term for species that produces males only to mate with mother or sisters

The non-random mating of individuals within a population is called Assortative Mating. Mating specifically with individuals that share similar traits is called Positive Assortative Mating. However, sharing similar traits doesn't imply being closely related.

The reproduction by two closely related individuals is called inbreeding. The opposite of inbreeding is outbreeding (a.k.a. outcrossing).

To my knowledge, a mating system where all individuals inbreed doesn't have a special term. Searching google.scholar for mating system inbreeding will show you a lot of articles that talk about mating systems where all individuals inbreed without needing to use a specific term for it.


Is there a risk of localised die-off when plants bud too early?

If you're talking about shoots or buds coming out of individual seeds, then those plants are probably doomed. Most seeds are "designed" as one-shot delivery packages. In this case, they'll bud, be killed off by a frost at some point during the winter, and then be spent.

For a perennial plant like a tree that buds year after year, the impact of an early blooming will depend on the species. As per a Q&A from Cornell (Will Warm Winter Wither Plants?, 2007), most plants growing in a temperate climate (like that of Britain) will have experienced warm winters before and will have at least some evolutionary adaptations to help them deal with occasional aberrant weather. For example, even if you do see some fresh buds on a tree this time of year it is likely that the majority of its bud primordia (the parts of the plant that will someday become buds) have not developed. Although you won't see regrowth in the spring of most of the buds that opened early, you will see normal development of the buds that stayed dormant during the winter.

As for the question of wider ecological change, one anomalous year isn't going to make a difference because, as you say, a large portion of the seeds/shoots/buds/whatever refrain from growing even if some are being tricked by the mild winter. However, if a string of mild winters cause significant die-off year after year you would start to see changes in the ecosystem. It works the same way for many with loosing their hair...


How can heart disease cause excessive sweating?

The answer lies in compensation. Take myocardial infarction, for starters. MI, if large enough, severely weakens the heart, and hence, at the same level of stimulation, it can no longer pump blood effectively, causing what is called Heart Failure (inability to pump enough blood). This causes an excess stimulation of the sympathetic nervous system (or more technically, neurohumoral mechanisms) in an attempt to compensate, which by its effects on heart contractility and rate increases the amount of pumped blood to match the need. This sympathetic outflow also causes increased sweating, nervousness, dry mouth etc. Sweating, nervousness are cardinal signs of acute MI.

Additional point: This compensation can only work in certain cases, say for example where the heart failure is due to blood loss with a healthy heart. But in cases like MI, this compensation is not an optimal response, rather it worsens the case, since increasing the workload on an ischaemic heart (ischaemic levels of atherosclerosis being the commonest cause of MI), further damages the wall leading to chronic heart failure and disease. This is the Broken Compensation Model for chronic heart failure. This is why we use Beta Blockers to abrogate the sympathetic system's (or more technically, the neurohumoral mechanisms') unwanted compensatory efforts, and the observed efficacy and increased longevity substantiates the validity of the model.

References:

I added them in a bit of a haste. They might not be the best references available, but they are considerably credible. Pathophysiology of heart failure, ventricular remodelling and the involved neurohumoral mechanisms are well-studied, and you shall get several papers on it on pubmed or google scholar.

Books

Robbins and Cotran: Pathological Basis of Disease 9th Edition
Hutchison's clinical methods 23rd edition

Papers and links -Heart Failure pathogenesis

Kemp CD, Conte JV. The pathophysiology of heart failure. Cardiovascular Pathology. 2012 Oct 31;21(5):365-71. (General overview of the pathogenetic mechanisms underlying)
CVphysiology.com(A relatively less technical review)
Kırali K, Özer T, Özgür MM. Pathophysiology in Heart Failure. InCardiomyopathies-Types and Treatments 2017. InTech.
http://bestpractice.bmj.com/best-practice/monograph/61/basics/pathophysiology.html

Papers and links -Sweating as a symptom of MI

National Heart Lung and Blood Institute
Bruyninckx R, Aertgeerts B, Bruyninckx P, Buntinx F. Signs and symptoms in diagnosing acute myocardial infarction and acute coronary syndrome: a diagnostic meta-analysis. Br J Gen Pract. 2008 Feb 1;58(547):e1-8.
Gokhroo RK, Ranwa BL, Kishor K, Priti K, Ananthraj A, Gupta S, Bisht D. Sweating: A Specific Predictor of ST‐Segment Elevation Myocardial Infarction Among the Symptoms of Acute Coronary Syndrome: Sweating In Myocardial Infarction (SWIMI) Study Group. Clinical cardiology. 2015 Dec 1.
https://www.sciencedaily.com/releases/2005/11/051122183817.htm
http://www.webmd.com/heart-disease/news/20051115/sweating-prompts-heart-attack-care#1


Cell biology - Resting membrane potentials

The resting membrane potential is the voltage at which there is no net flow of ions across the membrane.

Every ion will tend to flow down it's concentration gradient (this is just a basic principle of physics/chemistry). So, without considering charge, for a typical cell, potassium will tend to flow out, sodium will tend to flow in, and other ions will also behave according to their concentration gradients.

The other crucial part of the equation is the relative permeability of the membrane to each ion. This comes mainly from the presence of ion channels. At rest, a typical cell has more permeability to potassium than sodium.

That means that if the driving force for sodium and potassium is the same (it's not identical at 0 mV but fairly close), more potassium will move than sodium.

If the definition of resting potential is the potential where net flow of charge is zero, and considering only sodium and potassium, then rest has to be where sodium flowing in equals potassium flowing out. This situation occurs when the inside of the cell is negatively charged compared to the outside: the membrane voltage "holds" potassium in and "pulls" some sodium in, such that their currents are equal and opposite despite the higher permeability to potassium.

Note that the voltages we are talking about in neurons, on the order of 10s of mV, are very small, and electrical forces are very strong. The concentrations of positive and negative ions are almost exactly identical on both sides of the membrane: only a few ions actually have to move to make a (biologically) large membrane voltage. What is actually important is the permeabilities: that's what makes action potentials and other forms of neuronal signaling feasible.


Cornea is considered as an "immune-privileged" site and tissue, neither HLA nor blood grouping is required for allogeneic corneal transplant.

In terms of reference:
This could be one: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802514/


The Isreali outbreak (associated with changes in fish marketing) was reported in Lancet a few times. It was particularly important for identifying biogroup 3. I hope that might be helpful, but I'm not sure it will be. Since it was an important epidemic, I wouldn't be surprised if it was discussed in a visiting lecture by someone who wasn't part of the Isreal Vibrio study group.

I'm not aware of a soap dispenser case for V. vulnificus, but soap dispensers have been implicated in the transmission of other pathogens. Could it have been some other halophilic bacteria, possibly another Vibrio?


Does Rough ER (RER) produce phospholipids?

The endoplasmic reticulum (ER) is one of the largest continuous membrane bound organelle of the cell.

The rough ER and smooth ER share the same membrane and some membrane proteins can diffuse between them. At the same time there are specific markers for ER sheets (rough ER) and ER tubules (smooth ER). The terminology of rough and smooth come from early electron microscopy and biochemical work where large amount of ribosomes (polyribosomes) were found on the rough endoplasmic reticulum membrane, and less on the smooth. These membranes can be biochemically separated one being more heavy (RER because of attached polyribosomes) than the other.

In general the ER has several functions: protein synthesis, calcium storage, entry of the secretory pathway and lipid synthesis. It can not only produce phospholipids but also a large array of precursors for steroids and neutral lipids.

This is a topic of research itself but it is general thought/accepted that the smooth ER is the one responsible for the synthesis of phospholipids.

In reality, there are multiple ways to produce phospholipids (from recycled membranes, from lipid droplet stores, etc) and there are multiple possible pathways for producing lipids and lipids precursors (de novo synthesis). This also implies that there are multiple enzymes involve in this process. Now these enzymes are often ER membrane proteins and they can but do not always specifically localize particularly to one part of the ER.


Selection marker for a cytoplasmic vector that works at low expression levels?

Flow cytometry looking for your plasmid.

These folks labeled their plasmid with a proprietary fluorescent marker, then used flow cytometry to detect cells which had taken up the plasmid.

A novel rapid and reproducible flow cytometric method for optimization of transfection efficiency in cells

  An alternative and more direct method to using fluorescent reporter
  genes is to directly label nucleic acids with fluorescent dyes to
  track their intracellular delivery [16]...
  Using the non-enzymatic Label IT® Tracker TM Kits, any plasmid can be
  custom labeled in a simple one-step chemical reaction before
  introduction into mammalian cells [18]. Thus, both subcellular
  localization of the labeled DNA and expression reporter transgene can
  be monitored simultaneously following introduction of the labeled
  plasmid into mammalian cells [16, 18]...

  Herein, we demonstrate the development of a flow-cytometric assay to
  determine transfection efficiency by labeling a reporter plasmid with
  Label IT® TrackerTM. This method does not depend on co-transfection of
  two different plasmids and simultaneously quantifies cell death,
  uptake of the labeled plasmid during transient transfection, and
  expression of the target protein.

Even if only a small fraction of your cells take up your glowy plasmid, you will sort those out from the rest with flow.


What determines the duration of larval stage?

I actually see two different questions in your question. The first is "what determines the duration of the larval stage ?", the second is "why is this duration longer that the adult stage ?"

A) What determines the duration of developmental stages?

First, you must note that not all insects follow the same development process. Holometabolous insects (e.g. butterflies) have four life stages: egg, larva (with several instars), pupa and adult (or imago). On the other hand, hemimetabolous (e.g. bugs) only have three life stages, and some insects are ametabolous, i.e. no metamorphosis. Development time thus greatly depends on the mode of development. Of course, there can also be a huge variation within insects that have the same mode of development.
What else determines the duration of developmental stages ? (i.e. eggs/larva/pupa) A large combination of factors. Before they reach the adult stage, insects need to accumulate enough energy to undergo every developmental step and become mature. Resource quality and availability of course influence developmental "speed", but abiotic parameters such as temperature or humidity are also of prime importance. Actually, development time of many insects can be measured in degree days, which corresponds to the accumulation of temperature over time. For instance, larval-pupal development of the codling moth Cydia pomonella can go from 1 to about 6 months, according to temperature conditions.

