texts: What is the difference between a response element and a enhancer?

texts:
I have been confused as to the difference between a response element and an enhancer.

Wikipedia has the definition of response element as the following:

  Response elements are short sequences of DNA within a gene promoter region that are able to bind specific transcription factors and regulate transcription of genes.

Wikipedia's definition of enhancers:

  In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.[1][2] These proteins are usually referred to as transcription factors.

They seem almost the same. What are the main differences?

The only difference I can see is that response elements can both halt transcription or allow for it. While enhancers only promote transcription if the transcription factor is present.

Is this the difference between the two, or is there something else that differentiates them?


texts: How does DNA organise a cell's physical position within a body?

texts:
How do cells "know" where they are supposed to be in relation to other cells, in forming the physical shape of the body?

If you have ever tried to organise or choreograph the physical positions of a group of people on a field, for example for a dance or display, or even just to stand on stage at a graduation, you will know it takes a bit of communication and working out between the people, and the choreographer (who could be considered a kind of "central intelligence")

Analogy: If you give each person on the field a simple diagram or map (DNA) which shows where the final positions should be, they may or may not be successful, but they would definitely have to talk: "You stand here; I'll be next to you; Jo you need to turn a bit; etc, etc..."

How do cells do this, given than cells could attach and clump in any direction? Especially, how do cells coordinate with other cells quite distant? (Given how small cells are in relation to the shapes & structures of the body)

For example, in my diagram here, 4 cells are forming a specific shape (let's say they're building the corner of an ear or something.) Does cell A "know" where cell C or cell D is?

Please, I'm not after specific chemicals names or in-depth mechanics of cell physiology. I'm after a layman's description or a general principle that is at work.

Bonus related concept: Why/how does the body build a bone of such exact shape the first time around (in the womb) but when you break that bone later, the body seems to just slap bone material around all over, like a bad plasterer?

I've appended a list below of articles I've read (or attempted to read) to try to answer my question.

https://www.reddit.com/r/askscience/comments/3ln201/how_do_cells_know_where_they_are_in_the_body/
http://www.newswise.com/articles/how-do-cells-know-what-to-do-and-when-to-do-it
http://www.thenakedscientists.com/HTML/interviews/interview/1000544/
https://www.sciencedaily.com/releases/2014/10/141027085032.htm
https://www.ucsf.edu/news/2014/05/124831/how-do-our-cells-know-where-they%E2%80%99re-going


texts:
I dropped my phone onto the carpet and picked it up and saw this tiny mite crawling around on the screen.

It is too small to be a bed bug, but perhaps too big to be a dust mite (and doesn't look like the images I found).

Main image is an out of focus image with an iphone simtray for size comparison (the mite about 0.5mm).

The second picture from the left is the only one where I seemed to be able to get its head; all others it was moving away from my camera. I couldn't take any better photos so you'll need to click the image to see the mite in detail.
EDIT: I am in the UK


texts: If neurons come from neuroblasts which come from neuro stem cells that are embryonic, how is it possible for an adult to regenerate nerve tissue? Are neuro stem cells created during later stages of life, and, if so, where? Or is it solely a finite repository of stem cells somewhere?


texts:
I was just looking at some mouldy ginger found in the fridge under the microscope and was horrified/delighted to find (what looked to be) mites growing in it. I have searched the web and can only find references to red spider mites which these are certainly not. They were clear white and under 40x zoom about less than a mm across - does anyone know what they could be? Furthermore, what are they feeding on (ginger root is only ~15% carbohydrates - is that enough?) and has a minimal (~1%) amount of protein.

Here is a picture (sorry for the quality but the white thing looks to be a mite).


texts: Why does it hurt the next day after doing significant exercise?

texts:
I think this is a fairly common observation that if one does some significant amount of exercise, he/she may feel alright for the rest of the day, but it  generally hurts bad the next day. Why is this the case?

I would expect that if the muscles have undergone significant strain (say I started pushups/plank today), then it should cause pain while doing the strenuous activity, or during rest of the day, but it happens often that we don't feel the pain while doing the activity or even on that day, but surely and sorely feel it the next day.

Another example - say after a long time, you played a long game of basketball/baseball/cricket. You generally don't feel any pain during the game/that day, but there is a good chance it will hurt bad the next day.

I am trying to understand both - why does the pain not happen on that day, and why it does, the next day (or the day after that).


texts: Why are the neurites from hair cells to spiral ganglion cells called axons?

texts:
In Kandel's Principles of Neural Science I found the following figure which shows the innervation of the organ of Corti:

From the legend to this figure (30-10, p. 602):

  "The great majority of afferent axons end on inner hair cells, each of
  which constitutes the sole terminus for an average of 10 axons.[...]
  Efferent innervation of inner hair cells is sparse."

BUT: The depicted axons that "innervate afferently" hair cells seem to go into the wrong direction (downwards, not upwards). What do the (red) bulbs touching the hair cells represent. I guess synapses, but which one is the presynaptic and which one is the postsynaptic neuron? (I guess: The hair cell is the presynaptic neuron - it's a sensory neuron! But then the neurites emanating from it would be afferent dendrites of the ganglion cells, not axons. I'm lost. Might it be the case that transport along these neurites is active - like in axons, not passive like in dendrites? Or are they called axons because they are myelinated? Or is it because in bipolar cells it is not distinguished between axon and dendrite?)

Question: Why are these neurites called axons?


texts: We can localise cancer cells in the body. We can manufacture materials thin and hard enough to penetrate the body without harming it. So what stops us from creating an automated surgery where the patient lies down for some time whilst a machine locates cancerous cells and, using micro tubes, kills them one by one?


texts: What does characterization mean in a genomics context?

texts:
"The resulting libraries of gene sequences allow CDC and other
  laboratories to compare the genes of currently circulating influenza
  viruses with the genes of older influenza viruses and viruses used in
  vaccines. Through this process of comparing genetic sequences, called
  genetic characterization, CDC can make informed assumptions regarding.."

I'm unsure what genetic characterization means. What do the researchers actually here?


texts: Effect of steroid hormone on specific cells?

texts:
As steroid hormones can pass through the plasma membrane by simple diffusion because they are lipid derived hormones, it means that they are capable of passing through every cell of our body, BUT why are only specific cells responsive against steroid hormones?

For example, all of our body cells almost contains the genes for the development of secondary sexual characters but why do only specific cells show a response against these steroid hormones because the development of secondary sexual characters occur only in specific region of our body, that is, beard formation occur only in a specific region of the face, etc.

IN SUMMARY: When steroid hormones can pass through every cell of our body then why do they show only a localized response?


texts: What is the standard method for measuring soil and substrate acidity

texts:
Soils and other plant substrates differ a lot in their moisture content. In dry matter a pH is not measurable without adding water, but this has the problem of the resulting value not being independent of the amount of water added. In controlled conditions pKa measurements would be used instead as they are independent of the amount of water, but would this would require information about chemical composition that is generally unobtainable.

What is the standard way of reporting acidity of soils? I would think that there is probably some kind of measurement based on mass or volume. Or, perhaps the log scale renders the amount of water negligible for most purposes?


texts:
One summer (August) I was in Bulgaria (Dobrich province) and in the middle of the city I take picture of this bird:

He was making a sound like "Tchek-tchek" like the sound of a Eastern Olivaceous Warbler (lat. Iduna Pallida) but the greenish color make me think it is more a Icterine Warbler (lat. Hippolais icterina).
I found a song similar to the bird I saw on this page (second record).

It could also be a Common Chiffchaff (lat. Phylloscopus collybita) or a Willow Warbler (lat. Phylloscopus trochilus) as they are very common but the length of the tail make me feel it more one of the above (or another one) and the sound does not seem to fit.

Anyone can help on identification of this bird?


texts:
Upstate NY USA here.

I am trying to identify the type of insect that this is:

Top-side:

Bottom-side:

Is this a cockroach? If so what type/sub-species might it be? If not, what other type of bug have I stumbled across here?


texts: How many different colors can a normal human distinguish?

texts: I am not talking about asking a person to sit for 10 hours to separate one color. I want to know is the normal person in a normal life.  How many different colors can a normal human separate?


texts: What is this insect? 6 legs and black spots

texts:
What is this bug?

Details:
 - Georgia, (Southern) USA
 - Maybe 1-4cm in size
 - Seen near an open area/crack between an outer door-frame and door where it could have come from outside, or going from inside to outside since the temperature difference was noticeable in this area.

Thanks in advance!


texts: Can someone help me identify this Brazilian spider?

texts: Does anyone know anything about the identification of this spider? Sorry, but it's the only image I have. It was shot at 2004, January 25th (summer), at 11:27 AM, in Cerrado biome at Minas Gerais state, Brazil. It was walking over a Paepalanthus inflorescence (Eriocaulaceae), probably waiting to prey on its pollinators. A small section of web can be seen raised to the left (where it apparently comes from another inflorescence), touches one of the small flowers, and then it's apparently still connected to the spider, in a pattern that reminds me of Salticidae, though I'm not sure. I think its size is around 1 cm. I doubt a specific identification will be possible, but family, superfamily, subfamily, anything will be fine.


texts:
In my bio class, we learned that you can use restriction enzyme or PCR to linearize a plasmid. Linearizing by restriction enzyme seemed visual and intuitive but how do one linearize a vector using PCR?
I know how PCR works(at least I believe I do), since I watched couple of videos on YouTube explaining them.

But it is not connecting to me how PCR can be used to linearize a "circular" DNA. I have seen videos where a straight double stranded DNA was separated into single strands and using PCR to produce multiple copies with appropriate primers.

But if a plasmid, the circular DNA is not "straight" or linearized in the first place how do you perform PCR on it? Because if they are in a circular state during PCR the strand would never separate in to linear strands. Wouldn't you just have two sperated strands that are circular? E.g a small ring of single strand DNA and a bigger ring of single strand DNA. They are still in circular state after the strands split from each other. Please correct me if I am spitting out nonsense. I just don't see the visual here.


texts:
... when not killed by other members of the hive.

