Does a top heavy population grow, decline or stabilize? Imagine a population that has a larger proportion of older individuals than younger ones, what could possible happen to it in the future?

I am guessing that if the older individuals reproduce, the population will increase but as the older generation grow older they would eventually perish again decreasing the population. As they form the larger proportion, the net population would eventually grow but decline, but would the population then begin to stabilize or continue declining?

Your question leads to the field of structured population models, and I am afraid the answer is: It very much depends on the exact Leslie matrix!. The population may go extinct, may remain at stable size or may grow indefinitely (theoretically speaking), may increase in size and then go extinct, etc…

This is at least true if you make the assumptions that the rates that govern transitions between age/stage classes (survival, growth, reproduction) are  stable over time. Your scenario is explicitly dealing with transitory population dynamics, i.e. it is asking about the population fluctuations that will happen before the age-structured population stabilizes (assuming it does stabilize at some point).

To understand what will happen to your population you can model your population using a Leslie Matrix.

Leslie matrix

The Leslie matrix describes the age-specific survival and fecundity of individuals in a population. Shortly speaking, a population dynamic model using age-specific survival and fecundity looks like this:

Renaming the matrix and the two vectors you see above it gives: $n(t+1) = M \cdot n(t)$, where $n(t)$ is the vector of number of individuals in the population at each age and $L$ is the Leslie matrix, where the first row gives the fecundity of each age ($f_2$ is the fecundity of the individuals of age class $s$ where the number of individuals is a given time is given by $n(t)$) and the lower diagonal gives the survival probability ($s_2$ is the probability of surviving from age 2 to age 3).

So, basically to answer your question, define your Leslie matrix $L$, define $n(0)$ and iterate (left multiply your vector $n(t)$ several times) to see how the number of individuals change through time.

Leslie Matrix and Linear Algebra

The right leading eigenvector of $L$ gives the stationary distribution and the associated eigenvalue gives the growth rate $R$. If $0<R<1$, then the population size decreases through time if $R>1$, the population size increases through time. $R$ cannot be lower than zero (see Perron-Frobenius theorem to understand why). Many biologically interesting features can be extrapolated from the Leslie matrix such as the average lifespan or wether you'd better to introduce individuals of a age 1 or of age 2 (for examples) in a natural population in order to prevent its extinction. The sensitivity of the population to change in parameter (such as an increasing mortality rate at lower age due to a new predator for example). You will find more information on the Leslie matrix on the wiki article and on many other websites.

Other ways to model using a Leslie Matrix

One can also model age-structured population using right matrix multiplication (unlike the above example) and use row vector rather than column vector. The Leslie matrix may also be a function of various variables such as the population size. One can also extend the Leslie matrix to incorporate different class of individuals in the population (different genotypes or different sexes for examples).

Books

Charlesworth (1994) and Caswell (2001) are both excellent books to go deeper into the subject of structured population models, but may be challenging if you lack some background knowledge in linear algebra or population biology.

Hope that helps!

EDIT - R simulation

It's been a time I haven't programmed in R. So, I took the advantage of your question to have some fun and write a quick and dirty code. Below you'll find a R code that allows you to see how the age-specific population size varies depending on your initial vector $n$ and the Leslie matrix. I also add some instructions in order to change the number of age classes (because my code is not very flexible).

install.packages("ggplot2")
require(ggplot2)

######## Parameters

n = c(2,23,40,300) # initial age-specific population size. MNodify as you which. You can as well change the number of age classes

L = matrix(c(0,0,1,2,0.8,0,0,0,0,0.8,0,0,0,0,0.3,0), byrow=T, ncol=4) # Leslie matrix (Left multiplication). Modify as you wish but make sure it should always be a Leslie matrix. You can modify the number of age classes

nb_generations = 100 # Number of generations you want to compute

############

n_t = data.frame(age1=rep(0,nb_generations), age2=rep(0,nb_generations), age3=rep(0,nb_generations), age4=rep(0,nb_generations), Generation=1:nb_generations) # It is a data frame to keep track of age-specific population size changes through times. You will have to add more `ageX` columns if you want to simulate more than age classes

# print (n)
for (generation in 1:nb_generations){
    n_t[generation,1:4] = n
    n = L %*% n
#   print (n)
}

n_t2 = reshape(n_t, direction='long', idvar='Generation', v.names='Age_Specific_Number_of_Individuals', varying=c('age1', 'age2', 'age3', 'age4'), timevar='age') # Just to reshape the data for convenience!

ggplot(n_t2, aes(x=Generation, y=Age_Specific_Number_of_Individuals, color=factor(age))) + geom_line() + scale_color_manual(values=colorRampPalette(c("black", "grey"))(4)) # change the last number of this line according to your number of age classes.

You can see that there are important osciliations in the first 30 or so generations just as expected. Then, the population more or less stabilizes. You also see that due to a survival probability that is different from 1 for each age class, there is necessarily at equilibrium more individuals in age class 1 than in age class 2 and more in age class 2 than in age class 3, etc...


Is there any disease in adult human, other-than cancer, which-is resulted from mutation? On all environmental articles I read about 3 impacts of mutagens (say Cigarette/ Naphthalene/ EtBr/ Colchicine/ ionizing radiation/ whatever )...

1. direct effect on tissues, other than mutation, such-as burns, choke, cirrhosis of liver, Lesion in lungs etc. (no direct relation with mutation)

2. Mutation affecting development of organs and intelligence, in youngs; and hidden mutation not affecting adults but showing expression (birth-defects) in future progeny.

and

3. Tumor and Cancer.

Now, my question is, if an adult become exposed to some mutagen; the only visible effect of mutation (not about burns etc, talking about genetic-mutation) ... on that affected-individual; whether cancer is the only-possible disease? or it is possible to occur some-other sort of genetic disease  (not about future but only to that particular affected-one)

anything else should happen ... say exact opposite thing... uncontrolled apoptosis that gradually kills whole affected person (for say).

or for say due to a genetic-damage a person became unable to perform cell-division, so no wound healing. If once part of body become cut, and it remain open forever, never seals. (I never heard or read anywhere).

instead of cell-death, they could perform some-other malfunctions, too. Like turning-off certain normal function, say stopped transport of certain molecule, or say stopped a function like color-vision, or start to secrete / accumulate some metabolites same-way as inborn error of metabolism?

But could anything such happen other-than cancer?

Before answering your question, an important note. Not all neoplastic growth is malignant. A mutation may result in a benign growth, which is an outcome different from cancer. Not all of these change to cancers. Moreover, almost all genetic diseases may arise de novo as a germline mutation, and this mutation may be caused due to the environmental mutagen, and hence will be a non-neoplastic outcome of environmental mutation. The list of such genetic diseases is impossible to replicate here.

Assuming you are asking non-malignant diseases involving somatic (acquired) mutation as a pathogenetic event, here's a subset.

Some diseases with proven somatic mutation are:

Neurofibromatosis 1 & 2
McCune-Albright
Paroxysmal Nocturnal Hemoglobinuria
Incontinentia Pigmenti

For more details, have a look at this paper here.
Erickson RP. Somatic gene mutation and human disease other than cancer. Mutation Research/Reviews in Mutation Research. 2003 Mar 31;543(2):125-36.


How does the measeles virus form? I would like to understand how (if possible) the measles virus could start to infect a population that was theoretically isolated from any other population group. Put another way, can the measles virus develop within a person without external influence/inputs?

The question could be rephrased

Can a measle virus be created anew and not via reproduction from another virus?

The answer to which is "no".

The falsified idea that new life forms can jump pop up out of nowhere is called spontaneous generation. Spontaneous generation do not occur.

Note however that sometimes it may look like as if a new epidemic came from nowhere. The reasons is due to natural reservoir.

  A natural reservoir  or nidus (the latter from the Latin word for "nest") is the long-term host of a pathogen of an infectious disease.

An asymptotic carrier can be used as a natural reservoir

  An asymptomatic carrier (healthy carrier or just carrier) is a person or other organism that has contracted an infectious disease, but who displays no symptoms.

These reservoirs can keep the viruses (or other pathogens) alive in while from the outside it looks like the disease has been eradicated. At some point the virus can spread again making it feel like it came out of nowhere.

[..] my confusion is on how a population gets the first instance

There is no clear first instance. Modern day measle viruses evolved from an ancestor that was not the modern day measles. Just like there was no sudden first human (or any other species). There were just ancestors that evolved to become what we now call modern day humans.

You might want to have a look at an intro course to evolutionary biology such as understanding evolution by UC Berkeley for example.


Species with reproduction barriers that can both reproduce with a third species To start with, I do not have a sound knowledge in biology or any formal education in the area.

I was told that one of the definition of a species is a reproductive barrier, which means that if two animals can't reproduce, they are of different species. The barrier can be either the inability of the sperm to fertilize an egg, or a physical trait that inhibits reproduction, e.g. a cricket species that has a different mating song than another species or two species of flies, one that mates on yellow flowers, and the other on red flowers.

But what happens when, while two species can't reproduce, but there is a "chain" of "intermediate" sexual partners that can produce reproductive connection step by step. Like 6 degrees to Kavin Bacon, but with animal sex.

I'll try to explain with an example:

A Great Dane and a Miniature Pinscher dogs can't mate due to obvious size differences. But The Pincher can mate with a German Pincher (a slightly bigger breed of Pincher), which can mate with a Doberman Pincher. And the Doberman can mate with a German Shepard which can mate with a Great Dane.

I've also heard that such things happen with birds and crickets, where there is an original species, from which evolved several other, and while the original species (which still exists) can mate with all the new species. Some new species can't mate with some, or all of the other new species.

How are such species are defined, and at what point dogs stop being dogs anymore?

How are such species are defined, and at what point dogs stop being
  dogs anymore?

This is a bit like the is-Pluto-a-planet-discussion. A group of scientists have to come together and hold a big conference.
You have a few principles that you want to adhere to and then it's big groups of people making decisions.


