texts: Can different Chromobactierum strains have completley different colony morphology?

texts:
In the analysis of an unknown bacterial broth I observed a gram negative rod genus. Upon plating I observed small, dark purple and convex colonies; corresponding presumably to Chromobactierum. After then replating the purple colonies I then observed white fillamentous colonies that were gram negative and was subsequently able to make an identification that suggested the organism was either of genus aeromonas, vibrio or Chromobactierum. I found an article showing that Chromobactierum colonies dont have to be purple and can have a range of morphologies (see link). My question is: upon replating, can the morphology of the two colonies change so drastically?( assuming I had two different strains of Chromobacterium present)

Source:http://jb.asm.org/content/66/4/470.full.pdf


texts: Do animals other than humans have different blood types?

texts:
Humans have the ABO and Rhesus blood typing systems. I have two questions about it:

Why have we evolved these blood types?
Do other animals have different blood types as well?


texts:
I have some genes which showed copy number loss between two groups. Now I want to see the copy number regulation of those genes. I really don't know about this concept. Can anyone please tell me clearly about this like why we need to check regulation of copy number loss genes? And any idea how to do this?

Thank you


texts: By just looking at an unlabeled picture, how do you know it is a protein?

texts:
I'm learning about proteins and need to understand this concept. What makes this colourful ball of squiggles identifiable? Why is it a protein, and not any other biomolecule (like DNA for example)? What are the colours showing? What are the variations in the shape of the image?

Basically, the question is: What is this image trying to tell me about this protein?


texts: What bacteria shed harvestable energy from root zone organic matter?

texts:
I recently heard of a successful effort that harvests energy from soil at plants' bases due to apparently bacterial breakdown of wastes from the plants:

  Via photosynthesis a plant produces organic matter. Part of this
  organic matter is used for plant-growth, but a large part can’t be
  used by the plant and is excreted into the soil via the roots. Around
  the roots naturally occurring micro-organisms break down the organic
  compounds to gain energy from. In this process, electrons are released
  as a waste product. By providing an electrode for the micro-organisms
  to donate their electrons to, the electrons can be harvested as
  electricity. Research has shown that plant-growth isn’t compromised by
  harvesting electricity, so plants keep on growing while electricity is
  concurrently produced.

Apparently there is more research here, and this was particularly interesting (a PDF) as it states more clearly that we are indeed talking about bacteria:

  The PlantPower concept is based on the cooperation of plants and
  microorganisms to produce in-situ electricity. Plants take up carbon
  dioxide and water and capture light energy. This energy is stored in
  the chemical bonds of sugars produced, using carbon dioxide and water.
  Part of this chemically stored energy is transferred to the roots of
  the plants. This energy present in the root zone can then be captured
  by the so-called electro-chemical active bacteria. These organisms are
  capable to oxidize the organic matter present in the root zone and
  transfer the energy rich electrons to an electrode. The energy carried
  by the electrons can be used as electrical energy, after which the
  electrons react at another electrode with oxygen to form water.

I would like to understand this process as far as what bacteria or "micro organism(s)" are being leveraged here.  It seems that they are supplementing the soil with some kind of bacteria that acts in this specific way of releasing additional electrons that can then be harvested.

Any idea as to what kind of micro organisms or bacteria have this kind of reaction wherein they release or excrete harvestable energy (and apparently CO2 + H+) upon consumption of plant "excretions" (C6H12O6)?

After doing a bit more digging, I have found some, perhaps, interesting information from Wikipedia:

What ultimately confuses me here is that the other method noted earlier does not really emphasize any particular kind of plant and therefore I can't help but think that perhaps there are some other more useful bacteria for this scenario...


texts: How exactly is the sunflower seed pattern calculated?

texts:
I came across this https://www.mathsisfun.com/numbers/nature-golden-ratio-fibonacci.html

and the rotation simulator just below the first section says to type in a number for each rotation. But, it doesn't explain what it is actually calculating.

If I type a number, by what angle is it rotating each cell, how is it calculating the initial number of cells, and how is it scaling each cell with each rotation to look like a sunflower? This definitely has come up in natural phenomena before like the nautilus spiral and the fern, so I want to know the generalization behind this pattern.


texts: What Ultimately Controls DNA Transcription?

texts:
Transcription of DNA and further splicing of mRNA is regulated by various transcription factors, small nuclear RNAs and so on; similarly such related mechanisms as transposition of transposons.

All such factors and mechanisms, including those linked to inter-cellular signalling mediated by peptides and various so-called epigenetic enzymatic processes, require and are dependent upon transcription itself, in the first place of DNA codons.

What mechanism then is supposed ultimately to control the expression, eventually as peptides translated from mRNA, of information encoded in DNA; if it is not peptides thus encoded? That is, since transcription depends on transcription factors which themselves require transcription requiring further transcription factors, does this mean that in the entirety of its function, DNA controls itself?

How then can DNA and its transcription be conceived as a such a self-controlling function?


texts: How do cold conditions help organ transplants?

texts: Body organs are kept cold in-between explanting them from the donor and implanting them in the new host. How do these cold conditions help organs to stay viable while they haven't fresh blood, energy and oxygen supply?


texts:
Getting old
Hello community, I have been thinking about age, and I thought that aging is the reverse of how a biological system is able to fix itself over time. Actually, some species actually are able to reverse it completely, such as the jellyfish and lobsters for up to 400 years in the Greenland sharks. Moreover, by evolution principle, those species must've exchanged this ability over others, which is noticeable considering they're really adapted to their habitats.
What does research tell us on aging so far?

According to Britannica, aging affects many dimensions for all humans.

So, when scientists are talking about "a cure to aging", I cannot comprehend whether they're proving that those are symptoms of some biological factor (such as producing a certain gene, etc.) or whether all of them share the likelihood to appear more often over a certain age?

How can studying those species help science advance in research?


texts: Why can't the human eye focus blue light?

texts:
I recently noticed that it is hard to focus on blue light sources, especially at night. When observing a blue light source, e.g. a neon sign, it looks somewhat blurry. A sign with a different colour right beside it looks sharp.

I already know about the three kinds of cone cells in the human eye (I'm not a biologist) with their spectral sensitivity peaks in in short (S, 420–440 nm), middle (M, 530–540 nm), and long (L, 560–580 nm) light wavelengths [1]. But does the spectral sensitivity correlate with focus? Or does our eye lens refract blue light in a different way?

When I screw up my eyes looking at a blue light, it becomes less blurry, but then all the other colours are blurred.

[1] http://en.wikipedia.org/wiki/Cone_cell#/media/File:Cones_SMJ2_E.svg


texts: Why are some viruses not communicable person-to-person?

texts:
Below are two quotes from the CDC about Hantavirus:

  "Researchers believe that people may be able to get the virus if they
  touch something that has been contaminated with rodent urine,
  droppings, or saliva, and then touch their nose or mouth."

and:

  "You cannot get the virus from touching or kissing a person who has HPS."

This is hard to believe.  So, since human saliva is not a problem, can you be contaminated
by human urine or human droppings?  The only way for me to interpret this logically is to
say that this virus lives at the end of the digestive tract (for both rodents and humans)
and people can be kissed because they have much better hygiene than rodents.  Is there a
better interpretation?

Also, is there a simple reason why Hantavirus leaves the mouth (moving to the end of the
digestive tract) of an infected animal, but influenza does not?


texts: Is there any biosafety level scale for plant pathogens?

texts: Biosafety levels commonly defined on basis of human/animal pathogens, but what would be the biosafety levels for plant pathogens?


texts: What makes delayed onset muscle soreness stop occurring?

texts:
If someone lifts weights or takes a long jog after not doing it for a while, they can experience delayed onset muscle soreness (DOMS).

However, when they return to the same exercise days afterwards, the chance of a new DOMS episode occurring diminishes.

I used to think that it was partly due to muscle getting larger. However, an individual who trains themselves to lift 100kg, stops for 2 months and still manages to lift the same 100kg can experience DOMS (assuming that little has changed in the muscle size and force it can exert).

This leads me to ask: are there other biological phenomena involved, rather than just muscle size?


texts: When is the lactase in lactose-free milk active?

texts:
Recently we have started suspecting that one of our children has hypolactasia (lactose intolerance), and so accordingly I have had my first exposure to lactose-free dairy- and dairy-like products. In addition to soy milk and almond milk, we have recently purchased actual dairy milk that was labeled lactose-free. This gave me the impression that they had used some process to remove the lactose, but looking at the ingredients more closely, it seems that they simply added lactase enzyme to the milk to assist breaking down the sugars.

My question is this: when is the lactase enzyme active? Does the lactase activity begin right as it is added to the milk, or will it not become active until ingested?

Essentially, I'm wondering if this type of milk can/should be used in cooking or baking. High temperatures will certainly denature the lactase enzymes in the milk, but if the lactose has already been broken down, this shouldn't be a problem.


texts:
I know that there is a variable region on antibodies which can recognize a wide variety of antigens, and that germinal centers create more "fit" antibodies to respond to an infection.

So I was just wondering:

Does this process itself evolve? Only vertebrates have this type of immune system if I understand correctly, do we actually get better (faster/more efficient) at responding to disease?
Is there any antigen which antibodies don't recognize?
Can an organism be so efficient at this process of immune response, that it essentially never gets sick or dies of disease?
There are cases where organisms contain viruses which do not harm them. Could an organism have this relationship with all viruses? As in, no virus is actually a disease to them?


texts: Why isn't Bubonic Plague as virulent as it once was?

texts:
Although I am admittedly not anywhere near an expert on any topic, I still have a hard time understanding how Black Death and Bubonic plague are one in the same. Since plague still exists, with news stories about it every once in a while, and especially in places like India, why doesn't it spread with anywhere near the rate it did during the Middle Ages?

Obviously global society in general is much more sanitary than it was then, people also tend not to live in close quarters with animals today as they did then, however in places like rural India and China this lifestyle still takes place and plague still exists, so why aren't there large out breaks of plague in these areas if it indeed is Black Death?

