text:
Is there a way to use presence-absence data to inform a sampling design for a more specific survey?
I am currently in the process of designing a spatial survey to assess the abundance/density of woody debris across an ecosystem with multiple defined habitats (i.e. I am interested in not only the abundance across the entire system, but also any differences across habitat type). I have no prior data or similar studies to perform a power analysis to help determine how many sites I will need to address my questions, but I do have presence-absence data of woody debris within my study area. Is there a way to use this data to inform my design? I am likely going to be developing a small pilot study to collect enough data to run a power analysis, does presence-absence data help in any way?

What's your scientific question?

This might be better for CrossValidated. Power analyses always rest on some assumptions. You might be able to leverage presence/absence + some assumptions to get an estimate of variation in density, but you can also probably perform the power analysis with some sensible order-of-magnitude guesses about the degree of variation.


text:
What are the implications/predictions of the selfish gene theory?
Are there any testable predictions or implications of the selfish gene theory? Or it is just interesting interpretation of the observations/experimental data? If this theory is not falsifiable and doesn't generate any predictions, how can it be helpful anyway?

The Selfish Gene theory "can be defined as the idea that the gene is the ultimate beneficiary of selection".   Argren, in Selfish genetic elements and the gene’s-eye view of evolution lays out the history of the theory and the arguments for and against it.
The theory is almost certainly correct; and it's almost certainly incomplete. The theory is testable.  It predicts, for example, that there will be genes whose sole function is to self-propagate.  Those genes can't confer much fitness disadvantage to their host or they will quickly be weeded out of the population; and they don't necessarily need to confer a fitness advantage. But to the extent that different individuals have different versions of the same genes, the versions that convey a fitness advantage are likely to win the evolutionary competition.
There are, of course parasitic genes like transposons which impose a cost by requiring the host to adapt to their presence.  As long as the host is able to adapt without losing too much fitness, the parasitic genes can ride along for free.
The Selfish Gene theory provides useful insights, but it is incomplete, because combinations of genes,  arrangements of genes, and even genetic diversity within a population can provide a fitness advantage or disadvantage. Even genes are subject to "group selection", where gene A can provide a disadvantage unless gene B is also present, in which case A and B together provide an advantage. This leads to selective pressure to link the two, e.g., by placing them close together on one chromosome, which is analogous to a cooperative relationship between the genes that provides a mutual fitness advantage.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

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text:
ELISA troubleshooting
Hi,
Why does my elisa plate wells gives a brown color after adding the stop solution. I am giving a 4*5 minutes wash after each step. TMB gives it a proper blue color but when I add the stop solution (0.16M H2SO4), the color turns to brown. I am using all the reagents new. Any help will be appreciated.

The full oxidation of TMB ( 3,5,3’,5’-tetramethylbenzidine) is 2-electron process.  The first step (one electron oxidation) gives the blue product, which is then further oxidized to a yellow product (2nd electron) that is stable in acid.  At high concentrations this might appear brown.
You might also not be fully quenching, leading to a mixture of blue and yellow products (should be more greenish though).  In this case add more stop solution.
TMB chemistry:
Josephy, P. David, Thomas Eling, and Ronald P. Mason. "The horseradish peroxidase-catalyzed oxidation of 3, 5, 3', 5'-tetramethylbenzidine. Free radical and charge-transfer complex intermediates." Journal of Biological Chemistry 257.7 (1982): 3669-3675.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is it possible to cultivate cheek epithelial cells in a non-CO2 incubator?
CO2 is important for maintaining constant pH in cell culture. Unfortunately, I do not have access to such incubator and buying a new one is expensive. I found a cheap incubator online, but it doesn't support CO2. I'd like to ask if I can cultivate cheek epithelial cells in such incubator and if it won't negatively affect my cell culture. Another option is building a small CO2 generator inside the incubator. I made some calculations - I know how much CO2 I need to generate, how many grams and mL of solutions I need, moreover the build-up pressure is so small, it should not negatively affect the incubator.

