neuroscience - How does the eugeroic modafinil work?

The exact mechanism is not known:

Modafinil has wake-promoting actions similar to sympathomimetic agents like amphetamine and methylphenidate, although the pharmacologic profile is not identical to that of sympathomimetic amines. [...] Modafinil-induced wakefulness can be attenuated by the α1-adrenergic receptor antagonist prazosin; however, Modafinil is inactive in other in vitro assay systems known to be responsive to α-adrenergic agonists, such as the rat vas deferens preparation. [...] Modafinil is not a direct- or indirect-acting dopamine receptor agonist. However, in vitro, Modafinil binds to the dopamine transporter and inhibits dopamine reuptake. This activity has been associated in vivo with increased extracellular dopamine levels in some brain regions of animals [1].

A 2010 study has concluded that:

Recent evidence suggests that modafinil may block the dopamine transporter (DAT) and that the dopamine D1 receptor (D1R) may contribute to modafinil effects [2].

Another one confirms modafinil's dopaminergic activity:

These findings indicate that modafinil has a long duration of action, with alerting properties arising predominantly from dopaminergic activity [3].

It seems to be dependent on catecholaminergic signaling:

It binds competitively to the cell-membrane dopamine (DA) transporter and is dependent on catecholaminergic (dopaminergic and adrenergic) signaling for its wake-promoting effects. [...] Modafinil is an exceptionally weak, but apparently very selective, DA transporter inhibitor. [...] The conformational constraints on the interaction of modafinil with the DA transporter - and probably, as a consequence, its effects on trace amine receptor signaling in the catecholaminergic cell - are unique among catecholaminergic agents [4].

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References:

1. Drugs.com. Modafinil. Clinical Pharmacology. Available from http://www.drugs.com/pro/modafinil.html (accessed 29.07.2014)


2. Young JW, Geyer MA. Action of modafinil--increased motivation via the dopamine transporter inhibition and D1 receptors? Biol. Psychiatry. 2010 Apr 15;67(8):784-7. doi: 10.1016/j.biopsych.2009.12.015. PubMed PMID: 20132929.


3. Turner C, Belyavin A, Nicholson A. Duration of activity and mode of action of modafinil: Studies on sleep and wakefulness in humans. J. Psychopharmacol. (Oxford). 2013 Dec 3;28(7):643-654. doi: 10.1177/0269881113508173. PubMed PMID: 24306135.


4. Wisor J. Modafinil as a catecholaminergic agent: empirical evidence and unanswered questions. Front Neurol. 2013 Oct 7;4:139. doi: 10.3389/fneur.2013.00139. PubMed PMID: 24109471.

Can any protein be phosphorylated?

For one of the most comprehensive databases of protein post-translational modification (including phosphorylation, methylation, acetylation, ubiquitination, etc.), check out PhosphoSite. You can find links to sequences, diseases, motifs, publications, antibodies, mass spec experiments, structures, you name it.

cell biology - RNA or ribosome, which one moves during translation?

The ribosome moves relative to the mRNA by, in effect, pulling itself along it. If both the ribosome and the mRNA are freely floating and not attached to anything else (as in jp89's answer), the relative amount of movement should depend on their relative masses.

(Actually, it also depends on how much drag each of them experiences with respect to the surrounding liquid medium, but since I have no idea how much that is, and since it's probably highly conformation-dependent anyway, I'm going to just ignore that and just assume that the drag is also more or less proportional to mass, at least to first order.)

As it happens, a quick Google search and some back of the envelope calculation suggests that the mass of a ribosome and the average mass of an mRNA are both around a megadalton. Of course, the length (and thus the mass) of an mRNA varies quite a lot, so it would seem likely that sometimes it's the ribosome that moves mostly, sometimes it's the mRNA, and sometimes it's both.