Why doesn't the sperm die if there is citric acid and acid phosphatases in the semen? While studying I read that sperm needs alkaline medium for its survival.But when I studied the composition of semen it revealed that semen contains citric acid which acts as a sperm nutrient along with fructose.It also contain acid phosphatases.So in such sitution how can the sperm survive?

Citric acid is a weak acid so in the context of a buffered physiological medium (semen pH 7.7) it will not cause any significant acidification. Acid phosphatases are enzymes with a pH optimum below 7 (as distinct from alkaline pho sphatases). Their presence has no implications for the pH of semen, although it is interesting to speculate why an alkaline fluid would contain an acid phosphatase.


What is the mechanism responsible for the 'delay' in delayed rectifier potassium channels? I've been trying to find a comprehensive explanation concerning the nature of the 'delay' in neurons' delayed rectifier potassium channels. As it's written in my intro to neuroscience textbook, these channels are voltage gated and become activated when the typical neuronal membrane reaches an electrical potential of approx. -40mV. While the channel is activated at this point, it only opens up after a delayed period of approx 1ms.

I'm mostly trying to clarify that this isn't an confusion in wording and that delayed rectifiers aren't actually activated when the inner membrane reaches a charge of approx +40mV which would be correlated (at least in textbook examples) with the '1ms delay', but caused by the actually typical charge observed at approx 1 ms of delay during an action potential.

Thanks so much. Let me know if I can clarify something. I know this wasn't necessarily so well asked

These channels are slow to respond. After depolarization they are activated, but only after a relatively long time. Their closing kinetics are also relatively slow. A definition is give here.


Which patterns do I have to avoid when modifying the 3'-UTR? I want to change a pre-miRNA sequence (in my case the pre-miRNA is encoding in a 3'UTR of a gene) and then put it in a lentivirus to see if it is still processed.

After modification (permutation of ten regions of ~20 nt) which kind of newly appeared pattern I've to be careful about? I do not want to disturb the gene in which the miRNA is encoded

If your goal is to avoid regulatory elements, I would not believe any prediction program, since new regulatory elements are found every day.  The best way would be empirical and just clone and infect with a mutated 3'UTR and see if your gene's regulation is perturbed.  You could at least swap the entire 3'UTR with that from another gene to see if there are even any gene regulatory elements in the 3'UTR.


How long does it take for cancer to be detectable if it grows from a single cell? Assuming cancer has its origins at a single malfunctioning cell, how long would it take for that cell to grow from the point at which it is malfunctioning enough so that it can be detected by the immune system, to the point at which it be detected with:

Routine modern medical tests
Cancer specific blood test
Noticed by the host (symptoms)

The barriers you mention are outlined well in the classic Hallmarks of Cancer paper: http://www.cell.com/abstract/S0092-8674(11)00127-9

The main problem with finding a general answer to this question is the large diversity in cancers, and the resulting problem in defining what hallmarks are sufficient to call an individual cell cancerous. There are cancers that can't be detected by the immune system or blood tests and will hide for a very long time symptom-wise, and non-cancerous tumours that can be detected in various ways very early on.

Let's say for your timing reference you simply take the point of neoplasm diagnosis (for neoplasms that turn out to be cancers after testing). At this point, figuring out how much time this cancer has spent being cancerous is very difficult, and to my knowledge has never been done. It could be possible to determine:

The number of genetic or epigenetic malfunctions that made the difference between benign tumour and cancer for this particular neoplasm (once again, hard to define)
An approximate rate of acquiring those malfunctions. Conceptually, one could ex vivo culture the cancer and monitor the rate of aquisition of further mutations in cancer-related loci or epigenetic markers.

Depending on how that rate looks, it may be possible to reverse extrapolate the rate of acquisition before diagnosis, and thereby estimate an approximate timepoint of acquisition of the first proper cancerous malfunction.

Besides that, "it probably took more than a few days" is the only statement I can confidently make, although as far as biological theory goes, it's perfectly possible (though highly unlikely) for a cell to acquire a set of mutations sufficient to become cancerous in a single round of replication.


How many molecules are generally required for cell signallng processes for given cases? I know its really a broad topic but I am interested in just few cases:

Quorum sensing
neurotransmitters for the communication of images/ general information
hormones/pheromones

I actually want to know that does a single or hundreds of molecules are needed to communicate information from one cell to another.
I searched but approx number of molecules, I can't find anywhere.

A cell can interact with other cells in zillions of ways. You can send information from one cell to other cells via neurotransmitters, hormones, pheromones, electric signals, magnetic resonance ,leukotrines etc.

In general a single type of molecule is enough to send such information. Like you require only Acetylcholine(Ach) as neurotransmitter to transmit various nerve impulses.
But, even for a single type, you require thousands of molecules. Like 1 molecule of Ach can do almost nothing and would immediately be broken by Acetylcholinesterase. You require 1000s of such molecules.

You can modify the communicating information via different types of transmitters. You can use GABA or glycine to supress any information exchange or use dopamine to enhance it. But again you will need many molecules of GABA or Glycine.

For visual pathway,  you can use no. of types of transmitters like glutamate, glycine, gaba, dopamine, acetylcholine, substance P etc.
Neurotransmitters for visual pathway.

Hormones are transmitters that are required in small quantities. But,  again you require certain concentration. There is normal blood concentration of various hormones like 80 pg/ml for calcitonin.

Quorum sensing use transmitters like AHLs. Again a certain threshold value is required for them to act.

Again,  to produce these transmitters you have to go through a rigorous process of transcription, translation and post-translational modifications.
So, for cell to communicate a rigorous process is used.


Bacteria Replication I learned this at a lecture, but somehow I have trouble in understanding this. It is said that the bacteria such as E.coli need 20 minutes to divide, but its chromosome require 40 minutes to multiply. It is explained that the E. coli will have copied half of it, which will spend 20 minutes and after divided, it will continue another 20 minutes to complete the chromosome copy. However, it is said that each daughter cell will have one complete and half copy after they divide. I am confused that if the bacteria only spend 20 minutes to copy half of it, how  can each daughter cell could have one and a half?

Referring to the six stages in your diagram as Stage 1 through Stage 6, let's look at Stage 3: At that point, there is one bidirectional replication in progress, having made it about halfway around the chromosome. So it has 2 copies of the first half of the chromosome, and 1 copy of the rest, which is yet to be copied.  To get to this state of replication took 20 minutes.

Now the cell starts two new replications, one at "origin of replication" on each of the two copies of the first halves of partially replicated chromosome.  This is the state shown in Stage 4.  There are now three replications going on: the original, which is working on the last half of the chromosome, and two replications, which are working on (their own copy of) the first half of the chromosome.  All three replications will continue working for about 20 minutes.

We then get to Stage 5: the original replication has finished and the septum forms to separate the daughter cells.  The two replications started in stage 4 are continuing, and are about halfway down the chromosome.

The cells separate, and we are at Stage 6.  But stage 6 is the same state for each daughter cell as we had in Stage 3: a chromosomal replication that is halfway through (thus having one and a half copies).  It took 20 minutes to get from Stage 3 to Stage 6, where we are ready to double again.  During that 20 minutes, only one half of a chromosome had time to be copied, so it takes twice that (40 minutes) for replication of the whole chromosome.  This works out because the cell is doing three replications at once.


Name this green giant insect hanging on the wall This Insect was found on the wall of the Party Hall, Where I went to my Girlfriend's birthday party. This insect looks very greeny. I am in India.

You simply found Parasanaa donovani, Which is the large bush-cricket found in India and various countries in Southeast Asia.


Evolutionary chronology - if any, which species have evolved in the last 100 years I heared somewhere, I cannot remember where, that there has not been an evolution observed in our lifetime. In life science class, right at the start, we was doing the usual MRSGREN (how to tell if something is a living organism), and the tutor said that you can also tell something is a living organism if it evolves. So I asked if there has been an observed evolution in our lifetime. She said that there had been many but could not recite any off the top of her head, so the next week she handed me a piece of paper with 8 or so websites that aparrently corroborated her claim. I have not got the paper anymore but I recall there been on there the peppered moth or something. So I set out to look for a chronological list of evolution but could not find an authoritative one. I could only find something on wikipedia that indicated that species have been dying out for the past thousand years, but nothing saying that any have evolved.

Every single species in existence has "evolved" over the past 100 years. Evolution is a constant process. You are asking whether we can observe evolutionary change in a given species over a short time span, not whether evolution is occurring. I know this sounds like pedantry but it is a very important distinction.

That said, yes, of course we've seen evolution in action in short time spans. The classic example is the various bacterial species that have developed resistance to antibiotics. As very nicely illustrated by Garry Trudeau:

If you want more rigorous evidence than a comic strip, have a look at Wikipedia's page on antibiotic resistance or read Demerec, 1948(1).

Another example is described by Yona et al.(2) who show that subjecting yeast to high temperatures (heat stress) for a few generations causes genetic changes that help the cells deal with the stress. This is, clearly, evolution in action. In fact, they even show that the first response is the duplication of an entire chromosome (think of it as a crude, bludgeon-like solution) which is later suppressed by other, more subtle, compensatory mechanisms which arise to replace it.

Demerec, Milisav, "Origin of bacterial resistance to antibiotics." Journal of bacteriology 56(1), 1948
Yona et al., "Chromosomal duplication is a transient evolutionary solution to stress", PNAS, 109(51), 2012.


Spider Identification: Is this an Arizona Recluse? I found this spider in my toilet bowl. It was after dark. We live in Prescott Valley, AZ at around 5100' elevation at the edge of a development fairly close to the mountains in grass land.

I'm concerned its an Arizona Recluse (or Desert Recluse). We saw a few of these around the house during the warmer months; this is the first I've seen in a while since its gotten cold, but my wife just did some extra cleaning.

