Pharmacology Half Life Calculation I'm really stuck on this question. I'm being asked to find the half life of a drug.

The Vd is 50L/kg. The clearance is 0.1 L/hr/kg. The patient weighs 70 kg.
Equation is:
T1/2 (halflife) = 0.693 * Vd / Cl.
I keep getting 0.693 * 50 / 0.1
               = 346.5
The right answer is 14.4 days but I can't figure it out.
Thanks in advance

You have done the calculation correctly it is just the answer you have is in hours, try dividing by 24.

A  good method of checking answers is to use a trick which is horribly called "Dimensional Analysis". This basically means writing out your equations but use the units of each value rather than the value itself

so in this case you have T1/2 = Vd/Cl      (removing the unitless 0.693)

the units for this are then ? = (L/kg)/(L/hr/kg)

in this case the litres and the kilos cancel to 1/(1/hr) or just hours, comparing this with the correct answer which is in days should then be a little more obvious


Snake with orange spots found in South Florida I found this snake near my doorstep. What species is it?

Looks very much like a red rat snake (Pantherophis guttatus). Nonvenomous, and wonderful.


Trying to differentiate between the three muscle tissues with small pictures For an assignment I have to differentiate the three types of muscle tissues in these three pictures
.
I'm having difficulty seeing the striations and branches etc. because the pictures are so small. Am I missing something?

Without answering the problem for you, because you have not shown work yet to try to figure out which is which, let me tell you that you have three options.

Skeletal Muscle- striated, peripherally located nuclei, same thickness along length, non-branching
Cardiac Muscle- striated, few centrally located nuclei, branches and anastamosis
Smooth Muscle- non-striated, centrally located single nucleus per cell, tapering ends

Now, hopefully, based on your pictures, which are indeed sufficient for you to figure out which is which, you can answer your own question. Good luck!


Examples of animals with different number of chromosomes that can interbreed? When I was first started to write this question, I wanted to know how species evolve to have a different chromosomal arrangement, such as having two pairs of chromosomes instead of one? However, I think I have resolved my misunderstanding by reading:
http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/

My basic misunderstanding was that I thought animals with a different number of chromosomes couldn't reproduce, which appears to be wrong. My question is now, are there examples of animals that can interbreed that have a different number of chromosomes (particularly offspring that are not sterile)? Is there a species that is known to have a variation in the number of chromosomes (yet, somehow, hasn't yet resulted in complete speciation); or are there two species that can be interbred and result in fertile offspring?

Such examples are not that rare: multiple species are polymorphic for supernumerary (B-chromosomes), others are known to show intra-specific Robertsonian polymorphism (fusions of acrocentric/separation of metacentric chromosomes).

One very well studied example, which covers both intra- and inter-specific crossings, are isopod crustaceans from the Jaera albifrons complex. They show Robertsonian variation (and additionally sometimes B-chromosomes):

different species in the same location normally have different chromosomal numbers;
on the macrogeographical level at least some species show certain gradients in chromosomal numbers;
sometimes the same variation can be observed on the level of local populations.

Hybrids between species are viable and not sterile, but rare in nature. Fecundity of hybrids is lower than that of the parental species, and this seems to serve as an additional post-zygotic mechanism of species isolation.

Crossings between specimens of the same species with different numbers of chromosomes do occur in mixed populations and are also possible for parents coming from different extremities of the above mentioned chromosomal cline. In the case of mixed populations frequency of these hetezygotes is less than expected by Hardy-Weinberg. Such offspring is fertile, and its lowered frequency is associated with higher incidence of abnormal meiosis.

On the cytological level (normal) meiosis in a heterozygote individual is remarkable in showing trivalents instead of bivalents for the polymorphic chromosomes:

(a metaphase with a trivalent in the center and two bivalents) (from Staiger & Bocquet 1956)

In addition, in four out of five species of the complex chromosomal sex determination is of the following uncommon type: males are homogametic with sex chromosomes ZZ, while females are heterogametic with ZW1W2 chromosomes. So, females normally have in total an odd number of chromosomes and in their meiosis one observes a trivalent similar to the one shown above: the metacentric Z-chromosome conjugates with the two acrocentrix W-chromosomes.

Some references available on-line:

Lécher & Prunus 1971 (in French)
Solignac 1981 (English, on isolating mechanisms in general)
Lécher et al 1995 (a review in English)
Kappas et al 2013 (a review in English - see pages 23-26)

These are highly relevant to the question, but not accessible on the web:

Lécher 1967 (Cytogénétique de l'hybridation expérimentale et naturelle chez l'Isopode Jaera (albifrons) syei Bocquet)
Lécher 1967 (Polysomie autosomique chez l'Isopode Jaera albifrons syei Bocquet)
Staiger & Bocquet 1956 (Les chromosomes de la super-espèce Jaera marina (Fabr.) et de quelques autres Janiridae (Isopodes Asellotes))


Strange fast growing mushroom like entity I found this in my lounge today.
This room was cleaned less than 48hours ago, with no sign of this growth.

We sweeped and mopped, using the same floor cleaner we always do.

The two images below is of the same corner, but with the growth lifted in one image.

The consistency is like a fungus or mushroom and can probably be removed from the wall as one piece without much effort.

One of the walls close by do suffer from damp on occasion, but we have been in this house for over two years and have not had anything like this appear.

Please help!

This is dry rot. It could be one of several species, including Serpula lacrymans, Meruliporia incrassata and Fibroporia vaillantii. It is a fungus that feeds on and decomposes wood. Despite the name, some moisture is required for growth, so
it makes sense that your wall suffered from damp. The fruiting body will darken at the center as the spores appear.

Example images of dry rot fruiting bodies:

Photo by Seabrooke Leckie

Photo by Dave Brown


How to assess if biological measurements follow a normal or a log-normal distribution I am using a dataset composed by $m$ samples and $n$ features (genes). Each data point is real number.

I want to understand how to preprocess data before analysis, in particular: do data points follow a normal or a log-normal distribution?

I thought about using qqplots and searching for different tests to assess the form of the distribution, but I have a doubt:

Do I have to assess the form of:

each sample distribution
each feature (gene) distribution
the whole dataset ($m$ samples x $n$ features (genes))

?

From personal experience, nearly all count data whether from microarray or reads from RNAseq of some kind, requires a log transformation of the counts. Usually a small fraction is added to all values before doing so to zero protect. Log2(counts + 0.5) or some such.   This is independent of the treatments. If you log transform one sample, you will do the same for all samples. To examine for normality, a simple way is to look at the histogram of counts (by all samples or by each sample) before and after transformation. Roughly bell shaped -> proceed.

Pictures below from my data. Although the data are from RNAseq, microarray data should be similar.

R code here:

hist(t$counts,breaks=100,main="Histogram of Raw Counts from RNAseq")
hist(log(t$counts + 0.5,2),breaks=100,main="Histogram of Log2
transformed Counts from RNAseq")


Crispr complex in human cells? Is the crispr (where the parts of Virus DNA is saved) section of the DNA existing in human cells aswell or is it just in bacteria cells?

No analogues of the CRISPR-Cas system have been found in any eukaryotic species, including humans. So far, it appears to have evolved only in prokaryotes and archaea.

Reference: Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence


Why do classic psychedelics not cause withdrawal, despite high tolerance? "Classical" psychedelics, such as LSD, DMT, and Mescaline, are serotonin agonists that cause hallucinogenic effects. They are notorious for having rapid tolerance, such that after consuming such substances, one would need to (at least) double the dose to feel the same effect if taken daily. No other substance, not even opiates, have such a high tolerance curve.  While this tolerance contributes to the less-addictiveness nature of psychedelics, there is no observed withdrawal. Furthermore, because of the high Therapeutic Index, some users may consume large doses.

Wouldn't such tolerance result from 5HT downregulation, and therefore cause withdrawal? Is it something with serotonin, or is the mechanism different?

There is evidence that 5HT downregulation is what actually causes the effects of anti-depressants. This explains why it takes a few weeks for SSRIs to kick in. Perhaps, this explains why psychedelics can have an antidepressant effect? Perhaps, unlike other neurotransmitters, activation and downregulation of 5HT is not harmful?

https://www.ncbi.nlm.nih.gov/pubmed/7972628

Short answer
Withdrawal effects are generally associated with drugs that induce feelings of euphoria by stimulating the reward center of the brain, either directly (cocaine, morphine) or indirectly (alcohol, nicotine). The classic hallucinogens have little effect on the dopaminergic pathways and hence do not cause serious withdrawal effects as observed with other classes of psychoactive drugs.

Background
Withdrawal is defined by the WHO as:

  a group of symptoms [that] occur on cessation or reduction of use of a
  psychoactive substance that has been taken repeatedly, usually for a
  prolonged period and/ or in high doses.

The typical drugs that are associated with withdrawal are alcohol and other sedatives, opioids, and stimulants.

Alcohol and sedative withdrawal can lead to anxiety, agitation, and depression. Opioid withdrawal results in drug-seeking behavior that may continue after the physical symptoms have abated. Stimulant withdrawal (the ''crash") is associated with depression, malaise, inertia, and instability (source: WHO).

All these characteristic symptoms are basically caused by the fact that the nervous system counteracts the drugs effects and downregulates the receptor systems activated by the drug. Therefore, more and more of the drug is needed. Indeed, downregulation is one of the physilogical mechanisms underlying tolerance (Stewart, 1993):

  Tolerance refers to the decreased effectiveness of a given drug with repeated administration.

There are many factors underlying tolerance. For example, there is acute, short-term tolerance seen with cocaine use, but also a long-term tolerance form example seen in opioids. One factor in developing (long-term) tolerance is a downregulation of the receptor systems involved. Alcohol and other sedatives target the GABAA system. GABA being the primary inhibitory neurotransmitter in the central nervous system, it's not surprising that abstinence in a situation of tolerance results in over-stimulation of the nervous system (anxiety, agitation). Likewise, opioid tolerance results in mu-opioid receptor downregulation (Stafford et al., 2011). Given that mu receptors mediate positive reinforcement following direct (e.g.., morphine and other opioids), or indirect (e.g., alcohol, cannabinoids, nicotine) activation it is readily apparent why opioid abstinence results in the craving for the drug, as it is thought that after prolonged use, the user is unable to experience pleasure without the drug. At this point, the person is addicted (source: The Treatment Center). According to the NIH

  Addiction is defined as a chronic, relapsing brain disease that is characterized by compulsive drug seeking and use, despite harmful consequences.

