text:
Do cancer cells use as much NADH as normal cells?
Recent literature shows that cancer cells have a different electron transport chain mechanism from normal cells and both of cancer cells and normal cells use NADH as electron donors. So, is there a difference in the number of electron donors required between cancer cells and normal cells? What possible mechanisms could explain this difference?

Reference:
Huang, Huaiyi, Samya Banerjee, Kangqiang Qiu, Pingyu Zhang, Olivier Blacque, Thomas Malcomson, Martin J. Paterson et al. "Targeted photoredox catalysis in cancer cells." Nature Chemistry 11, no. 11 (2019): 1041-1048.
Kim, S. Y. (2018). Cancer energy metabolism: shutting power off cancer factory. Biomolecules & Therapeutics, 26(1), 39.

Could you please explain in your own words what is proposed. It is not apparent from the figure and “different ETC mechanism” conjures up some alternative form of the various complexes, which is highly improbable. I am not going to read the original paper to find out — questions here should be comprehensible in themselves.

Also see Warburg effect. http://en.wikipedia.org/wiki/Warburg_effect_(oncology)

"MAS" (according to one of the papers you quote) is the malate-aspartate shuttle. That is, electrons from cytosolic NADH cross the mitochondrial membrane, but the inner mitochondrial membrane is impermeable to NAD(H), a key point not very clear from your diagram/description

Short answer:
Yes, NADPH is definitely enriched in cancer cells, since cancer tends to rely more on glycolysis. That way, much less NADH is consumed into the electron chain. It was even proposed to treat cancer using NAD+ precursors to shift NAD/NADH balance: Santidrian et al. 2013

Tumor cells also generate high levels of reduced forms of NAD+, NADH, and NADPH as important cofactors and redox components (4, 5). These altered metabolic activities can be linked to mitochondrial dysfunction that inhibits OXPHOS, increases ROS, promotes uncontrolled growth, and causes DNA damage that further supports a metastatic phenotype

The energy metabolism in cancer might be one of the most skewed and dysregulated aspect of any cancer cell.
One reason is actively discussed: Hypoxia. Cancer grows. Fast. Faster than blood vessels can grow into the tumor to support it with oxygen. So the tumor is constantly suffocating. That's why cancer relies on oxygen independent metabolism (Glycolysis, aka the "Warburg effect"). In the later stages of cancer transformation however, it seems that a cancer cell can re-activate oxidative phosphorylation (OXPHOS, or mitochondrial electron chain with oxygen as terminal electron acceptor).
This review (Zheng 2012) name some very interesting reasons why that is the case:
Glycolysis yields more metabolic precursors for growth

i) Glycolysis is more suitable for cancer growth. Since proliferation of cancer tissues is faster than normal tissues, it not only needs energy, but also needs metabolic intermediates for the biosynthesis of macromolecules. Many intermediates from glycolysis and the truncated TCA cycle can be used to synthesize macromolecules, such as nucleic acids, lipids and proteins, which are required for cancer growth and proliferation (2,30).

Glycolysis generates Energy Quicker (despite being inefficient)

ii) Too efficient products of ATP may not a good thing for cancer cells. If cancer cells use high-efficiency glucose, ADP is converted to ATP. The high concentration of ATP will inhibit phosphofructokinase 1 (PFK1), the rate-limiting enzyme in glycolysis and pyruvate kinase 1 (PK1), and glycolysis will be inhibited. Inhibited glycolysis is unfavorable for cancer cell growth. Although glycolysis yields less ATP than OXPHOS, the speed of ATP generation in the former is quicker than in the latter, which is suited to the energy demands of rapid proliferation tissues such as cancer and embryonic tissues (11). Generally speaking, rapid proliferation tissues rely more on glycolysis for ATP production whereas differentiation tissues rely primarily on OXPHOS for energy production (13,31). If using glycolysis inhibitor 3-bromopyruvate (3-BP) treats tumors, it is more efficient for rapid growth of tumors than slow growth of tumors.

Glycolysis enhances Invasion

iii) Hypoxia is often observed in cancer tissues, and glycolysis offers growth advantage of cancers under this hypoxic environment (4). Glycolysis produces lactate which is released into the extracellular space. An acidic microenvironment provides a growth advantage to cancer tissues over normal tissues and enhances the invasion and metastasis of cancer cells (32,33). In addition, lactic acidosis inhibits glycolysis and favors aerobic respiration as a means of energy generation (14).

Glycolysis is less Cytotoxic

iv) Due to the decrease of mitochondrial OXPHOS, less reactive oxygen species (ROS) are generated, which are cytotoxic to cancer cells (34,35).


text:
Koshi and Goldstein substitution matrix
In their article (Context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)), more precisely in the substitution matrix displayed in Figure 2, one one hand, the legend says:
"Graphical representation of the probability of a mutation from the amino acid in a given row to that in a given column during an evolutionary time of 40 point-accepted mutations per 100 residues"
And on the other hand, I've noticed it is a lot more likely for an amino acid to be deleted than to be inserted (cf. screenshot, blue is low probability, orange/red is high probability).

Taken from: context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)
How could one explain that? If that was true, all proteins sequence would slowly become smaller and smaller, right? Is it because it doesn't consider when proteins sequences merge? (I'm no biology expert, I'm sorry if the vocabulary I'm using is not exact. You are encouraged to correct me).

You should always provide a complete citation; "Koshi and Goldstein" can be one of a number of papers, and you shouldn't leave it to your reader to guess, nor should you reproduce figures without a proper reference to where it came from.

I have made the necessary adjustments in my question. Thank you for your insightful feedback.

Year is helpful but still not a complete citation. You'll want the title, journal, page numbers; these days a DOI is a nice add. And "Koshi-Goldstein" makes it appear like you are talking about one person with a hyphenated surname, not two.

It seems that there IS a deletional bias across genomes Kuo & Ochman 2009:

Based on over 5,000 indel events in noncoding regions, we found that deletional events outnumbered insertions in all groups examined.

That would be one mechanism of genome shortening. However, there are mechanisms that also increase the size of the genome:

DNA polymerase tends to do "replication slippage". That's when DNA polymerase detaches from the DNA during replication and re-associates upstream. That way, whole genes can get duplicated (which is also a driver of evolution, since there‘s a second copy to mess around with)
Transposable elements (ancient viral sequences) keep replicating and re-inserting into the DNA.
Overall, natural selection keeps genes at full length and functional

So although small edits tend to be on the deleterious side, big edits are the opposite, causing an overall expansion of the genome.

Worth considering selection, too. Populations need not follow mutational biases if selection favors something different.

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Is there any reagent that can help me obtain the protein in a 14 μm tissue without damaging the morphology of the tissue
I need to extract proteins, but I want to protect the morphology of the tissue. Can I use lysis buffer directly？

The morphology of tissue is due in large part to proteins. Trying to extract them with lysis buffer will destroy the tissue.

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What is the the meaning of Coordinated effects in genetics?
I want to find the definition of Coordinated effects
in the paper enter the matrix link the author defines "Complex biological process" as

coregulation or coordinated effect of multiple molecular species resulting in one or more phenotypes. Examples can range from activation of multiple proteins in a single cellular signaling pathway to epistatic regulation of development.

I gathered that coregulation refers to the Transcription coregulator link

In molecular biology and genetics, transcription coregulators are proteins that interact with transcription factors to either activate or repress the transcription of specific genes.

But the term coordinated effect eludes me. Does it refer to the Coordination complex? And what is the context in biology? Several papers mention the coordinated effect but fail to define what it is.
Biology and genetics are new to me; I need more understanding of the general field. Naturally, the term might be standard, but it is just puzzling.

You deliberately omitted the second half of the author's definition: "Examples can range from activation of multiple proteins in a single cellular signaling pathway to epistatic regulation of development." If you are right, that the term is only used by these authors, then what is your problem? Within this paper, just stick to the author's definition.

Quite the assumption that I deliberately did that. That I would say is quite presumptuous. Moreover examples are not definitions. They might outline key factors but this is no definition

You're right, examples are not definitions, they're usually better than definitions.

It's the definition the authors use in their glossary, which itself is defined to be a collection of definitions (https://en.wikipedia.org/wiki/Glossary). Ergo you only provided half of their definition, which is a misrepresentation. I didn't say that you deliberately misrepresented the authors, simply that you deliberately omitted part of their definition. I don't see how you can argue against any of this.

Interesting point. My questions was not the term "Complex biological process" but the term coordinated effect. Even with brain krause comment an example is better than a definition. my argument still holds that the term coordinated effect is not defined in the paper and merely an example was given. Finally, arguing that examples are better do not help the reader understand the term. @acvill actually explained the term in the context

Coordinated, here, does not connote any special meaning above that of its English definition, nor is it referring to coordination complexes. Consider one of the definitions of coordination from OED:

Harmonious combination of agents or functions towards the production of a result

In your linked paper, the authors are using coordinated effect to refer to the cooperative or synergistic influence of multiple molecules or processes on a phenotype. I think this is most easily understood in contrast to the simple models of genotype-to-phenotype mapping that are often taught in introductory genetics courses, i.e. a single gene variant encodes a single factor that produces a fixed phenotype. A complex biological process is one in which the abundance, activity, and localization of different molecular components have an effect on the magnitude of a phenotype.

cheers! very well put. clear, concise and nicely outlined with comparison to the English dictionary. There are still concept that need to be explored but an overall great outline.


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Is it possible to change an amino acid within a protein but not affecting that protein's functions?
In the answer(source - Campbell Essential Biology with Physiology, self-quiz question), it's given that "if the change doesn't affect the protein's shape in any way then it's possible to do so". But practically, is it possible to amend a protein without changing its shape?

