What causes plants in the prunus genus to reach anthesis? In a related question, I ask how to trick fruit trees into flowering later in the spring by prolonging frozen ground conditions.

However, I'm starting to realize that I don't actually understand what triggers plants to flower in the spring in the first place. Possibilities include:

Photoperiodism
Air temperature
Soil/root temperature

It seems to me that this is a simple enough question. I'm guessing that plants in a certain genus would have a fairly specific genetic program that would stipulate when they should flower.
For example:

If root temperature is greater than X (for greater than Y duration), and daylength is greater than Z, then initiate flowering.

I'm not looking for the specific values (example x = 10 degrees C); the values would likely vary by species or even by plant. I'm just wondering what the primary variables are.

Here’s how it works. Every morning when the sun breaks over the horizon — no matter what time of year it is — a clock starts ticking inside the trees. After a specific number of hours, the plants’ cells start producing high levels of a molecule known as the FT protein. This protein is responsible for initiating processes that help the plant grow.

But the FT protein has a curious property: In the absence of sunlight, it curls up and dies. So when the sun sets, it degrades rather quickly and becomes useless to the plant.

Nilsson thinks this peculiarity is the key to the seasonality of certain flowering plants, including most trees that blossom in the spring.

If a plant is genetically programmed to produce lots of FT protein starting, say, 13 hours after dawn, the molecule will be abundant during the last few hours of daylight in the longer days of summer. And those few hours are enough to kick-start crucial growth processes. So the cherry trees do most of the heavy lifting for the spring festival — bud and flower formation — way back in the summer and early fall.

As autumn progresses and the days shorten, that same 13-hour clock — the number of hours will vary by species and even by individual plant — means that the FT protein will be produced in darkness, and it will degrade before it can work its magic. The trees take this as a signal to drop their leaves and stop generating new buds.

When winter arrives, day length and temperatures both reach their annual nadir. At this point, the plant goes through vernalization, a dormancy period that has enormous importance in protecting the trees, for reasons explained below.

In springtime, one might imagine that the FT protein process would reverse: The days get longer, the FT protein is produced during daylight hours, and the plant kicks off its growth process. Surprisingly, that’s not what happens.

While the cherry trees recognize the arrival of winter by sensing a decline in daylight, they detect the arrival of spring based on temperature. They wait for what’s called a “temperature sum”— basically a bunch of warm days in a row. (The precise temperatures and durations required vary by plant.) When the temperature sum is reached, the blossoms open. Of course, since the National Park Service can’t control the weather, peak blossoming doesn’t always coincide with the Cherry Blossom Festival’s lighting of the stone lantern and the Japanese taiko drummers.

The cherry trees’ habit of marking the start of winter by daylight and the end of winter by temperature is reversed in some other plants. Plant biologists, for example, base much of their genetic research on Arabidopsis thaliana, or mouse-ear cress, a small plant that belongs to the same family as cabbage. (“It’s the laboratory rat of the plant world,” says Nilsson, because its small genome enables researchers to closely observe its genetically based behaviors. ) The plant measures the arrival of winter by a drop in temperatures and decides when to flower in spring by day length.

Click here for the source of this information, hope this helps :)

-Sartoaster


How was the origin of CTVT parasitic cancer determined? The wikipedia article on CTVT says that the tumor cell has 57-64 chromosome while a normal dog has 78 chromosomes. Similarly while all chromosomes in dogs except the X and Y chromosomes are acrocentric, many of the CTVT chromosomes are sub-metacentric or metacentric. Reference is given for the data in Wikipedia though a subscription is needed to view the referred articles themselves, so I was unable to confirm the data. (Wikipedia is sufficient for me, though popular opinion seem otherwise)

In addition there seems to be numerous (in the order of thousands) differences in sequences.

  Their study showed that the cancer cells all originated from a common ancestor cell, not from the dogs themselves. Comparisons of the cancer DNA with dog DNA from reference samples held by the US Kennel Club and Crufts showed that it most likely originated at least 250 years ago from a wolf or an "old" Asian dog breed such as a husky or Shih Tzu, and spread like wildfire thereafter.

This was taken from Riddle of Infectious Dog Cancer Solved.

How is the conclusion arrived at in cases like this in general? What percentage / degree of genetic similarity is needed to identify something as belonging to a specific species?
How was the conclusion arrived at in this specific case? (I know I am greedy!)

Your answer to your titular question, How was the origin of CTVT parasitic cancer determined? is that cytogenic studies were done on the tumors. It arose in dogs and was logically assumed to be of dog origin, and was first characterized in 1876. The tumor cells were/are characterized by a rearranged karyotype, which is similar in tumors from in different parts of the world. (1969) Thus it was postulated that that the transmissible agent causing the CTVT is the tumor cell itself and that all worldwide CTVT have a clonal origin. (1985)

Your later question states:

  What percentage / degree of genetic similarity is needed to identify something as belonging to a specific species?

When a tumor arises in an animal (say a dog), it is automatically assumed that the cancerous cells, regardless of their ploidy, arose from that animal (in this case, a dog), not a different animal. Not all animals have had their entire genome sequenced, so this question as stated isn't answerable (although the genome of the dog has been completely sequenced). And certainly, not all tumor cell lines have been completely sequenced. The assumption of origin is made by looking at certain genes (e.g. histocompatibility genes) and others known to be species specific.

Since there are relatively few transmissible cancers (that is, where the cancer itself acts as the infectious agent), this is still a safe assumption. While I'm fairly confident more transmissible cancers will be found, I'm also fairly confident that they will be species specific, because in order to escape detection, they will need to be recognized immunologically as "self", as they must survive in the host at least long enough to be transmitted.

This is the case with canine transmissible venereal tumor (CTVT). It is also the case with the contagious tumor Tasmanian Devil face tumor disease (DFTD). Just as with the canine infectious cancer, DFTD cells in different individuals have identical, complex chromosomal rearrangements and are genetically identical to each other but different to the host devil.

  Spread of such an infectious cell line between unrelated individuals should be prevented by major histocompatibility complex (MHC) Class I antigens on the surface of the tumour cell, as Class I molecules play a key role in self/non-self-recognition. The recent emergence of the tumor (transmitted by biting) in the endangered marsupial Tasmanian devil (Sarcophilus harrisii) is an unfortunate exception. In the Tasmanian devil, the tumor is very aggressive and kills the host.

In the case of canine transmissible venereal tumor (CTVT), it was shown about five decades ago to be the same dog tumor being spread from dog to dog. The earliest studies were based on histological studies and karyotyping. Paraffin-embedded tumor samples still exist. More recently, with genetic analysis, it is possible to perform much more sophisticated testing on the tumor DNA.

  The transmissible agent causing canine transmissible venereal tumor (CTVT) is thought to be the tumor cell itself. To test this hypothesis, we analyzed genetic markers including major histocompatibility (MHC) genes, microsatellites, and mitochondrial DNA (mtDNA) in naturally occurring tumors and matched blood samples. In each case, the tumor is genetically distinct from its host. Moreover, tumors collected from 40 dogs in 5 continents are derived from a single neoplastic clone that has diverged into two subclades. Phylogenetic analyses indicate that CTVT most likely originated from a wolf or an East Asian breed of dog between 200 and 2500 years ago. Although CTVT is highly aneuploid, it has a remarkably stable genotype.

Your quote

  likely originated at least 250 years ago from a wolf or an "old" Asian dog breed such as a husky or Shih Tzu...

Has been disputed. Estimates vary widely, from 11,000 years to 250 years.

Canine TVT: Evolution of Somatic Tumour Cell as Transmissible Parasites
MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer
Clonal Origin and Evolution of a Transmissible Cancer


CRISPR/Cas for editing the human genome I know, that the CRISP/Cas approach for "cutting" the human genome is not completely suitable if we can't say not suitable at all. Because we have many repeats and this approach can bring to our genome additional breaks in DNA and after DNA-repair it causes unwanted mutations. If so, why scientist still continue to play with it (See the link, only 16% success chinese scientist got) ? And what other DNA-editing mechanisms we have? I might be wrong, so correct me please.

Thanks for explanation.

Chinese Scientists Defy Ethics, Double Down on Editing Human Embryos

Repeats aren't the problem with CRISPR. They stop you from editing repeats and repeat-like sequences, but in principle they can be worked around through careful design of guide RNA. CRISPR techniques right now do have problems with off target effects, but these problems may yet be solved. The CRISP/Cas approach to gene editing already has a lot of different variants and is under continual improvement, so there's no reason to think it won't get better. There's also no reason to think that the 16% figure there is only influenced by the use of CRISPR/Cas - it's an experiment with lots of other variables.


How does DNA codon (5`-3`) convert to mRNA? There is a problem I stumbled upon when doing a lesson on molecular genetics (Grade 12 level).

The lesson contains many tables in this format:

I don't understand how it got to the mRNA codon considering how RNA polymerase creates mRNA. From what I know already RNA polymerase reads the anti-sense/template strand (3`-5`strand) and synthesizes mRNA in a 5`-3` direction.

For example, using the first column with the DNA codon 5`-TAC-3`, I would automatically convert it to 3`-5` complementary anti-sense strand because of the nature of the enzyme. It would be 3`-ATG-5`. Now using that anti-sense strand I would find the complementary base pairs and the mRNA strand would be 5'-UAC-3'. This is not consistent with the example given by the lesson. I can understand how to get to the answer (just find the complimentary base pairs of the DNA codon given) but it goes against what I know.

Now if the table said (3`-5`) instead of (5`-3`) it would make sense. Am I misunderstanding a fundamental concept?

Your reasoning is correct and the table is wrong. The mRNA will have the same base sequence as the sense DNA strand (with T replaced by U).


How is color information transmitted from the eye to the brain via the optic nerve? I would presume that is has something to do with synapses and specific chemicals starting specific charges through the optical nerve's sub-components, and that this is somehow interpreted by the brain to configure an actual image; but in all honesty I have no idea.

The eye is obviously quite complex, and as I am not massively associated with all the terminology yet, I would be grateful for an answer in layman's terms.

