What limits chromosomal length? What are the upper and lower limits for chromosome length? Are these limits different in different species or kingdoms? If there is any limit, which cellular or molecular factors are reasons?

There is both an upper and lower limit which are species specific. The upper limit is caused by incomplete segregation of sister chromatids and subsequent trimming of the long arm(s). The reason for the lower limit is, as far as I can tell, unknown.

Upper Limit
Schubert I, Oud JL. 1997. There is an Upper Limit of Chromosome Size for Normal Development of an Organism. Cell 88:515-520.
Hudakova S, Künzel G, Endo TR, Schubert I. 2002. Barley chromosome arms longer than half of the spindle axis interfere with nuclear divisions. Cytogenet Genome Res 98:101-107.
Rens W, Torosantucci L, Degrassi F, Ferguson-Smith MA. 2006. Incomplete sister chromatid separation of long chromosome arms. Chromosoma 115(6):481-490.
In these papers they found that in mono- and dicotic plants and one animal, the chromosome arm length is limited to half of the average length of the spindle arm axis (the length between the centromeres). Due to the mechanism and its presence in both plants and animals, it might be reasonable to expect that other domains of life are subject to similar constraints. Schubert and Oud (1997) speculate that the spindle axis length is fixed species specifically.

These are confocal microscope images of dividing Vicia faba (bean) cells (Schubert and Oud, 1997). (a) Wild-type cell at anaphase. (b-d) When the chromosome arms are longer, the chromatids cannot be completely separated at anaphase. (e) Wild-type cell at telophase. (f, g) Longer chromatids cannot be separated sufficiently and a bridge forms between the two daughter nuclei. (h-j) The bridge is broken when the cell plate forms. (k) Wild-type cell at interphase. (l) Breaking of the bridge between cells with lengthened chromosomes creates irregularly shaped nuclei and micronuclei - these micronuclei represent loss of DNA from the genome and are eventually lost outright through further cell divisions.

Lower Limit
There is a lower limit, but it doesn't seem that anyone knows why, which makes it impossible to accurately define.

Schubert and Oud (1997): Data from various eukaryotic kingdoms indicate the existence of a lower limit of chromosome size for stable mitotic and meiotic segregation. Yeast artificial chromosomes do not exhibit normal meiotic stability until they are of a size between 120 to 500 kb which comes close to the order of size of native yeast chromosomes, in addition to functional telomere and centromere sequences (Niwa et al., 1989). For a Drosophila minichromosome, an island of complex DNA of 220 kb was shown to be necessary for proper centromere function (Murphy and Karpen, 1995). However, for stable mitotic and meiotic segregation an additional 200 kb of a flanking satellite sequence was required. For stable achiasmate disjunction of minichromosomes during meiosis in female Drosophila, 1000 kb of overlapping centric heterochromatin sequences are necessary (Karpen et al., 1996). Schriever-Schwemmer and Adler (1993) have shown that a minichromosome representing the small centric product of a translocation between chromosomes 7 and 15 of the mouse and comprising about 1% of the haploid genome got lost during meiosis in the female carrier organism while the corresponding product of a translocation involving chromosomes 4 and 8 did not. The latter was somewhat larger. Either this different behavior was due to the presence of essential genetic information on the small translocation product 4⁸, or the minichromosome 7¹⁵ was just too small for stable segregation, although it contained a complete centromere as well as telomeres. Finally, we have observed that the frequency of meiotic missegregation, but not of transmission to the next generations, is inversely correlated with the size of translocation chromosomes in Vicia faba (Schubert et al., 1986). Thus, the existence of a proper length range for eukaryotic chromosomes is obvious.
The physical reasons for the lower limit that still enables stable mitotic and meitotic segregation are less clear at present than the constraints for an upper limit of chromosome length

Of course, "present" in that paper refers to the late 90's but, in my admittedly brief search, I have been unable to find too much in the way of more recent results. The following paper seems somewhat promising, but I don't have access to it and can only quote from the abstract. It's not much more recent, either.
Schubert I. 2001. Alteration of chromosome numbers by generation of minichromosomes -- is there a lower limit of chromosome size for stable segregation? Cytogenet Cell Genet 93:175-181.

[A] lower size limit for a stable chromosome transmission … might be based, for instance, on insufficient lateral support of centromeres or on insufficient bivalent stability due to the incapability of chiasma formation.


Why eyebrow growth stopped after it has specific length? When comparing with hair that grow forever after we cut it, why eyebrow not. what gene measure current length of eyebrow so it stop to grow after specific length.

Activation of the mammalian gene Lhx2 leads to increased hair growth. Lhx2 is a transcription factor which regulates hair formation.

"...length of the hair is determined by the duration of the growth phase; for example, the growth phase for scalp hair can proceed for a number of years, while the growth phase for eyebrows last a few months."

Other genes that have been associated with hair disorders include: FOXN1, ALX4, HOXC13, MBTPS2, VDR, CDH3, HR and ANTXR.


Modularity of transcription factors I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying that PAX6 can be considered as 3 TFs in one protein, acting independently in different situations:

Relative roles of the different Pax6 domains for pancreatic alpha cell development

Does anybody know of more examples like this?

The NF-κB family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of RelA/p65, RelB, c-rel, NFKB1/p50, and/or NFKB2/p52 subunits. For example, the "canonical" p65/p50 dimer is activated in response to stimulants like TNF-α (tumor necrosis factor alpha, released in response to inflammatory signals like the presence of pathogens) and LPS (lipopolysaccharide from the cell walls of Gram-negative bacteria), while the RelB/p52 dimer plays an important role in the development of B cells (the immune system component that produces antibodies). The AP-1 transcription factor is also heterodimeric, containing proteins from the Jun, Fos, JDP, and ATF families, and there are numerous other examples of multimeric transcription factor complexes. This recent article in Nature Immunology (disclaimer: I was not involved in that research, but my old lab did similar work) shows DNA sequence-specific binding by different NF-κB dimers.

Polymerism in general, and dimerism in particular, are quite common modes of transcriptional activation and regulation. The large number of ways in which a relatively small number of transcription factors can be combined allows for the exquisite control of genes, responding to a huge variety of cellular situations. Unfortunately, it also means that mutations in key, common components can result in transformation, unrestricted growth, and the generation of tumors.


Do fish depend on plants for survival? As far as I know, all land life depends on plants for survival. Plants convert sunlight to energy using photosynthesis, herbivores consume plants, and carnivores consume herbivores. All the energy is coming through the sun and being gradually processed by this food chain. If plants were removed from the system, all animals would eventually die as they would run out of energy.
Do fish and other water creatures also depend on plant life in the same way?

Yes, photosynthesis provides nearly all of the ocean's biomass and energy. The best is to study oceanic food chains and webs.

It looks like there aren't enough plants in the ocean because they don't form huge reserves of foliage and branches... 10% of land plant mass dies and is replaced every year, and 100% of oceanic plants die and are replaced every week:
"Biologists set out to estimate the total biomass of phytoplankton and calculated that less than one billion tonnes of the single-celled microorganisms were alive in the ocean at any one time. There were 45 billion tonnes of new phytoplankton each year, 45 times more than their own mass at any given time. The phytoplankton would therefore have had to reproduce themselves entirely, on average, 45 times a year, or roughly once a week. In contrast, the world's land plants have a total biomass of 500 billion tonnes, much of it wood. The same calculations showed that the world's land plants reproduce themselves entirely once every ten years.
https://www.nature.com/articles/483S17a
Every step of the marine energy pyramid has about 10% efficiency, so the shrimps and zooplankton take about 10% of the phytoplankton energy, then small fish 1%, and big fish 0.1% of the plant energy.
For every 500,000 units of radiant energy that hit the ocean surface, 2% is converted to phytoplankton at the base of the trophic pyramid, and the 500,000 units are necessary for every 10 units that a tuna consumes. https://oceantracks.org/sites/oceansofdata.org/files/energytransfer.png
https://en.wikipedia.org/wiki/Marine_food_web
In biology, we typically study coccolithophores and phytoplankton to learn the marine food web.
Areal map of sea chlorophyll in Mg/m2.


Wheatgrass in thalassaemia In local newspapers there was a not so recent story about wheatgrass juice being "curative" in thalassaemia. Although I do not take the article at face value, it would be enlightening to know if there was any basis at all in the claims that wheatgrass juice or extract can help mitigate some symptoms of thalassaemia.

Wheatgrass juice or extract has shown some promise for reducing the required frequency of blood transfusions in thalassemic patients, possibly due to iron chelating activity.  However, few high-quality controlled studies have been conducted so it may be too early to form a definite conclusion.

References:

Choudhary, Dharma R.; Naithani, Rahul; Panigrahi, Inusha; Kumar, Rajat; Mahapatra, Manoranjan; Pati, Hara Prasad; Saxena, Renu; Choudhry, Ved P. (April 2009). "Effect of wheat grass therapy on transfusion requirement in β-thalassemia major". The Indian Journal of Pediatrics 76 (4). pp. 375—376. doi:10.1007/s12098-009-0004-6.
Das, Priyabrata; Mukhopadhyay, Ashis; Mandal2, Suvra; Chandra Pal, Bikas; Mishra, Raghwendra; Mukherjee, Debarati; Mukhopadhyay, Soma; Basak, Jayasri; Kar, Manoj (2012). "In vitro studies of iron chelation activity of purified active ingredients extracted from Triticum aestivum Linn. (wheat grass)". European Journal of Medicinal Plants 2 (2). pp. 113—124. doi:10.9734/EJMP/2012/1059.
Marwaha, R.K.; Bansal, Deepak; Kaur, Siftinder; Trehan, Amita (July 2004). "Wheat grass juice reduces transfusion requirement in patients with thalassemia major: A pilot study". Indian Pediatrics 41. pp. 716—720.
Mukhopadhyay, S.; Basak, J.; Kar, M.; Mandal, S.; Mukhopadhyay, A. (2009). "The role of iron chelation activity of wheat grass juice in patients with myelodysplastic syndrome". Journal of Clinical Oncology (Meeting Abstracts) 27 (15S). p. 7012.
Singh, Karnail; Pannu, M. S.; Singh, Palwinder; Singh, Jaswinder (January 2010). "Effect of wheat grass tablets on the frequency of blood transfusions in thalassemia major". The Indian Journal of Pediatrics 77 (1): 90—91. doi:10.1007/s12098-010-0002-8.
Tirgar, P. R.; Desai, T. R. (September 2011). "Investigation into iron chelating activity of Triticum aestivum (wheat grass) in iron-dextran induce iron overload model of thalassemia". Journal of Pharmacy Research 4 (9). ISSN 0974-6943.


