DNA adaptation in human life Does our DNA adapt by human lifetime? Or do we have the same genetic information from birth to death?
I mean: What is usually called "evolution" means "natural selection" like this:
http://www.youtube.com/watch?v=hOfRN0KihOU&list=UUsXVk37bltHxD1rDPwtNM8Q
-stronger animals have more descendants, so they make bigger percent of strong animals.
But does evolution work by some primitive genetics-engineering too? Thank you.

Lewontin's recipe

A very nice way to consider natural selection is through the lense of Lewontin's recipe. Evolution of a given trait (tail length for example) through natural selection occurs whenever the three following conditions are met:

There is variation for this trait in the population

This variation is caused by mutations

Part (or the totality) of this variation is heritable

Heritability is the part of the variance in a trait that is explained by genes. It can be measured as a parent-offspring correlation.

The variation of this trait is correlated with fitness

loosely speaking, fitness is an index of both fecundity and survival

You can take two minutes to think about how logical it is that changes in frequency of variants (natural selection) occurs whenever these three conditions are met. You can imagine any objects you want (pencils of colors for example) and simulate these three steps:

Variation

different pencils have different colors

Heritability

simulate that your pencils reproduce (asexual reproduction is conceptually easier to understand) and offsprings have similar (or even the same) color than parents

Correlation between trait and fitness

Pencils of different colors have different fitness.
For example each red pencils create two red pencils the next generation while blue pencils do not manage to replicate at all.

You can quickly see how the red pencils become more frequent in your pencil population through time. If you wait long enough your pencil population will be totally composed of red pencils. And you'll need to simulate a mutation in order to create a blue pencil. I think you understand the how different are the roles of mutations and natural selection in evolution with this example.

Genetic Adaptation During Lifetime of a multicellular organism

For a beginner in evolutionary biology, saying that a multicellular individual's genome does not change during its lifetime might be considered satisfying. In reality it is slightly more complicated. Two elements that are mostly influent very early in the lifetime of an individual have to be considered.

While most mutations occurs during reproduction, some mutations does also occurs during body growth or stated differently during cell reproduction (Mitosis). In consequence, some pairs of your cells share exactly the same genome while other pairs of cells have a sligthly different genome.
Moreover, once some mutations had occurred within the development of an individual, these mutations might influence the fitness of the cells and therefore some alleles (variant of a gene) might raise in frequency while others decrease in frequency (Natural selection). It is important to understand that this process of natural selection select for cells that have a higher fitness and therefore do not necessarily select for the cells that allows the individual to increase its own fitness.

I don't fully understand what you mean when saying: "But does evolution work by some primitive genetics-engineering too?" Could you try to rephrase this question?

Please, let me know if I answered your question!

Note:

Here is a good way to understand the difference between "gene" and "allele". A gene might be a called the "eyes color" gene for example, while the three alleles of the "eyes color"  gene might be callsed "blue eyes", "brown eyes" and "green eyes". In this sense, the alleles are the different variants of a gene. Mutations increase the number of alleles and natural selection reduces the number of alleles by selecting for the allele that cause its holder to have the greatest fitness. If you understood that, it is already good!

Note: Natural selection does not necessarily reduce the number of alleles, several alleles might be kept (polymorphism) in certain "types" of natural selection (frequency dependent selection and overdominance (heterozygote advantage), fitness varies in space and/or time, selection acts on different levels). The "type" of Natural selection that reduces the number of alleles after some time is called directional selection.


Can the shoulder bones grow after the growth plates have fused? Body builders have broad shoulders. If one start lifting weights after one's growth plates have fused, can one still increase the width of one's shoulders? If yes, does that mean shoulder bones can grown longer?
Which bones, (if any) can grow longer after growth plates have fused without causing an abnormal condition like acromegaly?

Regardless of growth plates, exercise does not cause bones to get longer or wider than they would have without exercise.
Each bone is like a sponge, it grows to a predetermined size as regulated by your DNA. Exercise makes the bone more dense and stronger. The more you exercise, the more stress your bones are under.  The bones respond by getting denser and stronger.

Like most organs/tissues, skeletal bone is constantly remodeling. Bone remodeling is a lifelong process where mature bone is removed (a process called resorption) and new bone is formed (called ossification). Cells called osteoclasts are responsible for the breakdown (resorption) while cells called osteoblasts handle new bone ossification. When we are young, we make new bone faster than we remove old bone and we increase our bone mass. Through our 20s this starts to shift, and we begin to lose bone mass faster than it is created. Source


Why are Mendelian mutations considered rare? I was reading the Wikipedia articles about genome-wide association studies (GWAS) and whole exome sequencing.

As I understand, GWAS is used to identify most common SNPs that are proved to be associated with a disease/disorder. On the other hand there is an article about whole exome sequencing method where it said that it is more sensitive to identify Mendelian mutations in contrast with the SNP genotyping methods used in GWAS.

As the graph shows below, there is a distinction between Mendelian mutations and common mutations. What exactly does Mendelian mutation mean (why do we call it Mendelian)? What makes a Mendelian mutation so rare but effective in contrast with common mutations? Aren't common mutations inherited with the same rules as Mendelian ones?

I will focus more on the question of rarity, which the comments have not addressed. Recall that natural selection is operating on the human population. Because of this, bad mutations of large effect (disease mutations such as CFTR in your figure) are very rare, because selection is removing them at some rate from the population (people with cystic fibrosis are unfortunately very sick and are not as fertile as healthy people), whereas mutations with very little effect are not subject to much selection. Paper one and paper two are reviews describing the population genetics in more detail.

As suggested by commenters, Mendelian mutations are so named because they are single loci of large effect controlling traits (approximately). Common variants, by this logic, must have very little phenotypic effect, because they are not purged by natural selection (assuming that they are deleterious, or disease-causing).

Rule of thumb: 'Mendelian' alleles can easily be used to predict phenotypes (like disease) and are acted upon by natural selection. 'Common' alleles are individually not informative about phenotype and are thus mostly ignored by natural selection. Not exactly true, but close.


nontechnical understanding of a mammalian expression system I just started working as an intern in the pharmaceutical industry. My background is in economics and I have pretty much zero knowledge of biology/chemistry. I am trying to build a basic understanding of some of the products I work with to better understand their place in the market. One (the most important) such product is a mammalian protein expression system. My questions are the following:
As I understand it the "output" of such a system is a protein, the "input" is DNA and the system itself is a cell, is this correct?
In the context of producing pharmaceuticals, would this system be used primarily for R&D, manufacturing or both?
I have read that an expression system consists of host cell lines, vectors, media and know-how. Would it be possible to explain in layman's terms what each of these elements is, and how they fit together?
Thanks

The general principle of the expression system is simple: it is a biological machine that uses cell media as its input (i.e. a broth of simple nutrients, including the protein building blocks) to generate its output, a specific protein of interest, according to its "settings", if you will, which is the DNA plasmid that describe which protein will be made. The cogs of the machine are carefully engineered mammalian cells that both create protein from nutrient, and multiply themselves to increase production capacity.
In a perfect expression system, there would be no need to know the underlying biology of the system: just provide the specified broth with a correctly formatted DNA plasmid, let it simmer for a specified duration at a given temperature, and voila!
The value proposition of a commercial system for its users is being as close as possible to this perfect system, i.e. not having to "roll your own" from first principle (after all, the general processes underlying protein expression are covered in an undergrad biology education) which would entail a great deal of effort and expenses. In some way, this is similar to the business model of cloud providers like AWS: abstract the low-level sysadmin-type stuff to provide a reliable platform for applications.
This is useful in both an R&D context (you can iterate on the protein and specific process steps for your product, not on the expression system) and a production context (you have a reliable expression system, that conform to regulatory requirements, with vendor technical support).
However, even the vendors have not entirely abstracted the biology of protein expression, and the specific working of the system is part of the differentiating features of a specific commercial product versus other products in the same line, and competing solutions from other vendors. You have asked clarification on a few technical terms:

host cell lines: The carefully engineered mammalian cells, which have been tuned to product protein in great quantity, while maintaining quality (e.g. avoiding aggregates) and, typically, specific requirement on post-translational modifications necessary for the application the protein was designed for. It must be easily to culture in large batch. There cells are a blank slate in which the DNA plasmid will be inserted to start useful production. A vendor's expression system will feature a cell line that tries to fulfil these something conflicting requirements.
vectors: How to format the DNA plasmid (= protein recipe) and get it into the host cell line. For mamalian system this will typically be viruses that can infect the host cell line to deliver the plasmid. The reliability and ease of use of the vector system, as well as compliance with regulatory standards in a pharmaceutical environment is also a differencing feature of an expression system.
cell culture media: Specific cell line will have different "nutritional requirement", as such vendors will have specific "recipes" for the nutrient broth in which to grow the cells of the system. This is more or less directly dependant on cell line, so less of a differentiating factor per se.
know-how: Biological processes tend to be messy, so some troubleshooting is expected even in commercial systems. Documentation as well as expert technical support can be an important selling point.

Ultimately you will need to understand to some degree the biology underlying the particular
expression system to be able to compare it horizontally to competing solutions from other vendors,
and vertically to other methods of producing proteins (e.g. prokaryotic expression system, cell-free systems), and, if you are in a customer-facing position, to be able to answer some domain-specific question on the spot. Here is an overview, here is another from a different vendor. I would suggest asking more specific question after perusing these.


How is Coenzyme A Transported to the Matrix? So, I've been researching cellular respiration on my own, and trying to keep track of most of the major processes. However, I do have one question left: I can't seem to find any sort of information about how Coenzyme A (I think it's made in the cytosol) is transferred to the matrix (the inside of the mitochondria, inside the inner membrane). Is it transported with a shuttle like for NAD+/NADH, a translocase like for ATP/ADP, or something else? Thank you for your time.

