E. Coli growth inhibited in Powdered Honey I ran into problem with my method validation since the E. Coli that I've spiked into my Honey Powder sample can't grow in the media. The media I've used is Merck CCA (Chromogenic Coliform Agar). I've also used the MPN method (3 tubes) using LST Broth with the same result.

Really appreciate if someone Can  lead me into why would this happen and give any suggestion on how to troubleshoot this?

Regards.

If I understood correctly you want to grow E. coli in the presence of honey, right?

This migth be the problem as honey inhibits bacterial grow. See here. Therefore, it also doesn't matter which medium you are using.


Negative spikes in neurons I'm new to neuroscience research and came across a term called negative spikes (sometimes also used in conjunction with terms biphasic spikes or positive-negative spikes), but could not find what it meant from scientific papers. Can a spike occur in a negative direction (hyperpolarization from the resting potential first, followed by depolarization) or does this term mean something else entirely?

Intracellular recordings of action potentials always show the same format with which you are familiar. There is polarisation which the stimulus reduces, a threshold is reached, there is a positive spike, then repolarisation, hyperpolarisation, a refractory period an a return to the baseline polarisation.

The term "negative spike" applies to extracellular recordings. These measure the potential between a point close to but outside the cell and a reference point. The inflow of cations into the cell causes a drop in extracellular potential, which appears as a negative spike in the recording.


Why is ab initio protein secondary structure prediction less reliable than alternatives? To predict secondary structure of proteins three types of Algorithms are used Ab initio, homology based and neural networks. Among these neural networks prove to be more accurate and give good results as compared to ab initio, especially when multiple sequence alignment and neural networks are combined the accuracy of results reach almost to 75%. My query is that what actually lacks in ab initio methods which reduced their sensitivity and specificity and lacks the ability to predict reliable secondary structures? (Some of ab initio based softwares that I have studied are Chau Fasman and GOR Method)

Preamble

In the comments @CMosychuk linked the most comprehensive text on ab initio I have seen this side of the year 2000 (Lee et al., 2009). It agrees that you've raised a good point.

  It is important to acknowledge that ab initio prediction methods
  solely based on the physicochemical principles of interaction are
  currently far behind, in terms of their modelling speed and accuracy,
  compared with the methods utilizing bioinfor- matics and
  knowledge-based information.

This is a good real life example of different philosophical approaches of inductive reasoning and deductive reasoning (AKA top-down logic) behaving as one might expect. Each specific software has it's own problems and advantages and may not fit into the below categories. I'll grossly simplify each approach in crude categories and then broadly explain why errors crop up in them.

Below, we'll discuss ab initio and why it goes wrong and then the alternatives including why they're currently generally more reliable. We'll round up with how ab initio is probably going to become realistically involved in reliable protein predictions.

Ab intio.

Figure showing the broad pipeline difference between ab initio and homology modelling.Nara Institute of Science and Technology.

Ab initio often works on the premise that physical laws can be applied universally in biology. As you are most probably aware, biochemistry is far messier than chemistry and often those physical laws appear bent if not completely broken. The goal of ab initio is therefore to combine physical properties with some fudge factors to account for a complex system. Due to the complexity of the system never being fully modelled, ab initio predictions are limited to what your input is. There are also limitations pointed out in the 2009 article:

potential energy functions.
conformational search engines
model selection scheme

What you can see now is that ab initio is missing something that the others have: biological experimental empiricism. Without that inductive reasoning ab initio modelling is very vulnerable to assuming far too much and oversimplifying the system (This xkcd springs to mind).

Although perfect ab initio prediction is the "Holy Grail" of protein structure prediction, currently if there is homology which provides an experimentally known structure then that is often more reliable.

Ab initio is not completely without merit. For relatively short proteins (100 residues) the accuracy has improved over the last decade (Lee et al., 2009). From the above mentioned article:

  ...the physics-based atomic potentials have proven to be useful in
  refining the detailed packing of the side chain atoms and the peptide
  backbones.

Homology modelling.

This type of modelling is a safe bet provided that the MSA is available and reliable. The premise here is that if two proteins look similar enough at a sequence level, and you know the structure of one, then probably there is structural conservation as well. The problem is that obviously, those small changes in sequence, or other contextual differences like post translational modifications, localised pH differences etc. might mean that the protein folds differently.

Machine Learning.

Neural networks are a form of machine learning. Conceptually, these use the same assumptions as homology modelling, but on a larger more sophisticated scale (not necessarily an advantage). A good example of “machine learning” winning out in terms of homology clustering and secondary structure prediction is that of HHpred. An algorithm will make subsets of "if" statements. If a protein has a certain combination of "ifs" and "nots" then it's safe to assume other proteins with the same "ifs" and "nots" have similar structures.

You need to know a lot of information about the dataset that you put in, and also one needs to know which of that information is relevant. If these conditions aren't thoroughly complied with the categorisation results will just be amplified errors, arbitrary categorisations, missing categories, or a combination of those three.

It's worth pointing out at this point that most modern secondary structure predictors use a combination of homology and machine learning.

A reasonable ab initio approach.

More recently iterative optimisation based on vague experimental data has become the standard practice shifting ab initio from a top down approach to something more inductive. Kulic et al., 2012 is an interesting example of such a modern holistic approach. It involves an iterative optimisation of ab initio protein structures based on experimentally derived structures.

Another excerpt from the 2009 article.

  Thus, developing composite methods using both knowledge-based and
  physics-based energy terms may represent a promising approach to the
  problem of ab initio modelling.


How do chromosome pairs get "paired up" for protein synthesis? If my understanding is correct, during interphase a normal human cell will have 46 chromosomes scattered about in the cell nucleus. These chromosomes can be thought of as pairs: there are two copies of "chromosome 1", one from mom and one from dad. Same goes for chromosome 2, chromosome 3, ... chromosome 22. Although we think of these as coming in pairs, are they actually attached or paired up in some way?

At some point, protein synthesis will take place via transcription. What I'm having trouble understanding is how and when the above pairing takes place. Does transcription occur independently for each of the 46 chromosomes? I don't think this is the case, because in my head I imagine that we will only get one set of proteins from the pair of each chromosome. Also, I'm unclear as to how dominant/recessive genes can come into play unless protein synthesis occurs as a function of both pairs of chromosomes.

I hope this is clear enough. Thanks.

Although we think of these as coming in pairs, are they actually attached or paired up in some way?

Chromosomes only pair up during metaphase I of meiosis. And meiosis only occurs during the production of gametes (sperm and oocytes). Say Chr1 from mom pairs up with Chr1 from dad. http://media.web.britannica.com/eb-media/76/94976-004-7D0416E7.gif

Mitosis is what happens when somatic cells (say in your toes) replicate.  Chromosome (inherited from your mom and dad) do not pair up in mitosis. Instead each chromosome is replicated

You are probably confusing chromosomes pairs (one copy from mom and another from dad) sitting side by side... undergoing chromatid crossover... with sister chromatids (ie the same chromosome which has been duplicated, so each daughter cell can have its own copy.) This forms the X shape that you think off when imagining a chromosome.

Transcription occurs on all 46 chromosomes. Aside from situations where the gene is controlled by parental epigenetics... both the paternal and maternal copy of the gene is active.

As for  recessive/dominant allele... it has more to do with the function of the protein. If the protein is produced by one allele in sufficient to give a normal phenotype, then the allele is dominant. A dominant negative tends to occur when the mutant allele codes for a mutant protein that can interfere with the normal function of the protein that is encoded. A common example is that the protein works as a pair. And is one member of that pair is mutated, the entire complex is non-functional.


How can I make legal mature female Cannabis plants to Flower in home during March (springtime)? In December 2019 I purchased 4 Cannabis seeds Legally in Canada.Two of my plants are now about 100 cm tall. I am using wide-spectrum LED grow lights and have fertilized them both. I started with 16 hours light per day and now have cut back to about 12 hours per day.I was told that these seeds were not auto-flowering.These seeds were from Tweed and were labeled "Baker Street Indica". The leaves are all healthy and dark green. Now I would like to stimulate flowering. As our days are getting longer I want to trick the plants into its Fall/Autumn flowering cycle. Any good ideas ?

Keep the plants in dark night for 12 h , 13h then 14h per night.
Keep the plants well fertilized with lower N , higher P and K.
Keep well watered with a dry period in between watering.
Keep the plants protected until the plants are ready to flower.


Protein inhibitory process I usually find substances that activates proteins, like ApoA-I, but I don't find substances that inhibit it.

So in an experimental design, could I consider the absence of a drug that directly acts on the increase of a protein could be considered an inhibitory process?

No, absence of an stimulating substance is not appropriate to consider as inhibition.

To see why, consider a situation where there are two such substances, substance A and substance B, which can both stimulate protein P (many such relations exist).  If you add only substance B, then protein P will be stimulated. Since P is being stimulated in this case, it would thus not be reasonable to describe the protein being inhibited by the lack of substance A.


Is it possible to have life in vacuum? I just got struck by curiosity now: Intuition says no, but I've never had confirmation of it.

As @terdon comments, dormant organisms can survive in vacuum. This includes lichens, bacteria, and even an animal: the ever-amazing and adorable tardigrade (Jönnson et al 2008). In 2006, tardigrades survived exposure to the vacuum of outer space with no appreciable difference in mortality compared to controls.

Tardigrade Hypsibius dujardini, a different genus than the ones sent into space, but probably equally hardy. Photo by Bob Goldstein & Vicky Madden (CC by-nc-ca via Goldstein lab - tardigrades on flickr).

Jönsson, K. I. et al (2008). Tardigrades survive exposure to space in low Earth orbit. Current Biology 18(17):R729–R731


What are "feeder cells"? What exactly are "feeder cells"? A paper I'm reading says they harvested the cells and then plated them onto feeder cells. What is the purpose? Is in order to promote growth?

Cultures of growth-arrested feeder cells have been used for years to promote cell proliferation, particularly with low-density inocula. Basically, feeder cells consist in a layer of cells unable to divide, which provides extracellular secretions to help another cell to proliferate.

