Short Answer: As the comments mention, this is a hot topic for pseudoscientists to use as a selling point for their supplements. There is limited evidence that dietary acid intake significantly alters bone resorption, especially in the setting of normal renal function. This paper should answer all of your questions (emphasis mine):

  Frassetto, Banerjee, Powe, Sebastian. Acid Balance, Dietary Acid Load, and Bone Effects—A Controversial Subject. Nutrients. 2018. 10(4),517.

    Abstract: Modern Western diets, with higher contents of animal compared to fruits and vegetable products, have a greater content of acid precursors vs. base precursors, which results in a net acid load to the body. To prevent inexorable accumulation of acid in the body and progressively increasing degrees of metabolic acidosis, the body has multiple systems to buffer and titrate acid, including bone which contains large quantities of alkaline salts of calcium. Both in vitro and in vivo studies in animals and humans suggest that bone base helps neutralize part of the dietary net acid load. This raises the question of whether decades of eating a high acid diet might contribute to the loss of bone mass in osteoporosis. If this idea is true, then additional alkali ingestion in the form of net base-producing foods or alkalinizing salts could potentially prevent this acid-related loss of bone. Presently, data exists that support both the proponents as well as the opponents of this hypothesis. Recent literature reviews have tended to support either one side or the other. Assuming that the data cited by both sides is correct, we suggest a way to reconcile the discordant findings. This overview will first discuss dietary acids and bases and the idea of changes in acid balance with increasing age, then review the evidence for and against the usefulness of alkali therapy as a treatment for osteoporosis, and finally suggest a way of reconciling these two opposing points of view.

This paper is open-access and I recommend you read it, but the conclusions summarize their findings nicely:

  7. Synthesis

    We suggest the way to put all of this information together is to agree...that bone alone cannot buffer the positive acid balance that one can calculate from measures of acid production and acid excretion. In addition, endogenous acid production goes up and down in an attempt to maintain systemic blood pH...

    Diets high in acid precursors add to the body’s acid burden. For the majority of people eating typical western diets with acid loads of ≤1 mmol/kg, whose renal function and acid excretory ability is normal, dietary acid loads would not be a readily detectable factor in altering bone mineral density leading to the development of osteoporosis. Other factors such as age, gender, race, and immobility are quantitatively more major factors in determining bone mass and bone breakdown.

    However, body retention of only 1 or 2 mEq of acid each day, barely detectable by current measurement techniques, buffered by muscle and kidney and titrated by skeletal base over decades, could potentially result in major depletion of bone mineral. Thus, we suggest that those older subjects with diminished renal function, decreased renal acid excretory ability, and lower buffering capacity due to lower muscle and/or bone mass, whose diets contain high net acid loads could potentially benefit the most from alkali therapies.

Long Answer: Although there's a wealth of pseudoscience on the internet relating to acidemia and bone composition, there is some truth to the idea that bone can be affected by pH. An excellent model to explore this concept is chronic kidney disease, as impaired renal function causes decreased H+ secretion, which results in a chronic metabolic acidosis:

  Kopple, Kalantar-Zadeh, Mehrotra. Risks of chronic metabolic acidosis in patients with chronic kidney disease. Kidney International. 2005. 67(95),S21-27.

    Metabolic Acidosis

      Severe chronic metabolic acidosis (i.e., the presence of excess hydrogen ions in blood) has two well-recognized major systemic consequences. First, metabolic acidosis, or acidemia, induces increased protein catabolism, decreased protein synthesis, and negative nitrogen and total body protein balance, which improve upon bicarbonate supplementation. Second, metabolic acidosis causes physicochemical dissolution of bone and cell-mediated bone resorption (inhibition of osteoblast and stimulation of osteoclast function).

    Metabolic Acidosis and Bone Disease

      Metabolic acidosis exerts multiple effects on bone. It causes the physicochemical dissolution of bone and cell-mediated bone resorption through the inhibition of osteoblast activity and stimulation of osteoclast function. These events are associated with a loss of calcium and phosphorus from the bone. Metabolic acidosis stimulates osteoblasts to release prostaglandins. This stimulates osteoclast function and inhibits osteoblast activity. Glucocorticoids can inhibit the production of prostaglandins by osteoblasts.

      Metabolic acidosis is also associated with a decrease in the content of bone bicarbonate. Additionally, bicarbonate supplementation in postmenopausal women is associated with decreases in urinary calcium, phosphorus, and increased osteocalcin levels, indicating a beneficial effect. Figure 4 shows the mechanisms relating metabolic acidosis with bone disease3. These observations suggest that uncorrected metabolic acidosis has adverse consequences on bone anatomy and physiology.

      Figure 4. The various mechanisms by which metabolic acidosis may contribute to bone disease. (From3).

From here, your questions can be answered:

Q: By consuming acidic foods, could one cause their blood to become acidic and therefore cause an acid+base reaction between their blood and bone?

A: Maybe. It is possible to induce a metabolic acidosis with diet:

  Adeva, Souto. Diet-induced metabolic acidosis. Clinical Nutrition. 2011. 30(4),416-21.

    The modern Western-type diet is deficient in fruits and vegetables and contains excessive animal products, generating the accumulation of non-metabolizable anions and a lifespan state of overlooked metabolic acidosis, whose magnitude increases progressively with aging due to the physiological decline in kidney function. In response to this state of diet-derived metabolic acidosis, the kidney implements compensating mechanisms aimed to restore the acid-base balance, such as the removal of the non-metabolizable anions, the conservation of citrate, and the enhancement of kidney ammoniagenesis and urinary excretion of ammonium ions. These adaptive processes lower the urine pH and induce an extensive change in urine composition, including hypocitraturia, hypercalciuria, and nitrogen and phosphate wasting.

And there is existing research on short-term effects of altered diet on blood and urine pH and composition, but the clinical relevance of these values is indeterminate:

  Buclin, Cosma, Appenzeller, Jacquet, Décosterd, Biollaz, Burckhardt. Diet Acids and Alkalis Influence Calcium Retention in Bone. Osteoporosis International. 2001. 12(6),493-99.

    The urine-acidifying properties of food constituents depend on their content of non-oxidizable acids or precursors. Acidifying constituents such as animal proteins may negatively affect calcium metabolism and accelerate bone resorption, thus representing an aggravating factor for osteoporosis...acid-forming diet increased urinary calcium excretion by 74% when compared with the base-forming diet (p50.0001), both at baseline and after the oral calcium load, and C-telopeptide excretion by 19% (p=0.01), suggesting a skeletal origin for the excess calcium output. This observation confirms that renally excreted acids derived from food influence calcium metabolism, and that alkalizing nutrients inhibit bone resorption. Further studies are needed to determine the clinical impact of dietary counseling for avoiding diet acids as a preventive measure against osteoporosis.

But best recent evidence does not support the idea that significant changes in bone composition could be induced by diet alone (see my "Short Answer" above).

Q: ...what salt would be produced?

There are many metabolic acids, but for simplicity, we'll consider H+. Bone bases are stored as alkaline salts (e.g. calcium carbonate, CaCO3, which is really Ca2+ and CO32-). So, if H+ comes into contact with calcium carbonate, you'll make carbonic acid (with H+ displacing Ca2+ to produce H2CO3 – you excrete the Ca2+, resulting in the hypercalcuria described above). Through the bicarbonate buffer system,  that H2CO3 will be converted into carbon dioxide and water, which you excrete from your body via respiration.


What actually happens to the human body during fasting/starvation?

Actually, the body goes into the fasting state about eight hours or so after the last meal, usually when the guy finishes absorbing nutrients from the food.
Normally, body glucose, which is stored in your liver and muscles, is your main source of energy. When in a fasting state, your body uses up the glucose that you have stored to provide energy. If you are still fasting after this store is used up, your body will start to burn fat to create energy, therefore leading to weight loss.
After fasting for a few days, there will be a higher level of endorphin in your blood which will cause you to be more alert and, weirdly, giving you a feeling of mental well being.
Eventually, if you are starved for too long, your body will start to break down muscle protein in order to create energy (that is why, during WWII, most POW's held by the Japanese were very thin - they were starved and in order to survive, their bodies had to 'eat' their own muscle)
Technically, starvation is when your body starts to eat your protein, i.e. Muscle.During starvation, your body will thin out, because your fat has been burned and your muscle is being 'eaten'. This obviously leads to weakness.
When your fat is being burned, you go through a detoxification process which is caused because any toxins stored in your body's fat are dissolved and removed from the body.
Your kidneys are very efficient in being able to maintain the body's water and salts, like potassium and sodium. But these can be lost through perspiration.
This eventually leads to dehydration which does many things to your body, like: not allowing for your body to regulate body temperature; your heart works harder (most of your water is in your blood (about %$60$) and when you lose the water, your heart has to 'catch' up and pump more to keep the blood flowing and cooling you down - now, your heart is working harder which could give you a greater risk of heat exhaustion); you can feel cranky, drowsy, confused, forgetful.
These are a lot of things that happen when your body is deprived of what it needs in terms of food and liquid.

This is what happens, and this is very general, when your body is in its starvation mode. I am sure that there are many more things, but I could only give a brief answer.


How can a brainless Cnidarian hunt and defend itself?

