texts: Is there any research on wolf and bobcat interactions?

texts:
I'm studying interactions between North American predators, specifically wolves, coyotes and bobcats.

There's evidence from data I've collected from game cameras that suggests a significant interaction between wolves and bobcats. However, I haven't found published literature or reports on interactions between these two carnivores besides a paper by Stenlund (1955) that suggests bobcats may benefit from scavenging wolf kills.

Does anyone know of any publications in peer-reviewed literature, government reports or even reliable observations from biologists in the field on interactions between wolves and bobcats?

Thank you!


texts: How does natural selection process escape from local optima?

texts: How does natural selection process escape from local optima towards global optimum in a fitness landscape during evolution?


texts: Formula for number of divisions required to form x number of cells (Mitosis and Meiosis)

texts:
In case of Mitotic Division, we say that if the total number of cells formed by mitotic divisions are $x$, then counting from the first cell onwards, we get $x-1$ divisions ($N$)

$N = x-1$

This is fairly logical to me

However, to find total number of meiotic divisions for $x$ cells, we use the formula
$x/4$ (In questions where we are supposed to find total number of divisions required for forming some number of seeds or pollen grains)

Shouldn't the formula be $N = (x-1)/3$ (Using the same logic as used for the mitosis formula)?


texts: Why do genetic testing companies (FTDNA,AncestryDNA,23andme) express DNA shared in centimorgans (cM) instead of in number of base pairs or in percent?

texts:
Expressing DNA shared in number of base pairs or in percent of total genome would be so much simpler and easier to understand for the customers.

.


texts: Why can't there be fructification of mycelium in submerged culture?

texts:
I am very new at this. I am wondering why fed batch cultures produce a lot of mycelia but no fruit. I thought the more mycelia you had, the greater chance of it forming a fruit body.

I am refering to this paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768415/ but there are many others with the same methodology. It seems to oppose fruit  body production to submerged cultures.

It seems to be submerged in water and in sugar.

It also seems you can have fruit bodies with a single mating type :
- Coprinus sterquilinus (The Fungi by Sharma)
- A bisporus and V volvacea (Chang Chiu)


texts: What in neurons and their connections changes during the process of learning?

texts:
I'm not sure if this question belongs more in physics or biology (or maybe even computer science)... but biology seemed to fit more.

What changes in the state of our brains when we learn things?  Because I looked on the internet and I learned about artificial neural networks, and every resource I've found teaches of neural networks that have weights that are trained/evolved and then are static at runtime; you simply train the weights and then once you use them in simulations, they never change.

Purely feedforward neural networks that rely on this can't react to new situations differently if they've experienced it before.  They react exactly the same each time.

I suppose that theoretically, a recurrent neural network that was big enough could really learn, but in practice, these have been used as purely memory slots for an existing method defined by the weights, not as storage of new methods of doing things.

So my question is, physically, chemically, biologically, what changes in the neurons and the connections between them when we learn things?  I don't think we really understand how it comes together on a grand scale yet, but I'm pretty sure we've figured out that much.  I want to learn how to model a simplified version of it mathematically/programmatically.


texts: Do cows chew in a preferential chirality?

texts:
One of the enduring myths in molecular physics, when talking about chirality as pertains the existence of enantiomers and the differences between them, is that the way cows chew is also chiral, i.e. the up-and-down and the around-in-a-plane movements combine in such a way that you can distinguish a cow chewing from its mirror image. This is mentioned in e.g. Wikipedia, among other resources.

A recent question in the Physics site asked for the source of this factoid, which turns out to be

  Movements of the Lower Jaw of Cattle during Mastication. P. Jordan and R. de L. Kronig. Nature 120, 809 (1927),

and this is a rather unsatisfactory source: they report on a survey that finds that 55% of cows chew in a 'right-circular' fashion and 45% chew left-circularly, but they then go on to disavow any statistical significance in the result:

  The number of observations was, however, scarcely sufficient to make sure if the deviation [in the ratio of the two kinds] from unity is real.

Given that this isn't a physics question, I thought I'd bounce it over to the mammalian behaviourologists out there: have there been further studies about which way cows chew? I imagine that they're out there, but I wasn't able to find them.


texts: Why does a Urinary Tract Infection cause a strong, persistent urge to urinate?

texts:
There are plenty of articles on the fact the a urinary tract infection (UTI) causes frequent and urgent urination. For example; on this National Institutes of Health webpage.

My question is:

Why does a urinary tract infection cause an increased desire and hence, a greater urgency to urinate?


texts:
I need a ppi network of cancer and it should have 200k to 300k proteins (nodes)
As the web inteface don't allow more than 2000 proteins to be visualized . I have downloaded the protein_links of homosapiens from the download section .
It has 11353058 link which means 11353058 interaction .
The downloaded file is a .txt How do we do  to extract cancer interaction from this huge set ?
What are the different ways to manipulate this file .


texts:
A space pod containing an astronaut drifts out to space and cannot be rescued. The space pod contains no insects, and the only bacteria present are those originally brought in by the astronaut. There is plenty of oxygen (assume 20%) and the interior is heated in the long term to 20 degrees C by a radioisotope heater.
The astronaut eventually dies through lack of food or water. His body is found many years later. What will the rescuers find? A body or a skeleton?


texts: Why were dinosaur skeletons so light compared to mammal skeletons?

texts:
I was watching a presentation by Dr. Jessica Theodor [1] who discusses (at 38:10), among other things, the skeletal structure of dinosaurs vs. mammals. "Dinosaurs have way lighter skeletons, which means that for the amount of material they can be bigger. If we start to look at sauropods, they have this really interesting set of structures, these big holes in their vertabrae...
it allows you to build a lighter, stronger skeleton. Mammals can't do that. It's not how we build our bones."

Why don't mammals do this? Are there fundamental trade-offs that make our (apparently) weaker, heavier bones better, or is it just chance that we haven't matched this development?

(Of course I'm open to the possibility that I misunderstood the talk, or that it was simplified to the point of inaccuracy on this point.)

[1] Jessica Theodor, Being Giant: Why are mammals not as big as dinosaurs? (2015)


texts:
Million of years ago there lived dinosaurs up to 36 m high. About 10,000 years ago lived Machairodontinae -compared to cats today they were huge. About 400,000 years ago lived Mammuthus trogontherii: it reached over 4 m at the shoulder. And these are just some examples.

Todays biggest living creatures look small compared to previous. So my question is, why are all creatures getting smaller? Why doesn't evolution generate any big creatures with size comparable to the dinosaurs?


texts: Meaning of "stripped" in "stripped antibody-depleted sera"

texts:
From a research paper:

FOLR1 autoantibody detection
The assay for identification of the presence and relative quantification of FOLR1 autoantibodies in serum samples was performed as previously published.41–43 Horseradish peroxidase (HRP) labelled anti IgG antibody (Cat#I8640 Sigma Aldrich) and IgM antibody (Cat#I8260, Sigma Aldrich) were used to detect IgG and IgM. Antibody-depleted sera (Sigma Aldrich) was used as negative control. Serum effect on blocking FA binding to folate binding protein was detected using HRP labelled FA (FA-HRP, Ortho-Clinical Diagnostics, Raritan, New Jersey, USA). FA in serum samples was removed as previously described. Unlabelled FA was spiked (0.01–2000 ng/mL) into stripped antibody depleted sera to generate the standard curve. The SuperSignal ELISA Femto Substrate (Cat#37074, ThermoFisher Scientific) was used as substrate for detection of HRP activity. Images were collected using a 96-well imager (Q-View Imager, Quansys Biosciences). Intensities were extracted from the images using Q-View Software. IgG, IgM and relative FA-blocking amount were calculated based on the standard curves.

What is the meaning of "stripped" in stripped antibody depleted sera? I think that "antibody-depleted sera" stands for "serum samples that contain a reduced concentration of antibodies". But why stripped? Does it mean that the authors applied some additional techniques to ensure an even lower level of antibodies in the serum samples?
I found it odd because the word "stripped" is used only in this particular place, and nowhere else. They mention 'antibody-depleted sera" earlier, without "stripped".


texts: In what ways does the number of legs affect an animal's functioning?

texts:
After much research, I've only been able to find specific examples of leg-number's impact on locomotion and dexterity (and/or object manipulation). I feel as though there must be other ways it has a role in an animal's anatomy and function.

Examples I imagined but couldn't evidence include;

Respiration rate (relating to S.A. for tracheoles in Arthropods).
Similar to no. 1 but not quite the same - the structure of the circulatory system.
Insects'/tetrapods' stabilty (especially regarding an ant's capacity for load-bearing).
The brain's capacity for higher order thought processes (does conscious control of more limbs limit this?).
Efficiency of thermoregulation (also related to differences in S.A.).

I would most appreciate an explanation for how a given animal's number of legs gives it an aptitude for a type of locomotion (such as sprinting, climbing or burrowing). I would also like simple yes/no answers to the ideas listed above - as to whether they are implicated in the number of legs.


texts: What is the meaning of "Rb is in the active state"?

texts:
I am reading about cyclins, cdks and Rb (Retinoblastoma) and some of the terminology is not clear to me.
I understand that when CDK phosphorylates Rb, it disconnects from E2F, and E2F can act as a transcription factor. My question is about the terminology.
My questions are:

When people say "Rb is active", do they mean "active = phosphorylated state" (where E2F is free from Rb) or do they mean "active = not phosphorylated state"?

Does "active cyclin" means cyclin is going to join CDK and cell cycle proceeds? or is "active cyclin = cyclin is not activating CDK and cell cycle paused"?

Active CDK means CDK is activated by cyclin and cell cycle can proceed?

In general, Maybe one can say that binding (Rb with E2F or Cyclin with CKD) means activation and disconnecting means inactivation?

Thanks!

(Image source: Kolch, Walter, et al. "The role of Raf kinases in malignant transformation." Expert reviews in molecular medicine 4.8 (2002): 1-18.)


texts: Which pathways/mechanisms could control some Synaptic clefts in series by Somatic Nervous System?

texts:
I listened a talk where the speaker said that this can probably be possible by Weak Quantum Cognition Theory.

