What percent of genetic disease are preventable? I like to know what percentage of genetic disease are preventable before birth?

Also, when we can detect all of them? I heard in a TV show a doctor said about 5 years later we can prevent all genetic disease! Is this estimation true?

There is no simple answer to either of your questions.

There are many monogenic diseases where mutations in single genes result in disease phenotype.

There are far more diseases that have a genetic component where mutations in one or more gene increase the baseline risk of disease and this risk is then modified by the environment the individual encounters throughout their life-time (see Multiple Genes).

To get an overview of the functions of genes that have been so far identified, mutations within them and the diseases they have been linked to see Online Mendelian Inheritance in Man (OMIM).

If you want to get a feel for just how complex genetics is then a recently published paper on the genetics of hair colour would be worth reading...

Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability


Who were "Dawson and Wilson" (mentioned as authors of an embryonic postmortem examination method)? A sentence from a Russian text I'm translating:

  Following the drug administration period, the pregnant animals were euthanized in order to examine the embryos using the method developed by Dawson and Wilson.

That made me curious. Who were they? Google fails to bring up both these surnames at once in response to queries like "Dawson Wilson embryo necropsy" etc. Maybe one of them developed an embryo examination technique, and the other perfected it?

This article (A Note on the Staining of the Skeleton of Cleared Specimens with Alizarin Red S) looks to be the one by Dawson.

Update: I think the Wilson your text is referring to is James G. Wilson, an important researcher on terathology. I can't find any reference to a single article, though.


Is there any scientific evidence that a human has ever grown a third set of teeth? This is about the possibility (or lack thereof) for a person to re-grow a new "permanent tooth" or set of teeth, to replace the teeth that grew after their milk teeth fell out.

I had earlier seen some anecdotal evidence on the internet that this would have happened to some people.

Anyway, what I wanted to ask is if there is any scientific evidence (e.g. properly recorded unusual medical phenomena) that shows that a person has grown a tooth (or a set of teeth) to replace their permanent teeth?

There are legitimate case reports in credited journals of hyperdontia, or the condition of having supernumerary teeth. Such cases are often associated with congenital syndromes-- cleft lip and palate, trichorhinophalangeal syndrome, cleidocranial dysplasia, and Gardner's syndrome. I included a case report and a comprehensive review for you below.

Case Report from American Journal of Orthodontic Dentofacial Orthopedics, 2011.

Comprehensive Review from Journal of Oral Science, 2014.


SARS-COV-2 replication speed What is the speed of replication of SC2? Any information, including in vitro data would be appreciated.
I would be interested to know the length of SC2 eclipse period, latent period and something like burst size.
Alternatively, per day CT values of qtPCR of COVID+ subjects would be also helpful.

According to Amy Rosenfeld, it is about 8 hours eclipse and 18-24 hours until "its done". Not sure if it means until burst or until the latent period is over. These times are in vitro and are cell line dependent. In vivo might be different. Burst size also cell depndent. Source: https://youtu.be/NP56XjzyPfQ?t=1301
In this video https://youtu.be/4S3DXXtRZZg?t=152, it is said, that each cell can produce up to 600k viral particles of SC2, but I'm not sure, what is exactly meant by the number. Later in that video: https://youtu.be/4S3DXXtRZZg?t=187 it is said, that the virus seems not to kill cells for about 5-6 days.


Reason for conversion of glucose to fructose in glycolysis In glycolysis, glucose is converted to glucose 6-phosphate so it can not diffuse out of the membrane. Then it is converted to fructose 6-phosphate.

Why is this? Perhaps it makes it less stable so it is easier to break down into pyruvate?

That is just a guess, is anyone able to provide more information about this?

Avoiding diffusion is one reason to phosphorylate glucose, the other is that it is removed from the osmotic balance between inside and outside of the membrane, so it can be transported at a high rate.

The Glucose-6-phosphate can then be used as a substrate for different pathways, namely glycolysis and the pentose phosphate way, and (depending on the organism) also be converted into glycogen and starch for further storage.

The reason for the phosphorylation lies further downstream in glycolysis: The isomerization by the glucose phosphate isomerase and the subsequent second phosphorylation into Fructose-1,6-biphosphate make the conversion and dedication of the molecule into the glycolysis irreversible.

Fructose-1,6-biphosphate is then cleaved by the aldolase into two C3-units: Dihydroxyacetone phosphate (DHAP) and Glyceraldehyde 3-phosphate (GA-3-P). GA-3-P is converted into DHAP, so that downstream only one metabolite needs to be processed.


Why does blood come from mouth when people are shot in the chest area? In almost every movie scene when a character is shot in the chest area, some blood comes from his mouth or sometimes even coughs blood before he dies.

Are these kind of scenes realistic/possible? If yes, why does blood come from mouth in this situation?

Substances such as blood trigger the Cough reflex, so if for any reason blood accumulates in the airways, it will be ejected this way.

If you have a look at chest anatomy, you can see how this could be caused (look at Trachea down to the lungs, aorta and the carotid arteries above the heart). A shot through the chest can peforate many large blood vessels, along with the airways, and cause leakage inside.

I would consider it quite hard to hit the aiways like that though, the bullet would have to enter the chest quite near the centre as the cough reflex is not triggered by substances in the lung itself, only in the airways. There may be other ways of blood getting into the airways, but I would assume that a scene with a shot near the breast and then blood coughing would be unrealistic.

Image source: Micheau, A (2010) ANATOMY OF THE MEDIASTINUM: ILLUSTRATIONS AND CROSS-SECTIONS. From: http://www.imaios.com/en/e-Anatomy/Thorax-Abdomen-Pelvis/Mediastinum-Illustrations


Does a specific blood group enhance the Plasmodium growth? I am maintaining Plasmodium falciparum cultures for past 6 months. For the blood culture, usually we lab members take turns  and donate blood for the culture. I observed that the parasite's normal growth cycle were fast and more healthy in B+ blood, little slow in AB+ blood. But on the whole the culture was maintained good but I really observed fast stage transitions in B+.

Is this really possible? Does a specific blood group have an impact on Plasmodium growth? Did anyone notice the same issue?

Thanks.

It is a well documented observation that Plasmodium (vivax and knowlesi) infection is dependent on the Duffy blood groups [1].

Individuals lacking the Duffy antigens (Fya and Fyb) have lower susceptibility to malaria. Plasmodium expressed Duffy Binding Proteins facilitate in establishing the initial contact between the merozoite and the RBCs.

However, Plasmodium has evolved to break this dependence on Duffy antigens [2, 3].

For, the ABO blood group system, it has been observed that the blood group-O is associated with lower severity of P.falciparum malaria in adults  [4, 5], which possibly happens because of reduced rosetting (binding of infected RBCs with uninfected RBCs) [5].

References:

Dean L. Blood Groups and Red Cell Antigens [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005. Chapter 9, The Duffy blood group. Available from: http://www.ncbi.nlm.nih.gov/books/NBK2271/
Ménard, Didier, et al. "Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people." Proc Nat Acad Sci, USA 107.13 (2010): 5967-5971.
Mendes, Cristina, et al. "Duffy negative antigen is no longer a barrier to Plasmodium vivax–molecular evidences from the African West Coast (Angola and Equatorial Guinea)." PLoS Negl Trop Dis 5.6 (2011): e1192.
Cserti, Christine M., and Walter H. Dzik. "The ABO blood group system and Plasmodium falciparum malaria." Blood 110.7 (2007): 2250-2258.
Rowe, J. Alexandra, et al. "Blood group O protects against severe Plasmodium falciparum malaria through the mechanism of reduced rosetting." Proc Nat Acad Sci, USA 104.44 (2007): 17471-17476.


Obtaining a mapping of RefSeq ACs to Uniprot ACs I am trying to obtain a mapping for RefSeq Accession Numbers to Uniprot Accession Numbers.

I can write a script to do this for a list of RefSeq ACs like this:

#!/usr/bin/python

"""
Derived from:
  http://www.uniprot.org/help/programmatic_access#id_mapping_python_example
"""

import urllib
import urllib2

url = 'http://www.uniprot.org/mapping/'

params = {
    'from':'P_REFSEQ_AC',
    'to':'ACC',
    'format':'tab',
    'query':'NP_511114.2 NP_004295.2 NP_031465.2 XP_004934106.1',
}

data = urllib.urlencode(params)
request = urllib2.Request(url, data)

# Please set your email address here to help us debug in case of problems.
contact = "email@example.com"
request.add_header('User-Agent', 'Python %s' % contact)
response = urllib2.urlopen(request)
page = response.read(200000)
print page

I am curious if there is a way to request the entire mapping of human genes to proteins.

I have tried to configure a query from the Uniprot resources, but I can't see how to get RefSeq data from this tool.

http://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606#customize-columns

I am happy to use a resource other than Uniprot.

You have a bunch of options:

You can use Biomart.
Biomart is a standalone tool, but also have a pyton and R libraries. So it gives you more options depending on your preferred programming language. This is a widely used tool and in general works well.

biomart http://www.biomart.org/
biomart python library
biomart R library (from bioconductor)
Biomart is widely used and have extensive documentation.

Use a python library called pyEntrezID
https://pypi.python.org/pypi/pyEntrezId/1.4.7
You can do all sort of conversions of ids, however I've never tried it.
You can try NCBI eutils or one of the Ensembl REST API endpoints


Septic Shock: I'll kill myself before you kill me Most of the deaths caused by extracellular bacteria don't actually result directly form their action. Rather, it results from an overreaction of the immune system to antigens such as LPS and LTA (Superantigens are bacterial toxins with an enormous power in originating immune responses; they are able to activate numerous T cells through a different TCR, which will produce too many pro-inflammatory cytokines, resulting in an excessive reaction by the body and causing self-tissue damage, etc), and it is this excessive reaction of the immune system which ends up killing the organism.

http://www.medicalnewstoday.com/articles/311549.php
http://www.medicalnewstoday.com/articles/305782.php?sr

How come, after all this evolutionary time, we have this self-killing mechanism? Why do T-cells have receptors to such generalized and potent antigens, which will frequently result in self-damage? Is it because at the point of infection that this happens, we would die anyway from it, so it doesn't alter fitness?

The important thing to recognize about the host response to sepsis is that it is actually a generalization of mechanisms used in local infection response by the innate immune system. When an animal has a local infection, such as at a wound site, innate immune cells such as monocytes and macrophages recognize 'generic' bacterial features, such as lipopolysaccharide (LPS). When they recognize these features, they respond by engulfing the pathogen and releasing cytokines that result in local vasodilation and inflammation. In this context, these responses are close to ideal. Vasodilation helps to isolate the area and promotes the recruitment of more immune cells.