@danieldelrey I honestly have zero knowledge
I've never studied biology before( as my subjects are maths, electronics, thermodynamics, mechanics and computer science ) but my school is forcing us to and now it's getting really difficult to understand things for me
So I just need it to pass my exam

Not only can it happen it is one way we study what are the functional components of a a particular protein . https://www.ncbi.nlm.nih.gov/mesh?Db=mesh&Cmd=DetailsSearch&Term=%22Amino+Acid+Substitution%22%5BMeSH+Terms%5D#:~:text=The%20naturally%20occurring%20or%20experimentally,enhance%2C%20or%20eliminate%20protein%20function.

What the authors are describing here is the idea that function follows from form.  Meaning that a proteins 3D structure is, in many ways, responsible for it's actions.
And yes, it is possible to change a residue without changing the proteins shape.  For example, changing a residue that resides on the outside of the protein from a positively charged one like Lysine to a positively charged one like Arginine (both residues are very similar) will not have any effect on the structure of the protein, in most cases. Same thing when changing an Alanine to a Valine: they are so similar to one another that it would be difficult to find a case where swapping them would cause the protein to change shape or for its function to be destroyed.

Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center.

@danieldelrey - There are proteins which are intrinsically disordered (https://en.wikipedia.org/wiki/Intrinsically_disordered_proteins) or that contain regions which are intrinsically disordered. In these cases it is the lack of a stable 3D structure that is responsible for their action.

@danieldelrey - When the original poster is asking about a proteins shape or conformation he's referring to a stable structure that persists through time (vibrations and all).  Of course the 3D structure of anything physical is responsible to some extent for its function, but that's a useless definition and irrelevant here.


text:
Help identify parasitic plant on oak seedling
See pictures below. I found five of them on a patch of oak seedlings in northern Turkey yesterday, they are about 2 centimeters in diameter and smell like grass.

Five months later:

I tried PlantNet and Google Lens before asking but nothing came up.

I've asked several botanists from North Caucasus, none of them know. Considering that it's green, it must be hemiparasite, like Viscum.

I wonder if these are galls formed by an insect. That may be who made the hole in the bottom in the third photo.

@JohnPolo Thank you both, I'll take a look.

I think these are galls produced by a wasp in the genus Andricus.
Here are some produced by A. polyceras:

However, there are many species in this genus so more detail would be needed to narrow it down.

This looks very much like it, thanks. What more detail would you like me to provide?

I'm not familiar with this group, but a positive ID might require dissecting the galls, or capturing the wasps that emerge for inspection. The other most similar species I saw was A. quercustozae, but most of the photos showed much more bulbous galls. I didn't see any with the really narrow bases that your photos show.

The oldest relatives of these found in amber are from about 50 million years ago. They inject up to 70 active mutagens and viroids that hey use to control hosts.

Couldn't find any more galls to dissect. I'll go ahead and accept your answer, thanks again.


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Identification of cellular membrane damage using a microscope and gram stain
I am observing E.coli under a microscope at 1000x with a gram stain, and I was hoping to identify potential cells with cellular membrane damage.
In my experiment, I had a negative control sample of E.coli and a positive control with penicillin. Both samples were on slides which were then stained and viewed. I know that penicillin would kill the bacteria but I was hoping to see some damage on the bacteria through a microscope.
Is it possible to identify which cells were damaged by the penicillin through a microscope?
Negative Control:

Positive control(Penicillin):

Why would you think you might see this? You should check the mechanism of action of tetracyclines...

Apologies, I used multiple treatments so I confused the tetracycline with penicillin. I edited the question and added the new image.


text:
Which reflex arcs work in Heart with extrasystoles?
I am researching what is triggering the extrasystoles - initial idea from this thread about Which ionic channels of Pacemakers can work in very low frequencies in extrasystole?
I am interested in the reflex arc with extrasystoles.
I am not completely sure if the intrinsic regulation of the heart can start specific stimuli.
I have now intuition that not possible.
What are the reflex arcs of the heart?

Not to be fussy about it, but it will help someone searching for your question.

Edits are always welcome :)

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What is the name of systemic tension of muscles?
I meat a overtrained friend (25 years old) who cannot rest.
He has all muscles and most of the skin very tense.
He is practising  regularly in gym and sleep badly.
He moves like a stick figure and has complained pains systemically.
The tenseness have now been some years.
I have met once before such a person who was about 90-year old body builder (male) who never run and did no stretching.
Ageing is not necessarily linked to this kind of tenseness.
I have not seen such tenseness in women.
So I think it is related to the muscles.
Possible pathogenesis. Probable causes of this kind of systemic tension

fibrinous inflammation starting from upper body

etc posterior, medial scapula;
middle inferior posterior clavicula

starting as membranous inflammation
long-term accumulation of fibrin and proteins in lymphatic system in interstitial spaces

proceeding on muscular membranes and through lymphatic system into axillary zone
axillary lymph nodes

deep injury of lymph conduction system as a consequence of decreased lymphatic drainage
proceeding into pseudomembranous inflammation in the upper body

starting from axillary lymphatic system
proceeding back to to the origin through fibrinous membranes as pseudomembranous to other parts (clavicula and scapula)

step by step proceeding into extremities and to lower body

eventually achilles tendon and foot Thian point glympadenopathy
hardening of foot muscles similarly as through upper body

Schematic drawing about the fibrinous inflammation

Possible other causes without citings to literature

right heart failure
systemic hypertension and defect in heart (etc fully patent foramen ovale; got idea from this discussion)

I am interested what is name of this kind of systemic tenseness, probably muscular origin.
What is the pathogenesis of this kind of tenseness?
Why is it systemic?

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How is the nasal secretion system of local immunity coupled with lymphatic circulation?
I started a thread about Nasal chronic Inflammation after influenza virus here.
However, I do not understand enough well the structure of the nose to answer the questions there.
I know that the lysed DNA (proteins) of small bronchial tree are circulated on the nasal epithelium.
I am not sure how this happens but my intuition is

first through lymphatic circulation
then on posterior nasalis membrane upward progression on the nasal membrane in the nares.

Picture about the nasal membrane.

Better pictures about the linkage of lymphatic circulation from the small bronchial trees into posterior nasal membrane are wanted.
However, I am not completely sure how this organisation occurs.
How is the nasal secretion system of local immunity (IgA) coupled with the lymphatic circulation around the back of the nose?

I know that the lysed DNA (proteins) of small bronchial tree are circulated on the nasal epithelium: Do you have a reference for this ?

@WYSIWYG Thank you for your question! This sentence was introduced by one leading researcher in the field last year in London. I contacted him about your question. I hope I can provide it to you.


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How does an engineered supressive Lethal (when present in 2 copies) gene drive spread through a population until causing population extinction?
I understand that at the molecular level a CRISPR mediated gene drive works by copying the altered gene (and the drive containing CAS enzyme, and guide RNA) into the other chromosome containing the wild type allele through homology directed repair...Lets consider  a suppressive drive that is designed to be lethal when the altered gene is present in Both copies of the chromosome (for example maybe organism is likely to die of a heart attack before reaching reproductive maturity)..... In a  lethal suppression drive as described above, Where is this copying  and homology directed repair happening. In the somatic cells of one of the “parents”, or the germline cells of  the parents during meosis/gametogenesis?  What happens when a organism containing wild type allele mates with an organism containing the drive?
If the drive and altered gene is copied in the somatic cells of the organism that was inserted in, then wouldn't the organism perish before, being able to pass on the drive/altered gene (given how our suppression drive is designed being lethal if both copies of gene are present)?
Or is this copying happening during when the offspring is a zygote (thus all off offsprings somatic cells), or the germline of the offspring? If the copying is occurring in the Zygote stage, all somatic cells of the offspring will contain two copies of the altered gene and will be Homozygous recessive for the altered deleterious gene. Then how will the offspring be able to mate and SPREAD the drive before perishing (or not being able to reproduce).
How is it ensured that drive copying only occurs during gametogenesis and does not alter the somatic cells in either parent or offspring? Because it seems to me for the drive and the altered gene to spread it can only happen during meosis/gametogensis...

Have you read, for example, the Wikipedia article on gene drives, or review articles like this one or this one?

Yes I read the Wikipedia and review article Did not quite clarify where and when the homology directed repair/copying is occurring for a suppressive gene drive.., Let us consider a suppressive drive that is supposed to kill organism before reaching reproductive maturity.  Is this occurring during gametogenesis of the organism that contains the drive? Because in suppressive gene drives having TWO copies of the deleterious gene kills the organism, but one copy is benign. So if HEG/copying is happening in the somatic cells wouldn't the organism just die before able to pass gene?

Crossposted on Medical Sciences SE

I have closed the copy on Medical Sciences as I believe it is a better fit here.

@MattDMo I think an answer based on those sources would be excellent.


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Production method of custom seed mir451? How to edit middle of a fragment?
I am trying to create a plasmid that produces mir451 targeting a new gene, so I need to alter the seed sequence. The seed sequence is 7 bp long, so I think that is too long for PCR mutagenesis. How do people generally alter sequences that would be in the middle of an amplicon? Buying it from gBlock or something is an option, but if I need to try multiple permutations that could get really expensive quickly. I haven't done any synthetic biology in a long time so sorry if this a basic question or it doesn't make sense. Thanks

I think 7nt is ok for site-directed mutagenesis, see older question here.
The size constraint comes largely from being able to have enough flanking homology 5' and 3' of the substitution on your primer (e.g. Figure 1 here). This provider suggests >=10nt of 3' homology, this other provider suggests at least 11nt on either side.
gBlock is almost certainly the fastest and removes the experimental error side, but if you need to screen a lot of combinations SDM seems workable.