Zhyvoloup et al. (2003) J Biol Chem 278: 50316-50321; emphasis mine:

  CoA synthase is localized on the mitochondrial outer membrane.
  Moreover, we demonstrate for the first time that phosphatidylcholine
  and phosphatidylethanolamine, which are the main components of the
  mitochondrial outer membrane, are potent activators of both enzymatic
  activities of CoA synthase in vitro. Taken together, these data
  provide the evidence that the final stages of CoA biosynthesis take
  place on mitochondria and the activity of CoA synthase is regulated by
  phospholipids.

https://www.ncbi.nlm.nih.gov/pubmed/14514684


How does Serotonergic (5-HT2A mediated) Psychedelia work? How does serotonergic (5-HT2A specific) psychedelia work? I've read that there are some theories that it might involve the induction of a glutamate release in certain regions of the brain involved in perception.

Brenton, the linked pdf is called "Multiple receptors contribute to the behavioral effects of
indoleamine hallucinogens". It goes into detail on a a few basic behavioral responses.  I don't know what your background is so if you need help understanding parts point them out to me and I'll give it a go.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110631/pdf/nihms267079.pdf

https://docs.google.com/file/d/0B0JUrCVOms3MdzdlYmh0SnBmOHc/edit (I'm hosting the pdf on my Google Drive if you aren't able to see the link hosted by the NIH).


can anyone identify this plant please? Seen in the med and have it in my garden

This is a climbing plant from the Genus Mandevilla. It's a genus native to the Americas.

Here is a photo for comparisson:

However, since the Genus Mandevilla has more than 150 species (let alone cultivar and hybrids), narrowing it down to a particular species may be very difficult in your case.


What is the meaning of 'primary' and 'secondary' sympatric speciation in this paper? Sympatric Speciation in the Genomic Era. Both terms are used throughout the paper.
I'm not able to make sense of these terms in the contexts used.
I've also heard the terms 'primary' and 'secondary' gene flow elsewhere on the same topic - are they related?
From the abstract:

However,  I  argue  that  genomic  studies  based  on contemporary  populations  may  never  be  able  to  provide  unequivocal  evidence  of  true primary sympatric speciation, and there is a need to incorporate palaeogenomic studies in  to  this  field. This  inability  to  robustly  distinguish  cases  of  primary  and  secondary divergence-with-gene-flow may be inconsequential, as both are useful for understanding the  role  of  large  effect  barrier  loci  in  the  progression  from  localised  genic  isolation  to genome-wide reproductive isolation. I argue that they can be of equivalent interest due to  shared  underlying  mechanisms  driving  divergence  and  potentially  leaving  similar coalescent patterns.

From the introduction:

Lastly,  I  consider  whether  primary  and  secondary  sympatric speciation represent a mechanistic dichotomy, I suggest that primary and secondary contact can leave a similar genomic signature, when speciation is driven by tightly clustered or  large effect loci. Arguably, the advent of affordable population genomic studies should place less focus on whether study systems result from primary or secondary contact and instead focus on the mechanistic aspects of the genomic architecture and making progress in identifying the conditions and processes under which natural and sexual selection can drive speciation, without extrinsic barriers to gene flow.

TLDR
Sympatric speciation and allopatric speciation with later migration into the same habitat were historically diffucult to distinguish without looking at palaeo-biological data. The paper argues that while palaeo-genetics has made this easier, it is still difficult to distinguish pure sympatric speciation (which it calls primary) and sympatric speciation with a geneflow from an geographically separated (allopatrically speciated?) subpopulation (which it terms "secondary sympatric speciation" or "speciation with secondary gene flow", "...with secondary contact" etc.).
Speciation
Speciation is the divergence of one species (with one gene pool) into two different species (with different gene pools). It is obvious that this will happen if subpolulations are geographically separated and continue to adapt to their local conditions (allopatric speciation).
However, Mayr suggested (back in the 1940s) that there is another type of speciation that happens while the speciating populations share a habitat, and, consequently, while gene flow between these subpopulations is maintained until the speciation process is complete. This requires strong selection pressure towards two different ecological niches each with their associated adaptations.
Empirical examples have been discussed and called into question again. One cool and frequently discussed example is that of the apple maggot in North America that has developed from the hawthorn maggot after the introduction of apples in North America.
Debate
Unequivocal examples for pure sympatric speciation are rare, leading to some debate about the merits of the concept. Sympatric speciation models (following Maynard Smith's models from the 1960s) as well as the reasons for skepticism towards them are illustratively explained for instance in this article (Felsenstein 1980), page 133-135.
The debate continues, today with additional, newer findings from genetics, palaeo-genetics, etc. This is what the article in the OP (Foote, 2018) was about. The pdf of the article (Foote, 2018) without paywall can also be found here. While Foote suggests that what pure sympartic speciation and speciation with secondary gene flow may never be unequivocally distinguished (without additional palaeo-genetic information), others are more optimistic, e.g. Richards et al. 2019 (without paywall on biorxiv). Coincidentally, Richards et al. have a very nice illustration (their Figure 1) that illustrates the issue the OP was asking about.


Calcium concentration in activated dendritic spines? What are the typical calcium levels reached in single postsynaptic spines following activation of NMDA receptors by an EPSP or backpropagating spike? Everyone seems to refer to that one Neuron paper (Sabatini et al. 2002) which reports experimental estimates of around 1 uM following single synaptic stimulation in CA1 neuron spines. However, most computational papers on LTP (even biophysically detailed models) work with much lower values for Ca2+ transients that do not seem to have concrete experimental support. I am trying to put together a realistic model for hippocampal spine calcium signaling, and would really appreciate it if anyone can point out other relevant experimental papers that provide estimates for spine calcium transients.

An earlier source for an estimate of ${[Ca]_{i}}^{+2}$ in spines comes from hippocampal slices of P13-P19 rats (Majewska et al. 2000). The resting ${[Ca]_{i}}^{+2}$ in this paper was ~80 nM and a back-propagating action potential (AP) elicited a response up to ~250 nM (change of ~170 nM). They included $F_{min}$ and $F_{max}$, the minimum and maximum fluorescence signal from a single AP, as parameters in the equation they used to estimate ${[Ca]_{i}}^{+2}$. This paper may be where the models you mention got their numbers from.

The resting ${[Ca]_{i}}^{+2}$ estimated in Sabatini et al. (2002), where they also used rat hippocampal slices from P14-P20, matches that found in Majewska et al. as it was ~70 nM. For the estimation of the evoked change in ${[Ca]_{i}}^{+2}$ after a single AP they used the maximum fluorescence increase from trains of action potentials at 62.5 Hz and 83.3 Hz as a parameter in their estimator equation, assuming that the calcium indicator was fully saturated at those stimulation frequencies. Their estimate for the change in ${[Ca]_{i}}^{+2}$ per AP was about 530 nM. They then reasoned that the buffering properties of the calcium indicator itself could reduce the change in ${[Ca]_{i}}^{+2}$. Thus they loaded several different calcium indicators with different affinities and at different concentrations, in order to manipulate the $\kappa_b$, the buffer capacity, of the calcium indicator. They observed a very strong linear relationship between $\kappa _b$ and the change in ${[Ca]_{i}}^{+2}$. By extrapolating from a linear fit on these data, they concluded that in the case where there was no calcium indicator in the cell —i.e. when $\kappa _b = 0$— the change in ${[Ca]_{i}}^{+2}$ per AP would be approximately 1 $\mu$M.

So the difference between these studies is that in Majewska et al. they used the maximum observed fluorescence of the calcium indicator in their data after single APs, whereas in Sabatini et al. they attempted to saturate the calcium indicator with high-frequency trains of APs. Furthermore, in Sabatini et al. they attempted to account for the buffering capacity of the calcium indicator itself, thus arriving at a more unbiased estimate.

Reassuringly, later work from the Yuste lab (the same lab as in the Majewska et al. study) could replicate the results of Sabatini et al. when they used similar methodology (Cornelisse et al. 2007). Their estimate for $\Delta{[Ca]_{i}}^{+2}$ for a single AP was also ~1 $\mu$M.


Do breasts size depend solely on fat amounts? I've read the first answer here on quora and it suggests that (not during pregnancy and breastfeeding) breasts differ in size only due to the amount of fats. However, there can be firm or soft breasts of the same size and this is somewhat disputing the claim. Also, women with firm breasts can find it painful when their breasts are squeezed while those with soft breasts are less likely to have the same experiences.

So, what makes breasts firm or soft given the same size?

You are asking two different, but related questions

  Does breast size depend solely on fat amounts?

First, breasts are made up of skin, blood vessels, ducts, fibrous tissue, and fat. There is variation between individuals and within an individual the relative composition changes with age, nutrition, and hormonal status. The size of each of those elements will determine the overall size of the breasts.

  What makes breasts firm or soft given the same size?

We don't know, but it's not fat. You can determine the relative amount of fat in breast tissue (fat is black, or radiolucent, other structures are white, or radio-opaque) using mammography. There is even a term for the ratio of non-fatty structures to fat (mammographic density) but physical findings by trained examiners regarding the firmness or softness of breasts do not correlate with the relative composition of a breast. This is tricky because breast density as it is defined in mammography is relative amount of non-fatty structures compared to fat, but you can't predict the mammographic breast density with physical examination of the breast.


Why do Humans not produce Vitamin C like other mammals? Why do most mammals produce their own Vitamin C?

Why do Humans not?

Humans do not produce Vitamin C due to a mutation in the GULO (gulonolactone oxidase) gene, which results in the inability to synthesize the protein.  Normal GULO is an enzyme that catalyses the reaction of D-glucuronolactone with oxygen to L-xylo-hex-3-gulonolactone.  This then spontaneously forms Ascorbic Acid (Vitamin C).  However without the GULO enzyme, no vitamin C is produced.

This has not been selected against in natural selection as we are able to consume more than enough vitamin C from our diet.  It is also suggested that organisms without a functional GULO gene have a method of "recycling" the vitamin C that they obtain from their diets using red blood cells (see Montel-Hagen et al. 2008).

A 2008 published study (Li et al. 2008) claimed to have successfully re-instated the ability to produce vitamin C in mice.

Simply as trivia: other than humans; guinea pigs, bats and dry-nosed primates have lost their ability to produce vitamin C in the same way.

