texts: Ion-exchange vs Gel Permeation Chromatography for proteins

texts:
For extracting Lysozyme from egg white which method would you recommend and please help me understand why.

Lysozyme has a higher isoelectric
point (pH 10.5) and a lower molecular mass (14 307 Da) than most proteins so both these methods make quite a bit sense. Use Sephahdax G100 for gel permeation chromatography and CM-Sephadex G25 ion exchanger for ion exchange.

From what I can understand, Gel Permeation will separate the egg white based on Mr of the various proteins and compounds. There is quite a bit of variation in the Mr of egg white proteins but lysozyme, in fact, doesn't have the lowest Mr as Cystatin and Ovomucoid have lower Mr. Furthermore, GPC requires around at least a 10% difference in molecular weight for a reasonable resolution of peaks to occur. The range of Mr is also quite broad in this method. Will this be disadvantageous perhaps? So GPC does have the plus side of it having a well-defined separation time due to the fact that there is a final elution volume for all unretained analytes.

Now Ion exchange chromatography is very specific in the nature of how the exchanger interacts with the mixture being separated. Lysozyme has a PI of 10.7 which is much higher than the rest of the proteins in the egg white. As with GPC we use 0.05M Tris-EDTA, pH 8.2, containing 0.05M NaCl as the standard. Can this setup result in Gibbs Donan effect or chromato- focusing ?

I'm currently leaning towards GPC as the option to yield the purist product especially seeing as it can be desalted afterwards with G25.

Please help guide me in the right direction. I'm quite new to this but am ready and very willing and keen to learn and expand my abilites.


texts: How does high-intensity aerobic exercise affect the brain?

texts:
I have been reading articles claiming that serotonin, endorphins and BDNF are produced during exercise, but they never mention the intensity or duration of exercise for this to happen.

To not make this question too broad, I want to narrow it down to, lets say, a 4-5k run over 20 minutes. Also, I want to restrict it to the body's response during these 20 minutes.

How will this affect the brain? Which chemicals do the body produce/release into the blood stream that could have an effect on the brain? And, how much?

I am asking because I am always curious about the mechanisms underlying the effects of exercise on the brain and because it's always difficult to find information regarding results of exercise; Googling mostly results in content marketing articles (like this one for Buffer).


texts: I'm doing some research on Harbor seal behavior, but I haven't been able to find much on general behavior such as personality,  quirks, ect. Does anyone have anyone have any firsthand experience with harbor seals that could tell me what their general demeanor is? Are they playful? Curious? Shy? What are some behavioral actions that you see them do often? How do they react with their social groups? Do they have obvious hierarchies or do they mostly ignore each other? Any information is helpful, thanks!


texts: Are there any examples of weighted edit distance genome alignments?

texts: It has been said that weighted edit distance is a preferred way to compare/align genomes in practice, e.g., when identifying genetically similar patients. I wonder if there are some concrete examples when weighted edit distance is used this way and I am particularly interested to see some example weight tables. Some links to research papers showing such examples would be very useful.


texts: Why would a human female have a sexual display despite male biased operational sex ratio?

texts:
why would a human female have a sexual display despite male-biased operational sex ratio?

In human society there is a male-biased sex ratio, due to female child rearing, which results from anisogamy. Human females sometimes expend great amounts of energy and resources performing display acts and doing things to attempt to improve their apparent quality to males. Human males tend to be eager, despite a certain level of socially imposed monogamy, and many males will mate with a low quality female. Why do human women do sexual display behaviors, when there are so many eager males to choose from?


texts: Isn't biological immortality strictly speaking impossible?

texts:
This question relates to both immortal cells such as cancers and organisms like the Hydra genus. Isn't it technically impossible for these "immortal" biological systems to live forever, even disregarding accidents and disease?

I am aware that they are considered immortal because they do not exhibit the usual degradation of functionality as they chronologically age. In cancer's case an up regulation of telomerase prevents the usual gradual depletion of DNA at the chromosomal ends limiting a cell's lifespan. But at the same time cancer cells and immortal organisms still undergo DNA damage and thus mutation (cancer cells even mutate faster as far as I know), wouldn't the stacking of these mutations at some point kill off the cancer cell line/immortal organism as some vital part of their metabolism is inevitably damaged?

Wouldn't true biological immortality require an organism with DNA that is either impossible to damage or if it could would always be perfectly repaired? (creating an evolutionary dead-end as well)


texts: How do I find the sequence of the phage BxB1 gene?

texts:
Specifically, I'm trying to find the sequence of BxB1 and its att sites.  I have success finding the att site sequences, but I'm having a bit more of an issue with finding the sequence of the actual recombinase.  I've looked through Genebank, but I can't find a definitive sequence of the BxB1 recombinase.

How should I go about looking for this sequence?

EDIT: One more thing I'm concerned about is the validity of the sequences that I do find.  For example, I have seen that Addgene has this pCAG-NLS-HA-Bxb1 sequence.  However, I'm not sure how to verify that this sequence is correct.


texts:
Can anyone identify this insect? It was sitting on my refrigerator.

Size: approximately 1 cm height, 1 inch across

My location: Bangalore, India


texts: Where does DNA fit on the Chomsky hierarchy?

texts: Since adenine pairs with thymine and guanine pairs with cytosine, this seems to imply that there's a trivial Regular Expression for DNA (i.e. it's trivially a Regular Language, which is Type 3 on the Chomsky hierarchy). With that said, is there a "less trivial" Regular Expression for DNA? Or, even better, is there a "deeper" grammatical structure for DNA, such as a Context-Free Grammar?


texts: RNA-Seq library normalization and experimental setup

texts:
I'm working on an RNA-Seq project and I am trying to figure out library normalization.  I'm aware of using the geometric means (e.g. cuffdiff) of the fpkm for the normalization.

However, I was wondering why people don't add some unique, known RNA sequence of known concentration into their sample prior to amplification.  Then after sequencing you would have some known measure by which to normalize your fpkm. I would think this would also be a way to minimize batch effects.

Is there a technical reason why this isn't done?


texts:
I am looking for an umbrella term for general "parts of the brain", esp. for (somehow arbitrary) "subsets of neurons".

For the tree of life there is an umbrella term for all kinds of taxonomic groups all down the tree. They are called taxa.

Domains, kingdoms, phylums all down to families, genus, and species are taxa:

In brain sciences there seems to be no such umbrella term which is generally agreed upon.

Which term would best include all of the following?

brain hemispheres
coarse brain subdivisions (cerebellum, cerebrum, ...)
cerebral lobes (frontal, parietal, ...)
the thalamus („a large mass of gray matter“)
nuclei (thalamic, ...)
Brodman areas
cortical layers
cortical columns
the limbic system
regions of interest (in fMRI)

All of these immediate suggestions don't fit perfectly:

(brain) region
(brain) division
(brain) area
(brain) volume
(neural) group
(functional) system


texts: Why E.Coli get bigger if they replicate faster?

texts:
When E. Coli divide faster, they tend to have larger volumes. If the same cells are grown in a poorer medium, they'll have longer replication cycles and shrink. What is the explanation of this phenomenon?

Refs.

http://book.bionumbers.org/how-many-ribosomes-are-in-a-cell/
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023126


texts: harvesting fertilized eggs from Tetraodontidae species?

texts:
I would like to know how easy/difficult it is to harvest fertilized eggs from Tetraodontidae species such as Tetraodon nigroviridis or Takifugu rubripes compared to zebrafish? Ultimately, I would like to know how much material would be obtainable from Tetraodontidae eggs to extract DNA from the nuclei.

I know zebrafish lay lots of eggs, and other model fish species like medaka lay much fewer of them, but I couldn't find any information about Tetraodon nigroviridis or Takifugu rubripes after some googling.


texts: Protecting an internal clevage site from restriction enzyme while cloning

texts: 2 restriction enzymes used to generate cohesive ends in a vector and foreign DNA(gene of interest you want to clone) also cuts the foreign DNA at an internal site. What are ways to overcome this?


texts: Distribution of nutrients throuought a drink made of plants?

texts: In an attempts to eat my veggies for the day in one shot, I blended together a bag of salad with some water. The mixture separated by density, a thick top layer containing the bits of leaves, and a bottom layer of just juice. My question is: how many vitamins and nutrients are actually found in the top layer compared to the bottom, and how efficiently would the body process them?


texts:
I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be wonderful.

This research project is more like a class where students are taught how to sequence a piece of plasmid via Sanger sequencing method, with paired end primers. For each plasmid there will be two entries (~1kbp each). Then the students would BLAST the sequence, mostly to see if there is any close match with certain related organisms.

The main purpose of this database I'm creating is to monitor the sequencing progress, as well as to single out the samples that need to be redone. So far, the record-keeping is not exactly accessible, hence the need for re-organization. Additionally, the students would need to be able to view their own results and enter the BLAST results themselves. The last condition seems to necessitate a web-server type of thing that the student can connect to enter their information.

The total number of bacteria clones containing plasmids are ~18k, which means there will be ~36k entries in this database. It would be great if there is anyway to manage the trace files of the entries, or if not, I think I can add a column for the file path.

Is there a database management program that is appropriate for organizing sequence and trace file, with easy access for data entry by multiple users? It would also help if the program don't have a high maintenance need.

Disclaimer: I have very limited knowledge with database structure, having only taken an online intro to database class. About programming language, I am still learning Python. This project is a way to force myself to learn more.


texts: This grows in Modiin, Israel. The leaves look like black locust (Pseudoacacia robinia) to me, but the branches are very knobby. Can anyone identify it?


texts: Perception of white in the absence of rods

texts: If the retina would not have any cones, one would be color blind. If white is the presence of all colors (in the matter of color mixture, not addition), then what would white look like without rods?


texts: Why isn't the insertion of a single nucleotide destructive for DNA?

texts:
As far as I know proteins are built by sequentially reading triplets of nucleotides.
But if at a certain point a nucleotide is inserted in the sequence, the following sequence of triplets is completely different.

For example:

AATACGGTACCATTA ...

AAT ACG GTA CCA TTA ...

But inserting a nucleotide B at second place we get

ABA TAC GGT ACC ATT ...