These sorts of small infections are very common for all animals (just about every creature cuts itself at least once), including humans, and the absence of this response would result in sepsis (not the immune response, but just sepsis itself) because the infection would not be contained. Control of such local infections is thus 'life-or-death' for all creatures—which is an extremely powerful selective pressure.

The other thing to consider here is when in nature are these local defences overwhelmed such that sepsis, and then septic shock, which is what you are asking about, occurs. The answer is that it does not happen very often. Transient bacteremia is relatively common (it even happens when you brush your teeth, see this paper for example), but overwhelming bacteremia, sepsis, is not very common in healthy individuals. It is generally a condition that affects weakened individuals and those who have already reproduced. We notice it far more now because it is a major cause of death for humans hospitalized for other conditions, as well as older people with pneumonia. Most of the primary causes of sepsis though—major wounds, pneumonia, weakened immune systems—would be death sentences in themselves in the absence of medicine, irrespective of the organism's response to the sepsis.

That is not to say it is completely invisible to selection, for example this paper, and others like it, demonstrate that the immune cells responsible for septic shock are regulated by hypoxia (a major feature of shock). However, it is reasonable to say that any fitness advantage conveyed by a reduction in the intensity of septic shock would be dwarfed by the fitness penalty paid if that reduction also reduced the efficiency of the response to local infections. For this reason, it is likely that septic shock is an evolutionary accident, a trait that exists in part because it is irrevocably linked to a set of highly advantageous traits (those involved in local infection response), rather than a trait that has been extensively selected on by evolution.

Note that this answer is my opinion only. To the best of my knowledge, there is no definitive answer to this question yet, and future research may prove me wrong.


What is this insect? Found in Peru I took the pictures today in Cusco Peru. It is the third insect of its class in a month. I never see it before. I thought that it is a wasp, but I think it's really thin to be a wasp. It's about 4 or 5cm.

I want to know what kind of insect is and if it's dangerous. Thanks!

So that looks to me like the Ophioninae family of wasps, genus Ophion. I'll query the list of known species to try to find a more direct match.

Some evidence exists which notes Ophion may sting when threatened, but at the same time (and I don't have the reference ready) it's believed that the sting contains no toxin.

As for a positive identification, it's difficult without examining the the features of the wasp extremely close up. Identification keys exist here.


Why not use Cu(OH)2 as a dye for protein electrophoresis? As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?

Copper hydroxide does not dissolve very well in water, which means you will have trouble soaking them into your gels.

Also, even if you managed to add enough copper hydroxide beforehand (in the wells), it is unlikely that the copper(II) ions, if any existes, will travel along with the protein due to its size. (Copper hydroxide itself does not have any charge.)

As for the paper Stella mentioned, the copper salts are used after electrophoresis to produce a negative image, which is exactly what you cannot do with copper hydroxide.


Expected bands in polyacrylamide gel I have something in my notes that doesn't seem right.

If I use restriction enzymes on a PCR product how many bands should I see provided I know the restriction enzimes will cut the DNA? If I use two restriction enzymes I expect two cuts then then gel should show three bands. Then, if I use just one enzyme and I know the enzyme will cut just once, then should I expect two bands? According to my notes one band is expected.

If your restriction enzyme only targets a single site on the DNA sequence then it will split each DNA strand into two fragments. If the restriction enzyme cuts every strand then you will see those two fragments. Note that if the two fragments have the same length they could appear as a single band when separated using gel electrophoresis.

If the enzyme doesn't cut everything the uncut DNA will also be present. This is why you should always separate some uncut DNA in the gel electrophoresis.


How strong is spider silk? Spider silk is pretty darn strong and all sorts of comparisons are made to steel. I'm more curious about the various moduli of spider silk and how it compares to other materials. What is the Young's modulus of spider silk? What is the bulk modulus of spider silk? What is the shear modulus of spider silk? In general how do those moduli describe the material properties of spider.

A simpler way to ask the question, what does it mean when it is said that spider silk is strong?

Wikipedia has a remarkably well-cited article on the subject of silks and their various biological isoforms and mechanical properties. With respect to tensile strength, spider's silk is as tough as high-grade steel.

Explcitly, dragline silk was measured by Pérez-Rigueiro at al. to be 600 ± 50 MPa with a comparison to silkworm silk.

Reference:

 Pérez-Rigueiro J, Elices M, Llorca J, Viney C. 2001. Tensile properties ofArgiope trifasciata drag line silk obtained from the spider’s web. Journal of Applied Polymer Science 82: 2245–2251 [pdf]


How would one determine whether a chemical will upregulate a certain class of proteins? I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity.

How would I go about this experiment? I'm assuming I would use some sort of assay but I'm not exactly sure how I'd go about it.

One way of examining this is by looking at the transcriptome as a whole before and after the introduction of the chemical. I would use microarray or next generation sequencing RNA-seq technology to look on the expression level of all the genes after the introduction of the chemical, some inert control and no treatment control.

Then, you can calculate the relative fold change in expression of all genes, under treatment vs. control. Next, you can do a GO term enrichment of the significantly upregulated genes, and see if the term "deacylases" shows significant enrichment in genes that are upregulated under treatment vs. control.


Why does the direction of endolymph flow oppose direction of body motion? In the semicircular canals, the endolymph always flows in a direction that is opposite to the motion of the vestibular apparatus itself. I’m having trouble grasping why this is, and I would greatly appreciate it if anyone could give me some physics insight into this.

The endolymph inside the ear, like any kind of matter, has mass and so is subject to inertia.  This means any change in speed and direction will be resisted.  The ear and semicircular canals themselves are fairly solidly connected to the rest of the body and so accelerate smoothly.  But since endolymph is fluid, it cannot be brought up to speed as fast, so it lags behind in moving.  So, as the ear moves forward, the endolymph stays behind and so in relation to the ear, flows backward.

This is like what you experience when a car or airplane accelerates: you "flow" backwards into your seat as the vehicle surges forward.


How is cognitive ability linked to the presence of sex chromosomes? Most cases of sex chromosomal abnormalities in humans have a case of learning disability or less developed cognitive abilities. Wikipedia says:

When additional X and/or Y chromosomes are present in 48,XXXY, 48,XXYY, or 49,XXXXY, developmental delays and cognitive difficulties can be more severe and mild intellectual disability may be present

So, the question is simply this: How is cognitive ability linked to the presence of sex chromosomes?

If you are thinking that, say, a chromosome 1 triploidy will not result in cognitive impairment... that's not quite right.  Almost all triploidies result in death.   Same with chr2, chr3, chr4...just about every chromosome is lethal if there are extras.
It's not so much that having extra sex chromosomes is bad for cognitive function, it's that having extra chromosomes is usually lethal, only a few triploidies are even survivable, and they all cause lots and lots of problems, including cognitive impairment.  Having extra sex chromosomes is the mildest one, and it results in lots of comparatively mild problems.


Phospholipid membrane fluidity if phospholipid had one type of fatty acid How would membrane fluidity change if the phospholipid membrane had only one fatty acid?

Cell membrane doesn't have just phospholipid inside.

Components who influence fluidity in cell membrane are:

1) Fatty acids length
2) The grade of unsaturation of these fatty acids
3) Presence of cholesterol

So, if composed of just fatty acids, excluding every other component (carbohydrates, channels proteins and, mainly, cholesterol), the answer would be yes, its fluidity will change drastically.


Does leaving land alone actually help nature conservation? I like nature conservation - the idea of creating protected areas where nature lives on its own and wilderness is "created" like that. Is is possible to raise the natural value of land only by leaving it on its own - I mean in the way that humans do not touch the land in any way (buildings, roads etc.)?

I know about some "private" protected areas in Europe, where NGOs thought this piece of land should be protected but the authorities failed to do so, so they bought the land and took care of it themselves (restricted public access to help conservation, removed invasive species etc.)

I wonder what does it take to correctly protect an area - is it OK to leave the land alone and never touch it again or is it necessary to take care of it somehow. I mean things like invasive species (I can imagine the normal "unprotected" nature is full of them) like various types of grass, invasive animals etc. I can imagine this may be largely location dependent (some parts of the world are more influenced by humans than others). My location is the Czech Republic.

I'll give you an example, because this question is pretty case specific. In Delhi, my hometown, they kept areas of the forest, the 'Sanjay Van' free from construction and people and only very recently started cleaning it up. As a result, an invasive variety of the Acacia tree (known locally as keekar) more or less took over the forest and has basically wreaked havoc on the wildlife.
I think better than just letting Nature take it's course, humans should help get abandoned areas back to a sustainable point, where it can integrate with the wildlife, but again, it depends on each area.


What gene targets associated with the new coronavirus (SARS-CoV-2) have been identified so far? One hypothesis for which we have some supporting evidence is that the new virus (SARS-CoV-2) "enters human cells through an interaction with angiotensin-converting enzyme 2" see here. Although it is still unclear what genes to target in order to prevent the infection (entry or reproduction).

Is there empirical evidence suggesting what genes can be modulated to fight the infection?

This is an interesting question. A recent study published on bioRxiv by researchers from Xi'an, China (pre-print) argues that CD147 can also be an entry receptor for the virus. They showed virus entry can be blocked by an antibody to human CD147.


Is this a Loranthus Europaeus? Location: Austria, Vienna Ottakringer Wald
Date: Feb 8

I found something beneath a tree with epiphyta , which I thought to be Viscum album but is vividly yellow instead of white and I found no leaves.

My search of subspecies of Viscum album initially revealed:

  Viscum album subsp. austriacum (Wiesb.) Vollmann. Fruit yellow; leaves 2–4 centimetres (0.79–1.57 in). Central Europe. On Larix, Pinus, Picea.

But then I began to think it shouldn’t be V. album. In illustrations of V. album there aren't the thin stalks between berries and branches as in my specimen.

Perhaps Loranthus europaeus?

You are quite right: it's Loranthus europaeus. Vienna was the prime example in our botany lectures where to see that plant without a fuzz.

c/p from the Flora of Vienna:
"Auf Eichen, vorzüglich auf Quercus pedunculata und Qu. sessiliflora, selten. Im Eichenwalde von Schönbrunn, auf dem Gallizin, hinter Neuwaldeck, hin und wieder; viel häufiger auf dem Bisamberge {A}. ... auf den grössern Donau-Inseln z. B. ... in der Lobau {C}."

