texts: Do ants use something similar to the honey bee "waggle dance" to instruct the rest of the colony where to find a food source?

texts:
In the 20 years since we built our home, we've just recently had our first ant infestation.

I'm familiar with the fact that ants leave scent trails to find their way back and forth between the colony and a food source.  So in my limited experience with ant eradication, I assumed that by taking away the empty ice cream bowl and scrubbing the scent trail which lead to it off the kitchen counter (multiple times with different household cleaning products) the ants would quickly give up their search.

My assumption was that the oncoming foragers would be confused by the abrupt end of the scent trail and wander aimlessly in the gap between where the trail had been scrubbed away and the former location of food.

However, what I’ve observed again and again is ants continuing to move across the scrubbed counter to the exact location of where the food used to be -- as if they didn't need the scent trail.  Their only confusion seems to be the lack of food at that spot.  This behavior will continue for several hours after the removal of whatever food had been there, despite multiple eradications and vigorous scrubbings of where the original trail had been.

Ants follow odor plumes to food sources according an answer in another Biology Stack Exchange post.
(Can ants sense food from a long distance?)

And from a link in the same Biology Stack Exchange post “If they [patroller ants] didn’t return to the nest, departing foragers would know it wasn’t safe to go search for food.” and “The ants can take advantage of sudden windfalls of food, but they don’t waste energy and resources if there’s nothing there.”
(https://wikkorg.wordpress.com/2015/04/23/ants-swarm-like-brains-think/)

Here are my questions:

Are ant scent trails strong enough to withstand multiple washings with soaps, detergents and disinfectants?

Can ants detect airborne food molecules in very small parts per million, even after the food and its odor plume have been removed?  If not, do ants use something similar to the honey bee "waggle dance" to instruct the rest of the colony where to find a food source?  Or both?

Why and how do they keep coming back to a place where there is no food, especially if (eradicated) members of the colony are not returning?


texts: Identification of an insect from Bangladesh

texts:
This is a video of the insect. Sorry, I don't have any still photograph.
Location: Savar, Bangladesh.

I've been suggested by an insect photographer that it is a caddisfly.

EDIT: Here are two images from the video


texts:
I’ve just learned about cell division and I noted that plant cells don’t have centrioles but still undergo cell division. I’ve read a few documents about it and wondered why plant cells don't have centrioles.

How is it that plant cells can divide without centrioles?


texts: anybody know what this might be, found in my bed. Pennsylvania, USA . Thanks


texts: I found two of these objects near a creek in Missouri. They feel like they are made out of bone but they do not look like any bone I have seen before. They also appear as though the could be some sort of plant part. I am having a very difficult time identifying them and any help would be appreciated.


texts:
what are the "next day" actions that one has to take, when accidentally ingests contaminated drink/food from Aspergillus or Penicillium or Candida fungus?

Is it feasible to take N-acetyl-L-cysteine supplements? What other measures minimize the damage from the mycotoxins?

What kind of supplements and/or treatments reduce the superoxides produced as effect of the mycotoxins?


texts: Is there a scientific proof that smoking spoils face skin?

texts:
I saw that cigarettes-smokers (more than 3 cigarettes per day) often have the skin of the face which is a little bit spoiled.

Is there any scientific proof that cigarette smoke (or the nicotine inside it) is a damaging fator for face skin?

Or it is just due to the skin-smoke interaction casued by the smoke that the person breaths out from the mouth?


texts: Are these 2 procedures to fight cancer (cancer "vaccine", and cancer drugs which can attack all tumours) related?

texts:
Last year appeared the new of a cancer "vaccine" (not a vaccine in the traditional sense) tested in animals for 4 types of cancer and which worked in 97% of the cases to eliminate already existent tumours.

Cancer Vaccine Trial

Now appeared the new of "cancer drugs which can attack all tumours" to be fast-tracked by NHS.

Game changing cancer drugs can attack tumours

I would like to know if both procedures are based in similar ideas (meaning the second one could have a similar effectiveness to the first one) or if they are completely unrelated.


texts: Near-zero water loss in a closed hydroponics system?

texts:
I know there are a lot of factors that would impact this...

Plant type.
Plant neediness (i.e., even sibling plants will possess different needs, defects, etc).
Automation efficiency.
Water & nutrients quality.

And that is barely touching the surface, but assume that...

We only have 1 healthy adult (meaning fully grown) plant who transpires 90% of absorbed water. The other 10% fuels photosynthesis, cell growth, etc..
Its nutrient levels/requirements are (somehow) perfectly monitored/satisfied.
The hydroponics system is enclosed s.t. nearly all the transpirated water is reintroduced into the water supply, rather than evaporated.
The recycled water is kept clean & nutritious by an automated system.

So my questions are...

Is it possible to create a system where the aforementioned 10% accounts for the only loss of water?
Am I missing any other significant source(s) of water loss?
Are there implementation factors which would jeopardize the plant's health?


texts:
I am somewhat of a newbie in evolutionary biology currently taking my first steps in bioinformatics. I was reading a paper when I came across the term  "constrained genetic elements", referring to sequences in the genome.

From what little I found googling the term, a constrained genetic element is a sequence/region in the genome that can be found preserved in many generations of a species. Is my understanding correct? What are the criteria by which those regions are identified?

The paper is Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures.


texts:
First time posting. I recently started working in the field of metabolomics. I have semi-quantitative (not absolute concentration) LC-MS data from in-vitro cell experiments under different experimental conditions.

What is the best way to normalize the data so that I can compare across experimental conditions correctly ( + across different cell types)? I've found many people scale their data using different methods (pareto scale, auto scale, zero mean)  each of these leads to different results when I run something like a PCA between experimental groups.

Thanks.

Jon


texts: Coiling of chromatids during cell division

texts:
What is exactly coiling of chromosomes?
I just heard about the names i.e paranemic, plectonemic, orthostichious, anorthospiral.
I have ecaxtly no idea of what phenomenon is this.
Also what type of coiling occurs during meiosis and mytosis type of cell division.
Could it be explained in detail....?


texts: Is there any evolutionary significance of downward facing nostrils in human beings?

texts:
The nostrils in apes and monkeys are almost at the front, but in humans nostrils (external nares) face downwards. Also a lot of non-primate mammals like goats have nostrils at the front.

Is it the increased cranial capacity in humans which pushed the nostrils downwards?

Is having a pair of downward facing nostrils, an advanced feature? If yes, then why?


texts: Why does size decrease across the sequence of human chromosomes?

texts:
The following graph shows a decrease in the number of base pairs per chromosome across the sequential set of human chromosomes:

Is this because chromosomes were originally numbered by their size on the karyotype?


texts:
My wife and I recently found out that we are going to have twins and so nearly everyone asks if we have a family history of twins.  Now I know that the answer for me is that it doesn't matter—as a man, I have no influence on my wife's tendency to hyper-ovulate.  And, of course, if we turn out to have monozygotic twins (we don't know yet), genetics plays no part.

Therefore the question only matters on my wife's side and only if dizygotic twins are known in her heritage. As it happens, we don't know of any twins on her side.  Given that many factors besides genetics are relevant to twins being born and we only know her family history for a half-dozen generations with any confidence, what are the odds that we would observe twins in her family history if she is genetically predisposed to having them?

Or, to put in another way, can I respond that nutrition and other factors were probably more important than genetics?


texts: Why are so many spermatozoa produced when only one of them fertilises the ovum?

texts: During fertilisation only one sperm can fertilise the ovum. So why so many millions of sperms are produced?? Isn't this a waste of energy?


texts: Are there people cured of HIV by means of HAART?

texts:
I wonder if there people who were cured of HIV only by means of highly active anti retro-viral therapy (HAART) or other drugs rather than by bone marrow transplant?

I know that HAART can suppress HIV below detectable level but are there people who stopped HAART and did not experience the HIV levels rising?


texts: This was found under a rock in a freshwater creek in Maryland. Stayed like this for while, then stretched out long, then contracted, and then JUMPED off the rock back into the water. Looks like a trilobite. Rock-colored.


texts:
In prokaryotes, GroEL protein (together with GroES) is required for protein folding.

Question: Can a bacterium survive without GroEL protein?


texts: Is there a way to determine how far and how fast an animal can run for based on geometry?

texts:
I was looking at research and finding that drastically different animals can fall under the same brackets for how far and how fast they can run, or that similar animals can fall under different brackets. For instance, a kangaroo could hop at 40mph for a couple miles, meanwhile an elephant can also run about 40mph but for only a couple miles. They're very differently shaped animals, and yet have a similar ratio of their sustained run to their stamina.

Conversely, humans can run for a very long time but maybe no more than 20mph for those in great shape, though they can do it for many miles, over 20 miles which is longer than an elephant can run for. Bears have very similar legs and feet to humans as they are both larger plantigrade mammals, but they can run at 35mph for their top speed and otherwise don't have as much stamina as humans.

Felines and canines are often thought to be similar in many ways. Wolves are known for being able to run and walk for long distances, often having more stamina than their prey and moving 10-30 miles in a day. But, their top speed is only somewhere in the range of 20-35mph. Lions have very similarly shaped bodies and yet are more adapted to run short distances at around 50mph. Similarly, dogs can run for long distances, but cats can jump much higher and not just in proportion to their body length but in terms of absolute length, despite having very similarly shaped bodies.

The reasons for these differences must have something to do with the combination of the geometry of their vertebral column, legs and feet over which their muscles are shaped as well as the weight of an animal. If an elephant was lighter, it would surely run much faster, probably comparable to a horse as its feet are already ovaloid and digigrade. And, if a dog was lighter, it would probably be able to jump higher than a cat. If humans were more massive, then they probably wouldn't be able to run as far, but would probably as fast or faster due to increased muscle mass that compensates. A horse and other horse-like animals seem to have a very good ratio of geometric features to mass that lets them run both very far and very fast.

