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Can the fungal form of Malassezia morph into the fungal form of Candidia when feeling threatened? Resistance Mechanisms
Malassezia feeds on oils in the carbon chain 11-24 and Candida feeds on sugars. I recall learning that when these types of fungus feel they are under attack, they can morph. Does this mean they can change into each other? This question deals with resistance and strategies for overcoming resistance through combination therapies.
"Malassezia (earlier known as Pityrosporum) species form the cutaneous commensal flora, which are associated with varied clinical manifestations ranging from benign skin conditions, such as tinea versicolor, to fungemia in the immunocompromised host.[1] There are at present 14 described species, namely M. furfur, M. pachydermatis, M. sympodialis, M. globosa, M. obtusa, M. restricta, M. slooffiae, M. equina, M. dermatis, M. japonica, M. nana, M. capre, M. yamatoensis, and most recently M. cuniculi.[2] Owing to their lipophilic nature, they colonize the seborrheic parts of the skin and they sustain themselves by using the fatty acids present in normal sebum. They cause skin disease in certain conditions such as overgrowth, descent into hair follicles, or inflammation. Though, by definition superficial mycosis do not extend beyond the cornified epithelium, these organism are seen in the ostium, central and deep segments of the hair follicle in Malassezia (Pityrosporum) folliculitis. Malassezia infections can manifest as superficial localized or can cause systemic infections in immunocompromised hosts."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4533528/
"The genus Candida includes about 200 different species, but only a few species are human opportunistic pathogens and cause infections when the host becomes debilitated or immunocompromised. Candida infections can be superficial or invasive. Superficial infections often affect the skin or mucous membranes and can be treated successfully with topical antifungal drugs. However, invasive fungal infections are often life-threatening, probably due to inefficient diagnostic methods and inappropriate initial antifungal therapies. Here, we briefly review our current knowledge of pathogenic species of the genus Candida and yeast infection causes and then focus on current antifungal drugs and resistance mechanisms. An overview of new therapeutic alternatives for the treatment of Candida infections is also provided."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708393/
"CONCLUSION
Morphological transitions are commonly observed among diverse fungal species. These cellular responses are accompanied by equally profound changes in cell physiology and structure. As noted above, the highly regulated process of fungal morphogenesis represents an adaptive response to specific stresses encountered in various microenvironments, including that of the infected host. Therefore, morphological and physiological plasticity allows fungi to rapidly adapt to changing extracellular conditions. Species-specific signaling and morphological features appear to be a direct result of fungal attempts to survive as new microenvironments, and their particular cell stresses, were encountered (Hogan and Klein 1994; Newman et al. 1995; Batanghari et al. 1998; Sebghati et al. 2000; Gow et al. 2002; Brandhorst et al. 2004; Rappleye et al. 2004, 2007; Gantner et al. 2005; Nemecek et al. 2006; Gauthier and Klein 2008; Nather and Munro 2008; Mora-Montes et al. 2011; Wang and Lin 2012; Wang et al. 2012). The concerted action of morphotype and physiological changes in the context of a particular environment are therefore critical for successful fungal adaptation (Butler et al. 2009; O’Connor et al. 2010). Defining the cellular machinery controlling fungal morphogenesis offers unique insight into our basic understanding of fungal life cycles and pathogenesis."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315913/
"Therefore, morphological and physiological plasticity allows fungi to rapidly adapt to changing extracellular conditions. Species-specific signaling and morphological features appear to be a direct result of fungal attempts to survive as new microenvironments, and their particular cell stresses, were encountered"

The majority of fungi grow in one of two growth forms: either as rounded or spherical cells (yeast fungi) or as a polarised branching mycelium (filamentous fungi). Such fungi are found throughout the fungal kingdom and are termed 'dimorphic'.
http://www.davidmoore.org.uk/21st_Century_Guidebook_to_Fungi_PLATINUM/Ch05_01.htm
Candidiasis is a fungal infection caused by a yeast (a type of fungus) called Candida.
https://www.cdc.gov/fungal/diseases/candidiasis/index.html
Pityriasis versicolor is caused by a type of yeast called Malassezia.
https://www.nhs.uk/conditions/pityriasis-versicolor/
Malassezia (Pityrosporum) folliculitis is a fungal acneiform condition
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970831/
Dimorphic means they can change from the fungal form of yeast to the fungal form of hyphae or filamentous fungi within their own species, not morph into another species. Its clear to me now.
Hyphae - Hypha. Hyphae are a highly polarized cell type and are the hallmark of the filamentous fungi, which make up the majority of known fungal species
https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/hypha


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If massive animals live longer, why do humans with gigantism die younger?
What I mean is humans suffering from gigantism (type 1 neurofibromatosis, Marfan syndrome, X-linked dominant acro-gigantism, et cetera) rarely live more than 5 decades (50 years).
The same can be said to wolves: wild ones rarely live more than 9 years, and domesticated wolves (dogs) can live up to 20 years if they are small like chihuahuas, beagles, and toy poodles, and no more than 7 years if they are massive like great Danes, mastiffs, and Rottweilers.
But, at the same time, horses can live 3 decades (30 years), but hamsters only live 4 years.

You are mixing gigantism, which is an anomaly, and the normal animal size. Wolves arenot chihuahuas with gigantism, but a different species.

In short many things determine life expectancy and the interplay between different factors will determine an individuals life expectancy and a species' average life expectancy.
How life expectancy links to size:

Among mammals there is an inverse relation between heart rate and life expectancy (mammals tend to average 7.3+/15.6 x10^8 beats per lifetime which appears to be a symptom of the fact that heart rate is a marker of metabolic rate and so there is a fixed 'metabolic lifetime' for animals (source). This is somewhat substantiate by metabolism variants in C. elegans and the link between metabolism and free radicals and DNA damage (source).
Larger animals are thought to have a slower metabolic rate by weight (not overall) due to scaling laws (see Kleiber's law) and how surface area and volume relate and change temperature regulation metabollic requirements.

Other factors that change life expectancy:

In breeding: a reduction in genetic variation caused by inbreeding (e.g. many dog species though the extent to which they are inbred will depend on the species) can lead to lots of underlying health issues that may reduce the lifespan independent of metabolic rate
Stress: Higher stress will reduce life expectancy
Nutritional abundance: reducing caloric intake may reduce metabolic rate and extend lifespan, though starvation will decrease lifespan

Gigantism:

Whilst the life expectancy for a species may be higher in general people with gigantism may live shorter lives than possible because of non-metabolic related reasons. For example many forms of gigantism are linked to hormones which promote cell division and growth which are also linked to forms of cancer.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

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What does it mean to "cure" microscope slides?
I am reading a journal paper and I have come across the following statement in the materials and methods section regarding the preparation of microscope slides:

Coverslips were washed once more with PBS, inversely mounted on
microscope slides with ProLongTM Diamond antifade mountant containing
DAPI (Invitrogen). Slides were cured for 24 hours at room temperature
before observation.

I am not sure what exactly is meant by the statement the "slides were cured". I have searched on Google for some answers but I have not found anything useful. Any insights are appreciated.

In this context, "cure" is a chemical term. Definition from Wikipedia :

Curing is a chemical process employed in polymer chemistry and process engineering that produces the toughening or hardening of a polymer material by cross-linking of polymer chains. Even if it is strongly associated with the production of thermosetting polymers, the term curing can be used for all the processes where starting from a liquid solution, a solid product is obtained.

So here it means that the slides were incubated at room temperature for 24 hours to let the mounting media harden. Of note, not all mounting media harden, some may require specific conditions to cure like UV light (example), and the curing step changes the properties of the mounting media like the refraction index. From the ThermoFisher website :

Formulations of mounting media that can add favorable properties such as optimizing the refractive index to match that of glass, preventing photobleaching, or preserving samples for long-term storage are widely available. Keep in mind that some require time to “cure” or harden. For mounting media that need time to cure, it’s important to let the sample fully harden before imaging so that you don’t inadvertently damage or destroy your sample by moving it around on the slide or cause photobleaching of your stained cells. Typically, the refractive index of the mounting medium will not reach its specified value until after it has fully cured, and its photoprotective properties will increase during the curing process. The degree of hardness after the mounting medium has fully cured will also vary; some will set like jelly while others will set like hard plastic

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What is the evolutionary advantage with two lungs (kidneys)?
What is the evolutionary advantage with two lungs (kidneys)? Most living beings only have one heart, one stomach. Most internal organs are not doubled and if one lung fails it is not exactly quite transparent due to having an extra lung. Before modern health care one failed lung would kill the individual.
The same can probably be said for kidneys.

Evolution does not have a purpose.  As for why things evolved that way, most animals are essentially tubes.  It would seem to take very little evolutionary change - basically a few mutations to the HOX genes - to create bilateral symmetry.

The heart is two-sided, each side doing pretty much the same thing, much like the lungs and kidneys. Could easily be separate, though wouldn't work as well together. Also, you should cite sources for your claims.

Does this answer your question? Why do some bad traits evolve, and good ones don't?

most organs come in pairs in vertebrates, (the heart starts as two separate organs embryonically) the digestive tract organs are the exceptions, you may want to reframe your question about that.

Humans and most organisms have bilateral symmetry.  Anything that is on the left side of the body will be on the right also.  Not everything can be in the middle, so ... you end up with two.  This is evolutionarily labile - for example, fish generally have one dorsal swim bladder, though it is derived from the lungs.  In a similar manner, the heart is formed by the fusion of primordia on either side during development - see UNSW for a cute video.

-1. Your thesis does not stand. The heart and other organs like spleen does not have bilateral symmetry.

Bilateral symmetry is of course an approximation - biology doesn't know theory.  But it is a good one.  For example, the spleen begins from the dorsal mesogastrium (the mesentery connected to the greater curvature of the stomach), making it, conceptually, an unpaired midline organ that merely reacts to surrounding circumstances.  In some humans the situation is more bilateral

Bilateral symmetry goes much further that the internal organs, of course, so bilateralism must be deeply embedded in the genes.  (Even structures like vertebrae are symmetric.)  So the question really should be why some few organs AREN'T paired or symmetric.