I don't see a violin shape, but this article points out that desert recluse's don't have a noticeable violin. It also looks like it has 3 sets of eyes, but the 4th may just be hidden due to the angle since it looks like the 3 I see in the pics aren't centered quite right. Anyways, if anyone has some insight I would be happy to know. The leg span was a bit bigger than a penny.

I don't think it's an Arizona recluse. Characteristic of all recluse spiders (including the five varieties found in Arizona):

  Long thin legs
  Oval shaped abdomen
  6 eyes in dyads (pairs)
  Uniformly colored abdoment with fine hairs
  No spines on legs
  Legs are uniformly colored
  Light tan to dark brown in color
  Distinct violin-shaped mark on on the back points to the posterior of the spider (less obvious on Arizona recluses)
  Body not more that 3/8" in length

Your spider has spiny legs. That, plus the fact that Arizona recluses are even less likely to live where humans do (as your article states), and are attracted to dry places, makes your spider an unlikely candidate, but I could be wrong.

Loxascelidae, Loxosceles reclusa


From where did the selfish gene get its selfishness? This is in reference to the book The Selfish Gene by Richard Dawkins. Further,

Because there is a law such as gravity, the universe can and will
create itself from nothing. Spontaneous creation is the reason there
is something rather than nothing, why the universe exists, why we
exist. It is not necessary to invoke God to light the blue touch paper
and set the universe going.
— Stephen Hawking and Leonard Mlodinow, The Grand Design, 2010

What was the spontaneous creation that led to this selfish gene?

This is a very introductory question to evolutionary biology. While the book "The selfish gene" is very pleasant to read and directly offer some key notions of modern evolutionary biology, it offers little to no introduction to the basics of evolutionary biology (it is not its goal). I highly recommend that you have a look at a short intro to evolution such as Understanding  Evolution by UC Berkeley for example.

Below, I give a very brief answer to your question but taking an intro course to evolutionary biology would probably be more helpful.

What is evolution?

Evolution is a change in allele frequency in a population through time

An allele is a variant of a gene (or any other sequence at any locus). A locus is a position in the genome.

How do alleles come to existence?

Alleles are created from previous alleles, through mutations. The process of mutation is random in the sense that the effect of the new allele is "unknown from the organism" which create this allele. The mutation just occurs and it just has some effect on the phenotype and the fitness.

What are the forces of evolution?

There are a number of forces that affect evolutionary processes such as genetic drift, migration and natural selection for example.

What is natural selection?

Natural selection is the change of frequency of of the alleles at a given locus caused by differential fitness among the individuals carrying the different alleles.

Why one ought to expect that altruism should not exist in nature?

Here the term selfish and altruism are defined in terms of fitness effects. An altruistic individual is one that is performing a behaviour (or having other phenotypic trait) that is positively affecting the fitness of an individual of the same species while decreasing its own fitness.

Imagine an individual (let's call him the "actor") that has a mutation causing him to be altruistic (in opposition to being selfish). Such "actors" will have a low fitness while its neighbours will take advantage of the altruism of the "actor". There is therefore a differential in fitness between those that are selfish (higher fitness) and those that are altruistic (lower fitness) which ultimately yield to a decrease in the frequency of the alleles causing the altruistic behaviour until it completely disappears from the population.

The above paragraph explains why one would expect that altruism should be absent from nature. However, the story is definitely not that simple. But this extension is a story for another time. You will have to understand the different between "true (lifetime) altruism" and "false altruism", you will have to learn some game theory and finally Hamilton's extension of game theory.

What Dawkins mean by selfish gene

In his books, Dawkins talks about selfish gene often to refer only to genes that are causing meiotic drive (which might be confusing) and to talk about the existence of inter-genomic conflict. There are various mechanisms that can cause meiotic drive. You can learn more about that in Haid and Berstrom 1995, Jeanike 2001 or Jeffrey and Neuman 2002 for examples.


How could I identify whether given RNA-seq data is paired end or single end I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans

In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702  ftp and downloaded sra file. Then I need to convert it to fastq file format. For this purpose I've heard that there is a sra-toolkit and within it there is  fastq-dump exacutable. However in order to use it, first of all I have to figure out whether my sra file contains paired-end or single-end read data. So my question is that how could I know the type of reads in the dataset (in the first link) ?

Without any information, I used --split_files flag of fastq-dump exacutable and it generated two 14 Gb  (both of them  are exactly 14.346.367.840 bytes) files and their name are  SRR1741330_1.fastq and SRR1741330_2.fastq Does it mean my dataset is paired end ?

As an another question (different but related with part 1). In the SRR1741330_1.fastq file, at some lines, sequences contains different characters such as CCCFFFFFGFHHHGJJJJI#1?FEIGGI... Before looking into these files, I have thought that these sequence lines should only contain the letters of A,G,T and C . What are these F,H,J,I,#,? etc..

My questions might be trivial and unmeaningful but since I'm a totally new person in this area, I could not understand them.

EDIT

New question

I wonder one more thing, since its related with previous part of my question I asked it here instead of creating new question. After I generate fastq file with dump_fastq executable, all the sequences are length of 50. Does it because of parameters of the dump_fastq executable or its related with original sra file? In other words, could I increase this length?

To find out whether a dataset was paired-end or single-end, go to SRA, click on a run, and look under "Library". Paired-end datasets will typically have "Layout: paired". Note that people don't always mark this correctly, which causes no end of headaches.

Regarding lines like "CCCFFFFFGFHHHGJJJJI#1?FEIGGI", that's the quality score line. Look at the fastq article in wikipedia for more details.

Edit: Regarding the updated portion of your question, no you can not increase this length. The sequences produced by Illumina machines are a fixed length and that length (or whatever length was submitted) is what you're getting. As a general rule, you'll get whatever sequence was updated (unless you forget the --split3 (or whatever it's called) option).


Is there a list with common mistakes in database entries? I am a university student at the department of Biology. As part of my assignment for the subject Bioinformatics, I was asked to refer to common mistakes in biological database (e.g. Uniprot). For instance, "dehydrofolate reductase". Is there any list with such common mistakes? Otherwise, in your own experience, could you mention some examples of similar mistakes that you meet regularly?

Microsoft Excel has a nasty habit of thinking it knows your data better than you do, and when it sees gene names like Mar3 and Sept7, it tries to be helpful and convert them to dates.

So anytime someone puts a long gene list in to Excel and takes it back out again, you see those genes and their relatives converted to dates.

This has been known for years, but you still see it in lots and lots of published papers.

According to http://dx.doi.org/10.1186/s13059-016-1044-7, almost 20% of article supplementary material gene lists made with Excel contain such errors.


How does Pothos grow in only water? The popular potted plant, Pothos aureus (or Epipremnum aureum) is happy to grow in a jar, with only water, for years. How is this possible when other plants need at least Nitrogen, Phosphorus and Potassium?

It is not possible, that a plant grows without any nutrients. Magnesium for example is needed in every chlorophyll, so there is no photosynthesis without magnesium. Another point is that plants can not get nitrogen from the air, so they have to get it from the soil and nitrogen is present in every amino acid, which build the plants proteins. Proteins are essential for every living organism. This are only two points and there are many many others why every plant needs nutrients like nitrogen phophorus, magnesium...

If it seems that Epipremnum aureum does only need water, maybe the plant gets its nutrients from a place you don't expect. Maybe the water is contaminated. Are there leafs falling into the water for example? Another possibility could be that Epipremnum aureum stored a lot of nutrients before it got only water but this won't last for ever.

I read your comment, thats why i think the nutrients have to come from the water. Additionally I found this publication about Calcium Deficiency Symptoms of Epipremnum aureum

I think you know that tap water or rain water isn't pure H2O. We just measured the tap water in Cologne, by ICP-MS. This is no official measurement, and we measured only once but I think its nice to see whats else in tap water.     Unfortunately we couldn't measure nitrogen, because normally the machine is used for plant extracts and there would be to much nitrogen.

Maybe your Epipremnum aureum gets enough nutrients from the water, I don't know if this is possible and how often you change the water.

Your pot could also be a source for nutrients if its not sealed up.

In conclusion the answer is that in general it is not possible, that your plant grows without nutrients. So there is a source which can be only detected by yourself, because you know the exact conditions under which your plant grows. I hope I could give you some hints.


How is magnet based bead capture used for indexing-first ChIP-seq? The context for this question can be found in this paper by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they

sort cells
sonicate chromatin
immobilize chromatin on Dynabeads with anti-H3 antibody
index chromatin (barcode)
pool samples
perform H3K4me3 ChIP
sequence

I am interested in the purpose of step 3 and how that contributes to step 4. What could be the purpose of essentially adding another IP step?

The Supplementary Materials (where all the methodology is described) mentions that "magnet based bead capture was used to efficiently add, wash and remove the different master mixes used in the indexing process." I'm somewhat confused as to how this adds efficiency, as I thought barcoding prior to sequencing is typically performed as a ligation step without selection (they perform the H3K4me3 ChIP after the indexing step anyway, so why select for histone H3 chromatin first?).

The anti-H3 antibody will precipitate all chromatin. They could have used an antibody against any histone monomer; that they initially used anti-H3 and then later used anti-H3K4me3 is coincidental. The idea behind the first immunoprecipitation is to immobilize the chromatin on the beads to allow easy recovery of pure chromatin after each step of the indexing process. These steps are seen in the supplementary material (4. Chromatin Indexing). For example, after immobilization, they perform end repair using specific buffers and T4 polymerase and polynucleotide kinase. These enzymes must be removed and the buffer exchanged before the subsequent indexing. The beads facilitate this process.


Why X-chromosome linked diseases happen due to recessive gene? All the X -chromosome linked genetic disease I have studied (Color-blindness, Haemophilia, Muscular dystrophy) happen due to a recessive gene.

At first, I thought it was because there could be a 'good' copy of that gene on the other X chromosome (in case of females). So that's why these genes are recessive. But this is a bogus reasoning, I soon realised.

