Typical neuronal firing rates across the human cerebral cortex I would like to find a scientific article (or articles), which would summarize typical neuronal firing rates in different parts of the human cerebral cortex.

Any good references on this?

Here's a good reference to start you off where you can access an atlas of different properties of neurons.
Cell types from the Allen Brain Institute

Remember that when you say typical firing rates you have to specify what kind of cells you are talking about because interneurons can fire faster for example than pyramidal cells. Also there are differences in basal vs active firing rates.


Why does excess dopamine activity in the pleasure centers results in less pleasure in schizophrenics? According to the dopamine hypothesis of schizophrenia, there is an excess of dopamine in the mesolimbic pathway (nucleus accumbens), and this contributes to the positive symptoms of schizophrenia.

I am not sure what the cause of anhedonia (reduced interest), one of the negative symptom of schizophrenia. If nucleus accumbens plays a role in the reward system and there is an excess of dopamine, isn't it the case that there should be an increase in interest, that is, no anhedonia?

Short answer
The dopamine hypothesis includes brain regions with reduced dopamine transmission as well. The prefrontal cortex in specific has reduced dopaminergic activity and is implicated in anhedonia. It affects pleasure seeking behavior through interactions with the nucleus accumbens.

Background
The negative symptoms of schizophrenia are less well understood as the positive counterparts. One thing is for sure, the dopamine hypothesis cannot explain everything. It is a very useful working hypothesis, but primarily based on the first generation antipsychotics such as haloperidol with mainly dopaminergic mechanisms of action. In turn, these drugs mainly and effectively target the positive symptomatology (excessive dopaminergic transmission).

Second-generation antipsychotics are more effective in treating the negative symptoms and are thought to actually increase cortical dopamine, as well as and acetylcholine release, as well as have a variety of effects on the glutamatergic system not shared by the typical agents first-generation antipsychotics (Meltzer, 2004).

In fact, the dopamine hypothesis has been improved and adjusted during decades of intensive research. One of the important things that has come out of this is that dopamine neurotransmission is regionally affected, with a prefrontal hypodopaminergia (prefrontal cortex, or PFC and a subcortical hyperdopaminergia (e.g. in the pleasure centers). An excellent review of the historic developments in the dopamine hypothesis was published by Howes & Kapur (2009)

Now on to anhedonia. Pleasure perception per se seems largely unaffected in schizophrenic people, it is the anticipation of pleasure that seems negatively affected. This is accompanied by reduced motivation and goal-directed actions to seek pleasure. Anhedonia is primarily attributed to disturbed interactions between the ventral (nucleus accumbens) and dorsal striatum (mainly the caudate) and the PFC and not so much in the experience of pleasure per se. In addition, insular cortex, amgydala and hippocampus may be involved. A dysfunctional coupling between the anterior cingulate and the insular cortex (the “salience network”) has also been linked to the failure to appropriately process reward in schizophrenia. Lastly, goal-directed actions needed to obtain the reward and dependent on the PFC is dependent on not only dopaminergic, but also adrenergic and other mechanisms. This is all nutshelled information and I would encourage you to read Milan et al. (2014), who have written an extensive and excellent review focusing on anhedonia in specific as a negative symptom. Fig. 1 is obtained from that paper and shows the complexity of anhedonia.

Fig. 1.  Cerebral circuits involved in negative symptoms, with a focus on deficits in anticipatory reward. source: Milan et al. (2014)

Reference
- Hows & Kapur, Schizophr Bull (2009); 35(3): 549–62
- Meltzer, Curr Opin Pharmacol (2004); 4(1): 53-7
- Milan et al., Eur Neuropsychopharmacol (2014)24(5): 645-92


How to measure surface area of plated bacteria? For my project, I'm growing Baker's yeast and probiotics in two liquid cultures before mixing them together and plating them.
I'm trying to measure the impact of the probiotics on the yeast.
How could I measure the amount of fungi on the plate, whether by cell counting or surface area?

You can count the individual colonies on the plate, with this number being the number of "Colony Forming Units" (CFU), as theoretically, only a single cell is needed to spawn a colony.

To do this though, you will need to do a serial dilution of your liquid cultures before plating, so you would have one plate of 10$^0$ dilution, then 10$^1$, 10$^2$, and so on, generally a ten-fold dilution is performed.

Hopefully this will yield at least one plate with a countable number of colonies, that is - not too many, and not too few - usually 30-300.

cfu/ml = (no. of colonies x dilution factor) / volume of culture plated

This usually yields a very large number, so it is common to then take the log of this number, and report that as your result.

And then you will be able to compare your results between probiotics. It's a very good idea to do replicates of each dilution!


What is the basis of the endocochlear potential? I am learning about the endocochlear potential. According to different sources, the ionic composition of perilymph is about as follows (in mM): 150 Na+, 4-5 K+, 1.2 Ca2+, 1 Mg2+, 120 Cl−, and 20 HCO3−; and that of endolymph is 1 Na+, 157 K+, 0.02 Ca2+, 0.01 Mg2+, 132 Cl−, and 30 HCO3−.

This means (in a naive attempt to quantify ionic charges) that the sum of charges in perilymph is 150+4.5+2*1.2+2*1-120-20 = +18,9.
And in endolymph it is: 1 + 157 + 2*0.02 + 2*0.01 - 132 - 30 = -3,94.

From these numbers, it seems like perilymph contains more positive charges than endolymph. How is it possible that the potential of endolymph is highly positive (80-90 mV) compared to perilymph? Shouldn't it be the other way around?

I have searched the forum and the internet for answers, but my question seems so basic (or based on a very fundamental misunderstanding) that I can't find anything of help. The only explanation I keep seeing is that the high potassium concentration accounts for the potential. However, isn't that outweighed electrically by the excess of negative ions in contrast to the perilymph?

About biological electrical potentials generally

Biological potentials on the order of tens of millivolts depend on very very few ions moving (about 1/100,000 of the potassium concentration, for example, for a typical neuronal potential).

Therefore, the sum of positive and negative charges in any compartment is always almost zero (to several decimal places and beyond measurement; if you say a ). Electrical forces are very powerful, and

Some previous answers that are related:

https://biology.stackexchange.com/a/57066/27148

https://biology.stackexchange.com/a/77925/27148

https://biology.stackexchange.com/a/81571/27148

The endocochlear potential in particular - this is really cool

Everything I said above basically can be summarized in a quick statement: you can't figure out potentials just by measuring ion concentrations and summing them up. If you counted all the ions (including charged proteins, etc), you'd get ~0 in any biological solution. Instead, you have to think about where the concentration gradients are and how particular ions are moving. Let's tackle the endocochlear potential... Hibino et al 2010 has an excellent diagram, adapted from their previous 2008 paper:

Let's walk through the key features here, focusing on panel (b). First, the general structure: there are three extracellular spaces, which are all electrically isolated from each other. Between these extracellular spaces, there are two layers of cells where all the business happens.

Between the perilymph and intrastria space, there are a collection of cell types all connected via gap junctions. We can treat them sort of like one big cell, I'll call it the syncytium. A sodium-potassium ATPase uses energy to pump potassium into the syncytium and sodium out (upper left of [b]). Additionally, because there is now low sodium in the syncytium, more potassium enters through NKCC channels, which are symporters that move 1 sodium, 1 potassium, and 2 chloride ions together.

Potassium  would accumulate in the syncytium, except there are Kir4.1 channels permeable to potassium on the other side of these cells, open to the intrastria space. So, potassium flows down its concentration gradient into the intrastria space. This also creates an electrical potential and makes the intrastria space very positively charged (shown as +90mV on the diagram; the syncytium would similarly get a negative charge from the flowing potassium, but that isn't shown).

Normally, not many ions would actually flow to create this potential (on the order of the 1/100,000 I mentioned above) and everything would stop there. However, there are another set of pumps and channels in the marginal cells. The marginal cells also pump potassium in, via the sodium-potassium ATPase and NKCC channels, keeping potassium concentrations in the intrastria space low, such that potassium continues to flow down its concentration gradient from the syncytium.

The marginal cells also have potassium channels on their opposite face, and these are open to the endolymph. The high concentration of potassium ions in the marginal cells and the positive charge in the intrastria space gives the necessary drive to push the concentration of potassium in the endolymph high.

Ultimately, there is a full circuit of potassium because potassium is flowing into hair cells from the endolymph, and then back out to the perilymph. The sodium-potassium pumps use energy in the form of ATP to maintain the imbalance between perilymph and endolymph.

Hibino, H., Nin, F., Tsuzuki, C., & Kurachi, Y. (2010). How is the highly positive endocochlear potential formed? The specific architecture of the stria vascularis and the roles of the ion-transport apparatus. Pflügers Archiv-European Journal of Physiology, 459(4), 521-533.

Nin, F., Hibino, H., Doi, K., Suzuki, T., Hisa, Y., & Kurachi, Y. (2008). The endocochlear potential depends on two K+ diffusion potentials and an electrical barrier in the stria vascularis of the inner ear. Proceedings of the National Academy of Sciences, 105(5), 1751-1756.


What tool to use to map reads (samtools, sequencher,...)? I am a beginner in Bioinformatics. I have 4 files:

2 fastq files (aln1.fastq and aln2.fastq)

2 bam files (aln.bam and aln.bam.bai)

I know that:

the raw file is aligned to hg19 human genome.
The sequenced file is pair-ended from Miseq sequencing platform.
This file is the result of an amplicon sequencing design.

I also have sequence information about the primers (4 forward and 4 reverse) and 2 adaptors.

And I have to answer these two questions:

What is the constitution of each read, for example (adaptor + primer + amplified
region) ?
Which gene region did those reads mapped to ?

My question is what kind of tool do I have to use to respond to these questions? samtools? sequencher? FastQC? Can anybody help me just to start because I am totally lost.

Thanks

Samtools is not an aligner; it is used to analyse alignments. FastQC is for analysing the read qualities and average composition. You can get to know the adaptor sequence by running FastQC.

The next step is adaptor trimming. There are many tools that do that. Trimmomatic is currently popular. You can find the adaptor composition of each read by subtracting the read length post trimming from the read length pre-trimming (this would be same for all reads).

