6
votes
2answers
752 views

How do I prepare and clone from E. coli DNA?

I'm looking for a protocol to get genomic DNA from an E. coli sample so that I can clone a small portion of it using PCR into a plasmid. (< 500 bp in this case). It seems OWW (Open Wet Ware) ...
9
votes
1answer
716 views

Can I elute my GFP-tagged protein off anti-GFP antibody using a peptide?

I would like to perform a modified co-immunoprecipitation assay using a GFP-tagged protein. We are going to bind the tagged protein to anti-GFP antibody then bind that to protein A/G beads, however ...
7
votes
4answers
158 views

How can I produce milligram quantities of an isotope-labeled DNA oligomer?

I'd like to produce a specific DNA sequence on a milligram-scale and 13C15N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs. I'm also ...
18
votes
3answers
378 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, ...
14
votes
1answer
540 views

Do large animals often evolve into smaller animals?

There are several examples where the largest animals were killed off preferentially due to a major ecological shift: The KT extinction event The Holocene extinction, as well as the major megafauna ...
9
votes
1answer
188 views

What are the clotting factors' effect on avascular necrosis development?

Do clotting factors tpa and pai-1 lead to degenerative osteoarthritis in the same way that lupus anticoagulant and prothrombin might? Is one of these pathways particularly detrimental during formation ...
30
votes
2answers
1k views

How do cockroaches resist the effects of ionizing radiation?

Cockroaches are very hardy insects. It is known that, among other things, they are able to withstand bursts of ionizing radiation that would kill a human being. The explanations of this observed ...
17
votes
2answers
317 views

Can an adult without genetic lactase persistence still develop a tolerance for dairy foods?

While investigating the rise of adult lactose tolerance, I came across the news that China has been encouraging its citizens to drink more milk, even though most of the Asian population lacks the SNP ...
5
votes
2answers
1k views

What conditions should I use for Gel Red staining?

What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often ...
10
votes
1answer
296 views

Examples of animals that co-opt toxins?

It is known that there are animals that acquire toxins through their diet or through their surroundings. The examples I know of include butterflies stocking up on alkaloids/glycosides while in the ...
11
votes
1answer
195 views

What histological stain can I use for beta-keratin?

I'm trying to find a histochemical stain for beta-keratin, the type found in Reptilia which is organized in beta-sheets. It's different than alpha-keratin which is found in mammalian skin, hair, ...
20
votes
1answer
13k views

How does cerebrospinal fluid circulate in the central nervous system?

Cerebrospinal fluid (CSF) is produced in the choroid plexus of the lateral ventricles and in the 4th ventricle of the brain. CSF then circulates through the ventricles of the brain and the ...
10
votes
1answer
884 views

How is Taq polymerase produced?

I've seen Taq polymerase being marketed as either "native" or "recombinant". I understand that the recombinant version is produced by specially modified Escherichia coli strains that have the gene for ...
16
votes
2answers
256 views

How do fairy rings propagate?

It was somewhat new to me that mushrooms usually aren't individual organisms, but are merely the visible bodies of a bunch of fungi living in the soil. I know that mushrooms emit spores to reproduce, ...
15
votes
2answers
5k views

How do the brain and nerves create electrical pulses?

I have heard that information is sent between the brain and peripheral nerves via electrical pulses or signals, but I don't understand how they create them in the first place.
35
votes
4answers
3k views

Life without DNA?

I'm by no means an expert in the field, merely a curious visitor, but I've been thinking about this and Google isn't of much help. Do we know of any lifeforms that don't have the conventional ...
14
votes
2answers
209 views

Why is there now only one Salmonella species?

Once upon a time, I chanced upon an old microbiology book that detailed the rather colorful world of enterobacteria. Salmonella in particular stood out, as it seemed there were a lot of species: typhi ...
10
votes
1answer
166 views

How can you identify if a person is homozygous for a certain allele?

I've been thinking about starting a small private research project. In this project I need to find out whether a person is homozygous for a certain allele. The reason for this is that I'm really ...
17
votes
1answer
237 views

Is there any convincing evidence for the existence of nanobacteria?

The existence of nanometer scale microorganisms has been proposed and used explain several phenomena including morphological structures in a martian meteorite (ALH 84001) and implication in the ...
10
votes
2answers
240 views

Which sequence characteristics influence the transcription efficiency of T7 polymerase?

The T7 polymerase doesn't transcribe all sequences equally well, the transciption efficiency can vary widely for different sequences. One well known requirement of the T7 polymerase is that the ...
11
votes
2answers
456 views

What are limiting factors for intron length?

For predicting genes from a sequenced genome, you need to set a maximum intron length. How long can introns get in animals? Is there some limit?
8
votes
2answers
974 views

How can rooted and unrooted (phylogenetic) trees be distinguished from one another

I understand that both are similar in structure But how can they be easily identified as one or the other? Is it simply based on the presence or lack of a named root (the root is identified as a ...
10
votes
2answers
937 views

Do human beings have pheromone receptors?