I see that there is no evidence at the moment, only theory.
I see no pathways by which this could happen directly such that the quantum entanglement and quantum superposition could happen.
They should happen in a series, but I see no system holding the signal going on.

I think this is a only a hypothesis, without any supportive  evidence.

Probably, some type of synaptic cleft can be controlled, but still I see no evidence or no pathway or pathways.

I do not understand which pathway/pathways this could happen.
What is the target mechanism? Presynaptic membrane or postsynaptic neuron?

Which are possible pathways that could control the secretion of synaptic cleft?


texts:
what snake is this and is it venomous?
Found on my house on Khao Yai, Thailand


texts: Why and how does falsifying sensory information work?

texts:
Some context, before the question:

Whenever I have a craving to binge on something sugary, I just prepare a cup of extremely bitter green tea (with 3 bags of tea) and I imagine myself binging on something sugary, but at the same time I take a gulp of this bitter stuff and let that sit in my mouth for a few seconds.

The very next moment, I immediately notice that the craving comes down and after a few more sips the craving completely goes away. I feel nauseous if I think about something sugary for another day.

Actual question:

Why and how does this work? Even though I consciously know that I am fooling myself, with a false sensory perception, why does my brain associate sugary treat to be revolting and poisonous(cause of nausea)?


texts: Why there are two types of medium (YPGlu and YPGal) in the *K. lactis* Protein Expression Kit?

texts: I am planning to use the K. lactis Protein Expression Kit from NEB for the expression of certain protein. I am not experienced with working with yeast. I started by reading the manual for this kit and I am a bit confused with the fact that there are two types of medium: YPGlucose and YPGalactose. Do I understand correctly that YPGlucose medium should be used for cell propagation while YPGalactose should be used for protein expression and if so, why is that?


texts: What does this equation about DNA replication mean?

texts:
Could someone help me understand this equation please? I found it in a paper which said that it was DNA replication, but why?

$\ce{dNTP + dNMP_{n} -> dNMP_{n +1} + PPi}$

I found that dNTP means deoxy nucleotide triphosphate and dNTP means deoxy nucleotide monophosphate. Deoxy nucleotide monophosphate is a monomer in DNA, but dNTP isn't.

I also would like to know if there is an equation like this in other processes in the central dogma (such as transcription and translation)?


texts: Pectoral fins in fish, why the terminology abductor and adductor for main muscle groups?

texts: Fish pectoral fins are roughly divided into large dorsal muscle mass, and a large ventral muscle mass. Just from that division and position of muscles, the ventral muscle mass seems to mainly lower the fin, flex it ventrally. And the dorsal muscle mass seems to flex it dorsally. While the compartments are termed "dorsal" and "ventral", the actual muscles are termed adductors and abductors. What is the rational for those terms?


texts: Can spider silk be synthesized to be used for 3D printing?

texts:
With the recent rise in 3D printing, I keep hearing about more novel ways to use the technology: cell 3D printing, liquid aluminum or plastic 3D printing. For example,   this Ted talk deals with printing a human kidney. What interests me is if the current technology can be adapted to print with spider silk. The silk has some amazing properties, and apparently there are multiple types of silk that spiders use.

I found this project: Spiderbot 3D printer.  Can spider silk actually be synthesized in large enough amounts to enable 3D printing?


texts: How fast is the blood flow in various vessels?

texts: How fast is the blood flow in different blood vessels, such as the aorta and capillaries?


texts: A missing endogenous retrovirus in humans, but present in gorillas and chimpanzees?

texts:
I have read an article about an endogenous retrovirus called PtERV1. It is present in gorillas and chimps, but is missing in humans (original study here).

According to the article, this retrovirus is very similar to HIV. And all of us (gorillas, chimps and humans) have a protein called TRIM5α to fight against PtERV1.

Nearly at the end of the article the author says: currently, there is no explenation for why the endogenous retrovirus (PtERV1) has never entered the human genome.

Is that a typo? Isn't a missing endogenous retrovirus just basic heredity? Especially because humans have the TRIM5α protein against PtERV1 just like gorillas and chimps, which indicate that we used to have it, but we lost it due to how heredity works.

Or did the author meant something deeper that the average user would not understand without a lot of pre-knowledge about genetics?


texts:
I have often heard a vague claim that bees help flowering tree populations survive.
As far as I know, bees take nectar and pollen concentrations from the flowers of flowering trees and use at least the nectar as a food source, but they don't take seeds out of these trees, so it's unclear to me how they help these trees survive in that regard.

Given that bees don't take seeds of flowering trees (and drop some when they fly) How do bees help flowering trees survive?
How does the taking of nectar and pollen away from flowering trees make bees symbiotically help such tree populations to survive and endeavor?


texts: What kind of sieve does one use to extract meiofauna?

texts:
Suppose I have a core of sediment, and I want to extract the meiofauna from it, in order to study these organisms. According to the sources I could find, this involves using a very fine (e.g. 45 μm) mesh that will filter out and retain the meiofauna (as they are larger than this e.g. 45 μm that I mentioned earlier, and so, will remain on the mesh).

I have found lots of information on the mesh size, how many μm it should be, etc., but barely anything else about what kind of sieve should be used.

So now, if I want to buy a sieve to use for extracting meiofauna, I don't know anything about what it should look like, except the mesh size. What should I care for besides that, if I want to buy one? Can I just buy any laboratory sieve provided the mesh is of correct size? Or do I need some special kind of sieve to conduct such study?


texts: Pluripotent stem cells are very popular and lots of research has been conducted to use these cells as a tool for drug discovery. My question is how many years would it theoretically safe is we could use iPS cells during the process of drug discovery?


texts: Found in garden ,Brisbane Australia at base of trees and amongst plants in open ground


texts: Physiological function of CFTR gene product?

texts:
I just need a clarification.

If I am to talk about the physiological function of the CFTR gene product? Then what should I do research and talk about?

The only physiological function that I can think of is the control of the thickness of mucus.

Is there any other ones?

On top of that, if i am to search for research paper for this topic. Do I just search for comparative study that compare the gene product in normal individuals and CF individuals in terms of mucus thickness?

Thanks


texts: Are there any proteins not found in the brain that are affected by prions?

texts: A prion is an abnormally folded protein that is capable of causing otherwise normal proteins to also misfold and become prions. They are responsible for causing diseases such as Kuru and Creutzfeldt–Jakob disease. These are both diseases of the brain. Are there any non-brain proteins that also have corresponding prions that can cause disease, or do prion diseases only affect the brain?


texts: How semi-synthetic cell with artificial DNA works

texts: I know that by now this is old new but I heard that a cell that used a synthetic pair of nucleotides, called X and Y, have been made. My question was, how did the cell understand the X and Y nucleotides during translation and how was it even represented in mRNA? It must have been represented differently, possibly using X and Y nucleotides only. That's the only way I can think of that causes the cell to make 172 amino acids instead of the usual 20. By the way I read this in the Discover magazine, January issue.


texts: species ID: garden bush from Bangalore, India

texts: Please help to identify this plant. It is a garden bush growing in soil. The pictures were taken in Bangalore, India.


texts: bee I found in Rochester NY, any guesses what species?


texts: What is the name of this plant I found in a park?

texts: I found this on Garret Mountain in Paterson, New Jersey, USA. Does anybody know the name of this plant?


texts: What does these $\Delta \Delta G$ numbers signify?

texts: I was reading a paper and came across this table showing  $ \Delta \Delta G$ numbers of different nucleotide sequences in DNA/RNA. I know that $\Delta G$ is free energy and $ \Delta \Delta G$ is relative free energy with respect to L. variegatus 5 S RNA gene. What does this numbers signify actually?


texts: Understanding the brain: how are neurotransmitters released in the brain?

texts:
I have a basic knowledge of how neural networks work. A potential difference is created that forces sodium, potassium, chloride, and calcium ions to flow which carries an electrical signal to the end of a synapse. From there, the presynaptic neuron releases neurotransmitters creating a potential difference to the postsynaptic neuron.

What I don't understand yet are the mechanics of which neurotransmitter will be released. Do the vesicles of each type of neurotransmitter have an energy threshold? If yes, when the highest energy threshold of a vesicle is achieved, does this mean all the other vesicles will release the encapsulated neurotransmitters?


texts: What decides the nocturnal periodicity of microfilariae?

texts:
Microfilariae, which are the larvae of filarial worms show a nocturnal periodicity of entering into blood in south Asia and China. This coincides with the biting habits of its vector.
The same very species in Malaysia, the larvae are present throughout the day and night but peak at specific time points (subperiodic). The vector there hase different feeding habits.

This understandably is beneficial to the worm.

What are the cues that the worm uses to understand day and night?

Reversing the sleep wake cycle also apparently reverses the periodicity of the larvae from nocturnal to diurnal.


texts: Why would the citrulline content of the watermelon be so high?

texts:
Citrulline is a non-proteinogenic amino acid (that is, citrulline is an amino acid that is not coded for in mRNA), and it is an important metabolic intermediate in the Urea Cycle. The Urea Cycle is critical for nitrogen (e.g. ammonia) excretion in humans as well as other mammals.

Citrulline is an interesting amino acid, given its vital function in the Urea Cycle, but also because it has such a high concentration in the watermelon. The name citrulline is actually derived from citrullus vulgaris, which is the Latin word for watermelon.

A notable fact about the watermelon is that the watermelon is the only food known to have such high content of citrulline. There are NO other foods that have such high endogenous levels of this amino acid.