Also, as shigeta and others have pointed out, there can be more than one ribosome attached to the same mRNA strand. That's going to make the mRNA move more (and, correspondingly, the ribosomes move less), since there are more ribosomes pulling it along.
Then there's also the protein being transcribed, which is attached to the ribosome but also being moved with respect to it. And I really have no idea how negligible the interactions with the tRNAs and so on are. It's a mess, but my guess would be that, usually, it's mostly the mRNA that moves, but that the ribosomes aren't completely stationary either (unless they're attached to something, of course).

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Ps. Here's an exercise for you, which you may try out if you happen to have a friend who works at a public swimming pool. Otherwise consider it a gedankenexperiment. You know those floating ropes that separate the lanes in the pool? Try getting your friend to let you into the pool when it's not in use and to release one of the ropes from the walls. Then get in, grab the rope with your arms and legs and try pulling yourself along it. While doing so, try to decide whether it's you or the rope who moves more. (Also, to more closely approximate the Reynolds numbers involved inside a cell, imagine doing this in treacle instead of water.)

genetics - Do antisense transcripts have different names than their sense strand transcripts?

If the anti-sense transcript is correctly annotated and in the databases (a very very big if), then it will have a different name. For example, the mouse Msx1 anti-sense transcript has the RefSeq accession NR_027920 while the sense transcript of the same gene is NM_010835.

In general, each transcript that is transcribed from a given locus has a different accession. The same is true for alternatively spliced transcripts. If a given gene has 4 AS transcripts, each of these transcripts will have a different, unique accession. The human insulin receptor gene, for example, has two protein coding transcripts, each with its own accession: NM_000208 and NM_001079817.

You may be interested in a recent analysis of cis-NATs in 10 species^[1] and also in NATsDB: Natural Antisense Transcripts DataBase^[2].

1. Osato N, Suzuki Y, Ikeo K, Gojobori T. 2007. Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice. Genetics, 176(2): 1299-1306, doi:10.1534/genetics.106.069484.


2. Li JT, Zhang Y, Kong L, Liu QR, Wei L. 2008. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Research, 36(15):4833-44, doi:10.1093/nar/gkn470.

bacteriology - Flow cytometry issues

I'm having problems with data analysis here.

I have flow cytometry data being collected on a Fortessa, and when I import them into FlowJo 8.7, all of my fluorescence values are systematically 10X lower than they are on the cytometer. No idea what's going on here, anybody can help? If you want screenshots and photos of the data, I'm happy to post them up.

genetics - Transcriptionally-mediated DNA damage

There seems to be some solid evidence that transcription promotes mutation because the untranscribed strand is able to form secondary structures which expose bases to chemical mutagenesis.

Here is a recent paper about transcription-associated mutagenesis:

Kim H et al.(2010) Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli. PLoS One 5(5):e10567. doi: 10.1371/journal.pone.0010567.

From the abstract:

During transcription, the nontranscribed DNA strand becomes single-stranded DNA (ssDNA), which can form secondary structures. Unpaired bases in the ssDNA are less protected from mutagens and hence experience more mutations than do paired bases. These mutations are called transcription-associated mutations. Transcription-associated mutagenesis is increased under stress and depends on the DNA sequence. Therefore, selection might significantly influence protein-coding sequences in terms of the transcription-associated mutability per transcription event under stress to improve the survival of Escherichia coli.

The authors cite a number of papers in their introduction which document the phenomenon that you could follow up. Just in case the focus on a bacterial system puts you off, the Kim et al. paper has in turn been cited in:

Wright et al. (2011) The roles of transcription and genotoxins underlying p53 mutagenesis in vivo. CARCINOGENESIS 32:1559-1567

Abstract in full:

Transcription drives supercoiling which forms and stabilizes single-stranded (ss) DNA secondary structures with loops exposing G and C bases that are intrinsically mutable and vulnerable to non-enzymatic hydrolytic reactions. Since many studies in prokaryotes have shown direct correlations between the frequencies of transcription and mutation, we conducted in silico analyses using the computer program, mfg, which simulates transcription and predicts the location of known mutable bases in loops of high-stability secondary structures. Mfg analyses of the p53 tumor suppressor gene predicted the location of mutable bases and mutation frequencies correlated with the extent to which these mutable bases were exposed in secondary structures. In vitro analyses have now confirmed that the 12 most mutable bases in p53 are in fact located in predicted ssDNA loops of these structures. Data show that genotoxins have two independent effects on mutagenesis and the incidence of cancer: Firstly, they activate p53 transcription, which increases the number of exposed mutable bases and also increases mutation frequency. Secondly, genotoxins increase the frequency of G-to-T transversions resulting in a decrease in G-to-A and C mutations. This precise compensatory shift in the 'fate' of G mutations has no impact on mutation frequency. Moreover, it is consistent with our proposed mechanism of mutagenesis in which the frequency of G exposure in ssDNA via transcription is rate limiting for mutation frequency in vivo.

homework - At what substrate concentration will an enzyme work at 40% of its maximum rate if its Km = 0.095M?

To be honest I know very few about enzymes and absolutely nothing about Michaelis–Menten.

However, when I "took the Michaelis-Menten equation, replaced v with 0.4Vmax, canceled the Vmaxes (one on each side), and solved for [S]", my result is positive:

0.4 * Vmax = S * Vmax / ( Km + S )
0.4 = S / ( Km + S )
S = 0.4 * Km + 0.4 * S
0.6 * S = 0.4 * Km
S = Km * 2 / 3.

human biology - Is reproduction intrinsically part of life?

Every species has the ability to reproduce. Of course, individuals within a species can be born with a mutation that keeps them from reproducing, or lose the ability to reproduce at some point in life. However, to say that once these individuals fail to meet that criteria they are no longer forms of life would be a fairly absurd semantics argument. It might be useful to note in an evolutionary sense that those individuals can no longer pass on their genes, which is could select against whatever it was the resulted in that individual being sterile.

You could probably reword the characteristics of life to stress species instead of individuals, but then theres a problem with microbes which have very poorly, or non-existent species. But in general, this is not something a biologist is going to lose sleep over.

zoology - How can an albatross stay airborne for months?

Albatrosses, of the biological family Diomedeidae, are large seabirds allied to the procellariids, storm-petrels and diving-petrels in the order Procellariiformes. They range widely in the Southern Ocean and the North Pacific.

Short tailed Albatross , Source: Wikipedia, DOR 16/09/2012

I read that albatrosses can stay airborne for up to a decade and that they can cycle brain activity between hemispheres. How do they do this feat, and how did they evolve this ability?

Possible points to consider:
immune system, predation, cycling solar output, weather, seasons...

behaviour - In the context of twin studies, what do 'unique environmental factors' and 'shared environmental factors' refer to?

I was reading this study on sexual behavior and they refer to both terms without clarification. Does 'unique environmental factors' refer only to the prenatal environment or does it include individual experiences with, say, illness as well? Would friends be considered a 'shared environment factor' or an 'individual environment factor?'

dna sequencing - Separating DNA Fragments by Gel Electrophoresis. Are all the strands for one size the same?

The answer to the part of your question concerned with average lengths of restriction fragments is: if the DNA molecule being digested is of random sequence, and is 50% GC/ 50% AT, then the probability of finding any given short sequence at any position is 1/4^N where N is the length of the short sequence. So, for example for a restriction enzyme with a 4-base recognition sequence such as AluI (AGCT) the probability is 1/256 and so the average length of an AluI fragment would be 256 bp. For an enzyme with a 6-base recognition sequence such as HindIII (AAGCTT) the corresponding number is 4096 bp. Please note that this is the average length, and is not an 'expected' length.

The answer to the part of your question about fragments of the same size co-migrating, how would you purify them on a gel for further analysis is trickier. I think the first thing to say is that you wouldn't do this for sequencing, and this is reflected in the various answers you have already received - sequencing no longer requires this sort of approach.