References

Li, Y., Shi, C.-X., Mossman, K.L., Rosenfeld, J., Boo, Y.C. &
Schellhorn, H.E. (2008) Restoration of vitamin C synthesis in
transgenic Gulo-/- mice by helper-dependent adenovirus-based
expression of gulonolactone oxidase. Human gene therapy. [Online] 19
(12), 1349–1358. Available from: doi:10.1089/hgt.2008.106 [Accessed:
31 December 2011].
Montel-Hagen, A., Kinet, S., Manel, N., Mongellaz, C., Prohaska, R.,
Battini, J.-L., Delaunay, J., Sitbon, M. & Taylor, N. (2008)
Erythrocyte Glut1 Triggers Dehydroascorbic Acid Uptake in Mammals
Unable to Synthesize Vitamin C. Cell. [Online] 132 (6), 1039–1048.
Available from: doi:10.1016/j.cell.2008.01.042 [Accessed: 31 December
2011].


Is it possible that nearly human mammals existed before the last mass extinction dinosaurs? From time to time I am hearing people discussing about the possibility that men and dinosaurs meeting some time ago.

The oldest mammal remains seem to be about 35 million years old, quite some time after dinosaurs have perished.

Also, it is very implausible for a primitive man to manage to survive near the dinosaurs (I think they would be very hard to handle even using current technology).

Question: is it even remotely possible for advanced mammals (nearly humans) to have coexisted with dinosaurs?

Is it possible that nearly human mammals existed before the last mass extinction dinosaurs?

Short answer

No!

Longer answer

The ancestor of all mammals lived about ~180 millions years ago (see here), so much before the Cretaceous–Paleogene extinction event (~65 millions years ago). The ancestor of all primates lived ~65 millions years ago (see here), so pretty much at the same time as the C-P extinction.

But please, don't picture the ancestor of all primates as something that is too human like. It looked more like a lemur, a tarsier or a loris, than like a human!

The first great ape lived about 14 millions years ago (see here) and the most recent ancestor of chimpanzee, bonobos and humans lived about 6 millions years ago (see here). The discovery of how to control fire happened about 1.5 millions years ago (with a pretty wide confidence interval, see the wikipedia article). The first generally considered Homo sapiens lived about 200,000 years ago (see the wikipedia article). The wheel was first invented about 5'000 years ago (see the wikipedia article).

Related: Who are humans' closest relatives, after primates?


How do similar environments on islands in close proximity result in allopatric speciation? I would like to ask a question on the very classic example of allopatric speciation seen in the Galapagos finches. Adaptive radiation occurred because the finches flew from island to island, so there is gene flow, and the different environments on the different islands provide different selective pressures that causes relative fitness of the same species of birds to change. Over time, more drastic changes occur and speciation event occurred.

What I am doubtful of is the extent of different selection pressures on speciation. Given that the islands are so close to each other, wouldn't it be safe to assume that these islands generally have similar types of plants, similar types of insects, similar climate, similar predators. If gene flow between populations of finches can occur across islands, why can't it happen for the other biotic factors "contributing" to the islands' characteristics? So how can such similar conditions/environments provide selection pressure that is different enough to result in speciation?

Your clarifications are very much appreciated!

The question is a bit confusing because it seems to be built on at least 5 misunderstandings.

Allopatry and gene flow

  [..] allopatric speciation seen in the Galapagos finches. Adaptive radiation occurred because the finches flew from island to island, so there is gene flow [..]

By definition, an allopatric speciation is a case of speciation where there is no gene flow. If there is gene flow, then you may still end up with a reduction of gene flow and a speciation event but that would not be called allopatric speciation.

The first event leading to isolation (that is to an allopatric scenario) might be caused by birds flying over to another island but this does not mean that the divergence between populations occurred with gene flow.

Relative fitness

  [..] the different environments on the different islands provide different selective pressures that causes relative fitness of the same species of birds to change.

It makes little sense to talk about relative fitness of a species. The relative fitness of an individual is the absolute fitness of this individual divided by the absolute fitness of a reference individual (generally a theoretically super fit individual) in the population.

Did you want to talk about competition between species? I don't think so as I don't know how this concept would fit in the rest of the question.

Assumption of similar ecology

  [..] wouldn't it be safe to assume that these islands generally have similar types of plants, similar types of insects, similar climate, similar predators.

No, it really is not a good assumption. In some extreme cases, climate can actually radically differ between two locations at less than 20 meters apart! The same is true for other variable making up the ecological conditions.

Species dependent migration abilities

  If gene flow between populations of finches can occur across islands, why can't it happen for the other biotic factors "contributing" to the islands' characteristics?

Because birds have wings! It is easier for a bird to fly to the next island than it is for a mouse.

Implicit assumption that selection is needed for speciation

  So how can such similar conditions/environments provide selection pressure that is different enough to result in speciation?

Speciation can happen in absence of divergence selection (esp. in allopatry). Genetic drift alone yield to population divergence too and can lead to reproductive isolation.

To my knowledge, the relative role of selection vs drift in causing speciation is not well understood though.


Precursor miRNA and a mature miRNA What is the main difference between a precursor miRNA and a mature miRNA?

It is often the case that we have more than one precursor miRNA but only one mature miRNA.  The miRNA-seq data contains only precursor miRNAs, so I was wondering if we could use the expression of the precursor miRNA as the expression of the mature product or not?

precursor miRNA is ~70mer RNA with a stem loop structure. It is cleaved by dicer to generate one or two mature miRNAs (from one or both the 'arms' of the stem ; called 3p and 5p which are ~22nt long). Refer to this review. (It is an old one and some facts might have changed, but the basics are there.)

Yes, there can be different precursors giving rise to same mature form. There are a few cases like that (check for entries like mir-x-y [where y can be 1,2,3,...], in miRbase).

Usually pre-miRNA is shortlived and is immediately converted to mature form. Therefore, in small RNAseq data, most miRNA reads (more than 90% [at least that's what I get]) come from mature form (pre reads would be longer [after adapter removal] and will contain sequences not retained in mature form). Most algorithms select for the mature reads.

It is difficult to determine which precursor gave rise to a certain mature miRNA, using an RNAseq data. The usual practice is to assign the average read count to each locus. E.g., for a mature form that has 3 precursors, each precursor is assigned 1/3 of the total mature reads. However, in most RNAseq experiments, the objective is to obtain the mature miRNA profile and which precursor gives rise to it becomes immaterial.


A hypothetical emergency situation This question was posed to me by my Biology teacher:

Consider a hypothetical emergency situation of a person shot by a bullet in the heart. The bullet goes into the body and comes out from it, causing a total of two "holes" in the heart, one each in the "dorsal" as well as "ventral" side of the heart. Blood starts coming out.

Now in an ordinary situation, if the blood continues to flow out, the person will die. But there is a twist, the person has been given an infinite supply of blood from some sort of medical equipment. (Nothing like this actually exists in real life, but you might consider this a "conceptual Biology textbook problem".) The person's heart beats at a normal rate of ~72/second.

Now here is the question :

  Considering, the "infinite" supply of blood available, will the person survive?

Will the heart develop some sort of clot or something similar to prevent further leakage of blood, as it forms due the cuts on arms or legs? Is some medical assistance required besides the "infinite" supply of blood?

NOTE : You might make the following assumptions ---

There is no doctor/surgeon to help. Just you and your faithful "machine".
The blood provided by the "machine" is 100% compatible with the blood group of the person.
The "machine" is connected in such a way that after the complete loss of the "original" blood of the person, now the blood provided by "machine" runs in the arteries of the person.
The veins and arteries of the person are 100% OK. The only part affected is the heart "perforated" by the bullet.

The person cannot survive for long, in spite of the infinite supply of blood.

In real life

There is no blood delivery system that can add blood to the vascular system as fast as it would be lost by two bullet holes in the heart. But I guess that's covered by your conditions.

As mentioned in comments, where would the blood go? Despite a thoracic entry and exit wound, blood volume inside the thorax would not squirt out of those holes fast enough to prevent a life-threatening accumulation of blood which would interfere with expansion of the lungs, so unoxygenated blood = death.

Theoretical

I suspect this is what your teacher was hoping would be the answer. Blood - like most things - will follow the path of least resistance. Which has a higher resistance, the aorta and arteries  (if it hit both the right and left ventricles, the pulmonary vasculature as well) supplying life-sustaining blood to vital organs, or two holes? Theoretically, there would be little resistance against blood flow through the holes, so no flow into vasculature means death.

Regarding clotting, nope. Rate of blood flow would preclude a functional clot.

In real life, even with surgeons at the ready, this is a deadly scenario. One hole: doable (depending on the caliber of the bullet); plenty of people have survived this event. Two holes, it would take particular circumstances and would basically be a miracle.


Is there natural occurrence of induced pluripotency / expression of Yamanaka factors and what is the evolutionary explanation of that? Is there natural biological processes in which the full (full reprogramming into pluripotent state) or partial (partial reprogramming, stopped before point-of-no-return, preserving the functional distinctiveness of the cell) induced pluripotency (https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell) and expression of Yamanaka factors occurrs? What is the evolutionary explanation of such rejuvenation factors? I would like to see the natural explanation otherwise it begs for the idea that the Universe is created with the human as the goal of it (anthropocentric hypothesis) and it is quite uneasy for me.

I guess, that natural reproduction processes can involve some kind of rejuvenation/induced pluripotency and they determined the existence of Yamanaka factors.

What is a pluripotent stem cell?

A pluripotent stem cell is a cell that can differentiate into any of the major tissue categories. Every animal exists as a collection of pluripotent stem cells at an early stage of development: if you are looking for an evolutionary purpose, that's where you should start, and the purpose is pretty obvious: you start as a single fertilized egg and end up as a complex collection of tissues, so at some point that one cell has to become a collection of tissues, and there is an intermediate step which is a pluripotent cell.

None of this has anything to do with induced pluripotency, however.

What makes a cell pluripotent?

The answer to this question isn't really all that unique to stem cells: all cell types are differentiated from others based on their expression of transcription factors. Transcription factors determine what proteins get produced (including other transcription factors), which in turn determines how a cell functions and what role it plays.

Pluripotent stem cells express pluripotent stem cell transcription factors. Yamanaka started with embryonic stem cells, and looked for transcription factors that were special to those cells.

What does it mean to make a pluripotent stem cell?

Given that the identity of a cell is based on the transcription factors it expresses, the way to make one cell type act like another cell type is to change those transcription factors. A cell is a pretty complicated environment: there are lots of different transcription factors and lots of other types of proteins, so it's possible that it wouldn't be feasible to reprogram a cell this way.

