Does Human being have potential to perform parthenogenesis? Wikipedia says:

Parthenogenesis can occur without meiosis through mitotic oogenesis. This is called apomictic parthenogenesis. Mature egg cells are produced by mitotic divisions, and these cells directly develop into embryos.
In 1936, Gregory Goodwin Pincus reported successfully inducing parthenogenesis in a rabbit. In April 2004, scientists at Tokyo University of Agriculture used parthenogenesis successfully to create a fatherless mouse.

Since human is mammal,does not the success of the experimentations hints at the possibility of parthenogenesis in humans,naturally?
If not,why is  parthenogenesis not possible in human beings?

'Possible' is a tricky word here. There are a lot of things that are possible that just don't happen, because they are so exceedingly rare; or that happen but are unknown because they are hard to spot.

As it happens, we know that parthenogenesis-like effects can be induced in humans, because we've done it. If you remember the cloning debacle around Hwang Woo-suk, it turns out that while he didn't clone anything, he did manage to induce parthenogenesis, so … good for him, I guess?

Whether or not it happens in the wild… we just don't know. It's possible that it does, but it's really difficult to look for, since women have sex and then subsequently have babies, and a vanishingly small proportion of them are ever DNA tested; so even if one in every one million live births (which is a lot) were the result of parthenogenesis, we might never, ever know.

Basically, it's definitively possible with external meddling; it may or may not be possible without, and it may or may not actually ever happen.


Can nociceptors die because of too much mechanical stress? In martial art people hit their body (e.g., with small bean bags) to become more insensitive to pain. Can the sensory neurons die during this procedure? I think this is just an urban legend. Instead, I think the skin receptors desensitize, but they don't degenerate by the constant mechanical stress. However, I cannot find any research in the topic.

As far as I know, adaptation of peripheral receptors, including pain receptors, is transient (Giniatullin & Nistri, 2013)

Instead, my educated guess is that the increase in subjective pain threshold plays an important role. Pain thresholds differ between the sexes (Chesterton et al., 2003), and depend on disease and physical status (Kosak et al., 1996). Repeated exposure to painful stimuli hardens one mentally (I have practiced martial arts for two decades ).

Morever, there is an interesting answer on Martial Arts SE on the question How should I expect my fist to change over time from punching? Here it is shown that extensive training stimulates the growth of additional skin and bone. Extra skin (calluses) may dampen the impact of painful pressure stimuli.

References
- Chesterton et al., pain (2003); 101(3): 259–66
- Giniatullin & Nistri, Front Cell Neurosci (2013); 7(245): 1-9
- Kosak et al., pain (1996); 64(3): 415–23


Isopropanol precipitation of DNA - duration and magnitude of cold storage DNA prep protocols often include a final precipitation step with alcohol, often isopropanol, where the DNA must be kept in the alcohol, at a low temperature such as -20C or -70C, often overnight.

What is the point of keeping it at low temperature? Is lower better? At what point do you see diminishing returns?

What about the time? Is overnight really necessary, or would, say, an hour suffice? Do lower temperatures result in quicker precipitation?

For the precipitation you use different reagents: First you add salt under slightly acidic conditions to make sure that the DNA precipitates in a less polar environment. This is achieved by adding alcoholes like ethanol or isopropanol.

It is commonly thought that a incubation at low temperatures enhances the results, but this is interestingly not true. There is a paper from the Bethesda Research Laboratories which is called "Ethanol Precipitation of DNA." which analyzes these relationships (temperature, time and alcohol concentration) in great detail, its definitely worth reading.

Figure 1-3 from this paper shows the influence for Ethanol (but I am pretty sure that this is not much different for isopropanol):

I would prefer ethanol precipitation to ispropanol whenever possible. Isopropanol co-precipates salts, so you have to wash a few times with 70% ethanol and it is less volatile than ethanol, so the drying step takes longer. Its also less effective cleaning organic compounds like phenol away and sometimes the pellets are harder to see.

On the other it can be useful when you have to deal with large volumes, since you only need 0,7 volumes of isopropanol compared with 2,5 volumes of ethanol.

Precipitations with Isopropanol are usually not incubated but centrifuged directly after mixing. Here is a protocol from my lab (which originally came from Qiagen, if I remember correct):

Adjust the salt concentration, for example, with sodium acetate (0.3
   M, pH 5.2, final concentration) or ammonium acetate (2.0–2.5 M,
   final concentration).
Add 0.6–0.7 volumes of room-temperature isopropanol to the DNA
       solution and mix well.
Centrifuge the sample immediately at 10,000–15,000 x g for 15–30 min
   at 4°C
Carefully decant the supernatant without disturbing the pellet.
Wash the DNA pellet by adding 1–10 ml (depending on the size of the
preparation) of room-temperature 70% ethanol. This removes
co-precipitated salt and replaces the isopropanol with the more
volatile ethanol, making the DNA easier to redissolve.
Centrifuge at 10,000–15,000 x g for 5–15 min at 4°C
Repeat the washing and centrifugation steps once more.
Carefully decant the supernatant without disturbing the pellet.
Air-dry the pellet for 5–20 min (depending on the size of the
pellet).
Redissolve the DNA in a suitable buffer.


curly braces in sequence motifs what do curly braces in sequence motifs stand for?
e.g. in

RTCRYBN{4}ACG

what is N{4}? moreover, i notice that in TRANSFAC matrix notation the N{4} is completely omitted:

NA  Abf1p
XX
DE  RTCRYBN{4}ACG
XX
P0  A     C     G     T
01  0.500 0.000 0.500 0.000 R
02  0.000 0.000 0.000 1.000 T
03  0.000 1.000 0.000 0.000 C
04  0.500 0.000 0.500 0.000 R
05  0.000 0.500 0.000 0.500 Y
06  0.000 0.333 0.333 0.333 B
XX
P1  A     C     G     T
01  1.000 0.000 0.000 0.000 A
02  0.000 1.000 0.000 0.000 C
03  0.000 0.000 1.000 0.000 G

moreover the MEME suite's transfac2meme completely ignores the second chunk of the matrix after the P1 row.

N is the IUPAC code for any nucleotide, so in DNA sequence an N signifies any one of the four bases could be in that position.

The {4} means 4 of the previous character in the pattern, or NNNN. In Perl regular expressions \d{4} means match 4 digits in a row, so the notation is quite similar.


What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification? I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an alternate technique to isolate a protein.

What exactly are differences in HPLC and FPLC (fast protein liquid chromatography) instruments, and why would FPLC be a better technique than HPLC to use with proteins? What situations make HPLC preferable?

The only difference between FPLC and HPLC is the amount of pressure the pumps apply to the column. FPLC columns have a maximum pressure of about of 3-4 MPa, whereas HPLC columns can withstand or require much higher pressures. As a general rule, HPLC columns won't work with old FPLC equipment; FPLC columns can go on HPLCs as long as the pressure can be regulated.

Manufacturers have been marketing separate equipment to handle these different classes of columns, but the trend seems to be heading towards machines that can handle both types of columns without issue. A GE rep told me a few years ago that they've improved the pumps on the AKTAs to the point that "they're technically HPLCs now." The term "FPLC" is probably on its way out.


Cancer in myogenic heart cells? Why cancer does not occur in myogenic heart cells? Is there any special ability in heart cells to resist cancer ?

As a preface, this isn't a comprehensive answer for everything. As MattDMo points out, some of the original answer was poor in it's presentation. In my update there's some supporting information to some expert testimonial, but this is mainly targeted at adult cases rather than pediatric cases, i.e. why would cardiac cancer be rare in an adult with no prior history of cancer. There's a reference #5 at the bottom which goes into some of the genetic conditions that result in rhabdomyocarcoma.
Cardiac muscle cells do not divide particularly often (though they may divide: Evidence for cardiomyocyte renewal in humans). This would be a good mechanism of resistance of heart tissue to a more typical or rapid cancer development, compared to say, the endothelium of a vessel or an interstitial/connective tissue cell. Not to say heart tumors are impossible, either, as rhabdomyocarcoma is a good example of a cardiac tumor. Moreover, here's an excerpt from this article on heart cancer:

“There’s not a lot of fatty tissue [in the heart],” Gaynor said. Even more, “the heart’s enclosed in a membrane,” he explained. Known as the pericardium, this fluid-filled sac may itself become engulfed by cancer, with tumors metastasizing to the outside of it, but still it does its job of protecting our precious hearts.
So, even though cancer can happen anywhere there are cells, your heart remains virtually immune due to its muscular nature and the assistance of the pericardium. Smart heart.

And then from Cancer Prognosis: Role of BMI and Fat Tissue,

Many prospective clinical trials have linked excess body weight—typically represented as a BMI of 25kg/m2 of body surface area or greater—with a higher risk of development of cancers, including postmenopausal breast cancer in women and esophageal, colon, pancreatic, endometrial, and kidney cancers in both sexes. The number of obese Americans will increase by an estimated 65 million by 2030, increasing cancer diagnoses by 500,000 (Lancet 2011;378:815–25).

So fat content has it's role in progressing cancers, determinately. Let's explore this part. The adipocyte isn't simply a storage for fat, it has it's own host of proteins it produces and secretes. In obesity, the adipose tissue becomes dysregulated in it's secretion of adipokines [1]. The book Adipose Tissue and Cancer by M. Kolonin, the author notes that two major adipokines, leptin and adiponectin, play a major role in tumorigenesis by induction of cell survival and proliferation pathways [2]. Also duly noted, increased circulating insulin and insulin-like growth factors due to insulin resistance results in mitogenic effects on tumor cells.
White adipose tissue has been shown by Pedro et al. to increase bioavailability of sex hormones such as estradiol, through increased aromatase activity and  "increased insulin and bioactive IGF-1 levels which downregulate the concentration of the circulating sex hormone-binding globulin, resulting in an increased fraction of bioavailable estradiol, but decreased testosterone production." The same study has a section on inflammation induced by adipose tissue in section 3.2, the entire article is rather long but they sum up some of the information into a figure,

Source: Pedro et al.
Generally speaking, and in reference to the expert testimonial above from Dr. Gaynor, the heart isn't a very fatty organ, and it's protected from the surrounding adipose tissue by the pericardium. You could also argue that the fast flow of blood through the heart would leave a smaller fraction of circulating tumorigenic molecules for ready uptake by cardiac cells.
Being said, and while I haven't any data for the molecular pathogenesis for cardiac tumors, nondividing epidermal cells have been shown to enter a proliferative state in response to inflammation [3]. We also see that adipokines have been implicated in heart disease due to pro-inflammatory effects [4]. My concession here is that the rarity of cancers in adult cardiac muscle cells is because this process is very slow, and it's aided in part by the sort of environment the heart finds itself in. We often see cases of cardiac tumors in children due to errors in development [5].


