text:
Cellular Respiration in Boiling Conditions
Here's the question:

Imagine that you are given 25 germinating pea seeds that have been placed in boiling water for 5 minutes. You place these seeds in a respirometer and collect data. Predict the rate of oxygen consumption (i.e. cellular respiration) for these seeds and explain your reasons.

I'm thinking that there will be no cellular respiration and thus no oxygen consumption because the boiling probably messes it up, but I'm not sure why that is...

What does boiling do to proteins? Why would that impact cellular respiration?

Does it denature the proteins in the Electron Transport Chain such as ATP synthase?

It would denature a lot of proteins, not only respiratory proteins. Denaturation means unfolding followed by incorrect refolding so the protein can't do it's job. Until recently, this was seen as permanent damage, however research published in ChemBioChem 2015 shows that the denaturation can in theory be reversed.

Extending on @ANONGOODNURSE, @SAPPHIRA and @JAMES.
Something you should know about proteins, they have primary, secondary, tertiary and quaternary structures all due to specific folding of the proteins. These foldings are mainly connected via hydrogen bonds to each other along with other bonds (Alberts et al., 2002). On the action of heat, the molecules composing the bonds are vibrated due to higher kinetic energy resulting in the breaking of the bonds which causes unfolding of proteins (Wikipedia denaturation of proteins). This phenomenon is called Denaturation of Proteins which causes the loss of protein function due to loss of shape.
Read this QandA in Reference.com for more information about denaturation of proteins.
Read this for more information about proteins: Molecular Biology of the Cell. 4th edition.
Link this idea to cellular respiration and how Electron Transport Chain and the Krebs Cycle (Citric acid cycle) involve proteins for the completion of the respective processes.


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Ion channels affected by gravity
In the literature I have found that action potentials behave differently when gravity is changed (cannot access fully).
Action potential properties are gravity dependent.
http://link.springer.com/article/10.1007/BF02870977
Are there any ion channels in the neurons that are more or less likely to be sensitive to changes in gravity?

Please link to the article abstract about gravity.

http://link.springer.com/article/10.1007/BF02870977Action potential properties are gravity dependent

I'd say this is a fairly niche area of research so it's unlikely this has been studied beyond the citations you will find in that article.

source: Stack Exchange

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sort: votes


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Genotype frequencies and fitness values in haploid population with clonal growth
I found a small problem, and I am not sure at all about my answers. If someone could correct it, that would be awesome.

Consider a heterogeneous population with the following genotype frequencies and fitness values (attention: haploid individuals with clonal growth!) :
ab : $ P_{ab} = 0.8, \quad \lambda_{ab} = 1 $
Ab : $ P_{Ab} = 0.1, \quad \lambda_{Ab} = 1.2 $
aB : $ P_{aB} = 0.1, \quad \lambda_{aB} = 1.1 $

Determine the average fitness of the population
After one generation, what are the new genotype frequencies and the average fitness of the population ?
What are their values in the long-time limit ?
Explain clonal interference in this context.

My answers :

Relative fitnesses values - we take the highest as reference (here: Ab):
$$ \omega_{ab} = \dfrac{1}{1.2} = 0.83   $$
$$ \omega_{Ab} = \dfrac{1.2}{1.2} = 1   $$
$$ \omega_{aB} = \dfrac{1.1}{1.2} = 0.916   $$

Average fitness of the population :
$$ \overline{\omega} = p_{ab}.\omega_{ab} + p_{Ab}.\omega_{Ab} + p_{aB}.\omega_{aB} = 0.8556 $$

$$ p_{ab}(t+1) = \dfrac{p_{ab}(t).\omega_{ab}}{\overline{\omega}} = \dfrac{0.8\times 0.83}{0.8556} = 0.776 $$

same for the others frequencies :
$$ p_{Ab}(t+1) = \dfrac{0.1}{0.8556} = 0.117 $$
$$ p_{aB}(t+1) = \dfrac{0.1 \times 0.916}{0.8556} = 0.107 $$

I know that the fraction of the fitter genotype will grow exponentially compared to the genotype of lower fitness. But how do you demonstrate that ?
I learnt that due to the haploid structure of the population, the two new alleles A and B are in competition under natural selection : this will lead to the loss of one of them in the long term (even if they are both advantageous for the organisme). Then how do I explain that we those data ? Does this mean allele B will disappear ?

Any help would be welcomed :)

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How does the hypothalamus get the information out of the blood?
The hypothalamus is a very important nervecentre which checks continuously how many hormones neurotransmittors and other molecules and information (like temperature) are there present, so it can keep a kind of balance in our body. But how does the hypothalamus do this? Does he has so much different receptors on his membrane for each type of molecule one or does it do that in a different way?

First of all, there is not such a thing as "the" hypothalamic membrane. The hypothalamus consists of multiple nuclei, and each nucleus contains numerous cells (neurons and glia cells).
The mechanisms by which the hypothalamus senses hormone concentrations in the peripheral blood are rather complex. In recent years, considerable research has been done to elucidate the central mechanisms underlying thyroid homeostasis [6], which involve the regulation of TRH release from the hypothalamic paraventricular nucleus [1, 2]. Therefore, my following explanations are focussed on the control of TRH secretion, but similar considerations apply to other hormonal systems [7-9].
First, hormones have to be conveyed by special transport proteins across the blood brain barrier (BBB). In case of thyroid hormones, this is accomplished by tanycytes in the circumventricular organs [3]. They control the transition of hormones from the blood to the cerebrospinal fluid (CSF), and partly directly to glia cells via the transport protein OATP1C1. In glia cells thyroxine (T4) is deiodinated to form the more active hormone triiodothyronine (T3). T3 is then transferred to neuronal target cells via the transporter MCT8 [4, 5], where it exerts its homeostatic effects by inhibiting TRH release. Hypothalamic TRH secreting cells have, however, multiple afferent signals. In addition to thyroid hormones they include clucocorticoids, leptin, alpha-MSH, norepinephrine, cocaine and amphetamine-related transcript (CART), endocannabinoids, agouti-related peptide, neuropeptide Y (NPY), GABA, galanin and probably multiple additional signalling substances. This enables the TRH neuron to act as an integrator of energy homeostasis [1, 2, 6].
Of course, the TRH-secreting cells in the respective hypothalamic nuclei have receptors for all afferent hormones and neurotransmitters. Some of them (e.g. for catecholamines) are located on the cell membrane, others (e.g. for thyroid hormones or steroids) in the nucleus.
As mentioned, similar considerations apply to other hormonal systems [7-9]. Recent research suggested e.g. the existence of a receptor-mediated transport system, which conveys insulin trough the blood-brain barrier [9].
1: Joseph-Bravo P. Hypophysiotropic thyrotropin-releasing hormone neurons as transducers of energy homeostasis. Endocrinology. 2004 Nov;145(11):4813-5. PMID: 15489313. http://www.ncbi.nlm.nih.gov/pubmed/15489313
2: Joseph-Bravo P, Jaimes-Hoy L, Charli JL. Regulation of TRH neurons and energy homeostasis-related signals under stress. J Endocrinol. 2015 Dec;227(3):X1. doi: 10.1530/JOE-14-0593e. PMID 26527565. http://www.ncbi.nlm.nih.gov/pubmed/26527565
3: Rodríguez EM, Blázquez JL, Pastor FE, Peláez B, Peña P, Peruzzo B, Amat P. Hypothalamic tanycytes: a key component of brain-endocrine interaction. Int Rev Cytol. 2005;247:89-164. Review. PMID 16344112.
https://www.ncbi.nlm.nih.gov/pubmed/16344112
4: Kersseboom S, Visser TJ. Tissue-specific effects of mutations in the thyroid hormone transporter MCT8. Arq Bras Endocrinol Metabol. 2011 Feb;55(1):1-5. PMID 21468514.
http://www.ncbi.nlm.nih.gov/pubmed/21468514
5: Bernal J, Guadaño-Ferraz A, Morte B. Thyroid hormone transporters—functions and clinical implications. Nat Rev Endocrinol. 2015 Jul;11(7):406-17. doi: 10.1038/nrendo.2015.66. Nat Rev Endocrinol. 2015 Sep;11(9):506. PMID 25942657.
http://www.ncbi.nlm.nih.gov/pubmed/25942657
6: Hoermann R, Midgley JE, Larisch R, Dietrich JW. Homeostatic Control of the Thyroid-Pituitary Axis: Perspectives for Diagnosis and Treatment. Front Endocrinol (Lausanne). 2015 Nov 20;6:177. doi: 10.3389/fendo.2015.00177.  PMID 26635726.
http://www.ncbi.nlm.nih.gov/pubmed/26635726
7: Thon M, Hosoi T, Ozawa K. Possible Integrative Actions of Leptin and Insulin Signaling in the Hypothalamus Targeting Energy Homeostasis. Front Endocrinol (Lausanne). 2016 Oct 20;7:138. PMID 27812350.
http://www.ncbi.nlm.nih.gov/pubmed/27812350
8: Herman JP, Tasker JG. Paraventricular Hypothalamic Mechanisms of Chronic Stress Adaptation. Front Endocrinol (Lausanne). 2016 Oct 31;7:137. PMID 27843437.
http://www.ncbi.nlm.nih.gov/pubmed/27843437
9: Blázquez E, Velázquez E, Hurtado-Carneiro V, Ruiz-Albusac JM. Insulin in the
brain: its pathophysiological implications for States related with central
insulin resistance, type 2 diabetes and Alzheimer's disease. Front Endocrinol
(Lausanne). 2014 Oct 9;5:161. doi: 10.3389/fendo.2014.00161. PMID
25346723,
http://www.ncbi.nlm.nih.gov/pubmed/25346723/


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Does the testicle's temperature increases with the body temperature during a high fever?
The testes is the male sexual organ. It is positioned outside the abdomen along with the scrotum. I would like to know if its temperature is independent from the body temperature due to its location.

Welcome to health SE:-) Sorry but I'm not actually getting your question correctly. Pls can you make it a bit clearer.

The question is quite vague. Please specify for clear answer.
However, although testicles are out of the body, but a part for sure. Due to pyrogen attack when the body temperature increases, literally the temperature of the testicles should be increased but clear research has not been found yet.
Please specify your question.


