texts: Physical activity in fasted state: Glucose for brain vs muscles

texts:
Let's consider this scenario:
You do sports in the morning in a fasted state (i.e. without consuming any calories after waking). Your brain of course needs glucose and your liver probably still has some of it in stock. So it keeps releasing it. Is there a mechanism to prevent the working muscles from consuming the glucose (so that the brain can be supplied longer)? If yes, how does it work?

(Please answer not too technically, so that people outside this area can also understand it.)


texts: What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?

texts: I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources describing the interaction energies/chemical potential/free energy for protein-protein interactions, however, I cannot seem to find any of these values for cytoplasm interaction with proteins. Any help would be appreciated. Please let me know if I am not being specific enough. Thank you!


texts: Mesoporous silica particles as anti cancer drug delivery method

texts:
If this question is a little off topic for Biology, I'm sorry. I've recently read a lot about mesoporous silica nanoparticles as a promising drug delivery method. The huge range of customizability of the particles, coatings, contents, etc. can pretty much tailor them to be effective in delivering most drugs to most target locations in the body (or to specific cells). The research is not new, and all the articles hail the method as a very promising way to treat for example cancer. However, as far as I know, these methods are not widely used today. Why? Is there some catch that I don't see?

I'm no biology expert, but if this is so promising, and the research is at least a decade old, some companies would have produced this (they already produce the particles) in terms of drug delivery. So why not? Is it a case of null-findings not being published? Is it actually used and I'm blind?

Thanks for your help!

edit: for those interested, here is a good review


texts: What are the difficulties/challenges against developing a coronavirus vaccine?

texts: Multiple groups of scientists are trying to develop a coronavirus vaccine but they are not yet being fruitful. What challenges or difficulties are there in the process that slowing down and/or causing failure in development of vaccine?


texts: Considering that the DNA needs enzymes, to be formed, however enzymes need DNA to be formed too. What biomolecule was created first?


texts: What is this pink angiosperm from Morocco?

texts: What is this pink angiosperm photographed in Morocco in spring? The diameter of the flower is about 2 cm. The petals are fused. The plant is crawling and did not have any erect parts.


texts: Why do most organisms have negative supercoiled DNA?

texts: It has been observed that in nature most organisms have negative supercoiled DNA and that few organisms have positive supercoiled DNA. Some of the organisms that have the positive supercoiled DNA live in strong acidic environments but are very rare compared to negative supercoiled DNA. Why wouldn't all organisms have the same DNA supercoiling? Does it affect their survival in any way?


texts: Why HIV patients have greater virulence of M.tuberculosis?

texts:
I am reading Murray Microbiology book.

Some facts

M. tuberculosis is an intracellular pathogen.
At the time of exposure, M. tuberculosis enters the respiratory airways and infectious particles penetrate to the alveoli where they are phagocytised by alveolar macrophages.
In contrast with most phagocytised bacteria, M. tuberculosis prevents fusion of the phagosome with lysosomes (by blocking the specific bridging molecule, early endosomal autoantigen 1 [EEA1]). NB probably here something relevant
At the same time, the phagosome is able to fuse with other intracellular vesicles, permitting access to nutrients and facilitating intravacuole replication.
Phagocytised bacteria are also able to evade macrophage killing mediated by reactive nitrogen intermediates formed between nitric oxide and superoxide anions by catalytically catabolising the oxidants that are formed.
Dissemination to any body site occurs most commonly in immunocompromised patients, like HIV patient.


texts: If the conditions within the womb are mimicked, and proper amniotic fluid with constantly recycling nutrients is maintained, is it not possible to obtain an artificial womb? Is there anything missing? I think, artificial womb, if possible, could open new ways to study human anatomy and development and further the research studies. Starting with test tube fertilization, one could observe the entire process of growth of a zygote to a fetus.


texts: Help ID this plant, quite possibly a weed

texts:
I found this plant near my South Indian home in Kerala, India. Most probably it could be some sort of weed. Anyhoo, is this plant of any medical or commercial value? Is it a remedy for something?

It has a white tap root with little veins off the main root
It has a really small yellow flower
It's leaves are similar to that of a clover, except for that it has three to five leaves

Merci d'avance!

(P.S. Forgive me if this is some very common plant that I should know about, I'm in 7th grade.)


texts: Is there any possible way to take a DNA test without using blood in humans?

texts: Is there any possible way to take a DNA test without the need to draw blood in humans? Any information will be useful for me.


texts:
I was reading on mammary gland development, and I found this (1):

As a girl approaches her teen years, the first visible signs of breast development begin. When the ovaries start to produce and release (secrete) estrogen, fat in the connective tissue starts to collect. This causes the breasts to enlarge. The duct system also starts to grow.

Wikipedia has an article about the duct system(2):

The development of the mammary gland occurs mainly after birth. During puberty, tubule formation is coupled with branching morphogenesis which establishes the basic arboreal network of ducts emanating from the nipple.

It goes on to say, developmentally, mammary gland epithelium is constantly produced and maintained by rare epithelial cells.

By the pubertal stage, the mammary ducts have invaded to the end of the mammary fat pad. At this point, the terminal end buds become less proliferative and decrease in size. Side branches form from the primary ducts and begin to fill the mammary fat pad.

In the end, I understood that the mammary alveoli (containing milk) are not formed during this. During pregnancy, the ductal systems undergo rapid proliferation and form alveolar structures within the branches to be used for milk production.
And from where is the milk produced? (Just for some more detail)

After delivery, lactation occurs within the mammary gland; lactation involves the secretion of milk by the luminal cells in the alveoli. Contraction of the myoepithelial cells surrounding the alveoli will cause the milk to be ejected through the ducts and into the nipple for the nursing infant.

Three questions:
An interesting case is one of neonatal milk.(3)

It is thought to be caused by a combination of the effects of maternal hormones before birth, prolactin, and growth hormone passed through breastfeeding and the postnatal pituitary and thyroid hormone surge in the infant.

The article doesn't mention anything about developement of mammary alveoli, though. How does that happen, then?

I know milk formation primary requires prolactin, oxytocin and indirectly, estrogen.(4) So does this process wait till pregnancy?(If yes, then the lobes and branches are devoid of any lumen, and they remain empty until pregnancy, which seems skeptical to me.)

Can lactation occur without alveoli formation?

1-
www.hopkinsmedicine.org/health/conditions-and-diseases/normal-breast-development-and-changes%3famp=true
2- https://en.m.wikipedia.org/wiki/Mammary_gland
3- https://en.m.wikipedia.org/wiki/Witch%27s_milk#:~:text=Breast%20milk%20production%20occurs%20in,not%20by%20prematurely%20born%20infants.
4- https://www.ncbi.nlm.nih.gov/books/NBK148970/#:~:text=Hormonal%20control%20of%20milk%20production,indirectly%20in%20lactation%20(2).


texts: Do transcription factors bind to both strands of DNA?

texts: Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. Any reference books, papers or links will be helpful.


texts: Does opening the lid of the spectrophotometer affect my results?

texts: If I'm performing an experiment using a spectrophotometer and I mistakenly forgot to close the lid on the spectrophotometer, would that affect my results?


texts: Reverse complement of reconstruction model for assembling reads

texts:
One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this problem is the reconstruction model, which calculates the minimal edit distance between a possible superstring (that contains all fragments) and each one of the fragments. What I don't understand yet is the fact that when calculating the edit distance for a given fragment, it's necessary to calculate the edit distance for the reverse complement of that fragment. An example of a fragment and its reverse complement could be:
 ACTGTCC fragment
 TGACAGG complement (the complementary strand as we know)
 GGACAGT reverse complement
According to the book I'm reading the ideia behind it is to find a superstring as short as possible that either the given fragment or its reverse complement must be an approximate substring of the superstring. I know that many mathematical/computational models don't have a biological sense for their way of soluting a biological problem, but this recontruction model I could think it's biologically reasonable to find a string that contains all the fragments of a certain region of a DNA sequence, and all the complement fragments, after all when assembling we can find both strand sequence. But a reverse complement is not something that exist for a given sequence, unless it has suffered some kind of break-recombination event, which is something not expected, mainly when talking about conserved regions. Do you any idea why this model takes into account the reverse complements ? Thanks in advance.


texts: Why people don't harvest Locusts when infestation happeds?

texts:
We've heard about tremendous amount of money losses even leading to famine due to crop destruction from locust infestation over and over again, but all these grasshoppers are a valuable protein, probably way more valuable than the destroyed crops. Although most people from many cultures won't eat such insects, these can be ground to flour and stored to be fed to omnivore livestock like pigs or sold for profit or exchanged for grains.

Is there edible energy in the insect swarms? Can this be made into livestock feed? If not, is the reason this isn't common practice biological or economical?


texts: What would need to be discovered to prove there is extraterrestrial life?

texts: Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment. What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA (or its Martian equivalent)?


texts:
I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying start/end sites have ended up being aggregated in E coli (while the full length protein expresses reasonably well). My question is what considerations one should use to determine start/end sites to maximize chances of getting soluble, purifiable protein. The criterion I used were:

Preferably loop region in known x-ray structure
Use hydrophobicity plots to minimize hydrophobic residues at both termini
3-4 residue linker between protein and affinity tag (GST/6xHis)

From personal experience with an earlier construct, this can turn out to be an idiosyncratic exercise but I was wondering if I was missing any crucial parameters.