What's read depth in VCF? There is an attribute defined as DP (Total Depth) in VCF file format. For example, http://www.1000genomes.org/node/101.

What does this attribute mean? If I get a value of like DP=128. How can be that be interpreted?

So the general sequencing analysis pipeline is to generate a bunch of read sequences, figure out how they match to a reference genome and align them, then call any differences between the reference genome and the sequencing reads. The following image, from the Broad Institute's Interactive Genome Viewer, may help you visualize what is happening here. As you can see in the image, the human reference DNA is found at the top of the window, and the sequence of bases for the current selection, at the very bottom of the window. Then each of the gray bars that you see below that is an individual sequencing read that matches to that particular location along the human DNA.

When you use a variant caller like Freebayes, it will list out information about locations along the reference genome that had differences in your actual sequences. For instance, as you bring up, DP or read depth. Looking back at the IGV image, you can see a location that had a lot of 'G' showing in the sequence reads, where the reference DNA has 'A'. Variant callers will pick up on this and list it as a possible variant. They will also tell you the read depth at that location which is the total number of sequence reads overlapping that position. In this case there are 21 gray bars (sequence reads) overlapping at that position, meaning that DP=21.

Even though it is not listed in the VCF example to which you refer, variant callers can also give other data like AO, which is times that a variant was observed, and RO which is the number of times the reference base was observed. This information allows you to decide whether or not an identified variant was a sequencing error, or a real variant.

For instance if DP=1, AO=1, RO=0, that means there was only a single read at that location and it was not what is listed in the reference genome. Because the depth is so low, and the error rate of a next-gen sequencer is somewhere between 0.5-5%, you cannot say that this is a mutation or just a sequencing error. However, as DP increases, you gain more confidence in whatever was called. So if DP=10, AO=10, RO=0 you can be quite confident that the reason you read an alternate base at a given location, it is not just a sequencing error because you read this location 10 times and every time you saw the same variant.

Let me know if I can clarify further.


Triosephosphate isomerase deficiency Triose phosphate isomerase deficiency, a rare condition, is the only glycolytic enzymopathy that is lethal. This deficiency is characterized by severe hemolytic anemia and neurodegeneration.

How can I relate this enzyme deficiency to hemolysis?

My attempt:

1- Accumulation of DHAP is causing intracellular fluid to be more osmotic leading to cell bursting.( Then why don't we see the same in outer cells?)

2-Lack of glucose may lead to less ATP production, Na/K pumps work less, thus disturbing membrane potential, which finally may cause hyper-osmic ICF and then henolysis. ( But why don't RBC take twice the amount of glucose?)

Source: Biochemistry 8th edition by Jeremy M. Berg John L. Tymoczko Gregory J. Gatto, Jr. Lubert Stryer

Unlike most of the cells in a human body, erythrocytes (or red blood cells) don't have mitochondria (because they are basically O2 carriers), and don't perform Krebs Cycle or Oxidative Phosphorylation. Therefore, they depend exclusively on glycolysis to produce their ATPs.

According to the Genetics Home Reference (from the NIH, National Institutes of Health) page about triosephosphate isomerase deficiency:

  The anemia in this condition begins in infancy. Since the anemia results from the premature breakdown of red blood cells (hemolysis), it is known as hemolytic anemia [...] TPI1 gene mutations lead to the production of unstable enzymes or enzymes with decreased activity. As a result, glycolysis is impaired and cells have a decreased supply of energy. Red blood cells depend solely on the breakdown of glucose for energy, and without functional glycolysis, red blood cells die earlier than normal. (emphasis mine)

Thus, since erythrocytes depend solely on glycolysis as energy source, there is a marked accumulation of DHAP toxic sub-products (Ahmed et al., 2003).

Sources:

Reference, G. (2017). triosephosphate isomerase deficiency. [online] Genetics Home Reference. Available at: https://ghr.nlm.nih.gov/condition/triosephosphate-isomerase-deficiency#genes [Accessed 16 Jul. 2017].
Ahmed, N., Battah, S., Karachalias, N., Babaei-Jadidi, R., Horányi, M., Baróti, K., Hollan, S. and Thornalley, P. (2003). Increased formation of methylglyoxal and protein glycation, oxidation and nitrosation in triosephosphate isomerase deficiency. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1639(2), pp.121-132.


Is this flying bug swarm termites? Found in New York city, approx 7mm Just saw a giant swarm of these fly out in between pavers and a door sill from a small crack in the ground here in New York City.  There seemed to be hundreds of them swarming out very quickly.  They are about ant-sized.  Are they termites?
Here are photos:

Yes it looks to be Reticulitermes flavipes aka the Eastern Subterranean Termite.


Are molecular machines encoded in the DNA? I don't know much, if anything, about molecular biology. I watched the "inner life of the cell" on Youtube which triggered my curiosity about how these molecular machines came to be. My simple understanding is that if these molecular machines are encoded in the DNA, then they are "evolve-able" by mechanisms such as natural selection. Is that case? And if so, can we identify which part in the DNA sequence have the encoding for these molecular machine such as the Kinesin? Do molecular motor machines get synthesized by the RNA as well?

Yes.

The "molecular machines" you are referring to are particular proteins.

The specific one you are referring to, kinesin, is involved in movement along microtubules, part of the structure of the skeleton of a cell, but other proteins act as their own kind of machine to do their own tasks: sometimes catalyzing a biochemical reaction, or responding to a type of stimulus, or forming a shape or structure, or combinations of all of the above.

Protein-coding sections of DNA are well-studied, and there are substantial databases of known proteins. If you go to wikipedia you will see a whole list of different kinesins, if you click on one, for example, KIF1A, on the right hand side it shows you it is found on chromosome 2 in a human, starting at 240,713,764 base pairs and ending at 240,820,308 base pairs. Information for the mouse is also located there.

Proteins in DNA-based life are all synthesized by first producing an RNA transcript from the DNA, which is effectively an RNA copy of a short stretch of DNA, which is then translated into protein. Other RNA molecules are involved in this process, too, as the rRNA part of the ribosome (sort of a 'protein factory') as well as tRNA which carries the amino acid components of proteins as they are being built. Transcription and translation are central to understanding biology at the molecular and cellular level.

Not only can all proteins, from kinesin to collagen, evolve, they all have evolved through natural selection and other evolutionary mechanisms, and they continue to evolve today in all living organisms. Without evolution, no biology would exist. RNA-based biology (today, mostly some of the viruses) is also subject to evolutionary mechanisms, so that isn't something unique to DNA, but rather to heredity and biology in general.


Could an action potential produce few or more neurotransmitters based on the stimulus received? I reckon that if you would be able to widen the AP width, it would produce more neurotransmitters in that larger time interval. Is that correct? Or does the neuron have a standard amount of neurotransmitters it releases in order to pass the signal post-synaptically?

(bonus: could it NOT result in neurotransmitter release, or does the definition of an AP include the release of neurotransmitters?)

Short answer

Widening of the action potential increases neurotransmitter release;
Generally, an action potential results in the release of about one vesicle of  neurotranmitters;
An action potential does not have to lead to neurotransmitter release - the chance being anywhere between 9 - 100%, depending on the synapse under investigation.

Background

Neurotransmitters are released in packets, called neurotransmitter vesicles:

Source: Science blogs

Vesicles are released via a mechanism involving Ca2+. When an action potential reaches the synaptic terminal, voltage-gated Ca2+ channels open, which leads to Ca2+ influx. The increased Ca2+ in the terminal leads to release of vesicles.

A study by Sabatini & Regehr (1997) showed that widening of the presynaptic action potential in rat cerebellar cells resulted in enhanced Ca2+ influx, which in turn greatly enhanced neurotranmitter release.

According to a study in rat hippocampal cells it was shown that, on average, a single action potential releases approximately 0.5% of the vesicle pool from the presynaptic terminal. The presynaptic vesicle pool was estimated to be 100 - 200 vesicles, which hence added up to 0.5 - 1 vesicle released per action potential (Ryan & Smith, 1995).

An earlier study of Rosenmund et al. (1993) confirms these findings in hippocampal neurons, and investigated the variability between different synapses in greater detail. They found that the chance that a single action potential released neurotranmitters was 9 - 54%. They reasoned that larger synaptic terminals, or terminals triggered by long-term potentiation have a higher chance of releasing neurotransmitter. Moreover, such terminals with enhanced release probability may also have a higher chance of releasing multiple vesicles per action potential. They predicted that 54% of release events from such enhanced terminals may release multiple vesicles per action potentials, whereas just 9% of normal terminals may do this.

References
 - Rosenmund et al. Science 1993; 262: 754-6
 - Ryan & Smith, Neuron 1995; 14: 983-9
 - Sabatini & Regehr, J Neurosci 1997; 17: 3425-35


What nutrients are best suited for growing E.Coli I am looking to grow E.Coli (In a nutrient agar dish) to be used in an E.Coli lawn and was wondering what specific nutrients should be used to ensure the E.Coli grows optimally? Any answers or links to relative resources are greatly appreciated!