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evolution or chance?
I was reading my chemistry textbook, when in the chapter on 'solutions', i came across a problem, which calculated the amount of oxygen that can be dissolved in 1cc of water at STP. Then they commented, "this amount is just perfect for aquatic and marine life. Had this been lesser, life in the oceans might not exist at all.' This raised the following question in my mind:
1)aquatic species of flora and fauna evolved over time to adapt to this concentration of dissolved oxygen, and their biological processes were also fine tuned based on the environmental conditions.
2)It really was fate that the dissolved quantity was just enough to support marine life, as the textbook said.
Which of the two is the actual scenario? My personal pick happened to be 1), but I have no proof of it. Can someone explain?

That is not really chance but referred to as the contingency of evolution. Any other oxygen concentration would - observed now, after a long time of evolution - seem to be just as perfectly matching.

Oh my. Do the authors provide any support for this claim? More importantly: what is their affiliation with creationist organizations? Well, back to science.
First, a note about your question. It might seem that you have sketched out two scenarios, but for the biologist, they are equivalent. We know two things: life exists, and life adapts. Yes, the specific circumstances on Earth have made life possible, and subsequently, life has adapted and fine-tuned itself to those circumstances.
Now to answer your question.
I really like the visual representation of the Life Timeline on Wikipedia. 4.1 billion years ago, earliest life appeared on Earth. At that time, all oxygen on the Earth's surface was bound in chemicals like CO2, iron oxide, etc. We are unsure whether the earliest life-forms originiated in the ocean, but we know they ended up there one time or another. The absence of athmosphetic and water-dissolved oxygen of course meant those first life-forms were anaerobes (lived without oxygen). In fact, oxygen was extremely poisonous for our teragrandparents. (We are the ~ 10^12th generation of life.)
So, aquatic life has existed without oxygen, and still exists, whether the solvabily of oxygen is 'perfect' or not.
Another fun fact debunking your chemistry authors statement: water oxygen saturation doesn't reach 100% at all times (linked article provides lots of great information about dissolved oxygen and life, by the way). Lots of life-forms requiring oxygen hence live in a world where the solvability of oxygen is even more than perfect. Furthermore, life exists (but doesn't thrive) in low-oxygen conditions (e.g. pubmed:9510533).

The claim is strange since many bacteria don't use oxygen, and since oxygen is indeed a by-product of early life (thus not using it. Oppositely, oxygen is indeed a poison for cells that they had hard time to protect against, then get able to have some use).
Moreover the amount of dissolved oxygen varies with places, depth, temperature, and along geological times.
So, answer 1.

It was quite clearly answering 1. I made it explicit :-) .


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dNTP concentration for reverse transcription from RNA to cDNA
Does it affect the results if I use the half of dNTP amount in a reaction that it says in my protocol?
I usually use 4 microlitres per reaction and this time I did a mistake and I used 2.
The final cDNA will be used for qPCR relative cuantification,so I am not sure if that will affect my results.

It depends on several parameters like what is the concentration of dNTP you use, the length of the DNA amplified, the polymerase and other PCR parameters. I think the best way to know would be to check the quality of your result via agarose gel electrophoresis.

You will probably be fine. Lower dNTP levels might reduce the amount of product you obtained since it is usually the primers or the dNTPs that run out near the end of the reaction. The only other effect I am aware of is that the reaction might be slightly less specific as dNTPs sequester magnesium which is a big factor in determining the stringency of the reaction.
You say how many microliters you used but it would be more useful if you mentioned the concentrations of the dNTPs and the desired final concentration.

Please cite content that supports your answer, opinion based answers are bad.


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How many proteins do all human ribosomes together produce per hour?
Very roughly how many proteins (chains) are synthesized in the human body per hour under normal conditions?
(And how many ribosomes does the human body have?)

Welcome to SE Biology. This question has multiple issues that will see it being downvoted or closed. There are two questions rather than one. Neither question is well defined. The first question is impossible to answer. This is due to the enormous error in such an estimation. There is variation at every level of a human body; starting between tissues down to translational initiation events on individual RNA transcripts. Also, every protein/polypeptide chain has a different length so every protein will take a different length of time to produce.

@Michael_A  It's not such a crazy question I think ... It should be possible to come up with at least a ballpark figure (say, correct within an order of magnitude) from bioenergetics.

@Roland, Changing the question to ask about the number of amino acids per hour would make a ballpark estimate feasible. Once that change is made I almost agree with you regarding the first question. The other issue is that there are two questions. Currently, there are two answers but each answer addresses a different question.

@Michael_A  But once we know the number of amino acids, this can be converted to number of proteins, since we know the average length of a protein in human cells. (Although we must assume that protein turnover rate is independent of protein size.) I agree it would be good to split the question in two.

@Roland, figure 3, shows the distribution of protein lengths in the genome is not normal. This is why thay specifically discuss median rather than mean length. Figure 3 highlights the fatal flaw in the assumption of an average length of the proteins in human cells, the need to take into account the expression of proteins. At any given time a cell is not producing 1 copy of every protein in its genome, it is producing the proteins that it needs. In the figure this lowers the median length to 248 aa.

@Michael_A  No, the shape of the protein length distribution is irrelevant. The key assumption is that the protein synthesis rate is proportional to its relative abundance (or equivalently, that turnover is constant). See my revised answer for a clarification.

I'm voting to reopen this question, as I think it's fully possible to answer it with some reasonable confidence.  We often overlook these quantitative questions in biology, but they are interesting and not as hard to answer as some may think --- it is not necessary to know a lot of details. I don't know the answer to the second question on number of ribosomes, but it should  be possible to figure out a rough number for this as well, by estimating ribosomes as a fraction of total protein. This has been done for yeast, see http://book.bionumbers.org/how-many-ribosomes-are-in-a-cell/

It's a so-called Fermi question. My colleagues and I found three or four different ways to answer it, all yielding similar results. I could have posted the answers if the question wasn't closed. The moderators should be more open-minded towards scientific approaches that they are unfamiliar with.

Regarding protein synthesis rate, here's an attempt at an estimate from bioenergetics:

ATP turnover in the human body is consider to be about 100 mol / day.
Protein synthesis is estimated to require about 1/4 of ATP consumption in a mammalian cell, and one amino acid elongation requires about 5 ATP, so about 5 mol amino acids are elongated per day, which translates to $1.2 \cdot 10^{23}$ amino acids per hour.
An average human protein is about 400 amino acids, which gives about $3 \cdot 10^{20}$ proteins per hour.${}^1$

I think this should be correct within an order of magnitude at least. (Unless I screwed up at some step in the calculation, it's getting late over here :) The most uncertain factor is probably the fractional ATP demand for protein synthesis.

${}^1$ The is correct with the following assumptions. Consider that the proteome has some (any) length distribution $p(n)$ where $n = 1,2,3 \dots$ is the protein length in amino acids, and $\sum_n p(n) = 1$. Let $r(n)$ be the total rate of synthesis of all proteins of length $n$. If we assume that this rate is proportional to protein abundance, $r(n) = t\ p(n)$, where $t = \sum_n r(n)$ is the total protein synthesis rate, then the total rate of amino acids per unit time is
$r_{AA} = \sum_n n\ r(n) = t \sum_n n\ p(n) = t\ \mu$
where $\mu$ is the average protein length. Hence the sought total protein synthesis rate is $t = r_{AA} / \mu$.

For your first question I think @Michael_A has explained why this question can't be answered.
And for the second one, I quote from bscb.org :

Ribosomes are found ‘free’ in the cytoplasm or bound to the endoplasmic reticulum (ER) to form rough ER. In a mammalian cell there can be as many as 10 million ribosomes (A single cell of E. Coli contains about 20,000 ribosomes and this accounts for about 25% of the total cell mass). Several ribosomes can be attached to the same mRNA strand, this structure is called a polysome. Ribosomes have only a temporary existence. When they have synthesised a polypeptide the two sub-units separate and are either re-used or broken up.

I don't like the last sentence in the quote. Very misleading. Almost everything in the cell turns over, but ribosomes have a long half-life compared to the time needed to translate a mRNA.


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How do you identify this particular snake shedding?
Aloha,
Snakes are illegal in the State of Hawaii, with the exception of the Hawaiian Blind Snake (Brahminy Blind Snake (Ramphotyhlops braminus)). I've read through a plethora of articles to no avail. It also doesn't help that snakes are virtually non-existent in the Hawaiian Islands.
I would like to identify this particular shedding, however, it has proven to be just as difficult as I predicted. Could anyone identify the species of this shedding?
Mahalo


text:
Why does the term "epicondyle" often refer to either of the two at the elbow end of the humerus?
Why does the term "epicondyle" often refer to either of the two at the elbow end of the humerus?
Example:

I understand that epicondyle means near a condyle, but there are several condyles in the human body:

On the femur, in the knee joint:

Medial condyle
Lateral condyle

On the tibia, in the knee joint:

Medial condyle
Lateral condyle

On the humerus, in the elbow joint:

Condyle of humerus (Condylus humeri)

On the mandible, in the temporomandibular joint:

Mandibular condyle

On the occipital bone, in the atlanto-occipital joint:

Occipital condyles

If something is unclear in the question, please explain, I'd be glad to improve it.

The humerus is the only of those that has a "protuberance"?

@kmm That would indeed explain. But is it true that the humerus is the only of those that has a protuberance?

There is a lateral epicondyle and a medial epicondyle of the humerus. "Epi-" is a Latin root meaning "near". Both epicondyles are near the condyle of the humerus.

Thanks. "Near the condyle of the humerus" -> Why the humerus in particular? I understand the "near the condyle" part.

@FranckDernoncourt - If you understand the " 'near the condyle' part", you have your answer. What more do you expect? Are you asking how many epicondyles there are? Are you asking what the equivalents are on the femur? Clarify, if you will. Otherwise be nice and accept (or at least upvote) this correct answer!

@anongoodnurse there are more than one condyle https://en.wikipedia.org/wiki/Condyle_(anatomy) . Why the humerus in particular? Just curious. Calm down. Why did you downvote the question?