As a physiologist citrulline is very interesting metabolically, but I wonder why the watermelon would have such a high concentration? Why would that occur? Would high citrulline content offer some type of competitive advantage to the watermelon in terms of out-competing other plants? As biologists, we usually think about things from a teleologic perspective in order to make sense of the world around us. With that perspective, is there a logical reason that citrulline would be so enriched in the watermelon? It seems very odd that it would be the only plant with notable quantities.


texts: When is strict sterile technique necessary? Cloning vs. protein expression

texts:
Background: I have previously worked with RNA, and then we use laminar flow hoods for any work where we do plating or inoculation of cultures while applying sterile technique. I am now working in a biochemistry lab. I'm told that I can work on a lab bench, while doing basic cloning for production of plasmids in E.coli, and don't need to use a Bunsen burner as long as I apply sterile technique (and in most cases I don't see people sterilizing the bench with enthrall prior to work). However, if I do any work which relates to expression of proteins - then I should use the Bunsen-burner while applying sterile technique.

Question: Is it really so that you don't even have to use a Bunsen-burner while plating (normal E.coli: XL1-blue cells)? in this case, why? Are there not always something in the lab which can grow on kanamycin plates? We don't use white/blue screening, we simply spread XL1-blue cells onto LB plates with kanamycin - then pick a averaged sized colony to make a LB-culture. It seems to me that we are just lucky that we usually pick the right colony (which we do confirm by sequencing after mini-prep).


texts: Gene knockdown vs gene knockout vs knocksideways?

texts: How are the techniques: Knock-sideways, knockout & knock-down different?


texts: How do you dilute forward and reverse primers for a master mix?

texts:
I apologize for the very naive question, but I'm just starting out in a high school biology lab and I am very confused.
If I have stocks of 100μM for forward and reverse primers separately, I can dilute them to 10μM very easily. But what if I want to make a master mix? I have 1000μL of 10μM for each primer, forward and reverse (not mixed). Would I just add 500μL of my forward primer and 500μL of my reverse primer for a mix of 1000μL in  which both concentrations are still 10μM?


texts: Human spine: Is the coccyx really fused?

texts:
Prologue: This post is about the adult (say, a 20 year old) human skeleton; I'm not particularly interested in infant skeletons.
The human spine has is composed of cervical, thoracic, lumbar, sacral and coccygeal vertebrae

 Image source

My school textbook (which has a history of possessing erroneous/outdated information) states:

The coccyx consists of 4 coccygeal vertebrae that are fused to become a single bone.

However, this Wikipedia article states:

Most anatomy books incorrectly state that the coccyx is normally fused in adults. In fact it has been shown that the coccyx may consist of up to five separate bony segments, the most common configuration being two or three segments.

Is Wikipedia correct?
If so, what is the (most common) number of bones that constitute the spine? Is the number of vertebrae that constitute the spine going to be different?

This other Wiki article appears to be particularly contentious:

A fully grown adult features 30 bones in the spine, whereas a child can have 33.

The cervical vertebrae (7)

The thoracic vertebrae (12)

The lumbar vertebrae (5)

The sacral vertebrae (5 at birth, later fused into one)

The coccygeal vertebrae (5 at birth, some or all of the bones fuse together but there seems to be a disagreement between researchers as to what the most common number should be. Some say the most common is 1, others say 2 or 3, with 4 being the least likely. It is counted as 1 in this article.)

I understand that there is little to no variation in the number of cervical, thoracic and lumbar vertebrae among humans, so they altogether constitute $\mathrm{7+12+5 = 24}$ vertebrae/bones (in this case, I believe "vertebrae" and "bones" are synonymous).
Assuming that the sacrum really is one fused bone (my question's regarding the coccyx, so I'm not going to question the anatomy of the sacrum in this post) consisting of five vertebrae (I think there's a bone-vertebra distinction here, so they aren't the same thing)
In that case, the cervical, thoracic, lumbar and sacral contributions are $\mathrm{ 24 + 1 = 25}$ bones, or  $\mathrm{ 24 + 5 = 29}$ vertebrae. (Right?)
According to the Wikipedia article I cited above (the second one), the adult human spine has 30 bones.
So the coccyx contributes $\mathrm{30 - 29 = 1}$ bone to the spine, or $\mathrm{30 - 25 = 5}$ vertebrae to the spine.
In other words, the second Wiki article implies that the coccyx is a single (fused) bone. However, the first article states that the coccyx is really composed of 3-5 (say, 4 on an average) bones.
This is horribly contradictory.

If the finer points of my question was lost, I'll restate them here:
1) Is the coccyx a single bone or multiple bones?
2) How many bones are there in the adult human spine?
3) How many vertebrae are there in the adult human spine?


texts:
After searching extensively I have been unable to find a name for this plant. It was found growing in the Eden Project Tropical biome in the UK. The flowers were approximately 7-8 cm across.
Any help greatly appreciated!


texts: Why Pan_troglodytes-2.1.3 Assembly renamed as a Pre in ENSEMBL?

texts:
I began working with panTro3 assembly of the UCSC. This assembly corresponds to CGSC Build 2.1.3. See here: https://genome.ucsc.edu/FAQ/FAQreleases.html

Now, I have to cross annotations with ENSEMBL (Indeed, I need to use Biomart tool: http://www.ensembl.org/biomart/martview/2e4aac505f5cf5e0ac255b4a215a056c). But It seems that between Release 64 and 65 they passed directly from Chimp 2.1 to Chimp 2.1.4. I researched some information and found that Chimp 2.1.3 renamed as a Pre! See here: http://pre.ensembl.org/Pan_troglodytes/Info/Index and here http://www.ensembl.info/blog/2011/06/10/new-pre-site-for-chimpanzee/

Is it a way to solve this problem? How may I use Chimp 2.1.3 assembly in Biomart with GrCh37 as reference genome (I was using an archived versions of the Ensembl: http://grch37.ensembl.org/biomart/martview/cbe191dccbe8e5a314cfebeaa8862ca0), but seems not possible to cross between different releases of the ENSEMBL.


texts:
The karyotype is performed on a cell whose cycle has been stopped in metaphase or pro metaphase, using colchicine or by other means. In the textbooks I read that during the S phase each of the 46 chromosomes is duplicated, giving, again, 46 chromosomes, but, and here I am deducing, 92 chromatids. When we perform the karyotype, we only see 23 pairs of chromosomes (46, that is), and, it looks like to me, the same number of chromatids (46 as well). What am I missing? Why can't we see 92 chromatids in the karyotype?

Thanks a lot for your attention.


texts: Can someone identify this brown spider in California

texts: Spider found on transit case from California. Approx 1 1/2 inches leg span. Is it poisionus?


texts:
I am currently taking a course called "Introduction to Machine Learning with ENCOG 3", and I have a question about how well the Artificial Intelligence (AI) algorithm for a "neural network" corresponds with how an actual neuron works.

In the course, they model a neuron like this:

x1, x2, etc. are voltage inputs, the wij are weights.  The inputs are multiplied by these weights and summed up by the neuron.  The neuron then has an "activation function" which then takes the sum of weighted inputs and calculates an output, typically a value between 0 and 1 (or between -1 and 1). You can think of the wij as representing dendrites (a higher weight means a more dense and thus conductive dendrite), and the output of the activation function as the voltage that gets sent down an axon.

The AI neural network algorithm creates a kind of intelligence by modifying the weights (wij shown in the picture).

My first questions is: Is this a good approximation as to how neurons actually work?  That is, do our neurons "learn" by changing the weights (dendrite density, conductivity)?  Or, is there some other mechanism that is more important (e.g. do neurons learn by changing their activation or summation functions?)

My second question is: If neurons really do learn by changing the density of dendrites, then how fast does this happen?  Is this a fast process like DNA replication?  Does the neuron quickly generate (or decrease) dendrite density when it receives some kind of biochemical signal that it needs to learn now?

I understand that much of this might not yet be known, but would like to know how well the AI algorithm corresponds with current theories on biological neural networks.


texts:
I am interested in fibroblast cells in human arteries. Here are the things that I am not clear at the moment and I could not find any answer from the literature:

What are the dimensions of these fibroblast cells? How big are they in terms of diameter and thickness? How big are they if they are comparing with the collagen fibers in the artery?
I think they have to attach themselves to the fibers in order to proliferate or differentiate. However, I do not know, do one fibroblast cell attach itself to one fiber and then "crawl" to another? Or do they "sit" on a network of fibers?

I will appreciate your help on this and will be even more grateful if you could provide me with some literature that I could find the answer to these questions.


texts: How deep could a human swim with SCUBA apparatus?

texts: Using normal SCUBA apparatus and wet suit, how much pressure can the human body withstand? This is assuming that they descend as gradually as necessary for their body to make adjustments. What would be first symptoms that they experience as they descend? And if they descend to the deepest depth that they can reach without immediate permanent harm, how long can they spend at that depth before time related symptoms set in?


texts: Need help distinguishing between a primary and secondary source

texts:
I am trying to figure out if the following article is a primary or secondary source.

I'm leaning towards secondary but here are my cases for both.

  Primary: Published in a peer-reviewed journal.

  Secondary: It seems to be mostly a summary of other works so it might
  not be original research.

Can anyone confirm this for me? Thank you!


texts: How did the tendency to perform death rituals evolve?

texts:
Both elephants and humans perform rituals when deaths occur.

However, I do not see any evolutionary benefit of this. The rituals take time, which apparently could be better spent hunting, foraging, traveling, mating, or grazing.

I am interested to know if these behaviours have any significance and whether they confer any kind of survival advantage.

A cursory google revealed nothing about this.


texts: PCR processes number of amplicons produced

texts: Beginning with 600 template DNA molecules after 25 cycles of PCR how many amplicons will be produced?


texts: How does DNA code for the actual *shape* of individual body parts/areas (NOT segments or Hox genes)?

texts:
Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and a better than average (for a layman) understanding of how DNA works.

I understand the process of Amino Acid being coded for by specific DNA nucleotides and the chains of Amino Acid forming specific proteins - however, I am unable to find information on the topic of how actual shape is determined / coded for by DNA (again, not Hox genes and body segments).

Here is an example of what I am asking about - please note that this is just an example and I'm not specifically asking about how eyes evolved. I'm asking how changes in shape/size/structure of any part of a body happens from changes in DNA.

It's generally held that eyes evolved (in very basic terms) from a layer of photosensitive cells on the skin, which slowly formed into a cup that could detect direction, then the cup eventually closing in to form a smaller hole, and then a lens, and so on.