Color vision in layman's terms:

The eyes contain a photosensitive layer much like a digital camera called the retina. In the center of this layer is a 3 mm-wide spot called the fovea that contains high densities of photosensitive cells, called the cones. Cones are photon hungry and operate only in bright light (photopic vision). They are called cones because of their conical shape. Rods are abundant in the periphery and mediate gray-scale night vision (scotopic vision).

The cones in the fovea are present in three types: red, green and blue cones - hence they convey color images much like digital pictures, namely as a bunch of pixels with a mixture of red, green and blue.

The cones in the retina are the first nerve cells (called neurons) in a long chain of neurons. The cones are hence called primary neurons. They connect to secondary neurons, namely the retinal ganglion cells (RGCs). These cells have long protrusions called axons. These axons bundle together to form the optic nerve. Each cone in the fovea connects to one RGC. The optic nerve extends from the retina to the brain. Information is sent through the optic nerve in the form of electrical pulses, just like a photosensitive chip operates in a camera. The information from the optic nerve eventually reaches the primary visual cortex in the brain, also referred to as V1 or striate cortex (Fig. 1).

In the visual cortex, there is a retinotopic map, meaning that a topographic representation exists in the brain that matches the retinal image. In other words, images are projected faithfully on the brain's surface as neuronal activity. The brain's job is to process these images further and generate conscious perceptions out of them; we see with the brain, not the eyes (a famous quote from Bach-y-Rita).

Fig. 1. The visual system. source: IEEE

References
- Kolb et al., Webvision. The Organization of the Retina and Visual System. Utah University
- Purves et al., Neuroscience 2nd ed. Sunderland (MA): Sinauer Associates; 2001


difference between "Petri dishes" and "Petri plates"? In microbiology, we often hear "we use Petri dishes to prepare our cultural media".

Which is correct — "Petri dishes" or "Petri plates"?

Typically you'll hear either "petri dishes" or "plates", not usually "petri plates". Either way though people will understand what you're talking about.


Can gelatine digestion make blood more thick? Can gelatine cause blood thickening if digested?

No, because gelatin is a mixture of collagen-derived peptides. When you eat them, they are first hydrolyzed by stomach acids into constituent amino acids. These amino acids are then absorbed from the small intestines as nutrients.


Do we need to drink less water in humid weather than in dry weather? From my understanding, humid weather means that the air has a lot of water in it. Therefore, someone who lives in this kind of weather would be hydrating himself just by breathing.

Does that mean that, to stay hydrated, one needs to drink less water in humid weather than in dry weather?

Of couse, I know that humid weathers are usually hotter, which accelerates dehydration. But in this case, let's assume the temperature is independent of the humidity of the air.

You don't get hydrated by breathing moist air. That may at best hydrate your respiratory tract. You should drink more water in dry weather because the body gets dehydrated more.

Humid weather is not hotter, it just feels more uncomfortable. But dry heat is actually more harmful, because it dehydrates you (not in the sense of extreme heat).


How can I tell if regulation is at the transcriptional or translational level? I was reading a paper, http://www.pnas.org/content/109/8/E471.short, where the authors claim that (e475)

  Translation of the TfR (Transferrin Receptor) is regulated through sequences in the 3′ and 5′
  UTRs (untranslated regions) of its mRNA. To study the regulation of TfR levels independently
  of translational control, we measured the levels of TfR-EGFP expressed
  from a plasmid lacking the regulatory sequences present in the
  endogenous TfR mRNA (Fig. 6A).
  Endogenous and GFP-tagged expressed TfR levels were reduced equally in
  response to Rabenosyn-5 depletion, ruling out an effect of this
  protein on transcriptional or translational control of TfR expression.

I believe I understand that the effect can not be post-translational, since TfR-GFP has no region for translational regulation and so it cannot be regulated by any translationally active regulating factor.

My question is: Wouldn't the statement above, that Rabenosyn-5 has no effect on protein transcription, require a proof that mRNA levels are not affected by this protein?

Fig. 6A, http://www.pnas.org/content/109/8/E471.figures-only

From the Methods section:

  Human TfR in plasmid cDNA was a gift from Tim McGraw (Weill-Cornell
  Medical College, New York, NY). Human TfR cDNA was subcloned in frame
  with EGFP in the Clontech pEGFP-N1 vector at the XhoI and BamHI
  restriction sites.

This TfR-GFP fusion protein does not have the endogenous TfR promoter. So it is not likely to be regulated by any TF that would directly regulate TfR transcription.

So they conclude that Rabenosyn-5 does not specifically regulate TfR expression.


Using evolution of bacteria against themselves We know that mutations happen regularly in bacteria and also that one bacteria might get the mutation and become stronger than the others and thus survive, causing antibiotic resistance as well. Can we deliberately make mutations in bacteria that would harm other bacteria but not humans. This would not only make them stronger and thus let them survive but would reduce the very need of antibiotics as they would be less virulent to humans?

Mutating Bacteria is a very plausible idea. If you mutate a particular strain of 'helpful' bacteria to become extremely positively selected for in the current environment then it is possible that the rest of the bacteria interacting with your new mutated will face heavy competition and eventually die out.

The major hole in the idea however, is that bacteria regularly undergo horizontal gene transfer which makes this idea extremely, extremely dangerous for humans. (If your mutated bacteria accidentally passes on the mutated gene to, say, a bacteria that causes Tuberculosis, it would initiate a pandemic. It is also equally possible that a dangerous bacteria might transfer its genes to your mutated bacteria.) It is generally accepted that mutating bacteria or other pathogens(most of which mutate at high rates) is generally a bad idea, because once released into the environment, the possibilities of the mutation going haywire are high(other mutations might make them dangerous).

Horizontal Gene Transfer: Transfer of genes due to recombination processes like Transduction, Transformation and Conjugation which can occur between bacteria of same or different strains, species, domains. etc


Poly-symbiosis? What's the name for this? A mutually beneficial relationship between two species is called symbiosis.

If multiple symbiotic relationships exist with a single common (dominant) species, is this called 'farming'?

A mutually beneficial relationship between two species is not called symbiosis, but is rather called "mutualism." The benefit is measured in terms of fitness; a combination of survival and reproduction. Symbiosis is the degree to which species are "together," which is used in terms of physical proximity or degree of dependency. Pathogens, for instance, have a symbiotic relationship with their hosts and physiologically depend on their hosts by feeding on them. Mutualism and symbiosis are often conflated, and should not be.
Let's dissect: "If multiple symbiotic relationships exist with a single common (dominant) species, is this called 'farming'?" It seems like you mean, if members of the same species increase each other's fitness. Reciprocal fitness benefits between species is called mutualism, and within species is cooperation. There are important differences between mutualism and cooperation from evolutionary points of view and they have vastly different intellectual histories. None of this is really called "farming," except for some ant-insect mutualisms, where ants raise and protect aphids for a reward (honeydew; i.e., plant sugars secreted by some insects).


Fluorescent protein tags and colocalisation We want study if 2 proteins A and B are co-located, for that we use 2 FTP(Fluorescent tag proteins) for each protein?and after the expirement these 2 FTP are co-located. Does that mean necessarily protein A and B are co-located?

"Are protein A and B co-located?" The answer is that it depends. Since your test question included the word "necessarily", this means that the answer to the test question is no. All you have to do is think of at least one plausible counter-example.

Here's a couple:

The flourescently tagged constructs were screwed up somehow, so A, B, and each of their respective tags were actually expressed as 4 separate proteins.
(As per BPinto's comment) the tagged constructs may co-localize even if A and B would not normally do so. This can happen if, for example, the tags bind to each other, or if the tags somehow cause both constructs to get transported to a particular organelle.


Proteoglycans vs Glycoproteins On the left, is my histology book, on the right there's qoura (the internet).
My histology textbook says that "unlike glycoproteins, proteoglycans have attached GAGs which often comprise a greater mass than the polypeptide core"

What I found on qoura is "The carbohydrate content of proteoglycans (10-15%) is far less than glycoproteins is (50-60%)"

I tried googling the question but couldn't find the answer so which of these is correct ?

More context would be helpful, but it's possible the data from the Quora post was incorrectly transcribed from a table on this biotech site, which states that the carbohydrate content of proteoglycans is 50-60%, compared to 10-15% for glycoproteins.

However, the first comment on that page suggests that the table was initially incorrect:

Hi Anne,
This is a great post, but the numbers for the carbohydrate content are reversed. It’s 50-60% for the proteoglycans and 10-15% for most common glycoproteins (and things like uromodulin and most mucins would be 30+% sugars).
Best,
Jared Gerlach

So that may be the source of confusion, here.  It seems the commenter is an expert in the field of glycan research, so the table is likely correct.


How is it that the WI-38 cell line isolated by Hayflick in 1962 is still very much around and not affected by the 'Hayflick Limit'? I have searched the net and I have not been able to come up with an clear answer.

Edit: Here is the para quoted from Nature http://www.nature.com/news/medical-research-cell-division-1.13273
"So began WI-38, a strain of cells that has arguably helped to save more lives than any other created by researchers. Many of the experimental cell lines available at that time, such as the famous HeLa line, had been grown from cancers or were otherwise genetically abnormal. *WI-38 cells became the first 'normal' human cells available in virtually unlimited quantities to scientists and to industry and, as a result, have become the most extensively described and studied normal human cells available to this day".*

The answer is that the majority of the cells were frozen from very early in their Hayflick lifetimes e.g. after 9 population doublings. They have been thawed out judiciously and only as needed thus preserving a lot of frozen stocks.  When an ampule of cells frozen at, for instance 9 population doubling, is thawed, the cells pick up where they left off and still have 41 doubling a to go.  So the magic of exponential growth combined with the fact that they keep dividing after being thawed has made for a decades- long supply . Does this answer the question to your satisfaction?


Why do we have five fingers? Humans (and other humanoid mammals) have five fingers in each hand.

Curious to know, why five? Wouldn't more fingers be more useful?

Is there any evidence that it used to be different and natural selection caused those with five fingers to survive?