B) Do insects have longer pre-reproductive periods that reproductive periods ?

It depends. There is a huge variation a) in the lifespan of all insect species, b) in the relative length of their developmental stages.
Some insects indeed have a very short adult life stage, relatively to their developmental stages. Mayflies are a classical example, but it's also true for many butterflies and moths of for mosquitoes, for instance.
On the other hand, it's not true for many other insects. Many Coleoptera (e.g. beetles, cockroaches) can have several-month long adult lives, sometimes way longer that their life as a larva. Bees are a more extreme example: bee queens need three weeks to become fertile, and can then reproduce during several years (same for ants).

C) Why do s̲o̲m̲e̲ insects have short reproductive periods ?

To my knowledge, the reasons are mainly ecological. Insects that have short adult lives are often fragile, flying insects that disperse a lot. They face an increased risk of predation as well as environmental fluctuations (weather, etc.) against which they are poorly protected. Besides their resources (e.g. sugar) may be scarce or poor-quality - some even do not have the ability to feed, e.g. mayflies.
What about evolutionary reasons? Developmental stages need some time because, as I said earlier, insects need to acquire a lot of energy to pass all developmental steps. I didn't even talk about metamorphosis, which is a complete cellular re-organization -that takes some time. On the other hand, adults just need to mate and/or lay all their eggs before they die. They don't need to live too long as they'll probably die soon anyway. Think about mayflies: they are less protected as free flying adults that as underwater-protected nymphae. And they'd better try to maximize egg laying in a reduced time.
Besides, note that there is a difference between potential lifespan and realized lifespan. For instance, parasitoid wasps can live up to 30 days in safe, food-abundant conditions - in the wild however, they often live just a few days.

References

https://www.terminix.com/blog/bug-facts/how-long-do-bugs-live/

Harvey, J. A., Cloutier, J., Visser, B., Ellers, J., Wäckers, F. L., & Gols, R. (2012). The effect of different dietary sugars and honey on longevity and fecundity in two hyperparasitoid wasps. Journal of insect physiology, 58(6), 816-823.

Müller, T., & Müller, C. (2015). Behavioural phenotypes over the lifetime of a holometabolous insect. Frontiers in Zoology, 12(1), S8.

Rafoss T, Saethre M-G (2003) Spatial and temporal distribution of bioclimatic potential for the codling moth and the Colorado potato beetle in Norway: model predictions versus climate and field data from the 1990s. Agric Forest Entomol 5:75–85


There was a 2011 study where they used a sensitive atomic magnetometer to try to detect a plant's magnetic field. They stated that:

  To our knowledge, no one has yet detected the magnetic
  field from a plant. Biochemical processes, in the form of ionic
  flows and time varying ionic distributions, generate electrical
  currents and time-varying electric fields, both of which produce
  a magnetic field. However, contrasted to muscle contraction
  and brain processes, which have a characteristic time
  scale shorter than one second, plant bioprocesses span several
  minutes to several days and the expected magnetic field from
  such processes is correspondingly smaller.

  Measurements with a sensitive atomic magnetometer were performed on the Titan arum
  (Amorphophallus titanum) inflorescence, known for its fast biochemical processes while blooming.
  We find that the magnetic field from these processes, projected along the Earth’s magnetic field,
  and measured at the surface of the plant, is <
   0.6 lG.

So according to this, no, you wouldn't be able to sense the magnetic field from a plant with a magnet.


Does the corpus callosum have a significant relationship with motor memories/ muscle memories?

This study tests the time it takes for patients with damaged corpus callosums to perform intermanual transfer motor tasks.
Patients drew a meaningless figure with one hand, then did it again with the other hand (And vice versa). Thus performing intermanual transfer.

All three patients displayed a significant benefit for transfer from the dominant to the non-dominant hand but not vice versa during proximal motor activity.

...the proximal transfer behavior was found to be similar for all patients in the healthy group.

From these results, a relationship exsists.


Do all mammals have a Ventricular system?

The ventricular system is common to vertebrates. It's also necessary for brain nutrition, assists in preventing under/over perfusion by exerting/releasing pressure, and forms part of the brain's glymphatic clearance pathway.

See also:

Totally Tubular: The Mystery behind Function and Origin of the Brain Ventricular System


Database of Multicellular and Unicellular organisms?

More like a comment:

It doesn't seem that such a database exists, but I think it's relatively easy to create a list of multicellular taxa and the rest should be considered unicellular. Since you use ncbi taxonomy, you can easily get higher-level parent for any species, so there is no need to define cellularity for individual species.

The challenging groups would be different algal and fungal taxa, but there are some good reference books. You also have to decide, whether to introduce a separate category for colonial/coenobial/filamentous organisms.


Epistasis when interacting loci are codons within a single gene

The Wikipedia article on epistasis has a section on epistasis within genes, which it terms intragenic complementation:

  Just as mutations in two separate genes can be non-additive if those genes interact, mutations in two codons within a gene can be non-additive. In genetics this is sometimes called intragenic complementation when one deleterious mutation can be compensated for by a second mutation within that gene.

It appears that many interesting examples of this phenomenon occur when the protein forms multimeric complexes. A multimer consisting of monomers with different mutations may function where a homogenous multimer of monomers of only one of the mutations might be inactive. See Turner et al., (1997) PNAS 94:9063-9068. The Wikipedia article mentions some examples of this under the term interallelic complementation or heterozygotic epistasis.

This reminded me of the phenomenon of protein coevolution that is currently being used to try to leverage evolutionary information to solve protein structures. When the homologous sequences of a protein are known in many different species, then a reasonable assumption is that mutations in protein residues that are in close spatial proximity will correlate, e.g. if a lysine is switched to an glutamate, then other nearby residues may mutate to accommodate the change in ambient electric charge. For more information on this effect, two very interesting papers are Hopf TA, Colwell LJ et al., (2012) Cell 149(7):1607-1621, where the sequences of a family of membrane proteins are used to predict their structure, and Skerker et al (2008) Cell 133:1043-1054, where the covariation between residues in a complex of two proteins is used to re-wire the specificity of one protein for another.


Experiments on abiogenesis in laboratories

Now the question you have is really very interesting and deep but the short answer is we still don't know enough to be able to decide

1.Precisely when an assembly of molecules and their interactions becomes a living organism and

2.We have no idea what the "alternatives" of what we know today as life are, so we can't be really sure what kinds of "other possible life forms" can be generated both in the laboratory and in the outer space on some distant planets.

In order to tackle the first question in the last decade or 2 new science has emerged-the field of synthetic biology whose goal is to "recreate" life in the laboratory from materials generally not considered to be alive-like cell membranes and DNA alone out of the cell but they are also trying to upgrade our current technology for manipulating the DNA of living organisms to the point where we can literally create new species in the laboratory. Here are some very good publications by the most renowned expert in the field of synthetic biology Craig Venter-here and here . These are seminal works for synthetic biology but if you want to know more you can search entire journals dedicated only to synthetic biology-here,here and here. There are actually hundreds of articles pertaining exactly to the answer of the question you are posing-what are the experiments we have done in the laboratory to recreate life in controlled conditions and how much we can "model" it to our own desires. Even if you only skim the abstracts of the articles in these journals you will be able to see how far we are in the de novo genesis of life and what we can do with our newest technologies to mimic the process by which the first cells arose. You would also find good work showing the prospects for manipulating current living cells to "synthesize" what scientists would consider new "man-made" species of bacteria. Although we aren't quite there yet the prospects are exciting at the least and really mind blowing at best. The discipline (I call it discipline because it isn't "just" a science but a combination of recombinant DNA technology, advances in the chemistry of large biomolecules, cutting edge genomics and proteomics, novel methods for computational modeling of metabolism and genomics and many more disciplines combined into one direction) is just in its "infancy" but even only what we can do now is enough to open the door for an entire new array of biotechnologies to come. However, I personally advise you to begin with the 2 papers of Craig Venter I already showed you and also this one and then go to these journals.

I would also recommend you seeing the reviews of Pier Luigi Luisi on the attempts of constructing self-replicating vesicles in the laboratory-here,here and here. He in my opinion is the man who has got the closest to actually achieving in the laboratory the synthesis of systems close enough to the living cell-self-replicating lipid vesicles. I think if we are ever to recreate life in the laboratory this is the closest shot we have. You might also be interested in this paper here and this here who pertain to the same field-the use of lipid vesicles as a simple way to recreate the origins of life and to build living cells in the laboratory.

Lately, there is also one brand new interesting paper from this year on the issue of creating molecules and systems of molecules capable of evolving themselves into more complex ones here.

Now on the second question-how to recognize what kinds of forms of life can exists in the universe, there is also a fast growing new science-the science of astrobiology whose goal is to devise a broader perspective on what life is. can be and how it can arise in the wide context of the cosmos. not only in the particular context it occurred here on Earth. There are 2 good journals pertaining to this field here and here which can give you very good perspective as to what the field is about and how it can shed more light both on what life generally is in the universe and how can we recreate it on Earth. I would also recommend you to read the articles Life as we don't know it, Defining life,How rare is complex life in the Milky way? and The potential of detecting "Life as we don't know it" by fractal complexity analysis. Those papers should be nice "introduction" to the world of astrobiology and if you follow through browsing the journals I just showed you can get a pretty good idea where we are today in the quest to answer your question.

You might also want to consider learning more about the origins of life. It also is a field directly related to the question you posted. Nice review on the topic is here and you can also check out this article and this article here. Then, you may want to check out the journal dedicated specially to investigation on the origins of life-Origins of life and evolution of biospheres and watch this online lecture on the subject.