EDIT: I also played around with the PDB file of the non-truncated protein to check whether huge hydrophobic patches were exposed on deletion of the domain(s), and I didn't find any such patches that could potentially be exposed and lead to aggregation


texts: Will gene mutations give rise to a protein that is shorter than the full length protein?

texts: What is the relationship between deletion or insertion of nucleotide in the gene sequence and the protein's length that is coded out from the mutated gene?


texts: Sansevieria falling back to the wild form via leaf cuttings but not via micropropagation

texts: I have heard that when you propagate Sansevieria via leaf cuttings, you get the wild form again. But if you use only meristem tissue, you can propagate the multicolored cultivated forms. What would be a possible explanation for this phenomenon?


texts: Short, concise, practical manual for doing experimental biology

texts: I am am physical scientist working in biology, and have recently started doing experiments. I would like a manual akin to "Numerical Recipes", but for the lab: straight forward, easy instructions on how to do the (100) most basic biology experiments - PCR, cloning, etc. I realize that a lot of these depend on kits, and specific equipment, but it seems like there still should be something that would give you the outline of how to do these experiments. Does anyone know of a resource like this?


texts: Why did some animals evolve inward-slanted legs?

texts: Something I noticed looking at reference images is some animals have legs that are slanted inward relative to the length of their body, like in the two images below. Why have animals evolved this instead of having their legs pointing more straight down like lions or elephants?


texts:
I was reading this article which states this:

  Classical Batesian mimicry, in which an undefended mimic evolves to
  look like a toxic model, is a parasitic relationship in which the
  mimic gains an advantage at the expense of the model

I don't understand why this mimicry is equivalent to parasitism. Do the authors call it parasitic because eventually it may cause threat to the model, as the predator learns that it is being fooled around ?

I don't see a clear and certain antagonistic relationship here. Can someone please explain.

EDIT

If it is the case that the mimic reduces the likelihood of the model being preyed then then outcome of this is dependent on multiple parameters.

The +/- effect of this interaction is not always certain (which on the other hand is usually certain in the case of a typical parasitism). The uncertainty can arise not just by evolution of the predator but by other factors such as population size and structure.

Considering all this is it correct to call a relationship as parasitism just based on one of the many possible outcomes ?


texts: Why won't this spray kill this bug (household insecticide); could it be so selective?

texts:
I have a can of bug spray. The label is in another language which I can not even type in order to do an online translation, but the ingredients are in romanized writing:

Metofluthrin  0.012% w/w
Phenothrin    0.100%
Cyphenothrin  0.100%

Wikipedia: Metofluthrin, Phenothrin, Cyphenothrin

I've been seeing small (3~4mm) dark flying bugs that seem to be able to take a direct hit. They may be grounded, but after a minute or two walking around and cleaning their wings, they fly away.

The spray worked very effectively on the cockroach I bought it for; this kind of thing happened about 90 seconds after a direct hit. Here they don't really infest as much as just wander in off the street and can't find their way out again.

I assume if I get rid of any residual sources of food or water the little flying things should die off. But I was really shocked to see them fly away undaunted after some serious aerosol action.

Here are some snapshots I took of the small bug trying to eat my spicy noodles. It's actually not so dark. Please please tell me it's not a tiny baby cockroach!


texts:
My question is about the CIGAR specification.

The documentation states:

M 0 alignment match (can be a sequence match or mismatch)

I 1 insertion to the reference

Q1: If I have a CIGAR string 99M170661N26M, does that mean I have 99 matches. Can that also mean 99 mismatches? What about 98 matches and 1 mismatch? The specification states it could be a sequence match or mismatch.

Q2: Assuming I'm doing an RNA-seq experiment. In my CIGAR string 99M170661N26M, does that mean my read aligns to an intron which has 17066 bases? Can I think like: "I have a spliced read which aligns to two exons and an intron. I have 99 matches to my first exon and 26 matches to my second exon. I have 17066 matches to my intron."?

EDIT:

Can I get the number of matches in my read? Does that even make sense? For example, how do I know if I have 10 exact matches?


texts: Which species of Agave are known to have inedible flowers?

texts: It is well documented that many species of Agave have edible flowers, however I keep coming across statements to the effect that "most species" of Agave have edible flowers. This implies that it is known that some do not, but I have been unable to find any specific references to species known to be inedible. I'm particularly curious about Octopus Agave (agave vilmoriniana), which I could find no confirmation either way, but would like to know any information & sources regarding the inedibility of any Agave species.


texts: Essential amino acids also have codons.Still they are needed by humans through diet?Will those codons do synthesize amino acids for some other purposes in humans or not?If so, what is the purpose?e.g?


texts: What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?


texts: Can you measure ECG from a single location?

texts:
I want to make a DIY bracelet to measure my ECG. All I need is the interbeat interval.

Can I design a bracelet on one arm only, with two electrodes slightly spaced from one another, and figure out the beat from the conduction timing differences down the arm?


texts: I read somewhere that the function of Golgi bodies is glycosylation and glycosidation. What is the difference between the two? I searched google but it gives complex answers.


texts: Parallels between pixelized image and the human retina

texts: On Wikipedia it is explained that the human eye has a certain 'resolution'. Does this mean that the retinal image consists of pixels? If yes, what shape would these pixels have?


texts: Organisms that use more than the 20+2 commonly occurring amino acids?

texts:
I know scientists have created synthetic bacteria, with a genetic code containing 6 letters instead of 4, with the aim of creating more complex proteins (using amino acids outside of the standard 20+2, the +2 being selanocysteine and pyrrolysine).

Are there any examples of already-known organisms that use more than the 20+2 commonly occurring amino acids, when translating from RNA codons to amino acid sequences using the ribosome? Post-translational modifications would not count, as the ribosome would not be directly responsible for the incorporation of the amino acid into the protein through that method.

Source: 22 proteinogenic amino acids
https://en.wikipedia.org/wiki/Proteinogenic_amino_acid


texts:
My textbook says:

  DNA is the heredity material which controls the properties and
  potential activities of a cell.

I couldn't understand how it controls properties of cell?


texts: How to determine whether changes of an allele's frequency are due to genetic drift or selection?

texts:
Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population:

Are there ways to determine whether a frequency shift for a specific gene/allele is due to genetic drift or selection? In other words: when we see an allele take over a population, is there a way to know whether it was selected or just 'got lucky'?

UPDATE: since apparently this issue is quite complex in experimental biology I want to clarify why I'm asking this and what I hope to learn.

I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift.

I'm applying a genetic algorithm to the optimisation of websites, where each gene determines an aspect of the user experience of that website. The question is whether the alleles I see emerging in the fittest solutions (= the best user experience, rated by visitors) got there by chance or actually contribute to the fitness of the candidate solution (= make a difference in shaping the user experience).


texts: Why is the "mango fly" called a "mango fly"?

texts:
Cordylobia anthropophaga, the mango fly, tumbu fly, tumba fly, putzi
fly, or skin maggot fly, is a species of blow-fly common in East and
Central Africa. Wiki page

Why is Cordylobia anthropophaga among other names called the mango fly? I can't seem to find anything online about why they gave it this name, and I figure they don't eat mangos.


texts: Can prawns be classified as fish, or is their position ambiguous?

texts: Today a zoologist told me that prawns and fish are very similar, but zoologists/taxonomists have put them in different categories because their distinction is unclear (like hydrogen in the periodic table). This completely bewildered me, as I know prawn and fish are in different classes because there is no similarity between them. I have no connection with biology now but studied it in high school — but even then, I could not believe it. Can someone please elaborate on this?


texts: Long-term-potentiation and memory. Where do we stand?

texts:
I was reading the answers to the question: How and where, in the human brain, are memories stored? and, as expected, LTP and LTD came out.

Every time I read about LTP/LTD there is always something that bugs me a lot.

When I read papers about LTP/LTD (OK, I should really say "when I browse", as I'm not exactly in that area of neurosciences, and that is probably the reason why I am confused by this) I always see these very neat experiments where stimulating a neuron in a certain way increases/decreases its further responses. Then, I look at the time axes on the graphs, or read the Methods, and I see that the LTP was induced and analysed few minutes after the stimulus.

So my questions are:

Is there clear evidence that LTP is involved in long-term memory (not counting 1 hour as long-term...)?
Has LTP/LTD been shown in vivo after long period of time (e.g. months).
For those who work in the field, is there a strong belief that LTP/LTD are the only phenomena underlying memory?


texts: What biological process was taking place?

texts:
A tub of a side dish, either tomato salsa or baba ganoush (eggplant), was left in a plastic bag for several months.  The plastic bag was not airtight, but was wrapped somewhat tightly around the tub.  Although it was supposed to be stored refrigerated, it was not (it was stored at room temperature).  It also was not supposed to be stored for such a long duration.

When the bag with the tub inside was eventually handled, it was noticeably hot.

What biological reaction was taking place that would generate that kind of heat, especially after months of storage?


texts: What are the differences in ultrastructure of cilia and flagella?

texts: Cilia and flagella are aimed for similar perpose, motion. And both of them show the (9+2) microtubule arrangement. They are nearly identical in structure. But to be more specific , where exactly does the little difference lie (except the 5-6 bridge) ?


texts: Exactly what biochemical factors control the intensity of an allergic reaction?

texts:
I think have a functional understanding of how an allergic reaction (Type I Hyper Sensitivity) occurs: basically the allergen causes production of antibodies that attach to mast cells and basophils. Later, if the same allergen binds to those antibodies, the cells release histamine and other unpleasant chemicals.

However, it's clear that the degree of allergic reaction varies a lot from person to person. For example, if my wife goes outside all day during peek grass pollen season, she'll end up with a sinus reaction, and not much else. If I go outside for a few minutes, I'll develop that, and if I stay longer, I'll get hives, weepy eyes, and so on.

Clearly I'm more sensitive to grass than my wife, but what exactly causes this? I can imagine a lot of possible factors!

Maybe I have many more antibodies (but why?)
Maybe I absorb more of the allergen per unit time (but why?)
Maybe my mast cells require less allergen to react (but why?)
Maybe my mast cells contain more histamine per cell (but why?)
...

So I guess my question is: What drives the variation in allergic hyper sensitivity responses?


texts: Does anyone know what marsupial this is?

texts: I know what this is a marsupial, but i'm not quite sure which one. Any thoughts?


texts: What's the name of the fibrous strands that hold the seeds in a pumpkin?

texts:
If you cut open a pumpkin, the seeds are suspended inside the pumpkin by some fibrous, slimey strands. You can see them in the middle of this sliced-open pumpkin:

I'm writing a post for the Cooking.SE blog, and am trying to find out the proper botanical term. Someone suggested that might be called the endocarp, but I want to make sure and also see if there is a more specific term.