@FranckDernoncourt - You're welcome. I also voted to close as unclear. Always happy to do my part to make a site - and its questions and answers - better. (Ha! you edited your comment. I DV'd because your question is unclear. That's one of the DV reasons (hover over the button and you'll see.)

@anongoodnurse what is unclear in the question?

@FranckDernoncourt the entire question is unclear. If you actually click on some of the links in the Google search you show, you'll see that there are several epicondyles - a lateral and a medial on both the humerus and the femur - and they are referred to as "the [lateral/medial] epicondyle of the [humerus/femur]", meaning the bone itself is referenced in the name. Google doesn't give a link as to where its definition comes from, but I suspect they said "especially of the humerus" because of lateral epicondylitis or "tennis elbow". You need to look at multiple sources to verify something.

@MattDMo unclear isn't the same as incorrect

@Franck I will admit I was unsure exactly what you were asking when I provided this answer. I will happily delete the answer but I still don't really understand what your question is - would you mind clarifying?

@HarryVervet "Both epicondyles are near the condyle of the humerus." ->  how about the Medial epicondyle of the femur? My question is: Why does the term “epicondyle” often refer to epicondyle of the humerus, whereas there are other epicondyles in the human body.


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Clarification of the brightness of bioluminescent proteins
One basic thing I'm not too clear on, which I would like to be clear on, is the brightness per mass unit of GFP or luciferase.  I was having trouble finding a resource that would state the brightness at least for standard GFP or luciferase per gram, for example.  Is there a basic rule for the maximum brightness for either of them?  I'm aware this might end up being a vague question, but I could use help clarifying this.  I found brightness as a product of the extinction coefficient and quantum yield but I wasn't sure how to translate that to watts.

Search quantum yield

So I understand that the quantum yield is the ratio of photons emitted to photons absorbed, but I still don't know what's generally the maximum brightness of at least certain kinds of GFP under a sufficiently bright light source, if that question makes sense.


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Anti malarial drugs and g6pd deficiency
Why does antimalarial drugs causes hemolysis in g6pd deficiency patients?
I know that g6pd protects the cell from oxidative stress by maintaining glutathione in reduced state but how does the antimalarial drugs cause the deficiency of gsh? I came across this(https://malariaworld.org/blog/hemolytic-anemia-and-antimalarials) site and it says:

The antimalarial activity of quinine and compounds vicine and convicine present in broad beans eventually follow the same path. In the gastrointestinal tract they are hydrolyzed to form unstable pyrimidine aglycones. They reduce red blood cell GSH and generate hydrogen peroxides and free radical species.

I highly doubt the last line, how does gsh produced not prevent the cell from hemolysis?

Antimalarials, fever, age (of the RBC), other drugs, and a host of other things increase oxidative stress in RBCs (which results in the production of H2O2.)
The line you point out as a problem is a bit confusing, but it is entirely correct. It helps to keep in mind that 'glutathione' exists in two forms in the cell: glutathione disulfide (GSSG) and glutathione (GSH). GSH is the reduced form. So a reduction in GSH (the reduced form) does lead to an increase of H2O2.
Another way to say it is that in the absence of G6PD, the amount of reduced glutathione is decreased.
Glucose is used by RBC's as food, and G6PD is needed to metabolize it. G6PD reduces a molecule of NADP to NADPH + H+, which then reduces glutathione disulfide into GSH (reduced glutathione). That molecule is used in the reduction of H2O2 to H2O.

If there is a deficiency of G6PH, there will not be enough NADPH to reduce GSSG, leading to decreased levels of GSH; H2O2 levels rise, and oxidative damage to proteins in the RBC occurs.

Glutathione metabolism consists, in large part, of its oxidation to the disulfide and recycling to the reduced form by the co-enzyme nicotinamide adenine dinucleotide phosphate (NADPH) by mediation of glutathione reductase (Figure 1⇓). Reduced glutathione is important in the detoxification of free radicals. In normal cells, NADPH is regenerated by G6PD during oxidative stress. Impairment of this step prevents reduced glutathione recycling, exposing the cell to oxidative damage. Alternative pathways to G6PD-dependent NADPH production exist in most human cells but not in erythrocytes, and the lack of protein synthetic machinery deprives the erythrocyte of the opportunity to replace enzyme that has been lost. For these reasons, these cells are uniquely vulnerable to oxidative stress in G6PD deficiency.

These damaged proteins bind to the red cell membrane, which is then processed in the spleen; the spleen removes the damaged part of the RBC membrane. A few passes of this, and the RBC can no longer maintain the integrity of its cell membrane, and it breaks up (hemolysis).
Glucose-6-Phosphate Dehydrogenase Deficiency and Antimalarial Drug Development

Oh! Reduce= decrease, I thought reduce means reduction ( as in redux reactions)


text:
Can viruses pass through sweat pores?
I have read somewhere that viruses and other microbes can not penetrate skin but what about sweat pores? Can viruses pass through these pores?

How would you expect that it would be determined that viruses cannot penetrate skin? Some theoretical method, performed by pipe-smoking tweed-suited academics at a blackboard, or by testing whether viruses can infect via skin?

'Pore' is a confusing term. Sweat is produced in sweat glands, and subsequently excreted through a duct, as indicated in the image below (sudoriferous ~).
In short, viruses cannot enter the body through these glands because the glands don't really open up into the body, but instead the inside of the sweat gland is lined with sweat-producing cells (fig 2 and 3).
A passive protection mechanism preventing infection is similar to the mechanism by which the bladder is guarded from infection through the urethra: even if some malignant agent were to enter the sweat duct, it is simply pushed out by the excreted sweat.

Figure one: Sweat glands in skin. Source: wikimedia commons.

(source: uwa.edu.au)
Figure two: Slide of sweat gland. Tightly packed secretory cells dump sweat into the lumen through exocytosis (see fig 3). Source: University of Western Australia.

Figure three: Exocytosis. The lining of the sweat gland contains cells producing sweat through exocytosis. Viruses and other pathogens cannot simply enter these cells, and also cannot 'slip in between' the cells. Source: wikimedia commons.

It would be great, if you can at least add the sources for the images. Additionally references for further reading would also be good.

Thanks for the feedback. I had the sources in figure alt-text, but this is much better. Will look at further reading later

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Importance of fate maps
I did some normal google.book search and found the two importance of fate maps-
1. They helped establish the idea that communication between different parts of an embryo leads to the formation of new cell types and have thus helped discover different signalling pathways.

2. They enable us to interpret experiments in which cells of the embryo are exposed to conditions that may alter their developmental fate.

I really don't know where to look for the experiments that support these merits of fate maps. So is my question,what are some experiments that support these merits?

A good place to begin is with the experiments of Hans Speymann and Hilde Mangold, done in the 1920s. They transplanted a piece of the dorsal lip in a newt gastrual to the ventral side of another newt gastrula with different pigmentation. Because of this transplant, a "secondary" embryo formed, on what would have been the belly, in addition to the standard embryo expected. (Some picture show this to be rather like a second head.) Use of differently pigmented embryos allowed the researchers to note that the transplanted dorsal lip material developed into a second notochord. But the interesting facet is the newly developing notochord induced the development of a new neural tube in the adjacent cells which were otherwise destined to become "belly stuff".
My appologies for not finding a great reference with diagrams, my source is the 7th edition of Biology, Campbell and Reece. Here's a very thorough reference, with diagrams, if you're up for it.
https://app.shoreline.edu/kwennstrom/spemannmangold.pdf
This work contributed to a Noble Prize for Speymann. The bottom line here is that tissues receive information from adjacent tissues that influence their developmental fate.
Later experiments showed that the inducing agent was chemical in nature


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Where am I going wrong in a Reactive Oxygen Species Assay done in N9 cells?
I have followed the modified protocol that was given to me by my senior (who was using for his RAW 264.7 cells - Reference article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308605/ ) for assessing ROS in N9 cells.
But, I am not able to standardize it in our lab ... every time there are variations in the results.
Protocol

Seeded 10,000 cells per well in a 96 well plate.
After 12 Hrs of growth, the spent medium is discarded and the cells were washed twice with PBS.
After the PBS wash, 50uM DCFDA was prepared in PBS and 100ul/well was added in 96 well plate and then incubated for 30 min at 37oC and 5% $CO_2$.
The DCFDA was removed from the wells, immediately and cells were washed twice with PBS.
After the wash, to standardize the protocol, the cells were treated with 10uM, 30uM, 50uM ${H}_{2}{O}_{2}$ as a positive control and 1mM and 5mM N-Acetyl Cysteine was used as negative control.
And a set of cells not treated with any compound (DCFDA/${H}_{2}{O}_{2}$/N-acetyl cysteine) are also used as control.
After treating with the compounds, the fluorescence was recorded in multi-plate reader at (excitation -485 nm and emission-530 nm) different time points with a 10 min interval - T0, T10, T20, T30, T40, T50, and T60.

We could not see in difference in different concentrations of ${H}_{2}{O}_{2}$ (newly purchased) and also with N-acetyl cysteine. We would expect to see some difference.
It will be a great help if you can suggest me where I might be going wrong with the protocol or is it anything to do with the seeding density of the cells.

Hi and welcome to Bio.SE! This is a good example of a lab-technique question as far as I can tell and I hope someone can point you to the right direction! I've made some formatting edits, but feel free to roll back.


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Do Alicyclobacilli produce carbon dioxide?
Do Alicyclobacilli, especially guaiacol producing ones, still produce carbon dioxide? Alicyclobacillus spp. are well known spoilage organisms in the fruit juice industry. Apparently there is no "blowing up" of the packaging (often caused by carbon dioxide production) which makes it difficult to visibly detect a potential contamination. Thus the question, do Alicyclobacilli produce carbon dioxide at all?

Alicyclobacilli are strictly aerobic and thus take up oxygen and secrete carbon dioxide, as opposed to the (facultative) anaerobic yeasts and bacilli that usually cause spoilage. So yes, alicyclobacilli produce CO2. But why doesn't the packaging swell? Compare the number of gas molecules in the simplest reactions for aerobic and anaerobic metabolism:
Aerobic metabolism: $C_6H_{12}O_6 + \underline{6 O_2} \Rightarrow \underline{6 CO_2} + 6 H_2O + 38 ATP$
Anaerobic metabolism: $C_6H_{12}O_6 \Rightarrow 2 Ethanol + \underline{2 CO_2} + 2 ATP$
Aerobes take in as much gas molecules as they excrete, while anaerobes (the ones producing ethanol at least) only make gas.


text:
databases for plant growth temperature and altitude
Does anyone know databases which have info for plant growth temperature.It could be specific numbers or categorization as 'cold, warm,tropical and etc' ?