Now we come to the conclusion that dopamine is central to addiction, also for drugs not directly activating it, such as alcohol and nicotine. The latter group indirectly release dopamine in the brain's reward center (the limbic system).

The classic hallucinogens stimulate the serotinergic system, and specifically the 5HT2A receptors (López-Giménez, González-Maeso, 2017), but fail to activate the reward centers in the brain. Indeed, all addictive drugs activate the reward circuitry of the brain, thereby producing the subjective “high” that the drug abuser seeks (Gardner, 2011). Tolerance to these drugs has rarely been reported (Smith et al., 1999) and LSD  rarely produces serious withdrawal symptoms (source: LSD Abuse Help. But in rare cases, tolerance can develop and is associated with 5HT2A receptor downregulation (Gresch et al., 2005) and the development of hallucinogen persisting perception disorder (HPPD). An LSD tolerance can be developed quickly, although it usually dissipates within just a few days depending on the user, their dosages and frequency of use. Long term tolerances are uncommon because users do not frequently repeat doses of LSD without taking breaks in between (source: Hallucinogens).

The SSRIs you mention basically work by downregulation of presynaptic 5HT1A receptors (Celeda et al., 2004), which are unrelated to the effects of hallucinogens.

References
- Celeda et al., J Psychiatry Neurosci (2004); 29(4): 252–65
- Gardner, Adv Psychosom Med (2011); 30: 22–60
- Gresch et al., Neuropsychopharmacology (2005); 30: 1693–1702
- López-Giménez, González-Maeso, Curr Top Behav Neurosci (in press)
- Smith et al., Psychopharmacology (1999); 144(3): 248–54
- Stafford et al., Pharmacol Biochem Behav (2001); 69(1-2):233-7
- Stewart & Baidani, Behav Pharmacol (1993); 4(4): 289-312


What is the IC50 exactly? I am reading the paper "Activity of the bcr-abl kinase inhibitor PD180970" but I don't understand how IC50 works on table 1. Can you tell with simple words and give me an easy example?

The IC50 is the concentration of an inhibitor at which you observe the half maximal inhibition. See the figure from the Wikipedia:

The IC50 can be seen as a way to measure the effectiveness of an inhibitor on a biological function as an enzyme. In the case of PD180970 you have an inhibitor which inhibits the p210 Bcr-Abl tyrosine kinase. The IC50 is the concentration at which 50% of the kinase is inhibited.

In table 1 different mutations of the tyrosine kinase are tested against the inhibitor to see, if the mutations have an influence on the IC50. This is important as PD180970 is considered as an anti-cancer drug and possible mutations would make it less effective here.


Need of Creatinine Phosphate In muscle cells most of the ATP's phosphate is with creatinine phosphate.

So why is the displacement of the phosphate group done ? Is it because creatinine phosphate would give it's phosphate more easily ? Is it done so that the negative feedback by ATP on mitochondria is not there and more and more ATP can be generated ?

Creatine phosphate is used as a buffer in high energy using cells, such as muscles. In a cell you have a pool of ATP, which is needed for things like muscle contraction, and then you have your pool of creatine phosphate, which can not directly be used as energy for muscle contraction. The cell only stores so much energy as ATP. And during high energy activities it can be depleted quite fast. The problem is that it takes a lot of time to make ATP through oxidative phosphorylation. And while glycolysis is faster, you dont get nearly as much ATP. Creatine phosphate solves this problem by acting as a reserve of ATP, so when ATP is depleted, the creatine phosphate can transfer a phosphate to ADP, and thus restoring ATP without needing to wait for glycolysis or the electron transport chain to complete.


How to determine the number of parameters in a phylogenetic model? I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?

The number of parameters depends both on the number of taxa and model of sequence evolution. The topology is not typically considered a parameter in the usual sense of statistical inference (as it is the a priori specified topology the likelihood was calculated on).

So, for example, if you infer a tree from nucleotide data for 25 sequences under the General Time Reversible (GTR) model with gamma distributed among-site rate heterogeneity and empirical stationary frequencies (this is commonly called GTR+F+G), then you would have 56 parameters with the following breakdown: 2n - 3 = 47 branch lengths (where n = 25, the number of tips), 3 frequencies (because these sum to 1, once three are known the other is automatically known, so we only count 3 estimated parameters), 5 substitution rates (there are actually 6 substitution parameters in GTR, but it is typical to set one, usually G > C, to 1, and estimate the others relative to this, hence only 5 estimated) and 1 alpha parameter for the shape of the gamma distribution of rates (gamma distributions actually have two parameters, alpha and beta, but for phylogenetics we usually constrain them to be equal).

In total, this gives 47 branch lengths and 3 + 5 + 1 = 9 model parameters, and 47 + 9 = 56


Does anyone have any TOPO directional cloning tips? I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?

I have lots of experience with the TOPO TA kit which is very similar to the kit your using. Here's a link to the TOPO Directional cloning product page which shows a schematic of the enzymatic ligation.

From your comments, you said you have doubly-digested the PCR product. This is likely your point of failure unless you are absolutely confident that your enzymes work at blunt ended DNA (which I can almost guarantee does not work). Restriction digestion of PCR products will only work if there are at least a few bases on either side of the recognition site so that the restriction enzyme is able to "grab on" to the DNA. What you are mixing instead, is blunt-ended PCR product DNA + cohesive-ended vector. This will not work under any circumstances as is.

There is a simple solution.

Add 3'-A overhangs to your PCR product directly. The back of the TOPO manual tells you how to do this as well as many other sources. Ligate this using your TOPO kit to produce a shuttle vector that you can then doubly digest your insert out and gel purify it. Then you may ligate this purified, digested DNA with your previously digested destination vector.

Note that in my hands and in others in our lab, topoisomerase is unstable and has a short half-life. It is especially sensitive to temperature changes (warming from -20°C to 4°C) which you wouldn't expect since it is designed to work at room temperature. The vector is not affected, but without a working topoisomerase, the ligation step does not occur and the DNA does not transform.

As an aside: If you plan on doing more cloning in the future and need to replace the kit, I would recommend getting the basic TOPO TA cloning kit, clone your PCR product (with 3'-A overhangs) into the vector, transform, pick white/light blue colonies for screening then cut out from the TOPO vector (the shuttle vector) for downstream applications. The fact that it is directionally cloned or not into the TOPO vector is of no consequence unless it also happens to be your destination vector.


identify this ant queen can anyone help me identify this ant queen, if it's an ant queen? I only assume it is because I caught another with wings which looks exactly the same. Thanks in advance..

There is only one segment between the thorax and the abdomen and the first segment of the abdomen is not elongated, which indicates this is a Formicinae.

Because the head width is similar to the thorax width from top view, this likely corresponds to a social parasite ant from the genus Lasius.

See ref below:

  Seifert, Bernhard. Die Ameisen Mittel-und Nordeuropas. Lutra Verlag-u.
  Vertriebsges., 2007.


Are there animal species with sex of an offspring determined by sex of preceding offspring? For instance, if an animal's first offspring is male, then all subsequent offsprings will be male too (the sex of first offspring could be determined randomly).
Does it happen in any species?

I can think of one (perhaps trivial) case where this happens. In insects with haplodiploid sex determination (like Hymenoptera) then almost all of a male's offspring will be female, as they will be diploid.


Help identifying an insect (I think it was an insect) While I realize this may be difficult without a photo, I'm hoping someone can say "This is a list of possible species given your location and description" and I can attempt to find a photo that matches from there.

I'm in NE Indiana. I think it was an insect. The species in question looked a bit like a leech, black and shiny but wasn't segmented and it was a bit flattened out (but not entirely), maybe an inch long. It wasn't tapered. Also I don't believe it made any attempt to bite me (or just wasn't around long enough to). Unfortunately it startled me so I smashed it pretty quickly so I didn't get a picture, but I got a good look and couldn't identify any legs, eyes, antennae. It moved fairly quickly, almost in a pulsating motion.
When I smashed it, there was only a bit of white, mealy paste left behind, the body almost seemed to liquefy.

If it hadn't moved so quickly and wasn't so small I'd have thought it was a baby slug. It's possible it could have been some sort of larvae.

I also don't think it was a leech because I found it on my body but I was in my home and can't think where I could have been that would have exposed me to one. I noticed it when after removing my shirt and lying in bed. So it was either inside my shirt for several hours without me noticing, fell out from the covers when I got in bed, or fell from somewhere after I got in bed.

This is not easy to answer without a picture. However, if it was unsegmented, it was definitely not an insect (which have a segmented body plan, both as larvae/nymph and adult). Your description also sounds nothing like an insect. However, the overall description fits fairly well with a flatworm (Phyluym: Plathelminthes), see e.g. Geoplanidae. They can resemble slugs or leeches, but both lack segmentation and antenna. Finding one inside your house sounds a bit strange though, as they generally prefer moist habitats.

Terrestial flatworms are relatively mobile and most are predators or scavengers

Example pictures:


How can you identify if a person is homozygous for a certain allele? I've been thinking about starting a small private research project. In this project I need to find out whether a person is homozygous for a certain allele. The reason for this is that I'm really trying to find out whether has a mutation that makes him/her not produce this chemokine. Thus I need to identify in an easy way which people are "normal", which people have the mutation in one chromosome, and which people have the mutation in both. About 1% of the population have the mutation in both chromosomes.

A primer would AFAIK not be able to differ between the heterozygous and the "normal" people.

Do anyone know how to approach this?

