Glucose 6-phosphate dehydrogenase: reaction mechanism

Disclaimer

I am not an enzymologist and this answer is based on work published in 1998, and the latest paper I consulted was 2000. Hence I cannot exclude the possibility that more recent work has modified the model shown here.

General Approaches

The general approach to elucidating the mechanism of action of enzymes has been as follows.

Historically, and before a structure is (or was) available:

Hypotheses of possible types of mechanisms would be made on the basis of the known mechanisms of non-enzymic chemical reactions.
Experiments with inhibitors might suggest what class of residues of the enzyme might participate in the reaction.
Experiments would be performed to get indirect evidence for the residues involved, e.g. by examining the effect of pH in relation to the pKa.

More recently, with structure determination less difficult and more common:

The structure would be determined and an attempt to identify the active site made on the basis of the position of a bound pseudo-substrate or inhibitor.
Residues near the substrate that might participate in the reaction would, thus, be identified.
A hypothesis of the role of these residues would be made in relation to the known chemistry (as in historical 2, above).
Experiments would be performed to test the participation of the residues — often by modifying them — and their proposed role.

Proposed Mechanism for Glucose 6-phosphate dehydrogenase

The structure of glucose 6-phosphate dehydrogenase (G6PD) was published in 1994 by Rowland et al. in Structure 2:1073-1087. To test their hypothesis of the mechanism, Cosgrove and coworkers constructed performed site-directed mutagenesis on G6PD and determined the structure of the mutated protein. On the basis of this they published a paper in Biochemistry 1998 37:2759–67 in which they proposed the reaction mechanism shown below.

The Nδ1 atom of His-240 is hydrogen bonded to the Oδ1 atom of Asp-177, forming a catalytic dyad. The Nε2 of His-240 is poised to act as a general base by abstracting a proton from the C1-OH of G6P, allowing transfer of the C1-hydride to the C4 position of the nicotinamide ring of NAD(P)+.

They summarize this as follows:

  “The results support a mechanism in which His-240 acts as the general
  base that abstracts the proton from the C1-hydroxyl group of glucose
  6-phosphate, and the carboxylate group of Asp-177 stabilizes the
  positive charge that forms on His-240 in the transition state. The
  results also confirm the postulated role of His-178 in binding the
  phosphate moiety of glucose 6-phosphate.”

Suggested reading and search approach

The classic text on enzyme mechanism is Alan Fersht’s Enzyme Structure and Mechanism published in 1984. This is clearly based on a limited range of enzymes, so its importance is not in finding the mechanism for a particular enzyme, but for understanding the principles involved. (You can pick up a second-hand copy very cheaply). Fersht has a more recent (2017) book in the same area — Structure and Mechanism in Protein Science but this is much more expensive. You can view the contents on Amazon.

Other suggestions are welcomed as comments.

My approach to searching for an answer here is worth mentioning as the question indicates the poster failed in his attempt. First I just did a Google search “reaction mechanism, glucose 6-phosphate dehydrogenase”. This wasn’t very useful, but alerted me to the fact that Google was prioritizing pages related to G6PD deficiency, a clinical condition on which much had been written. To avoid this I decided to focus specifically on structure, assuming that some of the papers would be proposing mechanisms. I tried three of the following four approaches (while idly waiting for a computer program to run).

Google search on “glucose 6-phosphate dehydrogenase, structure”. This did not appear to give me a direct hit, but brought up the three other sources I went on to try.
The Wikipedia entry on glucose 6-phosphate dehydrogenase. Half way down the page is a section on structure with a diagram of the substrate binding site, so I knew I was on track. The references on this page were not very useful, but the diagram indicated the structure was PDB 2BHL.
The Google search also brought up a Protopedia page, which I actually looked for directly. At first I was disappointed by the lack of information other than the structure, but the third of three references was a Cosgrove paper from 2000 which contained the words “catalytic diad” in its title. I went for that, and it led me back to their 1998 paper.
I could have tried the Protein Data Bank and searched for 2BHL (or just for the enzyme). 2BHL would have led me to a later paper in Acta Crystallographica, which does mention the 2000 Cosgrove paper in its introduction.


Based on the long legs and long antennae, I'd say you're correct that it's an orthopteran, very likely a cricket or one of its allies (i.e., suborder Ensifera).
Within this subgenus, the most likely candidate families are either the "true crickets" (Gryllidae) or "camel crickets" (Rhaphidophoridae).
Your photo is not nearly good enough to begin making more informed specific guesses. However, If I had to guess, it could possibly be a cricket in the genus Phaeophilacris, which are striped-leg crickets found in Africa.

See inaturalist for incidence of this genus in Africa.

You can see some photos of Phaeophilacris Bredoides here, with a few photos copied below:

 Source
You can read an interesting paper about communication in this genus here1

 1. Heinzel, H.G. and Dambach, M., 1987. Travelling air vortex rings as potential communication signals in a cricket. Journal of Comparative Physiology A, 160(1), pp.79-88.


Making antibodies is mostly nothing you do with transgenic microorganisms. To make an antibody you first have to immunize an animal with the correct antigen. This includes have an animal facility where you can keep animals under clean conditions. If you are looking for polyclonal antibodies (meaning a whole bunch of different antibodies with different specificities) you will boost the animal before sacrificing them and isolating their blood to purify the antibodies.
If you are aiming for monoclonal antibodies then the animals will be boosted as well, then sacrificed and their spleens isolated. From the spleens you make single cell solutions from which antibody producing cells are isolated and plated one cell per well of 96 or 384 well plates and cultivate them to identify cells which produce antibodies. These cells are fused with immortal cells to produce immortal hybridoma cell lines which secrete a lot of antibodies into the cell media. These antibodies still need to be characterized to make sure the really bind the antigen of choice and not something else (in the spleen a lot a these reactions take place).
Just for estimations: Making one batch of a custom polyclonal antibody in rabbit with a given peptide sequence will cost you at least 5000\$ to 10.000\$ the last time we checked for it. Monoclonals are more expensive. So making an antibody is quite an investment on the first hand.


Can a non-disjunction event occur in meiosis II (in the paternal gametes) to result in an XXY male?

The reason maternal non-disjunction during meiosis II can produce XXY offspring.

In this case, meiosis I occurs as normal so that after the first division the replicated homologous chromosomes, each consisting of two chromatids connected at a centromere, have separated. If a non-disjunction occurs at this point, haploid cells will not be formed. Instead, the sister chromatids of a replicated chromosome will not be separated and a gamete containing two X chromosomes will be formed. When this gamete combines with a sperm containing a Y chromosome, the offspring has the XXY genotype.

The reason paternal non-disjunction during meisosis II cannot produce XXY offspring.

This is similar to the maternal case except that after meiosis I, in one cell will be two YY chromosomes while the other cell will be two XX chromosomes. When non-disjunction occurs (assuming it occurs in both divisions), these chromosome arrangements remain the same and two cells are formed. One with two XX chromosomes and one with two YY chromosomes. If either of these gametes combines with a female X gamete, either XYY or XXX will be formed but never XXY.


Essentially, yes, "proteins that we consume form new proteins that are different".

The processes are each of them topics for themselves. In short, consumed proteins are digested by peptidases (enzymes) in the stomach, breaking them down into their consituent amino acids. These are absorbed in the gut and transported in the blood to all cells. These take up amino acids and attach them to tRNA molecules which are used in translation to form new body proteins.


How is a specific fragment isolated for PCR amplification?

There are a number of primer testing tools that will compare primer sequences against the genome to ensure specificity, or help you design specific primers to amplify a specific region. One place to start is NCBI Primer BLAST; the linked page explains how to use it to generate primers to amplify a specific gene.

Doing PCR on genomic DNA can be a bit tricky, though, since you have to deal with a lot of confounding factors like DNA accessibility, contamination, and PCR inhibitors that get through your purification procedure. In addition, genes often contain huge introns, so you're going to end up doing PCR on an extremely long template (which is very hard or even impossible, depending on the size of the gene) and you'll end up with the whole gene sequence with introns which is not what you need in order to express it as a transgene.

Instead, I'd recommend purchasing a cDNA clone of your gene of interest and amplifying it from that. cDNA is made from the spliced mRNA sequence, so it will be a much more managable length and will prevent problems with alternate splicing.

If you go to the NCBI page for a gene, on the right sidebar under "Related Information" you'll see a link to Order cDNA clone. This will give you a few options to purchase a purified plasmid containing that gene for around \$60 - \$90. It will be much easier to work with this plasmid than genomic DNA and it will definitely save you time and money, especially if you're still inexperienced at molecular cloning.

Of course, it's not 2003 anymore and there's a good argument to be made that the whole idea of doing molecular cloning yourself is a waste of time and money. If your budget allows it, the easiest and fastest way is to pay a company to synthesize your gene for you. Genewiz, for example, offers snythesis for $0.28/bp, but you can probably get a better deal if you shop around.

The advantage of synthesis is that you can get the exact sequence you want cloned into exactly the right vector done perfectly the first time. If you don't have experience with it, trying to clone a gene yourself will take longer and cost more money than you think. It's better to just get it synthesized so you can move onto your real experiment.


How to identify active protein in a complex mixture?

This is a classical protein purification problem - you have to find ways to fractionate your mixture so that each fraction can be assayed for the activity you are interested in. When you find the active fraction you then subject that to a different type of fractionation.

Salting out

The solubility of proteins is affected by the ionic strength of the buffer. If the ionic strength is raised above a critical value (which is a characteristic of an individual protein) the protein  will precpitate, usually without being denatured. By doing a series of such precipitations at increasing ionic strengths a protein mixture can be fractionated according to this property. The salt used is ammonium sulphate, because of its very high solubility. You can find more details at this Wikipedia page (ammonium sulphate precipitation).