"Häufigkeit des Vorkommens: häufig bis sehr häufig"

(Confused about the contradicting "rare" and "frequent to very frequent" statements, but anyway.)

Here are some more pictures.


Does mixing alcoholic drinks really make you more drunk? There is plenty of anecdotal evidence ("beer after wine and you'll feel fine, wine after beer will make you feel queer") that mixing alcoholic drink types leads to a stronger effect, but I can't find any true studies.

In fact the only studies I found are looking at mixing energy drinks and alcohol (mixing with energy drinks increases motivation for more alcohol (in college students) [1]), and discussed mixing caffeinated beverages with alcoholic ones [2].

Are there any studies specifically looking at mixing alcoholic drinks? They would have to compare people drinking the same amount of alcohol, but some people mixing, others drinking the same thing. Maybe even a cross-over study design? Same people do both, one after the other? The only way to get an unclouded answer!

I am also interested in the follow-up why question: Why does mixing some drinks make you more drunk? Presumably it is something in wine (for example) that interacts badly with something in beer at the chemical level (the metabolites maybe)?

Marczinski CA, et al, (2012). Mixing an Energy Drink with an Alcoholic Beverage Increases Motivation for More Alcohol in College Students. Alcohol Clin Exp Res, epub. doi: 10.1111/j.1530-0277.2012.01868.x
Touyz LZ, (2011). Mixing drinks and concocting troubles. Curr Oncology, 18(6):262-3. PubMed; FullText.

There are some very general answers to your question.

Definitely, there is a lot of magical thinking. We as humans are very prone to anecdotical evidence and extrapolations from incomplete data, even more so when we are drunk.
As an interesting "proof" is the fact that the German counterpart of the saying "beer after wine and you'll feel fine, wine after beer will make you feel queer" is "Wein nach Bier, gönn' ich Dir, Bier nach Wein, lass es sein" -- which means the exactly opposite of the English saying (beer after wine is bad, wine after beer is fine).

Many kinds of alcohol contain unwelcome additional substances, for example fusel alcohols. Definitely, "mixing" broadens the range of these additions.

Mixing can lead to a misperception about the actual amount of alcohol that was taken in. Many people who would not drink a vodka and drive have no problem driving after a half a liter of beer (which contains same amount of alcohol two shots of vodka).


Microbiome Context for Amino Acid Essentials and Non-Essentials Given what we are now learning about the diverse mix and variance of microbiomes (aka bacterias via human gut project), is it possible that synthesis of aminos can be done by specific bacteria and therefore provide the "essentials" if atomic ingredients are available in digestive tract?

If your body was filled with highly specialized bacteria living in nutrient-rich conditions, what you suggest could happen*.

But in practice, you're not filled with such bacteria, and most of the bacteria in your body are living in rather harsh conditions for rapid metabolism.

That said, gut bacteria do produce a range of other useful nutrients. Look for a review on gut microbiome metabolism, and you will find a number of examples.

*Some basic calculations:
Say we take an optimistic estimate for productivity of 1g AA/g biomass/day. (It's what they got in this paper (one of many) that characterized a strain of Corynebacterium glutamicum engineered to produce lysine for industrial purposes and growing in a bioreactor. There are better strains now, but still, let's call that an unbelievably optimistic estimate of what a bacterium in the body might produce in the right conditions). How much bacterial biomass is in the body? Not a trivial question to answer (How much weight/volume do microbes occupy within the human body?) but let's go with the middle of the road estimate of 1kg. So 1 kg of awesome lysine-producing bacteria might potentially produce 1 kg of lysine a day. Googling around for dietary requirements seems to get you somewhere in the 1-5 g/day range. So assuming vaguely similar productivities for other amino acids, we've got plenty of room to spare if we assume that our bacteria are highly specialized for this function and are exposed to friendly, oxygen-rich and nutrient-rich conditions.


Derivation for drug half life The formula in textbooks for $t_{\frac{1}{2}}$ of a drug following first order elimination is generally given as $$t_{\frac{1}{2}}= \frac {\ln(2).V_d}{Cl}$$where $V_d$ is the volume of distribution and $Cl$ is the clearance.

Shown below is my attempt to derive the formula but I don't know where I'm going wrong.

Assuming first order kinetics of elimination, the rate of elimination ($R$) would be proportional to the plasma concentration ($Cp$)

$$ R = Cp . k$$

Where $k$ is the rate constant.

For calculation of $t_{\frac{1}{2}}$, since this is a first order elimination, $$ t_{\frac{1}{2}} = \ln(2)/k$$
Substituting,
$$ t_{\frac{1}{2}} = \frac{\ln(2).Cp}{R}$$
Since $ Cl = R/Cp$, substituting would give,
$$ t_{\frac{1}{2}} = \ln(2)/Cl$$

Since both the formulae don't match (this one doesn't have a $V_d$ term at all!), where have I gone wrong? Also then how is $Cl$ different from $k$?

According to the correct formula, $k=Cl/V_d$. How is that so?

EDIT

Volume of distribution is the apparent volume of blood the drug takes up and is given by $$V_d = \frac {Dose}{Pc}$$

Clearance is the volume of blood that has been cleared of the drug in unit time and is given by $ Cl = R/Cp$

Correct me if the basic definitions themselves are wrong.

Well, $Cl = R/Cp$ is correct, but $R$ is not $Cp \cdot k$.

Given $X(t)$, the actual quantity (ie weight or moles) of drug in the system, $R$ should have the dimension of $\frac{dX(t)}{dt}$, that is $weight \cdot time^{-1}$ or $mole \cdot time^{-1}$ because the base definition of clearance is given by $$- \frac{dX(t)}{dt} = Cl \cdot C(t)$$.

The volume of distribution $Vd$ comes into play when converting from $X(t)$ to $C(t)$. Following the same steps as you did :

$$ R = \frac{dX(t)}{dt} = \frac{dC(t)}{dt} * Vd = C_p  \cdot k \cdot V_d$$
because (due to 1st order kinetics)
$$\frac{dC(t)}{dt} = Cp \cdot k$$

  Substituting,
  $$ t_{\frac{1}{2}} = \frac{\ln(2)}{k}$$
  $$ t_{\frac{1}{2}} = \frac{\ln(2) \cdot C_p \cdot V_d}{R}$$
  Since $ Cl = \frac{R}{Cp}$, substituting would give,
  $$ t_{\frac{1}{2}} = \ln(2) \cdot \frac{1}{Cl}  \cdot V_d$$
  $$ Cl = \ln(2) \cdot \frac{1}{t_{\frac{1}{2}}}  \cdot V_d$$
  $$ Cl = k  \cdot V_d$$
  $$ k = \frac{Cl}{V_d}$$


Terminology for inefficacy of selection on recessive alleles I am wondering is there some proper terminology which is used to say that deleterious recessive alleles might be able to hide, reducing the the efficacy of selection, in diploid organisms/chromosomes.

I was thinking about Y chromosome linked mutation and their inability to hide from purging by selection behind other alleles by being recessive... perhaps something like recessive sheltering? e.g. "In the Y chromosome mutations are more easily purged because recessive sheltering does not occur" ?

I think recessive refuge is the term you are looking for (this is the best link I could find, sorry: https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/)


Why do mammals in the wild retain the "trait" of menstruating with blood? This question intrigued me a lot since if animals in the wild did have menstruation with blood flow, wouldn't all that blood be attracting every other predator in the vicinity?

I would guess that the answer is something like this: ever since the development of the placenta enabled females to carry their offspring longer and to develop more fully.  Upon birth they were stronger and/or their brains were more fully developed (in the case of humans).  The increased gestation time, made possible by the structures of the womb and placenta is probably an adaptation whose advantages are much greater than the increased risk from menstruation once a month.

Some anthropological studies indicate that in preindustrial societies that women do not menstruate very much as adults though.  If you subtract out the time that they are carrying infants and nursing, which both prevent menstrual cycles, females will miss years of menstruation with only a few months in between. I would assume this is a factor in the risk of menstruation for many animals.


Is Leptin Stimulated by Insulin Alone? What is the mechanism of insulin stimulation in the human body?

Is leptin release stimulated by circulating insulin directly? Which other factors are involved in the level of insulin release? My goal is to identify nutrients that aid/trigger leptin production and release without causing undue inflammation or body-fat storage.

I have to say that this seems like a really odd approach to figuring out your diet.  The question of whether insulin increases satiety has been more specifically studied in the literature, as has the satiety generated by equicaloric portions of various kinds of foods, as have the actual effects of various specific diets in human feeding studies.  If you do a bit of digging, I'm sure you can find studies relating high/low GI diets to medically important outcomes (weight loss, blood lipids, fasting insulin levels, etc.), as opposed to their effect on one proposed satiety/fat regulation hormone (leptin).  Your approach also ignores leptin and insulin sensitivity, which might be as important as the levels themselves.  As someone concerned with which foods to actually eat, empirical studies of actual diets seem like the best place to look.