From this paper's abstract:
Feeder Layer Cell Actions and Applications


Can suppression of the immune system help cure chronic diseases? I am not a biologist, but recently while reading an article on Scholarpedia about self-organization I encountered a fascinating biological observation concerning immune response to infections.  To quote the article:

  Whether the resulting patterns are stable or oscillating depends on the relation of the time constants. If the antagonistic reaction has a longer time constant than the self-enhancing reaction, oscillations or burst-like activations will occur. An example is the time course of an infection: The infection with few viruses could be sufficient to trigger a sickness since the viruses replicate themselves (self-enhancement). The antagonistic reaction, mediated by the immune system, is much slower. It takes a day to become sick, but a week to become healthy again. (What appears on a first inspection as a disadvantage is in fact a good strategy. If the immune system would be much faster, an equilibrium between virus production and virus removal would be established. After a single infection we would fight for the rest of our life against the virus. However, due to the burst mode, we become sick for a short while but the virus is subsequently completely eliminated).

Since the quote may be hard to parse out of context, I'll recapitulate: The writer is asserting that the immune system's response to infections is slower than might be physically possible because such slowness actually makes the response more effective.  By waiting a few days, the patient is sick for longer than they might be happy about, but when the infection goes away, it's gone for good.  If the immune system responded immediately to an infection, it might result in a low-level infection that persists indefinitely.

This makes me wonder: For chronic diseases, is the reason they are chronic related to the time scale of the infection vs. that of the immune system's response?  Could such diseases possibly be cured by suppressing the immune system for a time so as to get the "burst" effect alluded to in the quote above?

No, this wouldn't happen. The logic of your proposition assumes that chronic diseases are caused by the strength of the immune response being insufficient to kill off the virus, resulting in a long-term equilibrium between the amount of virus particles produced and the amount of virus particles killed.

In reality, this is not how chronic diseases work. Only a small amount of chronic diseases are caused by viruses. There are many which have other causes, not all of which can be defended against by the immune system - e.g. chronic depression is not curable by immune response.

But even if we focus on chronic virus infections such as herpes simplex, they are not sustained by the mechanism you describe. They happen due to the fact that our immune system simply does not know how to get them out of their new home within our body, they are just that good at hiding during latency. So even if you could cause a strong immune response all at once, it wouldn't kill all viruses at once.

Even if we have viruses whose serum presence depends on a constant growth vs. destruction dynamic (I don't know if these exist at all), an overly strong immune response won't be that good for the human host. Inflammation is a dangerous state, most of the unpleasant feeling you get when you are sick is not due to the virus itself but due to your own immune response, which causes the fever, muscle pains etc. associated with many acute infectious diseases. If we were to ramp this up, you'd probably get a fever high enough to cook you alive, or some other undesirable effects.

On a side note, I also doubt the author's argument which suggests that long-ish convalescence times evolved because shorter ones would leave the system in an undesirable equilibrium. Sure, an alternative reality is thinkable where the innate and adaptive responses described by Chris occur much stronger at the beginning, leading to steeper curves and shorter healing times. But the simpler explanation for that is that 1) our immune system is not perfect, and it evolved to the highest healing speed it could achieve, and 2) an immune system with higher acceleration would have been way too costly in terms of resources available to the body. An evolutionary advantage in having a low-acceleration immune system is a strong assumption for which I see no support, especially considering that the residual immunity provided by the adaptive immune system would prevent the dynamic equilibrium suggested in your quote.


How do I get the current "camera position" in PyMol so I can reuse it in scripts? I have a few protein models I want to take pictures of with various ligands bound.  It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same view is with zoom resi. 64, 152, 150 or the like, which isn't framed that well.

How can I manually position the viewport, capture it's parameters, and repeat it in the script?

I have found get_view, e.g.

PyMOL>get_view
### cut below here and paste into script ###
set_view (\
     0.590180993,    0.670941532,    0.448923886,\
    -0.507570565,    0.740831316,   -0.439937204,\
    -0.627747774,    0.031782545,    0.777776182,\
     0.000000000,    0.000000000, -417.497009277,\
     0.741809845,    7.078243256,   16.473480225,\
   329.157806396,  505.836212158,  -20.000000000 )
### cut above here and paste into script ###

but this doesn't work in a .py script, where I need to modify it to cmd.set_view(...), as it complains it wants just (or up to 5) arguments, not 18.  The wiki is vague about it, it just says

  PYMOL API

cmd.set_view(string-or-sequence view)


Systems identification in small neural network When analyzing data from cortex, we often try to understand what each neuron does in terms of its inputs from other neurons - a specific kind of a systems identification strategy. Most current approaches use generalized linear models for that purpose (Review article).

For very small systems like the worm c.elegans it must be possible to record from all neurons at the same time, at least optically. How well can we understand the output of each neuron based on its inputs in such simple systems? What are the best databases to ask such questions?

The reason I am asking this question now is because the human brain project that just got roughly a billion dollars in funding basically needs such data for every cell in the whole brain.

For very small systems like the worm c.elegans it must be possible to record from all neurons at the same time, at least optically.

While it is true that whole organism optical recording is technically possible in C. elegans, I'm not aware of any published work  where all neurons were identified and recorded from simultaneously and then combined with connectivity data in a systematic way.

I should note, that this isn't limited to C. elegans. Florian Engert's lab has published whole-organism recordings from zebrafish as well. At the moment, though, there are still technical challenges to work out before we get the input-output relationships you desire on a whole organism level. First off, the recordings aren't truly simultaneous, in the sense that it still takes time to build up 3D images from z-stacks. Second, the image processing to label neurons is not yet robust.  And finally, the most popular optical indicators  are based on calcium levels and thus provide only a proxy for membrane potential and furthermore they have limitations in time resolution, range and accuracy.

The field, however, is progressing rapidly and I suspect that these challenges will be overcome in the next few years.

  What are the best databases to ask such questions?

There are no database yet for C. elegans neural activity,  likely because the number of groups publishing optical recordings in C. elegans is still fairly small. But as more labs pick up the technique, I think the value of a database will become more obvious to the community and the OpenWorm project is providing some well-needed leadership in this area.

Finally, I should point out that in the end we may find that neural activity and connectivity provide only one part of the story. It is likely that in C. elegans neuromodulators and other "unwired" connections between neurons could play very important roles as well.


Amount of reverse transcriptase in µg or mM for qRT-PCR I am trying to calculate a titration amount for a molecule which I would like to use in my PCR samples. Different molecules have different densities so I would like to calculate the appropriate density of the titrated molecule. How many micrograms or microMolars of reverse transcriptase are used in qRT_PCR kits?

Reverse transcriptase (and most other commercial enzymes these days) is made recombinantly, then purified to varying degrees, using varying methods, among different suppliers (and sometimes between different lots from the same supplier). Some enzymes actually have multiple functional units combined in a complex, others may require a post-translation activation step like phosphorylation by a separate kinase in order to be fully functional. All of these variables can yield preparations of different molar concentration, but very similar activity. Therefore, companies like New England Biolabs have unit definitions for their various products based on activity.

Having dealt with NEB in the past, I know that they generally have a concentration for their products as well, so if you're doing experiments like an enzyme inhibition assay, you can dose for concentration as well as activity. It will vary from enzyme to enzyme whether your inhibitor will even bind to any inactive protein that may be present, in which case activity would be the better attribute to use in your calculations.


What impacts on metabolism are likely from the 6x increase in water consumption by Americans at restaurants since the 1950s? CDC data show that American water consumption in restaurant meals is 600% of what it was in the 1950s while meal calorie density has decreased (kcal/oz). What impacts is this likely to have on the metabolism of Americans?

My question is based on this infographic:

As mentioned by nico in his comment, this infographic is very misleading in that it presents quite uninteresting data in a way as if it was a sensation.

It claims the average meal drink has been soda which has increased by 6 times in size. Then it claims most of the volume is water. This is of course true. But while a substance solved in water barely increases its volume, it can still make a difference - soda and water are completely different things and the important statistic to look at here is not the amount of water drunk, but rather the fact that it is soda. Where I live, soda usually contains around 27g of sugar per 240ml (8oz) which is 9% of the GDA. So according to this data, people consume half their energy needs of that day with the drink they get in their restaurant meal.

The other statistic is about calories per ounce of the food. What sense does a statistic about that make? The only relevance of the calorie density of food would be the effect on how well it is digested, and for that only a calorie number isn't really helpful. The relative ratios of fibre, carbohydrates and fats would be much more useful in that case. The only interesting statistic here is that meals have almost doubled in size. The fact that the volume of meals has increased much more hints that there is a higher portion of less calorific foods, such as salads.

Impact on metabolism? Hard to say, this is a statistic about what people eat at restaurants, which is not really something that you expect to reflect their refular diet. It doesn't tell you anything about their general lifestyle, which would be the relevant statistic for effects on metabolism. If you only look at restaurant meals, those could look really unhealthy but on the larger scale, people balance it out in their every day diet and general lifestyle. If you had an additional statistic that shows that people actually eat a significiant amount of meals at restaurants, and they're the kind of meals described by the infographic you gave, that would have some implications.


Photosystem 1 and 2; P680/P700; Chlorophyll a/b I am getting slightly confused about how the above relate to each other. My current understanding is that P680 and P700 refer to the primary pigment reaction centres in Photosystems 2 and 1 respectively, with the numbers giving the peak wavelength of absorption. Now I initially thought that one of these primary pigment reaction centres must be composed of chlorophyll a and the other of chlorophyll b, hence the slightly differning absorption wavelengths. Instead, here it seems to suggest that the primary pigment reaction centre is always chlorophyll a. Most sources I have looked at do not specify what forms the primary pigment reaction centre (the Wikipedia article on photosynthetic reaction centre, for example, does not state for the general case of for photosystem 2; however it does mention that photosystem 1 has a special pair of chlorophyll a molecules at the centre).

So my specific questions are:

Is the primary pigment reaction centre in both photosystem 1 and 2 (i.e. P700 and P680) a pair of chlorophyll a molecules?
If so, what is chlorophyll b? Is it simply an accessory pigment?
Finally, if it is the case that the primary pigment reaction centre is chlorophyll a in both cases, how can it be that it absorbs at a different wavelength in the two photosystems if it is the same molecule?