Which is completely different.

However I know from theory that a single nucleotide insertion is not dangerous in most cases.

Could someone clarify my mind about this?


texts: Are there birds with knees instead of elbows?

texts: Are there any birds whose legs fold the same way human legs do, in a knee, instead of an elbow which is what all the birds I know have?


texts: Are simple esters like those used as flavouring agents metabolised into their constituent carboxylic acids and alcohols in the human body?

texts:
By this I mean to ask whether say ethyl butanoate is hydrolysed in humans into ethanol and butyric (butanoic) acid. This is of interest to me as a pharmacology researcher because butyric acid, for instance, serves as a potent histone deacetylase (HDAC) inhibitor and hence increases gene expression but it has very poor oral bioavailability and I am curious as to whether there's any theoretical basis for suspecting that using butyric acid esters as prodrugs would be a more efficient way of delivering butyric acid.

Here is the molecular structure of ethyl butanoate:


texts: What is the evolutionary advantage of getting hard nipples when being aroused? Why can they even be stimulated sexually?

texts:
I try to understand the evolutionary advantages of the body reactions of nipples and penises/vaginas. I'm confused, because I can explain the evolutionary advantage in a logical & consistent way for penises/vaginas, but not for nipples.

arousal causes stiffness

Penises are getting hard when aroused. I can make sense of that - it is evolutionary advantageous, because sperm is more likely to reach the uterus; therefore the likeliness to get pregnant is higher; therefore providing an evolutionary advantage.

But I can not make sense of nippels getting hard. I don't see any advantage that could provide. I mean, breast feeding causes stiffness through stimulation; but that is not sexual, I guess? I guess, breast feeding woman don't experience arousal because of the breast feeding?

sexual stimulation

Furthermore, why does nipple stimulation even cause arousal? I mean, why does it cause evolutionary advantages that we feel arousal when they are stimulated? Again, I can understand this part for penises/vaginas.


texts: How would a medication cause a one to maintain a different weight?

texts:
This isn’t really a medical question, I’m just really curious about this.

I was maintaining weight A and then started taking a medication that brought me to weight B. While on the medication, I maintain weight B. When I stop taking it, my weight goes down presumably to weight A.

The increase or decrease of weight in changing medications doesn’t puzzle me. It’s the maintaining of the weight.

Would the medication be affecting metabolism or what?


texts: Is "exhaustion" of the Hodgkin-Huxley membrane at constant stimulation a real phenomenon?

texts:
I was playing around with a simulation of the Hodgkin-Huxley model using their original parameters for the squid giant axon.

By applying a constant stimulation current to the model in resting state, an infinite train of action potentials is triggered, which seems reasonable. However, if the current exceeds a threshold, these APs die off very quickly as both the membrane potential and the ion conductances reach a steady state.

What is this phenomenon called? Is it a real phenomenon, or just an artefact of the Hodgkin-Huxley model?


texts: Is recombination suppressed in the males of all Drosophila species? Any other species?

texts:
Following up from this question, I am wondering if the phenomenon of genome-wide suppressed male recombination is limited to Drosophila melanogaster or is common to all Drosophila? The answer to the aforementioned question hints that this may be the case but has no reference on that, and doesn't directly state it.

For an added bonus, is this recorded in any other species?


texts: It is found in my apartment in Finland. I had to kill it to stop it from getting away before looking for the camera, but it looked pretty much the same alive and intact. It's length is about half a centimeter, and the younger ones look darker. It is often found in dark. Since their appearance, I often notice red and slightly itchy bug bite in the morning. The question is what is this insect?


texts: Comparison between Transmission Electron Microscope (TEM) to Scanning Electron Microscope (SEM)

texts: Can someone state the advantages of Transmission Electron Microscope (TEM) over Scanning Electron Microscope (SEM) and vice versa?


texts: How does heat shock transformation work?

texts:
What exactly happens when competent cells like DH5ɑ are heatshocked with DNA present? How does the DNA get inside the cells?

Specifically, why are all the steps necessary? What if you heatshock right after adding DNA? What if you don't put on ice after heatshock? What does the calcium chloride do? What actually happens when cells are "competent"? What governs transformation efficiency (besides obvious things like amount of DNA or cells)?

To make it clear what I'm talking about, I use a protocol like the following:

Take cells out of -80C and thaw on ice for 5 min.
Add 1 ul (~500 ng) plasmid DNA to 50 ul cells, mix gently with pipette tip.
Leave on ice for 30 min.
Put in 42C water bath for 45 sec.
Put on ice for 10 min.
Add 950 ul LB, put in 37C for 1 hour.
Spread 300 ul of the culture on LB-agar plates with appropriate selection.

I usually get thousands of colonies from this (in fact, often 1:10 or 1:100 dilution is necessary so I can actually get isolated colonies). Even if I skip the outgrowth, I still get hundreds.

I don't have my competent cell protocol, but basically I use that one rubidium chloride that everyone uses: DH5ɑ cells are washed with some buffers, suspended in a solution with CaCl2 and RbCl, then frozen in liquid nitrogen. I never actually measured, but usually the concentration of cells in the frozen aliquots is about 10 times as many as you would get from an overnight liquid culture (they are spun down and resuspended in a small volume).


texts: Factors That Would Promote Eusocial Development In Mammals?

texts: What would cause mammals to evolve to be more eusocial, like the naked mole rat did? What advantages does eusociality give in such scenarios?


texts: Is there a term for the opposite of intergenic?

texts:
I am looking for a term that describes DNA regions that overlap genes, i.e., non-intergenic DNA regions.
For example, say I am writing a paper about DNA-binding sites (i.e., DNA sequences that proteins bind to), but my paper focuses exclusively on DNA-binding sites that happen to overlap genes. What would my title be? "Non-intergenic DNA-binding sites are [...]" is one option, but I wonder whether a more appropriate term exists.
If I understand correctly, "Gene-overlapping" seems to be used for referring to genes that overlap other genes (https://en.wikipedia.org/wiki/Overlapping_gene).
Also, Google says that "genic" means "relating to genes".
Is any of my ideas appropriate? Or maybe another term?

To clarify what I mean by intergenic and non-intergenic, here is the figure from https://en.wikipedia.org/wiki/Intergenic_region. I added an example for a non-intergenic DNA region.

Explicitly, an intergenic DNA region is a DNA region that doesn't share any base with any gene. A non-intergenic DNA region is a DNA region that shares at least one base with a gene.


texts: Bacteria trapped in crystal inclusions found 'alive' after 50,000 years - what were they eating all that time?

texts:
The phys.org article Biologists find weird cave life that may be 50,000 years old describes the announcement by NASA Astrobiology Institute director Penelope Boston at the 2017 AAAS meeting$^{(1)}$ of micro-organisms found in small inclusions within crystals of hydrated [Calcium Sulphate][] (Gypsum) that had grown while underwater in a cave in Naica, Mexico. It is estimated that some of these organisms have been isolated within inclusions for as long as 50,000 years, and yet can grow and reproduce when carefully extracted and provided with fresh chemosynthetic nutrients.

(BBC Radio interview with Penelope Boston)

This particular discovery has just been formally announced so there is no peer-reviewed material to read yet, but it's possible someone here in Biology SE attended the meeting or has read further about the announcement.

50,000 years is a long time (for a bacteria, not a crystal), and if I understand correctly the energy source for these organisms is chemosynthesis. Put simply, wouldn't they have eventually used up all their food and died? I'm thinking the crystal is a good electrical insulator and the cave was dark, so there couldn't be external energy sources to replenish the oxidation state of the iron or sulphur or whatever they were eating.

The elevated temperature and ubiquitous radiation would have presented a relentless, potential source for DNA damage mechanisms, and repair would require a constant supply of energy. So I'm guessing there had to be some minimal source of energy to keep them viable, if not actually 'alive' for 50,000 years.

Is this thinking roughly correct? If so, what might that source of energy have been?

Below: Giant gypsum crystals in a cave in Naica, Mexico, from here. Note the person for scale at lower right.

(1) Currently 2017 AAAS meeting links are all re-directing to the 2018 meeting, so I can't find a link to the particular talk or session.


texts: Kin selection Vs altruism (social biology)

texts:
I know that this is a contentious topic and I found conflicting explanations online which is what prompted me to put his question up. In some papers, Kin selection is mentioned based off the concept of inclusive fitness (sum of direct and indirect fitness). However, Kin selection is said to be an altruistic characteristic. That being said, altruistic genes only propagate through indirect selection (since an actor gives up its own fitness and do not generally reproduce). In that case, isn't Kin selection based off just indirect fitness and not inclusive fitness as a whole?

In a webpage, it is mentioned that "Kin selection is the evolutionary mechanism that selects for those behaviors that increase the inclusive fitness of the donor.". In that case, how can kin selection be altruistic? Can someone shed some light on what Kin selection is exactly? Also, a proper definition for indirect selection would be good as well. Thank you.


texts: STRING ID - allelic differences and splice variants

texts:
STRING has protein (amino acid sequences) mapped to a single gene ID.
I have these doubts with respect to STRING ID.
I find that

1.All alleles of a single gene share the same STRING ID and
2.Especially in Eukaryotes, splice variants of the single gene(which might translate to different proteins) share the same STRING ID.

Does STRING take into account these two things like UniProt and have different IDs based on allelic differences and splice variants?If so,how?


texts:
Perennial plants species generate a new plant annually from the same parent root stock. At the end of the year that new shoot withers and dies, to re-appear the next year. Hence, the above-ground parts of perennials obviously age and die, but what about the rootstocks?

Are the rootstocks from perennial plant species immortal, or do these rootstocks age and die as well?


texts: Identify mystery insect found in Boston, USA

texts: This insect is approximately 2.5mm.  It was recently observed in a Boston USA shower.  Do you know what type of insect this is?


texts:
I've been reading up on beneficial mutations, and am curious when we discovered and documented the first one.

Can anyone point me to the first documented beneficial mutation?

Per request, let me try to clarify my answer a bit.
I know that we've been aware of mutations perhaps as long ago as the 1930s (I believe it was R.A Fisher who was one of the first to talk about them??).