Is it possible that Black Death has been miscategorised due to various historical circumstances and scholarly errors?


texts: Are we evolving to age slower, or to live longer aging at the same rate?

texts:
I wonder why most of us find senior people lovely and charming. Is it because to love grandpa and granny is vital to our survival as a species, in the same way as we love babies? If so, it would mean that we are either aging slower with time, or being selected somehow to love senior people despite their physical appearance, while they are aging at the same rate but living longer.

Update

Let's say every common characteristic among individuals of the same specie is product of evolution.
Many caracteristics are passed by the individuals to their offspring, but only those that were advantageous in some way or another allowed the offsring to survive and pass that caracteristic to their decendants in turn.
Our love for babies and elders is one of those caracteristics that we as indivudials of  a species have in common.
That make us to want our elders to be with us as much time as posible, just becouse our affinity with them.
This love for the elder have to be an advantaje that worthed to be selected by the evolutionary process, and this caracteristic is reflected in the tendency of the life expectancy to increase generation after generation.
One could say, that those elders that age slower would be more likely to benefit from the love of their offspring, than those that age faster.
On the other hand, to age slower may not make a difference at all, just because we love our elders despicte their physical appearance.
I'm considering the cultural and technological advantages that allow our elders to live longer to be a product of evolution too.

So my question is wheter we are evolving to age slower, or to live longer aging at the same rate?

As a side note, we are becoming more like what they call a super-organism, as most of os can only benefit of a longer life spam by living in society. Just like an anthill or a beehive. If that is true, we are not evolving to age slower.


texts: Can you help me identifying this spider?

texts:
I took this picture in Ohrid, Macedonia, it is the first time I see this kind of spider here.

This spider was 2-3 cm long and was outside in urban building.


texts: How is Microenvironment strictly defined?

texts:
I started to think this definition of Wikipedia:

  Microenvironment (biology), a small or relatively small usually
  distinctly specialized and effectively isolated biophysical
  environment (as of a nerve cell)

and I started to think which environments can be examples of its.
Joints, synovial joints with capsule, hyaline cartilage in capsules, ...?
I would like to get more examples of environments so I can think better definition.

What is Microenvironment?


texts: Fab fragments of antibodies to fight viral infections

texts: I was reading about Fab fragment and about using them to fight of viral infections. It seems that the Fab attaches to the viral receptors, which stops the viruses from attacking the cells. It seems that it has been done before. I was wondering, since Fab fragments can't activate immune response, what happens to the Fab-virus complex in the blood?


texts: Confusion related to the use of PCA to determine the background network

texts:
I was reading this paper related to use of gene expressions for predicting the drug response. I have this confusion, the paper has used PCA on the covariance matrix formed by the genes to get what is called the background network as they say.

I don't know the essence of background in this case. I know PCA gives us components which preserves the greatest variance and used for dimension reduction. What they mean by background network. Is it pathways ?


texts: Where can I find a compendium of microorganisms?

texts: I recently bought a microscope hoping to learn more about algae and bacteria and stuff. I've collected a few samples of pond water and found tons of algae and stuff, but I have no idea what to call the things I have found. I am wondering if there is a list of every known algae with a picture and some characteristics that would help me identify what I am looking at. I've looked around on the internet and haven't found much. Thanks


texts: Saw this bug this morning in Colorado. Looks like a giant wasp.


texts: What impacts on metabolism are likely from the 6x increase in water consumption by Americans at restaurants since the 1950s?

texts:
CDC data show that American water consumption in restaurant meals is 600% of what it was in the 1950s while meal calorie density has decreased (kcal/oz). What impacts is this likely to have on the metabolism of Americans?

My question is based on this infographic:


texts:
Please help me to identify this creature, is it harmful and possible solution of how to get rid of these in my house.

Please forgive me for bad image quality, some of these have white dot at the back(I guess male/female identification mark).
I am from north India, Punjab region
Please help me to get rid of these.

min size found: 3mm

max size found: 6-7mm


texts: Potential obstacles to growing nanoelectronics within living cells?

texts:
Say there was a nanotechnology allowing to "grow" and wire up electronic components/sensors measured only a few nanometers in cross-section, though spanning in length across microns. Say this was possible inside living cells (for the purpose of monitoring or even controlling living tissues at individual cell level).
Would such a technology be doomed in the bud simply because cells will immediately deploy antibodies to fight the foreign objects off, and either succeed in it (rendering the growing of said components impossible) or die if they can't succeed in it? Or are there chances to get the cells ignore the electronic components and live with them happily?
What are any other potential obstacles to this sort of technology from biological perspective?


texts: Why is Artemisinin Compound Therapy preferrable over Artemisinin therapy with regards to drug resistance?

texts:
How does adding other anti-malarial drugs to artemisinin, to obtain a "combined" therapy result in reducing the frequency of emergence of resistance?

  And it is given in the form of artemisinin combination therapy,
  combined with another anti-malarial drug, with the goal of reducing
  the frequency of emergence of resistance. (Cf source).


texts: Which of these components has C-H and COOH groups

texts:
A) Amino acids and triglycerides that have a carbon-carbon double bond

or

B) proteins and fatty acids

I think they are both true, but I should choose only one
I think that because since amino acids have COOH and C-H group, proteins do too and fatty acids have these groups too just like triglycerides with a double bond. But since I have to choose one I would choose B. Am I right?


texts: From school, I remember that for something to be considered life, it must be able to reproduce.  With the creation of seedless fruits (such as watermelon), would this be considered life as they don't have seeds so they can't reproduce?


texts:
What exactly does the term Haplogroup or Haplotype means?

How is it claimed that people belonging to the same haplogroups have common ancestors?


texts: Is hair made of protein or dead cells or both?

texts:
Some sources say hair is made of dead cells:

it's mentioned in many titles of Google searches, so I'm linking the Google search search

Other sources say hair is a protein filament:

Protein filament that grows from follicles found in the dermis, or skin

I don't think protein and dead cells are the same thing. Where am I mistaken?


texts: What is this beetle looking fly creature?

texts:
I found this fly in my back garden that looks like a beetle with wings and it hovers.

  ]1

  ]2

What is it?


texts: Are SNPs always in linkage disequilibrium with other SNPs

texts: Is it possible to have a SNP that is not found is be non-randomly associating with any other SNP?


texts:
I'm a bit confused by the concept of a minimum infectious dose (MID). It seems from what my research so far has turned up, that while any dose greater than 0 could potentially cause an infection, for most pathogens the likelihood of this occurring is low enough to be dismissed.

What I'm now trying to figure out is, what metric is used to define the MID? Is it the amount of the pathogen which is expected to cause an infection in 50% of those exposed (similar to an LD50?) Is there some other value used instead?

Secondly, is there a specified relationship between the received dose, as a multiple of the MID, and the likelihood of infection (for example if the MID caused an infection in 50% of people, then perhaps 2 MIDs would cause infection in 75% and 3 MIDs would cause infection in 87.5%).

Note, I am not asking about how the MID is empirically measured, but rather about the conceptual underpinnings of the concept itself. Also, any links you can provide to additional resources would be most appreciated. Google is useless these days now that the search results are flooded with nothing but SARS-CoV-2 specific articles.


texts: Can all oxygen be provided cutaneous in humans?

texts:
What partial pressure of oxygen is needed on the skin to completely replace the lungs function as oxygen receivers? Respiration has other functions too. I am only asking about oxygen intake.
Oxygenation through the skin could eventually be used against ischaemia like gangrene and covid clotting.
The skin might eventually be kept wet to improve oxygen diffusion through the skin, as this is the case with animals.
In normal conditions cutaneous respiration is 1-2% in humans. This means that with an atmosphere of close to 100 % oxygen and pressure of 10 bar, 50-100 % of a humans oxygen intake can be through cutaneous respiration.


texts: This term gets thrown around sometimes in biology articles, and I have a rough idea of what it is: during embryonic development, the tissue differentiates in a certain spatial configuration. Wikipedia also mentions that its two main mechanisms are regional specification and cell differentiation. However, I would really enjoy a thorough definition of the term (either in the form of an answer or a reference).


texts: Machine learning for light microscopy -- problems to solve?

texts:
I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The equipment and experience I have are:

Bright-field, dark-field, and phase-contrast microscopy
Modern laptop
56-core super-computer with >100 GB of memory (on request)
Intricate knowledge of machine learning algorithms and signal processing
PhD-level research skills
Programming skills that would get me to work at Google
Limited knowledge about biology, bioinformatics, and microscopy (yet)

I want to do some publishable research free from all academic hassle. I will do this solely on my own time, without hurry to publish, in an attempt to do something good for the mankind. I can throw a few hundred dollars on the project every two months (or abour 1000 USD per year).

Much of the biological research published in Science, Nature, PNAS, Cell, etc. are so specialized that I find it difficult to detect important problems I could have a good chance of solving given my skill set. Thus, I am asking your help:

What kind of software you always wanted for light microscopic research, but did not know how to build?
What are some important biological problems you would like to get solved? (For machine learning, problems with a binary decision task are particular well suited -- e.g. "does this person have malaria or not"?)
What are some recent, high quality reviews on open problems in biology?
Something else?

While my question is a bit broad, I think this goes under the "good intention" (or whatever it is called) SE policy.


texts: Are there any examples of viruses that have powered motion or do they all rely on passive diffusion?

texts:
Swimming, or any locomotion will presumably require energy which will in turn require metabolism which viruses lack supposedly.

Are they general able to direct their movement in any manner (e.g like sailing) or are they strictly limited to Brownian-like motion? If not, are there any exceptional examples that indeed can control their motion?


texts: Background (null) distribution for higher observed frequency of an allele

texts:
I am testing the hypothesis that being heterozygote at a certain gene locus, say X, increases the chances of having the good allele of X compared to being homozygote. I have data of more than 6000 individuals with their zygosity for gene X. What could be the background distribution of allele frequency for testing the hypothesis if the observed frequency of good allele is more in heterozygotes compared to one expected by chance.
Thank you so much.


texts:
I am looking to manipulate manually constructed phylogenetic trees (adding bootstrap values, markers to indicate trate loss/gain etc.) I came across a paper that used Macclade, however, this no longer appears to be a program that will run on almost all computers. Is there a useful alternative software package? I have tried Mesquite, but it does not appear to have the same functionality (although, I have probably just missed understood how to use it effectively).