With all this diversity in mind, what common denominators can be found to account for how the geometry of an animal determines its speed for its given mass?

For instance just as a very crude estimate, I would say animals with particularly long legs that are more closely aligned with the angle of their vertebral column have a tendency to run the farthest, but also the slowest. This might have something to do with how the elasticity of longer muscles and tendons is more efficient for repetitive motion, but not necessarily for propelling a body forward by keeping the force transferred from feet perpendicular to the ground up the leg and in the direction of motion.


texts: How stable is linear DNA transfected in eukaryotic cells?

texts:
I would like to know, with references from the literature, what is the half life of a linear dsDNA transfected in a mammalian cells.
For example, if I transfect human cells with a PCR product (500-2000 bp), that does not contain any replication or transcription signal, how fast will it be degraded by the cell (hours, days, weeks...)? Is there any difference in the half life if the DNA is in the cytosol or in the nucleus?


texts: I discovered a few of these while cleaning an outdoor fish pond north of Sacramemto California. What is this?


texts: Effect of respiration on Arterial pressure

texts:
I am trying to explain the effect of respiration on arterial pressure.
I am looking preferably some visual way to show it.

How can you show the effect of respiration on arterial pressure?

I am thinking some kind of figure which has the respiration rate and arterial pressure.


texts: Comparing Embryonic stem cell and hepatic stem cell

texts: So, currently, I want to compare transcriptome data for liver cell development. I found 2 data sets which start from stem cell, hepatoblast, and then adult cell. The first data set use hepatic stem cell and the second data set use embryonic stem cell. I am trying to map the difference in the gene expression during cell development, so it is important to make sure the state of the cell is same. My question is, is this stem cell comparable and can be grouped as 1 category? If hepatic stem cell and embryonic stem cell is different, is there something in common that probably can be used as basis of my analysis?


texts:
While doing morning-walk in Keweenaw Penisula, Michigan; I found this juvenile bird wandering around looking for her mother !

Can someone spot which bird is it?


texts: How does the body count time in the short term?

texts: So I've done some research and found out about the different circadian cycles that use chemical clocks to help us keep time in the long term (hours, days, etc.). This doesn't seem to explain how we can so accurately count seconds. Musicians can count time extremely precisely in even shorter intervals than seconds. Is it a chemical clock responsible? If you could explain the whole process to me it would be great. Thanks.


texts: Why does the cloned cat, CC, exhibit mosaic fur color?

texts:
Since fur color in this cat is from a sex-dependent gene, I see how calico cats occur. However, I don't fully understand why it happens in cloned cats.

When the cat is cloned, the DNA is taken from a somatic cell in donor and put into the egg of a surrogate. Wouldn't the DNA from the donor already have one of the X chromosomes inactivated to a barr body? Since one of the X chromosomes are inactive, wouldn't there only be a single color expressed?


texts: Do mucous membranes surround visceral organs?

texts:
Wikipedia claims that:

  A mucous membrane or mucosa is a membrane that lines various cavities in the body and surrounds internal organs.

The first part of that sentence is clearly accurate, but I cannot find any reference from Google Scholar or books that states mucous membranes surround internal organs.

The mucous layer lines the lumens of the body: digestive, respiratory,urogenital tracts, as well as cavities leading to openings such as the ears and nose, and forms the conjunctiva of eyes. The surfaces of internal organs don't fit any of these categories.

I think wikipedia is wrong about the viseral organ part, am I right?


texts: How to compare models of evolution to make assumptions about selection?

texts:
I'm having trouble understanding the concept of comparing models of evolution with LRT. I have following models: M0 (neutrality), M1A (negative selection) and M2a (positive selection) with following results from Maximum Likelihood:

M0: w=0.81; lnL=-5702.55
M1a: wo=0.50, po=0.65; w1=1.0, p1=0.35; lnL=-5650.21
M2a: wo=0.46, po=0.64; w1=1.0, p1=0.25; w2=2.38, p2=0.11; lnL=-5632.10.

I want to do the Likelihood Ratio Test to compare the models and make assumptions about the selective pressures on the analyzed sequences. So, first I compare M0 and M1a and calculate LRT=2(lnL1-lnL0)=104.68.

Now I want to take a look at a Chi table, but what am I using there? Am I supposed to used the po value for the M1a model? And if that value exceeds the value of the p-value in the table then the simpler model is chosen?


texts: How do molecular biologists determine biochemical pathways?

texts:
I'm new to this community, so hopefully this is the right place to ask this question.

I know my question is really general, but in all of my biology courses we are merely taught the chemical pathways of common reactions in cellular metabolism, but we're rarely told how these reactions were determined or discovered. What approaches do molecular biologists take to determine what molecules are involved in what reactions, what order the reactions take place, where they take place, etc.? Some of these pathways involve tons of steps, huge molecules, and a bunch of enzymes and proteins, and I just don't see how anyone could have pieced it all together. For that matter, how is the molecular structure of anything in the cell determined? For example, what was the setup of the experiment that determined that TNF-R1 even existed on the surface of the cell membrane, and that it triggers the apoptosis pathway? Another example is photosynthesis -- I could see how maybe we could find PS1/2, cytochrome complexes, etc. in a soup of blended up cells, but how in the world did we figure out what each one does and in what order?

The average cell is just so tiny and complex that it doesn't seem like there's any feasible experimental design that could lead to the discovery of these things. Please enlighten me!


texts: The effect on the efficacy and potency of a non-competetive antagonist binding to the active site of the receptor (dose-response curve)

texts:
According to the book "Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy" by Golan et al, non-competetive antagonists can bind to both the allosteric site and the active site.

I know that a non-competetive antagonist that binds to the allosteric site causes a decrease in efficacy, but no decrease in potency (see figure below). Figure A shows the agonist alone and the agonist together with a competetive antagonist. This causes the dose response curve to shift to the right, thus increasing the EC50 and decreasing the potency of the agonist. Figure B shows the dose-response curve for the agonist alone and agonist together with a non-competetive antagonist that binds to an allosteric site. As you see this type of antagonist causes a decrease in efficacy, but no decrease in potency is observed.

But how does a non-competetive antagonist that binds to the active site affect the dose-response curve? Does it lead to both a decrease in efficacy and potency? Unfortunately, there is no figure in the book to answer my question.


texts: NMDA receptor mediated plasticity figure reference

texts:
Because most of this research is over a decade old, finding a paper with a figure that clearly shows that (neuronal) synaptic plasticity (such as long-term potentiation/LTP) is NMDA receptor mediated has proven very difficult for me.

Is there a good reference for this?


texts: Why are primary sensory cells considered neurons but muscle cells are not?

texts:
The rough picture of cells involved in neural processing looks like this:

I wonder, why primary sensory (receptor) cells (like rods, cones, hair cells, Merkel cells) are consensually considered neurons (accidently having no synaptic input, but synaptic output), while muscle cells are not (even though they have synaptic input, but accidently no synaptic output).

The last cells that are unequivocally neurons are the motor neurons. Curiously, the first cells that are unequivocally neurons are mostly called "ganglion cells", not "ganglion neurons".

Is it all just a manner of speaking/matter of parlance and words? I believe not.

I received an interesting answer from Quora:

  "Muscle cells are derived from mesoderm, sensory cells (like all
  neurons) are derived from ectoderm."

But is this all that is to say? What’s the “deeper” source of this asymmetry? In the beginning there was only one type of cell, which was both sensory and muscle?


texts: Why do many humans have bad eyesight, such as near-sightedness, which hampers performance in a wide variety of tasks? Shouldn't there be evolutionary pressure towards better eyesight?


texts: I ate a ripe guava, rife enough to be broken with hand, i later saw that it has white worms with one black end crawling inside it, are these worm harmful, i had unripe guava of same batch though most of them had small black spot inside, but no worm crawling, what are these crawling worms, were they present in guava from unripe stage or infected only after ripening ?


texts: What in fast food fries have that regular fries don't?

texts:
Why is it that a french fry from a fast food restaurant doesn't seem to spoil the same way as one that one would cook at home?

PS: If given enough time will fast food french fries eventually decompose; if so, how long?


texts:
Some patient who have low White blood cells need  WBC Transfusion do resist infections.  What is interesting, doesn't transfused WBCs cause temporary autoimmune disease ?   Like recognising patients organs as foreign ?
just like in the organ transplantation.
Regards.


texts: There is a growing interest in the applications of non-equilibrium quantum dynamics to describe biological processes (I'm not talking here about Penrose's old theories, but new stuff -- quantum coherence in light harvesting, magnetoreception etc.). What is the biologists' take on this? Is this just a whim of physicists looking for grants, or a serious part of biological research?


texts:
Several places on the internet seem to purport that animal sacrifice is painless because exsanguination causes no pain. That sounds unscientific to me and an attempt to appease culture than than using science. For instance this question on the se and others like it on the internet. Is there a difference between pig and cow anatomy that makes religious slaughter of the latter less painful?

Could someone comment on the validity of this research?

Schulze W, Schultze-Petzold H, Hazem AS, Gross R. Experiments for the objectification of pain and consciousness during conventional (captive bolt stunning) and religiously mandated (“ritual cutting”) slaughter procedures for sheep and calves. Deutsche Tierärztliche Wochenschrift 1978 Feb 5;85(2):62-6.


texts:
What are the units of $N$: the colonies of bacteria or the viable cell count?