Differences between comatosed states and brain death What are the neurological, physical, etc. differences between someone who is in a coma (one that is not medically-induced) and someone who is colloquially deemed "brain dead" (being physically kept alive by machines)? Is there a certain minimal brain activity that is present in a comatosed state that is not present in brain death?
I found a decent definition here which defines the difference as:

Brain death: Irreversible cessation of all functions of the entire brain, including the brain stem. A person who is brain dead is dead, with no chance of revival
Coma: A state of profound unresponsiveness as a result of severe illness or brain injury

I can find other similar, vague definitions in a few other places.
I am wondering what is different about the neuronal structures or electrical activity between brain death and coma. Is there simply no (zero) neural/electrical activity with brain death, whereas there is with coma? What would be physiologically different with brain death that would prohibit such neuro-electrical activity?

I'd recommend reading a review paper on disorders of consciousness, which cover the spectrum of minimally conscious states, vegetative states, and coma. Brain death is outside the context of disorders of consciousness, but is often discussed for comparison. Nico Schiff is one expert in the area; I've attached a reference to a review he coauthored at the bottom and I'll draw mostly from that review in this answer.
Schiff and Fins write, with some bolded emphasis by me:

At present, brain death is diagnosed if clinical evidence of the complete loss of brainstem function is present at the bedside and the patient demonstrates a failure of ventilatory drive in the setting of documented hypercapnia (significant elevation of blood partial pressure of carbon dioxide over a chosen threshold) — the ‘apnea test’. Fulfillment of these criteria should invariably associate with an ‘empty skull’: no sign of any metabolic activity or blood flow measured by positron emission tomography, a ground truth linking the biological model to the clinical assessments

The first two statements are most relevant clinically; PET is not commonly used except in research and rare cases of uncertainty. Biologically, brain death is when the brain is...dead. There is no recoverable neural function. The signs are a lack of any brainstem reflexes, including lack of respiratory drive. Additionally, other potential causes of these symptoms (such as pharmacological causes) must be ruled out.

Coma is a state of unconsciousness, but some brain functions are preserved. Again from Schiff and Fins:

Both comatose and vegetative state patients are unresponsive to environmental stimuli, although reflex movements may be present; in neither condition are goal-directed behaviors initiated. Comatose patients lack state variations and typically remain in a closed-eyes state that is unchanging even when presented with the most vigorous stimulation.

Comatose patients do not meet the criteria for brain death described above, but do have a complete inability to respond to stimuli and do not make purposeful movements besides reflexes. Schiff and Fins (and others) compare this state to deep anesthesia. Though your question posits that there should be some distinction between medically-induced and one that is not, there is really no functional difference. The possibility of recovery is tricky to assess, but generally patients who spend a long time in coma have a worse prognosis than those that do.
The clinical approach is different. A brain dead patient is dead. Nothing can be done to recover function; potential for organ donation can be considered, but there is nothing medically to do for the individual. For a comatose patient, it's more complex, and decisions need to be made regarding the level of medical support to provide given expected prognosis in both probability and extent of recovery.

In brain death, the neurons are dead. The lack of electrical activity is not because they are in some quiescent state, it's because they are dead. With coma, it's less clear except that there are signs that some neural function remains. Coma is really a clinical state, not a biological one. It's not always possible to determine the level of irreversible damage in a comatose patient, nor the extent of possible recovery.

Schiff, N. D., & Fins, J. J. (2016). Brain death and disorders of consciousness. Current biology, 26(13), R572-R576.


Do people with colorblindness have less cones or no cones of a certain type? https://en.wikipedia.org/wiki/Color_blindness#Red.E2.80.93green_color_blindness

  Protanopia (1% of males): Lacking the long-wavelength sensitive retinal cones,

  Deuteranopia (1% of males): Lacking the medium-wavelength cones,

Do they lack all those cones, or are they just (severely) short?

This is a complicated case, as it can have multiple causes.
The genes which are coding for the long (L, yellow) and medium (M, green) wavelength photopigments are located head-to-tail on the X chromosome. This is the reason why this colors are affected much more and especially in men (which only have one copy of this chromosome).

What seems to happen mostly is that the photopigment of one type of cone cells (and their neuronal connectivity) is missing, while the density of the cone cells is still the same. This means that the cells are they, but are not functioning. See these publications (when you have problems getting the articles, let me know in the comments, I can help):

The density of cones in the fovea centralis of the human dichromat
Color-deficient cone mosaics associated with Xq28 opsin mutations: a
stop codon versus gene deletions.
Functional photoreceptor loss revealed with adaptive optics: an
alternate cause of color blindness.

What can additionally happen in some cases is that these cones have a different pigment than they should have. See the third paper above for details.


Is it a valid generalization that kinases catalyse reactions involving energy transfer and utilization? The Wikipedia entry for kinase states that "a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules [such as ATP] to specific substrates".

ATP is the energy currency of the cell, so, would it be accurate to say that a kinase catlayses reactions involving energy transfer and utilization within a cell?

Your (original) description:

  a kinase helps chemically deliver or metabolize stored energy within a cell

sounds a little more like what many ATPases do: they are using the energy from ATP to do some energetically unfavorable work, such as moving molecules or ions against their concentration gradients. However, kinases have a broad range of different functions.

In some anabolic pathways, yes, kinases are helping to deliver stored energy in the form of phosphate groups onto 'building blocks' of other molecules, and this stored energy can be used for future reactions.

However, when a kinase phosphorylates another molecule (often a protein) to regulate its function, I wouldn't really say that it is delivering energy, just that there is some energy cost to doing the business of flipping cellular light switches, and ATP is readily available as a source to do that. One big advantage of using kinases in these sorts of reactions is that, because a fairly large energy input is required, such reactions don't occur easily by mistake or just due to thermal energy.


How do mushrooms react to being grown in a microgravity environment? I'll use Agaricus Bisporus as an example mushroom. If cultured in potato dextrose yeast extract agar, will the resulting growth grow in a normal pattern? Will the sporocarps emerge from the surface (assuming there is one) properly? Will they develop inside the agar, or emerge an an angle?

Will the plant develop at a normal rate, and to normal proportions?

There were some experiments done in microgravity in longer space shuttle missions. The reports show that the fungi develop relatively normal but grow in random orientations instead of orientating upwards. See this images:

The upper image shows fungi grown on earth which are subjected to normal gravity. The lower image shows fungi (actually only the fruiting bodies) which are grown during 7 day on the Spacelab D2 mission. The fungi obviously have a way of detecting gravity to let their fruiting body grow upwards. The image is from here, the article contains more information about this.
There is also a publication in this topic:

Mushrooms in microgravity - Mycology at the final frontier


Why we utilize dextro glucose and levo amino acids? Our body only digest dextro(Right handed) glucose and levo(Left handed) proteins and can't digest Levo glucose and dextro proteins. Why?

Our body synthesis levo proteins. What is the reason?

Our body digests only certain type of enantiomers like L amino acid and D sugars because enzymes are specific for their substrates stereochemistry meaning they will only recognize a particular enantiomer.So I hope this answers to your first question.
Now, why we only see L amino acids and D sugars, there is some interesting hypothesis listed in this article.Here is the link
http://guava.physics.uiuc.edu/~nigel/courses/569/Essays_Fall2006/files/Rajan.pdf

I am adding some answers I found from research gate here, which includes
1)I think the prevalence of L-amino acids in biological systems is a quirk of our evolutionary history; there's no reason D-amino acids wouldn't work chemically, but once early life forms started building proteins out of L-amino acids, L-amino acids became abundant an it became selectively advantageous to use L-amino acids because then you could use the amino acids you obtained by eating someone else. It's a matter of compatibility; if you use D-amino acids, you have to build them all from scratch, because you're not going to find them in your environment. As long as you use L-amino acids, you don't even need to maintain the de novo synthetic pathways; you can just eat something that has those pathways (hence the 'essential' dietary amino acids).
2)There are a couple of reasons for biological homochirality.
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 preferentially 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.
3) Morozov, L. 1979. Mirror symmetry breaking in biochemical evolution. Origins Life Evol Biosphere 9: 187-217

But I think we have D amino acids also, as this paper says https://www.hindawi.com/journals/scientifica/2016/6494621/

Hope this helps!


Why doesn't Clopyralid damage cool season lawn grasses? I use Clopyralid (3,6-dichloro-2-pyridinecarboxilic acid) to kill broad leaved weeds in lawns. From my understanding, it works by mimicking an auxin which affects plant growth. Naturally this pulls the chemical to the growing points (stems, roots) of the plant and disrupts the growth, killing the plant.

My question is: Why doesn't this affect cool season lawn grasses (Winter rye, fescues, bluegrass)? It is also considered safe to use on some warm season grasses, but in my experience the results are not always good.

Auxins are a class of phytohormones involved in plant growth and behavior. Auxinic herbicides, such as clopyralid, induce an overinduction of the auxin response in susceptible plants (kelly & Riechers, 2007). From the Kelly & Riechers 2007 article I quote:

  [Auxinic herbicides] cause various growth abnormalities in sensitive dicots, ranging from leaf epinasty and/or cupping and stem twisting, to thickening of stems and roots, and ultimately chlorosis and necrosis [...]. Lack of phytotoxicity in grasses has been attributed to several factors, including anatomical differences in vascular structure and differences in ability to metabolize the herbicide [...]