As I said, "other organs" in plural, with spleen being but one example, which do not have bilateral symmetry. What is the mechanism of all the other non-bilateral symmetric organs? With respect to the spleen in particular, it just begs the question: what makes the stomach non-bilateral symmetric? You can say they just compete for the same spot and randomly eking out a space and deforming each other. Why do all of them not have two or more which can all be arranged bilaterally? Another question is why we do not have more equal distribution of people having their hearts and spleen situated

randomly on either sides of the spine.

The nodal signalling pathway is clearly involved, which can be traced back to the clockwise motion of cilia in some species.  But I have not kept up with recent developments in this area; you should find more with a little research.

@Hans the heart actually starts as two sperate organs embryonically. the only organs that do not start as pairs are the digestive organs (stomach, liver, pancreas, spleen) because the digestive system starts as a single tube.

@John: Wow, really? Does the heart start out as two bilaterally symmetrically embryonically? If so, my previous other question still remains: why do we not have equal number of people having left situated and right situated single-organ heart and bilaterally symmetrically situated two-organ heart?

@Hans the heart starts as two unconnected blood vessels. this may help https://open.oregonstate.education/aandp/chapter/19-5-development-of-the-heart/ I have a whole answer in the unclosed question about this. https://biology.stackexchange.com/questions/100928/why-do-we-have-two-kidneys-but-one-liver/100935#100935 Your questions about bilateral symmetry are great questions I suggest asking them as a stack questions (look for identical questions first) but in short is comes down to shoving 30ft of digestive tract in 2 feet of torso and the fact we are no longer laterally narrow fish.

Two of the duplicated organs work better (e.g.: also kidney) or even enable something new (e.g.: depth perception for eyes). Source

Two hearts? Two brains?

Same applies to animals with multiple hearts or brains. https://www.mentalfloss.com/article/52337/3-creatures-more-one-heart And https://medium.com/illumination/the-animal-with-many-brains-that-makes-us-rethink-intelligence-1fc5e1325bcb

@d-b: Vertebrates do basically have two brains, separate left and right hemispheres with interconnections between them.

-1 for the falsehood. 1. Why is 2 the optimal rather than 3 or 4 or more like the number of teeth? 2. It is not true for other organs like the heart and spleen.

My answer addresses OP’s question (what are advantages of multiple organs). The question  is not, why different animals all are not the same / why they occupy a given niche in the evolutionary landscape (and hence experience different tradeoffs). Additionally Mike Serfas great answer well explains the developmental possibility of two organs.

@jamesqf they also have two hearts that fuse into a single one during early embryonic development.

Eels have two lungs and so do lungfish and all vertebrates, so the design is at least 375 million years old, although vertebrate lungs have developed different air flow systems, i.e. birds and iguanas. No vertebrates have a very small and big lung as far as I know.

Rib punctures can affect one lung which fills with fluid.
Stick and tooth punctures can actually cause air to escape the lung through the chest, a condition that can sometimes be survived in th wild, but less likely with only one lung.
Pulmonary infections can cause a lung to fill with water, so having two lungs gives some extra protection.
Breathed in objects like twigs can sit inside a lung for many years and cause weakness, for example a man coughed up a twig from his lung 14 years after having breathed it in while playing in a hedge with friends.
Two lungs may also bring higher surface area and higher performance than one lung.

Most of your points are deadly in a non-civilization (i.e., for all animals except humans living in a society that offers some surplus food etc) context, even if you have a spare lung. Re the surface are, that is why lungs are "wrinkled", and that works fine with a single lung.

-1. None of your points answer the question. Regarding the last point, the fractal-like structure of each lung already increases the surface. It is not necessary to have two to increase the surface.

Actually, if your lung fills with water from a stick/rib/pneumonia, you will die irrespective of the fractal structure, which is not part of the question, but having two lungs will stop the liquid spilling into the second lung and choking the vertebrate in question, and two hemispherical spheres have a surface area of 3.14+1.4, i.e. 30% bigger.

@d-b Humans have only lived as a civilization for 10,000 years, previous to that they were hunter gatherers with very low populations because the surplus-giving crops did not exist, and they inherited their lungs from other primates and the primates from basal placental animals.... Two hemispheres have 30% more surface area to place the wrinkles on in the first place, so a 5 liter double-hemisphere lung is equivalent to a 7.5 liter single spherical lung, approximately.

Given the total volume and a geometric shape  the more isolated domain of the same size one makes the more surface area one gets in the form of $n^{1/3}$ where $n$ denotes the number of isolated geometry. So for $n=2$ there should be $2^{1/3}-1~26%$ more area. It is not clear what you are computing and where 3.14+1.4 comes from. If you split a sphere into two hemispheres, the area increases by 50%, not 30%. More importantly, it is not the outer shape and area we are looking at. It is the ultimate (inner) surface shapes, i.e, alveola sacs we are talking about,

not the exterior shape which has nothing to do with respiratory gas exchanges. One needs only more and smaller alveolar sacs. So there is no need to separate into two largely isolated domains if our objective is just to increase the gas exchange surface. You do have a point in asserting the risk diversification. That though begs more questions. Why we do not have more than 2 lungs? Why do the other organs such as the heart and spleen have only one isolated unit?

The lungs and the windpipe both lead straight into the middle of the lungs and provide better air and blood distribution than if it was a sphere. https://cdn.britannica.com/s:690x388,c:crop/20/125820-050-F1FD8A7E/veins-arteries-human.jpg Do you also disagree about the  protective effects outlined in the first 4 bullet points, and disagree with only the last one? What about the puncture, pathogen and fluid protection afforded by two lungs? The heart and spleen can't absorb pathogens and twigs and get pierced by ribs as easily as the lungs can.

Let us continue this discussion in chat.

Please check out my response to your last comment in the chat.


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How could a cell only have chromosomes from father or from mother?
How could arrangement one even be possible? How could a cell only have chromosomes from father or from mother?

[Image modified from "The laws of inheritance: Figure 5," by OpenStax College, Concepts of Biology, CC BY 4.0]

Hi! I suggest you read the guide on how to ask a good question: https://biology.stackexchange.com/help/how-to-ask
For example, you might add an explanation on why you think the example is not reasonable, and we may be able to help you.

That graphic is just confusing you.
The cell doesn't keep track of all the chromosomes from Mother versus all the chromosomes from Father so it can sort them out later.  That I know of!  [I don't think imprinting counts because its effect varies between genes]  But the paternal and maternal chromosomes are still separate before meiosis - there hasn't been any meiotic crossing over during fertilization or mitosis!
So by chance, in this diagram, two chromosomes from one parent went one way, and two chromosomes from the other parent went the other.  For 2 chromsomes the odds are 50-50.  For 3 chromosomes the odds would be 1/8+1/8 = 1/4.  For 23 chromosomes the odds would be 1/4000000.
However, the figure isn't finished misleading you!  During prophase I, there is also chromosomal crossover which exchanges segments between the two chromosomes.  So even in that very rare case when a child inherits one parent's form of all chromosomes ... it is still mixed in with stretches of the other parent's DNA.
I like OpenStax, but they are still in an early stage.  Their graphics are weak and many errors can be found.  But as long as you keep up this attitude of challenging your sources and asking questions, you can thrive using resources like this.


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Are there known genome sequencing issues in E. coli?
Despite the fact that the human genome project was declared "complete" in 2001, there are even now still gaps due to difficult-to-sequence regions of the genome such as telomeres and centromeres. Only last year was the first entirely complete chromosome sequence produced.
Telomeres and centromeres, however, are specific to eukaryotes.  Are there similar challenges with prokaryotes? A recent publication on a gapless E. coli sequence implies that there are indeed typically gaps, but I can't tell whether this indicates any systematic challenges, as with the human genome.
Thus, my question: are there known genome sequencing issues that currently make it difficult to acquire complete genome sequences from common lab strains such as E. coli?

Generally, gaps in genomes occur due to failure of de novo assembly -- the DNA can be sequenced accurately, but cannot subsequently be placed into a contiguous assembly due to alignment ambiguity with adjacent sequences.  In eukaryotes, telomeres and centromeres are difficult to assemble from short reads because they are highly repetitive. In bacteria, repetitive regions of the genome can cause similar problems when assembling from short reads.  Such regions include CRISPR arrays, integrated mobile elements (e.g. transposons), and gene duplications.1,2
So, what made a short-read no-gap assembly of E. coli strain C difficult, specifically? Alignment of the original short-read assembly 3 to the long-read reference 4 with Mauve 5 gives positions and length of gaps.

The first gap in the ordered short-read assembly (left-most red line in the figure) occurs at position 15,085 in the first contig and is 320 bp long. Looking at the same region in the long-read assembly, this closely corresponds to a 236 bp tandem repeat (CTGG × 59) at position 14,848. The authors of the short-read paper used 150 bp paired-end MiSeq reads to create their assembly, which, after adapter trimming, would likely not give enough sequence context flanking the repeat region to span it with a single read, thus creating a gap. This is just one example, and the rest of the gaps could also be repeats or other aforementioned mobile elements.

Treangen TJ, Abraham AL, Touchon M, Rocha EP. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev. 2009 May;33(3):539-71.
Ricker N, Qian H, Fulthorpe RR. The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics. 2012 Sep;100(3):167-75.
https://www.ncbi.nlm.nih.gov/nuccore/MNKV00000000
https://www.ncbi.nlm.nih.gov/nuccore/CP029371
Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004 Jul;14(7):1394-403.

Does this mean then that long-read sequencing, like with PacBio or Oxford Nanopore, shouldn't expect to run into any gap issues in E. coli and similar?

The key point is that many regions that cause short-read assemblers to fail (causing gaps) can be spanned by long reads. Repeated regions and tandem repeats in bacteria tend to be on the order of hundreds or thousands of bp long, and can therefore be captured by single long reads, which can be >10k bp for Nanopore and >100k bp for PacBio.

