molecular biology - How do proteins and genes participate in learning?

The storage of memories in cells is rarely thought of on the protein level of the cell. Cells are usually given a developmental state, but no memory. A cell may become a liver cell, cancerous, or diabetic, but this is not memory, but a physiological change in the cell which is usually not reversible to a previous state.

For example cancer treatments are entirely focused on identifying the cancerous cells and killing them. Internally the genomes of cancer cells often have deletions and duplications. They are cancerous, they have not learned to be cancerous. Though not as dramatic, it is now thought that cellular differentiation which creates different types of cells is heavily influenced by epigenetic modification of the genome; the DNA is marked by methyl groups which dictates the state of the cell by modifying the gene. This is mediated by proteins for sure, but is quite complex and not well understood at this time. Epigenetic markers can even change gene behavior between generations of offspring as well, though that is not usually called memory.

How is information stored in the brain? This is thought to be reflected in the organization of the neurons in the brain. There are many kinds of neurons. They can be distinguished by the sorts of axons and dendrites that emanate from the cell body. They can also be distinguished by the chemical variety of neurotransmitter they use (there are a score of different molecules). So to a great extent the type of cell and the specific proteins it chooses to use to mediate information is very important.

That being said, information is currently thought to highly related to the placement of the axons and dendrites connecting the neuron to sometimes scores of other cells, sometimes touching the cell body, other times other dendrites or neurons. As neural activity ensues, the cells will reconfigure their connections by physically moving them.

More recently, investigators have tried to understand the genes which internally modulate the neural signals within the cells. This nobel prize lecture discusses how the CREB/MAPK pathway can modulate Long Term Potentiation - the shape of the neuron response to a signal over time (days or hours).

Taken as a whole, you can see that memory is likely to be stored on several levels at once - the kinds of cells (dictated by differentiation) involved, structural arrangement of the neurons (axons and dendrites connecting to various cells and places on cells), as well as internal signaling circuitry that generates and modulate the electrical and chemical activity within the cell.

"Marker protein" only refers to a protein that you can follow to see some sort of activity in the cell. A typical example is Green Fluorescent Protein, which is colored, fused with a protein of interest. It has no specific meaning regarding learning I think.

microbiology - Is it plausible that eukaryotic organelles like flagella and cilia are the result of endosymbiosis with spirochetes?

This was a claim by Lynn Margulis explained over at this link.

The sense organs of vertebrates have modified cilia: The rods and cone
cells of the eye have cilia, and the balance organ in the inner ear is
lined with sensory cilia. You tilt your head to one side and little
calcium carbonate stones in your inner ear hit the cilia. This has
been known since shortly after electron microscopy came in. Sensory
cilia did not come from random mutations. They came by acquiring a
whole genome of a symbiotic bacterium that could already sense light
or motion. Specifically, I think it was a spirochete [a
corkscrew-shaped bacterium] that became the cilium.

And why would our bodies incorporate spirochetes as part of our basic functionality?

There are many kinds of spirochetes, and if I’m right, some of them
are ancestors to the cilia in our cells. Spirochete bacteria are
already optimized for sensitivity to motion, light, and chemicals… If
I’m right, the whole system—called the cytoskeletal system—came from
the incorporation of ancestral spirochetes.

homework - What are all possible vectors for unicellular human parasites?

I got the given question. They want the following pieces of information about protozoological human parasites:

disease - parasite - vector.

There are 10 proteogenic diseases at the Wikipedia. I added the corresponding parasite and the vector next to them:

1. Malaria - Plasmodium - Apicomplexa


2. Amoebiasis - Entamoeba histolytica - sarcomastigophora


3. Giardiasis - Giardia lamblia - no vector


4. Toxoplasmosis - Toxoplasma gondii - no vector


5. Cryptosporidiosis - Cryptosporidium - Apicomplexa


6. Trichomoniasis - Trichomonas vaginalis - no vector


7. Chagas disease - Trypanosoma cruci - insect


8. Leismaniasis - Leishmania donovani - sand fly vector


9. Sleeping sickness - Trypanosoma brucei gambiense - tsetse fly vector


10. Dysentery - Entamoeba histolytica - sarcomastigophora

I am unsure what I should answer to the question since it is asking "all" possible vectors for unicellular human parasites.
There are many possible diseases, much more than the given ten in my opinion.
It seems also that there are many possible ways of getting the infection for each disease.