Hence, grasses seem to be protected due to anatomical and metabolic differences. Specifically, auxinic herbicides seem to kill dicots and spare monocots (Song, 2014). Song explains, and I quote:

  However, the underlying molecular mechanism of how auxinic herbicides selectively kill dicots and spare monocots is not understood yet [...]. Early research has
  proposed that the selectivity of auxinic herbicide is because of either limited translocation or rapid degradation of exogenous auxin, altered vascular anatomy, or altered perception of auxin in monocots [...] The difference in vascular tissue structure between dicots and monocots may contribute to the selectivity of auxinic herbicides. In monocot stems, the vascular tissues (the phloem and xylem) are scattered in bundles, and lack a vascular cambium; in dicot stems, the vascular tissues are formed in rings and possess a cambium.

So in all, the exact mechanism of specificity between monocots and dicots is unclear, but may be related to structural and/or metabolical (pharmacokinetical) and/or different pharmacodynamical differences between monocots and dicots in general. Dicots are susceptible to auxin herbicides, while grasses, being monocots, are protected.

The complexity of the auxin hormonal system (Song, 2014) may explain why differences exist between grass species, but this is speculative.

References
Kelly & Riechers, Pesticide Biochem Physiol 2007;89:1–11
Song, J Integr Plant Biol 2014; 56:106–13


What signal processors comprise an Event-Related Potential system for EEG? So my 30,000 ft. understanding of the EEG signal processing data flow is:

Capture raw EEG data ("raw waveforms")
Run these raw waveforms through a Signal Processing Framework that consists of 1+ "nodes"/processors, where each processor is doing some kind of transform on the raw waveform. In doing so, new information is unlocked from the raw waveform that was previously hidden
Perform individual analyses on this unlocked data based on what suits your research/application

So first off, if the above understanding is misled in any way, please begin by correcting me!

Assuming I'm more or less correct, my specific application at hand is that I want to correlate certain raw waveforms with events (such as "thinking of a turtle", "moving head up and down", etc.). I believe Event-Related Potentials are what I'm looking for, but...

What I'm struggling with is: what does my "Signal Processing Network" need to look like in order to implement ERP? From an architectural perspective, I'm looking for this "network" to take raw waveforms in as input, and to output events, like the few I mentioned above.

Is FFT a player here? Some kinds of filters? What processors comprise an ERP system, and what does their respective "network" (data flow pipeline) look like?

Event-related potentials are an issue in many aspects of physiology, not just in EEG analysis, so this answer is more general.

The main problem is that electrical or other signals that are associated with some "event" are typically much lower in magnitude than the background noise in the system being examined. Electrocardiograms are the exception in this regard. The trick then is to get the event-related signal out of the noise.

This is done by multiple repetitions of the "event" combined with signal averaging. You mark the electrical record with the time of each event, line up portions of the record by the event markers, and average the lined-up signals around the multiple events. This can be the full waveform for sensory evoked potentials, or if you are examining action potentials in a nerve, the histogram of post-event occurrence times of action potentials.

The particular signal-processing mechanisms used have evolved with technology. I'm old enough to have known people who 60 years ago recorded electric neural activity on magnetic tape and processed the data, after analog-to-digital conversion, on what were then state-of-the art computers with 65,000 words of memory. Even then, there was discussion about the best technologies to use for specific purposes, as this 1959 MIT monograph indicates.

The main problem, the low level of event-related signals to the noise from other electrical activity, still remains 60 years later. The noise is biologic rather than technical, so more recent improvements have more to do with ease and speed of processing rather than the fundamental signal-to-noise problem. For event-related potentials, use whatever technology allows you to collect the electrical data along with linked notations of the event times, then to average the signals synchronized on the events to build up the signal out of the noise. In a standard clinical application of brainstem auditory evoked potentials to evaluate hearing, you may need to average over 500 or more stimulus presentations.

This signal-in-noise problem is also seen in functional magnetic resonance imaging (fMRI) of brain function, which must consider not only the signal over time but also differences among brain regions within individuals and differences among individuals. The Wikipedia page on fMRI goes into some detail on methods for getting specific signals out of the background noise. You should pay particular attention to the issue of "Block versus event-related design" on that page. My understanding is that for "events" of the type that you consider, like "thinking about a turtle," the block design works best in fMRI. The paper by Thierry et al, provided in the helpful answer by @Christiaan, shows how to apply this type of blocking approach to EEG measurements during presentation of visual stimuli.

The methods in that paper by Thierry et al also indicate the type of practical care that is used in professional analyses of this sort. The authors go into detail about the nature and placement of the electrodes, choice of which electrodes to use for analysis, signal-sampling rates, and so on. For example:

  Scalp activity was digitized at a 1-kHz sampling rate from 64 Ag/AgCl electrodes distributed throughout the scalp according to the 10–20 convention using Cz as a reference. Impedances were kept below 7 kOhms. The electroencephalogram was filtered on-line between 0.01 and 200 Hz and off-line low pass at 35 Hz using a zero phase-shift digital filter. Eye blink artifacts were mathematically corrected, and signals exceeding $\pm$ 75 $\mu$V in any given epoch were automatically discarded.

Reading papers like this are probably the best way to learn about what's involved and to find people who can teach you how to do it.


What neurons' projections comprise the olfactory nerve (Cranial Nerve 1)? Recently, I have been learning about olfaction. To my surprise, I am having a heck of a time finding explicit information regarding which neurons' axons are comprising the olfactory nerve. I am aware that there are several cells types that are relevant in the olfactory bulb: mitral cells, olfactory sensory neurons, tufted cells, and many more. However, I have not been able to find any source that definitively states from which neuron type the projections that comprise the olfactory nerve arise from.

I keep seeing articles that seem to imply olfactory sensory neurons comprise the olfactory nerve, but this doesn't seem right to me. My understanding is that the projections that emanate from the olfactory bulb and terminate in the brain constitute the olfactory nerve. The only thing I can think of is that the "olfactory bulb" is actually being considered "part of the brain"...in which case, the olfactory sensory neurons are technically peripheral neurons.

If that is the case, what exactly are the olfactory bulbs? Are they part of the telencephalon? Are they an outgrowth similar to how the optic nerves are outgrowths of the telencephalon and therefore not "true nerves"?

Olfactory receptor neurons (ORNs) in the olfactory epithelium in the nasal cavity project to the olfactory bulb; this projection is Cranial Nerve 1 and it's more of a collection of fibers rather than a highly organized nerve.

Your surprise or confusion is probably based on this:

  My understanding is that the projections that emanate from the olfactory bulb and terminate in the brain constitute the olfactory nerve

...which is false: the olfactory nerve is the step prior to the olfactory bulb. The olfactory bulb is part of the brain.

I'll add that I have seen poor diagrams of the brain that point to the olfactory bulb and label is as cranial nerve 1, which is false or at least misleading.


Immune system initial response One thing i can not still comprehend about the immune system is the following:

A bacteria is first recognized by neutrophiles. But then neutrophiles have to have the ability to release chemotaxines upon the recognition (or the bacteria?)? Its not mentioned anywhere in my script how macrophages and other non abundant innate immune cells come to the source of an infection in details.

On the contrary it's not neutrophils that initially recognize a threat, but rather distressed epithelium, and immune cells like DCs or macrophages that are already distributed in the tissue that recognize pathogen- or damage-associated molecular patterns (see PAMPs and DAMPs). The primary response to these patterns is the secretion of cytokines.

Among the many cytokines secreted include a subset known as chemokines, from the Greek work for movement. The combination of chemokines and cytokines induce chemotaxis of immune cells circulating in the blood, such as neutrophils, by telling these cells that the nearby tissue is inflamed. IL-1ß, IL-6 and CXCL2 are examples of neutrophil attractants secreted by macrophages and monocytes. Complement fragments like C5a are also known to induce an inflammatory response, inducing the secretion of these molecules.


Is there any difference between hydrogen acceptor and hydrogen carrier? As what i have learnt, hydrogen carrier (NAD+ and FAD) gets H (H+ and e-) from glyceraldehyde 3 phosphate dehydrogenase or Pyruvate dehydrogenase, and then transport H to electron transport cycle.

Do NAD+ and FAD act as hydrogen acceptor, hydrogen carrier, electron acceptor, and electron carrier?

Does this mean hydrogen acceptor = hydrogen carrier = electron acceptor = electron carrier?

Actually, both NAD and FAD accept a hydride ion, H$^-$ (a proton with two electrons), not a hydrogen atom (a proton with one electron). For this reason, I would not refer to NAD or FAD as "hydrogen acceptors" or "hydrogen carriers" at all. It just gets confusing. (I guess you could call them "hydride acceptors" if you want, but it's not common terminology.)

"Electron acceptor" is the right name for NAD and FAD when discussing a redox reaction where they in fact accept electrons, in the form of an H$^-$ ion. Pyruvate dehydrogenase which you mentioned is one such example. This is not unique to biology, it's standard chemistry terminology: any molecule that accepts electrons in a redox reaction is (cleverly ;-) called an electron acceptor. For example, oxygen is an electron acceptor in combustion reactions. So "electron acceptor" is just a name for the role that the molecule plays in a redox reaction.

"Electron carrier" refers to the fact that NAD (and also NADP, and quinones, and some cytochromes ...) can carry electrons between reactions that occur at different places. For example, after NAD picks up an H$^-$ ion in the pyruvate dehydrogenase reaction to form NADH, it can carry the two electrons over to complex I where it donates them to ubiquinone. (And here, NADH acts as an electron donor, while the ubiquinone is the electron acceptor.) So the term "carrier" emphasizes the transporting role of the molecule. FAD is actually a bit different in this respect, because it is not soluble; it's a prosthetic group bound to certain enzymes like Complex II, and therefore it cannot really carry anything anywhere, or at least not very far. So to be precise, I personally would rather not call FAD a carrier. But maybe that's just me.


How long can a unicellular organism live without nutrition? What happens after that? Does it depend on the domain? Say I have three unicellular organisms: a eukariote, a bacterium and an archaeon. If I cut off nutrition from them at the same time, how long will it take for them to die? What will their death look like, and do they actually need to die? If so, why?