Is it always a consequence of exile (denial of some resource, etc) or does some organ fail regardless of circumstances?


texts:
Why are some people affected so differently by auto-brewery syndrome differently if the syndrome seems to be caused by the single organism saccharomyces cerevisiae? It is known that the syndrome has been used to waive DUI charges — like most recently for this New Yorker whose blood alcohol level was 0.4 but she had none of the usual symptoms of intoxication, even though she had ingested alcohol earlier that day. She also carried out most of her daily activities normally, even with high levels of alcohol in her system.

On the other hand, there was another case where the carrier experience the effects of auto-brewery syndrome differently:

  Cases involving the yeast Candida albicans and Candida krusei have
  popped up in Japan, and in 2013 Panola College Dean of Nursing Barbara
  Cordell documented the case of a 61-year-old man who had frequent
  bouts of unexplained drunkenness for years before being diagnosed with
  an overabundance of Saccharomyces cerevisiae, or brewer's yeast, the
  same yeast used to make beer.

The quote can also be found at the link of the CNN article.

Could the difference in symptoms and effects due to variations in how the carrier bodies could deal with the overabundance (maybe depending on age, gender, or ethnicity) or are they attributed to variations in the nature of the yeast?


texts: Role of Intermediate Filaments in cell - cell signalling

texts:
A passage in my textbook mentions briefly that the role of intermediate filaments in the cytoskeleton is to enable cell to cell signalling by extending between special junctions and alowing cells to adhere to basement membrane

What does this mean?


texts: What was the biological mechanism that allowed Tarrare to eat so much?

texts:
Are there any conjectured mechanisms that cause Tarrare's extremely oversized stomach and abdominal cavity? Along with his superhuman appetite of course.  Whether from a medical perspective or a genetic one (I.e a potential diagnosis that is perhaps quite similar or the genes that would be at play).

Even correlated genes and their subsequent mechanisms that are being affected could be an interesting addendum.

*I would like to make sure that any answer is also trying to explain the enlarged esophagus and abdominal cavity(seen during autopsy) along with the appetite, sweating, and other observed manifestations of an underlying condition(see Death section of Wiki for info and associated source material in book "Two-headed Boy and other Medical Marvels").


texts: From an information perspective, are both strands of DNA necessary?

texts:
I am learning about the genetic code, replication, and transcription, and I have a question about whether or not both strands of DNA are really "necessary".

In replication, at a high level, we are taking 2 strands of DNA and creating 4 of them. Part of my question is: suppose hypothetically that the genome only consisted of a single strand (instead of the double helix), couldn't replication just as well occur by turning 1 strand into 2 (instead of 2 into 4)? I suppose this could be done by taking advantage of complementary base pairing as usual, and then splitting the two strands?

In transcription, I believe only one strand of a gene is read by RNA polymerase, so I don't think think the second strand is "necessary" here.

Can someone shed some light on this for me? I realize this is pretty speculative, and DNA is what it is, and does what it does. but I think this sort of question will allow me to see deeper into tits finer workings.


texts:
So I am trying to figure out a threshold for an activity driven model. That is described in this paper: https://www.nature.com/articles/srep00469

That is I don't see how the researchers got R0 to be between 0.2 and 0.5 (page 6). If they are using gamma=-2.1 and epsilon=10^-3 and threshold is defined in equation 4, my calculations give me threshold of 2.020396043515874.

Now if the power law distribution (activity) is a random number i.e. this:
http://mathworld.wolfram.com/RandomNumber.html

this yields average activity of 0.005489691793543477 using this equation:

((1-gamma)/(2-gamma))*((1-(epsilon**(2-gamma)))/(1-(epsilon**(1-gamma))))

so then following equation 4, the threshold is 2.020396043515874, but that's not what Figure 4 (B) is showing so I'm very confused.

I would really appreciate if someone could clear this out for me.


texts:
I've just finished reading The Hidden Lives of Trees by Peter Wohlleben, which I thoroughly enjoyed.

According to the author, the advantage of shaking the leaves is that both sides of the leaf are exposed to the sun, and therefore both sides can photosynthesize. This would be in contrast to other species, where the underside is reserved for breathing and transpiring. However, to me (a complete amateur), the underside of a quaking aspen seems paler in colour and doesn't "look" like it's any more suited to photosynthesis than the underside of any other leaf.

In addition, I can't find any other sources that back this claim. Most other sources (for example https://www.nature.com/scitable/knowledge/library/case-study-the-glorious-golden-and-gigantic-13261308/) seem to claim the shaking of the leaves reduces the risks that come with too much sunlight, which damages the leaves and actually lowers the rate of photosynthesis.

My question is therefore, what is the most convincing advantage the quaking aspen gains from this characteristic ?


texts:
I am interested in positive charged polyacrylamide to electrophorese molecules I am interested in.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643323/
http://onlinelibrary.wiley.com/doi/10.1002/bip.360300309/pdf

The articles shown above use allyltriethylammonium bromide (ATAB), but I am not sure which chemical they mention.

Or is there any other chemical to add to acrylamide to get positive charged polyacrylamide copolymer?


texts: Is there any measurement I could perform after RT that allows me to check the efficiency that the procedure had? Nanodrop cannot be used as remnants of RNA and poly T primers mask measure, or?


texts: What's the difference between a plant and an animal?

texts: Are there some living things where the distinction between plant and animal is blurry or unclear?  I wouldn't know where to put something like yeast.  I also thought of photosynthesis, but then I heard that some salamanders have photosynthetic cells.  So, what's the difference between a plant and an animal, formally?


texts:
Was diving a few days ago at Jervis Bay (Australian East Coast - temperate). Water temp 20 degrees C, depth 5m. Spotted this creature in the sand. About 150mm high. It isn't sea-pen (Cnidarian) as it doesn't retract if touched and is wrong shape. Has polyps 20mm long all over stalk. Its soft. I've never seen one before. Took a few snaps as I was sure everyone else would say they knew what it is. No-one does. Is it a soft coral? If so, what's it doing growing on sand in temperate water. It looked quite healthy but we've never seen any others there.
I wish I'd taken better photos now :)


texts: Do Japanese have a different pelvis position than Europeans?

texts:
I was watching a show that made the claim that European women's pelvis is tilted more forward compared to Japanese women's which places their butts higher up.

Is this information accurate?


texts: what would be the scientific name of this variety of dove

texts:
recently i came across a small dove who had its feathers tied by a rubber band so that it $would'nt$ fly. it looks some what like this

i was stunned by seeing it as i have never seen a dove in brown colour. and after staring it for some time i noticed that it's feathers or hairs near the neck region were made into a cluster that makes it look like $spike$ $hair$ $style$

so in short what would be the scientific name of this dove ??


texts: Is the mutation rate in pseudogenes higher than in coding regions?

texts: Coding genes are subject selective pressure that are not present for pseudogenes, that would suggest that pseudogenes have a higher mutation rate than coding regions. If so, how much higher?


texts: How did genome duplication in jawed vertebrates allow gene specialization?

texts:
I am currently reading from Chapter 15 in Principles of Life, 2nd Edition:

  Many gene duplications affect only one or a few genes at a time, but in some cases entire genomes may be duplicated. When all the genes are duplicated, there are massive opportunities for new functions to evolve. That is exactly what seems to have happened during the course of vertebrate evolution. The genomes of the jawed vertebrates have four diploid sets of many major genes, which leads biologists to conclude that two genome-wide duplication events occurred in the ancestor of these species. These duplications allowed considerable specialization of individual vertebrate genes, many of which are now highly tissue-specific in their expression.

My question is: how exactly does duplicating a genome enable specialization of genes? In other words, after vertebrates underwent genome duplication, how did one copy of the genome become "highly tissue-specific"?


texts: Why is extracellular measurement of action potentials so different from intracellular?

texts:
I had read in a paper that present a low noise amplifier the following:

"...This level of input signal is larger than both typical action potentials (<500μV) and local field potentials (<5 mV). If a larger input signal is expected, the amplifier’s supply voltage can be increased at the expense of higher power consumption.We verified that our neural amplifier works in a real recording environment by using it to record action potentials in the robust nucleus of the arcopallium (RA) of the anesthesized zebra finch. Data were taken with a carbon fiber electrode (Kation Scientific, Inc.) electrode that had an impedance of approximately 800kHz at 1 KHz. A long extracellular trace and a short extracellular trace recorded from our amplifier (normalized by its gain) are shown in Figure 2. They were found to be identical to that recorded by a commercial neural amplifier (A-M Systems, Model 1800)."

Link:

  http://www.rle.mit.edu/acbs/pdfpublications/journal_papers/woradorn_tbcas_neural_amp.pdf

Please, can someone help me to understand how we can measure an action potential as shown in figure 2? We know that action potential amplitude is approximately 70mV as shown in figure 1 but figure 2 shows that is approximately 70μV.Is this possible?