Optimal is a funny thing; it depends upon what you want. The purpose of the bacteria, is probably the most important aspect when considering the nutrients. There are many recipes capable of growing E. coli. What does optimal or best mean to you and why? Is selectivity or differentiation a factor? How important is cost? Are you aiming for industrial level production or just testing. Do you have a bioreactor? Or are you looking for something low tech... maybe from food-mart?

For what it's worth, you might find minimal salts media and solid state fermentation interesting.

Different strains like different nutrients, of course. So, phenotypical tests are sometimes helpful when figuring what an undescribed strain likes (and doesn't like).

That being said... I can offer a little insight here.

"+" for growth/utilization;  "-" for weak or no growth/utilization:

                 E. coli    E. coli inactive**  E. coli 0157:H7

Pectin                 -            -                   -
Dextrin                ++           ++                  -
Sucrose                -            -                   +++
Glycerol               +++          +++                 +++
Stachyose              -            -                   -
D-Fructose             ++           ++                  ++
D-Maltose              +            ++                  ++
D-Raffinose            +            -                   +++
α-D-Glucose            +            +                   +
α-D-Lactose            +            -                   ++
D-Trehalose            ++           +++                 +++
D-Galactose            ++           +++                 +++
L-Fucose               +++          +++                 +++
L-Rhamnose             +++          -                   ++
D-Sorbitol             +++          +                   -
D-Mannitol             +            ++                  ++
Methyl Pyruvate        +++          +++                 +++
Tween 40               -            -                   -

Gelatin                -            -                   -
L-Alanine              +++          +++                 +++
L-Arginine             +            -                   -
L-Histidine            -            -                   -
D-Serine               +++          +++                 -
L-Serine               +++          +++                 +++
D-Aspartic Acid        -            -                   -
L-Aspartic Acid        +++          +++                 +++

D-Glucoronic Acid      +++          +++                 +++

Citric Acid            -            -                   -
L-Malic Acid           +++          +++                 +++
Acetic Acid            +++          +++                 +++
Acetoacetic Acid       +            +                   -
L-Lactic Acid          +            -                   -
Mucic Acid             ++           -                   +++
D-Malic Acid           +            +++                 +++
Propionic Acid         ++           ++                  +++
Formic Acid            +            -                   +

D-Salicin              -            -                   -
Lithium Cloride        +++          ++                  ++
Na Butyrate            +++          +++                 +++
pH 5                   +++          +++                 +++
8% NaCl                ++           +                   -
D-Serine (high)        ++           +                   -
Potassium Tellurate    +            +                   +++
Na Bromate            +/-           -                   ++

E. coli inactive** is lactose-negative, non-motile- often misidentified as Shigella


Exact terminology of natural selection You don't need to explain to me what the theory of evolution is, or how it works. This question is purely about what exact meaning the word "natural selection" is ascribed to.

There seem to be multiple meanings that are given to the term "natural selection":

The process by which, in a single generation of species, the most fit individuals tend to survive. The "things that are being selected", are the individual organisms, and the "moment that selection took place", is the moment that these individuals reproduced or failed to reproduce, or alternatively, the moment that they died or survived.
The process by which, over many generations, the genotypes that result in highest fitness tend to to be selected for. The "things that are being selected" are the genes, and the "moment that selection took place" is not a single instance in time or a single generation, but a long time-span. In fact, I sometimes hear the idea that natural selection is already selecting for genes even if those particular genes don't exist in any organism. For example, if natural selection is selecting for "height", and there is a gene X that would increase height, then it is said that X is being selected for even if X does not yet exist.

Are both of these interpretations generally accepted?

"...in a single generation of species, the most fit individuals tend to survive.".  This is not correct. "Fitness" in an evolutionary context refers to how many offspring you produce. It has nothing to do with how many pushups you can do.
Yes, individual organisms are selected, and the selection process involves differential survival (to reproduce).

"The process by which, over many generations, the genotypes that result in highest fitness tend to to be selected for. "

This is largely correct.

"The "things that are being selected" are the genes..."  Yes and no. It is individuals that are selected. They live or die, depending on their traits, which are encoded by genes.

Darwin noticed the extreme physical variations that humans could create in dogs, and pigeons by selective breeding. He thought that the same process could occur in nature, and termed it "Natural selection".


Orientations of codon and anticodon So 5'-AUG-3' is the start codon on an mRNA transcript

Does that mean that the tRNA anticodon is 5'-CAU-3'?

Here, I see that the tRNA anticodon for methionine is UAC, and the chart doesn't specify which end is 5' and which end is 3', but I'm guessing it's 3'-UAC-5'. I thought nucleotides are supposed to be written 5' to 3', and that's a norm, but apparently it isn't the case here? Am I missing something?

The tRNA anticodons are both complementary and anti-parallel. That means for $5'-\text{AUG}-3'$, the tRNA anticodon would be $3'-\text{UAC}-5'$.

The image has the mRNA oriented with the $5'$ end on the right end. It shows both, complementarity and anti-parallel configuration. The reference you cite might have cited the anticodons $3'\rightarrow 5'$ and mRNA codons $5'\rightarrow 3'$. In general, we usually cite the codes from $5'\rightarrow 3'$ but it doesn't matter until it is explicitly specified or unambiguous.


Partial pressures of different gas in human blood and how they are calculated? In Respiratory Physiology, we use the $P_x{O_2}$ and $P_x{CO_2}$ in blood at different regions of the peripheral circulation. From my Chemistry knowledge I know that $P_x$ of a gas in a solution is the fraction of total pressure caused due to the gas dissolved. But in blood $O_2$ is present mostly as $OxyHb$ and $CO_2$ is also present as $CarbaminoHb$ & $HCO_3^-$. In blood their dissolved state fraction is very low. Now my question is how do we measure the $P_x$ of any gas ($O_2$ or $CO_2$) in blood and what is the logic here? [x means either arterial blood or venous blood]
Here is the data I'm talking about.(https://i.stack.imgur.com/lA1M5.jpg)

As a notation note, I never seen your $P_a{O_2}$ notation used except for referring to arterial partial pressure ($P_v{O_2}$ would be venous). Generically, partial pressures are usually noted as, for example, $P_{O_2}$.
When we talk about partial pressures in biology, we literally mean the partial pressures: that caused by dissolved gas.
Hemoglobin-bound oxygen is not the same as gaseous oxygen, nor is carbonic acid the same as carbon dioxide. Neither contribute to the partial pressure. They do relate to the total oxygen/carbon dioxide carrying capacity of blood, but this cannot be measured directly through partial pressures.
See this Q&A for a situation this comes up: Why is arterial pO2 normal in carbon monoxide poisoning?
In medicine, it is common to use oxygen saturation as an alternative measure of blood oxygen concentration; this refers to the percentage of oxygen binding sites of Hb that are saturated.
It is important to realize that the partial pressures of dissolved gases will eventually reach equilibrium with the surrounding atmosphere; the lungs are a great gas exchange organ (that's their entire job), so blood leaving the lungs should have partial pressures that approximate those inspired air (in practice, there is some discrepancy because the lungs are very humid and also are constantly refilled with $CO_2$ from blood, so water vapor and carbon dioxide contribute a substantial gas pressure that pushes out other gases: see the similarity between arterial blood and alveolar gas in your data table and the differences between atmospheric gas and alveolar gas).
Clinically/in a lab, we measure these things with a machine that just magically gives the numbers. I looked for a simple description of how these machines actually function, and found https://acutecaretesting.org/en/articles/understanding-the-principles-behind-blood-gas-sensor-technology to be useful. In summary, $CO_2$is measured by exposing a captive solution to the gas and measuring the pH, giving an indirect (but accurate) measure of $CO_2$. $O_2$ is measured with a reducing current. It's also possible to measure concentrations of arbitrary compounds more directly with gas chromatography - colleagues of mine have used this for anesthetic gases, for example.


When you blow through your nose while holding it closed to "depop" you ears, why do you sometimes feel it in your eyes? After your ears have "popped", for example on a flight, I heard you are supposed to hold your nostrils closed and blow through your nose to readjust the pressure to the normal level. Why do you sometimes feel a pop in the corner of your eye when you do this?

The sinuses connect the ear, nose and throat as well as the tear ducts of the eye. The pressure created when holding your nose and blowing is transferred to any area it can get to; in this case, the eyes and ears.


Why do lychee seeds come in different shapes? I've been eating lychee fruits recently and noticed that every once in a while (in about 1 of 10 fruits or so) the seed in the fruit is shriveled, while in other fruits from the same batch the seeds have regular ellipsoid shape:

Top: regular seed, bottom: shriveled seed

The fruits with the shriveled seeds don't look or feel or taste any different from those with the regular seeds.

It seems like a binary trait, i.e. seeds are not more or less shriveled, they are either shriveled or not.

Why are the seeds so different? Do they come from different cultivars, or it's some kind of Mendelian development, or maybe some kind of a plant disease?

The shrivelled seeds are aborted seeds, known as 'chicken tongues'. Some cultivars of lychees mainly produce fruits containing chicken tongues. These cultivars are usually considered more desirable, because they have more flesh.

Source: https://www.crfg.org/pubs/ff/lychee.html


Action potential attenuation in unmyelinated axons vs demyelinated axons I learnt that action potentials travel much faster along myelinated axons, and when these axons are demyelinated the action potentials travel much slower and sometimes die out. Why do action potentials die midway in unmyelinated axons?

Myelinated axons have schwann cells around them, electrically insulating the neuron axons except for gaps in the sheath which are called the Nodes of Ranvier. The insulation increases the speed of transmission of action potentials.

Without myelination conduction signals along the nerve can be impaired or lost.
There are some diseases E.g. Acute disseminated encephalomyelitis where myelination is lost.


Is too much CO2 in the air toxic? I know that if there is too much CO2 in the air we will have too much greenhouse effect.

I would like to know if there is too much CO2 in the room, something like 3% while there is also more that adequate oxygen for us to breath. will we live or die? why?

CO2 forms carbonic acid in water, which helps to dissolve rocks and mountains in envitonmental science. It would slightly acidify your body with what is called a weak acid.