Sea anemones are members of the phylum of Cnidaria. Distinguishing features of this phylum are radial symmetry and the presence of cnidocytes, or stinging cells (like the ones found in jelly fish). These cells have a mechanical trigger and if activated a subcellular harpoon is fired and paralyzing and painful toxin is injected. A cnidocyte diagram is shown below (from Wikipedia):

The Cnidarian nervous system is relatively simple indeed. The Cnidarian nervous system is decentralized and diffuse, and it basically consists of reflex arches. It is referred to as a "nerve net" as shown in the following schematic of a sea-anemone's nervous system (picture from Florida Int. University):

The presence of cnidocytes and a mesh nervous system basically answer your question:

1) Feeding: Whenever a prey touches the sting cells, it gets harpooned and paralyzed. The mechano-sensory cells sense touch, and drive nervous cells in the mesh. The nervous cells activate contractile epithelial cells in the arms of the anemone that push the prey inside the mouth. Then digestion takes place and the mouth serves as anus once digestion is complete.

2) Defense: the cnidocytes operate by mechanical triggering and no nerve cells are necessary.


Identify this large, beige or pine cone-colored squareish beetle and/or the pine cone it's on?

This is Tessaratoma papillosa, also known as the lychee giant stink bug. It is a pest for lychee trees, this is probably the reason for this warning sign. See the image for comparision:

See also this page for more information.


What's the difference between constitutional samples and tumor samples?

Constitutional samples do, as you surmised, refer to germ cells (sperm or ovum). Hence they have 1 copy of DNA instead of 2.

Tumours, as they acquire more mutations, often have aneuploidy, or different numbers of chromosomes, and can also have increased incidence of Xn chromosomes where X > 2. This is polyploidy for humans and organisms with normal 2n chromosomes.


How to calculate percentage of DNA that ancestors contributed?

The answer I'm going to give is more or less copied from Graham Coop's post, but I'll try and summarise it here.
A single generation ago, we have 2 ancestors. If we go another generation back, we have 4 ancestors (your 4 grandparents). If we assume that there is no inbreeding within the ancestral population, every time we go back a generation, the number of ancestors doubles.
On the other hand, the amount of your DNA you inherit from each relative halves each generation. You get ~50% of your DNA from your mother and ~50% from your father. These are inherited in large blocks which are split up by recombination events. If you go back a generation, you inherit ~25% from each grandparent.
However, because of stochasticity in how recombination occurs, you don't inherit exactly 25% from each grandparent. What you really inherit is a value distributed around 25%. There is a nice discussion of the ins and outs of it here. As an extreme example, if your parents and grandparents transmit entire chromosomes without recombination, then it is possible not to inherit any DNA on that chromosome from the other grandparent.
It's quite unlikely ($p=4$ x $10^{22}$) that you don't inherit anything from a single grandparent. However, as you go back through generations, it's increasingly likely there are some relatives who don't contribute anything to your DNA.
For example, 8 generations back, there's around a 20% chance that any given ancestor didn't contribute anything to your genome. Therefore, we can say that the number of genealogical ancestors a given generation back is one minus the number of ancestors who contributed nothing. This is why, even though 10 generations back we might have 1024 ancestors, perhaps only around 50% of them will have contributed anything to your DNA.
I'm not entirely sure about how the figures in this book were calculated; whether it was from simulation or not. However, the results should be more or less the same as how Graham Coop calculated it in the above post.


Isotype control antibodies in Flow Cytometry

I don't believe that the Isotype Control Antibody makes the antibody bind more specifically but rather ensures that your signal is specific to your antibody.

The Isotype Control Antibodies tend to bind to the non-binding domain of the antibody, typically the constant (Fc) domain. By measuring the concentration of the control antibody, you can determine what percentage of your light signal comes from your primary antibody and not from non-specific binders to your light source.

This is very similar to having secondary antibodies in your assay.

Random link showing that I'm not making stuff up


Is it considered feasible to genetically improve plants for better Carbon dioxide breakdown?

I'm not sure from your question if you're clear on the relationship between carbon fixation and 'energy', so just to be clear: carbon fixation in photosynthesis is the process of capturing CO2 and using it to store light energy in the form of carbohydrates. More CO2 capture = more harvestable 'energy'. Improving the efficiency of photosynthesis therefore captures more CO2 and generates more harvestable energy in the form of carbohydrates (edible or not).

There are three carbon fixation pathways in plants: C3, C4 and Crassulacean acid metabolism (CAM). The relative efficiency of the different pathways depends on the environment; for example, C4 plants are able to more efficiently fix carbon in drought, high temperatures, and limitations of nitrogen or CO2.

Because of this, scientists are indeed interested in engineering crop plants to use alternative carbon fixation pathways. One such project is the C4 Rice Project: http://c4rice.irri.org/.


Cellulose - why is it fibrous and not granular?

Cool I got something right :D

Cellulose is a linear polymer and therefore makes a fiber. I guess the linear in this case implies fiber. Amylose has a helical structure to it i think. Here is an image I found that shows the difference.


Maybe, cells should be contained under BSL-2 and agents (viral particles etc) under stricter BSL-3? That is, after immortalization you can keep cells under lower security.

  Biosafety Level 2 builds upon BSL-1. BSL-2 is suitable for work involving agents that pose moderate hazards to personnel and the environment.

  Biosafety Level 3 is applicable to clinical, diagnostic, teaching, research, or production facilities where work is performed with indigenous or exotic agents
  that may cause serious or potentially lethal disease through the inhalation route of exposure

  CDC Biosafety in Microbiological and Biomedical Laboratories, Laboratory Biosafety Level Criteria

As of HEK 293 cells, check this out:

  Biosafety level 2 practices and containment facilities for all activities involving HEK-293 cell lines.

  HEK 293 Cell Line Risk Assessment - IBC


Do females retain oogonia after puberty?

From Developmental Biology, 6th edition I learned the following:

In humans, the oogonia divide to form a limited number of egg precursor cells. In the human embryo, the thousand or so oogonia divide rapidly from the second to the seventh month of gestation to form roughly 7 million germ cells. After the seventh month of embryonic development the number of germ cells drops and most oogonia die during this period, while the remaining oogonia enter the first meiotic division. These latter cells, called the primary oocytes, progress through the first meiotic prophase until the diplotene stage, at which point they are maintained until puberty.

Hence, at puberty the cells from the lineage of oogonia are called primary oocytes. So from a terminological perspective, you are correct that no oogonia are thought to be left at puberty.


The sound in question is called the Korotkoff sound:

  If the pressure is dropped to a level equal to that of the patient's
  systolic blood pressure, the first Korotkoff sound will be heard. As
  the pressure in the cuff is the same as the pressure produced by the
  heart, some blood will be able to pass through the upper arm when the
  pressure in the artery rises during systole. This blood flows in
  spurts as the pressure in the artery rises above the pressure in the
  cuff and then drops back down beyond the cuffed region, resulting in
  turbulence that produces an audible sound.


Not sure, this what you need, but here you can find a detailed description of how photosynthesis efficiency can be measured in the field, with a list of modern devices. In short, it's about measuring the uptake of CO2 and release of H2O of individual leaves.


Take a look at this schematic of a mature mRNA.

[source]

The coding region (ie the part that is translated) is between the start and stop codons, but the 5' and 3' untranslated regions (UTRs) are also transcribed by RNA polymerase; these are part of the first and last exons, respectively. The transcription start site is labelled right in front of the 5' UTR. For the purpose of this answer, transcription termination can be said to occur at the poly(A) signal (the poly(A) tail is added post-transcriptionally, as is the 5' cap).

To be clear, the point I'm hopefully making is that transcription does not involve codons. RNA polymerase does not stop at the stop codon nor does it start at the start codon. In fact, it doesn't even "know" what codons are.


Chemistry of phosphodiester bond formation by DNA polymerase

I found this paper, which goes very deep into the molecular details of the individual steps of this reaction and also discusses how this is coupled to nucleotide selectivity.

The 'basic' details about the reaction (quoted from this section, which also has a nice figure):

  The polymerization reaction proceeds by a simple nucleophilic attack
  of the 3'OH of the primer on the α-phosphate of the incoming dNTP
  followed by the elimination of pyrophosphate [...] The reaction uses a
  "two metal ion" mechanism in which metal ion A activates the 3'OH as a
  metal hydroxide while both metals A and B stabilizes the developing
  negative charge on the α-phosphate in the transition state.

The metal ions are Magnesium (Mg$^{2+}$) and are properly positioned by the enzyme structure and some additional amino acid side chains also help with the activation of the reaction.


A lower supply of blood does not mean no supply of blood, so my guess is there's generally enough to keep stuff alive for some time. But if the supply is restricted for long periods (think frostbite), then stuff starts to die.

Also, the sensory neuron endings in the skin are normally just one long projection from a cell body, the major components of the neuron are protected by being located in e.g. The Dorsal Root Ganglion.


Are there COVID-19 citizen science projects to compare habits and outcomes?

I think you are looking for a very specific design of 'citizen' projects. But, if we relax a bit your criteria, there are some examples. Here, and here, for instance. One worth discussing, I think, is what Google has done for mobility tracking. Yes, the users did not 'opt-in' the study, but in essence, they provided the data!


How might I break down bread into glucose in a model of the human digestive system?

Amylase would be worth a try. The enzyme breaks down bread (starch), and you can buy it relatively cheaply online or probably at a chemist. Amylase is secreted in your saliva and in your stomach, so it would be most realistic if it was added in your model at those two points.


Would tattoos be considered a phenotype?