So my question (based on that example), would be, how does DNA (or a change in DNA) code for "create an indentation on the surface of the skin at this location". Or, "Deepen the indentation repeatedly until it is a cup". And so on.

More basic examples are "make the hind legs on a mammal slightly longer" or "make the cranium on an ape slightly larger". The question is not dependent on body part or animal type but is specifically about how DNA, in general, operates.

Hopefully the question is clearly stated and not too long - I welcome any suggestions on how to clarify the question.

Thank you!

--added--
canadianer's comment gave excellent information regarding some general principles that are involved, but I'm still hoping to find (if it's possible) a more precise and detailed answer to this.


texts:
I've tried to google this but everything that comes up are things like "mathematical neuroscience" rather than the other way around.

Specifically, I'm interested in the workings of a mathematician's brain that sets her apart from others. For example, is there evidence to be found in MRI scans or EEG recordings of mathematicians as to why they excel in math?


texts: What's the physical meaning of Svedberg unit?

texts:
Sedimentation coefficients, using a centrifuge, are expressed using Svedberg unit (symbol S, sometimes Sv). Wikipedia states that $S = 10^{-13}$ sec but I also saw in a book that actually $S = 10^{-13}$ sec/$\text{rad}^2$. Which of these is correct?

I know that a 50S ribosome has higher molecular weight than a 30S ribosome and for that reason the 50S would travel faster (on a test tube placed in the centrifuge) than a 30S, but if substitute S by $10^{-13}$ sec, for me it's a little bit-non intuitive, because 50S would be $50\cdot{10^-13}$ sec (and that is greater than $30\cdot{10^-13}$ sec), which means it takes more time to travel? Obviously not, so what's the physical meaning of time in this situation?

In response to Alan Boyd:

"In other words, at 1x g a 1S particle will travel at $10^{-13} m\cdot s^{-1}$" or $10^{-12}$?
Indeed 5.5h is a reasonable value but I still cannot understand the significance of the ratio between velocity and acceleration which corresponds to Svedberg units (in seconds).
Maybe $50\cdot{10^-13}$ sec is the time that our ribosome takes to reach the terminal velocity in the fluid? That would make some sense, for example, if I drop an unfolded A4 paper to the ground the time it will take to reach terminal velocity will be lower than the time a A4 folded paper will take to reach it's specific terminal velocity, which is higher than the velocity from the unfolded A4 paper, because the area is larger (the friction force acting on it will be very high) which is consistent with the observations that are made (in centrifugation objects with larger surface area will travel at a slower terminal velocity). What do you think ?


texts:
I would like to consider an old growth forest ecosystem such as a large part of the Amazonian forest. It is common to refer to such beautiful forests as a source of oxygen for the world. For example, the expression Amazon: Lungs of the planet is very common (e.g. this BBC article). I would like to question such an expression.

Questions

My questions are:

Does an old growth forest ecosystem produce more oxygen than it consumes?
Does an old growth forest ecosystem fix more CO$_2$ than it produces?

My Intuition

I understand that such a forest can be an important carbon storage and that if we were to cut the forest down, burn the wood and pour concrete on the soil (to prevent regrowth), then we would definitely release a fair amount of carbon in the atmosphere.

That being said, I am wondering whether, as of today, these forests act as carbon sink or not. It feels to me that while trees accumulate carbon and produce oxygen while growing, this carbon is released when they die and in an old growth forest a tree must die for a new tree to grow. If carbon is being fixed, then it has to go somewhere and I think it is almost by the definition of an old growth forest that there is no more room for more carbon accumulation (competition among trees prevent it). So I would tend to think that calling the Amazonian forest the "lungs of Earth" is very misleading.

Some random WWF article

This WWF article seem to suggest that, contrary to my intuition, the answer to these two questions should be "yes".


texts: Why glycoproteins are better than non-glycoproteins in fulfilling biological tasks?

texts:
I have just an intuition that the carbohydrate part of glycoproteins help them to fulfil those tasks like in plasma membranes.
You can also get many more receptors if you can use carbohydrates too.

For instance, glycoproteins are necessary in recognising white blood cells. Antibodies are examples of glycoproteins. So they play a crucial role in our innate and adaptive immunity: MHC interaction with T cells in adaptive immunity.
Other examples: necessary in platelet aggregation and adherence, components of zona pellucida and connective tissue. Some hormones are also glycoproteins so necessary in humoral adaptive immunity: FSH, LH, TSH and EPO.

But why glycoproteins are "better" than proteins without carbohydrates moiety in fulfilling biological tasks?

I still see that both are important, but why the one is better than the other one.

In other words: Are there any biological tasks that only non-glycoproteins can fulfil, not glycoproteins? Are non-glycoproteins necessary in some essential biological tasks?

I think the answer to the last two questions is "yes", so why would one say that glycoproteins are better in fulfilling biological tasks than non-glycoproteins.


texts: Why are there three stop codons but only one start codon?

texts: I was wondering whether there is any specific reason that there are three stop codons but only one start codon in prokaryotic and eukaryotic cytoplasmic mRNAs.


texts: Does a plant have to have leaves to produce fruit?

texts: Is it possible that a plant can still produce fruit, even though it may not have leaves? Are there any plant species that can produce fruit without leaves?


texts: Collagen, are fibrils arranged in overlapping fashion too just like tropocollagen?

texts: Collagen molecules (tropocollagen) are interlinked into fibrils, with a banded structure showing the spaces ("lacunae") between the molecules. Do fibrils in turn also interlink in a similar way, or, do fibrils run from end to end in the fibers?


texts: How to recover all protein ses into refseq database

texts:
I'm actually trying to download all the virus protein sequences available in the NCBI database.

I guess the link is this one: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/

How could I get all the protein sequences in fasta format into one file ? Does someone have codes to do that easily?

Thank you very much.


texts:
"Gorlin's Sign" is the ability to touch the tip of the nose with the tongue.  It is present in half of people with Ehlers-Danlos syndrome, but is also present in a minority of people without that disorder: among them, both me and one of my sons.

Is it known whether this trait is hereditary?  If so, is it a simple genetic trait (e.g., is it sex-linked, Mendelian)?


texts: Why do cats meow but lions and tigers roar?

texts:
So as far as I know the cat animals are related to each other by evolution. (Please correct me on this if I am wrong?)

How come the big cats; lions, tigers et.c. roar but smaller cats like house cats meow?

Has the evolution of meowing contra roaring been backtracked?

Is it possible to tell from the anatomy of a cat and a lion what differences cause the meowing and the roaring? Is there some peculiarities in the design of their voice boxes which cause the differences in sounds?


texts: Are the seeds in a single capsicum fruit genetically identical?

texts:
Hopefully not a too-basic question for the venue. I'm a chile pepper growing hobbyist and have spent some time searching around and reading up on pepper (angiosperm) reproduction, but I'm not getting a clear picture of the details.

It seems like flowers have multiple ovules and it seems like one pollen-grain landing on the stigma leads to fertilization of a single ovule. And it seems like that process produces a single seed.

But that fertilization also prompts fruit growth and flower death and capsicum fruits have many seeds, never just one (that I've ever seen).

So, does each seed have a potentially different father? Or are the multiple seeds generated through a reproductive/cloning process that I'm not seeing written about? Or something else?


texts: Any species returning to the land twice throughout their evolution?

texts:
Here's a question from my son I've found interesting enough to ask here. There are plenty examples of species returning back to the water environment, like dolphins, sea lions, walruses, some snakes, crocodiles etc.

The question is - are there any evidences that in evolution of certain species there was return to the land twice, that is, they've came from sea, then evolve as land species, then, again, evolved to somewhat marine or fresh-water and, finally, turn into land species again?

UPD Chordate are the most interesting but any example, even plants, would be nice.


texts: Are insects capable of gliding on the air with their wings spread, similar to birds?

texts: Sometimes birds can use the air to float on with their spread wings. Now, the wings of insects are too small to see if they can do that too. So is it possible for insects to do this also, or can't they hold their wings spread or is the air drag not enough?


texts: Were we able to create vitamin B12 in past?

texts:
All herbivores produce vitamin B12 de novo. Gorillas, for example, are "vegans" so I suppose some human ancestor was also herbivore.

Have we ever been B12 self-producers? If so, why have we lost that ability and do we have to obtain B12 from our diet? Have we just gotten "used to" being omnivores (i.e., we don't need self-production anymore)?


texts: Why is wombat scat (feces) shaped like cubes?

texts: I've heard that wombat scat is cube shaped, but I don't understand how that can happen. Has anyone studied the phenomenon? What would the evolutionary pressure have been to cause this?


texts: I've been trying to match this wasp to photos, but it seems like every species has something that doesn't quite match up. I killed it in my home in Indiana, USA. My best guess is a Northern Paper Wasp (Polistes fuscatus). Does that seem right? I read they can sometimes be dark in color like this one.


texts: This snake was killed in graveyard Peshawar (Pakistan). I just wonder what is this? Is it a snake? Baby crying sounds were reportedly heard from graveyard in Peshawar after months of search the sounds of baby crying were identified and this snake was killed. I have a video. I just want to know what is this?


texts: Can muscles remake pyruvate from lactic acid, or does it have to go to the liver in the Cori cycle?

texts:
When the muscle is exercising, and only anaerobic respiration is done, pyruvate -> lactate to regenerate NAD+. Lactate is then transported out of the muscle and into the liver, to regenerate glucose, which is then shuttled back to the muscle (the Cori cycle).

I was wondering whether once the muscle stops exercising, the muscle itself could regenerate pyruvate (using lactate dehydrogenase), or whether muscles always release their lactic acid to the liver? Or maybe there is no way of knowing this (how would this be tested experimentally...).


texts: Why have people much more different cells than rice plants, while they have roughly the same number of genes?

texts: Rice plants have about two times as much of genes in their DNA than humans have. Then how is it possible that people have much more different cells than a rice plant has?


texts: Repair wrong DNA pair after ending replication?

texts:
If there are wrong DNA pair, for example A=G, is there mechanism that could repair such things - after the replication was finished?

