Sexing fish from a tissue sample I am a member of a local fish club, we have a lot of different aquarium fish and would like to trade them amongst us. We all have a few fish that don't form pairs and would like to see if they pair up with someone else's. But as you can imagine keeping track of all the fish would be extremely hard and pointless if they were the same gender, so someone suggested we should buy a microscope and sex them via tissue or blood sample. But none of us has any experience doing that or if that is even possible, so we need some expert advice on the matter.

I wish to know if you can tell the gender of a fish from a tissue or blood sample and what equipment do you need (how much magnification in a microscope)? We work with discus and other cichlids, and countless marine aquarium fish.

For the sake of being specific I restrict my question to Discus fish, however, I would like to know if any general principles of tissue-sample based identification exist, for different species of fish.

As already pointed out by Remi, you can identify the sex from a tissue sample only if there is a genetic (such as chromosomal) sex determination system (by using techniques such as PCR or in-situ hybridization). However, different species of fish employ different mechanisms of sex determination:

  Focus on or attachment to genetic systems involving X and Y
  chromosomes must quickly be shed in studies of sex determination in
  fish due to the diversity of mechanisms utilized, and, by doing so,
  the researcher can explore alternative regulatory mechanisms that hold
  important clues for understanding sex determination in general. The
  biology and ecology of fish is sufficiently diverse to provide unique
  examples of sex-determination mechanisms, yet they possess many of the
  same processes and pathways that are used in other vertebrate systems.

   Devlin, Robert H., and Yoshitaka Nagahama. "Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences." Aquaculture 208.3 (2002): 191-364.

Though Devlin and Nagahama comment (above) that fishes also employ the same signalling pathways as other vertebrates for sex determination, study of these pathways to determine the sex would be extremely difficult as you may be aware that the cell-signalling and the gene regulatory networks are highly complex.

Fishes are highly sexually dimorphic (including Discus) and the sex can be easily identified (with some practice) by visual inspection. Microscopic identification would be both money and time consuming. Morphology based identification can be automated (when the machine is trained sufficiently). You can have a look at this article1 which is about using image analysis to score salmons.

1.    Merz, Joseph E., and William R. Merz. "Morphological features used to identify Chinook salmon sex during fish passage." The Southwestern Naturalist 49.2 (2004): 197-202.


Figuring out if populations from two regions share the same Neanderthal haplotypes I am going to preface this post in that I am not sure if it belongs here, but considering it has been ignored everywhere else I have tried I thought it is worth a shot. I am a graduate student who is still relatively new to bioinformatics and is currently utterly and completely lost.

I am studying Neanderthal ancestry in modern populations from two different regions of the world. These two regions have relatively similar levels of Neanderthal ancestry, and they aren't that far from each other. I have SNP data from an Affymetrix genotyping array (the data are in Plink format) for these populations as well as for the corresponding sites from Neanderthal and Denisovan genomes.

Using the SNP data, I need to try to find out if they have Neanderthal haplotypes in the same parts of their genome. I've found a map of putative Neanderthal introgressed haplotypes from 1000 Genomes Project's European and East Asian genomes (http://akeylab.gs.washington.edu/Vernot_2014/all_haplotypes_populations.bed.files.tgz).

I am trying to figure out where the individuals from each regions have Neanderthal haplotypes and how they differ between regions. Does anyone have guidance on how I could proceed?

What I am saying here is the way I would approach the problem. And as such this post is meant to give you some direction. Please do not hold me responsible if you do not get the expected results.
First off, I don't know how the Plink format works, you would do well if possible to convert that to a BED/GFF/GTF file somehow.
I looked up the file format, and most of your columns are significance scores. For a start I would use the BH FDR & p-value as a preliminary filter and later use the Bonferroni corrected p-value.
Wiki link to FDR
The wiki link should also give you an idea why I say later on move onto bonferroni.
Interesting questions asked on cross validated for FDR

Provides a vague idea on FDR
Provides a relation between p-value and FDR: Re-read the answer a few times and you'll get it.
Check out the books if you want some understanding of Statistics

Using the SNP data, I need to try to find out if they have Neanderthal haplotypes in the same parts of their genome. I've found a map of putative Neanderthal introgressed haplotypes from 1000 Genomes Project's European and East Asian genomes

I looked up the file, these are regions with an average span of 73.4kb across the entire genome. So what you want to do is map the "statistically significant" SNPs from your plink file to these regions.
If you don't know how, check out the UCSC genome browser. A detailed step by step would be too big an answer, but the overview goes something like this;

Choose your reference genome from assembly
Create two custom tracks, here you can upload your SNP data in bed format, which is the easiest to make. Link to format And add the existing haplotype population.bed file.
Go to intersection, to create an intersection between these two tracks.

This will give you an idea as to which of your haplotype regions are present in the population.
Ofcourse, it isn't that easy, because you have to make a consideration here. Do you choose to say the population is carrying that haplotype if a single SNP is present in a region which spans 73kb? That is more than the average size of a gene in Humans.
As far as the Neanderthal and Denisovan genomes are concerned. I would again point you to the UCSC genome browser where they have the Neanderthal and Denisovan assemblies and their corresponding variants mapped to the Human genome (assembly hg19). You can again get these files and see where the neanderthal/denisovan variants lie in the haplotype file using the same approach. Finally you can then use these two overlaps to find where your variants had mapped and if any ancient variants had mapped in the same region. You must also make consideration for Insertions and deletions within the genome, so the variants may not map at the same location but it will map nearby.
UPDATE

You can check out this link for retrieving allele frequencies from 1K genomes, for the overlapping variants. I never meant that you would use the bed files for finding allele frequencies. What I outlined is;

Use the haplotype population regions as a template and overlap your significant affy SNP variants on it.
Next, because the Neanderthal and Denisovan variants are mapped on the hg19 or hg18 assembly, you map back those variants to the same regions
Find the regions where an affy SNP and an ancient SNP exactly overlap

What I understand from your comment is, you have already done step one. And you want to know the allele frequencies for a particular ancient variant. You need to do step 2 and 3 before coming to allele frequencies.
Then you can look up the allele frequency of the variants which mapped exactly at a position which had an ancient variant in the 1K genome vcf files.


What differentiates neurons in different parts of the brain? For example: what makes a neuron in the hippocampus of the brain different from a neuron in, say, the amygdala, or the frontal lobe, or anywhere else in the brain? Do neurons in different parts of the brain have different structures, or are they differentiated solely by location?
By "different structure", I mean things like receptors that other neurons don't have and things like that.

During development of the brain neurons undergo several steps of differentiation. They transition from neuronal progenitors to mature neurons, resulting in different types of neurons, characterized most prominently by their primary neurotransmitter. During the differentiation, different genes are expressed, which in research is used to label specific cell types (to e.g. observe their distribution in the brain). Since timing is important in development and neurons migrate to their side of action, later born neurons often display different features than earlier ones. The final differentiation is also dependent on the environment, meaning surrounding cells can influence the outcome.

Not just neurotransmitters, also other surface molecules, types of synapses formed, morphology and many other genetic differences influence neuron function and their diversity. Each brain area has many different neuronal cell types, some are similar between brain areas, while others might be very specific to one area. As an example, there is a microRNA, expressed in only 6 neurons of the nematode worm C. elegans, that is essential for their specific function to sense CO2 by repressing other genes (publication).

Taking the example of your question, here is a paper on the diversity of GABAergic neurons in the amygdala (there are several different types of neurons having the same neurotransmitter but expressing otherwise specific markers, which results in different specific functions in the circuits). The author compares them to GABAergic neurons in the cortex (including hippocampus), where a similar function might be taken over by a different cell type (expression profiles are distinct due to different lineages and environments and can be labeled by different markers).


Possible to Gain More Weight than the Food You Eat I was wondering if it's possible to gain more weight than the mass of the food you eat. At a first look, this is impossible because of the principle of mass conservation, but are there other things to take into consideration?

For example, fat contains carbon. Does the body use the carbon we breathe to produce the fat necessary to store any energy we don't use? And a relevant question: how efficient is human fat at storing energy, compared to what humans normally eat?

No it is not possible.  Humans are heterotrophic organisms, which means that we use organic molecules (i.e., food) as a source of nutrients and energy.  We use the nutrients to add mass to our bodies.  These nutrients are the familiar carbohydrates, proteins, lipids (fats), etc...  During digestion food is broken down into simpler organic nutrient molecules that are then used to make our body tissues.

So even if we only used food for nutrients we could not gain more weight than the food we consume but note that the food is also used for energy. This means that some of the mass of the food that we eat is not used to add mass to the body but is "burned" as metabolic fuel.  The mass of the food used for energy is expelled from the body as waste in the $CO_2$ that we exhale and in the metabolic waste in the urine.

The carbon in the air is mainly $CO_2$, which is an inorganic molecule.  Only autotrophic organisms like plants can use inorganic molecules as a source of nutrients.  Since inorganic molecules usually contain less potential energy than organic molecules autotrophic organisms need a different source of energy.  Plants use sunlight.

Finally, fat contains about 9 Calories per gram whereas a Big Mac has about 2.4 Calories per gram so fat has almost 4 times the energy of a Big Mac.

(Calories are the amount of heat that is released if all of the energy in the organic molecules is released so it is an estimate of how much energy the body can get from food)


Get Parent GO terms of GO term vector? I have a vector of GOIDs that are specific GO IDs outputted from an enrichment analysis. I want to cluster my GOIDs by their parent GOID term. I used GOstats to do my enrichment analysis, and I have noticed there is an inducedTermGraph, which outputs a graphNEL object of direct children and direction parents of the GOIDs you query. If you set parents=TRUE and children=FALSE, your graph includes only parent nodes which relate to your GOID query.