Thanks that's helpful, I'll probably go with gblock first then maybe try SDM to test sequences if its cheaper


text:
Is it viable to make liquid potassium ferilizer through dissolving very small amounts of potassium chloride in water
I wasn't able to find fertiliser online that was simply potassium chloride and I didnt want to source my potassium chloride solution from potassium sulphate or other general NPK fertilisers for my experiment on the effect of varying K+ concentrations on a plant. maybe 50,100,250,1000 ppm solutions. Or is there another element or component of fertilisers, perhaps compounds that lead to nurtient intake that I am overlooking in my methodology

If you have potassium sulfate (or carbonate) you can precipitate using Calcium salts (nitrate etc). Not all, just most.

the issue here is the chloride not the potassium.  Potassium chloride is very soluble in water. but you could be killing your crops/garden when you spray it on.
Most plants do not tolerate much Chloride ion.  With a limit of 500mg/kg of chloride in soil you will not be able to use much of this stuff.
that's wny potassium phosphates are much more desirable.  the phosphate will be consumed by the plants.


text:
Are afterimages centrally regulated?
As I understand, negative afterimages might be induced by retinal cone bleaching or neuronal adaptation. I have heard that some experiments have suggested that afterimages can be centrally regulated. Is this true, and if so, what is the evidence?

I’m voting to close this question because it is not a question about a problem in biology, but a request for literature about a subject. This would have been obvious if you had finished the [Tour], as one would expect of new users to this site.

Welcome to SE biology.  Generic queries and requests for literature reviews aren't in scope for the forum. If you have a specific question you could edit this or post a new question.

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.

@David asking for help with literature is neither listed on the "do" list nor on the "do not" list. I do not know if it was my question that necessitated your tone or something else.

@Michael_A thank you! I updated my question, hopefully, brought it into the scope of the forum.

@aninstance The scope is much better, but we expect questions to be supported with some prior research. So, when you say you understand something to be true, it's best to provide a citation/reference where you found that information. When you write "I have heard that", it's best to specify where you've heard and what specifically was said. Probably also worth clarifying what you mean by "centrally", as the meaning of "central" depends on your point of reference.


text:
How do shoot apical meristems know which leaf arragement to set out based on DNA?
Shoot apical meristems are responsible for leaf and stem growth.
However when developing, how does the meristem develop the arrangement of the leaves? Like, alternate, opposite, whorled or basal.
Ive tried to search for any answers but to no answer.

Very briefly, leaf growth inhibits the growth of newer leaves.
Aspects related to this inhibition (distance from the old leaf, inhibition over time, architecture of the growing shoot, etc.) influence where on the stem the next leaf will appear. By varying the details of these parameters, one can model leaf arrangements that match most of the common leaf arrangements found in nature. Presumably there are genes that control aspects of these parameters.
https://phys.org/news/2019-06-unusual-japanese-recalculation-equation-leaf.html
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007044


text:
What is the area around a plant that is under its phytochemicals/secondary metabolites influence?
Is there a dilution threshold as a function of distance or some general measure regarding the area around a plant that is under the influence of its phytochemicals?
I'm looking for a objective value so I can proceed with a sample of aquatic macroinvertebrates in this area. I know it is something difficult to determine because of n factors, though any general, peer-reviewd information would be appreciated.

Welcome to SE Biology. This question is interesting but currently too broad to answer. Rewording to a specific plant (or group of plants), phytochemical, and aquatic macroinvertebrate (or group) might help.

I was pretending to address the effect of secondary metabolites from the white ginger lily (Hedychium coronarium) on aquatic entomological fauna according to different distances/buffers, expecting to find some threshold for functional diversity or other response variable. This is still an incipient idea that I need to refine.

Your comment has the kind of information that we would need to answer the question, directly including it in the question usually works best for useful answers. Also, you will need to directly @  for them to see your comment. Though that is also not working so well for me here for some reason.


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What is the difference between a semi-permeable membrane and a selectively permeable membrane?
What is the difference between a semi-permeable membrane and a selectively permeable membrane in cell biology? Is a selectively permeable membrane a type of semi-permeable membrane? Please help.
I think the semi-permeable membrane allows passage to only solvent molecules while a selectively permeable membrane permits the movement of solvent molecules along with some selected solutes. Am I correct in my understanding?

Welcome. I can understand your confusion, but there is a lot online about this. Using your exact phrasing, the top Google hits explained the difference. What do you understand about each type of membrane? (Asking to understand exactly the point where your confusion starts.) What were your search terms? If English is your first language, how do you understand semi and selective in general? Please click the edit button to include details and a quote from one of your sources. Thanks!

Not quite. Semi-permeable membranes permit diffusion of anything limited only by size. Anything bigger than the pore size can't pass (there are different pore sizes in different membranes.) Selectively permeable membranes allow certain select molecules/substances to pass and nothing else, independent of size. They are made to allow a particular substance to diffuse through. Does this answer your question?

Yes, thank you very much.


text:
Identify a spider which is consuming a fly
can you please identify this spider which was found on indoor banana plant eating(?) a fly?
Located in central europe - Czech Republic, Moravia region. Photo taken in April 23rd. Banana plant is located indoor, behind the window facing southwest side. 228m above the sealine. Googled "webless spiders" but couldn't find anything similar to this one.

Please [edit] your question and add some details like: when did you see this? What time of year? Can you be a bit more precise than "central Europe"? How about habitat? Was this in a house? On a mountain?

Please edit your question to begin title and sentences with a capital letter. This is the form in both English and Czech.

This is something in the Thomisoidea family (Crab and Running Crab spider superfamily).
You can review the community-observed species of crab and running crab spiders in Czechia here: https://www.inaturalist.org/observations?place_id=8264&subview=map&taxon_id=367176&view=species
The two stripes down the carapace are unlike Philodromus, where the stripes in Philodromus are at the edges of the carapace while in this photo, there is clear space between the stripes and the edges of the carapace. In North America, I would has assumed this was Mecaphesa (in the Thomisidae family), but Mecaphesa does not seem to exist in Europe.
But Europe (and Czech, in particular) has the Triangle Crab Spider (Ebrechtella tricuspidata) (this genus does not exist in North America). This Triangle Crab Spider has the same key indicators as in this given photo: short - almost dwarf-like - hind legs. Brown-striped front legs. Green abdomen. Two stripes down the carapace with remaining spacing on the outsides.
This photo was observed in Czechia:

The observation and identification can be found here:
https://inaturalist.org/observations/61869636

thanks for an answer. so according to photos here: https://en.wikipedia.org/wiki/Ebrechtella_tricuspidata the example on the photo should be male, right?

correct. Here is a gallery of males: https://www.inaturalist.org/taxa/360081-Ebrechtella-tricuspidata/browse_photos?quality_grade=any&photo_license=any&term_id=9&term_value_id=11&layout=grid&place_id=97391
and here is a gallery of females:
https://inaturalist.org/taxa/360081-Ebrechtella-tricuspidata/browse_photos?quality_grade=any&photo_license=any&term_id=9&term_value_id=10&layout=grid&place_id=97391


text:
Why is there a negative sign before voltage in the gate variable functions of the Hodgkin-Huxley model?
In Hodgkin and Huxley's articles (1952, J. Physiol.; 1990, Bulletin of Mathematical Biology), the gate variables are formulated as

In particular, as $V$ increases, $\alpha_n$ decreases and $\beta_n$ increases, as shown below:

However, in many other textbooks, e.g., Spiking Neuron Models and Fundamentals of Computational Neuroscience, as well as quite a few websites like HHsectionOnly.doc (illinois.edu) and Hodgkin-Huxley Model | SpringerLink, there is always a negative sign before $V$.

I CAN'T UNDERSTAND why there should be a negative sign. If so, the monotonicity of $\alpha_n$ and $\beta_n$ will be inverted, which is not the real case.
What makes me even more confused is, when I remove the negative sign, I cannot obtain valid results through programming.
In a word, I wonder why there should be a negative sign before the voltage. What's its physical interpretation? Thank u in advance!

Voltage is a potential difference. Membrane potential is a difference across a membrane. When you calculate a difference A - B or B - A, you get a number that has the same magnitude but opposite sign. So, if A is inside a cell and B is outside a cell, how do you know if the difference should be noted A - B or B - A? The universe won't tell you, you've got to make a decision. It's helpful if everyone makes the same decision and it becomes a convention.
These sorts of conventions are everywhere in physics: there's no real reason that protons shouldn't be thought of as "negative" and electrons as "positive", for example. All the math works out the same way, but it's helpful if the whole field uses the same convention.
Similarly, the field of neurophysiology has settled on thinking about things from the perspective of the inside of cells. That means, by convention, when we say a membrane has a "negative" voltage, we mean that "inside is negative relative to the outside".
Hodgkin and Huxley initially used the opposite convention in their experiments and papers. There's nothing right or wrong with that, but it means if you are using the typical convention that a "negative membrane voltage" means there is more negativity inside the cell versus outside, you'll need to multiply voltage by -1 when you use the original HH paper equations. See also e.g. http://nelson.beckman.illinois.edu/courses/physl317/part1/Lec3_HHsection.pdf - search for "sign conventions" for the relevant discussion.

Thank you Bryan. You really helped me a lot.


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How to calculate the osmolality of Hepes solution?
Here is an excerpt from Kollmann et al. (2020, J. Physiol.):

This ring was placed in a recording chamber continuously perfused with 37°C aerated Hepes solution containing (in mM) 136 NaCl, 10 glucose, 5 KCl, 10 Hepes, 1.2 MgCl2, 2.5 CaCl2 (pH 7.40) at a rate of 11 ml min-1. Hypoosmolality of the Hepes solution was established by reduction of the NaCl content to 33 mM (94 mOsm kg-1 H2O), 58 mM (144 mOsm kg-1 H2O) or 83 mM (194 mOsm kg-1 H2O).

