The transpiration of a single tree will likely not impact the ambient temperature around itself in any measurable way, especially at any distance greater than that I've already mentioned.


Where would vegetarians/vegans get a substitute of hemo/myoglobin from? As far as I understand, there is a difference in the iron absorbed from meat than from other sources like grains and vegetables.

If this is the case, is it possible that not ingesting the hemoglobin and myoglobin found in meat leads to some kind of deficiency in a protein or iron itself that creates some symptoms similar to anemia, like fatigue or headaches? Or, is the iron found in non-meat products just as viable as that found in meat-based products?

The following informations is taken this source. It also lists some references. If this doesn't answer your question let me know in the comments.

Iron is found in food in two forms, heme and non-heme iron. Heme iron, which makes up 40 percent of the iron in meat, poultry, and fish, is well absorbed. Non-heme iron, 60 percent of the iron in animal tissue and all the iron in plants (fruits, vegetables, grains, nuts) is less well absorbed. Because vegan diets only contain non-heme iron, vegans should be especially aware of foods that are high in iron and techniques that can promote iron absorption. Recommendations for iron for vegetarians (including vegans) may be as much as 1.8 times higher than for non-vegetarians.

Some might expect that since the vegan diet contains a form of iron that is not that well absorbed, vegans might be prone to developing iron deficiency anemia. However, surveys of vegans have found that iron deficiency anemia is no more common among vegetarians than among the general population although vegans tend to have lower iron stores.

The reason for the satisfactory iron status of many vegans may be that commonly eaten foods are high in iron.For example, you would have to eat more than 1700 calories of sirloin steak to get the same amount of iron as found in 100 calories of spinach.

Another reason for the satisfactory iron status of vegans is that vegan diets are high in vitamin C. Vitamin C acts to markedly increase absorption of non-heme iron. Adding a vitamin C source to a meal increases non-heme iron absorption up to six-fold which makes the absorption of non-heme iron as good or better than that of heme iron.

Fortunately, many vegetables, such as broccoli and bok choy, which are high in iron, are also high in vitamin C so that the iron in these foods is very well absorbed. Commonly eaten combinations, such as beans and tomato sauce or stir-fried tofu and broccoli, also result in generous levels of iron absorption.


Why do RNAi pathway proteins exist in the nematode when they can cause them harm? When dsRNA is injected in plant, Dicer cuts it and prevents disease.
Why would the plant parasite, M. incognita - a nematode,  die when dsRNA was injected in it? It should have saved it.

Again, to be more clear M. incognita has Argonaute protein and other RISC components for eliciting RNAi. This causes its death.

Then, why does the worm have such factors which cause its death?

There are many studies that have used RNAi against the plant parasite M. incognita. The fundamental idea is that RNAi is directed against one of the vital genes of this nematode. Since, RNAi causes downregulation of the target gene, the nematode dies (or becomes ineffective in infecting) because of the loss of function of these important genes. As you might know about the process of RNAi, dsRNA (or hairpins) are cleaved by Dicer and the small single stranded RNA products, called siRNAs, associate with Argonaute proteins to form RISC (RNA induced silencing complex). The RISC will cleave RNAs complementary to the siRNA.

If you see any of these articles you will notice that the dsRNA is not injected into the nematode; it is expressed in the plant. Nematodes (such as this one and C.elegans in which it is quite well studied) can take up dsRNA from the environment via the RNA transporters present in their cell membranes (See this post).

Now, coming to your question on "Why do RNAi pathway proteins exist in the nematode when they can cause them harm?"

endo-siRNA and miRNA mediated silencing pathways have critical roles in the nematode development and other miscellaneous functions (See this review). As you already know, RNAi can also serve as a defence against dsRNA viruses.

It is us, humans, who have exploited this pathway to develop tools for molecular biology and for targeting parasitic organisms. There is certainly a likelihood that the host plant may express the dsRNA against the nematode during the course of the evolution of its anti-parasitic defence system (it is however not the case now). Not just RNAi, there are many other examples of endogenous pathways of a pathogen being exploited to kill the pathogen.


Activity of DNA glycosylase I am wondering how DNA glycosylase works from the chemical point of view. Sometimes in papers I can see that they are doing activity assays with 1M NaOH and I am trying to understand why using 1M NaOH is more factual? Thank you for any help.