Edit

In "Morpho-Physiological Aspects of Productivity and Quality in Squash and Pumpkins (Cucurbita spp.)" §C.1, I see this:

  In the central portion of the fruit, a mass of tough fibers, together with vascular strands connected to the seeds, comprise the placental tissue. The endocarp is made up of small, thin-walled cells that form a membranous tissue that adheres to seed, becoming a transparent skin on dried seeds. (emphasis added)

Am I reading correctly that the name for this part of the pumpkin is "placental tissue", and that the endocarp is just a thin layer on the seeds themselves?


texts: Do muscles still hold glycogen reserves if there is no carbohydrate input

texts:
Afaik skeletal muscles take glucose from the blood to store it localy as glycogen, to be used in the case of intensive exercise.

Does this still happen

if the calorie input is exclusively made up of fats and proteins?
while fasting / starving?

I know that muscles can run on fatty acids and ketone bodies.
And that the liver can create glucose by gluconeogenesis.

But is this "backup"-glucose still used to refill the glycogen stores in the skeletal muscles in those two respective cases? (while resting)

If not, how would the performance of exercises like sprinting, that normally make use of those stores, be affected?


texts: I have heard that a reference genome such as humans is generated by randomly choosing samples from a group of donors. But why do we call the DNA sequence generated as a reference? Why should we believe those few samples can represent all humans, from which we need to align with?


texts: Electronic cigarettes (e-cigs), any health risks?

texts:
Background:

An electronic cigarette (e-cig or e-cigarette) is a battery-powered device which simulates tobacco smoking patented in 1963 by Herbert A. Gilbert.

It generally uses a heating element known as an atomizer, that vaporizes a liquid solution. Some solutions contain a mixture of nicotine and flavorings, while others release a flavored vapor without nicotine.

Question:

Are there any health risks uniquely associated with e-cigs as compared with normal cigarettes?


texts:
Recently, I've stumbled upon a fact, which hasn't bothered me for many years. The fact is that all universal 16S primers are written as "[FR][0-9]+" (in regex notation), that is they have a position with respect to a reference. I've read through many papers, wherein these primers were introduced, and most of the time the authors say nothing but "E. coli 16S". Anyway, in one case I've found that it is in fact the reference K12 E. coli. But the problem is that it has 7 distinct rRNA operons: rrnA, rrnB, rrnC, rrnD, rrnE, rrnF, rrnG. Do you have a reference showing a particular operon used for the 16S position notation?

Edit

Figure 2. Hypervariable regions within the 16S rRNA gene in Pseudomonas . The plotted line reflects fluctuations in variability amongst aligned 16S rRNA gene sequences of 79 Pseudomonas type strains... (Bodilis et al., 2012)


texts: Is reproduction intrinsically part of life?

texts: If all of the characteristics of life are required for something to be defined as living, how can we account people or other life that can not reproduce?


texts: Why is translocation of food in the phloem still a debate?

texts:
I currently take tertiary-high school biology and I am taught that translocation of food in the phloem occurs by the pressure flow hypothesis.
I would like to ask why it is still a hypothesis, and what are arguments against it. If possible are there any scientific literature or journals for me to chew on? Thanks in advance.


texts: Why genes are assumed to follow multivariate normal?

texts: I wonder why gene expression data are very frequently modeled by multivariate normal distributions. What is the reason for those strong assumptions that the genes follow multivariate gaussian? Are there any reasons specific for genetics other than the reasons for general gaussian assumptions (the ease of calculation, etc.)?


texts: Is an athlete's heart rate after exercise greater than a non-athlete

texts:
I was just wondering
And if it is greater or lower how does this benefit an athlete
Also what is the averaged number of heart beats per minute


texts: Can you get enough water by eating only fish?

texts:
Scenario: In a boat in the middle of the sea, no freshwater or food stores, no desalination equipment, no rain, but you can catch fish and eat it raw. Can you get enough water this way to survive, let's say for 14 days? (Enough clothes to protect against cold, shade available)

2, 000 g of raw Pacific cod contains 1,650 mL water, 350 g protein, 2,200 mg sodium (source: usda.gov)

By my calculation, you would need to excrete 2,800 mL of urine to excrete urea from protein metabolism (8 mL urine per 1 g protein; source: nap.edu), so after eating fish you would be in the negative water balance for more than 1,150 mL solely from urea.

My questions are strictly about fish as a water source, not about other water sources or survival time:

Does protein really expel so much urine that makes fish an inappropriate source of water?
Any other appropriate source of water from fish, apart from eyeballs? Can you somehow squeeze the water from fish?


texts: What is the average Leg-to-Foot Length/Width Ratio?

texts:
I'm making a program that estimates a probable size (widest width and longest length) for a human's foot given the length and width of the leg to which it is attached. However, try as I might, I can't seem to find the average foot-to-leg size ratio. Does anyone know this? It would be even better if you have different ratios for males and females.

As a note, I don't want to know that this varies depending on certain circumstances, just a good average number that will let me generate people who aren't grossly out-of-proportion


texts: Gel Electrophoresis - loading dye and more

texts:
I'm a student new to molecular biology coming in from an eco-evo background looking for tips from you molecular pros! It seems that I'm running quite a few gels. The loading dye I'm using is Gel Loading Dye, blue (6X). The supporting document calls for 5uL:25uL reaction and 10uL dye:50uL reaction. Here's the problem: I'm trying to get my PCR to work and so I'm doing a lot of 'just checking' trials where I only load 2uL of reaction to each well from different 20uL PCR reactions. What volume of Gel Loading Dye, blue (6X) should I use when running only 2uL of PCR product

My goal now is to learn to do a DIG in situ hybridization to localize the distribution of mRNA of a gene I'm interested in so any tricks and tips would be greatly appreciated!


texts: Why do smaller mammals move intermittently?

texts:
I was watching a nice little video on youtube but couldn't help but notice how snappy smaller animals such as rats and chipmunks move. By snappy I mean how the animal moves in almost discrete states pausing between each movement.

Is this a trivial observation or something inherent in the neuro-synapse or muscular make-up of these animals?


texts: Amino acids in human cancer cells expose dextrorotation?

texts:
I would like to know if the amino acids in the human cancer cells are dextrorotatory or levorotatory.
I mean the majority of them.
They expose levorotation just like the amino acids in the normal cells or they are different?

I mean in general. Maybe some particular types of cancer are significantly different from the rest.

I'll try to make the question more on-topic: The amino acids in cancer cells are also levorotatory, just like the amino acids in the normal cells?

This book: Breaking the Cancer Code: A Revolutionary Approach to Reversing Cancer says "We know that tumor cells grow in dextrorotation" - so I wonder where the author(s) know that from. They must be speaking about amino acids inside tumor cells, when they say "tumor cells"


texts:
How can a mixture of unspecified phages be separated (into singular phage strains)? I.e, what are the main methods?

My research shows it can be done using CsCl centrifugation and affinity chromatography, but both seem laborious, the latter also requiring the phages to be already available in pure form.


texts: i don't need Taq polymerase. Just need normal DNA polymerase. So the main idea is preparation polymerase directly from Lactobacillus without using cloned vector. My idea is electrophoresis using agarose gel and calculating the isoelectric point of Polymerase based on protein sequence to know where they will migrate after electrophoresis. Is it possible for this idea ?


texts:
I came across this slide:

Now I haven't understood what the last two grey colored lines mean. Can't ORFS be of any size? What is overlapping frames here?


texts:
I am in Northumberland, UK. This is growing in my veggie plot and cannot find out what plant it is....looks like a triffid!! It is one stem growing out of the ground and has many stems growing on the side of the main one which lie along the soil with no roots appearing.

I placed a couple of pea pods beside the brick to show the size. Hope someone can help. Thank you.


texts: What is the scientific name of this leaf?

texts: Has anyone seen this before? I got it from India as a gift but I have no idea what it is called or how to take care of it. Thanks


texts: Why would the stroma have a higher pH during photosynthesis?

texts:
Here is a question form my test.

  If you could measure the pH of the interior of thylakoids and the
  surrounding stroma during active photosynthesis what would be the
  relative pH of each?

The answer is C.

  the stroma would have a higher pH

I understand that proton gradient is from stroma to thylakoid space, but that does not mean stroma would have less protons than thylakoid space, if stroma would have a higher pH, then the proton will never flow from stroma to thylakoid space, right?


texts: Does all the citrus fruit contain Citric acid and Ascorbic acid?

texts:
While reading a sixth class book about acid bases and salts. I figured that that citrus fruits like lemon, orange etc.. contains citric acid. But in the same book they also given that amla contains Ascorbic acid. Amla being a citrus fruit should contain Citric acid. I am just confused with this.

  Just tell me whether all the citrus fruits contains both citric acid as well as ascorbic acid.

I checked in wikipedia & also in oxford dictionary.


texts: What is the Gaidukov Phenomenon in algae?

texts: Apparently the Gaidukov Phenomenon occurs in algae so as to enable the algae to absorb the maximum light for photosynthesis. How does this happen?


texts:
I just found this caterpillar in my garden. I’m about to mow the grass for the first time. Can I safely handle it? What type of caterpillar is it?
For reference, I’m in Leeds, UK. Here are some pictures:

It’s about 5cm long and 1cm wide. Thanks


texts:
Bacteria produce something called a biofilm.

I have found a few definitions; some say it is a complex of live and dead bacteria and others say it is a layer on cell wall.

What is it made of?
What is its purpose?
How do we combat biofilms when we encounter them?


texts: Floats of Algae, a house-made conjecture

texts:
Background

In North of Scotland there are many seaweed types. One is a green algae (chlorophyta).

They are full of 'bubbles'. According to web searches one of those bubbles (there are two types you can notice by sight) are spores; the other ones are called floaters.

According to searches, Kelp (or brown algae) floaters are full of gases. But we find most of the Chlorophyta full of water, some of them contain bubbles but tiny ones.

Conjecture

The water inside could be of a lower density than the sea water, instead of air bubbles.