Anyway, here are a few relevant citations to help answer your question:

This study found a increase in serum leptin levels in type I diabetic children who started insulin therapy:
Flück CE, Kuhlmann BV, Mullis PE. "Insulin increases serum leptin concentrations in children and adolescents with newly diagnosed type I diabetes mellitus with and without ketoacidosis." Diabetologia. 1999 Sep;42(9):1067-70.
http://www.ncbi.nlm.nih.gov/pubmed/10447517

A slightly smaller study asked the same question, and found no increase in leptin levels:
McCormick KL, Mick GJ, Butterfield L, Ross H, Parton E, Totka J. "Leptin in children with newly diagnosed type 1 diabetes: effect of insulin therapy." Int J Exp Diabetes Res. 2001;2(2):121-7. http://www.ncbi.nlm.nih.gov/pubmed/12369715

An in vitro study of rat fat cells does indicate a direct increase in leptin secretion/production when given insulin:
Barr VA, Malide D, Zarnowski MJ, Taylor SI, Cushman SW. "Insulin stimulates both leptin secretion and production by rat white adipose tissue." Endocrinology. 1997 Oct;138(10):4463-72. http://www.ncbi.nlm.nih.gov/pubmed/9322964 http://endo.endojournals.org/content/138/10/4463.full

...and in human fat cells:
Wabitsch M, Jensen PB, Blum WF, Christoffersen CT, Englaro P, Heinze E, Rascher W, Teller W, Tornqvist H, Hauner H. "Insulin and cortisol promote leptin production in cultured human fat cells." Diabetes. 1996 Oct;45(10):1435-8. http://www.ncbi.nlm.nih.gov/pubmed/8826983

Leptin levels are positively correlated with insulin levels and BMI (presumably as a proxy for fat mass?):
Lambrinoudaki I, Christodoulakos G, Panoulis C, Botsis D, Rizos D, Augoulea A, Creatsas G. "Determinants of serum leptin levels in healthy postmenopausal women." J Endocrinol Invest. 2003 Dec;26(12):1225-30. http://www.ncbi.nlm.nih.gov/pubmed/15055477

Thierry Thomas, Bartolome Burguera, L.Joseph Melton III, Elizabeth J. Atkinson, W.M. O'Fallon, B.Lawrence Riggs, Sundeep Khosla, "Relationship of serum leptin levels with body composition and sex steroid and insulin levels in men and women" Metabolism Volume 49, Issue 10, October 2000, Pages 1278–1284 http://www.sciencedirect.com/science/article/pii/S002604950041783X

This study found a positive relationship between changes in insulin levels and leptin levels, though it sounds like only in women. (I don't have the full text to check, and the abstract was ambiguous):
Widjaja A, Levy JC, Morris RJ, Frayn KN, Humphreys SM, Horn R, von zur Mühlen A, Turner RC, Brabant G. "Determinants of within-subject variation of fasting serum leptin concentrations in healthy subjects." Exp Clin Endocrinol Diabetes. 2000;108(3):208-13.
http://www.ncbi.nlm.nih.gov/pubmed/10926318

So based on an incomplete and cursory literature search, it seems likely that injecting insulin increases leptin production, as do some other activities that tend to increase insulin.  The evidence for causation in humans is not totally clear cut, though suggestive.


Why is my peripheral vision better for seeing in the dark? I often walk around my house at night with the lights turned off and one night I noticed that looking straight at an object with very little light available made the object disappear from sight but if I directed my visual else where I could clearly see the object in my peripheral

Its down to the structure of your eyes. The eyes are made of rods and cones, which have difefrences in detecting light.

Now, compare the images below.

As you can probably see, the peripherl vision is predominatlty due to your rods, and your central vision made of cones.

  Measured density curves for the rods and cones on the retina show an enormous density of cones in the fovea centralis. To them is attributed both color vision and the highest visual acuity. Visual examination of small detail involves focusing light from that detail onto the fovea centralis. On the other hand, the rods are absent from the fovea. At a few degrees away from it their density rises to a high value and spreads over a large area of the retina. These rods are responsible for night vision, our most sensitive motion detection, and our peripheral vision.

(Taken from: http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html)

You can read about the photorecptors of the eyes here:
http://webvision.med.utah.edu/book/part-ii-anatomy-and-physiology-of-the-retina/photoreceptors/


Is there any websites that provide the DNA sequences of food samples? We can get many DNA sequences at NCBI websites for free. Is there any websites that provide the DNA sequences of food especially meat, for free?

When I read papers regarding food authentication, they only stated the exact DNA sequence for the primers only, not the DNA sequence of their food samples. Why primers? Is it because scientists from the same field can guess what the sample's sequence will be?

Alternatively, if there's no site that shares the DNA sequence of food samples, is there any other place where I can get DNA sequence of mixed species or mutation? For free.

I am not aware of any websites that provide full DNA sequences for food products specifically. In the context of your question, by "food samples" I am assuming you are chiefly referring to meat, fish, and dairy products (the headline-making categories of food fraud), although similar principles are applied to plant products, oils, rice, and other natural products.

PCR

There are a wide variety of genetic techniques used to detect food fraud or adulteration. These techniques do not look at the entire genome of the animal or plant from which it is derived – that would be extremely expensive and unnecessary. Instead, scientists look at particular parts of the genome that they know will likely help them distinguish one species from another.

This is where the primers come in. DNA primers are short segments of DNA that are used to initiate replication of segment of DNA, and is the vital component of PCR that determines which part of the genome will be amplified. Once the PCR product is amplified, it can be analysed by a variety of techniques. For instance, if the PCR products of various species are known, they can simply be run on gel electrophoresis which separates the DNA products by size. Thus if a band of an unexpected size appears on the gel you know there has been some contamination. There are also more automated methods of detecting fragment size via electrophoresis.

Examples of where these techniques has been used has been to detect:

cow's milk in buffalo mozzarella cheese (López-Calleja et al., 2004)
king bolete mushrooms potentially mislabelled as slippery jack mushrooms (Moor et al., 2002)
domestic pig meat in wild boar products (Conyers et al., 2012)

From the López-Calleja study on mozzarella, one of the gels looked like this:

The PCR was run to detect cow's milk in buffalo cheese. Lane 1 corresponds to 100% cow's milk (it is a very bright band), lane 2 is 10% cow's milk, ranging down to lane 6 which has 0.1% cow's milk (a very faint band), and lane 7 is the pure buffalo cheese which shows no band. Therefore, this assay could be useful to rule out contamination with cow's milk.

Real-time PCR

Running gels is a somewhat old-fashioned way of doing things, and there are better ways to make use of PCR technologies on a larger scale. Real-time PCR is the technique now routinely done to detect food fraud. This is a variant of PCR, which (as the name suggests) allows one to quickly see which PCR products are being produced, in what quantity, and there is no need to run a gel.

For example, real-time PCR has been used to detect:

horse and donkey DNA in otherwise-labelled meat products (Chisholm et al., 2005)
pork adulteration in commercial beef burgers (Ali et al., 2011)
Atlantic cod, Atlantic salmon, and European plaice in fish products (Hird et al., 2012)
honey containing pollen from a specific region (Laube et al., 2010)

An example of what the read-out from the real-time PCR is given below. This example is from the Ali study on beef burger adulteration. The letter A was 100% adulterated (i.e. contained 100% pork instead of beef), letter B contained 10% pork, and so-on to E which contained 0.01% pork. F had no pork. The more pork contamination there was, the sooner on the plot (in PCR cycles) the contaminant reached detectable levels:

About the sequence

As you will see from reading about these techniques, it is not so much the sequence itself which is important – it is fragment size or other properties of the region analysed by PCR that is most practically useful. Sometimes the PCR product may be sequenced for comparison purposes, although I do not believe this is done as a routine screening for food fraud.

Keep in mind that PCR is just one of a number of genetic techniques used in food safety. For example, DNA barcoding and SNPs are also useful techniques that are used in this field. The technology is constantly improving and evolving and no doubt more refined and efficient methods are being developed to detect food fraud.


Did insects and arachnids diverge before or after moving to land? Question: Are arachnids and insects so distantly related that they were already diverging before their (independent) emergence(s) on land?

I am curious to know what the fossil record and molecular evidence has had to say so far about such questions.

To the extent that arachnids and insects might not be any more closely related to one another than they are to crustaceans, and crustaceans are mostly aquatic, it does not seem impossible/implausible to me that the terrestrial transitions of insects and arachnids could have been independent of one another. In fact, considering that wood lice are crustaceans, one can conclude that there have already been at least two independent terrestrial transitions for arthropods, so postulating a third seems less of a stretch to me.

I suppose the thought process behind this is related to this question. Specifically, to the best of my knowledge, flight emerged several times among distinct insect lineages after appearing on land, in cases of convergent evolution. The fact that no lineage of arachnids ever evolved winged flight while many lineages of insect evolved flight independently of one another suggests that the "fundamental recipe" for insects and arachnids is substantially different, i.e. that they are not as closely related as one might have otherwise thought.

Those are two very separate questions. Arachnids include terrestrial groups such as spiders, scorpions, and other arthropods. Arachnids are members of Chelicerata, which includes horseshoe crabs, Sea scorpions (extinct), and probably Trilobites (extinct). Chelicerates evolved in the marine environment, and invaded land afterwards. Arachnids and Insects evolved on land. Hexapods are nested within Crustacea, in a group called Pancrustacea. The likely sister taxon of Hexapoda (Insects, including Protura, Collembola and Diplura) are Remipedia, which are aquatic. See Misof et al. 2014 for the most complete molecular phylogeny, with dates. http://science.sciencemag.org/content/346/6210/763


Why do feces vary so little in color? Why do feces vary in color so much less than the food they are results of? E.g. you may eat food of all kinds of different colors but the resulting feces will almost always be some shade of brown.

The main reason for the color of our stool (or feces) is the presence of bilirubin, a breakdown product of the hemoglobin. The amount of it causes different variations from yellow to dark brown. When the passage time of the food in the intestine and the amount of bilirubin is constant, the color changes very little. Illnesses like diarrhea, which cause a lower passage time have therefore a ligher color because a lower amount of bilirubin can accumulate.

The color of the stool can also indicate illnesses of the internal organs, white stool (or pale clay like colored) can for example indicate problems with the biliary system (drainage system of the gallbladder, liver and pancreas).

You can find some more information here and here.


How does air pass through when we breathe through the mouth? When you sleep with your mouth open, does air pass through the nasal cavities? If not, how will you describe the air that enters the mouth?

The oral cavity and the nasal cavity merge into the trachea which yield to the lungs. As a consequence one can breath in and out through the nose or the mouth.


What is the difference between polar and charged amino acids? Chemically polar amino acids have an uneven (AKA  polar) distribution of electrons over their surface.

Charged amino acids have a charged ion in their structure. This is probably where my knowledge is a little shaky!

I guess I am confused at this point. Does this just mean that charged amino acids are really polar amino acids? If that is correct that would explain why I have seen histidine categorised as a charged amino acid, but has no clear ions.

All amino acids with side chains that are charged at physiological pH are, by definition, also amino acids with polar side chains (e.g., lysine or glutamic acid). The converse is not true; in other words not all amino acids with polar side chains are necessarily amino acids with side chains that are charged at physiological pH (e.g., threonine or asparagine). The pKa of the nitrogen in histidine's imidazole ring is quite close to physiological pH, and in some situations would be charged and in other environments would be uncharged. In either case it would be considered polar (or largely hydrophilic in nature).


How does a pine cone open? When a pine cone is wet, it remains closed. However, when it's dry it opens again.

From the perspective of physics or biomechanics, what is the mechanism that allows a pine cone to open and close as I've described?