This is very dependent on the organism within each of the groups you mention. While for the most part, archea are the extremophiles and have the ability to withstand many extreme conditions, nutrient limitation survival greatly varies. I think you could easily find organisms in each group that could withstand nutrient limitation well.

A good example would be yeast, which is a single celled organism you may have actually worked with. If you take laboratory yeast, in their diploid state, and starve them, they will undergo meiosis, and in their spore form, live for a very very long time without nutrients, protected by their ascus (which is actual their dead mother cell).

Yeast can also completely desiccate and still live. When you pick up an active yeast packet for baking, those yeast have not only been starved, but have been completely sucked dry of their water. Yet when you add water back, they live (though a great number of them will die).

I think in general, most single celled organisms have a certain tolerance for low nutrient conditions. This does happen to them a lot. All it means is they slow their cell cycle down, stop dividing, and just undergo a caution period. There is all sorts of signaling in the cells that sense the nutrients, and slow growth based on their conditions.


What does "chlorophyll photosynthesis peak" mean in relation to photon wavelength? When reading about how green / leafy plants work,
I saw that they have chlorophyll A & B, which allow the plant to use the energy from light by capturing and transforming.

When reading about Chlorophyll, I saw some charts showing "peak points" for each type for light wavelengths. Apparently, each chlorophyll type has both peak points.

Since from further reading I learn that plants can use all the light in the visible spectrum for photosynthesis, I'm wondering (my questions >>):

What do "peak points" of wavelength correspond to / stand for?
How does light peaking in red spectrum (say around 630nm) differ to (or affect plants) compared to light in red spectrum peaking at 680nm (which I gather is Chlorophyll A peak-ish)?
When same amount of radiant flux is projected to leaves on different wavelengths, one far from a chlorophyll peak the other near, which one gives more energy to plant and why?

First thing to note is that the absorption spectrum of chlorophyll A and chlorophyll B is similar but not the same. The reason for the appearance of absorption spectra is because the light is composed of photons of light.  Different photon has different  oscillation frequency and energy. The essence of Chlorophyll absorption is absorbing photons. After chlorophyll absorption of a photon, the electron transition from the ground state to the excited state, and get water electronic from the water cause decomposition. Only phonton that has resonant vibration frequency with electrons, and can meet the energy requirements of electronic transitions in order to be absorbed by chlorophyll. The Photon energy of different wavelengths of light is different. This is also the reason of different wavelengths of light affect chlorophyll light absorption.

Simply explain the absorption spectrum:

280 ~ 315nm  has small effect of plant morphology and physiological processes
315 ~ 400nnm absorption rate is small, impact the photoperiod, prevent stem elongation
400 ~ 520nm (blue) Absorption ratio of of chlorophyll and carotenoid in this light is maximum, it has the greatest impact on photosynthesis
520 ~ 610nm absorption rate is not high
610 ~ 720nm (red) low absorption rate.  It has a significant effect on photosynthesis and light cycle effect of  chlorophyll.
720 ~ 1000nm Low absorption rate, stimulate cell elongation, impact of flowering and seed germination
1000nm converted into heat

p.s. white light is a mixture of light


Violation of the law of energy conservation between photosynthesis and respiration? For the production of one glucose molecule in the Calvin cycle a plant uses 18 molecules ATP, but when the same glucose molecule is oxidised — first in the cytoplasm and then in the mitochondrion — it can obtain approximately 36-38 molecules ATP. How is the theory of conservation of energy maintained here?

The Fallacies in the argument

The question contains two main fallacies (some would say sleights of hand) in the energetic comparison of glucose synthesis from CO2 in the Calvin cycle and glucose oxidation via glycolysis, the tricarboxylic acid cycle and the electron transport chain:

  The descriptions of the two reactions are incomplete — important co-substrates are ignored.
  The formulation of the question seems to assume that the energetics of a biochemical reaction series is reflected solely in the
  interconversion of ATP and ADP, rather than the free energy changes
  that occur in all associated reactions.

Detailed explanation

To make a valid comparison of the thermodynamics of glucose oxidation to CO2 with its synthesis form CO2 we have to consider the single reversible reaction:

 (The ‘6H’ may appear rather odd, but it is accounted for in the reduction of cofactors etc.. We cannot include oxygen in the equation because it is not involved chemically in the synthesis of glucose. Therefore for this treatment the electron transport chain is not included, although it is discussed later.)

The reaction from left to right is associated with a certain decrease in Gibbs free energy (ΔG) and that from right to left in a corresponding increase of the same value. In a non-biological context this might involve the evolution and use of heat energy, but in the cell it involves the chemical energy of bonds between atoms. We therefore have to consider all the chemical reactions to which the reaction above is coupled, i.e. which receive or transfer free energy. The additional reactions and the free energy changes they involve can be found in the chapters on glycolysis, the tricarboxylic acid cycle and the Calvin cycle in Berg et al. and are (omitting water, hydrogen ions and inorganic phosphate):

From which it can be seen that the chemical energy input required for synthesis is greater than that obtained, contrary to what is asserted in the question

What about the ATP?

Yes, the cell oxidizes NADH and FADH2 and uses the free energy change to build an electrochemical gradient, the dissipation of which generates ATP (30 molecules per glucose molecule is the current estimate). However that is separate process, with no counterpart in the Calvin Cycle, where the NADPH is generated from photosynthetic reduction and not from ATP. However, if you perform a naive ‘currency conversion’ at the rate of 3ATP per NAD(P)H and 2ATP per FADH2, the balance is: input for synthesis 54 ATP, output from oxidation 38 ATP, i.e. the same general result as above.

Popularizing science is not easy, and those who make the effort can be excused for equating energy with ATP (often as clip-art lightening flashes). However if you wish to study metabolism you need to think scientifically about chemical thermodynamics and free energy. The fact that the hydrolysis of ATP to ADP is accompanied by a decrease in Gibbs free energy is not particularly chemically remarkable in the context of the free energy changes of other chemical conversions in the cell (including NAD(P) oxido-reductions). What is remarkable is that the cell has evolved enzyme that catalyse reactions in which the free energy change from this conversion is not lost as  heat, but can be used to offset the +ve ΔG of a reaction to which it is coupled. Reactions involving NAD(P)H do the same thing, but they are limited to reductions, and the free energy change is inconveniently large.

Why the accepted answer to this question is a red herring

The accepted answer addresses a different question to that posed. It cites a calculation of the photon energy required for converting carbon dioxide to glucose. This is irrelevant to the thermodynamics of the Calvin Cycle, which can occur in the dark. It is relevant only to the efficiency of the use of photon energy in phosphorylating ADP and reducing NADP+ (incidentally in an open system) — a distinct reaction. The thermodynamics of the reactions the question refers to — glucose / carbon dioxide interconversion processes — do not involve the generation of their co-substrates.


Burns' "To a mouse" - what species of mouse? What's the most likely mouse species Robert Burns is referring to in his poem "To a Mouse, on Turning Her Up in Her Nest with the Plough".

Burns farmed near Ayr, which is on the Firth of Clyde in Scotland. So the mouse of his poem would have to live in that area in the late 18th century. The creature obviously was living in an open field in December in a nest made of "leaves an' stibble [stubble]". From the poem's title it appears like the nest was constructed underground. "Sleekit" refers to sleek coated as in shiny fur. A clue to the mouse's diet is given by "A daimen icker in a thrave", ie grain. According to Wikipedia: "Scotland has no population of the Edible or Hazel Dormouse, or of the Yellow-necked Mouse, and the Harvest Mouse's range is limited to the southern part of the country."

The poem is here: http://en.wikipedia.org/wiki/To_a_Mouse

It could be Wood Mouse(Apodemus sylvaticus).

Courtesy : redbubble.com


How is the blood volume of a living organism measured without killing it? How is the blood-volume of an organism measured without killing it?

Note:The blood-volume of an organism is defined as the total volume of blood present inside that organism.

Polynomial gives a good hint. By adding in a known tracer of known amount that should only circulate in the blood stream, the concentration of the tracer when completely distributed will give the volume of distribution.

If the tracer only stays in the bloodstream (and that's a fairly large IF), then the VD will be equal to the VBlood. However, as many pharmacologists know, interactions with proteins and cells can skew that number. The blood volume is also reduced by the volume of the blood cells. However, using Andrei's method of dilution, one can merely swap the cell counts with the tracer concentration.


How does natural selection affects seasonal polyphenism in animals? How does natural selection affects seasonal polyphenism in animals?
In this Wikipedia article there is a following statement:

Since these animals in widely separated groups have evolved
separately, the similarity of coloration is due to convergent
evolution, on the presumption that natural selection favours a
particular coloration in a particular environment.

By looking at e.g. snowshoe rabbits, how can it be that natural selection "favors" a particular coloration during winter and summer? Is not the environment causes coloration without any "benefit" for these animals? How can it be proved, that these animals change their coloration because it is useful for them?

[H]ow can it be that natural selection "favors" a particular coloration during winter and summer?

Camouflage for example. In regions, where it snows some animals would take advantage to have a fur colour that match the substrate in which they live and they may therefore be selected for having a white fur in winter and a non-white fur in summer.

Consider for example Lepus lepus in summer

vs in winter

  How can it be proved, that these animals change their coloration because it is useful for them?

There are a whole lot of possible experimental design.

Considering seasonal coat colour in response to predation, a simple and obvious approach would be to experimentally dye the individuals and see how their survival varies depending on the colour they have been dyed.

Sometimes, you may have a sister clade that is non-plastic which it might be of interest to test against (depending on the exact question at play).

  I'm more interested in ecological impact on coloration [..] I'm looking for the articles providing evidence

Cases of local adaptation (such as Hoesktra 2006 for example) or other evidence of natural selection on coat colour such as differential selection among lineages are probably way more common. But if you are specifically interested in seasonal variation then, here are a few papers I could find with a quick google scholar search showing selection on seasonal variation for fur colour.