You could use a 3-primers strategy, where you have a common primer, one that only amplifies the mutant allele and one that only amplifies the wt. This may or may not be feasable depending on the type of mutation.
DNA from het people will amplify both product, while homozygous will only amplify one (wt or mutant).

Of course then, linking the mutation of a gene to the lack of a chemokine is not necessarily straightforward.

To be honest, however, I would use a different approach: take people who don't produce the chemokine, and people who do (simply by dosing the chemokine in the blood). Now sequence the gene in the two groups and look for mutations.


Why would stablising selection ever happen? If the aim of evolution is to allow an organism to better compete against rivals, why would stabilizing selection ever happen? If you're not selecting the most highly adapted competitors at either end of the spectrum then how would a species progress?

It occurs when a beneficial characteristic has been developed over time and it would be harmful to stray from it.  In these cases it is not the individuals at the fringe (as you put it the most adapted) who are the best adapted.

I think it may help if I answer with an example that is widely promoted by AQA in their A2 Biology syllabus.

Stabilising Selection in human birth weight

It is harmful for an infant to be born with a very low birth weight. They are much more vulnerable to heat loss due to their high surface area to volume ratio and consequently their respiratory demands are very high.  Pre-term babies (which account for 67% of low-birthweight infants(1)) are particularly susceptible to respiratory problems (lack of surfactant in the lungs), cardiac problems (Patent ductus arteriosus - the lungs are still bypassed when the umbilical cord has been cut) and dangerous intestinal problems (Necrotizing enterocolitis) amongst many other conditions can all be fatal (further information on mentioned conditions) and are reflected in high mortality rates at these low birth rates.  It is therefore not beneficial to be on the extremes of birth weight.

Similarly, delivering a child of too high birth weight can cause complications with delivery if the head and shoulders are too wide to pass through the mother's hips.  Therefore the other extreme of high birth rate is also not beneficial and will not be selected towards.

This leads to selective pressures in both directions, stabilising towards a mean birth weight as shown below:

This is an example of evolution not pushing a species forward but ensuring that individuals have the best chance of getting to reproductive age themselves.

(1) Martin, J.A., et al. (2007). Births: Final Data for 2005. National Vital Statistics Reports, 56(6).


Can an enzyme be activated without allosteric inhibition or activation? Are there ways by which an enzyme may be activated or inhibited by non substrate molecules other than allosteric activation or inhibition?

Apart from what Phototroph mentioned in their answer (competitive and non-competitive inhibition), an enzyme can be activated/inhibited via covalent modification of the protein (post-translational modification) such as phosphorylation by protein kinases (phosphorylation is the most common modification).


Can any one identify this insect from Lokhandwala, Mumbai India? I found this insect on my bed. I have never seen such creature before. Can any one identify this?

It's looks like a Leaf-Footed Bug (Homoeocerus Sp., Coreidae).

Source: https://www.flickr.com/photos/itchydogimages/17774939209

Source: https://www.flickr.com/photos/itchydogimages/6211603956/


Is a single polynucleotide necessarily and always a nucleic acid? I am confused. I know that a DNA molecule is made of two polynucleotides.

But does each polynucleotide represent one nucleic acid? If so, a DNA molecule is made of two nucleic acids, right?

Or do the two polynucleotides (that form a molecule of DNA) make up only one nucleic acid? If so, a DNA molecule is only made of one nucleic acid, right?

There are two types of nucleic acids: 1) DNA --> which is double-stranded, so it's made of only two polynucleotides 2) RNA --> which is single-stranded so it's made of only one polynucleotide. So if we get back to my original question "Is a single polynucleotide necessarily and always a nucleic acid?" --> the answer is no, for DNA is a nucleic acid and it is made of two polynucleotides.


What is a catalytic domain? I have to answer a few questions from an article I'm reading, and I am just really confused on defining "catalytic domain." I have to relate it to the antibiotic Teixobactin. Is catalytic domain the same as the enzyme's active site?

The catalytic domain is roughly referring to the same part of the protein as an active site and may be used interchangeably in some circumstances:

See here, where "catalytic domain" redirects to "active site."

There is, however, a difference:

From a free online medical dictionary:

  active site:
  the place on the surface of an enzyme where its catalytic action occurs.

From Wikipedia:

  catalytic domain: structurally conserved (tertiary) structure containing the catalytic function of the protein.

To further clarify: the catalytic domain is the 3D structural independent folding unit of the protein that contains an active site, while the active site (aka "catalytic site) is the area located within the catalytic domain where substrate molecules bind and undergo a chemical reaction.


Regarding inherited fertility in animals If an animal is fertile does it follow that both its parents of the same species (not necessarily the same species of the offspring)? Was it Mayer who said a fertile male and fertile female of two different species, if they 'reproduce' and the offspring survives it won't be fertile. Reproductive isolation I think this is called. So if an animal is fertile then both its parents should be of the same species, right?

No it isn't necessary that the parents should be of the same species. Mules (male donkey X female horse) have been found to be fertile (reference). The wikipedia page on hybrids lists many inter-species hybrids that are fertile including Beefalo (Domestic male cattle X american bison). There are also many canine hybrids which are fertile. Wholphins have been found to be fertile.

  A wholphin or wolphin is an extremely rare hybrid born from a mating
  of a female bottlenose dolphin (Tursiops truncatus) with a male false
  killer whale (Pseudorca crassidens).

So in short, for a hybrid offspring to be fertile, it doesn't necessarily need to be of the same species.


Why do people remove excess solution after they put on a coverslip? Today, my classmate and I stained a slide of cheek cells. After we put on a coverslip, our teacher said that we are supposed to remove excess solution using a tissue.

Why should we do this? I am so confused

Neither of the current answers fully answer the question.

The amount of liquid underneath a coverslip should be just sufficient to hold the coverslip and sample onto the slide. If there is too much water, the surface tension would become reduced, allowing the coverslip to fall off the slide.

Additionally, minimising the amount of water between the coverslip and the slide would ensure that the z-axis variation in your sample is minimised, therefore reducing the likelihood that your sample will have different focal points across the sample.

This UCLA guide on microscopy slide mounting explains it (emphasis mine):

  Small pieces of filter paper (Whatman #1) are placed around the edge of the coverslip to absorb excess mounting medium. If your specimen is tissue culture cells or frozen tissue sections, this should not harm them. This does two things: a) it allows the coverslip to come as close to the specimen as possible and reduces the depth of the field. You will get less focus aberration if you do this judiciously. b) the coverslip will be a lot less likely to float around on the slide and move which could specimen damage. The surface tension between the coverslip and slide will be much higher. You will also be much better able to seal your coverslip to the slide.


What are Antihistamines doing in a baby? In his song Lullaby, Tim Minchin sings:

  Your nappy is dry and your tummy is full
  Of enough antihistamine to chill out a bull
  Yet still all this gringing

According to Wikipedia, antihistamines are used against allergies.

So, why is there antihistamine in his baby's tummy and why is it supposed to make her sleepy?

This song most likely refers to an off-label (and usually inappropriate) use for certain antihistamines like Benadryl. They are sometimes used by parents to sedate their children, functioning through the exact physiological mechanisms @Chris describes.  Parents use it inappropriately as a means of behavioral control for active or upset children to make them more docile or sleepy, such as for airplane rides, etc.  It's not recommended by most pediatricians, because even though adverse (bad) side effects are usually rare, it is an actual medication with another primary mechanism of action having effects on many body functions, not a medication designed as a sedative.


What does the acronym ‘PIN’ stand for referring to PIN proteins in plants? There are so called PIN proteins, or PIN-formed proteins, in plants. What does this acronym mean?

Wikipedia briefly explains the function of the protein but not the origin of the name.  It's not explained even in the link-linked review paper, if I'm not missing something.

Like many genes and gene products, PIN proteins were named for a mutant phenotype and PIN is not actually an acronym; the source in your link does actually explain this (emphasis mine):

  The significance and function of AtPIN1 was discovered through the phenotype generated by the loss-of-function mutation in the gene: mutant plants fail to develop floral organs properly and generate naked, pin-like inflorescences, which gave the name PIN-FORMED (PIN) to the family

Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., & Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters. Genome biology, 10(12), 249.


Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar? Agar is a relatively cheap substance from red algae.  And it contains a saccharide agarose as well as a small amount of pectin.

Agar is used for culture plates as is, but for DNA gels a grade of agarose, I guess with the pectin removed.  What happens when a gel is run in agar?  i.e. why remove the pectin?

If you can guess, how is the pectin removed?  I know there are enzymes that might do it, but not sure what's really used.

The answer to the first part of your question can be found on Wikipedia:

  Agar is a heterogeneous mixture of two classes of polysaccharide:
  agaropectin and agarose. Although both polysaccharide classes
  share the same galactose-based backbone, agaropectin is heavily
  modified with acidic side-groups, such as sulfate and pyruvate. The
  neutral charge and lower degree of chemical complexity of agarose make
  it less likely to interact with biomolecules, and, therefore, agarose
  has become the preferred matrix for work with proteins and nucleic
  acids.

This page compares the result of using agar gels to that of using agarose:

The second part of your question: here's a patent, although I have no idea whether this method of agarose purification is widespread.  Propylene glycol purification of agarose does seem to pop up a lot.  I think people who  purify their own agarose use that method, but I am not sure if biotech companies have other methods.

EDIT: it's propylene glycol, followed by ethylene glycol, that is commonly used, but PEG has been used at least once.


Can gene-gene interactions result in gene expression? I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge.

The format of the input data is shown in the image.

Now according to what I studied, a Gene Expression Matrix has its rows represent genes, columns represent samples such as tissues or experimental conditions and the numbers in each cell refer to the expression level of a particular gene in the particular sample.

And that Gene Expression is the process in which information from a gene is synthesized to obtain Gene Products. The process of Gene Expression is that it undergoes a transcription process where a transcription factor attaches itself to the gene and then results in the formation of gene product.

But the input data apparently shows gene-gene interactions.

As a result of this I am extremely confused.