You might find these maps useful. I am not sure where you live, but most plants will list what region they will grow in on their seed packet or online.
You might also find luck by searching ESRI or ArcGIS maps to find more information.
http://www.ahs.org/gardening-resources/gardening-maps


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What is the meaning behind Kcat / Km?
I'm trying to understand enzyme kinetics, the formula for Km and Kcat make sense to me.

Km , the substrate concentration at which the reaction rate is half of Vmax
Kcat, used to describe the limiting rate of any enzyme-catalyzed reaction at saturation. Most of the time
  Kcat just equals K2 (NOT the case when there are
  more reaction steps)

I can find information about the calculation of the specificity constant (Kcat / Km) and what it means:

specificity constant,the rate constant for the conversion of E + S to E + P

However I can't find any detailed explanation WHY you should devide the Kcat by Km. Secondly Km is HALF of Vmax (so actullay at half saturation) but Kcat is at full saturation, deviding these two numbers makes no sense to me. So to summerize I'm asking : What is the "meaning" of the division of these two consants?
definitions are derived/edited from Lehninger principles of biochemistry

Just as $k_{cat}$ represents the rate of reaction at saturating substrate concentration, $k_{cat} / K_m$ represents the rate of the reaction at negligible substrate concentration.
If we take a look at the standard one substrate/one product Michaelis–Menten kinetics rate equation:
$$v = \frac{k_{cat}[E][S]}{K_m + [S]}$$
We can imagine what happens when $[S] \to 0$, we see that when $[S] \ll K_m$, the denomiator can be reduced to $K_m$, and thus the rate equation becomes
$$v = \frac{k_{cat}}{K_m}[E][S]$$
Or in other words, $k_{cat} / K_m$ is the (pseudo-)second order rate constant between the enzyme and the substrate, when $[S] \ll K_m$.
In fact, when you get into more complex rate equations (like inhibitors, pH effects, and kinetic isotope effects) there's a decent argument (one often made by W.W. Cleland) to be made that the two key constants for enzymatic reactions are $k_{cat}$ and $k_{cat} / K_m$, and it's $K_m$ that should be thought of as the "derived" constant. (The fact that we write the rate equation in terms of $k_{cat}$ and $K_m$ is a historical accident - we could have just as easily had $ v = \frac{k_{cat}\Phi [E][S]}{K_m + \Phi [S]}$, where I've arbitrarily chosen $\Phi$ as the symbol for $k_{cat}/K_m$.)
This still leaves the issue of why $k_{cat} / K_m$ is often referred to as the "specificity constant" of the enzyme. The reason for this is that if you have a single enzyme in the presence of two different substrates, you have a competitive inhibition setup. The math is a little dense (see here or here for examples), but the end result is that the ratio of reaction rates for the two substrates is related to the ratio of their respective $k_{cat} / K_m$'s:
$$\frac{v_a}{v_b} = \frac{k_{cat,A} / K_{m,A}}{k_{cat,B} / K_{m,B}}\frac{[A]}{[B]}$$
This actually makes intuitive sense, with the right mindset - the only stage where the two substrates are competing (where you make the decision to do reaction A versus reaction B) is when they're binding to free enzyme. "The rate when you only care about free enzyme" is equivalent to the negligible substrate case. With negligible substrate, all you have is free enzyme - there isn't enough substrate to have appreciable amounts of substrate-bound form, and the rate of enzyme-substrate encounter is much lower than the rate of product formation, meaning that in the steady state you don't have appreciable amounts of product-bound form, either. Thus the $k_{cat} / K_m$ for a particular substrate is representing how good the free enzyme is at performing that reaction.

Thankyou nice explanation! However there is one thing that's not quite clear for me because your example with two substrates for the SAME enzyme makes sense now (negligible [S] --> [S] <-- Km etc.) However Kcat/Km is also used to compare between different enzymes, doing that the argument about low [S] is not valid (unless they are both using the same substrate offcourse) or am I missing something? @R.M.

@RickBeeloo Do you have a particular example of the sort of comparison of $k_{cat}/K_m$ between different enzymes that you're talking about? Because you can certainly compare different enzymes via $k_{cat}/K_m$ -- just like you can compare different enzymes based on $k_{cat}$ or $K_m$. Comparing based on $k_{cat}/K_m$ gives you information about rates in the low (respective) substrate regime, just as comparing $k_{cat}$ gives information about rates in the high (respective) substrate regime. - I'm not sure if you're talking about this sort of comparison, or something else.

This ratio is more often called the "catalytic efficiency" and it's a bad measure. In many cases, enzymes are only better when they have a higher kcat, because the substrate concentration is always way above the Km. Using the ratio when this is obviously the case is just misleading imo, but this happens way too often.
In some cases it could be a useful measure to compare to enzymes. For example if you're unable to measure at higher substrate concentrations. You'd just have the initial slope of the [S] vs vmax graph. At low concentrations this slope approaches kcat/Km.
The kcat/Km ratio doesn't represent something real, it's just a lazy way to compare enzymes, combining two numbers that each represent something different into one number that's only looking good because it's one number.

"There is an upper limit to Kcat / Km, imposed by the rate at which E and S can diffuse together in an aqueous solution. This diffusion controlled limit is 10^8 to 10^9 , enzymes with a Kcat / Km near this range are said to have achieved catalytic perfection"(Lehninger) This would be a strange assumption if the value "doesn't represent something real' ? @VonBeche

I don't think that value is based directly on kcat / Km. It can be described in this way because Km = (k-1 + k2) / k1. But someone else might be able to help you more here, I'm not that at home in the maths behind this.


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Do macrophages engulf material in the epidermis?
This question comes from how tattoos work.  From what I understand, the ink particles are something like 100 nanometers in size, which is too big for macrophages to remove them in the dermis.  What I would like to know in that case is are macrophages able to go into the epidermis, or is that too far for them?  In other words, would material in the epidermis just leave the body after that part of the skin grows out?


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Drugs with unknown mechanism of action
I want to get a list of FDA-approved drugs with unknown mechanism of action. I think that there should be a database where for each drug there is a short field "mechanism", but I haven't find one. Do you know any database where I can find such information? Another possible way is to use text-mining programs to analyze scientific libraries like PubMed and find the drugs which names often occur together with words "mechanism" and "unknown". Are there any good programs which can do it? Any other suggestions are welcome too, of course.

Are there any  drug "approved" in medical-science (not-about the alternative medicines); whose working principle we do not know? at least partly?

There are a lot! Most drugs bind many targets, and nobody knows for sure which targets are responsible for the drug action. For example, look at wide-used drug modafinil (http://www.drugbank.ca/drugs/DB00745)


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How harmless bacteria on skin defence against harmful bacteria?
I have read that there are some harmless bacteria live on skin and they also have role in protecting body against some harmful bacteria but how do they do so? I mean how these bacteria are able to resist other bacteria which are harmful?

Another way to look at this is, you have a limited amount of skin. "Good" bacteria competes for space on the skin with "bad" bacteria. They kind of strike a balance where harmless bacteria are more common. That protects you in that say you have a microabrasion on your skin; it's less likely to be invaded by harmful bacteria than not as-pathogenic bacteria.

Relations between organisms in complex ecosystems are various, so I won't give an exhaustive answer, only keys to understanding.
First, you need to consider that a bacterium harmful to humans is not necessary harmul to other bacteria. So there is no reason why our skin microbiota will only target/resist to human pathogens.
What's more, microbes are not inherently harmful to us. Their dangerosity also depends on the capacity of the skin to block them 1.
Then, microbial defence mechanisms depend on the kind of relation they have to the potential pathogen: competition, parasitism, predation, etc.
The article cited below will give you a nice overview on the topic.

1 Cogen, A. L.; Nizet, V.; Gallo, R. L. (2008) Skin microbiota: a source of disease or defence? British journal of dermatology, 158, 3, 442-455; doi: 10.1111/j.1365-2133.2008.08437.x


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Does the genome make sense without knowledge of the ovum?
Much of the literature for laypeople seems to consider (and to spread
the idea) that an animal (or a plant, I guess) is characterised by its
genome. I do not know whether the same goes for more professional
literature. Even on this site, the tag genomes is defined as The
entirety of an organism's hereditary information, which seems to imply
that it contains a description of all that can be be inherited.
It seems to me that attempting to define an animal with the sole
knowledge of its genome (let alone recreate it as envisioned by some people) does not
really make sense, without the complementary knowledge of the cell
structure of the ovum that has to interpret this genome.
This question seems never to be seriously addressed in lay literature.
Is it the case that this decoding machinery evolves much less than the
genome itself? This could be expected, since changing the decoder has
usually more important, global and drastic effects than changing the
genome, which may result in a very localized effect. Hence, changes to
this machinery are less likely to give a viable being.
To refine that question (unless the moderator prefers this to be a
separate question):
Is there any study of the diachronic evolution of that genome decoding machinery in a
given species, or of the synchronic differences between species, which
would probably give a measure of the speed of diachronic evolution of
that machinery?
When two close species cannot mate, is it analysed (for some cases) whether it is due
to difficulties in combining the two genomes, or to the fact that the
ovum of one cannot properly interpret the genome of the other?

Don't forget that the initial cell machinery provided in the ovum is quickly replaced by that of the newly-formed zygote. (e.g. ribosome half-life is about 5 days). Also, and perhaps this analogy does not hold, but kickstarting a bike might be very different from driving down a road, but the engine itself defines the properties of the vehicle, not the way in which the engine was started.

You might want to rephrase the question to ask about the general case of converting genotype to phenotype, because "the ovum" has nothing to do with it -- obviously, since the vast majority of living things do not have ova. Moreover as you suspect you have two unrelated questions here -- genotype to phenotype, and speciation, which have very little to do with each other.