Broadly speaking it most likely is. The exact meaning of phenotype has changed quite a lot over the years. There isn't a clear distinction between what should or should not be included in the definition, and reasonable people can disagree on sound arguments.
Phenotypes were defined by Johanssen in 1911. His definition was "All “types” of organisms, distinguishable by direct inspection or only by finer methods of measuring or description, may be characterized as “phenotypes.”". So in his definition a phenotype is a class of individuals that share a common observable property. Take Mendel's experiment: short and long peas are 2 phenotypes. From heredity we can infer multiple genotypes. An identical phenotype (tall) can result from 2 different genotypes (tall-tall, or short-tall). That is why the distinction is important, because truly understanding genetics will require not only to understand the genetic makeup of individuals (we have more or less solved that), but more importantly how the genes are expressed into a phenotype. Keep in mind all of this was speculated long before we actually found out what genes were. Ironically, Johannsen thought it was an idle pursuit: "The question of chromosomes as the presumed “bearers of hereditary qualities” seems to be an idle one. I am not able to see any reason for localizing “the factors of heredity” (i.e., the genotypical constitution) in the nuclei.".
At the time, genes were really thought to produce strict discrete categories of individuals that were slightly smoothed out through random individual variations. Over time it became obvious that Mendelian traits were more the exception than the rule and that trying to classify individuals in discrete categories was not really helpful. So over time phenotype became to used for traits instead of individual. That's the way I hear people use it today at least (i.e. we would call "being tall" a phenotype of peas, and not "all peas that are tall").
So the modern definition of a phenotype is the observable characteristics of an organism, anatomical, physiological or behavioral. The first 2 points are easily accepted and uncontroversial. But there is debate about what exactly should be included in "behavior". I'm going to ignore behavior for now.
An important point, and I think this is where there is disagreement between Remi.b and me, is that a phenotype must have a genetics basis. I realize this is not explicitly mentioned in any definition, but that is very much the way people mean it. And if not, the definition is totally meaningless. Take the example of a monkey missing a finger congenitally. This is a phenotype, it is due to its genes. If the monkey is missing a finger due to a fight, this is not a phenotype because genes have nothing to do with it (again, ignoring behavior for now).
So, in my opinion, what would not be a phenotype is something that you could conclusively prove to have no genetics basis whatsoever. That's an extremely (impossible) hard case to make. But in retrospect I was perhaps to quick to include behavior in the definition, and this is due to my own biases as a behavioral neuroscientist.
I think this is the narrow definition of phenotype and I don't think anyone would disagree up to that point. You might notice that there has been no mention of evolution so far. It is because genetics and evolution have been developed independently, and even though everybody was quite aware they must be 2 sides of the same coin evolution is not directly relevant to the genotype/phenotype distinction.
This is when the definition of phenotype started to be extended beyond purely physical traits (people included behavior in phenotype but they mostly meant things like gait that require a behaving animal to measure, but it is not behavioral in the broad sense). I see 2 reasons for that change, and R Dawkins was largely involved in popularizing these ideas. First as genetics and evolution started to be integrated together, it became obvious that genes must be selected through evolution, and that phenotype must reflect something related to fitness. W. D. Hamilton did important work on the topic and his ideas were popularized in the "The Selfish Gene" from Dawkins. The second idea is the ethological "revolution" from Tinbergen and Lorenz. Until then animals were seen as automatons (following Descartes) that behave the way they do because of simple conditioning. Ethologists showed that complicated behaviors such as courtship or altruism are instinctive, and therefore must have a genetic basis (Hamilton also worked on altruism a lot). A new generation of scientists pushed things even further with people like E. O. Wilson who studied the social life of insects, J. M. Smith who showed that individually detrimental behaviors can be optimal at the scale of a population etc.
At this point it became clear that the definition of a phenotype was too narrow, because behaviors are (at least partly) related to genes and therefore must have been shaped by evolution. This is the idea put forward by Dawkins in his second book "The extended Phenotype" where he explicitly makes the case that the definition of phenotype should be enlarged to include behaviors such as courtship, nest-making and the like (Dawkins was a student of Tinbergen so it's not entirely surprising he is biased to like animal behavior). Although these 2 books became very popular and widely read in the general public, they were actually meant mostly for biologists. Note that the extension of the definition of phenotypes shifts the focus from pure genetics to evolutionary theory as the rational for extending phenotypes is that more stuff than pure physiology contribute to fitness. That's not entirely relevant to the genotype/phenotype distinction but there is a great interview of Smith by Dawkins where he discusses a lot the history of genetics, evolutionary theory, and the socio-political debates behind it (link below).
So today some behaviors are widely, and I think uncontroversially, thought to have a genetic basis and therefore should be considered a phenotype. This is the second part of the disagreement between Remi.b and me (which derives from the first). If phenotypes must have a genetic basis, then how do you know that a behavior has a genetic basis or not? The gold standard is to show heritability of the trait in a twin-study. If the trait co-occur more in identical twins than fraternal twins, and/or in identical twins raised separately than expected from chance, then you know with confidence that this trait is partly genetically determined. Most famously, for example, this is known to be true for sexual orientation. So I am not saying that a phenotype can only be inherited. Obviously a random mutation is a phenotype but has not been inherited. But to show that a behavior is genetically determined I don't know how you can do that without showing heritability (but I'm not a geneticist so maybe there are other ways). Siddhartha Mukherjee's The Gene is a very good summary of the state of the art in that area.
So where does that leave us concerning phenotypes and tattoos? Well if you agree that behaviors should be considered phenotypes, such as courtship, nest-making in birds, aggressive displays in monkeys... Then I see no reason not to include tattoos in it. Any criterion you apply to "animals" should apply equally to humans. Some birds decorate their nests with flowers as part of courtship. The question left is whether it has a genetics basis or not, and I think you are very likely to find that getting tattooed would co-occur more than expected from chance in twins. Of course the tattoo is not genetically determined. It's probably something like open-mindedness, but a tattoo is observable and open-mindedness is not. This definition of phenotypes means that you can more or less already include quite a lot of things in it. So I can see why someone would disagree with extending the definition of phenotype beyond pure physiology. But clearly phenotypes must be linked to genetics otherwise the definition is purely meaningless.
Johannsen W. The Genotype Conception of Heredity. The American Naturalist 1911;45:129-159.
Dawkins, R. (2016). The selfish gene. Oxford university press.
Dawkins, R. (1982). The extended phenotype (Vol. 8). Oxford: Oxford University Press.
Tinbergen, N. (1951). The study of instinct.
Lorenz, K. (2013). The foundations of ethology. Springer Science & Business Media.
Smith, J. M. (1982). Evolution and the Theory of Games. Cambridge university press.
Wilson, E. O. (2000). Sociobiology: The new synthesis. Harvard University Press.
Siddharta, M. (2016). The gene: An intimate history. Scribner, New York, 9-9.
https://www.youtube.com/watch?v=0b0Nm_L3TKg&list=PLVV0r6CmEsFzJSvAc4MBuUP_GrjO1lLHp


Transmission of disease from mother to fetus

Pregnant mothers can indeed pass on various microbes to their fetuses but it is not always directly through the placenta, as the placenta can be protective.  Although the blood of the mother and fetus do not mix directly, the two can interact.  Maternal proteins can flow across to the fetus, as maternal antibodies are actually the source of a newborn's immune system for a few months, and maternal immune cells have even been found in fetuses, which of course means other cells or viruses can get across.

HIV is a good example for your question, actually.  HIV can infect newborns through the placenta, but the majority of infections occur during birth, not in utero.  Birth is a pretty bloody process, and the rupturing of the amniotic sac exposes the infant to anything in the mother's blood, which is when most infections occur.  For HIV specifically, physicians can all but prevent mother-to-infant transmission by administering anti-HIV drugs just before birth.

Here is a list from the CDC of some STDs which details how infections may be passed on to newborns; most clarify that it mainly happens during the birthing process.  That being said, plenty of diseases will cause transplacental infections.  Usually they are viruses, as viruses are simply smaller, but there are definitely bacterial and parasitic examples, such as Borrelia duttonii, Trypanosoma cruzi, and Toxoplasma gondii.  Here's a list of bacterial ones and here's a list of viral ones.


How can you tell if a protein-coding gene is nuclear or mitochondrial?

I have limited my answer to refer to humans, but the advice generalises to other eukaryotic cells.

In human cells, almost all of the genes that code for proteins are located in the genome, which is located in the nucleus. The mitochondria have their own genetic material, however, the mitochondrial genes only encode for 14 proteins. The answer to this question also notes the existence of extrachromosomal circular DNA. There are also a number of proteins (1192) that are verified to exist but their genomic location is currently unconfirmed.

In your comments you mention ATP1 and note that it is called a membrane protein. The gene is located on chromosome 19 in the nucleus. The protein, that is encoded by the gene, can be found in a variety of places, including the nucleus and also the mitochondrion. The gene for Cytochrome c oxidase subunit 1 (CO1/COX1) is encoded in the mitochondrial genome and it localises to the inner membrane of the mitochondrion.

The links in this answer all point to Uniprot. This is what I use to get an idea of the basic functions of proteins. The database includes information genes but its primary purpose is to describe proteins and their functions. The information is roughly correct, it is not perfect. It includes a many species and links to a number of tools, including the gene ontology which attempts to characterise proteins using a controlled vocabulary.


What is the name of this whorled-leaf tree in India?

Bucida molineti also called geometry tree


How are there alternative initiation codons?

Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNAfMet (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable interaction. But apparently, only two-bases-interaction between the start codon (GUG, UUG) and the fMet-tRNA anticodon are sufficient for the initiation of translation (1). I will look more into the literature.

1. Initiation of translation in prokaryotes and eukaryotes


Why does hypocalcaemia cause increased muscle contraction?

Consider the pathophysiology of tetany, which is the involuntary contraction of muscles caused by hypocalcemia.

From the tetany wikipedia page:

  Low ionized calcium levels in the extracellular fluid increase the permeability of neuronal membranes to sodium ion, causing a progressive depolarization, which increases the possibility of action potentials. This occurs because calcium ions interact with the exterior surface of sodium channels in the plasma membrane of nerve cells and hypocalcemia effectively increases resting potential (rendering the cells more excitable) since less positive charge is present extracellularly. When calcium ions are absent the voltage level required to open voltage gated sodium channels is significantly altered (less excitation is required).