Regarding your questions #1 ("Is the primary pigment reaction centre in both photosystems a pair of chlorophyll a molecules?") and #3 ("How can it be that it absorbs at a different wavelength in the two photosystems if it is the same molecule?"):

Both reaction centers in Photosystem I and Photosystem II contain only chlorophyll a. According to Lodish (Molecular Cell Biology):

  As in the bacterial reaction center, at the center of each chloroplast photosystem is a pair of specialized reactioncenter chlorophyll a molecules, which are capable of undergoing light-driven electron transfer. The chlorophylls in the two reaction centers differ in their light-absorption maxima because of differences in their protein environment. For this reason, the reaction-center chlorophylls are often denoted P680 (PSII) and P700 (PSI). (emphases mine)

Regarding your question #2 ("If so, what is chlorophyll b? Is it simply an accessory pigment?"):

Chlorophyll b has a different molecular structure (and, therefore, a different absorption spectrum) and it's less abundant in the chloroplast than chlorophyll a. Here is an image depicting their molecular structures and absorption spectra:

(a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated in the red box, are responsible for the green color of leaves. β-carotene is responsible for the orange color in carrots. Each pigment has (d) a unique absorbance spectrum. Source: "OpenStax College, The Light-Dependent Reactions of Photosynthesis. October 16, 2013."

Both chlorophyll a and b are present in the antenna complex. Still according to Lodish:

  As in photosynthetic bacteria, each reaction center has an associated antenna that consists of a group of light-harvesting complexes (LHCs); the LHCs associated with PSII and PSI contain different proteins.

However, most of chlorophyll b is associated to PSII antenna complex, not PSI, which is one of the main differences between PSII and PSI.

Source: Lodish, H. (2000). Molecular cell biology. 4th ed. New York: W.H. Freeman.


Is a nature possible where animals do not kill each other? like the title suggests, i always wondered if its possible that nature would work without animals killing each other. Where they just eat plants. Like one special plant for each animal. If they eat to much of them away they also will stop multiplying to much, so there will never be too much of one species etc, terefore balance. I am sure there could be other controlling mechanism for balances.

:)

No, even herbivores will eat other animals, and predation goes down ot the cellular level.  Also something has to be ating your dead and will have a huge evolutionary pressure to evolve toward predation with no predators present.

Animals by definition have a much better profile of nutrients for other animals.

Deer routinely kill and eat birds, eggs and even dead rabbits. In nature food is food and evolution does not care where you get it from. Carnivores will and have evolved from an herbivorous ancestor when no carnivores are present.


Has there even been a clinical study where healthy volunteers consented to be infected with a pathogen? I am curious if there has ever been a (modern) clinical study where a healthy volunteer was purposefully infected with a pathogen in order to test the effectiveness of a therapeutic or preventative measure (like a vaccine)?

If not, would the FDA allow for ethical exceptions in cases where there is an extreme case of urgency (like in a pandemic)?

Obviously these would be willing volunteers who signed waivers, etc. So Nazi experimentation, the Tuskegee trial, and other studies without total consent from the participants wouldn't qualify here.

Edit: Self-experimentation wouldn't qualify here either because the bioethics of self-experimentation are different than testing on others.

This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology. I'm glad we encourage such questions from curious people who want to learn more.

One can't easily separate ethics from how biology is done, as much as some people have tried. (Though I suppose some have made bioethics into a separate and successful media career, so it can be done in that way.)
In addition to the comment-answer about the Tuskegee Study, Nazi doctors in Germany performed experiments without consent, which included infecting concentration camp prisoners with the bacteria that cause tuberculosis.
Your question is about volunteerism, however, and the victims of the United States and Nazi Germany did not give full — or any — consent to experimentation.
In this week's issue of Nature, there is a news article which interviews bioethicist Nir Eyal about a recent preprint, of which he is a primary author.
In this interview and in the preprint, your very question about coronavirus vaccine research, specifically, is discussed, as it concerns the matters of consent, ethics, and safety of doing accelerated biological research about this virus in a time of emergency.
In answer to your first question about modern clinical studies, Dr. Eyal notes:

Are there any precedents for infecting healthy people with a pathogen?
We do human-challenge studies for less deadly diseases quite frequently. For example, for influenza, typhoid, cholera and malaria. There are some historical precedents for exposure to very deadly viruses. The thing that demarcates the design that we propose from some of these historical instances is that we feel there is a way to make these trials surprisingly safe.

As an example, there was a challenge trial for malaria performed in 2012. Healthy individuals were bitten by mosquitoes carrying the malaria parasite and then treated with antimalarial therapies.
Clinical trials are done under the aegis of government agencies with review and approval processes, some of which are described on the FDA web site. IRBs or Institutional Review Boards provide oversight:

Under FDA regulations, an IRB is an appropriately constituted group that has been formally designated to review and monitor biomedical research involving human subjects. In accordance with FDA regulations, an IRB has the authority to approve, require modifications in (to secure approval), or disapprove research. This group review serves an important role in the protection of the rights and welfare of human research subjects.

History does guide us to worry about the ethical issues surrounding medical trials, especially under exploitative regimes that leave people to fend for themselves during a time of global crisis:

Do you worry that countries with authoritarian governments could conduct such studies on vulnerable groups, such as prisoners or members of persecuted minorities?
We would only recommend conducting the studies in an ethical fashion, with fully informed consent. Vaccine makers want to sell their product to other countries. They want to publish their scientific articles in prestigious journals and there would be many obstacles if their trial doesn’t adhere to widely accepted standards.

But in the modern age, in non-corrupt regimes, science does aim, for the most part, to do the right thing, and there are methods and regulatory mechanisms in place to try to enforce societal standards that move us past the days of Tuskegee and Nazi concentration camps.


Can anyone identify these flowers? I'm mostly interested in the maroon and white ones in the center, or the purple and white ones in the front left corner.  They were in bloom in a garden in July at the Buffalo Harbor.  Any help would be appreciated!!

The sign agrees. They are petunias. The specific variety of the red ones is raspberry swirl. I don't know the specific variety of the purple ones.


What sample sizes are ideal for carrying out Bayesian Skyline Plots? I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 polymorphic sites within each population and one dominating haplotype that comprises almost 90% of the population (the rest being rare haplotypes). Because, BSP uses Coalescent processes for the calculations, the sample sizes would have a effect on the results. I wanted to know if sample sizes of around 30 (for DNA alignments of 700bp) would be ideal for carrying out the analysis and expect reasonably good results ?

I found a PLOS one article that might help. In this they used similar numbers you're planning to use (if i get your question and the article's data right).

  The influence of the sampling scheme was investigated by drawing 40 samples in three different ways: 1) all 40 samples from a single deme, 2) 4 samples from each of 10 demes and 3) one sample from each of the 40 demes in the structured population. These correspond respectively to the local, pooled and scattered

(taken from the above linked article)

So depending on your sampling scenario your 30 samples seems to okay.

Also this is a link for the BEAST FAQ that might be helpful.


Calculating ultrametric distance matrix I am fairly new to phylogenetic analysis, so I'm guessing this is a basic question. If I have a bunch of aligned sequences, and I ultimately only care about pairwise distance (e.g. for calculating phylogenetic diversity) then is there any way to make sure these distances reflect an ultrametric tree without having to first calculate the tree itself? From what I can tell, to create an ultrametric distance matrix I have to first calculate an ultrametric tree and then use this tree to get distances. But this seems a bit backwards to me, since I can create a pairwise distance matrix without needing to create a tree, but I can't tell if there is a way to ensure that this matrix assumes some sort of underlying molecular clock so as to make sure the distances reflect an ultrametric tree.

I assume I'm just fundamentally failing to grasp something. Any help would be much appreciated.

In my understanding you cannot skip the tree construction, since there is no guarantee that the pairwise distances are compatible with a tree, even for non-ultrametric trees. That is, to create a pairwise distance matrix that reflects patristic distances between tree leaves you need to create a tree first. Even without the ultrametricity condition.

The complicating factor here is that distance matrices compatible with trees must also respect distances to unobserved internal nodes...
This blog post about how to make a tree ultrametric might be relevant.


Why my base-quality in alignment is not perfect? I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error.

wgsim -e 0 -r 0 sequence.fa seq_0_1.fq seq_0_2.fq

To my knowledge, this is a perfect simulation. Next, I give the paired alignments to bwa for alignment.

bwa mem -M sequence.fa seq_0_1.fq seq_0_2.fq > P0.sam

Now, I check the ASCII of base quality (column 11 in the SAM format, the specification is here).

head -n 3 P0.sam | cut -f11

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

According to this page, the ASCII (in order of quality) is:

!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

Question: My experiment is supposed to be perfect, so my base-quality metrics are expected to appear near the right-end of the list (like x,y,z). However, my metric I is no-where near the top of the list. In particular, I'm unable to achieve anything from J to ~. Why?

When fasta reads are aligned they are by default assigned the phred score of 40, which in phred+33 encoding is represented by I. Phred+33 uses ASCII characters from ! to I:

!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI

Phred+33 was originally used by sanger machines but it is now used by all popular platforms such as Illumina, Ion-torrent (also Ion-proton) and Roche 454. Since most platforms now use phred+33, most aligners also assume it by default. You can specify other quality encoding formats if you want (such as phred+64 or Solexa).

Have a look at wikipedia page on FASTQ format for the different quality encoding formats.


What plant have I collected? I have collected this plant from the soil in a park in Belgium. I thought it was a child of a plant which was growing nearby but when the leaves started to grow I realised it is a different plant.

When I was collecting it, it was at the stage of having only the seed leaves (still visible in the photo) which are elongated and about 2.5 cm long. In the park, on the ground from where I collected it, these plants were growing in large quantity close to each other. After about 1 week from bringing it home the leaves started to appear. Now about 3 weeks later the leaves are about 2-3 cm long.

Could you help me identify it?

Further clues

First of all, this plant is very abundant in the park but I can also spot it in other places, e.g. close to sidewalks within a walking distance from this park.