@iayork I cannot well rephrase my question because I am not competent enough
to use most words and concepts with precision. I am rather naive on all this, but
shocked by presentations I found too simplistic. I refer to ovum as the
only way I know to specify the context that initially interprets the
genome - assuming there is such a specific initial phase, which I am
note sure of. Also I first considered the issue for animals. Actually
I wonder whether reproduction can always be separated from cellular
differentiation (same genome, but machinery uses it differently)

The short answer is that there is elaborate machinery needed to convert genetic information into a phenotype; that's nothing to do with the ovum; and it's hardly ignored in biology as it's the topic of intense research.  It's difficult to answer your question any more than that since it seems to rest on so many incorrect assumptions.

@iayork Actually I am not assuming more than what you just said: I meant to
say that genetic information is meaningless without knowledge of the
machinery that will convert it to a phenotype (I did not know to
express it that way). The rest (ovum included) is just my failed
incompetent attempt at expressing it in a more concrete way. My
question is only why most presentations for non specialist are
ignoring that fact. I do expect biologist to deal with it, but is
there a reason this is not explicited for the wider public, to avoid misconceptions. Maybe I
should indeed rephrase.

Nice question! Let's start by talking about different forms of heritability.
What is heritable?
Here is a list of things that can be inherited. Some of them are only ('mainly' would be more correct that 'only') transmitted to the offspring while others can also be transmitted to any individual in the population.
The term epigenetics is used with several meaning. In its narrowest sense it refers only to modifications (typically methylation) on top of the DNA sequence or on top of histones (histones are proteins around which the DNA is wrapped). In its broadest sense, it refers to any element of hererdity that is not caused by the DNA sequence. In the below list, I will avoid using the term epigenetics.
What can be inherited:

DNA (obviously)

Modification of the sequence of DNA

Methylation on DNA

Modification of (typically) methyl group added on nucleobasis

Methylation on histone

Modification of (typically) methyl group added on (typically) the tails of the histones.

Environment (or rather macro-environment)

The term environment can be used with different definitions. Histone modification is generally considered as being the environment of the genome typically. I will however make a (somewhat) arbitrary distinction between this micro-environment and the more intuitive macro-environment
Individuals affect their environment and therefore can shape the environment for their descendents. An obvious example is a beaver dam which last longer the the life of a single beaver. Two key concepts here are niche construction and Ecosystem engineering. You should have a look at the post Does modern theory of evolution include modification of physical environment?

Memetics (See wikipedia > meme)

A meme is any idea or element of culture that can be transmitted. This type of inheritence is particularly important is species that have high cognitive abilites such as humans.

In this kind of discussion, there is often someone who stand up to talk about plasticity, developmental noise and mutational noise to mess things up. I will just consider them as phenotypic trait and will not much attention to them for the moment (even though part of my research is focused on these three concepts).
Consideration of the non-genetic inheritence in the literature
I like that you noticed that "the tag genomes is defined as The
entirety of an organism's hereditary information". Such definitions are common and grounded in an old view of inheritance. As listed above, there are other things than the DNA sequence that is inherited by the offspring. While all biologists know that, it is true that few really acknowledge the existence of these other forms of inheritence in their daily thoughts.
Some authors have argued that these other types of inheritence must not be neglected. Odling-Smee and colleagues wrote a whole book on the subject (Niche Construction: The Neglected Process in Evolution). Some have even argued that we should rename our theory of evolution to the light of the existence of non-genetic inheritence (see Laland et al. 2015). My feeling is the vast majority of biologist recognize the existence of these types of inheritence but do not consider that it is worth a renaming of the theory of evolution (current named modern evolutionary synthesis). Some would not consider this renaming necessary either because they neglect the important of these other forms of inheritence or because they just don't think it is worth renaming our theory even in the recognition of the importance of these other processes.
Viewing the cell as a decoder can be misleading
In your question, you are suggesting to view the cell as a decoder of DNA. IMO, this is misleading. In this discussion, I will exit science and enter in the realm of philosophy (identity).
What is generally considered as the mechanism of decoding DNA is actually part of our geome itself (consider typically the importance of tRNA and rRNA). If uneasy with basic concept of gene expression you might want to have a look at an intro course such as Khan Academy from the section Classical and molecular genetics to the section Gene regulation.
Also, I would argue that all the elements that are being transmitted to the offspring shall be considered as being the offspring. If it turns out (which we actually pretty much know is wrong) that histone modification explains more in the phenotypic variance than genetic variance, it would intuitively be unfair to see histone modification as just being a decoder of the genome. We would rather be tempting to see histone modification as central and the DNA sequence as a side-effect.
Layman literature
You say "This question seems never to be seriously addressed in lay literature". Richard Dawkins book called the extended phenotype, while maybe not directly addressing your question does a good job at playing out with thee concept of environment vs gene separation. You might want to have a look at it.
Note that the laland et al. 2015 cited above is easy to read and would be a good source of information for a layman.

I think the reason for the simplification in many contexts is that the machinery that converts genotype to phenotype is ALSO specified in the genome; yes, it is necessary to have that machinery present for cells of all types to function and to create new cells (whether single-cellular or multi-cellular), but this machinery itself is not really inherited; the machinery (proteins and functional RNA) that exists in a founder cell cannot be inherited except in a very unusual and extreme cases.
There can be differences in translational machinery, for example see wikipedia, but precisely because as you write, "changes to this machinery are less likely to give a viable being" - that means that changes to this machinery are most likely to be lethal and therefore do not persist in a population.
Failures of fertility between species are due to simpler factors, and the transcription machinery is highly conserved across many species that are not cross-fertile.

Craig Venter made his first synthetic bacteria by first making a synthetic genome containing all the genes required to run a bacteria (Mycoplasma. mycoides). His team then inserted this synthetic genome into related species of bacteria (Mycoplasma capricolum). The synthetic genome than took over the cell and over time turned the cell from one species to another. http://www.nature.com/news/2010/100520/full/news.2010.253.html
So... just because it does not make sense to your gut, does not make it wrong. Gut feelings are great... it is how we think the world should work. A short hand. But just because we think the world should work one way, does not make it so. The world and biology has many antigut concepts.


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Types of heparin
My textbook(biochemistry 4th edition, U. Satyanarayana) says that the following structure is of heparin
and it's name should be D-Glucuronate 2-sulfate, N-sulfoglucosamine 6-sulfate.
 I searched on internet but could not find this kind of heparin.
So could anyone give credibility that this structural compound is heparin?
Atlast what is the criteria that determines whether the compound is a heparin?

Why downvotes? Am I wrong?

This structure is exactly the same structure as found on wikipedia at the very top the page. Other variations are also shown elsewhere on that page.
Perhaps you are being misled by the presence/absence of hydrogens on the sulfate groups? The way your textbook shows it is a more physiologically relevant way as those groups would be deprotonated in normal biological conditions, but this doesn't really change the chemical structure. Heparin is normally administered as a salt.
Further, heparin is a polysaccharide chain of varying lengths (more information on that same wikipedia page) - it doesn't really make sense to say that heparin's chemical name should be "D-Glucuronate 2-sulfate, N-sulfoglucosamine 6-sulfate" - this is the name of only one disaccharide in a long, long chain. Your textbook doesn't say that either, the little "n" in the lower right corner is very important and indicates a chain of unspecified length.

on what basis we classify those(other variations)  as heparin?

Wikipedia shows iduronate on the very first pic while the book depicts glucuronate.

Sorry, you are correct; if you read more on the wikipedia article it mentions  the composition of heparin which includes both - it really doesn't matter much which are depicted. Heparins are just glycosaminoglycans of a variety of subunits - there is no one specific chemical called "heparin" but they all have roughly the same biological function - welcome to biology :)

This link might help you sort out some of the details in terms of where the boundaries are between heparins and similar compounds.


text:
How do poiklotherms survive at different temperatures even though enzymes work at specific temperature?
Since enzymes have an optimum temperature at which they are able to catalyze the reaction best and increasing the temperature above optimum can even damage them, how do poikilotherms survive as they change their body temperature according to environment unlike homeotherms. Also wouldn't their metabolism stop with increased temperature?

Instead of viewing poikilotherms as having the same temperature as the environment, view them as lacking an internal thermoregulatory system. Poikilotherms indeed suffer from not having the ability to regulate their internal temperature.
Homeothermy is ecologically advantageous, allowing optimal functioning at a range of temperature. Poikilotherms, therefore, are more restricted in their habitat range, have to depend on external mechanisms for maintaining temperature (eg: Hibernation, Shade-loving lizards, burrowing in desert animals) or simply die due to environmental change (eg: poikilothermic fish are the earliest to die from a thermal runoff into a water body).


text:
Why is trypsin digestion required for proteomic studies?
I know that trypsin is used for proteomic studies, but I do not understand why trypsin digestion is necessary/important.

Welcome to SE biology. Could you edit your question to make it clearer. Proteomics is not a synonym for mass spectrometry. I think you want to ask Why is tryptic digestion used prior to mass spectrometry?

Trypsin digestion allows you to cut proteins into smaller polypeptides, masses of which can be determined by mass spectrometry and then translated back into possible amino acid sequences. Trypsin cleaves after specific amino acids. Altogether, this allows you to identify proteins.


text:
How is randomness of the branch migration process ensured?
Branch migration (part of genetic recombination) is a random process. It looks like Ruv-ABC proteins are mainly responsible for this process, but how is randomness ensured? After all, it can only be a quasi-random process - i.e. molecules don't behave randomly. Is it thermal motion perhaps?


text:
Where is the H+ ion in this step of glycolysis coming from?

(from Fundamentals of Biochemistry by Voet, 5th ed.)
In this step of glycolysis, I'm not seeing where the $\ce{H+}$ ion on the product side is coming from. It seems to me that the G3P's aldehydic H is replaced by phosphate, and that H is given to $\ce{NAD+}$ to make NADH. So where is the extra $\ce{H+}$ coming from?

Look at what you are substituting  OPO for

I've reverted the question to its original. Clearly the answer to the question needs to take into account the ambiguous nature of the equation, which does not make it clear whether it is meant to be a stoichiometric representation of the reaction occuring on the enzyme (which must involve discrete species) or adherence to a convention (which I assume, like Berg et al. is not explained) in which Pi is used to represent the fact that the reactive species (orthophosphate?) is in equilibrium with other phosphate species. Thanks @tomd for putting me right here.