I found an interesting article in Scientific American (Coates, 2005), and I quote part of it:

  The condition of having no more than five fingers or toes [...] probably evolved before the evolutionary divergence of amphibians (frogs, toads, salamanders and caecilians) and amniotes (birds, mammals, and reptiles in the loosest sense of the term). This event dates to approximately 340 million years ago in the Lower Carboniferous Period. Prior to this split, there is evidence of tetrapods from about 360 million years ago having limbs bearing arrays of six, seven and eight digits. Reduction from these polydactylous patterns to the more familiar arrangements of five or fewer digits accompanied the evolution of sophisticated wrist and ankle joints--both in terms of the number of bones present and the complex articulations among the constituent parts.

So Coates states that around 360 million years ago there were tetrapods with more digits (6, 7, 8), but that this was reduced to 5 about 340 million years ago. Losing things in evolution is generally relatively simple, yet re-gaining them is hard. So while there is still a tendency for evolution to create species with less digits, there are no examples of land dwelling species with more than 5 digits.

The author reasons that more digits do no good on land as more digits impair locomotion. Most polydactylous species were indeed found to be aquatic.


What kind of microscope should be used to view biological structures (such as spores) roughly 5 µm in length? I would like to be able to identify genera of fungi based on the shape, size, and colour of spores. So the requirements are:

Must be able to view a 5 micrometre object clearly with reasonable resolution
Must be true colour
Must facilitate the measurement of an object within reasonable accuracy (500 nanometres would be nice)
Should be inexpensive (\$100-\$400) fingers crossed
Bonus: Be able to take photos

What type of microscope do I need? What magnification/resolution? Is there a good rule of thumb relating size of object with magnification?

How do I find and purchase a decent microscope after defining my requirements? Any tips?

Blue light is ~450 nm, so does that mean I will not get very good resolution?

(For the sake of context: I have absolutely no formal experience in biology, but I have recently taken an amateur interest in mycology and might enrol in an undergraduate course as part of my degree at some point.)

I think you have a good question, but if you want to get a good understanding of the issues you raise with it, then you really ought to consider spending some time reading this optical microscope primer. In my opinion, you need not bother with taking an undergraduate course at a physical university. As an intro to biology (which is not really necessary if all you want to do is look at small things in a microscope and understand what you're seeing), you might want to consider enrolling in this free class, but if all you want to do is look at small things and have a basic understanding of what you're seeing, I think all you need to do is read the primer.

If it was me, I'd read at least some of the primer before investing the money in a microscope. Otherwise you're just taking a blind leap of faith from someone's (perhaps biased) suggestion.


Must I HPLC-purify my PCR Primers for amplicon sequencing with PacBio SMRT? I would like to order some primers for amplicon sequencing. I am using universal tag primers (unusually long 30-mers recommended by PacBio for SMRT, both F&R) + barcodes (16-mers).   The resulting order of 192x46bp oligos is prohibitively expensive, because of the recommended HPLC purification. The increased expense is related to purification and to the increase in minimum scale (amount) required for ordering.   My question is this: what are the worst-case scenarios (and likelihood thereof) if I do not HPLC-purify primers for PacBio SMRT sequencing?  I am generally looking to make the process of sequencing heterozygous RT-PCR products less expensive, so additional advice in that vein would be terrific, especially from experienced users.  Additional, minor and clarifying side-questions. The PacBio recommended primer, the Universal Tag 30-mer primer seems a bit long to me, and possibly unnecessarily so. Does anyone know why they would insist on a 30-mer? It's a bit irritating that there is no specific reason given, and combined with the unnecessarily long symmetric 16-mer barcodes, and 5’-block (5’ NH4-C6), they are pushing up the cost for little transparently good reason. Perhaps I am wrong. Any offered reasoning on these points would be appreciated.

I am at the same stage as you right now. I am assuming that you are planning a 2-step amplification: first one with the universal primer and second one with the barcoded primers. So, this has been my rationale and experience on this.
HPLC purification
If you are generating your own primers and not buying the plate from PacBio it is better to get HPLC purified oligos. The idea behind using HPLC purified primers is that the oligo synthesis may produce truncated products (primers with deletions usually towards the 5' region) in little concentrations. According to IDT, each base addition has an approximate error rate of 1%.  Therefore, longer products have a higher probability of deletions; the number of expected errors would be 0.01 × length of the primer. For a 46nt primer (16nt barcode + 30nt universal sequence), the percentage of deletion-free products would be ~63% (Poisson probability of no deletions). So, you can expect 27% truncated products with approximately 1.2 deletions per product†. Therefore there is some likelihood that the truncated products may mess up your barcode. However, the probability of the deletions specifically in the barcode regions would be less than this estimate.
5' NH4-C6 modification
This modification makes prevents the ligation of the PCR products. You generate the final library by re-amplifying the PCR products of universal primer, with the barcoded primers. The product will also contain a little amount of the template, which you do not want to be ligated to the sequencing adapters. Again, this would be very less: for example if you take 2ng of the template and your yield is ~1.5µg (I typically get this much yield even with a colony PCR of 25 cycles) then the template contamination is less than 0.2% (ideally you should calculate this with number of molecules instead of mass but since the template and product would have almost equal molecular weight you can use the latter also).
Why 16-mer barcodes
You can use shorter barcodes too but you should make sure that they are different enough such that any sequencing error would not make it difficult for you to distinguish between your barcodes. PacBio has an error rate of 13% for a single read; it reduces if you do the Circular Consensus Sequences (0.13^n where n is the number of rounds). When you have a large number of samples then it is better to use longer barcodes as you can reliably distinguish between different samples. They also recommend that the barcoded primers have a 5' phosphorylation. This will further increase your cost. The 5' phosphorylation will increase the ligation efficiency. It is technically possible to use polynucleotide kinase to phosphorylate the products but the efficiency of T4-PNK varies with the 5' base (Houten et al, 1998). In this case I would recommend pre-phosphorylated primers.
Why 30-mer universal primer
I don't have a good knowledge about this but I guess the reasons have to probably do with the molecular biology rather than the data analysis part of it. Demultiplexing can be done manually and it is not very difficult. Technically, a 20nt sequence should also suffice (usual length of PCR primers). Under usual circumstances, I don't think you are going to save a lot by using a 10nt smaller primer. The total length of primer (universal sequence + the template specific sequence) may go down from ~50+ to ~40+. Many oligo-synthesis services have an upper bound for HPLC purification; they would PAGE purify the longer ones. For example, the company that I order from has a cutoff of 50. So, longer primers have to be PAGE purified which would reduce your yield and increase the price. But usually you can negotiate with the company to allow your 1-5nt longer-than-cutoff product to be HPLC purified.

Summary
Some of these modifications would just improve the efficiency marginally and may be skipped if your data is not likely to be affected by a slight drop in efficiency.
So this is my final recommendation:

HPLC purification: not necessary but recommended for long primers (at least the barcodes)
NH4-C6 modification: not necessary
5' phosphorylation of barcoded primers: recommended
Length of universal primer sequence: can possibly be shortened by 10nt but probably that is not likely to reduce the cost significantly.

However, you can significantly reduce your cost by asymmetric barcoding. For example, if you have 100 samples then the minimum number of barcode primers needed would be 20 (10 pairs). You can shuffle the forward and reverse primers to create 100 combinations.

† Explanation of the error rate probability
Let $\lambda$ be the error rate per base (0.01) and $N$ be total number of bases (46). The error will follow Poisson distribution and the probability of errors would be:
$$P(X=k)=\frac{(\lambda N)^k e^{-\lambda N}}{k!}$$
For zero error i.e. $k=0$ the probability would be simply $e^{-\lambda N}$ which would be ~0.63
The mean number of deletions for the 27% that contain errors would be (see zero-truncated Poisson distribution):
$$E(X|X>0)=\frac{\lambda N}{1-e^{-\lambda N}} \approx 1.25$$


How to quantitatively measure work done by a biological system? Thermodynamic efficiency can be expressed as the ratio of Work done(W) to Energy invested (Q).

Thermodynamic efficiency= W/Q

How can one measure work done by a biological system?

Measuring the work done by a biological system seems pretty impossible. Imagine how many different ways one cell of your body uses energy (ATP). You can't really measure all the work done by every cell on a macro scale. Metabolic efficiency has been defined as... "health". That seems just a little ambiguous. That's why we use things like averages to determine if energy use is normal or not, such as in metabolic age.

In short, work is a more tangible term in discrete physics examples, but there is so much complicated energy use in biological systems that total systemic work can't be easily defined.


What is the proper naming of Aminoacyl-tRNAs? I want to refer to an aminoacyl-tRNA with the anticodon 3'-UAC-5' that is charged with methionine. What is the proper name for this molecule?

Minimal Answer
If all you want to do is exactly what you have specified, on the basis of a 2013 paper on the human tRNAs identified in the 1000 genes project, the format would seem to be:

Met-tRNAMet(CAU)
or
methionyl-tRNAMet(CAU)

Notice that the anticodon is written in the 5ʹ→3ʹ direction, as in the paper, and that Met is capitalized, as recommended in this IUPAC publication of 1970 (sic).
I do have reservations about this as I have been unable to find tRNA nomenclature recommendations (not even in RNA journals), and the paper concerns genes (although a different nomenclature is used there — transfer RNA-Met (CAT) 1-1 etc.). Furthermore, my recommendation to use CAU, rather than CAT (used in the quoted paper) is only based on my experience of scientists who work on tRNA, rather than their genes would use (although it can be justified in a broader context: see below).
A variation on this is to be found in a 2017 paper:
$\mathrm{Met\text{-}tRNA^{Met}{}_{CAU}}$
So I suspect there is no ‘official’ nomenclature.
Problems in giving a more comprehensive answer
The answer above is adequate in certain circumstances, e.g. in differentiating in a paper or a lecture between two species (e.g. with different anticodons, although this does not occur with methionine). The problems occur when you wish to distinguish one tRNA from all other tRNAs present in a cell or encoded in a genome. I list some potential ambiguities:

Initiating v. elongating Met-tRNAs (in the case cited)
Anticodons containing modified bases
Distinct tRNAs with the same amino acid specificity and the same anticodon
Cytoplasmic v. mitochondrial tRNAs in eukaryotes
tRNAs from different species

Possible solutions
Different Met-tRNAs
This is often most important as both initiating and elongating Met-tRNAs have the same anticodon but are structurally and functionally distinct. Differentiation is generally done by way of a subscript: originally ‘f’ or ‘m’, respectively, but for eukaryotes now generally ‘i’ or no subscript:
$\mathrm{Met\text{-}tRNA^{met}_f} \quad or \quad \mathrm{Met\text{-}tRNA^{met}_m}$
$\mathrm{Met\text{-}tRNA^{met}_i} \quad or \quad \mathrm{Met\text{-}tRNA^{met}}$
Anticodons containing modified bases
It was observed early on that the anticodons of tRNA contained modified bases — e.g. inosine, which had particular patterns of ‘wobble’ codon recognition (see my answer to another SE question). Therefore, in many cases it would be important to specifiy these — which is why I recommend using U, rather than T, e.g.