Any kind of help would be greatly appreciated. Thanks.

I don't know anything about your algorithms. But i will try to explain your the format of data that was given to you. I don't know your background in Biology, so i will assume it is not your expertise field and will make some simplifications of the subject.

What is gene expression?
To understand what is a gene expression, you need to understand what is a gene:

  A gene is a sequence in the DNA (composed of 4 bases A,T,C and G) that can be transcribed by a protein, in your context we will say it always start with a start codon (a codon is a triplet of DNA bases) and stop with a stop codon. It is usually around a thousand bases long. The transcription will give you a RNA, and that RNA can be translated (note the difference with transcribed) into a whole new protein.

Now the gene Expression is a measure of the amount of RNA from the gene you are looking for. In a cell you can have around 10000-100000 copies of that RNA; the raw count is not really stable as you can have extract two cells or three and it will change your "expression". Most of the time we normalize the count by the count of a bunch of known genes called housekeeping genes. The particularity of these genes is that their expression is quite stable.

  The figures you have are a ratio between RNA copies of your gene of interest and RNA copies of a stable gene (in term of expression).

What does G1(-/-) and wt mean?

Usually when we (biologist) call a sample wt it means wild type, in other words, a normal individual. G1(-/-) means that this sample is from an individual with the G1 gene inactive (could be obtained by genetic modification).

What is a gene-gene interaction?
An example of interaction first: let's imagine a gene coding for an enhancer (booster) of transcription. the presence of this gene allow another gene to be expressed in the cell, if this gene isn't present or isn't transcribed, the other gene won't be expressed either.

How can we see interaction there?

Let's look at line one, the control (normal individual), We see that G4 (column) is almost unexpressed (0.07). In normal conditions, this gene is not expressed. Now let's look at mutant G1(-/-) and G6(-/-), we see the expression of G4 is rising (0.37;0.23) compared to the control (wt).
We can suppose than G1 and G6 are acting as inhibitors of the G4 gene.


Where are epitopes located on HLA molecules? Normally HLA molecules present cellular and extra cellular proteins to the immune system; presumably the proteins in this case are where antibody /t-cells etc bind.

But when an organ is transplanted to a HLA incompatible recipient, are they binding to the HLA molecule itself? If antibody response was reliant on the proteome expressed in and around the cell HLA incompatibility wouldn't be such a problem.

What about auto immune diseases?

T cells in a graft see both non-self peptides associated with the non-self HLA molecules, and can also see the non-self HLA molecules regardless of peptide. (MHC is a broader term than HLA, and I will use MHC here.)

  Surface expression of CD4 or CD8 is commonly used to identify T-cell subsets that recognize antigen presented by class II MHC or class I MHC, respectively. This holds true for T cells that respond to allogeneic MHC molecules that are directly recognized as foreign, as well as peptides from allogeneic MHC molecules that are indirectly presented by self MHC molecules.

--Contrasting Alloreactive CD4+ and CD8+ T Cells: There's More to It Than MHC Restriction

Recall that as T cells mature in the thymus, they undergo negative selection such that those T cells that spontaneously recognize self MHC molecules are deleted, but there's also positive selection that ensures the T cells can recognize MHC features in general. That leaves many T cells that could spontaneously recognize slightly different MHC molecules (i.e. non-self) that are not deleted. That means that in a transplant, there are a large number of T cells that can recognize the non-self MHC in a non-peptide-dependent manner.  There's also a much smaller number that can interact with the non-self-MHC but only in a peptide-dependent manner; this is just by chance, in that that particular T cell receptor happened to have the shape that sees that non-self-MHC and the peptide.

As for autoimmunity, that's all peptide-dependent, as far as we know, barring some of the really horrendous infant-onset autoimmunities that result from improper T cell maturation in the thymus.


how to reconcile PDB structures' sequences via Uniprot references? I’m trying to reconcile structures  in PDB entries with their  sequences as reported in their chemList.polymer.dbref entries.

E.g.: considering structures for HIV integrase:

PDB:3OS0 references UNP:P14350, focusing on integrase (len=391)

>sp|P14350|752-1143
CNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQ…NRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE

PDB:2B4J references UNP:P12497, focusing on integrase (len=287)

>sp|P12497|1148-1435
FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGI…LLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED

Why should these sequences be so different?!

and in case you think I'm focused on a bit of noise: there are 42 other HIV integrase structures all referencing UNP:P14350, and 43 other structures referencing UNP:12497 (and 79 others referencing UNP:Q76353, very similar to UNP:12497), 22 referencing an entirely different UNP:Q72498.

None of them is integrase:

P12497
Protein    Gag-Pol polyprotein
Gene       gag-pol
Organism   Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)

P14350
Protein    Pro-Pol polyprotein
Gene       pol
Organism   Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)

Even if you meant the integrase product of the polyprotein, the second one is not even HIV.

From Wikipedia:

  Human Foamy Virus (HFV) is a retrovirus and specifically belongs to
  the genera Spumavirus. The spumaviruses are complex and significantly
  different from the other six genera of retroviruses in several ways.
  The foamy viruses derive their name from the characteristic ‘foamy’
  appearance of the cytopathic effect (CPE) induced in the cells.[1]


Gene & Protein nomenclature: N-Myc, c-Myc, et. al Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins?

I think I know that for genes, we use an italic font and for proteins, we use a regular font.

I think I've also learned that for human, all letters are in uppercase (eg. SHH) whereas for mouse, only the first letter is in uppercase and the remaining letters are in lowercase (Shh). (From http://en.wikipedia.org/wiki/Gene_nomenclature)

But I'm stumped with all the other "tags" (in quotes because that's how they seem to be used and I don't know how else to think of them) that I see floating around gene and protein symbols.

For example, Myc (MYC?).

I see these three articles in uniprot.org:

http://www.uniprot.org/uniprot/Q99417 for C-Myc

http://www.uniprot.org/uniprot/P04198 for N-myc

http://www.uniprot.org/uniprot/P12524 for L-Myc

These proteins are all in human, and yet their recommended names are not all caps; what's up with that? But even more confusing to me are the "C-", "N-", and "L-" letters prefixed to them. What in the world are those supposed to be indicating?

Are these all fundamentally different proteins (coded by different genes), but maybe related somehow to each other (thus the common three letters, 'myc' even if they are not all the same case and not all upper case as I thought was supposed to be the case in human), and they are just given these "C-", "N-", and "L-" tags to distinguish one from the other? Does one tag indicate an oncogene or a proto-oncogene? Why do I sometimes see "c-Myc" and other times, "C-Myc"? Does the case of the "C-" mean something? Is there some kind of key or legend I can look at to get answers to all these questions? I've found some explanations in Scott Gilbert's Developmental Biology textbook, but it still doesn't give me all the answers I seek here

I just want to understand how these tags and symbols are being used because it seems to me that when I read research papers (of which I've read many), they are used by different authors in different papers in ways that are not consistent with each other. Either that, or else I'm missing something very basic, which is why I'm asking here.

Thanks in advance for any help.

There is a useful set of links to nomenclature guidelines for all of the main genetic systems at this Wikipedia page. Personally, I think that the Saccharomyces cerevisiae system works best: it manages to cover dominant and recessive alleles of a gene, the name of the protein, how to refer to a related phenotype, and the use of a parallel convention for the designation of ORFs.

Unfortunately there is now no going back - there are many different systems and there is no hope of unifying them. When this plethora of naming conventions is combined with the reluctance of so many scientists to stick to the guidelines, we have a recipe for near anarchy.

Edit - On the specific topic of MYC nomenclature:

The v- and c- prefixes come from the early days of oncogene research. Viral oncogenes such as myc and src were found to be related to (derived from?) similar genes in normal cells. Thus v- means viral and c- means cellular.

This can be seen if you peruse the HUGO entries for the four MYC family members encoded in the human genome (extracts below). They all have an approved name which relates them back to a viral oncogene found in the genome of avian myelocyomatosis virus. This was the founder member of this gene family. Thus c-myc was the first myc-related gene found in the human genome, and is the one that is responsible for Burkitt's lymphoma. It is true, as @Leonardo says, that in tumours the expression of this this myc gene in lymphatic tissue changes due to chromosomal rearrangements, but this is not the origin of the designation c-myc.

  MYC
  Approved Symbol:      MYC
  Approved Name:   v-myc myelocytomatosis viral oncogene homolog (avian)
  Previous Symbols & Names:   "v-myc avian myelocytomatosis viral oncogene homolog"
  Synonyms:   bHLHe39, c-Myc
  Chromosomal Location: 8q24

  MYCL1
  Approved Symbol:      MYCL1
  Approved Name:   v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)
  Previous Symbols & Names:   MYCL, "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"
  Synonyms:   bHLHe38, "l-myc protein", LMYC, "myc-related gene from lung cancer", "oncogene lmyc"
  Chromosomal Location: 1p34.3

  MYCL2
  Approved Symbol:      MYCL2
  Approved Name:   v-myc myelocytomatosis viral oncogene homolog 2 (avian)
  Previous Symbols & Names:   "v-myc avian myelocytomatosis viral oncogene homolog 2"
  Synonyms:   bHLHe38
  Chromosomal Location: Xq22-q28

  MYCN
  Approved Symbol:      MYCN
  Approved Name:   v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)
  Previous Symbols & Names:   NMYC, "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived"
  Synonyms:   bHLHe37, N-myc
  Chromosomal Location: 2p24.3


What will happen if mitochondria had a structure like lysosomes? I wanted to know an explanation how the structure of mitochondria affects its function. Therefore, how would it turn out if its structure is like the structure of lysosomes, what is going to happen?

Mitochondria are double membraned organelles with an outer membrane which is a rod-like shape, and a convoluted inner membrane (Figure 1).

Figure 1

On the other hand, a lysosome is a single-membraned vesicle containing digestive enzymes, with no internal structure. Its function is to keep these dangerous enzymes in a compartment.