From How Do Pine Cones Open (Nature):

  The scales of seed-bearing pine cones move in response to changes in relative humidity. The scales gape open when it is dry, releasing the cone's seeds. When it is damp, the scales close up. The cells in a mature cone are dead, so the mechanism is passive: the structure of the scale and the walls of the cells composing the scale respond to changing relative humidity.

As to the reasons why:

  Pine cones usually appear open because this is considered a more favourable condition for the seed dispersal and germination. This usually happens when the weather is warm and when they touch water or in cold conditions, they tend to close to avoid destruction.

As to the physics/biomechanics of the pine cone opening/closing, there is an interesting article titled Hygromorphs: from pine cones to biomimetic bilayers that discusses objects that respond to environmental humidity to change their shape.

  Using the pine cone as an example that opens when dried and closes when wet, we quantify the geometry, mechanics and dynamics of closure and opening at the cell, tissue and organ levels, building on our prior structural knowledge.


Do people with congenital analgesia feel cold? There are a few diseases that cause an insensitivity to pain. This question asks about the relationship between the cold and pain, which got me thinking:

Is shivering a response driven by the sensation of cold, or a response to the pain associated caused by the cold? This is easy to work out by considering people that do not experience pain.

The key here is if people with congenital analgesia (AKA CIPA, CIP) shiver then we may assume that it is the sensation of the cold, not the pain and the cold, that causes the shivering.

Do CIPA patients shiver in the cold?
Does this mean that the shivering is caused by sensation pathways or
pain pathways?

Disclaimer: I am not an anatomist and do not claim to have a working knowledge of the nervous system. Please point out any and all obvious errors in this question that might explain why this wouldn't be the case in the comments or as an answer if its a big error.

Interesting question. Here what I think (I am not an expert in congenital analgesia so take it with a grain of salt).

The pain provoked by an high temperature is mainly transmitted via the receptor TRPV1 (a Ca2+-channel nocireceptor) while cold sensation is driven by TRPM8 and possibly, for noxious cold, via TRPA1 (two similar types of Ca2+-channels). Those receptors are known as the temperature sensors. As an anecdote, TRPV1 is what give you a pungency sensation when eating spices while TRPM8/TRPA1 give you the cooling sensation from mint.

Mechanical pain is transmitted via other receptors, including TRP channels, but this is not fully understood at the molecular level.

As far as I know, the encoding of pain, and more generally physiological sensations, in the brain are also not yet fully understood but it is very likely that the pathways taken by TRPV1 differs from the one taken by TRPM8/A1 which would suggest that it is possible that CIPA individuals experience high-temperature pain and cold differently at the molecular level and therefore might respond, to some degree, to one but not the other. This also probably applies to mechanical pain vs temperature-driven pain.

I would actually not be too surprised if CIVA people shiver even if not feeling any temperature sensations. Would be interesting to have the opinion or even better the observations of experts in this field.

P.S. I know this is not a definitive answer but I have not enough reputation to comment.


Is there a stem cell dye for education purposes? I need a dye that will stain stem cells (for this purpose the stem cells will proquired from chicken bone marrow).

This will be an educational hands on activity for young teenagers so ideally the dye should be:

Safe
Easy to handle
Stain quickly
Be relatively cheap
Present an obvious colour change under a low zoom microscope or the naked eye

I vaguely remember using a dye years ago that fits this bill, but cannot recall the name or company.

There is no specific dye for stem cells. You would have to do an immuno-histochemical staining for stem cell markers such as Sox2/Oct4 etc.

Usually stem cells have a distinct morphology (round and clustered). You can use Leishman's (or Romanowsky-Giemsa) stain.


Can neutrophils kill bacteria inside other cells? Are neutrophils able to get inside epithelial cells in order to kill bacteria. Therefore, even if a bacteria gets inside the epithelial cells can the neutrophils get inside the epithelium to kill the bacteria?

Also when the bacteria get into blood stream can neutrophils kill the bacteria?

I am not from a biology background. So, a simple explanation will be helpful

Are neutrophils able to get inside epithelial cells in order to kill bacteria.
  Therefore, even if a bacteria gets inside the epithelial cells can the neutrophils get inside the epithelium to kill the bacteria?

No. Firstly because bacteria (except for very special cases) do not enter epithelial(or other) cells - that's what viruses do. Second, neutrophils recognise bacteria based on markers on their cell wall. These markers can come from the bacteria themselves, or from the innate immune system (see complement system) that 'marks' the bacteria, in any case being inside another cell would protect bacteria from neutrophils. Cases are like these are handled by the CD8+ T-cells of the adaptive immune system.

  Also when the bacteria get into blood stream can neutrophils kill the bacteria?

Yes, that's their job and neutrophils are usually inside of the blood(stream), so they could find and kill bacteria there.


Cell cycle-regulated genes and mRNA I am a mathematician and my knowledge about biology is close to zero. I am reading a bioinformatics paper and I would like to understand a bit more about the biology task they are talking about. I cite here the first paragraph of the paper:

  The identification of cell cycle-regulated genes through
  the cyclicity of messenger RNAs in genome-wide studies is a difficult
  task due to the presence of internal and external noise in microarray
  data. Moreover, the analysis is also complicated by the loss of synchrony
  occurring in cell cycle experiments, which often results in additional
  background noise.
  [De Santis, Marianna, et al. "Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes." Bioinformatics (2013): btt671.]

I've searched online for some explanation of this topic and I understand that cell-cycle is a set of events that cells go through for duplicating themselves. I also understand that there are some molecules that are responsible for the regulation of the cell cycle. I know that mRNA is a class of nucleic acid that is responsible for transferring the informations from the DNA inside the nucleus to the ribosomes in order begin the amino acids synthesis. Microarrays are matrices obtained by DNA sequences inside some chip.

What is the cyclicity of mRNA? How is it related to the cell cycle?

I just need a very simple explanation, without any detail, as it is not my field but I am concerned to understand the background.

It is assumed that in order for a cell to divide it must progress through a series of gradual stages. At each of these phases certain proteins have to be manufactured through mRNA and/or modified post-transcriptionally in order to serve an specific proliferative or anti-proliferative role, which overall eventually orchestrates the transit to the subsequent stage.

Conventionally the cell cycle is comprised of 3 "interphase" stages prior to execution of Mitosis itself: G1 (growth, metabolically active), S (synthesis of DNA to duplicate genetic material in preparation for its splitting into two daughter cells), and G2 (gap phase where a numerous of quality control checks are undertaken in the form of surveillance of the newly produced DNA for example to ensure viability of the progenies).

Under these premises, the protein content of a cell at an specific phase is expected to cycle or oscillate in accordance with its requirements, and this is linked to mRNA cyclicity as the most direct responsible process for modulation of protein abundance. It is then related to the cell cycle in the sense that in order to transit from the G1 phase for instance, proteins involved in DNA synthesis will need to be produced, and thus protein factors released for the transcription of those certain mRNAs to take place.

Experimentally such dissection of cell cycle-regulated genes is tricky. Extracting mRNA from pure sub-populations of cells at specific stages of cell division is challenging as the isolation of such cell sub-populations is normally through chemical enrichments and sub-optimal synchronisation procedures. The signal to noise ratio is not ideal under these circumstances.

In brief, the cell cycles through stages in order to divide and such cycling is in itself due to the cycling of certain proteins, the most renown ones are called precisely "cyclins", which are protein markers of cells division. Cyclin D, E, A, B prevail differently at different stages of the cell cycle as a result of the balanced equation of mRNA transcription and post-transcriptional protein modifications (phosphorylation events mark them for degradation for example).
Overall an intertwined and well-coordinated process.

*** EDIT

For a suitable selection of some basic bibliography on the subject, robust sources covering the subject with rigour (less specific and dense than the journal articles I comment bellow) please refer to the following links:

Molecular Biology of the Cell
Molecular Cell Biology
Cell Cycle Regulation
The Cell Cycle Principles of Control

& even a review of the latter here.

HTH


Why pouring salt in the wounds is painful? Pouring salt in the wounds is so painful. I am sure you all experienced this. whats happend there?

De salt particles are alien bodies and can damage the tissue by mechanical means (This would also happen if you pour sand into an open wound). Also, the exposed tissue is vulnerable to dehydration, wich happens faster if the osmotic pressure is higher. Finally, nerve tissue is particulary sensible to changes in the ion composition of its sorroundings, so the added sodium may affect the action potential of the nociceptors.


Does avocado and orange have a common ancestor? While I'm eating my orange, I felt as if I was eating avocado. It might be genetic manipulations perhaps but it made me think if they have a common evolutionary ancestor. Is there?

Here is a website that presents very accuerately the tree of life: tolweb.org/tree

Yes, they have a common ancestor just like any other living things! How closely related are they?

Both species are:

Eukaryotes (cells with a nucleus)
Archaeplastidae (plants)
Angiosperms (flowering plants)

Then, they split their way! Here is the tolweb.org page that correspond to this speciation: http://tolweb.org/Angiosperms/20646

The avocado is in the Laurales family: http://tolweb.org/Laurales/20672

The orange is in the Rutacea (sapindales, rosids, eudicots) family: http://tolweb.org/Sapindales/21051.

You can use the left arrow on the tree of these pages to come back through times and see the different speciation event that seperate both species.

While the orange is a eudicots, the avocado is part of the magnolids. The oldest fossil records of an angiosperm lived about 132MYA (see Crane et al., 2004). So the two species diverge for quite a long time! In order to give a comparison, they are as distant than humans and rabbits (it is a rough personal estimation, I don't have any reference for that!)

Note: The orange is called Citrus sinensis in latin. The species originated in China. The avocado is called Persea americana and it originated in central american (as their names indicate).

I don't know what make you feel that they are closely related. Maybe someone might say some words about their chemical compounds (and their flavour) but at first glance these two fruits taste very differently to me. Or maybe they have some remarkably similar phenotypic traits due to convergence evolution... I don't quite know about that!


How can I measure bacterial alkaline phosphatase activity? I want to measure alkaline phosphatase activity using PNPP in my mutant bacteria strains, but all the protocols I found involve purification of the phosphatase (which I have no need of).

Does anyone know a good protocol which involves using only the supernatant, without purification of the enzyme? What is the preferred buffer for the reaction?

I found this kit that appears to be compatible with biological samples.  Rather than buying the kit you may also be able to imitate / modify their protocol to do the assay with your super natant.


Can a species populated solely by males be saved from extinction? How, if possible, can a species be saved from extinction if the only surviving population are males that cannot reproduce with each other?

