texts: What statistical test would you recommend to compare two animal behavior sampling methods?

texts:
I am doing a lab where I am comparing the scanning method and focal animal method. Each method will give me the following:

Scanning method: occurrence frequency for each behavior (%),
focal animal method:the occurrence frequencies (%), as well as the duration for each behavior.

I was thinking a chi-squared test or a t-test somehow but I'm not sure which to do or how to format them. Should I somehow compare the occurrence frequencies?
Not sure if this info is useful, but I normally use R for my statistical test but have never used my own data, only example data. I was going to record my data in excel and import it into R. Thank you in advance.


texts: Are there critical points in ecosystems?

texts:
Some days ago, I was thinking (partially) about the complex balance that is needed for an ecosystem to exist. I got curious about the existence of some sort of critical point, something - that when taken out of the system - makes life vanish.

Is there a single species that when took out of one ecosystem destroys the life in it? Perhaps there's not a single species, perhaps there could be a minimal set of species in which this could happen.

Excuse me for the poorly formulated question. I'm not a biology student, I just get random curiosities from time to time.


texts:
I've been studing population growth models, but there's something I can not find that's fustrating. That's a formula for the variance in population growth. I know that other models can be aplied, but I want to start with the simplest case.

Let's assume a population is growing exponentially as defined by:
$N(t) = N(0)W^{t}$

The parameters $W$(absolute fitness in my definition) tell us that the time for division (if the species reproduces binarally) is given by an exponential distribution with $\lambda = \dfrac{\ln W}{\ln 2}$

So I see a model for $N(t)$ and a random variable associated with this model. What is the pdf, expected value and variance of $N(t)$? The expected value I expect it to be given by the first equation (or the value to be the same) but what about the variance?


texts:
I live in the Netherlands and it is getting fashionable to compost with worms. After investigating a few websites I noticed that most websites suggested that I cannot feed the worms leftovers from citrus fruits. This seems logical. I then started noticing that people advise against feeding the worms cooked food.

I'm no biologist but I cannot imagine a reason why cooked food is bad for the worms. Could anybody explain why this might be in layman’s terms?


texts: How much total RNA can be extracted from Drosophila brain

texts:
I am wondering how much total RNA could be extracted from a single D. melanogaster brain.
I could not find this information from the literature.

The closest hit was this paper, that claims that 16-21.9µg of total RNA can be extracted from 100 brains, which translates to at least 160ng for a single brain.

I also found in the supplementary material of this paper that 1µg of total RNA was extracted from 5-10 fly brains, which would also make > 100ng for a single brain.

I am asking the question because I am envisioning to perform RNA-seq of single Drosophila brains. The standard Illumina TruSeq library preparation protocol works with 100ng of total RNA. Thus I am wondering if this is realistic, or if I should rather target low input library preparation protocols.


texts: How can trees be able to transport hundreds of liters of water all the way up to the crown and out in the leaves?


texts:
I heard a lecture from a supporter of urine therapy and he claimed that urine is not only good disinfection but also as rich source of minerals. To me, these two advice seemed contradictory.

In addition, the supporter emphasized one should use his own urine - and yet, as an example of the magical effect of urine therapy we got a story of a boy who was hooked by jellyfish but was saved by a nearby doctor who used urine of his own. Apart from that I see no reason why urine should work against toxins better than a water or a disinfection (they don't).

Though, I know a very qualified doctor who advocated this treatment. What do you think?


texts: What is the common diet of food-related IBS patients? Besides most patients being lactose intolerant, what other intolerances do they face?

texts: I am currently writing a paper on irritable bowel syndrome, and I was wondering what the common diet of a patient with food-related IBS consists of. I've already begun discussing the pathogenesis of the disorder, but I want to start making a connection between food and IBS. I understand that most patients tend to be lactose intolerant, but I am also interested to see if there are any other common intolerances associated with IBS.


texts: Is there any checked case of "involution"?

texts:
I know that strictly speaking the term "involution" referring to the evolution theory doesn't hold any meaning. Organisms keep on evolving and changing with time, that's all.

But the following situation could perfectly happen:

Some event causes some organisms to evolve certain characteristics that allow for a better survival, but with time that event stops and what was previously and advantage for these organisms, now it's a disadvantange, and to adapt to the new situation what they do is to exactly remove these characteristics and they end up being exactly the same as they were previously to the change. It could be considered that they have "involutioned".

Are there checked examples of this? (Not just as theory, examples of organisms where this "involution" has been observed). I'm specially interested in "complex" organisms, I think this is not that far fetched to happen to organisms like bacteria, virus or the like. But for more "complex" organisms I guess it's too much of a coincidence.

Edit: I'm putting an example to clarify:

Let's imagine we have a huge amount of plants of the same species which can grow extremely fast (in the way they could simulate 100000 years in evolution in one hour) and we have an atmosphere for them that is the same as current one. (Not realistic, but let's make the thought experiment). We also put some put of these plants apart.

Little by little we go changing all the carbon dioxide in that atmosphere with something, like, for example, nitrogen, it's to expect, that, with time, some plants will appear to better use the nitrogen, at least up to the point where they can survive, as carbon dioxide is every time lower and lower and plants not adapted to this end up dying.

When we finally have only nitrogen processing plants we start the opposite, we start filling little by little with carbon dioxide, it's to expect that the contrary would happen.

Now, if a biologist were to observe the plants that were set apart at the beginning and the new created plants he wouldn't be able to tell where each plant is from, unless he was aware they were separated to do the experiment.


texts: I was doing research on Regalecidae, and I came across an online database. Here, on the database, there are 12 matches for Regalecus russelii. At the bottom of most of these pages, there is a related file, which shows the original record for each sighting. On these original records, it always lists the specimen as Regalecus glesne, not russelii. Why is this? What species are they really?


texts:
In most biomes on earth, and certainly in the most densely-populated, the best camouflage color or pattern for an animal would be a variant of green, so as to blend in with the leaves and grasses of the surrounding environment.  Whether predator or prey, the art of not being seen is hugely important in the natural world, and yet to the best of my knowledge there isn't a single mammal on the planet with fur that is even partially green.

Is there a reason for that?  It seems like animals have evolved some pretty crazy color patterns to break up their silhouette or blend into the background, but why haven't any mammals taken the obvious route of "look like leaves"?

Is it really THAT not-easy being green?


texts: Which plasmid can express T7 RNA polymerase in mammalian cells?

texts: Does anyone know what plasmid could express T7 RNA polymerase in mammalian cells, I would like to transfect it with other plasmid containing Gene Of Interest under control of T7 promoter. Thanks a lot!


texts: Same target receptor different mechanism of action?

texts: If different drugs have the same receptor as a target, does that imply that they have the same mechanism of action?


texts: Does precipitation influence the UV spec reading?

texts:
I have been checking my sample for Hydroxyl radical scavenging activity. I have dissolved Hydrogen peroxide in Phosphate buffer. My sample is clear and reagent is also clear but when I have mixed my sample extract with Hydrogen peroxide reagent a precipitant is formed. Control is very less than solution that is kept for reaction to proceed. So I am getting an answer in negatives (230 nm). Is that formation of precipitate affect the absorbance of the solution? Does precipitation increase the OD value compare to clear solution?
 Mine is mushroom powder. It is extracted with Ethanol. Extract is dried and finally it is dissolved with solvent above said. That has been used for Hydroxyl radical scavenging activity. Hydrogen peroxide 0.01 milli molar reagent is prepared with Phosphate buffer. First i have taken reading for H2O2 and added extract kept for ten mins and took reading. in 230 nm..


texts:
I saw this animal (probably insect) in my house in the Netherlands:

I have searched on the internet but was not able to find what this is, I first thought it was a kind of dragonfly, however there are only two wings which is not usual for a dragonfly. Any suggestions what this is?


texts:
The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:

$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$

, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by

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

$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$

, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.

Question

The above definition makes sense for one bi-allelic locus only.

How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for $n$ bi-allelic loci? Is it:

$$\sigma^2 = \sum_{i=1}^n \sigma_i^2$$ $$\sigma_A^2= \sum_{i=1}^n \sigma_{Ai}^2$$ $$\sigma_D^2  = \sum_{i=1}^n \sigma_{Di}^2$$

Here is a related question


texts: How are targets formed for axon growth cones (CNS)?

texts: Axons have growth cones which find a route to their target using multiple methods (guidepost cells, attraction to target, etc...). My question is, what is the process that actually forms the target? For some given Axon A1 of Neuron A, why does it skip Neuron B, and go straight for Neuron C? How is a target formed on neuron C for Neuron A to connect to? Are there are any articles/readings on this topic? There is also the process of following the path of a pioneering axon. Does following a path of a pioneering axon take precedence over other forms of signaling? Does distance play a factor in choosing a target (Eg: Axon growth cone prefers closer target rather than distant target?)


texts: How many molecules of ATP are actually produced in aerobic respiration?

texts:
I have been through the process of aerobic respiration a few times in different text books and almost every book quotes a different value for the number of ATP molecules produced. The consensus seems to be 30–32, but why is there disagreement and why aren’t the numbers exact?

The possible reasons I can think of are:

Phosphorylation of ADP is not directly coupled to redox reactions.
The number of ATP molecules produced depends on the shuttle used to transport electrons from the NADH in the cytosol to the mitochondria, i.e.  whether it’s FADH2 which enters the ETC or NADH. (I have a silly question on that, but I need confirmation, does the electron carrier chosen depend on availability?)
The proton-motive force can be used to drive other cellular processes other than the production of ADP? (I'm guessing.)

Are these suggestions correct, or is there some other explanation?


texts: Are there enzymes for every given reaction?

texts:
This is a question that's been bugging me, and I haven't been able to find a definite answer anywhere.