Another issue pertaining to the question is the definition of life and how difficult it is to be formulated. If you become familiar with the issue you will understand why it's so difficult to tackle the problem of how to synthesize life, where it is throughout the universe and how it originated here on Earth. I recommend you these 2 seminal works on the definition of life here and here. But I would also recommend you to read this,this and this article to get a deeper look at the problems we face even defining life today. If we can't even agree on what life is how do you expect to be able to understand how it originated or how to create it?

Another direction you could also look at is our attempt to model and describe what we can call life at all levels it can appear-the field of artificial life. You can learn more about it in the journal Artificial life which deals with our attempts at modelling complexity in abstract systems close to the dynamics of the living ones. Yet another attempt at understanding the dynamics of the living is the interesting field of biosemiotics about which you can read short overview or get more accustomed into in its journal here. I think this list is more than enough to cover all the major directions your interests can take you on.

But to get "the bigger picture" of the question here you need to do much more than that and to follow virtually every publication pertaining to the definition, origin, synthesis and location of life throughout space and time and this can be daunting task, believe me, I do it every day since years! But despite the enormous quantity of papers and articles I go through there are always newer and newer things to discover and no matter how many hours I dedicate to this task and how much it fulfils me there are still gaps in my knowledge and am learning new things about different perspectives on the BIG question-What is life? all the time!

So, to give you an advice derived from personal experience-the question you tackle is really very interesting and fundamental one but even if it consumes all your time and efforts you would still not be able to follow everything which can be pertained to it, so my advice is to take only 1 or 2 approaches used in either of the fields I just described you and concentrate only on their keywords to follow the advances of the people behind them. Take something from synthetic biology, something from the origin of life field or something from astrobiology and visit the journals I just showed you from time to time to search with these keywords and see what is new. Then you would have good enough idea how close we are to synthesizing life in the laboratory and knowing more about its nature and origins. This is my long answer and the best advice I can give you.

Hope it helps :)


In many mosquito species (and other diptera) males make swarm to attract the females. The vast majority of individuals in swarms are therefore males (but there are always a number of females in them as well).

These swarms are a type of lek mating which is also very common in midges (thanks to @arboviral for this info). Are you sure those you see are mosquitoes and not midges?

In order to produce these swarms, they typically hover a recognizable element in nature to swarm around, such as a small tree, a bush, a big stone, etc... On a soccer field, players are a distinct element to swarm over!

Of course, females are attracted to $CO_2$, warm bodies and odour of sweat but this is IMHO likely not an important factor causing the swarms you see. See @Kiny's answer on the subject.

References:

Takken et al. 2006
Yuval et al. 1994

  Also, why is this in the evening?

Mosquitoes typically start mating at the beginning of the evening and then forage during the night. However, this varies quite a bit from species to species. Aedes egypti for example, forage day and night while species of the genus Culex forage only for a few hours after the sun has set.

Such variation in the timing of mating behaviour can lead to (pre-zygotic) reproductive isolation between lineages. Potential reasons for being active at specific times and not others include temperature management, easier to parasite for females during the night (only females bite), timing with flowers (as both males and females feed on nectar). I would not be able to argue for why a specific species shifted its circadian rhythm in a specific way though.


What is the difference between SOLiD, 454, and Illumina next-gen sequencing?

Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one.

Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further takes part in downstream light-producing reactions. The amount of light is proportional to the incorporated number of nucleotides. The DNA is fragmented and adapters are ligated at both ends. The fragments are mixed with agarose beads, which carry adapters complementary to the library adapters, and thus each bead is associated with a unique DNA fragment. The beads and DNA fragments are isolated in individual micelles, where emulsion PCR takes place and million copies of the single fragments are amplified  onto the surface of each bead. Each bead is placed in a well of picotiter plate (PTP), as the wells have dimensions such that only one bead can fit per well. Enzymes are added to the beads and pure nucleotide solutions are added with an immediate imaging step. On one side of the array a CCD (charge-optic device) camera records the light emitted from each bead. The first four nucleotides (TCGA) are the same as the start of the adapter, which allows for the emitted light to be calibrated according to the type of nucleotide added. The major disadvantage of this method is the misinterpretation of homopolymers (consecutive nucleotides, e.g. AAA or CCC). Such areas are prone to insertions or deletions, as the length of the stretch can be inferred only by the intensity of the light emitted. On the other hand, substitution errors are very unlikely. The 454 FLX instrument generates ~400 000 reads per instrument-run, as the reads are 200-400bp. The greatest advantage of this platform is the read length, which is the longest of all second generation technologies. Although sequencing on 454 platform is more expensive than sequencing on Illumina platform (40USD per Mega base versus 2USD per Mega base), it could still be the best choice for de novo assembly or metagenomics applications. (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).

Illumina is the most frequently used one. The DNA to be sequenced is fragmented into about 200 base strands. Adapters are ligated onto the ends of the fragments and one of these adapters is hybridized on a flow cell. Illumina essentially utilizes a unique "bridged" amplification reaction that occurs on the surface of the flow cell. Localized PCR reaction is performed, and each of the hybridized pieces of DNA will get locally amplified to generate clusters which will have the exact same molecule. Subsequently, the DNA sequence is determined by adding a primer on one of the ends of the molecule. A mixture of modified nucleotides is added. Each one of them carries a base-specific fluorescent label attached to it. Also, each one has the 3' OH group blocked which ensures the incorporation of one nucleotide at a time.  The flow cell is placed under a microscope and when light is shined on its fluorescence, the emission light shows which base was incorporated on each one of those clusters. The Illumina read length is approximately 35 bases, but over billion reads are generated at a time. The major error type is substitution, rather than deletion or insertion (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).

The SOLiD platform utilizes the use of DNA fragmented library, which is flanked by ligated adapters. The fragments are attached to small paramagnetic beads and emulsion PCR is performed to amplify the fragments. In contrast to the other sequencing platforms, sequencing by synthesis is performed by utilizing DNA ligase, rather than polymerase. Each cycle of sequencing involves the ligation of a degenerate population of fluorescently labeled universal octamer primers. A specific position of the octamer (e.g., base 5) carries a fluorescent label. After ligation, images are acquired in four channels, followed by cleavage of the octamer between positions 5 and 6, removing the fluorescent label. After several rounds of octamer ligation, which enable sequencing of every 5th base (e.g., bases 5, 10, 15, and 20), the extended primer is denatured. Different primers can be used to examine the previous or next positions (e.g., base 3 or 6).  The platform can use primers which carry two adjacent correlated with label bases. This approach involves the examination of the bases twice in a cycle, which decreases the error rates. SOLiD read lengths are 25-35 bp, and each sequencing run yields 2–4 Gb of DNA sequence data (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).

References:

Mardis, E., Next generation DNA sequencing methods. Ann. Rev. Genomics Hum. Genet, 9: 387-402 (2008). DOI 10.1146/annurev.genom.9.081307.164359
Shendure, J. and Ji, H., Next-generation DNA sequencing. Nat. Biotechnol., 26: 1135-1145 (2008). DOI 10.1038/nbt1486


Can the knowledge about torsion angles alone be sufficient for specifying secondary structures of protein?

Its not true that the Ramachandran plot will determine the secondary structure of an amino acid.

Ramachandran plots show the sterically allowed phi/psi angles of an amino acid.  As such nearly all non-glycine amino acids are in alpha/beta spaces.  Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense orders. (alpha/beta/beta/alpha/alpha and etc)

The dihedral angles repeated in a pattern over a several consecutive amino acids create secondary structure (N>4 or 7 for helices - strands need other strands forming sheets).


Do diurnal birds of prey recognize each other by their appearance?

Having seen some nature documentaries about Penguins identifying their offspring using sound alone (even in flocks of hundreds of thousands of other birds), my immediate impression was that sound is likely to be more important with regard to recognizing individuals of the same species.

This is corroborated by Melissa Mayntz, a bird enthusiast, who has written a great account on birds use of their 5 senses (Understanding Bird Senses).

To summarize, she explains that whilst sight is a birds most important sense in terms of hunting and avoiding being hunted, their hearing is is their second most important sense and they use this to identify individuals;

  Birds hear a smaller frequency range than humans, but they have much more acute sound recognition skills. Birds are especially sensitive to pitch, tone and rhythm changes and use those variations to recognize other individual birds, even in a noisy flock.


Which frequency of UV light damages DNA?

Not only pure DNA, UV radiations are one of the main causes of skin cancer because they damage cellular DNA in skin cells. Talking about frequency range, two different types of UV radiations damage DNA in two different ways:

UV-A radiation damages DNA in indirect ways. UV-A radiation easily generates free radicals, such as hydroxyl and oxygen radicals, which in trun cause the main damage1. The damage caused by such radicals is mostly single-stranded breaks in DNA. In fact, it has only recently been established that UV-A radiations do damage DNA, while these were originally considered as not (or less) harmful2. UV-A also has immunosuppressize effects on the entire body and is also mutagenic for keratinocytes in skin.

Wavelength range: 315 - 400 nm

Effect: source
UV-B radiation is in fact what causes most damages and deadliest damages to DNA. UV-B radiation directly attacks DNA, it excites atoms of adjacent thymine molecules, which in turn form covalent bonds with each other and lead to formation of thymine dimers. These dimers, because of being bonded side-by-side instead of being bonded to opposite strand base, form a bulge which interrupts structure and function of DNA. Such dimers are removed by a process known as nucleotide excision repair, which involved about 30 diffeeent proteins3, meaning UV-B is more harmful for the body than UV-A. UV-B also causes double-stranded breaks in DNA, which are a major problem for DNA replication and a threat for cell's survival.

Wavelength range: 280 - 315 nm

Effect: source
Other effects of UV radiation on the body include damage to collagen fibers and vitamin-A in the body and accelerated ageing effects 4. Apart from this, UV radiations, because of harmful effects on DNA, are used for sterilization as they destroy microbes' DNA and thus prevent them from replication.