Zimova 2013 and Zimova et al. 2016 in snowshoe hares (which is listed in the wikipedia article)
Turner 1961 in pastry larvae
Maybe Ornborg et al. 2002 on blue tits


What Conditions must Drugs satisfy for them to be Deliverable via the Transdermal route? What Conditions must Drugs satisfy for them to be Deliverable via the Transdermal route? I assume a high $\log{P}$ (lipophilicity) would be one, are there any others?

Whether a drug can be delivered transdermally?  I think that carriers can be formulated to carry a small molecule through the skin into circulation, so I don't even know about lipophilicity. I believe if you spend enough money, you can overcome many of these problems.  I think that pharmacology might be just as important.

I think the first condition of a transdermal administration is that the drug cannot be effectively administered orally.  This is the most cost effective route go get a pharma compound into the body. It requires no devices, no fancy coatings or vaporizors.

Reasons that a pill (or its less popular cousins the suppository and sublingual tablet) cannot be used as the delivery system for a drug include effect of pH and other degradation of the compound in the GI tract, absorption rate from the GI tract and other factors such as effect of food in the system, other drugs which might interact in the system.

Another advantage of absorption through the GI tract is that this is the physiological system which is meant to be ingested and introduced into the body - its relatively fault tolerant, even if less of the drug actually reaches the blood stream.  There's more, but that's not a bad outline.

After pills and the like, the second choice is intravenous administration, which puts 100% of the drug into the circulatory system.   This has its own disadvantages, requires a clinical setting and the needle and breaking of the skin are not ideal in many cases.

If the drug needs continuous and non clinical administration there are many other means of drug delivery, including transdermal administration.  Differentiating these methods often includes making sure the drug is available specifically to the part of the body that needs it.  E.g. topical administration; putting on a medicated cream for a skin condition or use of an inhaler which delivers the drug directly to the lung for an asthmatic condition.

Transdermal administration has its own specific advantages; continuous distribution of the compound over long periods of time.  Disadvantages include: poor ADME properties for biologicals like antibodies and other proteins, low delivery concentrations where you need a large amount added (epinephrine, and maybe antibiotics come to mind).

Examples of successful transdermal delivery are testosterone gels and the nicotine patch.  Both of which apply continuous controlled low dosage that is important there.

There are three typical routes of drug absorption in transdermal delivery.  The drugs can diffuse through the membranes of dead cells of the stratum corneum, which works if the drugs are lipophilic enough.  They can diffuse around these cells, through the intercellular spaces, which can work for more polar drugs although this path is not usually as efficient.  The most extreme means are patches which contain tiny needles that can deliver straight through the protective layer of the skin.  With enough economic investment probably any sort of compound could be introduced through a patch.

Most of this is just cribbing off the notes from this lecture on coursera: Fundamentals of Pharmacology.  Its probably outlined on any pharmacology text.


Can the kidneys utilize ketone bodies for energy? Ketone bodies are water-soluble and should pose no problem to the kidneys because of solubility. If the kidneys are able to utilize ketone bodies for energy, then they must express the enzyme 3-ketoacyl-CoA transferase, correct?

Do the kidneys express the enzyme 3-ketoacyl-CoA transferase?

Can kidneys use ketone bodies as fuel?

Alexandria's answer:

This article's abstract says that 3-ketoacid-CoA transferase was found in the kidney: nature.com/pr/journal/v42/n4/abs/pr19972518a.html


What species does this moth belong to? It was found a few days ago in the state of Virginia, on the east coast of the United States.

Hemithea maybe, is as close as I can figure, although since there is so much variation between them it is very hard to tell.


What bug is this? I found several in my flat and I have no idea what kind of insect  is this? is it a moth larvea or a carpet bug?

That is the larva of a carpet or skin beetle, family Dermestidae.https://en.wikipedia.org/wiki/Dermestidae
These eat dried flesh, skin, and other dried organic matter. They are the bane of entomologists because they eat insect collections. They are used by bone-collectors to clean skeletons, and are the last insects to arrive at a corpse.


How do I change bond colors to something besides a different hue in Coot? I can modify the colors of carbons in Coot under Edit, Bond Colours..., but that only gives me different hues.  Is there a way to change the color to something less-saturated (or perhaps slightly transparent) so I can identify the "active" molecule I'm working on versus a template?

The menus seem no help, I'm wondering if there's some scripting magic that can do this.

You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example:

.

.... Because, from: http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html

  procedure: hilight_binding_site (imol, centre_residue_spec,
  hilight_colour, radius): hilight-colour is specified in degrees (round
  the colour wheel - starting at yellow (e.g. 230 is purple))

It looks from this like you only get to choose Hue (color_map_rotation) and not Saturation or Lightness, even with the script interface.

However, text can be full RGB

  3.28.3 (set-font-colour red green blue)

  where:

  red is an inexact number green is an inexact number blue is an inexact
  number


How can heart disease cause dizziness after eating? I have been reading several articles explaining dizziness after eating (see here and here), and both articles gloss over something that I found pretty remarkable.

Both articles claim that "heart disease" can cause one to experience dizziness after eating. For instance, as one article merely generalizes:

  A healthy heart is needed to pump blood faster during digestion. Certain heart conditions can lead to its inability to send enough blood to the abdominal organs, which may lead to a drop in blood pressure, resulting in dizziness and sometimes, nausea.

To me, this is pretty vague and uninformative. Making a blanket statement like "certain heart conditions can...lead to a drop in blood pressure" is like saying "not eating or drinking water can cause death."

I'm interested in are the hows and the whats: How does/can heart disease cause dizziness after eating, what are the reasons why this happens, and what are some examples of heart disease ("certain conditions") that cause this (as I'm sure there are many similarly-related diseases)?

Dizziness after eating, which can lead to falls and passing out, is called postprandial hypotension, and as the heart is indeed responsible for responding to hypotension by increasing it's rate - which can be seen in any number of clinical scenarios from blood loss to standing up too suddenly - failure to do so, for any reason including heart disease, can result in continued hypotension, which is experienced by most of us as dizziness.

Postprandial hypotension (PhTN) is defined as a fall in systolic blood pressure (SBP) of ≥ 20 mmHg occurring within 2 hours of a meal. This hypotension (hTN) can result not only in dizziness, but  may also cause syncope, falls, weakness, angina pectoris, and stroke.

Because PhTN is particularly common in older hypertensive patients, and older patients tend to have higher incidences of heart disease, it was initially thought heart disease was the cause. However, that didn't explain why some young people without heart disease have PhTN.

In truth, the mechanism of PhTN is not fully understood.

Normally after a meal, blood supply to the gastrointestinal (GI) tract increases, starting with increased flow through the left gastric and celiac arteries, followed by the mesenteric artery, which is more prolonged. Observations indicate that the postprandial hyperemia progresses along the GI tract in association with the movement of ingested food. The magnitude (25–200%) and the duration (3–7 h) of the hyperemia appear to depend somewhat on the composition of the meal. The increase in GI blood flow means there's less blood to circulate in the rest of the body (relative hTN). Normally this is corrected for in various ways.

Baroreceptors (nerve cells within arteries near the heart and in the kidney) are sensitive to rises, falls, and the rates of change in BP, but are especially sensitive to sudden falls in BP, which results in decreased baroreceptor firing. Autonomic Nervous System responds by increasing sympathetic outflow and decreasing parasympathetic (vagal) outflow. Sympathetic outflow leads to vasoconstriction (increased systemic vascular resistance, or SVR), increased HR (tachycardia) and increased force of contraction on the heart (positive inotropy). This leads to a partial restoration of arterial pressure. In people with PhTN, any abnormality at any point in the system will result in an insufficient rise in SBP to overcome the fall.

Therefore possible contributors to PhTN include inadequate sympathetic nervous system compensation for meal-induced GI blood pooling; impairments in baroreflex function; inadequate postprandial increases in cardiac output; impaired peripheral vasoconstriction, as well as abnormal responses to GI hormones released during digestion.

  Dysautonomic patients with postprandial hypotension fail to maintain systemic vascular resistance after a meal. This impairment in vascular response to meal ingestion may underlie the development of PhTN. Power spectral analysis suggests an impairment in the postprandial autonomic modulation of HR in healthy elderly and dysautonomic subjects, possibly predisposing to hTN when vascular compensation is inadequate.

Heart conditions that might result in an inadequate response to PhTN include low heart rate (bradycardia), heart valve problems (decreases cardiac output), heart failure (decreased ejection fraction equals cardiac output), patients with atrial fibrillation (decreases cardiac output because of inadequate filling of ventricles), heart attack (decreased ejection fraction), heart muscle disease (cardiomyopathy), severe left ventricular hypertrophy, people with HTN on medications which cause a lowered heart rate, etc.

Therefore, Postprandial Hypotension is an important hemodynamic abnormality in patients with cardiac diseases as well as autonomic nervous system abnormalities such as can be seen in Parkinson's Disease, diabetes mellitus, and others.

Postprandial Hypotension: Epidemiology, Pathophysiology, and Clinical Management
Association of postprandial hypotension with incidence of falls, syncope, coronary events, stroke, and total mortality at 29-month follow-up in 499 older nursing home residents.
Postprandial hypotension. Pathophysiological mechanisms and clinical implications in different disorders.
Postprandial hypotension in response to duodenal glucose delivery in healthy older subjects
Postprandial Hyperemia
Arterial Baroreceptors


How does Hemocytoblast constantly get formed into so many blood cells and yet remains there in the bone marrow throughout the lifetime? I mean, Hemocytoblast is a stem cell which is constantly being differentiated into daughter cells and leads to formation of all the blood cells (having short and limited life spans), so how come those stem cells remain there and continue to function, even when we grow up and finally grow old (i.e for 70 years approx)? The no. of those stem cells gotta be limited.

The trick for the stem cells lies in the way the proliferate and differentiate. See the image (from the reference 1):

Stem cells have the problem that they need to differentiate and maintain their population at the same time (subfigure a). This can either be done by asymmetric cell division which leads to one daughter which is still a stem cell and one which has been differentiated (subfigure b). Then it is possible that the cells divide only symmetrical (as shown in subfigure c) so they will either deliver two stem cells or two differentiated cells. And then it is possible (shown in subfigure d) that both possibilities are mixed and that symmetrical and assymetrical division occurs. Either way you get both: Differentiated cells and you still manage to maintain the stem cell pool.