Then you have to align your trimmed reads to a reference, using an aligner. Again, there are many aligners available; Bowtie, STAR and now a new one called HISAT. STAR and HISAT are faster than Bowtie.

Since you already have the alignments (aln.bam) to hg19, you do not need to perform alignment. You want to know, to which genes do these reads map to. This information is not available unless you have the genome annotations. The annotations are available in the form of GTF/GFF files. You can obtain the association between genomic locations and the reads using the BEDOPS toolkit as mentioned in this Biostars post.

I don't have much experience with this tool. What I would do is convert the BAM to SAM (using samtools) or to BED (using bedtools:bamtobed) and parse the columns of the SAM/BED file describing the read locations with the GTF file. See this link for the details on the SAM format. You can use any scripting language like awk or perl to parse.

Samtools does have an option to filter the reads according to regions specified in the BED format but it will not automatically annotate them.

samtools view -hL regions.bed aln.bam > aln_filtered.sam


What is this black and white worm in a white case? The case is very small and it's an off white color.

The thing living inside can come out of either end. It's a black and white looking worm. It will poke its head out and move everywhere!

They are all over my back porch and some are even coming in my house!

This is just a larva of a moth from the Family Tineidae, most probably Phereoeca uterella (known as plaster bagworm or household casebearer), or Tinea pellionella (known as case-bearing clothes moth).

As you can see, the larva of this moth...

  ... constructs a protective case from silk and camouflages it with other materials such as soil, sand and insect droppings. (from Wikipedia)

Here is a better picture of Phereoeca uterella, from the entomology deptartment of the University of Florida:

Here is the imago (adult), for comparison:


What proves that speciation is a pairwise process? I have been asked this questions by many biology students and even non-biologist without a pretty straightforward answer to give. We are quite accustomed to phylogenetic trees where a common ancestor becomes two different species and these new species become, each one, two more. But, Why is not possible that a species might divide in three different species? Or four? Or more?

What arguments support this conception of the evolutionary process? Also, if somebody has a good article explaining this, please provide me with the link or citation so I can refer my fellow biology students to it.

I offer this perspective in addition to what WYSIWYG has provided.

Phylogenetic trees are tools to model what has actually happened, or what some evidence implies has happened, to a population of entities that exchange genetic material.

These models fail, for instance, when describing the phenomenon of horizontal gene transfer since a tree is acyclic by definition. Consider a viral genome that has integrated into a host genome. The host now contains DNA from its ancestral lineage and the viral lineage. This process cannot be modeled by a tree.

Some founder population that is susceptible to exogenous genetic transformation may give rise to many distinct lineages, some of which your species concept may qualify as "new" species.


What would be the fate of protein made from D-amino acids after ingestion by humans? There are some natural peptides made of D-amino acids, rather than the L-amino acids normally found in nature. It is now possible to chemically synthesize artificial proteins made of D-amino acids.

If such proteins were ingested by individuals, how would they be metabolized and what consequences would they have?

One aspect of the basic biochemistry needed to approach this question is the fact that the enzymes that catalyse cellular reactions show various levels of specificity towards their substrates (reactants), including stereo-specificity. This is illustrated below (an ill-favoured thing, but mine own). The first example shows that the specificity of proteases may depend on the general chemical or physical nature of the substrate. The second shows the how stereospecificity works.

The enzymes that are relevant here are proteases, which are responsible for breaking down proteins to their constituent amino acids, which are then absorbed by the gut, and then the enzymes that would normally catabolize (break down) or metabolize (convert to other compounds) those amino acids. It is well known that the specificity of the enzymes is such that, even if the proteins were broken down to D-amino acids, these could not be used for protein synthesis.

I am not an expert in this area (‘for’ loops are more my sort of thing) but I found some pertinent references in a recent paper on D-amino acid analogues of peptides. To quote from the introduction to that paper:

  A useful consequence of this is that (D)-proteins are highly resistant to degradation and have low immunogenicity (7). The fundamental change in backbone–side-chain connectivity and geometry means they are not recognized as proteins by many (L)-proteins—including proteases. Consequently, (D)-proteins are reported to have greatly increased gut, blood plasma, and intracellular half-lives (8). Better cell penetration has also been reported in some cases (9, 10).

The references are:

Uppalapati M, et al. (2016) A potent D-protein antagonist of VEGF-A is nonimmunogenic, metabolically stable, and longer-circulating in vivo. ACS Chem Biol 11:1058–1065.
Rabideau AE, Pentelute BL (2015) A D-amino acid at the N-terminus of a protein abrogates its degradation by the N-end rule pathway. ACS Cent Sci 1:423–430.
Nickl CK, et al. (2010) (D)-Amino acid analogues of DT-2 as highly selective and superior inhibitors of cGMP-dependent protein kinase Ialpha. Biochim Biophys Acta 1804:524–532.
Brugidou J, Legrand C, Méry J, Rabié A (1995) The retro-inverso form of a homeobox-derived short peptide is rapidly internalised by cultured neurones: A new basis for an efficient intracellular delivery system. Biochem Biophys Res Commun 214:685–693.

So it would appear that the D-amino acid proteins are less likely to be metabolized and thus would be less likely to be useful as food. I do not understand why they would have low immunogenicity, but if this is the case it seems unlikely that they would cause allergic reactions.


What are the various types of plugs found in a bee house and how do they help us with identification? I have a Mason bee house with small tubes that is currently buzzing with life but I am completely clueless about what's in there. Some plugs seem made of clay, some of crushed leaves, some of resin, some look like just a little film...

I figure it's possible to learn about what is living in there (approximately) going by the type of plug, and maybe the size of the tube, but I don't know where to start. I'm in Eastern Canada if this makes a difference.

Not an expert on bees, but there 39 known genera of solitary bees in eastern Canada1.  That reference contains a key, so at very least you can start to identify your tenants when they emerge next year.

The clay plugs are due to one of the genera of "mason bees", but that doesn't really appear to narrow things down much.

Your area does have "leafcutter bees" in the genus Megachile that use cut leaves to line and separate the chambers of their nests1,2, so that probably explains the holes containing crushed leaves.

There are also "resin bees", but the only species in your area (Paranthidium jugatorium) I've read about that fits that description is supposed to nest in the ground.1

Finally, bees in the genus Hylaeus and Colletes are known to use a membrane rather than a plug.2

1: Packer, L., Genaro, J. A., & Sheffield, C. S. (2007). The bee genera of eastern Canada. Canadian Journal of Arthropod Identification, 3(3), 1-32.

2: Michener, C. D. (2000). The bees of the world (Vol. 1). JHU press.

ETA: A guides to wasps in your region from the Canadian Journal of Arthropod Identification may also be of help.


Question: What is CINWntUp and CINnormL? What is CINWntUp and CINnormL?

I read a paper that uses this two things as classes but Im not sure what they represent. I imply that CIN is referring to Chromosomal instability but I don't know what WntUp & normL refer to. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214593/)

From the paper:

  The dataset contains six colon cancer subtypes: class 1 = CINImmune-Down (116 samples), class 2 = dMMR (104 samples), class 3 = KRASm (75 samples), class 4 = CSC (59 samples), class 5 = CINWntUp (152 samples), and class 6 = CINnormL (60 samples).

CINWntUp and CINnormL are therefore two classes of colon cancer. You are correct, CIN is for chromosomal instability; WntUp refers to upregulation of Wnt, a signalling pathway involved in some cancers and named for a Wingless/Integrated phenotype in fruit flies and the homologous gene in vertebrates. normL stands for "normal-like."

See the original paper describing these classes:

Marisa, L., de Reyniès, A., Duval, A., Selves, J., Gaub, M. P., Vescovo, L., ... & Kirzin, S. (2013). Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS medicine, 10(5), e1001453.


Is RNase AWAY in the lab dangerous? I use RNase AWAY in the lab. I would like to know how dangerous this chemical is for health. For example, when I remove my gloves my hands smell because of the RNAse AWAY

RNase AWAY is marked for Category II skin corrosion/irritation and Category II eye irritation/serious eye damage. Recommendations by the MSDS followed by definitions as follows:

Skin contact Wash off immediately with plenty of water for at least 15 minutes. Remove and wash contaminated clothing before re-use. Immediate medical attention is required.
Eye contact Rinse immediately with plenty of water, also under the eyelids, for at least 15
minutes. Immediate medical attention is required.

SOURCE
DEFINITIONS FOR GHS LABELING
More information is included in the MSDS provided.
As for any smell, RNase away is reported to be a proprietary alkali hydroxide solution, so without any additional information it's difficult to tell.


Why I cannot find dendritic cells in blood smear? According to many sources including Wikipedia, there are haematopoietic stem cell derived dendritic cells in the blood.

figure 1 - haematopoietic cell lines - ref

Despite of this, when I examine a blood smear, I cannot find dendritic cells and I did not find any blood smear example on the internet, which depicts dendritic cells.

figure 2 - blood smear cell lines - ref

Why is that?

The dendritic cells are antigen presenting cells that process and present pathogens to the T Cells.
As such they are present in interfaces where foreign organisms are frequently present. Eg: Skin.
When these cells get activated i.e. come in contact with pathogens, they process them and move to lymph nodes to present the processed antigen.
Thus these immune cells do not circulate in blood once they reach the target tissue but reside in the tissues and found in lymph nodes on activation.
Further, from Kuby's Immunology:

Dendritic cells can be difficult to isolate because the conventional procedures for cell isolation tend to damage their long extensions. The development of isolation techniques that employ enzymes and gentler dispersion has facilitated isolation of these cells for study in vitro. - Kuby Immunology 5Ed. P.42
Since blood is the most accessible tissue for clinical studies, we set out to extend the findings that were reported in mouse blood to humans. However, when we tried to induce DC growth by adding GM-CSF to human blood, we identified actively proliferating DC aggregates only infrequently -
Proliferating Dendritic Cell Progenitors in Human Blood
By Nikolaus Romani, Stefan Gruner, et.al.


How to recognise the type of allele by pedigree analysis diagrams? It was said that this interference pattern is due to dominant allele. I fail to see that.
In general how to recognise the type of allele by pedigree analysis diagrams?