I have read various documented beneficial mutations since then, such as lactase example in humans, or cit+ in E.Coli.

What I'm curious about is when it was that we first identified and documented (scientific paper or article) an observed beneficial mutation, in any organism (not just humans).

So yes, Remi.b, your wording would have been what I was looking for:
"what is the first article that has documented a beneficial mutation, in any organism"

Does this clarify it enough?


texts:
What are the differences among the following competent cells DH5 alpha, Nove blue, and BL21? Why some of them are for cloning and others are for protein expression?

Any references where I could find the answer?


texts: Can an adult without genetic lactase persistence still develop a tolerance for dairy foods?

texts:
While investigating the rise of adult lactose tolerance, I came across the news that China has been encouraging its citizens to drink more milk, even though most of the Asian population lacks the SNP (single-nucleotide polymorphism) which conveys lactase persistence.

Is it still possible for an adult without lactase persistence to build-up a tolerance for lactose over time? If so, what's the mechanism?


texts: Generalism - specialism index in microbial ecology

texts:
I am doing research in Lipid metabolism in different yeast species and I would like to look into ecology of them.

I would like to classify them to a Generalist/specialist based on different Parameters (growth on carbon sources, pH, temperature,...).
I wonder if you have any experiences with that classification and if any of you know which indexes are used for that in microbial ecology?

Thank you very much for your answer!
Martin


texts: Do the claims in this paper have any degree of validity?

texts:
The paper The waiting time problem in a model hominin population talks about a problem of waiting time, etc. Is the methodology of this numerical simulation, and the conclusion right or is it wrong?

(A quick search reveals that the first author is an intelligent design advocate and apparently believes or believed that the earth is less than 10,000 years old)


texts: Why are men more susceptible to severe COVID-19?

texts:
It seems that globally, men are more susceptible to severe COVID-19 than women:

https://www.theguardian.com/world/2020/mar/26/men-are-much-more-likely-to-die-from-coronavirus-but-why

This is seen in other coronavirus diseases (SARS, MERS) but not respiratory diseases generally. Do we know the reasons for this?


texts:
I'm confused about the role of hydrostatic pressure compared to osmotic pressure.

Q1:If I have a U-tube with a membrane permeable only to water molecules and equal volumes of water on either side but only 1 side (side B) has NaCl, the osmotic pressure would cause water to move from side A to side B,correct ?

Q2.But then hydrostatic pressure would cause water to move back to side A.
So, the water would move from side A to side B until the effect caused by the hydrostatic pressure = effect caused by osmotic pressure ?

Q3. The last statement wouldn't be correct If I said that "water moves until the hydrostatic pressure=osmotic pressure" would it ?

and lastly, My friend said the water would move until the hydrostatic pressure on both sides was equal
Q4. If water is moving from side A to side B then the we have more water molecules at side B, how would side A ever reach the hydrostatic pressure at side B ?
Do I have a misunderstanding in the concept of hydrostatic pressure ? In this context, I understand that it is the pressure exerted by the water molecules on the selectively permeable membrane.

The more I google hydrostatic pressure the more lost I get because all sources seem to explain in terms of equations and physics and I'm only taking this for an introductory course in physiology.


texts: Transmission of HIV from Mother-to-Child Through Breastfeeding

texts: If a mother is HIV+ and was on medications which would help her deliver a HIV negative baby, can the baby contract the HIV through her breast milk?


texts: What is this animal looking like an Axolotl?

texts:
My friend caught a strange looking animal and he's saying it is an axolotl. I keep telling him it's almost impossible, since they are almost extinct in their natural environment and he caught it in St-Larent River (Quebec, Canada)

Anyone have any idea what it is ?


texts: Is the PCT of the nephrons of the kidneys of marine vertebrates to minimize the natural tendency for exosmosis?

texts:
For marine vertebrates, the concentration of salts outside their body (in the water, that is) is more than that inside their body. So, there is a natural tendency for exosmosis to occur.

To minimise this natural tendency for exosmosis to occur, these vertebrates would need to retain more salts inside their body.

I understand that the Proximal Convoluted Tubule (PCT) of the nephrons of the kidneys is involved in selective reabsorption of salts. So, making the PCT more coiled would increase the surface area of absorption, thus increasing the absorption, and therefore retention of salts in the body.

So, my question is: is the PCT of the nephrons of the kidneys of marine vertebrates more coiled than that of terrestrial vertebrates?


texts: Possible to breed human-adverse mosquitoes?

texts:
Some time ago I read a paper on fruit flies, in which the researchers bred a population of flies to avoid a particular fruit.  They did this by exposing the flies to two different types of food (say, e.g., grapes and bananas), one of which was poisoned and killed all the flies that ate it.

I forget the exact details, but I seem to recall that after about twenty generations they had successfully bred fruit flies that instinctively avoided the "poisoned" fruit, even when the fruit wasn't actually laced with poison.  (I think they alternated poisons every couple generations to ensure that they weren't breeding a distaste for the poison rather than the fruit).

I was wondering (1) if this sort of technique would work with mosquitoes and (2) whether such a change would be likely to persist.  It sort of seems like the answer to both ought to be 'yes', but if so then why has no one done it?  So I figure I must be missing something.  Some thoughts:

1) I forget which fruits the study used, but I remember that they were pretty distinctive.  Perhaps people are too similar to other prey animals for such discernment in mosquitoes?  Then again, we're bipedal and have much less hair than most mammals.  Probably smell different, too.  Those would seem to be pretty obvious traits.

2) On one hand, it seems like having fewer food sources would be evolutionarily disadvantageous, suggesting that the trait would not persist if released into the broader mosquito population as a whole.  On the other hand, I'm guessing that a much larger proportion of mosquitoes get swatted after biting people than after biting, say, a horse or a cow.  Which should make the 'avoid humans' trait evolutionarily advantageous and tend to spread throughout the entire population.

2b) Mosquitoes breed by the thousand, so clearly they can accept a large proportion of failure-to-breed from a species perspective, so swatting isn't a strong deterrent.  But neither should be failure-to-breed from starving be a strong deterrent, unless people are effectively the only prey species in the area.  Whether you lose 10% from swatting or 10% from starving, it seems like it makes no significant difference from a species perspective.

Anyway, I'm trying to figure out why this (apparently, or else someone would have done it already) doesn't work.  I figure I'm probably missing some key detail about mosquitoes or evolution that will solve the mystery, but I'm not sure what.

Edit: If it's not clear from the above, I read the paper on fruit flies quite some time ago (probably a decade or more, and no guarantee that it was new research then).  So some of my details could well be off.  If there's any reason to suppose that my memory is so excessively faulty as to make such a scenario implausible or otherwise questionable, please let me know.  I'm fairly sure I have the gist of the paper correct, which for the purposes of this question is that at least one type of insect can be bred over the course of a relatively small number of generations to strongly prefer one type of food over another, but not so sure that I'd stick to my guns if a subject-matter expert called it into serious question.


texts: Does glycerol in E.coli culture media somehow inhibit the lac-operon?

texts:
I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces protein expression at an OD of about 0.5 in the commonly used LB media (Lysogeny/Miller broth). IPTG is a lactose analogue that will induce the expression of proteins encoded in the lac-operon. I have been told that it is important to have a high OD before induction, because the added glycerol in the TB media (5%) will somehow inhibit expression of protein in the lac operon if it is not 'used up' before induction. However, glycerol itself should not inhibit the lac-operon from being transcribed (?).
I have several speculations about this: Could it simply be that TB-media has a very long exponential phase (rumoured to support an OD up towards 16.0, personally I routinely reached an OD of 10), and it is therefore not wise to induce protein expression too early (and thus has nothing to do with using up up the glycerol)? Another rational explanation that I came across is that glycerol might induce carbon catabolite repression, meaning that glycerol might inhibit the uptake of IPTG (or down regulate cAMP levels) and thus indirectly inhibit expression of protein from the lac-operon, but I found it a bit difficult to get a straight answer about this in literature.
Does anyone have some good references for these speculations?


texts: Do foods with preservatives become less toxic in the gut?

texts: Do foods with preservatives stay digestible for longer in the gut by not rotting as much (producing less toxins)?


texts: During my education in Iran, until now, which I must say that I'm graduating high school this year and will go to college next year, our biology book has said that there's some bacteria in our colons and those little cells live there and use the celloluse of our food and because mostly they are anaerobic they produce methane or hydrogen and hydrogen sulfide and so on and sometimes they are the reason of the smell of our farts. Also they produce little amounts of B and K vitamins which is good for us and also, by using cellulose they make the rejection of feces better and easier. Anyway I wonder that where do these bacterias come from? I mean are they with us since birth? Then it means they come from our mother's body but, wait how our mothers have them? But maybe they are not there since birth and they come to colon from the food we eat during our life, but why don't they die in stomach. Even if we think that they go there by eating food, passing stomach easily, what if we don't eat the "food that can have those bacteria", then could it be possible to some humans don't have those bacteria? But they can't have a good release of feces.


texts: How to do Sliding 80mer Window search against a database with fasta

texts:
I know how to do a 80-mer window search against a single protein

fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:0-80

FASTAbyGI15/378405189
fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:1-81 FASTAbyGI15/378405189
fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:2-82 FASTAbyGI15/378405189

....

This will give me the detailed results but I want to do the search against a database in Fasta like this website:

http://www.allermatch.org/allermatch.py/form

Can anyone help me?


texts:
I have read that IQ is highly heritable.

How could this be tested?

For honest testing, it seems to me that only children who were abandoned should have been tested, to exclude education effect. Was it really done?

UPDATE

Intelligence is one of the traits, that can be inherited both by genes and by education. You can't educate your children to have blue eyes, but you can educate them to count or to read.

So, to study heritability of intelligence, educational inheritance should be excluded.

I know that usual way to study heritability is to compare variability for monozygotic and dizigotic twins. Being sufficient for other traits, this method is highly insufficient for intelligence (which is obvious). Having identical perception system, monozygotic twins will respond identically to an education, so they will be more closely educated, even if IQ is completely independent of genes.