Figure 1

Figure 2


texts: Do humans have the hyaloid canal, after all?

texts: Most Google Images results for "eye anatomy" are pictures of eyes that don't have the hyaloid canal while some do (proof). Do humans have it, after all, or not? :)


texts:
I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself.
Thanks


texts: What do "e" "-" "C" and "E" mean in this output?

texts:
I have given an input of this protein sequence:

MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE

from this website  along with the option of COBEpro. Now the output sent by this site to my email is as follows:

Name: temp_prot

Amino Acids:
MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE

Predicted Continuous B-cell Epitopes:
MOST LIKELY EPITOPES:
0.82848577 39 TKALGIS CCCCCEE eee-e-e
0.82036375 39 TKALGI CCCCCE eee-e-
0.76503265 38 TTKALGI ECCCCCE eeee-e-
0.73178638 73 TSQPRGDP CCCCCCCC -eeeeeee
…

and a few more. Now can you tell me, if I consider the very first result, I was able to find TKALGIS in the parent sequence but could not find CCCCCEE. What is this CCCCCEE?
And what does this eee-e-e mean?


texts: The fastest vaccine developed is a mumps vaccine, which took 4 years. Where is the hope that we will find a COVID vaccine in less time?

texts:
I understand that doctors and scientists are working hard to find a vaccine, but is there a reasonable chance that we will find one in the time that scientists and politicians are suggesting?
I also understand that we have no choice but to socially distance and bithe our time to find a vaccine if COVID is anything like the flu, but what if it proves to be as hard as finding a vaccine for HIV? The first HIV outbreak occurred in the 1980s, and if I'm correct we still don't have a vaccine for it yet (even though we do have treatment for it so people could just live their life with it).
So my question is with all this in mind, how could there be a chance that we will find a COVID vaccine in less time? Is it just optimism, or is there actually reason to believe the vaccine will be produced say by the beginning of 2022.


texts: I remember hearing that the tumor where HeLa cells originated from was purple and jelly like, and I've seen pictures from studies with rats and HeLa tumors, and their tumors appear to also be purple. So what makes these tumors purple?


texts: Every now and then I got a glimpse of this bird which I'm pretty sure is not native to Northern Germany where I live. There are at least three of these birds around but I usually only see something quick and green somewhere in the trees. I finally managed to get some decent pictures so I'm hoping someone can tell me what kind of bird this is. I'm curious what biological niche this bird is likely to fill and which native species it might compete with.


texts: Does any lifeforms can make a haploid cell from any other cell without meiosis?

texts: Like the title says, is it possible to produce haploid cells without meiosis?


texts: Is it possible for a parasitic wasp to alter the behaviour of its host after emerging from it?

texts: I know that parasitic wasp larvae can live for a long time inside their live host (eg. caterpillar), but I always thought that they kill the host when they eventually get out of it. But I've seen a film, where it's shown that not only can a caterpillar survive the emergence of a wasp larva, but also the parasites infect the host with some kind of virus that changes the behaviour of the caterpillar to protect the wasp’s pupa. Is it possible and common among parasitic wasps? What species of wasps and viruses cause such effect?


texts: How would the human body adjust to sleep times if we were to live in a place with different day lengths?

texts: You sleep at night and are active during the day that's how things work for humans, but theoretically if a human whose parents lived on earth were to be born in another planet resembling earth but the difference was that this planet has an 8.5 hour day, what kind of changes will this person undergo?if a human who grew up on earth suddenly had to move to this planet how would his body adapt? what would be the difference between a person who moves to this 8.5 hour day planet with the person that was born there? and would the person who was born on this planet be active for 4.25 hours and then sleep for the other 4.25?


texts: How does gene affect organs development in eukaryotic cells?

texts:
I'm totally new to biology and apologies if you find this basic. The central dogma insists that genetic information flows in this direction:

  DNA -> RNA -> proteins

So far so good, it is very clear to me. The question comes here. How does this flow contributes to creating/developing organisms. I want to zoom out from molecular biology to a bigger picture of an organ.
I want somebody to tell me, how does genetic code in a zygote, results in creating organs just in secreting different proteins by different active genes?


texts: Neuron connectivity- how are they connected physically

texts: If Neurons are only connected through synapse and there is no physical connection,  how are they just suspended in brain layers?


texts:
When the post synaptic neuron begins to depolarise as positive sodium ions move into it and it reaches threshold- does the inside of the neuron actually switch to being more positive than the outside?

I thought depolarisation meant that the inside became less negative but still remained more negative than the outside, hence having a voltage of -55mV. If the inside became more positive wouldn't the voltage be 55mV?


texts: What kind of tree is this (Seattle, WA)?

texts:
This tree is a volunteer and I am hoping to find out what kind of tree it is.

Young tree

Leaf sample

Below is a more recent photo showing flowering.


texts: Why don't half of us have situs inversus?

texts: I don't see any possible evolutionary disadvantage in situs inversus(the condition where major organs are mirrored from their normal positions) when people with situs inversus can have a normal healthy life.


texts: What is the difference between cytokine and chemokine?

texts: I often see these terms being used in inflammation, and I'd like to know, are they synonymous with each other or do they mean different things? Also could someone provide an example of each?


texts: When should endocytosis inhibitors be used in cell binding assays?

texts:
I'm beginning to do some cell-binding assays and I would like for my proteins to not be endocytosed by my mammalian cells. Typical suggestions are for the cells to be kept on ice and that the binding experiment also occurs when the cells are chilled.

However, to be sure it has been suggested that I use endocytosis inhbitors. So my questions are, when are the endocytosis inhibitors necessary? How would I know that endocytosis inhibitors are necessary? Which ones would I actually use?

I recognize that there are both clathrin and non-clathrin mechanisms of internalization. Which mechanism would be more useful to study for an antibody-receptor interaction?


texts: HELP! How will pH 14 affect enzyme structure?

texts: If a substance is very alkaline/ basic, e.g. a pH of 14, does this mean that there are near to zero H+ ions (or it is possible to have such a situation where there are zero H+ ions and it is still alkaline) or does it mean there are lots of OH- ions relative to H+ ions? If so, how will this affect enzyme structure in very alkaline/ acidic conditions?


texts: How do scientists create specific mutations?

texts:
Suppose I want to create a mutant like Antennapaedia how will I go about accomplishing it ?

I know that radiation and certain chemicals are mutagenic. So do scientists subject animals to such mutagenic chemicals and then wait for their progeny to see what mutation it has got ? Are there any specific protocols to create a specific type(for eg.homeotic) of mutant or is it pure luck ?

Sorry if I am being too naive!


texts: How to do whole genome sequence alignment in R or Ruby/C++, any good language?

texts: I need to perform tuberculosis mutation analysis. First step I need to do is to align sequences in fasta format against one reference file. i tried CLC genomics workstation --- it hangs on 60 000 lines of fasta reference file for entire day. Please advise what technology and tutorial to use to do that task.


texts: What is the definition of "dry weight" and "dry cell weight"?

texts: As I understand it, the dry weight of something is its weight minus the weight of its water content. Is this the definition? What about dry cell weight?


texts: Is the 'fluttering feeling' when under stress neurological or physical?

texts:
I'm sure that everyone is familiar with the sensation commonly known as "butterflies in the stomach".  It is commonly experienced during periods of anxiety or stress (e.g. before high stakes job interviews or roller coaster rides) and apparently (after my web research) often felt in new romances without an obvious cause of tension.

However, whilst my googling did turn up an inordinate amount of rubbish regarding love-sicknesnes, I have been unable to find even a suggestion as to a mechanism as to the physiology behind this feeling.  Is it a sensation of physical change in the stomach (some sites vaguely mentioned the restriction of blood flow to critical organs but it was entirely unsupported) or is it neurological in nature?


texts: Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating)

texts:
Background

Quoting from Gillespie's book

  The level of inbreeding is measured by the inbreeding coefficient, $F_I$, which is the probability that two alleles in an individual are identity by descent.

The two possible alleles are $A_1$ and $A_2$ and their frequencies are $p$ and $q=1-p$, respectively. Gillespie goes on and give the expected genotype frequencies given $p$ (and $q$) and $F_I$

$$
\begin{array}{r|c|c|c}
Genotype & A_1A_1 & A_1A_2 & A_2A_2 \\
\hline
Frequency & p^2(1-F_I)+pF_I & 2pq(1-F_I) & q^2(1-F_I)+qF_I \\
\end{array}
$$

Question

Can you please help me to understand why those are the appropriate genotype frequencies?

Example of what is unclear to me

By the definition of $F_I$, I was expecting that the frequency of `$A_1A_2$ (and $A_2A_1$) would be $(1-F_I)$, that is the frequency (or probability) that two alleles in an individual are not identical by descent. I feel like the definition given above is wrong. Should it rather be something like the weight for sampling like individuals? That is if there were only two possible mates, one that is $A_1A_1$ and one that is either $A_1A_2$ or $A_2A_2$, then the probability for a $A_1A_1$ individual to mate with the other $A_1A_1$ is $F_I$.


texts: How do animals avoid the problem of inbreeding?

texts:
In humans, there are various cultural rules to avoid inbreeding (to the level of paternal cousins, nieces/nephews and uncles/aunts etc)

How do animals such as dogs avoid the problem of inbreeding? They do not have a record of their relatives and there seem to be many siblings in each batch for some animals. How does it work in the wild or among stray animals? Is their DNA somewhat resilient to these genetic disorders?

Likewise, how do birds handle this issue?

EDIT: I am not trying to breed animals, want to understand how it works in the uncontrolled wild when the young leave home early and are scattered.


texts:
What research guidelines is a person legally mandated to follow if they want to do medical experimentation on themselves?

There is a large amount of variation in the types of medical experiments so I wanted to ask people focusing on the change in practice as a function of the type of medical experimentation you do in the biological sciences (e.g., drugs, blood samples, tissue regeneration, testing medical equipment), including invasive and non-invasive studies. This question seemed almost equally suited to academia and biology SE, but given the focus on different types of biological experiments I felt this might be the more suitable site.

I am most interested on research practices in the United States, and anything touching FDA regulations would be great.


texts: Are there any half-evolved animals alive today?

texts:
I know that there are animals that are "simpler" than other animals but are there any that are half-evolved? Are there any animals with half-evolved functions, like arms, legs, etc?

This was part of the original question, but it was incorrect.

Saying that every species on the planet is "transitional" is an unacceptable answer because it only works on the assumption that macro-evolution is true.

Saying that all the transitional animals just died off also doesn't seem quite right. If all the previous transitional  animals just went extinct, then wouldn't we just have a few specialized species alive today? This wouldn't allow for the diversity we see today.


texts: Looking for source: Biologic reactions of people saying "no"

texts:
Searching for this topic is incredibly tedious because the word "no" is the main point of interest and I always end up on sites saying how "saying no is good for your health" but I am looking for the medical evidence of this claim.
I remember very faintly hearing about measurable physical effects on a person in a situation where this person says the word "no" to something.
There was an experiment where scientists (I suppose neuro-scientists?) were able to measure the effect of saying "no". Colloquially speaking the body was "closing" in a sense that the person went in some unconscious defence mode, stress levels were rising, change in muscle tone were measurable etc.
When I also remember correctly these effects were measurable even without exposing the person to a specific situation. Just saying "no" wholeheartedly triggered those effects.
Did someone hear about this one? I am looking for any clue to get more information on that.
Edit: I add to the excellent hint from Vadim: I am indeed looking for a credible source where experiments were conducted in a controlled manner and not someone sticking electrodes on people in the mall :D. And I also think this experiment would be hard to do right in the first place since you basically would have to deprive the people from any external stimuli which by itself would probably also already cause side effects.


texts: Does the leaves of papaya plant help in increasing platelets in a case of dengue?

texts:
In Kolkata and nearby regions, due to sudden and huge amounts of rainfall, there has been an outbreak of dengue, a disease spread by female Aedes mosquitoes. The outbreak has been so dangerous that dozens have already died in the villages.