Thank you, this is very clear @acvill. Out of curiosity, are the eukaryotic repeats much longer and thus harder to deal with, or are those readily addressed by recent sequencing technology as well?

I know less about eukaryotic repeats, but the background of this paper seems to be a good resource: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-1-r10.  If you have more questions, I'd encourage you to make a new post.

Summary
The publication of the first complete DNA sequence of Escherichia coli was for strain K-12 substr. MG1655 in 1997. Because of historical limitations in the technology used (rather than problems with repeat sequences or instability in the genome) this contained mistakes, which were subsequently corrected as the sequencing technology improved. An international consortium reported on this (and revisions in gene annotation) in a paper in 2006. Because of the extensive use of E. coli in biological research in the 20th century, many different strains have been used for different purposes and many sequences have been reported. The strain referred to in the question is strain C, which has only just been completely sequenced (or its sequence only just reported), presumably because nobody had the need to do so previously.
Technological context
The Wikipedia entry on DNA Sequencing contains the graphic reproduced below, showing the decline in the cost of sequencing between 2001 and 2019.

[Based on data from the National Human Genome Research Institute]
This decline in cost was the result of both improvement in methodology and automation, and also reflects the speed with which sequences can be obtained and hence the ease of repeating them. The E. coli DNA sequence published in 1997, and was only the seventh complete genome to be reported. The following extracts from the section of the paper on sequencing strategy gives an idea of the the various methodologies employed and problems encountered:

Sequencing was carried out in sections, with steadily improving technical approaches. The M13 Janus shotgun strategy proved to be the most efficient strategy for data collection and closure… The first 1.92 Mb… was sequenced from our overlapping set of 15- to 20-kb MG1655 lambda clones by means of radioactive chemistry and was deposited in GenBank between 1992 and 1995. Subsequently, we switched to dye-terminator fluorescence sequencing (Applied Biosystems). In addition to greater speed and lower cost, this new technology avoided electrophoretic compression artifacts, which, owing to its 50.8% GC content, occur in practically every gene of E. coli…The final stages entailed special attention to problem areas. The region between positions 0 and 22,551 did not yield a suitable I–Sce I fragment, so three lambda clones were selected to finally complete the genome. One of them was found to contain a deletion and had to be finished by shotgun sequencing of a long-range polymerase chain reaction (PCR) fragment.

Note in particular that newer, more accurate, sequences were combined with individual genes previously sequenced, and the reference to compression artefacts — the bugbear of separation of fragments by polyacrylamide gel electrophoresis. Not mentioned is the mistakes that can be made using the Maxam–Gilbert (chemical) method if one is not aware of the effect of methylation.
It is not surprising that there were mistakes in this sequence (and, indeed, in many much shorter sequences, often published in a hurry to obtain priority.)
Tracing the history of the K12 sequence
I think it worth explaining how I found out about the subsequent changes in the sequence, as the general approach may be useful to those that are not aware of it.
I started by locating the original paper by a simple Internet search. From this I obtained the accession number (an ID) of its deposition at GenBank — AE000137 — and searched for this on the NCBI website and found that it had been replaced by another entry, U00096. In the header of the entry, after the summary information regarding the organism and sequence, there is a reference section of the type:
REFERENCE   1  (bases 1 to 4641652)
  AUTHORS   Blattner,F.R., Plunkett,G. III, Bloch,C.A., Perna,N.T., Burland,V.,
            Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F.,
            Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J.,
            Mau,B. and Shao,Y.
  TITLE     The complete genome sequence of Escherichia coli K-12
  JOURNAL   Science 277 (5331), 1453-1462 (1997)
   PUBMED   9278503
REFERENCE   2  (bases 1 to 4641652)
  AUTHORS   Hayashi,K., Morooka,N., Yamamoto,Y., Fujita,K., Isono,K., Choi,S.,
            Ohtsubo,E., Baba,T., Wanner,B.L., Mori,H. and Horiuchi,T.
  TITLE     Highly accurate genome sequences of Escherichia coli K-12 strains
            MG1655 and W3110
  JOURNAL   Mol. Syst. Biol. 2, 2006 (2006)
   PUBMED   16738553
REFERENCE   3  (bases 1 to 4641652)
  AUTHORS   Riley,M., Abe,T., Arnaud,M.B., Berlyn,M.K., Blattner,F.R.,
            Chaudhuri,R.R., Glasner,J.D., Horiuchi,T., Keseler,I.M., Kosuge,T.,
            Mori,H., Perna,N.T., Plunkett,G. III, Rudd,K.E., Serres,M.H.,
            Thomas,G.H., Thomson,N.R., Wishart,D. and Wanner,B.L.
  TITLE     Escherichia coli K-12: a cooperatively developed annotation
            snapshot--2005
  JOURNAL   Nucleic Acids Res. 34 (1), 1-9 (2006)
   PUBMED   16397293
  REMARK    Publication Status: Online-Only

These three are journal references: there are 15 others which are just direct submissions to GenBank, most by Blattner’s group. Some of the earlier ones are marked as corrections. The later ones I assume are mainly concerned with the annotation of genes rather than the sequence itself. The latest date is 2014.
The authors of the 2006 Nucleic Acid Research paper write:

“Corrections to the original MG1655 genome are at 243 sites (totaling 358 nt), a correction rate 8 years later of ~7 in 105.”

They also make clear the problems of differences in what purport to be the same strains, which have mutated over the years through passaging and transfer to different labs (despite, no doubt, the best efforts to control this).
Reporting bacterial sequences today
Even in 2006 it required some effort to collaborate and correct a bacterial sequence, whereas today (2021) it would appear trivial to resequence any strain of interest. Thousands of E. coli sequences must have been determined. It may be of practical importance to workers using different bacterial strains to know when they have been sequenced, but it is now impossible to publish such in a standard scientific journal. It appears that the American Society for Microbiology has addressed that problem in a section of their journal (Microbiology) entitled “Resource Announcements”, which are little more than announcements of the deposition of a particular sequence. This would be the case for E. coli, strain C, which provoked this question.

I'm afraid that, while this is a nice summary of historical challenges, it doesn't really address the current state of play.

With all due respect, your question was about whether there were general problems sequencing E. coli and why a recent report made a point of the fact that the sequence was ungapped. I don't see anything about the current "state of play" in the question. It seemed necessary to explain why that the gaps in E. coli sequences were due to deficiencies in the technology when they performed, rather than structural problems, as in telomeres. And rather than just telling you this, I explained how to find this out for yourself, as your question seemed to indicate an ignorance of sequencing history.

Apologies; I thought that was clear from my discussion of systematic challenges and the nature of the organism, as opposed to technological challenges. I've added the word "current" to make it explicit.

@jakebeal Whatever. I try to make answers generally useful, rather than merely to the poster. I think this one is, as ignorance of the development of science and how to use GenBank entries is widespread.


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What does q stands for in Gq/11 alpha subunit?
Sorry for asking, I am not capable to find what does the q stands for in Gq/11 alpha subunits.

I know the term must have shown up somewhere between this paper in 1989 and another in 1995 referencing it.  The latter paper defines Gq as a broader class of proteins, and uses G alpha q for a formerly numbered clone.

@Mike Serfas Thank you. I am very appreciate that. :)

@MikeSerfas Since your comment seems to have been useful to the OP, do you want to turn it into an answer?

@LukasChumchal To make your question more useful for others, can you expand a bit to give context?

@jakebeal Thank you for noticing my question. I am actually studing for molecular farmacology exam right now and i know that my profesor said that she doesnt know that reason for this abbreviation. So this made me more curious about the it (i am very used to that abbreviation in biology have usually quite important reason behind it). I tried my best to actually find out the answer myself but failed horribly. Thats all what i can said.

@jakebeal I really can´t think of more specific reason/context for this question. It´s just really about the abbreviation. Nothing else. Nothing more.

@LukasChumchal This site has a very broad audience and subject matter, so explaining a bit more of what you're talking about would be useful. What is a Gq/11? What is its alpha subunit? Is this a protein? Is it a drug? Does anybody know what a Gq/11 alpha subunit does? Why would anybody care about it?  If you give a couple of sentences like that, it will help people who aren't sitting in class with your professor understand what your question is about.

@jakebeal you got a poit. However if you have no clue about stuff you mentioned, you are not capable of answer it anyway. So what is even point of adding more information about mechanism/role of Gq/11 in this case?

@LukasChumchal It will improve the information that you get, because it will demonstrate to people that you actually understand the subject you are asking about, rather than just being a lazy student who is pretending so that you can get somebody else to answer your homework. It will also help other people in the future who may be wondering about the same or similar questions.

@jakebeal I understood your point from your first comment. However do you thing that this question is really suitable for homework? I understand your life philosophy. However not everybody is in this times lazy individuals, who does not wont to work to archive some goal. Right now i feel like i am getting yelled by you becaus i was curious about this topic. Just you may try to actually find the meaning behind Gq yourself. I faild after reading 5 articles about it.

@LukasChumchal Apologies, I'm not trying to be rude, but to provide guidance on the typical expectations around question asking at StackExchange. You can read in the help center for more details: https://biology.stackexchange.com/help/how-to-ask If you're not interested in improving your question, that's fine, but be aware that as a result you may receive downvotes and the question may end up closed and deleted.

@Lukas while I disagree that it should be necessary to explain in your question all the details of how GPCRs work, what would have made the question better would have been to include references to the 5 articles that you have read for instance... It's not so much that we want you to make a 10,000 word essay on everything you know as we want to know where you're coming from and what you've tried so far.  It might not make much difference in this particular case, but for future reference, questions will be better received with such information included.  Thanks! Oh, and welcome aboard!