So, to study IQ heritability, subjects should be studied under different education conditions. I.e. they should be abandoned by parents and/or adopted separately.

My question is: was this done or not?

If not, then the question is, how education effects were eliminated?

Also I would like to know, if my reasoning about why just studying twins is insufficient is wrong.


texts: human sight at 1000x while looking into the mirror

texts:
I noticed that my eyeballs have the ability to see in what appears to be 1000x.
Setting the conditions: Look into a mirror while in a well lit room. (for me the lighting in my living room as opposed to the bathroom was not as direct and offered a better focus)  Position your face with your nose touching the mirror. Look at the twinkle of light that reflects off your eyeball. Stay focused on that twinkle with both eyes. Now, pull your face away from the mirror in order to focus your vision.  Position that twinkle of light directly to the center of your eyeball.
At this point that twinkle of light starts to look like a patch of cells under a microscope.  My left and right eye are different images.  My question: Am I looking at the cellular array that makes up my retina?   Eric McBrearty


texts: How did the double circulatory system evolve from the single circulatory system

texts: I already learned how the mammal circulatory system (double circulatory system) evolved from the reptilian circulatory system. How did natural selection evolve the reptilian circulatory system and the amphibian circulatory from the fish circulatory system (single circulatory system)? Did the reptilian circulatory system evolve from the amphibian circulatory system? If so, how? http://www.shmoop.com/animal-movement/animal-circulation.html shows what the fish, reptilian, and mammal circulatory system look like and https://universe-review.ca/I10-82-circulatory.jpg shows what the amphibian circulatory system looks like.


texts:
When sun rays shoot through my house from a window, sometimes if the lighting is correct, it will reveal a huge amount of floating particles and dust.

Are these particles dangerous to humans if you live with them constantly?


texts: By selecting sex cells after meiosis, would it be possible to create two offspring with inverse parental DNA of one another?

texts:
Would it theoretically be possible to select two sex cells after a male meiosis (filtering out the two where crossover had taken place) and combine each with two sex from a female meiosis (imagining they were all egg cells, even though only one would be) to create offspring with inverse inherited parental DNA of one another?
For example: If the mother's DNA is AB and father's is CD then the offspring could have AC and BD - inherited from both parents but completely different from one another.


texts:
Why are covalently closed circular plasmid DNAs naturally found in an underwound state ?

Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it because underwound state is energetically more favourable than an overwound state ?


texts: Can humans shorten their sleeping patterns?

texts: Can sleeping patterns be trained, or are they genetic? I read that a human needs to sleep at least 4 hours. Can sleeping time be reduced without having a negative impact?


texts:
If I were to take bakers yeast and put it in medium of minimal sugar(whatever quantity that would be) and rice(for a source of starch), could the yeast have a "evolutionary leap" and adapt to use the starch in its environment? I remember reading something similar in a report of E.coli bacteria and citrate adaption, under the heading:
 Catching evolution red-handed.

The passages in question are so:

  "Every night, the bacteria run out of the sugar glucose and go
  dormant. The following day around noon, a researcher plunges a pipette
  in and sucks up 1% of the culture to inoculate a fresh flask. Those
  faster at gobbling up glucose will send more of their descendants to
  the following day's pipette and, after a few weeks, descendants of the
  fastest one will be the only ones transferred as the mutation 'sweeps'
  to fixation."

Under the heading: The rise of Escherichia erlenmeyeri, (bold emphasis mine).

  "One morning, at the turn of generation 33,127 according to the lab's
  log book, a massive increase in turbidity was recorded on the vial
  labelled Ara-3. The sugar-starved bacteria had suddenly 'discovered' a
  vast new source of carbon by importing citrate, a pH buffer that had
  been in the growth media all along, and it sent the population size
  through the roof. "

So if I understand this correctly, there is evolution going on through the differential reproductive success of the bacteria, via their fitness which is affected by the glucose levels?

This "pressure" caused a type of "hopeful monster" in the form of Escherichia erlenmeyeri, the bacteria that could metabolize citrate, in which it didnt have the means to do so before.

So then could I replicate this concept with baker's yeast and starch metabolism and hope for similar results hypothetically? Or am I misunderstanding this?


texts: Is there a term to quantify how spread a character is on a phylogenetic tree?

texts:
Is there a term which can quantify how 'spread out' a particular character is on a tree? I want to distinguish between a character which is only restricted to a particular clade vs. a character that occurs all over the tree.

ETA: by 'all over' I meant it may be restricted to a few branches but those branches are spread out over the tree. It need not be ubiquitous. e.g. the character marked in blue on  compared with the case where these three branches are in a small clade.


texts: Can the basement membrane of blood capillaries expand?

texts: I have been doing some rudimentary research into the basement membrane and found the it contains collagen fibers which are known for their elasticity.  Does this mean that the basement membrane can expand in capillaries?


texts: What are the factors that control the speed of propagation of neuronal signals?

texts:
If we consider an analogy between a wire and a neuron there may be some resemblance between the factors controlling the data flow rate. For example the increased width of wire leads to decreased resistance etc; similarly increasing or decreasing the thickness of myelin sheath may have an effect on the conductivity or data transfer between neurons.

Are there additional factors that can control the speed of nervous conduction?


texts: How can I text-mine full-text articles from PubMed?

texts:
I want to do a text mining study using full-text versions of articles I find on PubMed. My intended search protocol will be roughly as follows:

Search PubMed using a gene name (and any alternate names) as the query, all matching papers are subjected to Step 2; my understanding is that this will return articles that mention the gene in their abstract
Search full-text for any and all matches from a list of keywords; assign each paper a score based on the number of matching keywords; any papers that match have to be read by a human but the most relevant papers will have a higher score and get read first

The two-step search needs to be repeated many times with different genes in Step1 so an automated approach is probably worth the time it will take to develop.
I know enough about programming that I could write a script to do Step2 if I had the paper as a plain-text document (I program in Perl but I also know a little Python) but I have no idea how I could automate the process of searching for papers, downloading them, converting them to plain-text documents that my program could work on.

I considered posting this in StackOverflow but have opted for this site because I have not ruled out the possibility that this can be done without doing my programming.

UPDATE: I have found one tool that might be very useful for exactly this problem. Unfortunately, I am not in a position to ask for a free trial so I cannot evaluate it. Even if it is an appropriate tool, I will most likely not be able to use it for my study.


texts: Is autoimmune disease associated with self-reactive B cells?

texts:
I'm a bit of an amateur, so excuse what may be a very naive question, but I somewhat understand how B cells that are self-reactive (bind to endogenous epitopes) are selected out during development. I also know that autoimmune disease is caused by the immune system persistently attacking specific components of the body, which sounds a lot like self-reactive B cells.

Is autoimmune disease associated with (dare I say caused by?) errors in this self-reactive B cell selection process? Any useful references so I can hopefully become less amateurish?


texts: Can some one identify this plant with really sweet smelling flowers?

texts:
Could someone help identifying this plant?
The flowers on it have a very sweet smell, similar to the night queen.


texts: How do axon terminals report to the soma?

texts:
It is important to bear in mind that the distance between a neuron's axon terminal and its soma can be extensive, up to about 1m in the human body. The fastest transport along the axon is 400mm/day (For this purpose I suppose Source: Wikipedia).

Of course the axon terminals also need to be supplied with a steady stream of proteins to maintain normal turnover, for example the terminal may need enzymes which metabolise the neurotransmitter, membrane proteins for signalling, vesicle coating and membrane fusion proteins etc.

However, sudden changes are possible in the level available of a certain protein. An example could be sudden depletion of SNAREs (required for vesicle fusion in neurotransmitter exocytosis) caused by botulinum toxin.

My question is, does the terminal somehow report back to the soma in any way if a certain protein needs to be made available more or less? And if so, how? Especially considering that retrograde transport, according to Wikipedia, gets up to 200mm/day only. If that was the mechanism for feedback, it would create a large discrepancy between signals received at the soma and the terminal's actual state.


texts: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?

texts:
Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops?

In software development, these constructs have the following functions:

IF-statements: An IF statement executes the code in a subsequent code block if some specific condition is met.
WHILE-loops: The code in a subsequent code block is executes as many times as specified, or as long as a specific condition is met.
Function calls: The code temporarily bypasses the subsequent code block, executing instead some other code block. After execution of the other code block the code returns (sometimes with some value) and continues the execution of the subsequent block.
GOTO-statements: The code bypasses the subsequent code block, jumping instead directly to some other block.

Are constructs similar to these present in DNA? If yes, how are they implemented and what are they called?


texts: I am working on pectinase enzyme assay. I incubated 900 ul of substrate for 10 minutes in the water bath, followed by adding 2ml of DNSA reagent, then 100ul of enzyme extract added finally i read the absorbance @ 540 OD. However the values are high. How can I troubleshoot high enzyme blank values in Pectinase assay ?


texts: Why is selfishness the 'obvious' strategy?

texts:
Thinking of behaviours an organism can adapt, at the very base an action can always be either selfish or altruistic (cooperative).

Usually, selfish behaviour is assumed to be the preferred choice and the question is how altruistic behaviour comes about.

But if reciprocal altruism can give both participants a higher benefit than their respective costs (which it usually does), why would selfish behaviour (in the sense of behaviour which reaps benefit at another entity's expense) be what we assume to happen? If evolution tends to optimise things, why does it not optimise this?


texts: How does energy conversion happen (chemical to mechanical?) in moving body muscles?

texts: From my understanding, the brain sends electrical pulses through neurons to different part of the body to initiate a movement. My question is, how is the movement realized? For example, in a train, steam engine is used to convert heat energy to mechanical energy to move the engine. Similarly, in the body, I understand the energy is stored in chemical form. How is this converted to the mechanical motion of a body part?


texts: Why are essential fatty acids so essential? I know that if taken less then it would cause diseases, but what metabolic role do they play? Are their importance is just because of their structural role?


texts: Why does the brain produce cannabinoids?

texts:
I've been reading lately about the brain producing cannabinoids. I was introduced to this idea by the Wim Hof Method which has been shown to increase the amount of cannabinoids (that is, compounds simulator to those found in cannabis) produced by the body.