This question is a bit broad. You have to understand a lot of concepts to figure out the nature of the allele. I'll just point out some basics:

If an allele is dominant it should affect both males and females equally (not X-linked)
If one of the parents shows the trait (while other does not) then at least one offspring should show the trait (basic Mendelian segregation)
If both parents show the trait and one of the offspring does not then it means that the parents are heterozygous and the allele is dominant.


Can the brain influence gene expression? A neuroscientist told me (according to my hazy memory) that the brain/nervous system can have an epigenetic function, ie directly regulate gene expression.

I'm not a biologist, but she talked me through how it worked, and I know enough of the basics to follow along and think it sounded reasonable.  I think the conversation was based on some post-doc research she was doing.

A quick google search (Maybe I don't know enough jargon to get a productive answer) brings up a chap called Bruce Lipton, who completely agrees, but who also, according to wikipedia "remains on the sidelines of conventional discussions of epigenetics, basically ignored by mainstream science".

So what gives?

Are there (a possible chain of) mechanisms by which the subconscious mind can affect gene expression?

As has been pointed out in comments, the brain can certainly affect gene expression; but so can anything in our bodies, because the blood stream is super good at carrying stuff around the body to wreak havoc.

But I'm going to take a somewhat uncharitable view of this question1; and assume that what you are asking about is high-level mental processes affecting gene expression throughout the body, which is not a thing that happens.

The basic concept to bring forwards here is that the brain is hell-a layered. The brain is an extremely complicated organ, and while it's not a complete mystery, it's not an organ that we generally can be said to understand, at least not on the level that we can be said to understand in major terms how, say, the liver, kidney or spleen works.

What we do know is this: The brain forms a massive network of neurons; the shape of which informs our personality, memory and cognitive functions. Even our simplest thoughts involve, by necessity, thousands of neurons, and anything more complicated than 'Fire!' involves tens, hundreds or thousands of thousands (millions) of neurons.

At the same time, it's important to understand that our brain does a lot of things that we're not directly cognisant of. For one, our brain controls our breathing. As you're reading this, you'll discover that you take control of your breath, but also that you haven't done so for several hours at the very least, and maybe not for days or weeks, and you haven't died from hypoxia yet. Our brains do these kinds of things all the time, and we hardly ever notice.

Genetics are a very, very, very low-level thing. Way lower of a level than mere breathing, genetics is the engine that drives decision making at a cellular level; which is so far removed from consciousness that it's hardly imaginable.

And this is where layering really comes into play: While recent research indicates that brain cells have hijacked DNA replication techniques to store memories, most of our actual thoughts exist only on levels that are so much higher than the nuts-and-bolts of our brains that the physical structure of our brains don't even come into play.

Essentially, thought as we understand it doesn't exist within individual neurons, but only within the relationship between neurons. When it comes to cognitive or metacognitive processes, things like genetics becomes an implementation detail isolated from the higher-level system as a whole. The underlying physical structures can affect gene expression, but do so not as a response to thoughts or subconscious desires, since these don't exist in the individual neurons; but as a response to primal needs like "more sugar for the brain!" or "more oxygen for the brain!" or "more protein for the brain!".

In other words: While the (sub)conscious mind can affect gene expression, it does so in terms of resource management, not in terms of how body tissues act, because the mind as it is has no physical concept of bodily function.

1: Uncharitable, yes, but it does make the question more illuminating and interesting, IMHO.


How long does each of the stages in meiosis take? For each stages of meiosis (i.e. Interphase, Prophase I, ...), I wanted to know the time between each stages either in percentages or minutes. However, while I could find the cell cycle for mitosis like the image (original link), I couldn't find such thing for meiosis. Does anybody know anything about this?

If you take a look at the figure directly above the image you posted in the link you posted, you'll see a very different set of figures.

It turns out, time spent in different phases of the cell cycle depends on species, cell type, and conditions, specifically, the presence of cell cycle regulating signals like cyclins. You can also read about that in the link you posted.

Meiosis is similarly varied. For example, in a female human, oogonia start meiosis while the female is still a fetus. Meiosis is then arrested in prophase 1. Further progression in meiosis doesn't occur until puberty at the earliest. Spermatogenesis in a human male, on the other hand occurs over a 64 day period. Since oocytes sit in prophase 1 for ~ 13-50 years, they will have a very different proportion of time spent in each phase. You can read about this in Costanza Physiology, chapter 10.


Is this mammalian embryo blastocyst, gastrula or only phase between them? The picture shows the formation of early blastocyst and late blastocyst.
The middle embryo has embryoblast.
My professor says that blastocyst in general has embryoblast and trophoblast.

Embryoblast is the inner cell mass but the thing has none of it.
The last embryo does not seem to have inner cell mass anymore.

Is the last embryo in the picture anymore blastocyst?

The given thing seems to be "the single layered blastocyst that will give rise to gastrula", Wikipedia Gastrulation. The given stage seems to last very short time. It probably should be called phase between blastocyst and gastrula so that the thing is not blastocyst and not gastrula.

What is the right name for the given thing in mammalians?

Again, the thing (2) is idealized and probably does exists at all. It is an idealized picture. It is really a mistake to call such a thing blastocyst like Wikipedia does. The thing should be fixed not to confuse other people.

There should be real pictures instead of such idealized ones.


How can a brainless Cnidarian hunt and defend itself? Cnidaria, such as jelly fish and sea anemones are radial symmetric en feature a simple body plan. One notable aspect is the lack of a brain. Hence, there is no central guiding structure, no mind or will if you like. Nonetheless, they are known to be predatory (such as the sea anemones), and are quite effective in defending themselves as well (such as stinging jelly fish). How does a diffuse nervous system allow Cnidaria to feed and defend themselves?

Sea anemone devouring a crab:

Sea anemones are members of the phylum of Cnidaria. Distinguishing features of this phylum are radial symmetry and the presence of cnidocytes, or stinging cells (like the ones found in jelly fish). These cells have a mechanical trigger and if activated a subcellular harpoon is fired and paralyzing and painful toxin is injected. A cnidocyte diagram is shown below (from Wikipedia):

The Cnidarian nervous system is relatively simple indeed. The Cnidarian nervous system is decentralized and diffuse, and it basically consists of reflex arches. It is referred to as a "nerve net" as shown in the following schematic of a sea-anemone's nervous system (picture from Florida Int. University):

The presence of cnidocytes and a mesh nervous system basically answer your question:

1) Feeding: Whenever a prey touches the sting cells, it gets harpooned and paralyzed. The mechano-sensory cells sense touch, and drive nervous cells in the mesh. The nervous cells activate contractile epithelial cells in the arms of the anemone that push the prey inside the mouth. Then digestion takes place and the mouth serves as anus once digestion is complete.

2) Defense: the cnidocytes operate by mechanical triggering and no nerve cells are necessary.


Fisher's Fundamental Theorem of Natural Selection Ronald Fisher discovered what he, with humility, called the Fundamental Theorem of Natural Selection. This theorem says (in its modern terminology):

  The rate of increase in the mean fitness of any organism at any time ascribable to natural selection acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time.

As I understand it, it sounds alike the standard equation that we learn in the first class of Introduction to evolutionary biology

$$R = S \cdot \frac{V_G}{V_p}$$

In words: the response to selection equals the selection differential times the genetic variance of the trait under consideration divided by the total phenotypic variance of the trait under consideration

But how can we prove/demonstrate that Fisher's fundamental theorem of natural selection holds true?

I don't ask for empirical evidences that support this claim but for a theoretical/mathematical proof/demonstration of this claim.

I don't think that you need to look further than the Price equation, which is basically a proof of a generalized version of Fisher's fundamental theorem. Price had a series of papers in the 70's that derived and applied the Price equation (e.g. Price, 1970; Price, 1972a), but most relevant for your question in probably Price (1972b).

A nice summary of Price's legacy can be found in Frank (1995).


What are names of the colon delimited fields in this FASTA header? The human chromosome DNA data in Ensembl release 96, here is in FASTA format.

Reading the Wikipedia article on the FASTA format, I understand the first line, prefixed with >, is variously referred to as a "comment" or "sequence headers". However, looking at FASTA files from different sources, it appears this first line is quite variable in actual content.

What are the colon separated fields in this FASTA header (as found above on the Ensemble FTP site)?  Most fields are guessable, but an explanation of each field would be much appreciated.  I believe the 46709983 is the number of base-pairs in the chromosome.

>21 dna:chromosome chromosome:GRCh38:21:1:46709983:1 REF

Finally, how should I have figured out the meaning of the header notation for myself?  Is there a list of common or known header formats?

According to ensembl's website (albeit somewhat buried in a page about downloading data via FTP) it says:

"The header line in an FASTA dump files containing DNA sequence consists of the following attributes : coord_system:version:name:start:end:strand This coordinate-system string is used in the Ensembl API to retrieve slices with the SliceAdaptor."

A brief rundown of these attributes as I understand them:

coord_system- Is simply the coordinate system used to locate a particular feature within an assembly: "chromosome" and "BAC clone" are common examples as described here.
version- This is the current version of the assembly reference. And refers to an Ensembl archive as detailed here. (Yours appears to be from the human GRch38 assembly).
name- This seems pretty self explanatory. In this case we are looking at chromosome 21.
start- Again, self explanatory. Any complete chromosome or contiguous sequence is going to start at "1".
end- End of the fasta sequence. [start] - [end] + 1 = total length
strand- This refers to orientation (i.e. forward or reverse strand) 1 is forward (-1 is reverse)

Here is a link to a pdf containing this information and more about using Ensembl (see page 23)...

Unfortunately, to answer your final question, there is no easy way to come across this information and there are as many ways of labeling fasta files as there are sequence databases. Sequence repositories have come a long way in the last 10 years but there is still a lot of work to do toward standardizing data formats and making databases more user friendly.


Why is a gene for a fluorescent protein used rather than one for an enzyme that produces fluorescent molecule? Green fluorescent protein (GFP) is a small protein that emits bright green fluorescence in blue light. It was first isolated from the jellyfish.

The gene coding for GFP can be expressed in bacteria, and so it is often used as a marker to show successful uptake of a gene by the bacterium.

What is the advantage of using the gene for GFP to produce easily detectable fluorescence, rather than using a gene for an enzyme that produces a fluorescent substance?

Ps. The original question I got was to explain about the disadvantage, which is that GFP may not fluoresce very brightly and so may be difficult to detect.