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Relationship between BMI and age?
I'm trying to study how age as a confounder may affect the relationship between commute mode and BMI (and design a research proposal).
To explain age as a potential confounder, I compared age to commute mode and then age to BMI. I found a weak association between age and BMI in my data.
In the literature does anyone know if BMI is expected to change with age? Is there a linear/ other relationship form? Please could someone attach any papers/ links for help.
Also, does anyone know what a clinically meaningful BMI is too? Would a change of 1-2 be important?

interesting - well thought! whether "important" could depend on what interests you, and may could only be answered after your model is complete. from the perspective of study design, you might run into the question of how sensitive your study / model should be (e.g.: should it be able to possibly be able to measure whether a BMI difference of 1-2 should have an impact on the entity you are interested). The relationship between BMI and age might depend on country etc, but at least in the USA is not linear (https://dqydj.com/bmi-distribution-by-age-calculator-for-the-united-states/ )

In (US) NHANES 2011-2012 data there is a significant quadratic relationship for 16+year olds:  males:  E(BMI) ~ 21.26 + 0.03age - 0.003age^2, females:  E(BMI) ~ 18.2 + 0.47age - 0.004age^2, highly statistically significant.  But the R^2 are not large (3% and 5%).  This is with around n=3000 in each group.  (I just pulled the NHANES data and ran the regression, so I don't have a citation).


text:
Are 2A cleavage sites functional in bacteria?
In mammalian cell lines, 2A self-cleaving peptides are frequently used to for expression of multiple genes from a single transcript. They've got some issues, e.g., leaving some proteins as fusions, but so do all of the other options, so 2As are a pretty good choice for many situations.
I have found 2As being used in many other organisms as well, including yeast and plants, but they seem to generally not be used for bacteria.  I've found a couple of articles (e.g. [1], [2]) that do claim to have successfully used 2A sequences in bacteria. If this actually worked well, however, I would expect to see it much more widely used.
Are 2A sites in fact functional in bacteria and, if so, are there any issues that inhibit their use there?

2A self cleaving peptides do apparently work in bacteria (as the papers in your question suggest), but it seems that they are not commonly used in these chassis simply because they are not needed.
For context, in prokaryotes, translation is initiated by the ribosome binding to a shine-dalgarno (SD) sequence on the mRNA. These SDs can be placed anywhere along the mRNA strand, and so multiple SDs can be present. This means that translation can begin at multiple points along the mRNA, and hence proteins can be co-expressed by one promoter by including multiple RBSs and stop codons within the expression unit (i.e. promoter-RBS-CDS1-stop-RBS-CDS2-stop-terminator).
However, in many eukaryotes, translation begins at the 5' end of the mRNA where the ribosome is assembled, and scans along the mRNA until it finds the start codon. Once the protein has been synthesised and the stop codon reached, the ribosome falls off of the mRNA. This means that if there was another CDS encoded after the first stop codon, it won't be translated.
It should be noted that it is possible for eukaryotes to generate mRNA encoding multiple proteins, but as it was assumed for a long time that this was unique to prokaryotes, there is less research for this in eukaryotes. This paper has some useful information: https://academic.oup.com/femsyr/article/2/2/215/536601.
Because of these differences, for most applications, if co-expression in bacteria is required it is much simpler to add in multiple RBSs and stop codons than to rely on something like 2A peptides which, as you mentioned, do not always work and can result in fused proteins. However in eukaryotes, techniques such as 2A peptides are important considerations for co-expression as poly-cistronic mRNA (mRNA encoding multiple proteins) seem to be much less common.
This doesn't mean that there aren't applications for 2A peptides in bacteria, but they are much more specific and hence their use doesn't turn up so much in the literature.
These wikipedia pages have some good reading and references:

https://en.wikipedia.org/wiki/Internal_ribosome_entry_site
https://en.wikipedia.org/wiki/Eukaryotic_translation

Disclaimer: I don't work with eukaryotes so most of the information about gene co-expression and how common it is has been gathered from reading for this question.

Very interesting, thank you! This is the opposite of what I was guessing, given my past experience where eukaryotic techniques don't work in bacteria because bacteria have a more constrained toolkit.

A potential advantage of 2A peptides over multiple RBSs is that the former ensures a 1:1 ratio between the resulting proteins.
Also note that 2A peptides are not actually cleaving the peptide chain (i.e., there is not proteolytic activity involved). "Cleavage" is instead the results of ribosome skipping.


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How to find a model organism's standard data about proteome size and genome size?
I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc.
I found www.uiprot.org
and I made a table which is wrong according to my prof.

for example, I searched "Saccharomyces cerevisiae" on the site.
https://www.uniprot.org/proteomes/UP000002311

I wrote 6,049 on protein. and clicked the link "GCA_000146045.2 from ENA/EMBL" on Genome assembly and annotation.
https://www.ebi.ac.uk/ena/browser/view/GCA_000146045.2

I clicked "Assembly Statistics" on the right box and wrote the total length.
where am I wrong?
It seems there are so many samples about a species. I don't know which is standard reference for the model organism. I want data as a general knowledge like on the text book
and I found model organism database sites on wiki
https://en.wikipedia.org/wiki/Model_organism_database
I don't know how to use these sites. they give me complicated sequence browsing but I only want just proteome, genome size. what should I do?

EDIT.
professor didn't tell us about strains. he just gave the table at the top of this post with data about E.coli by red text as a example.

this is what professor showed on his next lecture, which is other student's answer.
professor didn't mention which is correct or wrong, he asked if the student is sure about the source(Yu Nie) and if the source is reliable.
anyway, comparing this to my table, Mus musculus and Drosophila have significant difference.
Mus musculus other: 39,412, mine: 55,474
Drosophila other: 30,443, mine: 22,117
I searched again about these.

Mus musculus have only two result, it seems I should have chosen standard rather than close to standard.

but about drosphila, they have no standard. (I chose random one)
https://www.uniprot.org/proteomes/?query=drosophila+melanogaster&sort=busco&desc=no
where can I find about Drosophila?

when your professor asks about proteome size, do they mean number of proteins or length of proteins? usually the second is what is meant.

@Maximilian Press number of proteins.

I see nothing wrong with your method -- uniprot is a good resource. If your professor expects statistics for specific species / strains, they should supply unique identifiers or accession numbers for those organisms, at least. Did they give more information about which numbers in your table are wrong, specifically? Can you quote the wording of the assignment?

@acvill I added what you asked.


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Statistician confused about exact SNP data type
I'm from a statistical (not biological) background, and I'm very confused about what exactly is the "data" associated with a SNP. Below, I'll explain things as best I can--please correct me if any point is wrong or otherwise unclear. Assume we're working with humans, since the following will change depending on the species. (Assume all cases of interest are biallelic.)
When a locus has an allele on least one chromosome, the measurement AA, Aa, or aa is called a SNP (pronounced "snip"). Therefore, using statistical language, SNPs are three level factors--this is the data associated with a SNP. As said earlier, if the factor has 1 level (ie it's only aa or only AA) then it's not a SNP.
Sometimes for humans it seems like people say a SNP is actually just one allele (so a two level factor, a or A). How is this possible? Do people sometimes only measure one allele instead of both to get the genotype?

Could you provide the source where they refer only to one allele?

@Hachiloni There is no one source, but this is an example: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0218306 . See the paragraph which begins "Second, we compare three SNP codings..."

You have laid out what your knowledge of SNPs in an admirable fashion, except for one important thing. You do not state what SNP stands for. The name describes the concept: single nucleotide polymorphism. A polymorphism is literally a difference in shape (here a difference in the physical form) of an object. The object is the DNA sequence of a gene, and the difference is in a single nucleotide. It is not defined by whether the alleles are Aa, AA or aa — just by the fact that at this position different bases are found (generally 2, but could be 3 or 4). Do what you will with your statistics.

Thank you, @David. That's a very helpful point--I ignored where the term "SNP" came from completely. (I've edited the answer to address that I'm focused on the biallelic case.) I'm not focused here on what to do with the data (i.e. what statistics to do), just what the data itself looks like. I believe this is a biological question since it's certainly not statistical. If the data was "a" or "A", would you think that's SNP data? Or must the data be "aa","Aa", or "AA" to be SNP data?

I don’t know. But surely there is a vast literature on this. I read (skim) papers in Nature on large comparative genome projects which refer to the incidence of SNPs. There was one in February. The impression I get is they are just looking at whether different bases are found at particular points and how many there are in the genomes they have sampled. You would really have to find the references to their methods and check yourself (unless someone else here knows).

@David Thanks again for your helpful perspective.

I think the prevuious answers provide lots of valuable and relevant information, but let me add additional prospective:

As noted, SNP is a single nucleotide polumorphism, whereas notation AA, Aa, aa, etc. may refer to many other types of mutation: e.g., these could be whole genes, differing on many locations. Another common type of mutation is insertions/deletions, where one gene may lack whole segments (rather than  contain different nucleotides).
SNPs are used in particular contexts, where the change of genome is insignificant: e.g., when treating highly conserving human genome or when treating a variable genome on a short time scale, where only few changes happen. In this case we take the most frequent/initial genome as the reference and describe deviations from it as SNPs ("snips"). This is not always, possible - e.g., when multiple alleles are present (a single nucleotide can be in four states, A, C, G, T and all of these may have to be accounted for, e.g., when analyzing the evolution of viruses).
Depending on the problem, one may want to discuss population genetics of an organism in terms of genotypes or in terms of allels - even when a single organism carries multiple allele (e.g., two copies in a diploid organism). AA, Aa, aa are genotypes, whereas A, a are alleles. SNP is a change in allele rather than in a genotype. (But I do admit that biological language is often unprecise.)

Wow, thank you. This is incredibly helpful and fills in a lot of missing gaps for me.