A problem of this disease is that, the platelets in blood are decreasing abnormally. For example, a patient had 120 thousand platelets when checked at night, but when checked on the morning, it drastically reduced to about 20 thousand. This particular patient could not be saved.

Many people say that the juice of papaya leaves (leaves of Carica papaya) helps in increasing the platelets in blood. Some doctors say it's wrong, while others say that it does effectively help. Even tablets and powders have been made, but the confusion persists as to whether they are effective or not.

I could not find any good information on the net. Can anyone, with scientific arguments, answer this question?


texts: What is the purpose of an siRNA screen in drug discovery?

texts:
In the paper "A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle" by Martin et al. the authors try to disrupt the Ebola life-cycle by screening which human genes participate in it's replications:

In order to identify host factors involved in the EBOV life cycle, we performed a genome-wide siRNA screen comprising 64,755 individual siRNAs against 21,566 human genes to assess their activity in EBOV genome replication and transcription. As a screening platform, we used reverse genetics-based life cycle modelling systems that recapitulate these processes without the need for a BSL4 laboratory.

This helped them find a pathway.
What is siRNA screening and how does it help find a pathway?
The tag [rna-interference] references siRNA:

A post-transcriptional mechanism of gene-regulation/silencing mediated by small RNAs (siRNA)

However, I can't tell if siRNA refers to "small RNAs" or the whole process.


texts: Are there organisms that "branch more" near the leaf?

texts:
(I'm a computer scientist)

Tree branching is a fractal patterns in nature. I know stems typically branch in two at each level (self-similarity). I guess there are plants or other organisms that branch in 3 at each level (still self-similar).

But are there organisms where the stem first branches in 2, then at the next level branches in 3 or more? And maybe at the next (maybe the last) level branches even more, say in 7? It doesn't need to be the stem of a plant, it could be any part of any organism (fungi,...), e.g. the "flower part" of a plant, or a micro-organism.

I'm looking for places where just the branching factor changes, but otherwise little else. What I'm not looking for "branch by 2, branch by 2, branch by 2, and then the very final step is one level of fascicle where branching is 5". I would be fine it's "branch by 2, branch by 3, then fascicle where branching is >3".

I'm trying to find if there is something in nature (e.g. organism, geological, or physical structure) that follows this pattern found in a computer science algorithm, RecSplit, which I co-authored.

Like the following: it first branches in 3, and then branches in 8. The actual numbers don't matter to me, it might as well be branch in 2, then in 3, then in 5, or so.


texts:
Let's say I ordered seeds of a plant online. Then, I plant the seeds and grow a few plants. Then I take the seeds that the plants produced and separate them based on each plant.

Is it possible that I could then use those seeds to continue growing plants that have a desired characteristic? For example, if I wanted to grow taller and taller plants could I just keep planting seeds from the tallest plant? Or would I need to use a different method or technology to do this?


texts: Names for the degrees for symptoms from drought (or other damage) done to trees

texts:
Looking out my window, I see trees suffering from drought. I once knew the name for the degrees visible, but I have forgotten and can't find it on the net.

Attempt at describing "level of dryness"

Level 1

The tree is completely without leaves (at a season where it should have at least some leaves).
Level 2

The tree has at least some bushels of leaves on the main branches, interspersed with dry areas without any leaves.
Level 3

The tree has leaves all around the main branches (those which are attached to the stem), but not on any secondary branches.
Level 4

The tree has leaves on the main branches and secondary branches.

Explicit question

What are the names for those levels, or other levels, in case I missed some?


texts: What is Growth and how can we define it to be a defining property of life?

texts: I was reading a book and it said that internal/intrinsic growth is defining property of life and not extrinsic growth as saying accumulation of dust on a book makes it a bit bigger, even if it is by a few mm but since it's just a deposition of material and it can be removed, so it's not living. Now, if we see intrinsic growth then I had a doubt. Say we took a piece of log and dipped it into the water. Then the log will also grow in size and this growth is from inside, but the log of wood isn't living. So, I was in doubt that how can I define growth for a living.


texts: How can I find and get sulfate-reducing bacteria? Where and how can I store them for a long time?


texts: Can plants break down cellulose for energy?

texts:
I know humans and other animals start using their own proteins as food when starving. This made me wonder if a plant that is deprived of sunlight, after using up its sugar reserves and other carbs, could break down parts of its own woody structure in order to feed the rest of itself.

Googling yielded no useful results, which leads me to think the answer is no. I've never heard of plants themselves possessing cellulase, only certain animals.

Additionally, I would imagine that cellulose is not easy to transport, so it would have to be decomposed by the region of tissue surrounding it - which obviously couldn't last for long before that region died due to cannibalizing itself.


texts:
I know that most fungi are not differentiated into tissues. And tissues are groups of specialised cells aiming to perform a collective function. Does it, then, follow that most fungi do not have distinct cells for distinct functions, and that all their cells are essentially the same? I am slightly skeptical of arriving at that conclusion; but if it is true, then I believe that it would be reasonable to say that there is no difference between the cells that give rise to spores and those who don't. How is it possible, though, for cells to be structurally similar but capable of performing varying tasks?

To summarise,

Do tissue-less fungi have no dissimilar cells and all are exactly the same in all respects? I believe that the answer to this question would also be applicable to other multicellular organisms as well.
Can it be possible for two structurally similar cells in fungi to be adept at two different tasks? This too seems to be extendable to incorporate all other multicellular organisms.


texts: How to choose right volume of DNA and SYBR Green

texts:
I'm testing fluorescence level of a sample having dsDNA, SYBR Green and milli q water but I'm facing difficulty in choosing right volume of dsDNA and cons level of SYBR Green.

Details of sample: dsDNA:1000 nano mole, SYBR Green:1X (1000 times diluted from original stock)

Sample_1: dsDNA (3ul) + SYBR Green (5ul) + milli q water (27ul)

Sample_2: dsDNA (3ul) + SYBR Green (5ul)

Result: In first sample I haven't got any signal but in second case I got( But I want 5 times higher then what I got).

Please tell me how it work and how these things depends on each other. I'm not a biologist if possible suggest me resource as well.


texts: Deducing protein sequence length from gene DNA sequence length

texts:
Is there a standard way to deduce protein sequence length from gene DNA sequence length of the gene coding for it?

Naively I had assumed that amino_acid_seq_length / 3 -1 (deleting one for the stop codon)ought to work but apparently not always. Is there a better way?

Let's assume the gene is eukaryotic, specifically a plant gene.

e.g.

Or


texts: What is the resistance of a single human cell? I know different cells will have different values, some examples would suffice. I did not find any such information on the internet.


texts: Why do people with type O blood have anti-A and anti-B antibodies?

texts: People with type O blood have anti-A and anti-B antibodies, even without receiving a transfusion. Why?


texts: If the half life of Caffeine is ~6 hours, why do people consider it ineffective after its half-life?

texts:
Caffeine has a half-life of ~ 6 hours in the body.

So assuming you take 200mg of caffeine, after 6 hours there should still be 100mg of caffeine in your body.

Then why is it generally said that after 6 hours caffeines effect should wear off? Shouldn't it only be diminished since there is still 100mg of caffeine in your body?


texts: What are the exact reason causing missing calls in a VCF file from exome sequencing?

texts:
My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is recorded as "./." at the GT field. From googling I learned that they're not homozygous reference genotype ("0/0"), but missing calls due to some sequencing ignorance.

In order to make my data "cleaner", I thought it's better to filter out the loci with missing calls if there're not too many of them. I also checked the corresponding "DP" of the loci with and without missing calls. For example:

chr1:123 GT:DP 0/0:2 1/1:4 ./.
chr1:234 GT:DP 0/0:10 1/1:11 1/1:20
chr1:345 GT:DP 0/1:40 1/1:37 0/0:78
chr1:456 GT:DP 0/1:7 0/0:23 ./.
chr1:567 GT:DP 0/1:34 1/1:39 0/0:58

In the above toy example, there're 3 people and 5 loci. I checked the mean DP of all 5 loci and I found that the mean DP of loci with missing calls (1st and 4th loci) to be significantly lower than the mean DP of loci without missing calls (2nd, 3rd and 5th loci). Is that a coincidence? Or are there any specific reason that the loci with missing calls have lower coverage than the "normal" loci? Thanks!


texts: High Current (Speed) Transfer Buffer Recipe

texts:
Does anyone know an effective buffer mix to use for high current Western transfers?  We are successfully using the vendor's premixed buffer to transfer a wide range of protein sizes to PVDF membranes at 1A/25V for 10 min.  We get great results with the vendor's expensive buffer.

I haven't been able to find a non-proprietary recipe that works.  The best ones we have hold the 25V, but then have a decrease in conductivity (increase in resistance) where they will start at 1A, but drop to 0.4A by the end of the 10 min.  The vendor's buffer seems to hold the high current and results in better transfers.

I don't know if it will be helpful to list all the variations I've tried in detail, but they have revolved around modifying a traditional Towbin buffer plus SDS, more glycine/Tris, or MgCl2.  These were all various suggestions from people around the department, but I haven't found much published evidence for a buffer under these conditions.

I realize 1A (and no I don't mean 1mA) is a lot of current, but the vendor's system works really well.  Any pointers on what I might try/add would be appreciated even if you don't have a worked out protocol.

Edit: Info from the MSDS indicates it has 3 reagents:

Listing of dangerous and non-hazardous components:
Proprietary Reagent K
10-20%
Proprietary Reagent EB II
5-10%
Proprietary Reagent S
1.0-2.5%
7732-18-5 water
50-100%
·
.....
Solvent content:
Organic solvents:
0.0 %
Water:
74.8 %
Solids content:
25.2 %

[I'm not sure if this MSDS info should be put here, just because I'm looking for someone who has already used a high current buffer they know the formulation for, not a guess to what I have.]


texts:
Consider two identical pieces of paper.