This is the plant in the original environment from where I collected it:

I could also find it growing in a pocket of a tree - this suggests to me that the seeds might have fell from a height, so this plant might be a tree (?)

The ground of the park is largely populated by wild garlic. Other than that, some nearby plants are a hornbeam and elderberry.

Here are some further photos of surrounding plants that might be a hint for you:

You definitely have a seedling with prominent cotyledons still present.

My initial guess is Acer pseudoplatanus (sycamore maple, or just called "sycamore" or "planetree maple" in parts of Europe)

 Source: Wikimedia

You can see a detailed image of an A. pseudoplatanus seedling here and a time-lapse of a seedling growing to the point of cotyledon release in Neil Bromhall's youTube video.

According to the range map available from Euforgen, A. pseudoplatanus is present (blue) throughout Belgium:

As for confirming nearby adults, you're looking for a tree that looks as follows:

 Source: Blue River Nursery

For more information regarding identifying the adult, please see Virginia Tech Dendrology


What does "novel, predicted deleterious, within autozygome" mean in genetics? I am a medical student and just got involved with a genetic lab and research. I read a lot phrases like: "Although no mutations have been reported in this gene, we think this variant is interesting because the nature of the variant (novel, predicted deleterious, within autozygome).

Can anyone explain it to me?

For a genetic variant:

novel - Not previously reported in the scientific literature.
predicted deleterious - There are reasons to suspect the variant could cause abnormal effects in a person.  This may be in part from where the variant is located (e.g. what gene), what problems were observed in persons having the variant, and many other considerations.  See the "Variant interpretation" section of this paper for more detail.
in autozygome - "Autozygous" refers to parts of the genome which are identical on both maternal and paternal chromosomes because of common ancestry of the two parents.  The autozygome is the collection of all such segments for a person, and is larger in cases of inbreeding, as when the parents are first cousins.  Autozygous segments are (usually) entirely homozygous, that is, all alleles are the same since they come from the common ancestor. (In normal segments, there will be a mix of matching and mismatching alleles.) The importance of homozygous alleles, of course, is that a recessive allele will be expressed in the person when both alleles are the same.  (Related papers: "Autozygosity mapping with exome sequence data", "Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes".)


how to quantify toxicity When going through this link, Table 1, what are the numbers mentioned there? How is one quantifying toxicity?

Usually, toxicity is given in the units of mass of the substance per unit mass of body mass of the organism that will kill 50% of the organisms in a species if those organisms ingest the toxin at that dose (e.g. mg/kg, ng/kg). This measurement is called the median lethal dose, and is often abbreviated as LD50.

In your table, they only provide the mass of the (average) dose of the substance needed to kill the organism listed, as can be seen by the (mg) after the words "Toxic dose". They likely multiplied the LD50 of the toxin by the average mass of the organism to obtain those numbers. Based on Google's estimation that a mouse has an average weight of 0.68 oz (0.019 kg), and on this table of murine LD50 measurements, I calculated that for tetanus toxin, the lethal dose in the average mouse is 3.8x10$^{-8}$ mg, which is basically what your table provides, which supports my guess on how they obtained their numbers.

The other values listed under "Lethal toxicity compared with" appear to be ratios, given by the formula [lethal dose of toxin above]/[lethal dose of toxin on left]. Using Wikipedia's LD50 for Strychnine in mice (2 mg/kg) and the tetanus toxin LD50 from my previous source, I obtain the exact ratio that they do (1x10$^6$). The lack of units makes sense, as ratios are unitless.

Source on LD50


Where to obtain metabolic pathway datasets I've been looking through the files available at www.reactome.org along with some others but I only find images/pdfs of metabolic pathway diagrams. Where is the actual data these pathways are drawn from? I imagine there should be some kind of directed graph representation. I'm limited to freely available datasets, so unfortunately I'm not able to check out those such as KEGG.

KEGG is definitely your choice!

It is possible to get the whole list(s) of pathways: http://rest.kegg.jp/list/pathway (reference pathways) or http://rest.kegg.jp/list/pathway/hsa (for human).

Then you can use these IDs to retrieve information about individual pathways: http://rest.kegg.jp/get/hsa00053 (GeneBank-like format), http://rest.kegg.jp/get/hsa00053/image (image), http://rest.kegg.jp/get/hsa00053/kgml (KEGG xml). It will take a while, of course, and I'd recommend not to overload their server and make delays between queries. With the GeneBank-like format batch querying is also possible: http://rest.kegg.jp/get/hsa00053+hsa00061

This should likely be a one-time or at least rare operation, because of the load on their server (and I don't think they make big changes very often). You can retrieve info for new pathways, once they appear in http://rest.kegg.jp/list/pathway/...


Is there a difference between Luria Broth and Lysogeny Broth? Is there a difference between Luria Bertani and Luria Broth? Or are they both the same thing? Is it necessary to autoclave LB medium after it has been made?

Although both names are quite common, both are wrong. In the original paper from 1951 Bertani was studying the lysogeny in E.coli, hence he called his media for this purpose "Lysogeny Broth" or LB in short. In the subsequent decades this name was transformed to "Luria Bertani" or "Luria Broth", which is incorrect. See the references 1 and 2 for more details.

For the second question: It is absolutely necessary to autoclave the media after preparation to avoid the contamination and growth of microorganisms which are present in our environment. Only making the media sterile makes sure that we can work with defined microorganisms.

References:

Studies on Lysogenesis I.
The Limitations of LB Medium


Are there electron or proton receptors in our nose? We can easily smell chlorine gas and its irritating odour, but we cannot smell oxygen gas. Do few protons and electrons make such difference to our olfactory receptors?

Chloride (Cl2) carries 34 protons and electrons.

A common example of a relatively heavy odorless gas is CO2, carrying 22 protons and electrons.

All noble gases are odorless. The heaviest, naturally occurring noble gas is Radon, which has a proton count of 86. Ununoctium, an exotic artificial element with atomic number 118, is a noble gas too. However, with a half life of approximately 0.9 ms it's difficult to sniff out whether it's really oderless.

Sulfur hexafluoride is odorless too, with a proton count of 72.

Hence, the atomic number per se is not the determining factor reason for generating the sensation of odor.

What determines whether a compound generates the sensation of odor I am unsure of, but the above compounds mentioned are all chemically inert. Note that Ununoctium decays rapidly, it doesn't react with anything. I have not been able to verify whether inertness always means odorless, but with the above examples I am inclined to believe it holds true. However, the reverse is definitely not true, as carbon monoxide is odorless, but reactive.


Genetics of epilepsy Is epilepsy genetically inheritable? If yes, is it dominant?

Sometimes!

The causes of epilepsy are legion.  There's a massive Wikipedia page listing various causes, and, wow, I get tired just reading the table of contents.  None of those are genetic causes, but it should perhaps therefore be not surprising to learn that the genetic causes of epilepsy, although the minority of cases, are also quite varied.  Apparently most of the causative genes involve ion channels (whether voltage- or ligand-gated), but there are a truly large number of genes that can be related to epilepsy.

This 2011 paper has quite a lot of information.  Some facts it presents on the genetics of epilepsy:

Something like 1-2% of all mutations in mice present with epilepsy symptoms.
Concordance is around 50-60% for monozygotic twins, and 15% for dizygotic

The majority of twin concordance is likely from the same (genetic) cause

Monogenic causes (versus complex causes of epilepsy) account for around 1-2% of human cases.

In direct answer to your question, there is this paragraph (emphasis added) explaining the rough breakdwn:

  Monogenic inheritance is suggested by the familial aggregation of cases that share a similar phenotype and are distributed in the pedigree according to a Mendelian mode of transmission: autosomal or sex-linked, dominant, or recessive. Autosomal recessive epilepsies are often associated with structural or metabolic abnormalities of the brain and with neurologic comorbidities, so most of them are not in the category of idiopathic epilepsies. Examples of these are pyridoxine-dependent epilepsy (PDE), several progressive myoclonic epilepsies (PMEs), and some malformations of cortical development (MCDs). Most of the monogenic idiopathic epilepsies follow the pattern of autosomal dominant inheritance, implying the presence of multiple cases in successive generations and male-to-male transmission.

In short:

If it's genetic, it's likely to be complicated and controlled by many genes
If it's controlled by one gene, it's likely to be dominant

The paper also presents the following table which may be of interest, listing monogenic causes of epilepsy:


Why do some drugs require you to take them in an "upright position"? A friend of mine was taking the supplement Metamucil and on the container it says to take in an "upright position." Why would this be necessary? Doesn't your digestive system push food/liquid downwards anyways?

Metamucil is taken as a drink. You're more likely to aspirate versus swallow when drinking supine if you're ill with impaired swallowing reflexes.

It's also recommended that you take bisphophonates standing up so that gravity, and a glass of water, make sure the drug passes into the stomach. It can be highly corrosive if it gets stuck in the esophagus.


Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO? Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops?

In software development, these constructs have the following functions:

IF-statements: An IF statement executes the code in a subsequent code block if some specific condition is met.
WHILE-loops: The code in a subsequent code block is executes as many times as specified, or as long as a specific condition is met.
Function calls: The code temporarily bypasses the subsequent code block, executing instead some other code block. After execution of the other code block the code returns (sometimes with some value) and continues the execution of the subsequent block.
GOTO-statements: The code bypasses the subsequent code block, jumping instead directly to some other block.

Are constructs similar to these present in DNA? If yes, how are they implemented and what are they called?

Biological examples similar to programming statements:

IF : Transcriptional activator; when present a gene will be transcribed. In general there is no termination of events unless the signal is gone; the program ends only with the death of the cell. So the IF statement is always a part of a loop.
WHILE : Transcriptional repressor; gene will be transcribed until repressor is not present.
There are no equivalents of function calls. All events happen is the
same space and there is always a likelihood of interference. One can
argue that organelles can act as a compartment that may have a
function like properties but they are highly complex and are
not just some kind of input-output devices.
GOTO is always dependent on a condition. This can happen in case of certain network connections such as feedforward loops and branched pathways. For example if there is a signalling pathway like this:  A → B → C and there is another connection D → C then if somehow D is activated it will directly affect C, making A and B dispensable.