We know there are thousands of enzymes (proteins, let's ignore catalytic RNA for now) that catalyze many different reactions, and they do this because they have the correct shape to fit the substrates.

Theoretically, given some reaction, can an enzyme be created to catalyze that reaction? Or is there some reaction that it's not possible to catalyze with an enzyme? Can any given shape be created out of polypeptide chains? If not, what determines the shapes that it's possible to create?


texts: What the "due to" means in the definition of heritability?

texts:
According to Wray and Visscher,

  heritability is formally defined as the proportion of phenotypic variation (VP) that is due to variation in genetic values (VG).

My question is, what does “due to” mean here?

My first thought is that its meaning is causal. By using Pearl’s causality framework, I’d think that we could say something like:
I have a variable T (trait), and a pool of genes (G) as cause. Also, other variables (not genes) also cause T, let’s call them U. Thus, it seems that this is a (simple) causal model behind heritability:

However, let’s say the trait is accent. It is unlikely that genes have a causal effect on this trait, so the arrow from genes to this trait would not exist. However, if we measure it in some way, we will probably be able to compute the heritability of this trait, especially because white Americans, for instance, speak with a different accent than Afro-Americans (thinking about the USA). So, we should conclude from this that the “due to” in the definition above has nothing whatsoever with causality. It is talking about correlation: how much of the variation in the trait we can associate with genes. So, if we have the following causal model (to make things simple), we would still be able to compute the heritability of a trait.

However, the only effect of gene on accent is mediated by an environmental variable (segregation), which has no direct effect whatsoever of genes.

So, my question is: does heritability depend on having a causal model? If so, are estimates done with an explicit causal model like a DAG? Do they try to control for confounding and other things that may cause a biased estimation?


texts:
Just a general question about trophic levels. Traditionally, it's thought as much as one order of magnitude of energy is lost as one moves from trophic level to trophic level. I am confused here since it seems to me the energy content of certain primary consumers is more if not equal to an equal number of producers. Take a 1 acre lot of grass vs a 1 acre lot of cows; surely the calorie content in the cows is more than that in the grass no? A one ounce cut of beef has more calories than an ounce of grass. I could imagine for plankton or insects, maybe the energy content is not as conserved since they can store less energy and eat less. So my question is whether this one order of magnitude drop is a rule or just a 'rule of thumb' or if I'm framing the whole thing wrong.

Thank you


texts: How do fatty acid and polyketide synthases handle the varying size of their substrates?

texts:
Polyketide synthesis involves six modules, each containing certain common constituent enzyme activities (KS, AT, KR) that are involved in extending the chain (see e.g. Dutta et al.(2014) ). The growing polyketide, attached to acyl carrier protein, is passed on from one module to the next.

An analagous situation is seen in the single Fatty Acid Synthase complex. How can the same enzymes in later modules recognize what is a structurally different intermediate? Surely this contradicts the idea of substrate specificity of enzymes.


texts: Isolating the gene of interest for protein production

texts:
For protein production, the gene of interest is inserted in an expression vector and introduced into a suitable host for expression. But how is the gene of interest for the desired protein isolated from the organism which possesses it?

One way could be to synthetically make the DNA sequence coding for that protein. Another could be to identify the gene of interest from a pre-existing genomic library or cDNA library of that organism. Are they the only methods?

The organism's entire genome could be taken and cleaved with restriction endonucleases, and a Southern blotting technique (i.e. electrophoresis followed by probe hybridisation and autoradiography) could be used to screen the gene of interest from the fragments produced. Of course, for this the gene sequence must be known beforehand, in order to synthesise the probe. Is this method also adopted? It seems inefficient - given that the fragments are assumed to have the intact gene of interest, and the gene should have been sequenced beforehand.


texts: Can someone identify this species from the pea family? The plant was photographed in Morocco in spring. The location is south of Marrakesh at the foot of the high Atlas, in a dry riverbed.


texts:
I have an engineering background and have been assigned a project to look into to failures during E.coli fermentation process using the data available before/during/after the process

I have learnt some of the procedures involved in the process from SIP/ CIP and few things about inoculation during fermentation. But I am still lacking some basic knowledge of E.coli fermentation process using glucose and other media components. I consider and value these steps with extreme care during this project.

Any suggestions for resources from where I can learn about this process at a more basic/ intermediate level without focusing too much on any individual step.

I have looked at this youtube video and found it helpful to understand the fermentation process but I am looking into E.coli fermentation in particular, so I have posted my question here. I learnt a good deal about what OD measurement is, d02 values, KLA etc. during this project. I am looking for resources or suggestions to understand how these parameters affect E.coli fermentation process

Bioprocessing Part 1: Fermentation

I also browsed through BiFlo reactor product pages to try to understand some basic information about E.coli fermentation.

E. coli Fermentation Using a BioFlo® 110 Bench-Top Fermentor

I can provide more information if it helps anyone to provide some suggestions. I don't have biology background. So I am not aware of any decent textbooks or papers to read about E.coli fermentation process

Thanks


texts: If women need more dietary iron than men, then do blood donors also?

texts:
My understanding that women's dietary iron requirements are slightly higher because I've heard the only way of losing iron from your body is by losing blood, and this happens in menstruation. This got me thinking if someone donates blood does their dietary requirement increase also?

Also, related to this, when a person gives blood we're told that our body remakes the blood we've lost, does this replenish the iron in the blood also, or is this "newly created blood" absent of the iron normally present in our blood?


texts: Which process is right to describe V(D)J recombination? RAG-1 and RSS recurring process

texts:
I'm studying V(D)J recombination. I think I have two incompatible books about explantaion of the process. Which is right?

In Molecular Biology of the Cell 5th Ed., firstly RAG (-1?) combines to RSSs of V and J genes independently. After that, a hairpin loop is formated by paring random(?) RAGs.
In Janeway's Immunobiology 8th Ed., RAG complex (RAG-1 and RAG-2) has two sites for RSSs from the beginning. And in the figure, V gene is firstly recruited for a site. J gene combines to the RAG complex after V gene.


texts: We came across this snake when were on a hike in a typical dense forest in the Philippines. . Been wondering if this snake is venomous or not.


texts:
Why have humans developed ears capable of hearing sounds that are (never?) heard in nature.

Is it known why humans developed the ability to hear up to 20 kHz when all the relevant noises are below 8 kHz? (at least in my experience) Or why was it beneficial to hear in that range?


texts: Were Telomeres the Master Key to Abiogenesis

texts:
Knowing as we do now that all manner of complex organic molecules and viscelles/micelles form spontaneously in various environments, from hot vents perfect for basic hydrophobic H-C fatty acids and stable charged H-C-O-P hydrophobics - to volcanic glass micro-chambers, clay-layer geometry and water ice fractal symetry,  that all combine to create ideal nanoscale everywhere rapid self assembly scenarios for various amino acids etc that in turn can form RNA like segments and combinations... I can't help but wonder what scenario is best situation pre-biotic that can form Telomeric sequences.

It seems to me, an instinctive feeling after viewing so many bioscience and life origin videos, that in all the random prebiotic assembly and disassembly of molecules, the perfection of replication lies in repetition that first needed a master start and stop sequence control, as master of other sub gene start stop codons.

Of course a myriad of biophysics factors come into play in origin theory and I am far from expert but I wonder if anyone can provide solid
references about abiogenisis and telomeres?

Tough question to word here, and too vast a topic when I try and narrow the web searches.  However, the amino squences for telomeres are finite I believe and so before life kept repeating itself what molecules in what environment crates the combination best?


texts: Is a FoldScope microscope suitable for plant cytogenetics?

texts:
I have recently been getting more interested in amateur botany, and have some background in genetics and genomics (PhD+). I have used standard light and confocal microscopes but don't have much expertise in microscopy.
I often find myself wondering what the ploidy is of some plant that I'm looking at, as I know that this is a major life history feature and genetic variant in wild plants.
I was curious whether a cheap little scope like a foldscope would be an adequate microscopy instrument for looking at the cytogenetics of a (probably rather crudely prepared) plant sample, assuming that I can come up with a suitable home protocol. (I don't currently have access to lab space.)
I have found this question, but it doesn't really explain much about the required parameters for cytogenetic microscopy.
So:
1) What microscopy parameters need to be satisfied to do cytogenetics?
2) Does a foldscope meet them?
3) If not a foldscope, what other cheapo scope would work?


texts: What flower is this?  All help would be appreciated


texts:
I am looking for a database(or any kind of information source) of cancer cells, which has information about the speed of reproduction of these cells, how fast they grow, etc.

So I could make my simulation as accurate as possible, as close to reality as possible (I am working on developing a software that simulates how cancerous cells spread).

Edit

  Are you interested in growth rates in culture or in vivo (e.g. tumours)

Okay, I am a noob in biology, so let me explain it like that.
I am using Voronoi graphs for simulation, so I think that I am interested in tumor level, how each cell interacts with each other, and thus how fast can cancerous cells overpopulate healthy(or other cancerous) cells.


texts: Help ID this South Indian fruit-bearing tree

texts:
So there's this fruit-bearing tree near my house in Kerala, South India. A senior neighbor of mine tells me that this fruit is edible. I tried it out, and it tastes alright. I want to ID this plant, know its botanical name, as well as whether it has any medical/commercial/culinary application.