@user257566 I also come from non-biological background, so I probably encountered similar issues in understanding these things. For population genetics I recommend also the Gillespie's little book. It is somewhat sketchy, but might be easier to work through than real pop gen stuff: https://www.amazon.com/Population-Genetics-John-H-Gillespie/dp/0801880092

SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism"  only means there is a variability (between individuals) in a single letter in a specific position in DNA sequence. It depends on the speaker how they decide to describe the variability; wether they choose to focus on the possible sequences and say for example "There is only A or T in this position" or they focus on possible human genotypes and spells out all combinations (AA, AT, TT).
What constitutes as SNP data depends entirely on research question, used organism (diploid/haploid/polyploid) and experimental design.
Article you link in your comment uses oat lines and not individuals from outbreeding population. Oat like arabidopsis is naturaly highly self polinating so creating highly homozygous inbred lines is relatively easy. In this case it is reasonable for the researches to expect only AA or aa genotypes in each line.
Edit: Since you asked for more examples where the researcher chooses to focus on alleles instead of genotypes. Many SNP genotypes distribution fit Hardy-Weinberg equations. If that is the case, the frequency of genotypes can be calculated from an allele frequency in population. The researcher might ask: "Is the frequency of allele a different in population/group 1 from population/group 2?" They collect data from indivuduals in group 1 (AA, AA, Aa, Aa, aa) and group 2 (Aa, Aa, aa, aa, aa). They decide to treat each allele as independent measurement (not dependent on individual it comes from) and poll the data: group 1 (AAAAAAaaaa), group 2 (AAaaaaaaaa) and then they do simple binomial test to answer their question.
Note: Even if Hardy-Weinberg equilibrium is not met, the questions about of allele frequency are is still valid biological questions (with slightly different use/interpretation down the line).

Thanks. Could you provide other examples where it's reasonable to only focus on the value of one allele (when ploidy is at least 2) to constitute a SNP? Your argument for the linked paper seems to be that researchers who care about the genotype can only measure one allele, which is interesting but circumvents the core problem I'm having.

Thanks for including the interesting edit. Not to bleed you dry here, but unfortunately due to my limited biological background, any allusion you make it completely lost on me. Could you clarify with examples what you're describing in the last sentence on when HW is not met?

I can refer you to Khan academy on HW principle. HW has several asumptions any of which can be not true in a real population. What I ment to say is that even in this situation it is still meaningful to talk about allele frequency. For example when a species is highly self polinating (like oat) resulting in more homozygots than expected from HW, we can still ask: is one allele more frequent in eg. high altitude population?

Let me give you a back of the envelope calculation. The size of the human genome is 3 billon base pairs (BP). There are about 30 thousand genes in the human genome. Therefore, the size of a gene would be around 100 thousand BP (DNA does have non-coding regions, regulatory regions etc. Also a gene vary in size from a few hundred BP to more than 2 million. For the sake of simplicity, we can stick to this calculation). On the other hand, there are 5 million SNPs in human genome. Therefore, There would be a SNP in every 600 BP.
So, we can say with certainty that there would be genes that have more than one SNP. My suggestion would be, as @BagiM pointed out, do not confuse microscopic concepts with macroscopic ones.

Thank you for sharing your perspective. By "a or A" I meant an allele at a single locus, by "aa or Aa or AA", I meant a pair of alleles which constitute a genotype (in a human). Could you clarify what you mean by switching between microscopic and macroscopic?

SNP is a microscopic concept and Allele is a macroscopic concept. Allele is a very broad term and the molecular basis of this term could be numerous (@Vadim discussed it in his answer). The term was coined by Mendel himself. That too a long time before DNA was discovered. "a SNP is actually just one allele" -- is a wrong statement. There could be multiple SNPs inside an allele.

Thank you for clarifying my terminology--that's very helpful. I'm referring specifically to an allele as a variant in one base pair, and a genotype (for humans) as a pair of such alleles still at one base pair but now across two chromosomes. So my question is specifically about which one (between these two microscopic things) is used to represent SNPs.

None. SNPs are not defined in terms two chromosomes. Huge collection of DNA sequences are compared and specific positions on the sequence are found to show this polymorphism (which we call SNPs) while other regions of the sequence remain relatively conserved.

Ok, by none do you mean the former? The single loci?

SNP or not is something independent of how many chromosomes or alleles you are working with. To me, your question does not sound valid. Could you try to rephrase the question? Are you asking it for a specific allele or chromosome? If so, please look up what are the SNPs defined on that allele or chromosome from a genome data bank.

As said earlier, if the factor has 1 level (ie it's only aa or only
AA) then it's not a SNP.

If there is any variation in that base in your population, then it is a SNP, even if you are not looking at a heterozygote.
Anyway, if you are talking about a SNP, people will generally refer to it by its base, not be the name of the allele it generates.  (And actually lots of time, the alleles are not named as simply as A and a.  That notation is helpful when dealing with perfectly Mendelian middle school genetics homework problems, but in the real world, most data doesn't fit that paradigm.

Thanks. That quoted passage is in fact saying if there's no variation (ie if its only aa or only AA that have been observed). Further, it's been a while since I've been to middle school so it's helpful to know what's covered there for context. However, I'm not talking about how to name SNPs (personally, I'm familiar with rs numbers for that.) Instead. I'm talking about what values they take. Names for things are helpful for me here than the concept they represent.

Why would you have notation for different alleles if there was no variation in any population?


text:
Why is there a notch in the Na curve for an action potential?
Just out of curiosity, why does the Na curve dip down like in the figure below? I can't seem to find an explanation!

AP? Please do not use non-standard abbreviations in questions, especially in titles as they defy the indexing system this site relies on and confuse readers.

Please [edit] your post to include the source of your figures — you should always include reference information for quotes and images. Also, are you asking about the left panel or the right panel ? ——— I made what I believe to be corrections to your title (nudge makes no sense in this context) — please check that the new wording is consistent with what you were trying to ask.


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How come Draq5 stains cytoplasm and membranes under confocal
Just an imaging question on the back of my head.
For nuclear counter stain, Draq5 has been an excellent choice for many people over many years. And I too love it.
The working principle of Draq5 is the nuclear dye Draq5 binds to doubles strand DNA, especially d-A and d-T. That is to say it is very specific to stain nucleus DNA, minimal binding to mitochondria DNA, and no binding to RNA. It is also a very good live cell permeant dye.
In practice, we use it to stain cell nucleus and then perform image analysis, the primary objective in image analysis is identification of the cell object, usually through nucleus staining. No problem, Draq5 does this perfectly, I can see my image crispy clear.
Next, it comes to the estimation of the entire cell, that is to find cell membrane boundaries. A huge advantage of Draq 5 is it also stain cytoplasm and cell membrane weakly, allowing the accurate detection of cell boundaries. Comparing this to Hoechst dye, which also stain nucleus and weakly cytoplasm only for estimation of cell boundaries. This is unlikely a Draq5 non-specific binding, since data from resistant cancer cells that have membrane drug pumps still retain Draq5 very well.
I'm not a chemist so that one thing in the back of my head is:
Why does Draq5 bind cytoplasm and outlines cell membranes that well? Given it is highly specific to bind A/T in double strand DNA grooves. Presumably the dye is binding to its cytoplasm target and membrane target via different mechanisms. Can someone explain that?

Welcome to Biology.SE! Please provide more details and tell us what you already know (this provides context for answers and helps demonstrate that you have done the expected prior research). In particular, if you are seeing an unexpected pattern of staining it would be helpful to include images showing 1) the expected pattern (e.g. from prior research published using this dye — make sure you include reference information and links for these) and 2) what you are seeing (including details of the cells type/tissue, growth, and staining). ——— Off-hand I would guess that you are seeing an artifact.

Unsure if question ultimately seeks practical advise. If so: Ensure application to living cells and avoid fixing and permeabilization. If problem persists: do saturation curve with concentrations spanning some orders of magnitude.

Sorry, I was just lost in my thoughts and posted the half baked idea. Here I have updated my thinking. @tsttst, the staining of cytoplasm and cell membrane happens within its working range, this is actually the advantage of Draq5. In my own experiment Draq5 intensity far from saturation, I can see it over the range set by 16 bit camera, intensity is about the same as my TMRE.


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Is publication an important criteria to get a post doc in microbial ecology?
I am a researcher in microbial ecology , currently searching for post doc in European countries. I have publication less than 1 impact factor. Will this hinder my chances of getting selected . Please suggest?

Welcome! You might get a good answer (or find a similar one answered) on http://academia.stackexchange.com ; Personally, I would recommend to rephrase your question slightly to invite recommendations that will help you further (rather than getting a yes/no answer), e.g.: "Only published in low impact journals - how to maximize chance to do a PostDoc position in Europe?". You could possibly also add other information (e.g.: whether other students in your current department publish similarly).

We can also migrate the question to academia, if you want to.

I agree that this is not the best community for this question, since it is not really about biology. But to give a glimpse of an answer:

Having publications in high rated journals certainly increases your chances of getting a postdoc position.
It also depends on the general level/rate of publications in your field: in some fields having a few publications after a PhD is normal, while in the others the first publication may appear in press years after you graduate (not counting the thesis).
Then again, a publication in a top journal does not necessarily testify to one's abilities - e.g., if you are one among a few dozens of authors.
Networking and personal recommendations are often as important in getting positions as having publications.


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Are genetic crosses between asexual organisms possible?
To my knowledge (Please correct me if I am wrong), genetic basis is the key in defining species. When we encounter an unknown species, we can sequence it's genome and compare the genome with other known organisms from the genome data bank and see if there is a significant similarity. If no significance were found then we can call it a newly discovered organism. Also careful study of genetic crosses between species pairs and partially isolated sub species to identify general patterns in the genetics and origin of reproductive isolation helps to answer the question of speciation. Then how would we cross asexual organisms like many bacteria or protists? Is it possible to cross asexual organisms? If not, how do scientists study their genetics and define species of asexual organisms?

What do you mean by "genetic basis is the key in defining species"? If you are assuming that the "definition" of a species is related to the ability of individuals to produce fertile offspring then you need to learn more about 'species concepts'. You could start with this post. This post is also very relevant.