So, why X-linked genetic diseases happen due to a recessive gene? Maybe not all. But why some are recessive?

First of all, most observed mutations are recessive (see the answer to this question; in brief: homozygous carriers are strongly selected against, heterozygous carriers are not affected only if the allele is recessive). So you wouldn't be surprised to find the same pattern on the sex chromosomes.

A good way to think about the specialty of recessive alleles on the X chromosome, is to think about why these diseases are most often visible in males (and you are on the right track there) ... Most alleles causing heavy disease - be it a mutation on the autosomes or the sex chromosomes - are rare (it is for the same reason they are recessive which is described in more detail in the answer linked above; it is due homozygous carriers being affected by purifying selection again) and therefore female carriers are most likely heterozygous and therefore healthy. In males, however, a carrier is always affected by the disease because the carrier is hemizygous.


Difference between modules in KEGG Module The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?

M00115 is a pathway module (NAD biosynthesis) whereas M00542 is a signature module (EHEC/EPEC pathogenicity signature).

From the KEGG page on modules:

  pathway modules – representing tight functional units in KEGG
  metabolic pathway maps, such as M00002 (Glycolysis, core module
  involving three-carbon compounds)
  signature modules – as markers of phenotypes, such as M00363 (EHEC
  pathogenicity signature, Shiga toxin)


How do antibiotics combined with a non-Western diet affect weight loss? Wikipedia describes a Western diet as:

  ... higher intakes of red and processed meat, butter, high-fat dairy products, eggs, refined grains, white potatoes, french fries, and high-sugar drinks.

In the following article there is information about research done that suggests mice eating a high-fat diet while taking antibiotics become obese:

Scientific America: How Gut Bacteria Help Make Us Fat and Thin

I was wondering whether there has been any similar study to see what happens to obese mice or humans that take antibiotics while eating a non-western diet such as the Mediterranean diet, which this Guardian article suggests does not cause weight gain?:

The Guardian: High-fat Mediterranean diet does not cause weight gain

I don't believe elevated polyunsatured fatty acid consumption falls under the tendencies of the western diet, and may be more reminiscent of the Mediterranean diet, so hopefully this answers your question. This study took mice with elevated blood and tissue omega-3 levels, and were used to identify if high levels of omega-3's could prevent the deleterious effects of excessive antibiotic use on gut microbiota. Regarding microbiota diversity, antibiotics are known to create an imbalance between bacteroidetes (decreased) and firmucutes (increased) - this study evidenced that the omega-3 mice were able to rapidly recover their bacteroidetes composition and reduce the amount of firmucutes present in comparison to the control, which in short is good news, as this also prevented later-life obesity in the omega-3 mice in contrast to the obese controls.

For skeptics of microbiota-influenced weight loss (and I know there's many), there is quite a bit of literature out there describing the relationship between gut microbiota diversity and energy expenditure. The short description is that elevated bacteroidetes (in proportion to firmucutes) is associated with lean phenotypes, that diet is very much capable of modulating gut microbiota over short periods of time, and transplanting microbiota compositions into obese individuals has definitively shown an effect on metabolism. The only problem to a gung ho microbiota therapy is, no one knows the gold standard for microbiota composition.


How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid? I have a list of taxids that looks like this:

1204725
2162
1300163
420247

I am looking to get a file with taxonomic ids in order from the taxids above:

kingdom_id      phylum_id       class_id        order_id        family_id       genus_id        species_id

I am using the package "ete3". I use the tool ete-ncbiquery that tells you the lineage from the ids above. (I run it from my linux laptop with the command below)

ete3 ncbiquery --search 1204725 2162 13000163 420247 --info

The result looks like this:

# Taxid Sci.Name    Rank    Named Lineage   Taxid Lineage
2162    Methanobacterium formicicum species root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobacterium,Methanobacterium formicicum   1,131567,2157,28890,183925,2158,2159,2160,2162
1204725 Methanobacterium formicicum DSM 3637    no rank root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobacterium,Methanobacterium formicicum,Methanobacterium formicicum DSM 3637  1,131567,2157,28890,183925,2158,2159,2160,2162,1204725
420247  Methanobrevibacter smithii ATCC 35061   no rank root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobrevibacter,Methanobrevibacter smithii,Methanobrevibacter smithii ATCC 350611,131567,2157,28890,183925,2158,2159,2172,2173,420247

I have no idea which items (IDS) correspond to what I am looking for (if any)

I'll copy/paste my answer from StackOverflow here also.

The following code:

import csv
from ete3 import NCBITaxa

ncbi = NCBITaxa()

def get_desired_ranks(taxid, desired_ranks):
    lineage = ncbi.get_lineage(taxid)
    lineage2ranks = ncbi.get_rank(lineage)
    ranks2lineage = dict((rank, taxid) for (taxid, rank) in lineage2ranks.items())
    return {'{}_id'.format(rank): ranks2lineage.get(rank, '<not present>') for rank in desired_ranks}

def main(taxids, desired_ranks, path):
    with open(path, 'w') as csvfile:
        fieldnames = ['{}_id'.format(rank) for rank in desired_ranks]
        writer = csv.DictWriter(csvfile, delimiter='\t', fieldnames=fieldnames)
        writer.writeheader()
        for taxid in taxids:
            writer.writerow(get_desired_ranks(taxid, desired_ranks))

if __name__ == '__main__':
    taxids = [1204725, 2162,  1300163, 420247]
    desired_ranks = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
    path = 'taxids.csv'
    main(taxids, desired_ranks, path)

Produces a file that looks like this:

kingdom_id  phylum_id   class_id    order_id    family_id   genus_id    species_id
<not present>   28890   183925  2158    2159    2160    2162
<not present>   28890   183925  2158    2159    2160    2162
<not present>   28890   183925  2158    2159    2160    2162
<not present>   28890   183925  2158    2159    2172    2173


NAG, FUC molecules in PDB files In some proteins (such as 4ZXB, 6CE9 which are respectively apo and halo forms of insulin receptors), I see ligands such as FUC (ALPHA-L-FUCOSE) and NAG(N-Acetylglucosamine). No matter which paper I checked I see no explanation for these ligands and therefore I assume they have to do with the experimental procedure but I do not quite understand what is their role. Do they stabilize a particular state of the protein? Note that the proteins above are determined by different methods the first one X-ray crystallography and the second by electron microscopy. I have no technical knowledge about the neither method so any input or link to a paper that actually explains them would be appreciated.

Thanks

The insulin receptor is a glycoprotein. This is discussed, albeit briefly, in both papers for the structures you mentioned and the glycosylation is visible in the structures themselves. You can get more info in the following paper, among others:

Sparrow LG, Lawrence MC, Gorman JJ, Strike PM, Robinson CP, McKern NM, Ward CW. 2008. N-linked glycans of the human insulin receptor and their distribution over the crystal structure. Proteins 71(1):426-439.


Why doesn't a substance like loperamide promote analgesia? Loperamide is frequently used to slow gastrointestinal motility.  It is available over the counter (in the US, I don't know about elsewhere) without any regulations whatsoever, yet it's derived from an opiate.  Knowing that the opiates slow the intestinal motility, it makes sense that it shares the same side effect.

What doesn't make sense to me is why it doesn't share the same primary effect of analgesia?  Clearly it binds to opiate receptors in the gut, but are they the same subtype as those in the CNS?  Or is it that the structure of the drug is such that hardly any crosses the blood brain barrier?

This is more of a chemical question I think, but the gist of it is that, unlike its predecessors difenoxin (Motofen) and diphenoxylate (Lomotil), it was specifically designed by Dr. Paul Janssen and other researchers at Janssen Pharmaceutica to have limited bioavailability from the gut (it is easily first-pass metabolized through cytochromes), as well as being too lipophilic to be dissolved in water and thus administered intravenously (and thus, junkies hoping to get a "hit" from loperamide through injections will be sorely disappointed), while still retaining its ability as a μ-opioid receptor agonist to the receptors in the myenteric plexus (resulting in the slowing of peristalsis). (Difenoxin/diphenoxylate in fact is administered with small doses of atropine to discourage abuse.)

In addition, efflux mediated by P-glycoprotein in the blood-brain barrier helps retard the entry of loperamide into the CNS. The concomitant administration of a P-gp inhibitor like quinidine (a stereoisomer of quinine used as an antiarrythmic) with loperamide, however, will cause respiratory depression and other CNS effects that are characteristic of μ-opioid receptor agonists.


Cell biology - Resting membrane potentials Why do we say there is an overall negative charge on the intracellular side of the plasma membrane at rest, and an overall positive charge on the extracellular side when both potassium and sodium are positively charged ions, and they are in relatively equal amounts on either side? It seems to me that both sides should be positively charged, and I can't get my head around it.

The resting membrane potential is the voltage at which there is no net flow of ions across the membrane.

Every ion will tend to flow down it's concentration gradient (this is just a basic principle of physics/chemistry). So, without considering charge, for a typical cell, potassium will tend to flow out, sodium will tend to flow in, and other ions will also behave according to their concentration gradients.

The other crucial part of the equation is the relative permeability of the membrane to each ion. This comes mainly from the presence of ion channels. At rest, a typical cell has more permeability to potassium than sodium.

That means that if the driving force for sodium and potassium is the same (it's not identical at 0 mV but fairly close), more potassium will move than sodium.

If the definition of resting potential is the potential where net flow of charge is zero, and considering only sodium and potassium, then rest has to be where sodium flowing in equals potassium flowing out. This situation occurs when the inside of the cell is negatively charged compared to the outside: the membrane voltage "holds" potassium in and "pulls" some sodium in, such that their currents are equal and opposite despite the higher permeability to potassium.

Note that the voltages we are talking about in neurons, on the order of 10s of mV, are very small, and electrical forces are very strong. The concentrations of positive and negative ions are almost exactly identical on both sides of the membrane: only a few ions actually have to move to make a (biologically) large membrane voltage. What is actually important is the permeabilities: that's what makes action potentials and other forms of neuronal signaling feasible.


