texts:
Earlier today, I undertook an exam which featured a question regarding the stickiness of mucus in a person diagnosed with CF's. We had to explain why they had stickier mucus than a 'normal' person, given that CF changes the protein channels used for chloride ions to move through osmosis. This confused me, becuase I thought osmosis was through a permeable membrane, and active transport used a protein channel. I have googled it and I have been proved neither wrong nor right.

Basically, I want to know if osmosis requires or uses a protein channel, or the exam board wrote the question wrong and should have put active transport instead.

(Sorry for the waffle, I just felt some clarification is needed)


texts: How many diseases can be linked to disruption in the microbiome of a human?

texts: I was listing to the radio and heard recent research found a link between children and higher cases of asthma when certain bacteria are missing from the microbiome. How many other diseases can be linked to a disrupted microbiome and are there ways in repopulating missing bacteria?


texts: Can both the overlapping genes (in opposite strands) produce proteins?

texts:
I have recognized that both the forward and reverse transcripts from a genomic location code for protein products. Both do occur/express in the tissue of interest. In order to eliminate by chance probability, I have screened my entire list of genes and there are 6 different examples. I would appreciate if anyone having the knowledge about such exceptions could guide me further.

Is this phenomena of protein being coded from both directions (of a given genomic location) possible? Are there any known examples?


texts: What is a good multiple alignment of large genome sequences when working with limited hardware?

texts:
I need to align bacterial genomes (namely mycobacteria, over 4 Mb in length), and my choice would have been either 'muscle' or 'clustalW'; however these algorithms are too memory demanding for such long sequences thus I can't run the multiple alignment on my machine.

Is there any other program that I could use to align multiple bacterial sequences?


texts: Does the dissociation of serotonin receptors and their ligands really take hours?

texts:
If I understand the principle of neurotransmission correctly, then after binding to a receptor on the postsynaptic side, neurotransmitter molecules must be dissociated from the receptor and removed quickly from the synaptic cleft (see this book).

This article states that the off-rate $k_{\text{off}}$ for the 5HT3 receptor and some ligand is approximately $43 * 10^{-6} s^{-1}$. If we ignore the binding process for now and denote by $C$ the complex formed by 5HT3 and the ligand, we can describe the dissociation process by the following simple differential equation:
$$
\frac{dC}{dt} = -k_{\text{off}} * C
$$
(see Wikipedia).
Using the $k_{\text{off}}$ from above, we get that the half time of this dissociation process is $\frac{\ln{2}}{k_{\text{off}}} \approx 16116s \approx 4,5h $. A similar $k_{\text{off}}$ rate for all other kinds of 5HT receptors binding serotonin can be derived from the dissociation constants found in the Ki Database.

But wouldn't that mean that, when serotonin is released from the presynaptic axon terminal and the 5HT3 receptor binds it, not even half of the neurotransmitter molecules are dissociated from the receptor after more than 4 hours? That seems to clearly contradict the statement from the beginning of this post - so is something wrong with my calculations or does it really take that long? Or have I understood something completely wrong about the principle of neurotransmission?


texts: Cloning two fluorescent proteins with different promoters in the same plasmid?

texts:
I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform B. subtilis at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and Marston, 1999), because this plasmid can be used for homologous recombination at this specific locus.

Now the problem is, because of a few reasons (i.e., the locations of the restriction sites, keeping the spc resistance gene and deleting the current GFP gene), if I want to clone two genes into this plasmid, they will be very close to each other (~10bp). Will this be a problem either technically or biologically after transformation? I don't think that possible read-through will be bad, as I want one of the fluorescent proteins (pHluorin) to be continuously expressed. Maybe an option would be to clone the two genes in opposite directions?

This is the current genotype of the plasmid:

Ori amyE5' currentGFP Spc amyE3' bla


texts: What are the advantages of heterologous expression systems?

texts:
I am doing research in a lab and I am relatively new to wet lab work. Many experiments that people are doing in my lab include overexpressing a protein of interest from another species (e.g. mouse) into CHO cells via transfection. I have learnt that these are examples of heterologous expression systems.
I was wondering in general, what are the advantages of heterologous expression systems? I have read that you can use them to study the function of a protein in a well-defined, controllable environment. However, I was wondering what other benefits/uses are there to these kinds of experiments?
Any insights are appreciated.


texts: Do local potentials always precede action potential?

texts:
Do all stimuli change the membrane potential to a value lower than threshold potential first, and then by summating end up in an action potential?
How do voltage-gated ion channels detect this change in voltage and respond adequately by opening?


texts: Explanation of the ‘cherry red spot' in Tay Sachs disease

texts:
In Tay Sachs disease, a hallmark symptom is a cherry red spot in the macula of the eye surrounded by a halo of white.

I understand that the ganglion cells, which are higher in numbers around the macula rather than in the macula, accumulate gangliosides due to the hexosaminidase deficiency, and thus cause the surroundings of the macula to appear white, but I don’t understand why the macula is red.

It is said that in Tay Sachs disease, the macula is the only normal region of the eye, but isn’t the macula supposed to be yellow, as it is referred to as the yellow spot?

Moreover, I’ve read that the red color comes from the choroid blood vessels, but isn’t the choroid black? It contains blood vessels, yes, but it is pigmented. The hindmost layer of the retina also happens to be a pigmented epithelium. So what is the explanation of a cherry red spot?


texts: A strain of my hair has a grey spot in the middle, how is this possible? And why does it happen?

texts:
My hair is usually brown and black, I haven't dyed my hair for two years and if I had this would be strange. A strand of hair went from black(roots) grey (middle) then light brown(bottom).

How does hair change color along its length? And why does this happen?


texts: Problem on number of amino acids that an alien can use

texts:
A new life form discovered on a distant planet has a genetic code consisting of five unique nucleotides and only one stop codon. If each codon has four bases,what is the maximum number of unique amino acids this life form can use ?

I tried this and got 624 (Using permutation method 5×5×5×5 = 625). But the answer given was 3124. Please help.


texts: What makes DNA sequences most different/recognizable from a biological perspective?

texts:
We can pretty easily quantify the amount difference between two different strings/sequences of characters. For example, if we take the words trebuchet and trebucket, we can say they have a Levenshtein distance of 1 (only one character-edit's worth of difference).

From a linguistic perspective, that distance is very noticeable, whereas the difference between compliment and complement is much less so. Even though both pairs are only one edit apart (respectively), not all differences are equally distinguishable.

What is the biological equivalent of this when it comes to DNA binding proteins and RNAs? How do I identify which DNA sequences are more recognizably distinct from each other? For example, if we took a DNA binding protein that recognizes the sequence TGCCTCGAA, is it more likely to misrecognize AGCCTGGAA than TGCCAGGAA (or vice versa) as its target sequence?


texts: How do I find samples/patients in TCGA (the cancer genome atlas) that had radiation therapy?

texts:
I want to correlate the expression of a gene (for sample the KRAS gene) with survival and if the patient received radiation therapy using any suitable TCGA (the cancer genome atlas) dataset. However, I have so far been unable to figure out what patients have received radiation therapy.

Any suggestions?


texts: It’s about 2 1/2 inches long and had a little tail on the end. Also has short feelers that almost look like a moles.


texts: Creating a Phylogenetic tree using DNA sequences

texts:
I was wondering given DNA samples, how can we create a phylogenetic tree? I mean I don't even want to have actual DNA sequence. Can I generate small samples, like reads of a length 100 or 1000 of nucleotide chains and figure out how they are related.

Suppose we have two reads of DNA samples, for brevity let's have them really small like: AAAGGTCTTGA and ATAAAGTGTA. I can run the sequence alignment algorithm on the strings and I will get {"A", {"", "T"}, "AA", {"G", "A"}, "GT", {"C", "G"}, "T", {"TG",""}, "A"} So basically what alighns then where you have indels or substitutions. I can easily now write up a function that calculates how close are these two strings by giving positive weights for matches strong negative weights for indels, etc. Now I want to know if these two guys with really short DNA are related or no. What is the mathematical measure of relatedness? And after I do Multiple Sequence Alignments and get similar results how do I build a tree from it.


texts: Naively, I thought that germ cells are diploid (in diploid species like human/mouse at least). Then, germ cells undergo meiosis and become haploid. I thought this was the critical change that defined these derived cells being named gametes (spermatozoon/ovum) rather than germ cells. However, I read that while XX mammalian germ cells undergo meiosis during embryonic development, XY germ cells don't go through meiosis until well after birth (puberty). This would mean that female gametes arise over a decade before male ones in humans. Is there an accepted definition of when germ cells differentiate into gametes and the terminology?


texts: can a point mutation cause a frameshift?

texts:
During translation initiation, a tRNA loaded with Methonine binds to the small ribosomal subunit. Subsequently, a mRNA molecule, recognized by the 5 cap, binds to the small subunit, and the tRNA scans the mRNA molecule for the presence of AUG which is the start codon. A point mutation could result in the the sequence AUG to be present after the ribosome binding site, but upstream of the "true" start codon.

Question 1:Will translation start at the mutated site?

Question 2: Could the mutation result in a frameshift, with a truncated protein as a consequence?

I have not found much information about this. I did find one homepage, with lecture notes from a genetics course at University of New Mexico referring to this type of mutation as a start-gain mutation.

http://www.discoveryandinnovation.com/BIOL202/notes/lecture14.html

"Start gain. A start-gain mutation is a point mutation creating a new ATG start codon upstream of the original start translation site. If the new ATG is close enough to the original one (so that it is within the processed transcript and downstream of a ribosome-binding site) and in frame, it will be used to initiate translation, adding amino acids to the amino terminus of the original protein. It is also possible for a start-gain mutation to be out of frame, which will not affect translation of the original protein. In general, start-gain mutations have a low impact on gene function."

I have not come across the term start-gain mutation before, but it sounds like what I am describing.

Question 3: If the start-gain mutation is out of frame, why will it not affect translation of the original protein?

Question 4: It is my understanding that the start codon sets the reading frame, and not the bases prior to the start codon. If the bases prior to the start codon are also "read" in triples, which position in the mRNA transcript sets the reading frame?