If you were forced into this position for some reason then I can think of two things that could help: the first option would be to run the analysis on an acrylamide gel when you can get much better resolution of different fragments (all 50 bp fragments are not the same molecular weight), but this is really only useful for small fragments (100 bp or less). However the most likely way out of the co-migration problem would be to purify the two comigrating fragments as a mixture and then ligate them into a vector whereupon each recombinant would carry one or other of the two fragments. This is really going back to the original reason why molecular cloning revolutionised things - it allows the 'biological' purification of DNA fragments followed by production of these fragments in large amounts.

You mention "special base pairs that are lacking a hydroxyl group" so clearly you are thinking in terms of Sanger (dideoxy-) sequencing, in which case you could clone directly into an M13 phage vector so that you could make ssDNA for direct sequencing. By sequencing a number of clones you would find two sequences, one for each fragment. You would still have to find a way to decide which one was the fragment that you were actually interested in, however.

Like I say, things just aren't done in this way anymore.

taxonomy - Could someone recommend a book for surveying species?

Judging from your response to Gurav in the comments, it sounds like introductory zoology and plant biology texts would fit the bill.

For zoology, we teach from Hickman et al's Integrated Principles of Zoology. It outlines the major phyla, their defining characteristics, with plenty of specific examples scattered throughout. There are nice little problem sets throughout, and it goes into a solid amount of detail for a first or second year zoology course.

For plants, I've used Graham et al's Plant Biology, which takes a similar general approach. Though it's perhaps a bit broader, and less species-focused.

Both of these books outline the major relevant groups, and use 'representative' species to illustrate various biological points throughout. They might be a good place to start!

embryology - What is a zygote?

Conventionally, a zygote is considered to be formed the moment that a spermatozoum, penetrates the cell membrane of the ovum and yields its genetic material into the ovum. Effectually, however, there is a lag between the instant of fertilization and the fusion of the male and female pronuclei. In mammals, the duration of this lag period is ~12 hours. There are also additional actions that must be completed before the first mitosis as in most mammals, including humans, the ovum is actually in the second metaphase of meiosis at the time of fertilization.

human biology - How to map the Gene name to its Gene Symbol?

I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes in its name as

gene1:    chromosome 12 open reading frame 52

May I know how I can find its corresponding gene symbol as

C12orf52

Is there a mapping table or tool I can use ?

Thank you very much,

dna - How to learn molecular biology through pubmed research articles?

There are in fact various books where each chapter is written like a published review. These are not text books, but they are very technical. Off the top of my head I can think of this one for example:

Hatfield DL, Berry MJ, Gladyshev VN. Editors. (2011) Selenium: Its molecular biology and role in human health, 3rd Edition. Springer.

Like all such books, it consists of various chapters, each of which is a short review of the relevant topic by leading authors in the field. The problem with this is that a certain level of knowledge is assumed. Using your example, you won't be able to understand the original DNA paper if you don't understand the results of X-Ray crystalography experiments. Published articles assume that the reader is already an expert and they won't explain basic concepts.

A better way would be to read your textbook and then, once you have read and understood a chapter, look into that chapter's references and read through those. Most serious textbooks include published articles at the end of each chapter, if yours does not, get a new textbook.

Finally, another choice would be to read a review article. Those of the Trends and Current Opinion series are particularly good. They tend to be very well written and, most importantly, highlight the seminal papers in their references. Just pick one that is about a subject you are interested in and then look at the references. The important papers in the field will be marked with • and seminal works with ••. So, read the review and then read the •• papers.

biochemistry - How does GTP help in the step of codon recognition?

GTP based structural changes (even motor actions) are very common in biological systems. For e.g. G-proteins, Rab-GTPase (vesicular transport), Ran-GTPase (Nuclear export/import).

So all these GTP-bound proteins make use of an intrinsic or assisted GTPase activity to convert GTP to GDP. This conversion causes change in the structure of the associated protein. Going back to the GTP bound form requires proteins called GEF (Guanine nucleotide Exchange Factors).