Wavelength range: 10 - 400 nm (complete UV spectrum)

References:

Svobodová AR, Galandáková A, Sianská J, et al. (January 2012). "DNA damage after acute exposure of mice skin to physiological doses of UVB and UVA light"
Halliday GM, Byrne SN, Damian DL (December 2011). "Ultraviolet A radiation: its role in immunosuppression and carcinogenesis"
Bernstein C, Bernstein H, Payne CM, Garewal H (June 2002). "DNA repair/pro-apoptotic dual-role proteins in five major DNA repair pathways: fail-safe protection against carcinogenesis"
Torma, H; Berne, B; Vahlquist, A (1988). "UV irradiation and topical vitamin A modulate retinol esterification in hairless mouse epidermis"


First of all MHC stands for major histocompatibility complex. There are two types of MHC.

MHC type one is present on all of our cells with a nucleus. The purpose of these protein complexes is called antigen presentation. T-cells cannot recognize free antigens on their own, it has to be presented to them in the proper way. This is what these proteins do. In every cell there are lots and lots of proteins, that get digested to small polypeptides (short aminoacid sequences) by proteases during the natural recycling process. The cell takes a small portion of these polypeptides and presents them on its surface through MHC I complexes, that the immune system can read. This is like the cell saying to the immune syytem that "hey I got these proteins in me". Now if the cell is infected (by a virus most likely) then the "attacker's" proteins get digested and presented as well and its like saying " hey I'm infected and the attacker has these proteins".

MHC II serves similar function but it is only present on professional antigen presenting cells (APCs). These complexes present peptides derived from proteins consumed and digested through phagocytosis or receptor mediated endocytosis. It's like saying "hey we got a larger attacker and it has these proteins"

So, long story short T-cells cannot recognise antigens on their own it needs to be presented to them on MHC complexes and then and only then can they be activated.

Edit: A list of useful articles in the topic of antigen processing / presentation for further details:

January 14, 1998 14:59 Annual Reviews AR052-12
Annu. Rev. Immunol. 1998. 16:323–58
MECHANISMS OF MHC CLASS I–RESTRICTED ANTIGEN
PROCESSING Eric Pamer and Peter Cresswell

Cell, Vol. 76, 287-299, January 28, 1994.
MHC-Dependent Antigen Processing and Peptide Presentation: Providing
Ligands for T Lymphocyte Activation

Terry Y Nakagawa, Alexaiider Y Kudensky
The role of lysosomal proteinases in MHC class Il-mediated antigen processing
and presentation
This one may require subscription.

and the wiki page :)


Oligonucleotide purification with desalting

Oligos from well-known companies are pretty good to my knowledge. Problems begin after 100-300bp oligos/dsDNA fragments.

What I suggest is PCRing your vector like that:

          Primer F: ---------------------__________
vector: ======|v site for 36 bp insert v|==========...
        Upstream                        Downstream
        ______----------------- : primer R

Legend:
__ portion of primer annealing to vector
-- portion that is your insert of interest

Then you can actually just transform that PCR into e. coli, which will seal two nicks together and propagate your vector. Treating your PCR reaction with Dpn enzyme will ensure that all template DNA is removed.


When should you use a stringent plasmid?

The three general advantages are:

Lower expression. If your plasmid is expressing something toxic to cells at high levels, reducing the amount of DNA can reduce expression.
Lower plasmid burden. If you are concerned about the stress imposed by maintaining many copies of the plasmid, low-copy plasmids are helpful.
Population homogeneity. Relaxed plasmids tend to replicate such that there will be a wide distribution of # plasmid copies/cell. Meanwhile, stringent plasmid replication is tightly coupled to the cell cycle itself, so the number varies less. In certain cases it may be desirable to control the number of plasmids per cell.


Is consuming proteins different vs. consuming amino-acids and how?

To put it shortly:

Proteins have properties that individual amino acids that make up the protein does not have.
Similarly the individual amino acids have properties that the protein does not have.

This is analogous to elements vs compounds.

The site referenced below quotes 3 experiments done to examine this phenomena.

All experiments compared effectiveness of whey protein with that of essential amino acid (EAA) supplements. Experiments 1 and 2 involved old people while experiment 3 involved young people.

Conclusion of experiments is as follows:

Both EAA and whey protein (15 g of EAA and 15 g whey was taken by the respective groups) induced muscle growth, however EAA had better anabolic effect as compared to whey.
In this 3 groups were compared. 15 g of whey vs 6.72 g of EAA vs. 7.57 g of non-essential amino acids. Whey had higher anabolic effect as compared to EAA while the third group showed no improvement. This additional anabolic effect is attributed to unknown mechanisms. The anabolic effect was measured using a different method add compared to the first experiment. So results may not be comparable.
In this 3 groups of young men were compared. The first group was given carbohydrate (30 g) and EAA (15 g) drink, the second group liquid meal containing same quantity of EAA and total 850 calories while the third group was given both. The conclusion:

The third group, as expected had the highest anabolic rate
The first group (protein and carbohydrate drink) had better anabolic rate when compared with the liquid meal group though they both took the same amount of EAA. The difference was in carbohydrate content. The liquid meal had higher carbohydrates content when compared with the first group.

Whey has insulinogenic effect invitro. Whey also has the same effect whether taken before or after exercise while the protein drink has better effect when taken before exercise.

Among amino acids leucine, when taken alone has anabolic effect comparable to a mixture of EAA.

In conclusion:

  However, whey contains various bioactive peptides that act to enhance recovery and potentially in other ways that positively effect the adaptive process to exercise (12). These bioactive peptides are not found in EAA, BCAA, or Leucine, and appear to be a unique quality to dairy proteins. So what we can't say is that these aminos are the deciding factor in whey's effects...or that we can use one in place of the other (interchangeably) in all cases.

http://www.vpxsports.com/article-detail/supplements/whey-protein-versus-amino-acids-whats-the-difference

Please read the article which has more details and graphs and references for further study.


Why can't the human eye focus blue light?

The same thing happens in photography when you see an image with colorful shadows of objects on it - this is called chromatic aberration. Check this wiki page if you're not familiar with. Now this happens because the lens in the objective has different refractive properties for different wavelengths or if go the other way around different wavelengths refract differently within the same material. This is why the famous triangular rainbow prism is capable of separating the sunlight to rainbow. So back to the question: in our eye there is the eye lens that is responsible for focusing. Let's assume that it is homogenous enough. So when light enters into our lens it refracts to separate colours and our lens is not complex enough to fully compensate for this. The second picture is a good approximation of the human eye lens in shape.

Edit: so when you focus one color perfectly the others will be blurry a bit since those will be out of focus due to different refraction.

taken from: http://commons.wikimedia.org/wiki/File:Prism-rainbow-black.svg

taken from:http://en.wikipedia.org/wiki/Chromatic_aberration#/media/File:Chromatic_aberration_lens_diagram.svg


ELISA is Enzyme-Linked ImmunoSorbent Assay (capitalisation to point out source of acronym).

You can read about the various ways to do an ELISA here.

In your case this was probably an indirect ELISA. All ELISA techniques make use of the fact that proteins stick to plastic. In your case the protein components of the saliva, including the virus (the viral coat is proteinaceous) will stick to the wells. After rinsing out the sample the wells are treated with another protein (usually bovine serum albumin (BSA)) to completely block all available protein binding sites. At this stage these wells will no longer bind protein non-specifically, but will bind anti-EBV Ig because of the presence of the EBV particles bound to the plastic. This bound anti-EBV can then be detected with a secondary antibody. The protein complexes will build as follows:

plastic/EBV/rabbit anti-EBV/goat anti-rabbit IgG-HRP conjugate

It would also be possible to do this experiment as a sandwich ELISA. In this format the wells would have been pretreated with anti-EBV serum (or purified anti-EBV IgG) then blocked with BSA. At this stage these wells will no longer bind protein non-specifically, but will bind EBV because of the presence of the EBV-specific antibody. Once samples have been incubated in these wells (so that any EBV can bind to the antibody coating the wells) another antibody (raised in a different animal) is added, and this will bind to the EBV that has been captured by the original antibody that coats the wells. This latter antibody is then detected with a conjugate. The protein complexes will build as follows:

plastic/mouse anti-EBV/EBV/rabbit anti-EBV/goat anti-rabbit IgG-HRP conjugate

Your description of how to get the antibodies is basically correct, except that the primary antibody will probably have been raised in rabbits or mice, and certainly not in humans.

Added later: I didn't read the first question carefully enough. An ELISA is an assay because it measures something. It is based on a binding reaction mediated by an antibody-antigen interaction (immunosorbent). It is enzyme-linked because the secondary antibody is present as an antibody-enzyme conjugate. It is the amount of this conjugate that remains bound at the final step which is what is measured - the assay is set up so that the amount of this enzyme is a measure of the amount of the original molecule that is being assayed.


How do people measure how many calories or proteins/fats/сarbohydrates are in some food?

Messured by the amount of energy it will take to raise 1 degree celsius in 1 kg of water. You really can never go by what the packaging says either. All depending on how food is prepared, even your digestion differs the count person to person.


How can hyperthyroidism induce osteoporosis?

T3 stimulates osteoclast formation. Osteoclasts are cells that break down bone tissue. They are essential for bone growth in children, because they allow bone remodelling. However, elevated stimulation of osteoclast formation leads to osteoporosis in adults, where bone remodelling is not necessary.

In hyperthyrodism, T3 levels positively correlate with levels of calcium ions in blood, which confirms the break down of bone tissue. Calcium ions are then excreted in urine, because they cannot be efficiently reabsorbed. This constant loss of bone tissue cannot be reduced with high calcium diet, only by drug treatments that affect T3 levels.

Definitely can recommend further reading, especially regarding different types of thyrodism:

DOI: 10.1002/jcp.20041


Is it possible to make a contagious cure to a virus?

Fun question!

I think that to make a transmissable ("contagious") antiviral vector, you would need to design a virus that can infect people and that codes for something like an antiviral drug compound, which targets specific viral proteins.

As easy as that was to write down in one sentence, I think that execution would be extremely challenging.