Any help/recommendations would be appreciated


texts: How can we know which alleles are together on a chromosome?

texts:
This illustration says that if the two homozygotes pr+ pr+ vg+ vg+ and pr pr vg vg are crossed to produce a heterozygous offspring (pr+ pr vg+ vg), then:

this cross gives us exactly what we need to observe recombination: a
fly that's heterozygous for the purple and vestigial genes, in which
we know clearly which alleles are together on a single chromosome.

(My emphasis.)
Source: Khan Academy - Genetic Linkage & Mapping

I can't see the logic of this: surely if there were four chromosomes involved instead of two, wouldn't we get the same result via independent assortment?
In this scenario, the red-eyed, long-winged fly would have pr+ on chromosome 1, pr+ on chromosome 2, vg+ on chromosome 3 and vg+ on chromosome 4.
Conversely, the purple-eyed, vestigial-winged fly would have pr on chromosome 1, pr on chromosome 2, vg on chromosome 3 and vg on chromosome 4.
As the mother and father are both homozygotes (the mother for the dominant alleles and the father for the recessive alleles) the offspring couldn't fail to inherit pr+ and vg+ from the mother and pr and vg from the father, and the offspring would be the same as in the illustration.
I can't see how we can get any information as to whether genes are on the same chromosome or not from this crossing (unless we know they are on the same chromosome before we do the cross!).
I'm sure I've got my own logic wrong - can anyone enlighten me?


texts: Estimate parameters from epidemic curve: how to proceed?

texts:
I am trying to build an epidemic model based upon the SIRD model, but I need to estimate the parameters for this model (α = infection rate, β = recovery rate and γ = mortality rate).
What is the procedure to estimate these parameters directly from epidemic data? For instance, I have tried to get γ from the cumulative mortality rate for COVID-19 in China; I have found that the function Holling type III (y=ax²/b²x²) looks more like the data:

As starting parameters, I used the maximum of the cumulative curve for a and a subjective number for b.
How can I find the best fitting parameters for this function based on the data? Is there a procedure in
R?
Also: if this approach is correct, would the parameter b correspond to γ? Can I do the same for α and β?
And: can I apply this sort of regression on the raw data instead of the cumulative curves?
Thank you


texts: How to remove bad lanes in ImageJ Westernblot analysis

texts:
I use ImageJ to do an analysis of a Westernblot Image.

If everything goes as wanted the workflow is fine. But if I do something wrong creating a lane there is no undo for a lane and also no way to remove all lanes that I can find.

How do I get back to my original image or undo a lane creation?

I'm using 1.49e on Mac OS


texts: Directed evolution: Point mutation vs Insertion-Deletion vs Shuffling

texts:
When attempting enzyme function improvement via Directed Evolution I can see three different strategies to generating variation for the gene sequence:

Point mutations
Insertion / Deletions
Shuffling

Is there a systematic difference between how successful each of these approaches are likely to be for a particular gene or in general? Does one choose one over the other approaches in any specific project based on any characteristics / goal differences?

A related question: On a methodological front, I know one can use error prone PCR to get #1 i.e. point mutations.

What are similar techniques for #2 & #3? i.e. How does one execute gene shuffling or Insertion / Deletions in practice?


texts: How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?

texts:
In this link, it states:

  It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).

I do not understand how polyadenylation protects the intracellular RNA from ribonuclease. I always thought that polyadenylation was a way to mark RNA for degradation, not protect it from degradation. Perhaps it is speaking of protection from exoribonuclease only and not endoribonuclease?

Can someone explain this?


texts: It is said that PCT, DCT, Henle’s Loop reabsorb the filtrate. Does that mean they absorb the filtrate again? If it is actually reabsorbed to medulla then why it is said that PCT, DCT or Henle’s loop reabsorb the filtrate?


texts:
By consuming acidic foods, could one cause their blood to become acidic and therefore cause an acid+base reaction between their blood and bone?

I ask this because i recently discovered bone is a base, as its chemical formula is approximated as Ca10(PO4)6(OH)2 where the (OH)2 suggests bone is basic and thus prone to a neutralisation reaction with acidic blood. If so, what salt would be produced?


texts: Can a mother somehow positively affect fetus during pregnancy?

texts:
My mother keeps telling me that I like to study and have a predisposition to it because she was a student when she was pregnant. I highly doubt it, because I can't find any logic in these words.

I heard that a lot of mothers try to do something to positively affect their fetuses. For example:

Listening to classical music.
Learning something.
Singing or playing musical instruments.

Can these activities somehow affect a child or is it just a myth?


texts: I was wondering what is in the mosquito bites, which causes the swelling of the skin at the bite and also the itching. I know that the mosquito injects some stuff, but what is it?


texts: What kind of fish is this? Spotted or largemouth?

texts: I don't know if this is a weird looking largemouth bass or a spotted bass. It was caught in southern Oklahoma. Please help! Thanks.


texts: Are there proteins with multiple motifs?

texts: Does each protein adopt a single specific structural motif (zinc finger for example) or are there any proteins with multiple motifs along the chain?


texts: Does the effect of light on melatonin release adapts to light level over long periods of time?

texts: Or do you go to bed with low levels of melatonin when you stay behind a computer screen all day?


texts: Are any invertebrate nephridia (proto/meta) homologous with vertebrate kidneys in the sense that embryologically they also begin together with the genital system?  When did the embryologic association between reproduction and osmoregulartion/metabolite elimination begin in terms of evolution?


texts: Got stung by this flying bug in Death Valley and Arches, what is it?

texts: We camped in Death Valley and these guys were attracted to light and ended up stinging us. Didn't hurt as bad as a bee Sting. Any ideas what they are? Couldn't find them doing a Google search or image search.


texts: Is the leading strand consistent in the same chromosome with multiple replication forks?

texts: If a chromosome has multiple origins or replication, do those origins necessarily pick the same DNA strand as leading and the same one as lagging, or can they be of opposite orientations, sending replication forks in opposite directions and therefore picking different leading vs lagging strands?


texts: How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has?

texts:
I know that some amino acid substitutions are more effective in causing antigenic drift than other substitutions based on their location in the 3d structure of the HA protein (proximity to the receptor binding site).

I would like to be able to determine using a program whether a virus will be dominant based on multiple factors including genetic difference from the previously dominant virus. How can one know how much bigger of an effect one AA substitution will have on the antigenicity of a virus compared to another?

Any help is much appreciated.


texts:
What species of bird is depicted on this coin?

http://www.artic.edu/aic/collections/citi/images/standard/WebLarge/WebImg_000100/139651_846511.jpg

Thanks in advance for your help!


texts: determining genome-wide exogenous binding of pathogens to host genome?

texts:
I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice genome to the advantage of the pathogen.

It's an interesting concept but left me wondering how one would determine de novo the binding of these pathogen effectors into the host if one didn't know them. What would be the steps to determine where are the pathogen's TFs binding the host genome?

Edit: there is the possibility of not knowing which proteins bind to the host genome, so what would be the way of developing the antibodies in this case?

Reference:

 Li T, Liu B, Spalding MH, Weeks DP, Yang B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology 30: 390–2.


texts: 'Big ideas' behind constrained selective breeding (optimization)

texts:
I'm looking for help in finding the 'big ideas' behind a project I'm beginning and want to make sure I'm not missing anything since I wasn't trained in Biology.
My idea is investigating constrained selective breeding, say, a farmer who wants to balance crop yield with artificially selecting a desired trait (can't select too strongly because this will reduce yield). I've found many models for selection and found Haldane's classic useful but I'm not sure how to incorporate a constraint.


texts:
My university's -80 freezer just broke down and the repair will take 4 months according to the vendor. Is there any other way to preserve cells? Maintaining lot of flasks until the freezer is repaired is not viable option.

Is there any alternative to cryopreserve cell lines without -80 freezer?.


texts: When life first formed in earth's ocean, was it salty yet?

texts:
Do we have any tangible proof, e.g. by studying fossils of primitive life forms, that during their time the ocean was already salty, and at roughly similar levels to today's, or on the contrary, that water has no or very low salinity?
Did life had to adapt to dramatic changes in sea water salinity, as it has (I believe) for changes in air composition?


texts: Why do people and animals stretch out their bodies and what is causing this behaviour?

texts:
I noticed that my cat which is only 6 months old has started stretching its body from time to time. Then I thought that this motion doesn't seem very natural from another cat's viewpoint, so my cat probably didn't try to imitate some other cat all of a sudden and learned it like that. This action must have been caused by something else then. Or at least that's what I think.

Both animals and people stretch their muscles from time to time, but it doesn't seem to be caused by memory of others doing it. So how does this action originate in them?


texts: What happens to the food you accidentally aspire?

texts:
I'm well aware of the health effects of aspirating solid food and liquids, but I'm interested in the reaction of the body on the biological level to the strange body on our lungs.

After I almost aspirated corn, I started to wander: what does the body do when food got on our lungs?

Will it be eventually absorbed? Destroyed by our white cells? Or just lie there forever until it fully decomposes?

The body has mechanisms to prevent food to get into the lungs, so the body is aware that eventually some food will get into the lungs. As a result, it makes sense to believe that our body would have a mechanism to deal with such issue if all other mechanisms fail ( coughing and etc.,) yet I couldn't find anything on Google.


texts: DAPI staining showing unknown artefacts?

texts:
Dear fellow researchers,

I have been facing some problem with staining nucleus with DAPI. I use the standard protocol for fixation 4%PFA+0.1% TX-100+2%BSA.

I use 0.2ug/ml conc. of DAPI for 5 minutes. Before mounting my cover slides, the nuclear staining is very specific and no artefacts were visible. However, after mounting (with Sigma-Aldrich mounting medium), I have started observing artefacts. Images are attached for your reference.