Question

Any information on this respect?


texts: Why do Mangoes have a single large seed, and not multiple small ones?

texts: I was just thinking about this, wouldn't it make more sense for a mango to have multiple seeds, as it would allow more seed propagation?


texts: Can a human being live without any carbohydrates?

texts:
Nowadays low-carb is in fashion, but what I recently wondered is whether a human can live without any carbohydrates at all?

Of course this would be hard to do in reality, as most food will contain proteins as well as carbohydrates, but let's assume it would be possible to circumvent any carbohydrates.


texts: Solving a Pedigree Between Heterozygous Half-Cousins

texts:
A man who is a known heterozygous carrier of oculocutaneous albinism marries his half-cousin (they share one common grandparent) as shown in the pedigree below. This trait is transmitted as a fully penetrant autosomal recessive. What is the probability that this couple will produce a child with this disorder?

A. 1/2
B. 1/4
C. 1/8
D. 1/16
E. 1/64

My calculation was 1/2 (for II-2 as he must be carrier) * 1/2 (for II-3) * 1/2 (for III-2) * 1/4 = 1/32. Please help me out by proper explanation to your steps and point out my mistakes. The correct answer given is 1/64. Pedigree shown in the image below.


texts: What is the maximum electric potential that can occur in the human body?

texts:
Neurons can generate a voltage, if there is an action potential. Also, membranes where an ion concentration gradient is present, generate some membrane potential.
What I wish to know is, which cellular element in the human body creates the greatest potential differences? And how high can they be so high? Are there also biochemical reactions, where significantly high electric/electrostatic voltages are important? How strong are these?


texts: Cloning a coding gene into a non-expression vector

texts:
Does it make any sense to clone a CODING gene into a NON-expression vector?
doing this will only give us multiple copies of the gene, while we could run  PCR instead (Let's say we know the gene sequence)


texts: The exact points of muscle attachment and the "equal and opposite force" that skeletal muscles apply

texts:
I've been trying to make a simple simulation of the human body executing some motions in Mathematica (the details are irrelevant), but I need to know some more information about muscles and how they exert forces. To simplify the problem/question that I am asking, take just the bicepts for example. Suppose that you have just the chest, upper arm, and forearm attached, and ignore the rest of the body (and by that, I mean either remove or treat it as rigid, with the exception of the joints in question, which would therefore be just the shoulder and elbow joints).
One relevant idea that I should point out is that I'm simulating the guy basically jumping, and, whilst in the air, your body is in an inertial frame, meaning that Newton's Third law applies. Under the assumption of a constant moment arm, the usual simplifying assumptions that are made here, etc.. (actually, see the hyperlink below), does contracting JUST your bicepts cause an equal and opposite force at the shoulder, or just the elbow, and is this typical of muscles in the human body?
When the bicepts contract, if they're attached to the shoulder/chest they will (theoretically) pivot the upper arm towards you, while if they're attached to the upper arm they may pivot it backwards, the other way (I think). If they're attached to the upper arm, then the diagram here is essentially what I'd use, but if the muscles went all the way through to connect I'd have to basically "add" an additional segment to the diagram depicted in the link, and the muscle would pass directly over the upper arm, instead, for the purposes of contraction, attaching your forearm directly to your shoulder. This is why I think it's a problem of where the muscles seem connected.

Which of these is a more accurate representation of how human muscles accurately attach things, and therefore exert equal and opposite forces when they contract (and is what I've said so far even correct??)? Alternatively, how accurate is the image depicted in the hyperlink in the above paragraph?

Thank you in advance, so so much
Added TLDR; does (-from a conceptual viewpoint-) flexing purely your bicepts function to bring your forearm and UPPER ARM closer together, or is it really bringing your forearm and SHOULDER closer together? Is this how muscles work in general?


texts: What happens to dextrorotatory amino acids in humans?

texts: As indicated by this question, most of the amino acids in the human body have the L-chirality. As enzymes also have handedness, what happens to the D-amino acids that end up within the human body? Are they simply excreted? Are there enzymes (perhaps not in humans) that convert a D-amino acid to a L- one?


texts: Predictive Single Nucleotide Polymorphisms (SNPs) for Bipolar Disorder

texts: Are there any validated SNPs that are either predictive of developing bipolar spectrum disorder or are associated with its pathophysiology?


texts: Why are the shells of birds' eggs fragile but not those of other creatures?

texts:
In my limited  understanding, eggs of oviparous creatures other than birds have a flexible outer membrane.
Is there any obvious reason that bird eggs should have fragile shells?

Notes

I'm asking why birds seem to be a special case. If all other oviparians manage perfectly well without shells, what is it about being a bird that requires the extra resources to form a shell?

I believe birds are considered to be modern-day dinosaurs. Didn't dinosaurs have leathery eggs?


texts:
Recently I have just discovered that a certain amount of the mobile phone frequency can be absorbed by human tissues.

For example, this is the SAR info of iPhone 4s:

Head: 1.180 W/kg 1 g
Body: 0.491 W/kg 1g
Hotspot: 0.491 W/kg 1 g

http://en.wikipedia.org/wiki/IPhone_4S

so hotspot means a hot spot on human body right?

Then question is:

What are hot spots on human body?


texts: How is in-vitro fertilization technically achieved?

texts:
I failed searching on Google technical details about how in-vitro fertilization is achieved. I'm referring to the toolset and its use, rather than the chemical or biological aspects of the process. I often watch on TV how a needle penetrates into a human egg to fertilize it with sperm, but provided that a human egg sizes about 100 microns, I come up with the following questions:

Do there really exist needles so thin to penetrate a 100 micron cell? In such case, how are these needles manipulated without breaking or losing them in the lab?
How do technicians manipulate the needle with such micrometric precision?
How do technicians keep the human egg still so they can break into it with the needle without pushing the egg away?

Not sure if these questions sound naive, but I haven't been able to find any simple answer to them on the Internet.


texts: Species Identification: Small white maggot/larvae, Missouri USA

texts:
I'll try to give as much information as I can, because I don't know which information will be more important.

We woke up this morning to these little white worm/larvae in the house. We are located in the northern portion of southeast Missouri. We live next to some horses and cows. We have 1 inside dog and 1 outside dog. I'd say more of the worms were found in the kitchen (Tile floor) but some were also found in the living room (Hardwood floor).

This is a side view of the worm.

This is a perspective view of the worm. (About a 1/2 inch long)


texts: Why did high A+T content create problems for the Plasmodium falciparum genome project?

texts:
The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply that it prevented them using a clone-by-clone approach:

  Also, high-quality large insert libraries of (A + T)-rich P. falciparum DNA have never been constructed in Escherichia coli, which ruled out a clone-by-clone sequencing strategy.

And that it made gene annotation difficult:

  The origin of many candidate organelle-derived genes could not be conclusively determined, in part due to the problems inherent in analysing genes of very high (A + T) content.

Question:
What is the biological significance of high A+T content, and why would it cause problems in genome sequencing?

Ref:
Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., Paulsen, I.T., James, K., Eisen, J.A., Rutherford, K., et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419 (6906), 498–511.


texts: Can "human exclusion zones" in national parks for preserving Wolves and Grizzlies be a good idea?

texts:
There are National Preserves in the National Parks where some human activities are permitted. But can it make sense to create "exclusion zones" so no human would be permitted in a certain area, not even scientists or researchers just so Grizzlies and Wolves can have a whole world to themselves ?

I know we won't be able to find out how those species are doing, but would there be any benefit ? Has any country ever tried that ?


texts: Let's say you get a a cut on your finger. Will the fingerprint be regenerated to matched your original fingerprint and if so, how?


texts: Can you "fight" a coma or serious illness?

texts:
In an article about the latest earthquake to strike Mexico, I read that a rescuer said to someone in a gurney, "Fight for your life, please!"

I've seen similar things in TV shows and movies where a character is in a coma or seriously injured or ill.

But how much—if anything—can mentally "fighting" a coma, injury, or illness do?


texts: How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

texts:
I have two datasets, from different sources, that I need to compare.

The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library counts, and have calculated enrichment/depletion (positive and negative values with no upper or lower bound).

The second set is a set of protein sequences for which I calculate amino acid frequencies (positive values from 0-1).

The goal is to calculate a similarity between the two datasets. Typically I have two of the second type of set (protein sequences) and I calculate similarity based on the amino acid frequencies... What's the best way to convert enrichment/depletion to frequency so I can compare?

Example deep sequencing data, for position 77 of the protein:

$$\text{enrichment} = \log_2\left(\frac{F_S}{F_N}\right)$$

Where $F_S$ is selected frequency and $F_N$ is naïve frequency.

I came up with a possible solution for frequency equivalent from enrichment ($F_E$) but am open to thoughts if it's good or not:

$$F_E = \frac{\displaystyle\frac{F_S}{F_N}}{\displaystyle\sum_\text{amino acid}\frac{F_S}{F_N}}$$


texts: Why do we see better on stretching our eyelids to the side?

texts: I've often noticed that on stretching my eyes to the side I see a lot better. On searching, I read that this happens because the cornea reshapes itself (due to the ciliary muscles). But is that all, or is there a more accurate biological explanation for this?


texts: Why does Porous-tube Nutrient Delivery System cultivation improve nutritional quality of Okinawa spinach (Gyruna bicolor)?

texts:
I wrote a review paper and it involves in growth system of a plant “Okinawa Spinach (Gynura bicolor)”. A research of (Wang, Fu, & Liu, 2015) reported that Porous-tube Nutrient Delivery System (PTNDS) cultivation enhanced calories from 139.5 to 182.3 kJ/100 g dry matter, and carbohydrate from 4.8 to 7.3 g/100 g dry matter and reduced the amount of protein from 7.3 to 4.8 g/100 g dry matter and ash from 1.4 to 1.0 g/ 100 g dry matter, compared with hydroponic culture. PTNDS cultivation also accumulated the nutrition elements of Ca, Cu, Fe and Zn, and reduced Na concentration.

The reviewer asked me that “why the plant grown in PTNDS reduced the total ash but why improved accumulation of Ca, Cu, Fe and Zn.? “My major is food engineering and I’m not expert in this field.
If this area is your expertise or someone knows the answers? Please help me out with it. Thanks very much.