So, when Ca2+ levels are low, action potentials are spontaneously generated, leading to muscle contraction.


Is Sinus node conduction necessary for heart beating?

The SA node is not necessary for contraction of the heart.

The reason that this works is exactly what you mentioned: schematics.

They are in sequence, but within that sequence, there are multiple autonomous signal generators in the heart, where spontaneous depolarization occurs to initiate contraction: the SA node, the AV node, and the purkinje fibers.

The SA node fires the most rapidly, 60-90 times per minute - which is the average normal heartrate, because in most people the signal for contraction arises from the SA.

The AV node fires at 46-60 times per minute.  If it receives the signal from the SA node then it depolarizes in sequence like the normal sequence we learn.  But if there is no SA node signal received, the AV node will depolarize on its own.

The last "generator" are the perkinje fibers.  If there is no signal from previous nodes, they will spontaneously depolarize.  However, they depolarize VERY slowly, at a rate usually under 40 bpm.  This severe bradycardia is potentially life-threatening, but allows the heart to keep some circulation going if there is a sudden complete AV node block - but prompt treatment is critical.

Regarding the lack of necessity of the SA node:

In fact, in some cases of supraventricular tachycardia (for example IST, see here) that are not responsive to conservative treatment, they will actually ablate (surgically destroy) the SA node in order to slow the heartrate down because a persistently extremely high heart rate can be dangerous.

Good question!


I2D vs STRING for protein-protein interactions

I just looked and it seems I2D use the PPI from 5 organisms to predict interactions in those organisms, which have not yet been experimentally demonstrated, so its interolog PPI prediction tool by design (http://genomebiology.com/content/pdf/gb-2007-8-5-r95.pdf), where as STRING can be used to see what proteins are known to interact with a given protein, and what evidence is present for a particular interaction, which you then get a (confidence like) score.


While I can't find any specific sources regarding bacteria eating enamel, I highly doubt this is what's happening in our mouths. I doubt this because your point is likely true - minerals in enamel provide no added benefit to the bacteria. I would ask a dentist about this to be sure though.

However, what is certainly true is that the acid produced by the bacteria in dental plaque is what causes tooth decay and gum disease. More specifically, S. mutans is the primary culprit behind dental plaque. Most notably is that S. mutans is an anaerobic organism and because it doesn't require oxygen to respirate, the pathway results in lactic acid as a by-product. This lactic acid is what makes enamel prone to demineralization and if untreated, can irritate your gums, causing gingivitis. It's also worth noting that not all bacteria will do this - not even all anaerobic bacteria that release lactic acid will do this. S. mutans is likely one of the few bacterial species that can survive in your mouth because of it's ability to withstand low pH environments in your mouth and form biofilms - able to nicely stick onto teeth.

S. mutans has no need to munch through enamel or gums. Much of what it breaks down for respiration can be easily obtained from the food and drinks that are left behind after a meal - mostly sugars such as sucrose.


What is the difference between fibrogenesis and fibrosis?

I would say fibrosis represents an abnormal accumulation of fibrous tissue usually collagen fibres. Where as fibrogenesis is the process of formation of fibrous tissues be it collagen, reticulin, elastic, oxytalan..


How to know if your breathing is normal?

What you are looking for is a spirometer. There are different types of spirometers serving different purposes like the Incentive spirometer and the peak flow meter. I would suggest that you go through the wikipedia page on it to get more info.


Yeast absorption of different spectra of light

Most of the loss of light being transmitted through individual cells is not absorbed, rather it is scattered (redirected from its original direction to a new one without loss of energy).  There is actually not very much in cells that can absorb visible light, and virtually nothing at all that can absorb many red or near-infrared wavelengths.

Scattering does depend on wavelength, but the relationship is very complex.  For scattering from small cellular components (mitochondria for example), Rayleigh scattering dominates, which will decrease with the 4th power of wavelength, so that green light will scatter much more strongly than red.  For larger components that are comparable or larger than a wavelength (nuclei or whole cells), scattering will increase much more slowly.  The relationship between the direction of scattering and the size/wavelength is even more complex, but is very useful in applications like label-free cytometry where cells can be sorted based on scattered light.

600-800 nm light is a reasonable choice because it will not damage the cells unless the power level is very high, although using shorter wavelengths may give you more sensitive measurements.


That is correct. When plasmodium infects red blood cells, it consumes the hemoglobin in the cell, leaving the heme behind, which they can not metabolize (heme is a heterocyclic porphyrine ring with an iron atom coordinated in the center). Since the heme (or $\alpha$-hematin) causes the production of reactive oxygen species and thus oxidative stress, it has to be removed from the cell. This is done by the conversion into the insoluble and inactive hemozoin (or $\beta$-hematin). This crystalizes in the cell and is not causing any harm to the parasite. See here for more details.

When the parasite finishes this development step, the cells burst and set their interior free into the blood stream. Among the substances released in this step are hemozoin and also glucose phosphate isomerase which stimulate macrophages to secrete cytokines and other factors which then cause the fever and the shivering observed in malaria.

See here for more details:

Hemozoin Induces Macrophage Chemokine Expression through Oxidative
Stress-Dependent and -Independent Mechanisms
Malarial pigment hemozoin and the innate inflammatory response.
Effect of malaria components on blood mononuclear cells involved in
immune response.


For people who work in microbiology labs, what software do you use to manage your strains?

I would go for StrainControl Laboratory Manager. Works perfect and covers all needs of a lab. Do not go for all the "free" stuff since they rely on a active sponsor and your data is never safe.

StrainControl is free for 3 months and if you want to continue use it you simply purchase the Admin password and all your data is saved.


Sodium/potassium-exchanging ATPase (EC 3.6.3.9):

  An enzyme from the plasma membrane of animal cells that catalyzes the efflux of three Na(+) and influx of two K(+) per ATP hydrolyzed.

You can read about the mechanism on Wikipedia:

  The pump, after binding ATP, binds 3 intracellular Na+
  ions.
  ATP is hydrolyzed, leading to phosphorylation of the pump at a highly conserved aspartate residue and subsequent release of ADP.
  A conformational change in the pump exposes the Na+
  ions to the outside. The phosphorylated form of the pump has a low affinity for Na+ ions, so they are released.
  The pump binds 2 extracellular K+ ions. This causes the dephosphorylation of the pump, reverting it to its previous conformational state, transporting the K+
  ions into the cell.
  The unphosphorylated form of the pump has a higher affinity for Na+
  ions than K+
  ions, so the two bound K+
  ions are released. ATP binds, and the process starts again.


The fundamental importance of R.E.M. Sleep. (Rapid Eye Movement)

REM sleep stimulates the brain regions used in learning. This may be
  important for normal brain development during infancy, which would
  explain why infants spend much more time in REM sleep than adults (see
  Sleep: A Dynamic Activity ). Like deep sleep, REM sleep is associated
  with increased production of proteins. One study found that REM sleep
  affects learning of certain mental skills. People taught a skill and
  then deprived of non-REM sleep could recall what they had learned
  after sleeping, while people deprived of REM sleep could not.

  Some scientists believe dreams are the cortex's attempt to find
  meaning in the random signals that it receives during REM sleep. The
  cortex is the part of the brain that interprets and organizes
  information from the environment during consciousness. It may be that,
  given random signals from the pons during REM sleep, the cortex tries
  to interpret these signals as well, creating a "story" out of
  fragmented brain activity.

Source: link


The oncologist seems to be incorrect.

Antibodies are created all over the body inside secondary lymphatic organs (lymphatic nodes) or any other mucosal associated lymphatic tissue (MALT).

B cells mature in the bone marrow and finish their maturity in the periphery, then they can live in lymph nodes, MALT, spleen, omentum or other structures and they can create antibodies in all of those structures.

In regard of your localized infection question, you are right. When a pathogen enters the body the B cells closer to it are in the lymph node that is closer to that site and thus there is where the antibody response will take place. That is why when you have a sore throat (throat infection) your tonsils are swollen (they are lymphatic organs too).


Is the amount of blood that flows through every vein and artery per minute really a constant?

I think the question is not whether the blood flux is constant in time, but rather in space: if 5L/min is the flux through aorta (in given physiological conditions), then at the same moment 5L/min will cross the capillaries. This is volume conservation, for a closed system filled with an incompressible fluid, see this sketch:

If 5L are pushed through the main pipe, the same volume needs to be pushed through the system downstream of it.

Then comes the fact that the system is not perfeclty closed, and some water (and solutes) will "leak" in and out, as @inf3rno points, so this is only approximatively true. Another limitation is that vessel walls are actually elastic, so a change in vessel radius does occur during blood flow. However I believe it is a fair approximation.


What is the difference between transport proteins and effector proteins in gram-negative bacteria?

Is there any difference between the function of transport proteins and effector proteins?

Yes. In this context, the term "effector proteins" refers to proteins that are inserted into a host cell on infection to modulate host cell processes. Effector proteins are inserted into a host cell using a secretion system. The proteins involved in the secretion system are transport proteins, but the effector proteins themselves have a wide variety of functions. They include enzymes, transcription factors, and protein-protein interaction partners, and they have been shown to regulate many host cellular processes, from metabolism, to vesicular trafficking, cell adhesion, and apoptosis.

You can read more about this here.  This review has an interesting perspective, and the Wikipedia page on Bacterial effector proteins isn't bad either.