How can dopamine modulate synaptic strength? Does dopamine act on G protein coupled receptor, leading to more Ca2+ channels on the postsynaptic knob?

Also, how is the specificity of the location (of the brain) that dopamine acts on controlled? Or is it controlled at all? Is this chemical associated with addiction?

Yes, dopamine receptors (D1-D5) are G protein coupled receptors,  which act primarily on adenylatecyclase (changing cAMP concentration, which activate proteinkinase A, which phosphorylates other proteins in turn such as CREB... you can find the pathway in the following article). D1 receptors activate adenylatecyclase, D2 inhibit its activity.

I wouldn't say it directly alters the Ca2+ channel concentration per se, the article says however it can modify their state.

According to this article, G proteins of these receptors could also have different effects (alternative effects through G-proteins such as activating phospholipase C, which results in IP3 formation which results in Ca2+ influx to cytoplasm from ER which acts on proteinkinase C) or new research suggest that it could also act through G protein-independent mechanisms via interactions with ion channels.

  specificity of the location (of the brain) that dopamine acts on controlled?

The idea is that cells with certain neurotransmitter may induce growth of cells with same transmitter, thus forming specific circuits. I don't know however how specifically this happens and how the cells communicate to form specific connections (like dopaminergic connection from substantia nigra to basal ganglia) during development. I'd bet on some morphogenes. Someone else might know better :) .

Yes, dopamine is associated with addiction, as it's part of the reward system in brain. Many drugs inhibit its transport from synaptic cleft into the cells, which means prolonged activity, brain senses positive effects you can see when you've done something good (reward).


Why is the human body able to repair a broken bone and not a heart muscle? The human body can repair skin/organ laceration, fractures, even repair nerves - albeit the duration and rate of recovery differ.

Why can the heart muscles not repair themselves?

Part of the answer may be(*) that in bone, you have still stem cells everywhere (blood capillaries that grow until checked and osteoblasts), i.e., also in the vicinity of the wound. The same applies to skin, by the way, where the epidermis continues to produce skin layers until eternity. This facilitates repair enormously, as new cells won't have to move far to take their place.

Contrast this with heart or spinal cord, where the placement of the cells took place in early development when distances were small and most cells were undifferentiated. Also, no tissue like epidermis was left in the vicinity that could act as a near source of new cells.

(*) I said "may be" because 1. I have no ref for this, and 2. I have no idea to what extent other factors are involved. I would be thankful for counterexamples.


What differences in effect does fast repetitive exercise have compared to slower muscle-building exercise? As a drummer who likes to play high-energy music (fast, aggressive metal) it's safe to say I burn a fair amount of calories when doing so. But I've been drumming for over a decade and despite the amount of it that I've done, it hasn't really had any (visible) effect on muscle growth. Every time I drum I try and push the limit of how fast I can go until I start to ache, so I'm definitely doing something to the muscles in my arms and legs, but it definitely isn't building mass.

I remember reading somewhere that speed based exercise can actually reduce muscle mass as the body tries to make itself more efficient, but heard no evidence to support this or an explanation of how.

Can someone please explain to me how exercise such as fast drumming affects muscle growth and development in relation to traditional muscle building exercise like lifting weights?

I am looking for a explanation of the biology behind this by the way, not fitness advice.

Clarification - for non-drummers, the "speed exercise" I'm referring to is what are called blast beats, where the aim is to keep an often inhumanely fast repetitive beat going. It's common in more "extreme" music such as death metal. While trying to maximise efficiency by minimising the amount of effort required is the goal, the muscles required are undergoing a rapid contraction-release cycle, often sustained for minutes at a time, and sometimes for an entire song.

Your body creates muscle after an exercise through a process where it fuses muscle fibers together to form new muscle protein strands called myofibrils. these myofibrils increase in size as workout intensity increases, leading to muscle growth. Muscle growth occurs when muscle protein synthesis happens faster than muscle tissue breakdown 1.

Since you are never really increasing the amount of strain on your muscles(i.e. by adding more weight to a workout) there is no incentive for your body to create more myofibrils, rather it will just replace the ones that were torn during your drumming.


What is the difference between a myofibril and a myoblast? (In skeletal muscle) I read that a muscle fibre (myofiber) is formed when myoblasts fuse.
https://teaching.ncl.ac.uk/bms/wiki/index.php/Skeletal_muscle#:~:text=The%20multinucleate%20feature%20is%20established%20in%20myogenesis%20where,cells%20%28each%20muscle%20cell%20is%20one%20muscle%20fibre%29.
On google I saw that a muscle fibre is formed from many myofibrils.
https://biologydictionary.net/myofibril/#:~:text=Myofibrils%20are%20long%20filaments%20that%20run%20parallel%20to,are%20made%20up%20of%20repeating%20subunits%20called%20sarcomeres.
Does that mean that myoblasts and myofibrils are the same thing?

Myoblasts are the embryonic precursors of myocytes (also called muscle cells). Myoblasts differentiate into muscle cells through a process called myogenesis.
A myofibril (also known as a muscle fibril) is a basic rod-like unit of a muscle cell. Muscles are composed of tubular cells called myocytes, known as muscle fibres in striated muscle, and these cells in turn contain many chains of myofibrils.
So, to answer your question, No. These two are different and one is the precursor of the other.


Why is mutation rate high in introns? Principle of genetics mentions

  The fact that introns accumulate new mutations much more rapidly than exons indicates that many of the specific nucleotide-pair sequences of introns,excluding the ends, are not very important.

Though 'are not very important' is not true as introns do have a number of functions (both discovered and undiscovered).

But why is DNA polymerase less efficient at replicating introns? Is it known?

Not less efficient, but introns are under less selective pressure than exons. Exons actually encode the protein. A single bp insertion will ruin a mRNA encoding a protein by causing a frame shift in how the sequence is read.

However the same is not true for introns. 1bp insertion even if the intron has function such as transcription or translation factor regulation has a higher chance of not damaging anything important. Simply because such factors are spaced apart and the space is not really important.

http://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375
https://www.ncbi.nlm.nih.gov/pubmed/17570818


True anatomical/physiological explanation for "metaphysis" etymology The anatomy textbook1 I use for my students states that the prefix meta- means "between:"

  The metaphyses (me-TAF-i-sez; meta = between; singular is metaphysis) are the regions between the diaphysis and the epiphysis.   [my emphasis added]

This sounds reasonable given the explanation. However, I have never seen meta- applied in this manner; more generally, the suffix meta- usually seems to refer to "after."

In fact, Dr. Toby Arnold's Glossary of Anatomy provides the following etymology of the word metaphysis:

  metaphysis: Greek meta = after, and physis = growth; hence, the end of the shaft of a bone alongside the epiphysial or growth cartilage  [again, my emphasis added]

The latter explanation is somewhat underwhelming, but the etymological usage fits more with my prior experience with meta-.

So, which is it?

Can someone find a reputable source definitively indicating a clear anatomical/physiological explanation for why meta- was used in the case of "metaphysis"?

A webpage on EnglishLearner.com reports that our earliest usage of the term "metaphysis" came from an obstetrician named William Dorland (1864–1956) in the early 20th century. I couldn;t find additional info.

1. Tortora, G. J. and B. Derrickson. 2014. Principles of Anatomy & Physiology, 14th edition. John Wiley & Sons, Inc., USA.

meta-:

  word-forming element of Greek origin meaning 1. "after, behind; among,
  between," 2. "changed, altered," 3. "higher, beyond;" from Greek meta (prep.) "in the midst of; in common with; by means of;
  between; in pursuit or quest of; after, next after, behind," in
  compounds most often meaning "change" of place, condition, etc. This
  is from PIE *me- "in the middle" (source also of German mit, Gothic
  miþ, Old English mið "with, together with, among"). Notion of
  "changing places with" probably led to senses "change of place, order,
  or nature," which was a principal meaning of the Greek word when used
  as a prefix (but also denoting "community, participation; in common
  with; pursuing"). (Etymonline)

physis:

  The growth plate, or physis, is the translucent, cartilaginous disc
  separating the epiphysis from the metaphysis and is responsible for
  longitudinal growth of long bones. (The Royal's Children Hospital Melbourne)

Anatomically and physiologically, meta- in metaphysis means next after physis (growth plate or epiphyseal plate) and refers to the changing (growing) part, which is in between the non-growing parts of a long bone (diaphysis and epiphysis):

  The metaphysis is the wider portion of a long bone adjacent to the
  epiphyseal plate. It is this part of the bone that grows during
  childhood; as it grows, it ossifies near the diaphysis and the
  epiphyses. (Orthopaedicsone)

Picture: Parts of the bone (Radiopedia, Creative Commons license)


Questions about apoptosis Is apoptosis a part of cell division?
Can apoptosis occur if DNA is damaged beyond repair?

I think this question could basically be summarized as "What is apoptosis?"  I will attempt to give a brief answer to that question, answering the two aspects of the question along the way.

Apoptosis is at its root programmed cell death (PCD).  It is basically when a cell (healthy or not) dies so that it can be replaced.  It is happening all the time in multicellular organisms such as me, you, and the lion in the zoo.  Basically, it allows all the cells to be replaced as the tissues of the body grow.

For instance, as your skin grows, cells in the dermis are dividing to produce a new epidermal layer.  At the same time, cells on the outside are dying (at the stratum corneum) so that the skin does not grow infinitely and we aren't covered with 20 inches thick of skin by the ends of our lives.

The same thing is happening in, for instance, the liver.  As the liver cells split, old ones are also dying.  This allows us to rebuild the liver to its normal size after a surgery in which we remove a section of it.  We simply have to stimulate cell growth so that it counterbalances PCD (apoptosis) and the liver grows to its normal size.