Making the anti-virus out of another virus seems necessary to me, as there is little alternative. You would need something capable of efficiently spreading from host to host, that can generate many copies of its therapeutic payload and that is relatively simple to engineer. A virus is the only thing that I can think of that fits the bill.

You could theoretically engineer an antiviral virus that is mostly non-pathogenic to other people, although this wouldn't be perfect. Even if it didn't code for specifically pathogenic proteins, it is a foreign molecule that is likely to raise an immune response, risks integrating into an important location in the host genome and would divert cellular energy to production of its proteins and away from other cellular processes.

Say that you get this to work, that it's minimally harmful to its host and can effectively target the more pathogenic virus, against which you've designed it. What happens when the job is done? Is it still in the host body, pumping out more copies of itself and/or its antiviral proteins? If so, then it could end up causing more damage to the host in the long run, as it uses host resources to fill cells with no-longer-helpful foreign molecules.

Given more thought or time (than I have), you could probably image more ways to tweak the design of this theoretical anti-virus, but as a brief answer, I think that the above considerations can give you a quick idea of what it would take to bring this system from the realm of science fiction to that of hard science. :-)


Why do so many people have group O blood?

There are many different variants of O (all loss-of-function) indicating that this mutation has arisen many times in the human population. The prevalence of O is indeed taken as evidence of balancing selection. Various pathogens use the A or B antigens as receptors. The cited paper presents evidence about the phylogeny of the ABO gene in human populations and reports that there is clear evidence of balancing selection.

We propose several hypotheses for the cause of [balancing selection], which most likely involved interactions with multiple pathogens at different geographic regions and timescales.
Calafell et al (2008) Evolutionary dynamics of the human ABO gene. Human Genetics 124: 123-135


Is local equilibrium a reasonable assumption for evolutionary processes?

Nothing is at a genome-wide local equilibrium. Graham Bell wrote fairly extensively on this (IIRC).

Some loci

will be at what are likely global optimums (e.g. Cytochrome oxidase)
will be at local but not global optimums (e.g. low-fitness malaria resistance vs. high fitness malaria resistance: for the extremely cool story check out this page)
will not be at any optima because the environment shifts too quickly (e.g. loci clearly under frequency-dependent selection, such as MHC).

So, in general, it depends what you are trying to model. If you want to model a specific kind of evolutionary change, then model that kind of evolutionary change. If you want to model a different kind of change, then model that kind of evolutionary change. Natural populations will likely follow any model some of the time, but will probably never follow any model all of the time.


One possible reason to not filter for linkage disequilibrium is to produce peaks/hits with multiple SNPs, thereby clearly indicating a region of a causal genotype. For example, in the manhattan plot below, each point represents a SNP, the higher it is in the plot the more it relates to the phenotype.  We see that in each of the peaks multiple points are significant due to linkage disequilibrium.  If instead we had pre-filtered all of these points out then a peak has a greater choice of representing some type of error in data collection, since there is some probability that there is some error in each SNP, but not much chance of the error occurring in all the SNPs of one peak.

I am unclear why not pruning for linkage equilibrium would prevent an additive, or any model from working.  After all a GWAS is just a series of regressions between the genotypes of one SNP and one phenotype.  In this single SNP frame of reference the LD does not affect the calculation of the betas.  Zooming out, all of the significant SNPs should group together because of the LD, thereby indicating only a few regions and not causing an increase in the false error rate.


I thought this was an interesting subject and I had some time to do a little search around today.  I can't find anything better than the review you point out. All I can do is add a few interesting notes since 2001.  Nothing really turns over Rattenborg et al.

Sleep is itself a poorly understood process and most of the theories of the necessity of sleep can teeter precariously with discoveries like this report that baby dolphins and killer whales and their mothers simply don't sleep at all for the first few months of life.

The Rattenborg review is only guessing, but I think its clear that there is a cost to unihemispheric sleep, even if we don't know what it is.  Cetaceans and birds and perhaps reptiles having unihemispheric sleep are all cases where there are perpetual and strong selection forces that maintain the ability in these animals.  Without constant predation experienced by tasty ducks or the vagaries of being an air-breathing underwater mammal, animals quickly lose their ability to sleep with one half their brain, one assumes because the ability to maintain it is particular and easily lost with variation.  Modelling work of the hemispheres in sleep indicates that the connections between the hemispheres are modulated between the two modes of sleep - there may be advantages to such brain structures for instance.

This blog post is a good read though and a bit more recent, though most of the references are from before 2001. Dolphins do use both hemispheres to sleep, but just not very often (about 15% of the time), indicating there is some advantage even for these animals.  Seals may alternate between bi and uni-hemispheric sleep when they are on land and at sea.

If you were wondering if there was something you were missing - I'd say no.  At the time of this writing THIS web page is the sixth hit on a google search for the term 'unihemispheric sleep'....


Why doesn't the ambient lighting condition change the perception of colors we see on a monitor?

The phenomenon you are referring to is color constancy: The apparent hue of a reflective surface remains constant even when changes in the spectral power distribution of the illuminant alter the wavelengths reflected from it (Mather, 2008). In other words, despite substantial changes in illumination, we usually experience the color of an object as being constant.

The spectrum of wavelengths that enter our eyes is jointly determined by 1) the spectrum of the illuminating source (a variable), and 2) The spectral reflectance properties of the object (a constant).

To achieve color constancy, an object's spectral reflectance is the constant color parameter that needs to be evaluated.

Any information that better characterizes an object's spectral reflectance is a cue to colour constancy. This includes (Mather, 2008):

Local color contrast. Cone excitation levels of one surface relative to another remains constant when both surfaces experience the same change in illumination. Relative cone excitation levels are invariant ratios useful for achieving colour constancy.
Color adaptation. Adaptation reduces the contribution from the source illumination by lowering activity in the most highly active cone classes.
Global contrast. Global spectral changes generally represent changes in the illuminant; localised differences usually correspond to reflectance differences.
Luminance highlights. Glossy surfaces offer near-perfect reflections of the illuminant, which can then be factored from the rest of the scene.
Mutual reflections. The pattern of reflections that arise from different surfaces, under the same illumination, carries valuable information about the reflectance properties of each surface.
Range of reflected spectrum. This gives an indication of the breadth of the illuminating spectrum.

A graphical example of the effect of lighting conditions is found below (Fig. 1.)

Bowl of fruit photographed under artificial daylight (left), hazy day light (middle) and clear blue skies (right. Source: Mather (2008)

The most powerful cue to constancy is thought to be local color contrast (Mather, 2008). In other words, the relative contribution of the different cone classes stays constant, despite differences in the spectrum of the illuminant.

In your example, the object (paper) is not represented by a reflectance, but as an image; a representation taken out of its context, and it will appear yellow. Even if the ambient lighting is the same, as in your example, the monitor displays a 'real' yellow color, which has a different spectrum, because it is not a reflectance, but it is generated by a light source: your monitor; as mentioned in the excellent comment of @AMR. The real sheet of paper will have a different reflectance spectrum. Hence, both photo and real sheet will be interpreted as a function of ambient lighting by your visual system and they will appear different.

Even when your image was printed as a photo, the color is obviously different from the white sheet of paper. So the ambient light has a different effect on the reflectance spectrum of the photo and the real sheet.

Also the global contrast is different: the photo with a different spectral content than the real sheet is re-placed into the context of ambient lighting. Hence, the photo it is out of context and will be re-interpreted.

Reference
- Mather, Foundations of perception and sensation 2nd ed. Psychology Press 2008


what if there is a door for which our immune system has no key?

The Native Americans and smallpox

First I want to note that some of the posted answers are not quite accurate. For example, smallpox ravaged the Native American population because they did not have high-affinity MHC molecules for it, which is an evolved trait. MHC molecules must be capable of binding to a large class of peptides, at least weakly, to allow their presentation. There are only a finite number of MHC alleles in a given individual, and they tend to represent the most commonly found classes of foreign organisms.

The Native Americans were equally capable of creating anti-smallpox antibodies as any European, but that process was significantly slowed down due to not having MHC alleles which promote the presentation of smallpox, allowing the virus to accumulate to lethal levels before a sufficiently mature immune response could be mounted. You can bet that the survivors were the ones with MHC alleles that promoted rapid recognition of the virus!

Somatic hypermutation and affinity maturation

The way antibodies work is, B cells undergo both genetic recombination and an intentionally increased mutation rate called somatic hypermutation. This results in a virtually uniform distribution of new antibodies. These new antibodies are actually pretty bad at binding antigens, and at best, only roughly approximate them. This is one reason the first exposure takes so long to eradicate. When an antibody that weakly matches is found and the number of B cells rise, some of them begin to induce additional mutations to their antibody, a process called affinity maturation. The mutations that result in breaking the antibody end up discarded (those B cells die), whereas those that have an even stronger affinity result in the clone of B cells being positively selected for. This goes on and on until the resulting clone of B cells produce extremely high-affinity antigens.

The result of this is that virtually any possible "door" will have a "key", even if it is poorly fitting. Over time (and subsequent exposures), the key is fine-tuned. The only way a persistent antigen could evade an immune response, short of interfering with the immune system is if the antigen is extremely similar or identical to a self-antigen.

Some pathogens can avoid an immune response in indirect ways, such as frequently changing exposed antigens either by switching genes or through rapid mutation, covering the cell surface with self-antigens or innate, non-protein material, tucking conserved regions that act as epitopes deeply inside a protein, releasing molecules that inhibit the immune response, etc.

Foreign antigens resulting in production of anti-self antigens

An interesting thing to note is that, even if the antigen is similar to self, it will still often be detected. This can be highly problematic because selection against anti-self antibodies occurs when the B cell is first developing, during somatic hypermutation, but not during affinity maturation. A weakly binding antigen that is similar to a self-antigen may then stimulate the production of anti-self antibodies since the antigen is different enough from self that B cells specific to it are not negatively selected, but similar enough to self that the changes in affinity maturation are sufficient to convert it into an anti-self antigen (in other words, an antibody x steps away from targeting self-antigens results in negative selection, but affinity maturation results in y changes to the antibody, where y > x). This is one reason why some viruses can trigger auto-immune diseases.