Wang, M., Fu, Y., & Liu, H. (2015). Nutritional status and ion uptake response of Gynura bicolor DC. between Porous-tube and traditional hydroponic growth systems. Acta Astronautica, 113, 13-21.


texts: How can I evaluate the hydrophobicity and/or surface charge of a protein?

texts:
How should I evaluate protein surfaces in terms of hydrophobicity and surface charge properties of the surface.

Particularly I am looking to compare hydrophobic patches or surface charge between two proteins, from .pdb or Fasta sequences for example.

The goal is to study protein adsorption mechanism in the context of protein purification.


texts: Current human behavior as a genetic heritage

texts: People: I have doubts about genetic heritage, but let me explain the context which has shown up this doubt for you: I was debating about sexism and the following question were put on the discussion: What kind of behavior, most of them come from men, is cultural and social, and what is a genetical heritage from our ancestry? Because I have a feeling that plenty of these behaviors that can be considered, maybe not correct, but at least justifiable. If you have some literature about this subject I would greatly appreciate it.


texts: Do organisms use detergents to fight off viruses?

texts: Common advice against contracting bacteria or viruses is to wash your hands because soap dissolves the viruses' shell. Does any organism exploit this effect to protect against infection, e.g. by having detergents in their mucous membrane? If not, why not?


texts: Biologically, how prevalent is hair loss on a nuclear submarine? How can prolonged exposure to radiation levels typically present on a nuclear sub affect a person, say over a year or even more?


texts: What is a "homologous pair" of chromosomes in cross joining or cross over?

texts: I never understand if the chromatids attached at the centromere is a homologous pair, or the male and female chromosomes?


texts: Meaning of the word "targeted" in a description of chromatin immunoprecipitation

texts:
From a research paper:

The ChIP assay demonstrated that CIC physically binds to the promoter region of FOLR1, PCFT and RFC1.
Compared with IgG control antibody, CIC antibody enriched 4.1-fold more targeted FOLR1 promoter DNA, 13.8-fold more targeted PCFT promoter DNA and 4.2-fold more targeted RFC1 promoter DNA (figure 3B).

As far as I understand, the authors used chromatin immunoprecipitation to look whether and to what extent the CIC gene influences the promoters of folate-related genes (FOLR1, PCFT, and RFC1). And well enough, they discovered that the antibody to CIC precipitates more "promoter sequences" compared with the control antibody (IgG).
What does the word "targeted" mean here? If I remove this word, the meaning seems unaffected to me. In my Russian translation, I just omitted this word, because it does not seem to bear any additional meaning, but I'm not sure.
Can one simply omit "targeted" or does it have a meaning?


texts: Has it been demonstrated that the memory of human brain is just connections between neurons, not "long" molecules such as RNA or proteins?


texts:
In Wang et al., the authors state on page 663 at the top that

  Furthermore, Bax-/- Bak-/- cells were completely
  resistant to paclitaxel-induced apoptosis.

What's the meaning of the -/- notation? Bax and Bak are proteins involved in apoptosis.


texts: Antibodies stored in freezer instead of fridge

texts: Someone from my lab put the box of antibodies in the freezer instead the fridge.  Can I hope that they will still work?


texts: Has human skin pigmentation adaptation and evolution ceased?

texts:
Before asking this question read

Why human skin colour disprove natural selection?
Does darker skin color make it easier to live under sun?

though neither posed the same question or provide the answer to the present question.

In Modern Human Diversity - Skin Color published by The Smithsonian National Museum of Natural History the document in pertinent part states

  As early humans moved into hot, open environments in search of food
  and water, one big challenge was keeping cool. The adaptation that was
  favored involved an increase in the number of sweat glands on the skin
  while at the same time reducing the amount of body hair. With less
  hair, perspiration could evaporate more easily and cool the body more
  efficiently. But this less-hairy skin was a problem because it was
  exposed to a very strong sun, especially in lands near the equator.
  Since strong sun exposure damages the body, the solution was to evolve
  skin that was permanently dark so as to protect against the sun’s more
  damaging rays.

  ...

  The darker skin of peoples who lived closer to the equator was
  important in preventing folate deficiency. Measures of skin
  reflectance, a way to quantify skin color by measuring the amount of
  light it reflects, in people around the world support this idea. While
  UV rays can cause skin cancer, because skin cancer usually affects
  people after they have had children, it likely had little effect on
  the evolution of skin color because evolution favors changes that
  improve reproductive success.

  There is also a third factor which affects skin color: coastal peoples
  who eat diets rich in seafood enjoy this alternate source of vitamin
  D. That means that some Arctic peoples, such as native peoples of
  Alaska and Canada, can afford to remain dark-skinned even in low UV
  areas. In the summer they get high levels of UV rays reflected from
  the surface of snow and ice, and their dark skin protects them from
  this reflected light.

Cases: Lighter skinned populations who migrated to tropical regions (for example, Mennonites in Belize, Boers in South Africa, Belgians in Congo (DRC)) and darker skinned populations which migrated to non-tropical regions (for example Africans in Britain, Africans in the northern U.S. States and Alaska, and Africans in Canada), where the diets of the populations take on the diets which in part led to the specific pigmentation, and the sun applies the same amount of light (UV; other spectrums) to the population as the population where darker or lighter skin adapted, or evolved.

Given the parameters provided, a lay person might conclude that they should be able to migrate to a specific tropic or non-tropic region of the world, take on the diet which led to the melanin production and skin pigmentation which the article states influences adaption or evolution, and over N fixed generations, or an unknown period of time, though eventually, their skin pigmentation will adapt or evolve to the population planners' desired pigmentation; that melanin production and skin pigmentation is not fixed, that evolution and adaptation as to skin pigmentation is continuously ongoing in the human population on Earth circa 2019 CE - and the claim is capable of being reproduced, observed and objectively measured using the scientific method.

Have any scientific studies been performed which substantiates or refutes by observable measurement the theory or claim that environment and diet have an effect on melanin production and skin pigmentation within the scope of any timescale ("One generation, two generations, ten generations, 10-20 generations")?


texts: How many coronavirus particles are in the body at the peak?

texts: How many coronavirus (or other common virus) particles are in the body at the peak? How far it multiplies? Are there billions, trillions or other number of them?


texts: Are there insects who can or try to avoid colliding with raindrops?

texts:
Some insects are very fast. Does this mean that they are capable of finding a way through falling raindrops without getting wet?

Probably they don't do that at all, because riding on a bike or in a car they don't avoid colliding eather?!


texts:
Wikipedia:

  Nested polymerase chain reaction (Nested PCR) is a modification of
  polymerase chain reaction intended to reduce non-specific binding in
  products due to the amplification of unexpected primer binding sites.

I understand that there are two steps and one of those steps involves a non-specific primer followed by a specific primer...

But this does not seem to have sense. What is the purpose of running a non-specific PCR just to hit it with a specific primer afterwards?

What do we gain when doing a nested PCR?

Practical example:
We are planning on sequencing human skin microbiome. Would the ratios of different bacterial species differ if we would use the nested PCR products for sequencing, as compared to standard PCR?


texts: Relationship between the ambiguity (wobble) at codon position 3 in elongation and codon position 1 in initiation

texts:
In prokaryotes the usual observed start codon frequency is AUG > GUG > UUG.

An explanation for this is that

  AUG is the most common initiator codon because it forms the most stable interaction with the CAU anticodon in fMet-tRNA

But does this have anything to do with the more general wobble rules?

  Codon-anticodon pairing takes place according
  to the wobble rules (Crick 1966). During translation,
  base-pairing occurs in the usual way (A with U, and
  G with C) between the first and second nucleotides
  and the second and third anticodon nucleotides. The
  wobble rules state that in the pairing between the
  third codon nucleotide and the first anticodon nucleotide,
  there is a certain amount of play, or "wobble."
  This enables G in first anticodon positions to
  pair with U or C in codons, U with A or G, and I
  (inosine) with U, C, or A. In first anticodon positions,
  C pairs only with G, and A (very rare) only
  with U. These rules are fundamental to all discussions
  of codon capture. Table 1 shows anticodons
  in the universal genetic code as predicted by the
  wobble rules (Crick 1966).

I'm confused because that seems the exact opposite of what happens in the start codons' case, i.e. the "play" is in the first (not third) codon nucleotide in the start codon case. And the table in this last paper only gives CAU Met as the only pairing for CAU, so no wobble.

Am I interpreting this correctly and there's no "Crick" wobble in the AUG > GUG > UUG start codon, but rather another wobble-like mechanism that explains the start codons' first nucleotide wobble-like behavior?


texts: I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of phenotypic effects with some additional metadata. Thank you in advance.


texts: What species of wasp is this? And how to get rid of them?

texts:
Yesterday while moving a chair in my garden I got stung by a group of wasps. During the night I went hunting for their nests and managed to neutralize 3 of them: one was in the chair's legs, about the size of a child's fist and with a dozen on them inside. It was made of grey hexagonal cells, similar to paper in appearance.

(Sorry for the blurry image, I was a bit scared :-P)

Then I've found another one in a water hose tube that was slightly smaller, but quite active.

And finally a third one in a vase, it was very small, only had a couple of cells in it and wasps were working on it, almost as if they were building it from scratch.

Given the number and size of the nests I'm afraid that they could be spreading in the garden. I have already noticed that a couple of them survived the massacre of last night and I'm worried that unless I kill every of them they might keep nesting.

I don't know much about the hierachical society of wasps, but I was not able to identify the queen (although I haven't checked every single one I've killed). Reading online I've found that killing the queen might mean that the worker would eventually die.

So what kind of wasp is this? What can I do to make sure that they do not keep bothering me?

EDIT: by the way, I live in northern Italy


texts:
I encountered the term selective constraint in Huber et al. 2015, page 4 (last paragraph) in:

  If invariable  sites are included in the   analysis, then both the methods of
  Kim   and Stephan (2002)  and Nielsen et  al. (2005)  may be  sensitive
  to    assumptions regarding selective constraint  and mutation rates.

but the context does not quite help.

What it the definition of selective constraint?