References:

Asymmetric and symmetric stem-cell divisions in development and
cancer
Asymmetric cell division of stem and progenitor cells during
homeostasis and cancer
Asymmetric cell division


How do different tissue culture matrices affect background in fluorescent microscopy? In response to my previous question, I've been reading up a little bit on poly-D-lysine, Collagen I, Collagen IV, laminin, and other tissue culture coatings that promote cell adhesion. I've always assumed that anything other than standard TC-treated plastic or glass would significantly increase background, but perhaps my views on background fluorescence are a little outdated. Does anybody have experience with these in a fluorescent microscopy/high-throughput screening environment?

Specifically in my case, I'm looking at endocytosis and trafficking of a labeled protein into the lysosome. I'm labeling the protein with the pH-dependent dye pHrodoTM from Molecular Probes, which supposedly has very little fluorescence at neutral pH, but becomes very bright as the pH drops when endocytic vesicles become lysosomes. This theoretically means that a final wash step is not needed, but with a matrix coating on the plates I'm worried about background.

So, what is the current thinking as far as background fluorescence of the various TC matrices is concerned? Does the background come from the matrix itself, or by the fluorescent dye becoming adsorbed to it? Is it wavelength-dependent? Fortunately I may not be stuck with my poorly-adhering cells, and I may not need supplemental matrix at all in the end, but I still want a better understanding of how it works.

Extracellular matrix (ECM) fluoresces, especially Collagen and Laminin. The maximum is in the DAPI and FITC channels and the fluorescence becomes weaker towards longer wavelengths. However, since the coat on the TC flasks is very thin, I would not expect this to be a problem. The best thing is just to try it. There is also a quite famous document available which might be of help:

Autofluorescence: Causes and Cures


How does Topoisomerase II inhibition affect cancer cells? Topoisomerase II poisons represent some of the most important and
  widely prescribed anticancer drugs currently in clinical use. These
  drugs encompass a diverse group of natural and synthetic compounds
  that are commonly used to treat a variety of human malignancies. At
  the present time, six topoisomerase II-targeted anticancer agents are
  approved for use in the United States, and additional drugs are
  prescribed elsewhere in the world. These agents all act as traditional
  topoisomerase II poisons and function primarily by inhibiting
  enzyme-mediated DNA ligation.

Briefly describe what TopoII does and how it works. Explain what "inhibiting enzyme-mediated DNA ligation" means.

My thoughts for the first question are Type II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and
supercoils. They use the hydrolysis of ATP. It changes the linking number of circular DNA by ±2. After the ends are
cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re-
ligated. This  allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units.  It also
promotes chromosome disentanglement. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzymes are not allowed to ligate. This is
prevented by not allowing the formation of a phosphodiester bond.

Cancer cells grow much more rapidly than most cells in the body. What would be the consequence of "inhibiting enzyme-mediated DNA ligation" and why might this be particularly deleterious in cancer cells?

I am really unsure on this one.

I have looked at the Wikipedia answers to this question and they are wrong.

First question:

In general, topoisomerases are enzymes that relieve supercoiling in DNA strands and tangling in chromosomes. Type II topoisomerases is special among eukaryotic topoisomerases, considering they use divalent metal ions and ATP hydrolysis in their active site. The enzyme cuts both strands of the DNA helix simultaneously (double strand break) in order to manage DNA tangles and supercoils. It changes the linking number of circular DNA by ±2. After the ends are cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re- ligated. This allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzyme to re-ligate the DNA strand after it is cut. In other words, the prevention of a phosphodeister bond between nucleotides.

Second question:

In normal cells, DNA topoisomerase II plays several vital roles, mainly to relieve DNA tangles and coiling. This is done by generating "transient double strand breaks" in the DNA strand, which can sometimes cause harmful translocations and damage. Damage of this type is linked to certain specific types of leukemia. This intrinsically "harmful" quality of DNA topoisomerase II can be exploited in cancer cells due to their high replication rate . Certain cancer drugs, such as etoposide, act by altering the active site of topoisomerase II, preventing (inhibiting) the enzyme from ligating cleaved DNA molecules, causing permanent DNA breaks (and inhibiting replication). The fast replication rate of cancer cells ensures that there are large amounts of the enzyme present in the cell, increasing the effectiveness of any Topoisomerase II poisons. However, this drug can also act against some other types of tissues with large amounts of Topoisomerase II, such as cardiac tissue. Also, cancer cells are constantly in a growing/replication cycle, so they exhibit large amounts of the isoform Topoisomerase IIa, the type that is most likely to produce permanent and detrimental DNA breaks.

Source:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647315/


Why don't the female lions in a pride help their male lion to protect their children from other males? I watched a dozen of videos taping the fights between male lions; none of them involve female lions assisting in the fight. It is also known that the male lion who take-over the pride will kill all the under-age lions.
Why don't the female lions help their male lion such that their offspring won't be eliminated?
From an evolutionary perspective, the female lions will surely fight for their children as raising a new child is costly. Though they will most likely not fight to death. Even if a lioness does not have any child yet, her older sisters might already have a child so help defending the entire pride is the optimal strategy, although the younger sister might only contribute half of their strength comparing the older sister, as the child is not her direct offspring.

Alright, after watching a few more documentaries, here is what I found:
Lionesses do try to expel nomadic males, even if the male lion is not in presence.  On the other hand, I am still yet to find a single video taping the male and females collaborating to expel the invading lions.
When invading a pride's territory, the nomadic brothers will usually not attack first, even if there is only one "lion-king" in the pride. The nomadic brothers might think that the females will help the lion-king to protect the territory; otherwise the brothers will just simply attack as it is a 2 to 1 odd.
The nomadic brothers will usually disrupt the pride's food-supply first. As the pride usually have many cubs to feed, it consumes much more food than the nomadic brothers, and the lion-king is then forced to launch his attack first.
The fight between male lions are usually not lethal possibly due to male lions' body structure. Most of time the nomadic brothers are expelled, but sometimes the lion-king is wounded or expelled from his own territory.
After being wounded, the lion-king cannot protect his cubs. The nomadic brothers then start to find and kill the cubs. The females do sometimes try to protect their cubs, but their attacks can only lightly wound the male lions as males are well-protected by their hairs. In contrary, the males can one-hit the youngsters.
Cubs close to 2-year-old do try to run away and the females do sometimes help them by providing them food, even if the females seem to be obedient to the new dominating males. In this video the lioness even decide to run away from the original territory to raise-up her children and half-children: https://www.youtube.com/watch?v=eMgPf83uDec.
After all cubs are killed or expelled, the females lose the motivation to fight against the invaders, and the new pride is formed.


Why do mitochondria waste energy? In a mitochondria, it makes ATP by using energy from NADH and FADH2 electron to pump H+ into the inter-membrane space then use the ATP synthase to bring the H+ back into the matrix while using the proton motive force to create ATP.

My question here is, why does mitochondria do this, I mean, in terms of energy I think it is a waste of energy. For example using energy to put water on the top, then generating energy by making to water come down should make some unneeded energy loss.

Its because NADH is a powerful reducing agent. If you leave high concentrations of NADH in the cell, it would actually wreak havoc on the cell.

This is actually the reason why peroxisomes just remove FADH2s because they find no use for the extra energy and simply remove it.

So heres the simple answer. Energy is not always a good thing, because stability also matters. ATP is simply a good way to store and convert such energy.


Cold water sour taste Recently I underwent a wisdom tooth extraction, and while there is still numbness I have observed something peculiar. If I drink cold water, it tastes sour, however the same effect is not observed with room temperature water or hotter. What is causing this effect?

Here is an educated guess: firstly the typical dental anesthetic is lidocaine which tastes very bitter. Secondly, a bitter taste if often misclassified as sour. Thirdly, sensory thresholds (the amount of a compound required to detect its taste) is temperature dependent and lower at cooler temperatures. In other words, I assume that drinking cold water made you able to detect small remaining traces of bitter lidocaine that were too small to detect at warmer temperatures, and that you misclassified as sour.

Wei, Y., Nedley, M. P., Bhaduri, S. B., Bredzinski, X., & Boddu, S. H. (2015). Masking the bitter taste of injectable lidocaine HCl formulation for dental procedures. AAPS PharmSciTech, 16(2), 455-465.

https://www.sensorysociety.org/knowledge/sspwiki/Pages/Sour-Bitter%20Confusion.aspx

McBurney, D. H., Collings, V. B., & Glanz, L. M. (1973). Temperature dependence of human taste responses. Physiology & Behavior, 11(1), 89-94.


Is it possible to perform selection of plants without seeds? When a plant spread using roots or branches I believe new plants keep same genome.

Many plants don't have fertile seeds. How it is possible to improve quality of genome (perform selection) for such plants?

Should we wait for natural mutation to spread across entire plant?

Strawberry is a good example of such plant and we know large verity among this species. How was it achieved?

Most commonly by breeding with a related plant - if there is one. Mutagenesis is an old technique that technically can work.

If one part of the plant has mutated, of course you can take cuttings or plant tissue culture samples.

strawberries can be bred and characteristics selected for.
https://en.wikipedia.org/wiki/Breeding_of_strawberries

A good example of a difficultto breeed plant is bananas
See
http://www.promusa.org/blogpost363-Who-s-breeding-bananas


First neurotransmitter? Cnidaria are considered to be the first phyla to develop a nervous system. Nervous systems having 1, 2 and three neurons are considered to have appeared first in Cnidaria, with 2-neuron nervous systems having already specialized neurons for sensory and motor functions.

This takes us to the first synapse, which is thought to be of chemical nature, as the sensory and motor neurons in early Cnidaria utilized a chemical to communicate. This would be the first chemical to be used as a neurotransmitter, but which was it?

