How to Design an siRNA Experiment? I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein.

From what I understand, I will need to pick two specific siRNA's from  a screen of multiple siRNA candidates. As a negative control, I should also make a non-sense scramble siRNA. Of course the specific siRNA should show a significant knock-down of the enzyme; the control should not affect expression. As well, there should also be a validated positive control (such as GAPDH) and a mock treated control.

Is this experimental design sufficient? What are some common things to keep in mind, or pitfalls to avoid when doing siRNA studies?

First you should decide whether you want to design an shRNA or use siRNAs.

If you want to use shRNA you should look at the rules that "Mad Scientist" mentioned. You can insert mismatches but make sure not to disrupt the secondary structure. You can use RNAFold to verify.

shRNA always has issues and you have to optimize your design, test it by realtime PCR or Northern blot etc to confirm the production and the concentration.

You can design siRNAs and there are online algorithms to help you design one.
You have to choose a sequence which is specific to your gene. This step is important for both shRNA and siRNAs in order to minimize/avoid off-targeting.

A common practice is to use a pool of siRNAs for a single gene. Pooled siRNAs are commercially available for many genes.

For the experimental controls you would need to do two experiments:

mock siRNA treated; which wont affect any gene
Your siRNA treated

then test for a reference gene such as GAPDH and your gene. A good reference gene should be the one which is not expected to change expression. GAPDH may not be a good reference always (for example in cases where metabolism is affected). The choice of reference gene is intuitive and depends on your prior knowledge of the system. Instead of GAPDH you can also transfect GFP and quantitate that as a control (spike in).


Why is liquefactive necrosis only seen in brain? Liquefactive necrosis is a type of necrosis uniquely observed in brain. This occurs due to breakdown of cellular proteins by the action of hydrolytic enzymes.
In other parts of the body, usually a different form-coagulative necrosis is seen.

What makes the brain so unique that this form of necrosis is only limited to brain?

Liquefactive necrosis is indeed only seen in the brain in the absence of infection, but it is also seen in the case of some bacterial infections.  The reason is that liquefactive necrosis is, as you said, caused by the release of digestive enzymes and constituents of neutrophils.  Bacteria will, under some circumstances, release those enzymes, causing the cells to be devoured.
The fact that liquefactive necrosis is seen in the brain in the absence of bacterial infection is in part due to the fact that neurons have a higher lysosomal content, leading to a higher tendency toward autolysis, and in part due to a high concentration of neutrophils which swarm into an affected area.

Sources:

What happens after brain tissue dies?, PathologyStudent.com, 2012
Liquefecative necrosis, Medigoo.com, 2016
Necrosis, Cell (Liquefactive, Coagulative, Caseous, Fat, Fibrinoid, and Gangrenous), Rotimi Adigun1; Steve S. Bhimj, 2017


Do plants experience the following feelings I am not a student of biology,in other words I have not read biology much.

But I read that plants have life and so my question is the following:

  Suppose I take two saplings of two different varieties of hibiscus(or any other tree variant) and I put them in the same pot and allow them to grow up.
  Suppose they grow up and become well grown plants after say 4-5 months.
  My question is:

  Will the two saplings experience any feelings for each other,in other words will they become friends or share any relation with each other.
  Suppose one of them is attacked by insects and its growth gets shunted,will the other plant also experience some feeling for it.

  If I uproot one plant will the other one feel lonely or any other kind of feeling as if its counterpart is missing.

If someone cares to answer the above questions,I would be very grateful.
Thank You

Wikipedia defines emotion as "any conscious experience characterized by intense mental activity and a certain degree of pleasure or displeasure."

Plants do not have a central nervous system and therefore no mental activity so they certainly don't have emotions in the sense that humans and animals can have emotions. However plants feel/detect being eaten and they can communicate this to other (related) plants by releasing volatile organic compounds.


Why do humans grow taller than their ancestors? I'm taking the Introduction to Genetics And Evolution course and in the first lecture it was said that:

  Evolution in a biological sense is simply a change through time. And very importantly, that is change through time over generations. So for example, the human species, hundreds or thousands of years ago was much shorter than it is today. Over the course of those generations, the human species has grown taller. That change is an evolutionary change.

I'm wondering why we become taller than our ancestors? Now we almost don't fight with other species and can live doing something that doesn't require physical strength. It's more logical to me if we would become shorter.

A likely misunderstanding of yours

Now we almost don't fight with other species

Misunderstanding about selection
As you will go through this course, you will understand why this sentence makes little sense. A change in allele frequency via natural selection is caused by a fitness differential among genotypes within a population. The existence of a competitor species would eventually affect this fitness differential but there is no need for a competitor for having a selection pressure.
I think you are having the view that selection is a process that allows a species to be better at coping with a competitor but this is wrong. Selection will increase the frequency of individuals having high fitness in the population. The resulting population may well not be a better competitor.
False opinion that we are not competing with other species
Also, about nearly 50,000 people are dying every day from infectious disease (UN press release). So, we are definitely still "fighting" with other species. Adaptation to malaria in humans is a famous case study (see this answer and its links).
Also, according to reuters (who fail to link to their source), the worldwide cost of pests in agriculture is estimated to about 540 billions USD per year! So yep... competition there is.
What selection pressures are there on human height?
Review paper recommendation
Stulp and Barrett 2016 is a review paper on the evolution of height in humans that you might want to have a look to have a clearer picture than what I will give here. It is easy to read. I highly recommend having a look at it.
They cite a lot of papers. I won't cite them again below but I will just attempt to make a vague summary of the parts which I think will interest you the most.
What selection pressures are there on human height?
The question appears to not be that easy to answer. In humans, height is highly heritable and there is a lot of variance in height among populations. It is likely that different selection pressures may have acted on different populations.
There are a diversity of selection patterns
In short, selection pressures on height include intra and intersexual selection. Taller adults seem to have a reduced mortality rate. Taller women have a lower risk of complications when giving birth. However, in both men and women, the correlation between height and number of offspring varies a lot from study to study (and likely from population to population). In the USA for example, men having the highest number of offspring are of intermediate height (balancing selection).
It appears that epigenetic variation also have an important impact on height Simeone and Alberti 2014 and there might have a sex-driven intra-locus conflict on height (Gilks et al. 2014; Stulp and Barrett 2016)
There is evidence of current selection on height
We have a fair number of evidence that height was and is still under selection in humans but we think that the exact pattern of selection pressures acting on it is quite complex. Note that there is evidence that height is still under selection today.


How does the brain recall information? In computers, finding a single word is realized through serial attempts across all available connections to find a specified target.

How does the brain solve this? How does the whole process, from the command to recall some memory to actually "play" its algorithm look like?

By "recall" I mean literally, attempting to bring back an image, a word, a melody or any remembrance from memory.

This is a great quesion! There is lot of work still being done on this. Unfortunately I don't think I know enough about CS or computer engineering to make analogies, so I'll give a quick crash course and some examples instead and hope you find it helpful. Long story short though is that we are just now making really exciting headway into how memory might actually be stored and recalled and its usually a very dynamic, active, and possibly even stochastic process, not really like a search algorithm in a computer at all.

The brain works differently than a computer in that it encodes all of its information in frequency of signal firing and the patterns of firing between circuits with varying stregnths of connections based on experiences. Frequency is dependent on the neuron itself and patterns of firing between circuits are dependent on where the neurons project to, and how strongly they interact with the next neuron. At this very basic level memory is stored and recalled by placing proteins in the membranes of neurons that are strongly activated to make them easier activated in the future. These are sort of the first steps toward memory. This is called long term potentiation and just means that this neuron is primed to fire more readily and stronger in response to similar input in the future.

To build on this,  there is a classic example of this occuring and causing sensitization ( an exaggerated response to the same stimulus) in conditioning experiments in the sea slug Aplysia. Aplysia has a reflex where it will withdraw its gills slightly if you touch its siphon. You can pair a shock to the tail (unconditioned stimulus) which elicits a large withdrawal of the gills, with a conditioned stimulus (touching its syphon to elicit the withdrawal reflex) to get the sea slug to associate the two. The end result is that the sea slug will learn/"remember" to withdraw its gills fully in the presence of the syphon touch. No learning cannot happen without recall of some sort, and in this example the slug was associating and learning from two "circuits" to produce a different behavior.

In something a little more complex than a slug, memory and recall still functions much the same way, its just the circuits that are interacting are entire brain regions. Most people view the hippocampus as acting sort of like a relay center and boot loader for different memories by taking external input and sorting them to the right parts of the brain. A good example of this would be the difference between dorsal and ventral streams of information in the brain. For a really basic breakdown of this phenomenon there are two areas of your brain that I will focus on - the parietal lobe and the temporal lobe. The parietal lobe is known to be involved in spatial processing, and the temporal lobes are known to be involved in semantic and auditory processing. When information enters the brain (eyes, ears, nose etc.) it will be processed by sensory structures, sent to the thalamus and hippocampus to be "relayed" to the right areas of the brain. Relayed in this case is going to be dictated by whatever connections and how strong they are in the brain. In this case from proteins expressed in the cellular membrane that make some neurons in the hippocampus more responsive than others, so they are more likely to fire. Then, it depends on where they are projecting to that determines where they information is sent.

It just so happens the brain is arranged in such a way that neurons projecting dorsally, or to the parietal lobe I mentioned, will tell you "where" the stimulus is, and those projecting ventral to the temporal lobes will tell you "what" it is. This is achieved because these lobes are highly interconnected to even more regions in the brain and send their processed "where" and "what" info as input to other regions. These regions will all fire a certain way in response to this information and that pattern of firing can be considered a recollection or memory. Sorry that this is dense and so crash course-y but I hope it is helpful in clarifying how the brain recalls some information. Of course this is  a developing field and we are learning more about how it functions every day. These are just some classic examples.