The following answer only deals with theorical feasability

Can a species populated solely by males be saved from extinction?

Short answer : No, not with certainty
Nuanced : yes, in some species, it could be possible
It varies in function of how you determinate the sex of your species.
Sex determination is a wide topic, see the appropriate wikipedia page
Some reptilian species are not sexually determined by chromosomes but by temperature. An example is the painted turtle, of which thermal sex determination has been studied by Carrie Lynne Morjan in an article titled Temperature-dependent sex determination and the
evolutionary potential for sex ratio in the painted
turtle, Chrysemys picta
Thermal sex determination allows you to get 2 different sexes from the "same" genome, as temperature will be the driver of the hormonal differentiation.
Cross-species cloning: influence of cytoplasmic factors on development, by Sun and Zhu states that cross species cloning has been successfully made with fishes and mammals.

Nevertheless, cross-species NT has succeeded in cloning some endangered mammals, such as the gaur
In fish, a type of relatively primitive vertebrate, cross-species NT [nuclear transfer] could be achieved in quite a few genetically distant species

It means we are able to use as a mother and egg-layer a different, albeit related, species.
We can, with a massive grain of salt, hypothesize that we could, in a specie solely constituted of sperm producing male, use the oocyte of another specie to clone it, then use the thermal differentiation to make a female out of our clone.
However, I am not aware of any information about how much genome and spermatozoids genetic payload is modified by the sex differentiation. Therefore, it is possible that sex-determined genes cannot produce a sexually naive clone.
For more information, and if you want to research more about it, I recommend you to see the current state-of the art in de-differenciation technics and DNA-demethylation for cloning.
I hope I provided a sufficient answer for you.


What happens to fecal matter if it's continually re-eaten? After class today, the topic of eating one's one fecal matter came up. There was a sharp divide as to how people thought the defecations would change. I realize this is a bit of an odd question but understanding it would help me understand how our body handles waste.

One theory was that the body would continually reuse some elements of the fecal matter such that, eventually and with no other input, nothing would be defecated.

Another theory was that there are elements in the fecal matter that the body would never make any use of, so it would continually get excreted (up until the person died, of course).

Could someone please explain the likely outcome of continually and only eating your own poop (assuming you could stay alive long enough)?

In a healthy person, stool weight depends mainly on the quality and quantity of the diet. The mean stool weight of a normal defecation is about 320 g [1].

Dry weight of fecal matter contains [2]:

30 % bacteria
30 % undigested food and fiber
10-20 % fat
2-3% protein

Let's do the math (the only nutrients in feces are fats and proteins):

20% * 320g = 64g of fats which can release 64 * 9.3 = 595 kcal of energy
3% * 320 = 9.6g of proteins which can release 9.6 * 4.1 = 40 kcal of energy

That's about 650 kcal. 2,000 kcal is a rough average of what people eat in a day. But your body might need more or less than 2,000 [3].

As you can see, fecal matter can't supply enough nutrients. Continuously (re)eating feces and only feces will lead to denutrition, less feces and death.

References:

Seyed Mohammad Kazem Hosseini Asl MD, Seyed Davood Hosseini MD. Determination of the Mean Daily Stool Weight, Frequency of Defecation and Bowel Transit Time: Assessment of 1000 Healthy Subjects
shigeta's answer on What is the composition of human feces?
HowStuffWorks.com. How many calories does a person need daily?


Identifying flying insect from southern Poland / Upper Silesia area Yesterday evening, I spotted this quite huge insect at my home in southern Poland (the exact location of the place). Unfortunately, I have only a very low quality pictures available at the moment:

Some details:

found in southern Poland / eastern Europe,
about 3 cm long,
quite fat (if I may say so),
seems to have 4 pairs / 8 legs in total,
airborne / able to fly (though quite slowly).

The quite huge (as per typical insect in Poland) size of this species was kind of surprise for me, but its behavior was even more surprising to me:

As pictured, it was able / willing to rest (copulate?) one on another even in groups of three (I failed to picture this), remaining still / not moving at all even for as long as half of hour.
After such resting / copulation ended or was interrupted the species on top was thrown off, falling down to the windowsill beneath.
It was then lying there up-side-down on its back, again remaining still and not moving at all even for 10-15 minutes.
Then it was kind of waking up from some kind of stasis, turning over walking a little bit around the windowsill.
Then it was flying up, flying around a little bit.
Finally, it was trying to rest / copulate with the species still on my window's mosquito net (or with the couple being there).

And then, the whole cycle was repeating until (late evening) only one species remained on mosquito net, which was also gone late in the night (not found the following morning).

Found it, with a lot of help from my local neighbors. It is Melolontha melolontha or cockchafer.

From English Wikipedia:

The cockchafer, colloquially called May bug or doodlebug is a European beetle of the genus Melolontha, in the family Scarabaeidae.
Once abundant throughout Europe and a major pest in the periodical years of "mass flight", it had been nearly eradicated in the middle of the 20th century through extensive use of pesticides and has even been locally exterminated in many regions. However, since an increase in regulation of pest control beginning in the 1980s, its numbers have started to grow again.

Here, where I spotted this insect (Upper Silesia) it is called in local language (in Silesian language) "julik", which is quite correct, since they seems to appear in July.
However, as per above cited part and as per Polish counterpart to above cited article, officially this insect is called after May, either "May bug" (English) or "Chrabąszcz majowy" (Polish). Most likely because adult forms of this species appears mature by the end of April and through May.


How long do human egg cell grow up? I read article about alcohol harm where written that child may bear with birth defect cause mother used to drink alcohol 10 years ago so egg cell stay damages that long.

I don't believe that human egg cell wait for such long time until activated.

How long human egg cell grow up until sperm fuse it?

How long human egg cell grow up until sperm fuse it?

Ovules are made while the female is still in the uterus of her mother. The ovules (in the form of ovarian follicles) are kept in the ovaries for a long time, and just a month before leaving the ovary (ovulation), the ovarian follicle (and the future ovule) gain in size. In other words, the ovules are slightly older than the age (counting from birth/labour) than the person carrying them. You'll find more information on wikipedia > ovule > ovule Development, oogenesis, and ovarian follicle.

Does it address your interest about alcohol consumption?

Now, I don't think this question/answer address your interest about alcohol consumption. Whether or not the ovule is create by a division that happen just a day before ovulation  or many years earlier doesn't change anything to the fact that this ovule has experienced alcohol consumption (either directly or in the lineage) before.

Where to ask the question that I suspect interest you the most

If you want to question the article you read about alcohol consumption, the best you could do is to go on Skeptics.SE, link the article, quote something from the article and ask "is it true?"


Relationship Between Evolution and the Increase of Entropy of Earth I was confronted by this question:

Biological evolution of life on Earth, from simple prokaryote-like cells to large, multicellar eukaryotic organisms,

A) has occurred in accordance with the laws of thermodynamics.
B) has caused an increase in the entropy of the planet.
C) has been made possible by expending Earth's energy resources.
D) has occurred in accordance with the laws of thermodynamics, by expending Earth's energy resources and causing an increase in the entropy of the planet.
E) violates the laws of thermodynamics because Earth is a closed system.

Answer:  A

However, I do not understand. Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased.

I would answer D... Where am I going wrong?

However, I do not understand. Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased.

The universe and the earth are not equatable. Earth is not an isolated system. Life causes entropy of the earth to decrease. This is offset by increased entropy of the sun, which is the primary source of energy for the earth. Overall, the entropy of the universe increases.


Why does ostrich and other birds like pigeon swallow stones? I have read in my book that birds swallow stone to help in their digestion process. What is the need of swallowing stones? And how does it aid them?

Birds do not have teeth so stones help in the process of grinding food.

Before even going to the stomach the food it starts to be processed in the "Crop". However is in the "Gizzard"  that the stones play a big role helping this muscular sack to mince and grind the food (the link sends you to an image of an open gizzard with pebbles inside).

Food and stones are present at the same time into this organ, therefore during peristaltic and contraction movements the friction between stones and food allow more efficient grinding.

Here you can a detailed description of the chicken digestive system that can be largely applied to birds in general.


Cooking with sawdust In a book about post-war Japan (Embracing Defeat, Dower) the author mentions a process for making sawdust at least partially edible, so it could be used in recipes in a 1:4 ratio with flour for cooking. The author says the sawdust was "fermented," as I recall.

My question is whether this is anything more than marginally possible. After all, kimchee, yogurt, beer, and other fermented foods aren't necessarily easier to digest. Is there a fermentation process involving bacteria that break down cellulose that might make wood even slightly nutritious?

My impression is that in forests the process of breaking down wood does not initially involve bacteria but other microorganisms; on the other hand, ruminants such as cows use bacteria to help them metabolize.

Thanks for any insight.

Yes. I think it would certainly be possible for raw sawdust to be made digestible by humans through some sort of fermentation process with some kind of microbe or another.

Pickling (as is done with kimchee and cucumbers and lots of other fruits) uses naturally occurring bacteria that are artificially selected for by using a strong brine solution so that most microbes die but the ones that naturally survive in strong brine also convert the organic materials they find (raw cucumber or cabbage) into different organic materials (pickled cucumber or pickled cabbage in the case of kimchee).

If you could find a microbe that could digest wood (there are many I'm sure; the gut bacteria in termites provide evidence of at least one or some), and if you could find a way to select for that particular microbe, then fermenting sawdust for nutritious human consumption becomes feasible. The only remaining problem is finding that particular microbe whose excretions were digestible to humans.


Turning off the IP3 cascade After PIP2 has been converted into IP3 and DAG by phospholipase C (PLC), some of the IP3 opens calcium channels in the endoplasmic reticulum and calcium ions can enter the cytoplasm. However, it is unclear to me how this IP3 cascade is terminated. Is IP3 somehow degraded, do high calium concentrations result in closure of the calcium channels or is there some other mechanism?

IP3 is indeed degraded, this is done by a specific phosphatase which is called "Phosphoinositide 5-phosphatase (INPP5A)". It catalyzes the reaction in the following way:
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O $⇌$ 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate
The enzyme cuts of the 5'-Phosphate group and leaves 1,4-Inositolphosphate, which is subsequently recycled. The schematics looks like this in the left side (figure 1 from the reference):

Reference:
Inositol trisphosphate 3-kinases: focus on immune and neuronal signaling


Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors? I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a heat map how their expression varies across clusters. Can any one give me a hint on which tool or method I can use to find out which of my genes code for cytokine receptors?