Scenario 1: On both something is drawn in black ink. If the difference between the areas covered in black ink is sufficiently small, I cannot see the difference between the two drawings.

Scenario 2: Now imagine that the same parts are covered with ink, but their color differs. Again, if the difference is sufficiently small, I cannot see the difference.

Firstly: what causes this? I am aware of the terminology of just-noticeable differences/limina, but do not understand precisely what causes them. Is there some discretization of continuous signals going on that causes `nearby signals' to be treated the same way?

Secondly: one person may have better vision than another, but are there physical constraints that are the same for any two persons and that imply that if the difference in scenario 1 or 2 is sufficiently small, no two persons will be able to see a difference?

Addenda: I phrased the question informally by not defining what a `small difference' is, trusting/hoping that this does not lead to confusion. If desired, such statements can be made precise by adopting appropriate distance functions. In scenario 1, one way to measure distance between two areas covered in ink could be to use the Hausdorff distance; likewise, one way to measure the distance between colors in the second scenario could depend on the difference in responsivity of the three types of cone cells.


texts: How urination prior to blood test may give error?

texts:
Source: Textbook of  Practical Physiology, 4th Edition

  according to it urination within 30 minutes is a precollection factor that may alter the results of blood test.

I am unable to comprehend how urination could affect the blood sample. Urination will just result in excretion of urine already formed and stored in the urinary bladder, so how its loss could lead to error in blood sample?


texts: What is this snake in South Florida, USA

texts:
I observed this snake for about 10 minutes. It was slithering back and forth in about 50x20 yard (50x20 meter) area. Just kept going back and forth (then I left). There was a similar snake at the same time in roughly the same 50x20 area, but they didn't seem to be paying attention to each other.
This is in South Florida, near Naples, Florida, USA.
I took several pictures, but I think this one is the clearest.


texts: Which chromosome of the two contained in a haploid cell goes into the diploid cell after fertilisation?

texts:
I am totally new to biology and I have a very stupid question. In the typical representation of meiosis, haploid cells contain two different chromosomes, resulting from the crossing-over process. But diploid cells have two homologous copies of each chromosome, usually one from the mother and one from the father. So, since there are two identical copies of the same chromosome for each parent, it means that each haploid cell brought only one out of two chromosomes into the zygote. My question is: how is this chromosome selected? Is it a combination of the chromosomes contained into the haploid cell? Is it one of the original two, while the other one is discarded in the fertilisation process?
I'm sorry if my question is not clear. Thanks.


texts: When I searched for the causes of common cold, I found out that it's only cause is the spreading of virus and that it's a myth that you get cold when you get wet. If that is true then how does the virus start to spread if no one else is having cold? Or Simply, Can you get cold by yourself without the virus?


texts: What terrestrial Gastropod (specifically snails) has the fastest reproductive rate?

texts: I am looking to do a series of experiments to test the adaptation of snails to different environments (Controlled environments in a lab setting. No organisms would be released into the wild under any circumstances.), and to also test the potential rates of specialization to an environment or food source, and speciation in a snail species (obviously more experiments would have to be done with many species before the results could be generalized). To do this, I need a snail species that has a very short time between the oviposition and sexual maturity of the species, and that are not extremely difficult to raise or breed in a lab. Any help or leads would be appreciated!


texts: Why are there two replicase proteins translated from tobacco mosaic virus RNA?

texts:
I’m trying to understand how TMV is expressed and have read (here) that there is a large and small form of the RNA-dependent RNA replicase. These are translated from the same region of the genome, the larger arising from read-through of a leaky stop codon.
Why are there two forms of the replicase? My first impression was that each might produce a sub-genomic RNA, one for the movement protein and one for the capsid protein, but can find no reports confirming this.


texts: Coacervater were more like Viruses or Cells?

texts: The answer considers them as first formed living cells as they were precursor of life. But they had no lipid bilayer nor any cellular organization, shouldnt they be more like Viruses ,or like Prions and Viriods ??


texts:
I am looking for a reference to help me understand what is meant by acronyms such as : H3K9me1, H3K9me2, and H3K9Ac.

I know that these are all histone proteins, but is there a general nomenclature algorithm for all cellular proteins? Are H3K9me1 and H3K9me2 just different proteins that methylate the same region? What is meant by H3K? Etc.

Thanks!


texts: What causes Paresthesia (Pins and Needles) at a cellular level?

texts: I've looked it up in plenty of places like the Wikipedia page and such, and it is clear that the most common cause of Paresthesia is either a fair amount of pressure on a specific patch of skin causing lack of blood flow to the specific nerve endings in that limb (not to be confused with a stop in blood flow to the limb altogether) or a much stronger amount of pressure on that patch of skin for a shorter amount of time. This, although the most common cause, is not nearly the only one, which could be anywhere from simply sleeping on the wrong side of the bed to a lethal injection. I'm wondering what happens to the nerve cells that are affected at a cellular level, and what causes it at a cellular level. The level at which pounds per square inch aren't what is being noticed.


texts: Expression/Mechanism of ROR1 in healthy tissue

texts:
ROR1 is currently under investigation as a therapeutic target for cancer (1). A number of studies show different cancers may have their metastatic potential reduced, or become apoptotic through targeting or abrogation of ROR1 (1-3). ROR1 itself is show to have a number interactions (either through crosstalk or interaction) with some known tumorigenic markers; these include c-Met, PI3K, Akt, Wnt5a, EGF, c-Src (4-7). In terms of metastatic potential, interactions with vimentin, Snail/Slug, cadherins, ß-catenin, and CXCR4/CXCL12 were also identified (1, 8). Some of these are via expression of CREB. In terms of ROR1 is tissue, abnormalities that lead to death were noted in newborn mice that has ROR1 knocked down (9). A notable mechanism for ROR1 in development was in neuroprogenitor cells in which ROR1 regulation status determined whether these cells differentiated into neurons or not (10). It's also found that neural, heart, lung and kidney tissue in adults express some form or another of ROR1 (11). More recent studies suggest ROR1 downmodulation may present toxicity for some subsets of normal tissues (12).

The question, now: Are there any empirical studies that illuminate the potential mechanism of ROR1 in healthy, adult tissues? This is from a treatment toxicity standpoint, since the subsets of affected cells seem to be rather slim. I can understand why the effect on metastatic potential can be significant from the fetal neural cortex development (the need to migrate the neurons into position). We also see a truncated version of ROR1 in some instances. If anyone can shed some light, thank you in advance!

References

Cui B. et al. Targeting ROR1 inhibits epithelial-mesenchymal transition and metastasis.      Cancer. Res. 73, 3649–3660 (2012).
Hojjat-Farsangi, M., Ghaemimanesh, F., Daneshmanesh, A. H., Bayat, A. A., Mahmoudian, J., Jeddi-Tehrani, M., … Mellstedt, H. (2013). Inhibition of the Receptor Tyrosine Kinase ROR1 by Anti-ROR1 Monoclonal Antibodies and siRNA Induced Apoptosis of Melanoma Cells. PLoS ONE, 8. doi:10.1371/journal.pone.0061167
Daneshmanesh AH, Hojjat-Farsangi M, Sandin A, Khan AS, Moshfegh A, et al.. (2012) Monoclonal Antibody Against ROR1 In Chronic Lymphocytic Leukemia Cells Induced Apoptosis Via PI3-kinase/AKT/CREB pathway. 54th American Society of hematology (ASH), Atlanta, USA, 8–11 December.
T. Yamaguchi, K. Yanagisawa, R. Sugiyama, Y. Hosono, Y. Shimada, C. Arima, S. Kato, S. Tomida, M. Suzuki, H. Osada, T. Takahashi. NKX2-1/TITF1/TTF-1-induced ROR1 is required to sustain EGFR survival signaling in lung adenocarcinoma. Cancer Cell, 21 (2012), pp. 348–361
Fukuda T, Chen L, Endo T, Tang L, Lu D, Castro JE, Widhopf GF, II, Rassenti LZ, Cantwell MJ, Prussak CE, et al. Antisera induced by infusions of autologous Ad-CD154-leukemia B cells identify ROR1 as an oncofetal antigen and receptor for Wnt5a. Proc Natl Acad Sci USA. 2008;105:3047–3052. doi: 10.1073/pnas.0712148105.
Gentile A, Lazzari L, Benvenuti S, Trusolino L, Comoglio PM. Ror1 is a pseudokinase that is crucial for Met-driven tumorigenesis. Cancer Res 2011;71:3132–41.
Zhang S, Chen L, Cui B, Chuang HY, Yu J, Wang-Rodriguez J, et al. ROR1 is expressed in human breast cancer and associated with enhanced tumor-cell growth. PLoS ONE 2012;7:e31127.
Teicher BA, Fricker SP. CXCL12 (SDF-1)/CXCR4 pathway in cancer. Clin CancerRes. 2010;16(11):2927-31.
Nomi M, Oishi I, Kani S, Suzuki H, Matsuda T, Yoda A, et al. Loss of mRor1 enhances the heart and skeletal abnormalities in mRor2-deficient mice: redundant and pleiotropic functions of mRor1 and mRor2 receptor tyrosine kinases. Mol Cell Biol 2001;21:8329–35.
Endo M, Doi R, Nishita M, Minami Y. Ror family receptor tyrosine kinases regulate the maintenance of neural progenitor cells in the developing neocortex. J Cell Sci 2012;125:2017–29.
Reddy UR, Phatak S, Pleasure D. Human neural tissues express a truncated Ror1 receptor tyrosine kinase, lacking both extracellular and transmembrane domains. Oncogene 1996;13:1555–9.
Linked in text.


texts: Using viruses to treat altered or misconfigured DNA

texts:
Consider how a Retrovirus can modify existing cell DNA to 'execute instructions' on its behalf.