Thank you for your help.

GFP has a lot of advantages:

The detection of the fluorescence works directly and doesn't need a lysis step or the uptake of a reagent.
Fluorescence can be detected directly using a fluorescence or confokal microscope with the cells. This can be done while growing them on plates (works for bacteria and eukaryotic cell culture).
You can sort labelled cells using a flow cytometer.
direct tagging of proteins and their subsequent localisation on the cell is possible.
GFP is rather stable in the cells and not toxic.


What makes worms' eggs float or sink? In parasitology, while examining the stool sample, one important thing you do is test whether the eggs float on water or sink. We never did that since our coursework limits itself to microscopic examination, but we still are expected to remember examples of eggs under each
category.

So my question is, what makes flotation such an important criterion? And how is it done? How do you know if the eggs are floating or not? Does it depend on from where you take the sample (as in, add the stool sample to water and then either take from top or bottom)?

Another interesting thing we are expected to remember is that the fertilized eggs of Ascaris float while unfertilized ones sink. What's the basic funda behind all this? What's in fertilization that changes the buoyancy?

Okay, I found the last part of your question the most interesting and can't give a full answer to that, but I just noticed I can answer the rest so here goes.

How it works (the simple version)
It works on the principles of buoyancy. The eggs and oocysts are less dense (lighter) than the fecal flotation solution and, consequently, they float on the very surface of it. The feces themselves are more dense (heavier) than the fecal float solution and, as a result, they sink to the bottom of the solution, out of the way. Commonly used flotation solutions include sodium nitrate, Sheather's sugar solution, zinc sulfate solution, sodium chloride solution and potassium iodide solution.

The eggs of some important parasites (for example. Schistosoma species and Fasciola hepatica) are more readily diagnosed by fecal sedimentation (sediment) tests because their eggs tend to sink in flotation media.

What makes it so important?
Some parasite eggs float and some don't. Faecal flotation is a simple, rapid and helpful diagnostic that narrows down the agent causing the clinical signs in the animal.

How it's done
Use a "Fecalyser", a commonly used test kit for faecal floats. The best stool samples to get are those that are fresh - straight out of the animal within the last 30 minutes where possible. Detailed walkthrough of the protocol here and video tutorial here.

Why is there a difference in the buoyancy of fertilised versus unfertilised eggs?
No idea, sorry.  Similar effects are seen in some insect eggs - Stomoxys eggs which sink mostly hatch, while floaters don't hatch. The fact that Anopheles eggs have floats and Culex lay egg rafts implies to me that their viable eggs would otherwise tend to sink too (this could be to do with oxygenation levels being higher at the surface, but I'm speculating here). During embryonation, a serosal cuticle forms which makes the eggs highly desiccation-resistant; non-viable eggs dry out. However, according to some sources online it sounds like for parasite eggs it's the unfertilised eggs which sink, not the fertilised ones.


Chitin, homo or heteropolysaccharide? My teacher told me that Chitin is a heteropolysaccharide but my book regards it as a homopolysaccharide.I am so confused

Even teachers are sometimes wrong. ;)

Chitin is a homopolysaccharide. This just means that it is made up of repeating units of the same monosaccharide - in this case that monosaccharide is N-acetylglucosamine. Other examples of homopolysaccharides are glycogen and cellulose.

The basic structure of chitin is shown below as a polymer of two N-acetylglucosamine units:

Homopolysaccharides can be linear chains or branched, as long as they are made up of just one type of sugar unit. A heteropolysaccharide is made up of multiple different monosaccharide units. Glycosaminoglycans would be an example of a heterpolysaccharide as they contain two different sugar units.


How to convert FASTQ file format into GTF file format? I have a plenty of FASTQ files (FASTQ is a standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer) and need to convert them to GTF format (gtf - file format used to hold information about gene structure which significant feature is that it is validatable: given a sequence and a GTF file, one can check that the format is correct. This significantly reduces problems with the interchange of data between groups).

I assume that (if those formats are popular files' standards) there must exist some software that easily converts information from FASTQ files to GTF file.
Did anyone hear about any such (is possible open-source) software? I am familiar with R statistical package and SAS and can learn Python on a fly.

Thanks for any help.

You should really read about both these file formats. As swbarnes mentioned, FASTQ and GTF hold different kind of information. GTF stores the annotation of a reference sequence. For example a GTF for a genome sequence will have the information about the locations of features such as genes, transcripts, exons, start codon etc.

FASTQ stores the sequence of a read obtained from sequencing along with the quality scores corresponding to each position.

As mentioned by others, asking for interconversion of these file formats, makes no sense.

I guess what you are asking for is "How to obtain novel annotations with a FASTQ file at hand?"

This also depends on what you want to annotate.

The sixth column in a GTF file refers to a score; you can assign expression values to different features. You can calculate expression using the read counts. If these are RNAseq reads then expression can be measured using packages like tophat-cufflinks, RNAstar or some others.

If you are doing ChIP-Seq then you can generate a GTF with a new feature called TFBS (transcription factor binding site) and annotate the locations. A popular package used for ChIP-Seq analysis is MACS, which takes your reads and outputs the TFBS in the form of a BED file which also stores co-ordinates. You can convert BED to GTF. You can also assign scores based on the read counts at different TFBS.

If you do not have a reference genome or if the annotation of the reference genome is incomplete, then you should first assemble your reads. If you have a reference genome then you can go for a reference guided assembly of the transcripts to obtain novel transcripts or splice variants; Cufflinks does this.

If you do not have a reference genome then you should go for de-novo assembly of your transcriptome and annotate the transcriptome for start codons or other features of processed transcripts. Velvet and Trinity are popular packages that do de-novo assembly.


Cellular Respiration in Boiling Conditions Here's the question:

  Imagine that you are given 25 germinating pea seeds that have been placed in boiling water for 5 minutes. You place these seeds in a respirometer and collect data. Predict the rate of oxygen consumption (i.e. cellular respiration) for these seeds and explain your reasons.

I'm thinking that there will be no cellular respiration and thus no oxygen consumption because the boiling probably messes it up, but I'm not sure why that is...

Extending on @ANONGOODNURSE, @SAPPHIRA and @JAMES.

Something you should know about proteins, they have primary, secondary, tertiary and quaternary structures all due to specific folding of the proteins. These foldings are mainly connected via hydrogen bonds to each other along with other bonds (Alberts et al., 2002). On the action of heat, the molecules composing the bonds are vibrated due to higher kinetic energy resulting in the breaking of the bonds which causes unfolding of proteins (Wikipedia denaturation of proteins). This phenomenon is called Denaturation of Proteins which causes the loss of protein function due to loss of shape.

Read this QandA in Reference.com for more information about denaturation of proteins.

Read this for more information about proteins: Molecular Biology of the Cell. 4th edition.

Link this idea to cellular respiration and how Electron Transport Chain and the Krebs Cycle (Citric acid cycle) involve proteins for the completion of the respective processes.


Concentration of degenerate primers should you dilute to? I'm a little embarrassed to ask but when you have for example four degenerate primers and the end protocol says that the final primer concentration should be 10 µM working stock, should you make the primers 10µM total (2.5 µM each) or 10 µM for each degenerate primer?

You can just add 2µl from each working stock (10µM) to your PCR mix of 20µl.

You can check this protocol.
Caution: The author has used $l$ instead of $\mu l$

He uses 5µl of each primer (20µM) in a 50µl reaction. This is double of what I mentioned. IMO it is best to try with a lower concentration and then increase it if necessary. Excess primer concentration can give rise to some nonspecific binding and amplification if the primers are not perfectly designed.

From this site:

  Using degenerate primers

  Because a degenerate primer is really a mix of different primers, only
  a fraction of the degenerate 'primer' will actually work in the PCR.
  One would therefore need to increase the primer concentration in PCR,
  sequencing reactions, etc. If a primer is 8-fold degenerate, the
  concentration should be raised 4-8-fold, and so on. However, for
  higher degeneracies, e.g., 64-fold, one cannot increase the primer
  concentration 64-fold and would have to try their luck with a
  5-10-fold increase only.


Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)? Why do 60S & 40S subunits make an 80S (not 100S) ribosome and, similarly, 50S & 30S make 70S? 60+40 is not equal to 80, nor is 50+30 equal to 70, so why are the subunits of the 80S and 70S ribosomes named so weirdly? I couldn't come up with any other mathematical explanation.

That's not a simple mathematical addition!

If those units were mass, for instance, you could (and should) add them: a 60g Lego piece combined with a 40g Lego piece will, of course, form a combo that has 100g.

However, those numbers are Svedberg units, which is...

  a non-metric unit for sedimentation rate [...] The Svedberg coefficient is a nonlinear function. A particle's mass, density, and shape will determine its S value. (emphasis mine)

Funnily enough, most of my students thought that that S stands for Sedimentation. However, it's a tribute to Theodor Svedberg, winner of the Nobel Prize for Chemistry in 1926.

Thus, in a oversimplified explanation, the prokaryotic ribosome has two sub-units. The large sub-unit sediments at 50s, the small sub-unit sediments at 30s, but the two together (that is, the whole ribosome) sediments at 70s, not 80s.

The same way an eukaryotic ribosome has a large sub-unit that sediments at 60s, a small one that sediments at 40s, but the whole structure sediments at 80s, not 100s.

Also, the rRNAs that constitute the sub-units have their own sedimentation rates (in svedberg units) as well:

For a detailed explanation with all math you need, the other answers here and here explain it beautifully.


Modularity score comparison between different algorithms in network analysis I used different algorithms for splitting my large gene network into different sub-networks using Cytoscape. I compared the modularity scores and decided that the algorithm with the best modularity score will be used for clustering the network.

My colleague came up with the argument that modularity scores can only be compared for different number of clusters being created by the same algorithm.

So, my question is if modularity scores can be used to compare between different algorithms or only in the case of the same algorithm producing different number of clusters.

Since the goal of modularity estimation algorithms is to find the community structure that maximizes modularity, it is valid to compare different algorithms based on their modularity estimate. However, i) it is not the only consideration for choosing a community detection algorithm, and ii) the obtained modularity estimate will depend on the particular structure of each network, e.g. its number of nodes. For a principled comparison between several different algorithms, see Yang et al. (2016). Based on multiple criteria, they identify the multilevel (or Louvain) algorithm (Blondel et al. 2008) as the overall best choice.