Tyr-tRNATyr(GΨA)

tRNAs with same anticodon
Gene duplication often results in tRNAs with the same specificity and the same anticodon. In some cases the sequences are identical, so there is no way of distinguishing them, but in other cases mutations will occur that do not change the function. To distinguish such species with a single base (here at position 40) the 1000 genomes paper uses the following style:

(G40) tRNAArg(GCA)
or
(C40) tRNAArg(GCA)

At the genetic level arbitrary numbering is used for human tRNAs, e.g.

transfer RNA-Met (CAT) 1-1
transfer RNA-Met (CAT) 1-2

whereas in Drosophila a variant of this style is used, e.g.

transfer RNA:Methionine-CAT 1-1
transfer RNA:Methionine-CAT 1-2

Cytoplasmic v. mitochondrial tRNAs
It is important to remember that the mitochondria of eukaryotes contain their own set of tRNAs, and to distinguish these if necessary by a preceeding ‘mitochondrial’. In Drosophila the symbol would be ‘mt:tRNA:Met-CAT’, and the name ‘mitochondrial transfer RNA:Methionine-CAT’.
Species
Obviously, one can specify the species by a preceeding adjective. I mention this to point out that set of tRNAs is different for different species.


What is topological crossover? I read about "topological crossover" in this paper, Table 1. What does this refer to?

You may not want to know. It really depends on how good your math background is.

  A topological crossover is a class of representation independent operators that are well defined once a notion of distance over the solution space is defined [1].

Let's first start with the definition of Topology.

  Topology is the mathematical study of shapes and topological spaces. It is an area of mathematics concerned with the properties of space that are preserved under continuous deformations including stretching and bending, but not tearing or gluing. This includes such properties as connectedness, continuity and boundary [2].

Later on in the paper they start to mention transverse topology which leads to Differential Geometry.

  In mathematics, transversality is a notion that describes how spaces can intersect; transversality can be seen as the "opposite" of tangency, and plays a role in general position. It formalizes the idea of a generic intersection in differential topology. It is defined by considering the linearizations of the intersecting spaces at the points of intersection [3].

To understand the underlining math concepts of this paper, you may need a rigorous background in mathematics. I would check the authors backgrounds to see if they are Physicists or Mathematicians.

Most students in mathematics generally take two courses in introductory real analysis and at least one course in abstract algebra before taking topology. The standard book for a first course in topology is by Munkres.

A book you may want to look into is Topology in Molecular Biology. However, the author is a mathematician, so if you are not, you may need to start with courses in analysis, topology, differential geometry before you tackle this book. I have never seen the book so I don't know how difficult it will be but here is the about the author from amazon:

  M.Monastyrsky is a professor of mathematics and theoretical physics
  at the Institute of Theoretical and Experimental Physics, Moscow, Russia,
  graduated the mathematical department of Moscow state university(1967),
  author of numerous papers in diferent fields of mathematics and
  theoretical physics including the monograph :Topology in Gauge Fields
  and Condensed Matter (Plenum,1993 ) and two other books:Riemann,Topology
  Physics, Birkhauser, Boston, 1999, 2nd ed. and Modern mathematics in the
  light of Fields medals, AKPeters, 1997.I gave invited plenary talks on
  many conferences and was the visiting professor of many universities
  and institutes including IAS(Princeton), Harvard, Princeton and Yale
  Universities (USA), Cambridge and Oxford Universities (Great Britain),
  IHES and Universite de Paris (France).


Explanation about cytogenetic notation What is the correct meaning of cytogenetic notation "inv(4)(p13q22)" ?

Inversions at chromosome 4, at the p arm 13 is inverted AND at q
arm 22 is inverted

OR

Inversions at chromosome 4, the p13 is
Swapped with q22

Those are the break points of the inversion. So chromosome 4 was cut at p13 and q22 and the fragment was reinserted in the reverse direction, giving a pericentric inversion.


What is this plant's scientific name? This is the picture of a tree in my college's botanical garden.

First I thought it to be a banana tree for its leaves but then seeing its lower part, I don't think it is a banana tree. So what is it's scientific name? I am just curious. Is it any hybrid or something like that plant?

Edit: This tree is from Bangladesh in South Asia. This tree is approximately 9-10 feet (I think, I cannot go near the tree). This picture is from Spring season.

The name of this plant is:
Ravenala madagascariensis
Check: wikipedia


Question about the DNA glycosylase enzyme assay/formamide gel loading buffer Often for the DNA glycosylase enzyme assay we can see that the DNA glycosylase is incubated with oligonucleotide in 37C and then reaction is stopped by addition of formamide gel loading buffer (80% formamide/1 mM EDTA, pH 8.0y0.1% bromophenol blue/0.1% xylene cyanol). How the reaction is stopped by this buffer?

Escherichia coli endonuclease III (which I will now refer to as Nth), and the human homolog hNTH1, has both glycosylase and AP lyase activity. The section of the article you're referring is describing an assay of lyase activity. The assay tested both Nth and hNTH1 as well as HAP1, a human AP hydrolase that cleaves 5' to the AP site. Nth and hNTH1 were found by this assay to cleave 3' to the AP site. HAP1 is dependent on $Mg^{2+}$ for catalytic activity. hNTH1 (and likely Nth, given the high conservation) are dependent on $Mg^{2+}$ for substrate specificity (Eide et al., 2001). hNTH1 and Nth contain an $Fe-S$ cluster that is involved in DNA binding (Thayer et al., 1995).
Originally I thought that the reaction is stopped with EDTA. EDTA is a chelating agent; it binds and sequesters metal ions and prevents their use by enzymes. EDTA would prevent catalysis by HAP1 and DNA binding by Nth/hTNH1.
However, Chris pointed out that the loading buffer contains 1 mM EDTA while the reaction buffer contains 5 mM $MgCl_2$. While the paper doesn't give the volumes of reaction and loading buffer mixed together, it is perhaps unlikely that EDTA chelation of $Mg^{2+}$ is the sole mechanism for stopping the reaction. The high concentration of formamide (80%) in the loading buffer could then be responsible. Formamide is commonly used to denature nucleic acids and, at high concentrations, would likely have an effect on enzyme function.
References

Eide L, Luna L, Gustad EC, Henderson PT, Essigmann JM, Demple B, Seeberg E. 2001. Human Endonuclease III Acts Preferentially on DNA Damage Opposite Guanine Residues in DNA. Biochemistry-US. 40(22):6653–6659
Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA. 1995. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 14(16):4108–4120.


How are elements like iron recognized and routed to the right places for use in the body? I asked this in Chemistry and it was suggested to ask it here. I wondered how the genome, which afaik does not contain iron or calcium as "reference" copies, nonetheless produces an organism that uses certain elements. If it create proteins which bind preferentially to iron or calcium, how then are such elements routed to sites where they can be bound? Are there proteins in addition to those which bind to elements that are responsible for routing? I should mention that I am a software developer and imagine mechanisms analogous to computer code.

A wikipedia source gives you general informations and precise details about the locations and methods of absorption and distribution. Reading the page is well recommended, I will add the quote to save others time:

en.wikipedia.org/wiki/Human_iron_metabolism#Dietary_iron_uptake :

  Like most mineral nutrients, the majority of the iron absorbed from
  digested food or supplements is absorbed in the duodenum by
  enterocytes of the duodenal lining. These cells have special molecules
  that allow them to move iron into the body. To be absorbed, dietary
  iron can be absorbed as part of a protein such as heme protein or iron
  must be in its ferrous Fe2+ form.

  A ferric reductase enzyme on the enterocytes’ brush border, duodenal
  cytochrome B (Dcytb), reduces ferric Fe3+ to Fe2+.[9]

  A protein called divalent metal transporter 1 (DMT1), which can
  transport several divalent metals across the plasma membrane, then
  transports iron across the enterocyte’s cell membrane into the cell.

  These intestinal lining cells can then either store the iron as
  ferritin, which is accomplished by Fe3+ binding to apoferritin (in
  which case the iron will leave the body when the cell dies and is
  sloughed off into feces), or the cell can release it into the body via
  the only known iron exporter in mammals, ferroportin.

  Hephaestin, a ferroxidase that can oxidize Fe2+ to Fe3+ and is found
  mainly in the small intestine, helps ferroportin transfer iron across
  the basolateral end of the intestine cells. In contrast, ferroportin
  is post-translationally repressed by hepcidin, a 25-amino acid peptide
  hormone.

  The body regulates iron levels by regulating each of these steps. For
  instance, enterocytes synthesize more Dcytb, DMT1 and ferroportin in
  response to iron deficiency anemia.[10] Iron absorption from diet is
  enhanced in the presence of vitamin C and diminished by excess
  calcium, zinc, or manganese.


In Study from Blue Brain they say position of synapses doesn't change even if they modify neurons, only when they change shape of neuron it changes? https://medicalxpress.com/news/2012-09-blue-brain-accurately-neurons.html

  We could vary density, position, orientation, and none of that changed
  the distribution of positions of the synapses.....

  They went on to discover that the synapses positions are only robust
  as long as the morphology of each neuron is slightly different from
  each other, explaining another mystery in the brain – why neurons are
  not all identical in shape

My question is why, and how come? Am I understanding it wrong?

It helps to go to the original article for more guidance:

Hill, S. L., Wang, Y., Riachi, I., Schürmann, F., & Markram, H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proceedings of the National Academy of Sciences, 109(42), E2885-E2894.