DNA glycosylases bind to dsDNA, flip a base out of the base-paired double-helical structure and cleave it off, leaving the sugar-phosphate backbone intact. This base removal renders the DNA susceptible to alkaline cleavage.

In this recent paper:

  Miyazono et al. (2014) A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi. Nature Communications 5: #3178

the authors monitor the activity of a DNA glycosylase using this phenomenon: after treating an oligonucleotide with increasing amounts of the enzyme R.PabI they treat the DNA with NaOH so that the oligo is cleaved, allowing detection of the result of enzyme action on a polyacrylamide gel, as you can see from this image, taken from their Figure 3.

Incidentally the same phenomenon is exploited when DNA is transferred to a membrane for Southern blotting. After electrophoresis the gel is soaked in acid which causes depurination (analogous to DNA glycosylase). It is then transferred to an alkaline solution. Although protocols often refer to this as a neutralisation step it actually breaks the DNA at the apurinic sites and separates the strands. This cleavage is important for effective transfer of larger fragments from the gel to the membrane.


Effect of light intensity on the frequency of stomata According to this article, the frequency of stomata increases with an increase in the intensity of light. What I inferred from this is, since the rate of photosynthesis increases at higher light intensities, more C02 is is required and hence the frequency of stomatal openings increases.

I know that the Light Harvesting Complexes inside chloroplasts use light to release electrons, which are then subsequently used in photophosphorylation. If we compare the process with the photoelectric effect, we shouldn't see an effect of the intensity of light, but instead we should see changes for different frequencies(which we already do).

So how does the rate of photosynthesis increase with higher light intensities?
Is the mechanism of light absorbtion by LHCs similar to that of a photoelectric cell?

You are misunderstanding photoelecric effect.

Intensity of light does not have effect on maximal kinetic energy of individual ejected electrons. Maximal kinetic energy of ejected electron is determined by energy it can get from single photon which is in turn determined by frequency of light.

However, intensity of light definitely does have effect on number of ejected electrons. More incident photons (higher intensity of light) result in more ejected electrons (and higher measured electric current).

In photosynthesis number of utilized photons is more important than their energy. Photon either does have enough energy for separating the electron (e.g. red or blue light) or it does not (e.g. infrared light). If a photon with energy higher than needed (e.g. blue light) is captured then the excess energy dissipates to heat.


What are the floating translucent little objects called in the field of view? Sometimes we see these small translucent shapes moving by when the eyes are open. When the eyes are moved they seem to follow that movement, but with a certain delay, as if they are floating in a thick viscous liquid. What is this phenomenon called?

I think you are talking about floaters (a.k.a. eye floaters or flying flies). You may want to have a look at this english.SE post in case you were not talking about floaters.

  Floaters are deposits of various size, shape, consistency, refractive index, and motility within the eye's vitreous humour, which is normally transparent.

You can read the wikipedia article to better understand the causes. These floaters are typically not microorganisms unlike you seem to think. Their scientific name is 'Muscae volitantes' and they are mostly caused due to degenerative changes in vitreous humour due to aging.


Why is living on land beneficial? When fish started developing the stronger limbs needed to walk(Slither?) onto land how was this beneficial? I cannot think of any form of food that would be helpful that would not be plentiful in water, but it must have been so as from what I can tell most beneficial mutations tend to be either a better way to either survive or obtain nutrients.

Insects were the first animals to conquer land. Vertebrates followed later. So there may not have been an absence of a food supply. Also, the ability to leap to land for safety to avoid a predator is useful if said predator cannot follow. similar in manner to flying fish.


What if a Point Mutation is seen in only half the coverage for its location? I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact.

I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20.

My primary question is: how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?

I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.

I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have homozygotes and heterozygotes at this SNP-position.