However, how can I extract the node names of these parent nodes??? See code below:

gene.ids <- c(51141, 84968, 140850, 388289, 406994, 677828, 693217, 100287428,
             100505685, 100506540, 101926966, 101927244, 101928659)
require(RnBeads)
uids <- rnb.get.annotation("genes")
uids <- sort(unique(as.numeric(na.omit(unlist(sapply(unlist(uids)$entrezID,
        function(i) strsplit(i, split=";")))))))
params <- new("GOHyperGParams", annotation = "org.Hs.eg.db", geneIds = gene.ids,
             universeGeneIds = uids, ontology = "BP", conditional = TRUE,
             testDirection = "over")

res <- tryCatch({
    hyper.genes <- hyperGTest(params)
  }, error = function(ee) {
    print("Errorfests.")
  })

go.ids <- summary(hyper.genes)[,"GOBPID"]
result <- inducedTermGraph(hyper.genes, id=go.ids, children=FALSE, parents=TRUE)
nAttrs <- list()
z <- attributes(result)$nodes
    names(z) <- nodes(result)
    nAttrs$label <- z
plot(result, nodeAttrs=nAttrs)

To answer @RickBeeloo's comment above I decided to include an answer with some detailed code. Basically to obtain the ancestors of any Gene Ontology (GO) term using the Bioconductor package GO.db we need a call to the AnnDbBimap object for the adequate ontology. For example if we want it for Molecular Function (MF) we would use GOMFANCESTOR like in the example:

library(GO.db)

terms <- c("GO:0008022","GO:0001071")
as.list(GOMFANCESTOR[terms])

$`GO:0008022`
[1] "GO:0005515" "GO:0003674" "GO:0005488" "all"

$`GO:0001071`
[1] "GO:0003674" "all"

Similar objects can be used for Biological process (BP) and Cellular compartment (CC): GOBPANCESTOR and GOCCANCESTOR. The only limiation is that you cannot mix terms from different ontologies (i.e. all BP, MF or CC). There are similar options to obtain the children of any given GO term (e.g. GOCCCHILDREN). The description of each term can be obtained with:

Term(GOTERM[terms])
                   GO:0008022                                           GO:0001071
 "protein C-terminus binding" "nucleic acid binding transcription factor activity"

All available mappings can be listed calling GO():

GO()

Quality control information for GO:

This package has the following mappings:

GOBPANCESTOR has 28477 mapped keys (of 28477 keys)
GOBPCHILDREN has 16829 mapped keys (of 28477 keys)
GOBPOFFSPRING has 16829 mapped keys (of 28477 keys)
GOBPPARENTS has 28477 mapped keys (of 28477 keys)
GOCCANCESTOR has 3897 mapped keys (of 3897 keys)
GOCCCHILDREN has 1317 mapped keys (of 3897 keys)
GOCCOFFSPRING has 1317 mapped keys (of 3897 keys)
GOCCPARENTS has 3897 mapped keys (of 3897 keys)
GOMFANCESTOR has 10021 mapped keys (of 10021 keys)
GOMFCHILDREN has 2046 mapped keys (of 10021 keys)
GOMFOFFSPRING has 2046 mapped keys (of 10021 keys)
GOMFPARENTS has 10021 mapped keys (of 10021 keys)
GOOBSOLETE has 2012 mapped keys (of 2012 keys)
GOTERM has 42396 mapped keys (of 42396 keys)

Additional Information about this package:

DB schema: GO_DB
DB schema version: 2.1
Date for GO data: 20160305


Goodwin oscillator explained Hello I have been reading papers about the Goodwin oscillator and I found that the equations are kind of tricky. Specially the part of the hill coefficient. In his paper "An entrainment model for timed enzyme synthesis in bacteria" from 1966, in the part of the differential equation of the mRNA concentration Xi, there is the term Zi and this term also exists in other books that talk about this oscillator. However, I don't know what it means. Goodwin never mentioned what this term means. I'm guessing it is about the hill coefficient, but still I do not quite understand well.
I share the link of a chapter book that explains the equations of this oscillator (page 244):

Biochemical Oscillations

Thanks for your help.

The ODEs for the Goodwin oscillator are:

$$\begin{align}
\frac{dX}{dt}=&\ k_1\frac{K_i^n}{K_i^n+Z^n} -k_2X\\[1em]
\frac{dY}{dt}=&\ k_3X-k_4Y\\[1em]
\frac{dZ}{dt}=&\ k_5Y-k_6Z\end{align}$$

If you assume $X$ to be mRNA and $Y$to be protein then $Z$ can be thought of as an activated form of the protein (lets for instance assume a phosphorylated form).

The Hill coefficient, $n$ roughly tells you how many monomers of the activated protein co-operatively bind to the promoter or the number of protein monomers that form a multimeric repressor complex which inhibits the production of $X$. $K_i$ is a measure of how strongly would $X$ be inhibited by $Z$. To be precise it is equal to the concentration of $Z$ at which the production of $X$ is half its maximum rate. (Similar to Michaelis constant)

What the model says is that at higher values of $n$ (>8) there are sustained oscillations (which are called limit cycles). At lower values the oscillations damp. Note that even for low values of $n$ sustained oscillations (but not limit cycle types) can arise if there is substantial delay in the loop. However these oscillations are not as stable as limit cycles to perturbations.

Have a look at this post.

These are some advanced concepts and you may start by reading this book by Steven Strogatz called Non-linear Dynamics and Chaos*.

*Strogatz, Steven H. Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering. Westview press, 2014. (latest edition);  ISBN-13: 978-0813349107; ISBN-10: 0813349109


How does one insert cas9 into animal cells? How could cas9 be inserted into cells by researchers looking to edit a genome? I imagine for engineering bacterial systems you could just put in the cas9 coding region in an expression vector, but is that how it is also done for eukaryotic cells?

If you are talking about the nuclease functionality of Cas9, then you aren't adding the Cas9 gene into the genome, you are transfecting it on a plasmid. Usually there is either some form of permeabilization done to the cells, or the construct is inserted into a viral vector in order to transfect the cells in tissue culture. In multicellular animals, you would need to use the viral vector route as would need to be done with any gene therapy technique. Addgene is a nonprofit plasmid repository that has many of the CRISPR/Cas9 constructs that have been developed, and they have an excellent resource on their Website.

You wouldn't really want Cas9 active in the cell after it has done its job, as you increase your likelihood of off-target hits. The target shouldn't be in the genome anyway if the targeting event occurred, because you have either substituted in another piece of DNA or you have cut the DNA and the DNA repair mechanisms have introduced random nucleotides in order to repair the double stranded break.

Eukaryotic cells, for the most part, cannot maintain plasmids. The Cas9 gene will be transcribed along with the guide RNA. The resulting protein/RNA complex targets the sequence of interest and makes a cut. When the cell replicates the plasmid will likely be lost, but the daughter cells will inherit the genomic edit made by the targeting event.

If you are looking to insert a different gene at the target site, say a reporter into the genome, then you co-transfect a linear piece of DNA with homology arms around the cut site so that that donor will be inserted via homologous break repair.

One of the Cas9 constructs that has bene developed has disabled the nuclease activity, so that the Cas9/RNA complex ends up acting as a binding protein to suppress the activity you are looking to study without actually deleting or replacing the gene. In this case you may look to insert the Cas9 cassette, in which case you would use a recombination event as you would with any other type of incorporation into the genome.


Absorption of digested food in small intestine My book says

  glucose , galactose and amino acids are transported into cells of villi via secondary active transport(sat). Fructose is transported by facilitated diffusion(FD) .short chain fatty acids , vitamins diffuse into cells of villi. From there all these are transported to blood by FD.

This site says the reason for using SAT: http://www.phschool.com/science/biology_place/biocoach/biomembrane1/glucose.html

But I want to know why fructose, vitamins and short chain fatty acids do not need S.A.T. and travel via FD (or just diffusion)?dont they get reabsorbed into small intestine ?

In general:

Hydrophilic/polar/charged molecules require some kind of assisted transport across a membrane
Hydrophobic/nonpolar molecules can easily diffuse across a membrane

Glucose, galactose, and amino acids are hydrophilic. Fructose, fat-soluble vitamins, and short-chain fatty acids are hydrophobic.

Glucose and galactose have similar structures (aldose/pyranose) and are both hydrophilic. Fructose has a slightly different structure (ketose/furanose) which affects the way it is transported. Basically, it has a ketone (rather than an aldehyde) so it is relatively less reactive/polar. Because it is hydrophobic, it can diffuse across a membrane more easily.

"Since the concentration of fructose is higher in the lumen, fructose is able to flow down a concentration gradient into the enterocytes, assisted by transport proteins." (Wikipedia) Based on this statement, it seems that the lumen maintains a higher [fructose], relative to the enterocytes.

As explained in your link, glucose is mediated via SAT to ensure one direction of transport: we want glucose going only INTO our bloodstream. The [glucose] in lumen decreases after a meal, but we want glucose to keep being absorbed (hence SAT).. Also, unlike fructose, glucose and galactose are highly regulated for use in glycolysis, so it is important to keep glucose in the appropriate cells. In particular, because of its structure, fructose enters glycolysis after the "rate-limiting" phosphofructokinase step in glycolysis.

Quick notes on fat-soluble vitamin and short-chain fatty acids: they're both relatively small and hydrophobic. Short-chain fatty acids can easily diffuse across a membrane, which is also made of lipids. (I recommend reading about hydrophobic effect if you want to know more about this).. Larger fatty acids require shuttles because of their size.

Regarding "reabsorption" into the small intestine:
Diffusion is the result of the random motion of particles. The more collisions in a higher concentration region eventually leads to a net movement "down a gradient." Using this logic: at some point, yes, the molecule may go back out into the lumen or go back in ("reabsorb") because it basically follows the gradient.

(I may come back to this post after learning more about it in a few months.. I used most of my answer based on what I learned in nutrition, o-chem, biochem)

Read more here about fructose metabolism


Why is the 3'UTR region highly methylated in most of the human genes? Most of the human genes are found to be highly methylated in their 3'UTR region (0.8-0.9%). I was wondering if there is any specific reason for this?