I usually keep my samples at room temperature for an hour to let the mounting medium settle down and then move samples to 4 degrees overnight and observe them the next day. I do not think that temperature here is an issue because the other marker did not show any problems.

Another issue is that the artefacts of nuclear staining are not ubiquitous. Even after mounting, some cells stained nucleus fine but others showed cytoplasmic or membrane staining.

Is there any reason that you guys can think of? Or if you have encountered similar situation before? Thanks in advance.

Why is DAPI giving artefacts with nuclear staining? - ResearchGate. Available from: https://www.researchgate.net/post/Why_is_DAPI_giving_artefacts_with_nuclear_staining [accessed Sep 18, 2016].


texts: Will a Codon result in same amino acid across organisms

texts: Will all organisms with the same 3 nucleotide sequence in the codon produce the same exact same amino acid. I read that the three nucleotide sequence will code for a particular amino acid. I did not understand if that is the case across organisms. Can someone explain this in simple terms.


texts: Does anyone have any TOPO directional cloning tips?

texts: I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?


texts: Would tattoos be considered a phenotype?

texts: I'm trying to understand how broad the definition of "phenotype" is. If someone gets a tattoo, would that tattoo be considered part of their phenotype?


texts:
What is the name of this bee pollinating a lemon tree?
Area: south-central Europe


texts: Can a human increase cold resistance through some practice?

texts:
Can cold showers, moderate underdressing in cold weather increase your cold resistance?
What is responsible for cold tolerance? It's physiology/psychology or it's genetic thing?

By increasing cold resistance I mean feeling more comfortable/survive in low temperature environment comparing to state before practice(cold showers, underdressing, etc).


texts:
I have encountered the term "two photon calcium imaging" in a few papers.
I have tried to look in the internet but can't understand what this technique actually is.
I will be very happy for recommendations for a good internet source.
For example:

what does the "two photon" means?
how does the implement look like?
Is it sensitive to absolute voltage or voltage changes?
Does all relevant (genetically engineered) neurons light in the same color?
Is it the color that is measured or the intensity of the color?
Is the purpose of this technique single neurons or brain pathes?

Thanks!


texts:
I want to collect small blood samples at regular intervals (e.g. every 8 hours or more often) over a longer period (weeks to months). To avoid having to go to a lab or doctor to have this done, I want to do it at home. I will need to extract mRNA from PBMC from the samples.

Assume a test tube in which you have a piece of filtration paper. You prick your finger and let a couple of drops of blood soak into the filtration paper, and then seal the sample in the tube, and immediately place it in your regular freezer.

How long will the mRNA survive under these conditions?

Will it be better just to let the sample dry out inside the tube (e.g. using a desscant), or store it at room temperature?

Will it be possible to store it for e.g. a week before sending the batch in for analysis?


texts: Light/Heavy Isotopes in Living Organisms

texts:
I was wondering, why are lighter isotopes (e.g. carbon-12 as opposed to carbon-13) preferentially used by life on Earth? Is their increased stability the only factor?

Thanks in advance!


texts: Apart from nerve cells and muscle cells, what types of cells do not undergo mitosis in adult man?

texts:
Neurons and muscle cells in adult humans do not have the ability to divide by mitosis, so they can not repair themselves and their cell cycle remains in the interphase. I’m looking for more cells with this feature. Are there other cells with this inability to undergo mitosis in humans or in plants?

In an adult human:

Do nervous cells ever undergo mitosis?
I wonder if all muscle cells do not undergo mitosis or if this inability only applies to cardiac and skeletal muscle cells.


texts: Voltage sensitive dyes technique: What is the underlying measure?

texts: I just discovered voltage sensitive dyes technique: first of all what imaging techniques do we use? And I have seen that figures are labeled with ΔF/F0, what does it stands for?


texts: What is the actual chance of sibling incest child suffering from a genetic disorder?

texts:
This is not a question about the (a)morality of incest or current laws. However, there seems to be a widespread misconception about the impact of sibling incest on the genetic health of the eventual offspring.

What is the average chance that an offspring of a random sibling couple will suffer from a genetic disorder compared to an offspring of any random unrelated couple?


texts: SARS-COV-2 detectability versus viability

texts:
This week (#47 of 2020) two meta-reviews were published in the Lancet.
Ct values and infectivity of SARS-CoV-2 on surfaces, a brief review published on 19 November in The Lancet Infectious Diseases, observed that culturable virus samples are correlated with Ct values of 29·3 (steel surface) or 29·5 (plastic surface), whereas Ct values of 32·5 (steel surface) or 32·7 (plastic surface) correlate with the detection of non-culturable virus.
SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis, published on 19 November in The Lancet Microbe, furthers this observation and concludes that by such metrics individuals infected with SARS-CoV-2 are not infectious after day 9.
Does this suggest an upper bound of nine days for viable virus in a standard environment (22°C, 40-60% RH) or may surface conditions be more hospitable than living cells?


texts: Is there a short-term, very strong anesthetic, which can be blocked/delayed by other substances?

texts:
Question migrated from World Building SE.

(For fictional use only, of course :) )

I am looking for an anasthetic which fulfills the following criteria:

very strong effect, induces a comatose state in a very short period of time
quickly wears off (30 minutes~) with only minor impediments to the recipent upon awakening.
Can be 'partially blocked' or delayed by the intake of some medicine or other substance (which needs to be not too uncommon). Maybe some receptors for the anasthetic are blocked by the substance or something similar. Ideally this would result in the recipent falling into a dream-like state for some minutes before the real effect kicks in.

Does the anasthetic have to be made up, or does something like this actually exist?


texts: Can humans live without their right atrium?

texts:
The right atrium  is one of four chambers (two atria and two ventricles) in the hearts of mammals (including humans) and archosaurs (which include birds and crocodilians). It receives deoxygenated blood from the superior and inferior venae cavae, the coronary sinus, and the anterior and smallest cardiac veins, and pumps it into the right ventricle through the tricuspid valve.

Can humans survive without right atrium? In this condition blood would fill the right ventricle directly, comparable to some animals like  frogs, toads, snakes and lizards. What advantages does the normal human heart have to this anatomy ? If we had this anatomy, where would the best place for pacemakers be, like the sinus node?


texts: The probability of indirect human fertilization?

texts:
What is the probability of conception in situations when sperm isn't directly ejaculated into the woman's vagina, like:

The man's or the woman's hands come into contact with sperm, for example when removing a condom. (Perhaps after washing them,) the hands later touch vagina, for example during foreplay to another intercourse.
The man and the woman taking a bath together, the man ejaculates into the water.
The man ejaculates on the woman's body, perhaps on or around vagina but not inside. (In this case it could also make a difference whether the woman has shaved pubic hair or not.)
The man ejaculates during receiving oral sex, (perhaps the woman rinses her mouth), the couple kisses, the man performs oral sex to the woman.

In all these situations, it seems possible that a tiny amount of sperm is eventually transferred into vagina indirectly. And since just a single cell is enough to fertilize, it seems that there is non-zero probability of conceiving.
How much care need to be taken to prevent conception in such situations? Does simply washing sperm away with water (+ soap perhaps) eliminate it?

If you think of similar situations that are similar, please don't hesitate to add them.


texts: Identification of a bird on the beach of a small lake

texts:
Last December in France (lake of Divonne, Ain) I took a picture of this bird looking for some food on the beach of the lake.

It looks like a specimen of the genus Anthus (Family Motacillidae) but as these specimen are quite difficult to identify (especially winter time), I would like to have some confirmation.

By the picture I found on different Internet sites, my potentials guess are (by order of confidence):

Water pipit (Anthus spinoletta)
Meadow Pipit (Anthus pratensis)
Buff-bellied Pipit (Anthus rubescens)
Eurasian rock pipit (Anthus petrosus)

The Eurasian rock pipit could be present in the region while migrating but this is the less probable in my opinion.


texts: What effects would be caused by exposure to common life forms with opposite enantiomer biology?

texts:
Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything.

What would the effects be of that human's exposure to other Earth life?

I assume that quick death from malnutrition would be inevitable, but would there be more immediate life-threatening consequences?

Would anyone who comes into contact with the mirrored person be at risk?

Would reflected bacteria pose an immediate threat to the ecosystem?


texts: What is the brightest color a light source that only emits blue frequency light can achieve?

texts: Let's say there is a luminous light bulb that only emits blue light, and you (or a camera if you prefer) look at it from a close distance. Will the maximum brightness perceived not have any "white" to it? Because there is no white light if it's all blue. Probably the brightest it could be would be solid blue? Therefore, blue photons could produce a range of color of black to solid blue depending on the luminous or amount of photons hitting your eye per second? If that's the case then what happens if you raised the intensity of the bulb to an extreme? Is there a cut off point where even if you add more intensity to the bulb, you still see the same solid blue color?


texts: What is the advantage of restriction enzymes cutting only at specific sites?

texts:
Bacteriophages have sequences which often do not have specific sites for restriction enzymes of bacteria to cut at and so can attack the bacteria.

Wouldn't it be better if bacteria had something "universal" like an enzyme that simply cuts the nucleotide sequence "randomly"? Is there any particular advantage of cutting at only a few restriction sites?


texts: Which of the two mitochondorial membranes relate to bacteria according to the endosymbiotic theory?

texts:
I seached for endosymbiotic theory in Wiki and I found this about endosymbiotic theory:

  Symbiogenesis, or endosymbiotic theory, is an evolutionary theory
  which explains the origin of eukaryotic cells from prokaryotes. It
  states that several key organelles of eukaryotes originated as
  symbiosis between separate single-celled organisms. According to this
  theory, mitochondria and plastids (e.g. chloroplasts), and possibly
  other organelles, represent formerly free-living bacteria that were
  taken inside another cell as an endosymbiont, around 1.5 billion years
  ago.

But I couldn't find any answer for my question, so I decided to ask:

According to this theory and differences between inner and outer mitochondria and plastid membranes, which membranes (outer or inner membranes) of mitochondria and plastids (e.g. chloroplasts) relate to bacteria?