The point of this paper is that they are looking at the statistics at which neurons make connections with each other in neocortex. Neocortex is a layered structure, and cells of a particular type are identified by the location of their soma as well as the structure of their dendrites and axons. A layer 2/3 pyramidal cell, for example, has basal dendrites that spread a lot in layer 2/3 and creep into layer 4, and an apical dendrite that extends and branches in layer 1. Therefore, it can potentially receive inputs from any cell that has axons in layers 1 -> 4.

One hypothesis is that the primary determinant of which cell types are connected to which is simply the morphology of each cell type. If one cell Type A has a bunch of dendrites in a given layer, let's say layer 3, and another cell Type B has a bunch of axons in layer 3, they will have a lot of opportunities to contact and make synapses.

A second hypothesis is that cells connect with specialized guidance cues. For example, dendrites of Cell Type A release a peptide BALover that is detected by Cell Type B, and causes Cell Type B's axons to grow toward dendrites of Cell Type A. In this system, you could still get lots of dendrites of Cell A in one layer and lots of axons of Cell B in the same layer, but caused by the specific guidance cues from A->B.

In the second situation, however, we would expect the arrangement of axons and dendrites within that layer to be non-random. That is, we would find processes of B in greatest density nearest to processes of A.

If you labeled a bunch of Cell Type A from one animal, and a bunch of Cell Type B from another animal, and overlay them, they should have just as many contacts as if you labeled Cell Type A and B in the same animal if the connections are random due to morphology. If, however, there are specific guidance cues involved, you would find fewer.

Hill et al. 2012 shows evidence in favor of the first hypothesis: they get about as many contacts if they take cells from two individuals and overlay them. This is what they mean by "random placement": not completely random in all dimensions but rather random within a layer in cortex, as if the cells are taken from two different animals. Certainly guidance cues are still used and are still important for setting up the structure of cortex, but it seems like individual cells are mostly just programmed to take up a certain shape, and that shape determines their rough probability of connections. This is a good thing for the Blue Brain project, because it means that they can use composite data from many animals to establish connectivity patterns.


Cutting off circulation How much force is required to cut off the blood circulation of, lets say the average human arm? I'm asking because i'm bored and want to try it on myself. I know that in just a couple of seconds with lack of blood flow you will lose complete use of your arm. I'm only going to do this for a second or two with people watching so please do not worry about safety!

The pressure you need to apply is equal to your systolic blood pressure, about 120 mmHg. This is about 163 g/cm^2.


Is it biologically possible for an adult's eye color to change? Can it be that the adult eye can change color? Specifically my question is about a unilateral color change, such that the color of one eye remains constant, while the other changes color over time. Can this happen? Or can it be related to light-scattering, or an illusion of some sort?

Short answer: The genes that encode eye color do not change, but the pigments in the eye can change due to external factors like diseases of medication.

Long answer: Yes, it is possible that the eye color of adults can change, and it can also only happen to one eye. It is then called Heterochromia. There are two possibilities for different colored eyes, either congenitial (genetic) or acquired. Since you ask only for eye color changes in adults, we can skip here the genetic reasons, as these show up in kids already. If you are interested in them, have a look into the Wikipedia article on Heterochromia.

The basis for our eye color is genetically determined, changes can later occur due to diseases (so if one experiences a change in eye color, it is always a good idea to consult a doctor) and also due to medications.

The eye undergoing a change in pigmentation can either lighten up or darken.

Fuchs’ Heterochromic iridocyclitis: (also known as Fuchs’ Heterochromic uveitis) The change is caused by an eye infection with different microorganisms like Toxoplasma gondii, Herpes simplex virus or Rubella (an probably others) but it can also have an autoimmune pathology. See reference 1 and 2 for more details.

Horner's Syndrome: This is a syndrome which mostly occurs in kids after damages to some nerves. This can lead to insufficient signals towards the pigment production and heterochromia. Rarely this can occur also in adults, where this is called acquired Horner's syndrome, see reference 3 for details.

Pigmentary Glaucoma: In this disease (also known as Pigment dispersion syndrome) pigment cells from the back of the iris float are seperated from the original place and float through the aqueous humor of the eye where they can produce pigment which over time changes the appearance of the eye. See reference 4 for more details.

Medications: Some of the medications against glaucoma (the prostaglandins latanoprost and bimatoprost) can cause a deeper pigmentation which will not always diminish after the end of the treatment. See reference 5 for more details.

Cancers: Some cancers as melanoma can also cause heterochromia, either when they are darker pigmented that the eye or when they are not pigmented. In both cases they influence the eye color. See reference 6 for more details.

References:

Fuchs' heterochromic cyclitis: review of the literature on the
pathogenetic mechanisms.
Associations of Fuchs heterochromic iridocyclitis in a South Indian
patient population
Acquired Heterochromia with Horner's Syndrome in Two Adults
Pigment dispersion syndrome and pigmentary glaucoma – a major review
Incidence of iris colour change in latanoprost treated eyes
Diffuse iris melanoma: Report of a case with review of the
literature


Is there a chemical that can be used to subdue ants only temporarily without permanent harm? I would like to know as I want to contribute to a biodiversity project that wants to create a database with ant feature measurements. I'm not sure if I like the idea of killing ants however (even though it's just a single ant with limited ability to suffer, I know) so I'm looking for a way to immobilize ants long enough to take some detailed measurements but without having to kill them or harm them permanently.

Related question: how could I clean the ant so that it's not marked with the chemical used in the perception of other ants?

I know that for the database they may require keeping the specimen (and therefore killing it) in the name of science so that it can be checked by others but I'm more concerned with the question whether in principle these measurements could be taken without permanently harming the ant and how this could be done in practice.

Thank you for your help!

CO2 is often used for temporary knockouts of insects. I've used it myself for fruit flies (Drosophila melanogaster), and it's quite straightforward and very effective to hit them with it until they're asleep. However, this was in a rather expensive lab that had CO2 on tap - not a particularly accessible method to the average person.

What I'd recommend instead is to chill the ants. Simply capture them and put them in the fridge for a while. Read this wiki article and go to the part about "quiesence" for more. Quote: "quiescence acts like an anesthetic". It's short term, non-harmful and fully reversible. Also much more accessible to someone who isn't working in a big expensive lab. I assume that the ants will stay still long enough for your measurements - if not: put them back in the fridge for a bit. And better yet, there's no chemicals used, so no need to clean the ant and there's no cost to you.


Why does fever above 102 herald a cancer patient's death? I was recently intrigued by a longtime hospice nurse's observation that her cancer patients die a different death than her Alzheimer's, multiple sclerosis, heart failure and COPD patients.

She stated that the cancer patients will typically develop a fever over 102 degrees during the last 48-72 hours of their life, something that is not normally seen in her non-cancer patients.

Any ideas on the underlying biologic reasons for this extinction burst phenomenon and how might this be related to the high fevers induced with Coley's Toxins?

I'm not sure I agree with that, but if I had to support that assertion, I would say that while patients with COPD, CHF and neurodegenerative diseases may die of hypoxia (no fever there), patients with cancer more often die of opportunistic infections.

In patients being treated with chemotherapy (and for some time afterwards as well), myelosuppression - that is suppression of white blood cells vital to fighting infection - is a major risk factor, and is the major dose-limiting factor of systemic chemotherapy.

However, as I stated, I don't agree that fever is a predictor of end of life in cancer patients.

In one large study of terminally ill cancer inpatients, infection was the cause of death in only 15% of patients. More common causes included congestive heart failure (24%), renal failure (30%), liver disease (30%), cerebrovascular disease (30%), pulmonary embolism (25%) - very common in cancer patients - and lung disease. (Overlap exists because of comorbidity.)

Another study of hospice patients found the major problems in terminal cancer patients were the presence of cognitive failure, weight loss, dysphagia, anorexia and dyspnea to be independent survival predictors in this population (which somewhat supports the above study.)

The National Cancer Institute's Last Days of Life–Health Professional Version does not even list fever as a predictor of end of life (EOL).

Among a few others, the late signs found highly specific for impending death in 3 days involved instead signs of cardiac, cerebrovascular, respiratory, and renal failure.

Similarly, a study in the journal Supportive Care in Cancer found that according to palliative care experts (78 professionals, including physicians, nurses, and others):

  changes in the following categories (each consisting of up to three phenomena) were considered highly relevant to clinicians in identifying and predicting a patient's last hours/days of life: "breathing", "general deterioration", "consciousness/cognition", "skin", "intake of fluid, food, others", "emotional state" and "non-observations/expressed opinions/other".

Coley's toxins have to do with treatment of cancer. I'm not sure that they have anything whatsoever to do with death from cancer.

Mortality, morbidity, and cost associated with febrile neutropenia in adult cancer patients
Invasive fungal infections in patients with hematologic malignancies in a tertiary care cancer center: an autopsy study over a 15-year period (1989-2003)
Last Days of Life–Health Professional Version
International palliative care experts' view on phenomena indicating the last hours and days of life.


Why nerve fibre is infatiguable?( is my conjecture correct?) According to this:

  A nerve fibre cannot be fatigued, even if it is stimulated for a long time. This property of infatiguability is due to absolute refractory period.

How is refractory period related to infatiguability?

My attempt: If there were no absolute refractory period, then there will not be closure of Na+ ions into cell, so there will be temporary deficiency of Na+ at that location, now if a new action potential arrives at that point then , due to lack of Na+ there will not be further conduction of it.

Is my conjecture correct?

One can imagine that each action potential causes a small amount of $\ce{Na+}$ goes inside the cell, and a small amount $\ce{K+}$ goes outside the cell, thus weakening the electrochemical gradient of both ions. If each action potential has (approximately) the same flux of $\ce{Na+}$ and $\ce{K+}$ then higher frequency of action potentials means more flux, thus a quicker depletion of the electrochemical gradients. The absolute refractory means there is a maximum firing frequency.

Thus the Sodium-Potassium pump only needs to be able to "recharge"  the maximal possible depletion of ion's gradients. If there was no absolute refractory period then theoretically the action potential frequency could be faster than the Sodium-Potassium pump can keep up. A abnormally fast firing rate in theory could deplete the potassium gradient and sodium gradient thus would result in a fatigued neuron.