This is in regards to the bacterial growth formula used during serial dilutions,

$$
N =N(0) e^{kt} \quad .
$$


texts: How did interspecies reciprocity involving cleaner wrasses originate?

texts: The small bluestreak cleaner wrasse (Labroides dimidiatus) will approach a much larger fish (for example a grouper such as Cephalopholis miniata), enter its mouth, and spends several minutes cleaning its teeth. How did this behavior evolve? Wouldn’t the first cleaner wrasse that was bold enough to approach a larger fish have been immediately eaten? Since, in this encounter, the behavior of both fish isn’t learned, it must be encoded in their genomes. How could the appropriate coding gradually evolve?


texts: I've heard that this has happened to a few people before in extenuating circumstances, but don't know where to search for more information on this.  Is there a name for this?  What are some major symptoms, and how does it affect the body?  How is it identified?


texts: What exactly does Curare do to the peripheral nervous system?

texts:
so, I was told:

  If you give them the right dosage it'll wear off within an hour or two.
  It was used for veterinary stuff until they tried it on a human and realized it only paralyzed you and didn't block the pain. I don't know the exact dosage but if you go over the limit it'll start to relax the lungs
  So the exact dosage will be exactly enough to paralyze them without injury.

SO, naturally, I was wondering, what exactly does Curare do to the peripheral nervous system?


texts: How to estimate heritability from breeding data

texts:
I have a lot of plant-breeding data (tens of thousands of results) that are composed of phenotypes of parents and offspring. The plants however went trough years of selection and it is not balanced. Moreover, I have a lot of inbreeding data. What is the best way to estimate heritability from this type of data, having the exact pedigree relations and the phenotypes (But no accurate environmental data).
Moreover, how would you estimate heritability from nominal traits (like color or resistance)?


texts: I was wondering if narrow sense heritability $(h^2 = \frac{V_A}{V_p})$ was heritable itself. $(h^{2'} = \frac{V_A}{V_{h^2}})$


texts: Does hunger necessarily mean that we should eat?

texts: People feel hunger sooner after they eat food that consists mostly of carbohydrates. For example, if someone eats a good portion of rice then most likely they will be hungry after a couple of hours. But should they eat again in such a case or is it just deception because of blood sugar hikes?


texts: How arteries split into smaller blood vessels?

texts:
I am not sure if I am asking question that is hard to answer precisely. I just have begun learning about anatomy and physiology and have watched bunch of human dissection videos online. I feel like sometimes introductory college biology courses get so stuck in teaching about the details and mechanism of biological processes that I have trouble envisioning the bigger picture of what is being explained.
I specifically am confused about the organization of blood vessels in a living human/animal body. Like when I watch dissection videos, it is very easy to see with naked eyes the larger blood vessels like aorta, the arteries that emerge out of it and runs downwards towards the diaphragm and lower body.  so on and so forth. But i find trouble coming across resources explaining how and where (or what location in the body) they start splitting into smaller vessels. Like how are arterioles and capillaries organized in the body? Are arterioles microscopic just like capillaries. Do these smaller blood vessels run through the inside of every organs, muscles, cells (like extracellular space) etc...?
If someone can explain this or point me to any sources/topics that can explain this, I would greatly appreciate it. Thanks.


texts:
Last summer I took these pictures of a member of the Syrphidae on my balcony (Switzerland, Geneva area, Alt. ~380m, June 2020 @19:14)
Pictures:

I hesitate between three species but it could also be another one:

Scaeva dignota
Scaeva selenitica
Scaeva pyrastri

Because the pale marks on tergites 3 and 4 seems parallel to the anterior margins of the tergites, I would eliminate the third one, especially because the marks are also more yellowish than white.
For the two other species, I am not sure because I checked many pictures on the internet, but some are wrongly tagged (google images results).
Any entomologist can confirm the exact species of this hoverfly?


texts: Are females more flexible than males in all mammals?

texts: It's common that human females have a more flexible body than males, (but I don't know why, so it'd be helpful if someone answers why so as well!) but does this apply to all mammals?


texts: Help identifying spider found in central Indiana US

texts:
I noticed this spider outside my garage tonight, and I'm curious if anyone can help identify what type it is.

A few details to help:

I live in central Indiana, United States.
I saw it for the first time at night.
It's body was roughly 3/4 inches (might be slightly bigger).
Each brick in the picture is about 2 1/8 inches.
It seems to have a black velvet like texture.
It was sitting on a gas pipe that leads into my house.
It was under a bush.

Sorry the pictures aren't great. Being under a bush and trying to use a flashlight made it a bit harder.

More photographs


texts:
When looking at the process of sleeping, most research I find point to a group of mutually inhibitory cells which form a sort of biological "flip flop."  There's cells that promote awakenness and cells that promote sleeping.  The process we typically think of as "falling asleep" is getting to the point where this transition can occur, but I'm interested in the transition itself.

How fast is this transition? In engineering, we'll typically measure the speed of such a transition as a 10-90 measurement: the time it takes to go from a 10% signal to a 90% signal.  Is there a similar measurement made in such biological systems?


texts: I found this Grasshopper in Goa/India. It was about 2cm long. I suspect it is from Cataloipus genus or Gomphocerinae subfamily. Am i correct or it also seems to be juvenile from some other species?


texts: Can human stem cells be stored for use by future family members as a way to combat generational diseases like diabetes


texts: How far up a limb can a severed artery retract?

texts:
This is about the application of tourniquets. I was taught a hand width above wound, but recently I read severd arteries can in some cases retract higher than that which would then bleed into the arm.

Doesn't matter if cut or tear, and if the limb is torn off or just the artery cut through, but on arms and legs, how far up can it retract?


texts:
The resistance in a blood vessel is equal to the pressure difference divided by the blood flow. Let us now say that a sympathomimetic causes vasoconstriction which increases the resistance. Does this primarily increase the pressure in the blood vessel? Does it primarily reduce the blood flow in the blood vessel?

In context, the filtration fraction of the kidneys is the GFR divided by the plasma blood flow through the afferent arteriole. The sympathomimetic would in general increase the filtration fraction by reducing blood flow. However, the GFR is also dependent on hydrostatic pressure which may increase if there is a rise in resistance. Therefore, shouldn't the filtration fraction change minimally due to the rise in GFR counteracting the fall in blood flow?


texts:
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?


texts:
I have intuition that sepsis with infection can cause:

spastic functioning of heart during systole
heart working spontaneously in snatches during systole
atrial fibrillation
first contraction of ventricles ends earlier
which follows Action potential from A-V node during relative refractory period
weak second contraction
long compensatory pause

which can be recorded as spikes in the time axis.

With arrhythmic (earlier myocardial infarction) patients, sepsis seems to also cause leaking of valves, weakened compliance of vessels and structure of the heart.

So there are creaking sounds in the spectrum spaces.

How do the symptoms of sepsis affect heart function?

I am thinking if it is possible that this leakiness of valves and weakened compliance last only for short term and occurs periodically, during which also the heart pumps more frequently load during extrasystoles.

Assume that everything listed above is possible.

Can temporary acute/chronic inflammation in the heart cause such symptoms such as sudden weakening of valves and only temporary weakened compliance of coronary vessels?

I think the reason can be thromboembolism which is causing the sudden spastic function and weakened function of vessels and heart structures.


texts: Why is there such a large evening rise of temperature and night sweats in certain diseases like TB, lymphoma etc?

texts:
I've heard that it's got to do something with the levels of cortisol which usually dampens the effects of IL-1, but when it's night time the cortisol levels are usually low so IL-1 response is exaggerated.

But why does it occur to a greater extent in diseases like TB and lymphoma? Why is the interleukin 1 effect during night so much greater in these diseases than in case of other viral and bacterial infections?


texts: Can anyone identify this bug, it's got six legs

texts: Hi I live in the midwest (Wisconsin), these have recently started appearing all over my basement. Anyone know what they might be? They are about 2.5 mm long and they are quite active. I don't keep any food items in the basement they they would be able to fed on.


texts:
I am looking for an embryological perspective on the following question.
I know about coelom derivation, but I want to know how haemocoel is derived and how it is fundamentally different from coelom.
True coelom is formed by the cavity formed in mesoderm. It is lined by mesothelium on both sides, whereas on the other side pseudo coelom is cavity which is lined by endothelium and mesothelium. However, the formation of haemocoel is not clear to me.
I have looked for in many books, but I have not been able to find an embryological perspective and what happens to coelom in which haemocoel is present.


texts: Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means?


texts: Need clarification on Coalescent with Recombination

texts:
I've been reading about recombination with coalescent. The link to that file is as follows:

http://www.stats.ox.ac.uk/__data/assets/pdf_file/0008/4688/Reading_for_Recombination.pdf

I get the part where it says (page 142) that the rate of a coalescence event is k(k-1)/2 and the rate of recombination is kp/2. The image they have on the same page shows the intensity of coalescence and recombination. But I don't quite understand how those have been calculated. I mean the first event is a recombination event and not a coalescence event. I know they are using the rate formula I've mentioned above but I don't understand what sequences they are considering. If someone can give me a detailed answer I would really appreciate that.

I've attached the image as-well incase you don't want to read the pdf :)


texts: How effective is water purification by boiling?

texts: Does boiling water kill all harmful bacteria, fungus etc from water, or it is just a myth and removes only few of microorganism?


texts: Did the construction of the Panama Canal lead to a huge change in the local marine ecology?

texts: Before the Panama Canal opened in 1914, its two ends were only 77 km apart over land, but the closest sea route was 32,000 km long (around the entirety of South America) and passed through much colder waters near Cape Horn. Therefore, I suspect that the Atlantic and Pacific marine ecosystems were more or less completely isolated from each other and contained very different species before the Canal opened. It also seems plausible that once the canal opened and a 77-km marine route opened up, these two ecosystems very quickly came into contact and may have reached a new, drastically different equilibrium. Is this correct? I could imagine the ecological effects being equivalent to the sudden creation of a 77-km bridge connecting the ecosystems of, say, the United States and Kenya.


texts: What is the best way to make a phylogeny from a list of genera?

texts: All I have is a list of about 500 eukaryotic genera, and I need a neighbor-joining tree to show their relationship.  I want to cast on top of this tree the loss of a particular enzyme.  Is the best way to do this to make a 16S phylogeny?


texts: Can multiple overt/covert intentions produce identical EEG readings?

texts:
With sophisticated techniques likes ERP, it is possible to correlate certain EEG activity with certain overt/covert actions.