And why do mitochondria need to have a double membrane?


texts: What vitamins exist for other animals but not humans?

texts:
As you probably know, humans are among the minority of animals that require Vitamin C and don't produce it ourselves. For whatever reason (multiple theories exist), we lost the ability. Meanwhile, the vast majority of animals out there that require Vitamin C simply produce it internally, so they have no need for food choices that contain it. Had it not been for the discovery of scurvy as Vitamin C deficiency, we likely wouldn't have ever known that Vitamin C exists at all as a requirement for human health.

Are there known to be cases in other animals of dependence on food containing vitamins that we humans produce ourselves?


texts: Is there selection against long proteins and long genes?

texts:
Background thought
Titin and TTN
Titin is the largest protein in the human genome with 33423 amino acids. Titin is coded by the gene TTN that must be at least $3 \cdot 33423 \approx 100kb$ long. Looking at NCBI entry for the gene TTN indicate that TTN is actually about 240kb long.
Transcription rate
The average transcription rate (Ref.) is around 1.5kb per minute. It therefore takes about $\frac{240k}{1.5k * 60}$ 2.5 hours to transcribe TTN in mRNA. This mRNA then need to be spliced before being available for being translated. Per consequence, I don't think it is possible for translation to happen in the same time as transcription but might well be wrong.
Translation rate
The translation rate is about 8.4 amino acids per second (Ref.). It therefore takes about $\frac{ 33423} { 8.4 \cdot 3600}  \approx 1$ hour to translate the protein. Sure, several ribosome can translate the mRNA in the same time but it still remain that it takes 1 hour to synthesize at least one protein.
Transcription + Translation rate
Assuming translation does not occur in the same time as transcription, the total time to create the first protein of titin is about 3.5 hours.
Half-life
The half-life of a typical human protein is 6.9 hours (Ref.). Intuitively I would expect a negative correlation between mRNA size and mRNA half-life.
Half-life and Transcription + Translation rate
Because the time to produce the first protein is about half the half life, it means that a quarter of every single mRNA that is being produced would never give rise to even a single protein because it would degrade before either before or after translation has started.
It sounds like an important cost and would be surprised if a gene or a protein could be any longer.
Question
Is there evidence of selection against long proteins and long genes?
Are there proteins that are much longer than Titin in other species?
Do I exaggerate the cost it represents, either by not considering that an average rate (such as transcription rate) is not representative of the actual rate for typically long gene/protein or by assuming that it is costly to create tons of mRNAs that won't never be translated?


texts: Why is maintaining a circadian rhythm important?

texts:
What are the real consequences of never maintaining a circadian rhythm?
How is circadian rhythm important for health and function? Where did it arise in evolution?


texts:
Phenetics (grouping of organisms based on similarity) used to be claimed to be an alternative to cladistics, but now it is widely accepted that phenetic analyses cannot be used to infer evolutionary relationships. However, phenetic methods like neighbor-joining trees are still being developed today.

Are phenetic analyses still valid today for purposes other than determining evolutionary relationships, or are they completely obsolete? Does anyone have an example of a recent paper that uses phenetic analyses in a valid way?


texts:
Most animals age via at least two mechinisms:

at a "macroscopic" level, basically wear and tear to the point where (on evolutionary time scales) it's more genetically advantageous to optimize for reproduction rather than longer lifespans.
at a microscopic level, e.g. shrinking of telomeres. This prevents cell division after a certain point (good to prevent cancer and other growths, bad for regeneration).

Do plants also age microscopically? If so, how are we able to clone (in the horticultural sense) plants?


texts:
Goal

I am trying to get a distribution of Exons and intron sizes in Three-Spined Stickleback (Gasterosteus aculeatus).

Data downloaded

I downloaded some data from Ensembl. More precisely, I went there, selected "structure" in the "attributes" and selected

- Ensembl Gene ID
- Exon Chr Start (bp)
- Exon Chr End (bp)

There are two issues in these data:

Some exons end before they start
Some exons overlap

The first point is I assumed due to reversion, so I just reversed the start and end position when there was such inversion. The second point is more problematic as I don't know what such overlap could mean realistically.

Can you help finding the distribution of exon and intron sizes in three-spined stickleback?

What I did with the above data

Preparation

# read data

d = read.table(file.choose(), header=TRUE)
names(d)= c("ID", "start", "end")

# Reverse exons when needed

toReverse = which(d$start > d$end)
s = d$start[toReverse]
d$start[toReverse] = d$end[toReverse]
d$end[toReverse] = s

Exon Sizes -> Looks good

# Exon sizes

ExonSizes = d$end - d$start
hist(ExonSizes) # Cool, looks good!

Introns Sizes -> Looks bad

# Intron sizes
# This is a little slow. One might have better to switch to C++.
# The idea is to look at the distance between the end of an exon and the start of the next exon within each gene.

d$ID = paste(d$ID)
IntronSizes = c()
uniquegenes = unique(d$ID)
nbgenes = length(uniquegenes)
i=0
exon = 0
for (gene in uniquegenes)
{
    i=i+1
    cat(paste0(i," / ",nbgenes,"\n"))

    while (TRUE)
    {
        exon=exon+1
        if (d$ID[exon] == gene) {
   IntronSizes = append(IntronSizes, d[exon+1,]$start - d[exon,]$end)
        } else
        {
            break
        }
    }
}
hist(IntronSizes) # There are negative values. I don't know how to interpret them.

hist(log(abs(IntronSizes))) # That looks good but I doubt it makes much sense!


texts:
Cattle breeders have improved the quality of meat over the years by which process?
A) artificial selection
B) directional selection
C) stabilizing selection
D) A and B
E) A and C

I know the answer is D. It is obvious that is artificial selection but WHY is it also directional selection? how do we know? I know the differences between directional, stabilizing and disruptive selection but there is nothing in the question that explains the quality of meat in relation to directional selection. so HELP!


texts: Is this 12+ foot plant a sunflower or hogweed?

texts:
I'm trying to determine what this is. The plant is well over 12-feet tall, had huge leaves, and a very thick stalk. People near me say it's a giant sunflower plant, but it hasn't bloomed or shown sign of flowers. My moral ag-knowledgeable friends say it's hogweed, which is very dangerous. Thoughts?

This is the plant .

Here's another picture .


texts:
I have done a blastx and use the outfmt 6 option, because I want to work in the tables format. When I do this I get subject ids of the type

  sp|Q7XJS0|ASHR1_ARATH, sp|Q39547|CUCM1_CUCME,

et cetera.

However, in this blastx output format I cannot find any option that will give me the descriptions of these blast hits.
Could anyone advice me how I can link these subject ids with descriptions of the sequences, e.g., 'amino acid transporter ANTL1-like'? I'd be much obliged.

j


texts: Hormonal effects of Luteinizing hormone on endometrium

texts:
What is the effect of luteinizing hormone on the endometrium?
A general answer to this query is that it only thickens it. The same could also be said for the effect of Follicle stimulating hormone (FSH) on the endometrium as well.
Where lies the difference?


texts: What causes a small bump in the arterial pressure plot?

texts:
In my book there is a plot of the arterial pressure against time.

From the plot, during heart contraction, there is greater pressure on the artery and during heart relaxation, there is lower amount of pressure on the arteries.

This makes sense because P = F/A, the surface area of the heart is smaller when it is contracted versus when it is relaxed, hence greater pressure.

But why is there a small bump while the pressure is decreasing from systolic pressure to diastolic pressure?


texts:
In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters and sons, and autosomes from the father to both sons and daughters. Only the small amount of genes present in the Y-chromosome and mitochondria are inherited solely within one sex.

Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory? What is the most sex-limited genome known to researchers?


texts: Is DNA mutation locally energetically stabilizing the DNA molecule

texts: I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done along these lines for the DNA.


texts: The human brain in numbers II-A: synaptic connections per structural type

texts:
The overall number of synapses in the human brain is roughly 1,000 trillion, i.e. 10,000 synapses per neuron.

I assume that each structural type of neuron (basket, pyramidal, ...) has a somehow characteristic average number of in-coming and out-going synaptic connections, i.e. not every type of neuron will have the same roughly 10,000 in-coming and 10,000 out-going synaptic connections.

  I am looking for a thorough overview of these characteristic numbers
  by structural type.

Ideally as a link to an existing resource, but if someone with a good overview over the literature would take the effort  to compile such an overview (like user another 'Homo sapien' thankfully did in his answer to The human brain in numbers I: neurons), it would be even greater.

What's for sure: such an overview will be a) not complete and b) only estimates, so don't worry about that.


texts: Are there proteins that stabilize mRNA:RNA polymerase or mRNA:ribosome complex?

texts: Actinomycetes are known for their ability to produce rich variety of natural products, and particularly, polyketides. Many of the genes that encode the biosynthetic pathways are pretty big, as they could reach 20kb. These bacteria most probably have some kind of mechanism that would ensure efficient transcription and translation of these long ORFs. This could be done in two ways: either by stablizing the mRNA:RNA polymerase complex, or by stabilizing the mRNA:ribosome complex. Have any of you heard of such mechanisms in bacteria?


texts: Will humans and animals be harmed by frequencies outside their hearing range?

texts:
The human ear (for example) is sensitive to frequencies from 20Hz to 20kHz. Any sound beyond that limit would not be heard by us naturally.

Will it harm us (effect our ability to hear) when we hear sound more than 20kHz continuously?
Or...