References
- Yang, Zhao, René Algesheimer, and Claudio J. Tessone. “A Comparative Analysis of Community Detection Algorithms on Artificial Networks.” Scientific Reports 6, no. 1 (August 2016). https://doi.org/10.1038/srep30750.
- Blondel, Vincent D., Jean-Loup Guillaume, Renaud Lambiotte, and Etienne Lefebvre. “Fast Unfolding of Communities in Large Networks.” Journal of Statistical Mechanics: Theory and Experiment 2008, no. 10 (October 2008): P10008. https://doi.org/10.1088/1742-5468/2008/10/P10008.


Are there any exceptional cases in which a person with O negative blood group cannot donate? Are there any exceptional cases in which a person with O negative blood group cannot donate or any case in which compatibility might not be established between O negative an any other blood group?

There are some situations, where, depending on the interpretation of Rh status, an exception could become possible. Rh +/- commonly refers to the D antigen. However, the Rh group has many antigens in it, including C and E. One can become sensitized to these other antigens and develop a hemolytic response to incompatible C or E type.

Dean L. Blood Groups and Red Cell Antigens [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005. Chapter 7, The Rh blood group.


Genomic instability of cancer cells in h&e image Is there are any books or papers on the topic of visual differences(analyzing H&E microscopy) of high grade cancer cells vs low grade cancer cells vs non-cancer cells?

In particular, I am trying to measure how much of genome was altered by analyzing images.

Histologic diagnosis of tumors is made using the so-called  WHO blue books.

Different tumors show different patterns of cellular and tissual aberrations.

On h&e  karyorrexis and  pyknosis  are examples histological markers of nuclear aberration.

A recent  paper reviews the salient visual and subvisual morphological changes of cancer nuclei and their possible cause or etiology and significance.


What kind of fish are these? This should be pretty easy. We have a tropical fish tank, and among a few other species we have an adult pair of these guys. The female is a live-bearer, and seems to be giving birth to two young at a time. However, I can't for the life of me remember what kind of fish they are.

The male is in the foreground, and the female in the background. Any ideas?

I believe it is a Red Wag Platy (Xiphophorus maculatus)


What temperature should mammalian B-Cells be stored at outside of the incubator? I'm working with murine B-cells. The general protocol is to keep cells on ice to keep them from dying but I've noticed that it makes these cells aggregate and precipitate out. I've heard suggestions that these cells should just be kept at room temperature. How would I be able to determine which conditions at which I should be keeping my cells?

I was trying to collect cells to prepare them for cell binding studies to antibodies and then assess the cells on a filterplate. Typically, you keep them on ice to pause the metabolic state as well as to prevent endocytosis of the bound molecules. However, that shift seems to cause settling. How do you troubleshoot the appropriate temperature to process cells and what are the usual scientific justification for making such decisions.

For the settling there's little you can do except agitation and using a taller thinner tube and larger suspending volume.

For the clumping however if the analysis permits it, adding serum to a [final] of 5% will help slow the clumping (in the short term). You can also filter out initial clumps by pushing the cells through a nylon mesh filter (they make these especially for flow-commonly used with fixed cells). I've analyzed cells on ice in dark probably as long as 6 hours after harvesting with little change in viability, however this is of course bad practice.


Ventral stream pathway and architecture proposed by Poggio's group Please can you give me a very brief explanation about all functions in the ventral stream architecture summarized in this figure:

This figure is from Serre et al.'s A quantitative theory of immediate visual recognition. Prog Brain Res. 2007.

I read multiple articles about this model, but I still don't understand the basic aim, especially behind the two operations (Gaussian-like and max-like operations).. So please can someone explain to me in details the ventral stream pathway (from V1-V2-V4-IT-PFC) including the two operations in this model.

For example : I don't understand how the cells in S1 are constructed...

This is a typical architecture of computation proposed as a model for ventral stream of visual processing in primates. It has a long history (e.g., Neocognitoron by Fukushima was 1980) and still widely accepted in machine learning (e.g., deep learning) and neuroscience.

It is motivated by the organization of V1 simple cells and complex cells. Simple cells in V1 can be approximately thought of as edge detectors at a specific retinal location. This is why on the figure you cite, they are represented as a circle with a bar (a cartoon receptive field). The simple cells can only detect things very locally, meaning if the edge appears at a different location in your field of view, it will not respond.

Mathematically, you can think of a spatial filter that detects an edge (e.g., oriented Gabor patch) multiplied to your retinal image, and summed. For example the filter below will detect match a 45 degree bar aligned on the hot-colored area, but will have less activity if the bar is shifted out of the specific position.

The complex cells in V1, on the other hand is still an edge detector, but has some location invariance. In other words, when the edge is slightly displaced, the response of complex cells does not seem to change. It is believed that this is because complex cells pull from multiple simple cells with the same orientation. This is what you see in your figure where a single complex cell pulls information from the same orientation simple cells but at different locations.

Mathematically, a soft-max operation or a max operation over the simple cell outputs can lead to a good complex cell model. But, it is not limited to such operations. In fact, quadratic or other nonlinear models are also widely used in computational neuroscience.

The full hierarchy for ventral stream is then simply obtained by extending repeatedly using the simple-cell-complex-cell analogy. For each stack simple cell layer extracts some local feature (by computing on the previous layer's complex cell's output), and complex cell layer makes it invariant over space. From edges in V1, one can get corners on the next layer, then complex contours, and all the way up to objects. At least that's how the story goes.


Coefficient of relationship and path of coefficient A path of coefficient of relationship is defined as

$$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$

This SE post discusses this definition

From this, the coefficient of relatedness between two individuals $B$ and $C$ is defined as

$$R_{BC} = \sum \rho_{AB} \rho_{AC}$$

, where $A$ is (I think) the last common ancestor of $B$ and $C$. The sum is over all possible path coefficients.

Source: Wikipedia

I am a little bit confused, I don't really understand this formula. One reason is the following. Let's assume that  $B$ has 2 paths and $C$ has 3 paths to go to $A$. If we denote $\rho_{AB,i}$, the path $i$ (or the $i^{th}$ if you prefer) between $A$ and $B$,

$$R_{BC} = \rho_{AB,i} \rho_{AC,i} + \rho_{AB,j} \rho_{AC,j} + \rho_{AB,k} \rho_{AC,k}$$

But the path $\rho_{AB,k}$ does not exist because there are only 2 paths between $A$ and $B$ (which are denoted $i$ and $j$). Also, there is no reason to count the path in a specific order and not another one. If we change the order we count the paths between $C$ and $A$, we can get:

$$R_{BC} = \rho_{AB,i} \rho_{AC,j} + \rho_{AB,j} \rho_{AC,i} + \rho_{AB,k} \rho_{AC,k}$$

, which is obviously different from the previous calculation of $R_{BC}$

Can you help me making sense of these formulas?

The expression $f = 2h-1,$ coefficient of inbreeding (COI) is a measure of homozygosity. Since in a randomly breeding herd (of cattle) we expect 50 per cent heterozygous and 50 per cent homozygous, the minimum for $2h-1 $ is 0. If the cattle's genome is purely homozygous (aa, AA) we have $2h-1 = 1.$ (h is total homozygosity--see Wright's paper, linked below.)

As we can see from this site, a basic calculation of relationship coefficient may not deal with f at all. For two descendants B, C, the quantities $f_B,f_C$ are an attempt to factor in existing relative homozygosity that the coefficient of relation (COR) would otherwise not capture. Likewise $f_A$ measures preexisting homozygosity in the common ancestor of B and C. If animal A is the product of siblings then the homozygosity could already be quite high and this would maybe have measurable effects on the vitality of a cross between B and C.

Now $f_A$ and $f_B$ vary between 0 and 1 so $s = (\frac{1+f_A}{1+f_B})^{1/2}$ varies between $(1/2)^{1/2}$ and $(2)^{1/2}.$ Note that the important thing here is relative homozygosity of an animal and its ancestor:

a. If the ancestor A and descendent B have the same known preexisting burden of heterozygosity we can disregard s (and f) entirely. Their COR will depend only on path distance.

b. The homozygosity of the ancestor A  tends to increase COR while that of B tends to decrease COR.

The expression $r_{BC }= \sum p_{AB }\cdot p_{AC}$ is somewhat confusing. On page 334 of one of Wright's earlier papers we can get a clear idea of the use of the coefficient.

He defines $p_{BA} = (1/2)^n (\frac{1+f_A}{1+f_B})^{1/2}.$ If the path from C to A is $p_{CA} = (1/2)^m (\frac{1+f_A}{1+f_C})^{1/2}$ then the total path BAC would be

$$ p_{AB,AC} = (1/2)^{n+m}(\frac{1+f_A}{1+f_B})^{1/2}(\frac{1+f_A}{1+f_C})^{1/2} $$

$$= (1/2)^{n+m}\frac{1+f_A}{[(1+f_B)(1+f_C)]^{1/2}}  $$

So the expression for the sum of such paths would be

$$r_{BC} = \sum_i p_{AB,AC} = \sum_i (1/2)^{k_i}\frac{1+f_{A_i}}{[(1+f_B)(1+f_C)]^{1/2}}   $$

in which $A_i$ is the ith ancestor through whom B and C are related. The total path length for a given term is $(n_i+m_i)$ which I abbreviated $k_i.$

So a less confusing expression for $r_{BC}$ might be:

$$r_{BC }= \sum_i p_{A_iB}p_{A_iC}. $$

Note that the sum is over all common ancestors back to some arbitrary generation.

A good example of this is Figure 11 at link 1 above.
It's really not ``dumbed down'' at all, it just leaves out the factor s, which for a carefully maintained herd may be close to 1 anyway.


Is it possible to make a contagious cure to a virus? In a TV series I've been watching The Last Ship, - spoiler alert - a scientist develops a cure for himself for a virus, but actually continues to remain a carrier, and sort of weaponizes the virus accidentally, killing 3 billion people. In response, another scientist develops a cure for that virus, a vaccine, and eventually makes that contagious by close contact as well, based on data gathered from the lungs of the scientist that infected/vaccinated himself with the weaponized version.