Could anyone enlighten me on why the body naturally produces cannabinoids in the endocannibinoid system other than the shallow explanation that they have any anti inflammatory effect?


texts: How to clean and preserve a cicada's molted exoskeleton (exuvia)?

texts:
I found a good quality molted exoskeleton (exuvia) of a cicada, about 3-4 cm long on the ground. I'm amazed at the completeness and detail, the exit hole is in the center of the back and you hardly notice it. The "claws" on each foot are sharp and you can stick it onto any surface with a bit of roughness.

It had rained and there is some mud on it. I'd like to gently wash it and then keep it.

Are there any particular guidelines or techniques I should know about? Can I just gently swish it around in soapy water and then let air dry, or do I need to take some precautions, or even use some kind of fixative? Humidity is high where I live; anything that can possibly support mold will get moldy if you are not careful!

Sorry I can't add a real photo right now but it looks a bit like the emptying exoskeleton in this randomly chosen photo from here:


texts: Are there any trees that prefer to grow on the floor of water bodies but protrude to the air? Specifically, those that prefer salt water or grow on shallow sea.


texts: Why does the Vas Deferens detour over the pubic bone?

texts:
I was surprised to learn that the vas deferens detours over the pubic bone instead of taking the obviously more direct path.

https://human.biodigital.com/widget?be=u1P&uaid=1ly5V

Because I would assume that the vas deferens is more prone to damage facing the front. Also its damage would put procreation at stake.

Hence my question: Is there a biological reason for this path? Some advantage which outweighs or balances its disadvantages?


texts: Could an organism theoretically produce a metamaterial-like structure?

texts:
I'm curious to know if this is physically feasible because during my reading up on synthetic biology and just general research i realise that life is capable of producing some exquisitely complex materials and biological structures and wondered if they could potentially recreate artficial materials that aren't found in nature well not yet anyway. Could such a structure evolve naturally or would it have to be designed or directed via synthetic biology techniques?

Thank you for your time.


texts:
I often see the term "carbon in the soil" (example) but I cannot figure out what it is. It's a positive goal too - people want agricultural techniques that do not deplete it.

What form does this carbon exist in and what are the major sources? How does it help plants and other organisms who use the soil?


texts: Ploidy of Central cell in embroidery sac

texts:
In the unfertilized embryo sac in angiosperms, is the central cell considered to be haploid or diploid? though it has two polar nuclei but both of them are haploid, so I don't think it can be considered diploid.
(Actually, I encountered a question that specifically asks the number of haploid cells in an unfertilized embryo sac.)

Please help.


texts: Is Insulin-Glucose dynamic Lotka-Volterra?

texts:
From Wikipedia:

The Lotka–Volterra equations, also known as the predator–prey equations, are a pair of first-order, non-linear, differential equations frequently used to describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey. The populations change through time according to the pair of equations:

\begin{align}
\frac{dx}{dt} = \alpha x - \beta x y \\
\frac{dy}{dt} = \delta x y  - \gamma y
\end{align}

This looks very similar to how Insulin and Glucose interact with each other in the body.

Glucose uptake release insulin and glucagon offsets the effect of insulin through glycogenesis.

Can the Glucose-Insulin dynamic be described as Lotka Volterra?


texts:
There is a bush in my garden that I love to observe, as it often has large rain spiders building nests in its leaves, but I occasionally notice large groups of an orange-headed insect on the leaves, and I can only assume that they are the primary prey item of the spiders, but I can't seem to identify them, and I only managed to get a picture of one this morning, as they usually run and hide if I get close enough for a picture.

It has a very similar morphology to a cockroach, in my opinion, but after looking over common species in the area, I still have no matches, it is around 2 - 2.5 cm. I have never seen them anywhere but this bush. I live in Johannesburg, South Africa.

I would really appreciate any help in identifying the species.


texts: Are there specific non-protein substances that pathogens release into their host?

texts:
Reading research articles, I have found out that proteins called effectors get released into the host cell when a pathogen attacks a host. My question is, whether pathogens also release non-protein substances?

Have these substances been extensively studied and classified? Is there a list of such compounds? Are these compounds unique to pathogens?


texts: programmatic fast search of 100-1000 short reads to a public server and obtain list of nearby genes

texts:
What are the options for programmatic fast searching of 100-1000 short reads to a public server and obtain list of nearby genes where the reads map?

Input: ~100-1000 short reads

Output: GFF list of genes it maps to or nearby genes

Genome UCSC is restrictive to the number of searches and AFAICS it won't allow programmatic use.

Any ideas? I've asked this question to another forum without much luck:
https://www.biostars.org/p/114124/


texts: Why does hair thicken and become more rough after a razor shave but not after one using a trimmer?

texts:
If a razor cuts only the hair, then how does hair thicken and become more rough with a razor shave and not after one using a trimmer? If both are used for hair removal, why is there a difference in hair growth?

I have been using a trimmer for 1 year, but the growth of hair remained unchanged.  When I started shaving with a razor, the hair growth thickened.


texts: What does the number after Vitamin B signify?

texts: Does the number after Vitamin B signify anything? For example what is the significance of 12 in Vitamin B12?


texts: Did animals evolve from plants? Did animals' ancestors have chloroplasts in their cells?


texts: What are the effects of the common cold in an immunodeficient person?

texts:
How would the virus causing the common cold (rhinovirus) affect the human body in the absence of a normal immune response? On the linked wiki page it is said that the runny nose and fever symptoms are in fact caused by the immune response, rather than the rhinovirus itself.

Suppose the immune system is severely impaired (immunodeficiency), how would infection with the rhinovirus affect the body? Would the host not develop any symptoms then?


texts: Does blue light cause stomata to open or close?

texts:
In my biology lecture notes, it says that blue light causes stomata to close.

But thinking about it logically, since plants absorb a high percentage of blue light compared to light at other wavelengths, so wouldn't it cause stomata to open?


texts: Why is it harder to sequence plant genomes than animal genomes?

texts: Plants seem to be less complex organisms than animals, but despite that there are less plant genomes sequenced. Is that because plant genomes are more complex, for example in terms of regulatory regions and transposons that make sequencing more difficult, or are there other reasons why the number of sequenced plant genomes is smaller than animals?


texts:
What does "Psychomodulatory" mean in the context of potentially psychoactive drugs? That is, in this journal article http://www.sciencedirect.com/science/article/pii/S0028390812001931 in the discussion (you will need special privileges to access the article via an institute or personal subscription or by paying for access) in the last sentence of the first paragraph it says

  However, euphol even when given in very high doses, (up to 100 mg/kg)
  it did not show any evidence of psychomodulatory effects in the CNS


texts: Do Type 1 (Slow Oxidative) muscle fibers also make use of glycolysis?

texts:
I'm aware that slow-twitch fibers make use of oxidative phosphorylation; however, I am unsure if this is done in conjunction with glycolysis and the krebs cycle? Do these muscle fibers go through all three stages of aerobic respiration, or just the final step? If not, where are they getting the precursors for oxidative phosphorylation (NADH, FADH2)? Would they use fatty acids and proteins as precursors in the krebs cycle (if applicable)?

Slow-twitch (Type IIB) seem to use glycolysis and then anaerobic respiration (forming lactate), right?

Any input is greatly appreciated!


texts: What is the importance of alkaline condition in biuret test?

texts: Biuret test aims to quantify the amount of protein in a given unknown sample. Biuret agent contains copper sulphate, sodium potassium tartrate and Sodium hydroxide. Coppper ions form the complex of purple colour. Sodium hydroxide is added to make the solution alkaline. Why is it needed to make the solution alkaline?


texts:
I am stumped by two questions:

Why do we take only the initial 10%(or may be 9.99999....%) of S conversion as the rate of the enzyme reaction. why not more than 10%?
Why doesn't the velocity keep on increasing linearly until the Vmax is reached (as all the S molecules get exhausted)

Research and attempts to answer:

Why v0's 10%?

Steady state kinetics apply when the [ES] is constant, on reaching 10% [P] (for a uni uni reaction) the backward reaction increases, increasing the [ES]?
On reaching 10% conversion the rate decreases, so we measure the optimum activity.

Why doesn't the velocity increase linearly until all the molecules are used up?

Since an enzyme's turnover number (kcat) is constant...
...

Disclaimer :

'have put two Qs together.
Didn't find relevant Q on BioSE.


texts:
There is an old forest near me that has lain untouched for at least 150 years and possibly longer. The forest is on a big hill which is surrounded by a marsh.

The great majority of trees in the forest are gigantic hemlocks with aspens a distant second. The aspens are only found in the lower lying areas.

I am puzzled why there are so few deciduous trees in the forest. Deciduous trees are the most common around the town, and hemlocks are relatively rare outside the forest. The only deciduous trees in the forest are maples, and the few maples that are there tend to look sickly.

Why would there be so few deciduous trees? Do the hemlocks kill them off somehow, or would it be due to the soil?


texts: Gene expression for mathematicians: where to start?

texts:
I am a PhD student in mathematics, and I will be involved on a project that aims to cluster (i.e. automatically group) people according to their gene expressions.

Well, the project looks very nice, but I have no idea of what gene expressions are and consequently how to model them mathematically. So here are my questions.

Is there a "Gene expression for dummies" manual that I can read, considering that my last studies of biology move back to the high school (10+ years ago)? Any suggestion, also divulgative books?

Is there a good reference to study how gene expressions are modeled under the mathematical point of view?


texts: What is the minimal focal length of the human eye?

texts: What is the minimum length to which the focal length of our eye can go, even when  considering the blurred images too.


texts: Are there any culinary fruits that are not botanically fruits or accessory fruits?

texts:
Many culinary vegetables are botanically fruits. For example, the tomato, bittergourd and the cucumber are generally considered culinary vegetables, but they are botanically considered fruits.

Does the reverse also hold true, in that are there any plant parts that are considered fruits culinarily, but are botanically not considered fruits or accessory fruits?


texts: Is Inosculation of Young Roots Impossible?

texts:
I have only seen root inosculation to occur on old surface tree roots. Planting trees closely together (almost) always results in a tangled mesh of individual roots. Even though they are quite tightly packed, they do not fuse/inosculate.