The "purpose" or "role" of the mitochondria is to do cellular respiration to provide energy (as ATP) to the cell. To do this, the mitochondria have many respiratory complexes (groups of proteins which make respiration happen) embedded in their internal membrane (Figure 2). As you can see in Figure 1, this membrane is convoluted with many folds; this is to increase the surface area of the membrane to have more space for respiratory complexes.

Figure 2

Moreover, these complexes pump out H+ ions into the intermembrane space. The fact that there is this thin intermembrane space allows for a buildup of H+ concentration which is crucial for ATP production (through the action of ATPase). This process is called chemiosmosis and you can learn more about it here as a starting point. A lysosome with only one membrane does not have an "intermembrane space", so this buildup in concentration cannot happen.

If you would like to learn more about mitochondria, I would recommend reading Power, Sex, Suicide: Mitochondria and the Meaning of Life by Nick Lane.


Question regarding an Escherichia coli reaction With respect to this link
http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-14479
Here the enzyme is mentioned and the two reacting compounds. Now , my question is
1. When these two compounds react, do they initially get attached to the enzyme before reaction?
2.If they Do both these compounds get attached to the enzyme, what is such an interaction called? Protein compound interaction??

As far as I can tell, enterochelin esterase (Fes) utilizes an Alpha/Beta hydrolase fold to catalyze it's reactions, which means there's a triad of catalytic amino acid side chains. Where Fes differs from other proteins in the pathway is an amino terminal lid domain which confers specificity to the substrates of Fes ((1) dictates this forms a deep pocket in the protein). I'm having trouble finding the exact catalytic amino acids, but homology modeling between IroE and Fes from the same source shows this may be a triad of Glu, His and Ser. If we kind of visualize what a catalytic triad's mechanism looks like, and the following image is a generic lipase/esterase catalytic site,

A sort of transition state is formed between the target molecule and the serine, where the water reacts with help from the asp/glu and histidine to catalyze the hydrolysis. You'd just call it protein-ligand interactions.


agglutination test using blood of the donor and the recipient we were told that agglutination occurs when the matching antibody react with its antigen on the RBC surface (as antibody B with antigen B)....
Also when blood transfusion, Donors plasma with antibodies is diluted , so when o-donor gives blood to  B-recipient , B antibodies ( of the donor) is diluted
........
My question is in lab cross-matching test  when we put recipient's plasma(o with b antibodies for example) on the donor's RBCs (B with b antigens)..... is there agglutination, If so, how would we know the right group then?....if not ,Why not?
if the whole thing is misunderstood ,i wish to be told how it's done.

Disregarding Rh factor for a moment: when you add A-antibodies to a blood sample and agglutination occurs, this means the blood contained A-antigens (A-type). The same can be said for a sample of blood to which B-antibodies are added (B-type). If agglutination for both antibodies occurs in separate assays on the same sample of blood, it means the sample contains both A and B antigens (AB-type). If the sample is said to be O-type, this means neither A or B antigen would be present in these cells. It's safe to transfuse O-type blood into any recipient due to this fact. What you also want to watch out for, is attack on the recipients RBC's by antibodies in the donor's plasma. This can result in a hemolytic transfusion reaction (HTR), but it's noted in the following text:

  Red blood cell incompatibility may also occur when the patient's RBC antigens are attacked by antibodies from the donor's plasma. This tends to be a minor problem because of the small amount of antibody present in the donated plasma, which is further diluted on transfusion into the recipient's circulation.

If you're in the lab doing a Coombs test, for example, you're checking to see if there are any extraneous antigens present that might results in a HTR. In a normal result, ergo there aren't any antibodies to RBC's in the sample mixture, you wont see any agglutination. This is for considerations outside of ABO antibodies, generally. If you're adding to B-type RBC's a plasma with known antibodies to B antigen, like O-type plasma, you can probably expect an event. To my knowledge, O-type plasma wouldn't be safe to give to anyone but an O-type recipient.

additional source


DNA gel extraction: chemical contaminants I am performing a gel extraction to purify DNA after a double digest with EcoRI and BamHI.  After the gel extraction I need to complete a ligation step before bacterial transformation.  The problem I am having is that the DNA after the gel extraction have some kind of chemical contaminant that won't allow me to quantify the DNA using the Nanodrop spectrophotometer.  I am getting very low 260/230 ratios.

Has anyone had some issues with this?

I am using the Qiagen Qiaquick Gel Extraction Kit.

Here are some possible reasons:

Your yield is very low, which you can infer from a low 260 absorbance. Either make sure your restriction digest is efficient or add more substrate to the digest reaction.
Carbohydrate contamination, which will cause high 230 absorbance. Wash the column one more time with buffer QG (the step is described in the Qiagen gel extraction manual; if you're already doing a wash with buffer QG, do an extra one).
You didn't dry the column enough and some ethanol from the wash remains in the sample. This can also cause high 230 absorbance and your sample with smell of ethanol. Place your column in an empty collection tube and spin it down for a long time (15-20 min). Don't worry, the DNA can withstand it.


Linkage between chromosomal loci and the Hardy-Weinberg principle Referring to the Hardy-Weinberg principle, which is always stated with respect to a particular locus on the chromosome, if we observe that two different loci are either always together in Hardy-Weinberg equilibrium, or never together in Hardy-Weinberg equilibrium, can this give us any information about the linkage between the two loci?

Linkage is a physical reality

Linkage refers to the physical presence of several loci on the same chromosome. Two loci that are said to be in close linkage mean that they are locataed relatively close to each other on the same chromosome.

Linkage disequilibrium is a statistical reality

If two alleles at two different loci are found on the same haplotype than expected by chance (that is more often than the product of the respective frequencies), then there is an statistical association between these two loci. We refer to this statistical association as linkage disequilibrium (abbreviated LD). If there is absence of statistical association, then the two loci are independent and we talk about linkage equilibrium.

Let's consider two bi-allelic loci. We will call the two loci A and B and the two alleles A0, A1 and B0, B1 at loci A and B, respectively. Let $p_{AB}$ be the frequency of the haplotypes that contains both A1 and B1. Let $p_A$ and $p_B$ be the frequencies of the alleles A1 and B1, respectively. Then LD between the loci A and B (called $D_{AB}$) is defined as

$$D_{AB} = p_{AB} - p_Ap_B$$

There are other related mathematical definitions of LD than $D_{AB}$, such as $D'_{AB} = \frac{D_{AB}}{D_{max,AB}}$ and the correlation of coefficient among the two loci $r_{AB}$.

Linkage disequilibrium and Hardy-Weinberg equilibrium

You will note that, knowing whether or not each of the two loci are in H-W equilibrium (or respecting the assumptions of H-W equilibrium; see this post) tells you nothing about LD among these two loci. For example, two loci can both be at H-W equilibrium but be in LD (or in linkage equilibrium). Similarly, two loci can both be at H-W non-equilibrium but be in LD (or in linkage equilibrium).

Linkage and linkage disequilibrium

Various things can affect LD. In theory, there is no need for linkage to have linkage disequilibrium. A strong epistatic interaction for early life survival between two loci (whether or not they are in the same chromosome) can eventually cause  LD. However, most of the cases of known LD probably concern pairs of loci found in tight linkage. There is a diversity of processes that lead to LD and reviewing them would be outside the scope of this answer.


In genome research, what is the problem in Mapping that may be caused by reads being too short? In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back to the genome, but a significant proportion of them do not align.

The question is: give some obvious explanations why the alignment of short sequences can fail, apart from possible contamination or technical difficulties during the preparation of the RNA.

I would answer it as because reads are short, and because of introns(since it is RNA)

Another scenario: There are some indications that the problematic sequences come from an uncharacterised plant RNA virus. What would you do next? What are the specific caveats with short sequence reads?

I got the above questions, I am a computer science student doing bioinformatics, any biologist could answer it will be well appreciated

Being a bioinformatician as well, I am not really what you asked for, but I work with plant genetics so I'll try and answer anyway.

What you are mapping is RNA. So, as you already figured out, splicing events will be a problem for end-to-end mapping of the reads. There are tools managing that, though, so let's assume you used one of them and still a lot of your reads do not map. To put in WYSIWIG's good point: Another event that can mess up with your alignments is RNA editing, although this is not too likely to cause a high proportion of reads to not align at all.

Some aligners might filter out "too short" queries, so make sure you are not using one of them.

Then, have you preprocessed your reads? If you have not, there might be adaptor sequences left. Or may reads have very poor quality, thus are also aligned with poor quality, thus might be counted as unaligned.

And then check what you are aligning to. Many published plant genomes are also of minor quality, including lots of unassigned bases. So, there could be large proportions of your reference genome that count in the genome length, but are only Ns and nothing will align there.

Last but not least, your thought about a virus could also be right. Depending on the experiment, there might be pathogenic RNA in your sample, so check against a suitable database.

If the problem is only that the reads are "too short" for whatever reason, try doing transcriptome assembly before comparing to your reference.


What animals stop other members of their species from mating and why? (In particular primates)

I know chimps do. Powerful alpha males chimp would beat up omega males that they caught mating.

I know gorillas do. Powerful alpha males gorillas would beat up omega males that they caught mating.

I know humans do. Politically powerful alpha males would jail or stone weaker omega "peasant" humans that they caught mating.

I know bonobo doesn't.

What about other primates/animals?

So what's the difference and why?

Reference:

  The alpha animals are given preference to be the first to eat and the
  first to mate; among some species they are the only animals in the
  pack allowed to mate. Other animals in the community are usually
  killed or ousted if they violate this rule.

http://en.wikipedia.org/wiki/Alpha_%28ethology%29

How do preventing and punishing others from mate improve ones' own gene pool survival? Are there similarity between primates (including humans) in this regard?

As the comments suggest, I think a little basic reading so you understand the definitions involved here might be appropriate.  The questions are a bit anthocentric, and I think that's why folks with a bit more biological culture might be concerned about the answers.

Alpha type structures can be found in all sorts of animals.  Sperm competition, where many males simply mate with the female and let the sperm work it out are also v common from snakes to mice to primates.