I think you cannot find a better answer then the following review:

http://www.nature.com/nrmicro/journal/v13/n6/full/nrmicro3456.html

It was published in 2015, and it gives a good overview about the secretion systems. Anyway, T6SS can also be virulent. Vibrio cholerae can use an effector of this SS to cross-link actin in the host cell and modify its morphology and its cytoskeleton behaviour.
In general I think that there is not a general order of virulence, also because the T3SS was discovered long ago. Whereas, the T6SS just recently, so the amount of information about its function is still somehow limited.

Hope this helps.


Short, concise, practical manual for doing experimental biology

Molecular Cloning is updated and in its 4th edition.  Every lab used to have it.  Its comprehensive, but really no book could be complete.


How are fragments isolated during shotgun Sanger sequencing?

In the original method, one would clone all of the resulting fragments into a suitable vector, and transform the collection into a bacterial host, to create a so-called library.  By plating the library clones under appropriate conditions you would have a collection of so-called clones, and each clone would be randomly selected and sequenced using the Sanger technique.


BMI limits in interpretation in people with high/low heights

The best procedure is going to depend on what exactly you're going to do with your data. Regardless, you should NOT exclude the BMI values. Just include the height, weight, and BMI. If you're simply reporting BMI as a characteristic of your study population, you can annotate that figure and let your reviewers and readers decide what to make of it. This follows the principles in Chapter 4 of Hulley's Designing Clinical Research. You want to get and maintain all the data.

If you're going run some further analysis on BMI, or if BMI is an outcome in your study, then you can evaluate the impact of a cutoff on your results, but you have to decide ahead of time how you'll do your primary analysis. I recommend using the entire data set (no height cutoff) for your primary analysis (because *there is no established practice for a BMI height cutoff in the general medical literature), and then running a secondary analysis that excludes those research subjects above some threshold (you can pick it, but depending on the size of your sample, 2 standard deviations could be reasonable). That secondary analysis would be a hypothesis generating analysis. If excluding very short and very tall people changed the results of your analysis, that's something to mention in your discussion and something to consider for the next study.

*If you're in a specialized field, then follow the practice of that field for your primary analysis.


What is Growth and how can we define it to be a defining property of life?

If you are just asking what does growth mean in the context of living systems then it almost always means replication of a unit: cell or genetic material (cell division, DNA replication etc).

Note that increase in cell volume or the inter-cellular space (accretionary growth) also happen in living systems and they are also considered growth. However, at a gross level these processes are indistinguishable from what is happening to wood that is dipped in water.

So growing is not an exclusive feature of living systems but still one of the defining features.


Why are the Galápagos islands so special?

Charles Darwin formulated his theory after travelling the world aboard the Beagle, here's the route. He found the Galapagos Islands particularly inspiring,

  'The natural history of this archipelago is very remarkable: it seems
  to be a little world within itself.'

This is a more detailed account of his relationship with the Galapagos islands, and there is also a book called "Voyage of The Beagle" (I think it is available as a free kindle download) which is basically his diary.

A big part of the reason it is so famous is because of "Darwin's Finches," which are 12 species of finch on the island that have all evolved to specific niches. This is one of the classic examples of evolution. Darwin noted the differences between the birds, thinking they were of different families, but it was later discovered they were all finches and the differences had evolved because of factors like the food they eat (seed eaters had fatter beaks.. etc).

The Galapagos islands offer opportunities to study evolution and adaptation because the islands are distant from the mainland, have differences between the islands, and migration between the islands is difficult. Studies like this one (which I happened to be reading at the time of the question being asked whilst writing a manuscript) are an example of how cool a place it is!


How do I generate a phylometric tree given species names?

Biopython may have a module for this. I know it can parses phyloxml files and render a tree. You can query the ncbi database for the xml files. Here is some sample code that will render an ascii tree given a phyloxml file...

from Bio import Phylo
tree = Phylo.read("examplephylo.xml", "phyloxml")
Phylo.drawascii(tree)

There is also support for drawing more graphically rich trees using matplotlib. There is a .pdf book for Biopython that you can download from this url http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

Hope that helps


The Y-chromosome only really contains genes relevant to sex determination[1], with estimates of protein-coding genes ranging from 50-450. For instance the SRY gene, also known as the testis-determining factor [2], is only found on the Y-chromosome.

Phenotypes such as eye colour are coded on the autosomes (i.e. not the sex chromosomes), and as such are determined by alleles inherited from both parents. As Koustav Pal mentions in his comment, many such traits are multi-allelic (i.e. determined by multiple regions of the genome), and are therefore more complex than first appear; eye-colour can change over time, and there are many more complexities that do not fit into the simple "blue", "brown", "green/hazel" categories [3]. This also applies to hair, so the child you mention could become more like their father as they grow older (or not!).

Because each individual posesses two alleles for each possible trait (one from their mother, one from their father - we each have two whole copies of the human genome in our cells*) a person can be a carrier for traits, such as blue eyes, whilst themselves having brown eyes. In fact the situation is so complex (>15 genes affect eye colour) that two blue-eyed parents could have a child with brown eyes [4] - the historical perspective was the brown eyes were dominant over blue eyes.

I have focussed on eye colour because it is a good case-in-point: there are clear genetic determinants and heritability, and it is more complex than the popular perception. Regarding hair (or skin) colour, single-gene mutations can cause pale skin and red hair [5], but beyond these cases the same rules seem to apply; that there are multiple genetic determinants (which means the Mendelian single-allele dominant/recessive model does not really apply) that affect the amount of eumelanin (which is dark brown) and pheomelanin (which is reddish) produced, with together combine to make the spectrum of colours we see in the population - it is not true to say that there are only blond OR brown haired people, as many people lie somewhere between [6].

This has not been an exhaustive review of these topics by any means, and there may be further evidence either way, but it seems quite clear that it is not unusual for offspring to not actually take the appearance of one or both parents. There are many traits you mention (such as build) that I don't go into detail, but there is emerging evidence that these are incredibly polygenic (caused by many small-effect genetic variants - e.g. height [7]) and as such could lead to the same phenomenon.

http://ghr.nlm.nih.gov/chromosome/Y
http://www.ncbi.nlm.nih.gov/gene/6736
http://udel.edu/~mcdonald/mytheyecolor.html
https://www.uq.edu.au/news/article/2007/02/eyes-have-it-multiple-gene-question
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095693/
http://udel.edu/~mcdonald/mythredhair.html
http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html

* well, most cells - red blood cells and gametes do not.


LTP and LTD are processes that operate on single synapses. We don't know how "memories" (there are several types of "memory") are encoded in the human nervous system. As a consequence, we don't yet understand the explicit link between some group of synaptically connected neurons, and a given memory.

So the short answer is "we don't know". Take a look at some of the other questions about memories in human brains: 1, 2


Is this a bedbug or a book lice or what?

This is not a bed bug, but some sort of book louse (order Psocoptera). Bed bugs have a more compact body shape, even in the early stages:
 (from http://www.bedbuginspectiongroup.com/facts/)
Compare this with a book louse, and I think it is much closer to your specimen:

(from https://commons.wikimedia.org/wiki/File%3ABook_louse_01.JPG)
Also, here is a page comparing them: http://bedbugger.com/2008/03/04/book-lice/
Hope you stay bed bug free!


I don't know how extensive. Let's run a simple data query and find out: Go to GEO at NCBI. In the "Gene profiles" window, type CD47, and hit enter to launch the query. At the top of the resulting page, use the link labeled "Limits" to restrict the 7000+ results to human by entering the term "human" in the "DataSet organism" window. So, there are 3700+ results. Look through them to get an idea of which cell types and under which conditions CD47 is expressed.

Let's try a second method. Go to the BioGPS portal. Enter CD47 in the appropriate window and run the query. From the results, select the row with ID # 961 as this represents the human gene CD47. The resulting gene expression/activity chart for Hs (human) will show you in more general terms where CD47 is expressed.


Left-handedness and Right-handedness - Are they genetic?

Handedness has, like many traits, a non zero heritability. You now should read the post Why is a heritability coefficient not an index of how “genetic” something is? to understanding what heritability mean.

In short, yes part of the variance in handedness seen in the human population is due to genetic variance.

You will note that footedness is highly correlated with handedness (wiki > footedness).

Note also that today, in the western world at least, it is generally considered unhealthy for the kid to force him/her to use its other hand (as the catholic church used to do). I am not sure what are the evidence for that but it is a totally different question.

References

McManus et al. 2013
Brandler and Parachini 2013
Harmour et al. 2014


Empirical evidence for species selection

A commonly used empirical example of species selection (a.k.a clade selection, lineage selection) is pelagic larvae in sessile ocean species. See Maliska et al (2013) for a recent paper discussing this in Tunicata and Jablonski & Hunt (2006) for larval modes in gastropods. The idea is to some extent really intuitive - pelagic larvae means higher dispersal rates, so the species will be exposted to and can colonize new environments. This can lead to speciation through adaptive radiation. Larger ranges also means lower extinction rates (e.g. through less population synchrony). If the trait is fixed within a lineage, this lineage as a whole will, as compared to an sister lineage lacking the trait, contain more species (i.e. species selection).

However, you can also argue that pelagic larvae will lead to higher gene flow between populations, which could inhibit speciation. Therefore, the effect of pelagic larvae, and how these mechanisms are weighted in practice, is really an empirical question (see Duda & Palumbi, 1999 and Jablonski & Hunt, 2006 for discussions on this issue).

Jablonski (2008) provides a nice general review of species selection (concept, mechanisms, theoretical models and data), and Okasha (2006) (chap. 7) is good for a theoretical/philosophical treatment of levels of selection. Also remember that traits are selected for at the individual level, but can (especially if fixed) still act on a lineage level.