What is the current consensus on whether or not humans have receptors that detect pheromones? If there are purported receptors, in what anatomical areas are they located? With what organ systems do ...
9
votes
2answers
191 views

bi-directional transcription experiment

We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic ...
11
votes
1answer
605 views

What limits the maximum spacing of Nodes of Ranvier and which organisms tend to have the widest gaps?

Assuming that a longer distance between gaps in the myelin sheath is beneficial for an organism due to the increased propagation speed, what is the limiting factor in determining the maximum spacing ...
4
votes
1answer
140 views

Bacterial chromatin binding data?

I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions. Can anyone point me to a source?
7
votes
1answer
114 views

What specific membrane adaptations do cells have for saline-rich environs?

Are the cells of marine animals and flora equipped with special ion exchange pumps to mitigate the effects of a saline-rich environment? Or have the cell's membranes adapted through structural ...
4
votes
5answers
474 views

What is a good miniprep protocol for the class room?

I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found: Using phenol/chloroform extract with phenol:chloroform:isoamylalcohol, isopropanol precipitation, ...
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 ...
17
votes
4answers
1k views

How to understand influenza strain designations?

What do the strain designations for flu mean? For example avian flu is classified as H5N1, what do the letters H, ...
8
votes
3answers
140 views

What are the limiting factors for gene length and number of exons?

I recently downloaded gene annotations for Homo sapiens from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have ...
11
votes
1answer
71 views

What are the mechanism binding histone code with alternative splicing?

There are some bioinformatical considerations showing that there is a significant correlation of some between histone code and alternative splicing; but what are the hypothesis about the underlying ...
14
votes
1answer
100 views

What are the main mechanisms of interaction between the nervous and immune systems?

We know from pop science that our psychological states have an effect on our immune systems ("worrying ourselves sick", etc.), but what are the actual mechanisms through which our nervous systems pass ...
17
votes
3answers
189 views

What is the optimal frame size for protein secondary structure prediction methods?

The whole question is What is the optimal frame size for the second and third generation protein secondary structure prediction methods? Justify your answer. I remember it has something to do ...
8
votes
2answers
413 views

Has anyone tried Gibson Assembly Optimizations?

Has anyone tried the chew back-anneal in vitro DNA assembly method (known as Gibson Assembly) for difficult sequences, like GC-rich sequences? How big constructs could you efficiently assemble? Did ...
11
votes
1answer
493 views

How to reduce edge effects in cell-based high-throughput experiments?

In high-throughput experiments where cells are cultured, treated, stained, and imaged in 384-well microplates, I frequently see significant edge effects. For instance, the following plot shows cell ...
21
votes
4answers
572 views

How many times did endosymbiosis occur?

According to the endosymbiont theory, mitochondria and chloroplasts originated as bacteria which were engulfed by larger cells. How many times is it estimated that this occurred in the past? Are there ...
16
votes
3answers
222 views

What is the reason behind choosing the reporter gene when experimenting on your gene of interest?

I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you ...
24
votes
6answers
3k views

How should I ship plasmids?

I shipped 10 µL of my vector miniprep to a collaborator in a 1.5 mL eppendorf parafilmed shut and stuffed into a 50 mL conical with some paper-towel padding. However, something happened on the way ...
11
votes
2answers
199 views

Under what conditions do dendritic spines form?

I'm looking for resources or any information about the formation of dendritic spines and synaptogenesis, especially in relation to how new connections are formed on a daily basis. Does the ...
9
votes
4answers
202 views

How can I avoid digesting protein-bound DNA?

I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion. When digesting protein-bound DNA, is all of the unbound DNA ...
15
votes
3answers
335 views

Is exon order always preserved in splicing?

Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or ...
24
votes
3answers
4k views

How long does antibiotic-dosed LB maintain good selection?

Various people in our lab will prepare a liter or so of LB, add kanamycin to 25-37 mg/L for selection, and store it at 4 °C for minipreps or other small cultures (where dosing straight LB with a 1000X ...
19
votes
1answer
528 views

Are lymphocyte sizes clustered in two groups?

Tortora writes in Principles of Anatomy and Physiology: Lymphocytes may be as small as 6–9 μm in diameter or as large as 10–14 μm in diameter. Those ranges are quite close to each others. Should ...
18
votes
3answers
764 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 ...
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. ...
9
votes
2answers
35 views

Resources for finding all drugs of a certain class

I may be embarking on a project involving a fairly extensive healthcare records data set, looking for the use of a particular type of drug (for example, "Proton Pump Inhibitors"). But these drugs are ...
11
votes
3answers
523 views

Human disease and associated phenotype database?

Does anyone know of any good databases that contain symptoms for diseases and other ailments in humans? I've tried working with UMLS, but thats been impossible to work with. I've also tried working ...
20
votes
1answer
2k views

How long do your eyes need to adapt to darkness and reach full contrast?

I heard you should wait some time until your eyes adapt to darkness and are able to see smallest luminosity differences, otherwise you might overlook faint objects in the ocular. Are there any rules ...
12
votes
1answer
1k views

Why does looking at bright light trigger sneezing in some people?

Why does looking at bright light trigger sneezing in some people? Are there any recent studies that have found a cause for this Photic sneeze reflex? The Wikipedia article only references studies ...

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