Will it harm when we hear a 19,999Hz sound (which is upper limit) continuously?


texts: Do the bacterial species X, Y, Z code for proteins A, B, C?

texts:
My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of
Campylobacter and Helicobacter code for a list of several proteins.  To put it simply I’ve been asked, “Do species X, Y, Z code for proteins A, B, C?”  The genomes of these bacterial species have been fully sequenced and I am able to retrieve the FASTA files for each of them.  I am having trouble deciding on the proper method to screen these genomes for the genes.  I have been given the names of the proteins, i.e. VgrG and HCP, but the amino acids sequences listed on databases are annotated to different species of the bacteria.  I seem to be stuck in a grey area and am having trouble connecting the overwhelming amount of resources available on the NCBI website.  I have not found a specific guide to perform this task - Could you please provide me with a solution to my problems?


texts:
One episode of Cosmos: A Spacetime Odyssey describes a mechanism by which microbes could travel between planetary systems. As a star's orbit takes it around the galaxy, it occasionally passes through dense interstellar clouds. Rocks thrown into space at that time from the surface of a microbe-harbouring planet could carry life to temporarily nearby planets of another planetary system, before cosmic radiation would sterilise such rocks.

It's an interesting idea for TV; but scientifically, how plausible is this mechanism? My main concern is whether the average number of "infected" planetary systems per passage through an interstellar cloud is estimable as non-negligible.

Note: the use of "panspermia" in the title refers only to the question of whether an occasional interstellar transfer of microbes is tenable, not whether Earth's life originated outside this planet. As I understand it, the mechanism described above is lithopanspermia.


texts:
In most books, Triceratops is listed to live between 68-66 MYA (million years ago), however some books list Triceratops as living between 70-66 MYA. The Campanian age ended about 72 MYA and then came the Maastrichtian. Many articles state that Triceratops is "late Maastrichtian" dinosaur. All these citations do not give a clear answer: when did Triceratops live? All sources agree that Triceratops lived up to the K-Pg extinction 66 MYA, but when did the earliest Triceratops live?
This may be vague question so put it more empirically: what is the oldest age that a Triceratops fossil is dated to? Not when the first fossil of Triceratops was found but what is the earliest age (in MYA) at which Triceratops are known to have existed? Are there Triceratops fossils from 68 MYA? And from 70 MYA?


texts: How do nutrients get to the cells they need to get to?

texts: I understand the basics of digestion. I know that nutrients get absorbed by the microvilli, enter the bloodstream and travel to the liver but after all that, what is the biological mechanism that guides these nutrients to the proper receiving location?


texts: How does core-conductor model correspond to an actual neuron?

texts:
Hi guys, looking at your average neuron, it is very difficult for me to imagine how this could be translated into a core-conductor model

On the neuron above, where would be the intracellular space and where would be the extracellular space? Also, where is this membrane we are talking about?


texts: Is the Hypothalamus part of the Central Nervous System or Endocrine System

texts:
Sorry for a certainly naive question.
Some references (for example https://faculty.washington.edu/chudler/nsdivide.html) seem to to indicate that the hypothalamus is part of the Central Nervous System. Others (for example http://kidshealth.org/teen/your_body/body_basics/endocrine.html) place it in the Endrocrine System. I would have said it is part of both, but then I read the two systems are distinct. Could anyone explain me to which one it belongs and why?

Thanks,

Gilles


texts: Pedigree - Dealing With Unknown Parent Genotypes

texts:
I'm dealing with a pedigree problem, and I'm having some trouble dealing with problems of unknown parental genotypes (where there are multiple possibilities). This is not a homework question; it's an exam practice problem.

The question asks: Suppose brother and sister 6 and 7 are mated. What is the probability that their first pup will be albino?

The answer choices are 1/4, 1/8, 1/16, 1/32, or Not Enough Info.

Here's my attempt at the problem:

Since #2 is black, and some of its offsprings ended up sepia, #2 must carry the sepia gene (since the male mate is cream, and sepia is dominant over cream). So, we know that #2 is $Cc^k$.

Now, the male mate can be either $c^d c^d$, or $c^d c^a$.

This means that in order for the offspring of #6 and #7 to be albino, we need:

1) Male parent needs to carry the albino gene (i.e. male needs to be $c^d c^a$).

2) Male parent needs to pass on the albino gene to both #6 and #7.

3) #6 and #7 both need to pass on the albino gene.

I think the probability that the male is $c^d c^a$ is $\frac{1}{2}$, since the male parent can be either $c^d c^a$ or $c^d c^d$.

If we draw out a punnett square, the probability that the albino gene gets passed onto 1 individual is $\frac{1}{2}$ (since we already know the offsprings are sepia, we only need to consider the genotypes that contain $c^d$).

The probability that #6 and #7 pass on the albino gene is $\frac{1}{4}$.

This led me to think that the final probability is then P(male parent has albino gene) * P(#6 inherits albino gene) * P(#7 inherits albino gene) * P(#6 and #7 pass on the albino gene), which is $\frac{1}{2}$ * $\frac{1}{2}$ * $\frac{1}{2}$ * $\frac{1}{4}$, which gives us $\frac{1}{32}$, but I do not feel confident in my answer. Specifically, I do not know how to account for the fact that the male parent can be either $c^d c^d$ or $c^d c^a$.

Is my thought process correct? If not, where in my logic did I go wrong? Thank you for your help.


texts: Is Homo sapiens the only extant species of genus "Homo"?

texts: Is Homo sapiens the only species of genus "Homo" that survived?


texts: Why does max heart rate decrease with age?

texts:
I have heard that max heart rate declines steadily with age, and can be approximated by the equation Max Rate = 220 - Age.

What is the physiological reason for this decline, and how is it consistent with the fact that most endurance athletes reach their peak cardiovascular performance at around age 30?


texts:
What are some of the standard books to study :

Biological Interactions: Symbiosis, Mutualism...etc
Concept of Limiting factors
Niche concept
Resource partitioning
Concepts of community change
Theories of climax
Models of Succession

P.S. I am looking for a book for beginners for studying ecology at UG level.


texts: What does 'proper' mean in the anatomical context?

texts: I've seen the word 'proper' in websites, lectures, etc., in the context of human anatomy. But I'm unsure as to what its definition is. For example, the 'oral cavity proper'.


texts: Can a same gene stretch from one chromosome to another separate chromosome?

texts: Can a gene continue on from one chromosome to another separate chromosome? For example, can part of an eye colour gene be on one chromosome and the rest of it be on the next chromosome?


texts: Why myelin sheat does not cover the whole axon?

texts: Is there an optimal lenght for myelin sheats to be effective and lead potential across the nerve cell? This has always bugged me.


texts: Is this a young Ash Bud Moth (Prays fraxinella) caterpillar?

texts:
I am building up a my knowledge of organisms that live on trees (not necessarily as pests, but in the respect of the biodiversity that depend on different tree species) and their interactions.

Living on the underside of Fraxinus excelsior, in northern Europe (N. France), I have found these tiny caterpillars (end of May/start of June). They are eating small patches of the leaf, and excreting black frass.

The ash leaf in this photo is 70 x 35 mm, and so the caterpillar shown in approximately 1 mm in length, but there are others up to 2 mm.

The photo above also shows the mines in the leaf.

Under a hand lens, the body is an opal/beige colour and it has two black patches on the body above the head. The body is very shiny and glossy and it looks wet.

From my internet research it looks like a young caterpillar of the Ash Bud Moth (Prays fraxinella)?


texts: regarding genetic disorders related to protein production

texts:
I am not completely familiar with biology, but i had a genetics course in college along with practicals. Forgive me if there is something wrong with my question.

Is there a genetic disease which results in partially functioning or complete non functioning of genes resulting in little or no production of protein for eg Muscular dystrophy.

so why can't we supply these protein from outside the way we do in the case of diabetes(insulin)?


texts: It has what appears to be antennas in both front and back and legs front and back orange coloured dots ob front and rear of a blackish brown body


texts: What causes skewed lanes in a DNA gel electrophoresis experiment?

texts:
In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)?

(These images were samples that I took from an online activity we did for class)


texts: How is CO2 and O2 separated in our body during breathing?

texts:
https://www.msdmanuals.com/home/lung-and-airway-disorders/biology-of-the-lungs-and-airways/exchanging-oxygen-and-carbon-dioxide

The image in the above link shows that CO2 and O2 both pass through the same membrane but still CO2 is exhaled and O2 is taken in the body.

Why doesn't the CO2 mix with O2 and stay in the blood ?

Why is only CO2 passed out through the membrane?


texts:
I've gathered that a centromere is a a region*  where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark regarding its physical structure and functioning.

At what point during DNA replication is the centromere created, and how is it created? How does it hold the chromatids together (what are its components)?

Specifically:

When it is being created (presumably during cell division) how is the positioning  of the centromere controlled? Which flags are used by the enzymes in the process of making the centromere to tell them that it is the right spot: a section of DNA that 'says' "Right part of centromere, to be attached to left part"?

Secondly, after their condensation into chromosomes (e.g. during prophase), are the sister chromatids physically intertwined around each other** for the purpose of joining, or are they simply adjacent?

Is there a 'loop' in the centromere slung over the adjacent chromatids to join them?
If they are intertwined, how is this achieved during DNA replication, whilst the non-centromere parts of the sister chromatids are not intertwined?

How does the centromere break down to allow the chromatids to separate (e.g. during meoisis 2 and anaphase)?

On a somewhat unrelated note, what in the centromeres do the spindle fibres attach to, and how do the tips of the growing fibres notice it to head it its general direction?

*(i.e. there is not a separate physical object dubbed 'the centromere', rather it is a collection of objects in a region)

**(That is, considering no other molecules than the chromatids, if you were to pinch the top and bottom ends of the left and right chromatids and pull them apart, could you separate them without them locking together (basically, do they intersect knot-theoretically)?)


texts: What is it called when an animal only has one type/variation of dentition?

texts: An example would be alligators that only have one type/shape of tooth. Not the variation in function and shape like seen in humans, which have canines, molars, incisors, etc


texts: Alternative to distilled water for pH test

texts:
I am looking to test soil pH in a remote location. The test results don't need to be perfectly precise, and a pH test strip should provide sufficient accuracy. However generally this kind of testing uses boiled distilled water - and in this location it will be very difficult to buy distilled water.

The location is off grid, and getting specialized equipment to the location is not an option. (This is for field experimentation with farmers in rural Africa)

The process I have seen used for this is:

Add 1 part boiled distilled water and 1part soil by volume, in a clean container
stir and leave to settle.
Test the water pH with a pH test strip

Would it be possible to use boiled rain water for this process, or would this be likely to contain impurities which would interfere with the test results?