Prokaryotic sigma factors confer specific promoter recognition to RNAP via Sigma subunit σ1.1, which acts as a DNA 'mimic' - occupying the downstream DNA binding site. This interaction is displaced only when the promoter region is bound, hence conferring the specificity.
Note that Sigma factor on its own cannot bind DNA, as σ1.1 binds σ4 in the unbound form, preventing binding to any sequence.
Source: Section 2. Structural Organisation of σ70 and Other Group 1 σ Factors in this paper

This is in contrast to eukaryotic transcription factors, which can bind to the DNA on their own - indeed the assembly of the general transcriptional machinery in eukaryotes (read: In Yeast) is stepwise and involves first the binding of TFIID to the DNA, then TFIIA, then TFIIB, before finally the Polymerase is incorporated into the growing complex. Source: Molecular Biology of the Gene - James D. Watson, p.g.449-454

In prokaryotes, the sigma factor needs to be bound to the core enzyme (forming the holoenzyme) in order for this promoter specificity to be achieved. Your book 'Principle of Genetics - Snustard and Simmons' is referring to the core RNAP, not the holoenzyme with the Sigma factor bound.

This is why sigma factors are often not included under the umbrella term of 'transcription factor' - they achieve the same functionality as eukaryotic TFs, but are fundamentally different in terms of their binding to the polymerase.

Often authors note that eukaryotes need TFs whereas prokaryotes don't because the point they want to convey is that eukaryotes use huge multiprotein complexes bound to the Polymerase, whereas prokaryotes just use the RNAP holoenzyme, giving Sigma factors a somewhat 'special' place among the transcription factors.


How does one insert cas9 into animal cells?

If you are talking about the nuclease functionality of Cas9, then you aren't adding the Cas9 gene into the genome, you are transfecting it on a plasmid. Usually there is either some form of permeabilization done to the cells, or the construct is inserted into a viral vector in order to transfect the cells in tissue culture. In multicellular animals, you would need to use the viral vector route as would need to be done with any gene therapy technique. Addgene is a nonprofit plasmid repository that has many of the CRISPR/Cas9 constructs that have been developed, and they have an excellent resource on their Website.

You wouldn't really want Cas9 active in the cell after it has done its job, as you increase your likelihood of off-target hits. The target shouldn't be in the genome anyway if the targeting event occurred, because you have either substituted in another piece of DNA or you have cut the DNA and the DNA repair mechanisms have introduced random nucleotides in order to repair the double stranded break.

Eukaryotic cells, for the most part, cannot maintain plasmids. The Cas9 gene will be transcribed along with the guide RNA. The resulting protein/RNA complex targets the sequence of interest and makes a cut. When the cell replicates the plasmid will likely be lost, but the daughter cells will inherit the genomic edit made by the targeting event.

If you are looking to insert a different gene at the target site, say a reporter into the genome, then you co-transfect a linear piece of DNA with homology arms around the cut site so that that donor will be inserted via homologous break repair.

One of the Cas9 constructs that has bene developed has disabled the nuclease activity, so that the Cas9/RNA complex ends up acting as a binding protein to suppress the activity you are looking to study without actually deleting or replacing the gene. In this case you may look to insert the Cas9 cassette, in which case you would use a recombination event as you would with any other type of incorporation into the genome.


How extensive was interbreeding among human species?

Interbreeding between H. sapiens and neandertalis was quite limited.

  Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability.

--Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans

  ... the interbreeding success rate between humans and Neanderthals was found to be below 2% (Fig. 2, Table 1, Fig. S1, and Table S1). Under demographic scenario A (Table 1), which is based on the most realistic demographic parameters, we estimate this interbreeding success to be even well below 1% (0.51%, mode of black curve in Fig. 2; 95% confidence interval: 0.33–0.89%). ...  If we assume that both species interacted for 10,000 y during the range expansion of modern humans (11), successful admixtures between Neanderthals and humans would have occurred, on average, only once every 23–50 y over the whole hybrid zone to produce introgression levels of 1–3%, which shows that they were extremely rare events.

--Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

Note that this technically doesn't touch on "interbreeding" but rather addresses successful interbreeding; sterile individuals won't be detected in this approach, and even sub-fertile individuals (whose lineages died out) will be underrepresented.

We have strong evidence that male progeny of sapiens/neandertalis crosses were either sterile or extremely sub-fertile:

  These results suggest that part of the reduction in Neandertal ancestry near genes is due to Neandertal alleles that reduced fertility in males when moved to a modern human genetic background.

--The landscape of Neandertal ancestry in present-day humans

And even apart from that, there's good evidence that hybrids were less "fit" (in evolutionary terms) than either parent:

  After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. ...  We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids.

--The Strength of Selection against Neanderthal Introgression

So it's very likely that the rate of interbreeding, per se, must have been higher than the roughly once-per-generation rate that can be inferred from genome analysis, but most of the hybrids were sterile, or poorly adapted.  Of course, this is exactly what you'd expect from interspecies hybridization; the number of successful sapiens/neandertal hybrids through the millennia of their interactions was probably lower than the number of fertile mules in the past few hundred years.


Under what circumstances and why is terrific broth preferred to LB broth for E.coli growth?

I have used terrific broth to grow up transformed E. coli so they grow faster.  Often people will conduct a transformation, screen the cells, and grow them up in broth for plasmid extraction.  This growth would be for 12-16 hours.  Instead a person could use terrific broth to grow up the cells and it would take may 6-8 hours for adequate cell density for plasmid extraction.  If you are trying to express a protein then I would go with LB.

Also, I learned recently that terrific broth is also preferred over LB when needing to express proteins after transformation.


What's the proper way to determine whether dose response curves +/- another variable (besides dose) are statistically different?

Good call on not using multiple t-tests. The reason being, assuming a 95% confidence interval, each time you run the test you are "allowing" a 5% possibility of making a Type I error - this means that you incorrectly reject the null hypothesis in favour of the alternative hypothesis. If you run one t-test, there's a five percent chance of making an error. If you run two t-tests, there's a ten percent chance of making an error.

Between a regression model, or ANOVA, it does not matter. As the mathematics behind each are pretty much equivalent.

What you really want to look for, is the slopes of both models. If the two models have a statistically significant difference between their slopes, then this is indicating an interaction effect.

Two examples of (some, but not all) possible interaction effects:

Carrier A & B have a similar effect on dose-response at 2mmol. But as the dosage approaches 10mmol, Carrier B causes a dose-response that is nearly double that of Carrier A.
Above 5mmol, Carrier B creates a greater dose-response. Below 5mmol Carrier A creates a greater dose response. At 5mmol the dose-response is nearly equivalent.


Common Errors For Low R Value in Bradford Assay

You could be measuring outside the dynamic range of the assay (you can only add so much / so little BSA to a certain amount of reagent).
You could be outside the linear range of your spectrophotometer, usually under 1 is fine, although some old/crappy ones might not even be reliable over 0.5.
If you're fast you're measuring your different concentrations also at different times. Bradford is a little bit time-dependent, so waiting the recommended time before measuring your standards is not a bad idea.

Probably it's still pipetting though, try pipetting at least 20 uL in every dilution step and see if you're still off.


I am pretty sure you cannot jump from an oak tree to an ape with whatever common definition of species you're using. But this is some kind of practical implication of your question.

The concept of species was already being used by Aristotle and was kept up to now although the grouping of living things into species might not be a clever thing to do. I don't think there is any non-arbitrary, logical way of making groups out of living organisms. Here is a podcast (It is in French, sorry!) that is interesting for those wanting to learn about how the concept of species evolved.

The case you describe is called Ring species. There has been lots of discussion in philosophy about the concept of species. The concept of species is unclear and if accurately defined, then in practice we don't really follow this definition to improve efficiency in how we name lineages. The term lineage has a much more rigorous meaning and is often of greater usefulness.

Ensatina eschscholtzii (a salamander; see DeVitt et al. 2011 and other articles from the same group) is a classic example of ring species.

You should definitely have a look at the post How could humans have interbred with Neanderthals if we're a different species? which discuss the concept of species. Some other sources of info include:

Species problem wikipedia
Reduction of species
The evolutionist view of the species concept: ESU
Stanford dictionary


What are the applications of predicting the structure of proteins?

Just off the top of my head, protein structure is very important for determining how proteins interact, for example determining molecular pathways or viral capsid structures. Knowing the structure of a protein can help scientists better understand what it does and how it does it. By looking at protein structures, scientists can determine exactly how a different allele for a gene causes changes in an organism's phenotype at a biochemical level. Predicting sites within a protein's structure that have an enzymatic function allows scientists to predict how various factors effect it's function. Differences in temperature or pH can have an effect on protein structure as well, and understanding how a proteins changes based on pH or temperature changes can help scientists determine how a protein functions in its specific environment.


What causes muscles to generate heat on contraction?

First, it might be helpful to talk briefly about what heat is. It is a form of energy - molecular energy. Basically, heat is the amount of jiggliness of the molecules of a substance or object. When we look at a hot object, it doesn't apear to be moving any more than a cold object, but on a scale much smaller than we can see, it's molecules are moving faster than in a colder object. Read this for more information if you want.

There are at least two things going on in muscle contraction (as well as in other metabolic processes) which produce heat. The first is the chemical reaction that powers muscle contraction. You probably don't want to get into great detail, but basically there is a molecule which your cells use to store power, which we abbreviate as ATP. When our muscles use that power, an exothermic chemical reaction occurs that "burns" ATP, breaking it into two pieces (ADP and phosphate). That reaction releases energy. Some of that energy is used in the actual movement of the muscle. But some of it just "jiggles" the nearby molecules. Again that jiggling is the very definition of heat.