Regarding the kingdom Animalia, which phylogenic tree is more common: Molecular Comparisons or Body-Plan Grades In the picture below, which I obviously do not own:

it depicts two different phylogenic trees, one which is based on molecular comparisons and another one which is based on body-plan grades. My question is which is more common or accepted in the current Biology world?

Image reference: http://www.zo.utexas.edu/faculty/sjasper/images/32.12.gif

Long story short, use sequence information if you can.

The long story long:
Sequence information and the trees generated from them are strictly more reliable than morphological characters. For instance: sharks are pretty much the same shape they were millions of years ago, but they've been accumulating genetic differences 'invisibly' that allows us to group the different kinds of shark accurately. Where genetic data is unavailable (paleontology as a rule, certain kinds of field taxonomy where it's cheaper to code the morphological features of each new beetle than sequence them all) morphological trees are still used. So in terms of which tree type is more common: It depends.

In terms of which tree type is more accepted, it's genetic data by a landslide. Genetic data by and large is much less affected by homologous structures and convergent evolution. In addition, it works on species that all look pretty much identical (imagine trying to code hundreds of bacterial species that are all closely related). Using highly conserved cellular machinery, trees for very distant species can be constructed. Using unconserved noncoding sequences trees for very closely related individuals trees can be constructed with a reasonable degree of accuracy.

Some examples: Mitochondrial Eve would be impossible to date with morphological characters. There's just not enough morphological variation between humans.
Opabinia is a really good example of how hard it is to classify things based on shape, especially when they're a weird shape.
Something you can do yourself: Human  and Thermodesulfator(seq) are about as morphologically distinct as two living things can be. One is you, and one eats carbon dioxide and breathes sulfate and hydrogen. It lives at the bottom of the sea and would be more at home in a cup of hot coffee than outside it. Nevertheless, the two species show ~50% sequence similarity using 16S, twice as much as would be expected by chance and easily enough to classify a third thing as more closely related to one or the other. Try it yourself if you like.


How are large snails able to climb trees? In answers to What kind of hot pink eggs are these? and the linked duplicate I found out that snails that live in the water will climb up a smooth stick or branch to deposit their eggs. Today I saw several large (8 to 10 cm) snails climbing trees both a relatively smooth one and one with considerably rough bark.

How do these large and heavy snails manage to adhere safely to the sides of trees and climb so high? Is it adhesion? Is suction involved?

click images for full size view

above: June, northern Taiwan lowlands in a damp area. They look similar to the species discussed in answers to What are these four large snails doing? below: from What kind of hot pink eggs are these?

The foot of the snail secretes a sticky mucus which allows the snail to climb even the smoothest surfaces. The mucus have two states: one in which it is almost liquid to lubricate motion, and the other - a very viscous one, in which the mucus is sticky and "glues" the snail to the surface. The mucus can alternate between these two states via the pressure the snail activates on it. The gluey state sticks the snail to the surface via adhesion.

Researchers discovered nearly 30 years ago that snail mucus has some unusual properties. It allows the animal to stick to a surface while moving, with the mucus changing its characteristics according to how firmly the snail presses on it.  The slime initially acts like glue, sticking the snail to the surface. But when the snail's foot presses down hard enough on the mucus, it becomes more liquid, allowing it to flow underneath the moving snail. Existing theories assumed that this special characteristic of snail mucus was always necessary for the snail to push off and move forward.

Cited from: https://news.stanford.edu/news/2011/april/snail-slime-trails-040611.html


How specific is the adaptive immune response? When you read about the adaptive immune response, you are often told that the response is specific to each pathogen - that the response is tailored. My question is - to what extent is this really true? And if it is true, how is the response tailored?

I understand that the B cell receptors (and, consequently, the antibodies produced by plasma cells in response to a pathogen) are highly specific. A pathogen will bind specifically to a B cell receptor on a particular B cell and particular antibodies will be produced for that pathogen. Again, T cells are specific for each pathogen.

But, it strikes me that there doesn't seem to be that much variation in what antibodies do. Each antibody is particular to its pathogen, but all antibodies work by doing the same few things, e.g. opsonisation, or inhibiting viruses from infiltrating cells. Yes the antibodies may be specific, but to what extent is it true that the antibody will produce a specific response to a specific pathogen? I mean, does the antibody for staphylococcus affect staphylococcus differently from the way the antibody for listeria affects listeria?

Again, each CD8+ Tc cell is specific to its pathogen, but they then seem to go about killing their target pathogen in very similar ways - inducing apoptosis or lysis via perforin and various cytotoxins. So, again, would the CD8+ Tc cell for influenza respond differently to the CD8+ Tc cell for norovirus?

The adaptive immune response is highly specific and is made to fit a specific antigen. The antigen binding sites are located on the ends of the two short arms of the Y-shaped molecule, as seen in the figure below:

The recognition site is made of the ends of one short immunoglobulin chain and one long chain. The ends (shown in yellow in the figure) are also called variable regions and are the key to the big variety of different antibodies.

When B cells develop, there B cell receptor (which is basically a membrane bound antibody) is tested if it reacts to components from the own organism. If not, they are released into the periphery (blood stream). These B cells are then called naive, since they haven't come in contact with an antigen. They express a B cell receptor which usually only has a weak affinity to an antigen - but the body produces quite a wide variety of these cells. (see the second figure).

When the body comes in contact with an antigen (like a virus), it is taken up by the so called professional antigen presenting cells (dendritic cells, macrophages, B cells) of the immune system, broken down into small pieces and these are presented to the immune system. This activates the affinity maturation of the B cell receptor, somatic hypermutation and finally the clonal selection of the cells, which produce the antibodies with the highest affinity (the strongest binding) to the antigen.

There are estimates that the human immune system can produce around 10 billion different antibodies. This variability is achieved by the genetic variability of the mutation of the variable region of the antibody (the whole process is nicely explained here).

For further information on this topic I can recommend reading the following articles:

Development of the immunoglobulin repertoire.
Immune receptor editing: revise and select.

The reaction of the body afterwards is always the same, as you state yourself. The specificity of the adaptive immune response is "only" mediated by the specificity of the antibodies. This also makes the system very strong against new pathogens, since only one part of the system needs to be adapted, while the cascades behind it (like apoptosis) are always the same and can be activated fastly if needed.

This can cause some problems, too. Think about self-antibodies, which occur in autoimmune diseases. Here the body can not distinguish between a legitimate immune response against a foreign antigen and those, which are from the own body.


Why does alum work on blisters in the mouth/cold sores? Alum used to be an age old tradition to treat sores in the mouth and it worked beautifully.Foes anyone know why Alum works on sores in the mouth ?

Alum has been shown to be effective in treating aphthous stomatitis (canker sores) and it is believed to be due to the compound's significant drying effect. Alum is known as an astringent - a chemical compound that tends to shrink or constrict body tissues. More information on alum's astringent properties are reported in this paper. As the infected tissue shrinks there is a decrease in pressure due to swelling and this less pressure around the nerves in the affected area. The exact mechanism is still under question.


Does common X-like picture represent one doubled chromosome or two homologous chromosomes? What is on common X-like picture of chromosome?

Here is the image from Wikipedia:

Are (for example) lower petals homologous to each other?

If yes, then why (1) is entitled as chromatid: one-half of two identical threadlike strands of a replicated chromosome? Homologous parts are similar but not identical.

If no, then why does human chromosomes are often denoted by Xs:

Do we have 23 Xs (females) or 46 Xs?

The "X" you see is a chromosome. The two strands that forms the X-shaped chromosome are called chromatids. As they are bound together (by the centromer), they are called sister chromatids. Note that chromosomes look like that only during the metaphase. Note also, that not all chromosomes have a centromer that is in the middle of the chromosome as it is obvious from the picture in your question.
Many species (including humans) have two sets of each chromosome. If you add the other chromosome in the picture, you would see a pair of chromosome. One chromosome of the pair is said to be homologous to the other one. Below is a cladogram during the metaphase of a human (I let you figure out the sex) showing each pair of chromosome.

Sister chromatids are identical (except for mutation during the last chromosomal replication). Homologous chromosomes are similar but not identical. Crossover occurs in between chromatids of homologous chromosomes.
Further comment on your figure
There are 23 pairs of chromosomes, that is 46 chromosomes. Your picture shows only one chromosome per pair, that is your picture shows only 23 chromosomes. In other words, your picture shows the haploid genome and not the diploid genome.


Identification of an insect (?) This one was found in the woods of northern Poland. It was about 5 cm long and crawling pretty dynamically. For me it seemed a little too big for a butterfly larva.

What is it called?

It's an  elephant hawk-moth, Deilephila elpenor. Here is an image from Wikipedia to compare with:


When can I assume individuals marrying into a pedigree are non-carriers? If I'm not told that they're non carriers, and if I don't have proof of their geneotype based off of progeny, when can I assume they're non carriers for a trait?

All the time.

Unless you are specifically told/shown they are carriers, they are assumed to be Wild Type and do not carry the mutation.


What is the fate of micronucleus DNA? Micronuclei are cellular structures that are formed as a by-product of, usually, defective mitosis. The piece of chromosome in a micronucleus may, or may not contain a centromere and the DNA is wrapped in a double lipid membrane.

I have tried to find information, but I failed to find out what the fate of these structures is within the cell once formed? And is the DNA within it lost for the cell?

Emergence of Micronuclei and Their Effects on the Fate of Cells under Replication Stress (2010) explores how micronuclei behave and determine cell fate. It found that micronuclei is pretty closely related to apoptosis. If the cells with micronuclei didn't go through apoptosis, there were instances where the micronuclei would literally just disappear. They were unable to determine if it was expelled by the cell or reabsorbed into the main nucleus. However, there were also cases where there would be an increase in the number of micronuclei.

They concluded that there is a number of ways for the cell to get rid of the micronuclei and they were unable to determine which is the most likely.

I was unable to find any more recent in-depth studies (that I could understand).