5% can cause acidosis and loss of conciousness, without lack of oxygen.

3% would devastate most chalk based sealife, corals and shells.

Perhaps lifelong breathing of 3% co2 would have serious effect on alkaline processes in the body, osteoporosis, and would have to be counterbalanced by the body to maintain its blood ph above 7.35, with alkaline chemicals like sodium.

Also check out this fact sheet.


What are the migratory patterns of Orcas in the Pacific Northwest? Do they pass by Vancouver in the Fall? What are the migratory patterns of Orcas in the Pacific Northwest? Do the pass by Vancouver in the Fall?

I know you can never predict the sightings of a wild creature, but I was wondering what the migratory patterns of orca pods are in October in the Pacific Northwest, and what the possibilities are that they may be passing through Vancouver?

How large is the population of the migratory orca pods passing in the fall (if one can even know that)?

Thanks!

There are three ecotypes of orcas which are all members of the same species but tend to display different behaviours, communicate differently and have different prey preference. The most common ecotype near Vancouver are the Resident Orcas, specifically the Southern Resident Orca population. This population is comprised of the J-pod, K-pod and L-pod. These populations feed mainly on salmon which as scarce in the Salish Sea during the winter. Therefore, resident orcas tend to disperse in search of food during winter months in the as far north as Alaska and as far south as Califorina.

As salmon travel to the ocean from inland rivers for food during the summer, the Southern Resident Orcas return to the Salish Sea to feed. By October, many salmon return to their natal stream to spawn and therefore, the abundance of prey for the Southern Resident Orcas depletes. During this time, orcas will begin to disperse North and Southward in search of more abundant prey but some will linger to feed on the salmon late for spawning.

If you're interested in more information about this population, check out Orcas of the Salish Sea


Databases for gene regulatory network graphs? What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported or embedded to another website?

For a free resource, try GenMAPP. Commercial products like Ingenuity Pathway Analysis do the same thing with prettier graphics and a curated approach to network-building, but access can be expensive if you're not affiliated with an institution that will foot the bill.


Which comes first, PCR or Gel electrophoresis? If I want to find out wither a group of patients have the abnormal BCR-ABL cancer gene, how do I benefit from the PCR and the gel electrophoresis techniques? I'm kinda lost trying to determine which comes first and what is the exact function of each device, I have read the whole gene cloning process in my biology book but couldn't absorb it because it's so complex.

PCR comes first. If PCR works right, then a specific product will be amplified. But you cannot see it in the little plastic Eppendorf PCR tube. That is what the electrophoresis is for. After you run PCR, you run the products on an agarose gel to visualize it (with the help of some flourescent dye). The agarose gel is just to see if the PCR worked.


How to identify the subspecies/breed of a bee I have been a beekeeper for a number of years and originally obtained my first colonies from a guy in my neighbourhood. However, when I sell bees to someone else, they typically ask what species of the European/Western honeybee (Apis mellifera) I have/they're buying. Technically, they're after the subspecies or breed (like Italian, Carniolan, Buckfast, ...), but I don't know what to tell them. I just call them local (or locally-adapted) bees.
Is there a way that one can find out the subspecies/breed I currently have? Perhaps through DNA analysis/sequencing or some other kind of scientific analysis? Regardless, is such subspecies identification available/accessible to the hobby beekeeper (should read as being relatively inexpensive)?
Images like the following are circulated to estimate one's breed:

However, traits are hardly a definitive assessment of a breed, especially if you consider how close some of the breeds are listed above. For example, what's the difference in a trait ranked 5 and 6, say.

I am not sure about apiculture, but in academic research it is typical that people use microsatellite markers for identifying subspecies of bees. Microsatellite are repetitive regions of the genome that are useful in at identifying different species/subspecies, as well as for generating pedigrees and paternity analysis. Different species/subspecies have different numbers of repeats in a particular microsatellites, and these differing number of repeats are heritable. People use microsatellites because they are cheap, easy to run and reliable for identifying species/subspecies. Because there can be many different alleles (or different numbers of repeats) at a given microsatellite locus, so you only need relatively few microsatellites in total to identify individuals.
An example can be found in this paper. They used 7 microsatellite loci and could reliably identify between different African and European sub-species. It is worth a read of the intro:

Recent population genetic surveys in human (Bow- COCK et al.
1994;DIRIENZO et al. 1994) and other mammals (GOTTELLE et al. 1994;
TAEOR et al. 1994) and in bumble bees (A. ESTOUP,M. SOLIGNAJC. ,M.
CORNUET and A. SCHOLL unpublished results) have shown that
microsatellites are highly efficient at differentiating
populations or groups of populations. In this paper, we investigate their
usefulness for honey bee population studies by adressing the
following specific questions: Are the three evolutionary branches
inferred from morphometry and mtDNA confirmed by microsatellite
data? Are microsatellites useful for differentiating sub-species and
populations within subspecies? How does the pattern of variability of
these markers vary between branches/subspecies/populations and which
factors may be invoked to explain it? Is it possible to assign a given
colony to its population of origin from microsatellite data and how do
the individuals from this colony cluster within the population?

References:
Estoup A, Garnery L, Solignac M, Cornuet JM. Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics. 1995 Jun;140(2):679-95. PMID: 7498746; PMCID: PMC1206644.


Which is the proportion of metagenomics reads that cannot be mapped in any genome? I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable?

I found a figure for viromics, which seems to indicate that only about 6% of the sequences correspond to known virus (http://www.pnas.org/content/111/29/10714.full). But I couldn't find a more general percentage.

I think this will vary greatly depending on the source environment. Your example (marine viruses) is probably due to the large diversity of ocean viruses of which most have no reference genome.

Referencing the Human Microbiome Project:

A total of 57.6% of the high-quality microbial reads could be associated with a
known genome (ranging from 33–77% for anterior nares and posterior fornix, respectively).

Other papers describing more recent k-mer based approaches for classification report between 40-90% classified to a known reference. See:

http://www.nature.com/articles/srep19233

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401624/


Models of quorum sensing for multi-agent systems Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model of quorum sensing that abstracts away from the details of the mechanism implementing it inside the agent, but keeps the key inter-agent properties like diffusion rate, range, and timing.

Is there a standard abstract mathematical model of quorum sensing used by biologists?

I am not interested in the particulars of a specific organism, but would like a general model I could apply to capture the 'gist' for any organism that relies on quorum sensing for part of its behavior.

Bernardini et al. (2007) provided an extension to P-systems incorporating the basics of quorum sensing, and Romero-Campero & Pérez-Jiménez (2008) have used their approach to model bioluminosity in vibrio fischeri. This approach is conceptually appealing to me, but that is because I am predominantly a computer scientists. Although P-system can be used for modeling biological systems (Ardelean & Cavaliere, 2003), they still feel fundamentally computer-science-y and are typically not published in orthodox biological venues. This makes me suspect there is a more standard approach among biologists, probably via dynamic systems and diffusion equations.

I found this paper[1], which might be relevant; it uses is a more chemically inspired approach. Another paper[2] also might be interesting, it takes a more dynamical systems approach.

My personal instinct would be to use ordinary differential equations: generate a population of cells in random positions, assign each cell levels of any relevant molecular species, and come up with a list of ODEs that describe the rates of change of the species in a particular cell in terms of gene expression, degradation, and diffusion. You should then be able to simulate the time evolution of the system just by solving the (large) system of ODEs given your initial conditions. Something like the approach in this paper[3] (read the supplemental info), only your cells would move around during the simulation, rather than remaining still as part of a tissue. The implementation would get thorny, because you would have to accommodate the motion of the cells as you solve the ODEs. I imagine that this could be accomplished by simply treating the initial positions of the cells as part of the system's initial conditions and then defining the ODEs that govern the rate of change in each dimension (either randomly, or perhaps they move in a coordinated manner) so that this aspect of the system can evolve during the integration.

References:

 Rai N, Anand R, Ramkumar K, Sreenivasan V, Dabholkar S, Venkatesh KV, Thattai M. 2012. Prediction by promoter logic in bacterial quorum sensing. PLoS computational biology 8: e1002361.
 Chiang W-Y, Li Y-X, Lai P-Y. 2011. Simple models for quorum sensing: Nonlinear dynamical analysis. Physical Review E 84.
 Lubensky DK, Pennington MW, Shraiman BI, Baker NE. 2011. A dynamical model of ommatidial crystal formation. Proceedings of the National Academy of Sciences of the United States of America 108: 11145–50.


Which ingested allergens can be transferred to a partner via bodily fluids? Can some allergens, such as peanut traces, appear in bodily fluids (saliva, sweat, semen, vaginal secretion) after ingestion?

I would like to know in particular intake of which allergens should be avoided to prevent allergic reaction of a partner due to contact with bodily fluids.

It depends on several factors: what's the biochemical nature of the allergen? Is it a protein? What's its size?

In short, the answer seems to be yes, to some particular cases. For instance, this paper deals with allergens from Brazil nuts transmited by the semen:

http://www.jiaci.org/issues/vol17issue03/10.pdf

According to the paper:

  We report the case of a 20-year-old woman with
  documented Brazil nut allergy who developed widespread urticaria and mild dyspnea after intercourse with her boyfriend who had earlier
  consumed Brazil nuts.

Of course, there is no general rule, and each case has to be individually analysed. This makes very hard, if not impossible, to answer your second question ("I would like to know in particular intake of which allergens should be avoided to prevent allergic reaction of a partner due to contact with bodily fluids"), because it depends on the case in question: the allergy, the allergen, the people involved etc.

This Scientific American blog post makes a good overview of the matter:

http://blogs.scientificamerican.com/food-matters/sexually-transmitted-food-allergens/


Do plant cells recycle carbon dioxide from their respiration during photosynthesis? It seems one of my colleague's biology textbook claims that plant cells, with presence of light, feed back 100% of carbon dioxide molecules from their respiration into photosynthesis. Can you say that carbon dioxide molecules, gas or dissolved, get transferred from the mitochondria to the chloroplast?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884119/
This paper found mitochondria move to be next to chloroplasts when exposed to light. So carbon dioxide is  more likely to be recycled in lighted conditions.