Are you familiar with CO2-independent growth media? (I don't know anything about culture of that cell population specifically, though)

Thank you very much. I am not familiar with CO2-independent growth media, but I will take a look. I planned to buy a cheap DMEM from eBay. I hope, there are some inexpensive media you mentioned, or at least a method to convert DMEM to such medium.

L-15 media does not require a CO2 atmosphere and according to Sigma-Aldrich this media is suitable for primary explants of adult human tissues.

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text:
Can I sterilize the equipment for experiments without an autoclave?
If I don't have access to an autoclave, can I sterilize my equipment in a regular pot. If so, what time is needed at about 110°C (I measured inside) for a proper sterilization?

Welcome to Biology.SE! We encourage you to do some research on your own and then ask questions informed by what you have learned (ideally with references to reliable sources). ——— Please also take the time to go through the [tour] and the help pages starting with [Ask] questions effectively on this site. Thanks!

It certainly can be done. Tyndallisation may as discussed on labmate may work well for your situation. If not, there are many other viable alternatives suggested.

**Tyndallisation:
  **
  Developed partway through the 19th century by English physicist, John Tyndall, the eponymous Tyndallisation was a commonly used
  technique by the microbiologists of the 1800s. Tyndall experimented
  with boiling beef broths to develop a method to sterilise liquids in a
  safe and comprehensive manner.
His research led him to the basic principles for Tyndallisation, a process by which medias are subjected to relatively short boils at a
  regular atmospheric pressure. This relatively straightforward method
  is still suitable for small labs, or research facilities which only
  require sterilised equipment part of the time.
It is not recommended to attempt to sterilise closed glass containers using this method, without lining them with cotton and
  capping them with foil – allowing for air to escape without being
  subjected to contaminants.
The process involves boiling fluids for 10-15 minutes before leaving to cool to room temperature and leaving it to sit for 24
  hours. Repeat this process another three or four times, by which time
  sterilisation should have occurred.
Naturally this method has reduced in popularity due to the requirement to continue the process for up to five days to achieve
  sterilisation.


text:
Which culture media is suitable for cheek epithelial cells?
A month ago, I tried isolating cheek cells from saliva and the experiment was a success, however, I was wondering if it is possible to cultivate these cells in vitro. I'd say it's possible, but I wasn't able to find any publications about this topic online, even on PubMed (I found one, but it was outdated and the part with used media wasn't clear). Is it possible to use just DMEM media and if so, how long will the cells survive in the media, or are there any other alternatives?

There are different kinds of epithelial cell basal media. These are also usually supplemented by different factors. I cannot find a medium specific to oral mucosa and the composition of the basal medium is difficult to find. This paper says that DMEM supplemented with human serum or conditioned with fibroblast supports growth of conjunctival epithelial cells.


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How long does it take to reset sense of smell?
I have noticed that when I go on vacation for several days and then come back home, there is a distinctive, relatively mild paint smell in my apartment complex. However, under normal circumstances, this smell is virtually unnoticeable to me.
What are the primary factors that cause us to become used to certain smells? And, is there any way to estimate how long it takes to 'reset' the sense of smell, so that these smells which we have become used to will again be obvious?

the term you are looking for is Olfactory adaptation or Olfactory fatigue https://en.wikipedia.org/wiki/Olfactory_fatigue#:~:text=Olfactory%20fatigue%20is%20an%20example,'out%20of%20the%20ordinary'.


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How much variation in the human genome for humans
We are currently learning about the Human Genome Project in high school biology. Wouldn't the human genome that was mapped be different from, say, mine if it was mapped? How much variation is there between individual humans in our genetic sequencing? I'm assuming there is not that much difference since multiple volunteers were used in the project. I did see another question that talked about mutation rate, so I'm not sure if that's the same thing.

Welcome to Biology.SE! This is a very basic question and thus appears to meet this sites criteria for a homework question. In these situations we expect you to do some research on your own and then ask questions informed by what you have learned (ideally with references to reliable sources). For instance the "Related" links led me to this question. ——— Please also take the time to go through the [tour] and the help pages starting with [Ask] questions effectively on this site. Thanks!