Logic gates have been constructed using synthetic biological circuits. See this review for more information.

Note

Molecular biological processes cannot be directly compared to a computer code. It is the underlying logic that is important and not the statement construct itself and these examples should not be taken as absolute analogies. It is also to be noted that DNA is just a set of instructions and not really a fully functional entity (it is functional to some extent). However, even being just a code it is comparable to a HLL code that has to be compiled to execute its functions. See this post too.

It is also important to note that the cell, like many other physical systems, is analog in nature. Therefore, in most situations there is no 0/1 (binary) value of variables. Consider gene expression. If a transcriptional activator is present, the gene will be transcribed. However, if you keep increasing the concentration of the activator, the expression of that gene will increase until it reaches a saturation point. So there is no digital logic here. Having said that, I would add that switching behaviour is possible in biological systems (including gene expression) and is also used in many cases. Certain kinds of regulatory network structures can give rise to such dynamics. Co-operativity with or without positive feedback is one of the mechanisms that can implement switching behaviour. For more details read about ultrasensitivity. Also check out "Can molecular genetics make a boolean variable from a continuous variable?"


Double Digestion with Restriction Enzymes Using Different Buffers I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site located on my insert, and since I am using 2 restriction enzymes in my digestion, I had little choice in choosing my restriction enzymes. The only two restriction enzymes that will work for me are Xmal and KpnI. XmaI uses CutSmart buffer while KpnI uses NEB buffer. The efficiency of XmaI in CutSmart buffer is 100% while the efficiency of KpnI in CutSmart buffer is 50%. Would it be easier to perform a double digestion using CutSmart buffer and 2x KpnI than to perform two consecutive digestions?

NEB double digest planner is suggesting to use 2.1 buffer for your combination of restriction enzymes (XmaI 50% and KpnI 75% activity). I would be more worried about the star activity of KpnI in CutSmart buffer than the lower activity. The latter can be overcomed by prolonging reaction time or using more enzyme.


Help understanding the word 'glycosaminoglycan'? In my biochemistry course I have to know about various polysaccharides and variants, and I am struggling with remembering them. I think it would help if I could break down their names.

For 'glycosaminoglycan' i think

-glycan just refers to the fact that it is a polysaccharide. Some, but not all polysaccharides have glycan in their name, e.g. glycogen vs amylase and amylopectin

-amino means there is an amino group somewhere in there?

That's all I can think of...

Glycosamines (or amino-sugars) are monosaccharide derivatives with an amino group substituting the hydroxyl group at second carbon. Glycosaminoglycans (GAG) usually contain repeats of a disaccharide unit one of the component of which is an amino sugar. GAGs are not strictly polymers of amino sugar monomers as the name might misleadingly suggest.


Identify this South African spider A family member saw this spider in her garden in the Cape Town area of South Africa. It's very attractive and I wondered what species it was?

Approx size is that it would fit roughly on a 3cm diameter circle.

Based on the location and image you provided, I suspect this spider to be Garden Orb-Weaver, belonging to the spider family Araneidae.

Just a side note: I used an app called iNaturalist to identify this spider. It is a helpful app to identify insects and plants.

Here is a similar image I found online:


Quantitative Comparisons of Phylogenetic trees I am working on a broad phylogenomic analysis of proteins involved in one particular cellular process.  I have constructed a phylogenetic tree for each protein.  I am now working on comparing those trees in order to extract categories (i. e., allele a of protein a occurs most frequently with allele b of protein b, etc.).  I have attempted to construct a super tree using clann, but the tree is extremely difficult to interpret.  I would therefore like to carryout a quantitative comparison (and subsequent categorisation) of each each tree, but it is unclear to me how to even begin this analysis.  Is there a standardised method for comparison of phylogenetic trees?

I don't know whether it's exactly what you need, but there are formal algorithms for tree comparison.

There are basically two approaches: one utilizing tree lengths (branch score distance) and the other one dealing with topologies only (symmetric-difference metric): details and references can be found in the manual to treedist from the phylip-package, which implements both.

PAUP* has a command under the same name (treedist), which calculates the symmetric-difference metric only. This metric is very intuitive: it describes the total number of partitions (= splits) present only on one of the two trees.


Misincorporation of dUTP into DNA? Uracil, the RNA base, has been replaced in DNA by thymine, (which has the same base-pairing with guanine). However the synthesis of dTTP (more usually written TTP) requires dUTP:

To what extent is dUTP (mis)incorporated into DNA?

There follows an attempt to answer my own question, which I think is important to consider in the general context of postings on SE Biology concerning uracil and thymine in DNA and RNA synthesis.

There seems to be little misincorporation because of the low concentrations of dUTP in cells.

Any small amount of misincorporation can be handled by the DNA repair system that exists in cells.

I base statement 1 on the work of Grogan et al., published in Biochemistry 50, 618–627 (2011). They showed that in both mouse and human cell lines that the normal concentration of dUTP (and dUMP) was low. I assume that this must reflect cellular activities of dUTPase and thymidylate synthase being sufficiently high to remove dUTP and dUMP, respectively as they are formed. When thymidylate synthase activity was inhibited by anticancer drugs, these nucleotides built up, as expected.
In support of Statement 2 I refer to a separate earlier study in fission yeast by Seiple et al. in Nucleic Acids Research 34, 140–151 (2006). They used the drug, 5-fluorouracil, to inhibit thymidylate synthase and found that it caused misincorporation of uracil into DNA with concommitant cell damage. The role of the DNA repair system in mitigating this damage was shown using a mutant in the Ung1 gene, which encodes DNA glycosylase — here the cell toxicity was much higher.
Although there are some inconsistancies between the different systems used, and difficulties of interpretation.  I think that they provide general support for the two postulates. It would be useful if it were possible to locate kinetic data on the relevant enzymes to test my assumptions regarding the reason for the low dUTP concentration.


How does ultraviolet light influence the decay process of wood? Given a piece of wood, how does putting it in the sun or not influence the rate of decay due to rot (assuming that it's in an otherwise humid environment)?

Ultraviolet light is microbicidal. See this post.
As I answered in this previous post, micro-organisms are essential for rotting. Since UV kills these microbes it will reduce the rate of rotting. The heat from sun will also dry the wood and further decelerate rotting.


Stem cell that can pass through blood vessel I know that blood cells can pass through the smallest of capillaries, but I was wondering is it possible for stem cells to pass through the smallest of capillaries?

In other words, is it possible for a type of stem cell therapy where stem cells are injected into the vein in the arm for example and the stem cell would pass through into the tissue through a type of targeted therapy involving ultrasound or magnetic field.

Thank you very much ,
everyone

Yes, stem cells can pass through blood vessels and capillaries (as @WYSIWYG points, these cells should be small enough to fit inside that capillary). The interesting thing is that they posses multiple mechanisms of transmigration. They are attracted by TNF-alpha activated endothelial cells [1] and can pass through by [1]:

leukocyte-like diapedesis
paracellular migration between endothelial cells
transcellular, directly through individual endothelial cells

  I am thinking of some type of encapsulated stem cells where ultrasound, heat or magnetic fields from the MRI would break up the encapsulation releasing the stem cell at the targeted area.

Note: I don't know if the following is plausible. It is just something I thought of and I consider it to be more effective than what you suggested.

Then what is the purpose of using stem cells that are capable of chemotactic movements and can go by themselves in targeted areas? The encapsulation you propose could be used to fit inside the cell a drug-containing capsule that would break upon external electromagnetic, ultrasonic (etc.) stimulation. This means that the capsule would also contain a substance capable of inducing cytoplasmic membrane lysis, so the drug could reach the interstitial space. Or the cell could be genetically engineered to secrete that drug, when available in cytoplasm, through exocytosis.

But why not get rid of that capsule? A cell could contain (for example) a cytostatic drug in its cytoplasm and also be fitted with membrane receptors for a specific tumoral marker. When it reaches the tumor, receptor stimulation should trigger exocytosis of drug.

References:

Teo GS, Ankrum JA, Martinelli R, Boetto SE, Simms K, Sciuto TE, Dvorak AM, Karp JM, Carman CV. Mesenchymal stem cells transmigrate between and directly through tumor necrosis factor-α-activated endothelial cells via both leukocyte-like and novel mechanisms. Stem Cells. 2012 Nov;30(11):2472-86. doi: 10.1002/stem.1198. PubMed PMID: 22887987.


double PCR with tailed primer I would like to make a double PCR with universal tailed primer. The first PCR would make a tailed amplicon. The second PCR would generate fragment labeled with fluorescent dye. Here is my protcole. Could you tell me if I am wrong ?

is my second PCR forward primer well designed to fit with the tail ?
What would be the ratio of primer to use if I want to merge the two PCR into one ?

Fist PCR ( works )

In bold, you have the tail M13(-20)

Forward : 5'-GTAAAACGACGGCCAGTTCTGCAGTTGTACTGAGTGAA-3'
Reverse : 5'-AAAGCGTGCAGCTGATATTT-3'

Mix for 1 sample

Water              = 15.8µL
MgCl2 (25mM)       = 18µL
Buffer (5x)        = 6µL
dNTP (4mM)         = 1.5µL
Forward(20pmol/µL) = 1µL
Reverse(20pmol/µL) = 1µL
GoTaq (5U/µL)      = 0.15 µL
DNA (50ng/µL)      = 1 µL

Second PCR ( not working = no fragment signal )

Forward : 5'-[FAM]-GTAAAACGACGGCCAGT-3'
Reverse : 5'-AAAGCGTGCAGCTGATATTT-3'

Mix for 1 sample

Water              = 15.8µL
MgCl2 (25mM)       = 18µL
Buffer (5x)        = 6µL
dNTP (4mM)         = 1.5µL
Forward(20pmol/µL) = 1µL
Reverse(20pmol/µL) = 1µL
GoTaq (5U/µL)      = 0.15 µL
DNA (50ng/µL)      = 1µL from my previous amplicon

I'm not sure to understand your query. I can say that in my lab we are also using fluorescent dye (for SSR detection). But we are doing it with a one step approach:

Our forward primers are like yours preceded by the fluo sequence (M13-forward primer). But instead of making a second PCR, we add directly the fluo primer (let's called it M13-FAM) in the first PCR. It is REALLY important to put your M13-forward primer in lower quantity than the reverse one (factor 10 for me). To achieve that I use 0.1mM primer solutions and I mix my primers before

For 96 wells (20µL/well)

Primer Mix

1.25 µL of M13-F primer
12.5 µL of R primer
240 µL of water

PCR Mix

200 µL of Primer Mix
20 µL of M13-FAM
Master Mix 1mL
Water 1mL


What Type of fly is this? its huge I found this stunningly beautiful Fly in a graveyard in Point Lonsdale Australia.  Can someone tell my what type it is Please.