When it comes to viruses and bacteria, genetic cross is just as a vaguely defined concept as species. The latter is often defined on the percentage of the sequence similarity (for viruses) or the percentage of common genes (for bacteria).
If we speak about simply mixing genomes of different organisms, there are many possibilities, how this could happen. Just to give a couple of examples:

Some viruses integrate their genome into the host genome. In some cases these integrated genomes cease being functional viruses, and may evolve to be functional genes of the host. This is truly a genetic cross. See here, for example.
Bacteria and viruses routinely undergo horisontal gene transfer in which genes from one bacteria are integrated into the genome of the other one. A typical bacterial species has a few hundred core genes, and thousands of genes that are present only in some specimen or borrowed from other species, which significantly vary from one bacteria to another. Thus, every individual bacteria or bacterial community can be thought of as a genetic cross.

Thank you very much for the write up. I knew about the reverse transcription process (I leant about it while studying HIV) and also horizontal gene transfer. But never thought these concepts could be related to crossing in any manner. It seems to me defining a species that do not undergo sexual reproduction is even more difficult. Especially with polyploidy and multinuclear cases.


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How long will a typical bacterial strain keep in a -80°C freezer?
I know that a -80°C freezer is the recommended means of long-term cell-line storage, and that cells will typically not last long in a -20°C freezer.  But how long will a typical bacterial strain (e.g., E. coli DH5-alpha) actually stay good in a -80?
Searching around via Google, I'm finding a wide range of answers, anywhere from only 3 months to indefinitely, so I'd like to try to get a better grounded way of estimating longevity.

For what is worth, our 6 year old agrobacterial strains in -70 freezer seem to grow just fine. However, I am not sure I would notice if some percentage of cells died, since we don't take precise amount of the mixture when taking a bit for growing.

Exactly: I'm finding lots of anecdotal data points, like this, which makes me very uneasy about predictability of lab operations.

How predictable do you need your storage to be? There are many things that can happen in several years time. Freezer can fail without people noticing until morning. Someone can forget bacteria outside after using them. If my strains die I can make new ones with the same plasmid. For important stuff, there are backups.

Right now, I'm just trying to find out what the baseline is with a standard -80 and typical operations in order to understand the level of worry that I should be starting from.

To be frank, there probably isn't one answer. It will likely depend on the organism and possibly the specific strain you're preserving, how they were cultured, the concentration and type of cryoprotectants used, and the starting concentration of viable cells, among other possible factors. In any case, the decline in viability is likely to progress slowly enough at -80C that you'll notice before total loss of viability, as long as you're using a sound practices.

If you're truly worried about it, in terms of continuity of operations, I'd suggest a regular schedule for replenishing or replacing freezer stocks, either by sub-culturing and generating new ones, or simply ordering new stocks (assuming you're working with commercially available strains).

There are viral strains preserved from 50+ years ago. RNA is generally more sensitive to temperature.

I'm a bit too busy to write a detailed answer, which for bacteria actually seems necessary as they seem to have more variability than viruses in terms of cryopreservation, but see https://academic.oup.com/femsre/article/29/5/897/547905 (in particular section 7) for quite a few details. (Alas that was written 15 years ago.) Strangely enough, for some algae, freezing turns out to select some sub-populations in the process. I have no idea if anything like that was observed for bacteria.

I suspect that it might vary depending on factors such as the species of bacteria, whether they can regrow from spores, and whether or not ice crystals formed inside the cells of the bacteria and killed them.

The actual practical limit may depend on the long term stability of the cooler. For example, firefighter need to be informed, and have access pipes from outside to flood the room and probably the cooler with liquid nitrogen. I am not sure, but I think something like this is done in some maximum security virology labs.

@BagiM In practice the important labs have a combination of 1) really good insulation (this is important for keeping costs reasonable, anyway), 2) battery backups, 3) off-site monitoring with automatic notifications, 4) on site overnight security that can handle the unexpected (by calling the appropriate person for whatever area has alarms going off).

The reason you haven't found a definitive answer is that it depends on several factors.
The first factor that comes into play if we consider only ultra-low freezers (- 80 °C) is the organism you're freezing. Thermofisher gives an approximate time of bacterial cultures viability between 1 to 10 years :
$$\begin{array}{|l|c|c|} \text{Condition} & \text{Temp (°C)} & \text{Time (approx.)} \\ \hline
\text{Super-cooled freezer} & \text{-80} & \text{1 - 10 years} \\
\end{array}$$
For ATCC, the shelf life is even shorter :

-80°C is sufficient for most bacteria and fungi for short-term storage (5 years or less)

However, in Table 1 from She and Petti (2015), we can see that the shelf life - for an ultralow-temp freezing storage (-70 to -196) - varies greatly both between the organism groups and inside each group : up to 1 year for the Streptococci group and up to 3 decades for the gram-negative bacteria for example.
$$\begin{array}{|l|l|c|} \text{Organism group} & \text{Cryopreservative} & \text{Storage duration (yr)} \\ \hline
\text{Streptococci} & \text{Skim milk} & \text{0.2 - 1} \\
\text{Mycobacteria} & \text{Skim milk} & \text{3 - 5} \\
\text{Spore-forming bacteria} & \text{Skim milk, glycerol} & \text{2 - 30} \\
\text{Other Gram-positive bacteria} & \text{Skim milk, sucrose, glycerol} & \text{1 - 30} \\
\text{Gram-negative bacteria} & \text{Sucrose, lactose, glycerol} & \text{2 - 30} \\
\text{Filamentous fungi} & \text{Glycerol, DMSO} & \text{2 - 30} \\
\text{Yeasts} & \text{Glycerol, DMSO, skim milk} & \text{2 - 30}\\
\text{Protozoa} & \text{Blood, nutrient medium with DMSO or glycerol} & \text{} \\
\text{Viruses} & \text{SPGA} & \text{1 - 30}
\end{array}$$
How the stocks are made and used are also important factors :

Among other things, ATCC recommends a gradual freeze and a quick thaw :

In addition to using a cryoprotectant, the rate of cellular dehydration during the freezing process can be managed by using a -1°C/minute cooling rate

Thawing should be rapid at 37°C

ThermoFisher recommends a high cell density as cell death will occur no matter what :

Also, the greater the cell density, the better the recovery is after thawing the cells. For most bacteria, a density of 107 cells/mL will result in adequate recovery if all conditions are properly maintained.

Cell death during storage is inevitable but should be minimized as much as possible

The number of freeze/thaw cycles is critical and thawing even partial should be avoided :

Try not to freeze/thaw your glycerol stock too many times. Placing the glycerol stock on dry ice while streaking onto LB agar will prevent it from thawing completely and will improve the shelf life. from addgene.org

Coming back to the initial question, based on the information above and some of the feedback in this discussion stocks of the typical E. coli DH5-&\alpha& stored at - 80 °C would probably last up to 2 or 3 decades maybe more but depending how you make them and use them it can be much less. To go further, depending on your workflow you may want to consider having working and stock vials to limit the number or freeze thaw cycles or using freeze-dried stocks for longer term storage.
Edit : One thing to keep in mind too is that frozen stocks shelf life is not all about cell viability upon thawing but also about "cell integrity". As mentioned by She and Petti (2015), van Griethuysen et al. have observed the loss of the mecA genes in 2 years old Staphylococcus aureus isolates frozen stocks.

The mecA gene was lost in 36 (14.4%) of 250 methicillin-resistant Staphylococcus aureus isolates after 2 years of storage at −80°C with the Microbank system (Pro-lab Diagnostics, Austin, Tex.). Further analysis of 35 of these isolates confirmed loss of the mecA gene in 32 isolates. This finding has important implications for the management of strain collections.
I personally experience a similar issue with a routinely used strain that lost its adhesive phenotype so we had to use the backup stock.

References :

She, Rosemary C., and Cathy A. Petti. "Procedures for the Storage of Microorganisms." Manual of clinical microbiology (2015): 161-168.
Van Griethuysen, Arjanne, et al. "Loss of the mecA gene during storage of methicillin-resistant Staphylococcus aureus strains." Journal of clinical microbiology 43.3 (2005): 1361-1365.

Richard Lenski's lab at Michigan State university has been doing long-term evolutionary research on E. coli and maintaining a "frozen fossil record" of their experimental populations every 500 generations since 1988. They still periodically release research papers comparing the physiology of evolved and ancestral populations. For example, this recent paper looks at populations collected at 2000, 10000, and 50000 generations. According to this timeline, they used populations frozen over 3 decades ago.
This doesn't guarantee that your specific organism will last that long, but it does show that freezer stocks can remain viable for longer than some research labs will even exist. Most of their protocols are on the website. I've had lunch with Dr. Lenski, and he's a pretty approachable guy. I'm sure if you emailed him with specific questions that aren't covered on the website, he'd try to find an answer for you.
References:
Changes in Cell Size and Shape During 50,000 Generations of Experimental Evolution with Escherichia coli. Nkrumah A. Grant, Ali Abdel Magid, Joshua Franklin, Yann Dufour, Richard E. Lenski, Journal of Bacteriology Mar 2021, JB.00469-20; DOI: 10.1128/JB.00469-20
Lenski Lab homepage: http://myxo.css.msu.edu


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When is it better for a gene to cause a biased sex ratio?
Because genes are selfish and want to maximise their transmission from generation to generation, if they can distort a population's sex ratio, isn't it always in their interest to cause a biased sex ratio? Or are there cases when distorting the sex ratio isn't in their interest because they decrease the overall fitness at the higher level, i.e., incur too much damage in the individual/population? Their main priority is still to subsist in a population before spreading, right?
Thanks in advance :)

I'm afraid that I'm a bit confused about what "subsist before spreading" is supposed to mean. Can you please clarify?

I’m voting to close this question because the anthropomorphic formulation of this question deprives it of all scientific meaning.