Ion exchange chromatography

Proteins have different intrinsic charges, and the net charge on a protein will vary with pH. This property is exploited in ion-exchange chromatography. In this technique the protein mixture interacts with a solid matrix carrying fixed charges. Under the correct conditions your protein plus others will bind to the matrix, while lots of other proteins won't. That's already a purification step, but you can then treat the matrix with buffers of increasing ionic strength. Weakly-bound proteins will be eluted from the matrix first, and as the ionic strength of the elution buffer increases proteins will elute in order of strength of interaction. By performing this procedure with the matrix in the form of a chromatography column and collecting eluate fractions you can achieve another step in the purification of your protein.

Size exclusion chromatography (gel filtration)

This technique is used to fractionate a mixture of molecules according to size. In this case the solid matrix that is used is charaterised by pores of a specific size. Proteins that are too large to enter the pores will pass through quickly;  small proteins will spend a lot of time moving in and out of the pores and so will pass through slowly; and proteins of intermediate size will spend some time in the pores. Essentially the average time spent passing through the matrix will depend upon size. Read more here.

These are just three of the possible fractionation procedures - others, including  hydrophobic interaction chromatography are described here). The key point to grasp is that using any one of these techniques will give you your protein in a fraction which also contains other proteins, but if you apply them sequentially you will progressively remove contaminants because each approach is based on a different physical property of proteins, and your target will have a unique combination of these properties.

At each step you will be assaying fractions to locate the protein of interest, and also running fractions on  SDS-PAGE to get a feeling for the number of proteins left. If you have an assay that lends itself to measuring some kind of unit of activity (as you would with an enzyme), then by also measuring the protein content of the active fraction you can express the purity as a specific activity (units of activity per mg protein). At each step in your purification this specific activity should increase because you recover most of the activity, but discard a lot of the proteins that were present in the previous material. The increase in specific activity can be used to assign
a purification factor to each step. A useful purification step will give a reasonable yield in combination with sigificant purification.

Finally, what order to do these steps in? I've listed them in a logical order - salt precipitation is a low-tech method that can give a quick first step and which has the advantage that it concentrates the target protein (since the precipitate is redissolved in fresh buffer). Size-exclusion chromatography doesn't deal well with large amounts of protein so is best left until later. However, protein purification is a craft, and an expert will use the available techniques according to the exact nature of the project.

UPDATE

From the tone of your original question I had inferred that you were a beginner, but from your comments, apparently not, since you are thinking in terms of mass spec as an endpoint.  A starting concentration of pg/mL is quite a challenge, and clearly you are never going to have enough material to see your molecule on standard gels.

Here are a couple of thoughts on aspects of your problem.

It seems that  in trying to purify minor components of serum a good starting point is to deplete the serum of its major proteins. This is a link to an imunodepletion product, and here is a related product from Biorad (no connection with either company and no recommendation implied).

I also found these papers which may be of interest. (Incidentally I think you'll find that each of the techniques I described is still used, perhaps just with modern instrumentation.)

Li,J et al. (2012) Purification, identification and profiling of serum amyloid A proteins  from sera of advanced-stage cancer patients. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES 889: 3-9

Fertin, M et al. (2011) Strategy for purification and mass spectrometry identification of SELDI peaks corresponding to low-abundance plasma and serum proteins. JOURNAL OF PROTEOMICS 74: 420-430

Finally, a quick look at the Wikipedia page on plasma reveals that brain natriuretic peptide seems to be present at the levels that you are considering  perhaps you should look for papers describing its purification.

Other than that I think you have to hope that a proteomics expert will come by and give you an expert answer.


What is contiguous premise culling and dangerous contact culling?

Dangerous Contacts were defined as premises where animals have been in direct contact with infected animals or have, in any way, become exposed to infection
Contigous Premises are defined as a category of dangerous contacts where animals may have been exposed to infection on neighbouring infected premises

Tildesley, Michael J., et al. "The role of pre-emptive culling in the control of foot-and-mouth disease." Proceedings of the Royal Society B: Biological Sciences (2009): rspb20090427.


This is very likely some species of Viburnum.

Viburnum is a genus of about 150–175 species of shrubs in the Adoxaceae family that are primarilly native throughout the temperate Northern Hemisphere.

All species of viburnum (as far as I know) have opposite leaves, as does the specimen in the picture.

Many species of Viburnums bloom in white in the last part of April through early May, and typically you have to pay attention to flower shape and often, more importantly, the leaf shape to differentiate species.

Without location information, an exact species ID is not guaranteed, but your specimen looks very similar to:

Doublefile Viburnum (Viburnum plicatum)

 Source: Dave's Garden

 Source: Missouri Botanical Garden

This species produces two rows of white flower clusters, with both small and large flowers, along the stem.

According to Wikipedia: Viburnum plicatum is a popular ornamental plant, both in its native area and in various temperate regions.

Based on the "double" flower types of your specimen, it's likely V. plicatum f. tomentosum:

  Cultivars with wild-type flowerhead structure are sometimes described as a separate botanical form V. plicatum f. tomentosum. They include 'Cascade', 'Lanarth' and 'Rowallane'.2[3] Two cultivars in this group, 'Mariesii'[5] and 'Pink Beauty',[6] have gained the Royal Horticultural Society's Award of Garden Merit.

Habit: A deciduous, multi-stemmed medium-sized shrub that typically reaches 2.5 3 m tall. [Source].

Leaf: ovate, 5-10 cm long, up to 5 cm wide; pointed apex and rounded leaf base; serrated leaf margin; 8 to 12 pairs of veins; pubescent underside; dark green leaf color. [Source].

Flowers: individual flowers form a large (up to 10 cm diameter) flat-topped cyme composed of showy infertile flowers surrounding unshowy fertile flowers. Blooms in May. [Source].


Forward or Reverse Strand: Is there a difference when encoding genetic devices?

First, I think you have misunderstood the concept of sense/antisense. These are defined individually for each gene, with the sense strand always referring to the coding (non-template) strand of a gene, and the antisense strand to its complement, the non-coding (template) strand. So in your plasmid example above, all genes are encoded by their respective sense strand, but which of the two strands that is sense for a given gene depends on its orientation. There is therefore no biologically meaningful sense/antisense concept for entire genomes, chromosomes or plasmids. Read more in the Wikipedia article on sense, and the answers to this SE Biology question.
Having said that, it should be clear that the expression cassettes pictured in figues A) and B) are completely identical. If you ignore the context around them (e.g. readthrough), their direction is irrelevant.

It also seems that genes are sometimes encoded on the reverse strand for no apparent reason, especially in plasmid backbones

Many commonly used plasmid backbones derive from vectors that date many decades back, to a time when cloning strategies were far from as flexible as today. Researchers were generally limited by the restriction sites occurring naturally in the DNA sequences. A gene's position and orientation with respect to its neighbouring genes might therefore be the simple result of lack of other cloning options - although I honestly doubt "wrong" orientation would even have been considered an issue. For an example you could read about plasmid pBR322 in this Wikipedia article, and references therein.


Is there any research paper which identifies left and right brained behavior?

In general I'd say "left and right brained behaviour" is total nonsense. I guess the origin of this kind of claim is a bad press release or something.

Let's start with something simple. Say hearing. When you hear a sound to your left ear, it is projected strongly to the contra-lateral side (right hemisphere), and weakly to the ipsi-lateral (left hemisphere) of your brain. So the brain response to a sound presented to the left ear is lateralized. Typically, this means that the other hemisphere is "more" responsible for processing the input. Similar thing happens for the other senses too.

So what is interesting about lateralized brain responses? Well, it would be very interesting to know for example are memories lateralized. It would tell something about the system: is it a kind of distributed system, where parts of a memory are scattered here and there, according to some logic, or is a single memory stored on a small area (and maybe only on the other side of the brain), etc. The distributed hypothesis seems more plausible according to recent research.

Let's talk about handedness next. Are you right handed? Or left handed? Or ... something between? Actually, even something like handedness is not a binary thing. It is more like a value on a range from 0 ("very left handed") to 100 ("very right handed"). This is taken into account in decent research, where ~1 hr per participant is used to assess that value (if it is relevant to the study).

So we have now talked about lateralization. How about the "left and right brained behaviour" then? In the URL you have provided it is implied that certain behavioural attributes are somehow related to lateralization. Lateralization of what? All the attributes, e.g. "being rational" depend on so many things: seeing, hearing, thinking, retrieving memories, ... that saying such a thing is not plausible.

Anyway, many brain processes are lateralized. That is the word to look up for for more information. But a thing like "behaviour" is too complex to be put to one hemisphere.

Reference: Accumulated wisdom from being a research assistant in a neuroscience project. (so you should trust pubmed.org more than me).


Is the motor cortex identical to the sensorimotor cortex?

The primary somatosensory and primary motor cortices are distinct cortical areas. According to the structural classification of Brodmann, the primary somatosensory cortex is referred to as Brodmann's areas 1,2 and 3 (BA1, BA2 and BA3). The primary motor cortex is referred to as Brodmann's area 4 (BA4). The primary sensory cortex is sometimes denoted by S1, and primary motor cortex by M1.

Source: My Brain Notes

The primary somatosensory cortex is concerned with the processing of somatosensory input, such as tactile stimuli coming from the skin. The motor cortex is concerned with executing movements and hence with motor output. As such, there is a functional as well as structural distinction between the two areas.

Within the primary somatosensory cortex, basic processing of somatosensory information takes place in BA3, while more advanced processing takes place in BA1 and 2. Neurons in the somatosensory cortex project to adjacent regions, including the motor cortex (Kendal et al., 2000).

Because the primary sensory and motor cortices are four strips of cortex closely situated together, and because they are functionally coupled at the physiological level, they are sometimes collectively referred to as the sensorimotor cortex.

Reference
Kendal et al. 2000. Principles of Neural Science


How does an electrical impulse spread in a muscle fiber spread from the motor end plate?