I wondered: Why can we not utilize lab-generated viruses to infect sick patients with a 'healthy' virus that would rewrite bad segments of DNA with something either correct or non-malus? This of course is assuming that we have a solid understanding of the relationship between genomes and precise viral functions, additionally that we had some sort of gene replacement functionality.


texts: Is it possible that there are two people in the world who belong to a different species?

texts:
There're over 7 billion people in the world and every one of them is different from everyone else. Is it possible that there are two people so different that they belong to different species (in the sense that they cannot reproduce to produce fertile offspring)?

This doesn't have to mean that there's someone in the world who's completely unable to reproduce with everyone else, just that these two individuals are so different that they can't reproduce with each other (they can still reproduce with other people who can reproduce with the other individual - a ring species system).

I'm particularly interested in an answer based on how much the genome varies between people vs. how much they vary against our closest relatives (such as Neanderthals). For example if humans and Neanderthals share 99% of their genes, and the largest variation among current humans is 0.001% of genes, then the answer to this question would be "no".


texts: Is RFLP markers are dominant or codominant?

texts: there are several markers used in molecular biology,. marker analysis. RFLP is most commonly used marker which having several advantages. is RFLP marker co-dominant or dominant ?


texts: When has an organism evolved enough to be called a new species?

texts:
Imagine that we take a population of horses, split them in half and place them in completely different environments. The two species will evolve separate from each other and because the environment is different, the outcome of evolution will be different.

But at what point can you say that these horses have evolved into two different species?

(I do know that they would probably go extinct if we conducted this exact experiment, but this experiment is just to give an example)


texts: What is a rough estimate of CO₂ saturation for high-yield or high growth rate plants?

texts:
Naturally, plants have individual photosynthesis capacities, but it would still be interesting to get a general picture of CO2 saturation levels for some common cultures. Where lies the optimal yield, growth rate, etc compared to the 0.04% in the atmosphere? What is this specific field of research called?

My first assessment is that there is no saturation level for individual plants, that each plant consumes CO2 according to its species' respiration level, and culture density is adapted to the species and practical circumstances such as the greenhouse construction. Is there a field of expertise in planning greenhouse constructions, and if so, what is it called?

It seems to me plants have already or can be genetically modified for heightened respiration. I'm not familiar with this field, further reading would be appreciated.

Would plants genetically modified for heightened respiration require nightly venting/oxygen infusion to support it?

Are there examples of cultures treated as respiration machines that are completely optimized for the capacity of their DNA?


texts: From a computer science perspective, how is DNA compared for various purposes?

texts:
I am very interested in privacy preserving technolgies, such as Microsoft PINQ and would like to see if this is applicable to DNA comparison.

  Given that I don't have a background in biology, I would appreciate it if someone could tell me how DNA is represented in a computer (in computer science terms), and how DNA is compared in a binary format (or logical equivalent).

The privacy preserving technology I'm using allows the patient to have granular control over what DNA data they share, and how it's used. The receiving agency (medical research, FBI, fertility clinics) will receive cryptographic proof of a DNA result, without exposing all DNA values.

I suspect that each of the following use-cases focus on a certain subset of data, and if the same information was presented to all of them, it would be a breach of privacy:

Combined DNA Index System, or CODIS
State DNA index system (SDIS)
National DNA Index System (NDIS)
FBI's 13-Loci
Other government's DNA matching requirements for inclusion/exclusion
Disease susceptibility via single nucleotide polymorphism (SNP), and related heredity
Paternity tests
Evolutionary patterns

Furthermore, based on my independent research, I understand that there are many ways to determine the DNA of a given sample.  What I don't understand is if every test has the same output? (e.g. are all chromosomes are returned, vs only 23? (or less))

The value-add I am trying to provide the patient privacy, while fulfilling all legal, moral, and ethical disclosures of data requested of them.  The recipient will have assurance the data is authentic, despite the inherent double blinding of the field data.

The cryptography allows for

Redacting (or black out) certain values
Anonymously compare a numerical value, (greater than, less than, equal to) without disclosing that value.
Prove, or verifiably disprove, that a value is not in a certain list of arbitrary values.
The agency to know which DNA testing firm generated the results
The DNA testing firm to not know who the patient is, especially in cases of partial disclosure of DNA data.

Your response will help me contribute what I believe to be the moral, ethical, and socially responsible way to handling PII and DNA data.  (yes it will be open source)


texts: How do prodrugs exactly work? Are there multiple varieties of prodrugs?

texts:
I have been reading about a (new?) prodrug of LSD, 1CP-LSD, which is being synthesized in the body to LSD.
However, I don't know how exactly. I read somewhere, that another prodrug of LSD, 1P-LSD was put  into a vial of human blood, and it was synthesized to LSD. Which is kind of hard to belive, that just exposure in blood synthesizes 1P-LSD to LSD. What processes in the body are responsible for this, are there another processes for synthesizing another prodrugs to their respective drugs?
Are there multiple varieties of prodrugs? By that I mean that they synthesize themselves using another method instead of one another.


texts: Can anyone identify this caterpillar / cocoon?

texts:
This insect is about 0.5 mm in length, so it is very small. It doesn't have legs I don't believe, I am not too good at this but I don't know if it's a worm or more like a cocoon for something.

I do find this alarming because I found this one underneath my bed sheet on the mattress. Now I do recall seeing something similar on the crack of the shaky tile floor, so I can't tell if it's just an apartment pest or it actually lives in mattresses.

Location: Toronto, Canada


texts: How does one predict the methylation pattern?

texts:
Suppose, we have a double stranded DNA like

5' AGCTAGGAGAGACCAGGTTCC 3'
3' TCGATCCTCTCTGGTCCAAGG 5'

Where would the methylated cytosine be? Is there any randomness?


texts: Can neurotransmitter concentrations in the synaptic cleft add up if there are several impulses in quick succession?

texts:
When an electric signal reaches a chemical synapse, the signal is transmitted using neurotransmitters. Afterwards, the neurotransmitters are removed from the synaptic cleft. My question is whether it happens in a normally functioning brain that neurotransmitter concentrations in the synaptic cleft add up if there are several impulses in quick succession? If so, does this serve any purpose? Or is the time between two impulses always long enough for all of the neurotransmitter to be removed from the synaptic cleft?

Edit: To further clarify (as the currently only answer does not really adress my issue), I am aware of the principle of summation, however I do not know whether this is actually caused by multiple neurotransmitter emissions "adding up" in the synaptic cleft or whether the postsynaptic membrane can just somehow remember if there was an increased amount of neurotransmitter recently.

To describe it graphically: According to this article, the concentration of serotonin in the synaptic cleft during a single impulse looks somewhat like that. Now when there is a quick series of impulses, does the neurotransmitter always get removed before the next impulse as on the right side of the following image, or can it add up as on the left side? And if it does add up, does this actually serve the purpose of temporal summation or some other purpose?


texts: Will dead cells in culture media have any significant impact on Live cells during incubation?

texts: I am generating stable cell lines and have something like 25+ culture flasks to take care of. Ideally I can let dead cells sit in the media with the live adherent without rushing to change media constantly - Will this affect growth of live cells - I don't want to hinder them as they are already sitting in high[] Hygromycin


texts: What is the name of this about 5cm high, grey, Beanie shaped fungus?

texts: I found those below some stone stairs in Germany. The grass gives you an impression of the size (I guess the grass is about 5-7cm tall)


texts: Double use of ATP in relaxing myosin & active transportation of calcium?

texts: Is the ATP molecule which is bound to the myosin head for relaxation of the muscle (i.e., to break the cross bridge) also utilized for active transport of calcium to the sarcoplasmic reticulum during muscle relaxation?


texts: Systems Biology of triacylglycerol (TAG) synthesis in Jatropha

texts:
I need the genetic regulatory network of TAG synthesis (Kennedy pathway) of Jatropha plant??
Or is there any way to convert metabolic pathway into genetic regulatory network?


texts: How to find the enhancer region of a specific gene?

texts: I am new to these concepts in biology and need some help understanding. My main concern is how to find the enhancer of my gene of interest, specifically the sequence of the enhancer. I am working on a project where I will be attempting to use CRISPR- mediated deletion of the promoter region and enhancer region in my gene of interest FOXN2, in MCF7 Tamoxifen resistant breast cancer cells. I already have the sequence for the promoter region from UCSC's GenomeBrowser, but I'm not sure if the enhancer region sequence can just be looked up on there or anywhere else. Do I need to do a protocol to find the enhancer region myself? I have seen many things about ChIP-Seq and that I may need to do that to get data to find my enhancer but I am just not sure. I plan to use the sequences of the enhancer and promoter region of my gene of interest to create gRNA for CRISPR. Thank you to anyone who can help.


texts: How does bonding between non-complementary bases occur?

texts: My teacher told me that when DNA polymerase makes an error (roughly every 10 million nucleotides?) that if, for example, it matches an A with a G that the error remains and is the main cause of point mutations. How do the two bases that aren't complementary remain bonded?


texts:
I was reading this question and I failed to fully understand the introductory part of it.

The OP (@Artem Kaznatcheev) says:

  Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection.

I don't fully understand it. Can you help me making sense of why assuming weak selection allows one to Taylor expand the selection function. I am hoping someone would answer by presenting a mathematical model that at first does not assume weak selection and show why assuming weak selection allows the use of a Taylor series to linearize the function. I'd like to understand which terms fall down and which terms left with this assumption.


texts: How can electric fields inhibit tumor growth?

texts:
In MIT's Technology review it is explained that electric fields can cause dividing cancer cells to explode, while these fields have no significant impact on non-dividing tissues. The original research was done by Palti et al.

What is the mechanism behind this? It does not seem to be related to thermal effects.