However, Yamanaka and colleagues tried to artificially make an adult cell produce those transcription factors observed in embryonic stem cells. Indeed, they found that if they used the right combination of transcription factors in the right environment, the cells started to behave like embryonic cells, and they could further make those cells differentiate into different tissue types. These transcription factors are the so-called Yamanaka factors.

Summary

An induced pluripotent stem cell is a cell that has been transformed to produce transcription factors that are found in embryonic cells. Transcription factors are what make different cell types different from each other, by controlling everything else that the cell produces. All of this machinery is ubiquitous in development, the only intervention that the humans are doing is to make a cell express genes it would normally only express if it was an embryonic cell.

All of this information is already present in the Wikipedia article you linked.

Takahashi K, Yamanaka S (2006). "Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors". Cell. 126 (4): 663–76.

Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S (2007). "Induction of pluripotent stem cells from adult human fibroblasts by defined factors". Cell. 131 (5): 861–72.

Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA (2007). "Induced pluripotent stem cell lines derived from human somatic cells". Science. 318 (5858): 1917–20.


Is there a biological explanation for perceived altered cognition whilst on cannabis? Cannabis has been associated with literature, arts, and culture for centuries. There are a few features of the drugs affect on the human mind that account for this, however it remains illegal in most countries.
In a very tangible way, cannabis causes a few alterations of perception, such as an altered sense of time and this is often exploited by police to see if a potential felon is intoxicated. Other psychoactive alterations that are attributed to a cannabis (AKA marijuana or weed) include a temporary sense of deeper metacognition, depersonalization, & derealization.
Whilst I'm aware that this is probably the result of the active compound THC, it's unclear how is this deeper feeling of cognition achieved from a physiological perspective? What is this process in the brain that changes the perception of reality?
Ideally studies mirroring the recent Cahart-Harris et al., 2016 paper would be ideal (but focused on THC rather than LSD). That paper identified key physiological features that correlated with the feelings of being "high" such as changes in brain blood flow, electrical activity, and network communication patterns.
Note I am not talking about long term IQ alteration, but rather the temporary affect the drug has on the brain's cognition.

There has only been little research on the neurocognitive and neurophysiological effects of cannabis. There have been introductory neuroimaging studies in mainly non-psychotic populations, which show that cannabis does not affect gross brain anatomy. On the other hand however, it has been proved that cannabis does acutely increase cerebral blood flow (temporarily; in the right hemisphere) on the long run, exposure will cause an overall reduction in cerebral blood flow.

There have been studies with animals where they used an active cannabinol called delta-9-THC to demonstrate enhanced dopaminergic neurotransmission in brain regions which are usually associated and known to be implicated in psychosis.

In humans the delta-9-THC causes psychotic-like states and memory impairments. The effect of a CNS cannabinoid system, on humans is still tested by neuroimaging studies.
The endogenous cannabinoid system is sensitive to contact with exogenous cannabinoids such as the delta-9-THC, which is known to impair memory in humans.

In a further study is was examined what impact chronic cannabis use has on memory-related functions by examination of the subsequent memory effect (SME) of the event-related potential (ERP). The study concluded that comparing the group to the control group that chronic users of cannabis have an altered memory related brain activation in the form of dysfunctional SME production which may also go hand in hand with reduced neural efficiency.

Several investigators studied the acute effects of cannabis specifically on attentional processing. Hart et al. (2001) studied the effects of placebo, light (1.8%), and heavy (3.9%) THC cigarettes in chronic, daily cannabis users and found no significant differences in the accuracy of response to attentional tasks. However, performance on a tracking task, which requires sustained attention, was found to improve significantly after the high dose of THC, relative to the other conditions.

In one study of 37 adults with a history of light cannabis use, acute intoxication with a high dose of THC resulted in significant impairment on a measure of impulsivity (McDonald et al., 2003). Another study (Ramaekers et al., 2006) found similar impairment on a task of inhibition in intoxicated, chronic cannabis users. The results measured where in a timespan from 0-6 hours after consumption.

In another study from 2010, researchers investigated "semantic-priming".

  Under the influence of cannabis, users showed increases in both automatic semantic priming and schizotypal symptoms compared with controls. When abstinent, cannabis users exhibited hyper-priming at long SOAs.

References and further reading:

Linszen D, van Amelsvoort T. Cannabis and psychosis: An update on course and biological plausible mechanisms. Curr Opin Psychiatry. 2007;20:116–20
de la Serna E, Mayoral M, Baeza I, Arango C, Andres P, Bombin I, et al. Cognitive functioning in children and adolescents in their first episode of psychosis: Differences between previous cannabis users and nonusers. J Nerv Ment Dis. 2010;198:159–62.
Bossong MG, Niesink RJ. Adolescent brain maturation, the endogenous cannabinoid system and the neurobiology of cannabis-induced schizophrenia. Prog Neurobiol. 2010;92:370–85.
Battisti RA, Roodenrys S, Johnstone SJ, Respondek C, Hermens DF, Solowij N. Chronic use of cannabis and poor neural efficiency in verbal memory ability. Psychopharmacology (Berl) 2010;209:319–30.
Hart CL, van Gorp W, Haney M, Foltin RW, Fischman MW
Neuropsychopharmacology. 2001 Nov; 25(5):757-65.
McDonald J, Schleifer L, Richards JB, de Wit H
Neuropsychopharmacology. 2003 Jul; 28(7):1356-65.
Ramaekers JG, Kauert G, van Ruitenbeek P, Theunissen EL, Schneider E, Moeller MR
Neuropsychopharmacology. 2006 Oct; 31(10):2296-303.
http://druglibrary.org/schaffer/hemp/general/mjeff1.htm


Unknown larvae in grey cocoon Location: Germany
While cleaning the windows today, I realized some dirt falling off the top of the window frame. By looking further, it seemed to be some kind of cocoon. (The first picture is very bad, I'm sorry)

Those cocoons were about 2-3cm long. There was a total of 6 cocoons.
Two were damaged by falling down.

The last picture shows the inner part of the second picture I think. The larvae(?) was about 0.8cm to 1cm long.
Not sure if it matters, but the window is an attic window, located at the third floor.
Do you have any idea, what kind of larvae it is?

This is a neophyte that has been recorded in Europe since 1979:
Sceliphron curvatum, in German also known as orientalische Mörtelwespe. Unusually large considering what else is buzzing around, but mostly harmless.
The nests, or rather individual larvae cells, are made of mud and while there are about thirty species in the genus, only Sceliphron curvatum is found in Germany - there‘s no other wasp or other insect in Germany that builds similar nest cells, especially the size is a good indicator. Your description of nest location in a window frame is typical, curtain folds or (vertical) nooks in furniture, e.g. shelves are also welcome. Our specimen picked a hiding spot behind a few books a few years ago.
Because of their size, there are usually some articles about them in the low-news summer media lull, describing baffled citizens and their “discovery”. A few less sensational descriptions, photos and further information can be found here (sorry, in German).
Nice find!


What is a positive epitope fragment What is a positive epitope fragment? I found one paper on the subject:

COBEpro: a novel system for predicting continuous B-cell epitopes by
Michael J. Sweredoski and Pierre Baldi

The group tries to predict possible epitope sequences for the generation of antibodies. This includes also non-linear epitopes where not all amino acids of the epitope are line up behind each other, but come in close contact due to a 3D-structure. To train their algorithm, they use data, where the boundaries of the epitopes and the non-epitopes are known and clearly mapped.

The "Dataset and Preparation" section in this paper contains the following:

  In this article, we used several different datasets to train and
  benchmark COBEpro. These datasets were derived from several different
  previously published sources: BciPep (Saha et al., 2005), Pellequer
  (Pellequer et al., 1993) and HIV (Korber et al., 2003). The BciPep
  datasets consist of epitope/non-epitope sequence fragments. The
  Pellequer and HIV datasets consist of whole antigen proteins annotated
  with precise epitope boundaries.

The "positive epitope fragments" are known and verified ("positive") epitopes from these datasets in the training database. The fragment refers to restriction of length to 20 amino acids which they choose to apply. Shorter epitopes got amino acids added so they get 20 aa long, longer got truncated.


Identify chromosome location from gene nucleotide or amino acid number I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of an amino acid or a nucleotide (for example, which lists the location as the ACADM gene, 985A>G (the nucleotide polymorphism) and 304 as the amino acid mutation (from Lys>Glu)). How would I go about now identifying the exact position of this on the chromosome? Eg: Chromosome 1, location 76123456?

Currently the only way I can think is to manually count 304 amino acids, or 985 nucleobases, from the start of the gene where the start location is listed. However this isn't practical. I downloaded some software (IGV & GenomeViewer) and can't see a way I can view the actual amino acid or nucleobase number from the start of the gene.

Option 1: You can use the SNP database, to see if it has (and it usually is) characterised before: The tutorial is here (http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioMed_Bioinformatics_NCBIGene_SNP.shtml)

Option 2: is to use a go to character function in a few text editors. If you are on windows, You can do it in Notepad++ (https://superuser.com/questions/487507/how-can-i-find-nth-character-in-notepad); if in Linux/mac, you probably know how to do it in vim (https://stackoverflow.com/questions/22862558/go-to-a-specific-offset-in-a-document). If using other text editors in Linux, ask around that community, and they'll tell you how to go about it.

Option 3: One another labour intensive but easy way to do it is to use the tools available online. I personally use NCBI for this, and play around with the region shown. This prevents you from counting. Once you get the local region, select a  few nucleotides  to the left and right, and use that as a search term in your sequence (find text and replace text)

Option 4: And my personal favourite, get the computer to do it for you like this: https://stackoverflow.com/questions/23662748/replace-a-nucleotide-at-a-certain-position-in-a-dna-sequence-file

If you are using IGV, it is said in the documentation here (https://www.broadinstitute.org/igv/Navigate) on how to search for regions and even insert mutations. Were you not able to make this work ?


Will tagging a protease with HlyA for secretion inactivate the protease? We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli isn't cleaved from the protein, it will remain attached to the protease in the extracellular matrix.

Will the protease still function and cleave the peptide chain at the n-terminal proline residue with the HlyA signal still attached?

