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why plants cannot use atmospheric nitrogen?
Earth's atmosphere constitutes 78% of Nitrogen, then why do plants need to absorb Nitrogen from the soil. Why couldn't it possible for them to absorb the atmospheric Nitrogen like they do in the case of CO2.
Most of the plants relies on other sources to fix their Nitrogen, why couldn't be there a single plant which can absorb atmospheric Nitrogen ?
Is there any ancient plant which is considered to be using atmospheric Nitrogen ?

I have done a simple research, I could only find that previously
  atmosphere is not so abundant with Nitrogen and plants developed
  mechanisms to use Nitrogen fixed in soil. So now they are following
  the same mechanism when Nitrogen is abundant in the atmosphere. Is
  this a valid answer ?

@anongoodnurse: I had seen that question while creating this thread.....but the answers are some what vague....I have came through some other answers but I cant find any reliable references in the answers given to that question.

Atmospheric nitrogen is inert and poorly soluble in water. It has to be converted to a soluble form before absorption.

@WYSIWYG: Can you please expand and add it as an answer

@Jay - the question (and the answer) is not "vague".

@anongoodnurse: I don't know the exact word for calling those answers which are having no references.

I agree with @anongoodnurse that the question is a duplicate. The answers there are, however, not satisfactory in that they do not give a clear cut answer. Hence, putting a bounty on that question would help. I understand 50 rep may seem a lot, but it would be the way to go here.


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Why are nausea and dizziness such common side effects from medication?
Why are nausea and dizziness such common side effects from medication?  If you go through your medicine cabinet and look at side effects, those might just be on every single bottle.  Is there some system in the human body that is very sensitive to any disturbance and causes nausea and dizziness?

This is very broad. Can you narrow it a bit down by naming specific medications? Additionally you have to understand that the information sheets provided by the companies are not medical, but legal information sheets. They have to name every side effect which occurs in a certain time frame after the intake.

I don't know I think the question is meant to be broad. An answer addressing the pathophysiology of these symptoms could have merit

Some medications because they are taken orally do cause nausea. Many medications, because they have an effect on blood pressure, or are central acting in some way, do cause dizziness. However, nausea and dizziness in particular are two highly subjective symptoms which are difficult to quantitate or verify, and which can occur with simple anxiety or stress. Several more such highly subjective and difficult-to-verify symptoms are numbness, tingling, headache, insomnia, fatigue and difficulty concentrating, all of which can be brought on by stress.
Switching for a moment to a drug with a measurable side effect of beta-blockers: erectile dysfunction (ED). In a study of men treated with beta blockers, the patients were separated into three groups with the following results:
a) the group who were not told the name of the medicine nor informed of the ED side effect had the lowest incidence of ED (3.1%)
b) the group who were told the name of the medicine but not informed about the ED side effect had a 15.6% incidence of ED
c) the group who were told the name of the medicine and informed of the ED side effect had the highest incidence of ED (31.2%)
Hypervigilance is an increase in attention to bodily cues or symptoms for any reason. It has been well documented in many studies that if you give one group of people a list of possible negative side effects, and another group a list of possible beneficial effects, then give both groups placebos (usually a small coated sugar or cornstarch tablet), the first group will experience negative effects while the second will feel better. The negative expectation producing a negative side effect is called the nocebo effect (the opposite of the placebo effect).
Interestingly, recent studies where anti-anxiety medications were administered before the nocebo dramatically decreased the nocebo effect.
For ethical reasons, in all clinical trials of drugs, patients in the treatment group and the placebo group must be given an extensive list (standardized) of possible negative side effects, introducing a negative expectation into both populations.
Two of the most common negative side effects in both groups are dizziness and nausea. Therefore, they must be reported as possibly occurring side effects with the medication.
This is not to say we're all imagining things. Nocebo effects have been correllated with reproducible effects on functional MRIs. They have a basis in reality, even if it's caused by negative expectations.
It's a problem being discussed a lot now by medical ethicists.
The influence of the nocebo effect in clinical trials
Avoiding Nocebo Effects to Optimize Treatment Outcome

anongoodnurse's answer is very thorough, but I would like to add one additional thing:
Nausea is in many ways the body's "default reaction" to anything being out of order with the body's chemistry; since most such things would once have been caused, the vast majority of the time of the time, by eating something toxic (or at least biologically active, and therefore probably toxic in large doses), which means that regurgitating stomach contents had a decent chance to expel the toxin and therefore save the person's life.
Because the effects of the medication are fairly light compared to toxic doses, the body rarely goes as far as actually throwing up (although people on prophylactic antiretrovirals, as one example, may disagree); the stimulus to do so is weak, so we feel only weak to moderate nausea rather than nausea strong enough to throw up.

source: Stack Exchange

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Do ring species exist?
In trying to understand evolution better, I have been looking at examples of speciation, and have thus come across the topic of ring species.  I have tried to find concrete examples of how these work, but have been unable to.  This paper deals with one of the frequently quoted examples of ring species, but concludes:

In conclusion, although ring speciation is theoretically
  possible, the few well-studied examples suggest that it
  occurs infrequently, because the dynamics of species’
  ranges are more likely to result in fragmentation, i.e. periods of allopatry, before the slow process of isolation by
  distance leads to sufficient divergence to allow for circular overlap.

The paper does, however, cite an article on a bird that appears to be a strong example of a ring species, but buying access to it is more expensive than a year´s supply of toilet paper.
Is there hard evidence that ring species exist?  And if so, what is the evidence and what does it teach us about the nature of speciation?

Good question +1. I don't think there is very obvious examples of ring species. There are however, examples that are quite promising such as the greenish warblers (Irwin et al., 2005) and the polytypic salamander (Moritz et al., 1995).

I'm not sure if I +1'd just for the toilet paper.

Please confine your remarks about access to scientific works to whether or not you have this. If you do not have access, someone here may help you or you may try to help yourself by emailing the author and requesting a PDF. I personally do not have funds to pay for others to read my papers but I am happy to respond to individual requests for reprints, whether or not this is in technical contravention of the agreement with my publisher.

You can get a free download of the paper from here: [https://www.researchgate.net/publication/12128943_Speciation_in_a_ring].  Or email the author(s) and ask for a reprint.

yes ring species do exist like the herring and lesser black-backed gulls in Northern Europe.

Have you read the Examples section on the Wikipedia page you link?

I looked at the sources for the examples.  For most of them I had to go through more than once source to find the primary article with the evidence, and I was unable to access several.  The few where I found the primary article with the evidence seemed more speculative than definitive.

Ensatina eschscholtzii is a classic example it is a salamander species. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1558-5646.2009.00722.x

While no perfect example exists, there are various different 'ring species' in nature where you have which species are able to interbreed with closely related populations, but there are least two "end" populations in the series. Examples include:

Alauda arvensis, A. japonica and A. gulgula: Species of Skylark birds that coexist around Central Asia

In central Asia, a northern form,, arvensis, a southern form,gulgula, and Oriental,japonica , coexist without interbreeding.These forms are separated
by a gap in distribution in northern China, but a morphologically intermediate
form, japonica, occurs in Japan. Northern japonica are similar to arvensis and
southern japonica resemble gulgula. -Ring species as bridges between microevolution and speciation

Lalage leucopygialis, L. nigra, and L. sueurii: Species of triller birds that coexist on Sulawesi Island.

The existence of ring species like this can, as biologist Ernst Mayr puts it, illustrate "how new species can arise through 'circular overlap', without interruption of gene flow through intervening populations…" and offers proof of speciation through a method other than allopatric speciation: speciation that happens when two populations of the same species become isolated from each other due to geographic changes.

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What is a detailed chemical explanation for describing how an enzyme may lower the activation energy of a reaction?
If you can provide some sound reasoning that touches on tertiary structures of proteins and does not use a lot of advanced chemistry jargon that might be really helpful, especially for an intro biology student.  I think my problem is that activation energy is lowered by an enzyme and I know how its like on the Gibbs Free Energy diagrams.  However I think I've been taking this as an axiom and I'm not really sure why.

Have you read the wiki article? What specifically don't you understand? How should we provide a detailed chemical explanation without using advanced chemistry jargon? You need to [edit] your question and explain exactly what you know and where exactly you're stuck. Otherwise, this question may be closed as violating our homework policy. "Homework" is interpreted to mean any academic or other assignment, test preparation, or task given in relation to a class, educational setting, or self-learning.

Take a piece of wood and set it down on a slippery surface. Now take a saw and without holding the piece of wood try sawing through the wood. Much of the energy will likely be dissipated by the board sliding around and you will expend a lot of your own energy trying to cut the wood without much success. Now take the wood and securely fasten it between two clamps, like on a work bench. Now use the saw and cut through the wood. All of the energy that you are expending is transferred to the cutting action and isn't dissipated because the wood cannot move around. The clamps are holding it in place

The clamps are like the enzyme. They provide a more efficient path to catalyze the reaction. Just as the clamps make each of your strokes with the saw more efficient than the exact same stroke when the wood was free to move on the slippery surface.

Nice description @AMR :) As an add-on - enzymes with multiple substrates often bind these substrates and bring them close to each other such that it is a near-perfect 3D confirmation to establish the bonding / breakage of chemical bonds.

I voted to close because "an enzyme" is too broad. There are many enzymes that may catalyze reactions in various ways.

I don't think this should be closed. It can be pretty easily answered, and I may even do so in the future.

@AliceD Thanks... If the OP had said that they were taking Biochemistry then I would agree that enzymes would not be specific enough, but they did say Intro Biology, which means at this point of first semester they may be around Chapter 8 of Campbell and they likely are just struggling with the basic understanding, although Campbell, goes into a little more detail, they are taking very broad brush terms. We aren't Academia SE where it is geared towards graduate students and professionals only, so I don't think it needs to be closed. You are right though that there are many types of enzymes.