The fruit is green when tender and red when ripe.


texts: Is it possible to have a mechanism to use carbon dioxide as a source of oxygen in human body?

texts: Is it possible to seperate O2 from CO2 and use it for energy In Human? Why Plants and not Humans can do it?


texts: TMB vs ECL for ELISA: which detection method is more sensitive?

texts:
I failed to find a comparison, does anyone know which ELISA detection method is more sensitive of these two: ECL, TMB?
Many thanks!


texts: How many oxygen atoms are used up in aerobic oxidation of one pyruvate?

texts: Please explain elaborately, if possible using the EMP, Krebs and ETS cycles.


texts: If one kidney can function just as well as two, why do humans have two kidneys? The cost of growing two kidneys must surely be quite high, especially since one kidney is all that is really needed.


texts: Why are mammals unable to produce Essential Fatty Acids?

texts: Why do we have to get them from our diet, and if they aren't taken in our diet we will face disease? Then why we don't have the enzymes which are require for EFA synthesis?


texts:
Normally I wash/detect with one primary/secondary-HRP antibody pair, strip, then wash/detect with the other primary/secondary-HRP pair which works well. However, I recently started working with a HRP-conjugated primary antibody for my protein of interest and wondered if I might add this together with the secondary antibody for my loading control to save the stripping and second washing.

Are there any general guidelines for Western blotting with multiple antibodies at the same time, i.e. changing antibody dilution?

An obvious first step is to make sure the HRP-conjugated primary isn't from the animal recognized by the secondary. I anticipate blotting with mouse HRP-conjugated anti-GFP and a secondary rabbit anti-mouse would not be a very good decision.


texts: Is there a vaccine against the plague (Yersinia pestis)?

texts:
There seems to be recurrent events of infections of the plage (Yersinia pestis), from the well known Justinian plague to the Black Death and to recent years. In fact, two cases were reported in China in November 2019. However, it seems there is not an effective vaccine yet. At least until 2013 there was no vaccine approved by the US FDA. There seems to be on-going research about vaccines for the plage.

Is then no effective vaccine against the plague? If yes, does it mean humanity is still at risk of yet another pandemic of the plague?


texts: How to conceptualize the action potential?

texts:
In my AP Biology class, we were taught that action potentials are not electrical impulses in the same way current travels through a wire. Rather, we were taught that action potentials are changing concentration gradients of sodium and potassium ions.

However, when I looked into modeling action potentials I saw capacitances, inductances, and currents--properties associated with electrical circuits.

My question: action potentials--are they electrical currents in the classical sense? If so, what is the charge that is flowing (is sodium and potassium ions?), and how is the overall charge neutrality of the body maintained?


texts: What equation to compare protein isoforms in a Western Blot?

texts:
The protein isoforms I am interested in comparing appear as distinct bands on the gel I have already run. I have an Excel sheet with optical density measurements I obtained using ImageJ; it looks something like this:

Lane    Iso1       Iso2       GAPDH
1       149.06     194.646    893.08
2       832.654    494.473    148.335
3       49.998     490.539    147.361
4       29.347     208.53     120.652

For the other proteins I've analyzed so far, I've been computing fold-change relative to my loading control, GAPDH, with the following equation:

Fold-Change = Log2(Protein/GAPDH)

I'm not sure how best to compare my isoforms to each other and considering the following two equations:

1. Fold-Change = Log2[(Iso2/GAPDH)/(Iso1/GAPDH)]

2. Fold-Change = Log2(Iso2/Iso1)/GAPDH

I've already computed both of these values for all my samples, graphed them and found that the resulting graphs look pretty different. Which of the two equations do you think is a better way to compare the relative quantities of these proteins?

Alternative equations are also welcome.


texts: What cells in mosses behave analogously to mammalian embryonic stem cells?

texts:
The Washington Post article Ancient life awakens amid thawing ice caps and permafrost describes the work of Peter Convey, an ecologist with the British Antarctic Survey and his team, and includes a discussion of some mosses that have survived over 1000 years in permafrost, and sprung to life once "revived" in a laboratory setting.
This passage caught my eye:

It’s not easy to survive being frozen solid. Jagged ice crystals can shred cell membranes and other vital biological machinery. Many plants and animals simply succumb to the cold at winter’s onset, willing their seeds or eggs to spawn a new generation come spring.
Mosses have forged a tougher path. They desiccate when temperatures plummet, sidestepping the potential hazard of ice forming in their tissues. And if parts of the plant do sustain damage, certain cells can divide and differentiate into all the various tissue types that comprise a complete moss, similar to stem cells in human embryos.

What are these cells in moss called, and how similar are their functions to mammalian embryonic stem cells?

Convey and his team announced that they had awakened 1,500-year-old moss that had been buried more than three feet underground in the Antarctic permafrost. (P. Boelen/BAS)


texts: Akt phosphorylation at Thr308 and Ser473

texts:
I am studying Akt signaling pathway. I know that phosphorylation at both T308 and S473 is prerequisite for full activation of Akt but wonder if phosphorylation/de-phosphorylation of one of them is prerequisite for another. In other words,

wonder if phosphorylation at T308 is required for phosphorylation at S473 or vice versa, or they are phosphorylated independently.
wonder if de-phosphorylation at T308 is required for de-phosphorylation at S473 or vice versa, or they are de-phosphorylated independently (wonder if there is any order of de-phosphorylation by phosphatases such as PP2A between the two sites)

If there is such order, can anyone suggests me some references?


texts: how to find full mitochondrial genome of plants in GenBank?

texts:
I am searching for full mitochondrial genome of a species of Malvaceae family.
To be more specific, I need the genus Corchorus. But I could not find the location where it is in gene bank. After searching in google, I found this, but here I did not found anything for plant.
Can you help me to locate its actual location?
Scientific classification from Wikipedia:
Kingdom:    Plantae
(unranked): Angiosperms
(unranked): Eudicots
(unranked): Rosids
Order:  Malvales
Family: Malvaceae
Subfamily:  Grewioideae
Genus:  Corchorus
L.


texts: Is it possible to extract tissue-culture material from a seed?

texts:
Here is the problem: Tissue culture is cloning, and all plants from the same mother plant are identical. On the other hand, plants grown from seed are all different. If parent plants are genetically diverse (not inbred), growing from seed is the best thing in the long run.

The problem starts when some plants have a low germination rate, or are difficult to grow from seed. We want to grow a large number of plants as fast as tissue culture does, but we want diversity. Suppose the plant can produce a large number of seeds or at-least can produce them easily.

Can we extract cells from the seed and grow them via tissue culture? Which part of the seed should be used, and how different it is from using vegetative parts such as the apical meristem?


texts: Why is sex pleasure giving activity but not childbirth?

texts:
Asking from an evolutionary viewpoint.

Sex is a pleasure giving activity so that it encourages reproduction and spreading of genes. But childbirth ,the most crucial part of the reproductive process, is equally opposite and many times hazardous to the health or even fatal to the mother.

why is that so? Not enough selection pressure (low death rate than succesful delivery rate)?


texts:
I have a list of orthologous gene IDs from the first supplementary file in here.

The gene IDs are of the following type:

EOG6STSR2
EOG60ZRJB
EOG6SBFJ2
EOG6P5KX3
EOG6B5PRW

I want to do the GO term analysis for these IDs. I tried mapping them to FlyBase IDs from OrthoDB and then using DAVID. But many of the orthologous IDs are not getting mapped to the FlyBase ones so I'm not getting proper results.

Is it possible to get the GO term analysis done directly for the orthologous gene IDs without mapping them to the FlyBase IDs?


texts: Coniferous trees in temperare rain forests

texts: In temperate rainforest, the dominant plant form is often coniferous trees (source). However, coniferous trees are also the dominant plant form in a very different climate and form a different biome (boreal forest). Why are broad leaved evergreen trees not so adapted in temperate rain forests as in tropical rainforests? What is the advantage of needle-shaped leaves in the climate with temperate rainforest?


texts: I would like to know what this insect is please

texts: Noted on the side of a tree in the Brazilian Atlantic Rainforest in Oct 2017. About 3-4 cm long . Middle of a very hot day.


texts: Do animals suffer from "Human" mental disorders?

texts:
It is tragic, but apparently Killer whales and Dolphins can commit suicide too (e.g. here)...

This suggests they can become depressed. I wondered whether they were "clinically" depressed like many people are, and what other mental illnesses have been observed in animals in general.

Questions

Which mental disorders have been observed in animals? Which animals?
What is the prevalence of these mental disorders in those animals?
Are the causes and treatments of these disorders similar to Humans?

Strange thought

Organisms that have not evolved the ability to make "conscious choices" cannot decide to end their life.


texts: Why are there no WINGED flying arachnids?

texts:
There seem to have been no arachnids flying WITH WINGS of any sort at any location or any time in the present or in the fossil record.  Why is this?

Rationale for question :

If the process of evolution can be expected to explore all (or large numbers of) possibilities open for adaptation of any form, why has this never happened for arachnids which have been present on land in large numbers of species and individuals for about as long a time as insects?

Arachnids were among the first air-breathing terrestrial creatures so have had this option available for all this time, with apparently no sign of wings at all.

Winged flight offers major advantages to creatures that have evolved it, and has been evolved independently by many branches of the animal kingdom and apparently over relatively short timescales among those that have done this (e.g. bats have presumably evolved flight since the kT extinction of about 65 MY bp).

Flight is easier for smaller animals such as arachnids, as insects have shown, and insects have also shown that flight for small creatures is possible in oxygen levels at present, and levels have been much higher at times in the past.

N.B. !! We all know about spiders ballooning on silk ! This question is about WINGED flight. Please do not waste any of your time or ours on comments about ballooning ! That does not allow directed purposeful flight as wings do and is not a substitute adequate to account for this absence.


texts: Data analysis of transcriptome sequencing data

texts:
I want to learn more about the data analysis and statistics on transcriptome sequencing data. I would like to read some important papers of the field and books and maybe some MOOCS, if they are available.

More precisely I have data of differentially expressed genes across different groups of individuals and I want to test, if the genes are more expressed in one group are the genes also more polymorphic?

