12
votes
3answers
725 views

Why do restriction enzymes tend to have an even number of bases in their recognition site?

When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases. I wondered if this was just a co-incidence, so I took the data from this ...
15
votes
2answers
2k views

Harmless virus?

Is it possible for a virus to live symbiotically with its host? Is the human body plagued with viral infections that do negligible harm, or even serve a beneficial role?
3
votes
1answer
503 views

Displaying nucleotide at a single position from RNA-seq reads in a BAM file

How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am ...
7
votes
1answer
4k views

Why does RNA adopt an A-form helix?

RNA is known to form an A-form helix, while DNA generally forms a B-form helix under physiological conditions. From left to right: A-form DNA, B-form DNA, Z-form DNA. Image created by Richard ...
3
votes
1answer
259 views

Where does meiosis II of oogenesis end exactly in tuba uterina - uterus?

I know that metaphase II ends at ampulla tuba uterina, but I am not completely sure where the telophase II ends. Is it in the triangular section of cervix uterii? I just have an intuition that the ...
16
votes
1answer
686 views

ATP cost for gene expression

How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?
4
votes
1answer
140 views

What are the constraints when growing an artificial brain?

Are there any experiments on growing artificial brains from brain tissue? What are the constraints? Will such tissue grown to the mass greater than that of human brain surpass it in intellect or it ...
10
votes
2answers
450 views

Antibacterial hand soaps (and related products); what are they good for?

From Wikipedia: Household use of antibacterials in soaps and other products, although not clearly contributing to resistance, is also discouraged (as not being effective at infection control). ...
10
votes
1answer
257 views

Is the minicolumn the unit of the neocortex?

There are many arguments for what the unit of the neocortex is. "Columns" seem to be the standard, but what exactly those are is extremely contradictory between individuals, cortical regions, and ...
7
votes
1answer
128 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
5
votes
1answer
767 views

Do eye muscles relax when you close your eyes?

I wonder whether the eyes muscle relax when you close them. Common knowledge told us the eyes muscle get tense when you stare at nearby object. If you close your eyes, you eye lids have 0 distance ...
9
votes
1answer
165 views

Is it correct to regard archeaic humans (i.e.n Neanderthals and Denisovans) as distinct species to Homo sapiens?

There is increasing evidence (e.g. here) that Homo sapiens interbred with contemporary homonins such as Homo neanderthalensis and the "Denisovans". Although these homonins do show differences in their ...
12
votes
4answers
410 views

Questions to ask to a panel of people that will be sequenced

Some genes have been shown to be associated with left-handedness. Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are "right or ...
5
votes
1answer
1k views

What is the distinction between F' plasmid and R plasmid?

Is there a difference between an F' plasmid that has taken up a chromosomal gene that conveys antibiotic resistance, and an R plasmid? Is a bacterium containing an R plasmid and yet lacking an F+ ...
12
votes
1answer
567 views

Sequencing the genomes of polyploid organisms

I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about ...
4
votes
2answers
2k views

How would a plant sprout and grow in a zero gravity environment?

Have any experiments been carried out involving sprouting and growing plants in a zero gravity environment? If so, what was the outcome? How did the plants sprout out of the soil without gravity? Did ...
9
votes
1answer
404 views

Why can you graft two unrelated cacti successfully, but you cannot do this on garden trees?

Any cactus can be grafted onto any other cactus, and even the most unlike of them grow together. My latest graft was a Schlumbergera truncata scion on an Opuntia microdasys rootstock. This kind of ...
3
votes
0answers
34 views

Can a cell culture insert plate be used with a vacuum manifold?

There exists 96 well plate setups for use with vacuum manifolds. Is it possible to use 6/12/24 plate inserts with the same setup?
3
votes
1answer
2k views

Why did the sensitive plant (Mimosa pudica) evolve its leaf-closing mechanism?

Why did the sensitive plant, Mimosa pudica, evolve its leaf closing mechanism? Does it heip in a heavy storm? Does it scare off whatever animals might think it a good meal?
9
votes
2answers
534 views

What is causing my problem with very low yields when isolating a 42kb yeast plasmid?

I have to isolate a large plasmid from yeast and transform it in E. coli. After transformation, I often get no colonies. One reason for that is the yeast mini prep hasn't worked or the DNA ...
7
votes
1answer
229 views

How do plants 'tell time' for circadian rhythms based on a ~24 cycle?

I've read that many plants have some sort of circadian rhythm where they perform a certain action on a cycle of about 24 hours, like the mimosa plant opening and closing its leaves. Obviously this is ...
7
votes
1answer
836 views

Does extracted DNA degrade after a certain time period?

For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression ...
15
votes
3answers
1k views

Transmission of epigenetic regulation through surrogate mother

I know the basics of epigenetics, but I do not know how epigenetic mechanisms are transmitted from parents to children (or if there is even enough literature to derive a consensus). My question is ...
18
votes
1answer
2k views

What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?

In prokaryotic translation, how critical for efficient translation is the location of the ribosome binding site, relative to the start codon? Ideally, it is supposed to be -7b away from the start. ...
3
votes
1answer
46 views

How can you improve solubility of colloidally dispersed substances?

If you solve collidally dispersed substances then the particles can form large colloids. This may block narrow passages and diffusion into dense structures may become completely impossible. What can ...
6
votes
1answer
626 views

How does water move throughout plants?