@MattDMo the wikipedia article does not say how enzymes lower activation energy. Actually it is not easy to find answer to this question by a simple google search and most basic level biochem textbooks also do not explain this issue properly.

@WYSIWYG The Wikipedia page does go into it briefly in the Mechanism section, after the stuff about substrate binding.

@canadianer ahh yes.. I just noticed. But I do think that it won't be very clear to many people. It is not that trivial. So I won't consider this a question a homework.

BACKGROUND
We should first understand what activation energy really is and what does Arrhenius equation mean. For any chemical reaction to happen you need to break some existing bonds in order to form new bonds. Breaking existing bonds consumes some energy; in other words you have to convert the reactant to an active form which undergoes a reaction readily. The energy that is required to do so is called activation energy.
It is essential to note that activation energy is an empirical term because it does not actually consider the reaction mechanism. The above example of bond-breaking and re-formation can happen in many ways. Some mechanisms may require less activation energy than the others.
The Arrhenius equation denotes the relationship between reaction rate and activation energy:
$$k=Ae^{-\frac{E_a}{RT}}$$
where $k$ is the reaction rate constant, $A$ is the Arrhenius constant (an arbitrary proportionality constant), $E_a$ is the activation energy, $R$ is the universal gas constant and $T$ is the absolute temperature.
This equation tells you that the rate of reaction decreases with increase in activation energy and increases with increase in temperature.
The temperature indicates the internal energy of the system i.e. the movement of molecules. Collision between molecules is essential for chemical reaction to happen and increased temperature increases the chance of collisions (due to higher molecular movement).

How do enzymes lower activation energy of a reaction?
They either do that by increasing the chance of interaction between the reactants or diverting the reaction to follow a different mechanism that has a lower activation energy.
As you know, the enzyme binds to the reactants and forms a complex. This effectively brings the reactants closer thereby increasing the probability of their "collision" which in turn increases the reaction rate. This can be further extended to the level of molecular orientation. The analogy presented by AMR in their comment is great. It is one of the mechanisms by which the free energy of the system would increase — by reduction of entropy. Clamping the substrate in place can expose its reactive groups to the co-reactants, thereby allowing the reaction to proceed faster.
In most other mechanisms of enzyme catalysis, the functional groups in the enzyme active site react with the substrate to form intermediates and these intermediates which have lower activation energy give rise to product faster than the substrate in absence of the enzyme.
It is to be noted that this entire process of catalysis adds a few extra steps to the actual reaction (binding,  formation of intermediates etc). The catalyst would be effective only if these combined rates are still faster than that of the uncatalyzed reaction.

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How will changing the concentration of a Tris buffer affect amylase enzyme activity?
For instance if you increase the amount of Tris but pH still does not change then will the enzyme activity still proceed normally?  If it does change the pH will it change enzyme structure and why?

I am a novice at biology, but googling "amylase ph" resulted in a recommended pH of 7.0 for "Human pancreatic alpha-amylase" . So wouldn't it depend on the pH of the Tris, which I forgot, since there are alot of different kinds of tris buffer preps? Googling "Tris" resulted in a wikipedia page with the pH being 8.0. So given that information, wouldn't it have less functionality?

Would increasing the amount Tris but no change in pH do anything significant?

To be honest, I wouldn't know. But increasing the amount of the Tris would cause a change in pH would it not? Unless you mean to balance it with something basic or acidic? And then in that case i still would not know. I always thought TRIS was just used to obtain the optimal pH for enzymes and the like and the pH was its reason for being used.

Assuming the Tris is chemically inert to the reaction, a higher amount of Tris will increase the buffering capacity (i.e. the pH changes less).

I realize I'm 4 years late, but wanted to give an answer to this. It appears that tris often has inhibitory effects on amylase activity. Adding more Tris will lead to competitive inhibition with the substrate and will skew the results.
Binding of Tris to Bacillus licheniformis alpha-amylase can affect its starch hydrolysis activity
https://www.ncbi.nlm.nih.gov/pubmed/18289113

After 4 years of working in enzymology I've got say tris is really tricky first of all when you use more tris to keep pH at the same as before you will need to re adjust the pH as tris is about 9 but most enzymes work around 6to7.5 (for alpha amylase it's 5.8) if you don't then your enzyme wont work properly ,it needs very low or high pH grade to destroy 3D structure of enzyme ,so we can simply say it will lost it's functionality , if you adjust the pH high concentration can cause some problem such as surrounding substract here amylase and not letting it to connect to enzyme in some cases acid you use to adjust pH has toxic effects on enzyme chlorine in this case but pretty sure the best way is optimization to understand the reaction.
Best regards .

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Why is the resting membrane potential of excitable tissue not affected by the extracellular sodium concentration?
I know that the resting membrane potential for excitable tissue (eg, nerve) is primarily determined by the electronegative difference between the inside and the outside of the membrane for potassium ions, as they are most permeate ion by far. And since the membrane is largely impermeable to sodium, it's diffusion potential is insignificant, as such it does not contribute much to the resting membrane potential.
However, is it not correct to think that if the concentration of sodium ions in the extracellular fluid drops, outward diffusion of the positive potassium ions will increase, because the outside of the membrane is now less positive (more negative), subsequently making the diffusion potential of potassium and the resting membrane potential more on the negative side and further from the action potential threshold. I am asking this because my professor was mentioning factors that affect the resting membrane potential, and he mentioned that the ECF concentration of sodium has no effect on the resting membrane potential.

I cannot imagine anyone being able to explain it more clearly than this webpage. Your question is addressed in the middle of the page.
It's easier to split the idea into two separate, but parallel ideas: electrical potential and chemical potential. Both sodium and potassium contribute to resting potential. Sodium affects the voltage (electric potential) across the membrane. However, their chemical potentials (difference-across-membrane) are separate. The key idea is that there is a difference between resting membrane potential and potassium equilibrium potential.
I quote a helpful thing to keep in mind:
In a neuron, the resting membrane potential is closer to the potassium equilibrium potential than it is to the sodium equilibrium potential. That's because the resting membrane is much more permeable to K+ than to Na+.

    If more potassium channels were to open up—making it even easier for K+ to cross the cell membrane—the membrane would hyperpolarize, getting even closer to the potassium equilibrium potential.
    If, on the other hand, additional sodium channels were to open up—making it easier for Na+ to cross the membrane—the cell membrane would depolarize toward the sodium equilibrium potential.

Hey. So if the resting membrane potential is indeed dependent somewhat  on the extracellular sodium ions concentration, wouldn't a drop in that concentration affect the resting membrane potential? If that's true I think the next issue is to only decide on how much of the sodium ion extracellular fluid concentration needs to drop before the resting membrane potential is affected in turn. Please also check my comment on the other answer. Thanks for replying, I really like Khan Academy as well.

This is a common misconception where ion concentrations and charge concentrations get confused.
Although the resting potential makes it sound like there is more "positive charge" outside than inside a cell, that difference is really really tiny, we are talking about a tiny tiny fraction of the number of ions in a cell (see for example Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?). For all intents and purposes, the sum charge of positive and negative ions is neutral both inside and outside the cell, to several decimal points.
If someone says the sodium concentration outside the cell changes they don't really mean just sodium ions, they mean sodium ions plus some equivalent number of negative ions. We can ignore those negative ions if they don't have any membrane permeability (see the Goldman equation: ions with no permeability don't count at all for membrane potential).
So in your question you already identified why extracellular sodium concentration doesn't matter much: its permeability is low and the extracelullar sodium concentration is already high. You should not think about adding extracellular sodium changing the charge of ions outside, you should only think about it as changing the driving force for sodium. The resting membrane potential is then a function of a sum of all those driving forces weighted by their permeabilities and calculated with the Goldman equation.
I won't do the math here, but if you actually were able to dump a bucket of just sodium ions, all with positive charge, in the environment outside the cell without a corresponding negative ion in solution, you would create something like lightning traveling at the speed of light and release enough heat to boil your apparatus.

Hey. So I have a couple of questions. 1- Why are should ions be separated from charges? In a biological system, aren't they the same thing. 2- Why can't it be said that the extracellular sodium ions concentration has changed without implying that some number of equivalent negative ions has changed as well? 3- And yes the amount of electrical charges participating in creating the resting membrane potential and action potential is relatively very small to the overall charge in and out, but doesn't that make it particularly sensitive to any change in electrical polarity?

Plus it seems to me that the diffusion potential for potassium is more dependent on the electrical gradient across the cell membrane, considering that at rest, with the potassium channels opens, the intra to extracellular concentration gradient for potassium is 35:1. So in a scenario where the extracellular sodium concentration drops, like in some sort of kidney disease, won't that affect the electrical diffusion potential of potassium, since this must affect the extracellular charge somehow right? even if the membrane is not permeable to sodium.

@Remoun It's really better to not think about charges because the differences in charges are so small: read the answer I linked about how small. The way you should think about resting membrane potential is that you have some ions, and they are all flowing down their concentration gradient according to the difference in concentration inside and out and how much the membrane is permeable to them. So you have some sodium flowing and some potassium. The resting potential is the voltage at which the number of positive ions moving out is the same as moving in.

Because there is more permeability to potassium, if there were no charges more potassium would be flowing out than sodium flowing in. The voltage at which the rate of potassium ions flowing out slows down to equal the number of sodium ions flowing in is the equilibrium potential.

Separating charge takes a TON of energy. You can't just remove a bunch of sodium ions without also removing some equivalent negative ions without creating the equivalent of lightning: a massive flow of charged positive ions away from where you added them rushing every other direction and messing up your lab pretty bad.

@ Bryan. I think that sodium ions as they exist in a fluid, whether in a body or lab, are in a hydrated state, which means every sodium ion is attached to more than one molecule of water through relatively weak hydrogen bonds that are constantly forming and reforming. Since I'm studying medicine, to my knowledge sodium ions can drop in the extracellular fluid either by inadequate intake through diet, or if they are "wasted" when they are not properly reabsorbed from urine by the kidneys (this may not be the only way for such wasting).