Skeletal muscle cells are excitable, like neurons. Enough summation of end-plate potentials causes the cell to reach threshold and fire an action potential (which then spreads throughout the cell membrane through positive feedback, just like a neuronal action potential).

There are some differences between skeletal muscle and typical neurons, like greater importance of chloride in setting resting potential in muscles, but otherwise their action potentials are driven by voltage-gated sodium channels, just like typical neurons.

You quote:

  the amplitude of EPP declines progressively with increasing distance from the end plate region.

which is true as long as the threshold potential isn't reached, and would also be true for subthreshold receptor potentials or post-synaptic potentials in neurons.

In the reference you link to, I assume you are referring to the mention of curare. Curare blocks the nicotinic acetylcholine receptor, so it is interfering with the end-plate potentials themselves, rather than the intrinsic excitability of the muscle.

See:

Philip M Hopkins, Skeletal muscle physiology, Continuing Education in Anaesthesia Critical Care & Pain, Volume 6, Issue 1, February 2006, Pages 1–6, https://doi.org/10.1093/bjaceaccp/mki062


What is the relationship between the light and dark reactions of photosynthesis?

ATP is a bad medium for storing energy as detailed here.

  ATP has a molecular weight of 507 Da
  Glucose has a molecular weight
  of 180 Da, and contains the same amount of energy as 31 ATP molecules


What's the physical meaning of Svedberg unit?

Wikipedia:

  The sedimentation coefficient is the ratio of the speed of a substance in a centrifuge to its acceleration in comparable units. A substance with a sedimentation coefficient of 26S (26×10−13 s) will travel at 26 micrometers per second (26×10−6 m/s) under the influence of an acceleration of a million gravities (107 m/s2). Centrifugal acceleration is given as rω2; where r is the radial distance from the rotation axis and ω is the angular velocity in radians per second.

In other words, at 1x g a 1S particle will travel at 10-13 m s-1 = 0.1 pm s-1

Particles with higher values of S will travel proportionately faster, and increasing g force will also increase sedimentation rate.

Let's look at the example of a 50S ribosome at 100 000 g:

rate of sedimentation = 10-13 x 105 x 50 m per sec = 50 x 10-8 m s-1

So how long to travel 10 cm = 10-2 m?

=10-2/(50 x 1010-8) s

= approximately 5.5 h, which seems about right.


Can ovulation and menstruation occur simultaneously?

Ovulation and menstruation don’t happen in normally cycling women at the same time. A basic outline of the hormonal cycle that triggers these events will make this clear.

Proliferative (a.k.a follicular*) phase
Beginning after menses (when the endometrium is thinned), the hypothalamus produces GnRH which stimulates the anterior pituitary to produce LH and FSH. These in turn stimulate ovarian follicles to develop. A dominant follicle produces estradiol which causes the endometrium to thicken (proliferate).

At a certain level of estrogen (actually estrogen/progesterone ratio), the feedback on the hypothalamus flips from a negative to a positive feedback loop. Thus, there is a GnRH followed by a LH surge. The latter triggers ovulation. Note that at this time the endometrium is stable due to relatively high estrogen levels.

Secretory (a.k.a. luteal*) phase
After ovulation, the high levels of LH trigger formation of a corpus luteum from the tissues left behind after ovulation. The corpus luteum makes progesterone. This hormone triggers a change in the endometrium from a proliferative to a secretory state. Progesterone also provides negative feedback to the hypothalamus and anterior pituitary, maintaining low levels of GnRH, LH, and FSH, so no new dominant follicles develop at this time.

If pregnancy does not occur, the corpus luteum will eventually (10-12 days) degenerate and stop producing progesterone. It is this abrupt drop in progesterone that triggers the sloughing of the endometrial lining. You can see these hormone shifts in an illustration like this:

The decline of the corpus luteum is correlated with a decline in serum levels of ovarian hormones including progesterone, estradiol, and inhibin A. Release from negative feedback provided by these hormones at the level of the hypothalamus and pituitary permits FSH to rise, and the cycle begins again.

You should now be able to see that:

Around the time of ovulation, the uterine lining is not fully developed and is stable due to the hormonal milieu. Menstruation does not occur.
Around the time of menstruation, FSH and LH are suppressed in a way that is not conducive to ovulation.

In theory, yes, of course there would be a lower chance of initiating a viable pregnancy (implantation rather than conception is the most obvious problem) were the endometrial lining to be unstable at the time of ovulation. The problem of luteal phase deficiency is along these lines. In this condition, the corpus luteum does not produce adequate progesterone during the luteal phase to develop the endometrial lining in such a way as to support a healthy pregnancy. However, ovulation and menstruation are still time-separated events for the reasons outlined above.

*Note that the first term is with respect to the endometrium; the second is with respect to the ovary.

Abbreviations:

GnRH - Gonadotropin Releasing Hormone; LH - Luteinizing Hormone; FSH - Follicule Stimulating Hormone

References

1. Anatomy & Physiology, Connexions Web site. Illustration is also from here.

2. Jerome Strauss, Robert Barbieri. Yen & Jaffe's Reproductive Endocrinology. September,  2013. Saunders.


Is ivy (genus Hedera) a shrub or an herb?

Woody plants are usually either trees, shrubs, or lianas. Ivies are lianas, they can have 40 years of woody growth rings and bark. The categories are flexible. It's an arbitrary division for convenience, it isn't that clear cut. Bamboos for example, are a woody grass.

https://weedwise.conservationdistrict.org/weeds/english-ivy#foobox-1/7/Untitled-4-copy.jpg

Does that count as a woody plant? yes it's a woody liana.


Can I simulate a previous and next sequence of my fasta files?

From the description of the model you are interested in, you probably don't need numerical simulations. A simple analytical expectation might be enough. But anyway, if you want to perform numerical simulations (maybe you don't want to assume panmixia), then there are a number of choices to you.

The simulator that you will need needs to be able to implement selection. It hence need to be a forward-in-time simulator and not a coalescent simulator. I personally have experienced with 4 different forward-in-time simulators; SimBit, SLiM, SFS_code and Nemo.

If I am not mistaken, SFS_code won't be able to simulate haploid individuals and will probably be slower than SimBit and SLiM. In SimBit, SLiM and Nemo you cannot do haploid either, however, you can set the cloning rate to 100%, which will essentially be the same as simulating haploids.

To my experience and generally speaking, SLiM and SimBit are faster than Nemo. Because your mutation rate is high and because your recombination rate will be very low (will probably be zero), SimBit should be very very fast and SLiM relatively slow. Also, SimBit will offer much nicer outputs for the statistic you are interested in than SLiM does.

Please note that I am the author of SimBit and I therefore might have a conflict of interest here. Here is the link to SimBit.


I do not know how to explain to a 6 year old how we are able to perceive colour. Does anyone know how this can be explained?

Well, depending on the depth you want to introduce her to, it can be difficult to explain to adults - much less children. You explained the basics well enough. Without going to the molecular mechanisms, here's a useful diagram:

Light will pass through the eye and Retina until it hits the Cones and Rods. That produces a reaction (which I'll address next) - which then causes signals to either resume or cease (Rods are, ironically, shut off by light - not turned on). These signals pass through Ganglion cells, through the Optic Nerve, and interpreted by the brain. When some cells are switched on, like a 3-Way traffic stop, they will prevent the information from other cells being transmitted.

A simple way of explaining it might be that inside our eyes are millions of teeny-tiny molecules that act like light-switches, and the brightness and color of light determine which of the "light-switches" are on or off.

If you want to go further into the actual mechanisms (or just have the background knowledge for future reference) the next diagram shows the mechanism itself (and the original in full-size since the one shown is squished if you prefer):

The big things to note above is the change from cis-Retinal to trans-Retinal which occurs after a Photon is absorbed. This causes signaling molecules to go a bit wild, open ion channels, and the depolarization of the membrane propagates the charge down the cell - much like a neuron.

  I have never quite understood this idea that an object has a colour depending on the light that hits it. Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours.

Well, let me stop you here. Low-light is a different situation than colored-light. Let's get the basics down:

Photons are absorbed by the electrons of the atoms that compose the molecules of an object. Whatever Wavelength of light is not absorbed by the electrons is reflected, and it's this Wavelength that we perceive as the color of the object as our Cones absorb the reflected light.

Photons can also be emitted when an electron moves to a lower-energy state. The Wavelength emitted by the electron is directly related to the difference between the High and Low energy states, as this diagram shows fairly well:

The emitted photons are the object's "Incandescence" - which is when an object produces a color of light by itself. The color you perceive is NOT going to change if the object emits incandescent light because the object is generating its own light. Neon signs are a great example: The gases being subjected to a current emit light, and will appear whatever color it's supposed to be whether or not it's a blue moon or sunset.

Photons which are reflected and not emitted - i.e. almost everything that doesn't have a power source - as I said above, are then absorbed by our Cones and our brain interprets the signals to produce a color.

The reason why objects that reflect light can change color is because not all environmental light is the same. Red objects will appear Black under Blue light because Blue light doesn't contain Red Wavelengths - there's nothing to reflect, so the object absorbs all of the available Wavelengths - the very definition of Black!

A lot of our color perception depends on ambient light, and most of the time - thanks to the Sun - that is a full-spectrum white light. Which brings me to answer the last bit of your question:

  What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours. What is that something?

Yes, there definitely is something inherent in both objects. That is: Their electron configurations absorb different chunks of the spectrum, and accordingly reflect different chunks of the spectrum. Although that's still a bit simplistic, since metals have some unique properties that other Elements do not. Their electrons exist in more of an "ocean" than around central atoms, but that's a whole other question.

As a fun bit of Trivia to impress your daughter when she's old enough, it's always a fun fact to know that the color Yellow is completely constructed in your head.