According to Choi et al. Genome Biology 2009, 10:R89, DNA methylation at both coding boundaries may regulate transcription elongation and stabilize splicing by reducing the occurrences of exon skipping.

From the abstract:

  Here we report a genome-wide observation of distinct peaks of
  nucleosomes and methylation at both ends of a protein coding unit.
  Elongating polymerases tend to pause near both coding ends immediately
  upstream of the epigenetic peaks, causing a significant reduction in
  elongation efficiency. Conserved features in underlying protein coding
  sequences seem to dictate their evolutionary conservation across
  multiple species. The nucleosomal and methylation marks are commonly
  associated with high sequence-encoded DNA-bending propensity but
  differentially with CpG density. As the gene grows longer, the
  epigenetic codes seem to be shifted from variable inner sequences
  toward boundary regions, rendering the peaks more prominent in higher
  organisms.

Their data (figures 1 and S2), however, do not support a generalized increase in the 3' UTR regions in either human T cells, mouse liver, yeast or flies.


Salbutamol's Pathways of Interaction and Classification Salbutamol is a very commonly used direct-acting β2-agonist.
This suggests me that it is sympatholytic.
However, it has sympathomimetic pathways, see PubChem for Sympathomimetic.

I am trying to think the group of Salbutamol.
Sympathomimetic or sympatholytic.

How can you classify Salbutamol into a group?

An agonist works with the receptor: a substance that initiates a physiological response when combined with a receptor; in the case of salbutamol (or albutarol in the US) they activate the beta-2 receptor on the muscles surrounding the airways. They are also known as sympathomimetics, as they imitate β2 adrenergics.

A blocker (or antagonist) is one that that blocks the action of endogenous catecholamines; for that reason, they are also called sympatholytic: antagonistic to or inhibiting the transmission of nerve impulses in the sympathetic nervous system.

It appears you have experienced a simple confusion in terms. Salbutamol/albuterol is definitely a sympathomimetic, used extensively on asthma and COPD.

Pharmacology and Therapeutics of Bronchodilators


Why is there a distinction between an *allergic* and an *immune* response? Our immune system has evolved to protect us against potentially dangerous non-self particles. I have difficulty in understanding why there is a distinction called an allergic response: what’s wrong with using the term immune response full stop? Surely a person’s immune system should react to a particle of grass pollen in EXACTLY the same way as it does to a non-self protein expressed on cells of some transfused blood. The mystery that I absolutely don’t understand is why our body can then differentiate the scale of the response.

The trouble is, you can't live without being exposed to all sorts of non-self particles. Some of those particles signal an actual threat to your health (proteins associated with a disease causing virus), some are nearly harmless (bee stings), some are completely harmless (grass pollen or cat dander), and some are potentially valuable as part of a food substance (seafood or peanuts). Ideally you'd like your immune system to respond to the harmful ones, and ignore the harmless or useful ones. An allergy is defined as an unneccesary immune response to a harmless (or nearly harmless) substance.
You do want your immune system to deactivate venom from a bee sting, but you don't want it to react so strongly that as a side effect your throat swells up and you can't breathe. Most people breath in grass pollen every day of their live with no ill effects, so those folks who have an allergy to grass pollen are being made miserable by their immune system to no good purpose.
Ideally the immune system mounts a full response only when the presence of particular non-self particles is associated with other signals indicating that something "bad" is happening which merits an immune response. However, the process by which the immune system is regulated is incredibly complex, involving feedback loops from hundreds of different chemical pathways and dozens of different cell types. The process is imperfect. Sometimes it goes wrong, and the immune system mounts an aggressive response to a harmless foreign substance or even worse part of your own body.


Does LSD "stay" in your fat storage and then "returns" back? This rumor was told me by a very anti-drug person. A stance I agree with only lightly.
The rumor was that when you take LSD, it stores itself in your fat storage, and then returns back in 3-6 months, returning back meaning there would be another series of effects of LSD (the trip).
Is this true? I highly doubt it. However, what I don't know, if the body is processing (burning?) fat and then processing substances (such as the rumoured LSD) found in fat stores.

I've heard this rumor for years, both from pro- and anti-drug people, and it is not true. According to this review of LSD's pharmacology, its half-life in the body is about 5 hours, with it being completely cleared within about 15-28 hours. There is no evidence that it accumulates long-term in fat, cerebrospinal fluid (CSF), or anywhere else in any pharmacologically significant quantity.
Reference:
"The Pharmacology of Lysergic Acid Diethylamide: A Review" CNS Neurosci Ther. 2008 Winter; 14(4): 295–314. PMID: 19040555 DOI: 10.1111/j.1755-5949.2008.00059.x


Why is an initiator tRNA required, distinct from the methionine tRNA used in elongation? I'm confused by why there is a need for different tRNA-methionine complexes for translational initiation and elongation.

This paper mentions that

  It is important that each type of methionyl tRNA be restricted to its separate function, as competition for tRNA by the initiation and elongation machinery could lead to serious problems for the cell

I don't understand what these problems may be.

I think the key to understanding this is to appreciate how different the initiation process is from the rest of translation.

The 30S ribosomal subunit recognises start codons via an interaction with the Shine-Dalgarno sequence that lies upstream in the mRNA. The remaining steps of initiation involve recruiting fMet-tRNA and, critically, placing it into the P site of the ribosome. In contrast, during elongation, aminoacyl tRNAs enter at the A site before their amino acid cargo is joined to the growing polypeptide which is held in the P site as a peptidyl tRNA. So you can see that the initiation process is special because of the need to prime the whole translation process by placing the first 'peptidyl' tRNA (actually N-formylmethionyl tRNA) into the P site.

There are two tRNAs for methionine, tRNAfMet and tRNAMet, and only the former is a substrate for the enzyme methionyl-tRNA formyltransferase. This effectively partitions the supply of methionine into two separate pools, one for use in initiation and one for use in elongation. In fact you could argue that initiation involves a different amino acid (N-formylmethionine) which is also coded by AUG.

Since an N-formylmethionine is essential for initiation, the simplest alternative would be to have a situation where a single species of methionyl-tRNA was a substrate for the transformylase. This would mean that N-formylmethionine would have to be allowed into the A site, and all those formyl groups would have to be subsequently removed from the internal methionines.

Update in response to comment from the OP

Having re-read the original question, I can see that I jumped the gun and actually answered a different question. The real question is much deeper.

Firstly, although the details differ, both bacteria and eukaryotes feed methionine through separate pathways for initiation and elongation.  Bacteria are discussed above; eukaryotes channel methionine through two different pools of tRNA, tRNAiMet and tRNAMet. Clearly this channelling is a universal feature of translation systems.

Next, let's look at tRNAMet abundances in E. coli. Since all protein-coding genes have a single start codon and, on average, a few internal methionine codons, we might anticipate that there would be more tRNAMet than tRNAfMet. But this isn't the case: according to Dong et al 1996 tRNAfMet is present at around 3x the level of the elongation species.

This suggests to me that there is something inherent to initiation that requires a higher level of the corresponding methionyl tRNA. Now you might say that this discrepancy is rather small but bear in mind that one of the properties of Met-tRNAfMet is that is easily rejected by elongation factors (reference). This is important because any charged tRNA can enter the A site before being compared to the current codon. By being easily recognised as 'wrong' for elongation, Met-tRNAfMet is, to some extent, excluded from the elongation process.

So far I have presented facts -  what follows are my own ideas.
If a single Met-tRNA species was used both for elongation and for initiation it would have to optimised for entry into the elongation process, spending time interacting with ribosomal  A sites. In order to maintain the level of free Met-tRNA required to drive initiation I conclude that much higher levels of this single Met-tRNA would therefore be needed. This in turn would increase the transient entry of this species into all A sites, and it would essentially act as an inhibitor of elongation.


How does an octopus eye react in free fall? according to Wikipedia:

  Attached to the brain are two special organs, called statocysts, that allow the octopus to sense the orientation of its body relative to horizontal. An autonomic response keeps the octopus's eyes oriented so the pupil slit is always horizontal.

so how would an octopus' eye react on the ISS (assuming the octopus has an aquarium or something it can live in)? In which direction would the eye be parallel to?

Statocysts are composed of a spherical structure with smaller granule statoliths inside; the orientation of these granules is recepted by cilia receptor cells. So in a situation like the ISS, statoliths would be randomly floating around, being recepted by cila receptor cells. At some times, the distribution of statoliths may be concentrated on one side, triggering random changes in the direction of the eye. So in this situation, the direction of the eye may be constantly changing.


Explaining natural selection in moth Industrial melanism is an example of natural selection. Can it be considered as a evolution due to anthropogenic action?

Evolution is a change in allele frequency through time. Alleles underlying moth melanism are changing through time in response to environment change, so indeed moths are evolving.

The environmental change is induced by human activities indeed. But the question of what is the cause of the environmental change causing the selection pressure is totally irrelevant to the question of whether there is such selection pressure.

Artificial selection is in essence the exact same thing than natural selection except that there is a goal (increasing milk production or making smaller dogs for example) that is decided by humans. In the moth example, the environmental changed is caused by human activities, but it has never been a goal for human to put selection pressure on moths to force them to change color. As a consequence, change in color melanism is an evolutionary process that is induced by natural selection, selection toward a new environment.

Evolution is not just the same thing as natural selection. The reason is that other mechanism than natural selection yield to change in allele frequency. One of them is genetic drift. You can have a look to this post to have a better understanding of what genetic drift is.

Hope that helps.


Using Canonical Correspondence Analysis on matrices with missing data I have a matrix of sites where not all the environmental variables I want to assess were sampled. In other words, there are sites with the whole set of variables sampled, and there are other sites where just some variables were sampled. Does Canonical Correspondence Analysis work with missing data for the environmental variables? If it does, what would be the effect of not including the missing values?

First, you cannot fully analyze pair-wise correlations between your environmental variables with NA values, and therefore cannot fully discount including covarying variables. If this is the case, you will not be able to know which of the covarying variables is responsible for any trends in your data.