It was wide as my thumbnail about 3cm long.

Could be a blue rutila fly (Family Tachinidae) http://www.brisbaneinsects.com/brisbane_tachinids/BlueRutiliaFly.html. Or the green rutila fly, which is similar.

Or the golden head rutila:


Can soap kill cockroaches and/or ants? If so, how? Is it possible to use dishwashing soap as an alternative insecticide? How would that and what are the components of the dishwashing soap that would kill the insect?

I'm not completely confident that the aforementioned post is a duplicate, because the question explicitly asks "Why do cockroaches burst from soapy water?" While this question explicitly asks "Can soap kill cockroaches and/or ants?"

The short answer to your question is yes.

According to this website:

  The soapy water kills [cockroaches] by forming a thin film over the
  roach's breathing pores that stays in place due to surface tension,
  causing the roach to suffocate.

Ants are killed in a similar manner (see this archived Reddit post).

For a more scientific read, check out this paper: Behavioral Responses and Mortality in German Cockroaches (Blattodea: Blattellidae) After Exposure to Dishwashing Liquid.


Do humans have any biological adaptations to eating cooked food? Humans have been cooking food for at least tens of thousands of years. The presumed reason why cooking took root in nearly all human cultures is that cooked food is easier to digest. However, cooking food can also generate toxic compounds such as polycyclic aromatic hydrocarbons, which would not be found in the uncooked version of the food. Considering that humans have been eating cooked food for such a long time, I am wondering whether humans evolved any adaptations to eating cooked food, e.g., that certain types of foods, when cooked, are more toxic to our closest relatives (great apes) than they are to humans, because we have more ability to metabolize the toxic compounds.

Humans are incredibly good at processing maillard compounds, which include both beneficial and mildly toxic byproducts of cooking. Humans are better at breaking them down than other animals. This is presumed to be an adaptation to eating cooked food. Malliard reactions are also a good indicator of when most plant and animal products are safest to eat via cooking, (browning) which may explain why humans on average show a preference for them or even adaptations to detect them. we are also learning that one place animal testing may be problematic is in dietary tests becasue of this.
extra reading on hominid adaptations to diet


Drosophila grey / yellow I am studying biology by myself via distance-learning. I have been trying to solve the following problem for a while now and hoped you could help me. As this is "homework" I would appreciate hints rather than solutions.

Drosophila has a gene "yellow body", $y$, on the X chromosome. The other, dominant, allele is "grey body", $y^+$.
When crossing female grey bodies  with male grey bodies we get 50% grey females, 22% grey males and 28% yellow males.

What is the genotype of the parents?

My work so far:

The genotype must be $Xy^+X?$ for the female and $Xy^+Y$ for the male.
There are two cases to consider: $?=y^+$ or $?=y$.
In the former we get $\frac{3}{8}$ grey females and $\frac{1}{8}$ yellow females and $\frac{2}{8}$ grey and yellow males each; that seems correct except for the yellow females.
In the latter, we get twice as many yellow females.

Perhaps the XXyy (yellow females) genotype is lethal but this doesn't help in determining the parents' genotypes.

If $? = y$ then cross-over from $Xy^+\mathbf{Xy} \; x \; \mathbf{Xy^+}Y$ would not eliminate yellow females.

I don't know of other effects to take into account, so I am stuck.

$ $

If you'd like to suggest resources (websites, textbooks $\ldots$) pertaining to this subject or on biology at this level in general, I would very much appreciate it.

Thank you.

Edit: I'd like to add an image for anyone having a similar problem.

Since Drosophila have the same system of sex chromosomes as human beings, (XY males and XX females).  Its clear that the sex determination is important - no females have yellow bodies. This is the key observation.

Amongst the males you have about 50%/50% Y/y phenotype.  This appears to be a classic sex chromosome related trait.  Does this help?  I can go further, but this should get you there.


I'm trying to unserstand Yamanaka's iPS cells paper Can someone please explain to me what is the beta-geo cassette and why is it used? I understand that it was inserted in the Fbx15 gene, and this gene is present in ES cells, and I believe this cassette is used as a marker of the Fbx15 locus, but why does it have resistance genes (beta-galactosidase and neomycin), what are they resistant for? What is their role? Thanks!

Suppose you want to insert a cassette in a gene.  How will you know it is there?  What if only a small percentage of cells are successfully transfected?  What if your reagents were bad.  You do not want to waste time on cels that did not take up your cassette.

Those resistance genes are for detection of the presence of the cassette in a cell (or colony derived from a single cell).  You can have other things ride along with your cassette that will let you detect its presence.  Neomycin resistance: if you grow the cells that you have engineered in the presence of neomycin, only the ones that successfully got your cassette will live because the cassette gave them resistance.  All the ones that did not take up the cassette, or took it up wrong will die.

An active beta-galactosidase gene can work on a substrate to make a blue color.

  An active enzyme may be detected using X-gal, which forms an intense
  blue product after cleavage by β-galactosidase, and is easy to
  identify and quantify.

Again this lets you detect cells (or colonies of cells) which have successfully taken up your cassette.


Identify an animal (Japan, urban area) I met this animal yesterday while walking along a small river in Yokohama, Japan. It came out of the bushes some 5 meters away from me, but while I was launching the camera app on my smartphone, it already went away into a fenced area where I couldn't follow and was quite far, so these are the best pictures I could take. It seemed to have something wrong with it's fur (either molting or sick). Could be a japanese raccoon dog (a.k.a. tanuki), although the images I found on Google don't look much like it to my untrained eye (maybe because of the fur), or some kind of a fox (looked even less likely). Tried asking locals, but they tend not to know anything about animals, unless those animals are either dogs, cats or foods. So, what is this?

EDIT: the size is hard to describe, I would say, it was a bit bigger than a big domestic cat, and also had different proportions - longer body, neck and legs.

I've been able to narrow it down to 3 species in Musteloidea, the weasel superfamily, but I think you observed a Tanuki that was suffering from scabies.

1) Tanuki / Japanese raccoon dog - 'Tanuki' - (Nyctereutes procyonoides viverrinus).
Visually similar to what you observed. The feet and face in particular seems to fit with a tanuki. Tanuki are often observed in urban areas in Japan and have been increasing in recent years. There are frequent reports of tanuki with scabies that have missing fur and a similar appearance:
(Google search for "tanuki" and "scabies":
https://www.google.com/search?q=%E7%96%A5%E7%99%AC%E3%82%BF%E3%83%8C%E3%82%AD

2) Common raccoon - 'Araiguma' - (Procyon lotor)
Since they were introduced in 1962 as pets, there are some wild populations in Japan, including in Kanagawa prefecture where you observed the animal.

3) Japanese badger - 'Anaguma' - (Meles anakuma)
Another possibility but I think it does not fit your observation.

There are a few other species in this superfamily but I think it is safe to exclude them due to a lack of visual similarity.


Analysis of post transplantation lineage tags I'm having some trouble understanding some bits of a study, mostly about the Sleeping Beauty system and TARIS model, from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408613/

I understand the concept, but not how it works technically. Can anyone explain it for me?

I can't find a reference to a "TARIS model" in the paper you linked, but we can break down the molecular circuitry of this lineage tag tracking system step-by-step.

The authors use a type of Tet expression system in order to tightly control the expression of a hyperactive Sleeping Beauty (HSB) transposase.  In the absence of doxycycline, the reverse tetracycline-controlled transactivator M2-rtTA does not bind the TetO operator. Jackson Labs has a very good summary of Tet-On (and Tet-Off) systems:

  ... rtTA is a fusion protein comprised of the TetR repressor and the VP16 transactivation domain; however, a four amino acid change in the tetR DNA binding moiety alters rtTA's binding characteristics such that it can only recognize the tetO sequences in the [tetracycline-responsive promoter element (TRE)] of the target transgene in the presence of the Dox effector. Thus, in the Tet-On system, transcription of the TRE-regulated target gene is stimulated by rtTA only in the presence of Dox.

In the presence of doxycycline, the transactivator drives expression of HSB from the constituent promoters of the TetO operator.  HSB contains DNA binding motifs that specifically recognize the direct repeats (white triangles) and a catalytic domain that excises the direct repeats and the DNA they flank, which contains a transcription stop signal (Tn-STOP).
Excision of the Tn-STOP signal allows for expression of DsRed driven by a strong synthetic promoter (CAGGS, first described here).  The excised sequence is then inserted somewhere else in the genome.
Because successful Tn-STOP excision is concurrent with transcription of DsRed, red fluorescing cells can be selected and prepared for NGS.  HSB transposition is "random", so two different transposition events are unlikely to target the same insertion locus.  The specific insertion site can then be used as a molecular fingerprint to identify the progenitor stem cell after replication and differentiation.


How didn't large, highly active dinosaurs overheat? The cube-square law seems to be the deciding factor when it comes to biological heat management. Small organisms with large surface areas relative to their volumes, like mice, need fast heartbeats and huge energy consumption relative to their size to keep themselves warm. Large organisms like elephants with small surface areas relative to their volumes need slow metabolisms and fairly little energy consumption relative to their size to keep from overheating.

But, dinosaurs. Most research seems to indicate they were basically warm-blooded (yes, that wording really bothers me too, but research as recent as 2015 states that they seem to lean decidedly toward warm-bloodedness, though they are technically somewhere in between). Modern-day creatures of that size tend to divide neatly depending on whether they live on land or in water, with the former being fairly inactive and herbivorous and the latter sometimes able to support the metabolic needs of predation by having water to help disperse the heat.