In case the sodium ions is wasted from the body, as in the case or some kidney malfunction, they are lost along with their hydration shells, dragging some water along. so I can't imagine a scenario where there is actual separation of charge on the magnitude you've described.

In any of those cases where sodium concentration drops, another negative ion drops as well, trust me. Regardless of being hydrated. This is basic electrochemistry.

Use the Goldman Equation - it's always correct, if you think of something where it doesn't work then you are approaching something wrong.

Re: “For all intents and purposes, the concentration of positive and negative ions are the same inside and outside the cell, to several decimal points.“ Here do you mean charge or ion concentration.

@user237650 I see now the way I worded it was vague. I meant that the ratio of positive:negative ions is 1 outside the cell, and also the ratio of positive:negative ions is 1 inside the cell.


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What insect is this with furry wings?
Found this on the wall of my house in Kuching, Sarawak, MALAYSIA It is a tiny black triangular shaped insect.

Possible duplicate of What's the name of this bug from Toronto, Canada?

Very nice macro. I really like the looks of these things and hate to kill them. :-( I keep my drains free-ish of biofilm so I don't have to.

That is a Moth Fly, also known as a Drain Fly. It is in the order, Diptera, family Psychodidae. https://en.wikipedia.org/wiki/Drain_fly

Here the animal's appearance helps in a more precise identification: we're looking at a species of Clogmia Enderlein, 1937 (see here for the only New World species of the genus); this may be C. albipunctata (Williston, 1893), but southeast Asia also features native species (for the original descriptions of several New Guinea species see Pacific Insects Monograph (15), accessible here).


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can a bacterium cell become a cancer?
I don't mean if a bacterium can be the cause of cancer inside a human. But can actually a bacterium changes in the way as normal cells change into tumor cells?
So gaining such characteristics of a tumor cell and if inside human body create a tumor mass?

related

A prerequisite for a cancer is that it is a type of cell within the human body that the immune system recognizes as it's own, and cancers are also generally multi-cellular. bacteria are unicellular and if they do reproduce wildly, then it's more of an infection than a tumor.

You ask two questions:

If a bacteria can get the same characteristics as tumor cells.
If such "bacterial tumor cells" actually can form a "tumor" within the
human body.

I assume that your question is not if bacteria can change in such a way that the can be confused with eukaryotic cells. This they cannot do. Bacteria cannot form organelles. Because they have no organelles they are solely dependent on their membrane for energy production. Because the surface area to volume ratio decreases with cell size there is a physical possible maximum size for bacteria. Here is some more in depth info on the subject.
So what characteristics can bacteria then have that tumor cells also have?
Well, according to wikipedia, a tumor is a mass of abnormal and excessively grown tissue (neoplasm) which may or may not be malignant. According to this definition bacteria could be tumor-like if the could form tissue and if this tissue could then grow abnormally or excessive.
And guess what? If you define tissue as "an ensemble of similar cells and their extracellular matrix from the same origin that together carry out a specific function." like Wikipedia does. Then you could argue that the biofilms some bacteria form are quite tissue-like since biofilms also contain an extracellular matrix, the cells within have the same origin and (in some cases) the bacteria can have differentiated functions.
However, the fact that bacteria can form biofilms does not make them tumor like. For that comparison to work mutated bacteria should be able to outgrow the rest of the biofilm. And while mutation that cause noncooperative/cheating/abnormally growing bacteria in biofilm are known, this kind of mutations cause the biofilm as a whole to grow slower. (source) In this sense comparing a biofilm to a colony of ants may be more appropriate than comparing it to tissue.
So to answer your questions:

Bacteria can form tissue-like formations, but when members of this formation do not cooperate anymore this typically leads to less growth, instead of increased growth.
Biofilms do form within humans. For example the bacterium Pseudomonas aeruginosa is assosiated with cystic fibrosis. And while cheaters exist among these bacteria, biofilms with high ratios of cheaters have a lower fitness. see this paper Therefor you would expect most biofilm within humans to be more tissue-like and less tumor-like.

No - when bacterial cells grow in an invasive manner in the body, this is termed a bacterial infection. When one’s own cells grow in an invasive and uncontrolled way, it is termed cancer.

This is exactly correct, but could do with some references, and possibly a little more about why these things are different.

Depends on how you define a "cancer".
The main hallmark of a cancer is cells with an agenda that can be summarized as "hungry, hungry, split".
Aggressive bacterial infections exhibit this behavior, digesting their host from the inside and quickly multiplying. Often, they spread quickly, which could be compared to going metastatic.
However, cancers have 2 advantages because they're technically human cells. This helps them dodge immune reactions, and makes a chemical "antibiotic" type treatment also difficult because it would be poisonous to regular human cells by definition. All of the known regular (non-personalized, non-immunotherapy) chemo treatments cause painful amounts of friendly-fire damage to regular cells.
Bacterial infections don't have this advantage - if they want to dodge immune reactions they have to figure it out on their own, and bacteria are so different from human cells that it's easy to make a chemical that selectively damages them with minimal side effects for humans.
Another cancer-like behavior that's possible in bacteria - benign to malignance. For example, suppose there's a symbiotic bacteria that mutates (or more likely, picks up a malicious plasmid) that turns it into an aggressive pathogen.


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Can a plastic degrading bacteria science fair project be recreated in a school lab?
i am just looking for a science fair project and am fascinated by this topic. i was wondering if a project concerning the isolation of plastic degrading bacteria could be done in a school lab. I am in grade 10. Anything helps!

This mostly depends on the equipment available in the school lab & as well as time and resources available. If you can add a few more details about either the equipment present in your school, it'd be easier to say what would be possible. The other way around if you describe in more detail what you'd like to do, it's easier to say what would be needed exactly.

I am not exactly sure of the materials needed since this is just the beginning stages of finding a project. From what I've researched, the main objective would be to isolate bacteria from soils, to test these isolates for ability to degrade different types of plastic and to identify these microbes. We have until December 14 to finish experimentation and would have help from a lab technician. Do you know if this type of project would be possible and what we should inform our lab technician with in order to help us? Thanks!

You should speak with your lab technician asap - he/she will know much better what exactly can be done in the lab and will need to done. Note that 2 months is a rather short timeframe to do an experimental project, esp. since growing isolated bacterial strains is not always straightforward


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Can a plastic degrading bacteria project be recreated in a school lab environment?
I am looking for a science fair project and am wondering if this could be a good idea. I am in the 10th grade. I am not exactly sure of the materials needed since this is just the beginning stages of finding a project. From what I've researched, the main objective would be to isolate bacteria from soils, to test these isolates for ability to degrade different types of plastic and to identify these microbes. We have until December 14 to finish experimentation and would have help from a lab technician. Do you know if this type of project would be possible and what we should inform our lab technician with in order to help us? Please reply asap as we don't have much time left to find a project. Anything helps. Thanks!


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At which temperature is the Tick-Borne Encephalitis Virus destroyed?
At which temperature is the Tick-Borne Encephalitis Virus destroyed? If there is no data specifically for TBEV, is there any data for typical temperatures at which other Flaviviruses / Flaviviridae / other similar viruses are destroyed? (Or if there's nothing specific at all, then viruses in general?)

A very basic model of virus inactivation is exponential decay.
You can describe exponential decay with the $N(t) = N_0e^{-\lambda t}$ equation, of if you want to use half-time, then with the $N(t) = N_02^{-t/t_{1/2}}$, where $N$ is the value which reduces by time, $t$ is the time, $\lambda$ is the exponential decay constant and $t_{1/2}$ is the half-life (the time required to reduce the actual value to its half).
Exponential decay looks like this on diagrams:

Figure 1 - exponential decay

Figure 2 - exponential decay on log scale is linear

In the case of your TBEV virus, the $N_0$ will be the initial virus titer, the $N(t)$ will be the virus titer by a specific time, the $t$ will be the time and the $t_{1/2}$ will be the half-life, which depends on many things; TBEV strain, temperature, dry/moist heat, pH, etc...
Now real life logarithmic diagrams of TBEV thermal inactivation are linear only by the first 30 mins or so (the inactivation is exponential during that period) as you can see on Figure 3.

Figure 3 - virus inactivation at 60°C
2004 - West Nile virus: recent experience with the model virus approach.
where $TCID_50$ is the tissue culture infective dose

By virus inactivation most of the articles like to use log 10 reduction factors. For example $3 lg$ or $3 log 10$ means in this context, that lowering the initial value to $10^3 = 1000$ fold.
According to this article most of the checked TBEV strains has an inactivation index (the reduction factor difference between two temperatures) around 1.7lg between 50°C and 37°C for 15 mins. So you need 15 mins at 50°C to reduce them at least $10^{1.7}=50$ fold. The reduction factor by this study was around 4lg by 37°C for 15mins (so the virus count reduces certainly not just because the heat, but other environmental factors).

Thermoresistance (Т50) of TBEV strains was tested by Ovchinnikova et
  al. method [17] using 24-hour cell culture grown in 96-hole plates at
  the presence of СО2. The thermoresistance was determined by
  inactivation index – difference in lg of titers of virus samples
  heated at 50°С during 15 minutes or unheated (4°С). In case of titers
  difference equal or less than 2.0 lg the strain was characterized as
  Т50+, from 2.1 to 3.0 lg – as medium, equal or more than 3.1 lg – as
  Т50-.
The values of lgTCD50/ml at 37ºС varied from 3.5 to 8.26. According to
  the thermoresistanse feature all tested strains were divided into
  three group: thermostable (Т50+) - nine strains; thermolabile (Т50-) –
  one strain; strains with medium thermoresistance – three strains. It
  should be noted that all strains isolated from I. persulcatus ticks
  collected in Krasnochikoiskiy district of Transbaikalia were
  thermostable.