Answering your questions directly

  What if there is no antibody in any cell against an antigen?

If for some reason no antibody were even had the slightest affinity for an antigen, then there would be no problem, and a pathogen would trigger an immune response because of another antigen. If for some insane reason every single antigen on a pathogen (there are many) was not even slightly matched, then no humoral immune will be invoked. There still may be a cellular immune response (e.g. for viruses), and the innate immune system would still be active.

  Does the immune system has antibodies against all antigens in the world?

The immune system has antibodies that bind a wide range of antigens, albeit weakly, and with high overlap. As a result, you could say that all possible antigens that are not too similar to self are countered by antibodies with at least some level of affinity. There is only a finite number of possible antigenic peptides, and of those, all that's needed is a weak interaction to trigger a full-blown adaptive immune response.

It's like going to an ophthalmologist. They don't have lenses for all possible refractive indexes, but they do have enough samples that, by trying them out, you can see which ones improve your vision. Going through this process allows gradual improvement, and eventually they are able to proscribe a perfect match.

  What happens if an antigen came into our body which has no antibody matching for it?

A single antigen, as opposed to a pathogen with many antigens? Ignoring the cellular immune system, nothing would happen. It would be treated virtually identical to self-antigens (i.e. it would be ignored). Depending on how the pathogen behaves, it could be wiped out by the rest of our immune system, contained in a local cyst, or even result in a lethal infection.


In general, DNA that encodes toxins can be incorporated in a viral genome and thus it can be expressed in the infected host inducing toxicity.
Here an example: http://www.sciencedirect.com/science/article/pii/S1438422104000542

Also, viruses can trigger allergic reactions (http://www.ncbi.nlm.nih.gov/pubmed/21980825) or promote them (http://erj.ersjournals.com/content/19/2/341).

Finally, there are some reports about viruses causing "with symptoms that mimic allergies" (https://www.youtube.com/watch?v=iDF07R1XHSk)


Is there a name for this phenomenon described in "Phylogenies and the Comparative Method"?

I've seen this termed "phylogenetic pseudoreplication", but I can't remember offhand where. I'll see if I can find it. Without a tree, the boxes and Xs essentially represent 2 data points. As Remi.b suggests, this is really just high phylogenetic signal.


In what forms do plants and animals excrete sulfur?

Sulfur is $3^{rd}$ most abundant mineral element in the body. Carnivores obtain it from Cysteine and Methionine in the animal protein which converted in to Glutathione.
Excess of sulfur is stored into Glutathione or oxidised to sulfate by sulfite oxidase which is eventually eliminated by urine.

[1]: Nimni ME, Han B, Cordoba F (2007). "Are we getting enough sulfur in our diet?". Nutr Metab (Lond) 4 (1): 24. doi:10.1186/1743-7075-4-24

[2]: Wikipedia on Sulfur metabolism


I believe it's a Patella pellucida or blue-rayed limpet. They live off seaweed in deeper waters, so it's not a surprise that you wouldn't see many live ones.

Picture from an interesting article: Blue-rayed limpet holds secret for windscreen transparent displays with no internal light source


How do CAM plants keep stomata closed by day and open at night?

As others already say in comments, the complete answer to this question is still unknown. However, the basic mechanism has been understood and has been summarized in the following diagram (from Wikipedia):

As you see, the mechanism is regulated by temperature instead of presence of light, keeping in mind that high temperatures are generally observed during the day and low tempertures at night. Temperature regulates, at the expression level, the activity of an enzyme PEP-C kinase. This enzyme phosphorylates PEP carboxylase (or PEPCase in short), which increases its activity. So lets see what happens when temperture is high:

During day:

high temperature inhibits expression of the enzyme PEP-C kinase, which decreases the activity of PEPCase.
activity of PEPCase is further reduced by an enzyme PEP-C phosphatase (this enzyme is active all the time, but its effect is reversed by PEP-C kinase).
due to respiration and photosynthesis, the amount of cytoplasmic malate is reduced (malate is converted to pyruvate to yield NADPH for photosynthesis, and pyruvate is used up in TCA cycle, whose by-product, $\ce{CO_2}$, is used up in calvin cycle).
due to this, malate is released from vacuole into the cytoplasm. This malate is not only used up in photosynthesis and respiration, but also further inhibits activity of PEPCase and expression of PEP-C kinase.
because PEPCase is inhibited, it results in depletion of malate in cytoplasm as well as vacuole.

During night:

at night, stomata open leading to increase in amount of $\ce{CO_2}$. Also, low temperature is unable to inhibit expression of PEP-C kinase.
when activity of PEPCase increases, PEP is converted to malate, which is then transported into vacuole. Also, increased concentration of $\ce{CO_2}$ increases photosynthesis.

Where is light required? As already said, the exact mechanism is still unknown. The mostly accepted mechanism is potassium ion pump hypothesis, but problems arise when we think about the initiation of this process in CAM plants. There are many hypotheses regarding this, and I will follow the one presented by Lee, 2010. Lets begin with the diagram (don't pay attention to the spellings):

initial stomatal opening is mediated by phytochrome in guard cells. The $\ce{H^+}$ pump in guard cells is also activated by darkness.
the maleic acid synthesized in other cells is also transported to the vacuoles in guard cells. There, the intracellular $\ce{H^+}$ (from maleic acid) is exchanged for intercellular $\ce{K^+}$.
increased concentration of $\ce{CO_2}$ also regenerates glyceraldehyde-3-phosphate and ribulose-1,5-bisphosphate, which lead to formation of sucrose via calvin cycle.
this sucrose is again transported to vacuole of guard cells, adding up to osmotic pressure. However, the major effect comes from maleic acid.
increased $\ce{CO_2}$ concentration and increased activity of PEPCase (as already explained) form malate and lead to further increase in the osmotic concentration. All this causes stomata to open.
during the day, malate is decarboxylated to pyruvate (as already explained), leading to decrease in osmotic pressure and thus, closing of stomata.

I hope this makes the concept more clear, but bear in mind that the above mechanism could later prove to be wrong as further studies on CAM plants help to find out the actual mechanism.


More context would be helpful, but it's possible the data from the Quora post was incorrectly transcribed from a table on this biotech site, which states that the carbohydrate content of proteoglycans is 50-60%, compared to 10-15% for glycoproteins.

However, the first comment on that page suggests that the table was initially incorrect:

Hi Anne,
This is a great post, but the numbers for the carbohydrate content are reversed. It’s 50-60% for the proteoglycans and 10-15% for most common glycoproteins (and things like uromodulin and most mucins would be 30+% sugars).
Best,
Jared Gerlach

So that may be the source of confusion, here.  It seems the commenter is an expert in the field of glycan research, so the table is likely correct.


Why shouldn't I clean microscope slides with a paper towel?

The main reason to avoid paper towels, tissues, and etc. is that they shed lint (paper fibers) which will be left behind on your slide and eventually interfere with your prep. They look small to the naked eye, but they are not small compared to the prep on your slide.

The other issue with paper towels and etc. is that there might be some particulate matter in the paper that's hard enough to scratch glass or optical coatings. This is more of an issue for optics - especially coated ones - than for cheap microscope slides, but it's something to consider.

If you're not mounting permanent preps then ultrasonic cleaning is probably a bit of overkill - although I have a surplus sonicator and it does a great job on a lot of tasks. It's generally sufficient to rinse the slide with distilled or deionized water and then follow up with (clean) alcohol. Optical purists will say spectroscopy grade methanol, but for home use any reasonably pure MeOH, EtOH or iPrOH will probably do. The main concern, again, is leaving behind particulates or residues. You can allow the slides to air dry if you're using pure alcohol, or use a piece of lens tissue (lint free paper tissue) to help them dry faster. I've also used Kimwipes in a pinch, but they're not truly lint free so not ideal. They're still much better than a tissue or paper towel.


Are humans the only species to suffer from impacted teeth?

According to Wikipedia
An impacted tooth is one that fails to erupt into the dental arch within the expected developmental window. Because impacted teeth do not erupt, they are retained throughout the individual's lifetime unless extracted or exposed surgically.
Now to your interesting question, there are case reports, that yes, animals, other than humans can also have impacted teeth.

Mandibular canine tooth impaction in young dog which was then made to erupt by surgery. Reference

Maxillary canine impaction in a persion cat. Reference

According to this article

Proper growth and development of the oral cavity depends on a series of events that must occur normally and in the proper sequence. Genetic abnormalities or trauma that affects either the developing tissues or the timing of their development can cause abnormalities. Defects that decrease comfort, health, or function require treatment; those that result in only an esthetic problem do not. Common developmental problems include persistent deciduous teeth, unerupted teeth, malformed teeth, malocclusion, and malformed jaws.


Reason for name "Motile sperm domain-containing protein 2" if it has nothing to do with sperm

As you can tell from the gene name, it contains a domain (a "major sperm protein domain)") that happens to have "sperm" in its name. That doesn't mean that the protein itself have anything to do with sperm. There are a lot of examples of gene names like this, where they're named after some random domain they contain until later their names are changed. MSOPD2 has only had a known function for a few months.

As an aside, if you actually work on this gene then one would hope that you would have taken the whopping 5 minutes required to figure this out in pubmed.


Oxygen masks can provide up to near 100% oxygen, whereas the atmosphere contains only ~20%. Typically, oxygen is provided in cases where patients' blood oxygen saturation is low or is likely to be low.

Giving a patient supplemental oxygen helps them to achieve oxygen saturation even if their breathing or circulation is impaired, and allows slightly more oxygen to be dissolved in the blood, which can be helpful in cases of blood loss or other traumatic insults.

I'm not sure of any cases where patients simply die immediately if their oxygen mask fails, outside of movies/TV; it's more of an issue of trying to provide the best outcome possible in a difficult situation.