What I'm wondering is: is there a risk for 2+ overt/covert actions producing identical EEG activity? Meaning:

Perhaps when I go to open/close my right hand, I produce certain neural activity (lets just summarize this as A1); where A1 is a specific set of wave signatures
Perhaps when I go to open/close my left hand, I produce neural activity A2 (a specific set of wave signatures that is distinctively/mathematically different than A1)
Perhaps there are 10,000 other movements I could make that produced their own distinct set of wave signatures (A3 - A10002), etc.
But perhaps when I think of sea turtles and pat my stomach at the same time, I produce the same set of waves as A2 (opening and closing my left hand)

My question is: is this a concern/possibility with EEG/ERP? In other words, can multiple overt/covert intents produce identical wave activity (hence, identical EEG readings)?


texts: Cat purring: What are some possible underlying mechanisms behind purring and bone remodeling and formation?

texts:
http://www.scientificamerican.com/article.cfm?id=why-do-cats-purr

The article above says that cats purr mostly when they're wounded or under duress. They hypothesis that cats purring leads to increases in bone density and bone healing. How is this possible? What are some physiological possibilities for something like this to occur?

I don't see any journal articles backing up any of these claims. Is it similar to how ultrasound in clinical trials works?

Is the cat purring affect formation of osteoblasts? What is possibly happening microscopically?


texts: I have some mouse tumours that have been snap frozen in liquid nitrogen following an in vivo study, and I thought it might be interesting to also determine the weight of the tumours. I was wondering if weighing frozen tumours would still be accurate, or if I should have measured them before they were frozen? Would one expect the weight to be significantly altered just by snap freezing samples?


texts: There are some psychologists who believe that dopamine is not released during pleasurable activities but before them; my understanding is that a little dopamine is released pre-reward in order to motivate us to complete the action and then a large amount is released when we consume/get the reward. Can you please explain this? Their argument is that dopamine release tells the brain that it is about to feel good and then the brain releases opioids to make us feel good. This doesn't make sense if when addicts take opioids, such as heroin, the brain is flooded with dopamine and the person feels good. In that case we could say that dopamine is responsible for the euphoria. Do you believe this to be correct?


texts:
In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other.
for example

SEQRES   1 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   2 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   1 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   2 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC

In that PDB ID: 1C58
What are this and What are represent the SEQRES?


texts:
"we reported ~2.66- Gb genome sequence of"
"we generated 191.5 Gb high quality reads"

I am very confused with these two quoted lines and I am not sure about giga byte or giga base pair.
and an additional question: How to count base pairs from a FASTQ file?
I have read numbers and length.


texts: Edema in lower leg and face is a symptom of Kwashiorkor. It is the most distinguishing feature of it which distinguishes it from Marasmus. Why would decrease in amount of proteins cause Edema? Why doesn't it occur in Marasmus (which is both protein and energy deficiency)?


texts: Enzyme inhibitors, reversible or irreversible?

texts: So far, I know about competitive, non-competitive inhibitors and allosteric inhibitor. Which ones are reversible and which ones are irreversible?


texts: Issues with Mutant Allele Fraction Preparation

texts:
I am currently trying to prepare mutant allele fraction (MAF) solutions for an allele discrimination qPCR assay. I began with plasmids cloned with the different desired alleles. I amplified the the plasmids via PCR using primers flanking the mutation site. The amplicons were purified and quantified using qPCR with primers that flank the mutation site. The quantification was done with an standard curve of Ct values plotted against the log dilution factor of the solutions, with an efficiency of 84.18%.

Based on the Ct values obtained, the mutant allele and wild type allele amplicon solutions were then diluted to the log dilution factor that would give a specific Ct value (using the standard curve).

When I amplified the 100% mutant and 0% mutant solutions, I obtained roughly the same Ct values (values differed by no more than 0.5). When I mixed the 100% and 0% MAF solutions to prepare 5%, 1%, 0.1% MAF solutions and amplified them with the same primers that flank the mutation site, the Ct values from each MAF solution differed by up to 2, when it should differ only very slightly since the total DNA content for each of the different MAF solutions are the same.

Does anyone have any idea why this is happening?


texts:
This is for AP Biology, but the assigned textbook chapter doesn't contain any information about the question.

  What are some difficulties animals had to overcome to reproduce on land?

Some disadvantages I brainstormed are

the formation of bones—need for vertical structure and support against gravity (?)
development of lungs

Are there any more?

Thanks,


texts: Question about microaerophilic parasite tolerance for oxygen

texts: Does anyone know what is the maximal concentration of oxygen that can be tolerated by the parasite Giardia intestinalis?


texts:
Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype association without evidence of replication.

However GWAS is no longer the domain only of human genetics and is being increasingly used on microbial species, pathogenic on humans, animals, and plants. However having read many of these studies (mostly in plant pathology) i can find no discussion of technical replication practices in their methods. In my own research I intend to conduct GWA between snps and gene presence-absence genotypes gathered by illumina sequencing, and phenotypes of virulence (as a continuous quantitative variable) when inoculated onto the host plant (which is wheat), of a large population of a fungal pathogen. i have inoculated 120 plants with 120 isolates of the pathogen, and i'm an additional replication cohort of 80 plants and isolates.

My question is, what is required to make these additional inoculations an 'independent' cohort?

The idea of independence in technical replicates is to correct for systematic bias present in the discovery cohort, I will likely grow these plants in a separate greenhouse bay for example (although since the different host-isolate combinations are randomised within the greenhouse even this may not be necessary); in a human GWAS different genotyping methods would be ideal in the replication cohort due to possible introduction of bias in the snp-chip, in my own study i'm unsure if this would be necessary as variants in my data will undergo stringent filtering prior to genotype calling.

If anyone could help point out to me what my possible sources of systematic biases are, i'd be very grateful.


texts: Acknowledging differentiation of species, in historical times

texts:
This is at least partly an historical question, and I am not even remotely a biologist of any sort, so apologies beforehand if it's a little obscure.

I often wonder how many distinctions were made in pre-Renaissance times, between species of animals.

For example, though I'm sure there have always been those with enough of an interest in nature to tell subtle differences, how were lemmings or voles, for example, told apart from rats or mice? Or did this recognition of speciation only come later, once more detailed (intrusive) forms of analysis became common?

I've looked up the etymologies for vole, lemming and hamster and all are dated post-Renaissance, so at least in these instances it may be safe to assume that people might simply not have noticed the differences before closer study took place. But I guess there are other animals where the same question applies (particularly smaller, harder-to-scrutinise animals where there are a large number of species similar at a glance).

EDIT: Vole means field (same root as wold), giving rise to the 19th c. term volemouse, meaning that originally, mouse and vole were indeed seen as one and the same -- proof of point.

P.S. Of course, this question need not apply solely to animal species.


texts: Are there special constants in biology that define organism's morphology?

texts:
In math, there are special numbers, like Pi (3.14159...) and e (2.71828...). In chemistry, there's numbers like avogadro's number (6.0221413e+23). For example a circle can be defined in terms of 2 * Pi.

Are there any significant constant numbers in biology that define the shape of an organism (ex: mammal)? I'm talking about stuff like shoulder to hip ratio or length of an organism, etc?

Here's an example that came to mind - different fetuses developing into different organisms. Is there any constant that is the same for these at some stage of development? Like the ratio of head to tail?


texts: Does antibacterial soap work chemically?

texts: Normal soap requires scrubbing, does anti-bacterial soap require scrubbing too? Since it (I assume) works chemically, can I produce the same cleansing effect without lathering with soap and using anti-bacterial soap instead? It could save me a lot of time showering in the morning.


texts: Is it true that oxygen levels in water limits fish size?

texts:
This answer says that breathing water is inefficient, and that may act as a limiter to the size of fish. I've heard this in a couple of other places as well, but cannot recall the sources. However, the Wikipedia page on allometry indicates that metabolic rate and oxygen consumption scale logarithmically with mass, which implies that the ratio of required oxygen to mass will be lower in larger animals than smaller ones. As such, I would think that the size of respiratory organs would shrink relative to the over-all size of the animal as it is scaled up. The answer linked above even says:

Gills grow in proportionate scales to body size, generally for every 100% increase in body size there is a 50-90% increase in gill size.

Which is entirely compatible with the (admittedly naive) application of allometric organ scaling. How, then, does access to oxygen limit fish growth?


texts:
From my understanding, in the sodium-potassium pump we have Na+ inside the cell and K+ outside the cell, thus forming a so called "salted banana." After reading my textbook I found many statements saying that "potassium ions tend to diffuse out of the cell...sodium ions tend to flow into the cell." I initially thought that when the action potential hits Na+ leaves the cell and K+ enters the cell, which to me contradicts the previous statement.

Can someone please clarify this and differentiate between the two?
I am trying to understand the action potential process as a whole.

Thank you !


texts: Why are oral polio vaccines advantageous over the killed ones?  I was told that the orally given polio vaccine prevents infection by causing intestinal immunity. How does it do that? Also, how does this make it superior over the intravenously injected polio vaccine?


texts: In-plane rotation of vectors of neural population responses

texts:
In this paper on fear conditioning, the following is given:

The n-dimensional population vector (activity of n neurons) evoked by the conditioned stimulus (CS+, auditory tone) before conditioning
The n-dimensional population vector (activity of n neurons) for the CS+ after conditioning

The authors describe that after conditioning, the CS+ rotates towards the Unconditioned Stimulus (US), representing a strengthened association between US and CS+ after learning.
They explain this rotation as follows: "The rotation towards the US representation reflected new CS+-evoked responses in cells previously lacking them." but also add that this is an in-plane rotation.
My question: I would imagine that newly active neurons would rotate the vector out of the original plane (as they add dimensionality to the representation). Hence how is it possible that the authors claim here to observe an in-plane rotation?


texts: How are bioremediation microbes removed from the environment once they perform their function?

texts: In the case of bioaugmentation, microbes are introduced into the environment to clean up and absorb a certain pollutant. My question is how is that microbe then removed from the environment once it performs its function?


texts: How long does it take to extract a tree core for dendrochronological analysis

texts:
I'm going to do research in the tropics and am considering using tree cores for part of my analysis. However, for my planning:

How long does it take on average to extract a tree core of a tree with dbh ~50 cm? Trees will vary in wood density between 0.2 and 0.8.