Is there a fundamental reason, such as the Casparian strip, that precludes the possibility of (young) root inosculation?


texts:
I live in a region with cold winters (ca. -40 C) and many quite small birds (sparrows, crows, ducks) stay for the winter.

How can the birds survive this?

As I understand it, smaller bodies will be less able to produce and retain heat. Despite this, birds seem to cope much better than humans, sitting in the cold all winter and even swimming in cold water. In comparison, humans lose mobility in their muscles when cold, and can suffer severe frostbite causing them to lose fingers, toes, or limbs from relatively short exposure to the same conditions.

What specific adaptations allow birds to cope so well in these conditions?


texts: What is the degree distribution of synapses per neuron in the human brain?

texts: I believe the mean number of synapses per neuron in the human cortex is around 6000.  What is the distribution around that average, either for the cortex or for the whole human brain?  E.g., is it normal, power law, etc.?


texts: One of my friends has seen this insect-like species in water in the mountainous area in Iran (near Qom).


texts: Is there evidence that some non-human species perform sexual selection based primarily on intelligence? How do they do this?

texts: I'm a biology amateur, but it seems like sexual selection is almost always performed based on physical characteristics, the outcome of physical contests, or some sort elaborate courtship. But do any non Homo-Sapiens perform sexual selection based on intelligence factors, like problem solving abilities? If so, how does the species accomplish this? I know natural selection as a whole would definitely favor intelligent individuals, but I'm curious if any species actually takes this into account when choosing mates.


texts: Large set of semen microscope images needed

texts:
As a course project I have to write an algorithm whose purpose is to analyze a sperm sample (total number, motility etc). In order to do that though, I need to have a sufficient number of images to use during the coding and testing parts.

Do you know if there is any dataset available with semen images? It would also help if the corresponding stats of the images are also given, so that I can use them as a benchmark to see how well my algorithm works.

Thanks in advance


texts: Random Mutagenesis vs Directed Evolution as Strategies to boost expression

texts:
Do people use random mutagenesis (say using UV) to generate host variants that have high expression of a metabolite / enzyme? I've seen it mentioned as a strategy but it confuses me as to why.

How does that compare to using Directed Evolution for the same purpose? Intuitively, random mutagenesis seems highly inefficient (since you have no control over which genes you mutate) given the combinatorial explosion even in something like E Coli's genome size. Am I making a mistake in this reasoning?

What are situations where one may prefer random mutagenesis over directed evolution? Are there any pros and cons to consider?


texts: Need to make a library of mammalian coding sequences

texts: I want to clone ~100 different coding sequences from human or mouse into an expression vector to analyze phenotypes in tissue culture. I can do all of the steps, but I'm not sure what I should use as the template for my reactions. Ideally, I would purchase a pool of full length cDNAs from a bunch of organs, and amplify from that. Less ideally, I can generate cDNAs myself, from multiple organs and pool them. Does anyone have suggestions on a template source?


texts: Why are bats the source of dangerous coronavirus pandemics?

texts:
Why do coronaviruses come from bats?

I mean, why precisely coronaviruses and not (for instance) herpesviruses?
It looks like bats host more zoonotic viruses (per species) than rodents, although they don't develop any sign of disease.

The article above says that rodents host more zoonotic viruses than bats overall (68 against 61), but at the same time most of the latest pandemics originated from bats.

It also seems that bats could be involved in the maintenance of ebola viruses.

My question is: why did these major pandemics originate from bats and not from rodents, although rodents host more zoonotic viruses overall?

We should also take into consideration that human-rodent interaction is usually more likely than human-bat interaction, except for people who consume bats (like Chinese people; this would (partially) explain why both SARS and 2019-nCoV developed in China).


texts: Short DNA triplex strands have been identified in various organsims. But, would injecting a single strand of DNA or RNA (with its bases complementary to the bases of DNA found in the major groove of a certain gene ) cause it to form a DNA triplex   at that gene?


texts:
In chemistry, I studied the decomposition of water as being $2H_2O_{(l)} \rightarrow 2H_{2(g)} + O_{2(g)}$. However, when water is split, the equation is $2H_2O_{(l)} \rightarrow 4H^+ + 4e^- +O_{2(g)}$. Why is that? How does $H_2$ just ionize?

Moreover, what is the mechanism for photolysis? I would have thought that splitting water molecules requires a ton of energy; yet it can be accomplished simply with light energy during photosynthesis?


texts:
The famous Hershey and Chase Experiment uses phages to inject genes into cells.

In the beginning, Professor Yamanaka injected 24 types of genes into cells to figure out which genes turn a cell into ES cells.

Did he also use phages?


texts: How good is information transfer between the hemispheres of the brain?

texts: I sometimes listen to lectures on my phone using ear buds, but occasionally with only one ear bud in. Is the other half of my brain losing out on any aspect of the lecture? Just how good is the corpus callosum at sharing information between the hemispheres?


texts:
I was studying the FitzHugh-Nagumo model with diffusion and I quite do not understand the meaning of it.

If we consider the system without diffusion,

\begin{equation}\label{FHN}\begin{cases}
\dot{u}=\mu\left( u-\frac{u^3}{3}+v+z \right), \\
\dot{v}=-\frac{1}{\mu}\left( u-a+bv \right),
\end{cases}\end{equation}

where $u=u(t)$ and $v=v(t)$, then it models the control of the electrical potential across a cell membrane. It models the action potential in neurons, for example. But this happens because in the system there is a stimulus current, $z(t)$. The system with diffusion

\begin{equation*}\begin{cases}
\frac{\partial u}{\partial t} = \epsilon D_u \nabla ^2u+\frac{1}{\epsilon}(u-\frac{u^3}{3}+v), \\
\frac{\partial v}{\partial t} = \epsilon^2D_v \nabla ^2v-(u-a+bv),
\end{cases}\end{equation*}

where $u=u(x,y,t)$ and $v=v(x,y,t)$, models exactly the same but just adding diffusion and removing the stimulus current.

How can it model the same biological behaviour if the stimulus current disappears?
Therefore, which is the exact meaning of this sistem (the second one)?

I've implemented numerically this system, and ploting $u$ in terms of $x$ and $y$ in a specific time, I get something similar to the following images:

https://chemoton.files.wordpress.com/2010/07/fitzhugh-nagumo-type-reaction-diffusion-system-i.png

Where the first image corresponds to $t=0$, the second one $t=10$ and the last one $t=100$.

What does this pattern formation mean? I do not know how action potential (which is modelled in this system) is related with these images...
Does this happen because the activated cells activate the ones in the neighbourhood (since diffusion acts)? Or this is wrong because the system only takes into account one single neuron?

Thank you so much!


texts: Why do trees prefer their sunlight a bit diffused?

texts:
I don't know what "a bit diffused" here means.

Do other plants also "prefer their sunlight a bit diffused"?

     Mount Pinatubo was the most powerful volcanic eruption in nearly one hundred years. Within two hours of
the main blast, sulfuric ash had reached twenty-two miles into the sky. By the time it was done, Pinatubo
had discharged more than 20 million tons of sulfur dioxide into the stratosphere. What effect did that have
on the environment?
      As it turned out, the stratospheric haze of sulfur dioxide acted like a layer of sunscreen, reducing the
amount of solar radiation reaching the earth. For the next two years, as the haze was settling out, the earth
cooled off by an average of nearly 1 degree Fahrenheit, or .5 degrees Celsius. A single volcanic eruption
practically reversed, albeit temporarily, the cumulative global warming of the previous hundred years.
     Pinatubo created some other positive externalities too. Forests around the world grew more vigorously
because trees prefer their sunlight a bit diffused. And all that sulfur dioxide in the stratosphere created
some of the prettiest sunsets that people had ever seen.

Dubner, Levitt. SuperFreakonomics: Global Cooling, Patriotic Prostitutes, and Why Suicide Bombers Should Buy Life Insurance (2009). p 176.


texts:
I have tried to make cDNA libraries from FFPE tumor blocks (highly degraded RNA) using the 3' end RNA seq protocol provided by West lab. Here is the link for the same.
http://med.stanford.edu/labs/vanderijn-west/Protocols.html
After PCR enrichment, a gel purification step follows. My trouble was, the fragments always gave rise to a smear rather than a band between 200-300 bp. Can anyone provide any suggestions as to why this may be happening?
Thank You


texts: Is this long black insect with semi-long antennae and a large segmented abdomen caught in the kitchen a larva or an imago? And what is it?

texts: This is in Northrhine Westfalia in Germany/Europe: we have those large longish and comparatively flat bugs (taking my hand below the plastic as reference, it should be about 4cm or 1 5/8in in length) or larvae in our kitchen occasionally.  For a larva, it seems to be lacking any soft parts.  It can raise its behind "threateningly" in the style of a scorpion but I doubt it's anything but mimicry.  Its large head reminds me of ant soldiers, though it is obviously out of scale.  I think it's mostly in the evening or night that we find one (and it's often because a cat stares at it in an obvious manner) and while it's usually the kitchen, that may just be because we are most frequently there.


texts: Can a brain be damaged by overstimulation?

texts:
I am wondering what, if any, long term health effects there are from high levels of brain activity.

I don't mean cases where a brain is being artificially stimulated, but rather where there is a high (as in the high end of normal, not as in shell-shock) sustained level of sensory input, or simply that the brain in question is "thinking too much".

Assuming a person could sustain high levels of neural activation, is there a chance that the brain could "strain" itself or somehow "wear out" or come to some other kind of harm?


texts:
The pectoral fins of a whale and a shark. Are they analogous organs?
I was looking at this question, and I saw that the two answers defined the range of 'same origin' differently. One said that sharks and whales have the same origin as jawed animals, (therefore they are homologous) and the other said that they had different origins, namely cartilaginous fish and mammals(therefore they are analogous). Now here's the question.