Second, I don't believe CCA will work with NA values -- you will either have to eliminate the observations containing those missing values or fill them in with column averages. However, both of these methods will have an impact on your results, so move forward cautiously.

Third, I wonder if CCA is even the way you want to go. nMDS (non-metric multidimensional scaling) is much less constrained than CCA. Additionally, it doesn't suffer from as many assumptions/limitations as CCA.

From McCune & Grace (2002):

  The following two questions can be used to decide whether CCA is appropriate: (1) Are you interested only in community structure that is related to your measured environmental variables? (2) Is a unimodal model of species responses to environment reasonable? If, for a specific problem you answer yes to both of these, then CCA might be appropriate

However, missing environmental data is still a problem in nMDS.


Are there any place in human body that safe to implant things and have large amount of blood run through? Suppose there was a fuel cell in the size of AAA battery that could convert human blood sugar into electricity. Assume it safe and efficient without causing allergic reaction. But to avoid the risk of it disintegrate and malfunction it should be put in a place that far away to any critical organ as much as possible. It also need to have large amount of blood to supply anytime

Which place in human body would be the best to put that device in?

No, there is no safe place.

Devices in contact with blood are subject to thrombosis and embolism. Even devices designed for bio/hemocompatibility are not 100% safe: they are used because the illnesses and diseases they treat are more dangerous than the side effects. Immune responses and platelet activation that occur in the vicinity of a device could also have effects elsewhere in the body, not just in the vessel you could potentially occlude.

Long term, these effects are reduced only because of healing over the exposed surface. You are proposing something which must be in constant contact with blood, which isn't really possible unless you plan to remove and clean it regularly.

On a side note, for the purposes you describe, there are already devices in development based on mechanical motion to do what you suggest (for example, the motion from walking) that are much safer and more feasible than using blood glucose, which is strictly in the realm of science fiction.

Lanzino, G., Wakhloo, A. K., Fessler, R. D., Hartney, M. L., Guterman, L. R., & Hopkins, L. N. (1999). Efficacy and current limitations of intravascular stents for intracranial internal carotid, vertebral, and basilar artery aneurysms. Journal of neurosurgery, 91(4), 538-546.

Wendel, H. P., & Ziemer, G. (1999). Coating-techniques to improve the hemocompatibility of artificial devices used for extracorporeal circulation. European Journal of Cardio-Thoracic Surgery, 16(3), 342-350.

Werner, C., Maitz, M. F., & Sperling, C. (2007). Current strategies towards hemocompatible coatings. Journal of materials chemistry, 17(32), 3376-3384.


What are golgi blobs? From a general google search I have come to know that golgi 'blobs'(also referred to as "golgi haze") are tubular vesicles formed during the interphase of mitosis.
I would like to be reassured and also learn more about this topic. If possible please include a diagram in your answer.

What are golgi?

Stacked array in the cisternae which are ought to connect vesicles and tubules
Made of >1000 different proteins
Has the ability to transform/alter in response to a cellular stimulation such as mitosis

Fragmentation of golgi during mitosis

  During interphase, the Golgi receives secretory cargo from the ER via the COP II vesicle formation pathway. Depending on their nature, secretory cargo then travel through the Golgi apparatus by a combination of vesicular transport involving COP I vesicles and cisternal maturation. A retrograde COP I vesicle pathway connects Golgi cisternae and the ER to allow recycling of Golgi enzymes and integral membrane proteins of the transport machinery such as the SNAREs. Two models have been proposed to explain the fate of the Golgi in mitosis. The first is the direct fragmentation model, where Golgi cisternae are consumed by continued COP I vesicle budding in the absence of membrane fusion, which is blocked in mitosis. This generates a pool of tubules and vesicles (Golgi haze) containing Golgi enzymes and structural proteins. The second is the ER recycling model, where forward transport into the Golgi by COP II vesicles is blocked, but COP I recycling back to the ER continues until Golgi proteins are redistributed to this compartment. Some Golgi proteins may then exit the ER via the COP II pathway, but these vesicles are unable to fuse with a Golgi compartment during mitosis, and remain in equilibrium with the ER.

A more detailed outline of the process of fragmentation of golgi apparatus can be found here and here

As I know "golgi blobs" are also referred to as "golgi haze".

Sources:

http://www.clfs.umd.edu/classroom/mocb639/Hamza_Golgi_Apr5_2005.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175146/
http://www.cbi.pku.edu.cn/chinese/documents/cell/xibaoshengwuxuecankaowenxian/cocb/15/15-4/15-462.pdf


Why are mules/donkeys aggressive when faced with predators but horses are not? I came upon an interesting quote after going down the rabbit hole on a variety of subjects. While deep in the data, I came upon this quote

  oat and farm animal owners likes to have mules with their herds because donkeys or mules will actually attack predatory animals such as foxes and coyotes.

Which raised quite a few questions in my mind. I was able to find additional sources as it relates to the predisposition of the given species.

Seemingly, donkeys and mules will act aggressively in confrontation with predators and attempt to attack to the point of killing many of them. Is there something about the physiology of a donkey/mule that makes them much less timid? Perhaps body structure? Seemingly a horse has equal or even better tools to try and defend itself.

Here are the sources (the first 2 are not the most authoritative by any means):

 Mule Behavior: Differences with horses and donkeys
Mule Facts
Donkey Behavior: A comparative study of donkey and horse behavior

So horses, donkeys, and zebras are all of the genus Equus. Mules are not a species, since they are the product of the cross-breed between horses and donkeys, and are sterile (therefore do not comply with the biological interpretation of species).
Given that 2 out of the 3 species from the species of the genus Equus are aggressive against predators (zebras see reference and donkeys), it might be possible that the "aggressive" behavior is the ancestral trait of the genus, and horses evolved afterward the behavior of fleeing before fighting. Furthermore, it looks like the "aggressive" trait is dominant over the "fleeing" trait since mules (cross-breeds between horses and donkeys) inherit the aggressive trait. There are no sources that necessarily say that a dominant trait is associated with ancestral (common ancestor) provenance, but for the case of single genes, this is the most likely scenario.
So if we think that horses evolved the trait of fleeing before fighting (being the "aggressive" trait the ancestral one), then one should ask why did they evolve such behavior (why is a cringy word for evolutionary biologists, but serves the purpose here). And this is probably due to the exposure horses had to different types of predators. I wouldn't be surprised if horses had more contact with human beings than donkeys or zebras, thus they evolved this behavior as a way of coping with extensive hunting.
Alternatively, some traits are not "modular" traits that can evolve independently from other traits. More often than not, complex behaviors, like the "aggressive" trait, are determined by a large number of genes, some of which have phenotypical effects elsewhere. This means that if a species has a "selective pressure" for one trait, other traits can also be modified over time as a causal effect of this selective pressure. Horses were domesticated long before donkeys were, and zebras haven't been domesticated at all. Domestication is usually conferred by a process of selectively breeding individuals that express the least amount of aggressiveness, or show signs/traits of "neoteny". If horses were selected to produce neoteny in the species, the non-aggressive behavior might also have been selected as a causal effect of this selective-breeding.  This would explain why horses, which have been domesticated way before donkeys have, do not show aggressive behavior as donkeys or zebras do.


What is GST RhoA fusion protein? Would you please explain to me what GST RhoA fusion protein means and how it differs from RhoA protein? I am a kind of doing an experiment using this protein.

GST is glutathione-S-transferase, an enzyme that binds reasonably tightly to glutathione. It is often used as a tag to purify proteins of interest. In your case, GST has been fused to RhoA most likely so that you have some means to purify it by applying it to a glutathione conjugated column. See here for more information.


Why is burn feeling 'slower' than touch? When you touch a hot object you first feel the touch and only after a second you feel the burn too, and if you detach your skin from the object the burn feeling continues for few seconds. I remember i've read something about why this occurs (something like 'burn neurons are slower than touch ones') but it's just a faded memory.

So i'd really appreciate your answers.
Thanks in advance :).

When you touch an object, a compression wave from the collision travels through your body at the speed of sound.  A sensor at any depth in your skin can pick up that signal at roughly the same time as the collision.

When you touch a hot object, heat from it moves into your body via conduction and to some extent radiation.  That heat flow moves much more slowly than the compression wave.  It will take longer for the heat pulse to reach a sensor that is deep in the skin and raise the temperature by a sufficient amount to cause signalling.

There may be further differences in the sensory neurons or in the reaction to the signals.  But there is a physical reason for the temperature signals to lag touch signals from the same object.

"Thermoception and Temperature Regulation" edited by J. Bligh, K. Voigt has some discussion of a study of thermoreceptors in rabbits.  It suggests both that

signal latency increases with increasing depth in skin
while most receptors has short latency, some receptors had much greater latency, and that this disparity in response may aid in determining temperature gradients within the skin, not simply reading instantaneous skin temperature.


ligand binding fluorescent protein does anyone know of a fluorescent protein that upon binding of a substrate its fluorescence is activated? i've been looking on this and perhaps my keywords are not the right  ones. Thanks in advance

There are only 3 classes of fluorescent proteins proteins known I think.  Two of them are relevant to your needs maybe.

The first are usually called 'fluorescent proteins'.  These proteins are usually derived from the A victoria jellyfish.  Its entirely passive in its fluorescence, but has been tuned to many levels of quantum yield and color.

There was a new sort of fluorescent protein cloned recently from japanese eels.  It is activated by binding to bilirubin.  Its so new that its not likely to be available, but there you go.

The third class would be the luciferases.  They are luminescent, not fluorescent but in producing light involves binding from a cofactor called luciferase which is oxidized to produce their light.  This is not really fluorescence since the electrical stimulation that causes light production is not from incident light, but since what you are looking for might not exist I wanted to remind you of the luciferases, which bind their redox substrates to activate.  The luciferin molecule actually varies as there are several classes of luciferase.  I think Flavin and NAD are the most common substrates.


Does pupil size affect image focus in persons with no lens? If an individual has no lens like Claude Monet (who had them removed).