Does Sansevieria trifasciata really absorb Carbon Dioxide at night? There's a claim that Sansevieria trifasciata (Mother-in-law’s Tongue) generates oxygen from carbon dioxide during the night.

This seems surprising to me: that process requires energy; plants generate O₂ from CO₂ through photosynthesis, requiring light. So not photosynthesis, and no CO₂ absorption, at night.

Am I missing something, or is this claim false?

This is an interesting topic!

Crassulacean acid metabolism is a second CO₂ fixation pathway where CO₂ is absorbed at night.  The CO₂ is fixed into maleic acid HOOC-CH₂CH(OH)-COOH which stores some of the CO₂ in the form of carboxyl groups.  During the day carboxylases release the CO₂ for fixation during the day.

This is an adaptation where the stomata open at night to take in the CO₂ and are closed during the day - the plants sort of 'hold their breath'.  The energy for this process is derived for glycolysis which were stored during the day (nice detailed review here).

The paper says that about 6% of plants (including Mother-in-Laws Tongue) do this and you can imagine with night breathing how closing the stomata during the day would really help with dehydration.  Its interesting to note that this is found in a wide variety of plants "CAM is found in five taxonomic classes, comprising monocots and dicots, encompassing 33 families and 328 genera".  That says that CAM is a pretty old development in plant evolution and not so expensive that it is easily lost.


What kind of "size" does SDS-PAGE separate by? What is the exact property of the protein that affects migration of bands in SDS-PAGE; is it length, volume, or mass?

For example, will GGGGGGGGGG (glycine 10-mer; mw <600) migrate more or less than WWWWW (tryptophan 5-mer; mw >900)?

The protocol for SDS-PAGE uses a solution of sodium dodecyl sulfate (SDS, also known as lauryl sulfate) to solubilize and linearize folded protein molecules and give them a negative charge that is approximately proportional to the length (and more or less to the mass) of the protein, depending on its sequence. Some sequences may bind the SDS more readily, while others may not, so the relationship between charge and mass/length is not perfect.

The linearized (and often reduced, typically with DTT or β-mercaptoethanol) protein solution is separated by polyacrylamide gel electrophoresis (PAGE), wherein the negatively-charged protein(s) migrate though the pores in a gel due to an electrical field applied across the gel. Smaller proteins run faster, and are visualized (by many different methods) nearer to the bottom of the gel, whereas larger proteins are closer to the top. Typically, a standard molecular weight marker is run alongside the samples of interest so that approximate molecular mass can be gauged. A number of situations may cause the samples to not migrate exactly according to their calculated molecular mass, including high levels of glycosylation, phosphorylation, or other post-translational modifications, as well as variable binding to the SDS as discussed above.


Identify arthropod with many legs in Mumbai Can someone please identify this ~5 cm long arthropod? I've been finding one of these every 2-3 days inside my apartment ever since rainy season started here in Mumbai (June).
The bulb portion is its head. The arthropod is capable of climbing walls.
Thanks.

Video of the worm (shot while brooming the floor. Hence the dirt)
https://imgur.com/a/0FZv3eQ
By the way, I've seen it 6 times in the last 2-3 weeks. Except once when I saw it on the bathroom floor, all other instances were during night time. So perhaps this is some sort of a nocturnal creature?

I'm pretty sure It's a millipede from the Julida order, that includes 750 species distributed in the northern hemisphere.
https://en.m.wikipedia.org/wiki/Julida


What is the biological function of nose, underarm, and pubic hair? What is the biological function of nose hair? In general, can we consider underarm hair and pubic hair to be vestigial structures?

From this article I quote

  Hair in the nose is one of the body's first lines of defense against
  harmful environmental pathogens such as germs, fungus, and spores.

  Another purpose for nose hair is to provide additional humidity to the
  inhaled air. As the air passes through the nasal passages, the mucus
  and hair provide heat and moisture. Humidity is an important factor
  for the rest of the respiratory system, such as the larynx and lungs.

  Hair in the form of tiny cilia also draw solid particles towards the
  interface between the nose and throat. Harmful debris is generally
  directed towards the back of the throat and esophagus for swallowing,
  while the filtered air continues towards the larynx and lungs.

If you look on an evolutionary perspective, the arm pit hair follicles as well as pubic hair have a type of sweat gland associated with them, called an apocrine gland, that begins to function at puberty and is widely associated with scent-communication via chemicals known as pheromones (reference).

Some other functions that are associated with pubic hair are:

Keeping the genitals warm.
Drawing attention to the genitalia.
It also decreases friction during intercourse (reference).

The nose hair is definitely not vestigial. As long as the armpit hair (between the body and arm in certain heavyset individuals) and pubic hair serve to reduce friction and male sweat serves to increase female hormones, I wouldn't call them vestigial (reference).


Organism with the greatest amount of gold as percentage of body mass I've read that the human body contains trace amounts of gold:

http://www.tellmehowmuch.net/how-much-gold-is-found-in-the-human-body.html
http://web2.airmail.net/uthman/elements_of_body.html

Are there other species that are known to have significantly higher ratios of gold to body mass?

And while there seems to be no definitive answer about the benefit of gold being in the human body, are there any species for which gold has demonstrative bodily uses or benefits?

Acidothiobacillus ferrooxidans can gain metabolic energy by utilizing gold thiosulphate complexes (Reith et al., 2007); Micrococcus luteus can oxidize methane to methanol using gold-containing enzyme (Levchenko et al., 2002).

However, for most organisms, gold is toxic (Wietkiewicz & Shaw, 1981); some bacteria actively detoxify gold: Cupriavidus (Ralstonia, Wautersia) metallidurans, Desulfotomaculum sp., Desulfovibrio sp., Hyphomonas adhaerens, Plectonema boryanum, Pseudomonas aeruginosa Salmonella enterica,  Shewanella algae, Spirulina platensis (Reith et al., 2007).

Reith F, Lengke MF, Falconer D, Craw D, Southam G (2007) The geomicrobiology of gold. ISME J. 1: 567-584.

Levchenko LA, Sadkov AP, Lariontseva NV, Koldasheva EM, Shilova AK, Shilov AE. (2002) Gold helps bacteria to oxidize methane. J Inorg Biochem 88: 251-253.

Witkiewicz  PL &  Shaw CF III (1981) Oxidative cleavage of peptide and protein disulphide bonds by gold(III): a mechanism for gold toxicity. J Chem Soc Chem Commun 21: 1111–1114.


Is it necessary to conduct a power analysis before beginning an experiment? I know that power analysis is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power analysis. Mostly, researchers seems to use a rule of thumb (three technical, three biological replicates is a common one).

Should I be doing a power analysis each time I design an experiment, or can I just use one of the common biology rules of thumb? If not, what are the consequences for the validity of my results? And is there a situation where I will be required to use power analysis, which makes it advantageous to get used to doing it now?

You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject.

Yes

It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you should do in collaboration with the person who is going to be helping you analyze your data. To address a couple points:

You'll see all kinds of researchers doing all manner of sloppy things when it comes to statistics and data analysis. Reading some journals makes me groan. You won't necessarily find it a problem for your field, but one should ask oneself if the goal is merely not to get called out by your peers, or to actually run a well designed experiment.
The consequences to the validity of your results lie in an increased risk of Type II error - the incorrect failure to reject the null hypothesis, or in slightly clearer English, finding no effect when an effect exists in reality. Which means, if you run an under powered study, you run the risk of doing the entire experiment, finding nothing, and being wrong. The consequences of that are myriad - first, it likely harms your chances to get published, as null results are often quite difficult to get into press. Second, if it does get into press, you've managed to get an incorrect finding into the literature, which will then be propagated in meta-analysis, reviews, and the minds of impressionable future readers. And then there's the chance you'll abandon a potentially productive line of inquiry because you couldn't be bothered to do power analysis.
One thing to also consider is that not having conducted power analysis somewhat limits your ability to chase after interesting sub-findings. If you've built your experiment on a shaky foundation, and then want to do a second analysis on a sub-set of your results, you almost certainly don't have the power for it.
There are times when you'll be required to do power analysis. If you do research that's clinically relevant, and you ever want it to appear in one of those journals, you may very well be required to show you had a properly powered experiment. And many grant applications require you do so. Even if they don't require it, some people will do a napkin math estimation of your power if they don't see it appearing in your application anywhere.

sjcockell is partially correct. To do power analysis, you at least need to have some notion of the effect measure you're likely to see. And these are indeed just estimations of what you'll see. But in nearly all circumstances, you'll likely have some ideas already. Are there similar experiments you can draw from? Your own pilot studies? A "feel" born of experience in your particular system?

It's also trivially easy to calculate power under a number of difference scenarios, to ensure your experiment is sufficiently powered if things go considerably worse than expected. For example, in a study I once did the power calculations for, we weren't sure what the ratio of exposed to unexposed subjects would be. So I ran it over a large range:

Which left me with the confidence that even if I was in my "worst case" scenario, I'd have reasonably good power at realistic effect sizes.

That's the true strength of power calculations. They'll tell you things about your study. What you need. What doesn't matter. Whether or not before you spend time and money pursuing an idea if you have a reasonable chance at success. Sit down with someone, take an hour or two (at most for a simple experiment) and do it right. Or ask CrossValidated for advice.


Hemoglobin question- how many alleles? So I know that Hemoglobin is made of 2 alpha and 2 beta subunits. The alpha consists of 2 genes on chromosome 16, and the beta of 1 gene on chromosome 11.
So why does Hemoglobin only have 4 alleles? Why is it not 6? In my way of thinking each alpha subunit consists of 2 genes, so 4 total. And each beta subunit consists of 1 gene, so 2 total. Together that makes 6. Confused! Thanks in advance

Meaning of Allele

The word "allele" is often used with two slightly different meanings in biology.