If there are likely to be impurities but there are approaches that can mitigate for them, please explain.


texts: Do skull bones have pain nerves (nociceptors)?

texts: I recently attended an awake brain surgery  for deep brain stimulation and it seemed to me that only the skin surrounding the drilled hole got local anaesthesia. I know that the brain itself does not have nociceptors, but what about the skull? And how does this compare to other bones in the body? Would you feel a hole being drilled in your skull? Would you feel your leg being chopped off if the surrounding tissue was numbed?


texts: Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?

texts:
I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory.
Note that I am aware of these posts:

best book for a comprehensive introduction to biology for a computer science graduate interested in undertaking research in bioinformatics
Introductory biology text for an outsider
Material recommendation: molecular biology for mathematicians and computer scientists

I consider my situation more specific, I am specifically dealing with DNA and RNA, so what I need is a basic text that deals with this two structures, rigorous but still accessible.
As an example I quote a paper I am reading:

(...) Inverted repeats are prevalent features of nucleic acids (...)

I would like trustable references for the fact that these features indeed exist, which is fundamental for my work, and maybe a shallow explanation for what they biologically imply, but I do not want to delve into what these features mean (It would be great to understand them from a biological perspective but that is not my priority)


texts: A word that includes plants and fungi, but not animals

texts:
Hello biologists and biology enthusiasts!
I am working on a project which includes information about plants and fungi. It would be very helpful for me if there a word that means plants-and-fungi, but I'm not sure there is. "Flora" only includes plants, but "biota" includes animals.
Thanks!


texts:
Is DNA helicase or RNA polymerase responsible for breaking the hydrogen bond between the 2 strands during transcription for eukaryotic cells? My textbook (WJEC Biology for AS level) says it is DNA helicase that breaks the hydrogen bonds while RNA polymerase catalyses the formation of bonds between RNA nucleotides.

  The enzyme DNA helicase breaks the hydrogen bonds between the bases in a specific region of the DNA molecule. This causes the two strands to separate and unwind, exposing nucleotide bases. The enzyme RNA polymerase binds to the template strand of DNA at the beginning of the sequence to be copied.

However, when I searched online, for example on https://en.wikiversity.org/wiki/Effect_of_hydrogen_bond_on_RNA

  Transcription can be explained easily in 4 or 5 simple steps, each moving like a wave along the DNA. RNA polymerase unwinds/"unzips" the DNA by breaking the hydrogen bonds between complementary nucleotides. RNA nucleotides are paired with complementary DNA bases. RNA sugar-phosphate backbone forms with assistance from RNA polymerase.

Then do RNA polymerase break hydrogen bonds? If RNA polymerase can break hydrogen bonds between strands then what is the role of DNA helicase in the transcription process?


texts:
It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well there are enzymes that simply work spontaneously and do not require such an influx of energy. However I can't seem to find any sort of list, however brief, that contains examples of enzymes that use ATP and ones that do not, or any indication of their prevalence. I could go one by one through each of the commonly encountered enzymes in the cell, but that would be tedious.
Is there any source where I could find what I am looking for? Or at the very least which of the major enzymes in the protein transcription/synthesis chain require ATP?


texts: Well to well variation in thermal cycler fluorescence?

texts:
We have an old BioRad ICycler Thermal Cycler with MyIQ single color fluorescent detector. While it's meant for RT-PCR, we've been using it for melt curves and binding assays for different types of RNA using thiazole orange as the intercalating fluorophore. However, when we tried to get serious about this assay and do things in triplicate we noticed that the well to well variation was terrible, making statistical significance difficult to get.

After reading through the manual I tried to get "persistent well factors" for the instrument to correct for this variation. However, the instrument's protocol for this requires heating to 95⁰C, so intercalating fluorophores won't work, the RNA melts and fluorescence is lost, so I tried with fluorescein. This didn't solve the variation.

So I tried to make my own well factors by making 10mL of Poly(rA) Poly(rU) RNA solution with thiazole orange and filling 96 PCR tubes with 100µL each and measuring fluorescence. Then I calculate the average fluorescence and divided the average by the value for each well to determine a factor, F, for each well. Then I tried to normalize subsequent experiments by multiplying each well's fluorescence by its F to get a corrected value. However, while this reduces the variation a little, it's still pretty bad.

Do you have any suggestions to reduce the well to well variation in these experiments or otherwise correct the data?

I have no prior experience with RT-PCR instruments, everything I know about it comes from playing around with the instrument. I don't know if I'm missing something really basic.

Step by step protocol

Prepared 1xSSC buffer, 150mM NaCl, 15mM Sodium Citrate, pH 7.5
Weighed 5mg Thiazole Orange, dissolved in 1mL Methanol
Diluted Thiazole Orange 1000 fold in 1xSSC
Took 71.4µL (100µg) Poly(rU) Poly(rA) solution, 1.4µg/uL
Diluted RNA with 8.93mL 1xSSC
Added 100µL diluted Thiazole Orange to diluted RNA, final volume 10mL
Set up 96 PCR tubes, used 8 channel pipette and trough to transfer
100µL RNA solution to each
Placed PCR tubes in all 96 positions of thermal cycler
Ran melt curve protocol, start at 25⁰C, increase 1⁰C every cycle,
60 cycles, so final temp is 85⁰C. Each cycle is 10 seconds.
Measure fluorescence every cycle.
Repeated melt curve 3 times, total of 4 curves.
Put data from each curve into spreadsheet. 96 data points at each temperature.
Averaged fluorescence across the whole plate at each temperature.
Used this average, standard deviation, maximum, and minimum
values to make the plots below.
Calculated correction factors for each well at each temperature by
dividing the whole plate average fluorescence by each well's
fluorescence for melt curves 2, 3, and 4. Averaged correction factors from each curve.
Calculated corrected fluorescence for curves 1, 2, 3, and 4 by
multiplying the averaged correction factor for each well by the
observed fluorescence for that well.
Replotted the corrected values to show reduced variation.

Data is shown below. I repeated the melt curve 4 times because the first melt usually has a lower intensity than subsequent melts. Y axis is fluorescence, X axis is temperature in celsius, and I plotted the average fluorescence at each temperature with the standard deviation along with the minimum and maximum to show how far outside the standard deviation some wells are falling. I calculated the correction factors for melt curves 2, 3, and 4 and averaged them. When I used these averaged factors on melt curves 2, 3, and 4 it did a good job at eliminating variation. When I applied the correction factors to melt curve 1, it reduced the variation, but not by much.


texts: In molecular docking, what is the difference between ligand and cofactor?

texts: In molecular docking aspect, what is the difference between the Ligand and Cofactor? Can a Cofactor be used like a ligand for docking with the target?


texts: Is this pCAMBIA co-transformation possible?

texts:
I would like to know whether the pCAMBIA1200 and pCAMBIA0380 be used for co-transformation of rice using Agrobacterium LBA4404.They probably have the same ori site so they belong to the same incompatibility group.So will they co-exist in one Agrobacterium strain and be transferred to the rice plant?

Please let me know.


texts: What happens to plants if they are exposed to "sunlight" 24h a day?

texts:
I just wondered if one could grow plants faster, if they were exposed to sunlight-like light all the time.

In a similar question which is not the same, I could confirm that plants have different processes going on at day and at light. However, it didn't answer the question about the consequences of permanent exposal to sunlight.

However, I don't understand what would happen if there was light all the time. What would happen to different plants if they are exposed to "sunlight" 24/7?

(Similarly: What is the "optimal" amount of sunlight time different plants have? Is it basically what is common in the environments they typically grow in?)


texts: Any difference between inverted microscope objective vs normal microscope objective?

texts: I'm planning to build an inverted microscope and I am not sure if I can use a plane achromatic objective of a normal microscope for the inverted microscope as well. Are there any specific needs for the objective of an inverted microscope?


texts: In phospho/pan analysis in Western blots, what is best way to normalise to an internal loading control?

texts:
I am analysing the expression of a protein kinase X that is a phosphoprotein through Western blots. I have labelled the membrane for both the phosphorylated form of the protein and also for the total target protein. I am comparing the expression of my phosphorylated protein between different experimental conditions.
For each sample, I have calculated the proportion of protein that is phosphorylated by dividing the phosphorylated protein signal by the total target protein signal. I have also done this to ensure that the differences in phosphorylated protein between samples is not due to variations in total protein levels under different experimental conditions.
However, I want to normalise this ratio to an internal loading control, since I think that it would be incorrect to assume that the expression of the total target protein is uniform between the different experimental conditions. I have read when comparing the expression of a protein amongst different experimental conditions, you need to use an internal loading control.
I have used a total protein stain (Ponceau S) instead of a housekeeping protein as my internal loading control, since studies have shown that expression of housekeeping proteins can vary between different experimental conditions and that the level of total protein between different experimental conditions is more consistent.
I am currently debating between the following two methods of normalisation:
(1) (phosphorylated protein X/Ponceau)/(total protein X/Ponceau)
(2) ((phosphorylated protein X)/(total protein X))/Ponceau
I think that method (1) is the more correct way to normalise the phospho/total protein X ratio, since you would want to obtain the relative abundance (to Ponceau) of both phosphorylated protein X and total protein X before calculating the phospho/total protein X ratio.
However, I would was wondering if anyone knows whether this reasoning is correct? Any insights are appreciated.


texts: What is this? Found in southern Illinois

texts: Found in southern Illinois in the driveway.  What is this?


texts: Never seen a spider with this pattern before

texts: Found this spider at work in the Leicestershire area of the United Kingdom. Never seen one with this kind of pattern on its back before so was curious as to what it is. (Size: 2-2.5 inches)


texts: Assumptions of the models for haploid and diploid selection

texts:
For a bi-allelic locus, the model for haploid Natural Selection is:

$$\frac{dp}{dt} =  \frac{pW_A}{pW_A + (1-p)W_B}$$

, where $p$ is the frequency of the allele $A$, which relative fitness is $W_A$. $W_B$ is the fitness of the allele $B$, which frequency is $1-p$. $\frac{dp}{dt}$ is the change in allele frequency through time.