Does it has to do with lethal mutations in non-coding regions? Does it has to do with selection interference?...


texts: Do animals suffer from tooth decay, such as cavities? Is it to the same extent as in humans, or do animal teeth decay more or less? If teeth decay in animals as well, are there natural strategies animals use to heal it? And, lastly, how do animals take care of their teeth?


texts: Are there any substance that are more dangerous at low dose than at higher dose?

texts:
It is commonly admitted that

  The dose makes the poison

which means as a person, the more I take a substance, the more risk I take for my health.

There is even an indicator called LD50 (see Median Lethal Dose), which specifies the 'lethal dose' at which 50 percent of subjects will die.

This might seems a stupid question but: are there any substances for which it is more dangerous to take at low dose than at higher dose? For example, you have to ingest at least 1µg of XXX because if you ingest less you will have health problem...


texts: What is this insect that I found under my bed

texts: Found it under a hotel bed in Las Vegas, what is it?


texts: Why the "cfr." in 'Cirrhipathes cfr. anguina' and not "cf."?

texts:
Recently I stumbled upon the species name Cirrhipathes anguina. In the literature it is often mentioned as Cirrhipathes cfr. anguina. What does cfr. mean? Does it carry the same meaning as cf.?

Edit: If the same, why is cfr. used in this case and not just .cf?


texts: What is the difference between Integrin to Cadherin?

texts:
My question is probably very basic but i couldnt get it in lecture and not from looking in the net.

  What is the difference between Integrin to Cadherin.

  By difference I am looking for say:

  structural difference
  functional difference

If i understand correctly both of them helps in cell adhesion.
But, probably in different way? or shortly, what is the difference?

Thank you!


texts: What is meant by "catalytic amount of a hormone"?

texts:
This textbook says:

  In the classic definition, hormones are secretory products of the ductless glands, which are released in catalytic amounts into the blood stream and transported to specific target cells (or organs), where they elicit physiologic, morphologic and biochemical responses.

What is meant by catalytic amount? Does it mean that amount required for catalysis? I know only renin which is catalytic and act as an enzyme, and many other hormones are non enzymatic so why the term catalytic is used in general sense?


texts: Why is thrombin time longer than prothrombin time?

texts:
Thrombin time (TT) and prothrombin time (PT) are two different clinical measures of blood plasma coagulation.

Both clotting tests end with the conversion of fibrinogen to fibrin; however, the TT skips directly to this conversion by adding thrombin reagent, while PT involves the entire extrinsic pathway. Despite the fact that PT involves the same clotting steps as TT plus several others, the normal range for TT is slightly longer than the normal range for PT.

Why is the normal range for TT longer than the normal range for PT when the former skips several clotting steps? Without background information about the normal ranges, it seems much more logical for the prothrombin clotting test to take longer.


texts: why is LPL (lipoprotein-lipase) down-regulated during fasting?

texts:
During fasting our body needs additional sources of energy and that's why triglycerides are broken down into fatty acids and glycerol. where fatty acids can be used to generate acetyl-coA and contribute to the citric acid cycle or build ketone bodies.

So if we are wishing to get more fatty acids why is LPL down-regulated although it's the enzyme needed to break down Triglycerides in lipoproteins?


texts: How many isomeres of sucrose can we use?

texts: It appears that of sucrose (C12H22O11) there are about 512 possible structures (nine carbon atoms are asymmetric= 2^9). And only one of this 512 forms taste sweet. Now it is known that human can't use all isomeres of amino acids but how many forms of sucrose can we digest or use in the glycolysis for our energy?


texts: What kind of spider has colonised my timber framework?

texts:
I'm in the south east UK. I have a site I'm doing intermittent timber work on, that's been left idle for much of the summer. When I came back it has huge webs strung from walls to beams and across the open spaces, everywhere, with the spiders in this picture sitting in them.

At a a guess they are about 30 - 40mm across (maybe 25 when 'sitting' with legs curled at rest close to body?). They sit in the middle of the webs, not hidden at the edges. The webs are quite strong and look like they are durable, as webs go.

Any ideas?


texts: How to cut out a specific named gene from plant DNA

texts:
Suppose one has extracted RNA from a plant, converted it to the corresponding cDNA & amplified it but now wants to cut out a particular, already-sequenced gene out from it, how does one proceed?

i.e. How does one cut out that particular segment of the whole DNA which one wants? Does one always find restriction sites (or rather cleavage sites)  at both ends of the desired gene segment & then one treats the cDNA sample with those specific restriction enzymes?

To get the gene shown below I'd find an enzyme that cuts at the GGCCAC site and another to cut at AAAAAA?


texts: What is the surface area of the human heart?

texts: I heard that the human heart had a surface area of 1000 square feet, and I thought that that cannot be true. So what is the surface area of the human heart and what are the different ways it can be measured?


texts: This insect was captured in Australia near Canberra. It has a very hard exoskeleton and is over an inch long. It seems to have 6 wings - 2 large pairs and one very small pair. I did not see a stinger - however I have no idea.


texts: What is this plant which closes its leaves when touched?

texts:
I came across this video on Facebook where a plant closes its leaves when touched. Unfortunately the video does not mention the name of this plant.

What's the name of this plant, and where can I see it?


texts: How can the symptoms of ovulation (pms or pmdd) occur if one is menstrating?

texts: Even if your period is lasting overly long. Wouldn't starting to ovulate end menstrating?


texts: Are exosomes useful as a transfection or delivery mechanism in gene editing?

texts:
The use of viruses as transfection or delivery agents for gene editing (CRISPR/cas9, etc) is well known. However, one problem with using viruses to deliver DNA into cells is the possibility of triggering an adverse immune response.

Cells already use exosomes to transport various cargo in and out of cells. Does this characteristic make exosomes ideal candidates for delivering gene editing cargo as well?

Also, are there any known examples or studies involving repurposing exosomes for gene editing? Specifically for CRISPER/cas9 applications?


texts: Models of quorum sensing for multi-agent systems

texts:
Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model of quorum sensing that abstracts away from the details of the mechanism implementing it inside the agent, but keeps the key inter-agent properties like diffusion rate, range, and timing.

Is there a standard abstract mathematical model of quorum sensing used by biologists?

I am not interested in the particulars of a specific organism, but would like a general model I could apply to capture the 'gist' for any organism that relies on quorum sensing for part of its behavior.

Bernardini et al. (2007) provided an extension to P-systems incorporating the basics of quorum sensing, and Romero-Campero & Pérez-Jiménez (2008) have used their approach to model bioluminosity in vibrio fischeri. This approach is conceptually appealing to me, but that is because I am predominantly a computer scientists. Although P-system can be used for modeling biological systems (Ardelean & Cavaliere, 2003), they still feel fundamentally computer-science-y and are typically not published in orthodox biological venues. This makes me suspect there is a more standard approach among biologists, probably via dynamic systems and diffusion equations.


texts: What is this plant growing on Asian spider-flower?

texts:
I found a densely-clustered plant (circled in red in photo) growing on top of an Asian spider-flower. I know what Asian spider-flower looks like. I'm in Chennai, India. What type of plant is this?

(Click the Image to enlarge it)


texts: In any way could the body store electricity supplied externally?


texts: How many times did photosynthesis evolve?

texts:
Was it a 1 and done thing? Plants seem to have developed photosynthesis by the endosymbiosis of cyanobacteria. Is the latter the one time in Earth's history that the process independently came about?
Any answers would be greatly appreciated


texts: Reading Jennifer Doudna's fascinating book on CRISPR. So she describes rare cases where a mutation in a single cell removes the gene responsible for a genetic disease. The cell proliferates and the disease is cured. What I don't understand is--aren't all the aberrant cells also still dividing and passing on the harmful mutation to their progeny? How does the single healthy cell edge out all the other cells to "cure" the patient.


texts:
How is it decided what type of food we want to eat? For example, sometimes you would like to eat some sweets but not a full meal, other times you'd like to eat some fruit, sometimes not and so on.

I have read somewhere that organism can detect whether we are hungry or not and it gives the effect so that we feel that we are actually hungry. But the question is: is there something that measures for example what is level of glucose or aminoacids or some fats in blood and specifies not only whether we are hungry or not but also what type of food we should eat to replenish lacking resources?


texts: How can I compare the STRIDE and DSSP output files of a particular pdb file?

texts: I have the pdb file of H-ras protein 5P21.pdb. I am supposed to compare the output of DSSP and STRIDE files after feeding this pdb file to respective servers. My question is how to make a quick comparison between these two results?


texts: Understanding the strategy of Sanger DNA sequencing

texts:
The Sanger sequencing method creates large numbers of sequences of all possible lengths, ending with a specific nucleotide, by terminating with a tagged (fluorescent) nucleotide at the end.

But if you already have fluorescent nucleotides of a specific base, why not just do regular PCR  with them, create a huge number of full length copies of the original sequence, and then simply see the locations where the nucleotide fluoresces to determine all the locations of that base. Why do we need a large number of copies ending at each possible location, as with the Sanger method?


texts: I had read about science working towards the creation of artificial wombs however I wonder how compatible are mammal wombs and connected systems to develop fetuses. What species are so compatible that they would be able to surrogate the embryos and fetuses of another species?


texts: Stabbing muscles when flexed and when relaxed

texts: Just a random question, would a sharp object pierce your muscle more(stabbed with the same amount of force) when the muscle is flexed or when relaxed?


texts: How is human cartilage immunised (protected) against pathogens since it does not contain lymphatic vessels?


texts: How conscious are mammals that mating leads to pregnancy and offspring?

texts: Does a pregnant female mammal know that its pregnancy is the consequence of a previous mating? Or are humans the only mammals which are conscious of it?


texts: Different number of flaps in heart valves

texts: Can anyone tell me why the different valves of heart have different number of flaps is it in any way related to evolution of homo sapiens.


texts:
I am wanting to learn (memorise) some of the tree of life; the classification of organisms. So I have come across a lot of kingdoms in my research. Basically, I don’t want to waste my time learning the wrong thing, so my question is this. Is there an official or most recent system of classification, some authority in organism classification that we look to? After kingdoms it seems pretty clear, the phyla in (say Animalia) seem pretty defined and uncontraversial.