Well first if a gene is not on a a sex chromosome there is little advantage in changing the sex ratio. This is why most of the ultra-selfish genes we know about are on sex chromosomes. A gene is not helping itself spread if makes more Male offspring unless one of two things is true, it is on the Y chromosome or there is already a bias making male offspring more successful. the latter actually helps keep populations rex ratios stable since if there are more of one sex generally having offspring of the other sex is an advantage.
The most impactful sex ratio altering genes we know about result in selfish sweeps where populations can collapse as they take over and eventually prevent mating entirely. but up until that final generations with no mates the gene in question has an advantage, evolution does not care about the survival of the species or population, if a gene can improve its own ability to spread at the cost of the population then so be it. fitness at higher levels is basically irrelevant. A gene is perfectly capable of spreading by favoring itself and driving the species/population extinct. In many ways run away sexual selection is this in a nut shell, detrimental to the individual and population but beneficial to the gene.

Thank you! This is a very useful answer.

First of all, we have to define what is meant by distorting the sex-ratio.
1) Changes to the sex-ratio as defined by the principles of the underlying Sex-determination system, can be seen as extremely unlikely:
In most species, sex is determined by inheritance of sex chromosomes, which based on meiosis results in a 50:50 sex-ratio. In this system, sex is determined by the presence or exact count of the sex-chromosomes (dependent on the species). Once this sex-system is established, I would personally see it as "frozen" and very unlikely to ever change. Other sex-determination systems are based on temperature and other environmental factors, and you can safely assume that evolution of their sex-ratios is based on advantages in the spread of the responsible genes. (Either through higher transmission rates within each population, or through a higher survival of the populations as a whole.)
2) Distortion of the perceived sex-ratio within the XY sex-determination system via TRD:
Transmission ratio distortion (TRD) occurs when one of the two alleles from either parent is preferentially transmitted to the offspring. This leads to a statistical departure from the Mendelian law of inheritance, which states that each of the two parental alleles is transmitted to offspring with a probability of 0.5. A number of mechanisms are thought to induce TRD such as meiotic drive, embryo lethality, and gametic competition. Importantly, such mechanisms only affect the sex-ratio, if the corresponding selfish gene sits on a sex-chromosome.
In this context, it is important to distinguish between true meiotic drives and killer meiotic drivers, as can be read in this review-paper. Killer meiotic drives often use complex [poison|antidote] systems, in which a tightly joined pair of a killer and an antidote gene together cause lethality in (haploid) gametes lacking the antidote containing chromosome after meiosis, while the poison is still present.
In general, drive alleles are predicted to be transient and evolutionarily labile. The transmission advantage enjoyed by drivers can allow them to become fixed in a population. After fixation, all individuals will be homozygous for the driver and exhibit no drive phenotype. However, if it affects a sex-chromosome, it could cause a bizarre state: On the x-chromosome, the mechanism would create a disadvantage in propagation due to the lack of male off-springs. On the y-chromosome, it might theoretically eradicate the whole population. By the way, such systems are considered for mosquito control.
Importantly, I would also like to address the gene R2D2 is an example of the true meiotic (see original publication), which is a “selfish” genetic element that exploits asymmetric female meiotic cell division to promote its preferential inclusion in ova (while the other female haploid cells die). However, against the suggestion of a commenter, this gene is NOT able to cause a distortion of sex ratio in mice, as females are homologous in X chromosomes; the ova always contains an x-chromosome.
So I will answer your question regarding selfish-genes, if it "isn't  always in their interest to cause a biased sex ratio" with a clear NO! Distortion of the sex-ratio is an extremely rare event that can result in strong disadvantages for the responsible gene, causing its own distinction.

real life sex linked genes like R2D2 in mice disprove your statements.

The op asked in bold letters of genes always try to change the sex ratio.

R2D2 is an example of the meiotic drive through asymmetric cell-division (female). The cell always contains the x-chromosome.

This means that R2D2 is entirely off-topic.

it is a selfish genetic element which changes sex ratios to change its own spreads in the population, thus disproves your middle three paragraphs. thus the bulk of your answer. other examples include selfish X chromosomes in Drosophila obscura, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1200995/

I will edit my text in the weekend to clarify my points.


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SARS-CoV-2 : does vaccination provide a better immunity than being sick and recover?
I recently read in the news that countries are thinking to offer a "green passport" based on the vaccination against SARS-CoV-2, allowing vaccinated people to do things with less restrictions than the non-vaccinated :
New York Times
BBC News
Bloomberg
IATA
If those passports are to be put in place, why do they not include people that were exposed naturally to SARS-CoV-2, this number being bigger days after days (60 millions people, 17/02/2021) ?
Does that mean that vaccines offer more immunity than being exposed naturally to SARS-CoV-2 and recover ?
My questions don't address the ethical aspect of implementing a "green passport", I'm only trying to figure out if vaccination offers more immunity than being exposed to the virus. A possible answer to this question can simply be "we don't know so far" because of the lack of feedback on a long term view.

The vaccine will protect you from severe disease, hospital stays and death. Isn't that enough?

Placebo-controlled trials are the gold-standard of evidence for something like this, but that's not really a possibility for assessment of immunity in previously infected individuals. Instead you'd need something like a prospective observational cohort study, which would need massive enrollment efforts and would likely still fall short of the strength of evidence provided by vaccine trials. My guess is that's why regulators are hesitant to make strong inferential claims about the strength of immunity after infection.

Perhaps the reason has nothing to do with the quality of the immunity, but is simply down to the fact that immunization can be well-documented, while having had the virus (especially a mild case that didn't require hospitalization) is not.  There's also the practical aspect that it would encourage more people to be vaccinated.

@Chris Yes of course I don't reject the usefulness of the vaccines, but it is another topic. My question is more focused on the immunity acquired by catching the virus compared to the immunity acquired by a vaccine.

@jamesqf Exactly, the immunity acquired by a vaccine is subjected to trials so it is certainly more documented than natural occurences.

@Genorme: You seem to have misunderstood me.  I meant that you can fairly easily document the fact that you received a vaccine, but if you only had a mild case, you can't really document that.

As @MikeyC and @jamesqf pointed in the comments, vaccines are better documented than the actual cases, whereas qualifying the immunity conferred by having recovered from Covid-19 would require large cohort studies.
However, one can follow up thir argument in many ways:

It would be reallys urprizing, if large-scale cohort studies have not been udnerway or already available by now: while nationwide testing may still be lacking in many countries, masive and repeated testing campaigns in specific regions are not a rarity by now. (see, e.g., here and here)
Hospitalization is not a necessary requirement for attesting a covid case - one could test unvaccinated persons for the presence of the Covid-specific antibodies.
There is much still unknown about the vaccines themselves - particularly about whether the immunity conferred is a lasting one, and whether.
Moreover, the fact that many people might have lived light cases of Covid does not make it easier for attesting the efficacy of the vaccines. Public authorities openly warn that the vaccine might be inefficient and a vaccinated person might be still a carrier of the disease.

In other words, "we don't know" is the most likely answer.
As the OP, I forgo the ethical issues raised by the "green passport" - these are not only those related to the restrictions on the individual freedom, but also the discrimination against the individuals to whom the vaccine is counter-indicated (e.g., allergics, pregnant women, people with weakened immunity, etc.)

It is said vaccines are over 90% effective. But I think natural obtained antibodies from Covid-19 and recovery offer more immunity than vaccines. The problem is that no pne can be sure to survive the infection.

I understand your opinion but it is not based on evidences, I am looking for a formal proof (if any up to date) that can confirm or infirm that immunity acquired by a vaccine is better.

We welcome new contributors to SE Biology, but ask that they read the [Tour] and the Help on answering questions. As the poster says, you are not providing an answer but an opinion unsupported by evidence, which makes your answer unsatisfactory for this question and answer site.


text:
The probability meaning of Covid variants
In the CDC webpage about Covid-19's variants the next sentence appears:

This (the United Kingdom) variant spreads more easily and quickly
than other variants.

In the ECDC paper about Covid-19's variants we can see that:

Several modeling studies corroborate the postulated increased
transmissibility of VOC 202012/01 (the scientific name of the United
Kingdom variant)

In a Nature article from last week written:

Several research groups suggested that B.1.1.7, which was first identified in the United Kingdom, was spreading more quickly than previous variants...

The probabilistic meaning of these sentences is not clear to me. Does this mean that the risk to be infected by the British variant is X times greater? E.g. if I was exposed to the British variant for 10 minutes, my chance of contracting is equal to the chance of contagion the original variant for 10 * X minutes?
Is there any nuance I miss?

The studies referenced do not have any such specifics about transmission probability.
What they observe is that a variant is becoming more common. Modeling the spread gives a different R0 value for the variants vs the reference strains:

In line with previous
modelling studies, the R0 for VOC-202012/01 was estimated as 75% more transmissible than other variants [35].
Davies et al. modelled data from three English regions to estimate that VOC 202012/01 is 56% more transmissible
(95% credible interval (CrI): 50-74%) than previously identified SARS-CoV-2 variants [32]. Danish modelling
studies performed in January 2021 estimated that VOC 202012/01 was 36% more transmissible than other
variants [ECDC communication with Danish authorities].

(from your second reference)
They infer that the variant is more transmissible because the modeled number of people subsequently infected per infected person is greater. The reasons for this cannot be easily determined by the methodology they refer to, and there is no simple way to map this onto probability of infection given some exposure; they are just describing what happens in real-world conditions, on average.
What you can infer is that there are some types of contact that occur in the real world that wouldn't result in transmission with the old strain that do result in transmission of the variant. This could be because more infected people produce enough virus to spread to others, it could be because shorter contacts lead to infection, it could be because infected people have different behavior that leads to more contact with people to potentially get infected; you can't tell the difference from these data.


text:
Why do microarrays require a priori knowledge of the genome?
Reading this paper they said this:

Contemporary microarrays emerged in the wake of genome sequencing
projects for one obvious reason: arrays require a priori knowledge of
the query genome

Why do you need a priori knowledge? Thanks.

How do you think people know what sequence to put on the probesets?