I hope that I am wrong in my statements.
It is my first course in Parasitology.

What would you answer to the given question?

How does a veggie-less diet affect the human body?

You'd be deprived of the vitamins and minerals which are found only in vegetables, but you'd live. There are vitamins and minerals in meat and other foods, plenty of them, and your metabolism would adapt to produce the proteins which are missing. Human body is a wonderful organism.

You wouldn't have a higher risk of cancer because cancer is a byproduct of life (the DNA repair mechanism and programmed cell death) and you can't get it by consuming meat or by not consuming vegetables.

You wouldn't gain weight if you're not consuming too much food. The math is simple, if you need 2000 calories, you'll gain weight if you're consuming 2050 calories of vegetables and lose weight if you're consuming 1950 calories of meat.

Your risk of heart disease wouldn't increase.

The only things which would change in this case would be the ones directly related to the nature of carbohydrates, proteins and fat. The carbohydrates in vegetables release energy slowly over a longer period of time, so if you'd eliminate vegetables you'd possibly be hungry more often. However, fat - and the glucose produced from it - would keep you going.

And you might have digestion problems because of lowered intake of fibers until your metabolism adapts.

bioinformatics - Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.

Here is my running command:

python scripts/oases_pipeline.py -m 25 -M 29 -o output -d " -strand_specific -shortPaired data/reads.fa" -p " -min_trans_lgth 100 -ins_length 300"

My library is strand-specific and pair-ended with length 67bp. The reads are shuffled as:

>0(left_mate_forwarded)
ACTC...
>1(right_mate_reverse_complemented)
TATA...

I got some transcripts, but are far from the transcripts annotated, also far from the result of Trinity. The longest contig from Oases is ~2500bp (vs. ~10000bp from cufflinks and ~6000bp from Trinity). The N50 value is also low. It only reports 20 contigs those cover full-length of some transcripts from Cufflinks (totally ~4000), while Trinity reports ~650.

The dataset I am using is a subset of S. pombe. Does it matter?

Could somebody help me point out whether something wrong here?

human biology - Why don't teeth glow?

Just to add a little more on the interface between optics and dentistry:

Whilst teeth do not phosphoresce, they do in fact autofluoresce.

The differential auto fluorescence of healthy tooth and carious tooth has been used for the early diagnosis of caries. (Gugnani N, Pandit IK, Srivastava N, Gupta M, Gugnani S. Light induced fluorescence evaluation: A novel concept for caries diagnosis and excavation. J Conserv Dent 2011;14:418-22 and http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-2-1-149)

To see teeth glow, or rather, fluoresce, they should be illuminated with short wavelength light, like blue light (wavelength 450 nm) and the teeth will glow green, which will be visible if the the blue light is filtered out.

Also see http://www.inspektor.nl/dental/qlfmain.htm#QLF%99%20Basic%20Principle

human biology - Why is the Patellar reflex not triggered when the tendon is extended slowly?

This effect you are observing has to do with the nature of the afferent neurons (Ia fibers), which carry a signal into the spinal cord and synapse onto motor neurons directly. See this text (scroll down to section 1.10) for a diagram. At their other end, these Ia fibers penetrate into the muscle and wrap themselves around the body of the muscle spindles, "[which] are specialized receptors that signal (a) the length and (b) the rate of change of length (velocity) of the muscle."

Because the main role of these spindles is to monitor the muscles for very rapid changes in length, the neurons have a static range which is optimized for these quick jerks (rather than firing over a wide range of velocities). When you are stretching the muscle slowly, the Ia fiber is not building up a sufficient depolarization to fire off an action potential.