How large is the range of 'same origin' when determining whether two organs are analogous or homologous? Is it as large as a Kingdom or a Phylum? Class? Order? Family? Or is there another criterion?


texts: The Semi-Conservative Model of DNA Replication: Question

texts:
My Campbell's Biology textbook contains the following diagram related to the semi-conservative model of DNA replication proposed by Watson and Crick. I have highlighted where my confusion arises in red:

So, I understand what goes on in the first replication--that's pretty much straightforward. However, what I don't understand is why in the second replication, the light blue strand isn't paired with a dark blue strand. After all, aren't the light blue strand and dark blue strand complementary, per the results of the first replication?

After the light blue and dark blue DNA strands separate to serve as templates in Replication #2, why don't we see two dark+light double-helices?


texts: Why don't materials and methods describe culture media in volume?

texts:
After reading several materials and methods sections of cell culture experiments, I have not seen the recipe for culture media ever described in terms of volume.

  Human adipose tissue was obtained from six samples of abdominal fat from female donors (age range: 20–45 years) after receiving informed consent and cultured as described in a previous study.[15] Briefly, samples were washed extensively with sterile phosphate-buffered saline (PBS) to remove contaminating debris and red blood cells. Washed aspirates were treated with 0.075% collagenase type I in PBS for 30 min at 37°C with gentle agitation. The collagenase I was inactivated with an equal volume of DMEM: F12/10% fetal bovine serum (FBS) and the infranatant centrifuged for 10 min at 800 rpm. The cellular pellet was resuspended in DMEM: F12/10% FBS and plated at 20000 cells/cm2 in T75 flasks in DMEM: F12 medium supplemented with 10% FBS and %1 Penicillin/streptomycin. After 24 h, it removed the nonadherent cells and expanded the adherent ADAS cells by serial passage. In this study, we used cells at passages 3–5 for all experiments and all experiments repeated at least in triplicate.

In this excerpt from the paper, Efficient transdifferentiation of human adipose-derived stem cells into Schwann-like cells: A promise for treatment of demyelinating diseases by Razavi et al, there is no mention of the volume of media used to culture the cells.

Moreover, there is no description of the height of the media in the dish, so it seems to me that from most cell culture descriptions, there is no way to properly reproduce the experiment simply by reading the paper.

Why do these sections fail to specify volume information?
Is there something that I'm missing here?


texts: Why is the probability of fixation of an allele equal to its frequency?

texts:
Introduction

In a panmictic population, the probability of fixation of an allele at a neutral locus is equal to its frequency at that time. I will refer to this probability of fixation as calculated at time $t$ as $P_{fix,t}$.

If $p_t$ is the frequency of the allele $A_1$ at time $t$, then the probability of the allele $A_1$ to reach fixation (rather than disappearing) is $P_{fix,t}=p_t$. Typically, the generation when the mutation occurred, the probability of the new allele to get fixed is $P_{fix,0}=p_0=\frac{1}{2N}$, where $N$ is the population size.

Question

This simple and classic result makes very good intuitive sense to me. However, I would fail to provide a mathematical proof.

Can you please demonstrate that $P_{fix,t}=p_t$?


texts: Gene perturbation, what is it used for, explain to computer scientists?

texts:
I am trying to build a gene regulation network, and I need some basic knowledge of it.

So, in gene research, we perturb genes. Such as knock down them?

Can people tell 2 or 3 experiment methods to perturb genes?
And 3 or more observations (phenotypes) after perturbation?

If it could be explained in the context of Microarray, it will be well appreciated.

The question is not that organised, if you can tell a whole story before the computational work started, I will thank you so much.


texts: How to convert bwa mem output to BAM format without saving SAM file

texts: I want to go straight from bwa mem alignment to BAM format as I don't need the SAM file and it takes up too much space. How do I achieve this?


texts: Why are there different species of bacteria?

texts:
The usual (high school or intro to bio) explanation for diversification of species comes from multicellular, usually sexually reproducing organisms, and seems to be closely tied to the biological species concept.  It is that once organisms are different enough, they will be unable to exchange genes and therefore gradually become more distantly related.

This is not really applicable to species of bacteria which can exchange genes through horizontal gene transfer (obviously not all can, but many can).  It seems to me that if HGT rates are low relative to mutation rates, the same process of diversification could take place.  However if they are high (and random), it seems like either species would not exist as discrete entities or would exist only because the environment was only favorable to specific collections of genes.

Is there a commonly accepted reason why species should exist among species which have horizontal gene transfers (ie is there a reason to expect that HGT rates will usually be very low), rather than bacteria existing as a continuous gradient?


texts:
I am a member of a local fish club, we have a lot of different aquarium fish and would like to trade them amongst us. We all have a few fish that don't form pairs and would like to see if they pair up with someone else's. But as you can imagine keeping track of all the fish would be extremely hard and pointless if they were the same gender, so someone suggested we should buy a microscope and sex them via tissue or blood sample. But none of us has any experience doing that or if that is even possible, so we need some expert advice on the matter.

I wish to know if you can tell the gender of a fish from a tissue or blood sample and what equipment do you need (how much magnification in a microscope)? We work with discus and other cichlids, and countless marine aquarium fish.

For the sake of being specific I restrict my question to Discus fish, however, I would like to know if any general principles of tissue-sample based identification exist, for different species of fish.


texts:
I just saw a video about the biology between sunburn, UVA and UVB and the different things we know about sunburn in humans. ( http://www.youtube.com/watch?v=ZSJITdsTze0 )

I wonder what keeps plants from getting sunburned?

By sunburned I meant that ultraviolet light injures the plant so that it requires some sort of healing process for the plant to be as healthy/strong/resistant to disease as a plant that isn't harmed.


texts: Is Mutation Theory still "valid" for complex organisms?

texts:
I'm afraid like most people I suffer from having learned "A History of Evolution" in school, rather than cutting to the chase and learning the actual "up to date" version of the subject. (Imagine if programming classes did the same thing and you were forced to learn FORTRAN and BASIC before learning JavaScript) So please help me fill in some gaps:

From what I have been taught, Natural Selection (or even Artificial Selection) is great for panning favorable genes from a species and bringing them to the fore, however, it does not introduce new genetic changes.

It is possible to introduce new genetic changes through mutations. When asexually reproducing organisms receive a mutation, they pass that mutation on to their offspring. Mutations are somewhat rare, and beneficial mutations even less so, but happen frequently enough to make a dent over a long period of time.

The problem I don't understand is with larger organisms, aren't those already rare mutations only passed onto offspring if they occur in the short-lived sperm or egg cells of one of the parents*? At the very low probability of a beneficial mutation occurring in a single cell of a male's leg, not only is it unlikely he would benefit by this mutation, but even if the male reproduced, this mutation wouldn't be passed on, and would die with the male.

Are mutations viable methods to introduce new variations in more "complex" organisms that reproduce sexually? Or is there another theory or system that bridges Natural Selection and Mutation Theory in larger organisms?


texts: How much of the total RNAs is tRNA? Some say 15% and some 20%. Those percentages came from my different teachers. Which is correct? And what are the functions of the extra arm (variable loop) of tRNA? My teacher said it was just for classification but an international textbook says its function is unknown.


texts: What is the formula to establish ec50 reproducibility with respect to dose response curves for some drug?

texts:
The EC50 is determined by fitting a standard curve to the experimentally obtained control values for each dose response curve using some software that does trial and comparison until satisfactory(nonlinear regression).

In the literature, it is mentioned that experimentally obtained control values for the dose response curves, are EC50 reproducible. To my current understanding meaning that EC50's obtained for different for several dose response curves are actually 'close enough'(in some formal statistical sense) together. Is there some procedure or formula for formally establishing EC50 reproducibility?

Thank you :)


texts: Does adding milk to cereal make it harder for our body to absorb the vitamins and minerals from the cereal?

texts: I add about 3/4 cups of Blue Diamond almond milk (unsweetened) every morning to a single serving of Cheerios. The milk contains filtered water, and I read that drinking water with food at the same time makes it harder for the small intestine to absorb the nutrients from the food. Has this been verified?


texts:
I have seen so many news and study online, saying exercise keeps body healthy in old age and keeps us fit? how is this possible normal tear and wear will become more with activity hence more mutation hence more loss. Why exercise help?

Tear and wear means lots of regeneration in our body, regeneration will lead to mutations, no regeneration is perfect, hence more regeneration's, more risk of bad DNA.


texts: What forms the base of the coral reef ecosystem?

texts:
Corals are small animals that form a symbiotic relationship with algae. The algae produce sugars for the corals and are in turn provided with needed nutrients and protection from predators.

That's all great, but it doesn't explain where the amazing diversity of fish, mollusks, crustaceans, everything else comes from. As far as I can tell, the whole point of the coral's success is that their hard skeleton protects them from all but the most specialized predators.

So if the corals don't directly add (much) energy input to the coral reef ecosystem, what is it that makes the reefs so productive and diverse? Or, put another way, what makes a coral reef environment more productive than simple phytoplankton floating in the open ocean?


texts: Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?

texts:
Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based on the thermodynamic stability of the sequence. The GC-rich stable hairpin together with the destabilizing U-repeat supposedly destabilize the binding of the polymerase enough to cause it to disassociate from the template.

What I'm looking for are specific requirements on the termination sequences that are not based on thermodynamics.

Are there any specific requirements on the hairpin sequence beyond a certain thermodynamic stability.
Are there any loop variants that are known to reduce the termination efficiency?
Does the shape of the hairpin, e.g. any kinks or bulges in it, have an influence on termination efficiency?

The typical requirements I read are 5-14bp and GC-rich, and I'd like to know if there are any more specific requirements, especially ones related to the structure and not the stability of the hairpin.


texts:
It is about 1-2 mm long. It also can fly and it stays on the wall.