So, according to this paper there are several answers...

Case 1: It is reabsorbed into the nucleus and most likely the information within is saved.
Case 2: It is expelled from the cell and the information within is lost.
Case 3: The cell undergoes apoptosis and all information is lost.


How to convert nanogram to picomole? I have lets say 10ng/uL of RNA. How can I convert it to picomole?

I need it to calculate how much magnetic beads I need. This is the product: http://tools.lifetechnologies.com/content/sfs/manuals/dynabeads_m270_sav_man.pdf

I do not know how much beads should I use.

Average molecular weight (MW) of a ribonucleotide = 340g/mol

Size of RNA = x

MW of RNA = 340*x g/mol

moles of RNA needed = y * 10⁻¹² moles (1 picomole = 10⁻¹² mol)

mass of RNA needed = 340*x*y*10⁻¹² g

Conc of RNA = 10*10⁻⁹ g/µl `(1ng =10⁻⁹g)

Volume needed for y picomoles = (340*x*y*10⁻¹²)/10*10⁻⁹ = 0.034*x*y µl

If your RNA is biotinylated then add the MW of biotin to MW of RNA


RNase and EtOH issue I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes RNase or should I be worried about it?

Addition: I am using eppendorfs directly from the bag. So they supposed to be RNase-free, right?

Thanks.

Ethanol is not a problem, we use it without any further precautions and it seems to be RNAse free. You should take the usual precautions you should take with all chemicals when you work with RNA, never use a spatula or spoon to get anything out of the bottle (unless you want to bake your spatulas all the time), always pour them to avoid any contamination.

We autoclave the Eppis once, this might be an unnecessary precaution. I think you can also buy them certified RNAse free, but I'm not sure if they are actually treated any different or simply more expensive.


How are fMRI responses to auditory stimuli measured? How can fMRI experiments be conducted which measure the response to auditory stimuli (e.g. music) when the apparatus makes such loud, nasty, and distracting noises? Are there quieter MRI tomographs in the meanwhile, or must the stimuli (transfered by earphones) be louder than the noise of the machine? How to measure the effect of a whishper then?

I could have found this article earlier, but as things go, I didn't. But possibly it contains most of what can be said to this question:

Jonathan E. Peellej, Methodological challenges and solutions in auditory functional magnetic resonance imaging, Front Neurosci. 2014; 8: 253


What causes a selective shift of colour perception after removing wavelength filtered glasses? Background

To improve sleep by reducing blue-light melatonin disruption, I wear night-glasses that filter short wavelengths (e.g. something like these). With these glasses on, both the top and bottom bars of this test image will appear visually identical:

(Source: Personally derived from this public domain image and released to public domain)

But the colour spectrum you "see" while filtering the blue light will not appear to be either of these bars; instead some partially de-saturated hybrid of the two. I think this is probably due to a pervasive blue wavelength of the LCD back-light regardless of defined colour contrast.

However, there is something else odd going on. If I wear these glasses for several hours and then remove them for some reason - all the blue colours I should see will be muted, partially de-saturated or even interpreted as a shade of green for at least several minutes afterwards (I haven't stop-watched the effect). Freaky.

Question

Why is this selective shift of colour perception occurring for a while after removing wavelength filtered glasses?

The short answer is you don't see light you see a reconstruction of your environment made by a learning organ, your brain adapts to changes in stimuli. Color in particular is tricky because there is no objective way for your brain to determine somethings color, it can only see the wavelength that reaches the eye which are affected by everything along the way including the color of your eye's tissues.  Your brain adjusts to the filter, until it sees the colors it expects to see again. It does this by becoming less responsive to some signals, in the case of the glasses the colors in between certain ranges. when the glasses are removed the brain is still largely ignoring those signals and has to learn to accept them again in exactly the same way it learned to ignore them.

You can do something similar with glasses that flip the visual field, (turn everything upside down). The work was done by This is a good article. Follow the link for more information. George M. Stratton, and after wearing the glasses eventually you start seeing things right side up again, then when you remove the glasses everything is upside down again, the brain has to again relearn to see right side up.


Trees ability to transport water How can trees be able to transport hundreds of liters of water all the way up to the crown and out in the leaves?

The most popular theory is the ‘hydraulic limitation hypothesis’ (Ryan & Yoder, 1997), which suggests that as trees grow taller, it becomes more difficult to supply water to their leaves. This hydraulic limitation results in reduced transpiration and less photo-synthesis, causing reduced growth.
It is known that in larger/taller trees water supply is limited by two factors — distance and gravity. Larger trees have a longer pathway of transporting tissue, this tissue is known as xylem. This is known as hydraulic resistance and makes it more strenuous for the water to move around in the tree. So now not only is the pathway long, but the water also has to beat gravity. Increased force is necessary to pull the water up to the highest leaves. Additional difficulty comes from the trees growing upright. Fast - growing/short trees frequently have shorter life-spans. They achieve their expeditious growth by having broader, wider xylem vessels, this increasing their hydraulic efficiency. At the same time this provides space for embolisms. An embolism makes it unable for a xylem vessel to transport water. Taller, slow-growing trees are longer-lived, this is caused by them having multiple xylem vessels, rather than having only a few wider ones like the fast-growing trees. Short-growing trees also have a more secured hydraulic system, preventing the forming of air-locks.


What molecular processes are involved in pseudopodial extension? I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular level? I am not particularly interested in the taxes that amoeba recognize, but rather the mechanism of response to these taxes.

The extracellular cue signal must be relayed to the cell by Rho family of GTPases, like in the case of filopodia and lammelipodia. This causes local actin polymerization leading to extension of pseudopodium.

For a casual reference you can check the wikipedia page on Rho family of GTPases. Cell biology books like MBOTC also have information on mechanism of cytoskeletal dynamics.


PCR master mix contents I am running PCR reactions with different sets of degenerate primers and I want to know what should go into the master mix

My usual master mix:

DEPC water
PCR buffer (-Mg)
25mM MgCl2
10mM dNTPmix
cDNA

On ice I add my forward and reverse primers to the appropriate PCR tubes, add master mix to each PCR tube, then right before I pop them into the thermal cycler I add taq and mix.

Is this a proper way of doing it? I get product but I'm thinking maybe I can improve it by changing what I add to the master mix. For example, is it better to add taq instead of cDNA to the master mix and then add cDNA before I start the PCR? Is it okay to add both cDNA and taq to the master mix together?

I always add the Taq to the mastermix. First it makes the handling easier and it avoids pipetting steps which can cause contamination and can also be forgot. Then the enzyme is very stable and will even tolerate room temperature without problem. Since we are going to heat this 30-40 up to 95°C, so this is clearly not problematic. Since the reaction mix is cooled, you reaction will not start. And even if it does, there wouldn't be much amplification due to the low temperature.

I usually add everything which is the same for all reactions to the mastermix (this can include the DNA as well). If I use more than one DNA I split the mastermix in half. This way you are not going to make different pipette errors for the template, which is especially important for realtime-PCR. I usually dilute the primers slightly so I can pipett bigger volumes (simply use a part of the water used to balance the PCR reaction). You can also premix primer pairs, if you want, I have never seen problems doing this.


Tree census data for Sweden/Scandinavia? Is anyone aware of any attempts to count or approximate the number of trees there are in Sweden or Scandinavia? I have a small popular science side project for which this would be useful

I would definatley look at data from Swedish National Forest Inventory (Riksskogstaxeringen). They have time series data of multiple variables (DBH, size classes, species, dead wood etc) from plots all over the country. Extrapolations based on these data should produce reasonable estimates of total tree count, and probably the most accurate one that can be obtained at the moment. As an example, this report (in swedish) includes graphs on trees/km$^2$ for different species and areas (page 17 ff), but this is only based on areas that can support productive forestry.


Plasmid addiction system in high-copy number plasmids Are there high-copy number plasmids that utilize a plasmid-addiction system?

According to the review by Kroll J, Klinter S, Schneider C, Voß I, Steinbüchel A. Plasmid addiction systems: perspectives and applications in biotechnology. Microbial biotechnology. 2010;3(6):634-657. doi:10.1111/j.1751-7915.2010.00170.x., there are high-copy-number Plasmid Addiction Systems (PAS), "specifically the addiction system depending on plasmid‐borne ORT utilizing the lac repressor."

  The lac repressor protein (LacI) binds to the lac operator (lacO) and therefore represses the expression of the kanamycin resistance gene. When IPTG is available as an inducer, LacI is titrated by lacO, and the E. coli cells were able to grow in media containing kanamycin due to expression of the corresponding resistance gene. The same result was obtained when high‐copy‐number plasmids harbouring lacO were used for ORT. In this case the plasmid was stably maintained over 72 generations (Williams et al., 1998).

ORT = operator repressor titration

ORT is one of the three main groups of PAS.


What is the difference between "cistron" and "gene"? I'm asking after reading the cognate wikipedia.en article on "cistron". I am still not sure about the difference between the two terms.

To me it seems valid to picture a "cistron" as the genome wide set of a specific gene's alleles ?

Thus if all copies of a gene bear recessive mutations all generating the same phenotypic trait (not necessarily the same mutation) no complementation is observed in a cis-trans test?

A cistron is a gene - here's how the word came about:

It's 1955. The proposed double helical structure of DNA has been published and the race is on to understand the implications of this for genetics. Geneticists have been working with genes for decades, but they don't know what genes are. Sanger has sequenced the two polypeptides of insulin, so the idea of a specific sequence of amino acids is established. The emerging molecular geneticists believe that genes will be explained by a feature of DNA, probably a sequence of nucleotides, but they don't know how. Crick and others are theorising about coding (i.e DNA > protein), but at this stage there is no genetic code, no mRNA or tRNA.