They should be able to still focus the images they see in a well light area if they shrink their pupils to a very small size like the Moken people right?

But they won't be able to see well at all in dim light, as focusing would require them to dilate their pupils which would make everything  very blurred.

Is this right?

Very nice question! You are right, in that small pupils will help to reduce the blurriness of vision caused by refractive errors.

Removal of the lens (aphakia) results in farsightedness. It is caused by a focus point that falls behind the retina as the absence of the lens prevents focusing of the image, causing a blurred image. The amount of blur is proportional to the pupil size (Colichia et al., 2008). See their figure 2 below:.

In the upper part you see a hyperopic eye, which has a lens that cannot accommodate sufficiently, comparable to an aphakic eye. the bottom part shows the result of when a pinhole is applied, namely a reduction of the blurred circle and improvement of the focus. This could also be achieved by having very small pupils such as when ambient light is very bright (and a characteristic of the Moken peoples when diving (Gislén et al., 2003). And indeed, under conditions of low lighting the pupil size will increase and hence blurring will be worse.


Why is dopamine or a dopamine-receptor agonist not pumped into the brain of Parkinson patients? I am aware that dopamine cannot cross the blood-brain barrier, but can't it be pumped inside the cerebrospinal fluid via some permanent tube implant? Wouldn't Parkinson patients chose that over succumbing to the disease? Why hasn't it even been ever tried?

Levo-Dopa is used as a first-line treatment of Parkinson's disease. Unlike dopamine, L-Dopa is able to cross the blood-brain barrier. There it is converted into dopamine. To prevent premature breakdown in the gastro-intestinal and circulatory system after oral intake, carbidopa can be co-administered. Also MAO-B inhibitors and COMT inhibitors can be applied to prevent breakdown of L-Dopa in the brain. Oral medication is preferable over invasive intracranial infusion of medication.

Conversion of L-Dopa into dopamine. Source: ADHD treatments.

Dopamine agonists are also in use. Unlike L-Dopa, dopamine agonists are not converted into dopamine. Instead, they mimic dopamine effects in your brain. They aren't as effective as L-Dopa, but they last longer and may be used alongside L-Dopa to smooth the sometimes off-and-on effect.

Parkinson's disease is not fatal, but it can reduce longevity. The disease progresses more quickly in older patients, and may lead to severe incapacity within 10 - 20 years. Older patients also tend to have muscle freezing and greater declines in mental function and daily functioning than younger people. L-Dopa treatment in the long run causes adverse effects, such as dyskinesias, toxicity, or loss of efficacy (Marsden, 1994).

Reference
- Marsden, Clin Neuropharmacol (1994); 17: S2:S32-44


Do ants have a "stay away" signal? Last night I discovered many ants entering my house through a window with an imperfect seal. I placed a poison ant bait on the window sill and within seconds they were feasting on it. This morning I noticed there were still many ants near the bait, but they were all bypassing it as if they were somehow warned to stay away. Do they have such a signal? If so, how would they know the bait is a problem? If not, what could cause them to be so interested last night and not interested at all today? (I can see that there is still plenty of food inside.)

Update: after a little bit more research, I decided that ants do not have a "stay away" signal, and that the only explanation for ignoring the bait would be a stronger scent trail leading somewhere else. Last night when I opened the window I found the jackpot. There was some sort of sticky substance all over the bottom of the window, and hundreds of ants celebrating the find. My conclusion is this was much more attractive than the bait, even though it was merely an inch away from their path.

It is a long time since I set in a Computer Sci (AI) talk about this….  This explains it a bit.

Once ants have eaten they return to the nest.
On the way back to the nest they put down a scent.
This scent fades with time.
Most ants follow the scent.
(A few ants walk randomly to find new food, or a new faster way to the current food.)

So if the agents eating your poison bait do not make it back to the nest, there is no scent trail leading to the poison for more ants to follow.     But the ants that went round the bait to find other food, did make it back to the next, so setup a new sent trail.

If a poison kills the ants quickly, the customer is likely to see dead ants and therefore buys more of the poison.   However a poison that kills the ants slowly, so the ants don’t die until they get back to the next, is likely to get more of them, as there is now a strong sent tail to the poison.


Taxonomic clasification of BLAST output I am working with Next Generation Sequencing. I BLASTed the bovine de novo assembled contigs to the NCBI nucleotide database. I got a matching with a lot of species i.e. different kind of bacteria, viruses and mammals. I want them to group in a logical way i.e. all the bacteria in one group (bacteria group) similarly viruses and mammals. This is hard to arrange manually, can anybody help how I can arrange my vast number of species into some logical grouping. Thanking in anticipation.

This is basically metagenomics.
Congratulations, you already did the most time consuming step.
There are several ways to go from there, but I will talk about the one I know best.
There is the metagenomic analysis tool MEGAN. It can read your Blast Output, if it is in the correct format (normal XML or tabular) and will automatically do what you want.
For a start, just use the default values, for more help you an then go to the Community Website of MEGAN for help.

Analysing your data may take a little, depending on how many contigs you have. But if you were able to blast them in reasonable time it should be no problem. As I said, you are through the most time consuming step already.


Is prion a term used to describe the normal form of the protein as well as the disease causing form? I've been reading my textbook and it refers to prions as a normal protein with a helpful function but it can turn into a disease causing form. However, I look in my other textbook and it refers to the word prion as solely being a disease causing protein.

I'd like to know which is the correct definition. Ie. Would I be correct in saying "The prion protein is normally involved in synaptic transmission but can turn into a disease causing form"?

Thanks in advance!

The normal isoform of the protein is called PrPC, which stands for cellular prion protein, while the infectious isoform is called PrPSC, which stands for scrapie prion protein.

According to Riesner (2003):

  The biochemical properties of the prion protein which is the major, if not only, component of the prion are outlined in detail. PrP is a host-encoded protein which exists as PrPC (cellular) in the non-infected host, and as PrPSc (scrapie) as the major component of the scrapie infectious agent. (emphasis mine)

If you search for "cellular prion protein" you're gonna find several papers that use the name prion protein to the normal isoform. Some examples:

Prado, M., Alves-Silva, J., Magalhães, A., Prado, V., Linden, R., Martins, V. and Brentani, R. (2004). PrPc on the road: trafficking of the cellular prion protein. Journal of Neurochemistry, 88(4), pp.769-781.
Ramljak, S. (2008). Physiological function of the cellular prion protein (PrPc_1hnc). 1st ed. Berlin: Logos-Verl.
Pantera, B., Bini, C., Cirri, P., Paoli, P., Camici, G., Manao, G. and Caselli, A. (2009). PrPc activation induces neurite outgrowth and differentiation in PC12 cells: role for caveolin-1 in the signal transduction pathway. Journal of Neurochemistry, 110(1), pp.194-207.
Martins, V., Mercadante, A., Cabral, A., Freitas, A. and Castro, R. (2017). Insights into the physiological function of cellular prion protein.

And many others.

Therefore, following this nomenclature, the answer to your question ("Would I be correct in saying 'The prion protein is normally involved in synaptic transmission but can turn into a disease causing form'?") is yes. The difference is the adjective: cellular or scrapie.

Finally, pay attention to this: you have two different questions here. In the title you say "Is prion a term used...", but in the last paragraph you say ""Is the prion protein normally involved in...". As extensively discussed in the other answer, the term prion alone (instead of prion protein) is normally used only when referring to the abnormal isoform. More on that here: https://www.cdc.gov/prions/pdfs/public-health-impact.pdf

Source: Detlev Riesner; Biochemistry and structure of PrPC and PrPSc. Br Med Bull 2003; 66 (1): 21-33.


Difference between taking tissue of cancer from secondary place or primary place Are there any differences when a surgeon takes tissue from secondary place (for example from metastasis) rather then from primary place (from an organ where cancer is) for morphological research?

I would disagree a bit with the previous answer. There are absolutely differences between the metastasis and the primary tumor. One result of this is that people very rarely die of primary tumors, but rather from the metastases of those tumors. The primary tumors will be quite heterogeneous and contain largely cells that have not undergone steps necessary for migration like epithelial to mesenchymal transition. After cells have metastasized they will be separate from the original primary tumor, and contain unique genomes. Because this is the more 'progressed' group of cancer cells, these are often the cells that need to be targeted. So, determination of the proper treatment strategy should be done on the metastasized cells.


Im struggling to see how these are presynaptic terminals/knobs and not post synaptic How are these presynaptic terminals ? The action potential is generated at the axon hillock and moves down the axon (in this case to the right) , then at the end of the axon should be axon terminals and presynaptic knobs. Shouldn't the dendrites shown here have post synaptic knobs with receptors for the neurotransmitters ?

The fibers in green are axons and axon terminals from other neurons, not the one colored orange.

Yes, there would be post-synaptic structures associated with these but those are not drawn in this cartoon.


Is the Common Cold an Immune Overreaction? It's my understanding that the majority of symptoms associated with the common cold (runny nose, inflamed sinus, slight fever) are essentially the result of the immune system's response.

I've never heard of someone dying of the common cold (unlike influenza), even in immune compromised people. As such, what damage would the cold virus inflict if there was no immune response? Would it be catastrophic?

Can someone die of the common cold?

No.
The common cold is a clinical syndrome restricted to upper respiratory tract involvement. By clinical syndrome, I mean it is the constellation of symptoms (rather than the consequence of a specific pathogen). As you mention, these symptoms are the result of the immune response, rather than tissue damage or compromised function as a direct effect of a pathogen or its toxin (e.g., the watery diarrhea in cholera).

As defined (see, e.g., Cecil Medicine Ch. 369), this clinical syndrome cannot lead to death.

  The common cold is an upper respiratory syndrome of rhinorrhea and nasal obstruction, frequently accompanied by sore throat, sneezing, and cough.

Can the viruses that cause the common cold cause death?