There is  a bit of ambiguity in the term of "microarrays", which is currently mostly used to relate to "microarrays" that detect nucleic acids through their sequence-mediated binding (see excellent answer below from Pascal). While much rarer, there would also be "microarrays" directed at other chemicals, such as proteins binding antibodies: https://en.wikipedia.org/wiki/Antibody_microarray

If the query genome is unknown, a microarray cannot be made for a target species. Microarrays have DNA fragments of what you want to amplify on them. Those fragments must be known.
From nature:

DNA microarrays are microscope slides that are printed with thousands
of tiny spots in defined positions, with each spot containing a known
DNA sequence or gene.

From wikipedia:

Scientists use DNA microarrays to measure the expression levels of
large numbers of genes simultaneously or to genotype multiple regions
of a genome. Each DNA spot contains picomoles (${10^{−12}}$ moles) of a
specific DNA sequence, known as probes (or reporters or oligos). These
can be a short section of a gene or other DNA element that are used to
hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called
target) under high-stringency conditions.

This answer consists of two quotations, neither of which is an answer to what in my opinion comes under the heading of "questions that show insuffiient thought to be worth answering". You state that "Microarrays have DNA fragments of what you want to amplify on them". This is incorrect. 1. There is no amplification "on" the fragments. — the cDNA generated from the mRNA may be regarded as amplified. 2. They are not DNA fragments. They are synthetic deoxyoligonucleotides. Please edit your answer such that it is is clear and correct.

Some good clarification. Maybe @David, you might consider editing the Wikipedia article.


text:
Waggle dance in the dark
Karl von Frisch discovered waggle dance [1] as communication system when bees talk about feed resources;
Long story short, using a polar coordinate system, bees dance to reveal flowers to sisters.
My question is simple: how can this be possible since bees are in hives, which are dark?
That is, how can a bee sees its sister dancing in a dark hive?

[1] https://en.wikipedia.org/wiki/Waggle_dance

You may want to look into the evolution of the dance, many of the different stages in its progression still exist, the most primitive form is done in the sunlight. https://www.nature.com/articles/43372

In bees that dance in the dark (not all do, some dance in the light) they don't watch the dance, they participate. The follow the dancer using their antenna and sound to keep track of them.

Beehives are often dark, so instead of watching the scout dance, the recruit bees follow the dancer using their antenna and the sounds produced during the dance to determine the directions to the food source.

https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/waggle-dance#:~:text=The%20dance%20conveys%20information%20about,directions%20to%20the%20food%20source.

I've never caught this detail in many books I read; just another side of this fascinating insect


text:
Chromosome Deletion Notation in Cancers
The cancer literature often refers to the deletion of certain sections of a chromosome (e.g. "17p del" or "Del(17p)" for the deletion of chromosome 17's p-arm.)
Does this mean both alleles of the chromosome were deleted for the specified cytoband (i.e., copy number analysis would show zero in this case)? Or does it mean one of the alleles was deleted, and thus one remains (copy number analysis would show a copy number of 1 in this case)?
Thanks


text:
What differentiates bound antibodies from unbound ones?
When an antibody is bound to an antigen, it can then stimulate a FcR receptor on a phagocyte etc. to respond to the threat. What stops 'free' antibodies from spuriously activating an immune response?
Even if an unbound antibody won't elicit a response, it can still hog the FcRs of expressing cells or cluster around them and degrade the immune system efficiency.
This article seems to imply that being bound to an antigen causes some change in orientation: "their Fc regions point outwards, in direct reach of phagocytes" but I don't really see how its bound state causes that any more than random movement.
It also states

The low individual affinity prevents Fc receptors from binding antibodies in the absence of antigen, and therefore reduces the chance of immune cell activation in the absence of infection

but I fail to understand the logic in that; let there be low affinity, but as much as a bound ab is somehow able to activate the FcR so can an unbound one, unless the bound/unbound state itself affects the affinity, something the article does not explain.

Keep reading further in that section: ”Many low affinity interactions are formed between receptor and antibody that work together to tightly bind the antibody-coated microbe. The low individual affinity prevents Fc receptors from binding antibodies in the absence of antigen, and therefore reduces the chance of immune cell activation in the absence of infection.” Also keep in mind that soluble antibodies are typically present only in response to an infection.

There are many related questions you can look at here.  Bear in mind that simply phagocytosing an antigen is different from "activating an immune response".  The antibody might be expressed in the membrane of a B cell, bind to a mast cell by its Fc region, or be phagocytosed after opsonization, or cause complement fixation, all with different effects.  But note a cell that engulfs unbound antibody cannot present the antigen it didn't bind to. :)

@canadianer Ii had seen that, but it doesn't seem to have any explaining power re. differentiating between bound and unbound ab's. See my edit. Thanks.

@MikeSerfas you're right that there is not antigen to present, but it should still degrade the efficiency of the system by hogging or wasting FcR interactions.


text:
Does hydrolysis of carbohydrates, proteins, and fats occur in the small intestine?
Does the hydrolysis of carbohydrates, proteins, and fats occur in the small intestine? I have researched this and just cannot seem to get a clear-cut answer. Perhaps I am misunderstanding something?
Any help and/or links to resources are appreciated! I just want to make sure that I understand this concept before moving on with other biology topics that I am learning.

Can you explain more about what you've learned and where exactly your understanding is lacking?

@BryanKrause I am not sure if I am lacking any understanding. I am taking high school bio, and I have been learning about the digestive system. So, I am not sure if hydrolysis of carbohydrates, proteins, and fats occur in the small intestine.

That's fine, but according to our homework policy we require that questions show their own research effort (not just state that the effort happened). This is part of how we avoid people asking questions here to just fill in the answers on their assignments, which we feel damages rather than assists learning.

@BryanKrause You know, I really appreciate that. I am so over the cheating nowadays because now I have to show proof of my research rather than just you trusting me (one bad apple spoils the bunch). Then again, I appreciate you taking the precautions. :) This is where I was finding my information, but I did not find what I was looking for...

digestion doesn't only happen in small intestine, but also in stomach and mouth even. search for what hydrolysis exactly means, then search for where do hydrolysis reactions happen in body, then search for digestion of carbohydrates, lipids and proteins and how do they happen.

@manidattas Thank you for your help! After some other research, I feel like hydrolysis of all three compounds does occur in the small intestine. I hope that I am understanding everything correctly; appreciate it. :)

This article section should give you enough terms and anatomy to answer your question the way you asked it. Once you know some names, look up the enzymes in other sources - you can use Wikipedia, but you can't trust it.  (Then try submitting an answer to your own question to help solidify your knowledge!)


text:
Do electron microscopy change the structure of the specimen due to the vacuum step?
Since specimens have to be prepared using the vacuum, would the pressure change affect the structures of the specimen?

What specimens ? It certainly does not bother  metallurgical samples.

You should specify the type of EM.  Transmission electron microscopy uses a tissue block not conceptually much different from paraffin-embedded sections for the light microscope.  Scanning EM often involves coating specimens with a conductive material, which in most cases probably changes their structure more than the vacuum, but there are other options... that answer would be more interesting.

I was thinking along the lines of biological specimens like Bowman's capsule, and this question popped up in my head when I was looking at an SEM, but I guess I was just curious about whether there would be any artefacts caused by the preparation stages of the vacuum.

There are several different ways to deal with the difficulties of imaging biological samples in vacuum. I'll go over the ones I'm familiar with.
TEM - plastic sections
The water in the specimen is gradually replaced with a resin which then solidifies, and slices about 100 nm thick are cut from the specimen and put into the TEM column at high vacuum. The chemical composition of the specimen is radically altered, but the shape of cells and even the arrangement of organelles inside can be preserved if the treatment is done well. Here's a representative image for this technique from http://www.cellimagelibrary.org/images/7722. You can see the endoplasmic reticulum with ribosomes and mitochondria.

TEM - CryoEM
The specimen is cooled so fast that the water in and around it solidifies without forming ice crystals, which would otherwise disrupt membranes, etc. The specimen is nearly identical to its natural state. These 'vitrified' specimens can be put directly into the microscope column, but they need to be maintained at liquid nitrogen temperatures. The size of specimen that can be cooled rapidly enough is limited to about 300 microns thick. A standard TEM beam doesn't penetrate well through samples more than about 200 nm thick; cryo specimens can be cut similar to plastic sections (though it's much harder than at room temperature), or by focused ion beam milling. Here's a representative image from https://www.pnas.org/content/117/16/8941 showing flagellar motors:

Environmental SEM
Larger specimens can be imaged without dehydration or coating in an environmental SEM (ESEM). This microscope has a high-vacuum chamber for the electron gun and lenses, and a low-vacuum chamber containing the specimen and detectors. This method can image larger samples, up to about 10 mm, close to their natural state, but isn't as high-resolution as the TEM methods. Here's an image from https://forschungsinfrastruktur.bmbwf.gv.at/en/fi/fei-esem-xl30-scanning-electron-microscopy_540 showing a small fish, you can judge for yourself how well the structure is preserved:

Love the images! And great answer


text:
Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles
First Question :
RNA interference - small-interference RNA
in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin
this Figure is Shown

my question is : if the foreign RNA is double stranded and the Dicer Cleaves it so it is still double stranded and Risc Forming with single stranded RNA ,i feel there is step missing here ? and how siRNA is finding those complementary RNA when they are in the cell in double-strand ? steps are missing or it is not essential or i myself miss somthing ?
Thank You

Welcome to SE Biology. Please finish reading the [Tour]. Note that you should only ask one question at a time. This is two quite distinct questions and needs to be split in half, deleted, and reposted. The second thing is that questions should be about specific problems in biology, rather than a help service for interpreting textbook diagrams. So you need to focus on the point at issue — Where does GTP hydrolysis take place in  *nameofprocess" — and then show that you have checked another text (NCBI Bookshelf has the other Cell Biology book — Lodish) to try to solve the problem.

@cisco_guy if you are still looking for resources, Wikipedia has a similar diagram outlining the formation of the RISC complex, with a step showing the degrading of the passenger strand. I recommend you read the rest of the Wiki and its references