Seymour Benzer, at Purdue, is working on fine structure of a genetic region in bacteriophage and in this year he publishes a key paper with that phrase as the title. Without going into a lot of detail about his experimental set up, he is studying a region of the bacteriophage T4 genome called rII. Wild-type T4 can form plaques on E. coli B or E. coli K12. Mutations in the rII region cause a large plaque phenotype in E. coli B so it is easy to isolate them, but these phage cannot produce plaques on E. coli K12 which sets the scene for a powerful assay for rare recombination events.

Benzer used this system to do very fine mapping of thousands of rII mutations because he was able to use the system to measure recombination frequencies, but what matters in the present context is that he was able to do a kind of complementation test (he called this pseudo-allelism). He was able to assign the rII mutants into two groups according to whether, in a mixed infection, they produced lots of progeny. So if he mixed two phage with different mutations and didn't get many progeny he put these in the same group. On the other hand if he did get a lot of progeny he placed the two in different groups. He called this approach a cis-trans test.

  "The application of the phenotype test to pairs of rII mutants leads to the division of the region into two functionally separable segments."

This is as close as he dared to go to claiming to be studying genes. He refers to 'functional units' but never uses the word 'genes' because at this stage that word belonged to classical genetics in higher organisms. In 1957 he proposed the word cistron for the functional unit defined by this type of test, and the word caught on, particularly because of its incorporation into the operon model with the idea of polycistronic mRNA. His other coinings, muton and recon were not adopted.

The two T4 genes/cistrons in the rII region of the phage genome are now called rIIA and rIIB.

  Benzer, S (1955) Fine structure of a genetic region in bacteriophage Proc. Natl. Acad. Sci. USA 41:344-354


Why do farts stink, but perfume does not? Why is it that natural things like farts, poop, halitosis etc., from which we are always surrounded smell "bad"; whereas manufactured products, such as perfume or glue smell "good" to most of us?

In my understanding, things smell "bad", because they are not good for us. But how are farts not good? And shouldn't artificial things like perfume or glue, which are relatively new to us, smell "bad"?

Why is it that natural things like farts, poop, halitosis etc., from
  which we are always surrounded smell "bad"; whereas manufactured
  products, such as perfume or glue smell "good" to most of us?

  In my understanding, things smell "bad", because they are not good for
  us. But how are farts not good? And shouldn't artificial things like
  perfume or glue, which are relatively new to us, smell "bad"?

Kind of a strange question but here is a quick and rough answer... There are at least three things to think of here.

Firstly, yes often natural things that are good for you have evolved to smell attractive, but not all natural things are good for you. Therefore a fart should not smell good just because it is natural. And it is likely that breathing farts non stop is not good for you.

Secondly, perfumes etc. have been chemically manipulated or designed to smell nice by human manufacturers - the preference for such smells existed before the specific perfume, the manufacturer simply designed a fragrance that was attractive.

And Finally... Not everything exists because of selection. Farts probably smell as a by-product of process of digestion rather than selection for avoiding them. Gas is produced during the digestion processes, the amount and odor (determined by the constituents of the gas) of gas will likely depend the efficiency of digestion and what is being digested. The dominant selection force affecting the odor is then probably related to digestive efficacy and selection against odor would only be (relatively) very weak.

It's better to digest food and fart a bit than it is to not digest but smell nice, digestion is quite important!


How does the brain know where a signal came from? What is the addressing system I am an electronic engineer so I am thinking about this from an electronics outlook.

How does the addressing system work, As I see it, the nervous system is small parallel branches attached to larger "serial" lines (spinal cord).

The serial line is then attached to the brain, but how does it then figure out where the message came from and then get the message back to the place it came from.

If I were to build a robot I would have an addressing system with each message and maybe some kind of error checking to make sure the messages don't become corrupted, but as it's not an electronic system I don't see how the brain could possibly do this. unless it is a fully parallel system and there is a single wire going from every sensor back to the CPU..

The brain knows where a sensory signal came from by what neuron is doing the signalling.  The incoming neuron is dedicated to signals from one source and, since it is not shared by other sources, does not need to have an encoding as to what the source was. When your toe touches something, the sensation causes a pulse which, amazingly, travels along a single nerve cell (neuron) up to the brain stem.  That neuron has its nucleus at a dorsal root ganglion located by the spinal cord, and has a fiber (axon) that extends to the source (toe) and another extending up to the brain stem.  This pathway is called the PCML pathway and the Wikipedia article has some readable details.  This page has a schematic and tabular summary, while this site has a good descriptive overview.

If a robot were built along the same sort of design, to determine what was happening at 1000 places in its body, it would have 1000 wires running to its central computer.  You probably wouldn't choose to use such a design, but then you probably wouldn't be designing a robot that has to build itself from raw materials.


How to write a stoichiometric matrix for a part of the Pentose phosphate pathway maybe this is more bioengineering than biology but I didn't find any such group.

So I got the following photo:

And I was asked to do the following for the network inside the red area.
1) Write the stoichiometric matrix for the network
2) Draw a pathway map for the network
3) Draw primary metabolite connectivity maps
4) Write the mass balance equations for primary metabolites

I know that for the first one the columns are the reactions taking place and the lines are the "chemicals". Should the markings on the columns be the same as the numbers that are written on each reaction? (like "3.1.1.31")
Almost every reaction can go in both direction, is there anything that says which chemical should get minus and which one gets plus?
My attempt at the matrix was:

As for the pathway map, isn't that basically the photo is given?
And finally what would be a "primary metabolite" in this case?

All help and hints very well appreciated!

This is not a particularly well written homework question. I'll try to give some hints based on how I interpret it.

1) The stoichiometric matrix. You have exactly the right idea. I would write the reactions as enzyme names or gene names instead of the EC numbers (e.g. G6PD or G6P dehydrogenase instead of 1.1.1.49). For the reversible reactions, there's no a priori reason to write them in one direction or another, but convention would be to make glucose consumption the positive direction. I would not include "glycolysis" as a separate reaction. I would also consider including cofactors and byproducts in the molecules affected by the reaction (e.g. CO2, NADP+, NADPH, (maybe ADP, ATP, NAD+, NADH also if those come up)).

2) Yes, it's basically what you already have. It's not a particularly great diagram, so you could draw it in a clearer way.

3) I have no idea what this means, but perhaps the next point will help.

4) Primary metabolite is not a super well-defined term, but I think in this context, I would say that the way they're intending the question, they're looking for a "total pathway reaction" that describes the net inputs and outputs of the pathway.

Something like this:

$$
X_1 G6P + X_2 NADP+ \implies X_3 GAP + X_4 FBP + X_5 CO_2 + X_6 NADPH
$$
(G6P=Glucose-6-phosphate, GAP=Glyceraldehyde-3-phosphate, FBP=Fructose-bis-phosphate)

I'll leave it to you to figure out what the X's are or whether I left anything out (since it's a homework assignment after all.)


How does a single-stranded RNA bind to a double-stranded DNA to form a "triplex structure"? If you have a single-stranded RNA that is complementary to a double-stranded DNA, how do they interact to form what my prof. calls a "triplex structure"?

e.g.

    UGCUGAUAGCUACG
ACGTACGACTA
TGCATGCTGAT

I don't understand how the DNA can form 2 bonds there?

DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g.

rCCCCCC
dGGGGGGGGGGGGGG
dCCCCCCCCCCCCCC

rUUUUUU
dAAAAAAAAAAAAA
dTTTTTTTTTTTTT

but it is now known to occur in more complex sequences. One of the best studied examples is in the promoter of the human DHFR gene:

  Gee, J. E. et al.(1992) Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J. Biol. Chem. 267, 11163–11167

In this work the oligonucleotide GR19 was shown to bind in a triple helix to SpI binding site I in the DHFR promoter (CR19 was used as a control). Triplex formation was detected by gel shift, and the specificity was confirmed by DNase I footprinting.

This effect is part  of the regulation of DHFR - the transcript from a minor upstream promoter binds to the major promoter, see:

  Martianov, I. et al. (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670

The structure of these triple helices involves a combination of Watson-Crick base pairing in the DNA duplex together with Hoogsteen base pairing in the RNA-DNA interaction:

Figure taken from:

  Morgan, A. R. & Wells, R. D. (1968) Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J. Mol. Biol. 37, 63–80


Are the ribosomes specific for each organism If we removed one ribosome from human and we put it inside horse, would the ribosome perform the as it would in humans or it will not work or somewhere inbetween?

One can prepare rabbit ribosomes from reticulocytes (immature red blood cells), and by providing a few cofactors required for an active extract, create an in vitro system that will translate virtually any eukaryotic mRNA that contains the correct sequence determinants. You can purify mRNA from your cells or tissues of choice, or you can synthesize an mRNA in vitro using a DNA template and an RNA polymerase. Either of these will be translated in a nuclease-treated rabbit reticulocyte lysate.

IVT (in vitro translation) extracts can be prepared from virtually any source (e.g., C. elegans shown by Bob Edgar in Cell ~ 1984). So I would predict that horse ribosomes would be happy translating human mRNAs, and human ribosomes would be happy translating horse mRNAs. The experiment you described, placing a human ribosome into a horse cell would be difficult to interpret because the endogenous horse ribosomes would already be translating the endogenous horse mRNAs, and so detecting activity from one additional ribosome could be challenging (even if you could come up with an experimental approach that gets that foreign ribosome in to the cell).

The take home message is that ribosomes, in general, do not care where the mRNA comes from--because ribosomes, as far as we know, do not have a way of distinguishing "self" from "other".


Species Identification: Coniferous tree, Italy I noticed it close to the place where I work, I live in Italy
Could you tell me the complete name of this tree?

Particular of the leaves

To me, it looks like a species of Taxus (Yew), for instance Taxus baccata. This is based on the flat needles, "flat" apparence/growth of the branches and the red berries. It's a bit hard to see what the red things are in your 3rd picture though (berries, shoots, flowers??). It should also have reddish bark where you can easily peal of loose scales. They can become very old (>1000y), have been used for many human purposes (woodcarving, medical purposes, bows), and all parts except for the berries are toxic.