Thanks


texts: How do t-lymphocytes become mature if thymus has lost its function?

texts: The development of t-lymphocytes are done by thymus and we also know that the thymus degenerates before puberty and we also know the maximum lifespan of WBC's is 15 days. So, how do t-lymphocytes become mature if thymus has lost his function?


texts: Effects of selection on effective population size

texts:
Background

The effective population size ($N_e$) is a central concept of evolutionary biology and is influenced by several parameters. For example: sex ratio bias affects $N_e$ $\left(N_e = \frac{4N_mN_f}{N_m+N_f}\right)$ and varying population size over time influences $N_e$ $\left(N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}\right)$. There is a post on how overlapping generations influences population size.

Question

Selection also influences the effective population size. Intuitively, I'd expect that the higher is the fitness variance, the lower is the effective population size as fewer individuals contribute to the next generation. Am I right? How (what is the mathematical formulation) does fitness variance influences the effective population size?


texts: What happens in our body when we get an electric shock?


texts: Which factors may affect a choice of an oviposition place in nocturnal moths?

texts:
Winter Moth (Operophtera brumata) is a small brachypterous (females have stunned wings - unable to fly) moth which places eggs on thick branches.

I would like to know which abiotic and biotic factors may play a role in selection of place for oviposition. Taking into account that level of humidity is probably the same on whole tree (and probably whole forest) and the branches are so thick that they are not distinguishionable from surrounding environment (and there is no accumulated heat to identify their orientation (south, north etc.)

What other factors may play a role?


texts:
This is for a mathematical research. I am building a model to identify severe dengue patients through the interaction of cytokines S1P,IL1b,TNFa,PAF and IL10.
For this I would like to know if there are any relationships among these cytokines. That is for example: when PAF increase S1P should decrease. or when IL10 increase Il1b too should increase likewise.
There are seperate articles on the individual effect of these cytokines but I couldn't find any that exhibit any kind of relationship among these cytokines.


texts: Why do some trees in California have dead brown leaves but also new green leaves?

texts:
It's Autumn 2015, and I just saw a tree that had mainly dead brown leaves but also some new small green leaves growing. Why didn't the tree just keep its old leaves? Does it think we are in spring already?

EDIT: To be clear, I had always thought that in autumn that all the leaves of a tree would fall off together, as a preparation for winter. It seems silly that the tree would then immediately grow some new leaves when it just decided to let all those previous leaves die. Why not just use that same energy to maintain those leaves?

I've taken some photos of the leaves and the trunk for help with identification.

More images of the tree can be seen at this Imgur link


texts: Which word is used to indicate that a vessel is "blood-filled" during a necropsy?

texts:
I'm translating a necropsy report, and one sentence says:

Синусоиды полнокровные. Портальные тракты сохранены, сосуды умеренно полнокровные.
The sinusoids are plethoric. The portal tracts are intact, with moderately plethoric blood vessels.

The meaning of the Russian word is "full of blood". There are three words in English: plethoric, congested, hyperemic. Which one is used more often in necropsy reports when describing the "blood-filledness" of blood vessels and tissues?
Per the comment below left by Bryan Krause: in my text, this feature, "full-bloodedness" of vessels, is clearly not pathological, because each of the several dozen animals has this "plethora of blood" in vessels in many instances across the document, and in the end the researchers come to the conclusion that the animals did not display any negative effects from the treatment.
I googled in Google Books using "congested vessels autopsy", "plethoric vessels autopsy" and "hyperemic vessels autopsy" and found all terms in use:


texts: Are there any studies of epigenetic difference between twins during their lifespan?

texts: Are there any studies of epigenetic difference between twins during their lifespan ? I ask because I wonder if there exist phases during lifespan, when environmental factors plays major role (expecially in early adulthood) - twins study should allow to distinguish between changes in epigenetic  profile caused by external factors and that from "inner dynamics" of organism.


texts: How can an albatross stay airborne for months?

texts:
Albatrosses, of the biological family Diomedeidae, are large seabirds allied to the procellariids, storm-petrels and diving-petrels in the order Procellariiformes. They range widely in the Southern Ocean and the North Pacific.

  Short tailed Albatross , Source: Wikipedia, DOR 16/09/2012

I read that albatrosses can stay airborne for up to a decade and that they can cycle brain activity between hemispheres. How do they do this feat, and how did they evolve this ability?

Possible points to consider:
immune system, predation, cycling solar output, weather, seasons...


texts: Is there a term for a procedure in which the chromatography column is washed with 20% alcohol

texts:
From a method description in a Russian document:

  After the chromatographic analysis is complete, the column is flushed with at least 2-3 volumes of water at a rate of 0.4 ml/min. The column is then mothballed (?) by washing it with at least 10-15 volumes of 20% alcohol at a rate slowly declining from 0.4 ml/min to 0 ml/min.

The word I translated as "mothballed" is konservirovat (консервировать колонку) in Russian. It has the general meaning of "preparing something for storage" (for instance, "preparing vegetables for storage by pickling").

In an effort to determine the correct terminology, I would like to know the reason why a chromatography column would be washed with 20% ethanol. Any recommendation on the standard biochemical terminology for this procedure, if it exists, would also be welcome.


texts: (Aquatic gastropod) Physae identification

texts:
I need help to identify a physa.
What are the identification keys to make the difference between:

 physa fontinalis,

physa marmorata

, physa acuta (syn. Physella acuta)

The difference that can been seen with the eyes, no microscope, and except their biotope? (As they are in my house, not in their biotope)

differences or identification criteriae? What are the right organs to check of the difference in eggs, etc.

There is a variability of color in snails, and a variability of sizes. One specimen in some conditions can be much bigger or smaller than the average, so it's very difficult to identify them.

Some aquatic naturalist here?

Important remark: I don't guarantee the pictures are accurate, the site posting the picture may have confused physae!

I got physae from a vendor, some have a pale body and a more yellowish or partially yellowish shell, some have the tip ot the antennae dark, and have a dark shell and a dark body. The vendor had them together, and it seems they interbreed, but I'm not sure if it's only one ssp or 2. I see nowhere color mutation of physae on the internet.


texts: Can compounds be predicted from Polyketide synthases gene clusters?

texts: I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this is largely what Warp Drive Bio is trying to do. How realistic is this technology?


texts: Overlapping genetic information in eukaryotes

texts:
In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do remember seeing quite a bit of variation in the direction of the overlapping genes (same vs different directions), the amount of overlap, and even the number of overlapping genes.

I know enough about gene prediction to take any computational predictions with a grain of salt--even those supported by transcript and peptide alignments. However, these cases have me thinking--does overlap of genetic information really occur in eukaryotes? I seem to remember learning (or hearing anecdotally) that it can happen in prokaryotes, and that seems to be understandable given the compactness of prokaryotic genomes. But can this happen in eukaryotes? Has this been studied, and are there cases that have been confirmed experimentally?


texts: Difference between Cary-Blair and Amies transport media for Staphylococcus and Streptococcus?

texts:
I normally use Amies medium, but I today heard that Cary-Blair is also possible.

When should you use Cary-Blair medium?


texts: Pasteurization and Bioavailability of Antioxidants in Beet Juice

texts: What are the effects of pasteurization on the antioxidants found in beet juice ? Does the process render most of the beneficial nutrients (betaine) useless and make them unable for the body to process as efficiently as it would with raw beet juice? Also, does the pasteurization process do this to most fruit and vegetable juices ? I appreciate any insight, I've seen a lot of conflicting reports and am curious of anyones thoughts. Thank you


texts: Why did the process of sleep evolve in many animals? What is its evolutionary advantage?

texts: The process of sleep seems to be very disadvantageous to an organism as it is extremely vulnerable to predation for several hours at a time. Why is sleep necessary in so many animals? What advantage did it give the individuals that evolved to have it as an adaptation? When and how did it likely occur in the evolutionary path of animals?


texts: How does low cysteine conditions affect pheomelanin production?

texts:
So we were studying this amino acid called cysteine. Specifically we were studying it's effect on melanin genesis.
Our teacher told us how excess of cysteine affects the melanin synthesis  by generating more pheomelanin. Low amount of cysteine promotes formation of eumelanin.
 He told us that if the concentration of cysteine is increased in cells then the above reaction starts producing pheomelanin in brown/black skinned people. I searched it on net and it seems to be true.
The question is that if someone who has fair skin (produces more pheomelanin) is forced to live in low cysteine condition, then what happens? Eumelanin production should increase. His complexion must change. But it doesn't occur anywhere. Fair skinned people affected by malnutrition remain fairskinned. How is this possible? The pheomelanin production must stop since they aren't getting enough cysteine. Then how...?

He also told us that onions contain large amount of cysteine yet it can't be used since it is destroyed by stomach acids.


texts: why should someone study mRNAs instead of miRNAs as a biomarker from liquid cell-free biopsy like from exosomes? Is it wrong to do it? Does it offer you something different? Thank you in advance


texts:
I found a wasp in one of my coffee cups about 1 hour ago. There was barely any coffee left but it had managed to get itself pretty much drenched in coffee. I took it out. Put it on a piece of paper and put a pile of sugar next to it. It started eating but it was in a pretty bad state. I came back half an hour later to check up on it and it had fallen down on the floor. It's state seemed to have worsened. Went from walking around to lying still and moving it's limbs.

What kind of damage did it suffer from the coffee and how would I go about maximizing it's chances for survival?


texts: Why do COVID19 serology tests focus on the nucleocapsid while vaccine efforts focus on the spike?

texts:
When I look at the specification sheets for many of today's serology tests like the new Roche test or the Abbott test, they use a nucleocapsid antigen in the test, looking for anti-nucleocapsid antibodies. Given that these tests seem to have high sensitivities toward past infection, it suggests that recovered patients seem to reliably generate an immune response to the nucleocapsid.

At the same time, a lot of the research into vaccines focuses on the spike protein: Moderna is developing a vaccine based on an mRNA coding for the spike protein, CanSino and Oxford combine an adenovirus carrier with a SARS-CoV-2 spike, and so on. I'm having trouble finding any vaccines that target the nucleocapsid peptide.