For validation, I tried to calculate the osmolality by myself. For example, when the NaCl content is changed to 33 mM, the osmolality should be
$$
33\times2~(\mathrm{NaCl})+10\times1~(\mathrm{Glucose})+5\times2~(\mathrm{KCl})+10\times1~(\mathrm{Hepes})+1.2\times3~(\mathrm{MgCl_2})+2.5\times3(\mathrm{CaCl_2})
$$
which gives 107.1 mOsm/L, i.e., 107.1 mOsm/kg. But 107.1 is largely different from what the author stated, namely 94 mOsm/kg.
When the NaCl content is changed to 58 mM or 83 mM, the osmolality should increase by (58-33)*2=50 mM, or (83-33)*2=100 mM. This is consistent with the author's calculation, i.e., 144-94=50 mOsm/kg, or 194-94=100 mOsm/kg. So, my calculation is correct at least in terms of NaCl. But how can I calculate the contributions of the remaining solutes correctly?
Reference: Kollmann, P. et al. Submucosal enteric neurons of the cavine distal colon are sensitive to hypoosmolar stimuli. J. Physiol. 598, 5317–5332 (2020).

I assume this is a measured osmolality rather than a calculated one. It's challenging to calculate actual osmolality because of incomplete dissociation of the solutes, see for example https://en.wikipedia.org/wiki/Osmotic_coefficient. There's also a subtle difference between osmolality (particles per mass) and osmolarity (particles per volume).
I believe HEPES can contribute to this effect because it will bond with free ions. Sugars do, too. The gap still seems a bit larger than I'd expect, some of that might involve the temperature of water when originally mixed versus when measured. If you're trying to replicate their methods, I'd get yourself an osmometer.


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Relation between image on retina and the real one: looking at the two objects that are 45 degrees apart, what's the distance in the actual image?
These are what I understand about the vision.

lights come through the pupil.
an inverted image of the real objects is formed on the retina. which is determined by the angles.
(so (a, d) and (b, c) look the same)
the retinal image is tiny(about 3~5cm?) and inverted.
our vision is somehow flipped and magnified version of the image on retina.

My question is: what's the relation between the actual angle on the objects and the distance appeared in the real vision. As shown above, what's the distance between two objects which are 45 degrees apart? On the retina, we can calculate the distance between the image of the two dots which are 45 degrees apart(for example, the image formed by a and c), but how do we know the distance between two dots on the real vision?
In short: What's the magnification rate? between the two(image on the retina and the actual vision)?

Usually we measure that distance on the retina just in terms of "degrees". For the rest of your question I think you actually just want to read about depth cues, specifically monocular depth cues. There are some existing questions here on that.

On your sketch, draw also the other eye next to the existing one, and repeat the drawing of light rays and image on the retina. This will help you understand how we can reason about depth and distance between objects.


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Why are deformable cancer cells associated with being more malignant or dangerous?
So I was watching a lecture that talked about circulating tumor cells/cancer stem cells, and the professor mentioned that deformable cancer cells tend to be more dangerous to us. Why is this so? Does it have to do with the cells' physical ability to metastasize or intravasize better? Is it possible deformable cells are more resistant to drug therapy? (The latter suggestion sounds kind of crazy to me but if anyone has insights, a potential answer, or a research paper on it, I'd really appreciate it!!)

What was the exact term the professor used? "Squishy cancer cells" is unlikely to yield good results on searching. Try deformability and metastasis.

I don't know for sure, but it could be something similar to what happens to RBCs where continuous peroxidation takes away their deformability so they break more easily and are taken up by macrophages when they get old. Deformable cancer cells may be similarly more stress resistant.

essentailly those cells are "stickier" because they are deformable and can adhere to a new site to begin growing easier. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386247/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386247/


text:
Found these bugs on a sticker in an old shoe box. What are they?

What are these bugs? I found them in an old shoe box on a sticker that was sitting on the carpet.

Hi, those pictures are really blurry. It would be helpful if you tried to take better photos, also with a scale to have a better understanding of their size.

I updated the photos, hopefully that is easier to see. Thank you!


text:
How does photosynthesis work exactly?
How does light reach the photoreceptors in plants? Does it need to travel through the plant or are the photoreceptors on the surface of the plant ?

I'd like to see that video. Can you please provide a link?

Quantum superposition has nothing whatever to do with time travel. You may have misunderstood what they were saying, or the video is tending towards the science-fiction end of things. Either way, it' doesn't sound like a good starting point for educating yourself about photosynthesis. As above, start with the Wikipedia article, then [edit] your question with what you need to ask.

@JiminyCricket  The title of the video is “we are from the future” and if it is true that the photons are put into a state of quantum superposition then technically it is like time travel, because all the possible realities where the photon should collide with other particles will collapse, & not occur, so rather than time travel it’s more like future assurance, all possible realities in which it does not reach its destination do not become actual therefor it has already reached its destination before it gets to it

@anongoodnurse https://youtu.be/15pOr1E6hvc

Thanks, @KeeganDavidson! That was interesting. I agree with Jiminy Cricket above; on the sci-fi spectrum. :)

The main thing about the video that is incorrect is the framing - the plants don't put the photon into quantum superposition and cause time travel of the information (nor are they near perfect efficiency)! It's a simple probabilistic function for the photo to reach a chlorophyll/photocentre. Yes, you could very weakly argue that "oooh we don't know where the photon is because it's quantum" which is sort of true, but it's much simpler than that. Lets imagine you had a million tiny ball bearings and a large board with lot of holes in it. Throw all the ball bearings at the board... cont

cont... Some hit and bounce off, a few go through the holes. The board is your leaf and the ball bearings are your photons. You must remember from basic atomic structure that atoms are mostly space - according to Dr Google, a Hydrogen atom is 99.9999...% space; if you could enlarge it to the size of the earth, the core proton would be about 200 m/600' (2 football fields long) across and the electrons circling around on the circumference of the earth. The forest analogy is more like running through the area of 37 football fields with 1 tree in the middle.

Scientific American has a helpful blurb, and here is part 1 and part 2 of a review about quantum effects in the light harvesting complex. It seems as though the chromophores in a complex can have quantum coherence, which does, indeed, lead to transfer of the photon energy from the harvesting complex to the reaction center with "nearly 100 percent efficiency."

The photoreceptors relevant to photosynthesis are the light-harvesting complexes. These are found embedded in the thylakoid membranes found within chloroplasts. To reach the thylakoid membranes, light from outside the plant must pass through the cell wall, cell membrane, cytoplasm, both membranes of the chloroplast, and some amount of chloroplast stroma. If the photosynthetic cell is not on the surface of the plant, the light would also need to pass through some number of intervening cells.


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Overlapping annotated regions among repetitive families of human genome
I am studying the repetitive elements in the human genome and I have come to know that some genomic locations are not uniquely described by a single repeat family. What's behind this uncertainty? Does it account, for example, for the variability among individuals? or is it a fact deriving from the limitations of our current technology?
The reason behind this question is a practical issue. My team is analysing the composition of some sequencing data and is mostly interested in the repetitive elements of human DNA. I can use the repeat masks that I download from UCSC database and count their abundance. My problem is that some repeat masks overlap at specific locations in the annotation track.

Welcome to Stack Exchange Biology. Please finish reading the [Tour] and then consult the Help on Asking Questions. I think that your question desperately needs clarification with an example. When you present your example be sure to provide a link. Without this I am not sure what you are talking about.

Can you give some motivation of why regions would be covered by a single annotation? For example, a coding portion of a gene is annotated as a gene, a transcript, an exon, and a CDS. That's 4 distinct annotations! If it's a transposase, it will also be annotated as a transposon, for 5 annotations. Having overlapping annotations is to be expected. I supposed you might mean repeat family annotations, but similar logic applies. Recombination of repeats etc. is rampant: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/, https://www.biorxiv.org/content/10.1101/2020.07.02.163816v1.full

Yes @Maxilimiam, I meant repeat_family_annotations. If I understand it correctly, you are alluding to the fact that some repeat families are associated to transposons elements and, as consequence of that, they are 'mobile' elements of the genome so it makes sense if some genomic locations can have multiple annotations.

@David, thank you for the clarification!

@AVO on the order of 50% of the human genome is repeats. Of that, >80% of the repetitive contents are mobile genetic elements (MGEs; see Table 1 of linked paper). So yes, when you talk about "repetitive DNA" you are generally speaking talking about MGEs. But the logic is actually that depending on what you mean by "annotation", you might have the same element annotated as a LINE, a SINE, an Alu, etc. (all MGE types), because these are sometimes chimeric or recombinant.


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How to deal with sample size and replicates
I need to perform several replicates of an experiment, say I have 3 treatments and 4 replicates. After performing the calculation of the sample size, I get n = 100 samples needed. This means that for each replicate I need 100 samples or can I split the samples among my replicates (i.e., 25 samples per replicate)?
Thank you.

Usually, if you want to draw conclusions about a population, we use representative samples which are adequately sized (sample size) and reflects all the features of the population. If calculations say that the sample size should be 100, we need 100 data points to make statistical arguments about the population based on these 100 data points (sample size).
You mentioned there are 4 replicates i.e. you counted 4 separate setups and so, if you divide 100 into 4 groups, each with 25 data points, you have, statistically, only 1 replicate with 100 datapoints, not 4.
Please don't forget to bring with you a pinch of salt.
Furthermore, in statistics, a rule of thumb is more the merrier.  In short if you ever get confused in situations like this, choose 100, not 25, in a manner of speaking. Of course your supervisor will wonder why his reagents don't last as long as it used to.


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Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability
I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like form similar to yeast. The species that I'm trying to work with is a gram-negative bacteria called C. Metallidurans. What's pretty cool about this bacteria is its ability to survive in environments that are high in heavy metals and produce pure gold from gold chloride. Any advice helps, thank you.