My dog and I are wondering: is this a biting midge, or another bug? A week or two ago, my dog started scratching, and it only increased. Not long after, I started getting bit by something that itches something awful. I thought it was fleas so got some medication and moved my dog out of my room. He stopped scratching immediately. After deep cleaning, I let him back in my room the next day. He shortly thereafter scratched again, but not intensely or frequently. My bites have continued.
I set out a flea trap (water, dish soap, flashlight on the water) and it caught the bug you see in the pic (it has only caught four of them).
Is that a biting midge, or something else?
Also, I'm in New York City.

https://i.stack.imgur.com/GC0iL.jpg -- close-up pic, color and pattern
https://i.stack.imgur.com/CVgnl.jpg -- several from a distance to show size
https://i.stack.imgur.com/rQqp4.jpg -- same one as in the first pic

The size is maybe as big as the hole a small nail makes in the wall, a very small ant, or a freckle.

It seems to be a Yellow-banded polybia wasp (Polybia occidentalis), a species of Potter wasp.

my doubts with this conclusion is that the abdomen of the insect in your photo is quite large compared to other observations of the species. Also, Polybia occidentalis is a species that exists in South and Central America, not up north in New York, Perhaps it is able to exist there due to the warm summer weather though I am not entirely sure.
It might be another species of potter wasp. Potter wasps are able to sting but rarely do so to large organisms and their stings don't hurt much. They usually prey on caterpillars and beetle larvae and use those to feed their own. They create these nests that look like a ceramic pot. each of these "pots" contains one larva of the wasp (along with all the food the wasp has collected for their larva when it hatches).
here's a photo of the pots (wasps seem to be willing to create these pots on pretty much any solid surface including under leaves):

Wasps are not parasites, they are hunters of other insects, if my identification of this species is correct, then you and your dog are likely not going to suffer any direct harm from this species let alone parasitic behaviour.


How do pet gecko lizards pose a health risk? Does having gecko lizards living in your house pose any health risk?

If you're referring to keeping geckos as pets, like all reptiles, amphibians and birds, they come with a small but finite risk of contracting salmonellosis. Having said this, the infection is easy to avoid if you maintain basic hygiene.

On a personal note, I know dozens (perhaps hundreds) of people who keep or have kept reptiles as pets and have yet to meet anyone who contracted salmonellosis. Basically, if you wash your hands after touching the gecko, keep it away from food preparation areas and don't put the lizard in your mouth, you should be fine.

If you're talking about geckos living free in your home, as is common in many tropical places, I have never heard of any health risks associated with them. If anything, I would think that the geckos would reduce health risks by eating insects such as cockroaches and mosquitoes that are prominent disease carriers.


Doubt on genomic code for nucleosome positioning? I was reading "A genomic code for nucleosome positioning" (by Eran Segal et al). And I am having 2 doubts.

The figure(b) in this image from the paper shows the graph of fraction (3-bp moving average) of AA/TA/TT dinucleotides of nucleosome dna sequence they analysed statistically as far as I understand.
What is 3-bp moving average here?
I also don't understand how they chose 0th position (the so called dyad).
Also what does it mean to have oscillations (correlation?) in this graph?

UPDATE : I am adding some supplementary information related to finding the dinucleotide fractions. Still I don't understand why is the fraction found so?

Dyad is the centre of the DNA that is wrapped around the nucleosome core (It basically is the centre of symmetry of the nucleosome). It is a common practice to set it at 0 thereby making incoming DNA half, negative and outgoing DNA half, positive.

By oscillations the authors mean that there is a periodic repeat of A/T dinucleotide. IMO it is actually not correct to call it oscillation which is mostly used in a time course dynamical sense.

I guess this is what is meant by the 3-nt moving average:

You have conditional dinucleotide probabilities for each position (As shown in the figure). Now you calculate the A/T dinucleotide probability which is:  P[A/T] = PAA + PAT + PTT + PTA

Now you find the moving average for 3 steps:

MA(n) = (1/3)×(P[A/T](n) + P[A/T](n-1) + P[A/T](n-2))

where n is the nth position of the DNA


Does DNA Ligase look for complementarity in sticky ends? Can DNA ligase seal two non-complementary sticky ends if the reaction is incubated at the optimum conditions ? I do almost 100% double digestion in the lab. However, during ligation, when I do a control without the insert, I still get many circularized vector and they cause massive false positives during transformation. Can ligase sealing two non-complementary sticky ends be a possible reason behind this ?