Any ideas?


texts: Why are carbohydrates the most common short-to-medium-term energy storage form in biology?

texts: According to this table, gasoline has a specific energy noticeably higher than fat and more than twice that of carbohydrates; even short-chain hydrocarbons like ethanol and even methanol offer an improvement in specific energy over carbohydrates. Given this, why are carbohydrates the most common short-to-medium-term energy storage form in biology?


texts: What is this growth on a Rosa rugosa stem?

texts: I saw many of these on my big old Rosa rugosa bush yesterday. What are they?


texts: By what mechanism does an obstructed bile duct cause excess fat in the stool?

texts: By what mechanism does an obstructed bile duct (for example gallstones) cause steatorrhoea (excess fat in the stool)?


texts: Why doesn't G-actin concentration fall once microfilament polymerization begins?

texts: I don't really understand why the monomer concentration on this graph will stay flat when the monomer concentration is above the Cc.


texts: What kind of microscope for ML/biological research?

texts:
I am a computer science student, focusing on machine learning applications. I have been always interested in biology but I lack any training in it. Now, I had an idea that I could introduce myself to biology more by buying a microscope, and doing some small (still serious, if possible) experiments.

Now, the problem one I am facing is what kind of microscope should I get? Preferred answer would outline what kind of research is possible to do with such and such microscope, and what is the typical price range for the system.

If there are any safety (e.g. does any of the UV leak from fluorescence microscopes?) or ethical concerns I would like to hear about them too. Thanks!


texts: What is the role of Aspartate Transaminase in gluconeogenesis?

texts:
I know that oxaloacetate cannot cross the mitochondrial membrane, but can instead be converted to aspartate, shuttled out, and then re-converted back to oxaloacetate.  What does this have to do with gluconeogenesis?

The traditional route is to convert pyruvate to OAA to malate in the mitochondria, shuttle the malate out, and then convert malate back to OAA in the cytosol.  If lactate is the precursor, then the conversion of lactate to pyruvate in the cytosol can generate an NADH, making the conversion to malate in the mitochondria unnecessary.  Thus, OAA is converted directly to PEP in the mitochondria by mitochondrial PEPCK and shuttled out to the cytosol to begin gluconeogenesis.

If we have these two pathways, what is the point of using aspartate?


texts:
Recently the toad from this video has been identified as an American Toad inside this post in Reddit. The original video mentions it was filmed in White Clay Creek State Park, Newark, Delaware, USA.

Calculating the water's wavelength based on the sound yielded a value of 0.5mm. Using the image's ratios, the toad's length can be estimated. The result was 7mm. Yes, a toad being 7mm long.
The purpose of this question is to ask both if it effectively is a species of American Toad and if it's plausible for it to be 7mm long.
Thanks


texts: Is it the sphincter that flexes when a human pushes a bowel movement?

texts:
Of course the sphincter muscle is at the exit point. To use a toothpaste tube analogy, if I want to squeeze out some toothpaste, it does me little to no good to jostle the nozzle; I need to squeeze the tube (which is analogous to the colon) to get the paste (payload) to come out.

So when a human is sitting on the toilet squeezing, is that squeezing flexing of the sphincter, or squeezing muscles along the sides of the colon pushing on it as one's fingers push on the tube to get toothpaste to come out.

If it's the sphincter that's getting flexed, how is that helping get a big log out?


texts: What are the methods for detecting anagenetic versus cladogenetic change?

texts: I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.


texts:
Are orthologs and paralogs examples of conserved genes? Orthologs are the genes or DNA that is present in 2 different species, having once been present in a common ancestor. It comes about by a speciation event. Paralogs come about by gene duplication events.

So, would we characterize these genes as conserved genes?


texts: Are there any creatures that will eat their own limbs or body parts to survive?

texts: I'm curious if there are any insects, bacteria or perhaps even large animals who would bite off their own limbs or body pieces to chew on in the desperate times of hunger.


texts: Why do people have darker skin in sunnier climates?

texts: I don't understand why darker skin is advantageous in hotter climates. Wouldn't it absorb more of the heat? I have heard that it reduces the incidence of cancer, but I would think absorbing more radiation would increase the risk?


texts: Double stranded nucleic acids are more 'durable' than single stranded nucleic acids?

texts:
I'm struggling with a question I've been asked.

"Why is double stranded genetic material more 'durable' than single stranded one?"

I know that double stranded genetic material is more stable due to multople strands. The single stranded isn't as stable as the double stranded since it lacks the second strand and therefore the bases are open.

Stable isn't the same as durable, and I've never heard in class that one is more durable than the other one. Did I miss something or is this just a mistake?


texts: Query individuals with both WGS and RNA-Seq data

texts:
Using the SRAdb R package, I am looking to query individuals who possess both WGS and RNA-Seq data on the SRA. So far I believe I have been able to query specific samples with both WGS and RNA-Seq experiments, however a specific sample, provided by the sample_accession, is not exactly what I'm looking for.

For example: I'm interested in finding human data in which one human was used to derive WGS data, and several tissues from that same human were used to derive RNA-Seq data.

Is there any easy way to accomplish this using SQL and/or R?

So far, this is my approach to identify samples that have both WGS and RNA-Seq data, using the local database, SRAmetadb.sqlite:

con <- dbConnect(SQLite(),'SRAmetadb.sqlite')
query <- dbGetQuery(con,
                    paste(
                          "SELECT
                            sample.sample_accession,
                            sample.scientific_name,
                            experiment.experiment_accession,
                            experiment.library_strategy
                          FROM sample
                          JOIN experiment ON
                            sample.sample_accession = experiment.sample_accession
                          WHERE experiment.library_strategy in ('WGS','RNA-Seq')
                          GROUP by sample.sample_accession
                          HAVING COUNT(DISTINCT experiment.library_strategy) = 2"
                        )
                    )

With this approach, I can see query contains 181 human samples that have at least one WGS experiment and one RNA-Seq experiment. That's great, but I feel I must be missing out on data that came from different samples but the same individuals.


texts: Does our immune system react on all bacteria?

texts:
In our body we carry a lot of bacteria. Some of them are bad for our health, but others are beneficial. For example bacteria may protect us against other pathogenic bacteria.

But is our immune system reacting to all bacteria, i.e. the good and the bad, or does it selectively target the bad? If yes, how does it differentiate between beneficial and pathogenic bacteria?


texts: Double mutant analysis with null mutants

texts:
My professor was talking about double mutant analysis with null mutants, and how double mutant analysis won't work with hypomorphs.  I really don't understand the concept of double mutant analysis.

He was talking about pathways - if A and B are in the same pathway, then you would mutate A and he said something about the phenotype being identical.  If A and B are in different pathways, you could mutate both of them and there would be a "stronger" phenotype.

He also said it would only work with null mutants, not with hypomorphs, because with hypomorphs some of the pathway would still be active, not completely shut off.

I really don't understand any of this - what a double mutant is, the whole pathway thing, why the phenotype is "identical" or "stronger", or why you use hypomorphs.  I would really appreciate a rundown on the idea of double mutant analysis because my professor's explanation was so unclear.  Thanks in advance.


texts: Are spinal nerves myelinated and unmyelinated at the same time?

texts:
I was trying to answer this question when I remembered that the somatic axon is myelinated, while both sympathetic and parasympathetic preganglionic axons are also myelinated. Are they only myelinated or are they both myelinated and unmyelinated? Thanks
Edit:
This is a question from an old lecture quiz (previous year) and unfortunately I do not have the answers for the questions. The wording of the question was

Spinal Nerves are
a.) myelinated
b.) unmyelinated
c.) answers a and b
d) none of the above"


texts:
Could someone please identify this mushroom?
Found in a garden situated in a mild Western European country.


texts: Are small CO₂ concentrations devastating to certain cognitive tasks?

texts:
A new study shows strong effects of what should be a negligible CO2 concentration.

The paper "Is CO2 an Indoor Pollutant? Direct Effects of Low-to-Moderate CO2 Concentrations on Human Decision-Making Performance" exposed people to three levels of CO2: 600, 1000, and 2500 ppm while keeping constant other factors such as ventilation, humidity, temperature, and indoor pollutant concentration. Of course, the participants didn't know how much CO2 was in the air.

At the 2500 ppm level, most cognitive performance measures were temporally reduced (they used the SMS management test). Some changes were drastic.

Since normal air is 400 ppm, 2500 ppm sounds like a lot. However, it is dwarfed by internal production. Humans exhale 50,000 ppm CO2 in the lungs, meaning that the lung air averages 25,000 ppm (as a rough approximation). The extra 2500 ppm is only a 10% increase in the average "atmosphere" that the blood is exposed to. Furthermore, people partially compensate increased P(CO2) with deeper ventilation (the effect takes much larger concentrations to be noticeable). Why would this extra 10% have such a strong effect?

Personally I am skeptical. This study has such high impact (millions of people's performance) that it needs replication. Maybe the hissing sound of the injector got people worried (more hissing at a higher concentration!). Maybe an experimenter (who knew the concentration) was watching the people and that subconsciously affected them.


texts: True or False: Vaccines are designed to protect against invaders that are encountered rarely, not all the time

texts:
I read the following statement in this article:

  Vaccines are designed to protect against invaders that are encountered
  rarely - not all the time

Is it true? If yes, why?


texts: How specific are Vitamin D promotors in the DNA?

texts: As far as I understand there are genes that get regulated by the amount of Vitamin D that comes in contact with DNA. How specific are those promoters? Are there promotors that for example only get activated by calcifediol but not by calcitriol or cholecalciferol?


texts: Can two protein secondary structures "overlap" in the PDB?

texts:
I have a technical question regarding the syntax in Protein Data Bank files.  In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:

HELIX    4   4 MET A 255  ILE A  265  1                                  11

SHEET    2   B 2 ILE A 253  MET A 255 -1  N  ILE A 253   O  ILE A 248

Now, as I understand the documentation, this means there is an alpha helix starting from residue "MET A 255" to the residue "ILE A  265".  There is also a beta strand from "ILE A 253" to "MET A 255".  We see that the alpha helix and beta strand share the residue "MET A 255".