Yes. Many viruses that cause the common cold also cause other clinical syndromes that can cause death. This occurs when viral replication moves to the lower respiratory tract. As an example, influenza viruses are responsible for 25 - 30% of common colds (see Bennett, Principles and Practice of Infectious Disease, Ch.58). When it moves beyond the upper respiratory tract, influenza is responsible for substantial mortality. Other virus families that are responsible for both a common cold syndrome and lower respiratory tract syndrome in immunocompetent individuals (e.g., bronchiolitis, pneumonia) include parainfluenza virus, metapneumovirus, adenovirus, and (rarely) coronavirus. Rhinovirus, responsible for 40-50% of common cold cases, is uniquely unsuited to lower respiratory tract involvement, because of its preference for the cooler environment of the nasal mucosa, replicating best at 33 C (Murray Medical Microbiology, Ch 56). However, in individuals with Severe Combined Immunodeficiency (SCID), lower respiratory tract involvement does occur. There are a number of case series reporting death due to lower respiratory rhinovirus. This is an example.

Can the common cold lead to serious illnesses other than lower respiratory tract involvement?

Yes. Other morbidity can occur as a result of the immune response that produces the common cold syndrome. Rhinorrhea and congestion can progress to a viral rhinosinusitis, a separate syndrome with its own complications, or a secondary bacterial infection, which can lead to bacterial sinus involvement and/or bacterial lower respiratory tract infection. Otitis media is another common complication, especially in children, and has its own potential complications. Asthma (and, generally speaking, most lung diseases) can also be exacerbated by what would otherwise be a simple common cold and predisposes to lower respiratory tract involvement. Asthma does deserve special mention, because rhinovirus associated exacerbations can be fatal, but this is a consequence of asthma rather than a common cold syndrome. Further discussion of these syndromes are beyond the scope of the question, but are discussed briefly in the chapters referenced above.


Immune response to IgA positive bacteria If certain bacteria can be coated with IgA in vitro, does that mean they are likely to elicit an IgA immune response?

Edit
I'm working on a project that involves IgA-Seq analysis. Bacteria are coated with IgA and then sorted for how much IgA they actually ended up having on them. I'm a biostatistician, so I don't know the biochemical details. But I'm assuming that the IgA binds to receptors on the surface of some bacterial more than others. I was wondering if that was related to immune response. I tried googling, but couldn't find much.

Depending on the precise details of the experiment, I don't see a particular reason to suppose that being coated with IgA should mean that they'll elicit an IgA response.
I'm assuming that the "coating with IgA" means that the IgA is binding like an antibody, through the variable region binding site on the antibody to some epitope(s) on the bacteria. The way antibody class switching works is that the epitope binding region of the antibody remains the same while the constant regions switch from IgM to IgG or IgA, etc. That means that the ability to bind to the bacteria appeared in a non-IgA antibody, so the ability to bind, per se, is more or less separate from the isotype of the antibody.
The factors that drive a response toward IgA are heavily influenced by location - a response on a mucosal surface is much more likely to drive IgA than one that's systemic (simplistically, because the cytokines and cell types involved are different in the different locations).
An alternate possibility is that the IgA is binding the bacteria through its constant (Fc) region, analogous to Protein A.  If the bacteria have evolved an IgA-binding capability in this way, one might guess that they did so because they need it as a defense, and if it's specific to IgA one might guess that it's because they tend to have an IgA-dominant response. But that's an inference, not a strong argument. As a counterargument to that, Protein A does (sometimes) bind to IgA and that's likely more of a side effect than a primary thing.
So I think the answer is "probably not, but you'd need more information to have a good answer."


Can a cell receive multiple copies of an insert when using different MOIs? I want to transduce a cell line with virus that carries a specific insert.
When using different Multiplicity of Infection (MOI), I expect to get different percentage of transduced cells, but is it possible to get more than one insert integrated in the cell genome?
I use high MOI and I always get 1 copy per cell, so I am not sure if increasing it a lot may also affect the number of in integrated inserts.

Yes, if you use a high enough MOI, you'll start to get double infections. Usually, anything >1 MOI will guarantee a high chance of double infections. If you're using a high MOI and only seeing single inserts, it might be due to your cells being difficult to transfect. If you look at this site: https://manuals.cellecta.com/lentiviral-construct-packaging-and-transduction/v10a/en/topic/lentiviral-titer-calculation it should give you a general reference for what % double transfected cells you should see. The difference between transfected cells and MOI % should estimate double infections assuming 100% efficiency.
Some cells are less efficient at being transfected, and it's a good idea to get a functional titer on your target cell line which is very easy if you have a fluorophore in the plasmid you're trying to insert.
I reread what you're getting at, and it's generally accepted that MOI under 0.4 won't give you double transfections.


Accurate Human Skull Model for Educational Purpose I want to buy a model of Human skull for education purpose. However, I really want a very accurate model and at a decent price. I got the info that many of the available skulls in the market are not accurate.  Can anyone suggest me one?

Also I want to know is there any regulatory body that certifies such
educational models regarding the accuracy etc.? If not then what is the way I can ensure that I am buying an accurate (or most accurate) model.

The best way to ensure you're getting an accurate skull, near as I can tell, is striking the "model" part of your question, and go straight for a real skull.

A cursory search revealed, for instance, Skulls Unlimited International, The Bone Room, and The Evolution Store although other providers probably exist as well.

A regulatory board for model skulls probably doesn't exist, given the apparent ease with which real skulls can be obtained and kept.


Evolution: One big population vs. many small populations Let's say I want to evolve a bacterium that is resistant to an antibiotic. I want to do this by growing initially clonal populations of bacteria in presence of this antibiotic for a long time.

I have two options:

Make one 50 ml flask culture
Make ten 5 ml tube cultures

What are the comparative advantages and disadvantages of these two? Clearly, the ten culture version is better at probing the space of all possible resistance mechanisms. However, what about the rate of evolution? If I just want to get a resistant strain as fast as possible, which one should I use?

Note that "antibiotic" is just a proxy for any selective pressure, and "bacteria" is proxy for any organism. If possible, I think it will be interesting to address the effects of sexual vs. asexual reproduction in the organism that is being evolved.

There is already a question, How does rate of evolution/innovation scale with population size? that is very similar. I think mine is different, because it is not one small population vs. one big population, but one big population vs. many small populations. In other words, I am attempting to control for number of selection/mutation events, and focus only on the stratification of the total population.

Note: This is not an area where I know the litterature well

Where are many counteracting processes to consider for this question. For instance, the rate of evolution will be affected by the rate of mutation, the distribution of positive and deleterious mutations, strength of selection, whether the fitness effects are small or large, if fitness effects depend on interactions between multiple mutations or single mutations with large effect, asexual vs. sexual populations, and processes such as genetic drift.

A recent review that is useful for your question is Lanfear et al (2014). They focus on how substitution rate is affected by effective population size, and go through both theoretical and empirical evidence. They conclude that in most cases, most mutations are deleterious, and that drift and selection are the most important effects in determining rates of evolution. They also state the effect of effective population size (Ne) is likely to depend if mutations are dominated by deleterious or advantagious mutations, and they expect the rate of evolution to be negatively correlated with Ne when deletious mutations dominate evolution and a positive correlation to Ne when advantagious mutations dominate.

A paper by Rozen et al (2008) indicates that while large populations are more effective in fixing mutations with large positive effects, small populations can be more effective in complex "rugged" adaptive landscapes.

  While such determinism speeds adaptation on the smooth adaptive landscape represented by the simple environment, it can limit the ability of large populations from effectively exploring the underlying topography of rugged adaptive landscapes characterized by complex environments.

However, this does not deal directly with the rate of evolution, but mostly about attaining the highest possible fitness in a particular fitness landscape. Another interesting paper is Desai et al. (2007), but I haven't looked through this yet.  However, they find (for asexual bacteria) that the speed of adaptation scales less than linearly with population size, and similar results have also been found in studies from Lenski's group. Their interpretation is that evolution is driven by multiple concurrent mutations of small effect and not one-by-one fixation of single mutations (which would favour large populations more).

For your case of evolution of resistance, I think one crucial thing is if you expect resistance to be driven by a few single mutations or combinations of many mutations that interact (related to whether resistance is "easy" or "hard" to evolve). From what I understand, the first case should favour a single large population (since they will fix mutations for resistance more quickly), while the second case might favour many smaller populations (since you might get more effective exploration of combinations of mutations)

These are just a few starting points in a very large field, and I hope that you find them useful.


What kind of spider is this? Found in my house in a Beltsville Maryland

I'm 90-95% certain that the spider in question is a Trachelas tranquillus, more commonly known as a "Broad-faced Sac Spider".

Broad-faced sac spiders are quite distinct in coloring; they have a dark gray/brown head (cephalothorax) with tan/light-gray abdomen, orange/red legs, and distinct pincers (which can be seen if you look closely). These spiders are also quite common for your area, and aren't a major threat to humans.

EDIT: I would like to mention that the images I provided (most likely) have enhanced lighting, and/or are much closer to the spider, so the leg color is (expected to be) lighter than what's depicted in your image.


What is the biochemistry of love? How is love induced between humans? Say, between mother and child, couples, etc.
Does the phenomenon of love exist in other mammals, too?

"Love" is a subjective phenomenon that can't really be applied to non-human animals because we can't ask them about their subjective experiences. However there is some clear evidence, especially in more social mammals, of caring behavior and social bonds for other conspecifics.

As far as biological basis, I suppose you could consider it biochemistry, the peptide hormone oxytocin is correlated with formation of social bonds between animals of many species (although Wikipedia isn't the greatest source, you will find this particular page is saturated with links to scientific literature). I would caution against the popular press treatment of oxytocin as "the love hormone" and caution against simplifying a complex set of behaviors to the action of one peptide, but certainly the evolutionary conservation and broad applicability suggest that this is indeed an important hormone in social relationships.


Do all human cells have all the same organelles? I know that not all human cells have nuclei (erythrocytes eject theirs before they are fully matured), but do all human cells have all the other organelles? The two I'm particularly concerned with are the Golgi apparatus and lysosomes.