Unless someone has actually done this specific fusion and reported on the activity, this question won't have an answer. I can't find anything about proline aminopeptidase fusions, but enzyme-HlyA fusions have been done that retained activity similar to the wild-type protein (examples: cutinase, β-lactamase). Your fusion might work fine or folding might be disrupted after secretion (either by the tag itself or by the absence of chaperones, if required). In other words, you need to try it yourself.

Bacillus subtilis is commonly used for secretory protein production and may present another/better option.


Microsatellites and Minisatellites: Which of these form the basis of DNA fingerprinting? I'm in a fix.

 Prepare yourself for a long read

We've just learned about minisatellites and microsatellites at class (okay, by "learned", I mean we were told their definitions and essentially nothing else... hardly surprising, since we aren't expected to know more than that at school).

Shortly afterwards, we touched on the topic of DNA profiling, and my textbook went on to state:

  Minisatellites are hypervariable and are specific to each individual. This uniqueness is employed in DNA profiling.

Which would imply that the repetitive DNA fragments used in DNA profiling (VNTRs - Variable Number Tandem Repeats) are (only?) minisatellites.

Fine.

However, the Wikipedia pages on minisatellites and microsatellites (I linked both of them earlier on in this post) mention:

  (Minisatellites and microsatellites)... together are classified as VNTR (variable number of tandem repeats) DNA. Confusingly, minisatellites are often referred to as VNTRs, and microsatellites are often referred to as short tandem repeats (STRs) or simple sequence repeats (SSRs).

If I interpreted this correctly, it's saying;

"Both minisatellites and microsatellites are classified as VNTRs. But when one normally talks about "VNTRs" he/she is referring to minisatellites. Microsatellites are, instead, commonly referred to as STRs/SSRs."

Okay, so far so good.

The Wikipedia page on microsatellites explicitly states that they (the microsatellites) are the ones you deal with in DNA profiling. However, the Wikipedia page on minisatellites carries no clear indication of their (minisatellites) use in DNA profiling.

Ugh.

And to compound my confusion, the Wikipedia page on DNA profiling states:

  DNA profiling uses repetitive ("repeat") sequences that are highly variable,called variable number tandem repeats (VNTRs), in particular short tandem repeats (STRs), also known as microsatellites, and minisatellites.

Which suggests that both minisatellites and microsatellites are used in DNA profiling (as they're both VNTRs), but microsatellites are more relevant in this regard.

Summing up what I said:

My textbook  says that DNA profiling makes use of VNTRs.
My textbook (and teacher) says DNA profiling makes use of only minisatellites.
Wikipedia says that VNTRs refer to both minisatellites and microsatellites.
Wikipedia says that VNTRs are typically mentioned in reference to minisatellites. Whereas microsatellites (which are strictly "VNTRs") are better known as STRs/SSRs.
Wikipedia says (explicitly) that microsatellites are used in DNA profiling. It doesn't mention minisatellites in this regard.
Wikipedia says that both minisatellites and microsatellites are used in DNA profiling, but minisatellites are use more often.

 This inconsistency over the three Wikipedia articles I've linked is seriously annoying

My question(s),

1) I'm told that VNTRs are used in DNA profiling. Does this refer to both minisatellites and microsatellites...or just minisatellites?

2) If only one of them is used, why disregard the other? They're both (technically) VNTRs aren't they? So shouldn't either of them work just fine?

1) I'm told that VNTRs are used in DNA profiling. Does this refer to both minisatellites and microsatellites...or just minisatellites?

Actually, it refers mostly to STRs. I worked a bit in forensic genetics and we always published works using STRs markers (one example here, there are plenty in the literature).

In addition, I would not be surprised if current forensic identification used SNPs instead, e.g. as proposed in this paper

2) If only one of them is used, why disregard the other? They're both (technically) VNTRs aren't they? So shouldn't either of them work just fine?

I really don't know, but I am sure that it has to do with one of a) level of variation, i.e. if minisatellites have lower mutation rates and are less variable, then they also are less useful, b) ease of genotyping.

Browsing in the web I found this website from which I understand that the minisatellites were the first to be used to perform DNA profiling (using a method different from sequencing) and that "modern" DNA profiling is performed using STRs. However, I insist that modern DNA profiling should be better performed using SNPs.


DNA Topology. Question on twists and writhes Hi guys there is a question which has been driving me crazy ever since I saw this video(https://youtu.be/az2c6UbEdug). At 4:50 the guy says that when a right-handed circular DNA starts forming a right handed interwounding writhe the DNA must adjust by twisting more(You can see the number goes up to 8 from 5 in the equation) and that when an interwounding writhe is done in the opposite direction it must twist less. To me this doesn't make sense at all. I thought that as you interwound to the right the twisting should lessen and when you interwound to the left the twisting should increase. Can someone explain(or show a very clear diagram/illustration which explains this) please??

It is all explained here in Wikipedia. If you want to make a 3D model of your own, you can use two pieces of tygon tubing (like the rubber hose for a Bunsen burner), that are both circularized and attached with connectors that can be opened and closed--that lets you simulate nicking and re-sealing the strands.


What is the biological significance of k-mer counting? There are many tools developed to compute the counts of k-mers present in a gene sequence. Jellyfish, Bloom Filter Counter, DSK Kmer Counter, KAnalyze, KMC 2 etc are some efficient software developed in last decade to count k-mers.

But in what purpose, these tools are used?

How they are serving biological community?

The applications for counting the k-mer occurences in a sequence are: building de Bruijn graphs [1] for de novo assembly from very large number of short reads, produced by next generation sequencing, fast multiple sequence alignment [2], and [3] repeat detection.

  Compeau PE, Pevzner PA, Tesler G: How to apply de Bruijn graphs to genome assembly. Nature Biotechnol. 2011, 29 (11): 987-991.
  10.1038/nbt.2023
  Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797.
  10.1093/nar/gkh340
  Kurtz S, Narechania A, Stein J, Ware D: A new method to compute K-mer frequencies and its application to annotate large repetitive
  plant genomes. BMC Genomics. 2008, 9 (1): 517-10.1186/1471-2164-9-517

To be clear, here is the biological significance of each of these applications:

Sequencing any genomes (bacterial, plant, mammalian) has become very cheap and easy recently with the next generation sequencing technologies. As opposed to the Sanger sequencing (the first generation), these produce as a readout very short sequencing reads, which have to be assembled into longer ones, and subsequently, into whole genomes. Counting the k-mers is part of the assembly process and this is its biological importance.
In order to compare whether proteins might have similar function, and thus belong to the same protein family, a multiple sequence alignment is performed. This is crucial step when annotating new protein sequences and studying their biological functions.
There are many repeats in our genome, as well as in plants. Repeated sequences are also involved in neurodegenerative diseases such as Hungtingtons, so being able to identify them is of medicinal importance.


why do sodium channels close with excessive extracellular potassium ions in cardiac myocytes? When there is an excessive concentration of potassium ions outside cardiac myocytes, the membrane potential surely goes up. I would have thought that this would make it easier for the membrane potential to go up past the threshold level, opening sodium ion channels and causing an action potential like at a synapse.

However, I understand that as the high concentration of extracellular potassium ions actually deactivates voltage gated sodium ion channels as opposed to opening them. Why does this happen?

Sorry if this question is pretty basic. We haven't covered anything nearly as complicated at school, especially not about cardiac cells.

Thanks for answering!

Short Answer

Depolarization block keeps sodium channels in a different state where they aren't available to open.

Longer Answer

The answer here applies equally to cardiac myocytes and neurons, and has to do with the gating properties of sodium channels (calcium channels have some similar behavior, which is also important).

Voltage-gated sodium channels at rest are pretty much all in a 'closed' state. The probability of a channel switching to an 'open' state increases with increasing voltage. However, those channels don't simply stay open indefinitely: they transition to third, 'inactivated' state. 'Inactivated' channels can't reopen. This helps keep sodium-mediated excitation brief and saves a lot of metabolic energy versus 'forcing' a cell to repolarize by only overwhelming the sodium conductance with potassium conductance.

Channels will stay in the inactivated state if the membrane remains depolarized. The probability of a channel switching from 'inactivated' to 'closed' (and therefore 'ready to open') increases with decreasing voltage. If a cell does not repolarize sufficiently, many sodium channels will stay in the 'inactivated' state. Further, channels that do switch to the 'closed' state could open, but not in synchrony. The eventual result is an equilibrium with a mix of sodium channels in open, closed, and inactivated states. There aren't enough 'closed' channels around to switch to open, there aren't enough 'open' channels to depolarize the membrane more, and as 'inactivated' channels switch to 'closed' there are other channels switching from 'open' to 'inactivated'.

This whole condition is referred to as 'depolarization block.'

Here's a helpful review on voltage-gated sodium channels that contains information covering what I discussed in my answer:

Catterall, W. A. (2000). From ionic currents to molecular mechanisms: the structure and function of voltage-gated sodium channels. Neuron, 26(1), 13-25.

You can also find lots more information in textbooks and elsewhere if you look for the term 'depolarization block.' Note also that I have simplified the gating transitions for voltage-gated sodium channels for the purpose of this answer, so some sources might explain a more complicated system; the general principles still apply to the question, though.


How do you turn a minimal CIF description into a complete one? I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition.  This page provides a batch script that I may be able to tease apart to suit my needs, but I thought there was a way to do this from within the CCP4 Program Suite GUI/job manager.

Maddeningly, I see in my project job history a couple "dictionary" jobs where I did this, but I utterly forgot how I set them up (forgive the asinine names):

When I try to use the Monomer Library Sketcher (under Refinement/Restraint Preparation) and open a CIF ("mmCIF") file, nothing happens.

Also under the sketcher, I can severely abuse the "Load Monomer from Library" and it looks like I get the right thing:

However, when setting up the above, it throws "Error: can't read "monomer_lib(code,n..." warnings, then when running it generates the Geometry file (seemingly successfully) then says that Libcheck failed when trying to create the coordinate file.

If there are other solutions, I'd be interested as well.  I've used PRODRG to create CIF files before with its draw tool, but it can be a bit clumsy, it ignores how I drew my double bonds, and it creates new names for all the atoms.