The second source of heat is probably much smaller: friction. In short, just about any time anything moves, nearby molecules get jiggled some more. Imagine trying to walk through a room packed full of harps. Everywhere you move, some of those strings get plucked and vibrate. It's a little bit like that. When your muscle fibers tighten and flex, they rub past each other and jiggle each others atoms. All of that jiggliness is heat, and the jiggling continues until it can transfer to some other medium, as when, sweat evaporates from your skin.


Absent a very specific learning objective, if (B) is correct, this is a poor question. In a high-school or undergraduate introductory biology course, I would say:

  (A) The bacteria cell walls prevented their explosion

Would be the correct answer, because of exactly your reasoning. This is what you're taught in introductory biology. You're taught that animal cells don't have cell walls. Bacteria and plant cells do have cell walls.

See The Cell

  animal cells are not surrounded by cell walls

Under this concept of a cell wall, red blood cells certainly don't have them.

However, red cell osmotic fragility testing comes out of a tradition that uses the phrase cell wall strength to describe the response of a red cell to osmotic stress. See Orcutt

  It appeared logical to us that a model based on a distribution of cellular wall strengths ought to reproduce the experimentally observed variation of degree of hemolysis as a function of osmotic stress.

All the same, if you were operating from that perspective, how would you distinguish between (A) and (B)? Here, we're not even taking into account the fact the primary mechanism for responding to osmotic stress in most animal cells, including the human erythrocyte, is regulation of ion flow, not the pressure of a rigid extracellular matrix. If the solution contained ouabain, which certainly does lyse human RBCs, would it be best to characterize the problem as "The blood cell walls didn't prevent their explosion"?

I would ask your lecturer to clarify the learning objective behind the question. As an interpersonal note, I'd point out that this is very different from asking him or her to justify the correct answer. Some (many...) teachers are oddly sensitive to any suggestion that they need to justify their expertise, especially when it comes to exam questions. If you make it a question about the learning objective, this should help you avoid triggering that particular sensitivity.


Is there any disease in adult human, other-than cancer, which-is resulted from mutation?

Before answering your question, an important note. Not all neoplastic growth is malignant. A mutation may result in a benign growth, which is an outcome different from cancer. Not all of these change to cancers. Moreover, almost all genetic diseases may arise de novo as a germline mutation, and this mutation may be caused due to the environmental mutagen, and hence will be a non-neoplastic outcome of environmental mutation. The list of such genetic diseases is impossible to replicate here.

Assuming you are asking non-malignant diseases involving somatic (acquired) mutation as a pathogenetic event, here's a subset.

Some diseases with proven somatic mutation are:

Neurofibromatosis 1 & 2
McCune-Albright
Paroxysmal Nocturnal Hemoglobinuria
Incontinentia Pigmenti

For more details, have a look at this paper here.
Erickson RP. Somatic gene mutation and human disease other than cancer. Mutation Research/Reviews in Mutation Research. 2003 Mar 31;543(2):125-36.


How does one maintain balance sleepwalking?

Balance is mediated by 3 things: the cerebellum, vision and the ear via the semicircular canal + vestibular nerve (i.e. the ear).

Sleepwalkers lack the visual feedback, but they have a functional cerebellum and semicircular system which is sufficient.

As for waking up and feeling disorientated, if that's when you get up fast that's because your semicircular system hasn't yet reset (as well as your blood pressure has just dipped).


The intermediate radio-ulnar joint is fibrous in arms.

[Source: Slideshare.net]

You can see the the interosseus membrane between radius and ulna which is composed of white collagen fibres.

Furthermore, there is a cartilaginous joint between epiphysis and diaphysis of humerus which is made up of hyaline cartilage. But it is lost during development and is absent in adults.


Phylogenetic algorithms: How to interpret multiple ML trees from the same dataset?

In short, you have chosen two examples that do not use maximum likelihood as you know it in other contexts. In most statistical contexts, the ML is a single number which can be calculated analytically, so it it always the same for a given data set. This is not the case for either MrBayes or RAxML but for different reasons.

MrBayes

The likelihood criterion in MrBayes is the marginal likelihood of the posterior, given effectively the data conditioned on the priors. This likelihood comes from a stochastic MCMC sampling of the parameter space. If all is well behaved, then the chains and/or runs will converge in the same general location. But then the different possible topologies need to be summarized in some way.

RAxML

RAxML generates essentially random starting trees by random sequence additions to build up trees. The subtrees are then rearranged to find a "best" tree. Again, different starting points may lead to different best trees. But if all goes well, analyses will end up with the same tree. This process is described in this chapter.

In both cases, if you start in a different place, you may end up in a different place. There may be many trees that are, within some criterion, equally likely. If you are familiar with parsimony methods, the analogy is that of multiple equally parsimonious trees.


First, the curves are not really logarithmic.

Instead, according to the Stevens' power law, the curves are of the form:

Perceived = k (actual)a

where "a" could be greater, less than, or equal to 1.

When "a" is 1, the curve is linear.

Examples of a=1 (linear), are:

brightness of a "point source briefly flashed"
length perception
cold perception of skin
radiant heat perception

If "a" = 0.5, the curve is a square root curve.  Brightness perception follows the square root (or de Vries-Rose) curve in some intensity regions, and a nearly-linear response in other (Weber's law) regions.

Examples of "a" being positive are perception of electric shock and perception of heaviness of lifted weights.

So, since the perception curves can be linear (a=1), more sensitive than linear (a>1), or less sensitive than linear (a<1), there is no general logarithmic property of neutrons that is responsible for the curves.


Do hormone drugs affect whether a person feels sexual attraction to males or females?

There is no evidence that postnatal hormone exposure can change the sexual sexual preference of an individual. However atypical hormonal stimulation of the fetus can induce homosexuality.

Homosexuality does not develop without a variety of social factors which are up-to-date mostly unexplained. But can develop without hormonal stimulation.

As real life examples there are a androgen antagonists for the treatment of of prostate cancer, which reduce the testosterone level in males. Under treatment the men often turn softer and more emotional, as described by their wifes. And there is beer which contains oestrogens and can induce the growth of female breasts in men. But none of this mechanisms has been observed to turn males homosexual.

Further Reading (second text is free fulltext):

[1] http://www.ncbi.nlm.nih.gov/pubmed/23397798

[2] http://endo.endojournals.org/content/152/8/2937.long


The parameter for setting the number of mismatches in standalone blast

There is no direct option like that but you can set percentage identity filter with -perc_identity

However, this is only for reporting. BLAST will still perform all the alignments. That is why I suggested you to use bowtie.

EDIT-1 (getting long for comment)

If you want a word type of search then use the -n option. But it always starts from the 5'end which is quite justified in case of miRNA because the seed region is in the 5'.

Setting -n to 0 means no mismatch in seed region. -l option defines the seed length; I would advise that you use something like 10. -e refers to maximum mismatches in the non seed region but it is not the number of mismatches; it means maximum tolerated sum of phred score of mismatches (fasta files are assigned a default phred score of 40 at all residues. So, for 2 mismatches you have to mention -e 80).

EDIT-2

Yes. Increasing mismatch and gap penalties would make the search more stringent if you have already specified a cutoff on score.


"Are these modifications the primary regulation mechanism for chromatin structure?"

It depends on how you define primary, we might currently think of histone modifications as primary because other regulatory mechanisms have not yet been well studied. Something else you can think of are the various regulatory proteins that interact with histone marks to modify chromatin.

I don't think you should imagine chromatin as assuming "the most compact structure possible until histone modifications are made to enable transcription" but rather histone modifications being a dynamic process with various transcription factors (a class of proteins) coming in and adding/removing histone marks as well as 'remodeling chromatin' (adding/removing nucleosomes)

As a sidenote, I don't believe much is known about the tertiary stage you initially mentioned so maybe that could play a huge role in the regulatory mechanisms of chromatin structure, it has just not been well explored.


Which range are the Therapeutic Indices of Currently-Prescribed Benzodiazepines in?

Wikipedia quoted this article as a reference for its statement about alprazolam having a therapeutic index of 100:1, although I can't confirm that, since I can only read what's immediately available in that link. There's a figure saying less than 100:1 for diazepam though.


Is there a normal human melatonin concentration to light level curve?

Found a few samples here: http://ars.els-cdn.com/content/image/1-s2.0-S0024320503008142-gr2.gif this shows the nocturnal melatonin peak, which is apparently very important for well being


I think 30 cycle PCR is maximum to see bands by electrophoresis in most of cases, because under the ideal efficiency, one copy could be detectable by 34 cycles of PCR. However, if your expected products are longer than 1 kbp, you might extend several cycles.

I usually add DMSO 5% in any PCR reaction. In my experience, DMSO would not interfere PCR reaction--you can amplify your fragments without DMSO; you could get PCR products with DMSO. Betaine sometimes work better than DMSO, so I am shifting my default reaction mix from 5%DMSO to 5%DMSO and 0.5M betaine.

For annealing temp, you can not tell which is better, lower or higher than the first trial which showed nothing. When increasing the annealing temp, primers may be able to access your target sequence more and you could get efficient amplification. So you might want to try both. If you have a PCR machine set various temperatures at once by gradient. You could include lower and higher temp together.

Alternatively, I sometimes use the touch-down method. You do not need to determine the best annealing temp in this case. If you just want amplified products, this could be a quick solution.

Additionally, hot start is also my default condition, because this could not ruin PCR reaction without hot start.

Basically, I change annealing temp. If I do not get good amplification and specificity, I change PCR enzymes. Changing PCR enzymes could mean changing buffer conditions because companies try to give unique features for their products.


Why are these nesting magpies building another nest

I found an article that explains secondary nests as backups in case of nest usurpation by other birds:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858914/
This is for black sparrowhawks losing nests to Egyptian geese around Cape Town. They measured number of nests built per breeding pair of sparrowhawks and found it to correlate with number of Egyptian geese present and especially their nest usurpation behaviour.