If I understand correctly you are preparing your cloning vector by digesting it with two enzymes that are 31 bp apart. If you have a high background of recircularized vector see if there is a unique restriction enzyme site within that 31 bp.  If there is, and if the fragment you are trying to insert also lacks that site, then a simple approach would be to inactivate the ligase, and digest the reaction with the third enzyme.  That should drastically reduce the background of recircularized vector.
If after gel purifying the vector backbone after the double-digestion, you get a  significant background of recircularization, then you can easily test your hypothesis about ligase ligating mismatched sticky ends: both of the starting sites should be gone and any sites in-between them should be gone.  Have you tested this?


Do birds have navels? This picture shows the development inside a bird egg:

This shows the connection of the embryo to the yolk sac.  Does this mean birds have navels?  And if so, what happens to the umbilical cord once the bird hatches?

All animals develop in this way, whether they are oviparous (developing in an egg) or viviparous (developing inside their mother, or live-birth).

From Wild Birds Unlimited:

  All mammals have navels or belly buttons where the umbilical cord distributes nutrients between a mother and her fetus. After birth, the umbilical cord is cut and a scar develops on the abdomen where the hole closes.

  Of course avians or birds hatch from eggs which are virtually self-contained life-support systems that only require warmth and oxygen to develop properly. Instead of an umbilical cord scar, birds have yolk sac scars at hatching. This is where the chick embryo is attached to the yolk sac. But don’t look for any bird belly button rings. The scars usually heal and become virtually invisible.

As for their umbilical cord, it looks like it falls off when the chick hatches if it is not fully absorbed along with the yolk sac, along with everything else contained in the egg (although there is not a lot of material left within the egg by the time the chick is ready to hatch).

  Inside a bird's egg there is a tiny cord that connects the developing embryo to the yolk sac. When the egg cracks open, the hatchling does in fact have a miniscule residual scar where the cord was.


How to understand influenza strain designations? What do the strain designations for flu mean?
For example avian flu is classified as H5N1, what do the letters H, N and numbers 5, 1 mean? Is it more than a simple string-identifier?

The sub-type is named for the broad classes of the hemagglutinin (HA) or neuraminidase (NA) surface proteins sticking through the viral envelope. There are 16 HA sub-types (designated H1 - H16) and 9 NA sub-types (designated N1 - N9). All of the possible combinations of these influenza A subtypes infect birds, but only those containing the H1, H2, H3, H5, H7 and H9 and the N1, N2 and N7 surface proteins infect humans, and of these, so far, only H1, H2, H3 and N1 and N2 do so to any extent.

Read more: http://www.fluwiki.info/pmwiki.php?n=Science.NamingInfluenzaViruses


Who was the first to talk about evolvability? "Evolvability is the capacity of a system for adaptive evolution." (source) There are several other definitions though:

Who was the first person to use the word "evolvability"?
Who was the first to introduce the concept of evolvability? in which article?

My literature searches have turned up dead ends, so this is less of a full answer and more of some groundwork, but Google ngrams suggests somewhere around 1931 for the first usage, with meaningful usages beginning in earnest int he early 70s.  Their book previews from that era are sadly lacking; I can't find the usage of the ones from the 40s and 50s they do list sadly, but there are definitely some misnomers that show up in programming.  There's a 1973 work and one from 1977 that at least appear to be the correct usage, with the one from 1973 using it as a "new" concept.


Recombination between DNA segments question In the diagram shown above, segments A and C are copies of a repeated DNA sequence, flanking a unique stretch shown as B. A and C are in an inverted orientation relative to each other, as indicated by the arrows. Intramolecular recombination between segments A and C would most likely lead to ...

duplication of segment B only
duplications of segments A, B, and C
inversion of segment B
deletion of segment B only
deletion of segments A, B, and C

I do not understand this question. Or how the answer was arrived it. Can someone provide some light on the subject? Is this related to transposons?