2013 - Genetic and Biological Properties of Original TBEV Strains Group Circulating in Eastern Siberia

According to another study TBEV required 6 hours of moist heat at 60°C for inactivation of 6.6 lg.

Vapor heating of a FVII concentrate in another study (which used
  lyophilization, followed by adding water to achieve homogenous
  moistening, then heating at 60°C for 10 hours, followed by heating at
  80°C for one hour in an airtight container under nitrogen gas
  atmosphere) was evaluated for its ability to inactivate HAV, HIV-1,
  TBEV, PRV, and MVM. HAV was readily inactivated within one hour at
  60°C (5.9 log 10 ). TBEV required six hours of this treatment for
  inactivation of 6.6 log 10 , and three hours were required to
  inactivate
  6.2 log 10 of HIV-1 and 6.9 log 10 of PRV.

2002 - Part 3a, Plasma and Plasma Products - Heat and Solvent/Detergent Treatments

According to this study TBEV is considered not heat resistant, so if you are worried for example about raw milk pasteurization, then I think boiling the milk for a few minutes is enough.

Due to the lipid envelope, TBEV is readily inactivated by heat
  treatment, detergents and organic solvents. Even though a viremic
  phase is common during a TBEV infection in several animal species,
  foodborne infection via contaminated meat or organs is unlikely due to
  the fast virus inactivation at elevated temperatures.

2011 - Scientific Opinion on an update on the present knowledge on the
occurrence and control of foodborne viruses

Thanks! This is very interesting, definitely very relevant and I'll certainly  upvote, but it doesn't quite answer my question... The "thermostable" strains are able to survive 50ºС, but how high does the temperature need to be to destroy them? The paper doesn't seem to have any data beyond  50ºС. Basically, I am looking for the minimum temperature at which it would be safe to assume that TBEV has been destroyed, regardless of strain.

@EugeneO I don't think you get the basic idea behind heat inactivation... I'll edit my answer.

Thanks for adding all this detail - I now realize I haven't made my question precise enough. I understand the concept of half-life / exponential decay. I guess the question I'm really trying to answer is, for a reasonably large reduction (let's say 3lg), and the most thermoresistant strain I'm likely to encounter, at what temperature do I have to treat it (given some reasonable fixed treatment time, e.g. 15min or 60min) to ensure that 3lg reduction will happen?

... And to add to that, I might as well ask the layman's question I'm really trying to answer. If I come back from a hike in the woods in Siberia with potentially live ticks on my clothes, and put the clothes through a wash cycle (e.g. 30min at 60 deg C), can I be reasonably assured that whatever viral particles that remain won't be enough to infect me? Is there any setting on a commercially-available washing machine (temperature, length of cycle) that will give that assurance?

(Actually, just noticed the part about "detergents" in the last article you linked, this may be my answer... But more details would be nice, this is not a theoretical question, I actually do go for hikes in the woods of Siberia so having additional data would certainly be reassuring :)

@EugeneO According to the linked articles, 3lg seems like achievable with 60°C, 30mins by every TBEV strain. Yes, detergents will boost the inactivation as well. Most laundry detergents contain e.g. proteolytic enzymes, which can help too...


text:
DNA preservation at room temperature
I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in their secure temperature-controlled facility, or "home DNA banking", where they somehow preserve the DNA such that it can be stored without damage "indefinitely", at room temperature. This is how they describe the technology:
"The  DNA is bound to a substrate and sealed under nitrogen gas with out patent pending process. This process allows the DNA to remain in a state of suspended animation and if the vial remains sealed the DNA has an indefinite shelf life. The DNA Memorial Home Banking may be banked in non extreme conditions and room temperature for future testing at home."
My question is basically this: Is there any scientific merit to their claims (i.e. is there anything peer-reviewed on the subject of room-temperature DNA preservation for many years, using technology such as the one they describe)? Can DNA preserved in such a way really be tested later in regular DNA testing labs (or will I need a specialized lab that knows how to deal with this unique process)? Is there any possibility of a full sequencing later of DNA stored in such a fashion?

If you would like to sequence this family member's DNA, why not sequence a sample now? Without a link, I'm not sure how to evaluate their process, but I would be skeptical. When I'm banking a DNA sample for future, unknown testing, I store it at -80 C.

I worked with museum specimens that were 40 years old, and dried, they were fine. They sequenced the Neanderthal genome. In my experience, DNA can be safely stored at room temperature.

DNA is already a pretty stable molecule. Storing it under N2 sounds like they have it precipitated form (i.e. lyophilised) - I would expect lyophilised DNA in a N2-only enviroment to last for a very long time. The biggest issue for using it later would probably be UV light exposure and physical fragmentation (which isn't a big problem for sequencing though).


text:
Does recombination increase the additive genetic variance for fitness?
On this article, first column, eighth line of the introduction:

By bringing together favourable alleles from different chromosomes, sex and recombination increase the additive genetic variance for fitness [..]

Can you please help me understanding why does recombination increase the additive genetic variance for fitness?
Note: In reaction @mgkrebbs comment, I think that given the subject of this article, when talking about different chromosomes, the authors actually referred exclusively to homologues chromosomes. My question concerns the second part of this sentence anyway: "Why does sex and recombination increase the additive genetic variance for fitness"?

Here is another question on the same article

This is a little tricky.
First of all lets be clear about 'bringing together favorable alleles' (or any alleles) represented by site mutations on 2 chromosomes:
--------A------------------
             X
------------------B--------

If the two dashed lines are two copies of the same chromosome, then a recombination event at X may produce:
--------A---------B--------

Allowing both A and B to be passed along to offspring.
Any given case of recombination might actually harm resulting offspring. But in cases where A and B together are beneficial, over the course of generations you will find AB genotype combinations show up more frequently in the population because of selection and competition.
Firstly each individual variant experiences some selection for fitness and many are lost.  Because of this, recombination will typically put two or more such variants together onto a single chromosome.  Recombination allows for individual mutations of benefit to pool together and collect into a single place.  This multiplies the chance that stronger combinations of mutations will show in the gene pool.  This increases the fitness variance - the most powerful combinations are more beneficial than any single variant alone.  On the other end detrimental combinations will also make some individuals exceptionally weak.
So its not just recombination, but recombination and selection which create favorable combinations of alleles in populations.  The link you give discusses how when selection is not strong, recombination is not so great, but we never seem to lose recombination where these conditions don't hold sway.
By comparison, consider a simple case where recombination does not occur where there is an A genotype and then one waits for B to show up on the same chromosome by random mutation.  That would take perhaps thousands or even millions of generations before such a thing happens at random.  Recombination is a powerful accelerator of evolution.

thank you. As I understand your answer, you explain the advantage of recombination just as it has been considered by Muller. But if I am not mistaken you don't address the question of why the additive genetic variance (you actually don't use the words "variance") increases thanks to recombination (or thanks to the combined effects of recombination and selection). Can you try to further elaborate your answer so that it explains why recombination causes an increase in additive genetic variance.

I don't think this response addresses the quote since this concerns crossing over.  The quote says "bringing together favourable alleles from different chromosomes", which doesn't involve crossing over.

"In meiosis and mitosis, recombination occurs between similar molecules (homologs) of DNA. In meiosis, non-sister homologous chromosomes pair with each other so that recombination characteristically occurs between non-sister homologues. In both meiotic and mitotic cells, recombination between homologous chromosomes is a common mechanism used in DNA repair." http://en.wikipedia.org/wiki/Genetic_recombination

@sigeta I agree with you shigeta. But I don't think your answer answers my question. I understand that if a highly beneficial mutation occurs before another beneficial allele on the same chromosome had time to reach fixation, then these two mutations can only be found in the same individual if recombination occurs. This concept is also conveyed by Gould when saying that "selection creates the fit". But I still don't understand why the additive genetic variance for fitness increases as a result of recombination.

Its tough to write answers here - remember that responders want to explain terms to other readers as well as the poster or they get complaints.  I thought I'd answered your question though.  Beneficial recombinations are among offspring; the vast majority of recombinations are probably less fit or have no substantial effect on fitness. Over time selection brings those combinations into common occurrence in the gene pool.  I didn't explain how selection works... maybe i need to define that in detail too?

Well the issue I'm struggling with is the idea that fitness variance is greater in a population where recombination occurs. This is not intuitive to me. I understand that recombination allows to bring to fixation several mutations that occurs in different individuals in roughly speaking the same time (It actually depends on the probability to occur in a chromosome already bearing the mutation which depends on the time difference between the two mutations and the selective coefficient of the first according to Haldane's law 1-P = exp((1+s)p).

@shigeta But why does this process increases fitness variance? I am not sure my comments will help finding out what point I am missing. I might still have some difficulties with Fisher's fundamental theorem although I asked a question about that some times ago. If you can pinpoint what I am missing, please try to edit your question to add some elements. Thanks a lot for your help.

I added a little bit here, but I'm not sure what the tie in to Haldane's rule is explicitly.  Haldane's Rule applies to specific cases where there is interspecies breeding and relates to speciation. Can you put in some links if you have any?  Or perhaps i've helped with what I've put up here.


text:
Influence of temperature on transcription, protein binding and decay rates
I am the kind of biologist who doesn't know much about molecular genetics and about the dynamic of biochemical reactions.
Question
My question concerns the influence of temperature on the dynamic of molecular genetic processes. Typically, I'd like to know how (quantitatively speaking, looking for the $Q_{10}$ for example) the following parameters get modified with temperature.

rate of transcription

UPDATE See How is the rate of transcription influenced by temperature?

protein binding to a DNA-binding-motif

UPDATE see influence of temperature on protein binding and decay rates

rate of protein decay

UPDATE see influence of temperature on protein binding and decay rates

rate of mRNA decay

UPDATE answered by @Chris below

Why do I ask this question?
In order to know what kind of default parameters values I should enter for modeling purposes in evolutionary biology. While our scope is large we decided we would consider parameters values that are observed in yeast.