I'm having trouble understanding this difference. Is it the case that recovered patients reliably produce antibodies to both viral components, but the nucleocapsid is better for testing due to cross-reactivity or other concerns? Or does a natural immune response target the nucleocapsid, while scientists think that the spike is a much better target because it's directly expressed on the cell surface or for some other reason?


texts: Is there a notion of RMSD for two different molecules?

texts: The (least) Root Mean Square Deviation is used for comparing different conformations of the same molecule. However one may be interested in comparing the conformations of two different molecules e.g. two proteins of different backbone lengths. So is there any method for comparing conformations different molecules such as a generalized RMDS?


texts: Can I breed the most productive hen by hatching eggs from the most productive ones?

texts:
Here is some hypothetical input:

I have a set of eggs.
I hatch these eggs and get chicken from them. Say, 100 hen that can lay eggs.
I have a hypothetical technology to track some parameters of each hen during their life - one of them is the moment a hen lays an egg.
I collect the data and find out which hen laid the largest amount of eggs during her productive period. I mark this one as the most productive.
I collect the eggs from the most productive hen in the generation.
GOTO 1.

Now, if I repeat this loop of death and life, say for 20 generations, hatching only eggs from the most productive hen, will it make next generations more productive and with each iteration or is it an oversimplified picture I have?

By performing this mental experiment I want to figure out if I can use it as a clear predictable factor influencing productivity of future generations.


texts: Found in my house in a Beltsville Maryland


texts: How much does capillary action contribute to blood flow to the human brain?

texts:
The BBC News Universal Wonders short video Why water is one of the weirdest things in the universe says after 01:50:

Water molecules can float upwards against the force of gravity. That’s because they love to stick to each other. They’re so good at it that they can actually pull each other up through tiny channels, such as the tiny blood vessels in your body. That’s how oxygen and nutrients reach the edges of your brain.
The same process, called capillary action, allows plants to move water from deep below the ground to nourish the leaves and branches that grow in the sunshine.

We learn about the importance of capillary action in water transport in plants, but I'd never heard that it was important for blood transport in Humans.
Question: How much does capillary action contribute to maintaining blood flow to the human brain? Is it a small effect compared to the difference between arterial and venous blood pressures, is it a substantial contributor?


texts: Non-coding DNA as a protection to deleterious mutations

texts:
We know that most part of our genome (at least 75 percent) is non-coding DNA. Can it be a way to protect the organism from mutations in important genes, such as the ones which control cellular cycle, as a mutations is much more likely to occur on these parts of the genome?

I've never been told if it could have such a function, and I thought about recently and wasn't able to find a clear answer.

So thanks in advance


texts: How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?

texts:
Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of degrading (or just inactivating) them.

This scenario seems more likely in eukaryotes, as they have capped 5' UTRs and a polyA tail at 3' UTRs that lend to RNA stability. How quickly and how much will an uncapped RNA degrade? What about the lack of a polyA tail?

Since prokaryotes lack these structures, I am restricted to the use of UTR regions in my particular instance. Is there any similar mechanism, whether in general or for specific proteins, that will allow me to exploit a UTR region for RNA inactivation in prokaryotes? Please keep in mind adding synthetic sequences to these UTR regions is certainly a possibility.


texts: Is there a known mosquito-specific lethal (for some relevant species of mosquitos) virus that you could safely (for the humans) put into the blood of living humans? Is it technically possible to engineer humans to produce such a virus?


texts: Identification of brown film inside a plastic water bottle

texts:
What could this film be at the base of a plastic water bottle?

Also observed one around the neck.


texts: In what does Genetic clustering and Cline sharpness differ?

texts: They are  both ways to measure divergence in species but I'm not understanding in what exactly the differ if both use hybrid zones and gene frequencies in the study.


texts: What are the units of Q10 (temperature sensitivity)?

texts:
$Q_{10}$ is the increase in a rate (e.g. activity of an enzyme) observed with a 10° temperature increase.

According to Wikipedia:

$$Q_{10}=\left(\frac{R_2}{R_1}\right)^{{10}/\left({T_2-T_1}\right)}$$

It is apparent that the units of $R$ (e.g. $mol/g/s$) cancel out, but what about the units of temperature? Does $Q_{10}$ have units? It seems the units would be "per 10 °C", but it is not clear how this comes from the referenced equation


texts: Does anyone know if the T7 phage promoter is efficient in mammalian systems?


texts:
Is dried grain considered dead or dormant botanically?

Related to a BH-SE question.


texts: How does Sodium Valproate cause neural plasticity

texts:
I have been reading a fascinating paper: Valproate reopens critical-period learning of absolute pitch

18 individuals were given Sodium Valproate (VPA) for a fortnight during which they trained on a pitch-training game. Results suggest that VPA reopens the plasticity window that normally closes by adolescence.

However, the paper seems to suggest that the exact mechanism of action is unknown.

  Valproic acid is believed to have multiple pharmacological actions,
  including acute blockade of GABA transaminase to enhance inhibitory
  function in epileptic seizures and enduring effects on gene
  transcription as an histone deacetlyase (HDAC) inhibitor (Monti et
  al., 2009). Of relevance here is the epigenetic actions of this drug,
  as enhancing inhibition does not reactivate brain plasticity in
  adulthood (Fagiolini and Hensch, 2000), but reopening chromatin
  structure does (Putignano et al., 2007). While systemic drug
  application is a rather coarse treatment, the effects may differ
  dramatically by individual cell type (TK Hensch and P Carninci,
  unpublished observations). VPA treatment mimics Nogo receptor deletion
  to reopen plasticity for acoustic preference in mice (Yang et al.,
  2012), suggesting a common pathway through the regulation of
  myelin-related signaling which normally closes critical period
  plasticity (McGee et al., 2005). Future work will address the cellular
  actions of VPA treatment in the process of reactivating critical
  periods. Future MRI studies will also be needed to establish whether
  HDAC inhibition by VPA induces hyperconnectivity of myelinated,
  long-range connections concurrent with renewed AP ability (Loui et
  al., 2011).

So it is saying that the standard use of VPA is to increase GABA levels (which keeps firing rate down -- it is used as an antiepileptic), however it also acts as an HDAC inhibitor, which means it causes unwrapping of chromatin and consequently increased mRNA transcription, maybe even transcription of genes that would normally be entirely deactivated in an adult.

So my guess is that some protein is getting produced that messages neurons to generate new axon/dendrite growth and/or new synaptic connections.

Can anyone clarify how VPA might accomplish plasticity?

EDIT (one month later): I have more detail, but I still can't quite make the connection. Here goes:

Neurites get wrapped by myelin/oligodendrocyte, which produces and exudes some of the chemical messagers {Nogo, OMgp, MAG}. The membrane surface of the neurite contains nogo 66 receptors (NgR-s) that get triggered by these messagers and inform the neuron to inhibit axon-growth. Somehow the 'HDAC inhibition' property of VPA is unwinding DNA enough to alter transcription rates of certain proteins, and one of these must be disabling the NgR.

But how is this happening?


texts: How sharp are the borders between Brodmann areas?

texts:
How does the border between two Brodmann areas look like in Nissl stains? How large is the transition zone where one cannot tell to which of the two areas a neuron belongs to? How many neurons are ambiguous compared to the number of unambiguous ones, roughly? 1%, 5%, 10%?

Is the inner connectivity of a Brodmann area greater than its connectivity with a neighbouring area across the border? Can this be seen in Nissl stains? Or is short-range inner-cortical connectivity somehow homogenuous over adjacent Brodmann areas?


texts: If hands are folded with both index fingers parallel, they will come closer and touch eventually?

texts:
I have a question out of curiosity. It is just something I found out/discovered:
if I fold my hands into each and let my two index fingers (see picture) be in parallel then they will eventually come closer to each other and touch.

How can this be explained?

Another thing I found out: if I fold my fingers on my left hand slightly and then with my right hand squeeze the wrist of my left hand (see picture), then the fingers of the left hand will fold more and more. Is this a coincidence of general?


texts: Why are there fewer ospreys in upper New England?

texts:
I have a book by the Audubon Society on building bird houses. In this book the chapter on ospreys shows their breeding range to include Canada and then a pocket around the Connecticut and New York coasts, but no upper New England (Massachusetts, New Hampshire and Maine).

This corresponds to my own experience. I have seen a lot of Osprey nests in Connecticut, but they seem much rarer in Massachusetts and New Hampshire. Why is this?

If the answer was that they prefer a warmer climate, then it makes no sense because they have a widespread breeding range in parts of Canada that are colder than New England.


texts: Why do I feel funny in my tummy when riding a virtual roller coaster?

texts:
I've ridden a virtual roller coaster on an Oculus Rift. I felt tension as I went up to the top, but more interestingly I actually felt my stomach drop when I went down the steep drop on the other side. Why can I feel this, when no forces are actually being applied to my stomach?

A bonus question: If you took someone that had never ridden a roller coaster, or even been exposed to rapid acceleration, and had them try a virtual one - would they feel the same stomach lurch as I did?


texts:
In the first step of glycolysis, the glucose ring is phosphorylated.
  Phosphorylation is the process of adding a phosphate group to a molecule derived from ATP. As a result, at this point in glycolysis,
  1 molecule of ATP has been consumed.

Is it the phosphate group, or the molecule, that is derived from ATP ?

http://www.sparknotes.com/biology/cellrespiration/glycolysis/section1.rhtml


texts: Anybody know of any sources/papers on wild animals identifying birds by their calls/sounds?

texts:
I'm doing a literature review about identifying birds, and was hoping to find some examples of animals being able to identify birds by sound (eg a mouse knowing the normal call of a sparrow is not the normal call of a sparrowhawk), but alas when I tried to search google for anything all I got was a bunch of pages showing humans how to identify bird noises, or apps to do the job for you, even making sure the word "animal" was included lead to the same results.

I vaguely remember watching a BBC show that had meerkats using a bird to alert them for dangers, but when I tried to find this online all I found were sources saying how it's actually a bird pretending to be a meerkat to score a free lunch, so if anyone knows any more about this I'd be grateful for any information.


texts:
Is light required for germination of every seed? If not, why don't some plants require it? Is there any difference in the quality and duration of light required ?