Not quite as ideal as I had hoped, but it works:

Get and install CCP4.
Obtain minimal CIF file from PDB or elsewhere.  Save to some folder easy to get at with the console.
Launch console and cd to folder with the minimal definition.
Run libcheck by typing it and hitting return

If it complains it's not found, the CCP4 bin directory may not be in your PATH environment variable.  You can get around this by specifing the full path to the program, e.g.: c:\CCP4-Packages\ccp4-6.1.13\bin\libcheck.exe (may vary with version)

Say "Y" or "A" at the _DOC: prompt for some more files, "N" if you don't care (I generally don't)
At the --> prompts, specify:

the input file, e.g.: file_l: ABC.cif
the monomer: mon: ABC
output file name: file_o: ABC_out

Leave a prompt blank and hit return to start processing.

If it runs successfully it might look something like this:

C:\Users\Nick>libcheck

  --- LIBCHECK --- /Vers 4.2.8   ; 02.06.2009/

  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
    N - means without DOC-file
    Y - with new contents
    A - means to keep old contents and add new information
        with DOC-file program creates batch file: libcheck.bat
 _DOC:n

 #
 #      Keywords:
 #
 #FILE_L:   < >  - additional library, " " means without this file
 #MON:      < >  - give info about this monomer
 ... (shortened) ...
 #SRCH: <N>/Y/0  - Y - global search, 0 - for MON from PDB_file
 #                 (only with NODIST = N)

 #---  type "keyword   parameters" and/or ---
 #---  press key "CR" to run program      ---
 -->file_l: ABC.cif
 -->mon: ABC
 -->file_o: ABC_out
 -->
 MON   : ABC
 -------------
 Output file   :ABC_comp
 Input user lib:ABC.cif
 _chem_comp.name "DRUG INTERMEDIATE"

          17          55
 "DRUG INTERMEDIATE"

 -------------
 Keywords:
 HFLAG : Y
 COOR  : N
 LCOOR : Y
 SRCH  : 0
 REF   : Y
 NODIST: Y
 ERROR ==> In the loop containing the item_chem_comp.three_letter_code
 ERROR ==> The number of expected items and the number existing items do not match
 ERROR ==> The number of expected items is    7
  NUMBER OF MONOMERS IN THE LIBRARY          :     1
                with complete description    :     0
  NUMBER OF MODIFICATIONS                    :     0
  NUMBER OF LINKS                            :     0
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  I am reading library. Please wait.
      - monomer"s description
  WARNING : monomer:ABC      - has the minimal description.
  now monomer:ABC      - has complete description.
  I will check it.
 * CIFile  : ABC_out_ABC.cif
 * PDBfile : ABC_out_ABC.pdb
 * Plotfile: ABC_out_ABC.ps
  I am writing new description to
  file: ABC_out.lib

C:\Users\Nick>

It yields the following output files:

(file_o): looks like a CIF file with lots of whitespace and records stripped out
(file_o).lib: the desired, complete definition file
(file_o)_(mon).cif: an even more minimal CIF file with only XYZ coords
(file_o)_(mon).pdb: a PDB file
(file_o)_(mon).ps: a document with a stereo labeled diagram, and lists of bonds, angles, chirality (centers?) and planes.  Can convert it to the easier-to-use PDF format using this http://www.ps2pdf.com/convert.htm, or other tools.


How is CO2 and O2 separated in our body during breathing? https://www.msdmanuals.com/home/lung-and-airway-disorders/biology-of-the-lungs-and-airways/exchanging-oxygen-and-carbon-dioxide

The image in the above link shows that CO2 and O2 both pass through the same membrane but still CO2 is exhaled and O2 is taken in the body.

Why doesn't the CO2 mix with O2 and stay in the blood ?

Why is only CO2 passed out through the membrane?

It all comes down to concentration gradients. In deoxygenated blood, which is what enters the lungs, the O2 concentration is relatively low and the CO2 concentration is higher than that of ambient air. On the flip side, the air that we breathe in has a higher concentration of O2 than deoxygenated blood. The alveolar membrane is thin enough that the gases can diffuse across this gradient almost instantly. And just like that, you have oxygenation of blood, and removal of CO2.


In (human) zygote cell differentiation, do we know how the cells coordinating the process know their current position? I've seen this question asked in a mature person -- e.g. lip cells will create more lip cells -- but how about in the developing zygote.   I've seen neighboring cells help determine the type of the new cell. Do we know how they know where they are located, and how many cells of a certain type have already been made, making "lips" complete, or teeth, etc.  So in summary:

1) how do the cells in the growing zygote know "where they are", assuming they need to, to determine what cells to build where for the body?

2) how do the cells know, when the cells of that type building a bone or lips or teeth, etc, are done, since obviously many participate in the process. ?

There's a protein called Bicoid in fruit flies (see https://en.wikipedia.org/wiki/Bicoid_%28gene%29) that determines the head/tail axis. I remember from biology class that there's a similar protein that determines the up/down axis as well, although I forget its name.

There's almost certainly something similar in humans.


Frog identification - two different frogs seen in New Zealand Me and my friends saw these two frogs in man-made ponds in an area which is undergoing development for residential use. Anyone able to identify these beauties?

Also would be interested as to how these frogs got there, as the pond wouldn't have existed 2-3 years ago and there are none nearby.

Location these were found can be seen in the following link:
https://www.pic2map.com/yibrir.html

the first frog(the green one) resemble GREEN AND GOLDEN BELL FROG - Litoria Aurea

Description of the frog -

Have golden-bronze colored spots
Have a black line from the eye to the nostrils
Found in northern Island

And coming to the second frog it resembles Southern Bell Frog - Litoria Raniformis

**Description of the frog - **

Have a distinctive black line running through their back
Found almost everywhere in new Zealand
They have black-brown patches on their skin (can increase in blackness based on the surrounding environment)

Coming to your question , the golden bell frog seems to stay in small temporary water ponds even puddles

On the contrary the southern bell frog lives permanently in a pond so probably it lives somewhere nearby

That'll be it


Sex determination in cephalopod? I see some source say octopus do not have sex chromosome. So what's the sex determination mechanism for cephalopods?

So far, you're right in that there is no hard method of determining cephalopod sex determiners.  Male and female share the same number of chromosomes, but are morphologically different, with the male developing a special arm for transferring spermitangia and the females often being larger than males (1).

Most research papers seem to focus on just being able to tell the sexes apart by behavior/anatomy (2) and have not yet broached on the How, except to note that they do not seem to have specific markers, which you've already noticed (1).

You can tentatively run with this, and keep an eye out for new research in Google Scholar, and decide that your race uses environmental signaling (3) to determine their sex.  Given how real life nature goes, you'd probably be in the clear as certainly one cephalopod species will use that method to determine sex. It also can segue into sequential hermaphrodism if you're interested in going in that direction.  It would certainly bring a novel element to your sophonts, rather than making an octopus "human". (Hypothetical extrapolation based on the previous version of this question in Worldbuilding.stackexchange)

But, to give you some ideas for environmental factors.  Some species of Daphnia will make parthenogenetic males when three factors meet: a short photoperiod, shortage of food and a high population density (4). The ever popular crocodiles have temperature dependent sex-determiners, with a narrow "sweet spot" to get a 50/50 male/female clutch (5). The green spoonworm determines it's sex as a larvae, if it lands on the seafloor it becomes female, if it lands on a female it becomes male and lives as a parasite inside of her.

Until further research, develop some form of environmental conditions that can be met naturally, or generated by intelligent octopi for what you want this question to answer.

(1) Coe, W. R. (1944). Sexual differentiation in mollusks. II. Gastropods, amphineurans, scaphopods, and cephalopods. The Quarterly Review of Biology, 19(2), 85-97.

(2) Mercer, M. C., Misra, R. K., & Hurley, G. V. (1980). Sex determination of the ommastrephid squid Illex illecebrosus using beak morphometries. Canadian Journal of Fisheries and Aquatic Sciences, 37(2), 283-286.

(3) Rider, C. V., Gorr, T. A., Olmstead, A. W., Wasilak, B. A., & LeBlanc, G. A. (2005). Stress signaling: coregulation of hemoglobin and male sex determination through a terpenoid signaling pathway in a crustacean. Journal of experimental biology, 208(1), 15-23.

(4)Kato, Yasuhiko; Kobayashi, Kaoru; Watanabe, Hajime; Iguchi, Taisen (2011). "Environmental Sex Determination in the Branchiopod Crustacean Daphnia magna: Deep Conservation of a Doublesex Gene in the Sex-Determining Pathway". PLoS Genetics. 7 (3): 1–12. doi:10.1371/journal.pgen.1001345. PMC 3063754 Freely accessible. PMID 21455482.

(5) Janzen, Fredric J.; Krenz, James G. (2004). "Phylogenetics: which was first, TSD or GSD?". In Nicole Valenzuela; Valentine A. Lance. Temperature Dependent Sex Determination in Vertebrates (PDF). Smithsonian Institution. pp. 121–130. ISBN 978-1-58834-203-4.


Are there any examples of proteins with no or minimal sequence identity, but highly similar structure? What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?

If none are known, what computational tools might be used to search for such examples?

This paper published last year, address the answer for your question, about computational methods, they mention 3 principal algorithms for structural alignment
of proteins:

Structural alignment directly at the level of C atoms.
The second class of algorithms first uses the SSEs (Secondary Structure Elements) to carry out an approximate alignment, and then uses the C atoms.
The final class of algorithms uses geometric hashing.

And finally you could find useful this paper for an example of this kind of analysis with structural analyses of metabolic families.

References:

 Venkateswaran JG, Song B, Kahveci T, Jermaine C. TRIAL: a tool for finding distant structural similarities. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 8: 819–31.
 Marsden RL, Ranea JAG, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, et al.. 2006. Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philosophical transactions of the Royal Society of London Series B, Biological sciences 361: 425–40.


ELI5 what is true breeding? In "Variation under Domestication", Darwin makes several references to the concept of true breeding:

  They believe that every race which breeds true, let the distinctive characters be ever so slight, has had its wild prototype.

And:

  I crossed some white fantails, which breed very true, with some black barbs.