The same model for diploid selection is:

$$\frac{dp}{dt} = \frac{p^2W_{AA} + p(1-p)W_{AB}}{p^2W_{AA} + 2p(1-p)W_{AB} + (1-p)^2W_{BB}}$$

, where $W_{AB}$ is the fitness of the diploid genotype carrying the allele $X$ on one chromosome and the allele $Y$ on the other chromosome. We define $W_{AB} = W_{BA}$ and therefore we use only the symbol $W_{AB}$ in the above calculations. Note: This equation assumes Hardy-Weinberg equilibrium.

Those equations can be found in any introductory courses in population genetics. For example, here is a source where you can find this same equation for diploid selection. They just express $q$ instead of $1-p$.

My questions are:

Do these models assume constant population size? Why?
Do these models assume threshold selection? Why?

Thank you!


texts: What is the main general difference between Mitosis and Meiosis?

texts:
I found such a clause:

  The general principle is that mitosis creates somatic cells and
  meiosis creates germ cells.

However, I cannot agree. Each gametogonium needs to go through mitosis before it can enter meiosis I. So in that case mitosis is happening with germ cells so the clause is false.

I would rephrase the sentence to be

  The general principle is that meiosis creates only germ cells with the possibility of a decrease in chromosome number, while mitosis can create both somatic and germ cells while the ploidy stays constant.

Ok, not perfect.

How would you say the main general difference between mitosis and meiosis?


texts: What do the text annotations in an electron micrograph mean?

texts:
I saw a photograph taken from an electron microscope, with some text.

I want to know what is the meaning of these numbers and letters?

Thank you! Regards.


texts: Practical utility of genes responsible for the biosynthesis of a useful compound in a plant

texts: Assuming a woody plant naturally has a valuable compound, say a kind of sterol. During an RNA-seq analysis, almost all genes involved in the biosynthesis pathway of this sterol were identified in the plant. I was wondering what are the benefits of this finding? If this study was done in a bacterium or fungus instead of a plant, the importance of this finding is clearer, at least for me, since these simple organisms can be the factory of valuable compounds by genetic engineering technology. But, what about a woody plant which cannot be engineered and grown in bulk?


texts: What is the secondary structure distribution per AA in the Human proteome?

texts:
If one would classify each amino acid to either be in a Coil, Beta strand or Alpha helix what would be the distribution of these classes in the human proteome?

Is it 33%-33%-33% or is it biased? If it is biased why?

I thought it should be around equal, but I run the whole proteome through PSIPRED, and I found the distribution to be 60% Coil, 30% Helix, 10% Sheet. Why is it so?


texts: Difference between intervertebral and vertebral foramina

texts: In the human spine, what is the difference between intervertebral and vertebral foramina? Is it just a matter of perspective and do they refer to the same thing or are they different?


texts: What is the word for being inured to loss of biological diversity?

texts: In the title.  The word has been coined relatively recently for the phenomenon of getting used to loss of diversity because of the gradual rate it happens at.  For example, not finding it strange that there are far fewer invertebrates around now than there were 30 years ago - car windscreens in the summer were covered in dead insects, whereas now that rarely happens.  Both time points are noticeably distinct in biological richness, but we quickly get used to the state of things now.  I can't find it on Google!


texts: How a person can transmit COVID-19 while his COVID-19 is still in incubation state?

texts: A person with SARS 2003 cannot transmit that disease while his SARS is in incubation state but how a person with COVID-19 is transmitting COVID-19 even though his COVID-19 is in incubation period?


texts: It is well known that if DNA occurs in the cytoplasm of eukaryotic cells, an immune response may be triggered through a myriad of DNA receptors and pathways as part of the immuno response. Yet, apparently the nuclear DNA does not induce any type of such response. Is it known why this happens? Is it just due to the fact that the nuclear DNA is immuno-privileged?


texts: Could random male-only-offspring mutation wipe out a species?

texts: If we can engineer the extinction of a whole species of mosquitos with male-only-offspring genetic mutation, how come such scenario never happened naturally in the past to other species? Or has it?


texts: How does pressure measured by sphygmomanometer translate directly to blood pressure?

texts: As per my understanding a sphygmomanometer when wrapped around the arm and inflated only measures the pressure of the air inside the cuff, doesn't it? How does that translate directly to the pressure value of blood flowing across the artery?


texts:
My 4 year old fell in love with this fish at the aquarium.

I'm trying to find out what species it is so we can learn more about it.


texts: ATP utilized in Glycolysis vs. Gluconeogenesis

texts: In glycolysis, the conversion of glucose to pyruvate results in a net gain of 2 ATP molecules. In gluconeogenesis however, the conversion of pyruvate back to glucose requires 6 ATP molecules.  Why does there seem to be an apparent loss of energy?


texts: Difference in callus formation during healing of bones of different origin

texts:
My study material from pathology states that during fracture healing after hemorrhage and coagulum formation the mesenchymal progenital cells from periostium that are closer to the fracture differentiate into chondrocytes and form hyaline cartilage, while the ones that are farther differentiate into osteoblast.

Result is production of hyaline cartilage in which enchondrial ossification and subsequent remodeling into lamelar bone occurs.

My question is: Does this enchondrial ossification also occur in bones in which Intramembranous ossification normally occur during development? (e.g. clavicle and some skull bones.)

NOTE:
in this stackexchange post and Wikipedia article on this topic, only chondrocytes are noted.


texts: Are there any animals that maintain white fur year round?

texts: Besides examples of rare albino animals, it seems animals only have white fur during the winter.  Additionally, and not coincidentally, the examples I've found live in the northern latitudes with predicable snow cover and have different colored coats in the summer months.  Are there any examples of animals that maintain a white coat of fur year round, or are there simply no environments that such a trait would be beneficial in?


texts: How long can Cholera bacteria survive in a dead host?

texts:
How long can cholera bacterium survive inside a dead host? Can they remain dormant in such conditions?

BACKGROUND

On a hill not far from where I live, there was a hospital operating since 16th until 19th century, for cholera patients, and a cemetery for those, who didn't make it. It was closed in 1st half of 19th century and until 20th century not even ruins of the hospital remained; the gravestones got lost under a layer of soil.

Currently, the area is being built over. Large amounts of soil are being excavated for foundations and basements of new houses. Rainwater falling on the piles of excavated soil floats down through driveways, backyards and gardens of houses down the hill, including my own.

Should I worry?


texts: Why are proteins in the insoluble form when they are in frozen water?

texts:
Why would lowering the temperature of water change the intermolecular forces so much that proteins once soluble in water, become insoluble? I know freezing can create a crystal lattice, but I don't see how temperature would connect to the inter-molecular forces of water? If it even does?

EDIT:  So why would a temperature decrease change how a protein interacts with a POLAR solvent


texts: Given an amino acid sequence, how to determine the structure (helix, beta sheet etc)?

texts:
Assume there's a short sequence of an amino acids.

MAKMGSKKKAGHGGKEKLENMGE

I am using molecular structuring softwares to look at secondary structure. But it's blackbox method. In plain theory, how to determine what structure the above peptide will fold into? There must be a basic set of rules, prior to all the complex maths, and modelling?

Based on basic rules I also want to know what and how a different amino acid contributes to the formation specificity.  Will add more details.


texts: Are there fishes with a double circulatory system?

texts: Our courseware materials say there are such fishes, but my Internet searches suggests fishes only have a single circulatory system.


texts: What’s the name of this insect that looks like a leaf? I found it in Taiwan

texts: Found it in a tea plantation. It can jump.


texts: What is this slug-like thing I found in my bed?

texts: what is this thing I found in my bed? Squishy like a slug, mildly freaked out, help? I'm in Scotland Edinburgh


texts: Do people often blow out the air from their lungs a lot when living in the cold condition to keep their lungs warm?

texts:
Do people often blow out the air from their lungs when living in cold climatic conditions to keep their lungs warm?

I ask this question because it could connect to how people in different areas construct linguistic sounds.

For example, the Germanic families of Language (German, English,...) use a lot of air from the lungs to construct the sound?

Is that because the Europeans living in cold climate often blow out a lot of air from the lung to keep warm and as a result gradually they construct air-driven linguistic sounds?

For people living in warm climates (ex: Sino-Tibetan language like Chinese, Thai), we mostly use the tongue to construct sounds, and we use very little air from our lungs to make sound.

I posted this question to some forums & some people said it’s baloney. However, there's one thing for sure, the environment shapes how local people construct sound. People construct the sound like that because it is constrained by something. One thing can not stand alone, it must be the karma or outcome of something else.


texts: Can someone identify this Brazilian bird?

texts:
Photographing and documenting the local fauna (Brasília, DF, Brazil - Near Coordinates [-15.696506 -47.860013]), I found this rather unusual-looking bird whose name I couldn't find:

(Image was now uploaded to Wikimedia under my account "AlephGuira")

Possibly useful information:

One was seen preying on
what looked like Taturanas (https://en.wikipedia.org/wiki/Lonomia), but due to their venomous nature, I'm not sure.
The observed flock was composed of 7 birds.
There seems to be sexual dimorphism (The other one, not pictured, seems to be smaller, has shorter head feathers, whiter wings and lacks the orange-pointed beak).
They were first seen on a Pequi Tree (https://en.wikipedia.org/wiki/Caryocar_brasiliense).


texts: Identifiying a conserved residue in multiple PDB structures

texts:
I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them.

Originally I wanted to extract the sequences from the PDB files with BioPython, align them and then use that alignment to identify the residue number in each PDB for my conserved residue.

But it turns out that is a bit harder than I expected. Parts of the sequence are often missing in the PDB. I don't see an obvious way to get a proper sequence out of the PDB files. Then there is the issue of mapping the conserved residue number back into the PDB file.

Is there any easier way to do this? It doesn't have to be BioPython, though that would be nice.