It would be interesting if someone could give both  physiological and evolutionary reasons.


texts: It was somewhat new to me that mushrooms usually aren't individual organisms, but are merely the visible bodies of a bunch of fungi living in the soil. I know that mushrooms emit spores to reproduce, but what has been bizarre to me is how fairy rings form. Why do the fruiting bodies arrange themselves in a more or less circular shape, as opposed to the random scattering one would expect from wind-borne spores?


texts: Do Schwann cells have Na+/K+ ATPase pump?

texts:
I was studying "Action Potential" and this question crossed my mind.
Another question is that, "Why does the action potential not occur in Schwann cells, or if it does, how does it occur?"
I know that many animal cell membranes have this pump, but I was not sure about this one.


texts: What is the opposite of a mutation (the regular state)?

texts: What is the term, if there is one, to describe the natural state of a gene? The one single word to describe it, just like mutation is the one single word do describe a deviation from that state.


texts:
The following question came up in my biology examination but I could not answer it:

  "What animal produces male gametes by mitosis?"

I know that some plants produce their gametes by mitosis in the gametophytes, but found no references to any animals doing so.


texts: Do the posterior legs of mosquito plays the role of antenna?

texts:
I have had this question for years and this stems from the observation that when I bring my hand close to a mosquito lying on some surface (e.g : wall) I see its posterior legs - which are in a strange posture then (going upwards - moving slightly toward my hand...
I wonder whether these legs have another role than standing ? Correct me if I'm wrong but in my humble knowledge some arachnids have the front pair of legs endowed with sensory function ,so is it a similar case with mosquitoes ?


texts: Does the complimentary base pairing of rRNA with itself play a role in its transcription?

texts: I have read that the termination of the transcription of mRNA involves a termination sequence in the form of a stem loop. As the structure of ribosomal RNA involves extensive internal base pairing, I wonder whether part of the mature rRNA provides the termination loop for its transcription.


texts: Book for artists' renderings of extinct species?

texts: I'm looking for a collection, in print or online, of pictures of ancient extinct species (i.e., imagined from fossil remains). Is there a good single resource for this? I'm interested in animals of all kinds, barring dinosaurs, and invertebrates. I'm not interested in recently extinct species but rather the very distant past.


texts: What is the best way to block cigarette smoke from the body?

texts:
Would it be better to hold your breath after smelling the presence of it or quickly inhale and exhale to get rid of it in your system(body)?

EDIT:
Changed from carbon monoxide to cigarette smoke.


texts: With respect to which METRIC is my DNA 99% similar to any other person's DNA?

texts:
I clarified my question, by editing the title. Using the comments  and links below, I have answered it myself:

The answer to my question is: The similarity is between 98.4%-99.9%, depending on which type of differences you include. The numbers relate to writing my and the other person's DNA as a long string, and compare differences (change of letter, missing/inserted letter). The most important differences seem to be SNPs (=difference in a letter in a gene-coding sequence) and account for 0.1% of difference between our 2 DNA's:

http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=110248
http://book.bionumbers.org/how-genetically-similar-are-two-random-people/

I have striked out the original question text, because it includes some motivation and interpretation, which seems false.

edit: It was suggested that the question is a duplicate to "Same" DNA vs genes but this might seem not to be the case, as this question just concerns the used metric (compare answer below).

99.9% vs 88%:

2 person's DNA is 99.9% the same (which goes down to 99% in some sources), e.g. http://book.bionumbers.org/how-genetically-similar-are-two-random-people/

Does this number include differences in copy-number variations and maybe other ?

On the other hand https://www.nature.com/scitable/content/global-variation-in-copy-number-in-the-13571 says that there may be up to 12% of some other differences (I am not sure what those differences mean).

Question:

I have been pouring through the internet and books, but have not yet understood to which metric this 99.9% number refers to? (I am a pure mathematician)

My hypothesis what it means:

If we look at a 1000 base-pair long snippet of the DNA of person A, then we will find this same snippet somewhere also in person B's DNA, with just one difference in one of the 1000 base pairs.

Now, if the latter is true, then this means that my DNA may still be significantly different than my neighbours, e.g. by containing a different number of repetitions in the non-coding DNA.

Ultimately, my DNA could be only, say, 2% similar instead of 99.9% (depending on the number of different repetitions), if we used as a metric the number of single base changes (including single deletions/insertions), we need to do to go from the DNA of person A to the DNA of person B (assuming we wrote down each other's DNA in one long string). Question 2: In fact, I would be quite interested to know how much the DNA of two people is similar using this last metric?


texts:
Recently I found out that the common houseplant Pothos (Epipremnum aureum) is toxic to cats and dogs due to the presence of "insoluble raphides." I have a lot of these plants around my house and my cat drinks water from the vase that they are in (I put drinking water into the vase that he always drinks from). He doesn't chew the Pothos leaves, he only drinks the water, is it still dangerous? I tried several times to give him water in an ordinary bowl, but he prefers the water that's associated with the Pothos plant, so I thought that maybe the roots of the plant excrete something nutritious (but I guess that's not the case, apparently...).
Is it harmful for an animal (cat) to drink water that has a Pothos plant immersed in it?
Also, my other cat does chew on the Pothos leaves (he goes crazy for them). Is it possible to have immunity and not be affected by the toxic chemicals? I read that chewing is supposed to provoke stomach irritation, but I would think that if the cat that chews the leaves suffered from irritation he wouldn't keep getting excited about chewing the leaves...
So what is going on? Many thanks!


texts: Do our belly buttons consist of scar tissue?

texts:
I read an interesting post on Facebook the other day saying that we all have a visible scar since birth - our belly button. This got me thinking (and research for me only found results regarding belly button piercing) is the belly button made up of scar tissue?

I seem to recall that there are some stem cells still within the umbilical cord (which is why doctors tell you to spend the money to have it saved (I think)) so I was wondering if scar tissue closed the hole left by our cut umbilical cord, or if the stem cells divided to produce normal skin tissue.


texts: A person sprayed with a dioxin, how long would it take for a dna change? Instant or over time? Would that person having children afterwards pass on any(if any) dna changes?


texts: Why do most plants reflect green and others other colors?

texts:
I have read that chlorophyll absorbs red and blue.

  As shown in detail in the absorption spectra, chlorophyll absorbs light in the red (long wavelength) and the blue (short wavelength) regions of the visible light spectrum. Green light is not absorbed but reflected, making the plant appear green. Chlorophyll is found in the chloroplasts of plants.

It did not mention what the difference in chlorophyll between a red leafed plant and a green plant?

Does chlorophyll only come in green?
 So what in chlorophyll determines if other colors than green are reflected in plants that are naturally red? If chlorophyll needed can only be green would not the color green and the red from a " pigment" look brown?

Japanese Blood Grass

Blue Selaginella

Solenostemon scutellarioides


texts: Does an organism have only certain antibodies for life?

texts:
Before birth, in the bone marrow millions of different B-cells are formed. These cells are differentiated and express different antibodies.

Are these the only B-cell types you will ever have? Or can the body generate new types of B cells, with new antibodies to deal with newly encountered threats?


texts: Is there a consensus on whether or not race exists on a biological level?

texts:
The most recent survey I could find was from 1985 which said that 16% of biologist disagreed that "[t]here are biological races in the species Homo sapiens."

I was wondering if there's been a change in this position.


texts: I read that the average cell will divide between 50-70 times before cell death. How, then, can human cells be constantly dividing?

texts:
Aren't those 2 statements contradicting each other?

See https://en.wikipedia.org/wiki/Hayflick_limit and e.g. http://book.bionumbers.org/how-quickly-do-different-cells-in-the-body-replace-themselves/.

Take stomach cells. If they divide every 2-9 days, doesn't that mean the stomach cells will all die in about a year (5 days x 70 division)?


texts: Photosynthetic Pigments vs. Chloroplasts

texts: What is the difference between Photosynthetic Pigments and Chloroplasts? I know plants have both but Prokaryotes (Bacteria and Archeae) only have the former.


texts: How to calculate extent of Sequence similarity

texts:
I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity.

I have a Problem Statement: we have a sensor (its like a magnetic compass and has a dial with twelve equal zones- 30 degrees each) that every second outputs where its pointing. The typical random output of the sensor may look like (for example):

  30 30 30 30 30 30 120 120 120 120 120 120 60 60 60 60 60 60 330 330 330 330 30 30 30 30 210 210 210 210 210 60 60 60 60 60 60 60 60 60 60 60 60 60 ……… etc.

We wanted to see if we can calculate a measure of similarity of two 4-minute sequence samples taken at different times during the day. (It would be great if we could state something like - the sequences are similar and there is a 1 in million (say) chance that we may be wrong.)


texts: Why don't myopic people see the world upside-down?

texts: I found this image while reading optical instruments in physics. If we look at the uncorrected rays, we see that the image they outline gets inverted. So why don't people with myopic vision see images as inverted representations?


texts: How do ants know where they are going without eyes?

texts: I know that ants have some sense of direction, but what is the physiology behind this sense?


texts: Why did many odd-toed ungulates become extinct?

texts: There were a lot of odd-toed ungulate animals in the ancient times but now just few of them survived. What is the reason for that?


texts: What is the expected number of children that need to be born for every possible point mutation to occur once?

texts:
I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write:

In the Paleolithic, with 100000 children per generation, it would have taken 8000 generations, or 160000 years, for each possible mutation to occur once.
Today, with more than a billion children per generation, every possible point mutation now appears about twenty times per generation, or almost yearly.

Using his probability, I get that you need 1 / (175 / (3 * 10^9)) (which is about 17 million children). But he writes that for the Paleolithic era, you need 10000 * 8000 = 80 million children! Can someone help me reason out how he got that number?
EDIT
My math was wrong :-) leaving up the og calculation. Here's the reference that he cites:
"Estimate of the Mutation Rate per Nucleotide in Humans" by Michael W. Nachman and Susan L. Crowell
In the abstract they write "The average mutation rate was estimated to be 2.5x10^-8 mutations per nucleotide
site or 175 mutations per diploid genome per generation."


texts: In splenectomized animals, where could red blood cells be released from, to explain an increased hematocrit after exercise or muscular contractions?


texts: This is one of the questions I wasn't exactly sure where to post. Basically, I want to make an X-Men parody, and for the part of Professor X I need to shave off my hair. Now I have a simple french crop, not really long or anything, but I was wondering if there's an estimate for how long it would take me to regrow my hair. Again, sorry if this is the wrong site, but I just thought "human body", so I guess it fits.


texts:
When HIV infects macrophages, it doesn't kill or destroy them immediately, but once it infects T-cells, they're destroyed. Why is that? As in why does it destroy T-cells and not macrophages or other cells.