Edited to add in reference to the conjecture:
Absolute refractory periods are cause by sodium gate inactivation, thus no matter how much current one adds the sodium gates will not open until sodium inactivation ends. However, over long periods of time (in seconds) and in the absences of a ionic pump, the lack of sodium (and potassium) gradients will cause fatigue.

However, "fatigued" neurons may not act like one expects.


What are these structures inside a cut open Allamanda blanchetti? As suggested by @tyersome in my previous question on the same topic which I posted yesterday, I have cut open few flowers of Allamanda blanchetti
in order to observe if any reproductive structures could be found.
I took 2 buds in different stages of opening as well,if they had some kind of bud pollination. But it seems there is no difference in the bud and bloomed flower.

then I found these  yellow long stiff hairs all stuck together, with some transparent secretion on them,no pollen. I think that these hairs cluster together to form this small star shape projection inside the flower we usually see when it is in bloom.

and this small green bulb like thing with a thread like extension to attach it to the base of the pedicel.
and then on further extending the incision this small swollen part almost like a ovary. But on its transverse section I didn't observe any ovules or placenta inside.

I don't have microscope or other high resolution equipment, I tried looking at it with a magnifying glass but no new details appeared.
So what are these structures? Do they enable sexual reproduction for the plant? Links to related reliable websites are also welcome.

The third photo gets to the heart of the matter. Here's an enlargement:

The gold-colored areas are the anthers of some of the stamens, the filaments of which are fused with the tissue of the petal.  (This is typical of the Apocynaceae, the family to which A. blanchetti belongs; they have epipetalous stamens, that is the stamens are "adnate" i.e. fused with the petal.) This is the male part of the flower; the anthers have the pollen grains which the plant is trying to get transferred to another flower.
Above the knife is the style.  This part of the female structure is a hollow tube which runs from the openings in the stigma (the out of focus green blob) down to the ovary (not in photo). The central part of the fourth photo is presumably the ovary (missing its style). The ovary contain the ovules which will become seeds after fertilization from pollen which sticks to the stigma and grows a tube down the style.


Do snail shells increase the number of rounds with age? Do snail shells increase the number of rounds with snail age?

Yes. Once secreted the shell cannot increase in size, so that the growth of the body is accompanied by continuous growth of the shell, i.e. by the gradual increase in the number of the whorls.

This also means that the topmost whorls are the oldest and the aperture marks the front of the new shell.


What software do I need to read-write cas9? and .dna files? I am still a complete beginner to crispr and I am still trying to learn what it is and how to actually use it. I now realise that you have to order the crispr components after you have actually designed them yourself in software that lets you design and alter the components.

Am I correct so far?

I am wondering if anyone could help me find which software I should use to design and or alter .dna files . Preferably free and open-source software. Are there any good tutorials for someone who wants to get more into crispr?

You have a long journey ahead. This guy spent about 4 years to learn what he is doing here.

He is using Snapgene software


Breathing under water Why can fish breathe under water but land mammals can't? How can fish extract oxygen straight from water but humans can't?

I'm taking this question at face value. Yes, fish have gills, but we also have a respiratory surface in our lungs so why couldn't we 'breathe' water and extract the oxygen (since extraction is a simple matter of diffusion from the content of the lungs into the blood).

Apparently we use 550 L of pure O2 per day. This works out as approximately 400 g.

The solubility of O2 in fresh water is around 10 mg L-1. Assuming a hypothetical situation where we could breathe water and extract all of the O2 from each lungful this means that we would need to breathe 28 L of water per minute, compared to the 8 L of air that we breathe.

Now of course water has a much higher density than air so that a lot of energy would be expended in moving this much water in and out of the lungs (which in turn would require us to consume more oxygen). Couple this with the fact that realistically we would only be able to use a fraction of the O2 dissolved in each lungful and you can begin to see why this is a non-starter.

Gills allow this problem to be largely circumvented by having a one way flow of water over the respiratory surface, which in the case of fish is often achieved at least in part by moving through the water.


How does chromosome fusion get fixed in the population? It's well known that one of human chromosomes is the result of fusion between two chromosomes in a primate ancestor. If we put anthropocentrism aside, it becomes clear that fusion events happened a lot of times, since chromosome count varies in different species.

Yet some people claim that while fusion event is probable, getting it fixed in the population is not, because it would require simultaneous mutation in two animals of opposite sex.

Could anyone explain in layman terms the scenario of this trait's propagation? I may only suppose that even if one parent has two distinct chromosomes and another a single fused chromosome, then two chromosomes may attach to the fused one, and then (probably) get fused themselves, thus leaving fewer and fewer specimens with distinct chromosomes in each generation. Is this a viable and likely scenario, or is some other way of propagation more likely?

Looking at this 2001 review paper by Rieseberg: http://evolution.powernet.ru/library/Scienc9.pdf (especially Box 2), drift and inbreeding are suggested ways that chromosomal rearrangements can become fixed. These forces are strongest small, isolated populations, such as populations experiencing the founder effect.

Another model discussed in that paper is the suggestion that some centric fusions (Robertsonian translocations) lead to little or no loss of fertility in the heterozygotes.


How to remove duplicate results from BLAST? If I run BLAST using a protein sequence (e.g. human p53), I get many matches to the same protein, presumably from different research projects. As you can see from the screenshot, all are similarly named and close to exact matches. Is there any way I can filter the results to get unique genes only?

BLAST against a non-redundant database (for e.g. nr and UniProt). nr contains all non-redundant sequences collected from different primary databases but nonetheless there is some redundancy. You can also specify (or filter out) the species if you are not interested in all species.

Finally, you can also choose the best hit (post-BLAST, using simple scripts).


What is an extinction test? In Stolerman & Olufsen (2001) I read the sentence:

After drug-appropriate responding with the training mixtures reached
85%, generalisation to ethanol was examined in extinction tests.

Here is the entire section from the article on the subject of extinction testing:

Extinction test procedure
Effects of test drugs were determined in brief extinction tests of 3 > min duration that took place twice weekly, with normal training sessions continuing on the interven- ing days. Initially, rats were tested once with vehicle and once with the training mixture; they all reached a cri- terion of at least 80% correct responding and they were all used in subsequent experiments. The effects of saline, the single drugs used for training and the training drug mixture were determined in 3-min extinction tests. The different drug treatments were given in random order. Prior to each test, two injections were always given (via the appropriate routes) to equate handling.

What is an extinction test?

It's a behavioral thing.
The abstract of the paper says: "...mixtures of two drugs from vehicle in two-lever procedures with food reinforcers..."

In operant behavior, rats (in this case) are trained to associate a stimulus (a tone, an odor, a light, etc.) with an action that leads to a reward, the association is trained by delivering a reward only when the 'correct' action is performed, e.g.:

stim A -> press left lever -> get a reward

stim A -> press right lever -> get nothing (or a punishment, but that is a whole different question)

One can quantify the performance of the animal by looking at the probability of responding left (in this case) when stim A is presented.

Now, we think of the association between stim A and left pressing as being reinforced whenever a reward is present, we call it extinction whenever the reward is not present, basically because the reinforced behavior will eventually extinguish, and we say its extinguished when the probability of response to the left and right is 50%.

"...generali[z]ation to ethanol was examined in extinction tests..."
basically means that they substituted stim A for ethanol (I imagine its all olfactory, just read the abstract sorry) and characterize the response to ethanol without ever reinforcing it, hence the extinction.


Evolution and the levels of selection Reading Okasha's "Evolution and the levels of selection" he talks about "the levels of selection problem." There is a bit of a problem with this opening chapter because, while he talks about why the levels of selection problem is a problem, he doesn't define what the levels of selection problem is.

The opening line from the book..

  "The levels of selection problem is one of the most fundamental in
  evolutionary biology, for it arises directly from the underlying logic
  of Darwinism. The problem can be seen as the upshot of three
  factors..."

I think what he means by the "levels of selection problem" is that selection acts on many levels, and what is adaptive at one level may be maladaptive at another. Therefore we can not define selection as acting at one single level, and studying it as such is likely to lead to incorrect conclusions - studying selection is not a simple process. Can anyone provide a firm definition of what Okasha, and the general community on the matter, mean by the "levels of selection problem"?

(Note: The factors are the abstract nature of the principles of selection, the hierarchical nature of biological organisation, and the process of adaptation via natural selection).

Reeve and Keller in the first chapter of Levels of Selection in Evolution (Princeton Univ. Press,1999) seem to address this question in the second item in the following paragraph.

  The purpose of this volume is to sample current theoretical and empirical research on (1) how natural selection among lower-level biological units (e.g., organisms) creates higher-level units (e.g., societies), and (2) given that multiple levels exist, how natural selection at one biological level affects selection at lower or higher levels [boldface added]. These two problems together constitute what Leigh (chap. 2) calls the "fundamental problem of ethology." Indeed, as Leigh further suggests, they could be viewed jointly as the "fundamental problem of biology," when genes and organisms are also included as adjacent levels in the biological hierarchy. This generalization has the desirable property of immediately removing the long-standing conceptual chasm between organismal and molecular biologists.

The authors suggest definitions of fitness that account for hierarchical relationships (the level of selection problem) by considering the effect of a trait (nepotism among social insects) on "adjacent" biological levels, such as individual and colony.

By measuring what they call 'absolute fitness force' they propose to eclipse what they see as spurious debate over the fundamental level of selection (genes vs. individuals, say).

A somewhat surprising aspect of their discussion emerges here:

"It is still embarrassingly common to read inaccurate statements...that frogs have to produce many eggs to ensure the survival of the species because tadpoles suffer extremely high rates of predation, or that wolves have evolved ritualized displays to establish dominance hierarchies because physical combats would be too disadvantageous for the species. These naive statements betray a widespread and persistent misunderstanding of the level at which natural selection most commonly operates."

Their point is that such statements focus on the wrong level of selection (group), and that stronger selection may occur at the individual level; their overall argument being that both levels should be factored in.

I cannot present this as a 'community definition' but it may be a representative example.


No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: introduction to Chip Seq . The same as autor of mentioned question I am a student of Applied Mathematics and I am doing my best to enter bioinformatics fields.