Thanks in advance.

I'm sure there are many ways to go about this (including literature research via PubMed), but for a start, I searched the GO term data base which, for the search term "cytokine receptor activity" returned this, which includes a number of genes which I can download as an excel file and match them with my gene set using R.


How do I generate a phylometric tree given species names? I have a list of species. I want to put those names into a tool and get back a visualized tree that includes names of shared order, suborder, family and genus.
Is there an existing tool that does this job for me or do I need to program my own solution?

(The solutuion in the other thread only shows the name of the species but not order/suborder/family/genus)

Biopython may have a module for this. I know it can parses phyloxml files and render a tree. You can query the ncbi database for the xml files. Here is some sample code that will render an ascii tree given a phyloxml file...

from Bio import Phylo
tree = Phylo.read("examplephylo.xml", "phyloxml")
Phylo.drawascii(tree)

There is also support for drawing more graphically rich trees using matplotlib. There is a .pdf book for Biopython that you can download from this url http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

Hope that helps


How does the hypothalamus get the information out of the blood? The hypothalamus is a very important nervecentre which checks continuously how many hormones neurotransmittors and other molecules and information (like temperature) are there present, so it can keep a kind of balance in our body. But how does the hypothalamus do this? Does he has so much different receptors on his membrane for each type of molecule one or does it do that in a different way?

First of all, there is not such a thing as "the" hypothalamic membrane. The hypothalamus consists of multiple nuclei, and each nucleus contains numerous cells (neurons and glia cells).

The mechanisms by which the hypothalamus senses hormone concentrations in the peripheral blood are rather complex. In recent years, considerable research has been done to elucidate the central mechanisms underlying thyroid homeostasis [6], which involve the regulation of TRH release from the hypothalamic paraventricular nucleus [1, 2]. Therefore, my following explanations are focussed on the control of TRH secretion, but similar considerations apply to other hormonal systems [7-9].

First, hormones have to be conveyed by special transport proteins across the blood brain barrier (BBB). In case of thyroid hormones, this is accomplished by tanycytes in the circumventricular organs [3]. They control the transition of hormones from the blood to the cerebrospinal fluid (CSF), and partly directly to glia cells via the transport protein OATP1C1. In glia cells thyroxine (T4) is deiodinated to form the more active hormone triiodothyronine (T3). T3 is then transferred to neuronal target cells via the transporter MCT8 [4, 5], where it exerts its homeostatic effects by inhibiting TRH release. Hypothalamic TRH secreting cells have, however, multiple afferent signals. In addition to thyroid hormones they include clucocorticoids, leptin, alpha-MSH, norepinephrine, cocaine and amphetamine-related transcript (CART), endocannabinoids, agouti-related peptide, neuropeptide Y (NPY), GABA, galanin and probably multiple additional signalling substances. This enables the TRH neuron to act as an integrator of energy homeostasis [1, 2, 6].

Of course, the TRH-secreting cells in the respective hypothalamic nuclei have receptors for all afferent hormones and neurotransmitters. Some of them (e.g. for catecholamines) are located on the cell membrane, others (e.g. for thyroid hormones or steroids) in the nucleus.

As mentioned, similar considerations apply to other hormonal systems [7-9]. Recent research suggested e.g. the existence of a receptor-mediated transport system, which conveys insulin trough the blood-brain barrier [9].

1: Joseph-Bravo P. Hypophysiotropic thyrotropin-releasing hormone neurons as transducers of energy homeostasis. Endocrinology. 2004 Nov;145(11):4813-5. PMID: 15489313. http://www.ncbi.nlm.nih.gov/pubmed/15489313

2: Joseph-Bravo P, Jaimes-Hoy L, Charli JL. Regulation of TRH neurons and energy homeostasis-related signals under stress. J Endocrinol. 2015 Dec;227(3):X1. doi: 10.1530/JOE-14-0593e. PMID 26527565. http://www.ncbi.nlm.nih.gov/pubmed/26527565

3: Rodríguez EM, Blázquez JL, Pastor FE, Peláez B, Peña P, Peruzzo B, Amat P. Hypothalamic tanycytes: a key component of brain-endocrine interaction. Int Rev Cytol. 2005;247:89-164. Review. PMID 16344112.
https://www.ncbi.nlm.nih.gov/pubmed/16344112

4: Kersseboom S, Visser TJ. Tissue-specific effects of mutations in the thyroid hormone transporter MCT8. Arq Bras Endocrinol Metabol. 2011 Feb;55(1):1-5. PMID 21468514.
http://www.ncbi.nlm.nih.gov/pubmed/21468514

5: Bernal J, Guadaño-Ferraz A, Morte B. Thyroid hormone transporters—functions and clinical implications. Nat Rev Endocrinol. 2015 Jul;11(7):406-17. doi: 10.1038/nrendo.2015.66. Nat Rev Endocrinol. 2015 Sep;11(9):506. PMID 25942657.
http://www.ncbi.nlm.nih.gov/pubmed/25942657

6: Hoermann R, Midgley JE, Larisch R, Dietrich JW. Homeostatic Control of the Thyroid-Pituitary Axis: Perspectives for Diagnosis and Treatment. Front Endocrinol (Lausanne). 2015 Nov 20;6:177. doi: 10.3389/fendo.2015.00177.  PMID 26635726.
http://www.ncbi.nlm.nih.gov/pubmed/26635726

7: Thon M, Hosoi T, Ozawa K. Possible Integrative Actions of Leptin and Insulin Signaling in the Hypothalamus Targeting Energy Homeostasis. Front Endocrinol (Lausanne). 2016 Oct 20;7:138. PMID 27812350.
http://www.ncbi.nlm.nih.gov/pubmed/27812350

8: Herman JP, Tasker JG. Paraventricular Hypothalamic Mechanisms of Chronic Stress Adaptation. Front Endocrinol (Lausanne). 2016 Oct 31;7:137. PMID 27843437.
http://www.ncbi.nlm.nih.gov/pubmed/27843437

9: Blázquez E, Velázquez E, Hurtado-Carneiro V, Ruiz-Albusac JM. Insulin in the
brain: its pathophysiological implications for States related with central
insulin resistance, type 2 diabetes and Alzheimer's disease. Front Endocrinol
(Lausanne). 2014 Oct 9;5:161. doi: 10.3389/fendo.2014.00161. PMID
25346723,
http://www.ncbi.nlm.nih.gov/pubmed/25346723/


Standard Classification of Disease I am working on a project for health center. It involves the creation of a database of all diseases. Currently I want to classify disease on the base of their category based on international standard.
Did anyone know where i can find one, I did a lot of research but was only able to come across this which seem not very useful to me: ICD

The two I know of off the top of my head are

OMIM : Online Mendelian Inheritance in Man. This is very good and very well organized but only deals with inheritable diseases, no infections etc.

Human disease ontology. From their webpage:

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Northwestern University, Center for Genetic Medicine and the University of Maryland School of Medicine, Institute for Genome Sciences.

The DO is probably perfect for your needs.


Insect Identification. Moth or dragonfly or? Found on the exterior wall of my house taking cover from the rain it seems. Wingspan is approximately 5cm. I live in the South SF Bay and it has been rather cold and rainy this week.

Found it. Amblyptilia acanthadactyla from Europe. He must be tired.

Update: It's a Geranium Plume Moth! Beautiful pics! I have geranium plants in my garden. Why have I never seen these? Thanks for the right find, Arthur!


How can I evaluate the hydrophobicity and/or surface charge of a protein? How should I evaluate protein surfaces in terms of hydrophobicity and surface charge properties of the surface.

Particularly I am looking to compare hydrophobic patches or surface charge between two proteins, from .pdb or Fasta sequences for example.

The goal is to study protein adsorption mechanism in the context of protein purification.

Since you have the structures the best option, in my opinion, is Pymol.

Hydrophobicity

Open Pymol. Load up your protein of choice. Download color_h.py which is a script from the University of Osaka that colours the residues according to Eisenberg's scale of hydrophobicity. Load this into Pymol by File->Run->PATH/TO/color_h.py. Then in Pymol run the following commands

show surface
color_h

Note that the script can be edited to use whatever scales you like. @mimat points you toward protscale and I would suggest the same. The Eisenberg scale is a rather old consensus scale. More up to date scales might be more appropriate in your case.

To start quantifying this, Pymol has tools for calculating solvent accessibility for example.

Additionally PDBSum and PDBe-PISA can estimate solvent accesible surface area.

Surface charge

Vacuum electrostatics

The quickest and easiest way to generate electrostatics is with the inbuilt vacuum electrostatics tools. In Pymol, select the action button (A)->generate->vacuum electrostatics->protein contact potential.

ABPS

Since the Pymol inbuilt electrostatics make a lot of assumptions, for publication it is best to get a much more accurately quantified surface map. However, ABPS is a bit more involved. Read the wiki if this sounds more like what you need.


Is the human body composition real? In Fullmetal Alchemist when Ed goes to disprove to Rose the Sun God's "miracle" to bring humans back to life by proving that science (in the form of Alchemy) can create people by saying

  Water (35 L), Carbon (20 kg), Ammonia (4 L), Lime (1.5 kg), Phosphorous (800 g), Salt (250 g), Saltpeter (100 g), Sulfur (80 g), Fluorine (7.5 g), Iron (5 g), Silicon (3 g) and trace amounts fifteen other elements.

I am wondering, is this composition true in real life? if so what are fifteen trace elements?

No, it's only a very rough approximation.

I actually made a spreadsheet to figure this out.

The rows represent the composition as described by the quote.  I translated each into its appropriate chemical formula and converted all measurements to grams.  Then I found the atomic weight of each.  The gray area represents the grams of each element made up from that particular description, which are summed up in the first summary line.  The second summary line are the values as specified in The Last Word's link, which are based on a 70 kg (154 lb) person.

You can see that while some of the numbers are in the right ballpark, most are still off by significant amounts (the bottom row is percentage error - negative means the anime was too low, positive that it was too high).


What are possible health risks to women having large numbers of children? What is the possible health issue the women would face in this record?

  The record for most children born to a single couple belongs to the
  first wife of Feodor Vassilyev of Russia. In 27 pregnancies between
  1725 and 1765 she gave birth to 16 pairs of twins, 7 sets of triplets,
  and 4 sets of quadruplets for a grand total of 69 children.