This sounds straightforward when thinking about it but finding hard evidence is not really easy. As this is too long for a comment, I have to put it in as an answer. Just a few thoughts: All enzymatic reactions are of course temperature dependent and usually have a temperature optimum at the specific living temperatures. For yeast this is around 27°C, for thermophiles this is much higher. For transcription an number of other factors including accessibility of the chromatin and the availability of cofactors play an important role besides the higher activity of one enzyme. This paper might be interesting for you: "Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response".
DNA binding should be a statistical process between association and dissociation at a given binding site. At higher temperatures the turn-over at the binding site should be higher (because there is more energy available to promote dissociation). T

The thermodynamics of DNA structural motifs
Thermodynamics of specific and nonspecific DNA binding by two
DNA-binding domains conjugated to fluorescent probes.

Thanks a lot Chris. You articles answered my questions for both the rate of transcription and the RNA decay rate. I asked a new question here for the two protein-related questions.

Great, I wasn't completely sure about it.


text:
How could be the "Eurasian magpie" bird won the "Mirror Test" where Gorillas failed
EURASIAN MAGPIE VS GORILLA
 VS
How could be the "Eurasian magpie" bird won the "Mirror Test" where Gorillas failed ?

In 1982, mirror tests on two, zoo-reared gorillas failed to demonstrate self-recognition. The authors wrote "[These studies]...suggest that the gorilla may be the only great ape which lacks the conceptual ability necessary for self-recognition." In 1993, a report was published that although six gorillas had previously failed to exhibit self-recognition.
The Eurasian magpie is the only bird to pass the mirror test. Researchers applied a small red, yellow or black sticker to the throat of five Eurasian magpies where they could be seen by the bird only by using a mirror. The birds were then given a mirror. The feel of the sticker on their throats did not seem to alarm the magpies, however, when the birds with colored stickers caught a glimpse of themselves in the mirror, they scratched at their throats - a clear indication that they recognized the image in the mirror as their own. Those that received a black sticker, invisible against the black neck feathers, did not react.
Reference

Birds lacks neocortex, the area where self-recognition was thought to reside. Then which part of the brain do birds like Magpies uses to process these complex cognition ?
Why do Gorillas failed the mirror test ?

Pigeons have also been shown to be self-aware
[1]: http://www.robertlanza.com/files/SCIENCE_Self-Awareness_in_the_Pigeon.pdf

I think the mirror test is not a reflection of overall intelligence. It is one of many ways to reflect cognitive properties what we think makes us human onto animals.

@ChrisStronks Neat!  However, as the authors state, "We have demonstrated that a pigeon can use a mirror to locate an object on its body which it cannot see directly.  We should not attribute this, however, to a pigeon's 'self-awareness' or claim that a pigeon has a 'self-concept.'"

Identifying oneself from a reflection needs relative comparison of particular movements and gestures from the image and thyself. Identifying from the mirror reflection is not always attributed to self awareness or overall intelligence, but there is still a complex mechanism working behind to enable this feature. The question mostly regards why gorilla(being a primate) failed and magpie(being a bird)achieved.

I think this website provides a pretty surprisingly thorough breakdown of avian brain anatomy, including historical contexts and debate around what exactly is homologous and what is not, and whether 'homologous' is a useful bit of information.
In short: It was thought until recently that the bird brain was just the core of the mammal brain with some layers peeled off, but it turns out to be more like a scale model, with many of the same parts. Roughly. Sort of.
So birds do not technically have a neocortex. They have a structure that looks like a neocortex, but it also looks like some other things. Gorillas do have a prefrontal cortex etc (even if they are smaller than in humans). The knowledge that structure X performs function Y in an organism generally implies little about a second organism, with or without structure X. Even features like 'wings are for flying' and 'fins are for swimming' have exceptions.

Nice answer (+1) - could you perhaps summarise the detail on the webpage you linked too?

Uh. Is the second paragraph deficient in some way? I've tried to summarize the salient points to this discussion.

The second paragraph summarises the general message of the site linked, but it would be good to expand on the detail of the first paragraph (partly in case the link ever goes dead, that would make the answer obsolete).


text:
What colors I am looking for in the TSA stain in this paper?
I'm just having a little bit of trouble and want to make sure that I am seeing the same things that the original researchers were seeing. This is the name of the paper Hair Cycle Control by Estrogens: Catagen Induction via Estrogen Receptor (ER)-α Is Checked by ERβ Signaling. Specifically, I am looking at Figure 2 with the tyramine signal amplification (TSA) images and am wondering what colors are supposed to indicate the presence of estrogen receptor (ER)? Take the statement:

ERα IR had its peak in telogen follicles and was intensely visible in
the dermal papilla and cells of the sebaceous gland.

When I look at Figure 2, T, I don't seem to be seeing any blue in the sebaceous gland?

Is it the case that the area I circled in red is the sebaceous gland with the smaller circles around the blue indicating the presence of ER-α, as opposed to the arrow the authors had placed?


text:
Is Einstein's mass energy equivalence ($E=mc^2$) relevant to biological systems?
I'm more than 100% sure that the kilograms I eat don't get directly converted to feces and urine.
I'm sure some of it goes to regenerating tissue that is constantly being disposed as well, and maybe some of it is  also being exhaled.
But I have a feeling that $E=mc^2$ might have something to do with the disposal of ingested kilograms.
We are constantly radiating electromagnetic waves in the nonvisible spectrum, we generate heat, we generate chemical bonds, all of these processes can convert mass to energy.
So I was wondering if $E=mc^2$ is relevant to biology?
Thanks.

Short answer
Any law of physics will of course be applicable to living beings. However, in the absence of mass gain and mass loss, the input = output equation for matter holds true and does not require any spontaneous creation and destruction of matter to equate. In other words, the effects of Einstein's discovery has no measurable/practical consequence on biological system (it is here but it is negligible) and the law of conservation of mass applies nicely.
Input and outputs of matter
There are two main sources of matter input:

Eating and drinking
inhaling (gas through the trachea and the lungs)

There are three main sources of matter output

excretion (urine and feces)
exhaling
sweating

The importance of inhaling and exhaling
Just to get an intuition about the importance of inhaling and exhaling matter in this input = output balance, note that when one make sport to lose weight, she/he principally lose weight through exhaling (see this popular video from SciHow). Similarly, trees mass mainly comes from  what they inhale (see this popular video form Veritasium)
Possible duplicate on Physics.SE
You might also want to read the How does mass leave the body when you lose weight? on Physics.SE.

No, the mass-energy convertibility has no practical relevance to biology.  The amount of mass produced or lost in the chemical reactions in biological systems is so small as to be immeasurable and is ignored for biological purposes (other than the conversions which happen as consumed radioactive elements decay).  One needs a nuclear reactor, atom bomb, or star to convert significant quantities of mass to energy.  Chemical bonding does convert between mass and energy, but the mass change is infinitesimal, as described in this question: "Do chemical bonds have mass?"

No, it is not. There are no nuclear fission or fusion reactions being performed in a biological context, for reasons that should be immediately obvious. Mass is not being converted to energy, or vice versa, when we generate heat or create or break chemical bonds.
Biological systems are covered by the laws of the conservation of mass and energy, so kgin $=$ kgout and Ein $=$ Eout. The inputs are food, beverages, and inhaled $O_2$, and the outputs are urine, feces, and exhaled $CO_2$. The making and breaking of various types of chemical bonds converts energy from one form to another, including heat.
I'm not sure what you mean by "electromagnetic waves in the nonvisible spectrum" aside from infrared light (heat).

Fission/fusion is not the only way you use $E=mc^2$. E.G. a water molecule weighs less than its constituent parts.

Are you sure that fusion and fission and energy to matter (and vice-versa) transformation does not occur in our body? It is obviously not an influential parameter in the input=output balance but it still occurs, doesn't it? I might be wrong, my knowledge in physics are a little shaky!

@DavidV and how does that happen?

@Remi.b yes, technically there is some radioactive decay of isotopes in our body. However, I said "in a biological context", meaning it has no impact on our biology - it just happens.

Ok it makes sense +1. I was pretty worried about this possible misunderstanding when I wrote my answer that I wanted to highlight it in yours.

@MattDmo the difference between the mass of the bound system and the unbound system gives you the binding energy. In a fission reaction this would give a tremendous amount of radiation, in the case of the creation of water it will give you a minuscule amount.


text:
Can multiple overt/covert intentions produce identical EEG readings?
With sophisticated techniques likes ERP, it is possible to correlate certain EEG activity with certain overt/covert actions.
What I'm wondering is: is there a risk for 2+ overt/covert actions producing identical EEG activity? Meaning:

Perhaps when I go to open/close my right hand, I produce certain neural activity (lets just summarize this as A1); where A1 is a specific set of wave signatures
Perhaps when I go to open/close my left hand, I produce neural activity A2 (a specific set of wave signatures that is distinctively/mathematically different than A1)
Perhaps there are 10,000 other movements I could make that produced their own distinct set of wave signatures (A3 - A10002), etc.
But perhaps when I think of sea turtles and pat my stomach at the same time, I produce the same set of waves as A2 (opening and closing my left hand)

My question is: is this a concern/possibility with EEG/ERP? In other words, can multiple overt/covert intents produce identical wave activity (hence, identical EEG readings)?

Why the downvote? This question is not a dupe, shows some basic research, is on topic, and is an SSCCE.

EEG/ERP are methods applied with a goal in mind. Your question asks for a concern, without defining the purpose to measure EEG/ERPs in the first place. That makes the question open for interpretation, vaguely defined and hence making the answer pob. That may explain the downvote, but I can't really speak for others

Thanks @Christiaan (+1) - but I (respectfully!) disagree, I don't think this is vague. All I'm asking is: is it possible for two distinct thoughts to produce the same electrical signature on an EEG?

That makes sense.  I +1d already.

Also,  don't worry too much about a downvote or two. It's all in the game. Upvotes give you more rep than downvotes take away anyway.

