bioinformatics - Organize sequence database

I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be wonderful.

This research project is more like a class where students are taught how to sequence a piece of plasmid via Sanger sequencing method, with paired end primers. For each plasmid there will be two entries (~1kbp each). Then the students would BLAST the sequence, mostly to see if there is any close match with certain related organisms.

The main purpose of this database I'm creating is to monitor the sequencing progress, as well as to single out the samples that need to be redone. So far, the record-keeping is not exactly accessible, hence the need for re-organization. Additionally, the students would need to be able to view their own results and enter the BLAST results themselves. The last condition seems to necessitate a web-server type of thing that the student can connect to enter their information.

The total number of bacteria clones containing plasmids are ~18k, which means there will be ~36k entries in this database. It would be great if there is anyway to manage the trace files of the entries, or if not, I think I can add a column for the file path.

Is there a database management program that is appropriate for organizing sequence and trace file, with easy access for data entry by multiple users? It would also help if the program don't have a high maintenance need.

Disclaimer: I have very limited knowledge with database structure, having only taken an online intro to database class. About programming language, I am still learning Python. This project is a way to force myself to learn more.

vision - Possibility of orthogonal view for a creature?

The answer depends on the distance between eyes, and width of the objects you are viewing.

The view of a separate object is close to the orthogonal view when the width of the object is equal to the distance between your eyes.

Hence the creature that has variable distance between eyes, and has large maximum distance between eyes, has most possibilities to view objects in orthogonal view. Snail comes to mind when I try to think about animal with variable distance between eyes, but its maximum distance between eyes is not that large.

When object is narrower than distance between eyes, you see it in "anti-panoramic view". You will see both left and right side of the object, which is impossible both in orthogonal view and in panoramic view.

Speaking about whole 180 degrees wide visble scene (wider for some animals), the answer is No. You cannot view the whole scene without perspective view, unless you have large number of "eyes" (sensors) that are spread over a large plane. There is no such animal, but you can artificially construct such "perceptor plane" using large number of photocameras.

When looking at the objects of width equal to distance between eyes, if your brain can direct eyes such that their viewing axes are parallel, and could integrated two pictures, then it would view perfectly orthogonal view. This is not what our brain normally does, though. But even with non-parallel view axes of eyes, what we eventually see when brain integrates different pictures the result is not par from orthogonal projection.

medicinal chemistry - Why does ice reduce swelling?

Swelling is one of the signs of inflammation. Inflammation involves release of histamine by mast cells present in the tissues. Histamine causes vasodilation and leads to leakage of fluid from the blood, along with which neutrophils and other WBCs also enter the area. They phagocytose microbes that might have entered with the injury.

Applying ice would cause vasoconstriction* (i.e. narrowing of blood vessels.) which would reduce the leakage of tissue fluid and hence swelling.

*If you wonder why ice(or any cool thing) causes vasoconstriction think why you turn pale in winter ? Vasoconstriction reduces blood flow to the particular area and hence the exchange of heat is reduced which conserves body heat in cold environments.

microbiology - Highly spherical Radiolaria; does this image accurately depict the organism?

If I understand correctly, Cenosphaera spp. is a type of Radiolaria, which is a type of zooplankton. The following is an image of Cenosphaera spp. is from the supplementary material (Figure S2) of the following paper:

F. Lejzerowicz et al., Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biol. Lett. (9) 2013.

Question: Does this image accurately depict the organism?

More specifically, in other images of this organism, there are numerous thorns pointing outwards. Is this thorn-less version a natural variation (or e.g. the result of the process of imaging the organism)? Also, is it largely a sphere with a hollow inside?

The authors give the following description of the process involved in obtaining these images.

Eighteen sediment samples were wet washed over 63 μm and 20 μm sieves. The >63 μm residua were dried and picked for radiolaria and foraminifera. From most samples all specimens were picked. Rich samples were divided with a dry microsplitter into fractions, from which at least 100 specimens were picked for each group. Specimens were arranged by taxa on micropaleontological slides. Radiolaria are classified on the generic level, according to the classification utilized by [8]. Foraminifera above the species level are classified according to [9]. In addition, for radiolaria, the 20-63 μm fractions were soaked in peroxide, then washed with tap water and propanol. For each sample, a few drops of suspended material was left on a glass to dry, covered with Durcupan ACM resin and a cover glass. The micropaleontological slides were analyzed under Olympus BX50 light microscope (electronic supplementary material, figures S2 and S3).

molecular biology - Just how light-sensitive is ethidium bromide?

Good question.

I found this reference in "Molecular Biology: A Project Approach"

A phenomenon called photobleaching occurs when ethidium bromide (EtBr) -stained DNA is illuminated by ultraviolet light.... This decreased fluorescence is presumably due to the dissociation of ethidium bromide from the DNA.

Ethidium bromide fluoresces when it is in a hydrophobic environment, such as when its stuck between two base pair stacks in DNA- water quenches its fluorescence.

I also found this article citing the fact that sunlight can break down EtBr but only when a catalyst of iron and titanium dioxide is there to catalyze the reaction.

A lot of the original characterization of EtBr as a stain is very old, so I couldn't access it directly online... It looks like the compound itself is pretty stable, but UV can, somehow interact with it when its bound to DNA to bleach it out.

evolution - Are genes associated with obesity selected for?

This is called the "Thrifty Gene Hypothesis" which was first used to explain why diabetes is so common. Basically it suggests that these alleles would have provided some kind of advantage, over the other possible alleles at that loci, until the environment changed. Then the environment changed and the allele became harmful. Environments are always changing and therefore favour different alleles (variant of a loci).

I suggest the genes linked to obesity in the modern world would, if tested on the old world populations would have been linked to being of a healthy weight. Further, those without it may have been skinnier and more likely to suffer from the disadvantages of being in such condition.

However, this paper present some counter arguments to the thrifty gene hypothesis. Speakman suggests that the genes responsible spread via genetic (allelic) drift rather than by positive selection. It is worth remembering that drift is very poor at spreading new mutations through large populations so there are also weaknesses to his arguments.

One example of a change in the favoured allele caused by an environmental shift is the DDT resistance gene in Drosophila which was present in the population at very low levels for a long period of time. As an aside, it possibly remained this way because it was subject to sexually antagonistic selection - beneficial to females whilst detrimental to males. It then spread through the population when DDT pesticides were used because it obviously became highly beneficial. Many other examples of environmental change leading to different selection are around, this is just one off the top of my head. Another is the Galapagos Finches in a drought in the late 20th century.

HTH, if not please ask more and if it does then please accept it!

pharmacology - Can a person become addicted to tea?

Yes, both tea (black tea at least, English speakers usually mean black tea when they say tea anyway) and coffee have caffeine which is addictive.

Apparently, being able to correctly reply to this question involves defining the word "addiction". My guess is that the negative connotation of the word "addiction" will cause some pressure to not use it.

Here's a recent review on caffeine addiction that says that caffeine is not addictive. I do not agree with their arguments but I'll leave it to the reader to judge.