Cell death is initiated, not by the DNA, but rather by caspase activity.  All cells have inactive procaspases which will destroy the cell as soon as they become active.  When what we call an initiator procaspase bonds with a procaspase within the cell, the procaspase is activated, and the signal is spread across the cell.  This initiator procaspase is usually triggered by a death receptor outside the cell.

More reading here


Have there been any experiments that duplicate chromosome copies from 23*2 to 23*3 or 23*4? Deinococcus radiodurans is an amazing bacterium with a fantastic survival rate. It can survive to high doses of radiation, in a complete vacuum and in hydrochloric acid.

How does this bacterium manage to restore damaged chromosome?
It is polyploid with 4 to 10 copies of the genome which are packed in a highly ordered manner.

Does this imply that creating multiple copies of the genome or inceasing DNA base repair activity would increase life span?
Is that even conceivable on bigger life forms?

It's an idea that doesn't hold much promise.
Individuals who show diploid/tetraploid mosaicism present "failure to thrive and multiple minor anomalies." according to:

Alonso L et al (2002) Tetraploid/diploid mosaicism: case report and review of the literature. Annales de Genetique 45 177-180

On the other hand, complete tetraploidy is apparently lethal:

Nakamura, Y. et al. (2003) A Tetraploid Liveborn Neonate: Cytogenetic and Autopsy Findings. Archives of Pathology & Laboratory Medicine 127:1612-1614.
Abstract
Cytogenetic and autopsy findings of a nonmosaic tetraploid male neonate, alive until shortly after birth at 37 weeks' gestation, are described. Oligohydramnios, intrauterine growth retardation, cranial abnormalities, and Dandy-Walker malformation were noted prenatally. Autopsy findings included cleft lip and palate; overlapping fingers; low-set ears; simian creases; hypoplastic external genitalia with undescended testes; Dandy-Walker malformation; slightly dilated lateral and third ventricles; hypoplasia of the cerebrum, pons, medulla, pituitary gland, thymus, lung, adrenal gland, and kidney; large ventricular septal defect; and enteric cyst behind the urinary bladder. The placenta was hypoplastic and showed no remarkable abnormalities, except for mild syncytial knots. Chromosome analyses of amniotic fluid cells at 31 weeks' gestation and the umbilical cord blood cells at delivery revealed a 92,XXYY karyotype. G-, C-, Q-, and N-banding heteromorphic studies demonstrated duplication of paternal chromosomes 1, 3, and 15, and maternal chromosome 22. In addition, the results of an analysis with 16 CA repeat polymorphic markers were consistent with duplicated inheritance of 1 paternal and 1 maternal haploid sets to the tetraploid patient. Therefore, it is most likely that the tetraploidy was caused by a cytoplasmic cleavage failure at the first mitotic division.

full text available here.


What is Colloidal biology and does it have any scientific background? There is the following bulletin published for the History of Chemistry Vol. 32: 105-118 in 2007:

“MOLECULAR” VERSUS “COLLOIDAL”: CONTROVERSIES IN BIOLOGY AND BIOCHEMISTRY, 1900–1940*

written by PhD habilitation research professor Ute Deichmann at the Leo Baeck Institute (LBI) in London and leader of the History of the Biological and Chemical Sciences Research Group at the Instritute for Genetics, University of Cologne.

Therefore, the question is: What is Colloidal biology, what are the basic differences between molecular biology and does it have any background in modern scientific community?

There are two antipodes: The molecular (or makromolecular) biology, which has the concept of large macromolecules which fulfill one task. This can for example be an enzyme which breaks down its subtrate. The properties and the structure of all molecules of the enzyme are the same and the factor determining the function of the enzyme.

The coloidal biology assumes that the function is granted by adding small amounts of an enzyme to water to form a colloid, which thenchanges the properties of the water in the way that it does break down the subtrate. Life was also explained as the sum of the functions of the colloids building the body.

This theory came up in a time when macromolecules and their functions where not very well understood. The better understanding of macromolecules rendered this theory irrelevant. This is also neatly sumarized in the conclusions section of the article you cite.


What is the energy balance of cooking? If I cook some food, I get apparently several energetic advantages:

thermal : the temperature of the food is closer or superior to the temperature of my body or internal organs, so I do not have to produce energy to warm it.
chemical : the transformations of the organic compounds during cooking operations may store energy in a potential form: more energy will be released by the digestive process from these compounds than from the raw ones.
mechanical : the food may become easier to chew, absorb, conduct in the digestive tract, leading to less muscular force used.
The cooking procedure may involve water immersion, and the water may penetrate the food and improve all three energetic aspects outline above.

(I may have forgotten a few things)

But what are the respective scale of these advantages, compared to the Joule intake of the raw food ?

Focusing on meat, for instance, is there an optimal cooking duration/temperature and eating temperature for human eaters, independently of personal tastes, for say, beef or chicken meat ?

If I cook some food, I get apparently several energetic advantages...

Let's make things a little more explicit. If you are talking of energy within the body, you are talking proteins, alcohols, fats, and sugars. You are not talking Vitamins or Minerals or any of the unique compounds (like specific antioxidants) that are available in the food.

  thermal : the temperature of the food is closer or superior to the temperature of my body or internal organs, so I do not have to produce energy to warm it.

You cannot eat enough to significantly alter the temperature of your body. The average American will eat roughly 5.4lbs of food per day - or roughly 2lbs of food per meal. Given that even raw food is at room temperature, the metabolic requirements to warm food you've eaten is negligible.

What's important is acidity and exposure. Food is generally broken apart and utilized by catalysts and proteins which have specific operating boundaries - which is why your stomach contents is acidic. However, your normal meals will not significantly alter your digestive capabilities either via pKa values or thermoregulation requirements.

What cooking can do is denature the raw food's proteins or compounds so as to make the usable energy sources more readily available. However, it can also just as easily destroy them (the 'char' on barbequed steaks is the meat exposed to high heat long enough to destroy almost everything but the carbon in the tissue). Whether a food gains or loses macronutrients depends upon the specific food and its preparation. A good example is potatoes, which are full of starch (sugars) in their natural state. However, french fries / frites / chips are often blanched before they're fried. The blanching dissolves much of the starch into water, leaving fewer sugars in the end product. However, the process of frying essentially adds fat to the food, and fats have a higher energy density than sugars so you have a net gain in caloric content.

  mechanical : the food may become easier to chew, absorb, conduct in the digestive tract, leading to less muscular force used.

For some foods, this is true. Steaming vegetables often makes them easier to chew/eat. The broth of stews and soups often contains micelles of fat and dissolved sugars, affording them greater and faster exposure to the digestive system. Keep in mind, you are not getting a net gain of caloric content from food by doing so, but merely reducing the time to utilization.

The calories saved by chewing less is going to be pathetically small, so to amend the previous paragraph: Yes, for some foods it's true that cooking will allow easier mastication and thus save energy. However, an extra chocolate chip or sip of spoon of rice could easily cover the energy spared.

  The cooking procedure may involve water immersion, and the water may penetrate the food and improve all three energetic aspects outline above.

If the energy source is water-soluble (that is: alcohols, ketones, and sugars) then water immersion - assuming you are also digesting the water solution after - will offer faster utilization, not necessarily more.

  But what are the respective scale of these advantages, compared to the Joule intake of the raw food?

Negligible in almost all cases. What cooking does is make things more palatable, has the potential to make micronutrients/vitamins more available (not macronutrients), and make the food edible in the first place as is the case with Taro plants, whose roots must be cooked in order to eat.

  Focusing on meat, for instance, is there an optimal cooking duration/temperature and eating temperature for human eaters, independently of personal tastes, for say, beef or chicken meat?

No. Cooking meat makes it safer to eat (unless you end up overcooking the meat and end up with a bunch of charred bone) and more palatable. Properly cooked meat has a very low chance of passing on parasites or other harmful organisms. Beyond that, there aren't compelling reasons to expose meat to heat - although as someone who's picked up stomach flus in his travels, it is a very compelling reason to do so.

*The above is based mostly on sporadically gained knowledge. If there are studies indicating otherwise, please alert me to them and I will rectify my errors.


Blosum matrix with probabilities instead of the positive and negative scores I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like to know the probability of LEU replaced by ASP.

Download the BLOSUM data and source-code from here. Unzip the archive which has several files.
The file called blosum'XX'.qij will have the co-occurence probabilities, and the subsitution probabilities can be calculated from them.

Also have a look at this article.


Protein-coding introns in mitochondrial genomes I am studying the mitochondrial genome and have read that some contain introns. However, these introns code for proteins. I cannot really understand this. Could someone tell me what intron in which mitochondria genome this refers to?

Mitochondrial genomes differ greatly in size, coding potential and even whether they are circular or linear. Mammalian mitochondrial DNA is small (11–28 kbp) and intronless. However the mitochondria of certain other organisms range up to 1000 kbp in size.

Certain sponges (demosponges) with large mitochondrial genomes contain type I introns and type II introns.  Although introns were initially thought to have no other function than to separate exons, the introns of certain nuclear genes have been found themselves to contain genes. This turns out also to be true of some of the mitochondrial introns. To quote from then introduction to a paper I found through an internet search:

  Most Group I introns encode homing endonuclease genes (HEG) and/or
  maturase of the LAGIDADG † family, while most Group II introns encode a
  reverse transcriptase (RT).

These introns are found in genes such as that encoding cytochrome oxidase subunit 1 (COI).

† This appears to be a misprint for the LAGLIDAD mutases, which are also endonucleases, and are involved in splicing the introns in which they reside.


How to preserve leaves between sampling (collection) and analysis? Suppose I spend a day in a forest, collecting different kinds of leaves, which I would like to analyze under a compound microscope. Now, obviously, measures should be taken to preserve the leaves some how. What would be the appropriate procedure? It seems (based on browsing the web..) that refrigeration could be one option. Is it scientific (used in published papers)?