The human eye only has Rho (Red), Gamma (Green), and Beta (Blue) color receptors which have the following absorption pattern (from photo.net):

What everybody sees as "Yellow" is actually when both the Green and Red receptors are activated at the Wavelength where they intercept above, which your brain interprets as "Yellow":

Because your brain does a lot of processing, despite having only three color receptors we can perceive millions of colors (and shades/tones). Now for a while everywhere you look you'll be utterly amazed at what's going on, and you rightfully should be. ;-)


How many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’?

It's one for every phosphodiester bond formed. 11 nucleotides, but only 10 bonds needed to join them into an oligonucleotide:

1  2  3  4  5  6  7  8  9  10 11
N--N--N--N--N--N--N--N--N--N--N
 1  2  3  4  5  6  7  8  9  10


Synapses are held together by adhesion molecules, like cadherins and neuroligins/neurexins, so they aren't just loose adjacent membrane, they are securely anchored in place.

The adhesion molecules serve both a structural and regulatory role, being important for synapse formation and plasticity.

Missler, M., Südhof, T. C., & Biederer, T. (2012). Synaptic cell adhesion. Cold Spring Harbor perspectives in biology, 4(4), a005694.


What is the darkest color human bowel movement can become?

The darkest stool in a healthy human is black. It can result from eating black licorice, blueberries, blood sausages, Oreo cookies or grape juice.

Other foods that may cause almost black stools: dark chocolate, beets, cranberries, prunes, dark green leafy vegetables, such as spinach or kale.

They are not nutrients, but natural or artificial dyes in the food, that can turn stool black.

Black, tarry and smelly stool is suspicious for bleeding from the upper gastrointestinal stomach (from mouth to stomach), since the acid in the stomach turns blood black.

Sources: (Medline Plus, OU Medicine, 25Doctors.com)


Why has evolution made neurons use spiking?

One of the many advantage of an all-or-none system is that resources can be conserved for timing events that require synchronized collaboration between many cells (like locomotion).  Binary behavior may also partially be a side effect of speed and efficient long-distance information transfer (which is one of the great advantages of neurons as cells in the first place).

It should be noted, however, that neurons aren't universally binary.  It is more accurate to say that neurons have binary properties that allow neurons to behave in a binary manner (but not all neurons do).  On top of that, many continuous (i.e. non-binary) processes underlie the neuron's excitability threshold.


How do you calculate the charge on a polypeptide chain with changing pH?

In theory, you can calculate the charge on every individual ionizable group (i.e. looking up their pKa and calculating charge by henderson hasselbalch) and just add them up to get the total net charge.

In practice you would need to measure it with something like isoelectric focusing, since polypeptides fold and certain groups end up interacting with other groups/being shielded from solvent, meaning you really can't calculate it accurately unless you had structural data and even then it would be extremely difficult.


How a nerve impulse reaches the correct destination?

OK, I think I can answer at the right level now.

Firstly, a nerve is a bundle of neurons, each neuron is like a fibre. So the sciatic nerve in the leg will carry fibres from the spinal cord to the muscles in the leg, like a data cable might connect many computers in an office to a server on another level.

Each neuron will form connections with a specific area on a specific muscle, at a specialised synapse called the "neuromuscular junction". When a signal travels down that particular neuron, it will release neurotransmitters that activate that particular muscle region. So by sending signals to the right neurons, the muscle to be activated and how much to activate it can be selected by the CNS.

A nerve impulse is a slightly misleading term as it refers to the collective activity of signals within the many neurons of the nerve, so an individual neuron won't register on an impulse. The signals in neurons are called "action potentials".

There is some information coding in the frequency of action potentials within neurons, but it is used to control the response of the muscle, rather than locate the correct muscle.

Wikipedia is pretty good on the subject if you know where to look:

neuron

withdrawal reflex

sciatic nerve


Short Answer
What you're referring to is called Delayed Onset Muscle Soreness (DOMS).
We don't really know what causes DOMS, but it's most likely caused by a cascade effect started my muscle injury. Also, we aren't sure if massages (or what type of massages) really help relieve the pain.

What is Delayed Onset Muscle Soreness (DOMS)?
Delayed onset muscle soreness (DOMS) is the sensation of muscular discomfort and pain during active contractions that occur 24–48 h after strenuous exercise. The initial symptoms are most evident at the muscle-tendon junction and thereafter spread throughout the entire muscle.(ref)
Physiopathology of DOMS
The mechanism is not completely understood and several theories have been proposed, namely: (ref)

lactic acid
muscle spasm
connective tissue damage
muscle damage
inflammation
enzyme efflux

The underlying cause is probably a conjunction of 2 or more of these theories. However, ultimately, the underlying transversal cause is muscle microtrauma. There are a few interesting findings that support this:

High-intensity eccentric contractions induce performance decrements and DOMS (ref),(ref)

Concentric exercises seems to cause no soreness (ref)

Eccentric contractions are high force and are associated with muscle damage (ref)

Creatinine, Potassium(K) (and sometimes Myoglobin) excretion (urine levels) and Creatine Kinase(CK), K and Neutrophil levels in blood are increased after intense exercise. This is also seen in acute rhabdomyolysis, a condition in which damaged skeletal muscle tissue breaks down. (Ref: Harrison's Principles of Internal Medicine, 17th Ed, Chapter 273: Acute Renal Failure)

The effects of massage on DOMS
A massage MAY indeed reduce pain in DOMS (ref), however, most studies' results are inconsistent and hindered by methodological flaws(ref) such as lack of control of the placebo effect or the subjectivity of pain.
A study by Smith et al suggests that sports massage will reduce DOMS when administered
2 hours after the termination of eccentric exercise. They also found lower CK levels, higher cortisol levels and a prolonged elevation of neutrophils in the blood of massaged groups (ref). This might mean lower muscle trauma and inflammation due to a reduced migration of neutrophils (to the muscle) and higher levels of serum cortisol.
The increment in the blood flow to the muscles during a massage might also be implicated in the process, by restoring oxygen and nutrients required to muscle remodeling. However, there is no clinical evidence of this fact and a study strongly rebutes this (ref)
Hyperstimulation of the nerve endings in the affected muscles might give a sense of pain relief, in a context of microtrauma. (ref)


Intestinal gas consists of ingested air and gas formed during digestion. Stomach gas consists of  15% oxygen and 7% carbon dioxide approximately; the remaining is nitrogen.
The air that we breathe contains about 21% oxygen; thus some of the swallowed oxygen is absorbed through the blood capillaries present in stomach. Carbon dioxide is synthesized by digesting food using gastric juices. Nitrogen is not absorbed.
The small intestine absorbs some amount of carbon dioxide and oxygen. And the remaining gas is passed further to the large intestine. In the large intestine,  most of the oxygen is removed and carbon dioxide is increased. New gases are produced mainly hydrogen because of bacterial fermentation. And these gases are absorbed by blood and later released via lungs.
Check out following links:
https://katesalevelbiology.wordpress.com/2017/02/14/human-gas-exchange-the-digestive-system-and-breathing/
https://www.gastrojournal.org/article/S0016-5085(19)33654-6/pdf
https://journals.physiology.org/doi/abs/10.1152/ajplegacy.1926.76.1.92
https://nyaspubs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1749-6632.1968.tb19024.x


Heritability in the narrow sense

Heritability in the narrow sense $h_N$ is the genetic variance $V_G$ over the overall phenotypic variance $V_P$

$$h_N = \frac{V_G}{V_P}$$

More information at Why is a heritability coefficient not an index of how “genetic” something is?.

Heritability in the broad sense

The heritability in the broad sense $h_B$ is the additive genetic variance $V_A$ over the overall phenotypic variance $V_P$

$$h_B = \frac{V_A}{V_P}$$

Decomposing of the genetic variance

Adding together the additive genetic variance $V_A$, the dominance genetic variance $V_D$ (and the epistatic genetic variance $V_I$) sums up to the overall genetic variance $V_G$. Here I will ignore the epistatic genetic variance

$$V_G = V_A + V_D$$

, where

$$V_D = x^2(1-x)^2(2\cdot M_{12} - M_{11} - M_{22})^2$$

$$V_A = 2x(1-x)(xM_{11}+(1-2x)M_{12} - (1-x)M_{22})^2$$

, where $M_{00}$, $M_{01}$ and $M_{11}$ are the measurements of the phenotypic trait in genotypes 00, 01 and 11 respectively.

Highly related

Why is a heritability coefficient not an index of how “genetic” something is?
Additive genetic variance with nn alleles
Additive genetic variance with nn loci


Two different Leucochloridium infected snails - different species?

An intriguing question. Because I have not conducted any formal research into the parasitic family of Leucochloriidae, I shall hazard two options which would not require genomic sequencing.

Principally, as you suggested, observing the banding of the broodsacs is one critical means to distinguish members of this genus. The study entitled 'A
REVISION OF THE FAMILY LEUCOCHLORIDIIDAE POCHE (DIGENEA) AND STUDIES ON THE MORPHOLOGY OF LEUCOCHLORIDIUM PARADOXUM CARUS' describes its broodsacs 'typically' to have green banding with dark brown and black spots. On the grounds that this indicator is liable to being variable, the next procedure may yield greater accuracy.
The secondary host of most Leucochloridium species, including paradoxicum, is an adult bird ranging from crows to finches in which the larval mircidia enter the bird's tract and develop into distomes through consuming the snail's infested tentacle. Moreover, if possible, determining the secondary host of the parasite may assist your taxonomic identification: the Leucochloridium often gives its host's left tentacle the resemblance of a maggot, attracting the American Robin, for example.
Ultimately, analysis of the distomes produced in the secondary host phase could allow you to discriminate at the specific level.
Information regarding Leucochloridium variae, available from: http://eol.org/pages/849160/details
The cruel world of parasites


Using the IMGT/GENE-DB service to find RSS

I'm not clear what "Locus", "Main locus", and "IGMT group" mean here
  exactly. Specifically, what is the difference between "Locus" and
  "Main locus"?