  This process does not destroy the macrophages.
  Unlike macrophages, helper T cells are destroyed.


texts:
Biology is the closest I could find to botany on SE.  Grafting can not occur naturally and so if a fruit does not have seeds there is no way it could reproduce in nature.

That logic makes complete sense to me so I am wondering why seedless fruits claim to not be GMO?

Take for example, Satsuma oranges.

Were they somehow crossed like a mule?  See here.  And then grafted over and over again?

It appears they occur naturally and are then grafted.  See here.

So the deeper question is does grafting create a "clone" of the grafted organism?

And deeper yet, what defines genetically modified ( GMO ) from simple genetic variation?


texts: Millions of colors in the visible spectrum can be generated by mixing red, green and blue - the RGB color system. Is there a basic set of smells that, when mixed, can yield all, or nearly all detectable smells ?


texts: Is it caused by inbreeding of many generations within an isolated population?


texts:
To clarify, I'm not asking about the common properties of living organisms, such as reproducing and having a metabolism, etc. What I'm curious about is, what is the difference between organic molecules and actual living beings?

For example, if a person's heart stops beating, they are technically dead, but all the chemical compounds and molecules are still there.. I guess another approach to this question would be "If we bring together all the atoms of a living being in the same exact arrangement, would that new thing be alive?"


texts: Why is ATP used as a source of energy rather than glucose?

texts: I'm struggling to pinpoint a misconception, but I don't think I understand why ATP is used as an energy molecule instead of glucose. I understand that glucose is respired, oxidised or combusted and produces energy in the form of ATP so I guess what I don't understand is why glucose isn't hydrolysed (like ATP is) when energy is needed instead of having to convert its energy to ATP first.


texts: Book recomendation: cell cycle regulation

texts:
I aim to study cell cycle regulation, can some of you suggest a good book or website that systematically explains the topic.
It should include-

Detailed account of Cyclin and cdks involved in different stages of cell cycle
Spindle assembly checkpoint
DNA damage checkpoint
Special roles of Rb and p53 proteins in cell cycle regulation


texts:
How  forgetting things is helpful for the brain or the human body  biologically? This web page

After some moment of being rude, selfish, or weak, either we are able to put it behind us, or the person who suffered at the result of our imperfection moves on. The reason for this is our ability to forget about it. We forget not because we have an imperfect hippocampus (our brain’s memory organ); it's actually an evolved solution. The ability to lose information allows new information to come in that is more relevant, more pertinent to an ongoing reality. Forgetting allows us to update.

and this Huffington post article

According to a study in Nature, our awareness is limited to only three or four objects at any given time. To be able to think at your highest level, you therefore must be very efficient at filtering out all of the background noise: Your racing thoughts, the ringing phone, your neighbor’s barking dog, and the list goes on.
The Nature study found that when participants were asked to “hold in mind” certain objects while ignoring others, there are significant variations in how well each of us can keep irrelevant objects out of our awareness.
The researchers concluded that our memory capacity is therefore not simply about storage space, but rather “how efficiently irrelevant information is excluded from using up vital storage capacity.”

provide some backgrounds.


texts: Why is chloride ion classed as a cofactor for amylase rather than as a coenzyme?

texts:
I am provided with the two following statements and have to prove which is true and which is false.

$\ce{Cl-}$ acts as a coenzyme for amylase
$\ce{Zn^2+}$ acts as a prosthetic group for carbonic anhydrase

Now, I know that statement 2 is correct.

But, I'm confused why statement 1 is wrong.

I know $\ce{Cl-}$ is the cofactor for amylase, but why is it not its coenzyme?


texts: How long does it take for blood to travel from the lungs to the fingertips?

texts:
I've noticed that a pulse oximeter at my fingertip lags my breathing effort by a noticable amount.  I conclude that it takes some time for freshly oxygenated blood to travel from the lungs to the fingertips.

What lag time should I expect? Is there a chart or study which provides an estimate based on heart rate?

Is the lag greater for fingers, or toes? Presumably toes, being further from the heart and lungs, but perhaps the circulatory system has a larger carrying capacity and evens it out for the legs and feet.


texts: What is this beetle and what are the strange antennae for?

texts:
I found this wonderful creature in my yard (I live in the south of France) last night:

It was about 2-3cm long, with a hard carapace and wings. It also made loud hissing noises when agitated. I am curious as to what species this is, I'm quite surprised I'd never seen it before cause the beastie is quite large and last night I found it because of the noise it was making. It was upside down and hissing like a kettle.

More than the specific species' name, I am curious as to what the large antennae are for. Does their shape and size somehow increase the beetle's sensitivity to whatever stimuli these are atuned to?

Alan Boyd's comment below helped me along a bit. I seem to have found a close relative of the ten-lined June beetle (Polyphylla decemlineata) pictured below (image source)


texts: What could I call such nucleic-acid-Sequence? A sort of palindromic sequence? is there any term called mirror repeat?

texts:
5'... ATGCC|CCGTA ...3'

3'... TACGG|GGCAT ...5'

or say

5'... AAGT|TGAA ...3'

3'... TTCA|ACTT ...5'

or in generalised way; on each strand;

ABCDEF|FEDCBA

Is there any terminology for such-sort of repeat? A sort of palindromic sequence? A sort of inverted repeat? or mirror-repeat?  Does they really exist in nature?
(I could not yet found any helpful answer in web, including wikipedia.)

UPDATE

I asked this question because the term "palindromic sequence" is not like the situation in OP but "palindromic sequence"  is like this:

5'... ATGCTTTC|GAAAGCAT ...3'

3'... TACGAAAG|CTTTCGTA ...5'

or  in general;

5'... A B C D E F | M N P Q R S ...3'

3'... S R Q P N M | F E D C B A ...5'

Where on single-strand there is no symmetry when read (3'---> 5') and (5' ---> 3').

BUT I'm not telling like that. i'm telling about a situation where a reflection-symmetry present in each single strand when read (3'---> 5') or (5' ---> 3').

like

5'... A B C D E F | F E D C B A ...3'

3'... S R Q P N M | M N P Q R S ...5'

From no angle it is a palindromic-sequence because the symmetry is not between 2 opposite strand.

This question came to my mind when for first- time I'd taught about palindromic sequence. I was unable to "literally" match it with verbal palindromes like "AND MADAM DNA" . Rather it was looking to me like

I EAT CAKE

EKAC TAE I

So I thought, if really there exist any sequence literally like "AND MADAM DNA"... whatever if there is any terminology for it or not.

  One other Q/A site mentions about a term "mirror repeat", with exact same  situation as OP,  but gave no reference and further biological importance.

    http://www.answers.com/Q/Mirror_repeats_in_DNA

  Latest revision of Wikipedia also mentions a term mirror repeat and everted repeat, but no further explanation and hyperlink is given.

  Another result from google search.

    URL: https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg


texts: Are ITS1 and ITS2 good for divergence time estimation?

texts:
I had a discussion with a colleague who told me internal transcribed spacers (ITSs) are not good for divergence time estimation:

Because they are non protein coding genes;
Because they belong to a gene family.

However, I was not able to find anything in the literature about that. Can someone please enlighten me?


texts: Does pepsin enzyme digest other enzymes like other pepsin molecules

texts: Pepsin digests proteins, as we know, but can it digest other enzymes that are actually made up of proteins, like digesting other pepsin molecules?


texts: Epidermal layer and muscle wall of colon?

texts: First of all,I wanted to ask that whether epidermis is present in colon ? And if yes than how is muscle wall present with respect to epidermis. Can anyone give me a pic that has both the epidermis and muscle wall of colon.


texts: Are hybrid-species individuals considered to be of the same species as their parents?

texts:
This question arises given the definition of father and mother as seen in the Spanish dictionary composed by the Royal Spanish Academy. Basically it says that a father/mother is a man/woman or a male/female animal that has engendered/given birth to an individual of the same species (Spanish: "especie").

The Spanish word "especie" could also be translated here as "kind", but let's assume it refers to its zoological definition. That definition would be mostly true, but what about mules or ligers?

In the case of mules, they are the offspring of a male donkey and a female horse. A male donkey is considered to be of the species Equus asinus, while a female horse is an Equus caballus. The mule is an individual of the species Equus asinus♂ × Equus caballus♀, but what is exactly that? It is the set resulting from the addition of the two parent species, or is it a complete, new species? In other words, are mules considered to be of the same species of a donkey or a horse? Or what they all have in common is just the genus?


texts: How do similar environments on islands in close proximity result in allopatric speciation?

texts:
I would like to ask a question on the very classic example of allopatric speciation seen in the Galapagos finches. Adaptive radiation occurred because the finches flew from island to island, so there is gene flow, and the different environments on the different islands provide different selective pressures that causes relative fitness of the same species of birds to change. Over time, more drastic changes occur and speciation event occurred.

What I am doubtful of is the extent of different selection pressures on speciation. Given that the islands are so close to each other, wouldn't it be safe to assume that these islands generally have similar types of plants, similar types of insects, similar climate, similar predators. If gene flow between populations of finches can occur across islands, why can't it happen for the other biotic factors "contributing" to the islands' characteristics? So how can such similar conditions/environments provide selection pressure that is different enough to result in speciation?

Your clarifications are very much appreciated!


texts: In which order did the cells of the immune system evolve?

texts:
Thinking about how complex the interactions between different types of immune system cells (T-helpers, T-Killers, Phagocytes, B-Cells etc.) are, it's fascinating how they all combine to get the desired effect.