So in the case of translation elongation, the elongation factor is a GTPase which changes confirmation upon GTP hydrolysis. This confirmational change twists the tRNA so that the bound amino acid moves closer to the peptidyl-transferase center (if P-site is in the left then the amino acid is bound to the rightward CCA tail of tRNA. The twist causes the amino acid to move leftwards- towards the P-site).

You can refer books like Genes by Lewin for details.

bacteriology - How effective are restriction enzymes in protecting bacteria?

Note that a given bacterium will probably have more than one restriction enzyme, so the viral genome probably won't ever run out of targets. Even if it did, restriction enzymes could suffer mutations that may change the specificity. When you talk about microorganisms, it's more accurate to think in populations rather than individuals, since the colony would be able to grow again if they have at least one cell. Viruses need a certain density to spread, so even if the bacteria cannot defend against, it may be able to survive simply because the virus run out of hosts before some cells can be infected. This is even easier if the bacteria have some kind of resistance form.

Moreover, restriction-modification systems aren't the only defense line against viruses. Many bacteria have a system called CRISPR-CAS that acts like an immune system, inserting RNA fragments into the bacterial chromosome and using them as "antibodies" by hybridization. In this context, you can assume that restriction-modification systems, alongside other nucleases they usually carry, act as an innate immune system, while the CRISPR-CAS would be an analog to acquired immunity.

Diagram of the CRISPR-CAS system. Source.

Furthermore, not every environment has the same viral density. Some habitats may be protected against viruses by some means, like the gut microbiota (the carbon intake goes through the stomach acid and tons of hydrolases, which is very destructive for viruses); while some others may have an incredible amount due to lack of biodiversity and high cell densities (this is the case of most extreme environments). E. coli, as a gut bacteria, would probably have enough with only restriction-modification enzymes (In fact, while it have a CRISPR system, it seems to be repressed), while many others will need more defenses.

biochemistry - Are there any methods to quantify H2O2 (hydrogen peroxide) which don't rely on horseradish peroxidase?

Amperometric detection of H2O2 can be performed without HRP, and gives high-resolution real-time readings.

You will find many different type of electrodes that are used in the literature to detect H2O2, including for instance MnO2-coated carbon paste microelectrodes or gold electrodes derivatized with cytochrome c.

Commercial electrodes also exists. For instance these from WPI are based on derivatized carbon fibers (although they do not specify with what, so I would not exclude HRP...)

Another option is that of using the H2O2-sensitive dye H2DCF (dihydro-dichlorofluorescein).

human biology - Perception of distant lights without glasses

I am fairly short-sighted and wear glasses pretty much all the time. Naively, I would expect that when I take my glasses off, the image I see should look very much the same as as a photograph that's out of focus, or an image to which someone has applied a Gaussian blur filter. In bright conditions this is mostly true, but at night if I look at distant point sources of light, the blurry halos around them appear to have quite a complex structure, and a fairly well-defined edge. Why is this?

To make it clearer what I mean, and at the same time to make a hypothesis about the answer, here is a public domain image of some lights, taken with a camera out of focus:

(image source.) Notice that the image cast by each light is not simply a uniform circle. They are each slightly hexagonal; they are slightly brighter around the edge than in the middle; and there are distinct nonuniformities in the brightness in the interior of each shape.

What I see is actually fairly similar to this but much more extreme. The shape formed by a light is much further from a circle, being very irregular in shape and distinctly elongated in one direction. (This latter is perhaps not surprising given that I have a strong astigmatism.) The bright edge to the shape, and the non-uniformities in its brightness, are much more pronounced than in the camera image.

Now, in the photograph I know that the hexagonal shape is due to the hexagonal aperture in the camera. This can be ruled out in my eyes because my pupils are definitely circular. (Unless some light also passes through parts of the iris?) I would guess that the bright edges are caused by diffraction, and that the nonuniformities are caused by defects in the lens and/or dirt on its surface. I suppose that diffraction and lens aberrations must be the causes of what I see when looking at distant lights without my glasses.