These are all of the ‘kingdoms’ I have found while researching. Some are called kingdoms in one source and not another. I know that some overlap others. This is just to throw every possible example out there.

Animalia, Apusozoa, Archae, Archaebacteria, Archezoa, Bacteria, Biliphyta, Chromista, Chromophyta, Ciliofungi, Cryptophyta, Eufungi, Euglenozoa, Excavata, Filastera, Fungi, Monera, Nucleariida, Plantae, Proteoarchaeota, Protista, Protozoa, Rhizaria, True bacteria, Viridiplantae

I don’t ask that you go through them and explain them. Only what the actual system of classificating organisms is. On that note. As far as I’m aware, there’s two types of domain systems. Two are Eukaryota, Archae/-bacteria, Bacteria. Another is Eukaryota, prokaryota. A clarification on this too would be appreciated.


texts: What is the proper naming of Aminoacyl-tRNAs?

texts: I want to refer to an aminoacyl-tRNA with the anticodon 3'-UAC-5' that is charged with methionine. What is the proper name for this molecule?


texts:
Building on this question,
I understand pretty clearly why forests are carbon sinks (trees grow, and there is carbon stored in soil and biomass).

What about the oceans, though? Are underwater plants the real actors here?


texts: What will happen if a scorpion pierces itself?

texts: If a scorpion pierces itself, will it die or immune to its poison? If it produces the venom its blood should be immune to itself poison.


texts: Why do eyes water in response to particular emotions?

texts: It is common for people to experience very moving situations (sad movies, etc) and have a physical reaction to it (such as crying). I am curious about how emotions can physically lead to the act of crying. Why/how does this happen? What is the mechanism?


texts: What is this soft cased worm-like creature?

texts:
Found this creature in the bathroom

Features which ought to help for identification:

Size = 1 cm
Soft casing
Can emerge from either end of its case and thus reverse the direction it crawls.
Many tiny legs.
Can walk pretty fast.

Found in the middle east


texts: Does polyploidy always isolate the polyploids from the diploid source population?

texts:
I am receiving conflicting information while researching polyploid speciation. On the one hand, some sources state that a polyploid can only reproduce sexually with polyploids having the same number of chromosomes. But I am also finding information claiming tetraploid x diploid reproduction in orchids, or tetraploid x triploid reproduction of orchids (for example,see  American Orchid Society, AOS.org).

Is polyploid sexual isolation always the case, sometimes the case, or never the case? Can someone clarify this?


texts: Can hormones of human body created artificially even i mean the hormones just consisting of bio chemicals and nothing else?


texts: Regulation of Cra protein level in E coli

texts:
Catabolite Activator/Repressor, Cra protein (formerly known as Fructure Repressor FruR) plays a significant role in central carbon metabolism of E coli. Its activity is inhibited by fructose-1,6-bisphosphate (FBP); Cra up-regulate gluconeogeneis pathways and down-regulate glycolysis and carbon-uptake pathways. I found enough literature on how Cra plays a regulatory role in metabolism.

However, I am unable to find out explanation of one experimental observation: with increase in glucose uptake rate the transcript level of cra decreases. What is the mechanism for this. Further, are Cra proteins degraded as the glucose uptake rate increase, if so what is the regulatory mechanism?


texts:
When the spinal cord is damaged, the connection between the brain and some part of the body may be lost.

To restore this connection, researches are considering either:

Repairing the damaged area so that the spinal cord works again.
Bypassing the spinal cord by connecting the brain directly to the affected part of the body.  This is done by implants in the brain connected directly to electrodes in the muscles creating a new circuit in parallel.

My question is has there been any attempt to bypass only the damaged part of the spinal cord?  To create a bridge over the damaged tissue?


texts: How is oxygen and carbon dioxide exchange mediated by hemoglobin?

texts: Oxygen is transferred by hemoglobin from the lungs to tissues, while carbon dioxide is transferred by hemoglobin from tissues to lungs. How is this regulated bidirectional transfer mediated?


texts: Can anyone identify what type of bug this is?


texts:
I am following the original genomic control article -
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.167.8448&rep=rep1&type=pdf

What's the role of $p_i$ in the article? It says that $p_i$ denotes the frequency of $A_i$ allele in population. Is it derived from Hardy-Weinberg equilibrium?

I would like to know how I should calculate $p_1$ for a specific data set.


texts: Does the human eye see things at twice the distance in a mirror?

texts: If I'm standing 3ft away from a mirror and looking at something in it that is behind me but 5ft away from the mirror, do my eyes see that object as 3ft? Or 8?


texts: Efficiency of plasmid DNA isolation from frozen E. coli cell cultures

texts: Has anyone isolated plasmid DNA from frozen (at -20degrees) E. coli cell cultures (not pellets)? Has that worked and if so, with what yields? What would be the quality of the isolated plasmid DNA if run on a gel? Would most of it be degraded or intact?


texts: What are the blue and white things on this Sunburst lichen?

texts: I am a amateur photographer I found some interesting things when I got home and looked at my photos. There are some blue/white cocoon. I  like structures on top of the sunburst lichen. I live in Colorado and took these photos on January 23.


texts: Is it true that oxygen has a diffusion rate in air 10,000 times greater than in water?

texts:
According to the Wikipedia page on the design of gills, oxygen has a diffusion rate in air 10,000 times greater than in water. Is that true?

The WP entry refers to: M.B.V. Roberts, Michael Reiss, Grace Monger (2000). Advanced Biology. London, UK: Nelson. pp. 164–165.


texts: UV light-induced mutagenesis during gel extraction

texts: this is a very short question I did not find the answer for online, neither on this nor other fora. At the beginning of my cloning protocol, I extracted the band with the sequence of interest directly from the gel upon electrophoresis, and failed to minimise the exposure time of my sample to UV (did not switch off the lamp between cutting of different bands). Now, the gel was sitting in the cast tray the whole while (altogether maybe 30 to 50 seconds), and I wanted to know whether this eliminates the risk of mutagenesis, or at least minimises it, due to the absorption of UV light by the cast tray. Thank you.


texts: Probability of all alleles represented in a sample

texts:
I'm trying to wrap my head around some formulas presented in the 1992 paper from Chakraborty Sample Size Requirements for Addressing the Population Genetic Issues of Forensic Use of DNA Typing, but I have not been able to.
Specifically, the right hand side of formula (16) and it's relation with formula (13).
$1-\sum\limits_{i=1}^{k}(1-p_{i})^{2n}$ (13)
$[1-(1-p)^{2n}]^{r}\geqslant1-\alpha$ (16)
Formula 13 indicates the probability, for a locus with $k$ segregating alleles whose frequencies are contained in the vector $p$, that all alleles are represented in a given sample of size $n$, and the right hand side of formula 16 indicates the probability of $r$ alleles to be represented in a given sample of size $n$.
First of all, why, based on 13, the expression inside the summation indicates the probability of an allele of frequency p, to remain unobserved in a sample of size n?
I tried to understand this from the Hardy-Weinberg equation but did not have any success.
Second, Why to take the expression in (16) to the r'th power?
Which biological concepts am I missing?


texts: Meaning of some unit of measurement of kinase activity

texts: I need help knowing what $cpm \times 10^3$ means in Figure 4(C) of this paper (https://www.sciencedirect.com/science/article/pii/S0022202X15323149#f0010). It appears to be a unit of kinase activity.


texts: biologically speaking, what's the difference between sleeping and just resting?

texts:
I can lay down in a rested position with my mind at ease, but no matter how relaxed I am or for how long i do it, it seems I'll still need sleep eventually.  What's the difference - what is occurring during sleep that can't occur now matter how relaxed or rested you are?

And if you know of any studies that have been done to try and mimic the benefits of sleep in a waking state - ie during some type of meditation or whatnot - I'd consider that relevant and interesting to know.


texts: Calculating chromosome number in meiosis: Why is the crossbreed between a fox and a dog (dox) sterile?

texts:
Given the following example/question (originally found here):

I worked out the haploid number of the dox to be 29 and the diploid number of the dox to be 58. 58 is an even number, so surely 29 homologous pairs of chromosomes can form for the dox to be fertile. Why is it sterile?

Thanks


texts: Unknown plant, can anybody identify this plant?

texts:
Location: Western Germany
Can anybody identify this plant from Germany ?


texts:
Sometimes it's difficult falling asleep for almost an entire night. You might feel like getting up and being productive instead, or 'pull an all-nighter'.

Or you can try to simply lay in bed to relax and rest, even though sleep does not kick in. In this situation, you may eventually fall asleep, only to be woken by your alarm just an hour or two later. Upon waking from such short sleep you can feel completely wrecked.

It leaves me wondering if you would feel more rested if you didn't sleep for just one hour. Maybe if you could relax throughout the night without really sleeping, you'd feel more rested by the time your alarm goes.

But is it physically possible to recharge as if you were sleeping without actually sleeping?


texts: From DNA data, is it easier to conclude that chimpanzees are our close relative, than it is to do a paternity testing?

texts:
Well, today I was contemplating on how to explain evolution, approaching with the dialectic method. When it came to why chimpanzees and us being so close in the tree of evolution isn't outright absurd, I formulated a witticism, "Well, today a glance at humans' and chimpanzees' DNA would confirm how much close we are. Compared to that, if you were to do a DNA paternity testing, you would have to do a bit more grunt work in that you would have to look for more nitty-gritty details that separate (and make similar) one human from another. So, ours and chimpanzees' closeness would actually be easier to conclude than to tell your parents apart from non-parents."

Well, was I correct? That this would be easier than that?


texts:
I've seen a patient who had a Vitrectomy (eye surgery) done on a single eye manifest massive swelling on both eyelids.

That seems like having my left hand swell after punching a wall with my right one.

Is this example in the eyes rare? How and why does it happen in the eyes? Does it happen anywhere else?


texts:
Say I have a disease that is autosomal recessive. If one was heterozygous for this trait, could the recessive gene still be expressed?

I know sickle cell anemia has a heterozygous advantage so it must be possible but what are the conditions for this to happen and also to what degree?