Lyophilization, aka freeze-drying, is probably the go-to method of microbial preservation without the need for cold storage. It's how bacterial strains purchased from commercial culture collections are typically shipped.
The process consists of first freezing cultures in a lyophilization buffer containing a mixture of cryoprotectant and lyoprotectant excipients, which is exposed to a strong vacuum (while maintaining sub-freezing temperatures) to sublimate the frozen water out of the mixture (source). The lyophilized powder is typically sealed in a glass ampoule filled with inert gas for long-term storage, but can also be packaged in any number of ways to for application-specific uses.
Unfortunately, there's probably not a one-size-fits-all formula that works best for every organisms, but there may be some approaches that are "good enough" for most. Under the right conditions, lyophilized cultures can be stable for years with minimal loss of viability, but I wouldn't count on it without extensive optimization and process validation. Also would not recommend it as your sole method of long-term preservation. Best practice is to always keep glycerol stock backups at -70°C or colder, and to have a plan in place for how often these stocks should be assessed/renewed.

Nice answer. I'd add that it needs some specialist equipment to freeze dry under the controlled conditions needed.

The answer to this strongly depends on the species of bacterium you are working with.
The only ones that I know of that are capable of withstanding any dehydration process are those that form spores. The spores are tough, long-lasting structures that enable the bacterial species to resist environmental changes.
Cupravidus metallidurans, the species you are working on is not a spore-former, so it isn't possible to fully dehydrate them. However, it is possible to form long-term stocks of many, if not all, bacterial species in glycerol and frozen at -80 C (ultra-cold freezer) sort of temperatures.

Most bacteria can tolerate lyophilization under controlled conditions, which essentially results in a desiccated powder. But it's a highly controlled process and the long-term stability of freeze-dried bacteria is more variable than that of frozen glycerol stocks.

@MikeyC true - I completely forgot about freeze drying. I was about to suggest you write it up as an answer, but then saw that you already had.


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Autotrophy vs. Heterotrophy in Chemotrophs
What's the difference between chemoautotrophs and chemoheterotrophs? They do both get their energy from high-energy inorganic particles, right?

"Auto" vs "hetero" in general refers to if they can generate their energy independently or require the consumption of another living thing to generate their energy Introductory Biology, 2.18. In the case of chemotrophs, they gather energy from chemical reactions that are not photosynthesis. The auto & hetero here refer to their ability to synthesize organic molecules on their own, instead of energy Microbiology, LibreTexts 5.1B.


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Did operon evolve after endosymbiosis and specialisation of mitochondria?
We know that all extant bacteria use the operon system as their mode of regulating gene expression, in contrast to eukaryotes, which use individual gene promoters as well as epigenetic mechanisms, supporting the idea that the first eukaryotes came from archaea as the 'host' in endosymbiosis, not bacteria [2]. However, the endosymbiont bacteria is suspected to be a bacterial phylum, supported by various lines of evidence: in short, an archaea enveloped a bacteria to make a eukarya.
An obscure group of protists was found to have mitochondrial DNA that used operon [1], but other than that, pretty much all eukaryotic cells have mitochondria whose mtDNA does not use operon, instead using similar regulatory mechanisms to eukarya including some basic epigenetics (methylation) [3]. A few operons, mainly for nuclear rRNA genes, have been found in chordates. But clearly it is not the norm.
Based on this, it would seem that operon evolved in prokaryotes some time after the endosymbiosis event, since the two are present mostly exclusively in independent domains of life. But recent research finds that operon seems to be fairly primitive (if I am interpreting [4] and [5] correctly) and could have arisen easily as a de novo insertion sequence, suggesting it would have come about earlier.
Does anyone have any expertise on whether this is the case? Did operon or mitochondria come first?
References
[1] Gray MW. Mitochondrial evolution. Cold Spring Harb Perspect Biol. 2012 Sep 1;4(9):a011403. doi: 10.1101/cshperspect.a011403. PMID: 22952398; PMCID: PMC3428767. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428767/
[2] Gautam Dey, Mukund Thattai, Buzz Baum, On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype, Trends in Cell Biology, Volume 26, Issue 7, 2016,
Pages 476-485, https://www.sciencedirect.com/science/article/pii/S0962892416300022
[3] Sharma N, Pasala MS, Prakash A. Mitochondrial DNA: Epigenetics and environment. Environ Mol Mutagen. 2019 Oct;60(8):668-682. doi: 10.1002/em.22319. Epub 2019 Aug 6. PMID: 31335990; PMCID: PMC6941438. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941438/
[4] Yuki Kanai, Saburo Tsuru, Chikara Furusawa, Experimental demonstration of operon formation catalyzed by insertion sequence, Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1673–1686, https://academic.oup.com/nar/article/50/3/1673/6511971
[5] Marco Fondi, Giovanni Emiliani, Renato Fani, Origin and evolution of operons and metabolic pathways, Research in Microbiology, Volume 160, Issue 7, 2009, Pages 502-512, ISSN 0923-2508, https://www.sciencedirect.com/science/article/pii/S0923250809000539


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Why does my cell subculture have these black dots like appearance?
I tried to subculture cells(hek293 cells) for the first time for a Cell Biology experiment, and here are the steps I followed:-
Cell subculture
(*the media is a mix of 10:1:0.1 of DMEM:FBS:Pen/Strep)

If cells are 70-80% confluency, please subculture the cells
Remove media
Add 5ml of PBS and wash the cells by tilting the culture dish few times
Remove PBS
Add 2ml of Trypsin/EDTA and mix well by tilting the culture dish few times
Incubate the cells for ~2min at RT (until cells are detached)
Add 5ml of media and resuspend well by pipetting
Transfer 7ml of Cells/meida/Trypsin/EDTA into a 15ml of conical tube
Centrifuge 300xg for 2min at RT
Remove supernatant
Resuspend cell pellet by tapping the tube 5 times.
Add 5ml of media and resuspend by pipetting
Add 10ml of media into a new 10cm culture dish
Add 1ml of resuspended cells into the culture dish (containing 10ml of media) (1:5 dilution)
Check the cells by a microscope
Put the culture dish into 37oC, 5% CO2 humidified incubator
Check the cells every day, and when cells are 80~90% confluency, do subculture.

I followed all the steps above to a T, and here is the cell culture under a microscope prior to culturing-

And the culture under a microscope post subculturing-

I don't really know what the numerous black dots are in the post-subculture cell culture. I also can't quite understand if I can see any of the cells in the post-subculturing culture. So, I wanted some advice on what the black dots might be, and if the subculturing appears to have been performed correctly. Thank you in advance!

Welcome to the Biology Stack Exchange. Please take the [tour] and visit the [help] for more information on this site and how it works. Please edit into your question which cell type this is, as that may help provide useful information on the effect you are seeing here.

Thanks a lot for your warm welcome and your suggestions! I have edited the question accordingly.

How long after subculturing is the second picture taken?

It was taken immediately after subculturing.

Were both images taken in similar conditions? The 'before subculturing' image on top looks like a dark-field image while the 'after' image below it looks to be bright-field

I'm thinking you are very new to cell culture - your first step should be to ask people in your lab.
You have a couple of problems here - it takes time for cells to settle and attach and start to spread out. Often several hours after seeding is needed for them to return to looking normal. Have a look at your cells now, as I've answered this ~24 h after you asked it. They should look more normal.
However, a lot of what you are seeing there is cellular debris. This indicates that you probably over treated your cells with trypsin and/or were very rough with your pipetting. It is normal to see some debris after seeding, but not too much.
In addition, your first photo shows massively over confluent cells, they are all tightly packed together and there are absolutely no gaps in the monolayer. This stresses the cells (even if they are not contact inhibited - HEK293 aren't contact inhibited), so they tend to attach more firmly than they should. This means that you end up treating them with trypsin for too long and then a lot of them die. You should be subculturing much earlier - there should still be about 20-30% of the culture area free of cells. The large, blobby areas in the top third of the first picture are not gaps in the monolayer - some of them look like senescent cells, and some are gaps left by dying/dead cells that haven't quite filled in yet.
HEK293 are a weakly attached cell line; in many instances you can tap the side of the flask firmly to detach them, you can even wash them off by pipetting. In my experience, you should only need a minute or less to detach them from cell culture vessel.
It might pay you to check the concentration of your trypsin/EDTA - often stocks are 10x or 100x rather than the 1x you need. Adding the wrong concentration will result in a lot of cell death as it is very hard to neutralize the trypsin.


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How does defining cell assembly by giving weightage to impact caused as opposed to strength of connections change our current paradigm?
Buzsaki, in his paper Neural Syntax: Cell Assemblies, Synapsembles, and Readers, seems to suggest that instead of using synaptic strength and connectivity as a defining feature, a (dynamically changing constellation of) neural cell assemblies could instead be classified based on the impact/output caused by their target "reader" neurons.
Primary question:
Is this an accurate reading of the argument?
His argument, in my understanding, is that the strength of upstream connectivities may not have a biologically meaningful significance unless the downstream potential is interpreted and acted on by the target reader neuron. Hence, interpreting the output/impact caused by the action potential of the reader neuron would provide insight into the nature of transiently formed assemblies as opposed to tracking down the linkages.
Therefore, while the synaptic strength of upstream neural assemblies increases the likelihood of stronger downstream potential, it need not be a requirement as even weakly connected upstream assemblies can gain significance if they activate the target layer. (Hence, the temporal window is a more deterministic classifier).
Secondary question:
Are there any compelling counterarguments to this hypothesis in the literature? Ideally including data supporting one hypothesis or another?

It would be helpful to link to the paper or provide a full reference. I'm not sure the question is answerable with anything but opinion and discussion though. Your post also seems to take as a straw man the idea that strength of connection is otherwise the sole defining feature - is anyone arguing that?

you might consider having this quesiton migrated to the psych/neuroscience SE. That might yield a slightly more relevant/expert group. I also second the suggestion to link the paper directly and try to find a more specific/answerable framing.

@MaximilianPress thank you for the edit. How do I migrate the question to the Psych platform? I did attach a link to the paper ( does it not open for you?)... but I guess it will be difficult to refer to one single paragraph since the question demands an understanding of the the whole concept of neural syntax that Buzsaki is getting at. Maybe I will let the question stay for a few weeks to see if anyone responds.