Although texts such as Berg et al. tend to refer to inorganic phosphate, $\ce{P_i}$,  as orthophosphate ($\ce{PO4^{3-}}$), the term inorganic phosphate is used because in aqueous solution at pH 7.6 several phosphate species exist, the predominant one being $\ce{HPO4^{2-}}$. If this is regarded as $\ce{P_i}$, then it is the source of the $\ce{H^{+}}$, and the equation balances.
Note added by David:
On checking I find, in contrast to Berg, Lehninger’s book defines $\ce{P_i}$ as monohydrogen phosphate ($\ce{HPO4^{2-}}$), and Fersht actually writes the equation of the reaction (16-1) with $\ce{HPO4^{2-}}$ rather than $\ce{P_i}$.

Ok, so do most sources assume $\ce{P_i}$ as being $\ce{HPO4^{2-}}$ or as being $\ce{H2PO4^-}$? It seems like the source of my image assumes $\ce{P_i}$ is $\ce{HPO4^{2-}}$.

Take a look at this link: http://www.statemaster.com/encyclopedia/ATP-hydrolysis .  It is about ATP hydrolysis which also releases Pi (the phosphate ion) but notice the resonance stabilisation. I think this is what anongoodnurse is meaning

This is very muddled. You are mixing up solubility and ionization, and if you want to discuss this you have to put the charges on.

@RickBeeloo No, the question is about the stoichiometry of the equation, it has nothing to do with resonance stabilization. In the link you cite the equation is balanced.

@David - I am not tech savvy enough to include both the superscript charge and the subscript. However, in truth, in cells, Pi does not exist as PO4-3. And ultimately, the H+ does, indeed, come from the solution, which has a number if weak acids and bases.

@tomd - I suppose it depends on exact definitions of inorganic phosphate. I'm glad you added your own answer.

I'm not sure that it's the right answer, but what it seems to me you are arguing seems better expressed as follows. Orthophosphate (3–) may be counterbalanced by N+ or K+ in solution, but will be in equilibrium with a much greater amount of the monohydrogen acid (2–). If orthophosphate is removed an almost equivalent amount of this acid will dissociate regenerating the orthophosphate, but also a hydrogen ion. This hydrogen ion could be the one in the equation. If this is what you intend I can edit your answer with the charges shown.

@David - I agree with what you say. If you can write in mathematic (I can only write English), I would be happy and grateful for your improvement to my answer, however you want. Many thanks.

I've now edited your answer. Do modify or revert it if you are unhappy with any aspect of it.

@David - Thank you, it's good.I looked at how you wrote it. It's like reading nonsense words (I could never have done it.) Again, thanks!

No problem. I've added a short additional note and regard your answer as correct.

Although an answer that I have contributed an edit to has been, rightly, accepted, I decided to add my own answer to clarify a couple of points.

The equation in the question is what is known as a biochemical equation, not a chemical equation. As this IUPAC document notes:

Chemical equations are written in terms of specific ionic and elemental species and balance elements and charge, whereas biochemical equations are written in terms of reactants that often consist of species in equilibrium with each other and do not balance elements that are assumed fixed, such as hydrogen at constant pH.

One should not, therefore, expect Voet’s equation to balance.

The 1974 paper of Buehner et al. on the crystallization of glyceraldehyde 3-phosphate dehydrogenase includes the following (net reactants in yellow, hydrogens in orange):

…which answers the question.
It is interesting that the IUPAC document defines Pi as orthophosphate, although this is irrelevant to the question at hand as none of the old papers I have looked at use the abbreviation Pi.


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Why is contractile vacuole absent in parasitic protozoans but present in free living protozoans?
I know that contractile vacuole helps in osmoregulation of protozoans and some nitrogenous wastes are also excreted through it. Since contractile vacuole plays an important role in protozoans, why is it absent in parasitic protozoans? I could not find the logic behind this.

No, you are wrong. Parasitic protozoans too have contractile vacuole, for example trypanosoma.
Also Wikipedia says:

Not all species that possess a contractile vacuole are freshwater organisms; some marine, soil microorganisms and parasites also have a contractile vacuole


text:
What is the evolutionary advantage of menstruation?
I was wondering why woman have fertile periods. Based on some simple reasoning I would expect that if woman were always fertile this would increase the chance of reproduction(one of the important things in life). But having menstrual periods would decrease this chance because only the period close to ovulation would result in fertilization.

So why did evolution result in woman having menstrual cycles?

Related http://biology.stackexchange.com/q/21715/3340

Human female ovaries only have a certain number of ova; none are manufactured in adulthood. Once they're gone (that's when menopause occurs), they're gone.
You can also ask, why did evolution result in a limited number of oocytes then? This kind of second guessing of physiology is endless.
In your scenario, an ovum would need to be released every few days in order to be fertile continuously. That alone would decrease the number of years that a woman could be fertile. Since a fetus needs about nine months to gestate, I think once a month fertility is more than adequate. The earth's population is already too large, which also translates as successful reproductively.
If a fetus could gestate in a month, I could see an advantage to constant fertility. But the disadvantages would also be great. How could a woman take care of so many babies? How could she possibly feed, say, six to nine babies a year with only two breasts? (Mammals that frequently have larger litters have more mammary glands.) How could her own body compensate nutritionally not only for the burden of feeding the fetuses but also of the babies?
Asking why didn't something evolve from a teleological standpoint rarely results in a satisfying answer. If constant fertility were advantageous, maybe it would be present.

But there are animals which don't have these cycles, so probably there should be another reason why we humans (and some other animals) got these cycles and others did not

@RickBeeloo - Are there mammals who don't have estrus cycles? Do these other animals physically care for their young through to near adolescence (age of "adolescence varies from species to species)?

Humans don't have estrous cycles, they have menstrual cycles (https://en.wikipedia.org/wiki/Estrous_cycle#Differences_from_the_menstrual_cycle ) so yes there are definitely mammals which don't have estrous cycles which is another good point in evolution (why menstrual cycles  and not estrous cycles or visa versa) @anongoodnurse

@RickBeeloo - Did I say humans had estrous cycles? I asked if you knew of any mammals that didn't have estrous cycles. You said, "But there are animals which don't have these cycles...". Since insects are actually animals, I know with great certainty that there are animals without estrous cycles. What you don't know doesn't make your argument more effective. There is no significant difference between menstrual and estrous cycles reproductively. One bleeds the excess endometrial tissue, the other reabsorbs it. Resorption may help avoid predation.

Yess I know there are animals which don't have estrous cycles and that's the whole point. Why are there mammals (like humans) which don't have an estrous cycle and mammals which do have estrous cycles, in other words what would be the advantage of having a menstrual cycle instead of a estrous cycle? I don't understand your confusion? @anongoodnurse

Reread my comment (which you did not answer); your question most certainly was not why do some mammals menstruate while others have estrus cycles (that's not "the whole point".)

@RickBeeloo you're talking in circles. Answer anongoodnurse's first comment.

Are there mammals who don't have estrus cycles? Yes humans. Do these other animals physically care for their young through to near adolescence (age of "adolescence varies from species to species)? Take snakes there is evidence that they take care of their offspring(https://www.reference.com/pets-animals/snakes-care-young-a731de15970742e4) And if I'm right snakes don't have cycles

The question asks about menstrual cycles. This answer going around the question because it conflates menstrual and estrous cycles.

@NickSandor - the original question did not mention menstrual cycles. It asked about periodic fertility. I answered the original question.


text:
How come Logs-Odds Scoring Matrix is symmetric?
I am studying Pevsner's Bioinformatics.
It is stated that Logs-Odds Scoring Matrix is symmetric at page 89.
But with given the equation to calculate the cells of the matrix, I find different scores for from cysteine to leucine and for from leucine to cysteine.
How is this possible?
Do we take the lowest value?
The equation used for constructing Logs-Odds Matrix from a corresponding Pam matrix is : $s_{ij}=10\times\log_{10}(M_{ij}/f_i)$
where $M_{ij}$ is the observed frequency of substitution for each pair aminoacids.
and $f_i$ is the probability of aminoacid residue i occurring in the second sequence by chance.

I'm voting to close this question as off-topic because it is about statistics, not the underlying biology. Please ask at [stats.se].

To answer this will require more information, given that most respondents will not have p. 89 handy. What is the equation you speak of?

Since I do not know what calculations you did. I am going to answer your
"How come Logs-Odds Scoring Matrix is symmetric?".
Let us assume that it is not.
So
\begin{equation}
S_{ij} \neq S_{ji}
\end{equation}
\begin{equation}
M_{ij}*f_j \neq M_{ji}*f_i
\end{equation}
Is this not in contradiction with Bayes theorem?. Yes.
So log odds matrix is symmetric.


text:
Vo2 of the brain is 21% of Q=13% or of the entire blood?
I am reading now the book which states that the Q (blood flow per unit of time) of the brain is 13% while the Vo2 (relative Oxygen used per unit of time) is 21%. Now my question is if the Vo2 of the brain (21%) is taken from the entire blood or from the part the brain gets (Q=13%)?  It is not clear on the book. I've attached the picture with the explanations.

What do $Q$ and $Vo2$ stand for?

Q stands for blood flow per minute, and Vo2 stands for relative Oxygen used per minute - as it's written on the chart.  I can assume that the letter Q is for Quantity and Vo2 is for Volume of o2 (oxygen).

TL; DR 21% of the whole body.
The VO2 numbers add up to 100%. You are looking at the way six major compartments of the body split the oxygen consumption. The brain takes 21% of the whole oxygen brought into the body by the arteries.
The Q numbers add to 100% too. The brain takes 13% of the blood coming out of the heart.
The picture is meant to contrast high-flow and high-metabolism organs. The kidneys take 20% of all the aortic blood, but use only 7% of the oxygen consumed in the body. The coronaries take 4% of the blood leaving the ventricles, but use a large 11% of the oxygen take in by the whole body.