I know! I've been on various StackExchange sites for many years now and know that - typically - one lone downvote/closevote can often trigger a "Mob Lemming Effect" and cascades into multiple users mindlessly repeating the down/closevote. And I've found that defending a question with my above boilerplate response usually helps prevent this Mob Lemming Effect from continuing any further :-)

That's an interesting point. The herd effect is indeed a common one. I often have the tendency to do the opposite. Comment and upvote after edits.

The close votes are for "unclear what you are asking".. You can add some background to your question if possible. Plus, I guess EEG may not clearly resolve between two "thoughts" that well. fMRI is something that you can have a look at. People have done experiments like the ones that you are suggesting using fMRI.

To curtly answer your question: given the sheer amount of different thoughts possible (billions I guess) and the limited spatial resolution of the standard EEG as well as the restricted number of characteristic parameters to describe EEGs (frequency, amplitude, latency) it is safe to say EEG is not suitable to characterize all of the brains processes. In fact, no state-of-the-art technique can do so, as far as I can see.

Thanks (as always) @Christiaan (+1) - however I feel like you might not be understanding my question. Let's take a concrete example: is it possible that blinking my left eye might show up (analytically-speaking) to have an identical "wave signature" as, say, wiggling my big toe? By "identical wave signature", what I really mean is "identical results/outputs on an EEG reading." Does that make more sense? Thanks again!

What christiaans Answer means is: Yes it is possible that different intents show up with the same EEG signature. This is due to the fact that the resolution of an EEG is not large enough to distinguish all possible intents simply because the parameter space resolved by an EEG is much smaller than the space of all possible intents produced by the brain.

Thanks for the clarification @Thawn (+1) - unfortunately since you are only leaving a comment I can't qualify you for the bounty, but your comment is immensely appreciated!


text:
Brain wave and motor movement correlation
I am trying to better understand which brain waves are generated when the motor system (arms, legs, muscles of any kind) are activated.
According to Wikipedia, several types (Beta, Gamma, Mu) appear to be generated when motor movement is present, but it is not clear which muscle groups/movements/characteristics generate which types of waves.
Also, I see the certain waves (Alpha an Mu for instances) appear to have overlapping frequencies. If their frequencies are the same, then what makes them different?

EEG is a summation of all of the neural activity, and as such, it is difficult to attribute a certain wave type to something of the scope as activation of the movement center (primary motor cortex).   fMRI scans are much more valuable in a clinical setting (in conjunction with other methods).  It's a snapshot and sum of electrical activity.

I don't think that we know yet the exact answer of your question due to the reasons told by @MG_MD

Thanks @aayushsrivastav (+1) - so if I'm reading that correctly, if I am hooked up to an EEG that is monitoring ALL waves, and have been sitting completely still for ~10 mins (to establish a baseline) and then immediately start doing a repetitive movement (say, blinking my eyes or opening/closing my right hand, etc.), you're saying that ALL the types (Alphas, Deltas, etc.) will start changing, and not just one particular type (say, only Alpha or only Delta)? Can you confirm/deny? Thanks again!

@smeeb To put it in the simplest way possible, yes.  You would have a baseline, then when you started to do all of these things you mentioned there would be a marked increase in many wave forms.  You would be thinking about moving, actually moving, and perceiving the movement.  These affect different areas of the brain and as such, the electrical output would increase. That's why EEGs are commonly used in a resting state (like sleep studies).  Also depth comes into play when using EEG, as it is mainly superficial electronic activity, not deep within the brain.

Thanks @MG_MD (+1) - if you (or anyone else) can place this in an answer and provide citations that back up the claims, I will happily award you/them the check + bounty!

EEG signals can be broadly analyzed in two  domains; the time domain and the frequency domain.
EEGs are often analyzed in the frequency domain, where signals are subjected to spectral analysis, by methods such as FFT. This is a classic type of analysis and is still used widely today. As you rightfully state in your question, EEGs are often analyzed in terms of frequency bands. In terms of voluntary motor activity, one study reports activity in the 15 – 30 Hz range when subjects performed wrist extensions and flexions (Halliday et al. 1998). This frequency range corresponds to the alpha (8 - 15 Hz) and beta (16 - 31 Hz) frequency bands in the EEG. Beta activity in general is associated with an alert state, alpha activity generally with a more relaxed state. Both make sense because the subjects were actively engaged in a task (alert), but the task was simple and likely kind of boring (relaxed). The authors conclude that the frequency range over the motor cortex represents (Halliday et al. 1998):

[...] [R]hythmic oscillations in the sensorimotor cortex [...] associated with voluntary motor tasks involving maintained muscle activation, such as position holding.

In the time domain a relatively straightforward response to record motor activity in the brain is asking a subject to perform a certain action, for example finger flexions. These events generate certain synchronized neuronal responses in the brain that can be measured on the scalp with EEG. However, a voltage response to a single event is typically swamped in background noise. A way top enhance the signal-to-noise ration is to repeatedly record the EEG in response to the same event. By time-locking the event with the EEG and averaging the individual event-related EEGs, the random background noise will be reduced (stochastic noise) and the event-related potential (or ERP) can be extracted from the EEG (Woodman, 2010). An example of an ERP to repeated index finger flexions is shown in Fig. 1.

Fig. 1. ERP to voluntary index finger flexions. Motor activity was recorded from the motor area. Source: Ball et al. (1999)
References
- Ball et al. NeuroImage (1999); 10: 682–94
- Halliday et al., Neurosci Letters (1998); 241: 5–8
- Woodman, Atten Percept Psychophys (2010); 72(8): 10.3758

I think this is a part of the answer, not the full answer because the question is 'brain wave and motor movement co-relation', not 'how EEG works'.

@aayushsrivastav - have you read the answer at all? Both sections are on movement and motor cortex. And I don't know how my answer even touches upon the workings of EEG  O.o.

the only thing in your answer that seems to be answering this question is "Beta activity in general is associated with an alert state, alpha activity generally with a more relaxed state. Both make sense because the subjects were actively engaged in a task (alert), but the task was simple and likely kind of boring (relaxed)." Can you please tell how time domain and frequency domain tells anthing about brain wave and motor movement co-relation?

As said by MG_MD:

You would be thinking about moving, actually moving, and perceiving the movement. These affect different areas of the brain and as such, the electrical output would increase.

Also, it is very rare that the brain produces only one type of waves as it is continuously processing millions of information, though we know the basic functions of all of those types (from here).
As to how EEG works:

The billions of nerve cells in your brain produce very small electrical signals that form patterns called brain waves. During an EEG, small electrodes and wires are attached to your head. The electrodes detect your brain waves and the EEG machine amplifies the signals and records them in a wave pattern on graph paper or a computer screen.

Source

Source of image
If you look at the image, th EEG has captured many waves of different types at the same time, which proves the staement of MG_MD.
For the "overlapping frequencies..." part:

For example there is the “mu rhythm” (which is actually alpha activity in the relevant sensory and motor cortical areas that happens when the arms/hands are not doing anything)...

Source

Interesting points, @Christiaan (+1) - it's not too late to weigh in with your own answer!


text:
What is the "leaky valve" between the esophagus and stomach?
When someone talks about there being a "leaky valve" between the esophagus and the stomach, what is the exact biological structure they are talking about?
This would be a structure that, when malfunctioning, causes stomach acid to leak into the esophagus.

The structure is called the lower esophageal sphincter:

Basically, its function is to prevent the contents of the stomach, including stomach acid, from "backwashing" into the esophagus. The stomach is protected from acid by a protective layer of mucus, while the esophagus is not, so any number of medical issues which cause problems with this sphincter may lead to erosion in the esophagus, which is quite painful and can lead to serious long-term consequences if not addressed.


text:
How can heart disease cause dizziness after eating?
I have been reading several articles explaining dizziness after eating (see here and here), and both articles gloss over something that I found pretty remarkable.
Both articles claim that "heart disease" can cause one to experience dizziness after eating. For instance, as one article merely generalizes:

A healthy heart is needed to pump blood faster during digestion. Certain heart conditions can lead to its inability to send enough blood to the abdominal organs, which may lead to a drop in blood pressure, resulting in dizziness and sometimes, nausea.

To me, this is pretty vague and uninformative. Making a blanket statement like "certain heart conditions can...lead to a drop in blood pressure" is like saying "not eating or drinking water can cause death."
I'm interested in are the hows and the whats: How does/can heart disease cause dizziness after eating, what are the reasons why this happens, and what are some examples of heart disease ("certain conditions") that cause this (as I'm sure there are many similarly-related diseases)?

Dizziness after eating, which can lead to falls and passing out, is called postprandial hypotension, and as the heart is indeed responsible for responding to hypotension by increasing it's rate - which can be seen in any number of clinical scenarios from blood loss to standing up too suddenly - failure to do so, for any reason including heart disease, can result in continued hypotension, which is experienced by most of us as dizziness.
Postprandial hypotension (PhTN) is defined as a fall in systolic blood pressure (SBP) of ≥ 20 mmHg occurring within 2 hours of a meal. This hypotension (hTN) can result not only in dizziness, but  may also cause syncope, falls, weakness, angina pectoris, and stroke.
Because PhTN is particularly common in older hypertensive patients, and older patients tend to have higher incidences of heart disease, it was initially thought heart disease was the cause. However, that didn't explain why some young people without heart disease have PhTN.
In truth, the mechanism of PhTN is not fully understood.
Normally after a meal, blood supply to the gastrointestinal (GI) tract increases, starting with increased flow through the left gastric and celiac arteries, followed by the mesenteric artery, which is more prolonged. Observations indicate that the postprandial hyperemia progresses along the GI tract in association with the movement of ingested food. The magnitude (25–200%) and the duration (3–7 h) of the hyperemia appear to depend somewhat on the composition of the meal. The increase in GI blood flow means there's less blood to circulate in the rest of the body (relative hTN). Normally this is corrected for in various ways.
Baroreceptors (nerve cells within arteries near the heart and in the kidney) are sensitive to rises, falls, and the rates of change in BP, but are especially sensitive to sudden falls in BP, which results in decreased baroreceptor firing. Autonomic Nervous System responds by increasing sympathetic outflow and decreasing parasympathetic (vagal) outflow. Sympathetic outflow leads to vasoconstriction (increased systemic vascular resistance, or SVR), increased HR (tachycardia) and increased force of contraction on the heart (positive inotropy). This leads to a partial restoration of arterial pressure. In people with PhTN, any abnormality at any point in the system will result in an insufficient rise in SBP to overcome the fall.
Therefore possible contributors to PhTN include inadequate sympathetic nervous system compensation for meal-induced GI blood pooling; impairments in baroreflex function; inadequate postprandial increases in cardiac output; impaired peripheral vasoconstriction, as well as abnormal responses to GI hormones released during digestion.