Or it happens only during replication?


texts: How to design a ChIP-exo experiment with controls?

texts:
Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment?  Is it even necessary to run a control (similar to input DNA for ChIP-seq)?  I'm looking for any references or forums that discuss this issue and experimental design?

This video (https://www.youtube.com/watch?v=8qLRI9Bqtso) briefly touches on this issue (t=32.45), indicating NOT to use an Input sample due to the Exo digestion.  However, I don't know how the community (or reviewers) feel about this?

Thanks for any help!


texts: Where do most mutations come from, mitosis or meiosis?

texts:
According to this (old) paper there are 10 times more mutations during meiosis than during mitosis. One reason for that is that recombination often causes replication error and therefore mutations. However, in many multicellular organisms, germ cells undergo many cell divisions (mitosis during development) before finally undergoing meiosis.

I think that intuitively many people (me at least) think of new mutations* that are transmitted to the offspring as mutations occurring during meiosis. I would like to have a notion of how important are the two processes (mitosis and meiosis) in generating heritable new germ-line mutations in multicellular animals.

Let's consider humans for example. Out of 100 new germ-line mutations transmitted to the babies, how many of those mutations occurred during mitosis (during the development)?

*I call "new mutations", any mutation that is transmitted to a baby but that was not present in any of the two eggs of the parents (even before the parents started the gastrulation).


texts: DNA gel extraction: chemical contaminants

texts:
I am performing a gel extraction to purify DNA after a double digest with EcoRI and BamHI.  After the gel extraction I need to complete a ligation step before bacterial transformation.  The problem I am having is that the DNA after the gel extraction have some kind of chemical contaminant that won't allow me to quantify the DNA using the Nanodrop spectrophotometer.  I am getting very low 260/230 ratios.

Has anyone had some issues with this?

I am using the Qiagen Qiaquick Gel Extraction Kit.


texts: unknown bird in Long Lake Michigan......chocolate brown head and neck, charcoal body and tail, ivory wings, top and bottom

texts: light chocolate head and neck w/ charcoal body and tail. the wings are ivory white, top and bottom from the body outwards. the colors are clear.....not mixed with other colors. no stripes or spots, etc. slightly smaller than a robin.


texts: Why do bees fly inside the gaps between the decoration on the exterior wall of a building and the wall?

texts:
My house has decorations around the windows on the exterior wall:
There are gaps between those decorations and the bricks of the building:
During the summer, there are always bees looking for those gaps so they could fly into them while I rarely caught them flying out. I wonder why do they do that? What do they do inside? Is there anything I should do about this situation?
I guess that maybe they want to stay in a cooler place since it's quite hot outside? However, it's also worth noting that they seem to be interested in only one particular side of one particular window since I have never seen this happening to other windows of my house.


texts: How can I tell if a certain marker is useful to date a phylogeny?

texts: If I have a phylogenetic tree for a genus, how can I tell if a certain protein would be a good phylogenetic marker to use if one wanted to use a molecular clock to date the age of some speciation event in that a genus? How can I look for it on a tree?


texts:
As I understand, each virus type can enter a particular cell type. For example HIV can enter CD4 & CD8 cells, while HBV can enter liver cells, some other viruses can enter other cell types like brain cells and cause brain diseases.

Is there any kind of virus that can enter all mammalian cell type so it can be used as a general gene transfer method?


texts: How does a cell regulate what leaves its vacuole?

texts:
Suppose a plant cell wants to take something out of its central vacuole. Some specific substance. Well if the vacuole is a bit of a soup of water and other dissolved substances, how does the cell get some specific substance out? Without letting any of the water/solution into the vesicle that's budding off? Or do they just let the solution right in?

Clarification: Since a vacuole is full of water and other dissolved substances, wouldn't that solution get into a budding vesicle? How is this prevented? Is it prevented?

When the cell is creating a vesicle, it starts pinching off part of the membrane, correct? My question is how the solution in the vacuole stays out of the vesicle, if it does at all.


texts: Are the subordinate genes of a repressed operon really "turned off"?

texts:
Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says:

  In addition to being physically close in the genome, these genes are regulated such that they are all turned on or off together. ... The ability to turn ... genes on or off as a group therefore provides an efficient way to quickly adapt to environmental changes. ... mutations affecting the promoter can prevent all of the operon's genes from being expressed, ...

The thing that confuses me is that I've also heard genetics aren't all or nothing, that genes can only be "down regulated" or "up regulated", not truly turned on and off.

Obviously, differing amounts of moderate levels of whatever effector is modulating the repressor could lead to different levels of downstream expression. But, what about situations where nothing is inactivating the repressors? Will the regulated genes be (for all intents and purposes) be turned off? Additionally (and relatedly), is it even a realistic scenario for an operator to always (or almost always) be bound to by such a repressor?


texts: Are restriction enzymes active at −20 °C?

texts: I have digested my DNA with NotI enzyme and put it in the −20 °C freezer without heat inactivating it. Can restriction enzymes work at −20 °C? Should I expect STAR activity?


texts: Is the squid giant axon the fastest conducting unmyelinated axon known?

texts: The conduction velocity of the squid giant axon can reach 30 m/s. Is there any known example of an even faster conducting unmyelinated axons?


texts: Why does bacillus thuringiensis produce bt toxin?

texts:
Background : B.thuringiensis produces an inactive crystalline toxin during sporulation which when ingested by an insect, gets activated and causes pore formation in gut , subsequently leading to death of the insect.

Question : What is the  role of the toxin in bacteria's own metabolism ? Does it "unintentionally" kill the insects or is there an evolutionary advantage gained by the bacteria ?


texts: If a dead snake reflexively attacks itself, why does it not always attack itself?

texts:
Recently there has been this video going around of a snake that had been decapitated.  Its body swung around to the decapitated head and the head attacked the body on "reflex".  Now we know that most reflex arcs bypass the brain.  So if it is the case that this strike attack is reflex then how is that suppressed when the snake is alive? Why aren't snakes always reflexively attacking themselves?

Here is the video.

Is this some other phenomenon than reflexive attack?


texts:
I was reading this article in wikipedia and came across this :

  It has been suggested that recombination takes place during G1, when
  the DNA is in its 2-strand phase, and replicated during DNA synthesis.

If For example - allele A is present on 1 and a is present on 1' and recombination happens such that a is present on 1 and A on 1' and then both get duplicated during S phase.

So how are the daughter cells going to be different from one another and from the mother cell in terms of phenotype? (obviously the alleles around these alleles are going to change)

How can this result in twin spotting in drosophila or any other trait occurring due to coming together of homozygous alleles by mitotic crossovers ?


texts: How many residues can a reliable ab initio structural model contain?

texts:
A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be reliably modelled.

7 years after that paper: I just attended a pre-publication presentation in which a 400+ residue structure had been modelled using I-TASSER. The speaker claimed it was reliable and it did fit well in the biological context, but it still needed experimental validation. Unfortunately they had no in silico validation scores to hand so I had no handle on how seriously I should take the model.

Ultimately, my question is how many residues can I-TASSER (other modern ab initio brands available!) reliably handle for a typical globular domain with today's technology?


texts: Is dietary fat directly stored in adipose tissue or is it immediately metabolized?

texts: I know that fat goes to adipose tissue and even sugar gets converted to fat and goes to adipose tissue, but what happens to fat (unsalted cow milk butter) I just ate? Will it give me energy now, or does it automatically goes to adipose tissues for future energy storage?


texts: Where do the Ca ions that causes neurotransmitter release from synaptic bouton, come from?

texts:
I hope the information you share will help clarify the following doubts and gaps in my knowledge:

Where do the Calcium ions in the influx (which then triggers the neurotransmitter vesicles) come from?
Are they traveling all the way from the ER of the neuron in the soma?
Are they stored locally within the neuron somewhere around the synaptic bouton?
Are they coming from outside the neuron cell?

And if you have some extra knowledge to dish out then:

Is it channels or pumps that cause this influx of calcium ions?
If these are channels then are they ligand-gated, voltage-gated or made more permeable via some other mechanism?

Thank you for reading :)


texts:
If one developing twin absorbs another, when does that happen?
Is it possible for an appendage or organ to develop and be the only remaining vestige of an absorbed twin, such as a hand or a mouth, or a heart?


texts: Why does hair know when it needs to stop to grow

texts:
I'm still not quite sure if head hair grows endlessly, or if it stops at some point, but that's not the question.

When the hair on my leg grows, it obviously doesn't grow endlessly, but it also stops at some point. I learnt that hair is dead matter, so why does the body know that my hair reached maximum length, and realizes I cut it when I did?


texts: How many generations apart can a DNA test for blood relations be valid?

texts:
Suppose an American suspects he is a descendant of George Washington and he has a strand of hair of George Washington. Can a DNA test be done to prove that he is indeed a true descendant of the great Founding Father?

How many generations apart can a DNA test for ancestry still be valid?


texts:
If an organ from person A is transplanted to a new human body B, is it possible that we can detect A's DNA in B?

How long until the organ's DNA is replaced by B's DNA so that we are no longer able to detect any signature of A?


texts:
I do know that the splint bones are vestigial (reduced non functional toes in this case) , in odd and even toed ungulates. Is there any evolutionary reason of why is it so?
What were the conditions that lead to it?


texts: Why do humans seem to be the only mammals that like spicy food?

texts:
Peppers evolved chemicals like capsaicin to discourage animals from eating them, and that chemical itself can cause internal damage if consumed in large quantities, though this is usually only a concern for the hottest of peppers (which people do eat).

Still, why is it that humans seem to be the only animal that often "like" spicy food?


texts: How to quantify quality of vegetables and fruits?

texts:
I am interested in knowing if there have been studies in quantifying the quality of vegetables and fruits. By simple examination, it is possible for us to identify if a particular vegetable is 'spoilt'. But does this transitioning from 'edible' to 'spoilt' happen instantaneously? Or is it possible to model this transformation by a random process?