Your original question did not have any link as you can see in the edit history: https://biology.stackexchange.com/revisions/114414/1 I don't know why you are mentioning "refer to one single paragraph" - no one has suggested you do that? I can migrate the question if you want; there is no way a user can do it on their own besides deleting and re-posting.

@MaximilianPress I think the edited question is not really quite right: I would not describe this as a hypothesis per se. It's an opinion; a scientific one, but still, an opinion. Like if someone said "the most important defining feature of a good meal is a balance of acid and fat", that's something where they can provide evidence of the importance of acid and fat but the "most important" part is necessarily opinion. That's what Buzsaki is saying: think about the outputs. Of course the outputs are connections, so saying "rather than connection weights" is also a bit misleading.

@BryanKrause I'm not sure that I understand the distinction that you're making between a hypothesis and an opinion. Questions of relative importance are critical to our ability to reason about phenomena. Is your point that the evaluation might be qualitative or subjective, or perhaps not testable? I don't have an opinion on the actual science here (connection weights etc.), so I left those parts of the question alone- I just rewrote the explicit questions until I thought that someone might be able to answer it more effectively.

@MaximilianPress Sure: subjective or not testable. I'm not claiming it's not useful, though.

I don't see reason for migration; the Q is suitable for both sites.

Ok @BryanKrause. Feel free to edit / roll back my edit as you see fit. Not my field, so I will defer to anyone who feels they can speak authoritatively!

This is a question and answer site about questions in biology for which an objective answer can be expected. You are trying to initiate a discussion about  a view that is apparently controversial (“How do you see?”). I see clearly that this is off-topic.

I’m voting to close this question because it is an attempt to initiate a discussion.

I think the edit to the title is an improvement and helps get closer to something answerable, thank you, though I question whether "our current paradigm" is really something that exists, there is absolutely no one specific paradigm in which people in neuroscience discuss networks of neurons or brain function overall. Maybe you can update the rest of the body to fit with this title, too?

@BryanKrause Great question regarding the current paradigm. Everyone had assumed the objectivity of time for the longest. But once someone took up the feat of defining it, the "assumed" definition became the current paradigm. Similarly, one of the objective assumptions we inherited about the brain is its stimulus-modulating-action property. However, the new proposed research-driven framework suggests the brain to be a self-organized output-modulating-input entity. Cell assembly (which also exists in the current paradigm) is an investigation to understand the brain's "organization" component.

@aztec242 I don't know about that assumption; I think people studying sensory versus motor systems tend to think in ways that prioritize the system they are studying. So, if you assume that an inherited assumption is stimulus-modulating-action, I think you're probably biased by thinking from the sensory side and ignoring the people studying motor systems.

I think this goes beyond the system one is studying and uncovers the researcher's (both motor and sensory) assumed definition of the "purpose" of the brain. The commonly defined purpose of the brain is to "understand" the objective world. This results in hypotheses and experiments exploring systems optimal at sensing & perceiving, modulating actions only when needed. The other approach suggests that the brain is more action-oriented, and prioritizes the maintenance of self-generated internal patterns heeding only relevant stimuli-derived changes.


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At what levels of muscle energy intake does catabolism start?
From my own reading, there are three ways used by the body to produce energy:

Alactic anaerobic (direct degradation of ATP and creatine phosphate for regeneration of ATP)
Lactic anaerobic (breakdown of muscle glycogen with lactic acid production)
Aerobic (breakdown of carbohydrates and fats primarily and secondarily of proteins)

My questions are:
1) Knowing that the anaerobic mechanisms (alactic and lactic) are triggered when the effort is intense and / or greater than body oxygenation capacity, it seems logical, at rest, the body uses mainly aerobic way for producing energy. Am I right?
2) If 1) is true, what are the conditions (trigger elements, trigger events) which lead to muscle catabolism (so protein degradation) in order to produce energy? ? Is it well the last resort used by the body to produce energy that is to say after degradation of total carbohydrates and lipids?

(1) is basically correct.  I don't see how (2) is related to (1) ? Also, there is no single answer to whether protein is the "last resort used by the body to produce energy", because different tissues of the body have widely different fuel preferences, and also it depends on the extent of fasting, level of exercise, amount of muscle and fat stores, and a bunch of other things. Can you be more specific?

Precisely, in a bodybuilding context, I would like to know the conditions which lead to muscle catabolism (so protein degradation) in order to produce energy?

Okay, can you please edit your question then so that it is specific to muscle catabolism during exercise.

@backlash that's an entirely different question.

1) Yes, most cells in the body derive energy from oxidative metabolism, unless oxygen is not available for some reason. There are some exceptions, for example red blood cells lack mitochondria and so have no respiration, and various types of rapidly proliferating cells such as activated immune cells have high glycolysis and lactate production (for reasons that are still not well understood).
2) The main fuel of exercising muscle is glycogen, which can account for 60-80% of energy requirements (article). Triacyglycerols (fat) stored in muscle tissue may account for most of the remainder (artice). Normally, muscle protein is not a major energy source during exercise. Some muscle protein breakdown has been observed after 2-3 hours of intense exercise (think marathon runners), when glycogen stores are depleted. See this review article.
If glycogen is not synthesized and stored normally while resting, then muscle may be more likely to catabolize protein during intense exercise. This can happen to some extent in diabetes, see for example this paper. There are also severe genetic disorders that disrupt glycogen synthesis, but those are very rare. I would guess fasting also makes it difficult to replenish muscle glycogen stores (and muscle triglycerides as well), so strenuous exercise combined with fasting might result in muscle protein breakdown, but I don't know of a study on this.

Prolonged fasting/starvation promotes muscle protein catabolism.
During starvation blood glucose must be maintained in order to provide fuel for red blood cells and brain in particular. Amino acids from muscle breakdown are used as gluconeogenic precursors by the liver and kidney. However fat is also mobilised and fatty acids are converted to ketones by the liver. Most organs/tissues can use ketones, including the brain (but not red blood cells or the liver). This use of the fat store reduces the body's demand for glucose and slows the process of muscle breakdown, allowing survival for weeks rather than days.


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Are Sciomyzidae fit to combat snails?
I read that Sciomyzidae are also called snail-killing flies, which immediateley made me think: "I need those"!
Questions:

Are they really fit to control snail over-population in my garden? and
if so where do i get them?

Short answers:
These insects live near water or marsh areas so that's where you can get them from. This is because many species of this group has larvae that are aquatic or semi-aquatic.  According to wikipedia:

The adults drink dew and nectar.

And it is their larvae that either prey on or become parasites of gastropods.
In this article the following is stated:

(...) Sciomyzidae is of interest from practical viewpoints because of their potential as biocontrol agents of aquatic snails carrying diseases (e.g. schistosomiasis and fascioliasis) and terrestrial, pestiferous snails..

So the answer is yes, they might be fit to use as biological pest control, yet they may not be suitable against all species. Details of their life cycle and their biology can be found in the linked article or in this book:
https://books.google.hu/books?id=vqE1AMIj-HUC&pg=PR16&lpg=PR16&dq=Sciomyzidae&source=bl&ots=pCVJJUu2cb&sig=M1F8GhR51VI1Y62htF7eX0kNpfo&hl=hu&sa=X&ei=AF0uVf_tKI3taNLhgIAL&ved=0CFgQ6AEwBzgK#v=onepage&q=Sciomyzidae&f=false

To be honest I did not read the whole book, but the title is quite specific for what you might need.

didn't think you read the whole thing and i won't do that either. But i agree that it sounds very specific to my question.


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Protein that exit from the cell - as marker
Searching for some protein, that I could use as extracellular marker for mammalian cells. I need to insert mRNA to cell, and to detect the protein outside the cell (not on membrane) if the mRNA successfully enter and been translated. (not GFP, I need protein that exit from the cell in big numbers)
Thank you.

You might want to check secretome analyses like http://www.nature.com/nbt/journal/v30/n10/full/nbt.2356.html

I don't know of any that are exported by all cells, e.g. both neurons and . All blood proteins, e.g. serum albumin are exported but by specific cells.

You can always express GFP or your favorite protein in a secretory vector like pSecTag or pSecTag2 from Invitrogen/Life/ThermoFisher/SuperUltraBioMegaMart. There are probably others, but those were the first ones I came across. They contain the mouse Igκ signal sequence for efficient secretion (so the website says, I've never used it).
I don't know the details of your experiment, but are you sure you want to use a secreted protein as a transfection marker? Remember, it's possible that only a small fraction of your cell population will take up the vector (or mRNA, if that's what you're using, but there are issues with that), but you will see secreted protein regardless of the number of cells that take it up.

Thank you! Looks good. It's ok, I just need to know if some cells get the vector, doesn't meter how many of them.

SEAP, secreted alkaline phosphatase, and vectors engineered to express fusions to this reporter gene may be well-suited to solve your problem.


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What does it mean: carrying the stably integrated gene
Reading this study
http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html
They writing

Multiple exogenous and endogenous genes can be simultaneously activated
  by CRISPR-on
We tested single, double and triple activation of a TetO::tdTomato
  transgene and the endogenous SOX2 and IL1RN genes (Figure 3A) in
  HEK293T cells carrying the stably integrated TetO::tdTomato transgene

Could you please help me to understand: They talking about exogenous gene. But saying "carrying the stably integrated". Does that mean that this gene (TetO::tdTomato) is in the cell genome (integrated to genome)? If so, what is the meaning of exogenous here?
Thank you!

According to Merriam Webster, an exogeneous gene is defined as " introduced from or produced outside the organism or system; specifically :  not synthesized within the organism or system—compare endogenous".
I believe they refer to the tetO::tdTomato transgene as an exogeneous, or not originating from the species of study

Yes thats what I am understanding from this too. Thank you.

@Barbos if this answered your question, please consider accepting it by clicking on the check mark to turn it green.