The documentation describes these as:

"Name of the initial residue."
"Name of the terminal residue of the helix."

The wording suggests that the "initial" residue is included, but I'm unsure of whether or not the "terminal" residue would be included.

  Question:  Should I consider this residue as belonging to both the alpha helix and beta strand?  Or should I consider the "terminal" residue as not belonging to the secondary structure element?  (Or something else?)


texts: Are there terrestrial plants that thrive on sea water?

texts:
Given the existence of coastal deserts such as in the picture below, I was wondering whether terrestrial plants can survive on sea water alone? If yes, why then do coastal deserts exist, instead of being grown over with belts of such plants along the shores?

If terrestrial plants thriving on sea water do not exist, then why? Especially given that there are marine plants like kelp and sea grass?


texts: What is the mechanism of antiperistalsis that occurs during vomiting? Why the peristaltic waves normally don't propagate in anal to oral direction? Please give logical explanation with authentic sources. :)


texts:
I found this image on the Internet, which features an African youngster holding up an animal for sale to a potential customer sitting inside a car. It appears to be some sort of dried and disemboweled animal.

What is the identity of the animal?


texts:
My main question is this: when you interpret gram stain results, does the majority color determine if its pos or neg?

We've been given unknowns and now have to determine what the organism is. I'm having trouble interpreting gram staining results. As far morphology they are all cocci and (sort of) in clusters but (this is the confusing part) they are both purple and pink. I understand that purple indicates gram+ and pink is gram-, but there should be one genus of organism not two. So shouldn't there be only purple or only pink, but not both? Should I be looking for the "majority" color and using that to decide whether I have pos or neg? That is, if its mostly purple, does that mean pos, ...but if so, then why are there still pink cocci on the slide?

I also understand why gram-pos appear purple, --that the crystal violet-iodine complex is retained due to thicker cell walls in gram-pos..... and thinner cell walls in gram-neg, so they are decolorized and appear the color of the counterstain.

Also I definitely did not see any rods in my slide, just cocci.


texts:
Doing some research into different forms of exercise and energy systems and I realized something odd about the way we talk about energy.

When we eat, we take on macronutrients that are broken down into their smaller components, but on it's face the assertion is that:

Fat = 9 Calories/gram
Carbs = 4 Calories/gram
Protein = 4 Calories/gram

However, when you look at the Krebs cycle, one acetyl sugar molecule generates 32 ATP molecules. Contrast that against Anaerobic metabolism and the Cori cycle, 1 sugar molecule generates 2 molecules (at a cost of 6 ATP in the liver later).

There are all sorts of fitness calculators out there, most of the calculations are based on the Assessment of Physical Activity and Energy Expenditure: An Overview of Objective Measures book, most of which was put together through measuring oxygen in put versus carbon dioxide output (in conjunction with heat radiation.  The clear problem with associating that with weight training and other anaerobic activities is that the other activities don't immediately create CO2 and don't immediately require O2. Some attempts have been made to make estimates based on lactate production in the blood stream, but I'm not confident in those results.

My question is, when there is anaerobic activity taking place, are we actually "burning" more base ingredients than we are exercising aerobically?

In other words, even if I'm only burning 100 Calories lifting weights, would I actually be burning the equivalent of 1,600 Calories based on the glucose I would have converted to ATP aerobially?


texts: Where should I start looking for an online gene library?

texts:
Is there an online library that includes all known genes in stored in their nucleotide form of all living organisms?

I'm presuming that such a database doesn't exist. So to kick of my search, how can I find a gene amongst all the other databases? Where is a good place to start looking for information about my gene given that it is a well studied sequence? The issue is that I have been provided with the sequence, but I just don't know what organism the sequence belongs to or what it codes for.


texts:
Can a Translocation of chromosomal parts occur between an autosome and an allosome?
If it occurs in between allosomes,what could be the effect of Robertsonian Translocation between an X and a Y chromosome considering the fact that the small product of a Robertsonian Translocation is mostly lost!??!


texts: Why pick just a single bacterial transformed colony

texts:
So after bacteria have been transformed to perhaps grow up a plasmid of interest, why pick only a single bacterial colony from a selective plate for further expansion?

I understand that this is to ensure that you are only working with a single genetic makeup because each separate colony is derived from only a single bacterium. What I can't rationalize is that if I am trying to expand and isolate a plasmid of interest, all colony expansions on a selective antibiotic plate should contain my plasmid. So is it really necessary to take only a single colony, because all colonies I pick should  be useful to me.


texts: What triggers the switch between aerobic and anaerobic respiration?

texts: I understand that when there is a shortage of oxygen cells convert the pyruvic acid from glycolysis to lactic acid to regenerate NAD+. What I don’t understand is how they switch to anaerobic metabolism occurs. Is there a certain chemical message that triggers this?


texts:
Why doesn't hair grow all over your face?

Surely hair on a face would have blocked the sun and kept it warm.

Or perhaps through natural selection we opted for hairless faces over hairy ones?


texts: Can DNA be used directly to determine the age of a mutation?

texts: I've studied that proteins found in a sample as biochemical evidences for evolution. Its variation in structure and configuration can be used to date the age when that mutation occured, effectively dating the sample. But can't DNA be directly used for the process? Proteins also require transcription and translation, increasing error. I think proteins make phylogenetic detection easier, but doesn't transcription and translation give more room for error?


texts: How does inbreeding depression cause infertility?

texts: My textbook states that repetitive self-pollination in the plants cause inbreeding depression which causes infertility thus plants develop techniques called outbreeding devices to encourage outcrossing. My question is how does inbreeding depression cause infertility?


texts: Effect on gene loss because of compartmentalisation of plastids/mitochondria/endosymbiont?

texts:
Considering the transfer of genes during endosymbiosis a gene transfer event (at least fundamentally, even if it's a special case), how does the fact that in this case the genes are inside a compartment, affect their gene loss, or incorporation into the host/recipient's genome (in context of gene transfer)?

I would imagine that the loss would be slower, recombination with other transferred genes less probable. But I can't find literature on the same. Any leads?


texts: Should there be a distance between the terminator of a protein with the promoter of another one?

texts: I want to do an overlap PCR to get the desired gene product I want. Can I put the promoter of the second protein just after the terminator of the first protein, or should there be some distance between them filled with random bases?!


texts: How do our sensory organs work automatically without our conscious effort?

texts: I wonder how our different sensory organs (e.g., eyes, nose, ears, etc.) work automatically without our conscious efforts or without our command. We don't have to tell our eyes how to see, our ears how to hear, etc. How does this work?


texts: Relationship between fatty acid chain and saponification number

texts: Why do long chain fatty acids have low saponification number? What is the relation of fatty acid chain( R)  with saponification number?


texts: Evolution from Mating types to different sexes

texts:
Imagine a lineage of multicellular organisms that had mating types and evolved their mating types into sexes. What are the possible mechanisms that might have brought this lineage to evolve sexes from mating types?

To my understanding of the definitions of sexes and mating types, the only diffenece between the two is that sexes imply gametes of different sizes. Is it correct?


texts: What percentage of RNA splicing happens during transcription?

texts:
Splicing can happen either during transcription, or directly afterwards.

I am reading about single-cell RNA seq, and according to this paper, they observed that 15–25% of reads contained unspliced intronic sequences.

Now assuming that the majority of reads from RNA seq will come from RNA that has finished being transcribed...

Does this suggest that 75-85% of all genes are spliced during transcription? In other words, are 80% of our genes fully mature (spliced) immediately following transcription?


texts: Difference between Category, Rank and Taxon

texts:
Is there any differences between the terms Category, Rank and Taxon or they all are same?

I remember an explanation which goes on like this:

Category and Rank are the same and are the categories of taxonomic heirarchy whereas taxons are the organisms present in those.

Is this correct?


texts: Is it possible to lose synapses over time?

texts:
I mean, what if a person is for a long time submitted to conditions in which his mental capacities are not explored, are the synapses undone? I've heard that drugs may cause such an effect, but what if the person is not submitted to drugs or any severe accident, may the forgetfulness be related to the simple lack of usage of a certain knowledge?

Is the lack of brain usage the main cause for Alzheimer's?


texts: Is there an instinct-driven body language for birds?

texts:
Over the last year or so, I've been observing house sparrows, because they are so prevalent in the northeast US cities. I noticed that a lot of sparrows, even in different cities seem to have very similar body language for communicating. I learned 3 expressions

Here's an example of a sparrow feeding their young. The young bird opens month and flickers its wings in what I can only describe as impatiently.

A sparrow swipes its beak along a surface at its feet - something food related?

A sparrow fluffs its feathers, turning into something like a tennis ball made of feathers.

I'm looking at this video of a sparrow raised in captivity, and it does 2 out of 3 expressions described here.

What interests me is if expressions like these are "local dialects" or universal, thus found across different geographies and times? for example, do sparrows in northeast US use the same expressions as sparrows in Australia? What about sparrows in the United Kingdom in the 1950s?


texts: Energy input during ATP Dephosphorylation?

texts:
What is the energy input needed to break the phosphor bond during ATP Dephosphorylation? How and when this will occur?

Many thanks for your answers.

Edit 1: I know how much free energy (∆G) is released with the hydrolysis of ATP, but I dont know how much energy is needed to start the hydrolysis of ATP.