So, apparently the "trick" to this question is in the wording. "between A and B" appears to mean one crossover somewhere in the B segment, which could destroy (delete) a gene in the B sequence if present at the cut.
The answer involving the horseshoe "trick" implies that the chromosome has looped so that the A and C sequences match up, an extremely unlikely condition. Then a crossover occurs while the loop is in place, also an extremely unlikely event.
Another problem is that the horseshoe solution apparently implies that it is a single chromatid that is looping to itself and forming the crossover. That's weird. I could more easily visualize a different solution: One chromatid is aligned tail-to-head with respect to the other chromatid (head-to-tail). This would allow the corresponding A and B segments on the two chromatids to match up, thus allowing a crossover point anywhere (except inside B) to result in an inversion of B. This is also weird.
These two solutions are much weirder and unlikely than a simple crossover inside B: Picture the two chromatids aligned a little off target so that one is cut at the start of B nearest the A segment, and the other chromatid is cut at the other end of B, nearest the C segment. The result is an uncomplicated deletion of the B segment from one of the chromatids and duplication in the other (no inversion). This scenario seems at least as valid as the "correct" choice given in the practice exam.
While I'm glad to have learned the "trick" in this question for when I take the exam, I consider this question "bad".


Population Dynamics problem concerning Allee Effect I am reading Nonlinear Dynamics and Chaos with Applications to Physics, Biology, Chemistry, and Engineering, 2nd Ed. (Strogatz 2015).  I came across a problem involving the Allee Effect which I have not been able to solve.
Problem:

I tried comparing terms with the Allee effect as stated on Wikipedia,  but it is still not clear to me how to solve this.  Can someone please help?

Since my last post, I have tried plotting several values for the parameters, and I solved for the zeros of this equation.  My guess, is that I am supposed to qualitatively analyze this plot and see that it is maximized for intermediate values of N.  I am including a picture from Mathematica of my work.  Please let me know if I am on the wrong track.

You're not interpreting that Wikipedia page correctly. That equation provides an example of the Allee effect, but is not exclusive.

The Allee effect occurs when the non-zero steady state of a system is not globally attractive, so that such populations may be stable at non-zero population levels for a long time, but are unable to recover once the population density drops below a certain threshold.

In terms of your problem, the tricky bit (conditions for global attraction) is done for you as it instructs you to find parameters so that $\frac{\dot{N}}{N}$ is maximum for intermediate (positive) $N$.

So when does $f(N) = r - a(N-b)^2$ have a maximum admitted at some positive $N$? This is a quadratic, so simple mathematics is enough.

$a>0$ is needed to ensure the parabola admits a maximum
$b>0$ is needed for the maximum is attained at positive $N$.
$r>0$ is also needed to ensure the maximum is positive. This is not clear from the information in the question, but the non-trivial steady states involve $\sqrt{\frac{r}{a}}$ and so $r > 0$ for these steady states to even exist.

So overall quite boring conditions and not a very satisfying question.

In general, a population $x$ with reproductive rate $b(x)$ and death rate $d(x)$ with dynamics $$\frac{dx}{dt} = x(b(x) - d(x))$$ displays the Allee effect if $b(0) < d(0)$. This is easy to prove with a basic grasp of ODE stability.


Is Klebsiella pneumoniae found in the throat of healthy people? Is Klebsiella pneumoniae found in the throat of healthy people?

Klebsiella species, including pneumoniae, are normal members of the healthy human oral microbiome.

Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota

Saliva microbiomes from 6 healthy adults were analyzed by 16S sequencing over a starvation timecourse, where oral microbes were cultured in minimal medium (PBS or 1:1 PBS:cell-free saliva).  Figure 1 shows that the genus Klebsiella is initially low abundance in the healthy oral microbiome, but the proportion of Klebsiella increases over the starvation timecourse in the two media tested.  An excerpt from the results:

  At day 1, several species of Streptococcus were recovered, as were Gamella sanguinis, Klebsiella pneumoniae, and Klebsiella oxytoca. At day 20, K. pneumoniae, K. oxytoca, Enterobacter homaechei, and Providencia alcalifaciens were the only recoverable species. Finally, at day 84 and day 100, only K. pneumoniae and P. alcalifaciens were recoverable under the conditions tested

Given the proximity of the mouth to the throat, I think it's fair to say that K. pneumoniae is likely a member of the healthy human throat.

If that's not convincing, you can check the supplemental data from this paper, which looked at 16S data associated with throat tissue samples from 29 patients with laryngeal carcinoma and 31 control patients with vocal cord polyps.  Looking at the relative abundance of different phyla, they found that Proteobacteria (the phylum containing the genus Klebsiella) accounts for 11% of the recovered 16S reads on average for all patients (range 0–67.1%).  The authors claim to have recovered 218 genera and >3000 unique OTUs at 97% similarity, though they only report the ~30 most abundant genera in their differential abundance analyses, and it doesn't look like they included the full dataset in this publication.