Abies alba might be an alternative (if the red things are flowers), but then the needle underside should be relatively white and they also look to broad, soft and shiny to me.

Some pictures:

(from wikipedia)

(from http://linnaeus.nrm.se/flora/barr/taxa/taxus/taxubac.html)

(from wikipedia, a 1200-year-old tree in Poland)


In which way would the yeast cell cope with the excess amount of methionine in the growth media? I guess that when there is surplus of methionine in the cell it is incorporated in the TCA cycle as a succinyl CoA, with cysteine as a by-product. But now the cell has the surplus of cysteine. What does it do with it? How does it remove excess sulphur from the cell? Would that process somehow influence NAD+/NADH balance?

In humans, cysteine first fills the glutathione pool (which itself is a reservoir for cysteine, apart from reduction equivalents and biotransformation). Excess cysteine can go three ways,

oxidation to sulfoalanine and further hypotaurine and taurine, via still unknown enzyme(s)
degradation to lanthionine and toxic H2S
degradation to serine and toxic H2S

Since cystathionine gamma lyase which (its L-cysteine desulfhydrase activity) catalyses 2 and 3 has homologues in yeast, my guess is that H2S is produced there too. Further oxidation of H2S happens through an ancient mitochondrial pathway which is highly conserved as well, yielding sulfite and sulfate. Sulfate then makes for a bit acidic environment but else is non-toxic.

I have linked to reactome.org entries where you can find references. Filling up the yeast's glutathione pool (if it happens) would move the NAD+/NADH balance to the NADH side, i.e., fill up reduction equivalents, too.


Why are plants unable to take up Phosphorus directly in their organic form like Phytic Acid? I am researching acquisition strategies of phosphorus by decidious trees. I am reading a lot that plants take up nutrients as their inorganic form. In the case of P according to literature this is mainly $H_2PO_4^{-}$ (Schachtmann et al. (1998), Hinsinger (2001), Buchanan (2015)). So far so good...

In forest soils for instance, Phosphorus is much more concentrated in the form of phytic acids (derivates of inositol hexaphosphate), which are organic acids. Not in any paper which I have read before, it is stated why organic P is not taken up directly, only that it is enzymatically cleaved before it is taken up as inorganic P. The best, which I have found so far is that

  Although organic P ($P_o$) is present in soil solution at higher concentrations than inorganic phosphate (Ron Vaz et al., 1993; Seeling and Jungk, 1996), direct uptake of ($P_o$) compounds by plants is considered unlikely. --Hayes et al. 2000

My problem - or rather limited understanding - is that I wonder, whether plants in fact do have the ability to take up nutrients directly as organic forms.  I would prefer not to take the presence of enzymes as a proof that organic P cannot be taken up directly by plants. Also phytate seems to be used in plant tissue for storage of P.

Unfortunately my understanding of biochemistry is limited, that's why I'm pretty sure that I am missing some basic facts, which could clarify the situation. My best guess so far is, that organic sources of P are simply too big to pass through the cell wall.

So my question is: are there certain structural or biochemical barriers or obstancles, which would prevent plant roots from absorbing organic P directly, or is it for some reason better to cleave phytates "outside" the cell?

I would be very happy if you could point me in the right direction. Thanks in advance

Sources:

Buchanan, Bob B.; Gruissem, Wilhelm; Jones, Russell L. (Hg.) (2015): Biochemistry & molecular biology of plants. 2. ed. Chichester, Rockville, Md.: Wiley Blackwell; American Society of Plant Biologists.

Hayes, Julie E.; Simpson, Richard J.; Richardson, Alan E. (2000): The growth and phosphorus utilisation of plants in sterile media when supplied with inositol hexaphosphate, glucose 1-phosphate or inorganic phosphate. In: Plant Soil 220 (1/2), S. 165–174. DOI: 10.1023/A:1004782324030.

Hinsinger, Philippe (2001): Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review. In: Plant Soil (237), S. 173–195.

Schachtman, Daniel P.; Reid, Robert J.; Ayling, S. M. (1998): Phosphorous Uptake by Plants: From Soil to Cell. In: Plant Physiology (116), S. 447–453.

https://en.wikipedia.org/wiki/Phytic_acid

I am not a plant biochemist but would make a couple of points that may or may not be relevant or helpful.

The living organisms that preceded plants had evolved a wide repertoire of systems for transporting ions across membranes, involving variations on a few general designs. Given the importance of inorganic phosphate in living organisms, phosphate transporters would have evolved early on.
Phosphate may have been more abundant in soil before sophisticated evolution of plants led to secondary metabolites like phytic acid. If this were the case it would explain why roots developed phosphate transporters.

This is not to say that it is impossible for organisms to develop transporters for more sophisticated molecules — there are many such examples — but in this case such a development would only be expected if there was such a lack and intense competition for phosphate that it would convey an evolutionary advantage.

This sort of question is always a matter of conjecture. One imagines there is a tipping point when the difficulty of developing a new system is outweighed by the advantage it would bring. This clearly hasn’t happened, but which of these factors is most important is difficult to say (for me, at any rate).


If oxygen deficiency is bad even for a short while, why do people swim? This may be trivia to many of you.

Textbook says the oxygen deficiency, even for a short while can injure our cells. Then why do people go for sports like swimming? (where rhythmic breathing is required yet, there's a practical possibility of holding the breath longer than usual inhale exhale process) I am looking for a reasoning from cellular biology/patho-physiology/respiration aspect. And not because swimming or any other such exercise is anyone's choice/preference.

So my question is: during sport like swimming, does the oxygen level in our blood drop below a critical level, that cells might suffer from lack of oxygen?

Also found some relevant information here.

Currently referring to this online text : Swimming Fastest: Physiological Responses to Exercise.

In this paper the authors measured decrease of arterial blood oxygen saturation in healthy and patients with sleep apnae (this latter part is not really relevant only the measurements in healthy individuals).

They found that fall of oxygen saturation depends on the initial saturation rate, but is not affected by the breath-holding time. As you can see on the graph at high initial saturation the fall rate per second is quite low. Here is the info in a table format:

At high initial saturation only mean 0.16% saturation drop occurs per second, thus in average a healthy individual looses 1% oxygen saturation approx every 5 seconds (I'd also like to note that the urge to breathe does not come from the lack of oxygen when holding breath, but from the accumulation of CO2). According to wikipedia normal oxygen saturation is between 100-95%, and only below 90% is considered hypoxemia /hypoxia (a medical condition where blood oxygen level is low). So if we look at the data in the table, it is safe to say that it takes approx 20s until the blood saturation level drops from 97% to 93% and another 5-6 seconds until it drops to 90% (with approx 0.5% saturation loss per sec at 93% initial saturation).

People who are conditioned by exercise have larger vital-capacity (they can breathe more air in for a single breath), thus have means to acquire more oxygen can compensate for the excess use of oxygen. During heavy sport activity like swimming it is unlikely that anybody will hold his/her breath for several tens of seconds.


Why should phospholipid non-polar tails be "protected" in the membrane bilayer? lipids are arranged within the membrane with polar head towards the outer side and non polar tails towards inner side, this ensures that the non polar tail is protected from aqueous environment.

My question is why should we protect non polar part ,will it destroy in contact with polar part?
 What should be the correct reason for bilayer arrangement?

What should be the correct reason for bilayer arrangement?

I'll answer your second question first, but there is an almost identical question on this site already: Why do cells have a bilayer?

There is water on the extracellular and intracellular side of the membrane. What's actually happening at a molecular dynamics level is the self-association of the hydrophobic lipid tail groups driven entropically by water. In other words the polar (hydrophilic) head-groups "prefer" interacting with the water (called the interfacial region) and the the hydrophobic tail groups "prefer" not interacting with the water. With those two preferences in play, the lipid bilayer formation we know and love emerges.

  why should we protect non-polar part, will it destroy in contact with
  polar part?

To directly address the first part of the question: no, nothing would be destroyed. The word "protect" isn't appropriate (it's a bit too anthropomorphic for my taste!). Here is a video showing the bilayer spontaneously assemble in a molecular dynamics simulation. Read the more thorough 2003 journal article for an idea of early MD simulations of the bilayer formation. As you can see nothing "bad" happens when the water collides with the lipid tails and the lipids aren't destroyed.

Interesting read: MEMBRANE LIPIDS OF THE PAST AND PRESENT. Good animations and explanations of different membrane formations.

For an academic perspective, I'd recommend a couple of reviews: Cournia et al., 2015 and Gerit et al., 2008.


Difference between fertilin and fertilizin I am confused between fertilin and fertilizin.Are these two same or different?
Here are a few sources i referred

Julian Lombardi (auth.) - Comparative Vertebrate Reproduction-Springer US (1998)
Page 210

Richard E. Jones - Human Reproductive Biology, Third Edition-Academic Press (2006)
Page 244

Bioregulators of Reproduction
edited by David Jagiello

google book image link

Please help me know how they are same or different ,specify their functions in detail and thanks for your help in advance !!!

Welcome to Biology SE.
Coming to your question, Fertilin and Fertilizin are different.
Fertilin
Fertilin is a sperm surface protein with an essential role in fertilization. It is required for the migration of spermatozoa through the oviduct, for binding to the zona pellucida, and for efficient binding to the egg plasma membrane. Fertilin consists of two subunits, fertilin alpha and beta, both of which belong to the metalloprotease-disintegrin protein family (ADAMs). Fertilin alpha and beta are made as larger precursors that are processed proteolytically at different stages of sperm maturation in the testis and epididymis. Fertilin alpha is processed first, most likely by a pro-protein convertase in the secretory pathway of testicular cells. Fertilin beta is processed later, while spermatozoa are in transit through the epididymis.(taken from this reference 1) Thus this protein is present in Sperm.
Fertilizin
Fertilizin is sperm-agglutinating substance (glycoproteins) present on Zona pellucida layer of the egg surface. Antifertilizin-fertilizin complex play a key role in sperm penetration. (Have a look at reference 2 &3 ). Thus, Fertilizin is present on egg surface.
Now look back at the images you provided with your question. Role of Ferilizin and fertilin-beta are clearly given.
References:

https://pdfs.semanticscholar.org/0043/f4525b6158d91a00682b86b1b9b15f726125.pdf

https://www.nature.com/articles/169548a0

https://www.journals.uchicago.edu/doi/pdfplus/10.2307/1537786


Conclusions from hybridization results A double stranded DNA was denatured in a mixture that included mRNA from a gene in the segment. The mixture was then cooled to promote RNA and DNA hybridization. The following figure the results.