Updated Question/s:
To break the phosphorus bond of ATP, must there be some input energy? What is the amount of this energy? Else how can break any bond of ATP without the supplement any energy?


texts: How to construct a sgRNA library with multiple samples?

texts:
I was wondering if anyone has already experience with constructing sgRNA libraries. We are interested in doing a knock-out experiment (loss-of-function) with 5 different conditions.
I have found this protocol from Joung et al.
In the protocol they have 10 different Fwd primer with no unique barcodes, only the eight Rev primers contains unique barcodes for different samples in KO.
Do I understand it correctly, that I can pool together only eight samples in one sequencing run with this protocol?
I would like to better understand the protocol of constructing an ngs library for sgRNA samples. If someone can point me to the right link/page?
Are there more complex library preparation kits out there which can deal with more samples?


texts: Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

texts:
Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis.

Of all the method listed on the Wikipedia page, the reference template method is my favourite as, it not only seems effective, but also was the idea that popped into my head before I did any study regarding this topic.

But, before I implement it in a project I am working on, I wanted to know if there are any common and obvious drawbacks/limitations that the bioinformatics industry faces quite often when using this scheme.


texts: Why it is important to vaccinate a human newborn within 24 hours since birth?

texts:
In Poland a newborn has to be vaccinated within 24 hours against hepatitis B and tuberculosis.

As I understand it is good to be vaccinated against both, I do not see the need to hurry so much.
Hepatitis B is transmitted sexually or by blood. The former vector is definitively unsuitable for a newborn, and the latter... Well, I do hope so far all Polish hospital adapted to Ignaz Sammelweis advice on antiseptics.
In case of BCG vaccine against tuberculosis (containing alive bacteria) there would be an additional risk if the newborn's immune system were in any way impaired which is unknown within first 24h. It is not that tuberculosis is common disease in Poland - is endemic (probably due to the obligatory vaccination indeed).

What possible biological benefits are there to vaccinate a newborn so early? Especially which of them prevail over possible risks of BCG vaccination?


texts: Why is there wide variation in genome size amongst groups of protists, insects, amphibians and plants, but less variation within groups of mammals and reptiles?


texts: Have there ever been as many mammals as there are now?

texts:
I apologize for the weird question, but based on a Google search it looks like this topic hasn't been discussed before. I'm hoping that enough information about population biology is stored in the fossil record to answer this question.

Humans have wiped out a lot of animals in a very short time, but I realized that mammals might be doing very well.

First off, humans are mammals, and there are 7.6 billion of us. That's quite a lot. I don't believe any other animal species of our body size has such a large population.

Second, humans have pets. A lot of them. And they're almost all mammals. Everywhere we go we take our cats and dogs with us. Many of them become feral and multiply prolifically.

Third, our livestock. With the growth of human civilization came the growth of meat consumption, which, naturally, meant a lot more cattle. I think I read somewhere that cattle are contributing more to global warming than cars, through burping.

Lastly, and probably most importantly: rodents. Cats chased us everywhere because rats chased us everywhere. They thrived on the grain we grew and their population exploded to the point that they became a global pest, and possibly humanity's greatest enemy.

So, my hypothesis is that there are more mammals now than ever before in the history of life. Not in terms of species diversity, but in terms of headcount. If this is true, it would be remarkable, since the rest of the Animal Kingdom is currently suffering through a mass extinction.


texts: Author statements (Readers) in biological nomenclature

texts:
I know that a binomial name may be followed by the name of the reader who has been the first to identify the species and to give it that binomial name.

It is not completely clear to me what the same of a botanist, zoologist etc. means if it is placed between parentheses, as in Blysmus compressus (L.) Panzer. Does it mean that Panzer gave that species the binomial name Blysmus compressus but it was Linnaeus that identified it as a species? I cannot find precise information on line, nor in my books...

Moreover, the pattern may get more complicated if we introduce the subspecies, for example another Cyperacea: Carex ferruginea Scop. subsp. macrostachys (Bertol.) Arcang.. It seems quite trivial to me that Scopoli (Scop.) identified and gave the species the name Carex ferruginea; as to the subspecies,  did Arcangeli (Arcang.) named it macrostachys after that Bertoloni (Bertol.) had identified it as a subspecies?

I thank any answerer very much.


texts: Did any warm blooded animals evolve back into cold blooded?

texts: Pretty much as title says - wondering if evolution can go from mammal back to reptile - either in theory or practice.


texts: Does mushroom likes low air pressure room?

texts: I know that mushroom likes high humidity and low temperature, but want to know that Does mushroom likes low air pressure room ? because of at low air pressure high humidity and low temperature can be achieved easily.


texts: What is the cause of singularity in phase response curve of human sleep and bright light?

texts:
I have no background in science as I am a computer programmer, but I am trying to get information on phase response curves, human sleep and exposure to bright light as I am trying to get to grips with a possible diagnosis of delayed sleep phase disorder.

The point marked phase delay is typically where someone would go to sleep and they would typically wake a couple hours after the peak marked phase advance. What is the physiological process that cause the move from delay to advance via the point marked singularity? In other words, why does light cause a delay initially but then cause an advance?


texts: Why is burn feeling 'slower' than touch?

texts:
When you touch a hot object you first feel the touch and only after a second you feel the burn too, and if you detach your skin from the object the burn feeling continues for few seconds. I remember i've read something about why this occurs (something like 'burn neurons are slower than touch ones') but it's just a faded memory.

So i'd really appreciate your answers.
Thanks in advance :).


texts:
More specifically, is nicotine in the concentrations that smokers receive when smoking cigarettes toxic? I know that in great enough concentrations it can be toxic (but then, so can just about anything else, including oxygen) and I know that in plants it is used as a defense against insects and can even be used as an insecticide. However, it has always been my understanding that nicotine is irrelevant as far as the harmful effects of smoking go.

I recently had a conversation with another biologist who had just quit smoking and had done quite a bit of research on the subject. He said that nicotine itself is in fact bad for you and, therefore, that tobacco-less alternatives to cigarettes (such as electronic cigarettes) are still harmful because of the nicotine alone.

Does anyone have any more information on this? Perhaps some references? Or, even better, a detailed explanation of the pathways involved? Again, I stress, not about nicotine's toxicity in general but about its harmful effects on vertebrates (preferably human) at the kinds of concentrations one could expect to ingest when smoking.


texts: I know that genetic diseases such as cystic fibrosis are often passed down through generations and are therefore classified as genetic disorders, but if a mutation occurs spontaneously, which for example leads to cancer, is this then classified as a genetic disorder?


texts: How are commercial steroid hormones produced?

texts:
Does someone know how oestrogens and androgens used for treatment are made? Is it with a GMO bacteria? Is it chemistry?

Thanks


texts:
From Black Jaguars in Belize?: A survey of melanism in the jaguar, panthera onca by John R. Meyer:

  There occurs in jaguars, as well as in leopards (Panthera pardus), a melanistic phase which has been much sought by zoos for exhibition purposes. This color phase was relatively difficult to acquire until the 1970's, by which time a few zoos, among them the Jacksonville Zoo, had begun to breed them regularly.

And likewise on the Wikipedia page for Black Panther:

  This "black cougar" was most likely a margay or ocelot, which are under 18 kg (40 lb) in weight, live in trees, and do have melanistic phases.

I don't understand this term "melanistic phase", which makes it sound like the jaguar has a period of time in which it is black.  However, it looks like it means something else, i.e., along the lines of What does phasing mean?, but I don't really understand that.

What does "melanistic phase" mean in regards to black jaguars?


texts: Is the quality of sleep dependent on sleep duration?

texts:
I've been facing this lately, where I will wake up in the middle of the night after sleeping for perhaps 2-3 hours and be wide awake, but when I go back to sleep, I wake up more tired than before.

Can anyone shed some light on this?


texts: What are stereological methods, similar to Saltykov Area Analysis, but specifically for parallel and equidistant histology slices?

texts: I've read Quantitative Stereology, by Underwood, and Saltykov Area Analysis works ok for my research, but I'm surprised there wasn't anything for equidistant parallel histology slices. Are there any methods specific for this case?


texts: Why do some proteins "use" a beta barrel structure instead of alpha helices in transmembrane space?

texts:
Most proteins are fixed in the membrane by alpha helices. But some use beta barrels.

Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil alpha helix structure could surely perform the same functions and given the vast number of proteins using alpha helices there might be some out there.

So my question is twofold:

Are these functions exclusive to beta barrels?
If so, what about alpha helices makes them unsuitable for those functions?


texts: $S_{0.5}$ vs $K_m$ values in enzyme kinetics

texts: What is the difference between $S_{0.5}$ values and $K_m$ values in enzyme kinetics?


texts: How can I keep HEK cells alive while expressing NMDA receptors?

texts:
I am trying to express functional NMDA receptors in HEK293 line cells for single channel recording experiments.

The HEK cells are maintained in the standard way (Thomas & Smart 2005) and transfected with NR1 and NR2x subunit cDNAs and also GFP, using either lipofectamine or calcium phosphate precipitation. GFP expression suggests successful transfection, but cells exhibiting green fluorescence are uniformly swollen and dead and it's more or less impossible to obtain a successful patch. Untransfected cells seem to remain perfectly viable.

On the basis that the toxicity might be a consequence of Ca2+ influx through open NMDARs, I've tried including a cocktail of blockers in the growth medium, including AP5, kynurenic acid and Mg2+, but the transfected cells continue to die.

Can anyone suggest anything else I should be doing to keep the cells alive? Or am I just on a hiding to nothing? Other researchers seem to have managed this (eg Medina et al 1995, Vicini et al 1998) and do not seem to be doing anything substantially different, so I'm a bit at a loss.


texts:
Please identify this bird? There are bright red feathers at the bottom of its tail. What do we call these feathers?

update:
Location is North India. Temperature is around 35° C.


texts: can we say that pumps are carriers that need ATP?

texts:
I know that pumps always use ATP , but i don't know what is the relationship between carriers and pumps .
are pumps a subdivision of carriers ?


texts: Does vitamin D affect melanin concentration?

texts: I am aware of the affect on vitamin D production by melanin (in sunlight) but I can not find any information regarding a reverse connection.


texts: If post transcriptional modification happens , how can a gene code for amino acids in a particular order?

texts:
Post transcription, introns are removed and exons are rearranged randomly. If that's the case (which it is according to the book EDEXCEL SNAB A2 topic 6) then shouldn't the protein produced be different every time? Shouldn't the order of amino acids be different? And if it is, doesn't that mean that the protein produced is different?