Dinosaurs, though, are an exception. Many of the fiercer predators were large, highly-active land-dwellers, three conditions that are mutually exclusive in modern organisms. How was this possible?

There has been a long debate whether dinosaurs were ectotherms or endotherms but  most of the recent studies (hypotheses)1 show that they were endotherms. In one of the most promising recent studies (in 2011), a technique called clumped-isotope thermometry2 (which is based on a reaction involving the bond between carbon and oxygen; and used in paleoclimate reconstruction) is applied to bioapatite (a form of calcium phosphate in bones and teeth) which acts like a thermometer.

  The nature of the physiology and thermal regulation of the nonavian dinosaurs is the subject of debate. Previously, arguments have been made for both endothermic and ectothermic metabolisms based on differing methodologies. Here, we used clumped isotope thermometry to determine body temperatures from the fossilized teeth of large Jurassic sauropods. Our data indicate body temperatures of 36 to 38°C, which are similar to most modern mammals. This temperature range is 4 to 7°C lower than predicted by a model that showed scaling of dinosaur body temperature with mass, which could indicate that sauropods had mechanisms to prevent excessively high body temperatures being reached due to their gigantic size.

  Dinosaur Body Temperatures Determined from Isotopic (13C-18O) Ordering in Fossil Biominerals
  Robert A. Eagle, Thomas Tütken, Taylor S. Martin, Aradhna K. Tripati, Henry C. Fricke, Melissa Connely, Richard L. Cifelli, John M. Eiler
  http://science.sciencemag.org/content/early/2011/06/22/science.1206196
  (emphasis mine)

However, a study as of 2014 claims that dinosaurs were mesothermic3 (meaning the blood runs neither hot nor cold, a thermoregulatory strategy intermediate to cold-blooded ectotherms and warm-blooded endotherms) based on the metabolic rates of dinosaurs by looking at changes in body size as animals grew from birth to adults.

  In early depictions, dinosaurs lumbered slowly, dragging their tails. More recently, we have imagined them lifting their tails and running. The question boils down to whether dinosaurs had energetic systems closer to those of rapidly metabolizing mammals and birds, or to those of slower reptiles that do not internally regulate their body temperature. However, determining the metabolic rate of extinct organisms is no easy task. Grady et al. analyzed a huge data set on growth rate in both extinct and living species, using a method that considers body temperature and body size. Dinosaur metabolism seems to have been neither fast nor slow, but somewhere in the middle—so, dinosaurs did not fully regulate their internal temperature but they were also not entirely at the whim of the environment; neither slow goliaths nor supercharged reptiles.

  Evidence for mesothermy in dinosaurs
  John M. Grady1,*, Brian J. Enquist2,3, Eva Dettweiler-Robinson1, Natalie A. Wright1, Felisa A. Smith1
  http://science.sciencemag.org/content/344/6189/1268
  (emphasis mine)

As we covered the thermoregulation system of dinosaurs, we can start with the question "How didn't large dinosaurs overheat?". As explained above, whether they were endothermic or mesothermic, dinosaurs had mechanisms to regulate their internal temperature not to overheat. There are theories that say that some larger dinosaurs relied on shade and dense flora to keep cool or they might have migrated due to seasonal changes. Other theories claim that they used large surface area organs (like long necks and tails) as a heat radiator4.

One of the most plausible explanations is that large dinosaurs displayed tachymetabolism. Tachymetabolic animals have high resting metabolic rates, usually resulting in endothermy and homeothermy. Further explanation of how big tachymetabolic dinosaurs coped with high heat loads5:

  BIG TACHYMETABOLIC DINOSAURS WOULD HAVE COOKED IN THE HEAT

  Myth: Because tachymetabolic rates scale to W0.75, while surface area scales to W0.67, it is almost universally believed that big endotherms suffer serious heat stress in tropical climes. Big dinosaurs, sauropods especially, should have had low metabolic rates to avoid this dire fate (Martin, 1979; Regal and Gans, 1980; Spotila, 1980; Reid, 1984; Schmidt-Nielsen, 1984; Carroll. 1988; Alexander. 1989; Prothero, 1989: Russell, 1989). Alternately. tachymetabolic sauropods needed well developed cooling systems (Bakker. 1980, 1986).

  Figure 5 This plot shows the time it takes high level endotherms to overheat if they store all internal heat production and exclude external heat by allowing their body temperature to rise to maximum tolerable levels. The mass range approximates that of adult dinosaurs (including lagosuchians), with the highest masses of mammals also indicated: note that giant endothermic dinosaurs would have been more resistant to overheating than giant mammals! Energy storage capacity is in kcal assuming a 6-8°C rise in body temperature (up to 46.5°C), with 0.83 kcal/kg stored for each 1°C rise in body temperature; total active metabolic rates are either 2.0 times endothermic standard energy production/bout, or only 1.3 times normal standard metabolic rates due to suppressed levels of activity and/or standard metabolic rates. The results are in good agreement with thermal tolerances observed among large tropical endotherms.

  Reality: This is a major misconception (Costanzo and Paul. 1978; Paul, 1988a. 1990a). Many tropical mammals have reached from 1 to 20 tonnes, but no classic reptiles have done so, exactly opposite the predicted pattern. Elephants lack well developed evaporative cooling systems. Elephants living in treeless habitats do not drop dead from heat stroke, even in the most dangerous conditions of an extremely hot drought when it is not possible to dump excess heat by radiation or evaporative cooling in the first place, and shade is not available. Instead, large bull elephants have the highest survival rates under such circumstances, again opposite the predicted pattern (Owen-Smith, 1988). Field biologists have long known that endotherms from 100 kg on up use a classic thermal strategy in which their great mass is used to store a relatively low rate of internal heat production for most or all of the day, body temperatures are allowed to rise 3-10°C, and water loss is kept to a minimum (Schmidt-Nielsen et al., 1957; Taylor. 1969, 1970. 1972: Gordon. 1972; Finch and Rohertshaw, 1979: Schmidt-Nielsen. 1984). The built up heat is then unloaded into the cool night sky. This makes large endotherms practically invulnerable to over-heating under the harshest conditions, small endotherms must seek refuge or quickly die from heat stroke or dehydration. The large size of dinosaurs may have been an adaptation for better coping with high heat loads with a tachymetabolic level of heat production (Figure 5).

References:

1. The Evidence for Endothermy in Dinosaurs -
 Top Ten Hypotheses http://www.ucmp.berkeley.edu/diapsids/endothermy.html

2. Paleoclimate reconstruction using carbonate clumped isotope thermometry
(John M.Eiler) https://www.sciencedirect.com/science/article/pii/S027737911100268X

3. Why Dinosaurs Were Like Tuna, Great Whites, and Echidnas http://phenomena.nationalgeographic.com/2014/06/12/dinosaurs-tuna-great-whites-echidnas/

4. Sauropod Necks: Are They Really for Heat Loss?
(Donald M. Henderson)
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077108

5. Dinosaur Studies - Commemorating the 150th Anniversary of Richard Owen's Dinosauria (By L. B. Halstead)

Further readings (supporting above theories or with different theories):

GEOL 104 Dinosaurs: A Natural History - University of Maryland -
Department of Geology -
https://www.geol.umd.edu/~tholtz/G104/lectures/104endo.html
Body Temperatures in Dinosaurs: What Can Growth Curves Tell Us?
(Eva Maria Griebeler)
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074317
Ecology and Behaviour of Mesozoic Reptiles (by John L. Cloudsley-Thompson)
Dinosaur Paleobiology (by Stephen L. Brusatte)
The Dinosauria (edited by David B. Weishampel, Peter Dodson, Halszka Osmólska)
The Complete Dinosaur (edited by James Orville Farlow, M. K. Brett-Surman)
Encyclopedia of Dinosaurs (edited by Philip J. Currie, Kevin Padian)
Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution (Phil R. Bell, Nicolás E. Campione, W. Scott Persons IV, Philip J. Currie, Peter L. Larson, Darren H. Tanke, Robert T. Bakker) - http://rsbl.royalsocietypublishing.org/content/13/6/20170092
Dinosaurs used nasal passages to keep brains cool - https://phys.org/news/2015-10-dinosaurs-nasal-passages-brains-cool.html


Why don't myopic people see the world upside-down? I found this image while reading optical instruments in physics. If we look at the uncorrected rays, we see that the image they outline gets inverted. So why don't people with myopic vision see images as inverted representations?

You have misinterpreted the nature of the light rays shown in the diagram in the question.  The two rays are representing light coming from the same (distant) point in the environment, that is, some small feature on an object is reflecting (or emitting) light in slightly different directions and reach the eye separated by a small amount (less than the width of the pupil).  The rays are almost, but not quite, parallel.  The two rays, coming from the same point, should be focused on the same point on the retina (as are the red rays corrected by the external lens).  The spread of the uncorrected rays in myopia or hyperopia sends them to different places of the retina, causing the image to be out of focus, not upside down.

The path of light from an entire scene can be illustrated like this:

As this diagram shows, the image is upside down for all of us, in focus or not.  That the image top is at the bottom of the retina is not especially important -- the cells doing the interpretation could have been located physically located anywhere as needed.


Bonding in the primary structure of a protein My textbook says:

  The amino group of an amino acid reacts with the carbonyl group of another amino acid at the end of a polypeptide chain. This condensation reaction forms a peptide bond. ... The precise sequence of amino acids in a polypeptide chain is the primary structure of the protein.

Later, it states that

  The primary structure of a protein is established by covalent bonds ...

Is the primary structure of a protein governed by covalent bonds or peptide bonds? Are peptide bonds a type of covalent bond?

Any help is greatly appreciated.

Peptide bonds (also called amide bonds) are definitely covalent bonds.
This is also mentioned in the first line of wikipedia entry: https://en.wikipedia.org/wiki/Peptide_bond


Why aren't mammals and reptiles considered amphibians? We've all heard it: birds descend from dinosaurs, so they're dinosaurs too. But this got me thinking: doesn't this mean that, for instance, all terrestrial vertebrates – including humans – are technically fish? A recent video by MinuteEarth and the Wikipedia article for "Fish" confirmed my shower thought hypothesis.