From the same site:

  A locus is a set of IG or TR genes that are ordered and are localized
  in a same chromosomal location, in a given species. […]
   A locus comprises the genes of different groups which participate
  potentially to the synthesis of a polypeptide of the same 'chain
  type'.

Main locus should have been Locus minus the orphons:

  A chromosomal orphon set is a set of IG or TR orphons (genes outside
  from the main loci) belonging to a same group and localized on the
  same chromosome in a given species.

However the Main Locus and Locus have the same options; Options for the Locus should have been chromosomes. They must have made a revision in the site but forgot to change the help. I tried setting all the options except any in Locus and selecting all for the Orphons; it yields no result. It works only if you set any in Locus. So it seems Locus option is useless; you can set the Locus as any by default.
 For confirmation it is best to ask the authors.

From the changelog:

  16 April 2012

  Update of the IMGT/GENE-DB Query page:

  The search criteria are organized according to the axioms IDENTIFICATION, LOCALIZATION and CLASSIFICATION of IMGT-ONTOLOGY.
  Addition of new search criteria:

  MolecularComponent (IDENTIFICATION)
  Locus (LOCALIZATION): includes main loci and chromosomal orphon sets
  Main locus: "all" value allows to search genes of all main loci.
  Chromosomal orphon set: "all" value allows to search genes of all chromosomal orphon sets

For details on the IMGT classification you should refer to this paper.

Fixing a Locus option does not change the IMGT dropdown box option but the results are different. If you try your example and set Main Locus as IGH and IMGT Group as IGKJ you would get no results. It is just a problem of the web interface. Apparently the search works fine.

Running the search

I searched with the exact same criterion as you mentioned and did not get any sequences smaller than 38nt. There must have been some bug which seems to be fixed.


What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

Lets state what a Mutation is first.

Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/GrCH38 from 2013, which are the most current genome assembly).

Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have been validated to be present in more than 1% of the population with the help of Genome-wide Association Studies.

Structural Variations: These are any mutations which cause a change in the organism's chromosome structure, such as Insertions, deletions, copy number variations, duplications, inversions and translocation.

For more please read Wiki Link here.

Thanks to WYSIWYG for his interesting question regarding SNPs.

This piqued my interest a bit, and to my surprise I found that the same actually applies to all other species for example chickens; This paper from way back in 2002 describes how EST mining was sometimes used to generate potential SNPs but also notes the possible false positives due to the possibility of RNA-Editing.

This paper describes the usage of SNPs to allocate bovine individuals to their source population. As does this paper which highlights the economic importance that SNPs may hold for identifying pure breeds and crossbreeds.

Apparently there are also SNP chips available for other animals as highlighted by this particular paper


When we say that something is a genetic marker we mean that we can establish its linkage to a chromosome AND that we have some way of discerning, or detecting, how the marker has segregated after meiotic recombination (this definition is only valid for diploid species that undergo sexual reproduction).

So, for example, in the fruit fly, Drosphila melanogaster, the white gene is linked to the X chromosome. Wild-type flies have red eyes, a mutation in the white gene yields flies with white eyes.  You can use genetic crosses (matings) to (a) show that the white gene is linked to only one of the four fly chromosomes, and (b) if you have other genetic markers on that chromosome you might be able to construct a genetic map showing the order and distance of the linked genes.

You can also use a DNA fragment from a chromosome as a genetic marker--if you have an assay that lets you track the fragment after meiotic recombination.  A Southern blot, using a labeled probe is one way to accomplish this (e.g. a Restriction Fragment Length Polymorphism or RFLP).  PCR that lets you detect a RFLP or a SNP serves the same function, and is much quicker than a Southern Blot (and requires less DNA starting material).

A QTL is just one of these "molecular" genetic markers that shows linkage to the trait you are assaying. So, for example, if you had RFLPs or SNPs sprinkled all along the human chromosomes, and if you had a way to detect the segregation of all those markers after meiotic recombination, then you could use DNA from a family with lots of kids of varying heights, where one parent was tall, and the other parent was short, to see if any of your genetic markers were segregating, or linked to the phenotype of height in the children (this example assumes that height in humans is a quantitative trait).


Can a protein go outside of nucleus after go inside with nuclear localization signal (NLS)

It seems that I need to add a NES (nuclear export signal) if I would like to make it able to export the nucleus : https://en.wikipedia.org/wiki/Nuclear_export_signal  .


How to relate human metabolic model reactions and cancer drug targets / reactome items?

Short answer:

For drugs with targets having a direct effect on reactions in the model:

Find the gene name for the target protein -> Find the Entrez Gene ID (or other gene identifier, depending on the model) -> Search the model file or database for reactions having a gene association with the gene identifier.

AND/OR:

Find the EC number for the target protein. -> Search the model file or database for reactions associated with the EC number (likely to miss many reactions or be imprecise).

EC numbers can be found in the UniProt database, while the HGNC database at http://www.genenames.org/ can be used to look up genes by name and find their Entrez Gene ID and other resources, including links to UniProt. Many other databases can also be used.

For drugs with targets having an indirect effect on reactions in the model:

Model/estimate in-direct metabolic effect yourself by using data on known regulatory effects to create new gene-reaction associations or modify the bounds on reactions affected by the drug.

Long answer:

To knock out or constrain a reaction based on data about a drug, you have to go from an entry in a drug database to an EC number or gene identifier consistent with the annotation in the model you are using. However, There is currently no standard annotation nomenclature for gene-protein-reaction (GPR) associations in metabolic models, and in general only direct GPR associations are encoded in model files.

Assuming that you have a metabolic model in SBML format (for example the RECON 2 model), reactions may have a gene association and/or be associated with an Enzyme Comission (EC) Number.1 However, several model reactions catalyzed by distinct isozymes (different enzymes catalyzing the same reaction) may be associated with the same EC number, and many reactions may not be annotated with an EC association. Therefore you might want to use the gene associations directly. Both gene associations and EC numbers are recorded in the "notes" tag for each reaction in the SBML file, and is not part of the SBML specification. (A proposal has been published for improving support for gene associations in the SBML format.2)

Using EC numbers:

Using EC numbers is the simplest, but not the most precise or possibly even usable solution. It is simpler than using gene associations, because genes may described using any of a number of identifiers depending on the database while any reaction is associated with at most one EC number. Once you know the target protein, you can look it up in the UniProt database, and find its EC number (if any) in the field "protein names". A simple example: The DrugBank entry for the cancer drug Fluorouracil (http://www.drugbank.ca/drugs/DB00544), links to the UniProt entry for one of its targets, Thymidylate synthase (http://www.uniprot.org/uniprot/P04818), where the EC number is given as 2.1.1.45. Searching the RECON 2 SBML file (or searching in BiGG at http://bigg.ucsd.edu/bigg/main.pl) for occurences of this number will show that it is associated with the "TMDS" reaction.

The IUPHAR database (http://www.iuphar-db.org/index.jsp) may also be useful.

Using Gene associations:

Genes are conceptually at least one step removed from the reactions their products catalyze, so one might argue that using EC numbers which actually correspond to reactions would be better. However, it is thinkable that a drug might affect only one of several enzymes which catalyze the same reaction and thus share an EC number. Furthermore,  annotation of reactions with EC numbers in metabolic models may be poor. Thus you may want to use gene associations to determine which reaction are affected by a drug.

Unfortunately, due to the large number of databases, a single gene may be described using many identifiers or symbols in different databases. You thus have to identify the gene coding for the product which is the target of the drug, and obtain the correct identifier for that gene which corresponds to the nomenclature used in the model.

Assuming again that you are using the RECON 2 model, it is an update of RECON1 which was made using the BiGG database3. Gene protein reaction (GPR) associations are therefore recorded using the gene names in BiGG. When ignoring the decimal and any following numbers, BiGG gene names appear to correspond to Gene IDs in the NCBI Gene database.5 A question on how to identify BiGG reactions  was also discussed at BioStar.6 However, you have the opposite problem: Finding a BiGG gene name from another gene identifier.

Using Fluorouracil as an example again, the DrugBank entry lists "Cytochrome P450 2C9" as a targeted enzyme, with the effect being inhibition. Following the link to the UniProt entry P11712 (http://www.uniprot.org/uniprot/P11712), we find that it has an EC number 1.14.13.- However, this EC number corresponds to a class of reactions (or rather, enzymes). There are also listed several additional EC number at the single reaction level, but as these may not cover or be associated with all relevant reactions, we'll use the gene association. Going back to the DrugBank entry (or just reading on the UniProt page), we find that the gene name is CYP2C9. Looking up this name at a suitable database, for example the HGNC database of human gene names at http://www.genenames.org/, we find the entry for CYP2C9 (http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=2623) and that its Entrez Gene ID is 1559. Searching for this gene identifier in the BiGG database, we find that four reactions are associated with this identifier (The actual association is to "1559.1"): P4502C9,P4502C92,P4502C93 and P4502C94. Note that none of these reactions have an associated EC number.

Defining your own GPR associations

Keep in mind that even in genome-scale metabolic models, a large number of reactions and processes are missing. While the term metabolism in its widest sense may be used to refer to all reactions occuring in a cell, metabolic models have so far been mostly limited to covering transport and inter-conversions of small metabolites. Processes involving signalling molecules and regulation of enzymes have been mostly or completely left out, along with critical processes such as DNA replication, DNA repair and apoptosis.  Because of the limited scope of the models, gene-protein-reaction (GPR) relations do not generally take regulatory effects into account, being limited to describing direct relations between one or more genes encoding (part of) a protein which directly catalyzes a reaction.

One could also model a very large number of indirect regulatory effects, but as current metabolic models generally do not specify these, you may have to construct them yourself. To find reactions in a metabolic model which are affected by a certain drug, you may have to "travel" several steps of interactions from the original target of the drug. You may consider using protein-protein-interaction network (PIN) data to help in this. You will have to consider the strength/importance of the interactions, something which may require a high degree of manual curation.