Effects of Polyphasic vs Monophasic sleep in humans Why do humans practice monophasic sleep cycles?

When altering one's circadian rhythm to a Polyphasic sleep schedule, how much would that affect development?

Is Monophasic sleep (once per day) chosen because of biological evolution or is it due to cultural influence?

Reading "Polyphasic Sleep: Facts and Myths (Dr Piotr Wozniak)", it is pointed out that infant humans do undergo polyphasic sleep. As this is where most of our development is obviously done, I do not know where I can further proceed with the question about how it would affect development?  Perhaps the issue is more how it would effect the day to day performance of a developed individual?  If this is the case then it is suggested by Dr Wozniak that this is likely to be highly disruptive to the individual

Those well-defined effects of natural sleep affecting stimuli on sleep patterns lead to an instant conclusion: the claim that humans can adapt to any sleeping pattern is false. A sudden shift in the schedule, as in shift work, may lead to a catastrophic disruption of sleep control mechanisms. 25% of North American population may work in variants of shift schedule. Many shift workers never adapt to shifts in sleep patterns. At times, they work partly in conditions of harmful disconnect from their body clock, and return to restful sleep once their shift returns to their preferred timing. At worst, the constant shift of the working hours results in a loss of synchrony between various physiological variables and the worker never gets any quality sleep. This propels an individual on a straight path to a volley of health problems...
It appears that polyphasic sleep encounters the precisely same problems as seen in jet lag or shift-work. Human body clock is not adapted to sleeping in patterns other than monophasic or biphasic sleep.

It would therefore seem that polyphasic sleep is certainly detrimental to health, if not development.
However studies into cognitive performance resulting from differing sleep patterns run by Dr Claudio Stampi (Published ISBN 0-8176-3462-2), he concluded that polyphasic sleep was more efficient than monophasic sleep.  Therefore it may be possible that polyphasic sleep patterns have no detrimental effect on development.

Individuals sleeping for 30 minutes every four hours, for a daily total of only 3 hours of sleep, performed better and were more alert, compared to when they had 3 hours of uninterrupted sleep

There are a couple of theories mentioned in the above book (beginning pg 5) which support the development of monophasic sleep as evolution rather than a social convention:

Polyphasic sleep is regularly seen in smaller mammals that have very high metabolic rates, requiring them to spend most of their time foraging or hunting.  Therefore a long sleep would be highly impractical for them as they would wake without the energy required to hunt their next meal. Humans do not have this need as they are larger and do not require such regular meals.
Monophasic sleep would be beneficial for the early human hunter gatherer as our eyes are not well adapted to see at night.  Therefore any time spent not using the daylight is wasted and any time without the light is not nearly as useful.  This makes it more beneficial to sleep for an extended period when the sun is down.

I am sure that social factors would have an effect, however I would imagine the evolutionary pressures to be more significant.
I really would recommend the book (http://sleepwarrior.com/Claudio_Stampi_-_Why_We_Nap.pdf) if you have not yet encountered it as I found it very informative and packed with references to studies that you may find helpful.


Plant cell question in age 12 science test Can anyone help me answer the questions in the attachment about plant cells. It was a question in my 12 year olds science exam. I'm baffled as I think he has given a good knowledgable answer but it wasn't awarded a mark.

Kind Regards
Matthew

From a picture like this one cannot actually say whether "part-A" is a mitochondria or chloroplast. That could even be some random vesicles or, to think even crazier, assembling viruses.

The question is really bad and the kid isn't really incorrect. Mitochondria as a guess is pretty reasonable too. However, the second answer is incorrect. I don't know what the kid wants to imply by "to absorb photosynthesis"; it is unclear to me.


How fast the brain recover itself at sleep? What can be done to accelerate this process? In Computer Science we have "Big O Notation" to describe how efficient is an algorithm at processing some task. Those can be linear, time constant, exponential among others.

Using that analogy, How much time the brain needs at sleep to recover itself from an intensive day at work/over stimulation/training/learning/etc?