I haven't yet found a decent explanation for how water moves throughout plants. It does seem to travel more efficiently upward than out or down. Why is that? How does it travel through the plant?
19
votes
3answers
389 views

Good source that explains the evolution of single-celled organisms “from scratch”

Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, ...
10
votes
2answers
141 views

Is there an equivalent to “Fields Virology” for Bacteria?

I've gotten a staggering amount of use out of my copy of Fields Virology as a general reference for "getting me up to speed" on whatever pathogen I'm currently looking at. I don't know of a similar ...
9
votes
1answer
284 views

How is the number of mitochondria in a cell regulated?

How does the cell regulate the number of mitochondria in a cell? What happens when there are too many or too few?
3
votes
1answer
423 views

How often can you reuse coomassie stain?

I usually heat to boil in the microwave, and stain for 12 minutes. How often can I reuse this buffer?
5
votes
3answers
1k views

How do you break up cell clumps when passaging?

I am working with HepG2 cells, and they really like to form clumps. Pipetting up and down in TrypLE does not seem to be very effective in breaking them up.
10
votes
2answers
560 views

Do insects with compound eyes have depth perception?

Do insects with compound eyes have depth perception? They fly as if they do, but their eyes are so close together it seems like the image would be 2 dimensional.
9
votes
1answer
581 views

Why are there nail growth differences between humans and other mammals?

When a cat is growing, his nails are growing with him to some extent. A grown cat has a fixed nail length that is not extending. By contrast, human finger nails just keep on growing, so we have to ...
4
votes
1answer
94 views

Is there a cheap and easy way to check for potentially unsafe UV exposure?

My lab has an older large Fotodyne tabletop UV transilluminator for visualizing gels. It has a UV blocking cover that hopefully reduces UV that passes through, but I've always been suspcious as to ...
9
votes
1answer
102 views

What is the base cancer rate for an arbitrary carcinogen?

Are all carcinogens equally potent? Is the relationship between dose and probability of cancer roughly equal, or are there some carcinogens that provoke cancer significantly more than their cousins?
5
votes
2answers
760 views

How to set up a slow cooling on an AB Veriti thermal cycler?

I want to incubate my sample at 50ºC and then slowly cool it down to 4ºC at a rate of 0.1ºC/s. I am using AB Veriti thermal cycler. Does anyone know how to set up the rate of cooling? It has to do ...
6
votes
2answers
289 views

What is a good Non Fluorescent DNA Dye?

Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? (We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak Signal even a low emission would ...
6
votes
1answer
452 views

X chromosome “weight”?

According to Wikipedia, the X chromosome has approximately 153 million base pairs, while the Y chromosome has only 60 million base pairs. Thus, the difference is roughly 93 million base pairs. My ...
7
votes
2answers
120 views

Is it possible to trace of the ancestry of a person by only using his/her genetic information?

Is it possible to trace the descent of a person only using his/her genome sequence?
7
votes
1answer
749 views

What is the mechanism of transgene integration (from expression vector to the host genome)?

How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium). I already cut some parts (NdeI-PciI) of the vector (pUC18) and ...
13
votes
1answer
195 views

What is the prehistory of amino acids in cells?

As a followup to Why 20 amino acids instead of 64? and What is the smallest number of amino acids required for life?, I am trying to understand the prehistory of amino acids in cells. All living ...
26
votes
2answers
572 views

What are the trajectories of flying insects?

Many flying insects tend to have very jagged trajectories. For moves of a fruit fly looks like a random walk. Is there any research on the properties of trajectories (e.g. their fractal dimension or ...
11
votes
1answer
220 views

How do you design a drug to be delivered to the CNS?

I have just started reading up on structure-based methods for drug design (this is completely not my field so apologies for stupid questions that will be coming along!) Clearly, some drugs are ...
6
votes
1answer
1k views

What is the average Leg-to-Foot Length/Width Ratio?

I'm making a program that estimates a probable size (widest width and longest length) for a human's foot given the length and width of the leg to which it is attached. However, try as I might, I can't ...
6
votes
1answer
195 views

What is the origin of “melting” in molecular genetics?

I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that ...
18
votes
3answers
781 views

How is RNAse contamination in RNA based experiments prevented?

Does anyone have any suggestions to prevent RNAse contamination when working with RNA? I tend to have issues with degradation regardless of whether I use DEPC treated / RNAse free water and filtered ...
2
votes
1answer
288 views

What is the structure and function of chromosomes during interphase?

Ok, it seems to be easy but I have probably ignored something by accident. Interphase is the phase where things are growing and the preparation for cell division happens. Its stages G1, S and G2. DNA ...
4
votes
2answers
550 views

What's the advantage of autocrine signalling?

In the antibody-mediated immune response, when the helper T cell gets activated by the costimulus (IL-2 and TNF-α secreted by the APC) which in turn produces IL-2, IL-2 acts in an autocrine manner. ...
13
votes
1answer
2k views

How does a plant grow before photosynthesis is possible?

During photosynthesis, a plant translates CO2, water and light into O2. I assume the carbon C is further used for the growing process. I wonder how the plant grows before the time where photosynthesis ...
8
votes
2answers
2k views

Are there any motile plants?

There are numerous examples of sessile animals (sponges, barnacles etc.) but are there any examples of motile plants? If not, why not? Surely mobility would have conferred an evolutionary advantage to ...

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