The science behind this might be totally ridiculous, or potentially realistic / possible I don't know. Is this possible? Can a vaccine / cure to a virus be engineered into a contagious version, to cure everyone in a chain reaction?

Fun question!

I think that to make a transmissable ("contagious") antiviral vector, you would need to design a virus that can infect people and that codes for something like an antiviral drug compound, which targets specific viral proteins.

As easy as that was to write down in one sentence, I think that execution would be extremely challenging.

Making the anti-virus out of another virus seems necessary to me, as there is little alternative. You would need something capable of efficiently spreading from host to host, that can generate many copies of its therapeutic payload and that is relatively simple to engineer. A virus is the only thing that I can think of that fits the bill.

You could theoretically engineer an antiviral virus that is mostly non-pathogenic to other people, although this wouldn't be perfect. Even if it didn't code for specifically pathogenic proteins, it is a foreign molecule that is likely to raise an immune response, risks integrating into an important location in the host genome and would divert cellular energy to production of its proteins and away from other cellular processes.

Say that you get this to work, that it's minimally harmful to its host and can effectively target the more pathogenic virus, against which you've designed it. What happens when the job is done? Is it still in the host body, pumping out more copies of itself and/or its antiviral proteins? If so, then it could end up causing more damage to the host in the long run, as it uses host resources to fill cells with no-longer-helpful foreign molecules.

Given more thought or time (than I have), you could probably image more ways to tweak the design of this theoretical anti-virus, but as a brief answer, I think that the above considerations can give you a quick idea of what it would take to bring this system from the realm of science fiction to that of hard science. :-)


Do any predatorial animals attempt to appear smaller? There are many animals that have behaviors or characteristics to make themselves appear larger than they are as a defense mechanism, such as butterflies have large eye patterns on their wings.

Are there any animals that do the opposite? That attempt to appear smaller in order to lure their prey closer?

I'm more interested in physical characteristics but behavior that does this, also counts.

In order to answer your question, two things must be demonstrated: First, we must demonstrate that the prey animal has perceived the predator. Second, we must demonstrate that the prey animal believes that it has perceived a small animal (which poses no threat).

There are several ways that a predator might achieve these outcomes. The first way is to present a small part of its' body as an independent animal, and the rest of its body as something innocuous, like a rock. There are many examples of this type of deception: you've already identified anglerfish lures. My personal favourites are frogfishes. Several other examples are discussed in the Wiki on Aggressive Mimicry.

Another way is to present the whole body in a way that makes it appear small, for instance by presenting a silhouette with a small apparent area to the prey. This has long been thought to be part of the foraging strategy of some ambush predators which have bodies with a small cross-section, such as pike and dories.

In addition to visual deceptions, some predators may use other signals to be perceived as animals that are smaller than themselves. Atkinson (1997) suggests that predatory Northern Shrikes impersonate the songs of smaller Passerine birds in order to lure them into striking range. This behaviour would also qualify as a predator attempting to be perceived as something smaller than it really is in order to gain prey.


What’s the Difference Between Grass and Sedge? What’s the difference between grasses and sedges? in terms of anatomy and classification.

Short answer
Sedges have edges, and they're in different families.
See Minnesota Wildflowers for a great summary with images.
 Long answer
Both are in the order Poales, but they are in different families:

Grasses = Poaceae (of the graminid clade)

Sedges = Cyperaceae (of the [non-monophyletic]1 cypirid lineage)

Some anatomical differences:

 Compiled using info from here and here

 Source: New York Botanical Garden

 Citations
 1. Bouchenak-Khelladi, Y., Muasya, A.M. and Linder, H.P., 2014. A revised evolutionary history of Poales: origins and diversification. Botanical Journal of the Linnean Society, 175(1):4-16.


What is the biological reason that some viruses cause sore joints (eg flu)? Frequently I have experienced sore joints during a bad bout of influenza. I understand that during time of sickness, white blood cells are deployed in the blood stream. I also believe that white blood cells originate or relate to bone marrow. I'm wondering if there is a relationship between each of these

My question is: What is the biological reason that some viruses cause sore joints (eg flu)?

Almost certainly what is causing the joint pain isn't the virus, but rather its the body's response to the infection.   Cells that are infected with viruses can release proteins called interferons. Interferons can act on surrounding cells and cause them to become less susceptible to viral infection.  Other cells, including your immune cells respond to a virus by releasing other proteins into the blood called cytokines.  Cytokines activate other immune cells and can stimulate the body to generate a fever and 'lock up' molecules of iron so they are not available to invading bacteria.

Some cytokines act on the bone marrow and cause the pool of 'reserve' neutrophils (a type of white blood cell) to move into the bloodstream.  Other cytokines shut down the lymphatic vessels, causing lymph nodes to swell up.   And other molecules such as histamine and prostaglandins are released and also play a role.

SO what you are feeling when you get ill from a virus (or a bacteria or parasite) is the effect of this 'soup' of cytokines, interferons and other 'mediators'.  You may have some combination of fever, muscle/joint pain, runny nose, malaise, fatigue etc.

In the US you'll see TV adverts for drugs used to treat Rheumatoid Arthritis.  These drugs include synthetic proteins that bind to a cytokine called TNF-alpha and  block its role in inflammation.


Where to find gene manipulation video (or photos) I hope Im not asking a dumb question!

Where can i find video of gene manipulation in action under microscope?
Like extracting a gene from a cell, fixing gene mutations, putting the gene in a vector, that kinda stuff. Is this too small to show in video or photos?

If i look up youtube all I find is scientists using lab machines and equipments except for under miscroscope!!!

From the comment section:

We don't have to see the actual changes. It's like chemists who will mix compounds together and obtain a new molecule. They dont see the chemical reaction per se but can test the new molecule to make sure what they predicted would happen had happened. Finally we often use fluorescent proteins to track some of the modification performed (which could involve a microscope). For the how, well that's a bit broad and involves too many notions to make a summary here.


Is it possible to become pregnant indirectly? Is it possible to become pregnant indirectly? For instance, if there is some wet semen left behind inside tight clothing, jeans for example, and a woman tries them on for a couple of minutes? What is sperm's motility after it's deposited on cloth in room temperature? Can sperm still swim inside from outside if it's near the vaginal opening in the cloth? What are the chances of pregnancy if the woman is/is not wearing any underwear?

yes this is possible, as long as the sperm make it onto the mucus membrane of the vagina. the LIKELYHOOD depends on the fabric and how much semen is in the fabric, if it's still clotted or not, and environmental factors.


Are our ears more sensitive to low or high pitched sounds? I am a Physics student who also love music and learned a little bit about Medical Physics. I know that the basilar membrane in the cochlear duct enables us to distinguish different frequencies. The different parts of the basilar membrane have different resonance frequencies and this leads to frequency dispersion.

I've also learned that the pitch of a tone is determined by the fundamental frequency, and the overtones just add timbre to the sound, and are difficult for common people to hear separately.

I think the above implies our ears are more sensitive to lower frequencies. However, this is obviously not true when we listen to a symphony, in which I think most people are more "sensitive" to the higher parts. And I think this is the reason while the melody is usually in the highest part in a song.

So I am confused. Are our ears more sensitive to high frequencies or lower frequencies? Is there a biological explanation of why we usually tend to hear the highest-pitch part of a piece of music?

Short answer
Our ears are most sensitive to the mid-frequencies.

Background
There are different ways of assessing sound level. The physical one simply determines the physical sound pressure level (SPL) in which all the frequencies weigh equally. This is referred to as C-weighting and is expressed in dB SPL.

Our ears, however, are most sensitive to intermediate frequencies, peaking at around 4 kHz (Fig. 1). The frequency weighting that takes this into account is dBA weighting.

The reason why we are most sensitive to mid-frequencies can be sought in the fact that sounds with frequencies around 4 kHz are amplified in the middle ear canal through the process of resonance. In effect, they are perceived 10 to 20 dB louder than other audible frequencies. The pinna also affect resonance and hence the outer and middle ear together join forces to create humps and bumps in the equal-loudness curves.

Normal equal–loudness-level contours for pure tones. source: Duncan (1996)

Reference
- Duncan, High Performance Audio Power Amplifiers
For Music Performance and Reproduction (1996): 1-18


Localization of B and T cell What does localization of B-Cell mean?? "Localization of B and T cell in allergens may not coincide". What does this statement mean? (I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

I think the reason you are having trouble discerning the statement is because it doesn't really make much sense, nor is it in my opinion sufficiently explained in the paper. The sentences preceding the it give a little explanation as to what the author may be getting at:

  So far, 1500 allergenic structures have been identified. Online allergen databases and allergy prediction tools are being used to find cross-reactivity between known allergens. Localization of B and T cells in the allergen may not coincide.

During an exaggerated immune response (allergy) the lymphocytes (B and T) will localize (travel or accumulate at) to the site of the antigen (allergen).

If I could guess I would say the author is stating that data has shown that no immune response is taking place (data generated by assessing the accumulation of lymphocytes near the allergen), despite the fact that these online allergen predictors say that an immune response should be generated.

The statement in my opinion moves to discredit these online allergen predictors.

I did look over some of the rest of the manuscript, and found two other ambiguities within.

The author does cite another paper in your sentence that may shed more light on this:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686541/?report=reader

An overview of it provided little clarity however.

I fear that only  a crystal ball or this question addressed to the senior author may answer your question with complete certainty:

Dr. Rajat Kumar De
Professor
Machine Intelligence Unit
Indian Statistical Institute
203 Barrackpore Trunk Road, Kolkata 700108, India.


A question about how the brain determines the source of a sound If a person's eardrum vibrates, let's say, 440 times per second for 1 second, how does the brain know its because 1 sound source vibrated 440 times, as opposed to 440 sources vibrating once, one after the other, or 2 objects vibrating 220 times per second, but out of sync with each other, or any other combination? Thanks.

If the sources have different locations then they won't reach the 2 ears at the same time, won't have the same loudness and spectral content (although here you describe a pure tone), so your brain will be able to tell them apart. There is a whole field of neuroscience interested in "causal inference", which describes how your brain makes this type of guesses. For example have a click and a flash been produced by the same source of different sources?