I believe that yes.

Here is more to read about:
https://bscb.org/learning-resources/softcell-e-learning/golgi-apparatus/
"is found in all plant and animal cells"

and explanation why so
https://sciencing.com/would-did-not-golgi-bodies-8657737.html

I am no expert in this but I was looking for it as well, I believe it is right.


Fastest and slowest action potential When our instructor asked us about the speed of action potentials in cells, I told him that action potentials and two-wheelers travels at similar speeds. He thought that this is an 'interesting' way of looking at it.

Needless to say after the class I tried to figure out the minimum, average and maximum speed of action potentials in neurons. Wiki helped but its not authoritative. Some place it says that the fastest is 110 m/s and other place it is 120 m/s. While slowest one varies between 7 m/s (in Rana frog) to 0.5 m/s (Nociceptors) on Wiki. The average speed would be hard to calculate.

I am looking for any references where slowest and fasted action potentials are described. They would be interesting cases to write a note for classromm.

You can search on Bionumbers.

Here is what I got after searching action potential:

Speed of action potential along non-myelinated invertebrate axons of ~10μm diameter = less than 1 m/s
Action potential speed in myelinated axon = 50 ... 100 m/s
Velocity of action potential in pyramidal tract at 37°C (in Cat Felis) = 164 m/s

It offers you references for every number.


Is it possible to have cancer and normal blood count at the same time? Does cancer always cause abnormal full blood count? I've read on the internet that some people who had advanced cancer, also had normal blood count. I can't find anything on the internet about this topic.

Cancer doesn't have to have a profound effect on the blood. Remember that a cancer generally starts off as an abnormal tissue growth or a neoplasm. As the tumor progresses into a malignancy, it has the potential to gain or lose functions, develop new cell types that shouldn't be present in a given organ, invade other tissues, etc. Because of this, in some cases of cancer patients may be subject to paraneoplastic syndrome, or cross-reactivity between something the cancer is doing and the normal tissues.

In the above-linked source, some hematologic paraneoplastic syndromes include (1) eosinophilia, commonly associated with a number of cancers, (2) granulocytosis, often associated w/ lung cancer, (3) Pure Red Cell Aplasia, commonly associated w/ thymomas. The list goes on, but in some cases blood testing is capable of assisting in diagnosis, especially in cases where cancer of the blood is the culprit (very obviously). To also be kept in mind, they note paraneoplastic syndrome only affects around 8% of all cancer patients.

In other cases, you'll be monitoring treatment. As we know, chemotherapy is destructive, and can cause a depletion of platelets or neutrophils, damage organs, etc. Complete blood count (CBC) testing will help oncologists monitor treatments in cancer patients.

Being said: Because individuals with a tumor/cancer may fall within normal ranges in a CBC test, and because these tests must be analyzed scrupulously due to several factors that influence them such as diet, multiple tests are often needed to arrive at a meaningful conclusion. On the basis of cancer itself, however, if it's a solid mass lodged in the liver for example, it's completely possible that blood counts are normal. What you may find, however, are biomarkers in the blood that are saying "hey, the liver is being damaged or dying" such as the enzyme aspartate transaminase. If the tumors are currently small, you may not find anything meaningful in blood tests, or that the blood is "normal." (the possibilities aren't exhaustive)

As a matter of real data I was able to find, Spell et al. was at least able to find some efficacy in CBC testing for colon cancer, to 84% sensitivity and 88% specificity, but you should suspect that individuals may still be asymptomatic under such tests regardless.


Disproportion in cranial nerve innervation? The cranial nerve innervation is highly disproportionate, as far as humans are concerned.  I am not sure of the advantage of being innervated by cranial nerve versus being innervated by a normal spinal nerve branches, if any.

If there is any advantage to be innervated by cranial nerves, why is there such a largely disproportionate distribution of these cranial nerves?

  Only the Vagus nerve (X) innervates parts other than the head of the
  animal. While there are 3 motor nerves just for the 6 eyeball muscles
  and the ciliary muscles (III,IV,VI), there is only one mixed nerve
  (X) innervating heart, gastro-intestinal tract and the respiratory
  apparatus and all smooth muscles therein. While there are three nerves
  for gustatory receptors, (VII,IX,X), one for retina (II), cochlea
  and vestibule (VIII) and the olfactory receptors (I) each, the
  entire plethora of intero-receptors in thoracic and abdominal viscera,
  aortic arch, external auditory meatus, tympanic membrane etc are
  carried by a single nerve (X). I am not sure if the disproportion is limited to the disproportionate area of innervation or even to the density of innervation in the target tissue.

Below are a few possible explanations that I came across while surfing the net, all without any strong arguments.

Is it because of the fineness of the senses in the head, i.e. the skin receptors in facial skin being higher than in the general body, providing a finer resolution of tactile reception? The special senses (vision, hearing, smelling and tasting) are also very fine in their resolution and might require more concentrated innervation and direct interpretation by the brain. But then the fingers and feet also have a high density of skin receptors, and the tactile sense can also be very fine (owing to several different kind of receptors) requiring dense innervation? Certain body movements (especially of hand) are very fine and detailed, requiring a very dense and co-ordinated motor neuron framework.
Is it because the cranial nerves, owing to some developmental restraint or functional trade-off, can only innervate areas close to its place of origin effectively? This might explain why 11 pairs of nerves innervate only the head region and only 1 pair innervates the remaining body. I have no idea about the validity and the reason of this claim.
Could it just be a random evolutionary outcome, there being absolutely no benefit of cranial innervation leading to random drift in the innervation patterns?

We can somewhat rule out reason 1 because fingertips are also highly sensitive to sensory stimulus. Moreover innervation is not solely about sensory inputs but also motor functions, visceral control etc. All the nerves required for the motor function and a significant portion of visceral control nerves connect to spinal cord.

Therefore in my opinion reason 2 is the most appropriate which automatically rules out reason 3.
Spinal cord is an advancement of neural organization in the chordates. Spinal cord can be viewed as a central cable in which all power lines merge (they still maintain their individuality [the spinal tracts]; they just get clustered to form an organized bundle). Evolution of spinal reflexes must have been a secondary event.

The case of vagus nerve and cranioaccessory nerve suggests that this is an ancient pathway to control the heart. Heart with a closed circulatory system is found in molluscs as well. Apart from the functional significance of the heart (which might to some extent justify direct cranial innervation), it is decently proximal to the brain as well.


What is the most appropriate way to normalize gene expression data? This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for microarrays.

For RNA-Seq data, there are methods of normalization which adjust for GC-content effect or other gene-level effects. It make sense consider these effects in the normalization of microarray gene-expression data?

Normalization of expression data is a big topic with new methods being published regularly. When approaching something like this you generally want look at people who have done similar things to what you've done, and then once you understand why they did what they did, you can ask what you need to do to answer your questions. Always keep your biological question in mind. For instance if you're measuring QTLs, you'll need to be a lot more careful than if you're just looking for genes effected by a knockout mutation.

In general you want to use quite different methods for RNAseq and Microarray data. The two data types follow completely different distributions (RNAseq gives you count data, microarray data gives you continous signals) and have different types of technical noise effecting them (GC content will effect both, but in a different way). Some methods can be used on both, but usually involve coercing the data into a different form (e.g. mapping counts to a normal distribution). The limma package for R can handle both, using different distributions, and is a good start. Newer, purportedly better methods exist for RNAseq, which I haven't personally used.


Can nervous disorders be cured? Will enough research be the answer? I have searched every nook of the internet and I couldn't find a clear and to-the-point answer. Well my story is that I am a young BSc student who wants to do research on neurological conditions because as far as my knowledge goes neurologists cannot do anything about ANYTHING, things like dementia and brain damage lead the person to become completely destroyed and then eventual death is what every doctor has to see. As of current.

So I am asking if we can develop eventually effective treatments for let's say OCD or Alzheimer's? Or that will never happen because of other factors in the ecosystem and it's the rule of the nature that some people are just unfit to survive? If that's possible, and about to happen in my life time -- i.e., I can contribute -- I am in. I am gonna get a doctorate in one of the life sciences and start doing something. Like discovering genes, or understanding the pathophysiology, or discovering drugs, whatever I am competent in and able to. I just cannot see people suffer like that.

Yes, levodopa type treatments for parkinsons.

epilepsy:
In 2017, 116 children were randomly assigned to undergo epilepsy surgery or receive medical treatment. After 12 months, 77% of the children who had undergone surgery were seizure free compared with 7% who received medical treatment.

Check news and histories of advances in neuroscience and neurology.

Every year drugs improve, it's best to stay objective in the face of mind dysfunction, meditate.


Do males ever produce the offspring? Are there any non-asexual species in which the male of the species produces the offspring?

If so, why are they considered male and not female?

Yes the males of a group of bony fish Syngnathidae can bear offsprings or as you say produce offsprings. This group includes Seahorses and Pipefishes. In some species the male have either a brood pouch attached to the trunk or its tail while in others the egg is attached to the trunk or tail laid by the female.The fertilisation takes place in the pouch or in water before implantation.

Here are some pictures :

1.Male seahorse with brood pouch and a slender female without a brood pouch

2.Male seahorse giving birth to a baby seahorse

3.Male Syngnathus sp.(pipe fish) with the brood pouch

Inset image C shows eggs in pouch of pregnant male and Inset E shows Embryos in the pouch of pregnant male. (Images taken from researchgate.net and peaubleue.org)

Now coming to your question

  why are they considered male and not female?

Though the males here bear the baby but the baby results from fertilisation of a sperm produced by the male (the same seahorse that is destined to bear the baby) and an ovum produced by the female (the other seahorse without a brood pouch).
The sperm / male gamete producing individual is a male and a ovum/female gamete producing individual is a female. The provision of being able to bear a child does not change the sex.

Note: Seahorse is an oviviviparous organism i.e they are organisms in which the fertilised eggs develop inside the parent's body until they are ready to hatch.

P.S. Brood pouch is a cavity outside the body of these fishes in which the eggs develop and hatch.