I cannot give a thorough answer right now (if I even find one) because I'm on my phone, but here are some papers that could inform the question in the meantime (or their abstracts at least!)
One element I have gathered so far is that the evolution of nervous systems likely involved not the evolution of wholly new molecules and structures, but the cooptation of existing structures for new purposes. Meaning the first neurotransmitters would have been pre-existing with some other purpose in early proto-neurons, not new molecules evolved expressly for the first synapses. One paper talks about neurotransmitters like dopamine being common across all life, including plants (no nervous systems there!). This does not answer which of these molecules would have been the first neurotransmitters however.
The abstract of this paper doesn't say much but the title is tantalizing:
https://link.springer.com/chapter/10.1007/978-3-319-20215-0_2
"New Trends and Perspectives in the Evolution of Neurotransmitters in Microbial, Plant, and Animal Cells"
This paper shows a unicellular eukaryote reacting to various neurotransmitters. If the full paper goes into the phylogeny some more it might be interesting:
https://sciprofiles.com/publication/view/0cc41fa28399e0e366d3199c3bcc48eb
"The Phylogenetic Background of Neurotransmitters in the Unicellular Organism Tetrahymena Pyriformis"
This paper's abstract says all I was saying about the development of neurons and synapses relying on pre-existing molecules and structures:
https://pubmed.ncbi.nlm.nih.gov/2830635/
"Evolution of Neurotransmitter Receptor Systems"
What I'm looking for to find how close science is to answering your question (or if it already has) is papers looking at the phylogenetic relationships of different neurotransmitters and related molecules. That might say a lot about which ones have been used as neurotransmitters the longest. I haven't found this yet but I'll try more tomorrow when I'm not on mobile.
ETA: will re-edit this comment later, but this paper answers your question I believe, or as well as any could at present at least:
https://cichlid.biosci.utexas.edu/sites/default/files/evoneuro/files/liebeskind_et_al_2017.pdf?m=1511200627
"Evolution of Animal Neural Systems"
This paper, which is available in full and is a review paper from 2017, looks at the evolution of every aspect of animal neural systems (i.e. nervous systems mediated by neurons, a concept the paper also defines because the line is apparently blurry). One interesting aspect of it is that while you point to Cnidarians as the most "primitive" nervous systems, the paper points out the latest evidence suggests Ctenophores are the earliest branch off the animal tree, meaning nervous systems either evolved convergently, or sponges lost their nervous systems secondarily, in which case Cnidarians would lose this special status.
The paper has a section about neurotransmitters, which says the following:

Several types of molecules are used as neurotransmitters; their evolutionary deployment in different synapse types across animals is fascinating and still poorly understood. Many are used widely in eukaryotes for intercellular communication, but some of the biogenic amines may be present in animals as a result of the late horizontal transfer of synthesis enzymes from bacteria(Iyer et al. 2004). For instance, epinephrine and norepinephrine are important neurotransmitters in vertebrates but not in protostomes (but see Bauknecht & Jekely 2017), whereas the opposite is true of octopamine and tyramine (Figure 4). Cnidarians make a set of neurotransmitters similar to those in vertebrates (Kass-Simon & Pierobon 2007), but Nematostella expresses most nonpeptide types in the endoderm near the pharynx and testes—only peptide transmitters are found in neurons(Oren et al. 2014)
Intriguingly, ctenophores seem to use a much more restricted set, as glutamate is the only well-validated neurotransmitter (Moroz et al. 2014). This is consistent with the theory that neurons arose independently in ctenophores and planulozoans because vertebrates and most protostomes use acetylcholine at the NMJ [neuromuscular junction I assume -my edit]. However, arthropods use glutamate at the NMJ, just as ctenophores do ( Jan & Jan 1976), and cnidarians probably use neuropeptides (Oren et al. 2014). Although sponges do not have true synapses, they use γ-aminobutyric acid (GABA), glutamate, and nitric oxide to coordinate contractions (Elliott & Leys 2010). Trichoplax individuals also lack synapses,but their secretory flask cells label for FMRFamide, suggesting a conserved role in transmission for this peptide class (Smith et al. 2014).

This gives at least a few names of neurotransmitters that are particularly conserved and candidates for neurotransmitters the common ancestor of neurons used (glutamate, acetylcholine; they may have been peptides, whatever that covers), and I think makes it clear that it is very much not known what those first neurotransmitters were.


Is rabies virus infectious outside host? Can rabies virus remain infectious on environment i.e on soil, grasses, leaves and water?

First off all we need to be 100% sure what does be infectious mean. According cambridge dictionary meaning of the word infectious is be able to past from one host organism (multicellular/cellular) from another. So this is actually biggest hole in your question.

But i think you mean something else then word infectious. In my oppinion you wanted to know if rabbies can survived outside of its host. The rabbies virus as many other viruses cannot live outside of its host. Rabbies is exists in "public reservoir". This fact only confirm its variety of hosts such as bat, bears, dogs etc. (technicly all warm blood species) and its long incubation period (for example 1-3 months in humans.

According this site:

Rabies virus is transmitted through saliva and brain/nervous system tissue. Only these specific bodily excretions and tissues transmit rabies virus. If contact with either of these has occurred, the type of exposure should be evaluated to determine if postexposure prophylaxis is necessary.
Contact such as petting or handling an animal, or contact with blood, urine or feces does not constitute an exposure. No postexposure prophylaxis is needed in these situations.
Rabies virus becomes noninfectious when it dries out and when it is exposed to sunlight. Different environmental conditions affect the rate at which the virus becomes inactive, but in general, if the material containing the virus is dry, the virus can be considered noninfectious.

To sum this:
Rabbies viruses need to have contact with host, typicly by biting. It is possible to be infected by other contacts such as kissing, licking not dry saliva, but still the virus cannot live long outside of body. So long incubation and variaty of possible host (most infected is bats) makes the true killing combination.


Is the ACh receptor more permeable to sodium ions? The AChR is permeable to sodium and potassium ions only and has a reversal potential of 0mV.

However the Nernst potentials for sodium and potassium ions is ~ +60mV and -88mV respectively. Taking a simple average of these two potentials would give an expected AChR reversal potential of -14mV; but that is not what we see.

My question is whether the reversal potential is pulled up to zero because of a greater conductivity to sodium than potassium ions, and if so, how the AChR selectivity filter achieves this.

Thanks!

Short answer

No.

There are differences in Na+ versus K+ permeability, but you have it backward: potassium is actually slightly more permeable; however, these differences are not the only factors influencing the reversal potential, and also, the reversal potential for a nAChR need not be exactly 0 mV.

tl;dr to the long answer

You need to sum before taking ratios rather than take a difference of ratios when computing a reversal potential for multiple ions together.

Before we get into the weeds...

In most sources you will hear something like the reversal potential for a nonspecific ligand-gated channel like nAChR is "about 0 mV" - this is going to vary in different cell types, in different conditions, with different recent activity levels, with different versions of the receptor, etc.

What's important to remember in all this is that -14 mV is also about 0 mV... In the context of excitable cells, what is most important is the reversal potential relative to the threshold for firing a spike or activating other channels. That said, I'm not actually saying the reversal potential for nAChR is actually -14 mV, there are a couple other factors missing...

What you are missing

The big one you are missing is that the concentrations of the ions matter, not just their ratios. For the reversal potential of a single ion, all we really care about is the ratio inside and out, which is found in the Nernst equation.

Averaging the reversal potential for two major ion species, like you have done, gives you a pretty good ballpark estimate (afterall, -14 mV is also about 0 mV!).

To get the actual reversal, however, you'll need the Goldman Equation.

We can simplify the Goldman equation for just Na+ and K+ in fairly standard conditions to something like:

$61.5 \mathrm{mV} * log_{10}(\frac{P_{Na} [Na^+_{out}] + P_{K} [K^+_{out}]]}{P_{Na} [Na^+_{in}] + P_{K} [K^+_{in}]]}$)

If the permeabilities are both :=1, and the concentrations of Na and K are equal and opposite, then indeed you will get zero. However, if that was true, you would also have equal and opposite reversal potentials for Na and K alone in the cell: in the numbers you gave, that isn't the case.

I'm not sure what numbers you used exactly, but I'll use my own example. If potassium is 5mM out, 140 mM in, the reversal potential will be -85.6 mV for potassium. If sodium is 140 mM out, 12 mM in, the reversal potential will be 63.1 mV for sodium (you can check my math with the Nernst equation).

If you combine these numbers in the Goldman equation above, you will get -1.2 mV: closer to zero than your -14 mV estimate.

They are so close because the ratio (140+5)/(12+140) is a lot smaller than the difference of the ratios (5/140) and (140/12): order of operations matters.

This is assuming identical permeabilities

However, the permeabilities aren't actually identical

There are many papers measuring relative permeabilities in nAChRs, I just chose one randomly as an example (happened to be the first Google Scholar result).

Nutter and Adams 1995 found the relative permeability of several monovalent and divalent cations, with Na as a reference:

Therefore, potassium is actually slightly more permeable than sodium. However, there are also other important ions that could contribute, even if they are found at lower concentrations than either sodium or potassium, and the example ion concentrations you find in a textbook might not apply in the systems you are studying. A source that says nAChRs are only permeable to sodium and potassium really just means that they are not permeable to another other important high-concentration ion: chloride. They are also simplifying things a bit for you, which is okay.

If I use the Goldman equation quickly with these data, I get a reversal potential (with just Na and K, ignoring other ion species) of -5.9 mV: still "about 0 mV" and still closer than your original -14 mV estimate.

But how are different ions with the same charge showing different permeabilities?

This is better off as a separate question, and probably easier to address with a more extreme case, like in selective sodium or potassium channels. However, like in those channels, in channels that we call "non-specific", the particular arrangement of amino acid residues (especially charged ones) at the pore can favor particular ions because those ions differ slightly in size.

Nutter, T. J., & Adams, D. J. (1995). Monovalent and divalent cation permeability and block of neuronal nicotinic receptor channels in rat parasympathetic ganglia. The Journal of general physiology, 105(6), 701-723.


How do mRNAs find ribosomes? After mRNA is released from the nucleus, the next process is its translation by ribosomes. By what physical, chemical or biochemical process does the mRNA reach the ribosome in the cytoplasm?