Thank you. Now I understand it (I also calculated all the vo2 in the chart and I got 100% and that proofs your things). But now I don't understand why there is not a relation or correlation between the Q and VO2, it means that it can be Q of 4% while the vo2 is 11% (almost 3 times than the Q!). Then my exact wondering is how could it be that a very small Q can supply a big quantity of vo2. By the way,  What does it mean "TL; DR" (in the beginning of your answer)?

TL:Dr means "too long ; didn't read", a frequent rebuttal on the Net for those who make too long an en explanation. It has been taken up in preemptive defense by those who write long explanations, like me.
The heart and brain use a lot of oxygen because they do intensive work, which require intensive burning of energetic substrates. The kidney is not a burner, but it needs a lot of blood in order to do its job - filtering -, effectively. Neither organ takes up all of the oxygen in the blood, but heart muscle and brain are making more of an effort compared to the kidney.

Thank you for your comment. I think that I didn't explained my question well. I've been asking, how could it be that a small amount of blood (e.g. in the heart 4%) can supply a big quantity of oxygen (vo2=11%)?

When blood leaves the brain or the kidney, it is not fully depleted of O2. Blood leaving the left heart has a hemoglobin saturation with O2 of nearly 100%. (Almost every Hb molecules carries the maximum, four O2 molecules.) Blood returning from the body through veins, mixed in the right atrium, has a saturation of about 75%. (That is, the average Hb molecule has three O2 molecules still bound to it.) Roughly speaking, the various organs take up only one of the 4 molecules of O2. Brain is striving a bit harder; brain venous blood saturation is about 70%. Kidney vein Hb O2 saturation is ~80%.


text:
GFP brightness calculation
So this question is part math, part biology, but I'm asking about the biology part here (or maybe the chemistry part).
Basically I'm asking about my attempt to calculate the possible brightness per unit mass of GFP, and I'm asking if it makes sense.  Here's what I've done:
(I'm ignoring the quantum yield which should be 0.8):
GFP molar mass=27,000 amus (27 kDa)
1 mole weighs 27 kilograms
therefore 1 gram=(6.02*10^23)/27000=2*10^19 molecules of GFP
Assumption that I'm asking about; I'm assuming in this calculation that GFP releases light from one excited electron (roughly 2.5 electron volts).  How many electrons are excited in GFP fluorescence?
(2*10^19)/(6*10^18), (the number of electrons in a Coulomb/amp)=3.3 amps
Brightness=2.5*3.3
=8.25 joules per gram
From Researchgate:
" The time constant of the fast, pH-dependent chemical process decreases with pH from 300 microseconds at pH 7 to 45 microseconds at pH 5..."
Given that's the case, that's roughly 3000 emissions (or 3333) per second (at 7 Ph), so
1 gram of GFP would have a maximum brightness of 24,750 watts, if there was enough UV light, or 25 watts for a milligram.
That sounds plausible, although high.  Does that make sense, or what part of this calculation was wrong?

According to https://www.jic.ac.uk/microscopy/more/T5_9.htm , only 80% of photons absorbed lead to photon emission. (It's "quantum efficiency".) In practice, numbers might be far lower for some other reasons. I recall that even one gram of eGFP was less bright than a 30 W fluorescent light bulb. I suspect that I could not excite all the GFP molecules as often as needed. They are quite sparse in solution, even at "high concentration".

But perhaps it could be brighter than that if the efficiency was maximized (i.e. the protein was spread out over a thin surface and completely concentrated, in theory, since it would have to be in some solution unless it was in powder form)?


text:
Confusion about Photosystem 2 with regards to lysis of water
I am slightly confused about the role of $\ce{H2O}$ lysis in PII. I know that this releases $\ce{H+}$ ions, which I think are important because they drive the production of $\ce{ATP}$ through F-Atpase across the thylakoid membrane. But I don't understand how else this is important? With my current understanding, I would think that it is perfectly sufficient for PII to receive photons to excite an electron in the primary pigment reaction centre, which goes along the electron transport chain to PI. Is the water lysis there to replace electrons lost by photosystem 2? If so, how is it controlled that the correct number of $\ce{H2O}$ molecules are lysed so that excess electrons aren't generated?

Generation of ATP via photons is the primary aim of the photosynthesis pathway, which is accomplished by the generation of a chemiosmotic gradient of $\ce{H+}$, which then drives the ATPase pump. All the other enzymatic setups are designed to just let this process run in the most efficient way.

I would think that it is perfectly sufficient for PII to receive photons to excite an electron in the primary pigment reaction centre

While you are partially correct in assuming this, since the ETC also participates in creation of a chemiosmotic gradient (Plastoquinone), such a mecahinsm would not be able to run repeatedly. Without the replenishment of the electrons of the PSII, it will not be able to initiate another round of electron transport. Hence, the oxidation of water is crucial in providing PSII the electrons it passed onto plastoquinone, so as to allow another round of photon-absorption and continuation of the photosynthetic process.

how is it controlled that the correct number of H2O molecules are lysed so that excess electrons aren't generated?

This is achieved by a complicated interplay of the enzymatic components within the PSII. In summary, utilizing the four stable oxidation states of manganese core in the redox center ($\ce{Mn}^{(2-5)+}$, four separate states of the center ($S1\rightarrow 4$) are formed. These states cyclically shunt one electron during each step, until a water molecule is bound to $S4$ which is then directly converted to $\ce{O2}$ by $P680+$, formed in PSII due to photon absorption, which is a strong reducing agent. Since the final step occurs only with water molecule bound to $S4$, which in turn is formed only by the cyclical transition between the various states of the redox center with systematic sequential loss of electrons, the overall process is very tightly constrained to extract only the limited number of electrons preventing any troublesome redox intermediates.
See here for some basic treatment of photosynthesis.

Thank you for your answer. Your answer and some additional reading allowed me to understand the role of water lysis! However there is one question that has come up for me which I cannot seem to find the answer to: so quinone B, after accepting electrons and hydrogen, transfers electrons to cytochrome b6f as plastoquinone/quinol. These electron are accepted by cytochrome b6f, to re-form quinone B, which is not lipid soluble. How is the quinone B replaced in PSII? It cannot diffuse back in the phospholipid bilayer as it came?


text:
How to predict future generations from heritability
The heritability of human intelligence is estimated to be around 0.5. There are of course various estimates, some lower, some higher. But let's work with this value of 0.5 for the moment.
I wanted to know how this relates to the trait value of future generations and read a bit about it. For example, in some related posts:
how should one interpret heritability is it related to r2
why is a heritability coefficient not an index of how genetic something is
how to interpret the breeders equation
Turns out the breeders equation gives us an idea about that. But we need a second variable: Selection.  I read that selection is based on the reproductive success of individuals with a certain trait value.  But how would I calculate this value?  Let's assume that the reproductive success is higher, for humans with higher intelligence. Let's simplify and say, the fertiliy rate of above average indivdiduals is 2.10 and the same value for below average individuals is 1.90. How would I plug those numbers into the breeders equation?
I tried the other way around. We know that intelligence is increasing over generations in western civilizations (see Flynn effect). Again, estimates vary (and can actually be negative) but we can work with an increase of 2 IQ points per decade. So lets say 5 IQ points increase from one generation to the next in a western civilization population. That would mean:
S = R/h²
S = 5/0.5 = 10
What would this value of 10 mean? How does this boil down to the reproductive success of individuals with certain trait values?

It might eventually help to also read the post How does Natural Selection shape Genetic Variation?. I tried to answer but have failed so far! I might try again tomorrow with a book in hands. +1

"How would I plug those numbers into the breeders equation?"  You would use those fertility rates in calculating the selection differential (S), which would essentially be a weighted intelligence average of the reproducers minus the population average (reproducers+non-reproducers).  So, if the population starts wih 100 IQ and those with 125 IQ produce 2.1 and those with 75 IQ produce 1.9 and those two groups are equally populated, the weighted intelligence avg of reproducers becomes (125*2.1+75*1.9)/4=101.25.  The selection differential is then 101.25-100=1.25.  Response is 1.25*.5=.625.  IQ moves to 100.625.  In your example, S=10.  That is, (x*2.1+y*1.9)/4-100=10, where x is the avg IQ of the above average group and y is the avg IQ of the below average group, assuming the two groups are equally populated.

Thanks. I got a slightly different result.  $$S=\frac{1}{\bar w}\sum_{i=1}^{\text{nb inds}}m_iw_i - \bar m$$ $$m_i = 125 \quad  w_i = 2.1 \quad   | i=1$$  $$m_i = 75 \quad w_i = 1.9 \quad | i = 2$$ $${\bar w} = 2$$ $${\bar m} = 100$$ $$S=\frac{1}{2}((1252.1-100)+(751.9-100)) = 102.5$$

I just realized that this might be due to the calculation taking $w_i$ as the value for couples. So for individuals we would divide by two. But then we would also have to divide ${\bar w}$ by two, and we get the same result. Maybe I got the formula wrong or am I misinterpreting something?

Is the top equation that begins with "S=..." yours or did it come from a text?  Our results are the same except you divided by 2.  I divided by 4 in order to get the average progenitor IQ weighted by the quantity of offspring produced (2.1+1.9=4 was the total quantity of offspring produced).

I got it from another post here (http://biology.stackexchange.com/a/16807/27686). Might be wrong. Your calculation seems logical anyways.

Meanwhile, I also found a paper here (http://www.sciencedirect.com/science/article/pii/S016028961000005X) and there is the following equation $$ S=\frac{1}{N}\sum_{i=1}^{N}(IQ_i - \overline {IQ})*\frac{CH_i}{\overline {CH}} $$ Where $CH_i$ is "Children of individual" and $\overline {CH}$ is "Average children in sample". But I do not really understand why we do not simply weigh with the number of offspring per individual as you did.

Can I ask what software you used to write these equations?