Its hard to say without you asking a more specific question, but the essential question is whether the competition occurs between the animals themselves or between the intermixed sperm of the males inside the female.  If that sounds gross, that's a typical reaction if you are not a monkey, snake, duck or mouse to name a few.  Different species choose different social roles in mating and for reasons that may be difficult to divine.

For animals in an alpha troop modality, the alpha male will eventually get older or weaker and the younger ones will have their chance to mate.  There is always tomorrow.  That's my very brief answer.

It might be worthwhile to take some time to read some about this - a page of response to your questions is not going to really answer your questions.  (I say this having answered several of them :).  I would recommend "The woman that never evolved" by Sarah Hrdy.  As a feminist in the 70s Hrdy decided to do a survey of primate male/female roles in mating, to try understand how human men and women became who they are (and who has not wondered this?).  This book will give you an idea of how so many different animals have come to different roles and possibly why.

Since I have a little time today, I'm adding a couple of tangential references:  Mice sperm have responded to sperm competition so much by evolving hooks on their heads and chain up together and swim together which enhances the chances of paternity.  Ducks are quite different.  they have a lot of forced copulation, but female choice of mate is still quite influential.  Duck vaginas are very complicated, with corkscrews and dead ends to make it difficult to copulate without 'consent'.


can a bacterial protease inhibitor cocktail be used for Western Blotting involving HUVEC cells and HT-29 adenocarcinoma cells? Dear fellow biochemists,

I need some advice on Western Blotting, more specifically the use of certain protease inhibitors with the RIPA cell lysis buffer and protease inhibitor cocktail. A Millipore technical representative recommended my using "539134 | Protease Inhibitor Cocktail Set III, EDTA-Free - Calbiochem" as a good general protease inhibitor cocktail.

I have another protease inhibitor cocktail which includes: AEBSF, bestatin, E-64, and pepstatin A (E.coli protease inhibitor cocktail) but it does not include the aprotinin or the leupeptin inhibitors. Is there a risk of proteolysis in a mammalian cell lysate without these latter 2 inhibitors? The specific cell types which we are using are: HUVEC (human umbilical vein endothelial cells) and HT-29 adenocarcinoma cell line.

In general, leupeptin (a cysteine, threonin and serine protease) and aprotinin (sometimes called Trasylol; trypsin inhibitor) are included in most mammalian cell lysate buffers. Whether you need them is really up to your protein of interest: if you know how it gets degraded in vitro, then you should be fine with inhibition of just those proteases. If instead you want to preserve as much protein as possible, then you should add them. Should you not use them, then yes, those proteases will degrade some of the cell proteins.

The good news is that you can buy aprotinin and leupeptin individually and supplement them to the necessary concentrations for a working lysis buffer.


Does neural network in brain form cycles? In other words is it possible for dendrite of neuron A to be connected with axon of neuron B and at the same time dendrite of neuron B to be connections with axon of neuron A (or similarly for any larger number of neurons)?

If so, are there any statistical data on number of such cycles in average human brain?

In general neural networks are a lot less simple and directed than ANNs or artificial circuitry - connections can be inhibitory or excitatory, vary widely in strength etc etc. So unsurprisingly yes, recurrence is observed in actual neural networks. I don't know of any statistics on the frequency of such network structures, or even if such exists. Our knowledge of the brain at this fine level is still limited I think, the more global attempt to map 'the connectome' generally consider things at a higher resolution.


Effect of transpiration on plant growth It is said that only about 1-5% of water used by plants is used in photosynthesis while the rest is transpired. Suppose that a plant grows in an environment where the temperature is not too high but humidity is very high, e.g. in the shadow of a forest. Would the plant grow faster if the humidity was lower? To what extent is the photosynthesis limited by reduced transpiration?

Mineral nutrients are conveyed up the tree via the xylem by transpiration. The phytohormone cytokinin that releases buds/shoots is synthesized in the root tips and is also conveyed via the transpiration stream. Transpiration is driven by the water potential of the air --> ln(rH); transpiration stops when the relative humidity is 100%.

Even though some species are able to generate root pressure that will force water plus minerals plus cytokinin up the xylem, growth must, nevertheless, be faster at moderate relative humidity than when rH is near 100% (because of the reduced availability of minerals for tissue synthesis in the lateral and apical shoot meristems).

Fertilizing will make minimal or no difference at 100% rH as there is not transport up the plant by transpiration. However, mineral nutrition could be via 'foliar feeding' wherein a fertilizer solution is applied to the leaves could be partially effective in overcoming the mineral nutrition issue of 100% rH. Minerals are then distributed by being actively loaded into/out of the phloem tubes.

Photosynthesis would be unaffected at 100% rH since all tissues would be hydrated. The consumption of water by PhotoSystem II, however, is the only mechanism that could cause some transport of water and minerals through the xylem when rH = 100% aside from root/stem pressure generated by osmosis.

REFERENCES:

Wikipedia - Mineral
Adsorption
Water ascent in plants: do ongoing controversies have a sound basis?
Chunfang Wei, Ernst Steudle and Melvin T. Tyree, trends in plant
science, September 1999, Vol. 4, No.
9
biology-pages: Transport of Water and Minerals in
Plants


Is the amount of the soil reduced when plants grow? According to the principle of mass conservation I think the amount of the soil should be reduced when plants grow. But this reduction is not typically observed. For example, some trees (big trees) grow so fast that if the soil was reducing due to the growing trees, it seems like no soil should be left around them (i.e. the soil surface had to go noticeably down). But it didn't occur. So, which matters are reduced by growing plants?

The vast majority of the mass of a plant is carbon-based which is obtained directly from the air via photosynthesis. So trees are, in a loose sense, solidified air!

And most of the mass that comes from the ground is water which, of course, is constantly being replaced when it rains (or by Charlie with her watering can).


What type of mutation causes Progeria? I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease.

I know that the LMNA gene codes for the "prelamin A" protein, and that protein contains a farnesyl group that is then not able to be removed (in the case of Progeria). The abnormal form (with the farnesyl still attached) of prelamin A is then called progerin, and attaches to the nuclear rim resulting in an abnormally formed cell nucleus, making mitosis impossible.

Is this a structural mutation? What sort of mutation is this?

Thanks in advance.

Hutchinson–Gilford progeria syndrome is almost always due to to a de novo mutation (i.e. not an inherited mutation) in the lamin A gene (LMNA). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is used it results in the deletion of information corresponding to about 50 amino acids internal to the protein and near to the C terminus.

During biogenesis of normal lamin A a C-terminal -CAAX motif is recognised as a signal for isoprenylation, in this case farnesylation. The added lipid group acts as a C-terminal membrane anchor. However this anchor is subsequently removed when the protein is proteolytically cleaved near the C-terminus, removing 15 amino acids including the C-terminal cysteine (by this point the three C-terminal residues have been trimmed away). The cleavage site for this final modification is missing in HGPS lamin A so the farnesyl group cannot be removed. The accumulation of unprocessed lamin A causes the observed defects in the nuclear membrane.

Eriksson et al. (2003) Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423: 293-298

Capell et al. (2005) Inhibiting farnesylation of progerin prevents the characteristic nuclear blebbing of Hutchinson-Gilford progeria syndrome. Proc. Natl. Acad. Sci. USA 102: 12879-12884


(Non-expert-question) What exactly do chloroplasts do when they "convert light into chemical energy"? Disclaimer: This question is kind of sprayed over biology, chemistry and physics.

Anyway, I had to learn more about photosynthesis recently, and although it is quite complex, I think I got it - except for one thing: Everywhere it is basically just said, that chloroplasts convert light energy into chemical energy. But seemingly no one is interested in how they do it. I couldn't find an explanation after some googling. Not even Wikipedia had something for me (at least nothing I was able to sort out of the technical jargon).

So my question now is: What exactly happens in this process? It'd be good if the answer wouldn't include to much jargon, because I'm not really experienced in the field. (Just the usual knowledge and a little more due to being interested in science in general).

I see you've given this a try, so here's a synopsis hopefully appropriate to both your current knowledge level and curiosity.

Light excites electrons in chlorophyll to a higher energy. Higher energy means less stable, those electrons want to return to a state of lower energy. The chloroplast is structured in such a way that the electrons, instead of just plopping back to the lower energy state in the chlorophyll to liberate the light they just absorbed, are handed off to another molecule. As the electrons get passed off to other molecules, they lose energy. All of this is taking place on a membrane within the chloroplast. The energy being "lost" by the electrons is harnesed to pump hydrogen ions across that "thylakoid" membrane in the cholorplast. The increased concentration of H+ within the thylakoid space is another form of energy that can do work. The work done is the creation of ATP.

We're not done with those electrons yet. They get passed off to yet more molecules, losing energy again in each hand-off. This energy is used to create additional energy-rich substances that will power the creation of energy-rich organic molecules in a process termed the Calvin Cycle. The Calvin Cycle, which creates the sugar G3P from inorganic CO2 from the atmosphere, also takes place within the chloroplast.

So, the chloroplast is a multi-talented factory for the conversion of CO2 into sugars. These sugars provide both energy and carbon, in a useable organic form, for other processes in the plant. Chloroplasts also contain DNA. This, and other evidence, suggests that chloroplasts, like mitochcondria, were once free living organisms that got co-opted by other organisms and now exist within cells in a mutualistic association (the Endosymbiont Theory).


Are there any animals that are both poisonous and venomous? From my layman understanding, animals that inject venom into the bloodstream by biting or poking are venomous. And ones that harm you when you eat them are poisonous.

Are there any animals (or plants) that fit both descriptions?

I'm guessing eating a venomous rattlesnake will give you an upset stomach but not cause enough damage to be classified as poisonous. And I'm pretty sure poisonous tree frogs don't bite into their prey and inject them with anything.

That is certainly an interesting question!

First, to clarify definitions:

To be considered venomous the toxic substance must be produced in specialized glands or tissue. Often these are associated with some delivery apparatus (fangs, stinger, etc.), but not necessarily.