The first, probably more appropriate usage is the one in Remi.b's answer: an allele is a variant of a gene in a population; there are many many possible alleles for a given gene, depending on the length of the gene, though typically only a few are common in a population and even fewer may be known.

The second use of the word "allele" is to mean "copy" of a gene; because those copies can be different, in this context an allele is a potential variant of a gene in an individual. For a diploid organism like a human, you might say that an individual has "two alleles" but what you really mean to say is that individual has "two copies of a gene, which could be the same or different alleles." The relationship between the two copies is called zygosity. I'd argue that this is a slightly sloppy use of the term, but nonetheless it is common and if you understand the meaning it is still clear.

Genes for hemoglobin

For hemoglobin, there are at least 3 important genes: two each encode alpha subunits, and the third encodes the beta subunit (there is also a delta and gamma subunit, but we can omit discussion of those for now).

For the beta subunit, each individual has two copies of the gene, which in human populations are typically thought of as one of two population alleles: either a normal allele or an allele associated with sickle cell anemia. Individuals with two of the sickle cell alleles will have sickle cell anemia.

For the alpha subunit, each individual has two copies of two different genes. There are alleles for each of those genes that produce non-functional products. Individuals with alleles that produce non-functional alpha subunits, for either gene, have Alpha-thalassemia. The severity of Alpha-thalassemia depends on how many alleles are present across the two genes that do not product functional alpha subunits.

Why 4 alleles for hemoglobin??

I suspect if you read somewhere that there are "4 alleles" for hemoglobin, that source was probably talking about Alpha-thalassemia in particular, in which case there are indeed 2 copies of 2 different genes so that an individual has four possible alleles. The severity of Alpha-thalassemia depends on the total number of defective alleles across the two genes, where having 4 defective copies is fatal, and having just 1 defective copy is not noticed clinically.

In the population, however, it is likely that there are actually many other alleles for each gene. For the purpose of describing disease, however, we can group these into "functional" and "non-functional" and say that there are two population alleles for each of these two genes.


Difference between spiking and firing In the article "A Topological Paradigm for Hippocampal Spatial Map
Formation Using Persistent Homology" by Y. Dabaghian, F. Mémoli, L. Frank, G. Carlsson I read some sentences with huge confusion concerning the use of the termss firing and spiking. Do they mean the same thing? It seems to me that when they say a place cell is firing or a place cell is spiking they refer to exactly the same thing. The confusion comes from using both words in the same sentence as in the following sample sentences from the article (emphasis mine):

  Indeed, a rat’s path through a small space can later be re-traced with a high degree of accuracy by recording hippocampal spiking activity during its explorations and then
  analyzing the location, size, and firing rates of a mere 40–50
  place fields [...]

  To understand what algorithms the brain might use to decode
  hippocampal place cell firing, then, we should rely solely on the
  information provided by place cell spiking activity [...]

  It is, in fact, generally assumed that neurons downstream of the hippocampus interpret place cell spiking patterns based on co-firing [...]

  It should thus be possible to trace the emergence of topological information as more and more spikes are fired [...]

  There are biophysical variables (firing rates, spike amplitude, etc.) [...]

In your quotes, the terms spiking and firing are used as synonyms. Indeed, both terms refer to the same phenomenon of action potential generation and in this context there is no physiological functional difference between spiking and firing.

However, note that in some contexts there may be a difference, namely some authors distinguish between a neuron spiking and bursting; the former referring to a tonic firing mode, the latter to a bursting firing mode (e.g. Ramcharan et al. (2000)).

Reference
- Ramcharan et al., Vis Neurosci (2000); 17(1):55-62


Resources to learn about marine life I recently saw the documentary series Blue Planet 2 and was mesmerised by it. Can someone recommend me some resources to learn about marine life? I am particularly looking for those that detail the habits and lifestyles of marine organisms.

P.S. - Hope this is the right stack exchange for this question

There are a lot of marine documentaries out there. These are some that I know of:

Shark (2 episode series in 2015);
Deep Ocean;
Life in the Blue;
Ocean of Giants (Nat Geo);
Ocean Giants (BBC);
Humpback Whales;
Ocean Voyagers (whales);
The Polar Sea;
Swimming with Killer Whales;
Ocean Wonders (no narration, just under sea footage of animal behaviour);
Martin Clunes: Man to Manta;
Nature's Great Events: Diaries (a couple episodes of marine ecology);
Dolphins: Spy in the Pod (a view on dolphin activity using dolphin-shaped cameras);

I watched these off YouTube:
Alien Reefs;
The Giants of Rurutu (whales);
Mucky Secrets: The Marine Creatures of the Lembeh Straight;
Reef Life of the Andaman;
Secrets of the Australian Ocean;
Oceans of Contrast (spends a lot of time on life on land revolving around the ocean, but there's reef life as well);
The Incredible Glowing Creatures of the Deep Sea: Documentary on Bioluminescent Sea Life;
Documentary on Coral: African Wonderful Coral Reef

Conservation type documentaries:
Sharkwater;
Mission Blue;
Chasing Coral;
Blackfish;
Sonic Sea;
A Plastic Ocean;
Shark Men (If you like reality style television series. They capture, tag and learn about sharks to protect them)

If you want a more in-depth resource for learning, you can also YouTube search "marine biology lectures"


How is Elysia chlorotica classified as an animal capable of photosynthesis? Elysia chlorotica is a kind of sea slug. Technically, it's an animal. However, it undergoes a process called kleptoplasty, which is the absorption of chloroplasts from algal prey cells which are then used to produce food. E. chlorotica uses these chloroplasts for 9-12 months at a time, and manages to keep them functioning. Also, E. chlorotica has absorbed some algal genes, however, none are related to photosynthesis, and none are expressed.
So, Elysia chlorotica is a sea slug that is capable of photosynthesis, but only after taking chloroplasts from its prey.
What I'm wondering is how do you classify something like this? I know E. chlorotica is currently listed as a mollusc in kingdom Animalia, but what if it fully absorbed its preys genome and was able to sustain chloroplasts on its own? Would E. chlorotica be considered a plant or an animal? Or something else? Is that even possible?
I know this is a lot, and maybe this forum isn't the right place for my questions, but any insight would be greatly appreciated!

Maybe you are familiar with the endosymbiotic theory which hypotetisays that the mitochondria (and chloroplast) was a little procrayote that got absorbed by larger organisme. At the beggining they were independent in an endosymbiontic relationship but in the process of evolution they merged to one organism from which all eukaryotes (plants). So yes, the process your describe is possible.
If it happens than the new organism is no longer E. chlorotica but a another which evolved from it, this creatue will likely still be clasified as an animal since there are non-photosynthetic plants and there are photosynthetic non-plants (algae, cyanobacteria), Therefore photosynthesys is not the definition of a plant.
The goal of the tree of life is to draw the "familiy tree" of all the living creatures. So, if we know one creature is an animal that gave rise to another one with a special ability we will still clasify it as an animal.


Where can I find hemagglutination inhibition (HI) assay data? I am looking for hemagglutination inhibition assay data for type A influenza virus. I've checked in databases such as fludb.com, however it seems to only have genetic data. A lot of the time, scientific papers don't include the HI assay data they used, so I was wondering if anyone knows where to find such data. I specifically need influenza type A HI assays, not influenza type B.

HI data comes in the form of titers (the reciprocal of the last well plate concentration of antibody that was able to inhibit the virus from binding to the blood sample and forming a shield on the well plate.)

Could someone please give me a link to a database with this information?

Thanks.

I don't think there's any universal database containing ongoing, widely representative HI assay output. The Antigenic Cartography group has made available some historical datasets that were used in published articles, such as

Influenza A/H3N2 data published in Smith et al. 2004. Science 305:371-376
Data from H1N1pdm09 assays in 2009/2010 (click on the links for html/Excel/OpenDocument tables)
Data published in Koel et al. 2013. Science 342:976-979

Trevor Bedford et al. make their large set of historical HI data described in Integrating influenza antigenic dynamics with molecular evolution available in DataDryad.


What is the best time to exercise So, after starting to gain weight on sitting in front of my computer too long, I have decided to take the plunge and maybe stick to an exercise regimen. As has been reported by some studies, exercising in the morning can be more beneficial than doing so in the evening. Now, personally, waking up in the morning is a huge chore for me. Furthermore, I have people advising me to hit the loo (toilet) before exercising as it may not be good for my health and leads to waste accumulation in the body. Now, search as I may, I cant find any basis that supports this theory. I understand that hygiene might be a factor but does exercising in the morning before going to the loo have any effects on health in general? Thanks.

WHO's definition about Health

  Health is a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity.

In other words, Good health means active life where you can express yourself freely, you can succeed and can make mistakes, can reach your goals, can understand your body and others, and can say no when you see your limit to yourself and others - and can set new targets to yourself, feel accepted in your society and accept yourself as you are.

Best time to Exercise for successful results in competitions - dependent on Age

Endurance atletes during ages 25-30 years in this answer about Why does max heart rate decrease with age?

Short-term and long-term effects of exercise on Vitality

There are many stages in your question in Physiology, Pathophysiology and Microbiology, for instance.
I can cover here only the surface:

very short effect of short exercise (20 min) on brain
long term effect of regular short exercise (20 min) on brain, hypothalamus and biologic clock - wakefulness (limbic system)
long-term effect of regular weekly exercise (3.5 h) on brain
long-term effect of regular weekly exercise (3.5 h) on body muscles
long-term effect of careful regular stretching and appropriate resting on congestion of body
long-term effect of regular weekly exercise (3.5 h) on metabolism
effect of regular exercise on circulation system (blood and lymph) - known to increase i.e. include temperature distribution and defence bodies distribution
short-term effect of short exercise on PTH secretion (calcium); autoregulation of renal blood flow with two major theories: myogenic mechanism and tubuloglomerular effect

where I only briefly cover one term in Pathology.
There are two unanswered questions about the renal function [Costanzo, 2013]

  (1) What component of tubular fluid is sensed at the macula densa? The
  major candidates are luminal Na+ and Cl−. (2) What vasoactive
  substance is secreted by the juxtaglomerular apparatus to act locally
  on afferent arterioles? Here, the candidates are adenosine, ATP, and
  thromboxane.

so to understand the effect of short-term morning training on PTH secretion, we should understand the two questions first.