EDIT: This isn't asking how a gene is recessive or dominant in a molecular level.


texts:
A recent review article, Oxidative mechanisms of biological activity of low-intensity radiofrequency radiation reached a surprising conclusion

  our analysis demonstrates that low-intensity RFR [Radio Frequency Radiation] is an expressive oxidative agent for living cells with a high pathogenic potential and that the oxidative stress induced by RFR exposure should be recognized as one of the primary mechanisms of the biological activity of this kind of radiation.

They suggest the oxidative stress can cause cancer and non-cancer pathologies.

This study has received next to no media coverage. With RFR impacting so many people it makes me wonder, is this study valid? I would expect this to be front page news given the large number of studies reviewed.

Are low-intensity radio-waves carcinogenic?


texts: How long it takes medium size dog's corpse being decomposed?

texts:
I am not a Biology student or expert. Moved the post from Pets SE.

Around a month ago, my 12 years old dog passed away. And I buried her in our front yard (mostly soil, 1 meter depth, wrapped in some cloth fabric material). The thing is I have a plan to sell my house, but don't have nerve to move away if my dog's corpse have not completely decomposed. There is a hard feeling to leave her like that, you know, the family bond stuff. So it will be relieving if her body are completely decomposed when that happen.

Background I live in Yogyakarta, Indonesia, which has tropical climate. But from the past few month, we have pretty unusual cold temperature during night until around 9 am, because of Australian Cold Monsoon. I mention this in case it has logical factor of how decomposition works.


texts: Is curling the fingers considered digit flexion?

texts: Is curling the fingers considered finger flexion and straightening the fingers considered finger extension? I feel like this is correct in everyday language, but I am not sure if it is correct in anatomical terms.


texts: How much does hearing deteriorate with age?

texts:
For the average person, what is the lowest volume of a pure tone at each frequency they can hear as a function of age?
I know some people lose hearing faster than other people, because they are exposed to loud sounds. So I am also interested in hearing loss induced by loud sounds as a function of frequency.
The brain can adapt to the hearing loss, thereby creating the illusion that a sound is just as loud as if nothing happened to their hearing. For that reason, I also wish to know what volume the ear transmits to the brain as a function of frequency and age.


texts: Why does the ova remain viable for only a day after ovulation?

texts:
The ova remains viable for approximately 24 hrs after ovulation to be fertilised by a sperm.

  ...chances of becoming pregnant increase dramatically if you have sex during the 5 days before ovulation and the 24 hours after ovulation.
  [source]

My question: what prevents it from remaining viable for a longer period?

My assumptions:

Could be because it is arrested in metaphase II so cannot undergo transcription
Could also be because its haploid
Due to progesterone effect.

So what is the real phenomenon behind this? Also note that, compared to the ova, the sperms remain viable in the female reproductive tracts for a longer time (approx. 4-5 days).


texts: In flowering plants food is transported in which form? I searched on google and found that it is sucrose. Why not glucose/fructose/starch?


texts: Identifying a lone bone found newar Rowena Crest, Oregon (USA)

texts: I was wondering whether anyone knows how to identify what animal the following bone belongs to.  I assume it a femur, but it seems rather short and squat.  The following photos show two views of this bone and I've placed a 15cm ruler in the frame with the bone.


texts: Why do water molecules diffuse along axons direction?

texts: I am studying tractography technique which aims to reconstruct bundles of axons in brain by following the diffusion direction of water. It is very interesting because it is non-invasive. It exploits the difference between grey matter and white matter: in white matter (axons) we find an anisotropic environment since there is a preferential direction of diffusivity of water molecules that is along the axons direction, while in grey matter the environment is isotropic since molecules do not move with a preferential direction. The diffusion of molecules is generally given by a difference of concentration of molecules between two points but they should move even though this gradient is not present because of the temperature so because of the fact that they have a certain thermal energy. Therefore my question is: why do molecules move along the axons direction ? Is there a biological aspect that causes like a difference in concentration between the starting point and the ending point ? Maybe the answer is trivial but since I am not a biologist I do not know it :) and I am not able to find something on web . It seems that I find only explanations for diffusion of water molecules from outside the cell to inside... I would like to know the reason why they move in the same direction of the axon.


texts: Does the anterior primary ramus of T6 innvervate the Rectus abdominis?

texts:
Anatomy and Human Movement Structure and Function writes in the section about Rectus abdominis:

  Nerve supply
  By the anterior primary rami of the lower six or seven thoracic
  nerves (T6/7 to T12).

What does "or" mean? Does it means that in some humans this happens and in some it doesn't?


texts: What causes midcycle FSH surge in the menstrual cycle?

texts:
I have encountered contradictory attributions to the causal factor of midcycle FSH surge. Whereas some sources attribute it to the relatively high estrogen levels (1), others say it is because of increasing amounts of progesterone (2).
I am confused.
(1) http://www2.hsc.wvu.edu/som/physio/classes/pcol260/classroom/notes/reproductive.htm
(2)
https://www.ncbi.nlm.nih.gov/books/NBK279054/#!po=1.17188


texts: Why is urine acidic (equilibrium of I/O, input  output)

texts: Urine pH is on average 6.0, net excretion of acid. Is that in balance with net input of acid?


texts: What are key factors when evaluating and comparing miniprep columns?

texts:
I'm looking to comparing different protocols for minipreps for plasmid DNA purification. What factors should I be looking at? A few things come to mind:

Cost
Yield
Time per step
Replacement with other reagents
Spin vs. vacuum
Color and caps or lack thereof


texts: How do chameleons signal cells to change color?

texts: I have read about how they can change color, but is there literature about the chemical signaling process they use to do so?  I read that it could be some combination of hormones and neurotransmitters, but I couldn't find specific information on the receptors or chemical mechanisms.


texts: Can the eye distinguish between pure and composite colours and how do we measure this?

texts:
Red light plus green light makes yellow light.

Suppose I shone a pure red light, say 650nm, onto the same spot as a pure green light, say 550nm. The eye sees this two-peak spectrum as yellow.

This presumably means we are tricking the eye, since a pure yellow light source would also be perceived as yellow.

Do the cells on our retina treat composite spectra equivalently to corresponding single-peak spectra? If not, how do we quantify the gap?


texts: What is the length of the centromeric repeat sequence in a human?

texts:
I'm looking for the lengths of the centromeres of human chromosomes.

The best I could come up with so far has been: The length of individual centromeric arrays was found to range from an average of 680 kilobases for the Y chromosome to 3000 kb for chromosome 11.

Here they say that "Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome." Which unfortunately is not the same as saying the centromeres compose 5% of the genome. (Or maybe it is? Biologists to the rescue!)

Ideally an answer would contain the length of the centromere in each chromosome, but a precise percentage for the whole human genome would be good enough.


texts: Does this patient have HHV6 or HCMV after transplant surgery?

texts:
I have been given mock results from a PCR test on blood samples taken from kidney recipient patients and their donors. The PCR reaction can detect single copies of viral DNA. I have been asked to determine whether 5 patients have been infected with either human herpesvirus 6 (HHV6) or human cytomegalovirus (HCMV) following kidney transplants. I have results for patients pre-transplantation and 1/3 weeks post-transplantation.

The results are as follows:

Donors:

Donor for patient A = HCMV+
Donor for patient B = HCMV+ & HHV6+
Donor for patient C = Neg for both viruses
Donor for patient D = HHV6+
Donor for patient E = HCMV+ & HHV6+

Recipients:

Patient A = HCMV+ before and 1 & 3 weeks post-transplant
Patient B = Neg for both viruses before, then HHV6+ at week 1 & HCMV+ at week 3 following transplantation but negative for HHV6.
Patient C = HHV6+ before and 1 & 3 weeks post-transplant.
Patient D = HCMV+ before and HCMV+ & HHV6+ 1 & 3 weeks  post-transplant
Patient E = HHV6+ before and HCMV+ & HHV6+ 1 & 3 weeks  post-transplant

Answers: I am guessing that Patient A was re-infected by donor A. Patient B was neg for both viruses, developed HHV6  week 1 but this test was neg week 3 & instead positive for HCMV – these viruses do not disappear, you either have it or don’t so assuming there is no contamination error then what virus did he develop post-transplant?? Patient C was HHV6+ prior to transplant but donor is neg for both, so what virus did he develop following transplant? I can see that Patient D was infected with HHV6 from donor post-transplant. Patient E was infected with HCMV from donor post-transplant.

I am struggling to determine what virus Patient A, B and C was infected with following transplant. Can anyone help? I know almost 100% of us are infected with both viruses but do not cause disease in healthy people, that both latent and active viruses show positive when in blood and that both viruses can re-activate under certain conditions such as via infected organ transplants and immunosuppression.


texts: Does the most common definition of "allele" include a change in phenotype?

texts:
I'm prepping an activity for my biology students on cystic fibrosis. There are about 2000 different mutations of the CFTR gene that cause CF. Since the final phenotype is pretty much the same, can I still claim that all these mutations represent different alleles?

I like to point out that genes tend to have more than two alleles - it's something that students really struggle with. But if every allele needs to have a different phenotype based on the standard definition, then this isn't ideal.

Thanks for the help.


texts: Bioinformatics - DNA binding, sequence-specific protein data

texts: I am a computer scientist and we are working on protein function prediction algorithms. Right now, we would like to examine protein-DNA binding properties computationaly. For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. I was looking on Gene Ontology and Protein Databank where I'd expect such informations, but I was unable to find it. Are such data presently difficult to obtain? Or are simply not collected? Or could you give me some direction where to look for such data. Thanks.


texts: What are the branches of system ecology?

texts:
What are the branches of system ecology that scientists research in nowadays? Or what can system ecology can applied to, or be used?

I have read its Wikipedia page, but sadly it doesn't answer my question. The most relevant section of it is the "Closely related fields", but again, it doesn't answer my question directly.

From what I understand, system ecology is a sub-field of theoretical ecology. It uses thermodynamic in physics to explain a biological system, with the help of network thinking and some technique of visualization. I have presented this in detail what I understand on my website.

Related: How is the Energy Systems Language used in ecology?