Before diving into the book, I never heard of the term, so I looked it up and found this definition in the Wikipedia article on Zygosity:

  A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes. The cell or organism in question is called a homozygote. True breeding organisms are always homozygous for the traits that are to be held constant.

But this is rather technical and it's not the kind of explanation I would give to a child.

What is true breeding, in simple terms? When is breeding not considered true?

In the context of Darwin's Variation under Domestication, "true breeding" is a phenotypic characteristic rather than a genetic one.  True-breeding organisms produce offspring that are identical to themselves, concerning some trait -- i.e. white fantails, when bred with white fantails, produce characteristically white offspring.  For diploid organisms, true-breeding typically implies that the parents are homozygous at the locus conferring the trait of interest.


What causes the variable/conserved structure in the 16S rRNA gene? See the image below for a visual representation of the 16S rRNA gene. It is composed of conserved and variable regions however I can't see to find a reasoning for why this is the case

Thanks

The structure of ribosomal RNAs involves double-helical stems, on the one hand, and loops or junctions, on the other. A comparison of small-subunit rRNAs of different sizes shows that, despite increasing complexity, a basic core structure exists. The is illustrated in the diagram below is adapted from Brimacombe, Trends in Biochemical Sciences (June 1984) 273–277.

From a structural (3D) point of view, both stems and loops are conserved, but as far as the nucleotide sequence is concerned, the helical stems are less conserved than the loops and junctions. This would appear to be because the main function of the helices is structural — so an A–U base pair can generally be replaced by a G–C (or U–A or C–G) base pair, whereas the loops are involved in interacting with various species — tRNA, initiation, elongation and termination factors, ribosomal proteins and the 50S subunit — which may involve more specific bases.

The main thrust of research on ribosomal structure (and what has interested me) is the relation of structure to function, but Carl Woese realized that, because of its ubiquity, rRNA was an excellent molecule for phylogenetic studies. Although, if one compares, say, mitochondrial ribosomes with mammalian ribosomes the sequence conservation is small, with different strains of bacteria it is much larger. This has led microbiologists interested in bacterial phylogeny to analyse the best regions for comparison in 16S rRNA, in terms of their degree of conservation, resulting in the concept of variable and conserved regions in the diagram in the question. (I find this terminology rather unfortunate because of its similarity to the totally unrelated immunoglobulins.) It appears that this is due to van de Peer et al. (1996), from whose paper I reproduce the figure below.

[Figure 3 of van de Peer *et al.*The most variable positions are in red, the most conserved in blue. Absolutely conserved positions are indicated in purple. Nucleotides present in E.coli but absent in >75% of the bacterial sequences considered are indicated in pink.]


What are the structural factors affect enzyme's Km? Is there any rules (should not be exact), to estimate the kinetic changes in an enzyme if I did any mutation on it?

If I cannot estimate the new kinetic values, is it possible at least to clarify or suggest any explanation for the new kinetic after mutating an enzyme depending on the point mutation I did on it?

So I want to explain the changes in the kinetic parameters (Km / Vmax) in my enzyme after mutating it, maybe depending on the 3D structure? or the charge/size of the new amino acids? Or any other factors I may use to suggest anything logical how and why those changes happened to my enzyme after mutating it?

I need that for my dissertation and I am still totally lost, any ideas (with the proper references) will be great. I really appreciate any help.

Computationally, using molecular dynamics (MD) simulations, it is difficult but not impossible, to quantitatively reproduce the effect of mutations on ligand-binding free energies, and activation and reaction free energies of enzymatic reactions. The most useful MD simulation methods for such a purpose are: free energy perturbation (FEP), linear interaction energy (LIE), linear response approximation (LRA), empirical valence bond EVB), and their combinations---developed by Arieh Warshel (The Nobel Prize in Chemistry 2013).

Mechanistically, mutations affect short- (van der Waals and electrostatic) and long-range (electrostatic) interactions with the surrounding environment, which comprises the rest of the protein and the solvent. Note that free energy is an attribute of an ensemble, not of a single 3D structure---which is why exploring a single structure of the mutated protein is unlikely to reveal the effect of the mutation qualitatively, not to mention quantitatively. One has to sample the conformational space of the protein---and MD simulation is the most efficient computational technique for such a sampling.

In summary, the effects are simple, but the system is extremely complex . . .

Klvana et al. (2012) Biochemistry 51: 8829-8843.

Klvana et al. (2016) J. Phys. Chem. B 120: 13017-13030.


If you have water on you, does it *actually* cool or down, or do you just *feel* cold? I'm sure many people have noticed after getting out of a shower or out of a swimming pool that moving air makes them feel colder. It seems like one way to beat the summer heat is with water and also moving air. But, does having water on your body actually cool you off more with moving air, or is that simply what it feels like because water cools differently than air?

When your wet skin experiences air flow over it, water will evaporate. Evaporation causes cooling, as energy is transferred from the remaining water molecules to the ones that evaporate - energy in water molecules is being experienced as heat. Less energy -> less heat -> sensation of cooling.

This is why you feel cold, as opposed to when you stay submerged in the pool, or your skin is dry and it is just air movement - no evaporation is taking place.


Alternative to distilled water for pH test I am looking to test soil pH in a remote location. The test results don't need to be perfectly precise, and a pH test strip should provide sufficient accuracy. However generally this kind of testing uses boiled distilled water - and in this location it will be very difficult to buy distilled water.

The location is off grid, and getting specialized equipment to the location is not an option. (This is for field experimentation with farmers in rural Africa)

The process I have seen used for this is:

Add 1 part boiled distilled water and 1part soil by volume, in a clean container
stir and leave to settle.
Test the water pH with a pH test strip

Would it be possible to use boiled rain water for this process, or would this be likely to contain impurities which would interfere with the test results?

If there are likely to be impurities but there are approaches that can mitigate for them, please explain.

Rainwater might not be the best option.

Rain water is naturally acidic due to the reaction of CO2 forming some weak carbonic acid [see here for explanation].

 Source: Wikipedia

As a result, pH of "pure" rainwater is usually between 5-6; usually around pH 5.6. See here.

  Most rainwater has a pH of 5.6 to 5.8, simply due to the pressence of carbonic acid (H2CO3).

Presence of any sulfur or nitrogen oxides in the air (perhaps from burning coal plants or city traffic from 100s of km away) would lead to rain becoming even more acidic. From environment.co.za:

  Sulphur dioxide reacts with water vapour and sunlight to form sulphuric acid. Likewise NOX form nitric acid in the air. These reactions takes hours, or even days, during which polluted air may move hundreds of kilometres. Thus acid rain can fall far from the source of pollution.


Identify fuzzy black quarter sized spider with orange on abdomen, in Minnesota Found this spider on my car in Minnesota near St Paul (USA). Total size including the legs (end of rear leg to end of front leg in picture) is probably about the size of a quarter.

This appears to be some species of jumping spider (family Salticidae).

  [Note that] All jumping spiders have four pairs of eyes, with the anterior median pair being particularly large.

In particular, I believe your specimen is Phidippus audax (Bold Jumper). Specifically, I believe yours is a subadult bryantae variant of this species.

 Source: David Hill 2014

From Wikipedia:

  The average size of adults ranges from roughly 13–20 millimetres (0.51–0.79 in) in length. They are typically black with a pattern of spots and stripes on their abdomen and legs. Often these spots are orange-tinted in juveniles, turning white as the spider matures.

Your specimen shares the orange abdomen with connected black "splotches" that leave an orange triangular dot in the middle. Also, notice your specimen has two grey lines on the posterior cephalothorax as well as black/white striped legs. Finally, 20mm is close to the size of an American quarter (~24 mm).

If you get a good look at the front of your specimen, you'll likely see that the chelicerae are an iridescent/metallic blue or green (a tell tale sign of this species and genus).

 Source: David Hill 2014

 More typical coloration (L) vs. bryantae variant (R). [Source: David Hill 2014]

P. audax tends to prefer relatively open areas to hunt and is commonly found in common in fields and grasslands, as well as on fences, exterior walls, and gardens. Finding one on your car, therefore, would not be so strange, especially given that they can jump 10-50x their own body length (Ruppert et al., 2004).

Phidippus contains some of the larger species of jumping spiders in the family, and it is almost exclusively a North American genus.

Specifically, P. audax is common in southeastern Canada, eastern and central United States and parts of northern Central America, and it has become increasingly common farther West.

Citation:

Ruppert, E.E., Fox, R.S., and Barnes, R.D. (2004). Invertebrate Zoology (7 ed.). Brooks / Cole. pp. 571–584


Are bananas C3, C4, or CAM plants? Are bananas C3, C4, or CAM plants? I have been researching for some time and cannot find the answer.

First of all, we have to think about the ecosystem in which banana exist. Obviously, the banana is in a rain forest. Rain forests are a very interesting ecosystem with lots of species. The climate is really hot and the atmosphere has high humidity.

Banana is definitely not CAM plant, because this kind of photosynthesis has usually cactuses and succulents. CAM plants usually have closed stromas during the day and open at night to protect from possible loss of water, carbon dioxide. This type of photosynthesis doesn't suite into the rain forest.

C4 plants are well known for Kranz anatomy of a leaf. They have special sheets to do secondary fixation of carbon dioxide. So according to this web I personally believe that banana is not C4 plant.

So according to this article the banana has C3 photosynthesis.


Method to recognize the age of a firebug from the pattern on its back Can I recognize the age of a firebug from the pattern on its back?

If yes, what pattern shows what age/stage?

Below is what I extrapolated from Wikipedia, but is there a more precise scale with more steps? (I could not find more than this with google).

Nymph: Adults:

The answer is more or less yes. Normally Firebugs (Pyrrhocoris apterus) go through 5 nymph instar stages (as do most Hemiptera), where they resemble the adults more and more as they grow. Only adults are winged and have have functional reproductive organs. This type of metamorphosis is called hemimetabolous or simple metamorphosis (in contrast to Holometabolism or complete metamorphosis). However, I cannot find a good overview of the instar stages of Firebugs to link to.