Evidences to some things

Short-term exercise can work sometimes as prophylactics for allergic symptoms.
I think the most important thing is the irritation of your skin which is the most important endocrine organ in our body.
Skin's temperature change secretes many hormones than help us to stand irritations from the environment.

What are the effects of short-term exercise in the morning depends on the patient at hand.
I cannot say much general.
For instance, if your heart is not strained; that it has too high T peak, too heavy exercise can cause you harm.

My personal experience

Short-term exercise suited to a person with no deficits in sleeping can help to alleviate symptoms of allergies and decrease stress in a normally physiological balances without viral infections,

but the real world is not that nice.
The problem comes if the patient has any disease that uses our immune system against us such as some viral infection.
The immune response is also the source of pathogenesis for many viral diseases.
Unlike for a bacterial infection, the ultimate goal of the immune response in a viral infection is to eliminate both the virus and the host cells harbouring or replicating the virus, [Murray, Medical Microbiology, 6th ed].
Actually, some drugs are immunosuppressant like cortisone, and some procedures like radiation therapy.

However, with some medication plans, you should avoid drugs, living styles and habits that immunosuppresses your body.
For instance, HIV patients with HAART medication plan (medication combination is antiretroviral but possible immunosuppressive pathways may exist in different conditions) that involves a strategy depending on the condition, since HAART medications are life-long and cannot be stop, so other conditions etc TBC must be treated first, to avoid too much burden on the body at the same time.
In a similar way, avoiding living style or habits that puts immunosystem down can help with HIV.
Doing sport when you have slept badly many days and feel exhausted, puts your body under immunosuppression.
So the state of the disease or your physical wellbeing determines when sport is useful and when not.

Other part of your question

To hit toiled before exercise is good because then

you decrease the risk of gastrointestinal bleeding and venous congestion.
effect of exercise on constipation is one topic here; depends on you, since there are many types

The more stuff you have in your colon and gastrointestinal system, the harder it is to use fully your muscles of your body.
Try pull-ups with more empty colon vs full one.
Pull-ups require many muscles from upper trunk and lower trunk.
You cannot use all your stomach muscles if something is blocking your middle body muscles.

Good Hygiene is the easiest way to decrease the risk of any infections caused by many factors.
I estimate that 2-5 % of people visiting public toilets wash hands correctly; one video here about how one should do it.
Many people leave their hands wet.
If you have infection in your body, you should not exercise because failure to resolve the infection may lead to persistent or chronic infection or death.
It takes much energy from our body to handle with infections.
To recover from training, it requires good balance of many factors.

Summary

The best time to do sport when you are healthy

you do not have any infections (viral particularly) because a failure to resolve the infection can lead to persistent or chronic infection or death
when you have prepared early enough for the exercise with enough sleep

where pathologies and/or teratologies are not limiting your process.
You compete only against yourself and then grow from that to see you how good person you are really.

The morning exercise in a body which has rested well before the exercise and prepared accordingly to the exercise can be useful because

short-term effects on the brain (process things during exercise) (See Figure 1)
possible short-term effects during day after the exercise

and if the exercise becomes a habit in a healthy person, then

long-term effects: increased metabolism and many other positive effects described above
and many other possible reasons from social to better self-esteem

when the the person listens to his body and stops when it hurts or something goes over; can rest accordingly.
Good motivation is useful in gaining good health.
Motivation is the strength and direction of the effort.
If you are interested in morning exercise, then you can set target and make a realistic plan.
Listen your own body and be able to refit your plan accordingly.
Actually, here is an important step that the consultation of many doctors can be useful; one doctor cannot always see the main problem for instance of prolonged and deepened allergic symptoms.
Consultation and discussions of other people can also be useful - like discussing where to help for this and this; who has enough capabilities to understand it.
The person cannot always know himself what is a main disease underneath.
Anything can come that postpone some training sessions.

Sources

Infectious disease courses 2015-2016
Gleeson. The effect on immunity of long-term intensive training in elite swimmers.
Anderson. Effects of Exercise and Physical Activity on Anxiety. 2013.
Laires. Exercise, magnesium and immune function.
Gunzer. Exercise-Induced Immunodepression in Endurance Athletes and Nutritional Intervention with Carbohydrate, Protein and Fat—What Is Possible, What Is Not?
HAART and HIV in DynaMed Plus. Visited 7.8.2016.
WHO. Health Education. Visited 7.8.2016.
...


Can human mRNA be translated in vitro by prokaryotes? As the genetic code is universal, can mRNA from a human cell be correctly translated by a prokaryote in a in vitro translation system?

Short answer: Yes, you can.

Usually these are coupled systems for transcription and translation. For these you clone the gene of interest into a vector which contains a prokaryotic promoter which is then used to generate the mRNA in the tube. This mRNA is then translated in the second step into a protein. This works very well, but the protein is missing the typical post-translational modifications of eukaryotic cells like glycosylations, as these are not existant in the bacteria.

These kits can be purchased of the shelf from the usual biotech companies. Mostly these are based on E.coli cell lysates. They work like shown in the figure (from here):


How is adrenaline (also known as "epinephrine") a ligand? I keep reading that adrenaline is a ligand, however, from what I understand a ligand is a molecule or ion which donates a pair of electrons to a central transition metal ion in a complex. If this is the correct definition of a "ligand", then how can adrenaline be a ligand?

The definition of "ligand" in the question, "a molecule or ion which donates a pair of electrons to a central transition metal ion in a complex" is clearly a more technical 'chemistry-type' of definition. Ligands in biology and medicine can be all sorts of molecules, though most of the time we think of them as molecules that bind to a particular receptor. Those receptors can be ion channels, enzymes, transmembrane receptors at the cell surface or within the cell in an organelle, nuclear proteins that control expression of genes in the cell nucleus (i.e. transcription factors), etc...the list could go on and on... In fact, more recently we have come to appreciate that compounds like bile acids - that were previously thought to be important only in fat absorption in the gastrointestinal/digestive tract - are also ligands for receptors that control gene transcription ("Farnesoid X Receptor") as well as increase energy expenditure in brown adipose tissue and skeletal muscle (through receptors like the "TGR5" receptor).

But... back to the question...

If a molecule binds to a receptor, then it's a ligand for that receptor. The ligand doesn't have to donate any electrons specifically to a transition metal. Most of the time in medicine/biology the binding of a specific ligand to its receptor is a reversible process that is dependent on the concentration of the ligand and the availability of the receptor (among other things). The specificity of ligand for the receptor is due to chemical factors like hydrogen bonding, electrostatic interactions (like positive charges attracting negative charges), as well as other chemical interactions beyond the scope of this question. As you can see from the picture below, the hydroxy groups (-OH) that are part of the serine residues on the receptor are hydrogen bonding with the hydroxy groups on the epinephrine molecule itself. Moreover, the carboxy group (-COOH) on the aspartate residue is binding to the positively charged amino (NH3+) on the epinephrine molecule.


Why does vaccine development take so long? The main principle behind a vaccine is to take a deactivated virus, "show" it to the immune system so it can "learn" how it looks like, so if and when the real virus does attack us, our immune system is already prepared for it. Vaccines have been developed using this idea even in the 1880's.
If that's the case, why does it take so much time and effort to develop a vaccine, for example, against covid-19? (and why are there several variants with different measures of reliability?) Is it only about balancing how strongly we damage the original pathogen, too much damage and our body might not learn the correct identifiers, and to little damage and it might still be active enough to cause the disease?

Roni Saiba's answer does a good job of explaining what goes into current vaccine development and why it takes so much effort, but I want to directly address the question of why we can't just grow some virus, kill it with UV and have a protective vaccine.
The answer is that not all immune responses to viral antigens are helpful in fighting infections of that virus. In some cases it can be harmful; antibodies to dengue virus of one serotype will attach to viral particles of another serotype but aren't able to inactivate them. The attachment of antibodies to active viruses makes their absorption by cells more efficient, and infections where this antibody-dependent enhancement occurs are more severe than first-time dengue infections.
Some viruses have evolved mechanisms to capitalize on this. The reason we need to get a new flu shot every year is that influenza viruses present a "knob" at the end of their glycoprotein that can change its structure and still retain function. This part is much more 'visible' to the immune system than parts of the virus that can't tolerate changes, so the immune response to this variable part outcompetes and prevents an immune response that would provide long-lasting protection. Conserved stalk-targeting vaccines are being intensely investigated for this reason. SARS-CoV-2 may have a immune-faking mechanism as well: the "spike" glycoproteins responsible for binding the ACE2 receptor and entering the cell convert to their post-binding form prematurely part of the time. Antibodies that bind the "post-fusion" form of the protein don't inactivate the virus, and this form sticks out more so may serve to compete for immune attention with the pre-fusion form that would provide protection if bound by antibodies.
In this last example, we can see that a vaccine made of killed SARS-CoV-2 virus particles would be useless if all of the spike proteins had converted to the post-fusion state. The mRNA vaccines therefore don't encode the natural spike protein, but a mutated version which can't convert to the post fusion state as easily:

S-2P is stabilized in its prefusion conformation by two consecutive proline substitutions at amino acid positions 986 and 987