However, I assume that they didn't all evolve simultaneously!  Is there any way to tell which immune cell developed first or any theories to that effect?  Perhaps that question is too specific, in which case was it humoral or cell mediated immunity that developed first?

You may find this paper helpful - unfortunately I'm still months off a campus so can't access it.


texts:
A relative brought back a plant cutting from a trip to Erythrea. The plant was in a garden, so I do not know whether it is native to that area. What I do know is that is lives happily outdoors, both there and in a mediterranean climate, in well-drained nutrient-poor soils.

Below is a picture of a cutting I have been growing indoors in the USA. It looks like a succulent; the shape and the presence of soft hairs at the junction of the green protuberances is somewhat reminiscent of a cactus. This plant is thin and about 25cm/10in high, but the mother plant is thicker and is about 30-40cm high (and the fleshy protuberances are not as developed).

Any idea what plant this might be?


texts: What is inside IDL (intermediate density lipoproteïn)?

texts:
I am studying about the endogene lipidcycle in the human body and I know that VLDL (very low density lipoproteïn) is made in the liver and that it contains triglycerides and cholesterol from your food but also made in the body.

Next with that, I know that VLDL brings triglycerides to the adipose tissue (or fat tissue) and to the muscles with help of the LPL (lipoproteïnlipase) just as chylomicrons do.

Enclosed; VLDL will go over to IDL (intermediate density lipoproteïn).

But what is the definition then from IDL exactly?
Is IDL just a smaller lipoproteïn then VLDL and does it only contains a sort of 'leftover' of the triglycerides? Or does it also contains cholesterol?

And if VLDL brings the triglycerides to the muscles and fat tissue, does it only contains triglycerides then? Or does it also carry cholesterol with it? If yes, what happens with the cholesterol then?

Because my book is only telling me about the transport of triglycerides to the fat tissue and muscles, but in the beginning it also says that it carry's cholesterol, and a little further in my book it even tells it can also carry cholesterolesters from HDL...
It's getting confusing...

Hope somebody can tell me what is exactly in all the kinds of lipoproteïns, where the lipoproteïns are all made, and where the products they carry come from, and where they go to. Because my book is being very indistinct.


texts: Can you measure plasma glucose with a regular glucose meter?

texts:
I'm wondering if plasma glucose can be measured with a regular glucose meter and strips like this. I know these meters are normally used to measure whole blood glucose, but can they measure plasma glucose levels as well?

Thanks.


texts: Is there an existing database of mutation rates for mitochondrial loci?

texts:
I'm wondering if there exists a database of mutation rates (transitions and transversions) for both mitochondrial loci (such as cytochrome c oxidase subunit I (COI)).

Due to the use of COI as a DNA barcode to identify animal species, this gene has a relatively high mutation rate despite being quite conserved across major taxonomic groups. Thus, substitutions in COI are expected to become diagnostic of species much more rapidly (also because of the 4-fold lower effective population size compared to nuclear markers).

The reason I ask is because I am developing a simulation algorithm allowing a user to generate random DNA sequences under a specified nucleotide evolution model (e.g., Jukes-Cantor, Kimura-2-Parameter). I would like to be able to specify realistic mutation rates of transitions and transversions in order to closely mirror actual substitution rates in COI.

Any insight would be much appreciated


texts: If crocodiles are k-selected, why do they supposedly "not age," as in avoid senescence?

texts: I recently saw a few sources stating that Crocodiles do not biologically age, implying negligible senescence. Basically, a 70 year old crocodile is in the same physical/health condition as a 7 year old crocodile. However, crocodiles are K-selected, meaning that populations are generally close to their carrying capacity. If they do not exhibit natural senescence, isn't that evolutionarily disadvantageous, because the younger crocodiles with more slightly more fit genes will not necessarily replace the older generations, meaning that crocodile populations would adapt to environmental changes significantly slowly. Can someone please explain to me how this lack of senescence can apply for this type of species?


texts: Are the social-distancing measures implemented against SARS-CoV-2 also suppressing the spread of other viruses?

texts: With social-distancing measures being implemented in many countries I would expect other viruses, like the ones that cause seasonal flus, to have also a hard time propagating in these circumstances. Are there any estimates or research (epidemiological models) I can check, about the possibility we are winning by accident a war against many other less alarming viruses?


texts: Why are there nail growth differences  between humans and other mammals?

texts:
When a cat is growing, his nails are growing with him to some extent. A grown cat has a fixed nail length that is not extending.

By contrast, human finger nails just keep on growing, so we have to cut them to keep an aesthetically pleasing look.

Nature clearly has a mechanism to control nail growth.

What is the most probable reason as to why this is not implemented in humans?


texts: In this video https://www.youtube.com/watch?v=os98s9kBlOI it is demonstrated that a moose leg bone can support until nearly 10 tonne before break. Is there any similar demonstration on human femurs? How much weight a human femur can support vertically before it is crushed?


texts: Could fish safely "breathe" pure oxygen in their water?

texts: I've heard it said various times before that humans can't breathe pure oxygen, or at least not for very long, before it would kill us.  But during a discussion on Worldbuilding, the difference between air-breathing and water-breathing came up.  It made me wonder: what would happen to a fish if it had pure oxygen, rather than the ordinary gas mixture of air, dissolved in its water?  Would it be safe, or have the same oxygen toxicity problems as humans?


texts: When is the second polar body extruded from the egg nucleus?

texts: When does the second polar body gets expelled from the egg nucleus during oogenesis ? I know that it occurs after the entry of the sperm into the secondary oocyte but does it occur before the fertilization or in the period between the entry of the sperm and fertilization ?


texts: Why did isopropyl alcohol not work as a disinfectant for E. coli in this experiment?

texts:
I recently performed a lab to test different concentrations (20-99%) of isopropyl alcohol and its inhibition of E. coli growth. My control was an antibacterial disk, and what I did was I dabbed the disk in each concentration and put it on the agar with the E. coli. I dabbed it enough so it wasn't soaking wet but it still had some liquid.

Unfortunately, I had no results at all from the alcohol-soaked disked, but I know the experiment should work because the antibacterial disks for all Petri dishes worked.

I don't know why the alcohol did not work at all though, especially since it is proven to be effective as a disinfectant at least for E. coli.

If anyone has a link with this exact lab being tested, or something similar (isopropyl alcohol and effect on zone of inhibition in bacteria labs) that would be amazing.
Concentrations 20,30,40,50,60,70,80,99%
-Disk diffusion, I put the bacteria by streaking across the quadrants
-I dipped the disks until it was soaked then dabbed enough to make sure it wasn't dripping
-Negative control:sterile disk In the middle, positive control: antibacterial disk on quadrant A
-I was going to measure zone of inhibition but there was none produced for all 12 plates except for quadrant A containing the antibacterial disk.


texts: What is the minimum atmospheric pressure at which bees can live/thrive?

texts:
Bees are amazing little critters. (Gosh, they're cute.) But what if we colonize Mars and start terraforming it? At what point will bees (and other insects) be able to live/thrive in that environment?
Obviously, there need to reasonable conditions:

total atmospheric pressure
partial O2 pressure and general atmospheric composition
no toxins
flowers to pollinate and get nectar from
a wider ecosystem to thrive in

For now I'm just wondering: What atmospheric environment do bees need to live on Mars?

Perhaps we should give them little space suits?


texts: Does a plant have to be alive for its roots to prevent erosion?

texts:
One argument often given in favour of saving current and planting additional plants/saplings is the roots hold soil together and prevent soil erosion.

Unlike plants that may be uprooted, a large tree may only be chopped down; its roots continue to remain buried. Do these, now dead, roots continue to prevent soil erosion, or does the plant have to be alive and kicking?

My guess is the latter, perhaps because absorption of water possibly 'compresses' the soil over the root.


texts: How can Taenia solium (tapeworm) lay 35,000 eggs per proglottid?

texts: As far as I know TAENIA SOLIUM is an acoelomate which basically means that the space between the alimentary canal and the gut is completely filled [or] occupied by the mesoderm and they do not have primary body cavity as well as secondary body cavity then from where does the space comes in taenia to store that huge amount of eggs


texts: Why do only two sexes exist for animals?

texts: Why, from the natural selection point of view, do only two sexes exist for animals?


texts:
So, I was reading about aneuploidy and how a zygote with one extra or less chromosome usually would not survive to full term. I suppose this happens because aneuploidy leads to some kind of protein imbalance. So, in case of monosomy we would have a shortage of proteins, and in case of trisomy we would have an excess of proteins.

On the other hand, a conventional argument for having two copies of each gene is that, if one gene gets corrupted because of some kind of mutation, we still have another copy that produces the correct protein. So, in case of a recessive genetic disorder, the zygote can survive even with half the amount of protein.

My question is then, why can't monosomic aneuploidy be looked at the same way? Moreover, I read that monosomic aneuploidy is almost always fatal, while trisomic aneuploidy is sometimes tolarated.


texts: Why are the kidneys called metanephric? What does the term metanephric actually mean? I tried to search that on Google but couldn't find the exact meaning.


texts:
Can I use dry seed, wheat for example, in place of young leaves for isolation and purification of genomic DNA for PCR amplification?

The goal of my experiment is to validate a novel gene which is either absent or present at a particular chromosome.


texts: References concerning the relative population sizes of predator and prey

texts:
In an ecosystem, say there are two species in a predator-prey relationship. What is the most typical ratio of these species' population densities? For instance, it could be that for every fox, there are ten rabbits. Actually, the precise ratios are somewhat irrelevant; mostly I would like to know if we can say that the number of prey is generally larger than the number of predators.

I would like references to articles, textbooks, etc. that contain information about such ratios.

Note that this is aimed at the number of species within a single ecosystem. However, if this information is hard to quantify (perhaps because it is hard to define where an ecosystem ends), global populations could be used as an estimate.

Forgive me if this is ill-defined or trivial, I'm a physicist by training.