Which strand is DNA/RNA?
What is source of the genetic material (Prokaryotic/Eukaryotic)?
Which segment is exon/intron?

You are almost right. I modified you picture a little bit to answer it:

Structure I is indeed DNA, structure II is processed RNA.
This is because in I you see loop structures which have no complementary part in the RNA anymore, these are introns (structure Q and the flanking loop regions to P). P is an exon flanked by two introns.
The end of the RNA is not complementary to the DNA because the poly-A tail has been added here.

The DNA is eukaryotic since you have introns and exons (which are not present in bacteria) and since the processed RNA contains a poly-A tail (which is also not present in bacteria).


How does the human body use energy? As far as I know the glucose gets processed from carbs and fats and as a result carbon dioxide, water and "energy" are released. The carbon dioxide and water are expelled by the body, and then energy is used by the muscles. But how exactly is it used? What happens to this "energy" and what is it exactly?

You can break down the energy expenditure of the human body in terms of the different organs which use it up: this is done in this biochemistry book for instance, http://www.ncbi.nlm.nih.gov/books/NBK22436/

You can also look at the detailed expenditure of each cell: although the amounts will vary according to cell type (neuron vs. muscle cell, say!), the "budget items" are the same. See this thread: Breakdown of energy expenditure at the level of a single cell


How to identify Ag nanoparticles in a solution? Doing an experiment involving the production of Silver nanoparticles using bacterial extracts. The issue is proving that they've been formed.
AgNO3 is added to the solution, and the reduction environment of the bacteria reduces into silver nanoparticles of various size, depending on many factors.
Color change can be seen, and a change in the UV-vis spec also, but beyond that, is there anything else that can be done?
The papers I'm basing this project off of have access to electron microscopes, I don't.
Is there any sort of biological assays that react to metallic silver? or maybe to Ag NPs?
Or anyone have any experience involving biologically producing nanoparticles?
I'll be asking in Chemistry as well for a possible chemical reaction of identify metallic silver.

This paper says that silver nanoparticles enhance the enzymatic reaction that happens in a normal ELISA assay. You should be able to observe a significative shift in UV absorbance comparing your bacteria to a control.

Otherwise, I'd think simply of lysing the bacteria and centrifugating the lysate. I'd expect the pellet to contain nanoparticles and to be somehow different (in color?) from a control pellet.


Molecular genetics textbook (free?) suggestion for first time I have never taken a molecular genetics course but want to prime myself for graduate school in the future. Does anyone have any suggestions or advice? A professor recommends "the molecular biology of the gene - latest edition" but I dont have too much money to spend on a text and simply prefer free/digital formats. ( less to carry)

I can’t comment otherwise this would be a comment, not an answer, sorry...

If you can’t lay your hands on a cheap (legal) text book that is of quality and in digital format then  maybe check out course material from MIT open courseware or something similar. As a further alternative, you should be able to find decent pop science books which are applicable and may be more useful than you think. The Epigenetics Revolution, for example, provided me with a really solid grounding when first trying get to grips with the subject.


When analysing phosphoproteins via Western blot, why is total protein level of the target protein recommended as an internal loading control? I am analysing the expression of a protein kinase via Western blots, and it is a phosphoprotein. I have labelled my membrane with antibodies against the phosphorylated form of the protein (using phospho-specific antibodies) and also for total protein (using pan-specific antibodies).
I have read that when studying phosphoproteins, you should normalise the phosphorylated protein signal to the signal for total protein. In this journal paper, it states that the Journal of Biological Chemistry recommends that “signals obtained using antibodies specific for phosphorylated epitopes should be normalized to the total protein level of the target protein”.
I have seen in other journal papers analysing the expression of a phosphoprotein via Western blots that they also normalise the phosphoprotein signal to total protein signal (of the target protein).
However, I am not sure why the total protein level of the target protein can be used as an internal loading control?
I have read in this handbook that internal loading controls are endogenous reference protein(s) that are present in all samples at a stable level and unaffected by the experimental conditions.
I want to compare the expression of my phosphoprotein between samples of different experimental conditions. I know that normally total protein stains such as Ponceau S or housekeeping proteins are used as an internal loading control and for normalisation.
But why is it recommended that you should normalise to total target protein (when looking at phosphoproteins), because one does not know whether the expression of total target protein will be stable between different experimental conditions? Any insights are appreciated.

It is because you don't know how your treatments affect the expression of the total specific protein; perhaps it down- or up-regulates the amount of protein being made, but the relative proportion of phosphorylation doesn't change. For example:
Imagine you have 4 samples from different treatments of which you have loaded an equal amount of total protein (lets say 50 ug total, note that this is too much to load on a WB for accurate quantitation; usually you want less than 10 ug). You run a western blot and find the following numbers (completely made up BTW) for the specific protein. In this scenario, 1 is untreated control.

10 ug
20 ug
10 ug
20 ug

You then try the phospho-specific antibody and get the following

1 ug
2 ug
3 ug
1 ug

What does that tell us about the 4 treatments?
Well, it tells us that 2 is up-regulating the total protein, but the relative proportion of phosphorylation is the same. In 3 phosphorylated protein is up-regulated (3x) but not total protein and in 4 total protein is up-regulated but phosphorylated is down-regulated (0.5x).


If a fully functional lab grown pancreas can exist, can it be used as a cure for type 2 diabetes? Is it approximately equivalent to say that if a fully functional lab grown pancreas exists, then a way to cure Type 2 diabetes could soon exist?

Recently I've already checked out that only the remission exists with some gastric surgery.

reference: 1)http://care.diabetesjournals.org/content/34/Supplement_2/S361

2) http://www.medscape.com/viewarticle/733691(full access require membership)

Since the consensus is that the underlying initial problem in t2dm is the development of insulin insensitivity in the presence of a normally functioning pancreas, then replacing that pancreas at a more advanced stage of the disease will not cause normalisation of glucose levels.

http://journal.diabetes.org/clinicaldiabetes/v18n22000/pg80.htm


Description of the paramaters in the packing parameter? For a phospholipid, the critical packing parameter is given by:
$$P=\frac{v}{a_0l_c}$$
And I know that

$v$ is the volume of the hydrocarbon tail.
$l_c$ is the critical length of the hydrocarbon chains.
$a_0$ is the optimum surface area of the head group.

But what do these actually mean?

For example what is the volume of the hydrocarbon tail, since it can't be simply the volume of all the atoms that make it up else this would be negligible? What is the critical length of the hydrocarbon tail? And What is the optimum surface area of the head group?

Following image from (Salim et al 2014) will makes thing clear to you,

When they say volume, it is volume of shape of lipid. Shape can be determined by many factors as described here. Following is modified images from (Sprong et al 2001) which will tell you how change differ in general. Here are examples of few common lipids.


Data Retrival from the GenBank? When I go to NCBI & Select nucleotide option there and in search box write For Example CNGA3 gene the page shows that there are 553 items.I know the method of downloading or retrieving the One item's or record's FASTA format but "if I have to download the FASTA Format of all the 553 items simultaneously without opening each link then what options should I use..?" If you know it then please help me.. ?

I think that using NCBI Gene would be a better option here:

Go to NCBI Gene http://www.ncbi.nlm.nih.gov/gene/
Enter your gene of interest, in this case CNGA3 (and optionally the species)
Click the species of interest (I'm assuming you are looking for human, the first search result)
On the information page scroll down and click on FASTA which will provide the sequence for the gene of interest.


What is the difference between kingdoms protistae and protoctistae? I understand that both kingdoms represent primitive eukaryotic organisms, and both contain both unicellular and multicellular organisms.

What are the points that distinguish one kingdom from the other?

First, just a correction: it's "Protista" and "Protoctista", not "Protistae" and "Protoctistae".

They mean the same thing. Those are just different names proposed by different taxonomists for describing the same group of organisms.

Protoctista (or Primigenum) was proposed by John Hogg in 1860.
Protista was proposed by Ernst Haeckel in 1866.

However, as it is common in taxonomy and nomenclature in general, things sometimes get a bit more complicated: some biologists, like Lynn Margulis, don't treat those two terms as synonyms. Particularly, I don't use her nomenclature.

Source:

Jstor.org. (2017). Protozoa, Protista, Protoctista: What's in a Name? on JSTOR. [online] Available at: http://www.jstor.org/stable/4331095 [Accessed 12 Sep. 2017].


Why do we need to close eyes to sleep? Out of all our sensory organs, we need to stop taking signals explicitly only from eyes in order to sleep. Even interestingly, those who are not able to receive signals from eyes (i.e., the visually challenged people) also need to close their eyes in order to sleep. I wonder what is the relation of closing eyes with sleeping. I think the reason might be related to the state of the muscles related to the eyes. Of course, even if it were the case that one could keep her eyes open while sleeping, the brain would stop paying attention to the signals received by the eyes -- just like the brain stops paying much attention to the signals received by the nose or the ears while sleeping even if these organs are not physically closed or prevented from receiving signals. But in the case of the eyes, they are physically closed while sleeping,  which makes me curious.