But I think this is not exactly what you were asking. If the signals are identical when reaching the ears then it becomes more of a philosophical question. If you place a microphone in the observer's ear and receive a perfect sine, does it matter that it has, in facts, been produced by multiple sources? That's the classical philosophical question of whether a tree falling in a forest produces a sound or not, if no one is around to hear it. Is a sound a physical signal or is it the percept it elicits in an observer? Take the example of color. If you compare 2 lights, one monochromatic red and one complex spectrum that looks exactly the same red. Do they have the same color or not? Due to the physiological limitations of your sensory organs they elicit the exact same response. Yet they are physically different. There is of course no clear or easy answer to this question as on one extreme you will end up arguing that there is no objective reality and on the other extreme you deny the obvious fact that we experience the world differently.

Shams, L., & Beierholm, U. R. (2010). Causal inference in perception. Trends in cognitive sciences, 14(9), 425-432.

https://en.wikipedia.org/wiki/If_a_tree_falls_in_a_forest


Do factors other than concentration gradient and membrane permeability affect the diffusion potential? If, hypothetically, the concentration gradients and the permeability of 2 different ions (Na+ and K+ for example) in 2 separate solutions are the same, will the diffusion potentials be different?
I'm trying to gain an intuition for the concept of diffusion potential and equilibrium potential.
It read this topic from 2 physiology textbooks but haven't really found an answer anywhere. I understand that the diffusion potential is the potential difference generated when an ion moves through a membrane down its concentration gradient. I also know that it is determined by both the concentration gradient and the permeability, but, does the type of ion itself matter if the charge on the ions is the same?

You can determine the diffusion potential mathematically with the Nernst equation. If it's not in the Nernst equation, it's not necessary.
The charge of the ion matters (including valance), the temperature matters. Some universal constants are in the equation but these don't vary.
Other factors that potentially matter are found in the other parameters, like the permability.


Would there be more amino acid residues in the extracellular or intercellular space? I am working on a bioinformatics project with HMMs and want to write some initiation probabilities for the location of amino acid residues. I know for different transmembrane proteins there will be different cases, but, in general, which regions of the protein would correspond to more AA residues: intracellular or extracellular? Or is there no general pattern?

Yes ,there are some patterns.
First you have to determine which group of membrane proteins you're talking about.
According to Molecular Cell Biology Lodish et al 8th ed chapter 13, there are 6 types of ER membrane proteins ( and therefore in the cell membrane)
The 6 types are type 1,type 2 ,type 3 , type 4,Tail anchored proteins ,GPI anchored proteins.
Nearly all AA residues in type 3 or  the tail-anchored type are located in the cytosolic side of the membrane ( their difference is in their N/C terminus orientation) whereas GPI anchored type has almost its entire AA residues in the exoplasmic side.
For other types there may not be a general pattern.
See E. Hartmann et al., 1989, P. Natl. Acad. Sci. USA
86:5786, and C. A. Brown and S. D. Black, 1989, J. Biol. Chem. 264:4442.
By the way , you can also think of it in another way. Antigens , Hormone Receptors , Structral proteins in exoplasmic leaflet of membrane usually have more AA in the exoplasmic side.


Why does an complete molar pregnancy not result in a clone? Complete molar pregnancy is one where an ovum devoid of nucleus is fertilized by a sperm after which the haploid set of chromosomes double to form a diploid set.

As far as my understanding extends if the sperm had Y chromosome the embryo will not survive.

However if the sperm has X chromosome the zygote will survive to have the 46 XX karyotype and will start to grow as molar pregnancy (which is basically trophoblastic tissue with no fetal parts, as answered by Anongoodnurse).

Why is there no proper fetus? Why can't a "female clone" of male parent form instead? Where is the defect as such?

The Question pointed out by WYSISYG contains data only from animal studies. Although it answers my question, I want more data obtained from study of human trophoblastic tissue (from the molar pregnancy).  Papers on imprinting which are linked in those questions have no mention of molar pregnancy although Prader-Willi and Angelman syndromes are mentioned (as cases seen in humans).

Oops, I corrected my question thanks to anongoodnurse. I mixed up complete and partial moles with each other.

"However if the sperm has X chromosome the embryo will survive to have the 46 XX karyotype and will start to grow as molar pregnancy."

Complete molar pregnancy is diploid, and there is no fetal tissue identifiable. It is a disease of the placenta, a uterine tumor (cancerous in some cases, non-cancerous in others); fetuses do not develop from such pregnancies, not haploid or diploid (though they are usually 46, XX). A male haploid 23,X replicates, but only trophoblastic (what should be the placenta) tissue results.

Partial molar pregnancies are triploid, and a fetus can sometimes be identified. However, it is non-viable, as polyploidy is non-viable in humans. Even if it were, the abnormal placenta could not support it.

Molar Pregnancy
p57KIP2 immunohistochemistry in early molar pregnancies: emphasis on its complementary role in the differential diagnosis of hydropic abortuses


Mechanism of antiperistalsis What is the mechanism of antiperistalsis that occurs during vomiting? Why the peristaltic waves normally don't propagate in anal to oral direction? Please give logical explanation with authentic sources. :)

What is the mechanism of antiperistalsis that occurs during vomiting?

Emetic agents in the bloodstream stimulate chemoreceptors in area postrema and nucleus tractus solitarius [1].
Nucleus tractus solitarius is connected to motor neurons in ventral medulla and hypothalamus [1].
Esophageal and gastric peristalsis is inhibited. Small bowel peristalsis is reversed. Esophagus and stomach don't have antiperistaltic movements [2].

  Why the peristaltic waves normally don't propagate in anal to oral direction?

Because of the mechanism of descending inhibition. Distension of the esophagus and intestine causes a reflex action that leads to circular muscular contraction just above the bolus/chymus. Longitudinal muscle also contracts (shortens) [3].

Reference:

Hornby PJ. Central neurocircuitry associated with emesis. Am. J. Med. 2001 Dec 3;111 Suppl 8A:106S-112S. PubMed PMID: 11749934.
Brizzee KR. Mechanics of vomiting: a minireview. Can. J. Physiol. Pharmacol. 1990 Feb;68(2):221-9. PubMed PMID: 2178746.
AUMSA. Digestive Physiology. May 2012. CC-BY-SA-3.0


Are receptors integral membrane proteins or peripheral membrane proteins? Integral membranes proteins serve as transporters. Peripheral proteins serve as cell adhesion molecules, antigens and enzymes. So what about receptors? Which proteins carry out the duty of receptors?

All the receptors I know about are integral, transmembrane proteins. It would certainly be possible for a receptor domain to exist on a peripheral protein that interacted with a transmembrane protein, but I don't know of any examples of this: an extracellular peripheral protein would tend to float away, which is a bit of a problem if they aren't intended for secretion.

There are certainly peripheral proteins that associate with the internal parts of transmembrane receptor proteins and may influence their function, but they are not themselves receptors.

I'm not sure about your question about "which proteins" - those proteins are most often named after their ligand followed by the word "receptor", or based on their function that is triggered by binding their ligand, or both (i.e., the AMPA receptor is a glutamate receptor that is also activated by AMPA; receptor tyrosine kinases are a family of receptors that are tyrosine kinases; the individual members of the family are typically known by their ligand).


What kind of animal can do this? When I was moving to another house, I found this plastic bag on the top of the cabinet of my old house. It looks like someone cut it all with a scissor, but no one have access to my bedroom, and it was not me.

I don't thing it could be rats. That bedroom was very tiny and closed, there's no way for a rat to enter.

The house is very near a university with a little "forest", there are many types of mosquito and little flying animals, but I can't imagine which could do this.

I'm just curious. (and not sure if "zoology" is the correct tag here, but I had to choose one)

Although your plastic bag tears are most likely due to light damage as @Chris mentioned above, there is a type of ant that chews its way through plastic, rubber and other manufactured polymers: Monomorium pharaonis, the Pharaoh ant.

It is capable of destroying many manufactured materials and is a great example of budding, a method by which new ant colonies form. They are very invasive and difficult to control.


Introducing evolution into the Hodgkin-Huxley equation How would the Hodgkin-Huxley equation change when the geometry of dendrites and axons are introduced?

Also can we model a situation of membrane activity during the corse of evolution, hence the equation would be subject to a periodic function ad it varies with time?

Taking the example of membrane transmission of electronic signals(in humans), can we model the change in conduction of the e-signal through the axon as its speed and geometry changes with evolution?

Although you mention evolution, I think what your question is really asking is in your last paragraph: what happens to conduction within dendrites and axons when geometry changes. There might be some evolutionary implications of this question, but you will also find vast variations in geometry among neurons in any one organism, as well.

You might want to look into expansions of Hodgkin-Huxley into compartment models that allow you to test the influences of geometry, see wikipedia for a list of different models at different scales of complexity.

There is a tool available called NEURON that is good for student or curious non-student experimentation, though you will have to read the documentation and hopefully find some examples that are close to what you want and then tweak them.


Role of drift in evolution of sexually dimorphic traits Is there a model for predicting how drift can affect the evolution of a sexually dimorphic (SD) trait? I've been trying wrap my mind around this paradoxical question; sexually dimorphic traits evolve due to sex-specific selection. So how can drift affect SD traits?

I've found the quantitative genetic equations (eq 1) in Lande 1980 very helpful for thinking about the parameters and how sexual dimorphism evolves.
Can this model be applied to a population bottleneck? Or comparing the degree of SD in a trait of two divergent populations (assuming s, Ne and other parameters remains constant).
$$
\begin {pmatrix}
\Delta z\\
\Delta y\\
\end{pmatrix}
= {1 \over 2}
\begin{pmatrix}
G_m B \\
B^{T} G_f\\
\end{pmatrix}
\begin{pmatrix}
P_m^{-1} s_m\\
P_f^{-1} s_f\\
\end{pmatrix}
$$

Edit: I've added the equation from Lande 1980, which models the phenotypic response for sexually dimorphic traits. I'm wondering how aspects of drift (Ne and fixation probabilities) can be merged with an equation such as this. From my understanding drift may affect the G, B and P matrices (that is the Genotype variance covariance, intersex (B) variance covariance and Phenotype matrices. One of the assumptions of this equation is that these matrices remain constant.

[C]an drift overcome sexual selection in the evolution of sexually dimorphic traits?