Thanks.


texts: What factors make a sequence evolve non-randomly?

texts:
On the wikipedia page about Fay and Wu's H, it talks about a non-randomly evolving sequence may be due to some selection acting or a selective sweep or population expanding/contracting. My questions about these factors that affect non-random sequence evolution are:

Does negative selection differ from a selective sweep because a sweep is a form of positive selection?
After a selective sweep, any rare mutations you see must have come after the selective sweep. Is it because they can't have come during it else they'd 'be diluted' by the positively selected alleles?
Population contraction can create a bottleneck, which makes all individuals come from a common ancestor. But how does population expansion make a sequence evolve non-randomly?


texts: How to differentiate between Bombus lapidarius and Bombus wurfleini?

texts: I am observing frequently different bumble bees in my garden (Austria prealpine-alpine region). One of them that I frequently saw is all black with red-orange abdomen (tail). From a very simple schematic poster I found I had concluded it would be Bombus lapidarius, but now reading a bit more on bumble bees I find it could as well be B. wurfleini. My question is now what would be the most obvious/simple way to discern between the two species?


texts: What roles do cyclooxygenase, lipoxygenase, and epoxygenase have in signal transduction?

texts: Besides oxidizing fatty acids to form prostglandins, leukotrienes, and epoxides, what other roles do cyclooxygenase, lipoxygenase, and epoxygenase have in signal transduction?


texts: Do desulfhydrase-catalysed reactions take place in animal cells?

texts:
It isn't a homework question. I'm just stuck with desulfhydrase reactions and am unable to find enough information in the usual places.
Any external source on this topic would be helpful.


texts: Is there any evidence for secondarily poikilothermic vertebrate?

texts: Is it possible that an endothermic physiology can evolve into an ectothermic (poikilothermic) physiology? I have a non-scientific gut feeling that it is irreversible. Whales and dolphins are evolved from land mammals, and they've remained warm blooded. While it doesn't give them any obvious advantage in the water, apparently they've compensated with massive amounts of body fat instead of devolving. If the ocean offers opportunity for mammals, then why haven't fish evolved to be warm blooded directly?


texts: How does cancerous tissue break down radioisotopes faster than normal tissues?

texts:
Apparently, many medical practitioners use radioisotopes to detect cancer in patients. From my textbook (McGraw Bio 12, pg. 10);

  Using a method called radioisotope tracing doctors can inject
  radioactive material into a patient and trace its movement in the
  body. For example, cancerous tissues in the body are characterized by
  a much higher level of activity than healthy tissues. Consequently,
  cancerous cells take in more glucose—a common cellular energy
  source—than healthy cells. Injecting a patient with radioactive
  glucose and then performing a positron emission tomography (PET) scan,
  such as the one shown in Figure 1.1, is one method to diagnose a
  cancerous tumour

Apparently, cancerous tissues break down radioisotopes at a much higher rate than normal tissues. But how?


texts:
I was reading Genetic Analysis (Sanders, Bowman) and saw the following figure summarizing the 1909 work of Herman Nilsson-Ehle in describing the genetic control of kernel color in wheat:

How did Nilsson-Ehle determine that the original pure-breeding parents were in fact homozygous for each allele?


texts: What determines the direction in which motor proteins go?

texts:
I know that kinesin motor proteins move towards the positive (beta) end of the microtubule, while dyenin motor proteins move towards the negative (alpha) end of the microtubule. However, because the microtubule is composed of repeating alpha and beta units in ABABABABAB fashion (as shown in the picture below), what causes motor proteins to move to the positive rather than the negative pole?

For example, if one "leg" of the kinesin is bound to a beta tubulin while the other leg is up and ready to bind again, what determines which alpha tubulin it binds to (since there is alpha in front and in back of the beta tubilin it is bound to)?


texts: aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

texts:
I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel.

I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about sensitivities of these recipes, and other advantages/disadvantages compering these two.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149902/

This article describes a recipe using aluminum sulfate.

http://onlinelibrary.wiley.com/doi/10.1002/elps.200305844/epdf

(NH4)2SO4 is used in this article.


texts: If DNA is the input, what is the output?

texts:
How does cells use the DNA inside them? I am looking on DNA as a strip of tape of Turing machine, but with machines its easy. I can read the tape and calculate the behavior of that machine. With cells its different we don't really understand the language of DNA.

So instead of trying to understand the language I was wandering if there are any particular behaviors of cells that we can associate to different "outputs" of the DNA tape.


texts: Can a chicken really be hatched outside of the egg?

texts:
This YouTube video (screenshots attached) claims to show Japanese schoolchildren breaking an egg into a kind of clingfilm "hammock in a cup", and then growing and hatching a chick from it in an incubator.

Is this really real?

My first immediate thought is, "If this can happen, why don't the eggs in my cupboard at home sometimes hatch? Why do I never see an embryo in my frying pan?"

Obviously the egg has to be fertilised, but depending upon where you get your eggs (like an "organic home farm" or something) this might happen.

If it's more a matter of temperature, how warm do the eggs have to be? For how long? (ie, Could a warm kitchen cupboard in a hot summer do it?)

What other biological requirements are there to make this work?


texts:
I have a question.
if you look at these two spectral diagrams (SPDs) from two different televisions that is calibrated to the same white point (D65) 6500K with a spectrometer.
The problem is that white still looks different to the eye here.
why does white look different is my question.

Television1
(pictures from avsforum)

Television2

A logical explanation would be great as i trying to figure out whats causing it.
is it the spectral power differences that causing it or is it the different distribution of the GREEN and RED with its more narrow peaks on television1 that causes it?
what i can see and what i understand is that Television1s spectral power will produce a more natural light as its more close to the warm light from an incandescent bulb.
Television2 reminds more of an typical LED lamp that we all know have a more harsh and poor light.


texts: Body size, what are the evolutionary trade-offs?

texts:
Background

Considering just the "Kingdom Animalia" branch of organisms. It is clear that bigger does not necessarily mean better - there is large variation in body size...

From the 94 µm long Tantulocarid arthropod (Stygotantulus stocki)

To the 25.5 m long Blue Whale (Balaenoptera musculus)

Questions

What trade-offs exist between having a particular body size (very large, very small) to other traits and factors?
Alternatively, what evolutionary/ecological advantages/disadvantages are there to having a large or small body size?

Thank you!


texts: How can I find a complete human genome file

texts:
I'm trying to figure out how I can download a file that represents the complete human DNA sequence. I don't care too much about the format – I'm able to write C++ code to parse it. FASTA seems like a simple format though. What I haven't figured out yet is where I can find a complete file – I have found what appear to be subsets of genes or other sequences or single chromosomes but aren't there 46 chromosomes to include or are some of those duplicates (i.e. 22 chromosomes + 2 sex chromosomes)?

On this page, I have found this list of files under "Human > Genome assembly: GRCh38" but it appears to be broken up by chromosome or something? If so, would I merge these? My goal is to display all the letters via projector onto a wall and I want to be able to point at it and tell someone, that's all the DNA for a human (not a subset). Also, to double check, it is a "genome assembly" I want right? By the way, I don't care about allele variants right now.

Please consider in your response that I am not familiar with much of the lingo, thank you.


texts:
In this guide i was reading for annotations, there is a diagram of chromosomes of D.mel, I am confused as to why the chromosomes are all attached to one another, is this picture taken in a certain stage of mitosis in which they are all condensed?

Original source
 (page 2).


texts: Mathematical relationship between membrane conductance and conduction velocity?

texts:
By what factor would the myelin need to decrease membrane conductance (gm) if you wanted conduction velocity in a 10 μm myelinated mouse axon to be 100 times faster than in a 10 μm unmyelinated mouse axon?

This is a question from a homework set. I understand WHY myelin decreases membrane conductance, and WHY decreasing membrane conductance would increase conduction velocity. I just do not understand how to calculate what factor specifically the myelin would need to decrease membrane conductance by.


texts: What is the difference between orthologs, paralogs and homologs?

texts: These three terms are often misused in the literature. Many researchers seem to treat them as synonyms. So, what is the definition of each of these terms and how do they differ from one another?


texts: Is this an eastern hemlock (Tsuga canadensis) seedling?

texts: I recently planted a few seeds gathered from a Tsuga canadensis cone in soil gathered from a garden full of weeds. I can't tell if what I have growing is a hemlock seedling or just another weed. See photo:


texts: What type of subsoil root structure provides better plant anchorage?

texts: Which type of root is better for good anchorage for small plants: tap roots or fibrous roots?. How about for trees:  tap root or a fibrous system?


texts: Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

texts:
I am using pymol to visualise the secondary structure of protein using its cartoon representation. The pdb file comes from a simulation, which contains multiple frames. After loading the pdb, its secondary structure (e.g. sheet, helix) could not been recognised. Surprisingly, if only one frame is kept, its secondary structure could be seen. So how to enable secondary structure recognition for a pdb file with multiple frames?

An example of the pdb file with multiple frames is shown below.

REMARK    GENERATED BY TRJCONV
TITLE     Protein in water t=   0.00000
REMARK    THIS IS A SIMULATION BOX
CRYST1  116.453  116.453  116.453  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  N   ASP     1      85.582  59.777  48.367  1.000.0000           N
ATOM      2  H1  ASP     1      84.882  59.067  48.507  1.000.0000           H
ATOM      3  H2  ASP     1      85.162  60.617  48.747  1.000.0000           H
... ...
ATOM   6615  OT  ALA   442      28.032  36.877  69.157  1.000.0000           O
ATOM   6616  O   ALA   442      30.092  36.087  68.677  1.000.0000           O
ATOM   6617  HO  ALA   442      30.072  35.867  69.597  1.000.0000           H
TER
ENDMDL
REMARK    GENERATED BY TRJCONV
TITLE     Protein in water t= 1000.00000
REMARK    THIS IS A SIMULATION BOX
CRYST1  116.384  116.384  116.384  90.00  90.00  90.00 P 1           1
MODEL        2
ATOM      1  N   ASP     1      75.052  41.097  56.132  1.000.0000           N
ATOM      2  H1  ASP     1      75.622  41.407  55.352  1.000.0000           H
ATOM      3  H2  ASP     1      75.602  41.357  56.932  1.000.0000           H
ATOM      4  H3  ASP     1      74.682  40.167  56.272  1.000.0000           H
ATOM      5  CA  ASP     1      74.032  42.157  56.202  1.000.0000           C
... ...
ATOM   6615  OT  ALA   442      45.292  49.247  90.922  1.000.0000           O
ATOM   6616  O   ALA   442      47.102  49.617  89.632  1.000.0000           O
ATOM   6617  HO  ALA   442      47.662  49.327  90.342  1.000.0000           H
TER
ENDMDL


texts: Where can I find trees preserved for hundreds of years?

texts:
I assume there are climate conditions that cause trees to be preserved, since there are fossilized trees, however, it may be extremely rare to find a tree in a nascent state of fossilization.