It's not a software, more like a code. It's called MathJax:  https://math.meta.stackexchange.com/questions/5020/mathjax-basic-tutorial-and-quick-reference


text:
Is sex linked inheritance independent of dominance?
I have a little challenge with what my lecturer said in class. I disagree with explanation but don't know how to convince myself. Please review and tell me your opinion.
Eye-color in drosophila is a sex-linked trait in which a white eye male was crossed with a red eye female. The F1 generation consist of 54 white eye and 49 red eye female; and 47 white eye and 50 red eye male. Explain.?
He said and I quote

"the white eye male will transfer the white eye allele to the F1 female generation while the red eye female will transfer her red eye allele to the F1 male generation"

I disagreed because his explanation didn't account for the red eye f1 female generation and the white eye f1 male generation.... I proposed that the female parent was heterozygous for the eye color trait..... Hence a cross shows that the phenotypic ratios for either eye colors for any sex is 1/4...In response he acclaimed there's no dominance since it's a deviation from medellian principle.

please dont post text as pictures.

Ok. Thanks for the correction. It's been taken. But any idea on the question.

Welcome to SE Biology. The feedback from Ebbinghaus indicates that an edit will improve your question, the picture should be removed and the text added to your question. Including an explanation of why you disagree with your lecturer will also improve your question. The chance of attracting good answers increases in conjunction with the quality of the question.

Drosophila follow the same sex determination as in humans, XY for males, XX for females. The eye colour is sex linked, that is, the genes for eye colour are only carried on the X chromosone in this case, not the Y (there are other linkages that are only carried on the Y, but that's not the case here). The wild-type colour, red, is dominant over the white eye colour. When speaking of inheritance of eye colour in drosophila males specifically, you don't need to consider dominance or recessiveness as males only get one copy carried on the X - either the wild type red, or white, there is no interaction between alleles. The dominance and recessiveness only comes in to play with the eye colour of females, as they get two copies, one on each X they get from the parents, in which case the heterozygous will appear red eyed, as will the homozygous for the red eye allele.
For the image: In this cross we have a heterozygous red eyed female (XWXw) crossed with a white eyed male (XwY). In the offspring you see that half of the females would be heterozygous for red eyes, thus presenting as red eyed, and half would be homozygous for white. In the males half would be red eyed and half white eyed as there is no dominance or interaction between alleles as they only have the single copy on the single X chromosome they have inherited.
Hope this makes sense!
With all that in mind, you are right, you will only get white eye males in the F1 generation if the mother in a cross is heterozygous for the eye colour trait.


text:
Can someone tell me if the example I wrote below is one possible answer?
Here is an imaginary mRNA sequence:
5’- THE BIG BOY SAW THE CAT EAT THE HOT DOG – 3’
Each 3 letter-word is equivalent to the codons in real mRNA.
What would the imaginary mRNA sequence look like if there was a deletion of two bases near the 5’ end of the mRNA? Write out the example above with the two-base deletion and 3-letter “codons” to explain your answer. Label the ends of your imaginary RNA and clearly show the mutation.
I used this: 5’- TBI GBO YSA WTH ECA TEA TTH EHO TDO G-3’. However I am not sure if writing in this form answers the question, can someone tell me whether this is correct and if not how should I change it?

No your answer seems correct, but are you sure they aren't asking you to delete the two bases at the absolute 5' end? In that case it becomes:
5’- EBI GBO YSA WTH ECA TEA TTH EHO TDO G – 3’
But if they're asking you to delete any two near the end, then you're correct.

Okay, is it necessary to put ... at the end of the 3' end for this question?

I don't understand, I haven't put three dots? It's just G – 3’

Yeah, that shows that the mRNA is going from 5' to 3' and that it's ending there


text:
Linkage disequilibrium
I want to know what ranges of value can D' in linkage disequilibrium take? Because I read in my book (An introduction to population genetics by Nielsen and Slatkin) that D' is guaranteed to be between 0 and 1. Whereas at the link provided below, it says D' can be between -1 and 1.
http://csg.sph.umich.edu/abecasis/class/666.03.pdf
Could someone explain this discrepancy? Because now I am totally confused.

The whole point about using D' rather than D is because D' is bounded between -1 an 1 for any allele frequency, while the bounds for D depends upon the allele frequency of interest.
Recall the definition of D
$$D = p_{ab} - p_ap_b$$
Let, $D_{min}$ and $D_{max}$ be the minimal and maximal values of $D$ for a specific allele frequency.
For $p_a = p_b = 0.5$, the  $D_min$ is when when $p_{ab} = 0$ ($D_{min} = -0.25$) and $D_{max}$ is when $p_{ab} = 1$ ($D_{max}=0.75$).
For $p_a = 0.8$ and  $p_b = 0.2$, the  $D_min$ is when when $p_{ab} = 0$ ($D_{min} = -0.16$) and $D_{max}$ is when $p_{ab} = 0.2$ ($D_{max}=0.04$).


text:
Can somebody identify this species of spider?
I ran into this cool looking spider in my yard in Banjaluka, Bosnia and Herzegovina.  It's about the size of a fingernail and unusually shaped (spherical). Could it be poisonous?

Location and size would help.

About the size of a finger nail. In Europe / Bosnia and Herzegovina. City Banjaluka.

The white cross on the body makes me think it could well be an Araneus diadematus. It is quite common and not dangerous for humans. It paralyzes its preys using some venom, though.

I agree with Araneus diadematus.  It's a fairly variable spider, but there aren't too many other options that I know of in the area.  Caveat - I'm not completely familiar with European spiders, and it's possible that there is another, similar Araneid in the area that I have not come across.  It's venomous, but like all known orbweavers, it's quite harmless to humans (and, indeed, to anything too large to get caught in the web).
Here's a comparison photo from Bug Guide - the spider in the photo is from the US, but the species is found all across the northern hemisphere.  The link goes to some information, and I've included another link to a good website on European spiders.

https://bugguide.net/node/view/3376
https://ednieuw.home.xs4all.nl/Spiders/spidhome.htm


text:
What is the meaning of "E-value" in the BLAST search?
After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that?
https://en.wikipedia.org/wiki/BLAST
This expectation or expect value "E" (often called an E score or E-value or e-value) assessing the significance of the HSP score for un-gapped local alignment is reported in the BLAST results.
If a lower E value means closer results to the query sequence, what is its difference to "Sequence Identity Cutoff"? http://www.rcsb.org/pdb/search/advSearch.do?search=new

You can find the definition here:

the number of hits one can "expect" to see by chance when searching a
  database of a particular size.

Also read some of the background information given to understand the meaning:

It decreases exponentially as the Score
  (S) of the match increases. Essentially, the E value describes the
  random background noise. For example, an E value of 1 assigned to a
  hit can be interpreted as meaning that in a database of the current
  size one might expect to see 1 match with a similar score simply by
  chance. The lower the E-value, or the closer it is to zero, the more
  "significant" the match is. However, keep in mind that virtually
  identical short alignments have relatively high E values. This is
  because the calculation of the E value takes into account the length
  of the query sequence. These high E values make sense because shorter
  sequences have a higher probability of occurring in the database
  purely by chance. For more details please see the calculations in the
  BLAST Course. The Expect value can also be used as a convenient way to
  create a significance threshold for reporting results. You can change
  the Expect value threshold on most BLAST search pages. When the Expect
  value is increased from the default value of 10, a larger list with
  more low-scoring hits can be reported.

If you want to understand the calculation I would highly recommend to read the BLAST course
Update
Identity is not the same as the E value
I would try to explain this as easy as possible so let's suppose a sequence:
query sequence: ATGCCGTGC

When you BLAST this (of course your sequence is much longer), you can get the sequence ATGCCGTGC, which will result in 100% identity (NOTE most of the time when you have 100% identity, you have the right sequence but I just picked 100% to make the difference clear. When you have lower percentages of identity the E value is much more important. So when you have 70% identity in different matches e.g. it is important to look a the E value to decide which match is the "right" one for your purpose), now you probably would think that's nice that's the sequence I was looking for. However this would be a mistake! Maybe this sequence is present many times in the database and this is just a random match, this is the point were the E value comes in. Looking at the E value this would be pretty high because you have a short sequence and the chance of matching this in a big database is really high so you can get an E value of let's say: 10. What this means is that you have a chance of finding 10 matches by chance when searching a database of a the current size in other words this match would probably be random! So it's much better to conclude if a match is "significant" based on the E value cut-off than on the identity. Further the choice of the E value is completely yours as said by WYSIWYG♦ as answer to a cut-off question:

E-value refers to the expected number of random hits for a given
  alignment score. Smaller it is more reliable is your match. There is
  no hard and fast rule for e-value cutoff. You can keep whatever you
  want depending on the level of stringency that you require. But you
  should note that for smaller sequences (< 30nt) there is always a
  higher likelihood of random matches. In such cases it is practical to
  relax the e-value cutoff.

Short simple example

Both of these sequences got the same identity but a different E value. What does this mean? Both of the sequences match the same amount(57%) of the amino acids however based on the E value you can say just as you said that the first match is less likely to be a false positive. I want to note one thing: Always take a look at the biological significance of your result. E.g. you extract proteins from a red blood cell and find proteins with a high E value for red blood cell proteins and a low E value for proteins from nerve cells. It's clear that despite the high E value the red blood cells are probably more biologically significant.

I re-edited the question. I feel that "E-Value Cutoff" and "Sequence Identity Cutoff" are the same? Also to clarify, the "hit" means the resulting sequences by BLAST? I think I do not need to know the details of the algorithm. I just want to know how the set the threshhold.

yes the hits are just the result sequences of BLAST, I updated my answer to clarify the difference between identity and the E value @ianselibai

thank you so much! I think I understand most of it. So it reduces the random hits. In that case, the lower of the E-value, the less likely for the "false positive" hits.

It doesn't really reduces the hits but it helps to make a choice about the significance of the hit, just as you said if the E value is low it's less likely that this match is a false positive. So in simple terms: the E value scales your score (based on identity and other factors) so that you can compare this to the other matches. I added a little example in my answer hopefully that will make it clear!

Sure, so for your "Short simple example", I guess, the first one is shorter than the second one?

I just closed the result but that's what you would expect indeed! However there are other scaling factors which can influence this but for that you should read the BLAST course

Sure, I use E-value = 0 to search, still can get hundreds of hits. Thank you for all your help!

If you want to restrict the matches you can try to use other scoring matrices and other parameters.

On the RCSB website, I can only increase the "Sequence Identity Cutoff".

try to use the offical BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi But you need to search some information about the paramters if you want to change these

sure, temporarily I will use RCSB