Dysautonomic patients with postprandial hypotension fail to maintain systemic vascular resistance after a meal. This impairment in vascular response to meal ingestion may underlie the development of PhTN. Power spectral analysis suggests an impairment in the postprandial autonomic modulation of HR in healthy elderly and dysautonomic subjects, possibly predisposing to hTN when vascular compensation is inadequate.

Heart conditions that might result in an inadequate response to PhTN include low heart rate (bradycardia), heart valve problems (decreases cardiac output), heart failure (decreased ejection fraction equals cardiac output), patients with atrial fibrillation (decreases cardiac output because of inadequate filling of ventricles), heart attack (decreased ejection fraction), heart muscle disease (cardiomyopathy), severe left ventricular hypertrophy, people with HTN on medications which cause a lowered heart rate, etc.
Therefore, Postprandial Hypotension is an important hemodynamic abnormality in patients with cardiac diseases as well as autonomic nervous system abnormalities such as can be seen in Parkinson's Disease, diabetes mellitus, and others.
Postprandial Hypotension: Epidemiology, Pathophysiology, and Clinical Management
Association of postprandial hypotension with incidence of falls, syncope, coronary events, stroke, and total mortality at 29-month follow-up in 499 older nursing home residents.
Postprandial hypotension. Pathophysiological mechanisms and clinical implications in different disorders.
Postprandial hypotension in response to duodenal glucose delivery in healthy older subjects
Postprandial Hyperemia
Arterial Baroreceptors

Vasoconstriction from sympathetic outflow is not generalized. It causes selective vasoconstriction, where skeletal muscles are excluded. I believe the viscera are also spared as sympathetic activation of viscera would inhibit digestion itself? Can you please clarify @anongoodnurse?

What I am asking is if sympathetic system will cause only peripheral vasoconstriction and not general vasoconstriction? Very nice answer BTW...

@CRags - the effect of sympathetic output is complex, involving not only norepinephrine acting on alpha receptors, but epinephrine, angiotensin II and vasopressin, among other vasoconstrictors. And, no, it does not have the same effect everywhere. The question was not about the sympathetic nervous system, but about PhTN. It's long enough! ;)


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same osmotic pressure of different solution
For example, There is a sugar solution with concentration $A_{1}$, how to determine the concentration of a NaCl solution which produce same osmotic pressure as the previous sugar solution toward animal's cell?
Is this ratio various between different kind of cells?
NOTE: the unit of concentration is not important between mass/vol or mol/vol. Because when one is known, the other is easy to compute.

Is A1 known? If yes, have you taken a look at this video?

@SPr, Yes, it is known.

This is a simple chemistry question. The answer is 0.5A₁ but I won't explain why. Read about colligative properties. I am VTCing this as a homework/General Chemistry question.


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Why do we need to amplify DNA sequences?
I am learning about biotechnology. I have no education in biology or chemistry and am simply interested in the subject of biotechnology.
I am wondering why we need to have multiple copies of a piece of DNA in order to do something with it (ie. PCR)? Why is one piece of DNA not enough? Is machinery not precise enough to work with one piece of a DNA sequence in order to do something with it?
I can understand that an experiment may fail. In that case, make 8-16 copies for assurance. But why an extraordinary (billions) amount of copies? What practical use does it have? What applications require there to be an extraordinary amount of DNA to be succesful? Do the billions of copies just increase the speed of the experiment by being able to quickly "fish out" a piece of DNA? I just can't quite grasp the idea.

Although your question about DNA has been answered, you need to be aware of the general limits of detection of molecules in the lab. If you thought you could detect one molecule of DNA, think about detecting one molecule of glucose. How much would that weigh? You can find the answer by reflecting on Avagadro's number — the number of atoms in a mole of a compound. This has a value of about 6 x 10^23, so there would be that many molecules in 180 g glucose! Catch one!

This is a question I also remember wondering about when I was younger in school. Now as a professional it's way too obvious to even explain. But i think it's an important and common question, which warrants an example or two from common daily lab practice.
Preface
You have to understand that DNA is a molecule. It's really tiny. It's not trivial to work precisely with it, nor detect it or discriminate two different pieces of DNA from each other, let along sequencing them. We make a lot of DNA through amplification so that we can prepare a sufficient amount to make reactions with.
Visualization
We usually make DNA visible by using chemical dyes that emit light (fluorophores) or incorporated radioactive pieces to make the DNA visible.
Here's a common case in the lab: we need to get enough DNA to use in subsequent reactions. When we work with DNA it is very rare that we obtain exactly what we want 100% of the time, or perfect yield. For example, we want to cut a piece of DNA once. But we have scissors (i.e. restriction enzymes) that will chop up the DNA multiple times, especially when we leave the reaction going too long. What we do is take 100 units of DNA, subject them to the reaction, and then view the results using electrophoresis using an agarose gel, for instance. We can then see 40 units of uncut DNA, 30 units of single cut DNA, and some 30 units of DNA cut multiple times (2+ times, so they are small fragments). We need enough single cut DNA to proceed with the next reaction, with full knowledge that there are no contaminating chunks of DNA. Typically there are many reactions in a row that we do to achieve anything in the lab. Cloning, in vitro amplification, sequencing, gene editing, preparing genes for transgenesis, creating RNAi probes, what have you.
More is better
Another case: if you want to know the sequence of DNA, you must sequence it. However, sequencing is imperfect and errors occur. To be sure, we re-sequence the same DNA many times to get a confident picture of what the sequence is like, beyond reasonable doubt. Sequencing DNA ten times is really more reliable than sequencing it once. This could be because of how the molecules behave in solution, or because of degradation, or tens of other things. You must understand this is also not specific to sequencing; a lot of reactions follow the same logic.
Amplification as a specification tool
By using primers in PCR, we can make sure we are obtaining what we want. In principle, this means that we can make a gajillion copies of something we are interested in (e.g. a gene), even from a single strand of DNA which may contain things we are uninterested in (e.g. the rest of the genome).
Some thoughts
This answer is certainly not extensive, but I hope it's a primer for you to understand that DNA work is just really smart nanotechnology, and we are not yet at the level of performing nanotechnology on single molecules, with full confidence, precision or efficacy. On the daily, we need enough to see it with our eyes so we amplify and react it with intercalating dyes to make them visible to the naked eye!

Thank you for the succinct answer. I was failing to understand the precision of current nanotechnology, and your practical examples (which sound really fun) really brought the point home.


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Which insect is this? They crawl like caterpillars and get metamorphed into orange moths
 They are like larvae which gets metamorphed into moth (orange colour with black spots) .They are multiplying rapidly and have spread all over our building.

Resembles wooly bear caterpillars while the moth you shown is very identical to black-banded orange moth (Epelis truncataria).


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Color of DNA, available absorption energy levels of DNA molecule, mutations
I have done a couple of DNA separations and observe that the clumped strands of DNA are white.
Is that an artifact of the chemicals used in standard separations? Or is it indeed the case that the DNA molecule in standard conditions does not absorb many or any photons in the visual range?
If that is right, can we use this as evidence for why visible spectrum light doesn't cause mutations, unlike say higher energy photons in the UV range?
Looking forward to your thoughts.

The reason why visible light doesn't cause mutations are simply because it has not enough energy. For this reason it doesn't penetrate far enough into the skin and has not enough energy to do the damage. DNA itself is not white, this is only because it is clumped together and reflects the light.

Thanks @Chris. Even in theory, can a visible spectrum photon cause a mutation?

@SimonS Some chemicals can be photo-excited to form reactive intermediates and these in-turn can damage the DNA. Visible light per se cannot do any damage.


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What initiates primase to add an RNA primer to a DNA strand and what makes it stop?
What initiates primase to add an RNA primer to a DNA strand and what makes it stop adding RNA nucleotides? Is there tags added to the DNA back-bone?

I'm studying "Biology" by Cambell et. al. and nothing is mentioned in the book.

Prokaryotic primases are activated by DNA helicase [1, 2] while the eukaryotic ones are triggered when they form a complex with DNA polymerase alpha and its accessory B subunit [2].
I couldn't find too much information about what exactly triggers activation, but according to De Falco M et al. (2004):

[...] synthetic function (of the prokaryotic primase) is specifically activated by thymine-containing synthetic bubble structures that mimic early replication intermediates. [3]

It stops when it finishes reading a DNA template:

The Sso DNA primase utilizes poly-pyrimidine single-stranded DNA templates with low efficiency for de novo synthesis of RNA primers [3].

References:

Wikipedia contributors, "Primase," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Primase&oldid=593928284 (accessed December 1, 2014).
David N. Frick, and Charles C. Richardson. DNA PRIMASES. Annual Review of Biochemistry. Vol. 70: 39-80 (Volume publication date July 2001). DOI: 10.1146/annurev.biochem.70.1.39
De Falco M, Fusco A, De Felice M, Rossi M, Pisani FM. The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity. Nucleic Acids Res. 2004 Sep 30;32(17):5223-30. Print 2004.