Is it possible to easily find trees that have been preserved for 200-300 years? By a tree, I actually just mean a preserved stump.


texts:
On Wikipedia, the entire microelectrode page states only the following:

  A microelectrode is an electrode of very small size, used in electrophysiology for either recording of neural signals or electrical stimulation of nervous tissue. Initially, pulled glass pipette microelectrode was used with later introduction of insulated metal wires. These microelectrodes are made from inert metals with high Young modulus such as tungsten, stainless steel, platinum and iridium oxide and coated with glass or polymer insulator with exposed conductive tips. More recent advances in lithography yielded to silicon based microelectrodes.

Can someone provide a more elaborate explanation of how it works?

Like ideally, I would like something as specific as the usual descriptions you see in introductory chemistry books for how emf works in a battery. In other words, I know how electric potential works, but I am not understanding the exact mechanism of the microelectrode works.

If there are many types of microelectrodes, just give me the properties of one involving small shafts of hollow glass filled with a conductive salt solution.

Pictures would be great.


texts:
I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem:

  Given the following DNA sequence, 5'-GGATCGTGCCACCATCCACCATCGTTA-3', if two introns are in bases 3-9 and 15-22, what is the mRNA transcribed? Give the answer 5' to 3'. Note that the first base is base 1.

And here are the steps that I took:

5'-GG ATCGTGC CACCA TCCACCAT CGTTA-3' (remove the bolded)
5'-GGCACCACGTTA-3' (new string)
take reverse complement
swap T's with U's

Is this correct? Or where am I going wrong?


texts: Could super-caffeinating somebody's bloodstream be dangerous?

texts: I'm currently planning out an RPG based on Misfits. Basically young offenders get super powers. I want one of the villains to have a really lame power that they use to become incredibly dangerous. I thought about using a power to caffeinate drinks. If someone used that to super-caffeinate somebody's bloodstream, could that hurt or kill somebody? Or would it not cause any real damage?


texts: How can the organic mercury compound Thiomersal be not dangerously toxic?

texts:
My intuition tells me that organic mercury compounds are absolutely toxic. Unimaginably, fundamentally, extremely and uncompromisingly toxic.

I know that is not true for all doses.

Thiomersal is the organomercury compound that was used in vaccines as preservative. It's use has been controversial outside of the scientific community.

I am not asking whether the use in vaccines is dangerous, to be clear:

The use of mercury as Thiomersal in vaccines it is not dangerous.

That is well-established beyond reasonable doubt. Far beyond.

My intuition tells me that any organomercury compound it so mind-blowingly toxic that I feel cognitive dissonance if I try to accept that, at some dose, it's not.

I'm totally aware that toxicity depends on dose, that the compound is toxic at higher doses, and the dose used is just low enough that it is not toxic.

But the dose used is still antiseptic and antifungal, and having anything in my body that contains mercury and carbon in a dose high enough to kill a form of life feels just not right.

I would not worry at all to get vaccinated with a vaccine containing Thiomersal, and if a physician would ask me whether I prefer a vaccine with or without it, I would answer "Whatever you think is best."

But still, on the abstract level, the feeling of "That can't be right" to have an organomercury compound in my body it pretty strong.

I know it is not dangerous, but:

How is that even possible?


texts: How do tight junctions in stratified squamous epithelia affect nutrient supply?

texts: In histology we know that epithelium tissue isn't vascularized so it takes the nutrition from Lamina propia (CT) via diffusion and in other hand we know all epithilial cells have tight junction which inhibits the flow of substance so how can it diffuse nutrients between themselves because of the tight junction how can they distribute nutrients, same way in capillaries which are endothelium  how interstitial fluid passes throw endothelial cells because of thier tight junction?


texts: Does severing the Corpus callosum, effect the brain's communicating ability?

texts:
With serious epileptic seizures, a treatment is to sever the corpus callosum, which stops the seizures. However, does this affect the communicating ability between the two hemispheres? Or how does this affect the brain differently? What are the consequences in the brain?

Thank you in advance! (If I've got this all wrong, please let me know.)


texts: What is this insect, the bite of which is causing deaths?

texts:
This insect is currently found in Kolkata, and in many parts of West Bengal, India. Its bite results in a fever, and if not treated immediately, the victim dies. This is the insect:

It seems that the insect belongs to the family of spiders due to its eight feet. But I can't conclude any more. Does someone know what this insect is, and how to be safe from it?


texts: How can human infants express chymosin with only a pseudogene at their disposal?

texts:
I read on the Wikipedia article about Chymosin http://en.m.wikipedia.org/wiki/Chymosin
It stated that chymosin is produced by gastric chief cell in human infants.
But it also stated that human only has a pseudogene for chymosin that does not actually encode the enzyme. On the other hand, another article show that gastric chief cell only secret chymosin in ruminant http://en.m.wikipedia.org/wiki/Gastric_chief_cell
How can infants express chymosin without a functional gene?


texts: Can two half-cut potatoes fuse back together?

texts: If I cut a potato in half, then I hold the two parts together, will the two halves fuse back into a single potato?


texts:
Well, I am not able to understand the exact difference between megasporocyte and archesporium. Also I'm not quite able to get, how or precisely from where do these arise?
Please help.


texts: Why metacarpus is considered hand proper?

texts:
This textbook states

  The hand (or manus) consists of the following parts: (a) wrist or carpus, (b) hand proper (or metacarpus), and (c) digits (thumb and fingers).

How could I justify why are digits not considered as hand proper? Hand is a prehensile organ and digits are of primary importance for prehension. So then how could metacarpus be considered as hand proper?


texts: I noticed spider cob hanging of my light bulb. That spider web was full of moving creatures. I quickly removed them and threw in the big. Wanted to find out what could that possibly be. I opened up light bulb and no traces to the ceiling. I found hundreds of them fallen on the floor, some where still moving. I do not have a good quality picture, but I have taken a video of it. Would anyone be able to identify? I live in Australia QLD, i think this could have been seeded by some fly?


texts: How to statistically test the predictability of evolution?

texts:
Can anyone recommend me an experimental study which tries to test the predictability of evolution? The closest works I found are the studies of fluctuation tests (f.e. classical study of Luria & Delbrück, 1943) which demonstrates that in bacteria, genetic mutations arise in the absence of selection, rather than being a response to selection. Is there any other point of view from which the predictability of evolution can be studied?

  Luria & Delbrück (1943) Mutations of bacteria from virus
  sensitivity to virus resistance. Genetics 28: 491–511.


texts:
After having a fun conversation with a friend regarding parenting, I actually had the general question arise in my mind of when did parenting actually start to take place?

But, first, I think we need to define what I mean by "parenting".  Specifically, what I am talking about is when animals decided to give birth to their young and not abandon them to immediately fend for themselves.  Instead, parenting is taking care of, and protecting children for a period of time (even a brief one) until they are grown enough to take care of themselves.

Also, I think it's worth not counting the actions of a mother or father hovering over eggs of unhatched offspring until they hatch.  True, this is a form of parental watching but I'm more interested in the general timeframe of when parents started watching over the general actions and "shenanigans" of their offspring in order to protect them from harm and to give them a better chance of survival.


texts: Biochemical Mechanism behind red hibiscus flower on a cream hibiscus plant

texts:
I have two 3-4 yrs old cream hibiscus shrubs in my garden. The shrubs seemed normal enough, giving cream colored petals with a red center. But soon I noticed that there are specific branches, which will consistently give completely red flowers. The leaves of this branch doesn't have any differences in shape or coloration, neither do the stem. On the days the red flowers don't bloom, there is no way to tell which branch it is.
Now my question is the reason behind the pigment change, is it due to a mutation?
I have read about complementary genes in Lathyrus sativus and epistasis for Cucurbita species. Is it a chain reaction in which a specific protein will result in red flowers?
If the red flowers produce seeds, then will those seeds give rise to red Hibiscus plants or cream ones?


texts: How are long time periods measured in biological systems?

texts:
Biological systems are pretty good at measuring fairly long times, for example, menstrual cycles (month), or puberty (years). Counting days or years seems to be implausible, and chemical concentration also seems implausible. What are the physiological processes that are involved in keeping track of such long periods? Is it just a long sequence of finite state changes?

I understand there are environmental correlates such as seasonal changes and relative position of celestial objects to measure the relative time, but regardless of these external cues, I suspect that a pretty good internal clock for longer time scale could exist. For example, the time to menopause can actually be thought of as a counting mechanism of a shorter clock which is the menstrual cycle. But, how does the body know when to stop growing? I cannot think of biological processes with such long time constants that is stable.


texts: It's obvious how a misdisjunction can result in klinefelter's syndrome (XXY) but I don't see how this can result in XYY syndrome. Your parents have a collective total of only one Y chromosome so how can any misdisjunction result in a child with two Y chromosomes?


texts: Can bigger persons generally resist g-forces better?

texts:
I've seen a claim that bigger persons generally resist g-forces worse than smaller in an undergraduate biology book. However this claim was supported by the argument that blood has to travel a longer way form the head to the heart.

However, I think this is not the only factor that matters. They generally should have a larger heart, but may need to pump more blood, so perhaps this cancels.

Questions:

Has it ever been tested whether bigger persons generally resist g-forces better? If so, what were the results?
If we only take scale factors in considerations, i.e. we take identical persons, but the one is 1.2 times as large as the other in all dimensions, what conclusion will we reach? What factors should we take into consideration?


texts: Who was the first to talk about evolvability?

texts:
"Evolvability is the capacity of a system for adaptive evolution." (source) There are several other definitions though:

Who was the first person to use the word "evolvability"?
Who was the first to introduce the concept of evolvability? in which article?