To quote : "When mRNA is produced, its introns are removed by spliceosomes and a different number of exons is put together at different orders which changes the sequence of amino acids in proteins."

Quote from the book:

  Genes contain sections that don't code for amino acids.

  These sections of DNA are called introns. All the bits that do code for amino acids are called exons.
  During transcription both introns and exons are copied into mRNA.
  The introns are then removed by a process called splicing -- introns are removed and exons joined forming mRNA strands. This takes
  place in the nucleus.
  The exons can be joined together in different orders to form different mRNA strands.

If this process happens,how can a gene code for a specific protein? This process means that exons are arranged differently, and this means that amino acids are arranged differently, and doesn't that mean that different proteins are going to be produced than the one coded for?


texts: What's the best way to measure/calculate the size of a light beam at the sample of a microscope?

texts:
I am using a microscope with an LED derived light through the epi-fluorescent port of a microscope.  I know that the "field of view" for a given objective is equal to the field number/magnification but I don't know that this is the actual area of illumination on the sample.  In my case, I am using a 40x objective with field number 26.5.

Secondly, if I were to use a pinhole filter between the light source and the back of the objective would this limit the area of illumination so long as the pinhole was smaller than the f.o.v. dimension?

I would be grateful for any answers, most of the information I can find on beam size at sample is related to spot size calculations of resolution.


texts: While preparing Jam we use sugar.Why? (can you elaborate in science language)

texts: Actually I was trying to find out the basic necessity of adding sugar in preparing jam.


texts: Is it true to say that the genome of trees includes or at least "encapsulates" the genome of mushrooms?

texts:
As a botany amateur, I know that mushrooms (which are of course studied in field of mycology and not botany) are dependent in trees or shrubs (and maybe also bushes) and that there are generally strong symbiotic relations between trees and mushrooms.

If mushrooms are strongly tree dependent and appear per tree species, is it true to say that the genome of trees includes the genome of mushrooms by some mechanism?


texts: What is the difference between a virus and virion.  Correct me if i am wrong but i think that one can simply say that " virus outside a cell is called a virion" and that this stage is used to go from one cell to another


texts: Is the Klein's bottle a good analogy to the relation between T-tubule and sarcolemma?

texts:
I am not quite seeing how the T-tubule and sarcolemma is connected. It says that the T-tubule is an "invagination" of the sarcolemma, which is sarcolemma folded from the inside to form a T-tubule

Can someone verify whether the following picture is a good presentation of this relationship?


texts: Is the efferent arteriole a pathway for filtrate through the nephron ?

texts: I am studying the urinary system. I have to identify what part of the nephron is not a pathway for filtrate. I believed the collecting duct is not a pathway for filtrate because once the filtrate enters this destination it is now referred to as urine, and no longer filtrate. I thought that inferred that it was not a pathway. However, the efferent may also be a strong answer because after glomerular filtration that small molecules that get filtered into the glomerular capsule are identified as filtrate. But the cell and proteins that do not get filtered are not, so not what are they referred to as non-filtered. However, later in the process of urine formation they become secreted back into the bloodstream through the peritubular network into the nephron at the distal convoluted tubule.


texts: What contributes to the variation of protein sequence across different species?

texts:
What contribute to the variation of protein sequence across different species (e.g. phenotype, environment, evolutionary pressure) and how do those factors contribute to the variation?

I have tried to search using google + google scholar but they generally show papers discussing why and how the protein conserved across species rather than why/how the protein diverged across species. Please help me on this and references/sources are very important and highly appreciated. Thank you!

An example to clarify my question. The gene CD81 is not identical among human, chimp, rat, chicken based on this identity matrix from ClustalW2. Why is CD81 not identical in all species? What factors cause the different in CD81s? How do those factors cause that (e.g. evolutionary pressure)?
#
#

Percent Identity  Matrix - created by Clustal2.1

#
#

 1: sp|P60033|CD81_HUMAN    100.00  100.00   93.22   82.55
 2: sp|P60034|CD81_PANTR    100.00  100.00   93.22   82.55
 3: sp|Q62745|CD81_RAT       93.22   93.22  100.00   82.55
 4: tr|F1NW06|F1NW06_CHICK   82.55   82.55   82.55  100.00


texts: Does food really give our bodies the energies that we have determined by burning them in the lab?

texts:
You are likely to have come across numbers like sugars 17kJ/g (4kcal/g) as the energy supposedly available to our bodies after eating. Yet these values have been determined using very artificial means, typically lighting up food with a red hot iron in a steel chamber at high oxygen pressure.

Many historic energy values have been proven wrong in the past. For example, salad leaves had zero calories in many historic energy tables before we realized that bacteria in our gut can break them down and we in turn can break down bacterial products, gaining back part of the chemical energy of the plant.

Are you aware of any research that has determined the energy value of different foods in more natural conditions, ideally in humans? I expect some calorie values to change from those determined by the bomb calorimeter, don't you?


texts: How is the acetone method different from QB buffer for extraction of plant protein?

texts:
I primarily work on animal tissue but I thought of running an SDS-PAGE for plant tissue just for fun. I searched for some protein extraction protocols online and I don't know which one to choose. One is the acetone trichloroacetic acid method where you use the precipitate (?) and chlorophyll stays in the supertanant while the other is a QB (full form?) extraction buffer which is similar to what we use in animal tissue (with a bit of DTT and PVP). Here, we use the supertanant after centrifugal ion and the chlorophyll stays in the loading sample(?). At least, this is what I gather. What are the functional differences and when to use which technique?

Since I'm planning to run a gel, which one would be the better technique?

Please correct me if wrong I'm new to this field

Protocols attached.


texts: Why are microtubules absent in and around the nucleus?

texts: I was going through fluorescence microscopy and found these four images. The top left corner shows the actin cytoskeleton (rhodamin phalloidin) and the bottom left image shows the microtubule cytoskeleton (Alexa 488). One thing I noticed is that the actin cytoskeleton is continuous throughout the cell as seen in the top right image (rhodamin phalloidin + DAPI composite), but in case of the microtubules, the nuclear position and microtubule localization seem to be mutually exclusive. I can't seem to figure out why this might be the case, and it definitely does not look like a coincidence.


texts: Is there a specific mechanism for the delivery of pain medication?

texts: For example, when one takes aspirin or ibuprofen does the chemical get dispersed to all pain receptor? My question really is, how does the chemical know where to target in the body? I figure wherever there is pain in the body that a certain signal is being produced; which possibly acts as a chaperone to direct the medication chemical where to bind and inhibit.


texts:
I saw this fish in an aquarium in a nearby house .I am not sure which species and sex this fish belongs to.

[![enter image description here][1]][1]

[1]: https://i.stack.imgur.com/oOAZx.jpg


texts: What is the evolutionary cause for various finger lengths?

texts: Why are the lengths the way they are with middle finger the longest?


texts: Does artificial heat (shower/tea) affect diurnal rhythms in humans?

texts:
I've been reading that over the course of the day, human body temperature follows diurnal rhythm with the lowest body temperature observed some time close to the middle of the sleep episode, while the peak body temperature is observed some time close to sunset.
Circadian rhythm on Wikipedia

I'm interested if humans have internal organ systems or brain "sensors" that "read" the body temperature as a part of synchronizing their own internal circadian clock to the master clock of the human body.

If there are indeed such sensors, then I'm interested if they can be thrown "off track" by artificial heat sources, like hot food, drinks or showers.


texts: What is the role of glucose in plasmid isolation?

texts: My understanding is that glucose is used in the resuspension solution to prevent cells from bursting by maintaining the appropriate osmotic pressure. Why do we even bother doing this? The cells are going to be lysed with the addition of the SDS+NaOH, and we have EDTA in the resuspension solution to chelate Mg, thus inactivating nucleases.


texts: Are four-leaf clovers mutations, developmental errors, or something more complicated?

texts:
What causes about 1 in 10,000 clovers to have four instead of three leaves? Will progeny(?) grown from its flower's seeds have a higher probability than that of also having four leaves?

From the Wired article The Mysterious Genetics of the Four-Leaf Clover

  A clover’s lucky fourth leaf is presumably specified in its DNA. But the clover genome is surprisingly complicated, and finding the genes responsible—and under what conditions—for the four-leaf mutation is a still-unsolved biological puzzle.

From the Wikipedia's Four-leaf clover: Cause  (emphasis mine):

  It is debated whether the fourth leaf is caused genetically or environmentally. Its relative rarity (1 in 10,000 clovers[ref]) suggests a possible recessive gene appearing at a low frequency. Alternatively, four-leaf clovers could be caused by somatic mutation or a developmental error of environmental causes. They could also be caused by the interaction of several genes that happen to segregate in the individual plant. It is possible all four explanations could apply to individual cases. This means that multiple four-leaf clovers could be found in the same clover plant.[citation needed] (emphasis added)


texts: Is it possible for an immune host to be reinfected and show symptom before swift recovery?

texts:
For example, let's say the pathogen is a virus, and the host was infected once but recovered purely on its own and thus retained a highly effective adapted immunity.
However, if we IV inject the the host with an overwhelming dose of virus, is it possible to infect some cells, cause some cell death before the immunity taking over and the host recovery? Is it possible to completely overwhelm the immune system and kill the host anyway?


texts: Do unique communities of bacteria form inside water storage in plants?

texts:
I assume that plants, like animals, have an ability to fight off bacteria that invade their cells (support: here and here.