Edit: The treatment in question seems controversial. A clinical trial showed improvement but it is not rock-solid data.


texts: Blast output - program to count the number of hits

texts:
I have to use the old version of Blast (not Blast+) to compare DNA sequences and I have to know the number of all hits. They are not given in the header and I have to know them for many many of blast outputs and its nearly impossible to count them (or to export them in excel). I think I probably have to write a 'Perl Script' and I did my best but I am not familiar with programming and it is not working. Furthermore I had a look on the internet and they are always comparing it to BIO Search. I have e code, which for me looks pretty good,but it also done a comparison with BIO Search, what I don't need/want.

use strict;
use warnings;
use Bio::SearchIO;

Usage information

die "Usage: $0 <BLAST-report-file> <number-of-top-hits> <output-file>\n", if (@ARGV != 3);

my ($infile,$numHits,$outfile) = @ARGV;
    print "Parsing the BLAST result ...";
    my $in = Bio::SearchIO->new(-format => 'blast', -file => $infile);
    open (OUT,">$outfile") or die "Cannot open $outfile: $!";

# print the header info for tab-deliminated columns
print OUT "query_name\tquery_length\taccession_number\tlength\tdescription\tE value\tbit score\tframe\tquery_start\t";
print OUT "query_end\thit_start\thit_end\tpositives\tidentical\n";

# extraction of information for each result recursively
while ( my $result = $in->next_result ) {
    # the name of the query sequence
    print OUT $result->query_name . "\t";

        # the length of the query sequence
        print OUT $result->query_length;

        # output "no hits found" if there is no hits
        if ( $result->num_hits == 0 ) {
      print OUT "\tNo hits found\n";
         } else {
      my $count = 0;

                # process each hit recursively
        while (my $hit = $result->next_hit) {
            print OUT "\t" if ($count > 0);
                            # get the accession numbers of the hits
       print OUT "\t" . $hit->accession . "\t";
                        # get the lengths of the hit sequences
                        print OUT $hit->length . "\t";
                            # get the description of the hit sequences
       print OUT $hit->description . "\t";
                        # get the E value of the hit
            print OUT $hit->significance . "\t";
                            #get the bit score of the hit
       print OUT $hit->bits . "\t";

                        my $hspcount = 0;

                        # process the top HSP for the top hit
            while (my $hsp = $hit->next_hsp) {
                            print OUT "\t\t\t\t\t\t\t", if ($hspcount > 0);
                             # get the frame of the query sequence
        print OUT $hsp->query->frame . "\t";
                                # get the start and the end of the query sequence in the alignment
                print OUT $hsp->start('query') . "\t" . $hsp->end('query'). "\t";
                                # get the start and the end of the hit sequence in the alignment
                print OUT $hsp->start('hit') . "\t" . $hsp->end('hit') . "\t";
                                # get the similarity value
                printf OUT "%.1f" , ($hsp->frac_conserved * 100);
        print OUT "%\t";
                                    # get the identity value
        printf OUT "%.1f" , ($hsp->frac_identical * 100);
                    print OUT "%\n";
                                $hspcount++;
                            }
       $count++;

                        # flow control for the number of hits needed
            last if ($count == $numHits);
        }
        }
}
close OUT;
print " DONE!!!\n";

May someone help me, please. I need a program, which first tells me the header and then the number of hits. I am a little bit desperate and would be so happy if someone can help me. That would be so nice. Greetings Tina


texts: Can you accelerate the growth of a plant by accelerating its surroundings?

texts:
I had this weird idea of making plants grow faster when I first visited an indoor nursery which used floodlights instead of sunlight. They turned on during the day and went off during night in cycles.

If the time period of the cycles are decreased, it would seem to the plants that the earth just switched to fast-motion. Will this trick the plants into growing faster?

If not the current generation, would the later generations of plants grown like this adapt to the new rhythm ?

(Given that the plant is provided with surplus nutrients to meet the new requirements.)

I would love to do the experiment myself if it would actually work!


texts:
I found this creature floating in the Mediterranean Sea, probably dead.
I tried looking it up in the Marine Species Identification Portal but I couldn't find anything like that. It looks like some kind of jellyfish or hydrozoan.


texts: Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?


texts: I would be interested in knowing how long it takes between the moment something touches our skin and the moment something is activated in the brain. Also how long does it take in total until we subjectively perceive something? And I would like to know whether this is dependent on which part of the body was stimulated (same latency for foot and neck?), or if it is dependent on the nature of stimuli (heat or mechanical). I would also be interested in that latency in the auditory and visual system. I tried searching for that but could not find what I needed due to the lack of the correct terminology.


texts: How does a glucose molecule enter the cell from blood vessel?

texts:
The transporters in the plasma membrane of the cells promote the entry of glucose molecules from the extracellular matrix to the cytosol of the cell. Could someone explain how does the nutrient molecule enter the extracellular space from the blood vessel?

For instance, in the context of the pancreas, the walls of the blood vessel is fenestrated. The literature also provides evidence for the presence of connexon in the endothelium of the capillaries.

My doubt is, the nutrient molecule that diffuses from the blood vessel reaches the cytosol of the cell through

Diffusing through connexon ?(or)
Does it reach the interstitial matrix(the fluid surrounding the cells) and then uptaken by the transporters present in the plasma membrane of the cell?


texts: Can anyone help confirm this tiny insect larvae?

texts:
Can anyone help identify this insect larvae?

Found: UK, autumn, in a bed.

Size: less than 2mm

The bed was searched thoroughly and no others were found, but is there likely to be more of them?

Thanks!


texts: If ants have an antibiotic gland, how can they spread hospital infections?

texts:
Wikipedia describes how antibiotics are produced in ants:

  "Metapleural glands ... are responsible for the production of an
  antibiotic fluid that then collects in a reservoir ... also referred
  to as the bulla ... From the bulla, ants can groom the secretion onto
  the surface of their exoskeleton. This helps to prevent the growth of
  bacteria and fungal spores on the ants and inside their nest."

So how are ants often cited as an important problem in hospitals, spreading infections from garbage and through the patients? Shouldn't their natural antibiotics prevent that?


texts:
I know that dynein arms and microtubules are involved in the contraction of certain parts of the flagella to produce a wave motion, but I don't understand they are related to the 9+2 structure of the basal body.

How do flagella work in prokaryotes and eukaryotes?


texts: Is it purely the nervous system causing vaginal lubrication (arousal)?

texts:
My girlfriend was watching some documentary on TLC about a paralyzed woman getting pregnant. I believe that woman still has some feeling, as she spoke about feeling the effects of a bladder inflamation. So supposedly, her brain could fire up her vagina to get ready for sex (in the sense that it gets lubricated and the labia get swollen).

But suppose a woman is paralyzed so they have no nervous connection from the brain to the vagina (or vice versa). Could she still be aroused in the sense of swollen labia, etc? (Presumably via some hormonal system?)


texts: Transport of newly synthesized proteins to cellular organelles

texts: In the nucleus the DNA is transcribed and processed to mRNA which is translated into proteins in the cytoplasm. What happens between the time a protein is made and that when it reaches the cellular organelle in which it functions? How is it transported to its destination?


texts: Zygote Implantation and Pregnancy Detection

texts:
In a normal pregnancy, the embryo (blastocyst) implants between 8-9 days after ovulation.  My understanding is that it is able to implant because the fertilized embryo produces a hormone that triggers the uterus to prepare for implantation.

At what point after this implantation can the first signs of pregnancy hormone be detected in the blood stream? (Hospital Birth Detection)
At what point after this implantation does the uterus prevent further embryo implantation


texts: SDS-PAGE and western blotting are both used to separate and isolate proteins. My question is, which technique should be used when? Does one of them has advantages over the other one?


texts: Chromosomal structures in S phase and Prophase

texts:
Of S Phase:

  Existing DNA molecule acts as a template to synthesize new DNA molecule. The cell doubles it's DNA, yet the number of chromosomes remain the same

Of Prophase:

  The chromatin condenses and during condensation, DNA strands untangle to form compact mitotic chromosomes

So in the S Phase, we're talking about chromosomes which contain double the number of initial DNA molecules, while the chromosomal number still being the same.
And in Prophase, there's condensation of chromosomes! But the chromosomes are already formed in the S Phase as per the sentence I have quoted from the textbook.

That doesn't make sense to me. I'm very confused.


texts: Is there any double staining method to visualise separate colour for plant tissue and fungal tissue?

texts:
Is there any double staining method for developing separate colour on fungal tissue and plant tissue when the said 2 types of tissues are intermingled?

Unlike my previous question, this question not necessarily need  to target specifically chitin and/or N-acetylglucosamine but looks for any principle to differentially stain intermingled plant tissue and fungal tissue.


texts: What type of white hard thing grows on lobster

texts: I have no idea how to explain it. It looks like mini white volcanoes growing on a lobster shell.  Is it bacteria or parasite?


texts: How much are phase-contrast and dark-field microscopy used in biological research?

texts: How much are phase-contrast and dark-field microscopy used in biological research today? It seems these were invented a long time ago, so I am thinking would it be a good idea to learn these techniques. (I will start an undergraduate program in biology next spring.. but I am still mostly interest how much the researchers use these technologies: if little, I should use my time better)


texts: Predicting host-pathogen gene interaction networks

texts:
Background

What we have are:

~20 genome sequences for a host species that come with gene annotations
Several sequenced genomes for parasite/pathogens of these hosts

Question

What are the possible ways of predicting gene-to-gene interactions or gene regulatory networks between hosts and parasites?


texts: Where is the pollenkitt material secreted? I think the tapetum would be a good candidate, since it provides nutrition to the pollen grains.


texts: Identifying statistically significant gene rich and gene poor regions

texts: I am just wondering If there any adapted way of Identifying significant gene rich and gene poor regions in each chromosome for a given genome say mm10?


texts: Why a brain's hemisphere controls the opposite side of the body?

texts:
As a physics student with very little understanding of biology, in a course about physics foundations diagnostic techniques I have come up with this question. I don't even know if it does make sense or not; in the latter case, please excuse me.

As far as I know, in the human brain the right hemisphere controls the motion of the left side of the body, while the left hemisphere controls the right side. Moreover, the part related to sight is on the back of the brain.

To me, it seems that there is a sort of opposition between the part of the body considered and the area of the brain that have to control it. Is this statement right? Only for human beings or also for animals? Are there any exception to this sort of pattern (if there is anyone)? Is there a logical reason to the fact that we show this characteristic and it couldn't be different from how it is?


texts: How do I compare bacteria growth curves?

texts: I have bacteria growth curves for 5 different temperature conditions and these were created using %red-light transmittance. How do I compare these growth curves? Should I calculate the growth rate and if so how do I do that?


texts: What's a good simple test for cDNA library quality?

texts:
How do I assess the quality of a cDNA library?