Short answer

Yes

Long answer

There are many ways to consider the effect of genetic drift. Here is one: One can approximate the probability of fixation of new mutations (using diffusion equations) with

$$P_{fix}≈\frac{1-e^{-4Ns} }{1-e^{-4s}}$$

, where $s$ is the selection coefficient and $N$ is the populations size. As you can see, a larger population size (the lowest is the genetic drift) corresponds to a higher probability of fixation of a beneficial mutation (to reach frequency of 1 in the population). If you don't have a good intuition of why genetic drift is inversely proportional to the population size, please have a look at this post. The most important point to keep in mind about the effect of drift is that when drift is high, every mutation pretty much behaves like neutral mutations.

This approximation is accurate under some assumption, for instance that the population is panmictic (=random mating). This equation holds true regardless of the reasons why a mutation affects fitness. The mutation may affect the activity level of an enzyme or it may influence how attractive an individual is to the other sex. So yes, in any case, a beneficial mutation may fix although it is deleterious (because of drift), or it may not fix although it is beneficial (because of drift).

A mutation might be beneficial in both sexes, detrimental in both sexes or beneficial in one sex and not in the other. In such cases, I suppose it is possible that the above equation must take a slightly different form. In any case where the mutation has a different impact on the fitness in each gender, I don't know how the above formulation would solve to but I'd think that you could simply replace $s$, by $\frac{s_m+s_f}{2}$, that is the average of the effect in both sexes (where $s_m$ and $s_f$ are the selection coefficients in males and females respectively). Intuitively, I think this should hold true as long as the sex-ratio is 1:1. The exact calculation of the probability of fixation doesn't matter to your question though. Note that mutations having the opposite effect on fitness in each gender often end up being on sexual chromosomes (if any) or at least being expressed in one sex but not in the other. In such case, a fixed mutation often end up being beneficial in one sex while neutral in the other. In any case, genetic drift will obviously affect the evolution of sexually dimorphic traits.

EDIT

  could you clarify "As you can see the highest is the population size (the lowest is the genetic drift),"?

The impact of genetic drift can be measured in terms of how it affects probability of fixation or how it affects the rate at which heterozygosity at a neutral site is lost. An intuitive explanation for why $N$ and genetic drift are inversely proportional can be found here.

  Are you referring to the positive correlation with P fixation and Ne?

Yes. I could have referred to that as to something else though. Note that the correlation between $P$ ans $N_e$ is perfect ($r^2=1$) because $N_e$ is defined on the concept of genetic drift.

Definition of $N_e$

Let's WR (stands for Wright-Fisher) be a population of size $N_{WR}$ where mating is random and there is no variance in fitness.

Consider now the population A. Let's its size be $N$. A experiences a given level of genetic drift based on its mating system, population structure, variance in fitness, etc.. the effective population size $N_e$ of A is (by definition) the size of the WR population ($N_{WR}$) that experiences the exact same level of drift, that is the same probability of fixation for a new mutation and the same rate of heterozygosity lose at a neutral site.


What is an interaction motif with respect to protein sumoylation? While am reading about protein sumoylation this morning I got stuck on sumo interaction motifs and consensus motif line. I heard the the word motifs for the first time. What does motifs mean in this context and What does canonical Sumo consensus motif ΨKx(D/E) mean also? Would you please elaborate the formula and thanks in advance.

A motif means a pattern. Since nucleotides and proteins have a sequence, they can have some patterns of sub-sequence that may serve some kind of function. For example TATA box in DNA serves as a promoter element. Similarly proteins can have some sequence motifs that can serve as recognition sites for binding partners (amongst other functions). Similarly there can be structural motifs in proteins, network motifs in big networks etc.

In this case the motif is a sequence motif.

From Gareau and Lima (2010):

  Many SUMO-modified proteins identified contain an acceptor Lys within a ψKX(D/E) consensus motif, where ψ is a large hydrophobic residue

This motif serves as a recognition site for the SUMO-Ligase.

Here,

K=Lysine
X=Any amino acid
D=Aspartic acid
E=Glutamic acid

From the below figures (Rodriguez et al., 2000), you can observe that ψ can be leucine (L) (original residue in Ran GAP1), isoleucine (I), phenylalanine (F) or valine (V).

I am not sure about the effect of double hydrophobic residues on rate of SUMO conjugation.


Meaning of "non-homologous virus" From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:

  More recently, concerns have been raised that HGT from genetically modified organisms (GMOs) could have adverse effects (Pontiroli et al., 2007). HGT of an introduced gene in a GMO may confer a novel trait in another organism, which could be a source of potential harm to the health of people or the environment. For example, the transfer of antibiotic resistance genes to a pathogen has the potential to compromise human or animal therapy (Bennett et al., 2004), transfer of a viral gene to a non-homologous virus may result in an emerging disease (Falk and Bruening, 1994) or gene transfer to humans has been controversially proposed as a potential trigger for oncogenesis (Ho et al., 2000).

What is a "non-homologous virus"? A virus whose species is the same but the strain is different from the virus taken as the donor for the GMO? Or just any virus (including viruses from different species) whose DNA or RNA sequence is different from the GMO donor virus?

Excuse me if the question seems too simple.

It simply means a two dissimilar viruses. If you read the paper Falk and Bruening, they are worried that if you place a viral gene in a plant (here we call that the transgenic gene), then natural viruses may "mix" it's genes with the transgenic genes and create a superior virus. The thought is, you are speeding up the evolution of the virus by taking a beneficial gene from a non related (non homologous virus), something that would probably take a long time.


Can antibodies be formed against white blood cells after blood transfusion? If antibodies are produced against other blood groups' red blood cells, why can't antibodies form against white blood cells, of any blood group? (even the same one, as MHC will be different in almost all individuals)

Antibodies and other immune responses do indeed occur against the donor's white blood cells. However, white blood cells are present in relatively tiny quantities (3-10 million WBCs per ml of blood vs 4-6 billion cells per ml).

Because the number of WBCs is so low, the immune reaction to them is also proportionally lower, with fever being a typical (and minor) complication of the reaction to WBCs. Some blood banks remove WBCs from blood to prevent these reactions.

For more information on the possible types of reactions to blood transfusions, see Wikipedia.

EDIT: Even in cases where the transfusion does not produce any symptoms, an immune reaction is most assuredly happening. In those cases, the immune system is simply killing off the foreign WBCs without any fuss.


Could a person become physically transgender through artificial means? Let's say there's a girl who carries a few masculine traits not normal in most girls, such as a high level of testosterone; we know there are countless reasons why something like this could happen, but could that girl have actually been concieved as a boy but modified before birth to become almost fully female, with only slight traces of male traits left? Is that possible through any sort of technology, or does biology even work that way?

For instance, if a male baby was injected with high amounts of female hormones before his birth, or really, anything else that could alter his gender, in any case could he start morphing into a girl, even if not fully? (Say, to the extent where he became more of a girl but still possesed a few common but not very specific/clear/exclusively male traits such as excessive body hair, etc.?)

A "high level of testosterone" must be made within the context of a particular sex. Men tend to have much higher levels of testosterone than women, but the testosterone production and levels within women vary widely - just as many hormones. Genetics, environment, diet, drugs, and workout regimes can all affect testosterone levels. A qualified physician will be able to tell where a person is after a test.
As for the rest... Every case of gender reassignment I've heard of and read about has occurred after birth. Read through this Johns Hopkins Magazine article from Sept. 2000 to get a fairly good understanding of when gender reassignment occurs and how it's handled. Here's a quick rundown (summaries, NOT quotes from the article):

Inadequate exposure to Testosterone in utero can result in ambiguous genitalia or other conditions such as 'micropenis' for an XY fetus. Up until the 1990's, regardless of chromosomal gender, children with the conditions would be reassigned as 'female' and had reconstructive surgery very early on.
Androgen Insensitivity is when an XY fetus is genetically incapable of utilizing male hormones and can involve several levels of insensitivity from "Complete" to "Partial". Complete insensitivity usually leads to fully feminine genitalia, while "Mild" or "Partial" can lead to partially or fully masculinized genitalia. Genitoplasty is an option for the latter cases.
CAH - congenital adrenal hyperplasia. This genetic disease causes the adrenal glands to produce excess androgens--the steroids that cause masculinization--a process that begins in the womb and can result in ambiguous genitals. However, CAH girls are generally more aggressive and display behavioral tendencies that more closely coincide with boys of the same age. Important to note: CAH children are genetically female (XX) and identify as female.

An extensive review of gender reassignments in 1997 had this to say about the consequences of surgically altering an infant's sex:

Considering this case follow-up, and as far as an extensive literature review can attest, there is no known case where a 46 chromosome, XY male, unequivocally so at birth, has ever easily and fully accepted an imposed life as an androphilic female regardless of the physical and medical intervention.

HOWEVER - as with all things scientific - there is dissent from the Johns Hopkins article above:

Preliminary analysis of the data, says Migeon, indicates that almost all of the patients are content with the gender in which they were raised. All but two showed a gender identity and gender role in accordance with their gender of rearing.

There is significant divergence that has not been reconciled in any trustworthy article I could find. The modern practice is to raise the child as their genetic sex unless significantly afflicted.
In adult transgender individuals, things like Hormone Replacement Therapy are part of a regime - along with surgery, acclimatization courses, and psychological evaluations - that can successfully result in a person presenting themselves and physically resembling another sex.
With adequate surgery, hormone therapy, and proper treatment all-around, it is practically impossible to tell whether a person is transgender without getting invasive or performing genetic tests.
As with all things that veer into a hazy area between medical knowledge (medical advice is not allowed on this website) and human biology: DO NOT use the above information to diagnose yourself or anybody you know. ONLY a qualified medical professional can perform the necessary tests required and give a qualified interpretation of the results.


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 type of reference for bacteria, but I only became aware of Fields as I was moving out of the field, rather than into it, so it's possible I've simply never heard of a suitable reference.

Any suggestions?

I might as well give this as an answer: the closest analog to Fields for bacteriology that I'm aware of are the two Bergey's manuals: Bergey's Manual of Systematic Bacteriology, and Bergey's Manual of Determinative Bacteriology. They deal with taxonomy and identification of bacteria (and even cyanobacteria and archaeans), with some emphasis on the medically important classes.