I am basically at the moment where I would like to annotate peaks with genes' IDs. To do this I am using ChIPpeakAnno R package from Bioconductor. I used below  code to annotate my reads (outputs from MACS) with genes' ID's

> library(ChIPpeakAnno)
> # data(package = "ChIPpeakAnno")$results[,3]
> macsOutput <- toGRanges(data="example_peaks.bed",
+                                               format = "MACS")

> data(TSS.human.GRCh37)
> macs.anno <- annotatePeakInBatch(macsOutput,
+                                                                AnnotationData=TSS.human.GRCh37,
+                                                                output="overlapping", maxgap=5000L)
> library(org.Hs.eg.db)
> macs.anno <- addGeneIDs(annotatedPeak=macs.anno,
+                                               orgAnn="org.Hs.eg.db",
+                                               IDs2Add="symbol")
>
> # no annotations for some genes
> as.character(head(as.data.frame(macs.anno)$symbol))
[1] "PTCHD2" "PTCHD2" "PTGER3" NA       "HFM1"   NA

but there occures that there are no genes' annotations for some peaks. Can anyone tell me why this might happen? And how to avoid this? Does this refer to the maxgap=5000L parameter? When creating output from MACS I set a parameter for length to be 10 000.

I had the same problem.
This how I solved it, I found the solution somewhere here, I don't remember where, and it worked for me.

macs.anno <- annotatePeakInBatch(gr_broadPeak, AnnotationData=TSS.human.GRCh38,
                                     output="both", maxgap=5000L)
 macs.annoL=addGeneIDs(macs.anno,"org.Hs.eg.db",c("symbol", "genename","entrez_id"))
 macs.annoDF=as.data.frame(macs.annoL)
   result=macs.annoDF[which(macs.annoDF$symbol!="NA"),]


Have there been any macro-evolution experiements? I'd like to start first by saying that I don't believe in creationism at all, nor any non-Darwinian-evolution explanation of the diversity of life on Earth. The theory, the fossil record, and the genetic, morphologic, and biochemical evidence are more than overwhelming in support of it.

Also, I understand that the term 'macro-evolution' is a "weasel word" invented by creationists to make a bogus distinction of two supposed kinds of evolution.

But for this question, I think the term is useful. I'm happy to take any corrections or qualifications in comments or answers.

I wonder if there has been any long-term experiment performed to attempt to induce 'macro' changes in a species-- something that would make this lab-based population considered to be a subspecies, or even a different species, if it were found in the wild.

I'm aware of the long-term E. Coli experiment that resulted in bacteria that developed mutations that allowed them to completely metabolize citric acid. I understand that's a change of a few genes (amongst other recorded changes).

What I'm looking for is something a little larger, more than a new protein. I was thinking something like 1. a new organelle, 2. a new type of cell or tissue, 3. a new organ, or 4. a new type of limb or radically different limb use (something like reptilian jawbones re-purposed in mammalian ears_.

I understand there are numerous incidents of organisms losing useless features, such as eyeballs in dark caves, flight ability, etc. For this experiment I don't think it's enough to show the loss of something-- genes turning off, but novel characteristics must arise. To rebut creationists, I think it's necessary to show 'new' information, not just loss of information (I'm speaking of the genes responsible for morphology).

With my laypersons' imagination, I was thinking of a species with a relatively fast reproductive cycle, put in an environment that had some selective pressures. Perhaps one without much room to fly, not enough food, but plenty of food in a water area where they couldn't normally get to it. Something that might encourage them to adapt to taking to water to exploit a new food resource.

Issue with the question

The question of what is an evolved phenotype that is "seemingly significant enough to the layman to be called macro-evolution" is very unclear and it makes it hard to answer.

Most experimental evolution are performed on lineages that have very short generation time (for obvious reasons) and on these lineages it is hard to even imagine the evolution of something that a layman would consider to be "significant enough to be called macro-evolution".

The whole issue is that one will probably consider a change in phenotype to be "seemingly significant enough to the layman to be called macro-evolution" if it occurs on lineages that have long generation time and therefore cannot be observed within a lifetime.

The question interesting. However, I think the best one can do is to look at the wiki article for experimental evolution who already offer quite an interesting list of examples. I tried below to highlight a few cases of eventual interest

Long term artificial selection on "large living things"

If one wants to consider artificial on "large living things", then probably artificial selection on crops and cattle will be a good place to look at. I think I don't need to list and make extensive description of how artificial selection has changed their phenotypes (and genotypes). Consider the pigs, banana and corn as examples.

A few evolved features that has evolved in labs in small organisms

We have observed evolution of multicellularity form unicellular organisms, observed new metabolic pathways and change in ploidy level just to cite a few major things that we evolved.

Lenski experiments

The Lenski long term experiments is the longest in lab evolution experiment performed today. They made a lot of different observations and not only the case of citric acid metabolization that you mention. Note that being able to metabolize a new compound is a pretty considerable evolved feature that only those who can't go further than considering evolution of extra legs as something significant would fail to appreciate.

Drosophila and Waddington's experiment

If one must restrict I suppose that looking at experimental evolution on Drosophila would be our best bet.

Change in allele frequency through selection is a relatively fast process. Creation of beneficial variants through mutations is often the limiting process. Cases where very different phenotypes exist in natural population and selection over these phenotypes (change in frequency only) will probably not be considered to be "impressive enough". However, one can consider Waddington's experiments (and further experiments inspired by Waddington's work) as an example of experimental evolution where standing genetic variance existed before the experiment started but was hidden in the environment they experimented (the exact process here might well be too advanced for a layman). Waddington in his experiments showed one can evolve Drosophila to have a double thorax or lose their halteres in only 20 generations.

Other Drosophila experiments

We evolved Drosophila to live in hypoxic conditions. It took about 200 generations that is more than 4 years. We have also selected Drosophila for cognitive abilities and food preference (and many other things).

Note on the term "macro-evolution"

The term "macro-evolution" hasn't been invented by creationists. It has been invented a long time ago, in 1927 by a russian entomologist. T. Dobzhanski and E. Mayr (two famous evolutionary biologist) have used this term without ever quite defining it. Because the term was never correctly defined, the vast majority of evolutionary biologist have either criticized the term.

It is true that the term is now sometimes used by creationist as any poorly defined term is one of the finest solution to build questions that can't be properly addressed due its lack of clarity.


Visual Quality Indicators for Soil and Plants I would like to know what are the visual indicators that can be used to determining the quality of the soil and plants by looking at the in-situ photos?
Can the following quality indicators be determined by visual check such that a decision making can be done?

Approximate Soil Salinity
Soil pH
Soil Moisture
Soil Content (red indicates presence of iron etc)

For Plants

Presence of weeds
Presence of bug infestation (perhaps different visual patterns to
identify kind of infestation)
Plant Health (rigid looking vs hanging etc)

The above is whats there in the top of my head, can this list be expanded and upto what degree the quality indicators can be relied upon?

Note: Soil salinity might not be easily determined if the excess salt doesn't precipitate (visible white layer on the soil can help determine the excess of salt hence its not a good visual quality indicator for most of the time.

There are numerous visual indicators for various type of plants that determine plant health. For example the rigidity of the leaves can help you determine that enough water is supplied to the plant (1). Now you can also determine the leaf shape and detect for presence of disease (2), pests (3), and plant health in general (4). This research however mentions no correlation between lamina shape and area so you would need wiser methods for your corrlelation methodology(5). Moreover, you can look at the fruit shape/sizes to determine if plants have been supplied enough nutrients(6). Another study which is worth mentioning is using chlorophyl to determine plant fitness but this cant be done insitu and you would need lab analysis (7)
All these are visual indicators for the plants itself. As far as soil is concerned is it more challenging because you can make soil and compost using various materials and methods so there is no general approach that can be used to determine the quality. So if soils is your primary concern then as @PolypipeWrangler mentioned looking at the plant fitness can help you determine soil quality.


What is the purpose of two cell divisions in meiosis? At the moment, my thoughts are that the two cell divisions are necessary for recombination to occur, although I am not sure. I cannot really see why technically, the chromosome from each parent cannot just recombine with the other chromsome when each is a single DNA strand and not in the form of two sister chromatids joined at the centromere. Something tells me that there are several reasons why there are two cell divisions. Perhaps the S phase of interphase triiggers some further stages of cell division such as cytokinesis, and the splitting of the cell will not occur unless some DNA replication has taken place? However in meiosis 2 there is no further DNA replication, so this can't quite be right...

For developing a 2N cell, we need a N cell from each parent. In any division(meiosos or meitosis), chromosomes are doubled at first. In firs meiosis a 2N cell in divided into two N cells and as you know these N chromosomes are doubled( 2N chromatids). In second meiosis a N cell is divided into two N cells but this time chromosomes are not doubled(in fact N chromatid cells)
1.Firs division in meiosis is needed because we need N cells to combine, if they are 2N the result of recombination is a 4N cell.
2.Maybe your question is: why a 2N cell is not directly divided into two N cells without doubling? the reason is same in mitosis and meiosos, it is because of a stage of division as you know it is called anaphase in which a kind of protein, connects centromer to centriol, this stage is needed because we need one chromatid of each chromosome in each cells so if this part is not done there is no guarantee to have all N chromosomes in both cells and in fact a kind of distribution is made.
( I hope that I could understand you, well.)


How do mutations of viruses lead to drug resistance? For instance, after starting zidovudine monotherapy against HIV, resistance develops against the drug because of a point mutation in the RNA transcriptase enzyme to which the drug binds.

So how does the virus ‘know’ to mutate this particular enzyme?

It doesn't. Viruses don't "know" anything. Mutations occur at random. Most of them don't do anything, or have a slight negative effect on the ability of the virus to infect and reproduce. However, there are billions and billions of viruses. Once in a while a random mutation will offer a significant advantage like immunity to an anti-viral drug. The viruses that have that beneficial mutation will then massively out-reproduce the viruses that don't have it. Eventually the population of viruses will consist mostly of individual viruses that have that mutation.


What species of butterfly/moth is this please? What species is this please?

It's really tiny. That's an oregano leaf.

Location: United Kingdom

Mint moth. We can only see the forewings on this photo. Single gold spot is the giveaway.