In conclusion, viruses and the immune system are very complicated. Simple vaccines work for some viruses, and don't work for others. When they don't work, the reason is always different, but hopefully I've communicated some general understanding of the background issues.
EDITS:
This doesn't relate to the rest of my answer but I want to respond to Ilmari Karonen's and there is not enough room in a comment.
Looking at the timeline for SARS-CoV-2 vaccine development gives a very misleading impression of how long it takes generally. This is because ~90% of the development work was already done before COVID-19 was ever identified, in the 18 years since the SARS-CoV-1 outbreak started in 2002. Vaccines against SARS were developed and tested up to phase I trials, but couldn't proceed further since the virus was eliminated. I discussed this in a previous answer to a similar question, but to expand/reformat, here's some of what we knew and had available on March 17th 2020, when the "covid vaccine timeline" begins:

Identified the receptor as ACE2, and knew that antibodies targeting the receptor binding domain (RBD) of the spike protein neutralize the virus. Protocols to test that these were also true of SARS-CoV-2 were already developed and validated. Without this there would have been a lot more trial-and-error experimentation and false starts with vaccine candidates that looked promising but didn't pan out in testing.
Animal models. There is no naturally-occurring model organism for COVID-19. This is a subtle point because other animals can be infected with the virus, and some develop morbidities because of it. However, these are different enough from what we see in humans that something that protects against the reactions we see in the animal can't be assumed to protect against the reactions that cause problems in humans. For SARS, researchers developed transgenic mice that used the human version of ACE2, and showed that the disease they got from SARS were analogous to the disease humans got. This took several years, and the colony was still available when the virus causing the outbreak in Wuhan was identified as SARS-like and researchers started looking for animal models. As an aside, in an interview on This Week in Virology that I can't find right now, one of the maintainers of that colony said they were months or weeks away from shutting it down and euthanizing all the transgenic mice when the pandemic began, so if funding had been just a bit tighter we probably would not be having this particular conversation now.
How to stabilize the pre-fusion form of coronavirus spike proteins had been determined from work on SARS and MERS vaccines.

In addition to these, a large amount of miscellaneous knowledge about coronavirus functions and the immune reactions to them had been accumulated, and this sped up development, and increased confidence in results, which allows vaccine candidate production and testing to proceed more aggressively.
Historically, vaccine development has taken years or decades of research after the need has been identified. Testing is still longer in many cases, but the current case is very unusual.


Plant respiration produces carbon dioxide, so why are plants regarded as decreasing its atmospheric concentration? In the absence of sunlight, plants give out the greenhouse gas, carbon dioxide. So why is it said that plants increase the concentration of atmospheric oxygen? Do they not increase the concentration of carbon dioxide and use the oxygen produced in photosynthesis.

There are two factors here.  First is that you have to look at the plant's net production over time.  Say for instance (I'm just making up numbers here) that during the day the plant takes in 88 g of CO2 and uses photosynthesis to convert it to 64 g of O2 that's released into the air, and 24 g of C that is incorporated into the plant.  Then during the night it uses 12 g of the stored C for respiration (combining it with 44 g of O2 from the air), leaving a net daily production of 12 g C that goes into plant growth, and 44 g of O2 in the air.

Second problem is perhaps better classed as either linguistic confusion (to be polite) or ignorance.  CO2 is not "pollution": it is a normal part - more accurately, a fundamental part - of the carbon cycle https://earthobservatory.nasa.gov/features/CarbonCycle on which almost all life depends.  The problem is not plants (or animals) releasing CO2: it's humans digging up lots of fossil carbon and burning it, thus increasing atmospheric CO2 concentrations beyond the levels to which the ecosystem has adapted.

Now that you've changed the question, it's even more important to read the basic description of the carbon cycle at the link.  (Honestly, wasn't this covered in your high school biology class?)  Again, the bottom line is that plants produce a net surplus of O2, which animals consume along with the plants, so that the cycle remains balanced.


Does long term use of antibiotics in humans actually lead to a greater risk of infection? I've read about the overuse of antibiotics leading to antibiotic resistant strains of bacteria, so generally does long term use of antibiotics breed these strains in the bodies of antibiotic users and increase the risk of various bodily infections?

does long term use of antibiotics breed these strains in the bodies of antibiotic users[,] and increase the risk of various bodily infections?

Yes to the first question (although I would use the words select for). No, not usually for the second question in the individual(*), yes in the population.

This should be looked at as a problem in populations of both people/animals and bacterial populations in general. Given time, any living organism will be favored if a mutation involving a selective pressure (like an antibiotic) is introduced, not only in those towards which the antibiotic is directed but also among the normal microbiota. The longer the selective pressure (antibiotic treatment), the greater the probability that a resistant strain of one bacteria or another will develop.

That's why there's a push (in studies) to limit the number of days of antibiotic use necessary to the least number needed which still proves efficient in eradicating an infection. (The trend is towards kill 'em quick and kill 'em all - higher doses for shorter periods, or make it strong and only long enough to cause the extinction of the illness-causing bacteria and not long enough for selection of resistance mutations.)

It is quite normal to have potentially pathogenic bacteria as part of one's microbiome. Usually other beneficial bacteria and conditions keep these in check. But antibiotic resistance, once selected for, can persist for longer periods of time than previously recognized (up to four years in one study). This gives even a small population of resistant bacteria to genetically transfer resistance to others.

Short-term use is less likely to select for resistance in one individual, but, in terms of populations of people, antibiotics are used so ubiquitously that resistant strains will be selected for in shorter treatment intervals by sheer numbers of people being treated.

  When resistant and susceptible organisms compete to colonize or infect hosts, and use of an antibiotic has a greater impact on the transmission of susceptible bacteria than resistant ones, then increasing use of the antibiotic will result in an increase in frequency of organisms resistant to that drug in the population, even if the risk for treated patients is modest. Antimicrobial use and patient-to-patient transmission are not independent pathways for promoting of antimicrobial resistance, rather they are inextricably linked.

"Long term use" in one individual is relatively uncommon and unnecessary, but if necessary, usually does more good than harm to that individual. Almost all (if not all) of the population of the bacteria you're trying to eliminate from one site will be susceptible to the antibiotic and will die, leaving, in a few cases, a few resistant ones that your body can handle naturally, or that can repopulate to "normal" levels without causing illness. But they are then there, the resistant ones, to spread within a population of the individual's microbiome, and the population of people. The next person with a problem, who might have picked up that resistant strain, will not respond well to the same antibiotic. Nor will the patient who was initially treated, if the problem recurs with an antibiotic resistant strain. So, as I said, yes and no.

That's why people (doctors, vets, and - with help - patients) should consider a risk-to-benefit-ratio whenever using an antibiotic. From that standpoint, it is always unethical to use an antibiotic for what is probably a virus, because the benefit to a patient is very small, but the risk - to that patient, who might suffer complications from its use, and to the population if a resistant strain is selected for - is relatively high. Better to wait it out to see if it is bacterial (if one can't test for it directly), and treat it if it does turn out to be. Of course, the risk of not treating in certain populations must also be considered: the elderly, the immunosuppressed, infants, and people with other illnesses or predispositions to infection.

It's not just use of antibiotics in patients/humans that causes problems; its use in any situation can lead to selection for resistance. This is well documented to occur in the meat industry, where a grower often tries to minimize the effect of cost-efficient but insalubrious growing conditions by giving antibiotics to the entire population of meat-animals (beef or poultry) to cut the monetary losses associated with potential illnesses.

It's a multifactorial, and often monetarily driven, problem. Doctors share the blame, but so do patients who demand antibiotics thinking they know better than the doctor, and who will doctor-shop until they find one who will do their bidding, or make a stink for the doctor who refuses. Some doctors still refuse, but they pay a heavy (non-monetary and sometimes monetary) price for doing so.

In the meat industry, it's always a monetarily driven process.

  This review focuses on agricultural antimicrobial drug use as a major driver of antimicrobial resistance worldwide for four reasons: It is the largest use of antimicrobials worldwide; much of the use of antimicrobials in agriculture results in subtherapeutic exposures of bacteria; drugs of every important clinical class are utilized in agriculture; and human populations are exposed to antimicrobial-resistant pathogens via consumption of animal products as well as through widespread release into the environment.

What YOU can do:
Do not take an antibiotic for a viral infection like a cold or the flu.
Do not save some of your antibiotic for the next time you get sick.
Take an antibiotic exactly as the healthcare provider tells you. Complete the prescribed course of treatment even if you are feeling better. If treatment stops too soon, some bacteria may survive and re-infect.
Do not take antibiotics prescribed for someone else.
If your healthcare provider determines that you do not have a bacterial infection, ask about ways to help relieve your symptoms. Do not pressure your provider to prescribe an antibiotic.

Antibiotic resistance: delaying the inevitable
Get Smart: Know When Antibiotics Work
Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome
Antimicrobial Use and Antimicrobial Resistance: A Population Perspective
Comparison of 8 vs 15 Days of Antibiotic Therapy for Ventilator-Associated Pneumonia in AdultsA Randomized Trial
Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria
Industrial Food Animal Production, Antimicrobial Resistance, and Human Health


Is it possible to get infected with HIV from old blood? Let's say that someone uses a needle which has some old blood infected with HIV. In this case, is it possible for them to get infected with HIV?

Yes, you can transmit HIV with infected needles/syringes. This is a quite common mechanism of transmission when drug addicts share and re-use needles and syringes and also in third world hospitals with poor hygiene standards.

A drop of blood is considered infectious at least until it has completely dried up (some research showed that it might be contagious for up to 5 days longer when the conditions are right, see reference 1 below). Mostly HIV is senstive against high temperatures (over 60°C), while it is stable at low temperatures. It is very sensitive against shifts in pH (below 7 or above 8) and also against desinfectants like bleach. Have a look at the references below, a lot of research has been done by Abdala et al. in this field. You can find his whole reference list here (it contains more articles in this field).

References:

Survival of HIV-1 activity after disinfection, temperature and pH
changes, or drying.
Survival of HIV-1 in syringes.
Survival of HIV-1 in syringes: effects of temperature during
storage.
Viability of HIV-1 in syringes: implications for interventions among
injection drug users.