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Is the nuclear envelope present in G1 of interphase?
Is the nuclear envelope present in G1 of interphase of eukaryotic cell? If so how does a method like Calcium mediated transfection get DNA past the nuclear envelope?

That is a very good question. I have done calcium phosphate transfections on primary hepatocytes, so I know it works on non-dividing cells, but I don't think there's a clear answer yet. The calcium ions released from the particles may help trigger nuclear envelope disintigration and allow plasmid DNA to enter. I'll try and find and find links to a couple papers I've read about it.

Alright, Paper 1 and 2 by Dana Olton are about Calcium phosphate nanoparticle transfection and intracellular trafficking. Leaf Huang has several papers about lipid coated Calcium phosphate for DNA delivery in vivo, 1, 2, and 3. And here is a paper about parvoviruses and how they enter the nucleus, which involves Ca.

To answer the question about nuclear envelope in G1 phase, yes it exists. The nuclear envelope is reformed at the end of Telophase after the 2 copies of the DNA are pulled apart, but before the two daughter cells are separated by cytokinesis. We can see the new nuclear envelope in these images:

Image from here

Nuclei visible near end of cytokinesis, centrosome still visible. Image from here.
As for how DNA gets into the nucleus without cellular division I don't have a good answer and I'm not sure anyone does right now. The nuclear envelope is a major barrier for non-viral gene delivery.


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Do all Gram negative bacteria cause septic shock?
Do all Gram negative bacteria cause septic shock? If they don't could they if you attacked them with an antibiotic that could lyse the cell? For example any antibiotic that attacks the cell wall, although I suppose that could be difficult with the gram negative wall, not to many gram negatives are susceptible to a wall attack.

all Gram negative bacteria can potentially cause septic shock, but septic shock is not limited to Gram negative cell wall lipopolysaccharides. Any infectious agent can cause septic shock, including gram positive and gram negative bacteria, fungi and even viruses (this is quite evident in the recent Ebola outbreak).[1]
The causative agents for sepsis/septic shock have evolved. Originally strongly considered to be related to Gram-negative bacteria, that is no longer the case. About 25 years ago, sepsis was considered to be a response to endotoxin thought to be relatively specific for Gram-negative bacteria. That Gram-negative bacteria were the most common causes of sepsis[2] resulted in trials that focused on  specific therapies for G negative endotoxins.
It is now recognized that sepsis may occur from bacterial, fungal and viral organisms. More recent epidemiology studies reveal that Gram-positive bacteria have become the most common cause of sepsis in the past 25 years. According to the most recent estimates in sepsis, there are approximately 200,000 cases of Gram-positive sepsis each year, compared with approximately 150,000 cases of Gram-negative sepsis.[3]
Fungal causes of sepsis have also grown at a rapid pace. Why this occurs may be two-fold: a general increase in nosocomial (hospital acquired) cases of sepsis, and more effective treatment of bacterial infections, thus promoting fungal infections to a more leading role. The increase of fungal nosocomial infections has also shifted away from the common Candida albicans organism to the more recalcitrant torulopsis, glabrata and krusei subspecies.[4]
So while the Gram negative Lipopolysaccharide or “endotoxin” is unique to Gram negative bacteria, cell components of Gram positive bacteria have been identified that appear to be biologically equivalent to endotoxin in stimulating the inflammatory response associated with sepsis and septic shock. These include a peptidoglycan layer outside the cell membrane of Gram positive bacteria as well as non-peptidoglycan polymers (such as the teichoic acids). They have been shown to stimulate the release of cytokines, specifically tumor necrosis factor and interleukin-1.[5]
[1] How Ebola Kills You: It's Not The Virus
[2] Septic shock in humans. Advances in the understanding of pathogenesis, cardiovascular dysfunction, and therapy
[3] The epidemiology of sepsis in the United States from 1979 through 2000.
[4] Nosocomial bloodstream infections. Secular trends in rates, mortality, and contribution to total hospital deaths.
[5] Sepsis and Septic Shock
Sepsis, severe sepsis and septic shock: changes in incidence, pathogens and outcomes

Regarding your connection to Ebola: As far as I remember the clinic in Hamburg decribed that the main problem with sepsis came from bacteria which leaked from the gut into the blood stream, causing problems. But this is most likely due to effects that the virus caused, so this is a bit of a hen and egg problem.

Without directly addressing your comment's content, I can say that a common misconception about septic shock is that it is a result of pathogens in the bloodstream. It's not. Septic shock in Ebola is due to a cytokine storm. Ebola virus appears to trigger a release of pro-inflammatory cytokines with subsequent vascular leak and impairment of clotting ultimately resulting in multi-organ failure and shock. The gut stuff is the result of GI end-organ failure.

Ok, this was an unclear formulation. Viable bacteria in the blood stream can be considered as one of the ultimate dangers. But still substances like LPS (which can cause septic shock) will find an entry route here.

@Chris - That's a good point. If you're interested in the medical side of this, here is some very interesting reading: Approaches to Clinical Management for Patients with Ebola Treated in U.S. Hospitals. It goes through everything we know about Ebola in the US-treated patients (except from Dallas). I didn't see any mention of positive blood cultures even in the patient requiring ventilatory support and dialysis (so very close to death).

The major factor defining Gram-negative (vs. Gram-positive) bacteria is the structure of the cell wall, outer membranes, and the moieties that extend out into the environment:

http://en.wikipedia.org/w/index.php?title=File:Gram-Cell-wall.svg
Gram+ bacteria have an inner plasma membrane and an outer, thick layer of peptidoglycans. This is what takes up Gram's stain. Gram-, on the other hand, have a plasma membrane, a thinner peptidoglycan wall, then an outer membrane consisting of lipopolysaccharides (also known as LPS or endotoxin) anchored into the membrane's phospholipids, along with various proteins within the membrane:

https://commons.wikimedia.org/wiki/File:Gram_negative_cell_wall.svg
Sepsis, a systemic inflammatory response syndrom (SIRS) can be caused by both Gram-positive and -negative bacteria, as well as viruses and fungi. In the case of Gram-negatives, the immune system is activated in response to the presence of LPS from extracellular lysed and intracellular antigen-processed bacteria, through the Toll-like receptor TLR4/CD14/MD-2 pathway. One can have a local infection, and still not develop sepsis. However, if the infection becomes large enough or the bacteria enter the blood stream in significant numbers, sepsis can occur. Not all patients with sepsis develop septic shock, which is characterized not only by a microorganism-caused SIRS and organ dysfunction/hypoperfusion, but also by chronic hypotension (low blood pressure) even after administration of IV fluids.
Structurally, LPS contains the highly-conserved Lipid A, which anchors the molecule into the outer membrane, a core oligosaccharide, and the outer O-antigen:

https://commons.wikimedia.org/wiki/File:LPS.svg
Lipid A is actually the most toxic segment of LPS (the portion recognized by TLR4 and MD-2), and while it is generally highly-conserved among different bacterial strains and species, studies have shown that different human-pathogenic species of bacteria have altered Lipid A from the "canonical" structure derived from E. coli. This can cause variations in the downstream signaling from TLR4 to NF-κB, potentially leading to immune system evasion.
So, to directly address your question:

Do all Gram negative bacteria cause septic shock?

They can, if present in sufficient quantities, but not necessarily through the same mechanisms. The immune system recognizes many different pathogen-associated molecular patterns (PAMPs) through a variety of TLRs and other pattern recognition receptors (PRRs) like C-type lectin receptors, Nod1 and Nod-like receptors, etc. Some work on intact bacteria, others recognize intracellular epitopes. Therefore, sepsis and, in severe cases, septic shock, can be caused by Gram-negative bacteria through LPS-independent pathways. While it's possible that lysing these bacteria chemically by antibiotics could potentially enhance the immune response, cells like macrophages are very good at recognizing foreign invaders and lysing them on their own, giving plenty of substrates to the various receptors. Also, keep in mind that dead cells may auto-lyse, so the antibiotics need not necessarily attack the cell wall itself, just kill the bacteria.


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How does a protein molecule enter a cell through the cell membrane?
I can't find a good explanation as to how a whole protein molecule enters a cell membrane. Is it through endocytotic vesicles, with the help of ATP? How does this occur?
Thanks for the help!

Are you asking about translocation, or about folded proteins passing through membranes?

Learning about both would be great!

Wikipedia has some information on translocation, and follow that up with their article on the translocon (the machinery that threads nascent peptides through the membrane). The Nuclear pore complex is a good example of a machinery that allows larger folded proteins through the membrane.

For now, I am going to suggest that your question should be closed because I think it needs a bit more focus to fit the shorter answer Q&A style of this site, but if you have any specific questions along the way, please post a new question or edit this question. I hope that helps :)


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Holder for 75 mm x 25 mm glass slides that can handle vibration
Hello Biology Stack Exchange,
I have an application where I have cells on a glass slide (dimensions: standard 75 mm length x 25 mm width  x 1 mm thick).  I want to vibrate/shake the cells rapidly while viewing through a microscope.
I have a piece of equipment that can produce vibrations, I just need to connect it to the glass slide somehow.
Are there any holders for glass slides out there that:

Firmly hold the glass slide
Enable me to somehow connect vibration equipment with the slide?  (Ex: screw into the holder, glue onto the holder, clamp onto the holder)
And still view the slides contents under a microscope?

Thank you in advance!

Welcome to Biology.SE!  I'm skeptical that you will be able to image actively vibrating cells, but that clearly depends on what sort of frequencies you are interested in (and your cameras frame rate/shutter speed).  Can you add more of that sort of detail to your question and maybe why you want to do this?  Also, have you considered using ultrasound to produce the vibrations?

@tyersome thank you for pointing out ultrasound!  Not bad thinking.  Per imaging active cells, I have previously adhered vibration motors directly onto glass slides, and I was still able to make out what was happening on the slide, even though it was very chaotic.