A generic overview of Heteroptera (True Bugs) can bee seen here
(from www.amnh.org/learn/biodiversity_counts):

This picture shows (at least) three instars + adults of Pyrrhocoris apterus (from http://www.projectnoah.org/spottings/17248017). The large nymph with 3 dots along the midline is the final 5th instar nymph:

However, due to hormonal disruptions there have been cases with even more nymph stages (6th and 7th instars with adult characteristics), but this is under unnatural laboratory conditions (e.g. Slama & Williams 1965 and Konopova et al. 2011). Konopova et al (2011) also has pictures of instar stages 4 & 5 (along with gene knowdown versions).


What kind of arthropod/animal is this? Can anyone identify this strange creature? I live in a very urban part of Montreal, Canada. It wasn't moving (seemed dead) and although the image is huge, it wasn't as big as it seems (a couple of centimeters).

It's a type of centipede.

Based on the long legs, I would bet on something like that:
http://en.wikipedia.org/wiki/Scutigera_coleoptrata

Or at least a Scutigeromorpha http://en.wikipedia.org/wiki/Scutigeromorpha#Scutigeromorpha


Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating) Background

Quoting from Gillespie's book

  The level of inbreeding is measured by the inbreeding coefficient, $F_I$, which is the probability that two alleles in an individual are identity by descent.

The two possible alleles are $A_1$ and $A_2$ and their frequencies are $p$ and $q=1-p$, respectively. Gillespie goes on and give the expected genotype frequencies given $p$ (and $q$) and $F_I$

$$
\begin{array}{r|c|c|c}
Genotype & A_1A_1 & A_1A_2 & A_2A_2 \\
\hline
Frequency & p^2(1-F_I)+pF_I & 2pq(1-F_I) & q^2(1-F_I)+qF_I \\
\end{array}
$$

Question

Can you please help me to understand why those are the appropriate genotype frequencies?

Example of what is unclear to me

By the definition of $F_I$, I was expecting that the frequency of `$A_1A_2$ (and $A_2A_1$) would be $(1-F_I)$, that is the frequency (or probability) that two alleles in an individual are not identical by descent. I feel like the definition given above is wrong. Should it rather be something like the weight for sampling like individuals? That is if there were only two possible mates, one that is $A_1A_1$ and one that is either $A_1A_2$ or $A_2A_2$, then the probability for a $A_1A_1$ individual to mate with the other $A_1A_1$ is $F_I$.

You're confused because you're failing to distinguish between 'identical' and 'identical by descent'. Some pairs of alleles would still be identical even in the absence of inbreeding.

We model the inbreeding by classifying allele pairs as IDB - always homozygous - or not IDB -  distributed according to Hardy Weinberg. The frequency of a pair of alleles being A1,A2 (or A2,A1) is thus the frequency under H.W.E. (2pq) multiplied by the chance of them NOT being IBD (1-FI). And conversely, a pair can be homozygous and not IBD - at frequency p 2(1-FI), or because they are IBD - at frequency p F I.


Michaelis-Menten equation; how to find the constants from enzyme activity experimental results? I was wondering what the constants in the Michaelis-Menten equation actually mean in experimental data of enzymes. How do I process the data to find Km and Kcat?

I did an experiment on catalase and its breakdown of hydrogen peroxide. I used a gas pressure sensor to track how much O2 was produced from the reaction over time. The following is an example raw plot of what I found. Point 0 is when I put the substrate and the reaction started (so I think I can call this the "maximum amount of substrate concentration" - in the Michaelis-Menten plot, it should be on the far right side.)

To find the speed of the reaction at each point, I thought of finding the slopes between each point, which basically equates to finding the derivative. Since the raw plot I found looks like a logarithm function, so I would predict that the derivative would look like a hyperbola (with x > 0). Indeed, this is the (crude) graph of the "derivative" of the previous plot, which looks like a hyperbola:

I believe that Kmax is the y-value of the first point in this graph - the initial velocity when the substrate is mixed with the enzyme. The substrate concentration is at highest at time 0, and the substrate concentration decreases as time increases.

So I thought, to make the Michaelis-Menten graph, I should flip the x-axis so that the substrate concentration is increasing along the x-axis. Yet, my problem was that if I do this, then the graph ends up not looking like the Michaelis curve...

What I would have wanted to find is the Michaelis-Menten curve, so that I can also derive the Km and Kcat values. Does anyone know how to do this? Or am I doing my steps wrong? Thank you very much for helping me!

Michaelis-Menten Curve:

Have you got data for different concentrations of hydrogen peroxode?

If so you should choose a time point that falls on the linear part of your time graph. And plot the rate at that time point for each substrate concentration.

That will give you a MM curve where you can calculate the values you desire. You cannot calculate them with just your time data that you have provided.


Do human-ape hybrids exist? Since humans and apes share up to 99% of their DNA, can they interbreed? For example, a horse and a donkey seem to be just as distantly related and produce offspring. Mules, however, are sterile. Would ape-human interbreds be sterile?

Although this question sounds easy to answer in the first place, it is not. The main problem between humans and the apes we are most closely related to is that we have 46 chromosomes, while the apes all have 48. At some point in the evolution of the humans the ancestral chromosomes 2 and 4 fused together to form our chromosome 2, leaving us with only 46 chromosomes (see reference 1).

This makes offsprings much more complicated, but not completely impossible. A good example for this are crosses between donkey and horses (donkeys have 64 chromosomes, horses 62) to get mules (male donkey crossed with a female horse) or hinnys (male horse crossed with a female donkey) which subsequently have 63 chromosomes and are infertile. There are even crosses possible between horses and zebras which even differ wider. Zebras have between 32 and 46 chromosomes (depending on the species) but still zebroids are possible. See reference 2 for some more details.

So far there has been no successfull attempt to produce such hybrids, although there have been some attempts to make them. Some information can be found in reference 3.

Besides this problems (which are also due to ethical restrictions), there is a study available that at least humans and chimpanzees interbred for at least 1.2 million years after diverging and still produced fertile off-springs. See references 4 (for a summary) and 5 (original paper) for details.

Based on this evidence, I would say it is possible for humans and apes to produces off-springs, however, this is relatively unlikely and they will probably be infertile.

References:

Origin of human chromosome 2: an ancestral telomere-telomere fusion.
The chromosomes of two horse x zebra hybrids; E. cahallus x E.
grevyi and E. hurchelli
Blasts from the past: The Soviet ape-man scandal
Human Ancestors May Have Interbred With Chimpanzees
Genetic evidence for complex speciation of humans and chimpanzees


Is it true that cats can drink sea (salted) water? Found somewhere in the Net, that cats can drink sea (salted) water.

This fact seems to me as being urban legend, not true (because the purpose of water in body apparently implies it should be clear).

What is true and how to explain?

Since cats are well adapted to dry environments, the question has some plausibility to it.

The book "Mineral Tolerance of Animals" suggests that cats may be able to tolerate slightly more salt in their diet than dogs (1.37 g salt/kg body weight for cats, vs. 0.64 for dogs).  However, these represent concentrations that were shown to be safe, not the maximum they could potentially tolerate. The reference in the book is Yu et al., 1997, and though the actual reference is not available in the Google Books version I believe it must be The minimum sodium requirement of growing kittens defined on the basis of plasma aldosterone concentration, so the goal was to identify minimum rather than maximum levels.

The ocean is about 3.5% salt.  The 1.37 value for cats came from kittens eating a diet that was about 2.5% salt, but another note in the book says that cats can safely eat a diet that is 3.8% salt, though they don't like it. I can't find the original reference ("Berger, 1979") for this claim, but I am pretty sure that this was with ad libitum water so they could flush out extra salt.  If so, cats would not be able to tolerate sea water unless they had another source of water as well.

It's often said that wild cats can get most of their water needs from their prey's blood.  It's also sometimes said (incorrectly) that the salt concentration of blood is like that of seawater; this is not true (blood is more like 1% or less NaCl) but it may be the source of the statement.


Is epilepsy more heritable from maternal side? I am thinking if paternal or maternal genetic line is the risk factor.
Mitochondrial DNA is coming from maternal line.
I do not know the pathogenesis of epilepsy so well that I could answer my question.

Is epilepsy more heritable from the maternal side?

Epilepsy is a neurological disorder characterized by hypersynchronous discharge of neurons .i.e abnormal electrical activity in the brain. Epileptic seizures caused primarily due to i) inhibition of inhibitory neurotransmitter systems such GABA neurotransmitters or ii) Enhancement of excitatory neurotransmitter systems such as nAchR. These conditions arise due to head injury, trauma and genetic factors. But there is no evidence as of now regarding Mitochondrial DNA taking part in inhibitory and excitatory systems. so, epileptic seizures are not specific in inheriting from any side (Maternal or paternal side) as far as pathophysiology of epilepsy is concerned.


Can you make sperm and eggs from the same person using in vitro gametogenesis? In a recent popular science article there is a discussion of the potential disruptive technologies that could become available with in vitro gametogenesis (IVG). Using skin cells you will be able to create either sperm or eggs. Thus, using stolen cells from Brad Pitt (simpler than getting his sperm) will allow a woman to have a nonconsensual child of him. What is not mentioned in the article and thus my question: Does this technique currently allow, (at least in mice), to make sperm from a female and eggs from a male? If that is the case, what will be the result of fertilizing sperm and egg from the same individual: a clone, a genetic "sibling" (not an identical twin), or neither of them?

At present (early 2017) the answer is No.

The trick to make spermatid like cells (ie they are not real sperm cells and need to be injected into an oocyte to accomplish fertilization) from ES and iPS in a dish was just achieved last year http://www.sciencemag.org/news/2016/02/new-method-grows-sperm-dish

The trick to make oocyctes from stem cells is not as complete and still requires an lab grown ovary to complete the process. http://www.sciencemag.org/news/2016/10/mouse-egg-cells-made-entirely-lab-give-rise-healthy-offspring.

The methods above still use ES cell of the appropriate gender. Female ES cells to make oocytes. Male ES cells to make sperm.  No info on female ES cells being driven to make sperm or even spermatid like cells.

That said... we have this paper http://news.nationalgeographic.com/news/2004/04/0421_040421_whoneedsmales_2.html, where a mouse is genetically engineered to produce oocytes that have imprinting patterns similar to a sperm. This genetically modified oocyte is then forced to fuse with a normal oocyte. Success rate was very low. 371 fused oocytes, 10 live births, 1 surviving to adulthood.