Source: Wikipedia


Regarding TIMP and MMP enzymes Are there substances that can promote TIMP enzyme production, or MMP enzyme production or supression in tendons?

Are there medical tests that measure quantities of MMP and TIMP enzymes in tendons?

For your first question

Both enzymes, are components of Epidermal growth factor receptor (EGFR) signalling pathway.

MMP is a matrix metalloproteinase, that triggers EGFR signalling, this can be done by a mechanism called transactivation

So, A signal from G-coupled receptor, or cytokine receptor could activate the cleavage of MMP,  then MMP converts to a ligand for EGFR activation

For example Angiotensin II type 1 receptor (AT1R) and type 2 receptor (AT2R) which are GPCR, there are evidence for crosstalk with EGFR, look for this paper. This could be linked with hypertension or inflamation. Also cancer, could trigger EGFR receptors by NMP's.

And finally tissue inhibitors of metalloproteinases (TIMPs) are the negative regulator of MMP's

This are only an overview of the whole biological process involving MMP, so I think there is no single answer to your question, but you can delimit the topic for a specific disease, and look for papers at google scholar.


Does animal blood, esp. human, really have similar salinity as ocean water, and does that prove anything about evolution? It is an often-repeated claim that human, and in fact all animal blood is salty because we evolved from aquatic organisms, and that blood has a similar concentration of salts as ocean water, or at least as primordial ocean water.

Is any of that true? Does science know what the salinity of the oceans was billions of years ago, and was it indeed similar to the blood of today's organisms? Does that knowledge prove anything about evolution and the origin of life?

I am wondering, because I tried to Google for the answers, and unfortunately all I could find were creationists referencing each other how it couldn't possibly be true because evolution is a lie in the first place etc., and they claim that there is no empirical research that would compare salinity levels of organims' cells and ocean water.

Short answer
Early sea water had a very different osmolality than blood plasma.

Background
The reference range of serum osmolality is 275–295 mosm/kg (mmol/kg) (MedScape). The osmolarity of sea water is about 1000 mOsm/l (Wikipedia), but it can vary substantially between different seas, namely between 642 and 1,480 mOsm/kg (Ninawe & Banik, 1998). Nonetheless, the range of osmolalities are substantially higher than that of serum. That's why we cannot consume sea water, without losing more water than gaining it (NOAA). According to Astro Biology Magazine, the salinity of early oceans 3.5 billion years ago, when life first developed, was even higher. So popular accounts that they are the same and that this has important evolutionary consequences are likely far-fetched.

Reference
- Ninawe & Banik, J. Mar. Biol. Ass. India (1998); 53(2): 230-36


Enzyme kinetics: recommended literature to grasp the concepts better I have had a few biochemistry courses, but I still feel confused and a bit scared each time they try to explain and apply enzyme kinetics or even chemometrics in different situation during class. On our last lecture we had kinetics regarding:

Pingpong reactions (with two substrates A, B):
$V_0 = \dfrac{K_{cat}[E]* [A][B]}{K_m^B [A] * [B] * [A][B]} $

General reactions (with two substrates A, B):
$V_0 = \dfrac{K_{cat}[E]* [A][B]}{K_m^B [A] * K_s^A * [B] * [A][B]} $

And we also had something about analyzing the "principle component" in multivariate data, from enzyme kinetic measurements (as effect of e.g. pH of temperature).
I really don't understand this, or how I would apply this - or analyze my data if I have two substrates.
Question: In general, is there a good web site which goes beyond the normal Michaelis menten analysis, or a very good book which explains both the basic and more complex scenarios regarding analysis/application of enzyme kinetics for biochemists?

I always used the book "Enzyme Structure and Mechanism" by Alan Fersht. (Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding is the latest version, published in 1998.) Both in some courses I did and when working on (complex) enzymatic mechanisms. It's a classic (so a bit old maybe), but it covers all the basics and includes most of the common complex mechanisms like ping-pong. I don't know if it will teach you how to analyze multivariate data, so maybe you need something else for that.


Crossing over : Holliday model In this figure out of the two heteroduplexes formed one is considered to be non-recombinant product(left) and the other recombinant product(right). My question is despite the exchange of middle DNA segment why is the right heteroduplex considered a non-recombinant product or patch. I've been reading two books:

Molecular Biology: Principles of Genome Function
By Nancy Lynn Craig, Rachel Green, Orna Cohen-Fix, Carol Greider, Gisela Storz, Cynthia
Molecular Biology
By Burton E. Tropp

both had the same illustration and descrpition.

Answer in brief

  Heteroduplex called patch does not have double-stranded recombinant regions, there is a new fragment in a single strand only. It means that the two strands are not complementary at that regions and as soon as DNA repair systems detects it, the mistake will be corrected. In case of heteroduplex called splice, there are double-stranded changes, which do not go against the complementarity principle and thus, they will not be removed or corrected in any way.

Diagrammatic Explanation

After horizontal and vertical resolution patch and splice are formed respectively.

A better version of this diagram with complimentary base pairing is shown below $-$

In patch the heteroduplexes formed have only a single stranded middle recombinant region which is not complimentary to the other strand when this is detected by the DNA repair system and corrected the duplexes formed are same as the original duplexes (before crossing over) so the products of horizontal resolution is called non-recombinant products.

In splice the heteroduplexes formed have double stranded recombinant segments with middle non complementary region which when detected and fixed by the cell's DNA repair system two duplexes are formed having recombinant DNA segments, so they are together called recombinant products. The recombination in splice is well represented by the reversal of terminal genes.


Dreaming after passing out I'll have few questions about passing out and dreaming. English is not my native language, and my biology knowledge is very limited. So bear with me.

What exactly is blackout? (in a really simple way)
Are there different types of blackout? (see below)
Do fainting, passing out, and blacking out mean the same thing?
Can someone have a dream/vision after loosing consciousness? (during blackout?)

I'm asking these because I had a similar experience and I'm trying to make sense of it.

We were goofing around and a friend of mine had me in an arm triangle. I suspect he choked me, because I lost consciousness for a few seconds, max 3. While in that state, I kind of had a dream or vision, whatever it is called. It felt like hours. This was a long time ago and I still remember the dream, but can't make sense of it. What I've seen was really interesting and I couldn't just let it go.

I'm not asking for dream analysis or anything, but the biological/neurological aspect of what happened, so don't get me wrong.

I'm also new in here, though not to stackexchange, so the tags might need a modification.

Fainting, passing out, and blacking out are all common terms for the same thing, a sudden loss of consciousness of short duration.  The medical term for this is syncope. It is caused by a decrease in blood flow to the brain, limiting the the availability of oxygen and nutrients to the brain cells.  Brain cells have high energy requirements, so this causes them to stop functioning, causing loss of consciousness and muscle tone.

There are many causes of syncope.  In the situation mentioned, a likely possibility is a pressure change in the carotid sinus which is located at the side of the neck. When sensed by a nerve, this can cause primitive parts of the nervous system to change the dilation of blood vessels and the beating of the heart in a manner that brings on syncope.

Dreaming during syncope is not uncommon and that fact may be useful in distinguishing syncope from epileptic seizures according to research by Chiesa et al..


identification of differentially expressed genes in RNA-seq analysis I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream processing.

Please give your suggestions.

Thanks in advance.

Unless you have a good reason, stick with the ones that the community at large uses most frequently: EdgeR or DESeq2.


What is the adaptive significance of temperature dependent sex determination? Why do some reptiles have TDSD ?  Is it because one of the genders is healthier than the other that only they, can survive high temperatures?

To my knowledge, it is still mainly unclear what are the enviromental factors that would promote Environmental Sex Determination (ESD; incl. TSD) vs Genetic Sex Determination (GSD; incl. with and without sexual chromosomes).

Environment variability and Climate change

Generally speaking it is thought that in variable environment, GSD might be more beneficial as an ESD mechanism could lead uneven sex-ratio and hence lower fitness (Pen et al., 2010).

Climate change can be very detrimental to species that use ESD. A sudden climatic change can cause a population to have a highly biased sex-ratio to the point where persistence is not possible anymore (Boyle et al., 2014).

Differential fitness variance among sex

On the other hand, ESD can allow parents to decide the sex-ratio of their offsprings (Randy, 2005).

Consider for example a case where sexual selection lead to a much high variance in fitness among, say, males than among females. Note that parents fitness and offspring fitness is correlated (because an obvious genetic correlation but also because some environmental correlation). In such case, parents that have a low fitness would prefer to produce females (that despite being unhealthy / ugly will still manage to have a decent fitness) while parents with high fitness would prefer to produce males (because very healthy / good looking males will have a very high fitness).

Charnov and Bull model

In Charnov and Bull (1977) own words (taken from their abstract)

  We propose that labile sex determination (not fixed at conception) is favoured by natural selection when an individual's fitness (as a male or female) is strongly influenced by environmental conditions and where the individual has little control over which environment it will experience. Our argument also applies to sex expression in hermaphrodites

According to wikipedia, there are a number of evidences for this model in the literature. I let you go through the cited papers for more information about what is the logic behind this hypothesis!

Evolutionary constraint

Changes in sex determination systems has not evolved that many times (in Reptilia at least; Jansen and Phillips, 2006; see this post for definition of Reptilia). It can be hypothesized that there might be a strong evolutionary constraint (see also phylogenetic signal) and hence looking for adaptive reasons for its evolution might be a moot point.


Database of known human proteins Is there an up-to-date database of known human proteins that is easily accessible using Python libraries?

GenBank includes human proteins and provides APIs for constructing HTTP requests to make searches. Examples are given in Perl, but if you prefer another programming or scripting language you are expected to write your own:

  Equivalent HTTP requests can be constructed in many modern programming languages; all that is required is the ability to create and post an HTTP request.

This approach has always served me well.

Uniprot seems similar in this respect.

SwissProt provides a package for BioPython which may be of interest. I don’t know if this is the library you are referring to — you don’t say, and I don’t use Python.