There are also some negative side effects of oxygen supplementation. Overall, Wikipedia has a reasonable overview of these, as well as the indications for oxygen supplementation.


Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?

I am not sure that I completely understand, it would be a little easier if you described the problem you are trying to solve or what the motivation is.

However, I think that some of what you want to do can be accomplished by inferring gene/protein trees for each gene/protein of interest across different species (including paralogs, maybe?). This will allow you to see discordance or correlation of evolutionary rates of different genes/proteins across species.

THis kind of analysis is built into HyPhy, though I have never used it. There are also somewhat less involved methods for measuring distances between trees.

You might also be interested in protein co-evolution methods, depending on the question at hand.

Your mentioning systems biology methods suggests that you have something rather different in mind, as none of these things I suggest are really systems biology IMO, but I'm not sure what it would be. Possibly you are interested in integrating e.g. protein-protein interaction or metabolic network information as well, but that would probably involve something more homebrewed that might integrate some of these things.

Hope that helps.


From this source,

  We answered this question on the show...

  We posed this question to Dr David williams from the Veterinary School
  at the University of Cambridge... David -  First of all, what actually
  makes something smell?   Molecules have to leave the smelly objects
  and get to your nose through the air and that means that these
  molecules must be very small and volatile.  That's to say they must be
  easily evaporated.  The chemicals that make dogs smell are mostly what
  we call volatile organic acids and they are produced by bacteria from
  the fats that are breaking down from sweat; and that's maybe why we
  find these body odours unpleasant.  They signal a presence of bacteria
  and decay and death to us.

  Their [dogs] skins mostly have
  Staphylococcal bacteria, which don't produce much in the way of a
  smell at all, but they've also got some yeasts too which are really
  pongy.   But why does the smell seem worse when the dog is wet?  Here,
  I think we have to go into some physics.  The amount of evaporation of
  a substance is related to the concentration of the compound on a
  surface it’s evaporating from and the amount of compound that's in the
  air, just above the surface.

  So how might that change when it’s wet?

  Well, if the organic acids are dissolved in water on the fur of the
  wet dog, as the water evaporates, the concentration of those smelly
  acids increases, so they'll evaporate more, so there are more
  molecules in the air for us to smell.  Diana -   A bit of evaporation
  can effectively amplify the amount of volatile chemicals that emanate
  from a dog’s skin, and Dr. Williams thinks it’s the same effect that
  causes that damp earth smell when it rains.  It may also alter how
  dogs interact with each other when they're wet.  So, if you have a
  dog, watch to see if it sniffs differently at other dogs on a dry day
  versus a wet one...

There's a start, sounds legitimate to me...


Is there life on other planets and if so how frequent?

OK, so we know a couple of things about life in the universe. Note, however, that this is not really an answer and is also not very biological in nature.

So, we don't know how life began on the Earth. However, do know that:

The probability of life evolving on a planet in the universe is non-zero (since we exist) and,
So far, we have not found evidence for life elsewhere in the universe.

So this leaves us with two main possibilities:

Life is rare in the universe.
Life is common in the universe but for some reason we do not detect it.

This latter possibility is basically a restatement of the Fermi Paradox which says

  "The universe is very big and there should be lots of alien life out
  there. Where is everybody?"

In the case that life is common, we can speculate extensively on why we have not detected  it so far. For example:

We haven't been looking long enough (SETI has been running for only a few decades)
We haven't been looking hard enough (the budget of SETI etc. is not large)
We haven't been looking in the right way. We are currently looking mainly in the radio regime, maybe aliens broadcast in X (where X is part of the E/M spectrum or something else entirely, e.g. gravity waves, tachyons)
Life is common, but intelligent life is rare (this would be my guess)
Life is common and intelligent, and doesn't want to answer (why? ask a xenopsychologist)

OK, so these are just some examples of "solutions" to the Fermi Paradox. There are many more which are much more exotic. My personal favourite of these is that we live in a simulated universe and the coders have not included additional alien life in the simulation. It would explain some strange "coincidences" about fundamental physical constants, but what simulation, no matter how good, would ever come up with cauliflower cheese for example?

However, until we actually detect life on another planet we will still be in the dark. The next generation of telescopes will be able to do this for nearby exoplanets if life is present on them and has affected the biosphere in a detectable way.

Edit - You mention "frequency models", but all we can currently say is that the probability of life on other planets is not zero - due to our existence - as I mentioned at the start

Some references:

A joint analysis of the Drake equation and the Fermi paradox, 2012, arXiv, Prantzos, N.
The Fermi Paradox, Self-Replicating Probes, and the Interstellar Transportation Bandwidth, 2011, arXiv, Wiley, K.B.
Interstellar colonization - A new parameter for the Drake equation, 1980, Icarus, vol. 41, 193, Walters, C., Hoover, R. A., Kotra, R. K.


No, there was nothing special about Henrietta Lacks, apart from the fact that her cells have been used for so many years (without her knowledge or consent, by the way). She was not immortal, her tumor cells were. The HeLa cell line comes from her cervical cancer cells. The rest of the cells of her body were not immortal any more than yours or mine are.

Such immortality is a classic characteristic of cancer, in fact it is a hallmark of tumor cells. Normal cells die when they are told to, apoptosis (programmed cell death) is a normal part of a functioning, healthy organism. Tumors are collections of cells that replicate uncontrollably and do not do what they're told, including dying like good little soldiers.

That is why we often use tumoral cells for cultures, since they have been immortalized, it is relatively easy to keep them alive in the lab. This means, essentially, that they produce an enzyme called telomerase which lengthens telomeres. In normal cells, the telomeres get shorter with each round of mitosis and when they get shorter than a certain threshold, they are targeted for apoptosis. Cancer cells are protected from this by the telomerase and can therefore undergo many more rounds of reproduction.

So, the cells are not special because of the person they came from, they are special because they are cancer cells.


I'm trying to figure out what the name of this flower is

That is a rose. At least we have such flowers around my flat and we called them roses for 18 years. See: Rosa Gallica


How are single cells sorted in an scRNA-Seq protocol by FACS?

I will append the previous sentence in your protocol, and put what might help you in bold:

  To  obtain  B  cells,  NK  cells  and  monocytes,  a  splenocyte  suspension  was  stained  with PE-Cy7-conjugated  CD19,  eFluor  450-conjugated  NK-1.1,  PerCP  Cy5.5  Gr1,  FITC TCR-β,  APC  CD11b  and  PE  B220  (CD45R).  B220+ and  B220neg (germinal  center)  B cells  were  collected  by  gating  for  CD19+(TCR-βneg)  cells  and  then  by  B220  against  theCD19  marker.  NK  single  cells  were  collected  from  the  CD19neg/TCR-βneg events  by gating  for  NK-1.1  positive  events  in  NK-1.1  vs.  Gr1.

The cell types in question have unique properties that can be stained for using (immuno)histochemistry, i.e. chemicals and/or antibodies. The antibodies themselves tend to be conjugated, i.e. they are covalently bound to fluorophores typically which are fluorescent. That means a cell type can be labeled by fluorescence, and the FACS machine can sort fluorescent cells from non-fluorescent cells.

They stained the different cell types with different markers. The markers are sufficiently different from each other to be able to use them together in some cases. For instance, whatever FITC is could be used simultaneously with PE-Cy7-conjugated antibody.

First, they collect two subsets of B cells (the B220 positive and negative cells) by using the CD19 marker (PE-Cy7-conjugated antibody that binds CD19).
Then, from one of the subsets, the B220 positive one, they sort another subset which is positive for eFluor 450 (which is conjugated with an NK-1.1 antibody). This collected subset fulfills their criteria for being NK cells.
This subset is used for single cell capture on a plate (e.g. for SMART-seq2) or using microfluidics (e.g. for 10X Chromium).

For a FACS machine, you can select the threshold level of e.g. florescence that will be used as a cutoff between positive and negative events (cells). This is arbitrary and is usually subject to trials.


Why we have just 2 teeth cycles, primary and secondary not more?

Humans are diphyodont animals, which means we are having two sets of teeth cycles, on contrast, the polyphyodont animals which are having multiple tooth cycles. The first deciduous teeth(milk teeth,baby teeth or primary teeth) then followed by the permanent teeth. Milk teeth develop from the embryonic stage and continue to develop for 6-7 years and gradually erupts forming the permanent teeth. The permanent teeth is developed and it pushes the milk teeth from the bottom which result in the shredding of milk teeth.

Most of these polyphyodont animals uses their teeth for more severe purposes like grabbing and slashing. Due to these massive work load, their tooth are considered as their main advantage for survival. Also their tooth are subjected to heavy flaws while they grab or slash, so having multiple tooth cycles help them ensure healthy teeth all over their life time. On the other hand considering the diphyodonts, their tooth have been using for chewing and grinding and they will having low flaws compared to the others. So from the evolutionary standpoint increasing the number of tooth cycles are not so economic for them.
Reference


Where are -HCl supplements absorbed in the human digestive system?

The hydrochloride ions are not what facilitate their absorption into the body. The HCl notation is from organic chemical reactions of a weak base (usually amines are involved here) with HCl to form a salt. The salt is what gets purified as a powder (otherwise the chemical remains in solution and can't be made into a pill/supplement). The bottle may say: "compound-HCl" or "compound HCl" implying that the two are chemically bonded together, but that is incorrect. What actually happens is that the compound is an ionic salt, in the form [compound]H+ Cl-. As far as absorption, that is entirely dependent on the compound(s) being absorbed. Once you swallow them, they dissociate back into the weak acid form and H+,Cl- ions.


(Web)app to search metabolic/signalling pathways

KEGG  http://www.genome.jp/kegg/kegg2.html

GLAMM http://glamm.lbl.gov/

I had to truncate to gluconolactone to make the search work in both cases.


Are prions a recent biological phenomenon?

Knock-out experiments on non-pathological prion proteins ("PrP") show damage to neurons. So there is evolutionary pressure to conserve their sequence and expression. Mutations to PrP and related regulatory regions appear to be deleterious and the organism will not likely get to reproduce.