When producers and retailers determine shelf life, is it only based on anecdotal knowledge? Is there a systematic process by which quality can be determined and quantified?

I shall be glad if you could point me to studies that look at time to expiry and hazard rates of vegetables under variously controlled environments. I am happy to have the data for one or more common vegetables or fruits.


texts: Drosophila biarmipes gene annotation, transposable element?

texts:
When doing an annotation of a contig31 of Drosophila biarmipes genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in blue below:

So according to the GEP(genomic education partnership) guide I was reading, I was to then BLASTP the amino acid sequence from these predicted genes to a non-redundant protein database. Using NCBI BLAST I did just that, and observed alot of results of significance (E value < 1 X 10^-5).

Many of the BLASTP results were somthing like:

Reading up on gag proteins I found they were related to transposable element activity, specifically reverse transcriptase activity. So then should I conclude that these regoins are showing a gene because they are a Transposable element, or the remenats of one?

I also found:

And reading on Wolbachia I found that there is Horizontal gene transfer with its genome and Drosophila in general, according to wikipedia:
http://en.wikipedia.org/wiki/Wolbachia#Horizontal_gene_transfer_and_genomics

So then, can I conclude the area circled in blue is a result of Transposable element, and not an actual gene belonging to D. biarmipes?


texts:
I am a biology student who has just completed drawing a food web for class. As I was making it, I learned that a food web is the sum of all feeding interactions. My teacher associated food webs with communities, but I do not understand what the communities of a food web are.

How are communities related to food webs?


texts:
My text book says:

  Platyhelminthes are unsegmented worms.

Moreover, tape worm (Taenia solium), which is segmented, is one of the examples of Platyhelminthes.

My question is: why a segmented worm is included as an example in Platyhelminthes (unsegmented worm)?


texts: What is this spider, and what is this object that emerged from its rear end?

texts:
I was observing this spider (caught in a Petri dish) under my microscope, when I noticed that a small, round object emerged from its rear end. It appeared to be black and white in appearance. I am guessing that it is an egg, but I am not sure whether it is one or not. The diameter of the object is approximately 300µm.

The spider seems to resemble Hasarius adansoni from photos:

The scale bars in the image are 5mm in length. The spider and the object are imaged together in the frame for scale.

Can anyone conclusively identify the spider and the object? The photo was taken in Singapore in November (although the seasons don't really matter in Singapore).


texts: Are there neuronal firing artifacts produced by head movement?

texts:
I'm experimenting with a consumer-grade ElectroEncephaloGram (EEG) sensor and have created the image below using the device. Because the sensor on the device does not use a suction cup, there are a lot of motion artifacts when the headband contact is poor (during motion).

This got me thinking - neurons have mass and thus inertia, and they are not glued to each other.  When the person moves (actually rotates) the head around, forces of inertia are applied to neurons/axons. I'm interested if such motion produces any kind of firing artifacts within the brain or how the brain filters out such firing?

This reminded me of this article: (5-HT and motor control: a hypothesis). Could it be that some neurons stop firing in response to movement?


texts: Is it possible to identify the wasp species/family by the nest?

texts:
I've seen a weird looking wasp nest recently.
Here's the picture:

I'm saying weird because it's the first time I see a nest that isn't a ball made of grey paper. Although this one is also made of paper, I don't understand where does the colour come from.

Is it possible to say, what species or family does it belong to?

(location is the North-West of Russia, close to Saint-Petersburg)


texts: Why a striped baby is not the result of a white and a black parent?

texts:
Someone asked me:

  If a striped cat is the result of a white and a black cat, why the result of a white woman and a black man is not a striped child?

I know the answer. I also know that the result of a black cat and a white one is not a striped cat. But I'm looking for a simple answer. I'm looking for an explanation without a genetics background required. I'm looking for a metaphor or something similar.


texts: Chemistry of the phosphodiester bond in RNA

texts:
I have been learning about the chemical structure of RNA, but I can't understand why all hydrogen atoms disappear in the phosophodiester bond between the riboses of RNA.

Phosphoric acid is $H_3PO_4$:

However, when it's connected to ribose the hydrogens disappear:

Where did the hydrogens go and why?


texts: Can human survive falling from 30,000 ft without a chute?

texts: If someone falls 30,000 feet without a parachute; what are the chances of survival if they landed in the water?


texts: Muscle involved in carrying load on head

texts: I have seen people carrying heavy load on their head especially in 3rd world countries, does carrying on head any benefit or harm, which muscle get strengthen in doing it?


texts: Why does Fallopia Japonica not cause issues in Japan to where it is native unlike other countries?

texts:
Fallopia Japonica (also known as Japanese Knotweed), is currently causing a huge issue in the English countryside where it was introduced. This is due to the fact that it spreads and grows rather quickly, its roots go roughly about 3m into the ground and are quite hard to dig up as there are so many of them interconnected and they are so firm. The only really absolute way of getting rid of them is chemical treatment for the soil which is obviously not so good for the environment nor that soil. This treatment is necessary due to the fact that even if one is to leave a very small amount of the root there, the plant is likely to still grow back quickly. All roots have to be fully removed for it to go.

However, in Japan, to where it is native, there is no such issue as there is in England and other countries where is it causing a mass problem.

This is probably due to the fact that the ecosystem is different and thus it will be balanced out and controlled by other plants in the ecosystem which aren't present here.

However, I have not yet come across proper research on this matter, so I was wondering if it is known why it isn't such a problem in Japan and how it is controlled and balanced out by what is naturally there, but isn't in the countries where it is causing an issue? Is there a specific plant which controls it? Perhaps an animal that eats it?


texts: Are there fundamental differences between the adaptive immune systems of higher primates and other mammals?

texts:
I recently attended a Leukemia and Lymphoma Society lecture in which one of the lecturers indicated that there are fundamental differences between the adaptive immune systems of higher primates and other animals.

The Wikipedia article on adaptive immune system seems to indicate that mammals share very similar adaptive immune systems.

I understand that there are (minor) differences between the B cells and T cells (and other cells) of different species, and that two species can differ in their susceptibility to a particular kind of pathogen (virus, bacteria, whatever), depending on small differences in cell surface proteins, etc.  I am not interested in these kinds of small differences.

Rather, I would like to know if there are any fundamental differences between the adaptive immune systems of humans (and other higher primates) as compared to other mammals.  For instance, are there particular kinds of adaptive immune cells in primates that don't appear in other mammals.  Or are there fundamentally different mechanisms (e.g. the mechanism of T-cells activating B-cells) or lymphatic system organs that are markedly different in higher primates as compared to other mammals.

In short, are there big differences in the immune system of higher primates that make them stand apart from the other mammals in the same dramatic way that thumbs and intelligence seem to separate them from other species?


texts: What evolutionary pressures pushed Galápagos tortoises to mature so slowly and live so long?

texts:
I read that they take up to 40 years (in the wild) to reach the age of reproduction and are thought to live over 100 years, with one in captivity reaching over 170 years.

Can someone explain in layman's terms how taking longer (especially spending years as a small tortoise) to reproduce was a winning trait, and how their biology delays the processes of senescence to the extent that it does compared to most other species?


texts: How do you increase eumelanin but not pheomelanin?

texts: Are Scientists currently looking into this?


texts: Why is it that I can understand speech through one ear better than the other ear?

texts:
First, I do a lot of music so I'm used to pick up details in sound and I have had hearing tests showing that my ears are quite well balanced, for my age, without any dead spots.

When I am in a social situation, I will hear people's voices equally well on both sides, however I will 'understand' dialog better on one side.

I remember reading many years ago that this is normal and there is a known reason for it, but I can't really find much about that topic.

Does anyone here know why this is happening?


texts: The title says it all. I'm just curious. I read that scientists mapped the genome for Malus Domestica, but I can't find a sequence anywhere.If this is a stupid question, I would appreciate if you tell me where I'm wrong in this!


texts: What is the use of having a surrogate mother in animal cloning?

texts: In animal cloning, an ovum is collected by an animal and processed to form an embryo after fusion, which is going to be inserted to a surrogate mother. So my question is that why can't the embryo be inserted the animal that gives the ovum as they are both maternal?


texts:
I went through a line in my textbook which read:

  "But for predators, prey species could achieve very high population densities and cause ecosystem instability."

I was not able to understand the meaning 'but for predators'. Can anyone please help me to interpret it's meaning?link to page where this line is mentioned

Edit: In terms of biology, I was unable to understand the meaning of the sentence,  and I wanted to make sure that I don't misunderstand things... And this is why I posted the question.. I feel that the answer given is correct and in case, you find better explanation, please do post.


texts:
I know of Anfinsen's experiments and I'm aware that some denatured enzymes may regain their lost activity through the removal of the denaturant agent. What I'm unaware of is how rare is it for a protein to be able to renature? Can all proteins do that? If not all of them can do it then how rare or common is it to find a protein which can be renatured?

P.S. To avoid answers like "depend on your denaturation process" let us assume that a protein can be renatured if it has been shown to renature in at least one experimental setup.


texts: Difference between Processing and Preprocessing

texts:
In the wikipedia article of emotion lateralization it is mentioned:

The right hemisphere is important for processing primary emotions such as fear while the left hemisphere is important for preprocessing social emotions

So I am wondering what exactly processing and preprocessing mean? What happens in preprocessing that they use this distinct word instead of mere processing?


texts: In our solar system which other planet could have been in the "habitable zone" in the past?

texts: With changes in our solar system, such as planets moving away from the sun and the reduction in solar radiation, which other planets in our solar system could have been, in the past, in a suitable zone for life to originate?


texts:
ANF as we know reduce the Na+ uptake and K+ removal in the distal tubules and it also functions as a Vasodialator (?) But again it says that ANF increases the Glomerular filtrate ? But if it is acting has a Vasoldialator (ie, antagonistic to Vasopressin) how is it increasing the GFR ? Shouldnt it lower the GFR ?

ANF - Atrial Natriuretic Factor also called Atrial Natriuretic Peptide

GFR - Glomerular Filtration Rate


texts: Why does an complete molar pregnancy not result in a clone?

texts:
Complete molar pregnancy is one where an ovum devoid of nucleus is fertilized by a sperm after which the haploid set of chromosomes double to form a diploid set.