Location: Lebanon.


texts: Longevity and extent of transfection after SARS-COV-2 vaccination with Janssen

texts:
The Johnson vaccine, unlike the RNA vaccines from Pfizer & Moderna, uses a vector containing DNA encoding for the SARS-COV-2 spike protein. This vector DNA needs to enter the cell, allowing for transcription and translation into viral spike proteins to occur (Fig. 1). These spike proteins are then exposed on the cell surface by the host cells, thereby exposing the antigenic epitopes, creating the immune response.
Basically, this turns the immune cells against their own host, because they are expressing foreign proteins on the cell surface. In effect, I presume, those host cells are subsequently destroyed by the immune system.
Now I was wondering if there has been any research done revealing the consequences of this auto-immune response. In particular how long does it take to get rid of all the transfected cells (or 'vaccinated cells' as they tend to be called) and what is the extent (volume/area affected) of transfected cells? Basically you are genetically altering the host's cells  that are subsequently attacked by the immune system. So I am basically interested in the pharmacokinetics of the vaccine I guess.
This safety report from EMA says that in 1 animal (from how many?) there was still genetic material after 180 days to be detected. However, the report says nothing about the extent of transfected cells nor anything about the auto-immune damage after the host attacks its own cells. No references are to be found either; it all seems to be about internal safety studies.
In retrospect I'd rather not have had the Janssen vaccine; I bet mRNA vaccines are a lot more instable, guaranteeing safe removal of the foreign genetic material.
Anyway, I'm drifting... In short, (1) how long does it take to clear all signs of foreign DNA from the host after Janssen, and (2) what is the extent of the cells that are transfected and subsequently attacked and damaged/killed by the host?

Fig. 1. Schematic depiction of the DNA vaccine from Janssen. source: Livingstone et al. (2021)
References
- European medicines agency, Assessment report COVID-19 Vaccine Janssen
- Livingstone et al., JAMA (2021); 325(15): 1575


texts:
I have a DNA sequence that makes protein 1. but now I have asked to:

compare the amino acid sequence of protein 1 with nine homologous proteins and make a multi sequence alignment (MSA) of the sequences.
Determine a consensus sequence for the proteins based on the MSA.
Find any specific parts of the proteins that are conserved, then explain why these parts are conserved.


texts: why is erythrocyte sedimentation rate higher in females?

texts:
erythocyte sedimentation rate should be independent of the sex.
what is the reason behind this sex bias and why does it increase during pregnancy and how does age influence it.


texts: Does repolarization of muscle fibers mean that the muscle bundle is relaxed?

texts: If I flex my bicep and continue to contract it does it mean that the muscle cells are in depolarizing state and not repolarizing?


texts:
Each year, large volumes of crop are harvested from fields.

Where does this biomass get replenished from?


texts: term for species that produces males only to mate with mother or sisters

texts:
In reading about unique reproductive strategies I've run into two closely related and comparatively unique mechanics.  Both involved a female who was born 'pregnant' with at least a male, but the male sole job was to impregnate the mother/sisters prior to immediate death, with the females never mating with a male other then their relative.  Thus, the outcome feels more similar to self fertilization of hermaphrodites then your traditional mutli-sex mating strategy.

I have heard of at least two species that did this.  One in which the son was born along with a batch of females that he immediately mated with, another where the son actually mated with his sisters while still in the womb, and the children would then eat their way out of the mothers corpse to be born (fun stuff!)

I also recall reading an article which said a mother would lay an egg to have a son who would mate with the mother to produce females and then immediately die.  However, this sounds so similar to the Haplodiploidy system that I wonder if the article I had been reading was simply misrepresenting a regular Haplodiploidy system by implying the males would never mate with other females (I read about it awhile ago so not sure, does anyone know if a species uses a haplodiplody system where the male never survive long enough to mate with other females?

I'm wondering if there is a name for this reproductive strategy.  Specifically for any strategy where a male is produced, but only as a means of providing DNA to mother or sisters; with no means to mate with non-familiar entities.


texts:
A while ago I received a pack of seeds described as Pycnanthemum Pilosum / Mountain mint. The seeds are small (below 1 millimeter) and brown:

Plants grown out of these seeds are around 40 centimeters high and spread widely. Leaves are bright green and smooth, around 3 - 4 centimeters long:

with strong minty smell (though quite distinct from let's say Mentha × rotundifolia or Mentha spicata).

Stems are square, with very short hairs.

Recently plants started to flower:

producing clusters (around 1.5 cm in diameter) of small (3 - 4mm long), slightly  flowers along the stem. Flowers are white, with light shade of purple. with no spots or other marks.

The plant started to flower in the first year after sowing (the plant is around 4 months old, planted outside, in Central Europe).

The plant doesn't really resemble Pycnanthemum pilosum descriptions I found online (for example this or this), which, among other differences, describe long and narrow leaves.

I wonder if someone can help me identify it. Thanks in advance.


texts: Is the SRY gene the sole responsible of biological male sex?

texts:
It's very well known that the Y chromosome is what determines maleness, but more specifically this seems to happen thanks to the SRY gene located on it. Some individuals have an XX karyotype, but because of unequal crossing-over between X and Y chromosomes during meiosis in the father, one of the X chromosomes ends up containing the SRY gene, and the individual develops into a male (De La Chapelle Syndrome).
So I was wondering, is the SRY gene all that's really needed for an individual to be, unquestionably, a male? It's kinda odd how XX males have male genitalia but are classified as intersex solely because their karyotype is a typical feminine one (which should be irrelevant given how they also possess the SRY gene).


texts:
Are there any non-asexual species in which the male of the species produces the offspring?

If so, why are they considered male and not female?


texts:
I wonder what the principal ways of (direct) cortico-cortical connections are.

I came up with the following possibilities:

vertical: a cortical neuron connects to another one in roughly the same cortical column, but in another layer
horizontal: a cortical neuron connects to another nearby one, preferably in the same or neighboring layer
"intragyric": a cortical neuron connects to another one in the same gyrus (see here)
interhemispheric: a cortical neuron connects to another one in the same (or neighboring) area of the opposite hemisphere

Are all of these relevant? And/or are there relevant but completely different ways of cortico-cortical connections, e.g. "intergyric"?

Addendum: Maybe too late I found a concise summary in the Wikipedia articles on white matter and association fibers (the latter term I wasn't aware of when I asked my question), which doesn't contradict and complements Bryan's answer:

intracortical (Bryan: "intracolumnar" vs. "horizontal")
short association fibers ("also called arcuate or U-fibers [...]  connect together adjacent gyri")
long association fibers which "connect the more widely separated gyri and are grouped into bundles" (often called fasciculi, but probably not exclusively)
commissural fibers (Bryan: "callosal projections")

There definitely seems to be no reserved name for something like "intragyric" fibers (see second addendum here).


texts: LacZ' selection: blue colonies despite ligation of insert

texts:
It has been suggested that bacteria transformed with pBlueScript vector, containing an insert in the middle of the lacZ' gene, can still give blue colour on X-gal, if the insert is small and ligated in-frame with the lacZ' gene (source: my course, ResearchGate).

I don't understand how it is possible that translation doesn't end at the stop codon encoded by the insert. Is this something to do with leaky termination? Moreover, even if leaky termination was possible, this would mean that there is ALWAYS a 1 in 3 chance of the insert being in-frame.


texts: What's this spring-like structure in the plant parenchyma cell?

texts: I observed a transverse section of an amaranth stem in biology lesson today. When I boost the magnification to 600X, I found this spring-like structure in one of the parenchyma cells near a vascular bundle. I could only find one of these in the section. Can anyone tell what structure is it?


texts: How two genomes adopt when cell goes to recipient's body from donor's body?

texts:
We often give blood to another following the blood giving compatibility chart. Heart transplant and similar transplants also brings one's cell to another's body.
My curiosity is, when a cell goes to the recipient's body from the donor's body, what actually happens with respect to the genome?
If the genomes do not merge to one, then how to identify one identically? How does DNA fingerprints, parent detection etc. work correctly? More generally, how does it maintain consistency?
Remarks:
My assumption was : "All the cells of one particular person's body carry the same genome or DNA information. And every individual has a distinct genome or DNA information". But after some study and some comments, I found that the statement is actually wrong.
However,  this article led me to break my wrong notion.


texts: What percentage of a Neanderthal's DNA could be in a Denisovan?

texts:
My questions arose from an online course video at 3:11-19

The professor mentioned that the Neanderthals were inbred with their cousins breeding together but the Denisovans were very diverse , with 70% Neanderthal's DNA, there was found mixing between Denisovans and an even earlier mysterious species.
The followings are my questions:

Did he mean that most of Neanderthals were prone to inbreeding? Why?
I'm not sure if that was exectly what he meant by 70% Neanderthal's DNA could exist in a Denisovan. If that were true, why not just called it Neanderthal if only 30% is not Neanderthal?


texts:
This is in Wroclaw, Poland.

I'll be here a few months and I've noticed that they come in large groups in the evening. They are everywhere outside, but I haven't seen any inside.
They seem to live in colonies because when you see one, there are 50 others next to it, all sizes (age I guess), but always the same type.

The large ones have body about 1-1.2 cm long but the colonies have some significantly smaller with them, like 1/4 of the size.


texts: Purpose of the conversion of 3-PGA to G3P in the calvin cycle?

texts: 3-PGA ($\ce{C_6H_7O_7P}$) is converted to G3P ($\ce{C_6H_7O_6P}$) before it is able to be made into glucose, with an expansion of 6 ATP and 6 NADPH. My question is why this process is needed and why the loss of 1 oxygen atom decides whether a sugar molecule can be synthesized into glucose. My take on this matter is that if they incorporate 3-PGA directly into glucose, they can save time and also energy in the form of ATP and NADPH.


texts: At what rate do chromosomal rearrangements occur?

texts:
How often do chromosomal rearrangements occur?

I am interested about these kind of chromosomal rearrangements that are passed on to the descendants, i.e. germ line chromosomal rearrangements. The value I am looking for is similar to the mutation rate but only take into account major mutations such as chromosomal rearrangements.

Supposing there might have some important variance in this rate among species, then I am interested in eukaryotes and particularly in plants. If needed, the answer can be split into the different types of chromosomal rearrangements (robertsonian translocation, other translocations, inversions, ...)


texts: Does cancer cells come from same process as evolution?

texts:
Here is how I understand it:

DNA replication is not 100% perfect and error can happen, this error can be good(evolution) or bad(cancer properties).
But its not the only source of cancer cells - DNA can be damaged by environment, and in rare cases it can receive cancer properties.

Am I correct?