I want to clone CDS copies of genes from a library, but I don't know what's a typical expectation of getting a full length clone even for a shorter gene (~1000 bp).  I know it doesn't have to be composed of full length cDNA for sequencing, but I'd imagine quality of starting materials is important there too.

Are there some common transcripts I can try to obtain from PCR that will tell me how fragmented the sequences are in there?

What's a typical result from a commercial cDNA library - are there any QC tests that are quick to run in the lab?


texts:
I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes RNase or should I be worried about it?

Addition: I am using eppendorfs directly from the bag. So they supposed to be RNase-free, right?

Thanks.


texts:
I did a flow cytometry experiment for the first time. I had three conditions: (1) unstained healthy monocytes (2) healthy monocytes stained with green/red (488/570) from the Live/Dead thermofisher kit (3) dead monocytes stained with the same green/red dyes.

I did those condition to know what graphs to expects, and learn the FACs process and analysis. Would appreciate it if someone can answer the following questions:

So I have two dyes in my samples and a control. Which flow cytometry channel should I use in my plots (FL1, FL2, FL3, or FL4)?
How to know the percentage of live and dead cells in each condition?
Anyone knows a free analysis software?
How practical is R to do flow cytometry analysis?


texts: Is there any problem with using a single stop codon with a single CDS in prokaryotes?

texts:
All protein coding sequences in the iGEM Registry are supposed to end with a double stop codon. Presumably, this is to decrease the potential for read-through, which could be problematic if one is putting together a polycistronic design.
If the design is intended to have only one CDS, however, and is targeted at a prokaryote (which have "backup" ribosome release mechanisms), then is there any problem with using only a single stop codon?


texts: How many frames per second do human eyes see?

texts:
I observed when a helicopter rotor or fan is spinning the blades blur making it impossible to count the blades, but after a certain speed the blades seem to become visible making it possible to count the blades. Cameras can also do this better.

Do human eyes have a frame rate? What is that called and the most a person can see?

This video in the link shows how these blades seem not to move by timing with the cameras frames rate.

https://www.youtube.com/watch?v=R-IVw8OKjvQ


texts: Why did scientists think humans had 100,000 genes (before the Human Genome Project)?

texts:
One of the major results of the Human Genome Project (HGP) was that humans have far fewer separate genes than previously thought. From a 2004 article about the HGP:

  Francis S. Collins, director of the National Human Genome Research Institute (NHGRI), said, "Only a decade ago, most scientists thought humans had about 100,000 genes. When we analyzed the working draft of the human genome sequence three years ago, we estimated there were about 30,000 to 35,000 genes, which surprised many. This new analysis reduces that number even further [to 20,000-25,000] and provides us with the clearest picture yet of our genome."

What was the old estimate of 100,000 based on? I assume that in 1994 no one had sequenced the entire proteome...

As Remi.b points out, the 100,000 gene estimate may be based on the one gene–one enzyme hypothesis. If that's true, did people before the human genome project think that there were 100,000 distinct enzyme activities? If so, what experiments/data were used to establish that number?


texts:
I want to do respiration process of an animal cell media in laboratory environment.

I don't entirely sure how to supply it with Oxygen to the process because it is a gas, but not a liquid.


texts:
I have been trying to extract RNA from soil without success. I have used commercial kits (The Plant DNeasy kit) because I did not want to buy a complete new kit (Soil) to do 5 extractions. Is there any "in-house" protocol that successfully extracts RNA from the soil? Or, is there any tip that would allow me to extract good soil RNA using the Plant DNeasy kit?
Thanks


texts: What would be the estimated cost sequencing?

texts:
I'm a newbie to the world of NGS, but I thought it might be a suitable and cheaper alternative to doing traditional Sanger sequencing for this particular application. However, I'm not so sure on how to approach calculating this cost, so I was hoping to reach out and see if someone could help here. This is for my grad school research project.

Problem Statement

I am about to make a rational library of ~1000 protein complexes belonging to the same family of proteins. There are 4 protein's plasmids to make per complex, and they are to be made by a combination of synthetic genomic cloning methods using cDNA, and multi-site directed mutagenesis on existing plasmids. Before testing their function as a complex, I need to verify that the cloning steps succeeded by sequence verifying each plasmid.

I could do traditional Sanger sequencing on each of the protein sequences, but given that each protein is ~2kb long, I would need 4 single direction sequencing reactions per plasmid to cover the CDS. In total, per protein complex, that's 16 sequencing reactions. At USD5 per sequencing reaction, each protein complex would cost USD80 to sequence. At 1000 sequences, that would be USD80,000 in Sanger sequencing.

I was thinking of doing something else - after creating the library, say in chunks of 384, send them for NGS on an Illumina MiSeq.

Request for Help

Given that:

I am not wedded to any particular NGS protocol,
Our only goal here is to, by one way or another, sequence verify the cloned plasmids.
1000 proteins is the right ballpark for the number of proteins that need to be sequence verified. 4 plasmids per protein complex.

What would be the appropriate sequencing strategy that could help us get way below 80K for sequencing costs?


texts: How will rising carbon dioxide levels in the troposphere affect photosynthetic producers?

texts:
Much discussion has been had about the affects of climate change on plantlife, but how will rising carbon dioxide concentrations affect the photosynthetic process itself? Since CO₂ is a reagent in photosynthesis, would we expect higher CO₂ to mean an increased rate of photosynthesis in a real-world context? Has there been any research on this?

I am thinking more of large-scale field tests rather than lab plants.


texts: What is the biological function of nose, underarm, and pubic hair?

texts: What is the biological function of nose hair? In general, can we consider underarm hair and pubic hair to be vestigial structures?


texts: Laying eggs vs giving birth: is there a connection with internal vs. external ears?

texts: I have heard that "The animals who have their 'EARS' outside their body give birth to their young ones and the animals who have their 'EARS' inside their body lay eggs." Is this true? Are there counterexamples?


texts: Is there a graph or ontology that maps diseases to its possible causes or causing diseases?

texts:
I am looking for a mapping, list, ontology or graph that shows the connection between a diseases and its (currently known) causes and/or risk factors.

For example a well known risk factor for acute kidney injury is diabetes. There are other diseases whoms risk factor is diabetes. This meanse diabetes is a risk factor for many diseases. Maybe if one traverses trough this dependencies and builds a graph out of it, there will interesting clusters and lineages.

I dont know if this is inherent knowledge or formulated somewhere in a formal and explicit way (e.g. as ontology).

There is http://disease-ontology.org/, but it does not contain any causes, risk factors, etc.

Thanks in advance!


texts:
This is my first post in this forum. I found the following insect at my kitchen in my apartment in Kolkata, India. Could you please help me identify the insect.
Thank you.
Best regards,
Saugata


texts:
My daughter (10th grade) is doing a science fair project on the toxicity of triclosan for the algae Selenastrum capricornutum. She is wondering the best way to measure the effect, given the limited resources at the school.

Should she use the school’s UV/Vis spectrophotometer or just do low-tech cell counting?
If she uses the UV/Vis, does she have to do a calibration curve where she manually counts the cells for some number of data points?
Or can she just compare %absorbance to the controls and before/after numbers?
Or is it already know for this particular algae at a particular wavelength that a certain %absorbance equals a certain number of cells?
If she uses the UV/Vis, does that indicate the total number of cells, dead or alive, or does it only measure live cells?

The trial is over 96 hours.    Thanks!


texts: How to grow a spirulina biofilm on a carbon/graphite cylindrical cathode?

texts: I am trying to grow a spirulina biofilm on my cathode for a fuel cell but it doesn't seem to be sticking to the cathode. I have a culture of spirulina  and I've submerged a few cathodes in it to try and develop a biofilm. This is not working. Is there anything I can do to promote spirulina growth on my cathode like coating it in glucose or something?


texts: Is sexual desire stronger in men than women?

texts:
Usually in popular culture it's considered men sexual desire is stronger than women. This seems to be congruent with the availability of sexual related items for men and women, such as magazines, movies, and more. Trying to understand if there is a biological connection to this, I found these paragraphs in some articles.

  Estrogen, progesterone, and testosterone are hormones that affect a
  woman’s sexual desire and functioning.

  When it comes to sexual desire, the most influential hormone is
  testosterone. Though it’s often considered a male hormone,
  testosterone — like estrogen– is present in both men and women, though
  the proportions differ between the sexes.

Hormones affecting sexual desire

and

  On average, in adult males, levels of testosterone are about 7 to 8
  times as great as in adult females.[7] As the metabolism of
  testosterone in males is more pronounced, the daily production is
  about 20 times greater in men

Testoterone

Is this greater production of testoterone in men related to a stronger sexual desire? Is there any research studying this, or studying differences between male and women sexual desire intensity in general?


texts:
Why doesn’t a basic side chain (R group) of an amino acid form a peptide bond in protein biosynthesis?

Consider lysine, for example, why can’t its side-chain amino group, –(CH2)4–NH2, form a peptide bond with the carboxyl group of the other amino acid? Is it due to orientation alone are their other properties involved?


texts: How do changes in temperature affect body weight in humans?

texts: What would be effect on weight of individuals if we bring a fully adapted (to cold climate ) human individual and a fully adapted to very hot climate individual to a moderate climate region?


texts: What is the best way to express two proteins in a mammalian cell?

texts:
I have two proteins and I will be preparing a vector with both genes for stable transfection. Each protein will have their own promoter and I will use piggyBac vector to insert a single cassette with both genes in it into the chromosomes. My questions are:

If I use the same promoter (CMV, SV40 or an inducible one) for both genes how would this affect the expression levels? I read in some papers that one of the genes might get expressed lower than the other. If you have first-hand experience I will be grateful if you share it.
If I use the same promoter for both, but put them far away (i.e. ends of the cassette) would the expression levels get affected again? It sounds simple enough but I think people would have published something if they had a good result with that.
If I use different promoters for each gene (e.g. CMV for one and Tet-inducible for the other) how would it work? I couldn't find a paper which used this and I would like to continue with this approach; therefore, if you have any experience I will be really grateful for any help.

I don't want to use IRES or 2A-peptide. I would like to be able to control this experiment in transcription stage.