You may want to see:

Mark W. Chase, Harold H. Hills; Taxon, Vol. 40, No. 2,  1991, pp. 215-220: 'Silica Gel: An Ideal Material for Field Preservation of Leaf Samples for DNA Studies'

Summarized, the process would be the following:

Place the leaves inside ziplock plastic bags;
Add ten times (minium) the weight of the leaves in silica gel;
After 12 hours (after which the degradation of the biological material is more likely), check the leaves by bending them: if they break cleanly, the leaf is dry;
Store in the ziplock bag, inside a box with an hermetic lid;
Refrigerate (if possible).

Note: Freezing by submersion in liquid nitrogen is also a viable approach, yet might be less practical


Brain + ethanol experiment suggestions needed I need to demonstrate the effects of ethanol on a human brain (or other brain with developed telencephalon) in vitro; ideally the effects on vigilance and/or memory.

Could you please suggest such an experiment?

What method would you suggest to demonstrate the effects of ethanol on NMDA receptors or membrane penetration by ethanol?

Edit in respose to the first comment by @MadScientist:

The point is to empirically demonstrate how ethanol affects the cognitive performance of brain (specifically vigilance and memory) and explain the biochemical nature of such an effect on an observable real example (not using computer simulations). It is aimed at mature layman audience.

The experiment has to be in vitro due to ethical and environmental limitations (well, I am not permitted to intoxicate mature students nor animals).

Demonstrating the effect of ethanol in the role of an NMDAR antagonist would be satisfactory as the chain of implications would be illustrated on a theoretical basis.

I have access to standard laboratory equipment on a university level, but the simpler it is, the better. As to the material, the same is true while a fresh brain slice will hopefully be available as well.

The main problem with what you are asking is that you want to show effects on vigilance and memory in vitro. That is just not possible: if you want vigilance and memory you need a live animal, there is no way around it.

Next point: you have an audience of non scientists, so you can lose them very quickly if you start speaking about NMDA, LTP or similar things without a clear explanation, so start with that: get a nice review (Pubmed is a good start, as always), and give a simple theoretical explanation of one of the mechanisms involved. It is then important to clearly explain the experiment you will perform, and what you are expecting to see in case there is an effect.

Unfortunately the best way to see effects on NMDA receptors would be electrophysiology. This is not trivial and, if you have never done it, I would not suggest going that way. However, if you have access to an electrophysiology setup you will most likely have access to someone who uses it, and that could make the experiment for you.

I am not an expert on this topic, but a quick research on Pubmed seems to indicate that alcohol can, for instance, reduce LTP in hippocampal neuron.
Maybe what you could do is having someone patch hippocampal neurons and show how an LTP protocol is used. You don't necessary have to show them the whole thing (I doubt anyone in a right state of mind would bare to stay until the whole experiment is performed in control condition first, and alcohol later...).

Also, the results of these experiments are often non obvious to analyse, so you should have some data prepared and analysed earlier and quickly show how analysis is performed, before showing the final results.

Calcium imaging experiments could also be used and would probably give results that are easier to understand for a laymen audience.

See for instance Fig. 1 or Fig. 5 of this paper (just the first one I found, there surely are other):
Ethanol alters calcium signaling in axonal growth cones.


Why do (almost) all energy carriers contain adenine? Unlike this question which is specific to just ATP, this one includes all energy carriers.

When thinking of common energy carrying molecules, I can think of Adenosine triphosphate (ATP), Nicotinamide Adenine Dinucleotide (Phosphate) (NADH/NADPH), Flavin Adenine Dinucleotide (FADH2), S-adenosylmethionine, coenzyme-A (derived from cysteine, pantothenic acid and ATP), etc. Recalling exceptions, I can only think of biotin (carboxylated) and uridine diphosphate glucose. Just talking about ATP, we could have called its preference over others just a matter of chance. But when so many carriers contain adenine, there has to be some selection against other energy carriers (or adenine was so lucky?). Note that when saying 'common energy carriers', I exclude GTP, CTP, TTP and UTP since they are not very commonly used (or at least their use is confined to only some metabolic reactions, unlike ATP which finds its use in almost all metabolic reactions requiring energy).

Why do the majority of energy carrier molecules contain adenine (or its derivative) instead of any other nucleobase?

This question is open for discussion i.e. everybody is welcome to post their (scientifically backed-up) opinion as an answer while none of those answers will be selected because of lack of conclusive proofs, which are very likely to remain elusive forever.

As @canadianer comments, this question is unanswerable, and it verges on being classified as ‘opinion-based’. However, because I do not find the answer from the OP appealing, I’ve set out a few points of my own. Hardly an answer — more a list of alternatives as food for thought.

I can imagine adenine being chosen for one of the following reasons (others are welcome to suggest additions):

Functionally best suited
Was there first
Easiest or cheapest to synthesize originally (which would explain why
it was there first, if this were the case)
Random choice

Let’s look at them in turn.

Adenine functionally best suited

There seems nothing in the function of NAD that suggests the adenine ring could not have been replaced by another of the bases, and we know that the free energy of hydrolysis of the beta–gamma phosphodiester bonds of GTP, CTP and UTP can be utilized in an analogous way to that of ATP, so this doesn’t seem very likely.

However one does wonder if a purine (rather than a pyrimidine) ring conveys some sort of advantage in that the other purine-based triphosphate, GTP, is used so widely in the (ancient and essential) process of protein biosynthesis. Perhaps the greater area of contact of the purine ring favoured interaction with proteins (if you don’t argue that these came later).

Adenine was there first

One might consider that early in the evolution of life the bases (or nucleosides and nucleotides) emerged one at a time, in which case the first might have been used for NAD etc. and stuck. One might also consider whether a two-base world preceded a four-base world. If A and U (but not G and C) were in the first RNA (which may have been single-stranded, so I don’t see that the GC content of contemporary thermophiles is relevant) then it may have been a choice between A and U, which A might have won because U is subject to spontaneous deamination (or for the protein-interaction argument mentioned above).

Adenine as easiest or energetically cheapest to synthesize originally

Clearly, the first base might have been the one favoured by chemistry in relation to its synthesis. Contemporary biosynthesis is unlikely to reflect primeval biosynthesis, but it is amusing to observe that adenosine biosynthesis is the only one that doesn’t involve NAD-dependent oxidation. Of course all the contemporary biosyntheses utilize ribosyl pyrophosphate, which requires ATP in its synthesis from ribose phosphate. (Talk about chicken and egg!)

Random choice that stuck

In the absence of any more sophisticated explanation, then it could just be this. Once a choice was made and enzymes evolved to use NAD etc. the choice of adenine couldn’t be changed (or there was no strong enough functional advantage to doing so).

Postscript: When and how did NAD appear on the scene?

One of the reasons I don’t favour the OP’s answer is because it envisages NAD arising after DNA genomes and as a separate entity. I would suggest that it is likely that RNA preceded DNA and that catalytic RNA was responsible for some of the early oxido-reductions. (The first ones were probably catalysed by iron–sulphur centres, either inorganic or associated with simple proteins.) It seem feasible that the nicotinamide ring was an elaboration of a ribozyme which was ultimately almost completely replaced by protein. The adenosine was retained with the functional nicotinamide because it could interact better with the protein. Gross speculation, and it doesn’t explain why adenine was the chosen base, but an antidote to thinking NAD evolved in the fully grown form we see it today.


Wax layer destruction from seed coats I'm working with some orchid species, and i encounter a specific issue. Some of those species deposits upon their seed coat a wax layer. This layer makes seeds behave in a very hydrophobic way. You cannot dispense them in a pour water.

That behavior has many impacts. One of the most significant is that it does not let water come in touch with the actual seed and then with embryo to make it sprout.

So i tried many ways to remove that layer but nothing actually seemed to work out.

I treated seeds with the following chemicals:

a) 1% NaOCl with some dish soap water solution for 10min. After throwing seeds into this solution you could see that they can be evenly dispensed in it and come in touch with the solution. But if you wash them up with pure water for example 3 times they are getting back their hydrophobic behavior.

b) 1% H2SO4 water solution for 10min. I thought that with this treatment waxes will be removed from the seeds but nothing like that happened. Maybe they had been better dispensed in the pure water comparing to the previous treatment but nothing significantly changed.

c) 93% ethanol solution for 1, 2, 3, ... 30min. results here were also very disappointed. While the seeds are immersed into ethanol, they were very well dispensed into the liquid without any hydrophobic behavior. After three washes with pure water, hydrophobic properties came back.

Treatment time seems not to play any significant role on the results.

My conclusion is that there is no destruction of the waxes with the above chemicals. The only thing that happened probably, is the creation of a Micelle around the seed, which make it for a while (the time that it was in the solutions with soap and ethanol) non hydrophobic.

Finally my question is, if there is any way to destruct chemically, to some grade the waxes. So even when you put the seeds in a pour water not be so much hydrophobic.

Thank you.

This paper describes dewaxing of sunflower seeds using various solvents. As you have already shown for yourself, using hydrophilic substances such as bleach and acids do not work well in removing the waxes.

Waxes are highly hydrophobic substances, and must be removed with either hydrophobic solvents (much like washing away acids with water at the emergency eye-shower) or detergents and water. The hydrophobic solvent mixtures used for lipid extractions recommended in WYSIWYG's link will likely work as well.


In the PR segment of an ECG, how come there's no current flowing? I don't really know how to phrase the question, but to put it as clearly as I can, I don't get why it is the P wave "flattens down" when the atria have completely depolarized. I get that the charge is uniform across the atria, but the ventricles are still polarized (and therefore of a different charge compared to the now completely depolarized atria), wouldn't this create a difference in charge and therefore a voltage to produce a current? I think this GIF can help explain my question better:

At frame 12:

I don't understand why there's no current flow and no deflection on the ECG leads despite the charge difference. Rather, why does the GIF deal with the current and charge difference in the atria and ventricles separately? I thought this all might be because of the fibrous cardiac skeleton, which acts as an electrical insulator, but that doesn't make complete sense either; sure it prevent current flow within the heart, but it wouldn't influence current flow outside of it, right?