So in the end, my question is mostly just, am I right about this? Are the shapes I see the result of defects in my eye's optics, and which specific anatomical features of the eye are likely to be their main causes?

metabolism - Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction

Well first off, we don't know how you sequenced the data. What did you actually sequence? Did you look at transcriptional activity using RNA-seq or did you do a full genome sequencing. Were there any paired-end reads? How did you create your library? Did you enrich the bacterial consortium for biomethanation activity?

Where do you reads map? The consortium complicates things but you will likely need to build a quality contig library before you do anything else. Without a doubt, much of your library will not map to anything interesting but you should still annotate the library by seeing where the reads map up. Identifying ORFs will be useful.

Likely, you will have a set of genes that will be involved with biomethanation. You should BLAST the bejesus out of your contig library for hits. Do they match any of your ORFs? Going the otherway, do your ORFs match any of the genes in EcoCyc or BioCyc. Do you need to use a larger database?

Is there any evidence that humans have faced extinction before?

There is ample genetic evidence for a population bottleneck following the out-of-Africa migration. This would account for the reduced genetic diversity found in non-African populations.

There is further evidence for an earlier major bottleneck that reduced the human population to around 10,000 individuals.

These kinds of studies are typically done now via Coalescent theory using whole-genome sequences.

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I just found this nice blog post summarizing the Nature paper I linked to.

genetics - How does sex differentiation work in Paracerceis sculpta, the sexually tetramorphic isopod?

Shuster, SM & C Sassaman (1997)
Genetic interaction between male mating strategy and sex ratio in a marine isopod. Nature 388: 373-377

As described in this paper, the chromosomal system of sex determination in Paracerceis sculpta is ZW=females, ZZ=males. Genetic evidence indicates that the morph of a ZZ male is determined by a second locus, Ams (alternative mating strategy) which exists in three allelic forms whose dominance relationship is Ams^β > Ams^γ > Ams^α. So for example, to be an α type male, an individual must be ZZ Ams^α / Ams^α.

That's the end of the answer, what follows is supplementary information.

The paper also describes an additional layer of complexity in the sex-determining system of P. sculpta involving sex changes in both directions. This is explained by a model in terms of two other factors: an autosomal locus Tfr (transformer) and a cytoplasmic factor ECF (extra-chromosomal factor) which interact as shown in the Table below (taken from the paper). However, this doesn't really add anything to the Ams story as far as male morphs are concerned, except that some of them start as females.

zoology - Transitivity of Species Definitions

There are many definitions of "species" which usually take the form

Two individuals are of the same species if ...

An implied (rarely made explicit) property of any sensible species definition is that the relation "is the same species as" should be an equivalence relation (the reason why this is sensible is that only such a relation partitions the set of all individuals into equivalence classes, that is, separate species). In particular, it should be transitive, that is

If A and B are of the same species, and B and C are of the same
species, then it follows that A and C are also of the same species.

It appears to me that all species definitions in use violate that property.

Are the Chihuahua and the Great Dane of the same species?

Not according to the "biological" species definition, which states:

Two individuals are of the same species if and only if they can produce fertile offspring.

Since that is (presumably) not true of Chihuahua and Great Dane, according to that definition, the two dog breeds are not of the same species.

However...

Let us say that the Chihuahua can produce fertile offspring with the Dachshund...

... and the Dachshund with the Golden Retriever...

... and that at last with the Great Dane as desired.

Then, if we assume transitivity, Chihuahua and Great Dane are of the same species - contradiction!

Are the Chimpanzee and the White Oak of the same species?

Intuitively, they are of course not, the very idea seems ridiculous. Sure enough, with the definition (a variation of the "genetic" species definition)

Two individuals are of the same species if and only if their genome differs in less than 0.5% of base pairs.

the two are indeed not of the same species.

However, we can again construct a "chain" of intermediate individuals, each of which is similar enough to its predecessor to satisfy the definition, eventually connecting Ape and Tree and violating transitivity again.