However, water often harbors quite a bit of bacteria in even unsuspecting locations (e.g., see here).

Moreover, plants store a lot of water in their vacuoles.

I was wondering, whether the water stored in plant cells tends to harbor bacteria...

If so, are the bacterial communities in such water-storage organelles unique to plant vacuoles or do bacteria get transferred with the water as it moves through the plant?


texts: How much DNA does a species lose after post-polyploidization genome downsizing?

texts: After whole genome duplication, diploidization takes place, right? A lot of changings in gene organization and expression involving genetic and epigenetic mechanisms (translocations, transpositions, deletion and / or insertion of sequences, additive or non-additive gene action, transposon activation, gene repression or activation, subfunctionalization, neofunctionalization and so on) cause the genome to shrink a little bit before the species karyotype stabilizes and establishes. But how much DNA, in average, is gone in such process? I guess I have read somewhere that the elimination of redundant repetitive DNA families, causes polyploidization to result in a DNA increase of about 1.5x and not doubling. Is it true? I really would like to have some references on this information or similar.. I did look for, but I couldn't find


texts: Found this on a nature walk in the town of Lincoln, MA, USA. Is this edible? I believe it is a type of fungus.


texts: I would like to learn how this plant is called. It grew together with the beans I had planted. The body of the plant grew overnight while the leaves took a couple of days to develop. I decided to keep it in a small pot I had laying around to see if it will develop any further....


texts:
I heard a friend say:

  I'm not drinking coffee this week. My body can only process the caffeine if I run at least 15km a week.

I found this claim fascinating - that exercise temporarily increases the caffeine tolerance of the body.

Caffeine side effects include:

Sleeplessness
Additional grogginess when waking up
Withdrawal headaches
Decreased empathy
A decreased ability to listen to orally spoken detail
A decreased ability to calmly think

My question is: Is there any evidence to suggest that exercise reduces the side effects of caffeine?


texts: How to filter the PBD databank for "single-domain proteins with full length 3D-structures solved"

texts: I am trying to reproduce a machine learning model that has been developed here. As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a background in biology, I am not sure how to filter the PDB databank for these kind of proteins. Any help would be appreciated.


texts: How are the correct tRNAs transported to the ribosome?

texts:
I have been trying to understand how the tRNA transporting the correct amino acid required by the ribosome reaches the ribosome. The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombard the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.

I can not imagine any other mechanism in the cell's cytoplasm that will somehow filter or push the correct tRNA+amino acid and move it towards the ribosome that needs it.

How do we explain this mystery?


texts: Are ribosomes assembled in rough ER and Golgi body, or in the nucleolus?

texts: I mean all the components, such as ribosomal RNA (rRNA) are synthesized in the nucleolus, but is the whole ribosome structure assembled in the nucleolus or is it also done in the rough endoplasmic reticulum and Golgi apparatus?


texts:
From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) :

  Both bacterial and eucaryotic tRNAs are typically synthesized as
  larger precursor tRNAs, and these are then trimmed to produce the
  mature tRNA. In addition, some tRNA precursors (from both bacteria and
  eucaryotes) contain introns that must be spliced out.

What's the difference between the two statements (and between trimming and splicing) ?


texts: Why is chlorophyll green? Isn't there a more energetically favorable color?

texts: Chlorophyll being green means it absorbs light in the red and blue area of the spectrum. Isn't this the high and low energy light? Wouldn't plants get more energy if they absorbed light in the green area of the spectrum instead of the red one?


texts:
The egg is from a dog's feces and it's a image of 400x.
I don't know the exact size but I think it might be Ancylostoma caninum (or Ancylostoma spp.)
Can anyone help with the identification?


texts: Why is statistical mechanics relevant to RNA and protein folding?

texts:
This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding environment (so basically a many body problem). So I don't understand how statistical mechanics, such as Boltzmann's law, come to play.

To my knowledge statistical mechanics and thermodynamics exist when we have an ensemble of particle such as in a liquid or a gas. So what is this ensemble for the RNA or protein folding problem?


texts: What is this New Zealand insect and what is it in?

texts:
What kind of insect is this?

Found in Early September at Jubilee Park, Dunedin, New Zealand. It was suspended from a silk thread (quite long, a few meters) to a tree above. It was climbing the thread, balling the thread as it went up. It looks like a caterpillar. What species is this and what is it inside of?


texts: Does osmosis occur when we have two different substances?

texts:
Assume that we have a semi-permeable membrane with water on both sides. First, straightforward, case: On the right side, we have a concentration of the substance A, and on the left side, we have pure water. Obvious effect: water flows from left to right.

Now, imagine we have a second case. We have the same membrane, and a water solution of A to the right. To the left, we have a water solution of a different substance, let's call it B. Now, what happens? I can imagine a few possibilities:

the system behaves exactly as in the first case, because the substances have no influence on each other
the system behaves as if it was a solution of A on both sides, with water flowing in the direction of higher concentration (because it only matters if there is something dispersed between the water molecules, but it does not matter what)
some interesting cross-influence effect happens
either one of the three things above can happen, depending on the particular combination of substances A and B

Which one is the true effect? What happens, and why?

If you need an example of the actual substances, let B be thiamine and A be plain sodium chloride, but I am interested in the general case.


texts:
I am interested in (rapid) polymerization or (rapid) long mollecule synthesishappening in the intracellular space.

Clearly protein synthesis or DNA/RNA synthesis are examples of elongation of molecules, but these are relatively slow.

I wonder if someone can suggest examples of polymerization processes that happen at a much faster pace, for example one monomer added to the mollecule every millisecond, or every few milliseconds.

The underlying question is: what is the fastest example of long-molecule elongation inside the cell? At physiologically viable concentrations, what is the fastest monomer addition process that we could find?


texts:
Most times when I hear a screech (such as moving a sharp object on a chalkboard thereby causing such unpleasant noise), my body twitches. There are also other unpleasant sounds that causes the twitching, but whenever it sounds only my dad, my brother and I that feels it, but my two sisters and my mum says they don't feel anything. My question is:

Is there any scientific term for this feeling?

Is it hereditary?

What happens in the body or brain when the sound is produced?


texts: Can someone help me identify this larva?

texts: I found this creature in my toilet bowl and very curious as to what it is. The main reason is I want to make sure this wasn't a parasite living in me.  Everything I've researched tells me this is some sort of fly larva, possibly a fungus gnat larva or a drain fly larva.  The fact that it has no long hairy like things makes me think it is not a pet flea larva.  This was in Southern California and it was almost exactly 1cm long.  Any help is greatly appreciated!


texts: Effective population size when the population sizes varies from season to season

texts:
Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in winter for example. In such case, the effective population size $N_e$ can be calculated by:

$$N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}$$

where $n$ is the number of generation per year (4 in my example) and each $N_i$ correspond to the population size in one season.

My question

Can you please provide an explanation of why this formula (based on the harmonic mean) holds true to define the effective population size?

source


texts: Reasoning for Stomatal Distribution Between Monocot and Dicot

texts:
When you compare the stomatal arrangement of bean and corn plants under a microscope, you notice that the corn's stomata arrangement is much more organized and linear then the beans. I am wondering whether there is an evolutionary explanation for why that developed?

One thing to note is that the morphologies of the epithelial tissue cells are very different, so maybe it is a natural consequence of that?


texts: When a human dreams does the brain activate the cones and rods in the eyes creating the images we see in dreams?


texts: What are the differences among food poisoning, gastroenetritis and diarrhoea?

texts: I have now studied a major chunk of my microbiology course without understanding the basic difference between the three. The terminologies seem to be confusing. Is it a necessity for food poisoning to be cause by bacterial toxins? My texts include Shigella, which causes dysentery under food poisoning. What are the operational definitions for them? Is food poisoning more of an epidemiological term? I understand that they aren't clear cut identities and there is significant overlap. But could someone please help out?


texts: Is genetic drift necessarily deleterious?

texts:
I read that genetic drift is random variation in the relative allele frequencies of a population.

This question however seems to pin genetic drift down to increasing deleterious allele frequencies. Is the answer to this question correct? I don't think that increase of a deleterious allele necessarily indicates that genetic drift is operating; it suggests genetic drift, because one would think that such alleles should decrease in frequency rather than increase, but random chance in a large population can also increase the frequency of deleterious alleles.


texts:
How common is complete heterochromia? (One iris is a different color from the other)

Are there any statistics available for this? If no, why not?


texts: Why would a python go after such large prey?

texts:
I read that most Pythons would go for smaller prey, around the size of a house cat, but that larger species enjoy crocodiles, deer and even a bit of antelope for dinner. But why?

Now, I realise that evolution is ongoing, and that even in the year infinity evolution can't be expected to result in any subjective measure of "perfection". But, even so, it seems odd to me that this behaviour could have survived the eons.

Perhaps I'm misunderstanding the animal's physiology and it's more mobile in this state than I expect, but isn't this animal utterly defenceless for the next couple of weeks while it digests its tasty snack? Couldn't something else now come along, rip open the snake, steal its crocodile then leave the snake for dead, all without encountering much in the way of effective resistance?

One possible answer I thought of was that other animals may not much like the taste of half-digested crocodile. Conceivably, one could stalk the snake waiting for it to start swallowing the croc, then grab it while the food is still relatively fresh. But I doubt any animal that's not already substantially stronger than the snake would feel too comfortable stalking it in the first place. Is that enough to explain why Pythons have gotten into the habit of apparently making themselves sitting ducks for protracted periods of time rather than simply eating less more often?


texts: Perhaps this is a tropical wasp. Can you identify it? Is it artificial?