The time includes labelling and storing in a bag, etc.

Tools: increment haglof borer. So I won't take a whole cross section, rather a small core of ~5 mm diameter that goes until the core.

And no picture because I need a more high quality image to be able to do my analysis.


texts: Evidence of condition-dependent sex-allocation in regards to humans

texts:
Coming from zero background in biology, I am looking for expert opinion on evidence regarding Trivers-Willard hypothesis (1973) and humans.

In short the hypothesis states that
if

"Condition" of offspring during their whole life are correlated
to that of their mother during pregnancy
Males have better on average better reproductive success (more genes in next generation) than female when in "good condition", and vice versa if you compare male/females in "bad condition".
Females objective is "eventual reproductive success" down the
generations.

Then it makes sense for females to vary sex ratio, more males when in "good condition" and more females when in "bad condition".

I think it is safe to say that plenty of evidence exists on assumption one. The second assumption seems more nuance in todays environment, but one would imagine that during most human history it does hold true. On the third one I think is safe to assume it is true based on the theory of evolution by natural selection.

Any (rigorous) reference (articles, researchers, journals) or comments would be superb!

Reported association that I am already aware of are:

Reduced gender ratio at times of war and famine (Ansari-Lari & Saadat, 2002; Song, 2012; Valente, 2015) and after natural disasters (Fukuda et al. 1998).
Darwin (Descent of man); Norberg, 2004; Almond & Edlund, (2007); Hamoudi & Nobles, (2014) divorce or "unmarriedness" correlated with lowered gende ratio.
Negative association between parents age and gender-ratio,  Jacobsen, Møller, & Mouritsen, (1999).


texts:
This is the picture of a tree in my college's botanical garden.

First I thought it to be a banana tree for its leaves but then seeing its lower part, I don't think it is a banana tree. So what is it's scientific name? I am just curious. Is it any hybrid or something like that plant?

Edit: This tree is from Bangladesh in South Asia. This tree is approximately 9-10 feet (I think, I cannot go near the tree). This picture is from Spring season.


texts: Where can I get numerical data for the PAR (photosynthetically active radiation) curve?

texts:
I'm trying to do some rough figuring to calculating efficiencies of various light sources for growing plants.  I'm hampered, however, by the lack of a curve to multiply by the spectrum of light sources to determine the amount of photosynthetically active radiation that a typical plant will absorb and use.

I can find curves like below all over, but I can't get numerical data in the form of tables. Is there some source from where I can get such data?


texts: Why are ducks more cautious than pigeons?

texts:
In my city park there are mostly two types of bird:

Mallard ducks
Rock doves (pigeons)

When I feed pigeons, they approach me very closely. Sometimes they peck the food that fell on my feet. If I hold my hand with food in the air some pigeons will land on my hand and eat.

In the same park there are Mallards, who are always very cautious and they try to maintain about 1-1.5 meters distance from me. They also run away when they see some rapid movement of mine.

Why are ducks more cautious? Why are pigeons more careless?


texts: Determine planar phyllotaxis characteristics

texts:
Is there any method to fast and precise count the number of spiral and the divergence angle on a planar phyllotaxis pattern?

The example of spiral phyllotactic arrangement of emerging flowers on Gerbera hybrida. (doi: 10.1093/jxb/erw489)

I'm looking for a method for characterizing any phyllotaxis pattern.


texts: Could there be a pathogen which does not activate an immune response?

texts:
In order for the immune system to be stimulated to produce antibodies, there must be a surface protein of the invading pathogen which binds to a receptor on B cell surface somewhat loosely. We need this first step for the initiation of the somatic hypermutation phase to produce specific antibodies.
But what if there is a pathogen which does not have such a surface protein? i.e. its surface proteins, if it has any, do not bind with sufficiently high affinity to surface proteins on existing B cells to trigger further aspects of the immune response.
One may argue that this is unlikely to be the case because:
a) naturally occurring pathogens evolve from existing ones, so the changes in the antigens will generally be minor. A new strain will have surface proteins that are similar enough to those of an existing strain for some loose affinity to present antibodies in the host.
b) I think, though am not at all sure, that pathogens need to invade cells to be dangerous.I'm not entirely sure what the nature of a pathogen which cannot invade cells would be. Perhaps not a pathogen at all? In any case, if the starting assertion is true, the dangerous pathogens have a surface receptor which binds with surface proteins on cells to enter them. What if many antibodies are based on the same proteins? (Though I have trouble believing this because the natural agonists of these cellular receptors are some biologically relevant and useful proteins, which we would not want an immune response to. For instance, a generally accepted mechanism of entry of SARS-CoV-2 into cells is by binding the ACE2 receptor, which has angiotensin II- a vasoconstrictor peptide- as an agonist.
So my questions are:
a) Could we synthesise a pathogen which has no surface proteins but which nevertheless does harm in some way? How could it do this harm?
b) Can we make a pathogen which has surface proteins such that it can enter cells or do damage that pathogens normally do, but goes undetected by the immune system?
In the above I have assumed that surface proteins (or perhaps also other surface molecular- maybe carbohydrates will do- are necessary for activating the immune response. If this is not the case, please let me know.


texts: what the best E-value cutoff in the miRNA homology search

texts: I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop sequence database? and the other main question is that which number of E-value is reasonably accepted as a lowest E-Value in the miRNA BLAST results? Also, what tool you suggest to perform miRNA enrichment analysis? for example we can use DAVID for gene (coding sequence) enrichment analysis. Using such analysis we are able to assign probable functions and biological roles to a group of miRNA (not only one miRNA). Any comments and idea is welcomed.


texts: How can a two genera share a latin name?

texts:
Recently, someone asked if species could share a latin name. In his answer, Remi.b said the latin name is unique to the species, and I think he is right.
However, this made me remember that I once stumbled upon a latin name that is shared between a genus of birds, and a genus of plants: oenanthe.

https://en.m.wikipedia.org/wiki/Wheatear

https://en.m.wikipedia.org/wiki/Water_dropwort

My question is: how come? Is it allowed for genera to share a name (not likely)? And why did Linnaeus, who named both, choose to do so? Error?


texts:
I know that white colour is perceived on excitation of red, blue and green cones simultaneously.

It is also said that a colour blind person doesn't see a particular colour and just perceives it as a shade of grey.

If their (for example all red) cones are affected, then how do they perceive white colour?

Clarification: Will a person with defect in red cones perceive white colour when green and blue colour only fall on his retina?

So, basically he will detect RBG and BG both as white.

If not then how will he be able to differentiate?


texts: Textbook Recommendations Covering The Adaptive Immune System

texts:
I will soon begin work on a project about immunology. I would like to read more about the main mechanisms of the immune system.

What books or articles could you recommend to me? In particular I am interested in the adaptive immune system.

I would appreciate if some of the recommendations are at an undergraduate level as I do not have a background in biology.

Thanks a lot.


texts: What are these white areas of coronary thrombosis?

texts:
Please, see the picture where the areas (1,2,3) look little yellow:

I think these areas are fat, platelets and/or air.
I think 3 is fat/platelets while 1 is air/platelets.
There also exists white thrombosis, which can explain something here.
However, I do not it is that because those white areas do not contain thrombocytes or leucocytes (not sure, since I have no more closer picture; probably you can see it from this).

I think at the moment that these white areas are endothelium-lined spaces.
However, I am not sure about (3).

What can these three areas be in the coronary thrombosis?


texts: What is the name of this flower (on a tree)?

texts: Here is a photo of a big red flower-like structure on a tree on Lama Island, close to Hong Kong. Does anyone know the name of the tree and what the black "berries" are attached to the "flower"?


texts:
I want to read some books about human evolution and about other extincted types of humans.

The book "Sapiens: A Brief History of Humankind" writes about history of agricultural and scientific revolution too, which is the part that is not interesting to me as it sounds more like history. However, I want a book about humans living millions years ago up to and before agriculture. I want to know how modern human evolved and what there were besides homo sapiens.


texts: Did bilateral symmetry evolved just once?

texts:
If I understood correctly, all bilaterians come from a single organism (the Urbilaterian) that showed this type of body plan for the first time at the end of the Ediacaran.

Does that mean that bilateral symmetry evolved just once in the entire history of life? Is it correct to say then that bilateral symmetry is not a feature of convergent evolution? That this is indeed a thing that evolution explored just that time in history and never again?


texts: How does shortage of oxygen halt the NADH dehydrogenase complex?

texts: I understand that in the absence of oxygen the functioning of cytochrome c oxidase stops because it is its substrate. However I don’t understand how stopping cytochrome c oxidase also stops the previous complex (the NADH dehydrogenase complex).


texts: On the effect of polluted air on health. Is it more gradual, or more immediate?

texts:
I've heard time and again that living in São Paulo (a large city in Brasil) takes 1.5 years from your life expectancy. The allegation is that this happens because of air pollution.

I am just wondering how air pollution harms humans. Is the effect cumulative? Or is it a more immediate effect that makes the elderly die sooner?


texts:
I have to determine the electrical charge of the next peptide chain:

C - E - H - P

I know that this page is not there to raise doubts about this style, but I have looked for resources on the Internet and find nothing. Please explain to me how to determine the net load according to pH and the isoelectric point, so that I can take this as an example.

My teacher told me to get the necessary data from this table:


texts:
Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence?