That article mentions brood parasitism (e.g. cuckoos) as another possibility for other birds, and I've seen references to duplicate nests with eggs in each. ( https://www.tandfonline.com/doi/pdf/10.1071/MU939286a )


Yes, your hypothesis is correct. There are more of them.

A few terms need clarifying here, just in case...

First, fluorescence is due to the property of a dye that can be conjugated to the antibody. Different fluorophores have different properties, some are more efficient than others. Some display strong "solvatochromism", i.e. they are happier in the hydrophobic environment (brighter and red shifted).

Second, DNA is stained not with an antibody but with the UV fluorophore DAPI, which shines brighter in DNA —same thing with ethidium bromide and Sybr Safe.

Now, if you are labelling a TF and they ought to be in the nucleus you definitely will have a brighter signal as you suggest. There will be a way-ever-so slight difference as the environment is less aqueous, but the nucleus is not that packed as on pictures.


Why are proteins in the insoluble form when they are in frozen water?

If proteins change from being water soluble to water insoluble it means that their three-dimensional structure changed, because this determines how the protein interacts with the water. Most proteins have hydrophilic residues on the outside in their normal structure configuration, which makes the soluble. If this changes and some of the hydrophobic residues come to the protein surface the protein may not be soluble anymore.

The process of the structure changing (sometimes also called 'denaturing') can be caused by a lot of different factors - basically everything that is different from the inside of a cell (for humans: ~37°, salt concentrations, ...). If water freezes then the ice-crystal lattice can force the proteins out of their normal conformation/structure, after thawing the ice they may not get their structure back on their own (this depends on the protein).

To give an answer to your edit: the temperature does not affect the solubility directly, the effect is indirect through a change in structure


Wasps are extremely territorial creatures. They also have great sight. Wasp colonies will send out foragers and scouts to look for uninhabited areas with food in which they can build a nest. Because wasps are so fiercely territorial, a scout wasp will generally stay away from an area with another colony already in it.

Because of this fact fake wasps nest works!!

Source: http://www.environmentalsociety.ca/main/wp-content/uploads/2011/05/Fact-Sheet-Wasps.pdf


There seems to consensus that it is not competition for tall food.  Giraffes actually often feed on resources that are lower than their maximum possible height.    See:

Simmons, R. E. & Scheepers, L. 1996. Winning by a Neck: Sexual Selection in the Evolution of Giraffe. The American Naturalist 148: 771–786

This paper put forth the idea that sexual selection is the reason behind long necks.  The idea is that longer necked males are dominant.  But this  theory has also been questioned.  See:

G. Mitchell, S. J. Van Sittert, J. D. Skinner. 2009.Sexual selection is not the origin of long necks in giraffes. Journal of Zoology 278, Issue 4: 281–286

So in the end there's no clear consensus.  Some papers have returned to the theory of competition for research in the past few years.To put it simply, no there is no consensus.


Here is a good article on the topic.

https://www.nlm.nih.gov/medlineplus/ency/article/003227.htm

But it's most likely due to the fact that a sun burn is an actual burn on the skin that can cause inflammation, inflammation can in turn cause fever. Also having a really bad sunburn can open you up more to the possibilities of skin infections. If this happens then once again you might get a fever due to infection. If you really want to find out more on the cause of fever after sunburn you need to examine the pathophysiology of fever and why fever happens. I bet my money on fever due to skin inflammation after a sunburn, I guess the real question would be why does inflammation cause fever since sunburn = skin inflammation

Here is a good article

http://antranik.org/inflammation-and-the-pathophysiology-of-fever/


Does myopia tend to decrease the risk for later hyperopia?

It is generally understood that we tend to become hyperopic as we age (reference). As to whether this aids in decreasing myopia is stated as marginal in papers. One paper titled "Is there a hyperopic shift in myopic eyes during the presbyopic years?" states that

  it was found that almost all hyperopic and emmetropic eyes showed an
  age-related hyperopic shift; but only a small proportion of myopic
  eyes shifted toward hyperopia, with others remaining relatively stable
  and still others increasing in myopia.

In a second study titled "Age-Related Decreases in the Prevalence of Myopia: Longitudinal Change or Cohort Effect?", it was found that there is a decline in the prevalence of myopia in older adults.

Some people in personal experiences have stated that their myopia has decreased (reference) while others found themselves wearing bifocals (reference). In closing, I would say that this is something that your Ophthalmologist may be able to predict better but it is not a given that your myopia would decrease. It may or may not be so with many factors like your eye shape coming into play.


How many ion channels on average must there be in one µm2 of neuronal membranes?

I expect your homework was already due, so...

You're supposed to remember what a membrane time constant is. I'll quote from page 12 of my (by now quite old) copy of "Ion channels of excitable membranes", by Hille:

  For biological membranes the product, RmCm, of membrane resistance and capacitance is often called the membrane time constant, taum.

Since you know tau and C, your goal is then to determine the membrane resistance. You also need to convert the capacitance to square microns (1e-14F per square micron). In this case: 1ms/1e-14F = 1e11Ohms, or 1e-11S, or 10pS. So on average there are 10 channels per square micron, assuming I didn't make any silly mistakes.


So in mitosis, the cell has to split itself into two cells; each daughter cell has a functional genome that may again split into more daughter cells. The cell replicates the DNA before dividing, so the error in replicating 3x or 4x is that upon division, the daughter cells will have more DNA than the initial cell, and every generation will have more DNA than the last. One replication ensures both daughter cells receive one functional genome. We can see the result of extra DNA in cases like Down Syndrome (trisomy of chromosome 21).
The cell controls this process by controlling the cyclins present in the cell temporally, namely cyclin-A and cyclin-E when we talk about DNA replication in S-phase,

From wikipedia,

Cyclin A resides in the nucleus during S phase where it is involved in the initiation and completion of DNA replication. As the cell passes from G1 into S phase, cyclin A associates with CDK2, replacing cyclin E. Cyclin E is responsible for initiating the assembly of the pre-replication complex. This complex makes chromatin capable of replication. When the amount of cyclin A/CDK2 complex reaches a threshold level, it terminates the assembly of the pre-replication complex made by cyclin E/CDK2. As the amount of Cyclin A/CDK2 complex increases, the complex initiates DNA replication.
Cyclin A has a second function in S phase, in addition to initiating DNA synthesis, Cyclin A ensures that DNA is replicated once per cell cycle by preventing the assembly of additional replication complexes. This is thought to occur through the phosphorylation of particular DNA replication machinery components, such as CDC6, by the cyclin A/CDK2 complex. Since the action of cyclin A/CDK2 inhibits that of cyclin E/CDK2, the sequential activation of cyclin E followed by the activation of cyclin A is important and tightly regulated in S phase.

Source: Cyclin A


Is lemon water an alkalizing agent in the body?

The blood pH is tightly controlled since variations are quite dangerous for us. Under normal circumstances the pH is 7.4 (with a normal range between 7.35 and 7.45). Below that we are talking about acidosis, above it about alkalosis. If the blood pH goes about 7.8 or below 6.8, death will occur. This pH is maintained by the Bicarbonate-buffering system, for details see here and here.
Food that we take up does not directly influence the blood pH (and there is also no reason for us to do so, since this is tightly controlled and regulated), so this is a health fad. Details that debunk this myth about it can be found here, here and here.


Why do we still have genetic disorders that show anticipation?

I can think of 3 explanations (not mutually exclusive) for the maintenance of important genetic disorders that prevent the sick carrier to reproduce.

Following what you said, the frequency of a given allele in a population is influenced by selection, drift, migration and mutation. Some disease present at low frequency can typically spontaneously de novo appear in a population. This is typically the case of cancer and trisomy 21 where new mutations (mutation in the broad sense) likely explain a big part of why such disease do not disappear through time.
Many genetic disease are carried out by recessive alleles. In consequence, only homozygotes for the recessive allele express the disease and the disease can persist through drift. Note the interesting case of hemophilia and Malaria resistant where the heterozygote actually has higher fitness than any homozygote (heterozygote advantage), particularly in regions where there is a high prevalence of malaria. In this case, the disease is not washed out of the population not only due to drift but also due positive selection on the heterozygotes.
Many so-called genetic disease actually have an important environmental component. For the Huntington's disease, the carrier of the autosomal dominant mutation does not necessarily express the disease. From wikipedia:

  The disease is caused by an autosomal dominant mutation in either of an individual's two copies of a gene called Huntingtin, which means any child of an affected person typically has a 50% chance of inheriting the disease.

As a result the Huntington's disease can still segregate thanks to drift in the healthy heterozygotes.


Cheap enzyme assay for a high school lab

There is the classic potato starch/iodine/amylase experiment:
http://dailynexus.com/2016-08-31/chemistry-101-the-classic-potato-iodine-blueblack-experiment-finally-has-an-explanation/

From memory, when you add iodine to a small piece of potato, the potato starch reacts to produce a dark blue/black colour.  The amylase enzyme in human saliva can break down the starch and remove the colour, which is effected by spitting into the test tube.

You might need to try titrations to work out how to do number 3.


Identifying whether amino acids are hydrophobic or hydrophillic

Does the side chain contain any Nitrogen (N), Oxygen (O), or Sulfur (S) atoms?  If it does, then chances are high that this particular R-group is polar (although it may not be charged).

The converse is also true, if the R-group lacks any of those three atoms then chances are high that the side chain is polar.  There are exceptions; Methionine has a Sulfur, but is quite hydrophobic (non-polar).  Tryptophan has a nitrogen but is non-polar.