Does apoptosis occur more at a particular time of day? I am interested to know if apoptosis (programmed cell death) occurs more frequently during daytime or nighttime hours, e.g. if apoptosis is associated with a circadian rhythm.

A simple search turned up a couple of articles:

Diurnal variations in the expression of radiation-induced apoptosis

The Circadian Clock Controls Sunburn Apoptosis and Erythema in Mouse Skin

However, I'm not sure how to interpret these and would appreciate the help of a biologist. I don't have a very good idea of the limitations of our investigative tools, or indeed whether my question is well-formed. Thank you!

Your question is quite well-formed, however all I can say so far is: I don't know. Maybe it is known, however I could not find any information on this in the literature. In general, little is known about the crosstalk between circadian rhythms and apoptosis. It is known that circadian rhythms regulate DNA damage repair, so I would assume that the same is true for other maintenance functions such as apoptosis of redundant or damaged cells.

I don't know which research tools are available to you, but if you want to look at the effect of the clock on apoptosis signalling in a simplified setting, I would recommend synchronising the clock of culture cells with dexamethasone (you'll find a lot on that in the literature) and then using the apoptosis read-out of your choice on samples of these cells taken in regular intervals. I recommend taking samples every 4 h over the course of 24-48 h. You can make this less tedious by synchronising separate batches at different time points. As read-out for apoptosis I recommend Caspase-3 / -7 activity, ideally by Western Blot or an enzymatic activity assay using Ac-DEVD-AMC or something similar.

If you want to have a look at the effect in a more complex, physiological model, you will have to use mice.

I hope I could help you a little. Good luck!


Spike protein production by mRNA vaccines? I am trying to understand the spike protein production mechanism of the mRNA vaccines, and during my research I learned that the mRNA (Moderna, mRNA-1273) vaccines hijack the cell machinery to produce spike proteins of SARS-CoV-2 by providing genetic material mRNA (which is encapsulated by lipid nanoparticle).
My question, which cells are subject to the vaccine particules (which factor determines the target cells?) Are produced spike proteins part of the cells (which interacted by the vaccine), or are these proteins emitted into the bloodstream like hormones so immune systems attack only the produced spike proteins?
I am asking this question to understand whether the cells which are used to create spike proteins are attacked by the immune system.

I am asking this question to understand whether the cells which are
used to create spike proteins are attacked by the immune system.

Yes, that is the aim of RNA vaccinations!
But don't worry, that's a good thing, as can be concluded from this review-paper, that emphasizes the advantage of RNA vaccinations to invoke cellular immune response:

Although subunit vaccines have been used successfully to elicit
humoral immunity against a wide variety of pathogens, they fail to
induce cellular immunity which is required to eradicate the
intracellular pathogen reservoir of many chronic diseases, including
viral infections such as HIV or hepatitis C.

Basically, the idea is that presented antigens from traditional vaccines are inclined to be presented via MHC2, rather causing humoral immunity, while after RNA transfection, cellularly produced peptides can also be presented on MHC1, causing cellular immunity.


Can/Do any spiders "release" their own web in the presence of a threat? Preface

We live in the north eastern US and have a spider that has setup shop next to our front door.  I've lived in this area my whole life and she's the largest spider I've seen.

We're too interested and afraid to do anything but let her be, so we've been watching her for the last couple of months.

The "Event"

My wife almost bumped into her web while we were looking for our cat tonight. (I mean she was really close). The spider was hanging around in the center of the web at the time.  A short while later my wife saw the spider scurrying furiously and then she crawled back into her hiding spot behind the shutter.  Next time I looked over, her web was completely gone - neither of us think we got close to it again during that short time.

I'd also like to point out that it was a bit gusty tonight, a rain storm was probably about an hour away.

We are wondering if something happened to her web, or if she took it down intentionally.  If she did, is this behavior common in spiders?

Other Information

She's got a blackish/yellowish bulbous body with the same color striped legs
She's about the size of a ping pong ball (including legs)
She hides during the day behind the shutter, but always comes out when the sun starts setting.
Unfortunately I have no pictures of her that aren't the underside, she never comes around the front of her web.
She builds a "classic" looking web, a hair longer than a foot in diameter with a couple of longer guy lines out to the door and the stoop. There are never any messages written in it.
She either never catches anything, takes her food back into her little den, or eats very quickly because I've never seen anything wrapped up in her web.
Our cat found his way home a couple of hours later

Photo

Thanks!

Building a web costs a lot of energy. From Wikipedia: "It is common for spiders to eat their own web daily to recoup some of the energy used in spinning. The silk proteins are thus recycled." https://en.m.wikipedia.org/wiki/Spider_web


Bioinformatics tool for "pairwise alignment" of complementary sequences? I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate efficiency of binding. After thinking about it, I'm essentially looking for "the opposite" of BLAST, in that BLAST looks for regions of similarity in sequences in the same orientation, while I'm looking for  regions of complementarity in sequence in the opposite orientation.

Does such a tool exist?

EDIT 1

To clarify, I'm looking for a tool that can detect the most optimal regions of complementarity in two sequences when both are aligned as such:

  5' TCGAAUAACTCGTCUGAUGAGUCGCUGAAAUGCGACGAAACCGTTAACGGA 3'

  3'   GTTTTACGCAAAGCAGCGTAAAGTCGCTGAGTAGTCACTTTAATGAC   5'

I'm not sure this is what you need since the sequences you posted are not actually complementary as far as I can tell. However, exonerate is one of the most powerful tools out there and can do this as well. Using these sequences as examples:

  >query
  TAGCTTATTGATGGGAGGAGAGTCCGTGCACATGACAGACCTTGGCTGTCCCAGACTGCAGGAAGCCCAGG
  >target
  CCTGGGCTTCCTGCAGTCTGGGACAGCCAAGTCTGTTATGTGCACGTACTCTCCTCCCCTCAATAAGCTA

And this command (should be run on a *nix system):

exonerate -m coding2coding -q qq.fa -t test.fa -s 0

I get this output:

C4 Alignment:
------------
         Query: query [revcomp]
        Target: target
         Model: genome2genome
     Raw score: 312
   Query range: 71 -> 0
  Target range: 0 -> 70

 71 :                                                          CCA       :  6
      CCTGGGCTTCCTGCAGTCTGGGACAGCCAAGGTCTGTCATGTGCACGGACTCTCCTCProTCAATA
      |||||||||||||||||||||||||||||| |||||| ||||||||| |||||||||||+||||||
      CCTGGGCTTCCTGCAGTCTGGGACAGCCAA-GTCTGTTATGTGCACGTACTCTCCTCProTCAATA
  1 :                                                          CCC       : 65

  5 : AGCTA :  1
      |||||
 66 : AGCTA : 70

vulgar: query 71 0 - target 0 70 + 312 M 30 30 G 1 0 M 26 26 C 3 3 M 11 11

C4 Alignment:
------------
         Query: query
        Target: target [revcomp]
         Model: genome2genome
     Raw score: 309
   Query range: 0 -> 71
  Target range: 70 -> 0

  1 :                      GTC                                           : 66
      TAGCTTATTGATGGGAGGAGAValCGTGCACATGACAGACCTTGGCTGTCCCAGACTGCAGGAAGC
      ||||||||||| |||||||||||+||||||||| ||||| ||||||||||||||||||||||||||
      TAGCTTATTGAGGGGAGGAGAValCGTGCACATAACAGA-CTTGGCTGTCCCAGACTGCAGGAAGC
 70 :                      GTA                                           :  6

 67 : CCAGG : 71
      |||||
  5 : CCAGG :  1

vulgar: query 0 71 + target 70 0 - 309 M 21 21 C 3 3 M 15 15 G 1 0 M 31 31

Basically it gives you two alignments, one reading the target 3->5 and the query 5->3 and one the other way around.

Alternatively, you could do a translated blast search, tBLASTx which will translate both target and query sequence and so, should find complementary regions.


How to remove bad lanes in ImageJ Westernblot analysis I use ImageJ to do an analysis of a Westernblot Image.

If everything goes as wanted the workflow is fine. But if I do something wrong creating a lane there is no undo for a lane and also no way to remove all lanes that I can find.

How do I get back to my original image or undo a lane creation?

I'm using 1.49e on Mac OS

ImageJ doesn't have a feature to remove individual lanes. But that shouldn't be a problem. All you have to do is draw the first lane correctly (I'm referring to size). Then press 1. Now, while the selection is still... selected, click inside it, but not on the number (where the cursor becomes hand), and drag it where you want the next lane. And press 2. And so on. Draw all your lanes.

Now, if you misplaced a lane, click the rectangle selection tool, then click on the lane number while the cursor is a hand. It will be selected. If you're having troubles with this, use the shortcuts Ctrl+1 and Ctrl+2 or the menu Analyze - Gels - Select Previous/Next Lane to select between lanes. The cursor turns to normal. Click anywhere inside the lane and drag it on the right place.

If the first lane was bad and you want to remove all lanes, just go to Analyze, Gels and click on Reset.


How do sharks and other fish conserve and gain water in marine environments? With the osmolarity of the average vertebrate being around 300mOsml, and salt water having an osmolarity of 1000mOsml, why does the water from the shark not leave to the salt water around it?

I presume the scales must act as a barrier to stop water form leaving, but with the blood vessels being exposed to the saline water in the gills, why does water not leave the body?

The mechanisms of osmoregulation is different for sharks (and other elasmobranch fishes) and teleost fishes.

In Elasmobranchs the body osmolarity is maintained equal to the seawater by Na⁺ Cl⁻ and urea. Toxicity because of high concentrations of urea (strong chaotrope) is counteracted by high levels of trimethylamine oxide (TMAO). So, the elasmobranchs do not need to drink water to prevent dehydration. But sometimes they do drink water for adapting to different salinity levels [1].

Teleost fishes, however, need to drink water in order to prevent dehydration. Initially Na⁺ and Cl⁻ are absorbed in the esophagus via cotransporters (Na-Cl/Na-K-Cl), thereby reducing the osmolarity of water. The cells that absorb Na⁺ maintain its low concentration by pumping extra Na⁺ in the Extracellular fluid, using Na⁺/K⁺-ATPase. Cl⁻ is also exchanged with Bicarbonate (HCO3⁻) via anion exchangers [2].

.