For example, I want a 1 kbp+ DNA fragment made up of copies of that exact 150 bp sequence.

I am performing optical tests on DNA strands, but the issue is that the DNA fragments that I am targeting are too small.

However, if the DNA fragment is just a repeated sequence of the DNA fragment I am testing, the tests will yield the same results. For that reason, I am trying to create a long strand of DNA from just one DNA fragment copied over and over.

Is there a procedure that I can follow to accomplish this?


texts: What is the name of the wrinkles occurring in people's lips?

texts:
I was wondering if there is a name for the wrinkles occurring in people's lips.
Just curious.


texts: Can Naegleria fowleri enter through wounds into the bloodstream?

texts: All the sources I've read said that Naegleria fowleri enters the brain through the nose. But lets say that someone had cuts on their arm or leg and they are swimming in water that is conducive to Naegleria fowleri growth. Could it enter the cut into the bloodstream and then into the brain or cause some other type of damage if it enters the bloodstream?


texts: I just found this outside my house while walking the dog. I was thinking it's some kind of slug? It's been raining a lot lately and today, so maybe that has something to do with it being on the pavement. I live in South Central Indiana, US. When it wasn't stretched out, I'd say it was 2-3 inches long.


texts: Found this critter this morning on a stack of clothes.  About the diameter of a penny and in my haste to rehome it, took only this photo.  The belly was golden brown.


texts: Peptide oxidation bias during sample preparation for LC-MS/MS

texts:
Problem description

In bottom-up proteomics, a commonly observed amino acid modification is the oxidation of methionine (Met-O). I wonder if the observed Met-O reflect natural protein oxidation or if they rather stem from oxidation during sample preparation.

Observations

During sample preparation, several factors could influence the Met-O:

Typical sample preparation protocols include reduction of the sample by either DTT or TCEP. This step serves to reduce disulfide bridges. I wonder if this step would also lead to reduction of oxidized methionines. Still, this reduction step seems to be used even in studies that analyse natural protein oxidation (e.g. Walker et al., PNAS, 2019, Methods)
Sample preparation takes several hours at least, typically the digestion is even prolongued over night. Several modifications typically happen during sample preparation or during the measurement, e.g. deamidations. I did not find studies about the extend of Met-O happening during sample preparation. Klont et al. report differences between Met-O in four different sample preparation methods, but it is not clear where the differences stem from. They could either happen during sample preparation or the four methods have different capacities of detecting natural oxidations.

My questions

Does the use of reducing agents modify oxidized methionines?
Do methionine oxidations occur during LC-MS/MS sample preparation and measurement? How strong is this effect?
Does anyone know a technique that discriminates native protein oxidations from those occuring during sample preparation? I found this publication, using 18O, but I cannot access it and thus cannot estimate if the protocol would be useful.


texts: How to build S16 rRNAs phylogenetic trees?

texts:
Here is what I know so far:

Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones.
There are stem regions in the S16 which I suspect are much less variable than the loops.

And here are my questions:

About 1., it is this the usual procedure?

About 2., do people use the loops or the stems to construct a phylogenetic tree? It they use stems, do they consider the coupling between stem bases? And, if they do so, where can I get a "map" of this coupling (preferably in a parseable form, not an image)?

In the other hand, is it correct to use a simpler nucleotide substitution model? which one?

Thanks in advance for any hints.

Lukjancenko O, Wassenaar TM, Ussery DW. 2010. Comparison of 61 Sequenced Escherichia coli Genomes. Microbial Ecology, 60:708-720, doi:10.1007/s00248-010-9717-3.


texts: Measuring protein concentration, Bradford vs. Nanodrop?

texts:
I know that the bradford assay is a very standard way of measuring protein concentration after e.g. a purification. However, in the lab that I work in now they normally only use nano drop at the 280nm wavelength.

How trustworthy is this concentration? Say that I e.g. get 2.5 mg/mL, could I really trust this?


texts: Are fish and reptilian scales homologous?

texts:
Wikipedia:

  Fish scales are dermally derived, specifically in the mesoderm. This
  fact distinguishes them from reptile scales paleontologically.

So aren't reptilia scales also dermally derived?


texts:
Barr's body is a spiral X chromosome. If I'm not mistaken, one random chromosome (a healthy woman) is inactivated in each cell. Which X chromosome is inactivated in a given cell is random. I've heard the example of a tricolor cat. The patched coloring is caused by the fact that  cells responsible for the color of each patch contain another inactivated X chromosome.

But what if a girl is a carrier of the Daltonism gene, why isn't she sick if a chromosome with this gene can be inactivated in some cells?


texts:
I'm very new to experimental biology and don't know much about it. So, i was looking to grow some bacteria in petri dishes and looked up how to do it. Unfortunately, I'm finding it difficult to get my hands on the 'agar-agar' required to make the culture medium. So, is it possible to use any other alternative which would give the same results? Like for example regular gelatin?

My school lab teachers have also shown little to no interest in helping me with my project, so I'm on my own here. Any tips would be greatly appreciated!


texts: Does the edge effect promote biodiversity?

texts:
I define the edge effect as:

A term used to describe what occurs at habitat boundaries where two bordering communities influence one another.

My question is whether it generally leads to an increase or decrease in biodiversity (both evenness and richness) and why.

Also, what are the biogeographic factors that impact biodiversity relating to this edge effect?

I believe that species diversity would increase, as at such habitat boundaries species that inhabit the bordering habitats and those that can also be found in habitat boundaries would be present.

I do remember reading that light intensity increases due to the edge effect and thus also allows for shade-intolerant species to thrive, but I do not understand why.


texts: Help identifying an insect by its remains

texts:
Yesterday i hiked in Bolsena lake, Italy. I felt this insect moving into my ear. So i smashed my ear and this is the result. Please tell me that there are no risks related to Lyme desease or similar.
Sorry for the bad quality of the photo.


texts: Why there is no vaccine against Human Immunodeficiency Virus (HIV)?

texts: I was informed by my teacher that this retrovirus changes its RNA, so there is not a drug which can recognize the RNA and somehow inactivates it. Are there any other reasons explaining why there isn't a vaccine for the HIV?


texts: How fast do stomata respond to environmental changes?

texts: How fast does stomatal resistance respond to environmental changes? Correct me if I'm wrong, but I assume that atmospheric humidity would be the fastest changing factor (e.g. rain storm on a dry day, or a warm change coming through). If the relative humidity changes from say 50% to 100%, how quickly will stomata open? And how fast in the opposite direction?


texts: I learn about the brain right now, and there are crossing of neuron pathways everywhere; in the thalamus, the medulla oblongata, the pyramidal tract... And I don't understand why? What is the reason to connect - for example - the right foot to the left part of your brain?


texts: Why do proteins targeted for chloroplasts require two signal peptides?

texts:
Question #11 of the GRE Biology Practice Test says that proteins targeted for chloroplasts require two signal peptides:

Targeting of a newly synthesized protein is most likely to require two different signal peptides for which of the following destinations?

(A) Plasma membrane

(B) Lysosome

(C) Cytosol

(D) Chloroplast (Correct Answer)

(E) Endoplasmic reticulum

I can't find a reference for this.

I understand that a ribosome starts the synthesis of a protein in the cytosol and a signal peptide takes that to the endoplasmic reticulum (ER) which finishes protein synthesis in the ER lumen and then the protein is secreted in a vesicle to its destination (if it doesn't become an ER membrane protein). What's the purpose of the second signal peptide to enter a chloroplast?


texts:
I am hoping that you can help me improve my understanding of transcription. :)  I have tried searching for the answers to all of these questions online already, but I have either had trouble finding relevant information or I have had trouble understanding it (i.e. it was too high-level for me).  I have also tried to answer my questions by browsing through different maps of genes (like this one: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr9%3A132847932-133136551&hgsid=709471277_W3A9vdobj2J7obkSXshDnCBnaTeK), but my questions are still unresolved.  Please note that I have come up with the following questions in my independent learning - these questions are NOT assigned homework.  In all questions, I'm referring to eukaryotic (linear) DNA.

Am I correct to believe that in a single chromosome, one strand of DNA is not the template strand for all genes within that chromosome?  For instance, let's call one ssDNA molecule "A" and the complementary ssDNA molecule "B"; together, A and B make up a single chromosome.  Am I correct to believe that in a single chromosome, the template strand for some genes will be A, and for other genes will be B?
If my statement in question #1 is correct, then does that mean that multiple genes within a chromosome can be transcribed in opposite directions?  Note that when I say direction, I do NOT mean 5' to 3' vs 3' to 5'.  What I mean by "direction" is looking from left to right.
Is it true that both strands of the double helix cannot be transcribed for a single gene in question?  Is this because the promoter will only be found on one of the strands?

Thank you in advance for your time!


texts: What happen's to a virus's capsid after it injects its genetic material into the host cell?

texts:
After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it just falls off. However, since it is now outside of a cell, there are no protein-digesting enzymes -- or are there?

What happens to it now? I'm guessing it doesn't just float around for all eternity.


texts: Are Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70 positively charged or negatively charged?

texts:
Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70,are they
positively charged or negatively charged ? And which other solvents can be used as a substitute to water for preparing solutions in each case ?


texts: Is this sentence about RER correct on Wikipedia?

texts:
While studying about Endoplasmic Reticulum on Wikipedia, I came across this sentence

  A ribosome only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol. This special complex forms when a free ribosome begins translating the mRNA of a protein destined for the secretory pathway.

To my knowledge, most proteins are synthesized and modified post-translation in association with RER. Then why is protein destined for secretory pathway mentioned?


texts: Does Darwin's Theory of Evolution refute Terence McKenna theory "Stoned Ape" theory of human evolution?

texts:
I haven't read it but I'm asking for a quick answer.