A common problem for any woman who has experienced pregnancy and childbirth is damage to the levator ani muscle, which comprises a portion of the "pelvic floor."

 from here

This can cause a number of symptoms, including urinary incontinence (due to an increase in pressure on the bladder from less effective muscular support), and possible prolapse of the bladder, uterus, or rectum into the vagina, again due to the weakening of the pelvic floor.


Intro Bio question: dihybrid punnet square Today we had our exam. There was a punnet square for two genes. and when I multiplied , for example, Ry × rY I wrote the answer as RyrY. When I returned back home I realized that I may have made a mistake because the book used to write them as RrYy. So is my answer write or wrong? why? I also freaked out because there were 16 boxes in the punnet square so does that mean that I'll lose 16 points? I got everything else in the exam correctly. So I'm freaking out because I don't know if I'm getting a 100 or 86 which will throw all my work the entire semester. Please respond as soon as you can. I feel like I'm having a panic attack.

Hah! You can relax. There's no difference between RyrY and RrYy, as there is no fundamental ordering of genes like that. That being said, the standard convention would be to write RrYy (or at least RryY), so if your grader is a pedantic hardass they might take off a couple of points, but probably not the whole 16.


What is considered incorrect for a cladogram's time axis? I am looking for help (and possibly references) regarding the correct mapping of time in a cladogram. As far as I know, it is considered incorrect to draw a time axis diagonally in a cladogram as shown below:

This setting would lead to conclusions like: Species B and ancestor b lived at the same time, because they would both fall upon the same place on the time axis. But we know this is incorrect. Or is this an acceptable positioning for a time axis?

The image below correctly represents the time axis, if I'm not wrong, using a vertical axis.

This positioning makes it clear that species B and b are not living at the same time. In this case, species B is alive and b is an extinct ancestor.

In your first example, each species becomes "frozen in time" once it evolves implying there is no further change. A slightly more complex cladogram will help.

Imagine the species A ancestor, after branching off the remote ancestor, serves as the ancestor to species E. You need to draw that line in some direction other than along A. Most popularily, that line would extend upward to the right. With the temporal axis as you first show, how did species E even evolve since A is frozen in time? Furthermore, the advantage of a vertical time axis allows us to see that species E appeared after species B and a bit before species C (horizontal dashed line).


Rejection of valid theories of biology on theoretical grounds Is there a theory in biology that was initially disregarded as false (because of critical or contrasting perspectives) and only recognized as important after a considerable time, possibly only in recent years, thus significantly impeding its development?

The idea that organisms with mitochondria derive energy from respiration through a proton motive force was considered controversial at the time.

This is the best reference I could find at the time:

  His theory explained that it was the energy captured from those protons
  returning to the matrix and not energy stored in an undefined
  high-energy covalent chemical intermediate that was then used to drive
  ATP synthesis. This Nobel Prize-worthy concept (1978) was so counter
  to the leading theories of the day that the field spurned it for the
  better part of a decade.

Pagliarini, D.J., Rutter J. Hallmarks of a new era in mitochondrial biochemistry 2013  Genes Dev.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877752/


Is there any alternative to x-gal white/blue screening for the monitoring of pseudomonas aeruginosa beta-galactosidase activity on agar plate? I want to screen a pseudomonas aeruginosa mutant library carrying a lacZ transcriptional fusion for dysregulating mutations. I tried to do it on xgal plates but the accumulation of the blue color makes the screening difficult. I saw that people are using macconkey or endo agar media for two-hybrid beta-gal screening in E. coli for instance. I wonder if it would be something to try even with pseudomonas (which would only possess the lacZ gene, so no permease etc...) and if someone here ever tried it ? Or if other beta-gal substrates could be used for this application ?
thanks
Julian

I think your problem will be even worse when you'd use MacConkey or Endo plates. You can see differences between different kinds of bacteria / expression of certain enzymes on those plates, but the coloring / decoloring is based on soluble compounds that easily diffuse.

Hydrolysis of xgal creates an insoluble product that's staying more or less at your colony. Of course it's not perfect and after a while you have a completely blue plate, but this would happen much faster with a soluble compound.

Try adjusting your conditions so you can look at the plate before it's completely blue. Things you could try: look earlier, plate them a little bit more dilute so colonies are further apart, use less xgal so your final coloring is less intense, look for some papers that use xgal for screening and steal their tricks.


Stomata during night (respiration) How does carbon dioxide from respiration diffuse out of the leaf during the night?

Do stomata close completely during night?

Leaves have no need to 'exhale' carbon dioxide - it gets consumed by photosynthesis.

Elsewhere in the plant, metabolic processes produce carbon dioxide. This escapes via inter-cellular gas channels that, in woody plants, terminate as lenticels (little pores) on the stem surface. Oxygen for metabolism diffuses into the plant in the same inter-cellular spaces as carbon dioxide diffuses out.

With roots, the oxygen necessary for metabolic processes is dissolved in water.

If you've meant to ask about leaf adsorption of carbon dioxide and when stomata close, it depends on what carbon fixation scheme the plant exhibits, CAM, C4, or C3.

You might want to also consult an  answer I gave to a similar question previously posed here.


Does anyone know good software for producing tanglegrams? I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for software with which to do this, and I have tried using Dendroscope and TreeMap, but can't get to grips with them.

I want to produce something along the lines of this;

Dendroscope

Using Dendroscope, I opened the provided example file trees.new. This opens a new window with 16 trees in it.

Shift click on the first two trees (Tree1 and Tree2).
Choose Algorithms $\rightarrow$ Tanglegram...
This will compute the tanglegram and open a new window.

At this point, I get:

There is nothing special in the trees.new file, just 16 Newick trees. So it looks like all you need is to have your trees in the same file or use File $\rightarrow$ Add from file.

I think that the tricky part is that your trees have to have the same tip labels, so that they can be lined up optimally. So in your example, Phalacrocorax pygmaeus and Pectinopygus excornis must have been named the same in the original Nexus file and then modified to produce the final figure.

TreeMap 3

TreeMap requires some preliminary setup. Basically you create a Nexus file manually. Using the 4taxonmatch file from the examples, you can get the basic layout. You have a HOST block and a PARASITE block. Within each one of those is a TREE block, which contains the Newick formatted tree.

The RANGE block inside the DISTRIBUTION block contains the mapping table. Here p maps to u, etc. This is the connection between host and parasite.

#NEXUS
BEGIN HOST;
TREE * Host1 = (u, (v, (w, x)));
ENDBLOCK;

BEGIN PARASITE;
TREE * Para1 = (p, (q, (r, s)));
ENDBLOCK;

BEGIN DISTRIBUTION;
RANGE
    p: u,
    q: v,
    r: w,
    s: x
;
END;

In contrast, you get the correctly labelled tree directly. See below.


What is the difference between intrinsic and extrinsic apoptosis? Hello my Professor has been teaching about apoptosis and sometimes makes the distinction between extrinsic and intrinsic. I am not sure if I know for sure what this means. Does this just refer to intrinsic is a cell doing itself while extrinsic refers to Fas ligand? Thanks.

In both pathways 'the cell does itself' the difference is in the reason.

In short:
Intrinsic apoptosis is a response to 'internal damage' eg. damaged DNA, chromosom rearrangement, hang ups in division, hypoxia, etc. that the cell senses itself and 'decides to commit suicide'. This is done by the mitochondrial pathway - release of cytochrome C from the mitochondria activates the caspase cascade that results in programmed cell death. This is like "I'm too damaged, I must die".

In the extrinsic pathway as you have mentioned is indeed related to the FAS ligand (and Fas/FasL being the main pathway for apoptosis), but that is not the only external signal as TNF (also known as TNA-alpha) binding to TNF-R1 (tumor necrosis factor receptor 1) may also lead to apoptosis. These pathways are usually activated by the immune system for example in cellular immune response. This is like "You're abnormal / dangerous / infected, you must die".

Both pathways activates the caspase cascade at some point that results in apoptosis. Either way the actual process of apoptosis is carried out by the cell itself in a programmed, regulated manner.

Source: http://en.wikipedia.org/wiki/Apoptosis
This papaer offers a great review on the topic, including both pathways:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/

I'd like to quote few  important parts to support my answer:

  The extrinsic, intrinsic, and granzyme B pathways converge on the same terminal, or execution pathway. This pathway is initiated by the cleavage of caspase-3 and results in DNA fragmentation, degradation of cytoskeletal and nuclear proteins, cross-linking of proteins, formation of apoptotic bodies, expression of ligands for phagocytic cell receptors and finally uptake by phagocytic cells.

(...)

  The extrinsic signaling pathways that initiate apoptosis involve transmembrane receptor-mediated interactions. These involve death receptors that are members of the tumor necrosis factor (TNF) receptor gene superfamily

(...)

  The intrinsic signaling pathways that initiate apoptosis involve a diverse array of non-receptor-mediated stimuli that produce intracellular signals that act directly on targets within the cell and are mitochondrial-initiated events.


What is an 'ex vivo' experiment? Simple terminology question:

Is there a hard boundary between in vitro and ex vivo?
Is there a hard boundary between in vivo and ex vivo?

Suppose a sensory neuron is electrically recorded in the following settings:

Surgically accessing through the animal's skin, and patch-clamped,
Tissue surrounding the neuron is almost separated, but still dangling from the larger part of the animal, and patch-clamped,
Same as above, but the slight dangling connection is cut,
The sensory neuron is isolated and put in an artificially oxygenated medium

The sensory neuron is assumed to have purely feedforward signal, and is perfectly healthy in all conditions. Which conditions, if any, are in vivo, in vitro, or ex vivo? (Feel free to propose better hypothetical experiments. I know this example is not the best.)

Am I the only one confused about these terminologies?

Ex vivo simply means "outside the normal, living organism", whereas in vitro means "within glass", usually in a cultured system.  They are not exactly same as there is no need for the work to be done in a culture system, although both are not in vivo.  Harvested tissue could be examined ex vivo without being in a test tube, or surgical systems could be tested ex vivo on artificial organ models.  In vivo requires the natural, living organism, although it depends on just how much you are perturbing the natural.

To answer your scenarios,

in vivo
ex vivo, as it is not within the normal organism, although I could understand someone taking issue with that; definitely not in vivo, which is usually for normal conditions only, even including temperature.
ex vivo
If you mean the artificially oxygenated environment of a tissue culture system, then in vitro; if you mean the artificially oxygenated environment of a lab bench with an open $O_2$ valve, then ex vivo would suffice.