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Proteases in the blood
I’m reading on hormones and the book talks about how peptide or amine hormones are easily broken down by proteases present in the blood plasma. This has led me to question the interactions between these proteases and the blood proteins of the blood (such as albumins and globulins). Does having proteases in the blood mean the blood proteins are constantly broken down? How do the blood proteins get anything done then? And what good do binding proteins do in protecting hormones during vascular transit when the binding proteins are also susceptible to blood proteases?
Edit: I’ve been requested to provide some quotes and references.

Because water-soluble hormones can dissolve in blood, many circulate as free hormones, meaning that most of them dissolve directly into the blood and are delivered to their target tissue without binding to a binding protein.

The book goes on to say

Water-soluble hormones, such as proteins, peptides, and amino acid derivatives, have relatively short half-lives because they are rapidly degraded by enzymes, called proteases, within the bloodstream. The kidneys then remove the hormone breakdown products from the blood.

These quotes were from Seeley’s Anatomy and Physiology, 10th edition.

When asking a question like this, it is usually best to cite the source that gave rise to the question. Also making a direct quote and attributing it to the reference makes it easier to determine the context of the assertion.

@AMR I have added some.

Basically it is that you are dealing with textbook vague. They don't define for you what relatively short half-lives is or the enzymes that are in circulation. IgG, which is the major immunoglobulin circulating in the blood has a half-live of between 11-21 days, depending on its subclass. Also the proteases may have certain specificities but not others. Certain proteins may not contain the moieties that the enzymes need to bind and catalyze the reactions and this acts to "protect" the protein from degradation. Without them providing the specifics of what they are referring to, its hard to say.

So is 11-21 days relatively short in the authors' estimations or are they referring to half-lifes on the order of minutes to hours? Unless they define it for you, it is difficult to say.

@AMR Can you give an example of a protein that does not contain a moiety to which enzymes can bind?

Well I don't know if this counts as this is an abhorrent form of a wild-type protein, but prions (PrP^Sc or PrP^TSE) are highly resistant to enzymatic degradation, even from Proteinase K. [Human Serum Albumin] (https://en.wikipedia.org/wiki/Human_serum_albumin) has a half-life of 20 days, and if I had to guess is much longer than what the authors of your text had in mind by saying "relatively short," so I would go out on a limb and say that those and Immunoglobulins are also resistant to serum proteases. If your text book gave a better definition than it would be easier to answer.

I think that you also have to remember that hormones are generally signaling molecules that induce transcriptional activity in the cells that receive them. They tend to be released based on certain stimuli, and most of the time, you only want them on for short periods of time, i.e., different stages of development, fight or flight, respond to changes that cause an imbalance in homeostasis, repair damages to cells and tissues. So you would want enzymes that can quickly degrade these molecules, in matters of minutes or hours, so that you don't over-respond to the stimulus.


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Why are lipid-soluble substances harder to excrete?
I understand why water-soluble substances can be excreted. However, why are they easier to excrete than lipid-soluble substances? Why can’t lipid-soluble substance be excreted just as easily in the kidneys?

Short answer
If you understand why hydrophylic compounds can be excreted, than it's kind of straightforward why hydrophobic ones can't - because they are not hydrophylic.
Background
The kidneys, through the production and excretion of urine, are the major gateway of clearing the body from toxins. Some toxins absorbed in the gastrointestinal tract can be excreted by the liver through the gall system.
Urine is watery and kidney's excrete water through ion homeostasis. Hydrophobic compounds do not dissolve in water and hence cannot be excreted by the kidneys. The liver has an important role in making hydrophobic toxins water-soluble. Often hydrophilic groups are attached to it in the liver, making them hydrophilic. If that can be achieved, they can be excreted through the kidneys. Hydrophobic compounds that are resistant to chemical modification tend to accumulate in the body in fatty tissues like the nervous system, for example the notorious polychlorinated biphenyls (PCBs).
Reference
- Chen. Activation and Detoxification Enzymes: Functions and Implications, Springer Science+Business Media (2012)

I guess what I’m wondering more about is what happens to those hydrophobic compounds that can’t be excreted. (Even if this doesn’t happen and the body makes sure they’re made more water-soluble, let’s say hypothetically it happens.) What happens to these substances then, if they aren’t dissolved in the urine?

I should add that by my previous comment, I meant what happens to them as they pass through the nephrons of the kidney. They still move through the nephrons, right? Then what happens, if they aren’t flushed out?

They accumulate, as said above

@lightweaver -They are, as AliceD stated, changed into more hydrophilic substances in the liver, then excreted, often through the biliary tract or the kidney.

@AliceD I understand they accumulate as fatty tissue in other places of the body. But I’m just not seeing how they end up as fatty tissue elsewhere if there isn’t a mechanism by which they are saved from being excreted in the kidney, so to speak. What happens to the fat-soluble compounds as they move through the nephrons? Accumulate within the kidney? (And if this entire scenario doesn’t happen, then hypothetically what would happen if it did?)

If I've interpreted your question right then I think this is the answer..
You have both lipid-solule and water-soluble in the filtrate.
Lipid-soluble substances can easily cross the phospholipid bilayer of cells lining the tubules and so are extensively reabsorbed by passive diffusion. Thus the kidney cannot actively excrete lipid-soluble substances. This means the kidneys cannot alter the plasma concentration of these substances.
Water-soluble substances are effetively trapped in the tubules. This means the kidneys can selectively secrete or reabsorb water-soluble substances via channels etc. So the kidneys can only control the excretion of (and actively concentrate in the urine) water-soluble substances.
Sorry I don't have a reference for you but you've probably already found an answer anyway since this was originally posted a year ago.

You need to understand how renal ultrafiltration works to answer this question.
In the glomerulus, hydrostatic pressure forces fluid (filtrate) across 3 barriers into the collecting tubule. The first is the membrane of the glomerular capillary, which has fenestrations (pores) which are about 8um wide; only molecules smaller than 8um and\or molecules that can diffuse across a lipid bilayer will pass this membrane.
Next, they must pass the glomerular basement membrane, which has a slight negative charge. Any negatively charged molecules will be repelled and not excreted.
Last, they must pass through the filtration slits formed by the interdigitations of podocytes that are applied to the glomerular basement membrane. This is also a very narrow passage and has a slight negative charge.
Now, none of those seems to immediately preclude hydrophobic molecules from passing through the glomerulus... but how do they get there? They have to be dissolved in blood! But that's impossible if they're hydrophobic- physiologically hydrophobic molecules are usually bound by proteins, which are hydrophilic but often have hydrophobic regions. Albumin is the classic example, and albumin is just slightly too large to pass through the filter. There is no carrier system that allows hydrophobic molecules to be shuttled to the glomerulus and then dumped off to be filtered.

Brian thanks for your effort on this answer - please add some references so that other users that are unfamiliar can understand what you're talking about and can read further if necessary


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Why does it take many sperm for one sperm to fertilize an egg?

Hundreds of acrosomes must undergo exocytosis to digest holes in the zona pellucida. This is one case that does not bear out the adage, “The early bird catches the worm.” A sperm that comes along later, after hundreds of sperm have undergone acrosomal reactions to expose the oocyte membrane, is in the best position to be the fertilizing sperm.

—Human Anatomy and Physiology, 9th edition (Marieb)
I’m having trouble understanding why this would be the case—the last sentence, that is. Perhaps it does take a lot of sperm to break through the zona pellucida, but why would any sperm that comes after have an advantage? Do the sperm cells die after the acrosomal reaction? If not, can’t the first few sperm cells be the ones in best position to attach to the oocyte’s receptors once the zona pellucida has been penetrated with the help of other acrosomes from other sperm?
Moreover, are the acrosomal enzymes degraded? Why would there be a need to have so many acrosomes if the enzymes can continue working through the zona pellucida? All you would need is time and soon the zona pellucida would be broken down, even just by a low number of enzymes, would it not?


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How Does NADPH Reduce 1,3-BPG?
If NADPH returns to being NADP+, then that means one proton and two electrons have been incorporated into 1,3-BPG. If only one proton and one electron were attached to the carbon in 1,3-BPG (removing phosphate), I’d understand, since there’s a single covalent bond between carbon and hydrogen which establishes stable octets. But there’s another electron hanging around. What happens to this one? Or am I totally mistaken about the whole process?
This is the chemical formula for G3P:

The Lewis diagram below shows the top part:

As stated, NADPH gave off 2 electrons, yet only one is needed to bond with carbon (orange). Where did the other electron disappear to?

NADPH is always accompanied by H+, and the electrons reduce as a pair. Otherwise, there will be no balance of charges.

And after NADPH reduces 1,3-BPG, it goes back to being NADP+. It loses two electrons. In 1,3-BPG, the hydrogen bonds with carbon, contributing one electron to the single covalent bond. My question is where the another electron has gone, if it’s not in 1,3-BPG and not in NADP+.

Sometimes the electrons react w/ oxygen to form superoxide, or react with surrounding hydrogen to form water

@Kendall So the electron does go elsewhere, and is not incorporated in G3P, correct?

Single covalent bond is a shared pair of electrons. For stable bond there should be 2 atoms with unfilled higher orbitals and at least a pair of electrons that is "distributed" among those slots.
UC Davis have hilarious page on that.

I have edited my question to show what I’m talking about better. A proton and one electron may be equivalent to a hydrogen atom, which can bond with a carbon atom. But there’s an extra electron that NADPH gives. What happens to it?


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Why does a fetus drink and urinate into the amniotic fluid?
I was reading this website saying that fetuses urinate into the amniotic fluid. It also mentioned that, because we drink the amniotic fluid, we’ve been drinking our urine for months.
However, why do we produce urine as fetuses? I always believed the placenta was our source of waste removal; then why have fetuses the need for filtering their blood through their own kidneys?
In addition, why would fetuses drink the amniotic fluid? Is there a benefit for doing that?