After it reach it's "specific time", I know that we dream, and that can take very few minutes. Last night I've dreamt of hardest college exams, even done my last one in 2011. So, dreaming time is a period where the brain clean itself from toxins? I've waked up early, so I should have "dreamed a litle bit more" to recover, or the dream it's just the output imaging of the brain recovery process?

What can I do to recover faster? Things like dimmer and silent ambient help better than the total time slept? How they affect and interrelate? If you can provide technical and scientific papers, it will help a lot!

Thanks a lot for your time and patience!

Edit: "Typed Bio O instead of Big O".

You should see some talks from TED about deep sleep.

One researcher summarized that adults generally need 8 hours every night to be at optimum strength. What is most important though is the Delta-wave sleep that occurs during very deep sleep.  To accelerate the process: It's pretty fringe research, what he said is early days... Alledgedly, playing a certain kind of noise triggered near the delta wave phase promotes Delta wave activity in the brain as measured with electrodes. it's essentially slow delta-synchronised seashore kinds of of grey noise played in sleep at the right moment. He said they were working on a device for it.

here's the talk.
https://www.ted.com/talks/dan_gartenberg_the_brain_benefits_of_deep_sleep_and_how_to_get_more_of_it

My own method to have amazing sleep is lots of nights at my girlfriends and to change mattress every few days mat my house, because my unconscious breathing is forced to exercise different muscles of the chest based on whether I am on a swimming pool matress, a futon, a cozy matress, covers similar to sleeping on a lawn. Physiology and muscles benefit from varied exercise, including the 8 hours of chest muscles during sleep. another matress for example I feel all the breathing in the lower belly. I just got out a pool matress for the last 2 nights on boards and rugs, and I dreamed that I was flying around the mountains and cities for about 3 hours and that other people were flying too, which is always nice. I swear I was sleeping a bit rough 3 days earlier on a normal mattres. other factor for me optimum warmth and lots of water for me:) i'm weird though because I had liver damage from a pesticide and following doctor care when I was 18 and I need drink more and sleep hot in order to sleep well.


Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1? My goals are to use a free webtool to:

Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic DNA.
Estimate efficiency and specificity of using the guide RNAs identified by the tool.

Unfortunately, when I tried to do this using the CRISPOR tool, the "Job Status" never advanced past the "Waiting" stage, even after 10 minutes. Attached is a screenshot to show what I see.

Specifically, I used the following settings in my query:

I named my sequence:

Mm Acaca block2 from BLAT alignment

In "Step 1" I submitted this sequence:

aactaaatct ccagcatctc catccccttc ttaggtttat ttattttatg ggtatgagtg
tatgtccgtg caccacatgt gtgcctggtg tctaccaagg taagtagagg tatacaaacc
cttggaattg aattatccac catgccgtca ggtgctggga gcaaattcag gtcctctttt
agagcagcaa gtatttccag ccacttagtc acctctgcag ccccttattt tcacagtctt
gagacaagaa tctcactctt tagcccatat tggcctggaa ctttaggcag tcctgccgga
gtttcagact gctgggatga caggcctgac ccattacgtc cactaaggat ggtttccttt
cctgtgagct agcagcatgt agactccaca aggctcctgg ggaagtgttg ttatagtatg
ttatagtata gttgcgaaag gaaggttttc agaagatatg ggtattacga agaaattcta
tgtaaagttt cttttggatt ctctgtttgt atAGATCCAG CATGTCTGGC TTGCACCTAG
TAAAACAAGG TCGAGACAGA AAGAAAATAG ACTCACAACG AGATTTCACT GTGGCTTCTC
CAGCAGAATT TGTTACTCGT TTTGGGGGAA ATAAAGTAAT TGAGAAGgta agttaaactt
actaaactat ttcgcttgaa gtatgtgaga tttcatgcct agatttgttg tttctgttca
aaaggatatt taggttttta gggactttgc ctttttatgc agggctatcc tttctgtctc
cctagcatgt tactaataca taatctcact gtgtacctgt gtttttacat

In "Step 2" I selected:

Mus musculus- Mouse- UCSC Dec. 2011 (GRCm38/mm10)...

In "Step 3" I selected:

TTTN-23bp - Cpf1 Acidaminococcus / Lachnospiracea

My questions are as follows:

Should I do anything differently to use the CRISPOR tool for my goals?
Are there other free webtools available for me to achieve the goals I outlined above?