Unlike our underwater ancestors, land animals have evolved eye lids or nictitating membranes to protect our eyes and keep them moist periodically by blinking. During the sleep state, closing our lids protects the eyes from drying out and getting damaged while unconscious.  In addition to the lids themselves blocking light stimulus (not totally), our eyes also roll back to attenuate light stimulation.  Fish also sleep and don't need eyelids to do so, thus closing eyes is not a prerequisite for the sleep state.

Textbook Source: Butler, Ann B.; Hodos, William (2 September 2005). Comparative Vertebrate Neuroanatomy: Evolution and Adaptation. John Wiley & Sons. p. 215. ISBN 978-0-471-73383-6.


What's the evolutionary reason behind feeling 'sorrow'? As it's established that life's design is a product of evolution, what advantage does emotions like sadness play in the life of an individual/species ?

I‘ll answer from a perspective I‘ve been studying in Psychology, but can‘t provide sources. If this is not within the scope of this SE, I‘d kindly ask to either add appropriate sources to my answer or close it.

Sorrow is an emotion that has specific cues and expressions like tears, distinct micro-facial cues (which are stable over practically all cultures according to studies of Paul Ekman et al.), a general tendency to withdraw from social settings.

This can be understood as communicating to other members of your group the need for consolation and social closeness, which would count as an evolutional gain.

Update:
I found an extensive article on the subject: http://www-personal.umich.edu/~nesse/Articles/Nesse-EvolutionBereavement-2005.pdf


Do similar adaptations result in similiar genetic code? Sometimes organisms within the same species evolve similar adaptations to similar living conditions without interbreeding.

Let's say we have two human populations which need to adapt to a colder climate, albeit one lives on the Northern hemisphere whilst the other one on the Southern hemisphere. Both populations develop hairy skin. Would the gene encoding the hairiness of the skin look similarly in both populations? Would this gene be at the same locus at the same chromosome in both populations?

Do similar adaptations result in similiar genetic code?

It can be the case but it is not necessarily the case. You sure can have the same mutation happening and raising in frequency in two independent lineages but you may well also have different mutations leading to similar adaptations in different lineages.

Example

As you talk about humans, let's take an example from humans. The ability to digest lactose (milk) at adult age has evolve several times independently. I just copy-pasted from this answer of mine

  Gene LCT

  Mammals have a gene (called LCT C/T-13910) coding for the lactase enzyme, a protein able to digest lactose. Lactose is a disaccharide sugar found in milk.

  Expression of LCT

  In mammals, the gene LCT is normally expressed (see gene expression) only early in development, when the baby feeds on his/her mother's milk. Some human lineages have evolved the ability to express LCT all life long, allowing them to drink milk and digest lactose at any age.

  Today, the inability to digest lactose at all ages in humans is called lactose intolerance.

  Three independent mutations

  Tishkoff et al. 2007 found that the ability to express LCT at an old age has evolved at least three times independently. Indeed, they found three different [SNPs][6] (stands for Single Nucleotide Polymorphism; it is a common type of mutation), two of them having high prevalence in Africa (and people of African descent) and one having high prevalence in Europe (and people of European descent). The three SNPs are G/C-14010, T/G-13915 and C/G-13907.

In this example we can know that the ability to digest lactose at adult age evolved at least 3 times independently. It is quite hard to tell whether it had evolved more than three times. It is indeed possible that the mutation G/C-14010 had occurred in two independent lineage but it would be hard to disentangle them today if the two lineages are not clearly geographically isolated (and in humans, very few populations are really isolated from the others).


How much of the human body is processed sunlight? So I believe (and correct me if I'm wrong--it's logic, not research) that the human body is pretty much all just processed sunlight based on the food chain.  How much, if any, of the human body is made up of materials that did not originate from the sun (e.g., various minerals or other trace elements)?

I think that Carl Sagan said it best:

  The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of starstuff.

The current view of cosmology is that every atom that isn't hydrogen, helium, or lithium was created in the fusion furnace in  the hearts of giant stars. These heavy atoms were then spread about the place by supernovas.

However, there's a lot more to the matter that makes up living creatures than just the atoms. The vast majority of the free energy that allows for the creation of intricate organic molecules with complex patterns of chemical bonds (e.g. protein, DNA, etc.) does indeed originate with our sun.


Do humans have Coelom? Kimball Biology 5e says

  Coelom is the main body cavity of many animals. It is lined with an epithelium derived from mesoderm.

Gilbert Embryonal Biology 9e says

  Coelom is the space between the somatic mesoderm and splanchnic mesoderm that becomes the body cavity. In mammals, the coelom becomes subdivided into the pleural, pericardial, and peritoneal cavities, enveloping the thorax, heart, and abdomen, respectively.

Then my lecture materials and the research site say

  Coelom is the secondary body cavity.

Finnish Wikipedia says that Coelom is only with invertebrates.
Again the Wikipedia page about peritoneum suggests that human has abdominal cavity and no coelom, and other mammalians coelom.

Does human have Coelom?

The confusing thing is the use of the word "OR", since I am not sure whether people are using it in different pages like "XOR" or like "AND" in normal speaking.

Wikipedia actually covers this:

  Most bilateral animals, including all the vertebrates, are coelomates.

Now, some coelomates have subsequently lost their coelom but primates (actually, I believe, all vertebrates) are not among them. In humans, the coelom forms, amongst others, the pleural cavity.

So, yes: humans do have a coelom that partitions into different, unconnected body cavities during development.


Can phylocode classify viruses? Can phylocode classify viruses? Based on what I found this system began in 2019, so there is not much information about it.
I know that the Linnaean classification system cannot classify viruses, but what about this new classification system (phylocode)?

PhyloCode is not a new system but it isn't popular yet and actually quite opposed by some.
It overlaps with the ranked based systems but does not nullify them, meaning that even if PhyloCode becomas popular the ranked systems will still be needed.
One might understand from your question that virus have no classification system, but they have. The common one is called ICTV.
PhyloCode can classify virus and there is already a classification for virus (ICTV)


sodium chloride and amylase activity So, I did an experiment on the effect of sodium chloride on amylase. and I found out the higher the concentration, the slower the activity.

Therefore, is it valid to make the assumption that when we consume food with starch and high salt concentration, it can affect our digestion of starch? like slower break down of starch?

I highly suggest you actually look at studies that analyze this and there should be a good number since amylase is a well defined enzyme. (Bailey K, Hopkins RH, Dolby DE)

Not only that but applying this type of logic to any problem results in bad conclusions and therefore is bad science. (Berkeley)

The process of proving something scientifically is something that follows a somewhat predictable route. I only say that because not everything follows this exact path.

There is usually a nicer looking picture though I cannot seem to find it.

(Source)

So to answer bluntly, no. You cannot make that conclusion with any stretch of the imagination.

Being that amylases are so well studied you may have your answer after a few google searches, but the case remains that it took many years of research to reliably say so.


What is this insect from India called? It was found on a roof in Jaipur, Rajasthan, North-Western India.

It appears like a pellucid hawkmoth (Cephonodes hylas; also called coffee bee hawkmoth). This belongs to the same family as the hummingbird hawk moths.

  From wikipedia

Many photographers have misidentified this one as the hummingbird hawkmoth (See the picture and the link below. So if you google hummingbird moth india, you'll get pictures of the pellucid hawkmoth too).

  Courtesy: Nitin Prabhudesai


What is the biological name of this plant? The plant was observed in a rural area near Digha.

This is Ageratum conyzoides, a flower of Asteraceae family.

The common Bengali name of this plant is Uchunti.

Other than this purple colour a white colour of this flower is also observed.


Oligonucleotide purification with desalting I have ordered 36bp oligonucleotides that anneal to each other and create sticky ends to be cloned in a vector afterwards. I have tried cloning many times with different methods and I failed. Now I started to think that my oligos are actually shorter than 36 nt since desalting is not an effective method and most of my oligos do not create complete sticky ends when they anneal to each other. I believe I have also found support for this. So, how much is it possible that most of my oligos are actually shorter than 36 nt ? Is this a good troubleshooting or 36 nt oligos not being purified with more efficient method should not really create a problem?

Oligos from well-known companies are pretty good to my knowledge. Problems begin after 100-300bp oligos/dsDNA fragments.

What I suggest is PCRing your vector like that:

          Primer F: ---------------------__________
vector: ======|v site for 36 bp insert v|==========...
        Upstream                        Downstream
        ______----------------- : primer R

Legend:
__ portion of primer annealing to vector
-- portion that is your insert of interest

Then you can actually just transform that PCR into e. coli, which will seal two nicks together and propagate your vector. Treating your PCR reaction with Dpn enzyme will ensure that all template DNA is removed.


How did sneezing evolve? Did we develop the sneezing mechanism to get rid of pathogens like bacteria and viruses in our nose?

Or did pathogens develop a way to make us sneeze to propagate themselves?

Or did we develop the sneezing mechanism, and then pathogens hijacked this pathway to benefit themselves?

I'm trying to understand why we sneeze so much when we get sick - is it our bodies trying to help us, or is it something the pathogen is causing to help itself spread? And if it's both, how did that happen?

Sneezing itself is a part of long story of human evolution.

Sneezing for early humans was as common as eating is for us. Early humans lived in caves which were full of dust and insects so whenever they wake up from sleep they sneezed intentionally to remove the dust and small insects from their nose, slowly this behaviour of early humans was proved to be beneficial and muscle memories remembered the Activity as a daily routine work and performed it to remove dust and any irritant in their nose or nasal cavity.
As they evolved they passed on their daily routine works to their descendants and this was also passed on , this way sneezing was slowly incorporated into the muscle memories and it exists till now as a way to relax is from external allergens.

There are several other theories too about evolution of sneezing and it itself demands great research .
 There is also a video on Veritasium on YouTube regarding the Sneezing whenever one sees light , this video too discusses this theory.
You should check that out too.