For example, if your drug affects HSP90, which is needed for correct folding of certain enzymes, you may consider creating a GPR stating that the gene for HSP90 (or rather, HSP90 itself) is needed for any reactions catalyzed by a specific enzyme to be active. This would be an indirect GPR, as HSP90 does not itself produce any part of the enzyme that catalyzes the reaction. As an alternative to on/off regulation through a GPR, you may consider searching for data on the ratio of correctly folded and misfolded enzymes in the presence and absence of HSP90, and apply bounds on reactions catalyzed by the affected enzyme to reflect this.


Why are these trees leaning, but no trees around them are?

There are several reasons as to why a tree might lean. Normally, it is a combination of some/all of the points below:

Weight distribution: Depending on the diameter of the trunk and especially the height of a tree, gravity can create problems. So the main question is how the weight of the crown is distributed over the tree's trunk.
Species variability: Different species of trees have different root systems, some go deeper and others don't. The depth and width of the root system are factors to consider when assessing a leaning tree.
Environmental factors: There are a variety of environmental factors that will contribute to a tree leaning. For example, a
tree that leans because it has grown towards the sun often has a curved trunk. The trunk curves due to the tree's ability to adapt over time to the changing
availability of sunlight. Its root system will grow to accommodate the “off center” weight distribution, up to a point. Additionally, storms or constant wind can obviously cause a tree to lean.
Structural damage: Leaning trees that don’t have a “sweep” (caused by wind) but tend to have a fairly straight trunk generally have a history
of structural damage to the root system or storm damage that has
caused the root system to slip, break, sink or simply fail to support the
tree in some fashion. If the trunk appears to enter the ground without
a mound of soil on the side away from the lean, then the root system
has sunk, either from rot, mechanical fracture, physical cutting of the root plate or soil subsidence. If the mound does exist on the back side of the lean, that's a sign that the root plate is being tipped
out of the ground and the roots have failed - either through mechanical wounding or structural failure. As roots break under stress from wind or off center crown weight pushing the trunk away from the soil holding the roots, the up-wind side of the root plate will tip out of the ground.

In addition, it may be worth mentioning that time plays an important role here too. Older trees will have been exposed to the forces of nature and plant pathogens for longer than younger ones so it certainly makes sense to take the life cycle of a tree into consideration, some live longer than others and thus may have been subject to wind while the other surrounding trees weren't "tall" enough to shield off any of the wind etc.

Sources: Georgia Forestry Commission - Leaning Trees - What's up with that


You can manually restrict the design ranges in Primer-BLAST screen.

First of all you should enter the targeted sequence. In this case, it will be NC_000012.12 which corresponds to chromosome 12 that has KRAS gene.
You should determine the position of variant that you interested in that chromosome. The KRAS G12D -or rs121913529- variant is in 25245350. position. You can find the position of specific variant on dbSNP.
For Sanger sequencing, the recommended size is 600-1000 bp. So, we should select ranges +/- 300-500 bp apart from the variant position.
For the left primer we choose From:25244850 To:25245050; for the right primer we choose From:25245650 To:25245850. And then submit.
Here are the primer-sets that you are looking for. :)


Can a cell culture insert plate be used with a vacuum manifold?

This company sells a vacuum manifold for 24, 48 and 96 well plate formats.


Ara H 1, Ara H 2, and Ara H 3 are the three main peanut allergies. AH1 and AH2 are typically higher-acuity anaphylactic type reactions. The molecular cause for this is that some Immunoglobulin E develop a serum sensitivity and bind directly to vicilin and conglutin (the active proteins in AH1 and AH2). There are actually 7 or 8 Ara H complexes, but it is believed the remaining ones have a lesser affinity for IgE, reducing the frequency of allergic reactions and thus their availability for relevant studies.

The prevalence of the allergy is generally attributed to a combination of exposure and genetics. Many people have a genetic predisposition to certain allergies, but to a certain extent the body must be exposed to the allergen before an allergy will develop. The high use of peanuts in the food industry, and even to a lesser degree in skin care products like lotions, can account for early exposure resulting in allergies.

From the other direction, some research suggests that early and frequent exposure from infancy through childhood (albeit the choking risk) can reduce the demographic prevalence of an allergy in a given population.


What does it mean to "write an image and GIF into the DNA of bacteria"?

The image was not in the DNA as such, only as an abstract representation that could be converted into an image from knowledge of the code.  Briefly, they encoded the image into DNA, using a couple of different strategies in which DNA represented pixels -- either with a single DNA base representing a pixel, or with a triplet representing a pixel.  Knowing the code they used, they could then extract the information and turn it back into an image.

Quoting from the original article, CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria:

  We began with an image and stored pixel values in a nucleotide code ... We first encoded images of a human hand using two different pixel-value-encoding strategies: a rigid strategy, in which 4 pixel colours were each specified by a different base; and a flexible strategy, in which 21 possible pixel colours were specified by a degenerate nucleotide triplet table ...  To distribute the information across multiple protospacers, we gave each protospacer a barcode that defined which pixel set (denoted as ‘pixet’) was encoded by the nucleotides in that spacer. Four nucleotides define each pixet, and the pixels of a given pixet are distributed across the image ...

Their 21-color strategy is outlined in this figure:

Note: The paper isn't open-access. If you want a full-access version, Church often puts freely accessible versions of his papers on his web site; this paper, #441 on his list, is still shown as "in press" there, but check back at intervals and maybe it will be available there


You are correct in thinking that because of the presence of the diphosphate linkage between the two nucleotides in NAD⁺, both of which will carry a negative charge at physiological pH, together with the positive charge on the nicotinamide N, it would be more chemically correct to write NAD⁻. However I think the idea of using NAD⁺ is to emphasise the N atom in the nicotinamide moiety, which is the 'active site' of the coenzyme.

As it says at the NAD⁺ Wikipedia page:

  Although NAD⁺ is written with a superscript plus sign because of the formal charge on a particular nitrogen atom, at physiological pH for the most part it is actually a singly charged anion (charge of minus 1), while NADH is a doubly charged anion.


The identification is done by sequencing virus samples and comparing them to reference genomes of viruses. By doing this, you can analyze how closely related an unknown virus is to the references.

For the nCoV this method shows it is 96% identical with a known bat coronavirus (see reference 1 for details).
As viruses accumulate mutations due to errors during replication, this method is also used to generate genetic trees of the virus to analyze how it spreads, map routes of infection and also if the virus has been introduced to humans more than once (reference 2 has a nice overview on this topic).

The problem here is: You need to have some known references for comparision, if you have a completely new virus which has never emerged before, this will not help. For this reason there are projects ongoing which collect samples to identify yet unknown viruses (see reference 3)

Discovery of a novel coronavirus associated with the recent
pneumonia outbreak in humans and its potential bat origin
DNA sleuths read the coronavirus genome, tracing its origins and
looking for dangerous mutations
Virome analysis for identification of novel mammalian viruses in
bats from Southeast China


Do any birds beside the family Columbidae (or any reptile or mammal) feed their young "Crop Milk"

In mammals there are only two species (known, there may well be others) where males lactate. They are both species of bats and this paper discusses the evolutionary mechanisms that could underlie male lactation. I have ignored human cases because they are more of an unusual occurrence (often brought on by severe dietary stress) rather than an evolved mechanism.

Other non-mammals include Flamingo and Penguins. There is also a species of fish, called a discus fish, which produces a mucus from its skin which the offspring feed on (here). I would hypothesise that this evolved originally for different reasons (defence, scent communication, excretion...) but offspring "discovered" this was slightly nutritious so fed off it, those genetically predisposed to doing such things then had higher fitness and the trait spreads. Evolution of greater or more nutritious mucus production would be achieved because parents that produce more/better mucus would have more offspring that reach maturity.

The paper by Kunz & Hosken is a good discussion on current evidence and the potential for evolution of male lactation.

I hope that answers your question, happy reading!


Thats a difficult one but my gut feeling is a 'bunting' and maybe a Rock Bunting juv ? - the bill is definitely bunting-like and there does seem to be a black and white eye stripe going on . There arent that many buntings in the south of Spain especially with a very warm brown colouring


Does the genetic sequence of SARS-CoV-2 end with 33 A's?

This is a poly(A) tail, which is a feature found in the majority of eukaryotic RNAs (especially mRNA) and is also not uncommon in RNA viruses (which essentially mimic endogenous mRNA for their own replication). As with mRNA, this poly(A) tail in coronaviruses is bound by poly(A) binding protein in the cytoplasm [1], which is involved in translation initiation. In coronaviruses, this poly(A) tail is also necessary for replication independent of its role in translation [2].

[1] Lin Y-J, Liao C-L, Lai MM. 1994. Identification of the cis-acting signal for minus-strand RNA synthesis of a murine coronavirus: implications for the role of minus-strand RNA in RNA replication and transcription. J Virol 68(12):8131-8140.

[2] Spagnolo JF, Hogue BG. 2000. Host protein interactions with the 3′ end of bovine coronavirus RNA and the requirement of the poly (A) tail for coronavirus defective genome replication. J Virol 74(11):5053-5065.


found this flying ant like insect in pune, help me identify it?

This is not a syrphid. It is a fly in the family Megamerinidae, genus Texara. Very little is known about their biology, and they are rather uncommon.


Why does the HLA show a high degree of polymorphism?

There are multiple explanations for the enormous polymorphism in major histocompatibility complex (MHC -- the general term for the equivalent of HLA in all species) proteins. In general they reflect resistance to infectious disease, with the details being mildly debated, and usually not mutually exclusive -- multiple reasons probably apply.

The overall phenomenon is called balancing selection (Wikipedia link), and the most common explanations for the phenomenon in MHC are heterozygote advantage (which is not quite the same as overdominance), frequency-dependent selection, disease-specific selection, sexual selection, maternal-fetal interactions, and drift.