To be poisonous, the toxins must be produced in non-specialized tissues and are only toxic after ingestion.

Interestingly, many venoms are not poisonous if ingested.[1]

I know of at least three species that produce both poison and venom. One is a snake (although not a rattlesnake, which are, in fact, edible): Rhabdophis tigrinus, which accumulates toxins in its tissues, but also delivers venom via fangs.[2] The other two are frogs: Corythomantis greeningi and Aparasphenodon brunoi, which have spines on their snout that they use to deliver the venom.[3]

[1] Meier and White (eds.). 1995. Handbook of clinical toxicology of animal venoms and poisons. Boca Raton, Fla.: CRC Press, 477p.

[2] Hutchinson et al. 2007. Dietary sequestration of defensive steroids in nuchal glands of the Asian snake Rhabdophis tigrinus. PNAS 104(7): 2265-2270.

[3] Jared et al. 2015. Venomous frogs use heads as weapons. Current Biology 25, 2166-2170.


Why does the refractory period of neurons only allow signals to pass in one direction? My textbook states that the advantages of the refractory period is that it means that action potentials are discrete and also that it results in signals only being able to pass one way,  but provides no explanation. Could anyone explain why this is?

The axon is an uniformly excitable structure; if you would stimulate an axon electrically somewhere in the middle, an action potential would be generated in both directions. Hence, an axon in itself does not have directionality.

Nonetheless, under normal physiological conditions, an axon  conveys action potentials from the dendritic region to the axon terminal, called anterograde signaling. The reverse direction, retrograde action potentials,  normally do not occur because signals arising in the dendritic region travel unidirectionally to the terminal. The reason why an action potential travels unidirectionally is because of the refractory period. Because the refractory period will cause the part of the axon that just generated an action potential to become unresponsive, the traveling action potential cannot generate another action potential in the retrograde  direction, because the only excitable region available is in the anterograde direction to the terminal (Fig. 1).

Fig. 1. Refractoriness. source: University of British Columbia

As an analogy, it's like a car driving across a road and throwing a temporary road block behind it that first has to be taken away before the road can be used again. This means that when a car leaves the parking lot and enters the road, it can never go back,  because it throws up road blocks that prevent it to return the way it came.


If all animals were to die, would all plants die too? Humans and many other animals are able to breathe because plants produce more oxygen than they need. I was thinking if all animals died all of a sudden, then wouldn't plants die too. Eventually they would produce too much oxygen and wouldn't have enough carbon dioxide to go through photosynthesis.

Animals are not the only organisms to respire without photosynthesizing. Fungi, many other eukaryotes and many bacteria respire too (and do not photosynthesize).

Now, if all animals were to suddenly die, there would sure cause a drastic environmental change for plants. Whether or not that would lead all plants to extinction is untestable and it is therefore impossible to give a definite answer. This type of question would be better suited for worldbuilding.SE. I personally doubt all plants would disappear.


Why are particulate matter toxic to humans? There are many studies on fine particles (PM2.5) and their fully negative effect on human health. There doesn't seem to have any positive aspect of inhaling particles, except very particular ones, but most often people smoke, and release all sort of unwanted and toxic PM2.5, same goes with for fuel combustion.

At a huge dose, we die within minutes, like in a gas chamber, at small dose below this hazardous health risk level, is it still dangerous to us? If yes, why aren't we equipped to fight them, I guess this smoke concentration and pollution level is very recent on human evolution scale, but at the lowest layer of life, bacteria may develop to break and eat toxic particles, does it happen it our blood? Is it hard to explain to a non-biologist like me?

Particulates can accumulate in the aveolae in the lungs. This leads to inflammation and tissue damage and scarring. This reduces the available surface area for gas transfer. Low level exposure over long periods is harmful. Asbestos workers are well known to get sick, but miners can get black lung or silicosis from inhaling mining dust, and farmers can get lung disease from inhaling dirt that gets blown up as dust. This damage usually isn't seen until they are in their 50s or 60s.


Why is oxygen and CO2 measured in pressure instead of mmoles/L like other ions? Na, K, Cl...All measured in mmol/L in plasma. Why is oxygen and CO2 measured in pressure (mmHg)? (I guess it has something to do with them being bound to RBC but I don't know why the difference).

As you suspected, hemoglobin is the reason why O$_2$ and CO$_2$ in blood are expressed as a pressure (mmHg) and not a concentration. Most of the oxygen in blood is bound to hemoglobin; the concentration of free oxygen in plasma is low because oxygen does not dissolve well in water (which is of course the reason why hemoglobin exists in the first place).

When the oxygen content of blood is given as a pressure, it refers to the partial pressure that a gas (air) must have in order to be in equilibrium with the blood. This might seem a bit roundabout, but it captures the effects of both solubility and hemoglobin. In essence, this pressure describes how much oxygen the blood can release, which is the critical parameter for oxygenation of tissues.

The molar concentration of free O$_2$ in plasma is proportional to the partial pressure over the liquid, a fact known as Henry's law. The proportionality constant is the solubility of oxygen in the liquid, about 1.3 10$^{-6}$ M / mmHg for plasma. So at 100mmHg, the plasma O$_2$ concentration is about 130 $\mu$M. For comparison, the O$_2$ concentration in an ideal gas at 100 mmHg is 9 mM, or 70-fold higher.

See for example this book chapter for more information.


Why does autosomal trisomy have more adverse effects than sex choromosome monosomy or trisomy? Autosomal trisomy syndromes are usually lethal but sex chromosome number related abnormalities do not lead to that much fatality. why?

It has to do with dosage compensation:

The Y chromosome contains relatively few genes. Interestingly, chromosome 21 and 18, which are over represented in the most common viable trisomies, are also relatively small.
Humans already possess a mechanism to compensate for additional X chromosomes: X-inactivation. Normally this inactivates one of the two X chromosomes in females but can also inactivate two in cases of X trisomy.

  Humans are much more able to tolerate extra sex chromosomes than extra autosomes. … Compared to autosomal trisomies, … sex chromosome trisomies are fairly benign. Affected individuals generally show reduced sexual development and fertility, but they often have normal life spans, and many of their symptoms can be treated by hormone supplementation. The ability of humans to tolerate supernumerary sex chromosomes is quite remarkable, as individuals can survive with as many as four sex chromosomes. This tolerance most likely relates to both X inactivation and to the small number of genes on the Y chromosome. In fact, when cells from individuals with more than one copy of the X chromosome are analyzed under a microscope, all but one of the X chromosomes appear as condensed Barr bodies, the cytological manifestations of X-chromosome inactivation. Supernumerary copies of the Y chromosome may be tolerated because the few gene products of the Y chromosome are not required for survival.

From: Chromosomal Abnormalities: Aneuploidies by Clare O'Connor (emphasis added)

An added bonus (and I feel as though I should actually write something myself), I recently read a paper studying trisomy 21:

Jiang J, Jing Y, Cost GJ, Chiang JC, Kolpa HJ, Cotton AM, Carone DM, Carone BR, Shivak DA, Guschin DY, Pearl JR, Rebar EJ, Byron M, Gregory PD, Brown CJ, Urnov FD, Hall LL, Lawrence JB. 2013. Translating dosage compensation to trisomy 21. Nature 500(7462):296-300.

Using zinc finger nucleases, they inserted a XIST transgene into chromosome 21 of cells derived from Down syndrome patients. XIST is a gene centrally involved in X-inactivation. They found that, by inserting it into chromosome 21, they were able to silence one and revert the trisomic cells to a more normal phenotype.


What could an increase in systolic blood pressure and decrease in diastolic mean? Sorry if this is a really simple question but my academic background is in completely different sciences. I recently made a computer game for an experiment that was related to anxiety and relaxation. One of the ways that I measured for success was to record participants blood pressure before and after they played the game.

There was a slight increase in systolic BP after playing the game, but not by a statistically significant amount. However the data shows a decrease in diastolic BP that is statistically significant. I've been trying to figure out why this might have happened but can't seem to find any answers. My brief overview of search engines and journals only seem to relate these changes to certain types of exercise. Which doesn't help as the participants of the experiment were asked to remain seated for 20 minutes by the time the second BP recording was made. Just wondering if anyone has any information in relation to relaxation techniques that might result in this pattern?

If it helps heart rate has mostly uniform throughout the experiment.

First, a couple of considerations

Heart rate (HR) is lower when seating, and even lower when lying. I assume that participants were seated when the first measure was taken.
Cardiac output is not constant during the day. Depending on the moment, some factors such as digestion have an impact in Cardiac output, so take that into account when carrying out the experiments.

Normal walking may cause that blood pressure pattern. I think that you should not consider the increase in systolic pressure if it is not significant, as something as simple as crossing your legs when seated can increase your systolic pressure and normally diastolic pressure provides more information for physicians. Relaxation techniques usually decrease heart rate, which can affect the blood pressure. However, the point in this case seems to be that HR remains constant. I suppose that Mean Arterial Pressure $(MAP)$ has decreased.

If we part from:

$\textit{MAP} = (CO \cdot SVR) + CVP$
where $CO$ is cardiac output, $SVR$  is systemic vascular resistance and $CVP$ central venous pressure.

$CVP$ is usually depreciable. $CO$ is defined by $SV \cdot HR$, where $SV$ is the stroke volume. Then, if the HR is constant, only $SV$ or $SVR$ could have changed. Maybe the heart is pulsating more vigorously, or a vasodilation is decreasing $SVR$. I find the latter more likely. However, I don´t know why the smooth muscle could be relaxing. Make sure that heart rate is not changing and consider your sample size.
I hope it helps, at least to focus you search on cardiac regulation. It is difficult to conclude anything without seeing the data but I tried to answer from my limited knowledge since I am not specialized in cardiac physiology.


Where can I find an image of the gut/anatomy of the mealworm? Specifically, I'm a student working on an experiment involving the dissection of the mealworm (Tenebrio molitor) but for the life of me, I can't seem to find an image anywhere on the internet. Speaking to Carolina.com also got me no results. We're looking to dissect the mealworm and extract its gut/GI tract. However, at the moment it seems like we're going in blind. Is there anyone out there who can provide some insight?