A paper here explores this question and demonstrates empirically that pathology-causing prions — normal PrP that refolds into a form that causes disease — themselves undergo selection pressure:

  In summary, prions show the hallmarks of Darwinian evolution: They are subject to mutation, as evidenced by heritable changes of their phenotypic properties, and to selective amplification, as documented by the emergence of distinct populations in different environments.

To the extent that organs susceptible to aberrant prions have undergone evolution, one could infer from this that prions themselves would be under selection pressure to adapt, as their host environment changes.

Further, there is another paper that discusses sequence-level similarity of PrP between clades:

  The presence of the human and mouse PrP genes within conserved syntenic groups (Sparkes et al. 1986) and the presence of aPrP gene in chicken (Gabriel et al. 1992) argue that the PrP gene existed before the speciation of mammals. In mammals, DNA sequences of the ORFs encoding PrP generally exhibit ∼90% similarity. As expected, the degree of similarity at the amino acid level increases to >95% when PrPs of different primates are compared (Schätzl et al. 1995) but is much lower when human PrP is compared with that of a marsupial (∼70%) (Windl et al. 1995). An even lower degree of homology is found when human PrP is compared with that of the chicken (∼30%) (Harris et al. 1989; Gabriel et al. 1992). Attempts to find PrP-related genes in lower eukaryotes have, to date, been unsuccessful (Oesch et al. 1991).

There is an estimation of 600M years of evolutionary distance between humans and chickens, back to their common ancestor:

  The last common ancestor of birds and mammals (the clade Amniotes) lived about 310 – 330 million years ago, so 600 million years of evolutionary time in all separates humans from Aves, 300 million years from this common ancestor to humans, plus 300 million years from this ancestor to birds.

This would suggest to me that PrP has been around for a while, at least 330M years and probably longer, and that aberrant and pathological folds of PrP would have been evolving since (along with PrP, itself).


No, absence of an stimulating substance is not appropriate to consider as inhibition.

To see why, consider a situation where there are two such substances, substance A and substance B, which can both stimulate protein P (many such relations exist).  If you add only substance B, then protein P will be stimulated. Since P is being stimulated in this case, it would thus not be reasonable to describe the protein being inhibited by the lack of substance A.


How do steroids travel in the bloodstream?

Steroid hormones are transported in an inactive form bound to proteins in the bloodstream. Androgens and estrogen are bound to Sex hormone-binding globulin (SHBG), while glucocorticoids and progestins are bound to transcortin.

References:

Transport of steroid hormones: binding of 21 endogenous steroids to
both testosterone-binding globulin and corticosteroid-binding
globulin in human plasma.
Plasma protein-mediated transport of steroid and thyroid hormones.
The Functions of Corticosteroid-Binding Globulin and Sex
Hormone-Binding Globulin: Recent Advances


Do lower animals have instinctive behaviors?

Short answer
'Lower' organisms like C. elegans exhibit innate behaviors. In fact, unicellular organisms [without any nerve cells at all] can exhibit instinctive behaviors.

Background
Let's start by defining the central terms here, namely Behavior and Instinct:

Merriam-Webster has a general definition of Behavior:

  [A]nything that an organism does involving action and response to stimulation

And according to the Cambridge dictionary, Instinct is:

  [T]he way people or animals naturally react or behave, without having to think or learn about it.

And Merriam-Webster defines Instinct more elaborately:

  Largely inheritable and unalterable tendency of an organism to make a complex and specific response to environmental stimuli without involving reason
  Behavior that is mediated by reactions below the conscious level

Hence, C. elegans' actions are indeed instinctive behaviors.

An interesting distinction here is whether behaviors in simple organisms should be indeed called behavior, or rather be classified as [lower-order] reflexes.
According to Merriam-Webster, a Reflex is:

  [A]n automatic, often inborn response to a stimulus that typically involves a nerve impulse passing inward from a receptor to the spinal cord and then passing outward from the spinal cord to an effector (such as a muscle or gland) without reaching the level of consciousness and often without passing to the brain, such as the pain-withdrawal reflex, or the knee-jerk reflex.

This is a typical schoolbook approach-based definition of a reflex. Strictly spoken C. elegans' behaviors would not classify as reflexes according to this definition, because invertebrates do not have a spinal cord.

Nonetheless, sea anemones show protective withdrawal responses by retracting their tentacles and oral disc. Some may even detach from the substrate in response to a variety of aversive mechanical, electrical, or chemical stimuli. And earthworms show rapid withdrawal responses mediated by giant nerve fibers when subjected to unfavorable stimuli, that are in fact classified as reflexes (Smith, 1991).

Indeed, Wikipedia defines a Reflex as

  ...[A]n involuntary and
  nearly instantaneous movement in response to a stimulus. Scientific
  use of the term "reflex" refers to a behavior that is mediated via the
  reflex arc.

Thus the question then becomes what is a reflex arc? The Medical dictionary defines a Reflex arc as:

  Route followed by nerve impulses in production of a reflex act, from peripheral receptor organ through afferent nerve to central nervous system synapse and then through efferent nerve to effector organ.

Hence, in all, instinctive behavior is appropriate general terminology. When in simple organisms the behavior can be directly linked to a responseive action to a sensory stimulus, the term reflexive behavior may be a more appropriate term than instinctive behavior as far as I can see.

To push the definition of instinctive behavior even further, we can conclude from all this that single-celled organism exhibit it too, as they can show simple instinctive behaviors, such as phototaxis and chemotaxis, where they change their direction of movement in response to light and chemicals, respectively (source: Khan Academy).

Reference
- Smith, ILAR J (1991); 33(1-2): 25-31


Is existence of different alleles for a gene a result of mutation?

I would like to understand evolution

The best way to do so is to start an introductory course on evolutionary biology. Consider having a look at evo101 for example.

  Why are there different alleles for a gene?

Because mutations bring variation. Note that not all genes are polymorphic. In other words, there might be genes for which, all individuals in the population share the same allele.

The existence of this genetic variance is absolutely central to the whole concept of evolution. In short, mutations increase genetic variance while natural selection and genetic drift reduce it.

  Is the different alleles of a gene are mutated versions of a gene?

Yes

  Why selection pressure favoured the existence of more than one alleles?

In the exception of cases of balancing selection (e.g. heterozygote advantage, negative frequency-dependent selection), selection does not yield to the existence of genetic variance, rather the opposite in fact. Selection "selects" for a given allele, which in turn reduces the genetic variance. Mutations bring new genetic variance in populations and selection reduces it. Genetic drift (another "driver of evolution") also reduces genetic variance.


What causes a small bump in the arterial pressure plot?

This bump is related to the closure of the aortic valve as a reaction to the retrograde blood flow which in turn gives small change in blood pressure.


A quote from a Discovery movie:

  Scientists have estimated that over the course of Earth's history, anywhere between 1 and 4 billion species have existed on this planet.

I know, I know... sorry. I hope someone has the original research, but in case no one does, or if you are just curious, and Discovery is fine for you, I decided to share what I know for the time being.


Can the liver prioritize it's metabolizing potential?

Aside from "toxins", the liver metabolizes a host of endogenous and exogenous compounds. Endogenous compounds are compounds that are normally present and produced within the body like ammonia and estrogens for example. Exogenous compounds are those like ethanol/alcohol, acetaminophen, and other drugs/etc that are not normally in the body but rather we take a mediations or recreational drugs, etc. Most of the compounds that the liver metabolizes are through a set of enzymes called the cytochrome P450 system, which includes numerous enzymes (too many to list here) that catalyze a number of reactions that help detoxify a substance and/or make it more likely to be excreted in the urine by the kidneys.

If the liver "sees" old and new compounds it doesn't differentiate between which it might metabolize first - that is based on concentrations within the liver. In fact, only if the compounds are metabolized by the same liver enzymes will they compete with one another. If they are metabolized by the same exact P450 enzymes, then the concentrations of each of these substances within the hepatocytes (liver cells) will determine which one gets metabolized more frequently. For example, if the concentration of substance A is much, much higher than substance B, then substance A is going to outcompete the other substance for the enzymes that metabolize it (similar to competitive inhibition in biochemistry). Most of the time, endogenous and exogenous compounds do not necessarily compete at the same P450 enzymes because there are so many different P450 enzymes within the liver.

The liver does not have any way of prioritizing different compounds, however, if the liver is exposed to a particular substance over a long amount of time then it may express more of a particular cytochrome P450 enzyme that metabolizes that particular substance. This is similar to alcoholics being able to metabolize a lot more alcohol than someone who has never drank alcohol previously.


Do Acyl Carrier Proteins and Conenzyme A have similar reactivity?

The acyl groups ligated to CoA and to acyl carrier proteins are actually attached to the same group (a phosphopantetheine group) as shown below, and so have very similar reactivities (i.e. group transfer potentials).


You do need two pairs of primers one unique to each species as you need a positive result to be confident that the thing you are looking for (cow or horse) is there.

There is no limitation on them being in the same place (with a different last base).

Usually this would be analyised by gel-electrophoresis and not by sequencing so you don't have to worry about getting the whole thing. This is because you are only looking for the presence or absence of PCR product.

When you do the PCR you will have 4 reactions, one which amplifies horse only, one which amplifies cow only and their negative controls (adding water instead of lasagna DNA extract). After the PCR you take a small amount of your PCR product and run it on a gel (gel-electrophoresis). If you see amplification in the negative controls then you have contamination and can't trust the result. Otherwise if you see amplification by the cow primers then cow is present in the lasagna and if you see amplification by the horse primers then you probably don't want to eat the lasagna. If you used both options for the first forward primer you suggested (blue) then all your bands would be the same size, if you used both the first (blue) and second (yellow) then you would get different band positions on the gel due to the different sized products which makes you feel more sure that you didn't make the mistake of adding the same primer pair to both tubes (it happens).

In the end it's simply a matter of style.