The answer to the first part of your question is: diffusion. After transcription and some processing, the eukaryotic mRNA is exported to the cytoplasm. Here it floats around until it meets a ribosome. Binding of ribosome to mRNA is facilitated by proteins called initiation factors (IFs) and the 5' cap of mRNA$^1$.
The second part of your question basically asks about cell-free protein synthesis using an RNA template. This has already been shown to work: one is reminded of the famous Nirenberg–Matthaei experiment$^2$, which ultimately led to the cracking of the genetic code. Nirenberg and Matthaei worked with bacterial cell extracts, but systems based on eukaryotic cell extracts have also been developed$^3$.

References and further reading:

Nelson DL, Cox MM. Lehninger principles of biochemistry. 7th ed (international edition). Basingstoke, England: Macmillan Higher Education; c2017. Chapter 27, Protein metabolism; p. 1077–1126.
Nirenberg MW, Matthaei JH. The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. PNAS. 1961 Oct 1;47(10):1588–1602. https://doi.org/10.1073/pnas.47.10.1588
Chong S. Overview of cell‐free protein synthesis: historic landmarks, commercial systems, and expanding applications. Curr Protoc Mol Bio. 2014 Oct 1;108(1):16.30.1–11. https://doi.org/10.1002/0471142727.mb1630s108


What is this insect? Seems to be in Indonesia https://www.facebook.com/gadik63/videos/707361412787259/

This video has me completely baffled.

https://en.wikipedia.org/wiki/Creatonotos_gangis

Creatonotos gangis is a species of arctiine moth found in South East Asia and Australia. It was described by Carl Linnaeus in his 1763 Centuria Insectorum.


Do male mammals other than humans have nipples? When I grew rabbits, I had a pair, one male and one female. And while the female's nipples were quite prominent, especially after giving birth, I don't remember the male having any nipples at all.

Do males of other mammal species, have nipples like human males, or is it a trait that's unique to Humans?

Most mammalian males have nipples. The duck-billed platypus does not have nipples but you begin to see development of nipples in marsupials (Park and Lindberg 2004) like the opossum and kangaroo.  Development of a complete nipple begins in the eutherian (placental) mammals.

The mammary glands develop early in the embryo along a pair of ridges called the mammary ridge, mammary lines, or milk line (shown in an adult human in the figure below, taken from Wikipedia). The nipples form along this line. In humans, this happens during the fifth week of development. Within a few days, nipples begin to form. The number of nipples pairs that form is characteristic of the species (e.g., 1 pair in humans to 9 pairs in pigs). The development of nipples occurs before sexual differentiation begins which, in humans, is during the sixth week of development. That's why both males and females have nipples. This same order of develop occurs in other mammals, revealing our common ancestry.

However, because the process is under genetic control, mistakes can happen. Occasionally, humans (and other mammals) can develop extra nipples, the so-called supernumerary nipple(s). The most common places that humans develop one or more supernumerary nipples are identified by the circles in the figure above. The actor Mark Wahlberg is not shy about showing his.

For a general overview of mammary gland development, Dr. Jacqueline Veltmaat has a nice web page that highlights her research in this area. For those interested in the more technical genetic aspects of mammary gland development, a paper by Watson and Khaled (2007) reviews the genetic processes that regulate development of the mammary gland in mammals, based on the mouse model system. The article covers all stages of mammary gland development, from the embryo through puberty to pregnancy. Their Figure 1 shows one row of embryonic mammary buds (labeled MB1 - MB5) in the embryonic mouse. In the case of the mouse, all of the mammary buds will develop into fully functioning mammary glands.  Another paper by Robinson (2007) discusses the signalling pathways during development of the mammary glands.

Literature Cited

Park, C.S. and G.L. Lindberg. 2004. The mammary gland and lactation. pp. 720-741 in Dukes' Physiology of Domestic Animals, W.O. Reece, ed.  (Publisher not identified.)

Robinson, G.W. 2007. Cooperation of signalling pathways in embryonic mammary gland development.  Nature Reviews Genetics 8: 963-972.

Watson, C.J. and W.T. Khaled. 2008. Mammary development in the embryo and adult: a journey of morphogenesis and commitment. Development 135: 995-1003.


Are there any pre-Holocene venomous animals? The novel (and subsequently movie) Jurassic Park featured a dinosaur called Dilophosaurus, that was purported to be venomous and had an ability similar to that of the extant spitting cobra. Unfortunately, the whole setup isn't real.

This got me wondering though. Modern venomous snakes, to give a particular example, ought to have had ancestors that already had appropriately modified salivary glands, and similarly for most other extant venomous species. (I suppose I'll restrict myself to vertebrates so as not to be too broad.)

I now ask: have fossils of animals that are likely to have been venomous ever been discovered?

Squamates

Extant venomous snakes do have venomous ancestors. Fry et al. (2006) reported on finding venom toxins more broadly within Reptilia, beyond the well-known venomous snakes and the helodermatid lizards. They show that varanid and iguanid lizards also have venom toxins.

The same group of authors (Fry et al., 2009) then reported on the use of venom in the extant varanid lizard, Varanus komodoensis (Komodo monitor). This is a different hypothesis than the usual "toxic bacteria" hypothesis for predation in these animals. They then reinterpret the skull of the giant (~5.5 m) varanid Varanus (Megalania) priscus. They conclude, based on anatomical similarity and the close phylogenetic relationship between it and V. komodoensis, that V. priscus' predatory mode was more similar to other varanid lizards, likely involving venom delivery.

Archosaurs

Discovery of a venomous clade within squamates, including snakes and several clades of lizards, does not imply venom more broadly within Reptilia. Specifically, it would not parsimoniously reconstruct the presence of venom in Archosauria, the clade that includes dinosaurs. However, Gong et al. (2009) interpret the teeth of the dromaeosaurid theropod dinosaur, Sinornithosaurus as having venom grooves. These grooves are similar to grooves in the teeth of Uatchitodon, a Triassic squamate from Arizona.

There is currently no solid evidence that archosaurs could spit, nor is there ever likely to be.

Mammals

Venomous extant mammals include the platypus (Ornithorhynchus), Solenodon, and some species of shrews. The venom gland in the platypus is a modified sweat gland on the hind limb, which includes an ossified spur. A similar structure has also been found in the basal mammalian taxa Gobiconodon and Zhangheotherium (Hurum et al., 2006). Hurum et al. (2006) described a similar structure in the multituberculates. As the most basal clade of Mammalia, the authors conclude that an ossified spur is apomorphic for Mammalia and that the ancestral mammal may have used it for venom delivery. This structure would have been retained more-or-less unmodified in platypus and lost in other mammalian lineages. The authors' conclusions are supported by the presences of a non-venomous spur in the other clade of monotremes, the echidnas.

Fox and Scott (2005) report that the Palaeocene (~60 Ma) pantolestid Bisonalveus browni also possessed teeth with venom delivery grooves.

Non-gnathostomes

Szaniawski, 2009 used similar logic based on grooved "tooth" elements to conclude that some extinct jawless chordate conodonts may also have been venomous.


Confusion regarding photosynthesis and respiration in plants During 24 hours there is a time in i.e. twilight when plants neither give oxygen nor carbon dioxide why is it so?

This also suggests that neither of the two vital processes i.e. respiration or photosynthesis is being carried out.

Well,
during twilight there is not enough sunlight so photosynthesis may  slow down or even cease but what about respiration?

You haven't directed us to any evidence for your assertion, so it is difficult to evaluate.

I'm not a plant physiologist, so I will argue from first principles:

photosynthesis consumes CO2 and produces O2:

6CO2 +6H2O -> C6H12O6 + 6O2

respiration consumes O2 and produces CO2:

C6H12O6 + 6O2 -> 6CO2 +6H2O

Plants do both of these things at the same time for at least part of the day. During the day, in a growing plant, photosynthesis will exceed respiration: a lot of the fixed carbon is fed into anabolic processes to produce "plant stuff"; polysaccharides, proteins, nucleic acids. This means that the plant will be a net producer of O2 and a net consumer of CO2. At night there is, of course, no photosynthesis and respiration will dominate and the plant will be a net producer of CO2 and a net consumer of O2.

At certain times of the day, twilight for example, there will be a transition between these two states, and the plant will pass through a state where there will be no net flux in either of the gases.


Traceability of a mature tree to its original seed via DNA Is it possible to trace a specific seed to a fully mature tree?  For example, Can a seed be traced to the full-grown plant based on DNA?  Would it be possible for me to catalog a seed DNA and then years later be able to identify the full-grown plant to that seed that was cataloged?

As the embryo of a seed typically contains many cells, it should in theory be possible to obtain DNA from a seed without disrupting it (there may be pragmatic issues with protocol, depending on the particulars of the seed).
If you have the DNA and each seed has been produced by a separate fertilization event, then each seeds DNA would be unique and it should certainly be possible to identify an individual genetically, just like it is with animals.
Not all seeds are genetically distinct however. For example, many plants will also produce seeds asexually under appropriate conditions, a process known as apomixis. If the seeds are being produced asexually, then your only hope would be to identify different mutations in different seeds, which is a much fainter signal and likely to fail for your intended purpose.


Functions of tracrRNA and crRNA in the CRISPR/Cas9 system I need some help about Crispr / Cas9.
The CRISPR/Cas9 technic consists (for bacterias) in "cut" bacteriophage's DNA, in order to make it unfunctional.
When the RNA is transcribed (RNA which is complementary to the bacteriophage's DNA), it will be associated with crRNA and tracrRNA to form the sgRNA (single guide RNA).
But I would like to know where crRNA and tracrRNA are from? and what are their function(s)/ goal(s).

Sorry If I made mistakes I'm French.

I have also been wondering the same thing for a while now and I think that the best answer that I could find after reading several review papers on CRISPR/Cas9 and online information, points to tracrRNA as serving the role of multiplexing with pre-crRNA which helps pre-crRNA mature to crRNA. This process activates the crRNA. I'm not exactly sure how this multiplexing action "matures" the pre-crRNA or what exactly that even means, but that is as much insight as the literature provides (see e.g. this abstract to a conference talk).

There most likely are some more important functions that have not yet been discovered for tracrRNA yet.