UPDATE: I emailed the folks at CRISPOR, and they informed me the site had been down, but they have since restarted it. Hopefully, their restart is sufficient, but I will leave my question up with the hopes that others can point me to more webtools.

Most online tools will only help you to design gRNAs for Cas9 because it is the one that is most commonly used. I found an online suite called RGEN tools that also has an option for AsCpf1.

However, if you don't find it satisfactory then my suggestion is that you either design your gRNA manually or write your own script (which won't be that complex).


Neuroendocrinal mechanism of parturition My book reads,

  "The fetus signals that it is mature by secreting certain hormones
  that diffuse across the placenta into mother's blood and cause the
  secretion of oxytocin from her posterior pituitary."

I would like to know what exactly are these hormones and their sites of production in the foetus, as well as their mode of action.

Also, I was wondering whether these hormones are released even during premature births? I doubt this because what I understand from the lines of my book is that it has to be a signal by the foetus that it is 'fully developed', whereas if it is not secreted it would not stimulate the secretion of oxytocin. This is creating a bit of confusion.

A detailed explanation would be a great help

Thank you

These hormones are progesterone and estrogens. They are actually secreted by the placenta, in increasing amounts as the fetus matures:

(Colorado State, R. Bowen)

You can see that the placenta produces both types of hormone in increasing amounts until birth. Additionally, the hormone relaxin is secreted by the placenta and thought to aid in parturation:

  Relaxin is a hormone thought to act synergistically with progesterone to maintain pregnancy. It also causes relaxation of pelvic ligaments at the end of gestation and may therefore aid in parturation. In some of the species in which relaxin is known to be produced, it is produced by the placenta, while in others, the major source is the corpus luteum. In some species, relaxin is produced by both the corpus luteum and placenta. - R. Bowen


How does blood pressure substantially drop in the capillaries and arterioles? Is this due to increased frictional resistance which decreases the velocity of the blood? You would think using Bernoulli's principle that the velocity of blood in the capillaries would increase due to the decrease in pressure but the inverse is true.

There are two main reasons why the pressure in the capillaries is lower than in the big arteries:

Arteries are elastic - they increase in diameter with every pulse, so the blood pressure is falling as the blood is moving along.
The total cross-sectional area of the capillaries is greater than the one of the big arteries.

Biology-pages.info

  The pressure of arterial blood is largely dissipated when the blood
  enters the capillaries. Capillaries are tiny vessels with a diameter
  just about that of a red blood cell (7.5 µm). Although the diameter of
  a single capillary is quite small, the number of capillaries supplied
  by a single arteriole is so great that the total cross-sectional area
  available for the flow of blood is increased. Therefore, the pressure
  of the blood as it enters the capillaries decreases.


How far can free radicals from UV radiation diffuse through the skin? UV radiation damages DNA through two separate mechanisms. Direct damage occurs when a photon is absorbed by DNA. Indirect damage occurs when a photon is absorbed by a chromophore, and the excited chromophore then reacts with DNA, or reacts with other molecules, forming free radicals and causing harm via an oxydative stress mechanism.  How far can these free radicals travel?  The Wikipedia article on indirect DNA damage states

  Unlike direct DNA damage, which occurs in areas directly exposed to UV-B light, free radicals can travel through the body and affect other areas—possibly even inner organs. The traveling nature of the indirect DNA damage can be seen in the fact that the malignant melanoma can occur in places that are not directly illuminated by the sun.

This seems extremely dubious to me, but I know very little about the topic and can't find any more reputable sources discussing the question. Can indirect damage occur in adjacent non-illuminated cells?  Can it occur millimeters away from the illuminated area? Centimeters?  Can UV light harm inner organs?

The life of the radicals decides how far they move.

This paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310837/#!po=6.92308 has a table of half lives of radicals, the longest lasting ones (the radical of nitrous oxide and nitrogen dioxide) have half lives of seconds.

Diffusion theough the skin would be slow

Technically the problem is "reactive oxygen species" (ROS) and "reactive nitrogen species" (RNS) that are the damaging chemicals that includes free radicals. The reactive species that are not radicals have a longer half-life or are even fairly stable and so could diffuse further before making mischief.

The wikipedia article has problems - that is mentioned on the talk page.