In utero, the growing little human is getting ready to be an independently functioning individual. While it is everything but that, it must be able to obtain fluids and nutrients through its mother's milk, and that from pretty much the first hour of its life.
To develop proper kidney function, the growing fetus needs to ingest fluids just as it will do post partum. Because a mini bar isn't available, it has to drink whatever is available, i.e., amniotic fluid and indeed, its own urine. Shortly after the kidneys start to produce urine, the fetal swallowing commences.
Amniotic fluid is 98% water and 2% salts and cells from the baby. Until the fetal kidneys start working during month four, amniotic fluid is made by the mother’s body. But after month 4, the fetus starts to make his contribution to the amniotic fluid by urinating into it (Penn Medicine). Production of amniotic fluid is then predominately accomplished by excretion of fetal urine (300 ml/kg fetal weight/day or 600 to 1200 ml/day near term) and the secretion of oral, nasal, tracheal, and pulmonary fluids (60 to 100 ml/kg fetal weight/day). Fetal breathing movements also contribute by efflux of lung fluid into the amniotic fluid. Removal of AF is predominately accomplished by fetal swallowing (200 to 250 ml/kg fetal weight/day) (Underwood et al., 2005).
The water in amniotic fluid originally comes from maternal plasma and passes through the fetal membranes. As the placenta develops, water and solutes from maternal plasma pass across the placenta to the fetus and then to the amniotic fluid (Underwood et al., 2005), see Fig. 1.
Swallowing its own urine is not only not dangerous, it is essential to proper development. A decrease in fetal urine production or excretion can result in a reduced amount of amniotic fluid (oligohydramnios). Oligohydramnios can result in fetal lung deformations (pulmonary hypoplasia) and increased risk of infection.  Fetal mortality rates as high as 80-90% have been reported with oligohydramnios diagnosed in the second trimester (Source: Patient Info).
If the fetus would have to prevent the production of urine in utero, the kidneys would have to remain nonfunctional during development, which would be disastrous once it is born. Renal failure is in fact pretty common in newborns, but can be fatal without proper treatment (Andreoli, 2004).

Fig. 1. After month 4, amniotic fluid is derived from maternal plasma that passes via the placenta, to the fetus and then to the amnionic fluid. Source: Underwood et al., (2005).
References
- Andreoli, Semin Perinatol (2004); 28(2): 112-23)
- Underwood et al., J Perinatol (2005); 25: 341–48

The fetal swallowing exercises the swallowing mechanisms and the fluid absorption paths of the digestive tract, which may be helpful. Note that since the kidneys need to function in utero, if the fluid used by them came only from the placenta, the volume of amniotic fluid would need to continually increase.

@lightweaver Why argue with almost a billion years of evolution; it seems to have gotten us this far.

@Christiaan I am fairly certain that Brian Griffin had a Minibar in utero.... :-)


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Permeability of Plasma Membrane
I’m having trouble grasping why small polar molecules can cross the hydrophobic region of the membrane and not ions. Won’t the polar molecules be attracted to the watery extracellular medium and not be inclined to move through the hydrophobic region? (This is my reasoning for why ions won’t go through.)
Also, why do lipid-soluble particles go through the membrane? I understand they have an affinity for the hydrophobic region, but won’t they want to stay there, sandwiched between the two watery layers? Isn’t that the point of the orientation of the bilayer? Why would the lipid-soluble particles move from the hydrophobic region into the watery interior of the cell? Furthermore, why are lipid molecules not repelled by the hydrophilic heads on the exterior of the membrane?

Polar does not equal charged. Polar molecules have dipole moments, but they do not carry a charge. Ions on the other hand are charged particles. There is a difference between trying to get something polar through the membrane and something that is charged through the membrane.

Passive diffusion.
This question specifically refers to passive diffusion.
Ill reiterate and clarify what was mentioned in the question.
Passive diffusion involves a molecule dissolving into the membrane, diffusing across it, and then dissolves in the aqueous solution on the other side.
The second part of your question can be answered briefly: this diffusion event occurs from time to time, and often at a high rate.

Importantly only small, relatively hydrophobic molecules are able to diffuse across a phospholipid bilayer at significant rates. Thus, gases (such as O2 and CO2), hydrophobic molecules (such as benzene), and small polar but uncharged molecules (such as H2O and ethanol) are able to diffuse across the plasma membrane. Other biological molecules, however, are unable to dissolve in the hydrophobic interior of the phospholipid bilayer. Consequently, larger uncharged polar molecules such as glucose are unable to cross the plasma membrane by passive diffusion, as are charged molecules of any size (including small ions such as H+, Na+, K+, and Cl-).
-Cooper, 2000

Hydrophobic fatty acids repel charge.
The additional or missing electron gives the ion its charge. The hydrophilic head groups of the bilayer are charged, but the fatty acid chains are not, and these repel charge.
There are also repulsive forces between hydrophobic and polar residues (hence the bilayer exists in water), however polarity is essentially a spectrum. A small relatively non-polar polar molecule will not experience enough repulsion to stop diffusion, but a larger, or more polar molecule might.
Active and passive transport.
Although not mentioned in the question, these ions and other molecules can permeate the membrane via protein channels that allow, often with great specificity, ions and large molecules to traverse the membrane.

In the structure of the bilayer, there are proteins sticking out through the membrane as either transmembrane (through the whole membrane), extrinsic (on the outside) or intrinsic (on the inside) proteins. These act as gates or channels to allow polar, water soluble substances through. This process is known as facilitated diffusion. Check out page 11 of this article
Some ions are allowed in but this is a mediated process of active transport, where ion channels or gates regulate it. This is seen in neurons during the movement of the electrochemical signal along the axon, however, this does not happen automatically, unlike facilitated diffusion.
As for the second part of your question i feel like you can check out this question here


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Does DNA polymerase I require a $3^\prime$ end?
DNA polymerase III adds nucleotides in the $5^\prime \rightarrow 3^\prime$ direction because it can only add nucleotides to the $3^\prime$ end of the previous nucleotide. This is why it requires a primer. However, does DNA polymerase I operate by the same criterion? Does it require a $3^\prime$ end of a previous nucleotide in order to bind successive DNA nucleotides?
If it does, then how can it do so for Okazaki fragments when each Okazaki fragment is unbonded to each other? It is the DNA ligase that finally catalyzes the phosphodiester linkage between the $3^\prime$ end $5^\prime$ beginning of two Okazaki fragments, isn’t it?
If it does not, then what’s the deal with telomeres? After each DNA replication event, the DNA gets shorter and shorter at the very ends because that final primer can be removed but not replaced by DNA via DNA polymerase I, correct? This suggests to me that DNA polymerase I requires a previous nucleotide's $3^\prime$ end to work with, and it has confused me regarding its action on Okazaki fragments in conjunction with DNA ligase.

DNA Pol I does require the 3' end of a previous nucleotide to initiate elongation.
Regarding Okazaki fragments, this is accomplished by the annealing of small RNA primers to the lagging strand part of a replication fork. DNA Pol I extends the lagging strand off of the 3' end of those primers, generating the Okazaki fragments. The RNA primers are later removed, leaving gaps between Okazaki fragments, which are later filled in through the combined actions of DNA PolI and DNA ligase.

In the case of telomeres, the final RNA primer can't be filled by DNA Pol I because polymerase requires a free 3' hydroxyl for the attachment of the first DNA nucleotide. After removing out the RNA primer, the first DNA nucleotide would need to be attached to the DNA nucleotide preceding it, which is not found in the case of the final primer on a telomere, since it's all the way at the end of the linear strand.
In this case then, DNA Pol I removes the RNA primer is removed by DNA pol I but cannot replace it with DNA, leaving a gap (step 6 in the following image).

DNA Pol III is involved, but the current understanding, as far as I can tell, is that Pol I fills in the gaps between RNA primers on the lagging strand, thereby generating the Okazaki fragments, while Pol III is more involved in the continuous extension of the leading strand. From this review (http://www.ncbi.nlm.nih.gov/pubmed/21622658), it looks like Pol I and Pol III interact during DNA extension in ways that still aren't fully characterized, so there may be some crossover.

@MarchHo - anytime! :-)


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Enzyme\Protein amounts in cancer
I am searching for source, that providing information about enzymes\proteins, in different types of cancers, that their amount in cell is significantly higher - comparing to normal, healthy cell.
Some pathways that exist in cancer in much more higher amounts.
For example - Telomerase.
Is there some sort of database for this information?

You could try expression atlas: http://www.ebi.ac.uk/gxa/home

Yes. The dbDEPC 2.0 database for example.
If you want to extend your search to pathways the best database I know of is the KEGG.
There are multiple databases out there. You might want to look at this wikipedia page.
By the way what you are looking for is called a cancer proteomic signature.


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Repair wrong DNA pair after ending replication?
If there are wrong DNA pair, for example A=G, is there mechanism that could repair such things - after the replication was finished?
Or it happens only during replication?

DNA mismatches and indels can be repaired after replication through an aptly named mechanism called DNA mismatch repair.
I'll briefly describe the mechanism in Escherichia coli, but it's similar in other organisms. A protein called MutS scans DNA for lesions caused by mismatched nucleotides incorporated during replication that escaped DNA polymerase proofreading. These are detected by the kink they produce in the DNA backbone. MutS recruits MutL and MutH; the former activates the latter, which is an endonuclease. MutH cuts the DNA backbone near the lesion in the newly synthesized strand (the one containing the misincorporated nucleotide). This strand can be identified because it has not yet been methylated, while the parent strand contains the original methylation. After cleavage, UvrD helicase unwinds the strand and an exonuclease digests it. The gap around the former lesion can then be filled by DNA polymerase III and DNA ligase.

[ image adapted from ]
Here's an interesting review in a Nature publication that discusses it in more depth, as well as the mechanism in humans:
Guo-Min L. 2008. Mechanisms and functions of DNA mismatch repair. Cell Res 18:85-98

Thank you! Only the link to Nature - page not found.