What is the name of the species of this butterfly? Well,I am from India and live in the northern part of the country.I commonly find these butterflies during winter or spring seasons.

The original image shot is:

I'm not an expert, but it looks like a male "common mormon" or Papilio polytes romulus

https://species.wikimedia.org/wiki/Papilio_polytes_romulus


What for a Kinase Assay? I am wondering why to use a kinase assay, since we can extract the proteins from cells and then do a Western with the specific antibodies we want to use.

There's a very simple answer: scale. If a drug company wants to screen a million-compound library to find which ones inhibit the kinase activity of a certain target, they're not about to do a million IPs and a million Western blots. Instead, they'll use recombinant kinase and substrate peptides, with a variety of readout systems to choose from.

Other reasons include not having a good phospho-specific antibody to the substrate, very low expression of the kinase and/or substrate, complicated protocols necessary to activate the kinase in vitro, lack of a good model system, and more.


Cannibalizing behaviour in ants Today I saw an ant question biology and was reminded of a picture I had clicked 2 years ago.

Here, you can see these black guys cannibalizing this other black guy.

To reiterate, these guys had their nest inside a tree. I had cornered one of them.

If I remember correctly the ant was walking fine and the only fault might have been that I lead the guy astray a bit (not further than the farthest guy in the colony) and near the colony I turned it on its back which lead to a lot of difficulty for getting up again (as any ant knows). I mean I waited maybe a few minutes but it just kept waving it's legs in the air.

So later on as soon as these other ants got sight of their lost friend when it was able to hobble back near the nest, they came over and just pulled him apart.

In the picture you can see the first guy just got to him and the others started aggregating as soon as this guy came over. Within five minutes some 10 or 15 ants were all over the place.

Which ant species is this?

Why did they murder/cannibalize a member of their own colony?

Is this a common behaviour among ants?

Scientific name: Camponotus compressus

Common name: Common Indian black ant

Camponotus compressus tending soft scale insects growing on a stem

Source:

Common Indian black ant
Wikipedia

Cannibalism is common in social insects. It is a way through which they control the population of the colony and conserve nutrients. Members of Hymenotpera (this ant being one) are very quick to consume injured eggs, larvae and pupae. It has been experimentally observed that when a colony of Zootermopsis angusticollis(a species of termite) was kept on a diet full of cellulose i.e. deprived of protein, they attacked their own kind. But cannibalism dropped to zero when casein was introduced in their diet. So it is safe to  assume that these ants too engage in cannibalism for the same reason, proteins.

Reference: This book.


How do we perceive acceleration? Today me and my friend were coming on motor bike and I was sitting opposite direction because I was holding something in my hand (and it was fun :P). When he started bike I felt very high acceleration. I asked him to go slow however he said he is going with regular speed. Then out of curiosity, me and him tried different velocities and different accelerations while me sitting on either direction of acceleration and opposite to it. To my surprise I 'perceived' more acceleration when I was sitting opposite to direction of acceleration. While searching how we perceive acceleration, surprisingly it is not very well known. I found following explanations,

We overestimate arrival time ( ref: this )
Endolymph from Vestibular system ( ref: Wiki ) [Not exactly acceleration but rather balance]
Interpolated motion segments ( ref: this )

My question, Is it just visual perception or special mechanism for detection of acceleration? In any of these cases, why I was feeling more acceleration while siting opposite than in direction of acceleration? [ My initial guess is because I didn't have any support and visual cues were messed up ]

Update:

I found this post but I didn't get any satisfactory answer from book referred in answer.

My question, Is it just visual perception or special mechanism for detection of acceleration?

Acceleration is a synthesized conclusion from a multitude of systems.

Most prominent is the Endolymph system you already mentioned:

As you accelerate, the endolympth and the otoliths within (small, calcified deposits) pass over the hair cells and produce action potentials which travel to the brain. The higher the magnitude of acceleration, the more action potentials will be sent.

This is also where dizziness comes from, as the endolymph and otoliths do not come to rest at the same rate, momentarily giving the brain two different interpretations of what acceleration you're experiencing.

There is also the Doppler Effect:

Based in the cochlear system of the inner ear this time, instead of the vestibular system, the doppler effect is interpreted by the brain and gives a very rough interpretation of both velocity and acceleration (if the velocity of the object happens to be changing).

Then there is the entire visual side of things. Motion blur and the speed at which the perception of objects change size are large contributors to our sense of visual acceleration, but almost all of this is done via complex manipulation of visual data in the occipital and frontal lobes.

There are also countless minor contributors: skin and join tension (the sensation of weight due to acceleration), ease of breathing, sensory cells in your hair if your hair is exposed to the open air while acceleration, blood pressure sensors (and numbness when the body can't compensate), etc.

  In any of these cases, why I was feeling more acceleration while siting opposite than in direction of acceleration?

My guess would be because your body is more visually attuned to facing the same direction as the acceleration, and when you were facing the opposing direction your mind overcompensated in an effort to protect you since you probably don't get a lot of opportunities to rapidly accelerate backwards over distances of more than a few feet.

Your brain might also have been panicking a bit because you couldn't see where you were going (usually very bad), and the heightened sensory state made the magnitude of the acceleration feel greater.

These are my best guesses, however. If someone has an academic source, please feel free to edit this answer!


What insect is this? I found it in Russia.

Where do they usually live? What do they eat?

Full length is approximately 2 cm.

This is a terrestrial isopod crustacean called a woodlouse (colloquially referred to as pill bugs, potato bugs, roly-pollies, sow bugs, etc.).

There are over 5000 species in the world with at least 64 in Russia (see Kuznetsova & Gongalsky 2012).

Habitat:

Woodlice are typically found in damp, dark places -- in the soil, under rocks/logs/debris, etc.

  Living in a terrestrial environment, woodlice breathe through trachea-like lungs in their paddle-shaped hind legs (pleopods), called pleopodal lungs. Woodlice need moisture because they rapidly lose water by excretion and through their cuticle, and so are usually found in damp, dark places

Description:

As with all Arthropoda, the woodlouse is a segmented animal with a rigid exoskeleton and jointed limbs.

However, this is not an insect! Insects have 3 pairs of legs while isopods have 7 pairs of legs.

The extended uropods on your specimen as well as the pereon-pleon junction, number of antenna flagella, etc. all are important for IDing to species. (E.g., see here).

Note: although many people associate these arthropods with the ability to roll up into a perfect ball, only woodlice in the genus Armadillidium and in the family Armadillidae can roll up into an almost perfect sphere as a defensive mechanism.

Diet:

Woodlice are generally detritivores, meaning they eat decaying organic matter.

Citations:

Kuznetsova, Daria M., and Konstantin B. Gongalsky. "Cartographic analysis of woodlice fauna of the former USSR." ZooKeys 176 (2012): 1.


Nervous System : Signal Translation If a device were created to monitor the nervous  signals from the heart, including stable heartbeats, rapid heartbeats, etc., and this device were capable of transmitting the "stable heartbeat" to the heart, would this have any adverse or advantagious effects for medical science?

Measuring the electrical signals (=nerve signals) from the heart is frequently done in medicine, it is called electrocardiography. It looks like this (from the same article):

Influencing the heartbear can also be done and is done by pacemakers. Depending on the patients necessities the can permanently stimulate the heart or do this only, when certain criteria are met which makes an intervention necessary to prevent cardiac arrest. Wrong stimulation can in fact kill people, since they go into cardiac arrest when the stimulation of the heart is not correct. This is why pacemaker patients have to stay away from strong magnetic fields which make their pacemakers fail and leave them without proper stimulation.

This technique of influencing the heart from outside is used by defibrillators, which use an electric shock to influence the heart beat. It is used for treating cardiac dysrhythmias, ventricular fibrillation and pulseless ventricular tachycardia, which all lead to death if left untreated. A special form are automated external defibrillators, which measure the an electrocardiogram and then decide by the form of it, if an electric shock is needed.


Do all organs of our body secrete hormones? My teacher says that all organs of our body secrete some kind of hormone so they are all glands.
Is the statement entirely correct without any exceptions?
Till date I am unable to find any exception for that statement.
Could anybody provide an exception if any present?

Good question! The major and most common endocrine glands in the human body include pituitary, thyroid, parathyroid, thymus, adrenal, pancreas, gonads and pineal gland, along with neuroendocrinol glands like hypothalamus. Some other, not-so-common, examples include heart (Anti-Natriuretic Factor), GI tract organs (gastrin, secretin, etc.), placenta (estrogen, progesterone, etc.), kidneys (erythropoietin, renin), skin (cholecalciferol) and adipose tissue (leptin)1. Even the lungs are known to secrete calcitonin2.

In spite of this, I can think of quite a few examples of organs which do not act as endocrine glands. That is because there is a difference between the organs secreting hormones and endocrine glands. The definition of endocrine glands is as follows1, 5, 6, 7, 8:

  Endocrine glands are glands of the endocrine system that secrete their products, hormones, directly into the blood rather than through a duct.

So, if these organs don't directly secrete the hormones into the bloodstream, then they are not endocrine glands. Leading this way, emotional tears are known to consist of hormones such as prolactin, ACTH and leucine-enkephalin3, 4. Thus, though eyes do secrete hormones, they are not endocrine glands. Also, not sure about this, but lungs still do not seem to fit in the category of endocrine glands.

In short, all the organs of the body might secreted hormones, but they all cannot be considered as endocrine glands.

References:

Endocrine gland - Wikipedia
[Hormone expression and opioid receptors in fetal and adult lung]
Gómez-Román JJ, Cifrián Martínez JM, Fernández Rozas S, Fernando Val-Bernal J.
Frey W. H., DeSota-Johnson D., Hoffman C., McCall J. T. (1981). Effect of stimulus on the chemical composition of human tears. Am. J. Ophthalmol. 92 559–567. 10.1016/0002-9394(81)90651-6
What biological functions does crying serve? - Biology Stack Exchange