I'd suggest reading the rest of the Wikipedia article on EKG rather than focusing on the particular cartoon you are using right now, because that cartoon does not depict the dipoles that are measured.

The key interpretation that you are missing is that the signals measured are not voltage differences between intracellular compartments of the heart (like between the atria and ventricles, or between the depolarized and polarized part of one compartment), but a moving dipole created during polarization changes.

As the atria depolarize, there is a wave of negative extracellular charge as positive ions enter cells, creating a dipole: there is more negative charge at the most recently depolarized point than ahead of the wave where cells haven't yet depolarized. This is the signal you measure. If you were to pause this process at any moment, those extracellular charges are free to move and the potential dissipates quickly.

There is too much conductivity in the extracellular space for the dipole to be maintained without the rapid polarization changes that occur when ion channels open. You can think of this as a high-pass filter; the amplitude of the dipole measured would approach zero as the speed is reduced regardless of static differences in intracellular voltage measured against some reference.

This is what happens during the brief "pause" between atrial and ventricular contraction: there is still a dipole, but it is much smaller as it travels through the AV node than in the muscle and would only be measurable from local electrodes. You begin to see the signal again once the ventricles contract.

http://umdberg.pbworks.com/f/Hobbie-EKG-1.pdf may also be useful.


Why can't the immune system start at the mating time? The immune system has a great role in our body. When foreign particles
enter our body, the immune system can recognize and start
defense mechanisms such as the complement system and others. But when sperm enters
into the female organism, why does her immune system not recognize this?
In that time which kind of mechanism is active in the woman's body?

These questions are not completely easy to answer, since the immune reaction in this area is not completely understood. There are two different mechanisms  which play a role here:

Semen is immunogenic and can cause the generation of specific antibodies against it in men and women. The main question here is if the presence of semen in the females reproductive tract is the consequence of a suppressed immune reaction or because it is not recognized. There are indications for both possibilities but I think the first is a bit stronger. The mucus from the vagina is immunosuppressive as well as the seminal fluid, which contains prostaglandins which have the same effect. Have a look at this article for some more background:

Sperm survival in the female reproductive tract: presence of
immunosuppression or absence of recognition?

For the situation in the uterus between mother and fetus the situation is better understood. This is the so called immune privilege of some tissues (among them are the uterus, testes and the eye) where immune reactions are suppressed.

The placenta forms an immunologic barrier which seperates mother and fetus. This is done by secreting immunomodulary substances and also by the subpression of some T cell subpopulations. For more details see here. This is a highly developed system to protect the developing fetus (which is foreign) from the mothers immune system.


Do plants have cellulases? I can't seem to find the answer to this. Not even Wikipedia could help- it mentioned bacteria and fungi that have cellulases but not plants. Using my own reasoning, I would think that

On the one hand it is better if plant cells do not have cellulases so that they do not break down the cell wall. Although maybe it doesn't matter because the cellulases would not reach the cell wall without being actively transported out of the plasma membrane.
Perhaps it might be useful for plants to have cellulase. I don't know if plants have any sort of immune system like humans, but plants also get bacterial and parasitic infections in their cells. Maybe plants should have some mechanism to destroy an unhealthy cell? In that case, the destroying cells would need to use cellulase, would they not?

At least some plants have cellulases which can be used to cleave primers from mature cellulose chains.
Cellulose synthesis requires chain initiation and elongation (the two processes are separate). CesA glucosyltransferase initiates cellulose polymerization using a steroid primer and UDP-glucose. Cellulose synthase utilizes UDP-D-glucose precursors to elongate the growing cellulose chain. In some plants cellulase is then used to cleave the primer from the mature chain.
Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119035/


Small, brownish bird with reddish spot around eyes This bird was seen in the Bourgoyen-Ossemeersen nature park, Ghent (Belgium) on December 3rd 2016. It is about the size of a common chaffinch.

We couldn't get a very good picture of it, unfortunately. What is the species of this bird?

It's a Chaffinch (Fringilla coelebs). From the first picture you see the
greyish head and orangish chick. From the second picture the typical whitish/greenish
wing bars. From the third pic the bricky belly.


What is this? Found in southern Illinois Found in southern Illinois in the driveway.  What is this?

Nice find! It looks to me like a Bush Cicada or scientificly Neotibicen dorsatus. It also looks like its injured, because we can see the white liquid around its wings and abdomen. Bush Cicadas tend to have a yellow or brown color but as shown here there is a wide variaty to the colourations that it might have:

Size (Adult, Length): 35mm to 57mm (1.38in to 2.24in)

Identifying Colors: yellow, brown, white, gold, black

North American Reach (Though Not Limited To*): Arizona; Arkansas; Colorado; Illinois; Indiana; Iowa; Kansas; Kentucky; Louisiana; Minnesota; Mississippi; Missouri; Nebraska; New Mexico; North Dakota; Oklahoma; South Dakota; Texas; Wyoming; Mexico.

Here are and some photos:

Adults:


PCR a plasmid with self-complimentary regions? I am trying to do a PCR using a plasmid as the template, pretty basic stuff. But the problem is that my forward primer just happens to bind to another location on the plasmid in the reverse orientation, in between the proper forward binding site and the reverse binding site. This isn't an example of non-specific binding, the sequences are perfect because the plasmid contains self-complimentary regions and my forward primer just happens to land right on it.

Here is a diagram:

Simply optimizing the melting point or magnesium concentrations probably won't help, because the sequences are the same. I'm doing this cloning to insert a reporter gene into the vector, and I need to place it very precisely, so I don't know if I can order a new set of primers, the insert needs to fit there.

The bad PCR product is about 500 bases shorter than the good product, but I only see the bad band on gel when I run a normal PCR. If I reduce the amount of forward primer and increase the reverse oligo, I can see the good band, but the bad band is still there and the total yield is much lower.

So my idea right now is to do an asymmetric PCR using the reverse primer only, then add forward primer to create the double-stranded DNA, then separate the good and bad bands using gel electrophoresis. But I don't have a clue how many cycles I should run each step, or how much forward primer to add, etc. Additionally, asymmetric PCR has low yield due to arithmetic amplification, but once I add the forward primers it can begin symmetric PCR and geometrically amplify both bands, but I think the shorter bad band wins out.

Does anyone here have experience with this sort of complex PCR, or suggestions to improve my yield?

From experience, your present problem will not completely go away no matter what you do.  The idea for asymmetric PCR is not a bad idea. However, you will only get linear amplification of the desired product from the initial single primer, so you will not "see" any product even after 30-40 cycles.  This first single primer PCR might also cause downstream problems with amplification of undesired products made during the second PCR (junk products).

I agree with comment #1, but then neatly cut the "visible" "good" band out of the gel.  Suspend (crush) the agarose band in sterile TE buffer, and then use an aliquot of that as template for a secondary PCR (use equal primers - maybe 30 cycles).  This should provide more than enough "good" starting template.

Alternately, you could design a new forward primer that does not have a bad secondary location on your plasmid.


Why did Fair Meiosis evolve? How and why did Fair Meiosis evolve?

I can hardly think that it provided a fitness advantage to the individual carrying the mutation. Why would it? Or did it evolve through lineage selection? Or was it some kind of pre-existing characteristic of meiosis that have no energy cost and therefore never disappear?

UPDATE:

I call fair meiosis the process of meiosis in which each chromosome has an equal chance of transmission.

I'm trying to make my questions clearer.

Is there any selection pressure in favour of alleles causing a fair meiosis? If yes, why? It doesn't seem to me to provide any advantage to the individual carrying this allele.

I think that Fair meiosis (I assume that you are referring to that chromosomes have an equal chance of transmission) can be seen as a byproduct of recombination at meiosis, which makes every chromosome a mosaic of maternal and paternal chromosomes. Therefore, selection does not act on chromosomes as a single unit, and "unfair" meiosis becomes meaningless. The "value" of "fair meiosis" most likely lies in the adaptive value of recombination.

Addition: To expand on the value of recombination, it has been suggested that the specific value of recombination is to break up linkages and thereby prevent meiotic drive (Haig & Grafen 1991, also see Okasha 2006). Haig & Grafen 1991 also specifically discuss selection for recombination. For an interesting analogy between economy and fair meiosis (veil-of-ignorance vs fair meiosis) see Okasha. 2012. Okasha notes that:

  In both, randomization is used to deprive self-interested agents (genes and individuals) of information about their identity, forcing them to adopt an impartial perspective.

In summary he also writes that:

  A gene that distorts segregation in its favour can spread despite reducing its host’s
  fitness. This harms genes at unlinked loci, who are thus under selection to
  restore fair meiosis if they can. One effect of fair meiosis is to equalize the
  interests of all the genes, thus ensuring they work for the common good.
  One way of achieving this is to destroy linkage, given that segregation
  distortion typically involves linked genes working in concert.

Okasha's paper also has a nice and accessible description of the biological process, and of the selective forces that are operating to counterbalance meiotic drive/segregation disorders.


Carbohydrates in acidic stomach How does the acidic environment in the stomach affect carbohydrate and fast digestion? Does it aid, impede or remain neutral in their digestive process?
Or do the carbohydrates, fats and proteins leave the stomach straight to small intestine once the churning is over?

As for the digestion of fats there are two digestive enzymes active in the stomach:

Lingual lipase (produced with saliva)
Gastric lipase (produced in the stomach chief cells)

Both have activity optima in the acidic pH range.

On the other hand, the salivary amylase that breaks down starch seems to be inactivated by the acidic environment.

Sources:

https://www.ncbi.nlm.nih.gov/pubmed/2134569
https://en.wikipedia.org/wiki/Gastric_lipase
https://en.wikipedia.org/wiki/Lingual_lipase
https://en.wikipedia.org/wiki/Alpha-amylase