As far as my understanding extends if the sperm had Y chromosome the embryo will not survive.

However if the sperm has X chromosome the zygote will survive to have the 46 XX karyotype and will start to grow as molar pregnancy (which is basically trophoblastic tissue with no fetal parts, as answered by Anongoodnurse).

Why is there no proper fetus? Why can't a "female clone" of male parent form instead? Where is the defect as such?

The Question pointed out by WYSISYG contains data only from animal studies. Although it answers my question, I want more data obtained from study of human trophoblastic tissue (from the molar pregnancy).  Papers on imprinting which are linked in those questions have no mention of molar pregnancy although Prader-Willi and Angelman syndromes are mentioned (as cases seen in humans).

Oops, I corrected my question thanks to anongoodnurse. I mixed up complete and partial moles with each other.


texts: How is honey not toxic to our epithelial cells?

texts:
Being a supersaturated solution of sugar, honey pulls the water out of cells it comes in contact with via osmosis - killing the cells. It also contains the inactive enzyme glucose oxidase, which when diluted with water activates and then converts glucose into gluconic acid and hydrogen peroxide - both of which are bad news for cells.

Honey also likely contains an antibiotic protein Bee Defensin-1, which is also bad news for bacteria. I didn't yet look into how it works so I don't know if it affects our epithelial cells.

Then some honey types (manuka) contain Methylglyoxal. Damage by methylglyoxal to low-density lipoprotein through glycation causes a fourfold increase of atherogenesis in diabetics. [1] Methylglyoxal binds directly to the nerve endings and by that increases the chronic extremity soreness in diabetic neuropathy.[2][3]

How is it safe to eat?


texts: Do all microRNA isoforms need to be known and sequenced to obtain microRNA expression?

texts:
From what I understand, microRNA are short "hairpin" shaped nc structures. When sequencing and counting miRNA, isoform miRNA are "found" which are subsections of varying length and possibly with some mutations or other differences to the "canonical" microRNA. The total counts for a miRNA are the sums of the counts for the isoforms which relate to that miRNA. [Please correct me if this is all wrong]

With regards to Next Gen Sequencing, a 'library' needs to be added which tells it what to sequence. Does this mean only "known" isoforms be read and counted or can "new" sequences (i.e. mutations) also be read and counted which were not known before sequencing started?

With regards to qPCR - does this technique only look for individual isoforms? In which case, if I want to know something about a particular microRNA expression would I need to do qPCR for each known isoform relating to that microRNA. OR, is it in fact easier to sequence microRNA expression with qPCR since sequences can be matched to the main hairpin structure with higher probability. (By easier I mean compared to say wanting to get the expression for a particular isoform since it needs to be matched exactly).


texts: Is biotin a hapten? If so, how does it work as a hapten in the human body?

texts:
https://en.wikipedia.org/wiki/Hapten

Hapten's aren't synonymous with allergens. It is defined as a foreign molecule that can bind to an antibody but does not evoke an immune response unless combined with a carrier protein.


texts: What are the pros & cons of site-directed mutagenesis? What are the alternatives?

texts:
For a lab course we have been assigned to "remove a stop codon, using mutagenesis, that is in the middle of a gene in order for the full gene to be expressed. This will then fluoresce."

To do this we are considering site directed mutagenesis, which can replace the stop codon, however is this a good method? Are there any alternatives to SDM using Quikchange that are better? What are the pros and cons of the SDM we are thinking of performing? To see if we succeeded we will then use DNA sequencing and gel electrophoresis.

Our overall plan looks like this:

Gathering plasmids from E. coli
Gel electrophoresis of the plasmid DNA
Perform the mutagenesis using Quikchange
Transformation by heat-shock
PCR
Use a lac promoter to produce the gene protein

One issue I could think of was, how do we make sure the primers carrying the mutation don't anneal to each other due to their complementarity?

Is overlap-extension a good alternative? Are there any advantages to using transposon-based or point-directed mutagenesis?

Thank you!


texts: Identification of a beetle found in a basement in Virginia, USA

texts:
Beetle found in basement in Alexandria, VA, USA

Approximately 5cm (2 inches) in length.


texts:
When an F+ bacteria conjugates with an F-, it makes the other bactaria F+ too. So on the long run, all bactaria should be F+.

Is there any mechanism that converts F- to F+? Could it be degeneration of F plasmid?


texts: Is there software or a website where I can browse extinct species?

texts: Is there any software/website where I can browse for extinct species? It must be based on real animals that are now extinct. It may be in animated versions.


texts: After reading about complement pathway and the complement components, I was wondering, does the C1q component attach to the Fab fragment or to the Fc fragment? The pictures in Janeway's Immunobiology are confusing and the text don't mention about this.


texts: What is the easiest way to measure a human body surface area?

texts: Looking for accuracy, cost-efficiency, and speed: this could provide useful information for determining individual bioinformatic calculations, pertaining to, for example cell type estimation, for personalized medicine regimens. I'm not sure why this question was marked as off-topic and closed.  The biological implications are grandioso.


texts: Are there known counterexamples to Hennman's size principle for muscle unit recruitment?

texts:
It is known that generally muscle units are recruited from small to large, and that typically also means slow to fast twitch.  This principle is called Hennman's size principle.

I've seen many articles backing this claim up.  However, I'm curious if there are any known situations where this principle is known to fail.  (Perhaps when there is a known impulse arriving shortly and it needs to be opposed by large fast-twitch muscle).

All I have found so far are articles which agree with the principle, but it seems surprisingly simple for a biological system.


texts:
Are there evolutionary theories as to why we (and most animals) sleep?

Some claimed functions of sleep include: restoration, waste clearance, memory processing, etc. But unless we understand why these functions are necessary (in the sense that the cost outweigh the benefits in terms of evolutionary fitness) and why they cannot be accomplished awake, we won't have a clear evolutionary theory of sleep.

Are there current theories on the evolution of sleep?


texts:
In the presentation of phylogenetic trees, the geometric shape of the trees often seems somehow arbitrary and is more driven by aesthetics than by informative reasons.

But wouldn't it make sense to give the geometry (distances and angles) specific meanings? Or is this already done (when it's done right)?

Some basic principles:

The vertical axis represents time (on a linear, logarithmic, or "anti-logarithmic" scale).
The horizontal axis represents the amount of genetic change (measured in appropriate units).
The line of one species (= population with virtually identical DNA) goes vertically from bottom to top.
The line ends when the species becomes extinct.
A new species branches off of an existing species by a horizontal line perpendicular to the line of the latter.
The length of the new (horizontal) line reflects the amount of genetic change.
At its end the line continues vertically.
There are no other branchings along the horizontal line.

By these principles and with perfect knowledge (and a good measure of genetic change) we would have a perfect rectangular tree like this:

But our knowledge isn't perfect: we know little to nothing about lots of intermediate species which didn't leave traces. Hypotheses about these unknown species can be reflected by inclined lines whose slopes can tell for example:

a) Their have been many pronounced genetic changes in a short period of time after the new species branched off. (grey: hypothesized intermediate species)

b) Their have been few small genetic changes in a long period of time after branching off.

  I'm looking for discussions/considerations of this kind of drawing
  phylogenetic trees (papers, web pages, or simply good search terms).

An interesting - and new to me - point of view is given in Joseph Ahrens' answer to this Quora question:

How do you interpret ancestry in phylogenetic trees?

What slowly becomes clear to me: It's about the interpretation of straight line segments, maximal straight lines, of horizontal vs. vertical lines, and nodes (= branching points) in phylogenetic trees, especially: which of them is to interpreted as a species?


texts: confusion in types and kingdom system of classification

texts:
I am a high school student and I want to ask: is the 'kingdom system' of classification (two-kingdom, three-kingdom etc.) different from artificial or natural classification? I am asking this because my teacher told me that these two are different things. He says that you cannot categorize the two-kingdom classification as artificial or any other type.
But I am little confused as to why we cannot categorize kingdom system classification into artificial, natural or any other type. For example, Linnaeus selected only a few characters to propose the two-kingdom classification. Then why can we not say that it is an artificial classification?


texts: Are single-celled organisms capable of learning?

texts:
I've read that the amoeba is capable of learning.  Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the evolutionary distance.

How does this species learn?  I would presume that there is a complicated chain of receptor mediated transcription regulation, but what are the specifics?  What types of receptors does an amoeba have to sense its environs?


texts: Length of upstream and downstream of tss important for gene regulation o

texts:
I want to find SNPs in the upstream and downstream regions of transcription start sites of some 42 genes implicated in a disease (on which I am working).

Are there any suggestions on what length should be covered both upstream and downstream? Is there a database which can give the transcription factor binding region of both upstream and downstream regions as a batch query? Or a paper to which I can refer for the search length for looking for SNPs?


texts: How does the brain know what to remember and what not?

texts: People remember some information for example when learning for an exam, or remember to go to a shop after work etc., but we don't remember usually much other stuff like people passing us, what was the weather some days ago etc. How does the brain know what to remember and what not, how does it filter important information from not important?


texts: Can someone provide resources on human electromagnetic frequencies?

texts:
Pardon all of my questions below.  I'm basically looking to find online resources regarding my inquiry.  If you can answer any of them off the bat, that would be awesome!!

It seems that humans and mammals give off certain frequencies from our nervous systems.  For example, dogs are able to sense when their master is coming home, even when their distance is close to a mile away.  Also, cats are able to sense when a human is about to die.  They can feel the frequency the person is giving off, and react differently.

Where can I learn more about this frequency that humans give off?
Has anyone ever done research on this subject?
Is this electromagnetic frequency or something else?
Are there devices that can measure this frequency that the human nervous system gives off?
Are there devices that can generate this frequency that the human nervous system gives off?


texts: What are the effects of sleep deprivation?

texts:
Having recently pulled an "all-nighter" while trying to fix a fatal bug in our release code, I started thinking of any health risks that I might have.