The best I could find which showed the inside of a mealworm not just the outside was this:

Taken from here. Hope this helps with your dissection.


Is there any evidence telling us what the oxidation state of early earth's atmosphere was? I ask this question in relation to the origin of life. I realise it would probably be better suited to a geology stack exchange, but it does not yet exist.

The Miller-Urey experiment gives a lab based demonstration of how organic compounds may have been produced. It recreates that conditions that are thought to have existed in the early atmosphere (Hadean period).

What this experiment relies on however is an assumption that the atmosphere lacked oxygen (reducing). The Miller-Urey experiment does not produce proteins if it is conducted in a oxidizing environment. I've seen that there is some debate over the oxidation state of the atmosphere, and the main evidence for a reducing atmosphere is that life wouldn't have been able to begin without it. Is there evidence supporting an oxidized early atmosphere, and if so, how did life come about?

There are wikipedia pages on Geological history of oxygenation and on Great Oxygenation Event

I don't know much about geology and someone else might be able to give an exhaustive list of evidence (and method of measuring) concerning the oxygen concentration on earth but that would be a very long answer I guess! Rather than a full answer, I give you a list of wikipedia pages below that will interest you and should help answering your own question.

Banded Iron Formation
Evolution_of_dietary antioxidants
Huronian Glaciation
Ice core


blastn: What substitution matrix is used? I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length.

For amino acids I am able to use the substitution matrices in Biopython (Bio.SubsMat.MatrixInfo).

However, I haven't found anything similar for DNA, so I read up and found that most systems use a match/mismatch scoring system where each nucleotide match and mismatch is scored and then the scores are summed. This works fine as long as I am only dealing with A, G, C, and T, but I run into problems when I get a sequence containing N or M and the like (meaning nucleotide unknown).

Is there a standard way to handle the situation with unknowns? That is, how do I score A versus N or M versus N?

Thanks in advance.

BLASTN does not use a substitution matrix. There are scores for match, mismatch and gaps which you can also define.

There is no feature available as of now to allow scoring of matches against unknowns. They are considered mismatches (as shown below). If these unknown are in the middle of a HSP, then you can probably re-score the HSP according to your scheme using a python script. If the N stretch is disrupting the HSP, then you can try relaxing the mismatch penalties and reduce word size (basically reduce stringency). I can't think of any other solution.

Query  1    CAGCGTCCANNTCCCGAGGTGCCGGGATTGCAGACGGAGTCTGGTTCACTCAGTGCTCAA  60
            |||||||||  |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  8    CAGCGTCCACCTCCCGAGGTGCCGGGATTGCAGACGGAGTCTGGTTCACTCAGTGCTCAA  67

Query  61   TGGTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACANNCTCCACCTCCCAG  120
            |||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||
Sbjct  68   TGGTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACAACCTCCACCTCCCAG  127

Query  121  CCGCCTGCCCTGGCCTCCCAAAGTGCCGAGATTGCAGCCTCTGCCCAGCCGCCACCCC  178
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  128  CCGCCTGCCCTGGCCTCCCAAAGTGCCGAGATTGCAGCCTCTGCCCAGCCGCCACCCC  18


How distantly related are eusocial insects? Aren't members of a species much more related than 1/4, 1/2, or 3/4? Possible Duplicate:
  How many genes do we share with our mother?

I went to a lecture that talked about the behavior of social insects in terms of their relatedness of genes. For instance, workers were 3/4ths related to each other, so it was in their gene's interest to care for each other instead of having their own, half-related offspring.

However isn't it the case that members of the same species are much more related than 1/2 or 3/4s? I've read that we share anywhere from 95-99% of our genes with chimpanzees. Also I believe I've read (perhaps in Pinker) that we share some 60% of our genes with daffodils.

So when they talk about the relatedness of social insects, and they say it's 1/2 or 2/3 or 1/4, aren't they really talking about the 1% to 5% of genes that are in play in sexual reproduction within the species? In other words, aren't I 97% + 1/2 * 3% related to my sister, assuming human beings share 97% of our genes?

In evolutionary genetic comparison, you are talking about members within species. They will share almost all genes, because if they didn't they would belong to a different species.

However, within species there exist different versions of the same genes, called 'alleles'. When we say that you are 0.5 related to each of your parents, we mean that statistically, 50% of your alleles should be those which your father has, and 50% of your alleles are those passed down from your mother.

Eusocial insects have different mechanisms. Bee males are produced without fertilisation, meaning that they only have one copy of each bee gene. When the male produces sperm, it only has this one set, so all sperms end up carrying the same set of alleles.

Females on the other hand have the normal double set, with two different versions of each gene. So if you look at one gene, half of the female's egg should have one version and the other half should have the other version. All females of one hive are produced by the same queen and the one male that she mated with. Remember, the male only has one set, so the versions coming from the male are the same in all female offspring.

This means a female's genes are made up of: 50% from the father (these are the same across all females) and 50% from the mother (where half the females have one version and half have the other version). Statistically, this means that looking at one gene, there is a 75% chance that two bees will have the same version of that gene.


Is this a simple Hardy-Weinberg problem? Phenylketonuria is a severe developmental disability due to a rare autosomal recessive allele. Approximately 1 in every 10,000 newborns suffer from this disease. Calculate the frequency of the allele causing this disease and the frequency of heterozygous "carrier" individuals.

What I've come up with is that this is a Hardy-Weinberg problem. Is this true?
My answers:
frequency of allele causing disease = 0.01
frequency of heterozygous "carrier" individuals = 0.0198

Too long for comment :

If you want to solve the question by Hardy Weinberg, there are certain assumptions involved :-

1.There is random mating. People do not choose their mates on the basis of whether they carry PKU gene or not & mating among close relatives is not there.

2.No new PKU mutations happen.

3.There is no difference in the reproductive capacity of people with or without PKU gene.

If your study population fulfills these criterias, you can apply Hardy-Weinberg to calculate frequencies of various genotypes.

Because this question is  homework ,such assumptions are not mentioned. And, at undergrad level,there is no other concept by which you can solve this question except HWE.

PS: Try to think what would happen if these assumptions are not fulfilled.

PSS: Even if you are solving a small homework question, do think about the logic behind every step. Though it may seem like a lot of work initially , it has enormous potential to teach you subtle concepts !


Does a microwave oven disinfect food? Imagine I am preparing food -- just about to put it into a microwave oven --  and some of it falls on the floor. Assuming it got some bacteria or other organisms (viruses?) on it, will the microwave processing disinfect it? What about worm eggs? As I understand, any living organism, given enough exposure to microwaves, degenerates. Is this true?

Microwave ovens can indeed kill bacteria in food by heating them to high temperatures. For example, this article found that microwave heating could kill all of the Salmonella bacteria in a chicken thigh sample:

  The effect of microwave heating on Salmonella Enteritidis inoculated
  on fresh chicken was investigated using a microwave oven (800 w) to
  determine the destruction of Salmonella Enteritidis isolated from
  chicken carcasses, in relation to the time of heating at two power
  settings: high (power level 10) and medium (power level 6); The
  relationship between heating time and temperature was also been
  studied. The destruction was 6.4 log cycles at time 95 sec for the
  high power level, and 5 log cycles at time 140 sec for medium power
  setting. After 110 sec for higher power level, no survival of
  Salmonella Enteritidis was detected in samples (100g), but at 140 sec
  for medium power level, these food pathogens were still present.

However, the main issue is balancing the amount of microwave exposure. Heating the food for too long will result in the food becoming dehydrated or burned, and heating it for too short a period of time will result in food poisoning.

This paper shows that insufficient microwave exposure can and will lead to food poisoning if there is a large amount of bacteria inside the food:

  Leftover samples of a savoury rice dish consumed by all six ill
  persons contained 6×103/gm Salmonella enteritidis PT4. The rice salad
  comprised boiled rice, raw carrots, eggs, cheese and curry powder. The
  curry powder and remainder of the pack of six eggs were negative on
  microbiological analysis. The rice dish had been prepared by heating
  in a 500 W microwave oven with a rotating turntable on full power for
  5 min.


Hand-eye coordination in 3D space A simple daily event has amazed me and triggered this question. I have read and heard about hand-eye coordination. It quite straightforward when you e.g. want to open a door or play Xbox. In this case either your hand is in your view or your hand will feel the buttons of your Xbox.

But when it comes to catching a ball or try to catch a falling object, our hand is totally out of our view since we are closely following the trajectory of the moving object. But meanwhile our hands moves in a 3D space and align it self perfectly in the path of trajectory correctly. This is what amazed me.

If you can see your hand and the object/ball simultaneously, its just a matter of moving our hand in the path of that ball/object. But having hands totally out of sight but catching the ball/object perfectly every time is amazing piece of nature's engineering.

How humans have achieved such a amazing piece of coordination in a 3D space without seeing where the hands are located?

Short answer
Proprioceptic receptors provide a feedback mechanism from the body to the brain, telling the brain what our limbs are doing and where they are with respect to the body without visual feedback being needed.

Background
Muscles, skin and joints contain proprioceptic receptors. They sense position and movement of our limbs and trunk, they register force as well as heaviness. Examples of such receptors are limb tendon organs and possibly also muscle spindles, which contribute to the senses of force and heaviness.

Proprioceptive sensations are influenced by visual input, but operate without it. The proprioceptive system is responsible for the ability to touch your nose with your eyes closed and the examples you have given related to catching a ball while not paying visual attention to the position of your hands.

Afferent signals from these receptors are combined and processed in the brain. Together they form information about limb position and movement. This information is mapped relative to a central body map to determine the location of the limbs in space.  The proprioceptive senses, particularly of limb position and movement, deteriorate with age and are associated with an increased risk of falls in the elderly.

Reference
Proske & Gandevia, Phys Rev 2012; 92:1651-97