As far as I know, Terence McKenna's theory of evolution in humans main concept is that a hominid has tried in their diet psilocybin mushrooms, and the experience they integrated changed their mind in a way that led to "us."


texts: What causes the noise when you crack a joint? Is joint cracking harmful?


texts:
During atrial contraction ("a" in the figure), why does the ventricular pressure match the atrial pressure? The ventricular pressure generally stays the same throughout passive filling until it reaches the point where atrial contraction occurs. Why is there a sudden change in the ventricle pressure during atrial contraction? I can understand the atrial pressure would increase when the atria contract, but the ventricles have not contracted yet so the ventricle pressure shouldn't increase. The ventricle pressure can increase greatly when the volume exceeds a certain value and the elastic tissue of the heart cannot stretch anymore. However, the volume here is only about 110ml, so it has not reached that point. I can only think of one explanation:

The pressure is equilibrated between two sides of an open valve.

However, this doesn't explain why the atrial pressure is slightly greater than ventricle pressure during filling; it also doesn't explain why the aortic pressure is slightly greater than the ventricle pressure near the end of ejection.


texts: Our bodies digest food using enzymes that have evolved to convert food here on Earth. Could we even possibly get nutrients from something we haven't evolved alongside? - Is it possible for humans to digest and live on food that isn't based on DNA or RNA?


texts: Mathematical representation of "gene signatures"

texts:
According to Wikipedia's definition, "a gene signature is a group of genes in a cell whose combined expression pattern is uniquely characteristic of a biological phenotype or medical condition."

While the above definition is very useful to understand the concept, I am looking for a "more practical" definition or, rather, a mathematical representation (e.g., a vector) of gene signatures. Hence my question.


texts: Do ringneck parrots reject eggs of other parrots in their nest / eggs touched by humans?

texts:
I've put up artificial parrot homes in my terrace. Parrots have been nesting there and have laid eggs in them.
Of late i have been observing a large gathering of crows and a few hawks perching in the nearby trees, like never before,  presumably due to the large number of artificial nests and feeders that i've put up for sparrows and parrots.
I observed that in one of the parrot nests, the mother/father haven't returned for almost a week now, and i'm worried for the eggs.
1) If i transport them secretly to another nest, will the host couple accept them ?
2) Can parrots sense if humans touch their eggs ? Will they reject them?


texts: What is this raptor on a building in California?

texts:
So I took this picture of a bird that was sitting just outside my workplace a few weeks ago:

At first I searched the internet for raptors in California and found the Cooper's hawk. It looked so much like this bird so I thought that must be it and left it at that. However I just recently came across this bird and also this recent hawk identification question and they both look very similar to my bird as well. So I realized I don't know what to look for when trying to identify this bird.

Does anyone know what this raptor could be?

If it helps, the specific location was the city of Tustin in Orange County, California (Southern California). It is about 10 miles from the coast.


texts: How is instinct carried from one generation to another?

texts:
How can non-structural information, specifically instinct (a fixed pattern of behavior that an organism reverts to as a response to certain stimuli), be passed on from generation to generation (such as an unborn baby's instinct to begin inhaling and exhaling amniotic fluid while still in the mother's womb to "practice" breathing, a sea turtle's inclination to enter the sea after hatching, etc.)?

Does DNA have anything to do with it? I can't imagine what else it could be, considering that the genome is the only thing an organism passes on to it's progeny.


texts: Can any animal ejaculate at will without physical contact?

texts:
Note: In this question, I'm asking about animals that have a penis that functions very similarly to humans. I've read some animals have dramatically different methods of copulation and physiologies, so for simplicity I'm only asking about males with reproductive systems very similar to mammals, birds, etc. However, if you feel a certain species deserves special note, please tell me about it.

Are there any animals that can ejaculate at will, while awake, without any form of physical contact with the sexual organs?

I read that a Muscovy drake everts his penis in about a third of a second and the accompanying video shows ejaculation once eversion is complete. This is so fast that I wondered how the male could aim accurately into a female's cloaca. I began wondering if the process was voluntary or involuntary, since a voluntary process seemingly would allow greater accuracy.

So, this led me to wonder are any animals capable of ejaculating at will without any form of physical stimulation to the penis or body?


texts: Molecular Cloning- Blunt end restriction endonucleases

texts: I work in a microbiology lab where we do a lot of cloning. I have always used restriction endonucleases to cleave the DNA to have sticky ends and not blunt ends. I currently am working on a project that suggests using a blunt end restriction enzyme, such as EvoRV, and then to perform a T-tailing of the plasmid, pl4440. My question is why do I not treat my pcr'd insert with a restriction digest just like I would the plasmid as the protocol suggests? How do I know the insert has ends that are able to ligate into the plasmid if I don't design the restriction sites into the primers?


texts: Effects of a constant magnetic field on the human body (especially blood circulation and ion channels)?

texts: Recently, while searching for the safety of MRI, I read in several places that hemoglobin and iron in the blood are not significantly affected by magnetic fields, so MRI is safe.  However, since the human body contains many kinds of metal ions, I'm wondering what effect would the long-term exposure to magnetic fields have on the human body, unlike in the case of MRI.


texts: What is the Darwinian explanation for hallucinogenic plants?

texts:
What advantage is there to being hallucinogenic when eaten by some or most species for survival? I can only think that perhaps it stops the organism from eating the rest of you as they are confused? Perhaps some animals seek out hallucinations thereby increasing the amount you are eaten so you can spread seeds?

I am not a biologist by any means but can understand basic biology any information would be gladly appreciated


texts: Why inhbition of RTK will not help in a case of mutant EGF?

texts:
I was given the following as an example for a quiz question but i don't understand the answer. Any help will be most welcome:

Question: Iressa is a Tyrosine Kinase Inhibitor. As a young oncologe, to whome of the patients will you recommand not to take this treatment:
a. Biopsia has shown that the EGF receptor is mutant
b. Biopsia has shown that the RAS protein is mutant
c. Biopsia has shown that the MAP Kinase stays in the nucleuous permanently
d. The treatment can help each of a,b,c, cases.

The right answer should be a. Can someone see why and help here?
I know that tyrosine kinase receptor is the inside part of the EGF receptor (where the two monomeres become a dimer and phosphorelate each other).
So, if the EGF receptor is mutant, shuldn't it help inhibiting it's continuation inside the cell and thus prevent to many EGF cascades?
Thanks!


texts: Are pseudogene counted as a subtype of long non-coding RNA genes?

texts:
Are pseudogenes regarded as a subtype of the genes for long non-coding RNAs?

I could not find the answer to this question in an internet search.


texts: Why is there such in interest in antibiotics against Pseudomonas?

texts: I keep finding information on anti-pseudomonal antibiotics, or information specifying the antibiotic has anti-pseudomonal activity. Is there anything peculiar to this bacterium when compared with other gram negative bacteria?


texts: How compatible are mammalian digestive systems?

texts:
I'm interested in what kinds of nutrients mammals extract from food and would like to know how similar are the outputs of these systems.

For example, if it is possible to successfully replace one mammal's digestive system with another mammal's one (all the connections are correct). Would the recipient survive or experience some form of malnutrition resulting in death?


texts: Is there an evolutionary basis for why women mature faster than men?

texts:
Females develop both physically and mentally earlier than males do. For example; females start puberty at an earlier age than males, and females brains mature more quickly than male brains.

  Girls have always developed earlier than boys - on average the onset
  of puberty happens between the age of 8 and 12 years in girls and
  between 9 and 14 years in boys.

Is there an evolutionary basis for this? Are there theories for why females mature earlier in life?


texts: Why did black swans to evolve black colouring?

texts: What environmental factor caused black swans, which are native in Western Australia, to evolve black feathers ? Note swans are either black or white, there are no brown or grey colurings, which can be commonly found in various geese and duck spieces.


texts:
I'm looking for the "earliest" specific site where the 3 following nerves' sensory signals "converge":

Trigeminal nerve
Median nerve
Superficial peroneal nerve

By "earliest", I really mean the first location in the sensory pathway (to the brain) at which these 3 nerves' sensory signals converge.  And by "converge", I mean "feed into each other". My understanding is that, with sensory nerves, all tactile reception roads lead to the somatosensory cortex, and so, I would imagine all the nerve signals converge/merge into one another at some point.

I would imagine the location I'm looking for is the brainstem, probably the pons, but I'm not a biologist and am looking for either correction or confirmation here. This uneducated guesstimate comes from two sources:

Wikipedia - which states that the cranial nerves feed into the pons; and
The fact that the median and peroneal nerves are spinal nerves, which ultimately feed into the medula, which then turns into the pons.

Am I right or way off track?

Please note: this is not homework!


texts: why do we tighten out muscles against cold?

texts: When I'm in shower and I want to open the cold water on myself suddenly I make my muscles so tight before I open the water and that helps so much in being able to handle the shock. Why does tightening of muscles help in handling the shock.


texts: Recommendations for an intro level virology textbook?

texts: I'm a college sophomore, and I was just accepted into a research lab that works with retroviruses. Since I haven't taken any classes on the topic yet, does anyone have recommendations for good, intro-level virology textbooks I could work through to learn some background information?


texts: How does CO2 gets diffused into the red blood cells?

texts:
Carbon dioxide diffuses out of the tissues and into the blood, where it is dissolved in the plasma. While some of the carbon dioxide remains dissolved in the plasma, most carbon dioxide diffuses into our red blood cells. In the red blood cell, some carbon dioxide binds to hemoglobin, forming what we call carbaminohemoglobin.

Do any other gases also diffuse into the red blood cells, if no why does only CO2 gets into the RBCs ?


texts: Do all RNA polymerase in Eukaryotes share the same transcription factors?

texts: I know that TFII proteins bind to cis elements in DNA and help initiate transcription for RNA polymerase II. But do RNA polymerase I and III also use these proteins when transcribing genes? Also, do all genes require promoters/cis elements? Do all genes put in a vector require promoter regions/cis elements?


texts: Is there a name for the behavioral phenomena of when animals like ants sacrifice themselves?

texts:
Title says everything about the first question.