Interesting. But... all amniotes, i.e. reptiles (and, by extension, birds) and mammals, descend from amphibians, right? If so, then why aren't they considered amphibians too?

Some named groups are not monophyletic (see this post for definition if needed). Fishes do not represent a monophyletic group. Groups like "fishes" are completely awful to define but everyone would agree that no, humans are not fish!

Now, it is important to understand for many terms, there might have a scientific and a popular definition of the term. For example, when people talk about reptiles, they talk about turtles, snakes, lizards, squamates but they don't talk about mammals. Hence by "reptile" they don't mean "Reptilia". Have a look at the post If dinosaurs could have feathers, would they still be reptiles?).


Solving a Pedigree Between Heterozygous Half-Cousins A man who is a known heterozygous carrier of oculocutaneous albinism marries his half-cousin (they share one common grandparent) as shown in the pedigree below. This trait is transmitted as a fully penetrant autosomal recessive. What is the probability that this couple will produce a child with this disorder?

A. 1/2
B. 1/4
C. 1/8
D. 1/16
E. 1/64

My calculation was 1/2 (for II-2 as he must be carrier) * 1/2 (for II-3) * 1/2 (for III-2) * 1/4 = 1/32. Please help me out by proper explanation to your steps and point out my mistakes. The correct answer given is 1/64. Pedigree shown in the image below.

From what I can tell, you are not including the probability of the grandfather being a carrier (it could be the grandmother who is the carrier). Calculation should go like:

P(Child is born with disorder) = P(II-2 is carrier) * P(I-2 is carrier) * P(II-3 is carrier) * P(III-2 is carrier) * P(Child is homozygous recessive)

P(Child is born with disorder) = (1/2) * (1/2) * (1/2) * (1/2) * (1/4)

P(Child is born with disorder) = 1/64


Difference in length of Okazaki fragments The length of Okazaki fragments in the lagging strand is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes.

  What (molecular mechanism, enzyme type ) determines the length of
  these Okazaki fragments?

  Moreover, which, longer or shorter, fragments would be more
  advantageous (energetically and considering accuracy)?

Longer fragments means less use of DNA ligase, DNA polymerase-I (prokaryotes) and other enzymes required to convert the okazaki fragments with dispersed RNA primers into a normal strand, and hence lesser scope of mistakes during replication in the lagging strand. Shorter Okazaki fragments improve telomere longevity, by reducing the capped-off portion after every division. Which of these views is correct?

I have found one more possible reason from Bruce Alberts' The Molecular Biology of the Cell: (Ch. 5 page 254)

  Nucleosomes are spaced at intervals of about 200 nucleotides pairs along the DNA strand , which may explain why new Okazaki fragments are synthesized on the lagging strand at intervals of 100-200 nucleotides in eukaryotes, instead of 1000-2000 nucleotides as in bacteria.

As already discussed by me and @SatwikPasani in the comments, increasing telomere longevity in eukaryotes by reducing the length of okazaki fragments, and consequently reducing the part of telomere cut-off after every division might be another reason for having shorter fragments in eukaryotes as compared to prokaryotes which do not contain telomeres.

EDIT : Having thought over it again, the relation between Okazaki fragment length and telomeres do not seem logical as only RNA primer length is important when considering telomere length.

Balakrishnan and Bambara (2013) explain the regulation of (and differences between) prokaryotic and eukaryotic Okazaki fragments in detail.


Erythroblastosis Foetalis If Rh- mother has Rh+ baby, the mother can become sensitized during first pregnancy and then if subsequent fetuses are also Rh+, there can be eryhtroblastosis foetalis.

I read that if mother is O- and baby is any +ve blood group other than O+ , then mother will not become sensitized during first pregnancy because a and b antibodies present in her blood will attack the antigen present on the fetus RBC and there will be no time for the mother to synthesize antibodies against Rh.

My Question : Can't the same logic be applied to all other blood groups? For example : A- mother and B+ baby.

if mother is O-

That means:

group O in ABO system: anti-A and anti-B antibodies
group Rh- in Rh system: no D antigen and no ant-D antibodies unless previously senzitized

  baby is any +ve blood group other than O+

ABO system: A, B or both antigens present
Rh system: D antigen present

So, the mother has anti-A and anti-B antibodies and her immune response will be directed towards the fetal RBCs containing A, B and D antigens. But, in theory, the immune system should also produce anti-D antibodies because of antigen presenting cells which will expose D antigens to T lymphocytes.

What is known is that if the mother already has anti-D antibodies, no other are secreted from fetal D antigens. This is how passive immunization vaccines work:

  This is done so that the fetal Rhesus D positive erythrocytes are destroyed before her immune system can discover them. This is passive immunity and the effect of the immunity will wear off after about 4 to 6 weeks (or longer depending on injected dose) as the anti-Rh antibodies gradually decline to zero in the maternal blood [1].

But the mechanism is not clearly understood:

  The most fascinating aspect of the story scientifically is that we still do not have a complete, mechanistic understanding of how this therapy works. The original hypothesis that Rh-immune globulin functions by clearing fetal Rh(D)-positive red blood cells from the maternal circulation, thereby hiding this foreign antigen from the maternal immune system, is inconsistent with the fact that passive immunization with Rh-immune globulin guides the fetal red blood cells directly to antigen presenting cells, the same cells responsible for initiating an immune response to foreign antigens [2].

References:

Wikipedia contributors, "Rh disease," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Rh_disease&oldid=615938189 (accessed July 28, 2014).
Eldad Hod. A Treatment for RH Disease. Available from http://pathology.columbia.edu/rh_disease.html (accessed 28.07.2014)


Can frequent ultrasound diagnostics be harmful? Are there any short or long term effects apparent in tissues if a zone (or the whole) of human body is scanned with ultrasonic waves often?

Ultrasound is considered a safe procedure (reference) which is accepted by the WHO as well (reference). There have been studies however, that show the link of ultrasound treatment to some undesirable traits.

Ultrasound could be possibly linked to a decrease in body weight on birth of infants (reference).

Frequent use of ultrasound may influence babies scanned to grow up left handed (reference)

A significant migration of neurons (change of neurons from their rightful area) has been observed in mice on exposing them to ultrasound at the prenatal stage. (reference).

A study has found detrimental affects to the brains of mice on exposure to ultrasound in the fetal stage (reference).

So based on these papers, I wouldn't call them a 100% safe but these tests all relate to repeated usage of ultrasound imaging. Ultrasound usage sparingly and on valid medical indication should not be a matter of concern.


When a muscle contracts, but not all the muscle fibers are activated, what happens to the remaining muscle fibers? I understand how motor neurons work, but I would like clarification on what exactly is going on when a muscle contracts. For the sake of simplicity, let's just use the bicep as an example. If I do a bicep curl with a weight that is the maximum weight my bicep can lift, all the muscle fibers in my bicep will be activated and contract(more or less). If I remove the weight and do the same bicep curl, now only a small percentage of the muscle fibers in my bicep will be activated and contract, because that extra force isn't needed. But, the whole bicep muscle is still contracting! It must be, otherwise wouldn't the other muscle fibers staying at regular length prevent the bicep from contracting?

So the only thing I could think of is that the unactivated muscle fibers are pliant and DO contract, they just don't initiate the contraction, but instead go along for the ride. So if you looked at the level of sarcomeres, in the activated muscle fibers, the myosin heads pull on the actin, causing contraction. In the unactivated muscle fibers, myosin heads are NOT pulling on the actin, but the sarcomeres are still contracting, due to the forces from the activated muscle fibers. Is this a correct interpretation of what's going on or am I wrong?

I don't think the unused sacromeres will contract though because every time you contract, it requires ATP and so it will be really expensive if you contract when you don't need to. I believe the unused muscle fibre will just be compressed or bent, since cells have a certain degree of compliance. I am guessing that is also why you won't feel your muscle as hard if you are not doing MVC


Are Pond Algae Edible for Humans? I've been farming freshwater fishes. After some time, i found some green algae grows there. When the algae dried, it looks like nori (which commonly used for sushi wrapping).

So, i wonder if those algae edible for human. Are the algae safe to eat?

Here's the picture:

I came across a this Wikipedia page which said blue green algae from ponds can be used as dietary supplement (in tablet form).

Many other articles on the internet like  here suggest it is included in many diets in many places across the globe.

However, without proper regulation one can include a heavy metal contaminated vegetable to their diet which is detrimental to health. Furthermore cyanobacteria are known to produce toxic substances known as microcystins which can cause damage to human organs as well.

So unless you are certain of the biochemical balance of your pond I would  recommend not integrating it in your diet. Rather you can find commercially available ones which your local regulatory authority(s) recommend for dietary purposes.


Do bacteria die of old age? I know that the cells of mammals at least stop dividing when they are old, and then die a programmed cell death. Then other cells have to replace them.

But in a bacterial colony, each cell replicates for itself. Obviously, if a division of a bacterial cell of generation N were to produce two new cells of generation N+1, and all bacteria died of old age at generation M, there would be no bacteria left around.

So how is it regulated in bacteria? Are their divisions simply unlimited? Does a cell never die and just divide forever?

This is a interesting question and for a long time it was thought that they do not age. In the meantime there are some new papers which say that bacteria do indeed age.

Aging can be defined as the accumulation of non-genetic damages (for example oxidative damage to proteins) over time. If too much of these damages are accumulated, the cell will eventually die.

For bacteria there seems to be an interesting way around this. The second paper cited below found that bacteria do not divide symmetrically into two daughter cells, but seem to split into one cell which receives more damage and one which receives less. The latter one can be called rejuvenated and seems to make sure that the bacteria can seemingly divide forever. Using this strategy limits the non-genetic damage to relatively few cells (if you consider the doubling mechanism) which could eventually die to save the others.

Have a look at the following publications which go into detail (the first is a summary of the second but worth reading):

Do bacteria age? Biologists discover the answer follows simple
economics
Temporal Dynamics of Bacterial Aging and Rejuvenation
Aging and death in an organism that reproduces by morphologically
symmetric division.