Simplistically, since MHC molecules are involved in protection against infectious disease, if there was only one MHC type then infectious agents that developed resistance to that type would be able to spread throughout the entire population readily. That means you as an individual are better off if your MHC is different from your neighbors', since you're likely to be more resistant to whatever pathogen is infecting them.

Many years ago I wrote a series of blog posts discussing the various evolutionary explanations in some detail, including dozens of references. The posts include:

Evolution of MHC: Elimination round
SEX! (… and MHC diversity)
Heavyweight championship: Overdominance vs. frequency-dependent selection
Testing overdominance in MHC: Can it be done?


Why do sharks continually regrow their teeth?

Actually, most animals with teeth are polyphyodonts - they regenerate teeth throughout their lifespan. This includes sharks, crocodiles, fish and some mammals (kangaroos, elephants and manatees). Diphyodonty (only replacing teeth once) is the exception. I have a vague memory from undergrad that the evolution of specialised teeth in mammal-like reptiles, and specialised jaw musculature (which happened at the same time) is/was believed to be the reason behind this - for a reason I can sadly no longer remember, tooth specialisation and tooth regeneration are incompatible. When I can find more details and a source for the latter I'll edit them in.


The leaves are most similar to this Mandevilla

It may be a hybrid periwinkle, in France and UK there are blue ones in wild and there are pink ones i.e. in Madagascar. If it's a periwinkle you can tell by the fruit and veins of the leaves. It can be a variant of Vinca minor. It has evergreen type leaves, it may be tropical. It is also similar to the Oleander family. Clematis and Ipomea have new foliage every year.

Also see this.


I have found an answer. The serine proteases on complement proteins actually have very limited enzyme substrate specificity. C1r only has two natural substrates, zymogen C1r and C1s, whereas C1s can only cleave C4, C2 and a few non-complement proteins. This was proven by superimposing the structure of serpins (serine protease inhibitors) with C1r and C1s. This analysis revealed that the access to these substrate-binding sub-sites is severely restricted, compared with digestive serine proteases such as trypsin. The trypsin or chymotrypsin-like pockets were only the primary specificity pockets. The strong preference displayed for Gln residues at P2 and Ile residues at P1 matched those found in physiological substrates of C1r, zymogen C1r and C1s. An example on how these specificity filters work can be seen when we substitute the Gln at P2 with Asn or Gly. To only allow Gln residues, polar or charged molecules will be placed where Gln’s residue’s polar head will be, and hydrophobic residues where the carbon chain will be.  When Asn is substituted for Gln, the shorter carbon chain will cause the polar head to overlap with the hydrophobic residues of C1r, which is highly detrimental for binding. Substituting this with Gly will eliminate the interaction altogether, so it will not be as detrimental, but the stability resulting from the Gln-C1r interaction will be lost.
More information in this article here.


How was the cama's life expectancy computed?

Since no source is given for the 30 - 40 years estimate in Wikipedia, we can't find out how the authors of the Wiki page reached that estimate, but 'someone made an educated guess' seems likely. There are a few reasonable ways that one might educatedly guess the longevity of the cama, but there are good reasons to treat those educated guesses with caution.

First, as you suggested, you could just estimate the cama's longevity from the life expectancy of camels and llamas. This is likely to fall in the right ball-park, but should be interpreted with caution: ligers (lion - tiger hybrids) are reputed to have high rates of premature death, and the same may well apply to camas.

Second, you could plug the animal's body measurements, metabolic-rate measurements, or similar measurements into a model which relates species' attributes to a measure of their longevity. Many different models of lifespan have been built (e.g. here), and if your goal is to get a rough estimate of how long a member of a particular species will live, those models are not a bad way of making a first guess. The 'this is a weird hybrid and might have issues with premature death' caveat still applies, though.


According to Psychoanalysis101.org, it is quite rare to be able to control dreams, though apparently it can happen 9according to the article.  Lucid dreaming is the term to describe when the person is aware that they are dreaming, further research and scepticism of lucid dreaming are outlined in this section of the article.


Is Nerve Growth Factor (NGF) commercially available?

recombinant human NGF is available for purchase.  You might not be able to buy it without some sort of a research lab affiliation.

http://products.creative-biolabs.com/symbolsearch_NGF_1.htm


How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

Your approach is correct but it is worth considering which database will work best for you. Questions to consider are;

Does the database provide a large search space for the organism(s) you're interested in?
Do its IDs work well for searching other databases?
How does the host database handle identifiers over time?

For protein sequences I would use;

Database; UniProtKB/Swiss-Prot(swissprot)
Organism bacteria (taxid:2) (or a subset)

The reasons for this are that I am comfortable with how Uniprot handles their ID's, they provide a large search space with includes clear delineation between reliable (reviewed) and other (unreviewed) sequences, and finally UniprotKB IDs map well to genes. The latter can be problematic. I also know that I won't have trouble searching PDB with UniprotKB IDs.
Despite using and liking the Protein data bank (PDB) I wouldn't use them for this kind of search as they are a structural database which reduces your search space. PDB has 8292 structures for E.coli compared to 23 017 reviewed and 1,335,860 unreviewed sequences in Uniprot. If you are only interested in structures then the PDB is an ideal fit.
I haven't used landmark.


Once the sperm reaches the cervix, through what does the sperm swim
  through to reach the egg?

It swims through the cervical mucus. Human sperm swim in a straight path in cervical mucus.

  Is the uterus completely filled with a fluid that allows the movement
  of the sperm, or does the sperm only swim through the endometrium
  (uterine lining)?

Yes, the uterus is completely filled with uterine fluid. They are attacked by many leukocytes while being helped by various contractions.

I would suggest reading the Suarez 2006 review. It has very nice information of all stages of sperm moment.


After the primer is removed from the leading strand, how does DNA polymerase I add dNTPs without a 3'-OH?

The leading strand post-initiation
First consider the DNA replication fork after initiation has occurred.
The 3′-OH primer on the leading strand is the 3′-end of the strand of DNA being synthesized in the 5′ to 3′ direction (circled in the diagram below, modified from Berg, Biochemistry). It is not removed because there is no need to do so. (The primer on the lagging strand is only removed because it is RNA.) So the problem posed in the question does not arise.
Remember that the reason for Okazaki fragments is that there is no DNA 3'-OH primer for the lagging strand, so a temporary RNA 3′-OH primer is generated instead, RNA polymerase — unlike DNA polymerase — is able to copy DNA without a primer. There is no such problem for the leading strand.

The leading strand at the origin of replication
As @canadianer points out in a comment, the remarks above do not apply to the initiation of DNA replication, the single instance where the leading strand must have an RNA primer. In the case of prokaryotes such as Escherichia coli replication proceeds in both directions so that a short time after initiation one has a replication bubble as shown in the figure below (adapted from Russel, iGenetics) :

It can be seen that, at the origin, the 3′-OH of the DNA from the lagging strand of the other direction of replication (boxed in red) can act as a primer for the DNA synthesis function of DNA polymerase I, after its exonuclease activity has removed a nucleotide from the start of the RNA primer on the leading strand.
References
Berg et al. Ch.27
The Cell, Ch. 5
Sandwalk: Blog page
Footnote
There was a typo in the original question which caused confusion about which strand the poster was concerned with. This answer assumes the leading strand.


white blood cells and cancer cells transport through lymphatic vessels

The "valves" are basically one way valves that just prevent backflow of interstitial fluid from the lymph into the interstitial space, so they do not specifically affect the flux of WBCs, cancer cells, etc. into the lymph vessels. In terms of a mathematical model of flux into the lymph vessels, you could use Poiseuille's law to determine the flow rate of interstitial fluid through the "valves", then multiply by the concentration of WBCs, etc. in the interstitial fluid to get the flux of the given cells into the lymph vessels. Of course, that is just one possible model for one parameter (cell flux).


Why are amino acids in biology homochiral?

I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very important pharmaceutical properties. I recommend this (1) review article if you are interested in the subject. It is also worth mentioning that D-alanine and D-glutamine are incorporated into the peptidoglycane of bacteria.
I read several papers (2, 3, 4) that discuss the problem of chirality but all of them conclude that there is no apparent reason why we live in the L-world. The L-amino acids should not have chemical advantages over the D-amino acids, as biocs already pointed out.
Reasons for the occurrence of the twenty coded protein amino acids (2) has an informative and interesting outline. This is the paragraph on the topic of chirality:

This is related to the question of the origin of optical
activity in living organisms on which there is a very
large literature (Bonner 1972; Norden 1978; Brack and
Spack 1980). We do not propose to deal with this
question here, except to note that arguments presented
in this paper would apply to organisms constructed from
either D or L amino acids.

It might be possible that both L and D lives were present (L/D-amino acids, L/D-enzymes recognizing L/D-substrates), but, by random chance the L-world outcompeted the D-world.
I also found the same question in a forum where one of the answers seems intriguing. I cannot comment on the reliability of the answer, but hopefully someone will have the expertise to do so:

One, our galaxy has a chiral spin and a magnetic orientation, which causes cosmic dust particles to polarize starlight as circularly polarized in one direction only. This circularly polarized light degrades D enantiomers of amino acids more than L enantiomers, and this effect is clear when analyzing the amino acids found on comets and meteors. This explains why, at least in the milky way, L enantiomers are preferred.
Two, although gravity, electromagnetism, and the strong nuclear force are achiral, the weak nuclear force (radioactive decay) is chiral. During beta decay, the emitted electrons preferentially favor one kind of spin. That's right, the parity of the universe is not conserved in nuclear decay. These chiral electrons once again preferrentially degrade D amino acids vs. L amino acids.
Thus due to the chirality of sunlight and the chirality of nuclear radiation, L amino acids are the more stable enantiomers and therefore are favored for abiogenesis.