What are the adverse effects of staying up for staying up for 42 hours, considering I took no caffeine or other stimulants, as well as no depressants such as alcohol?

Upon googling I found a lack of facts, what would be good is a list of effects and rough times that they start happening.  And any significant problems I would face, but moreover I would like to know what causes them?  Unfortunately I only studied Biology until GCSE (UK - SAT/TAKS Alternative) and might need some simplified explanations or links to help understand more complex tasks.

I'm not even sure if this question is grammatically correct, and my brain power has slowly dwindled, should I be worried?  I have read this and understand it to a vague extend.


texts: If a gene has for instance three alleles, p, q, and r, then could p be dominant to q, q be dominant to r, but r be dominant to p? Can a gene that is recessive to one allele not be dominant to another allele that is dominant to the second? If it can, what are some examples of traits that do this?


texts: How does caffeine (or any additional agents) act as a laxative when ingested? I'm interested in the metabolic/signaling pathway.


texts: Free-flowing cells and those that are stuck together?

texts:
I've been thinking about the development of an embryo from the zygote stage.

How is it that when cytokinesis takes place at that stage, the cells all stick together in a little ball, but later in life, some are not bound to others (red blood cells, sperm cells, etc.)?

In other words, how is it that some cells are stuck together and some are separated? How does this property develop?


texts: Confusion about Photosystem 2 with regards to lysis of water

texts: I am slightly confused about the role of $\ce{H2O}$ lysis in PII. I know that this releases $\ce{H+}$ ions, which I think are important because they drive the production of $\ce{ATP}$ through F-Atpase across the thylakoid membrane. But I don't understand how else this is important? With my current understanding, I would think that it is perfectly sufficient for PII to receive photons to excite an electron in the primary pigment reaction centre, which goes along the electron transport chain to PI. Is the water lysis there to replace electrons lost by photosystem 2? If so, how is it controlled that the correct number of $\ce{H2O}$ molecules are lysed so that excess electrons aren't generated?


texts: Death because of distilled water consumption

texts:
One of my friends said that I would die if I drank distilled water (we were using it in a chemistry experiment) I gave it a go and surprisingly did not die.

I did a bit of Googling and found this

It said that drinking only this kind of water could definitely cause death, as distilled water was highly hypotonic and it would make the blood cells expand and finally explode and ultimately cause death.

I wanted to know exactly how much of this water on an average was needed to be consumed to cause death.


texts: Validation by PCR of a lowly expressed gene in microarray

texts:
I am interested in validating the precence of a gene (FETUB) whose expression is in the lower quartile of the microarray (see figure in link).

https://drive.google.com/open?id=0B82aQne0d_mYWlFiMjRlb05CUVU

Do you think this gene would be detectable by PCR?

Thanks


texts: Is pathlength correction vital to be included while quantifying protein

texts: I am trying to quantify protein in serum/plasma samples. I have carried out biuret assay for my samples using microplate reader. While performing I encountered the doubt whether I should include pathlength correction, blank subtraction steps to get accurate value. Why and how to use these factors for quantifying using microplate?


texts: Trying to identify a bug that left a blood spot when killed

texts: Hi, this was flying around inside the car in northwestern Maryland, USA, yesterday. When I squished it with a tissue I was surprised to see a red spot that appeared to be blood. Cannot find a picture of this bug online and was hoping someone can identify it. Thanks in advance.


texts: What sample sizes are ideal for carrying out Bayesian Skyline Plots?

texts: I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 polymorphic sites within each population and one dominating haplotype that comprises almost 90% of the population (the rest being rare haplotypes). Because, BSP uses Coalescent processes for the calculations, the sample sizes would have a effect on the results. I wanted to know if sample sizes of around 30 (for DNA alignments of 700bp) would be ideal for carrying out the analysis and expect reasonably good results ?


texts: Is it possible to prove that a hand sanitizer can kill 100% of a person's germs?

texts:
We have a project for Economics, and we need to advertise something that consumers will be willing to buy. My group thought of "improved" hand sanitizer. So, instead of it killing 99.9% germs, we would make it kill 100% germs. Although, we are having a hard time trying to prove that our hand sanitizer can, but we can't change what our product is anymore, since we only have a couple more weeks until we pass the commercial.

Can anyone help us? Thank you in advance.


texts: Is it possible to get either a false positive or a false negative from a DNA paternity test and what would be the likely mechanisms behind this?  For example, is it possible that a father's DNA could have changed during his lifetime enough to be unrecognisable to that of his children?


texts: How can calcium be a kept as a local signal in the cytoplasm?

texts:
We went through this in my class last week and it doesn't make sense to me at all.

It's small and it diffuses in and out so easily so wouldn't it diffuse out quickly and thus not be a local signal? Or where it's stored in the RER does that change things?


texts:
I am working on ant resistant coatings that are meant to make a material resistant to ants or chewing through them. The question is - how do I get ants to attack the material?

I have considered leaving a plastic bag full of water that is coated in the material outside of an ant hill. Does anyone have any suggestions?


texts: How can I calculate Shannon-Wiener diversity index in caves with different kind of habitats and different sampling methods?

texts:
I would like to start a monitoring in different caves, compare caves of different age and length, and find out if there are any correlations between these factors and their diversity.

I was thinking to use the Shannon-Wiener diversity index and to use both pitfall traps and timed area search sampling methods. Can I get a single index value for each cave even if the methods are different?

And what about that caves which have stream or pools where the fauna can be very abundant? Even if I collect a sample of water, the abundance of certain species can be very high (e.g. copepoda).

Sorry for the banal questions but I have not experience with indices and statistics.

Clarification after comments:

I have about 20 caves to sample, I want to compare the fauna of these caves (richness and abundance). As I told they have differents lenghts, ages and others environmental features. Some of the caves have also streams or little pools (where I will take water samples to identify the fauna).

I have read some articles where the diversity indices were calculated using just one single methodology (traps or timed area search), and also for only one kind of fauna (acquatic or terrestrial).

The question is: Is there any methodology to get one single value of diversity index for each cave? (which considers both terrestrial and aquatic fauna). Or maybe in these conditions I can just get the number of species for each cave, without being able to compare their abundance?


texts: Would the amino acid profile of lab-grown human meat perfectly match the dietary nutritional amino acid requirements for humans?

texts:
Whey protein is the food which has the most ideal (yet not perfect) amino acid profile for humans, whereas gelatin for example has a very poor and incomplete amino acid profile for humans. Would human meat grown in a lab such as they are working on with the meat alternatives match our amino acid requirements perfectly since it is actually human tissue?
UPDATE: I was not aware of any hazards that could be involved with consuming human tissues, so I am expanding the question to involve if there is any way to produce human meat safely in a laboratory setting.


texts:
Which Starling Force is affected by Mannitol?

I am either thinking hydrostatic pressure of interstitial fluid (because it increases interstitial fluid volume) or hydrostatic pressure of capillary (because it is also increased plasma volume). I read that it deals with osmotic pressure but was unsure as it is a crystalloid and not a colloid.


texts: Can cancers caused due to viruses be contagious?

texts:
Generally, viruses are infectious in nature and there are several cancer-causing viruses that are known (i.e. oncovirus)

My question is:
Are these oncoviruses infectious in nature? If so, what is the way in which they can be transmitted?

(edit:just a background to connect the title and the question (as mentioned by user iayork):While reading my text(which led me to the doubt) I was considering the virus as a causal organism and the disease as cancer(malignant tumour cells).The cancer cells are non-contagious however I wanted to understand if the disease  was.Thus I was interested on the routes of the transmission of the viruses.Also note (which I had already asked user Chris in the comment) "most cancer disease are non contagious but if cancer disease was due to virus if it was contagious or not"


texts: How do legs of tiny insects/spiders like mosquito/Opiliones work?

texts:
I think I understand how legs of humans work. We have bones to which muscles are attached. Muscles can only contract / relax. By the combination of many different muscles we can make complex movements:

Image source: https://commons.wikimedia.org/wiki/File:1015_Types_of_Contraction_new.jpg

However, I have no idea how this works for insects / spiders. On the one hand, I'm not sure where the muscles should be attached to due to the exoskeleton. On the other hand, I have difficulties imagining that the same system works for legs which are this tiny:

Image source: https://commons.wikimedia.org/wiki/File:Spider-IMG_1630.jpg


texts: Why do membrane proteins at lower temperatures contain more alpha helices than beta sheets?

texts: Why do organisms found at low temperatures have membrane proteins with a higher percentage of alpha helices compare to beta sheets?


texts: A colony of humans are sent to an alien world, at what point would the descendants evolve to be genetically incompatible with Earth humans?

texts:
I recently heard about the evolution of the London Underground mosquitoes, and how they have changed genetically enough that they almost can no longer reproduce with above ground mosquitos. Since this change in the mosquitos occurred over a relatively short time frame, how many years/generations would it take for a similar process to happen with humans?

The thought experiment that comes to mind is this. Assuming we sent a colony of humans to a distant planet and didn't have any physical contact with them for x number of years, how many years would it take for the colony of humans to branch off enough genetically to be no longer be able to reproduce with Earth humans? This is assuming the planet is habitable but different enough to change the course of human evolution.

In other words, what would be an expected minimum number of years it would take for this colony's descendants to be removed from Earth humans to one day again be reunited and not be able to produce offspring between the now different species?

In other words, what would be an expected minimum number of years the would need to pass before they are reunited and are no longer enough of the same species to produce offspring together?


texts: Nonpancreatic digestion of tryglicerides

texts:
In an answer about coconut oil I can read

  the digestion of coconut oil does not involve in the Pancreatic digestive enzyme system

In both primary and secondary school I have learned that fat needs to be processed by pancreatic lipase as tryglicerides can not be absorbed.

Are medium-chain tryglicerides an exception (they can be absorbed), are there other (nonpancreatic) lipases in human digestion system, or is the linked answer wrong?


texts: Do different values of the smoothing parameter lambda for estimating the divergence times (in situ Sanderson 2002) will affect trait conservatism (e.g., Blomberg's K)?