The second question is: does the special case when ants apparently explode, https://www.washingtonpost.com/news/morning-mix/wp/2018/04/20/meet-the-exploding-ant-which-sacrifices-itself-for-its-colony/?noredirect=on&utm_term=.b56b0100a88b have its own name or does it fall under the same previous term?


texts: What is a inhibitory tone when talking about neurons?

texts:
In this SE answer: Could an "overactive" brain increase the chances of Alzheimer's Disease?

user @nico used the word inhibitory tone What does that mean?

More examples of it used:

http://www.ncbi.nlm.nih.gov/pubmed/18234887

http://www.cell.com/neuron/abstract/S0896-6273(11)00479-X


texts: How to do western analysis to lung tissue?

texts:
I am working with lungs from mice, and I want to do a western blot analysis to my samples.
I am having trouble with this because my images turn out very "messy", with a high background.
Perhaps I should filter my samples following their homogenization?
Has anyone had this problem and knows how to avoid it?
What is the best method to homogenize the samples?


texts:
A similar question but about teeth healing themselves is Do teeth have the capacity to heal?.

So I understand that teeth have the capacity to heal themselves to a certain degree. It appears to be that part of the reason they can't heal all of themselves is that they are not surrounded by cells. In that case why can't we grow teeth back?

If a tooth is grown in the gum, or somewhere else, it would be surrounded by cells and so should be able to grow back right?

It appears that sharks can grow their teeth back:

  New teeth are continually grown in a groove in the shark’s mouth and the skin acts as a “conveyor belt” to move the teeth forward into new positions.

Why can't we do this?


texts: Too few transcripts from transcriptome assembler Oases

texts:
I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.

Here is my running command:

python scripts/oases_pipeline.py -m 25 -M 29 -o output -d " -strand_specific -shortPaired data/reads.fa" -p " -min_trans_lgth 100 -ins_length 300"

My library is strand-specific and pair-ended with length 67bp. The reads are shuffled as:

>0(left_mate_forwarded)
ACTC...
>1(right_mate_reverse_complemented)
TATA...

I got some transcripts, but are far from the transcripts annotated, also far from the result of Trinity. The longest contig from Oases is ~2500bp (vs. ~10000bp from cufflinks and ~6000bp from Trinity). The N50 value is also low. It only reports 20 contigs those cover full-length of some transcripts from Cufflinks (totally ~4000), while Trinity reports ~650.

The dataset I am using is a subset of S. pombe. Does it matter?

Could somebody help me point out whether something wrong here?


texts:
My professor mentioned the resolution of the gel in gel electrophoresis. He stated that agarose has large pores and thus low resolution whereas polyacrylamide has the opposite.
I don't understand what resolution has to do with this. Can someone explain?


texts: Distinguishing between mitotic metaphase and metaphase II of meiosis

texts:
I'm sorry if this seems like a silly question, but I was brushing up on some cell cycle dynamics and realized that everyone was talking about the differences between metaphase I and II, and since metaphase II was so different from metaphase I (random orientation, tetrad, etc...) the distinguishing of the two didn't seem difficult.

However, I also always hear that metaphase II is similar to mitotic metaphase. In fact, I can't really figure out what the observable difference would be, though I'm certain this must be possible?

How exactly is metaphase II of meiosis different from metaphase of mitosis? I'm sorry if this seems like a silly question, but I haven't been able to figure it out.


texts:
From what I understand, the term operon is loosely defined to be a collection of genes that are found to be in the same proximity in a genome.

Some definitions enforce that an operon is only regulated by a single promoter and all of the genes are transcribed together.

If the above definition is strict, that would imply a couple of things

Genes are opposite strands cannot be in the same operon (since they cannot be transcribed together)
Overlapping genes cannot be in the same operon for the same reason.

I realize that part of the issue with these definitions stems from an ongoing investigation behind this phenomenon.  But are there strict standards surrounding the definition an operon? What is the minimal definition of an operon?

Relevant links

What is an operon?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161906/pdf/12864_2013_Article_6422.pdf
https://en.wikipedia.org/wiki/Operon


texts: Where does the carbon in new spring leaves of a deciduous tree come from?

texts:
When a leafless deciduous tree 'comes to life' in the spring and puts forth new leaves, where does the mass for these leaves come from? The tree has no leaves to make use of photosynthesis to get the carbon it needs to grow these leaves, so where does the carbon come from: has it been stored in the root system over winter just for this purpose? And if so, has enough been stored for the tree to produce most if not all of its new leaf growth for this season, or only enough to get a few leaves out that will 'take over' the task of providing carbon fixation (making sugars) via photosynthesis to grow the remaining new leaves?

It has been suggested in the comments that the new leaf buds were grown at the end of the previous season. It would seem to me that this strategy for new growth in the spring would be fraught with all sort of dangers from 'winter kill', so these buds would not remain viable come the next spring. So, are the sugars needed for new spring growth coming from the roots or last seasons leaf buds?


texts: I've read about safe doses of radiation, briefly. Why is there such a thing a safe dose? Can't any radiation give you cancer? Why is it more and more dangerous to take in larger and larger doses? Just because the body can't recover as easily? Is there something fundamentally more damaging about larger doses of radiation, as opposed to smaller more frequent doses? I suppose this could go to a health forum, but I don't know of one, and I came about this question via thinking about Physics.


texts:
My main question is why do people eat meat?
Can we not survive without meat?

I recently became a vegetarian and I have not yet felt any impact on my health. Can any one explain this phenomenon from the perspective of nutrition?


texts: Replicator dynamics giving probabilities greater than 1?

texts:
I have a linear replicator equation and I want to simulate its dynamics to find the resting point and hopefully the Nash equilibrium.

I defined strategies' payoff as  $ \vec f = C*\vec p+ \vec b$, where $C$ is a community matrix similar to the one in Lotka volterra models, $p$ is the vector of probabilities for each strategy and b is a vector of constants. From what I understand, this is very similar to the replicator dynamics for a linear model, except that I'm adding a constant.

However, when I iterate over $\vec p_{t+1} =  \vec p_t+ \vec p_t (\vec f- \sum\vec f \vec p_t) $,   $\vec p_{t+1}$ frequently gets values greater than one or smaller than zero, which from my understanding is not suppose to happen.

An example to show the issue:

$C = \begin{pmatrix} -1 && -1.1 && 0 \\ 1 && -1.0 && -1.1 \\ 0 && 1 && 0 \end{pmatrix}; \space \vec b= \begin{pmatrix} 0.7 \\ 0 \\ 0 \end{pmatrix}; \vec p_0 = \begin{pmatrix} 0.8 \\ 0.9 \\ 0.25 \end{pmatrix} $

In this situation,  the second element of $\vec p_1 $ equals 1.448550!

What could be causing this error? Am I calculating  the replicator dynamics wrong? Does adding a constant to fitness "breaks" the replicator dynamics? Is my understanding wrong and replicator dynamics can go above 1 or below 0?


texts:
Why does the answers to the problem found in the referenced pdf, differ from my calculation below? I am trying to understand the math from this pdf from an online tutorial I am reading and my own math does not give the same result: Can someone help derive their answer or confirm mine?

http://www.cs.columbia.edu/4761/assignments/assignment1/reference1.pdf
On page 13, I am trying to figure out how the weighted values are determined:

For example C_LL: 2.33 means the construct is [L_1   (L_2a L_2b)  L] and the center block is being counted as 1/3 for each so we get 4*(1/3) + 1 = 2.33 but the L_2a to L_2b i.e., the inside the block is not counted that should make it 2.66 right?

For C_LV: here there is obviously 4*1/3+1 and now the internal would be 2*1/3 which sums to 3 not 3.33. And now the internal one is counted.

I am confused. Any help?


texts: What is the shortest mRNA the ribosome can read to produce a peptide?

texts:
This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome.
In general, Glutathione has a "gamma" peptide bond, thus cannot be synthesized by the ribosome. However, is there an actual minimal length that ribosome can process?

I understand that the mRNA is more then just the codons, however, does it still require a minimum set of condos, e.g., say 18 nucleotides, to produce a peptide?


texts: Do the enzymes and compounds in saliva help with stain removal?

texts:
Does spitting on stains help with removal?
Saliva is high in amylase that should help with the breakdown of protein rich stains like blood and semen. It also contains antimicrobial enzymes and antibacterial compounds. Does semen contain any kind of surfactant agents?

So, my questions are:
Does spitting on a semen stain aid in or add to the cleanup?
On which stains are saliva beneficial and how long does it have to sit?


texts: Is there a maximum limit of connections between a pair of neurons?

texts: As neurons fire and work together, their connections strengthen. I was wondering if there was a limit on how connected neurons can be. If these neurons were constantly connecting then surely there would be an overload of connections at some point?


texts: Can anyone explain in a simple manner what is Fourier shell correlation (FSC)? And how is the conversion from 1D to 3D FSC?

texts:
3D FSC curves are used to show directional isotropy and global resolutions in cryo-EM maps. I am having a difficulty to understand the graphs since I do not have absolute clear idea about 3D FSC and sphericity in cryo-EM reconstruction. Attaching with this the DOI to the paper I am trying to understand.

doi:10.1038/nmeth.4347, nature methods | VOL.14 NO.8 | AUGUST 2017 |


texts:
Does anyone know what this is? I have lived in this area of northern Utah, USA for over 30 years and played with insects, snakes and spiders growing up here. However, until this week, I have never seen this insect before, nor anyone else we have asked. Suddenly they are all over our porch, patio, trampoline and house. This one is about the size of a lady bug, but we have seen some about double that size.

At first we thought it might be a beetle, but their shells are not bifurcated. Looking underneath, they have a long thin tube that they fold into their body that appears to be their mouths. We thought a weird tick, but they only have 6 legs. Can't seem to find anything similar online either.

Does anyone know, what it is?