BIOSYNTHESIS OF NONRIBOSOMAL PEPTIDES

Reasons for the occurrence of the twenty coded protein amino acids

Molecular Basis for Chiral Selection in RNA Aminoacylation

How nature deals with stereoisomers

The adaptation of diastereomeric S-prolyl dipeptide derivatives to the quantitative estimation of R- and S-leucine enantiomers. Bonner WA, 1972

The asymmetry of life. Nordén B, 1978

Beta-Structures of polypeptides with L- and D-residues. Part III. Experimental evidences for enrichment in enantiomer. Brack A, Spach G, 1980


if sperm contains only 50% of someone's DNA how can it be used to identify someone?

The comment from @User137 pretty much gets it: the mix of all sperm cells in even a small sample will contain the whole genome on average. So in the hair example in the comments above, there are probably a good number of dead cells hanging onto the hair, enough for analysis. Meiosis will redistribute the DNA sequences inherited from mom and dad randomly, so each sperm is in theory a unique patchwork of that person's genome, but overall the genome will be covered well. Single-cell work, on the other hand, is technically very challenging.

[edit: here is an article describing methods for low-input analysis of forensic samples. Unfortunately paywalled.]

To directly answer the OP on uniqueness: absolutely a single sperm is that unique for each person, in principle. There are lots and lots of genetic variants in each human, and everyone represents a unique mix. It is estimated that 1/1000 places in the genome of each person differ from any other person, on average (for substitutions). there are 3*10^9 places in the genome for this to be the case, which gives you a very large number of differences, ASSUMING that you can actually ascertain all those differences. [edit: for a discussion of these stats see here.]

The technical problem with forensics is that often they only look at a few places in the genome (microsatellites usually), because it is relatively expensive and hard even with recent technology to look at more than that in any detail. This leads to the non-trivial possibility of misidentification with the standard battery of loci. This possibility never goes away entirely, but it becomes very small with more data. I am not a forensic scientist, possibly they have gotten more comprehensive or the methods have changed in recent times.

[edit: here is a document that has what appears to be a readable introduction to DNA forensics, including technical discussions of some drawbacks of marker panels used by for instance the FBI of the USA.]


I think that immune rejection is not the only major problem in head transplantation.

We are quite skilled at suturing vasculature, but it's not fully solved yet how can you make new and proper connections in the spine?

Concerning your questions, if you just took these naive lymphocytes, they would probably get destroyed by the acceptor's immune system pretty soon. If this wasn't the case, the approach would already probably be in use for other transplantations too.

What you possibly could do is a bone marrow transplantation, where you would replace the bone marrow of the acceptor with that one of a donor. However this would cause the opposite problem, the donor cells attacking the acceptors body.

For now, lifetime immunosuppresion is the only working way to go.

To get a better idea about how exactly the mechanism of rejection works and the prospective future therapies, see for example: http://emedicine.medscape.com/article/432209-overview#a8


Partial pressures of different gas in human blood and how they are calculated?

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


Insect Identification. Moth or dragonfly or?

Found it. Amblyptilia acanthadactyla from Europe. He must be tired.

Update: It's a Geranium Plume Moth! Beautiful pics! I have geranium plants in my garden. Why have I never seen these? Thanks for the right find, Arthur!


(1) Chain Length

Will definitely affect melting point, as this website explains pretty well:

"Melting point principle: as the molecular weight increases, the melting point increases."

  (2) Number of Methylene groups.

This is another way of describing unsaturated from saturated fats. The more saturated a fat is, the straighter it is. Methylene groups cause kinks, which disrupts the Van der Waals forces along the rest of the carbon chain.

As such, from the link above again:

"On the other hand, the introduction of one or more double bonds in the hydrocarbon chain in unsaturated fatty acids results in one or more "bends" in the molecule. The geometry of the double bond is almost always a cis configuration in natural fatty acids. These molecules do not "stack" very well. The intermolecular interactions are much weaker than saturated molecules. As a result, the melting points are much lower for unsaturated fatty acids."

  (3) Ionized state of the fatty acid.

This will have a very minor affect. The fatty acid generally has an unpaired ester (-ate at the end) which can have a negative charge. However, from the link above again:

"However, in fatty acids, the non-polar hydrocarbon chain gives the molecule a non- polar character."

So even if the ester had a charge, the negative character is miniscule compared to the intermolecular forces exerted by the non-polar tail. Particularly since the charge can distribute amongst the two oxygen molecules which are conjugated, reducing the reactivity further.

  (4) Degree of saponification.

I'm not super-familiar with the degree of saponification, but from a quick overview of the process I'd say this wouldn't affect melting point - counter to my comment. The process of making soap involves only the acidic portion of the fatty-acid triglycerides. That portion of the macromolecule is going to be pretty much the same regardless of the fatty acid, so it will have nearly the same reactivity regardless of its chain length and conjugation.

What will not saponify are usually waxes - which are pretty much fully-saturated hydrocarbon chains with very few (if any) acidic sites. Parafin Wax, for instance, does not saponify, and has the formula ${C_{31}H_{64}}$.

  (5) Ability to alter entropy of water.

Like the degree of saponification option above, the ability of a fatty acid to alter the entropy of water correlates to the number of reactive sites throughout the molecule. As-such, unsaturated fats (those with methylene groups) are going to be slightly more reactive as pi-bonds are more reactive than sigma bonds.

So, given that this answer relies on a previous option, it's probably better to go with the previous option.

Ultimately, if I were answering the question I'd choose 1, 2 since the rest either depend on those two or are miniscule. However, beware that it's your question to answer and not mine.


How does stimulus reach neural threshold?

There is temporal summation of the stimuli. This is modeled in the Hodgkin and Huxley model .

To imagine the whole process, you should know that in the dendrites of the neuron, electric impulses are propagating passively ( the strength of the stimuli is decreasing over distance and time), in the axon the electric impulse is active ( in the form of action potential(AP) ).

Let me explain your second question with the help of mathematics:

Let's assume that T is the threshold value.

Func(x, t) is a function of the stimuli, where the depolarizing effect is decreasing with time and distance:

Func(A, t) > Func(A, t+1)

So after your assumption:

Func(A, 0) + Func(B, 0) = T

If we don't take into account temporal summation, in other words, if we are looking at only just one phase of the time, and A and B stimuli are not simultaneous, and in t=0, then there will be no AP.

Func(A, t1) + Func(B, t2) < T , where t1 != t2

But with temporal summation we can add previous stimuli into the equation. For example:

From the previous asyncronous stimuli, we got our two decreasing depolarizing factors, and over time we got one more stimulus from A, then with temporal summation they CAN produce an AP.

Func(A, t1) + Func(B, t2) + Func(A, 0) >= T,
if Func(A, t1) + Func(B, t2) >= Func(B, 0)

So after a depolarizing effect, the neuron enters into a hyperpolarized state and most of the sodium channels are inactive. This is called the refractory period. This is when, even A and B is applied simultaneously there will be no AP. And after the membrane potential gets back to his resting potential, then the whole process (including the temporospatial summation) starts from the beginning.


What is the protein sequence taken as input in the Path-A prediction system

Not necessarily, they can be enzymes, but they include a lot more (the whole proteome).

It takes a FASTA format file containing a set of query protein sequences from a single organism (a partial or complete proteome) and identifies those sequences that are likely to participate in any of its supported metabolic pathways
Path-A predicts the pathways supported by arbitrary sets of proteins, using validated prediction techniques based on sequence alignment and machine learning.


How can I interface cAMP signal or membrane potential from slime mold to an electrode?

For cAMP there is only one electrophysiological technique I've found.  You can use cyclic nucleotide-gated channels in the cell as a secondary indicator of cAMP activity.  When cAMP increases in the cell, these channel will fast gate which you should be able to pick up.

The issue is standard CNGC's are not overly sensitive to cAMP and are typically more sensitive to cGMP.  But there have been mutants created that have a high affinity for cAMP.  You can transplant these in and have an easier time with the detection.

This paper goes into a a lot more detail on it.


Can below-threshold potential changes of neurons convey information?

Electrical synapses (Gap junctions) can generate current to other cells without the emission of a spike. This sub-threshold interaction is proven to have functional implications in neural activity (eg. Retina).


What processes regulate the sex of offspring?

In theory spermatozoa are indeed produced in a 50:50 X:Y ratio. However, there are factors which can change the ratio, such as hormone-disrupting agents or even food.

Best known factor in the female body is timing. There are different theories of which The Shettles method is the most well known I think. In this theory they think that boy sperm are faster than girl sperm, but don't live longer. So to have sex around the date of ovulation highers the chance of getting a boy (their sperm is faster), but for a girl sex should be planned a few days before ovulation (they live longer). It is all theory, of course, so there are no guaranties.


It is definitely a crab - not anything spider. I originally thought it was a Sally Lightfoot Crab (a common crab on Madeira from the family of shore crabs) but I agree on your comment that it is more likely a Nimble Spray Crab (of the Flat Crab genus) as the specimen in your photo seemed a lot flatter than a shore crab (but I wasn't sure if it was just the shape of the rock).
The Wikipedia article on this species says that these are also referred to as another kind of Sally Lightfoot crab, and the fact that these are in a different taxonomic family from the other ones (the shore crabs) is a topic of debate.

They are observed in the coastal Atlantic and considered native to Madeira, but have recently spread into the Mediterranean

You can view a gallery of almost 200 photos of these crabs on iNaturalist.


Is the colour of a chrysalis predetermined?

Generally, in biology nothing is designed but if something is working it is saved for the future generations. Chemistry of colors is a complicated field, you can't just slightly modify single "color" molecule to get any color you want. Maybe in chemical sense the material of this shell can be easily modified to get shiny. Suppose it happened occasionally once due to sporadic mutation and no one dared to eat this chrysalis, which gave abundant progeny.