Possible duplicate of Why are the genomes of Humans 99.5% the same?

Hi Sarah, and welcome to Bio.SE! @tyersome I disagree that this is a "basic" or trivial question. So do the 500K genome project, gnomAD, ClinVar, Genomics England & BioBank, and countless other massive projects. Even post-sequencing, calculating the rate of variation is incredibly challenging. This question clearly is a fundamental question about genetics that has massive ramifications in rare disease, cancers, developmental disorders etc.

@David I think that I side with Sarah on this. Mutability (i.e conservation) and variation are fundementally different principles. Conservation (evolutionary constraint/mutability) are measuring changes of genetic regions over huge timescales by comparing homologous sequences in other species. Variation, however, is snapshot of what is currently varied in the population of a single species. Of course, there is a lot of overlap between constrained genes in gnomAD, for example, and highly conserved regions. Practically I'm not sure if this will be reflected in the answers...

@James — Perhaps we could do with a community wiki (whatever that is) on this whole topic. I think the current dispersed nature of questions relating to it makes it very hard to get a coherent view.

You are correct in saying that the human genome sequenced in the project was contributed by a dozen anonymous volunteers. However, the final sequence that is used as a standard reference is a somewhat arbitrary construct that represents a collection of consecutive segments taken from one or other of the contributors. It is a haploid sequence, plus a Y and an X chromosome.
Now you ask how different are the genomes of any two subjects, taken at random from a population. Imagine for simplicity looking at your own genome. For each of the 22 autosomes, you know you have two copies, one transmitted from your father, the other from your mother (for the X chromosome you have two copies, if you are a girl). Now imagine comparing the sequence of each of your pair of homologous chromosomes side by side; remember that they are derived from very different individuals (unless your parents are close relatives), so that they will not be identical, as they represent independent evolutionary histories.
Then, the question becomes: how much variation is there between the sequences of your paired chromosomes? And the answer is known: approximately every 1,000 base pairs your chromosomes show a base pair in one chromosome and a different base pair in the other; otherwise they are identical. The sites where this variation occurs are called SNP, for Single Nucleotide Polymorphisms (many other kinds of variation exist, but SNPs are the more common). We can generalize this observation, as it remains true for any pair of chromosomes chosen at random from any pair of subjects. Therefore, we can say that humans are identical for 99.9% of their genomes, whereas the genetic variation responsible for the differences that allows us to recognize ourselves as unique are limited to 0.1% of our genome.

I think this answer gives a good basic overview to the question, for further detailed reading it would be helpful to include links about the already mentioned SNPs and also the 1000-genomes project (which is essentially about exactly this question)


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Do bacteria select for "soap resistance"?
When people wash their hands with soap, this limits the spread of bacterial infections. That much, I am pretty convinced of. Duh.
What I don't get is how this doesn't lead to evolutionary pressure on the bacteria to become "soap resistant." I'm not talking about anti-bacterial soaps (I understand the FDA no longer recommends these), but just plain old soap and water.
The soap does something (I feel like I've heard a few mechanisms), but the net effect is that it makes the bacteria less likely to spread. How would this not lead to evolutionary pressure that drive bacteria to be less likely to be removed/killed/destroyed/whatever by soap?
Or is it not a problem because soap is just so "strong" that it's like evolutionary pressure for humans to survive underwater. Sure, if gradually introduced over 1MMM years, we might eventually get gills. But if you just keep drowning people, no one is gonna really evolve gills.

You make a reasonable analogy in the last couple of paragraphs - perhaps check out how soap works. There are 2 factors at play; chemical and physical.

Does this answer your question? Resistance to Antiseptics

I agree with @bob1. If you understand how soap works, you'll probably see why there's no selection pressure for soap-resistant bacteria. If after researching how soap works, you still have questions, please post what you found that confuses you.

Conceptually related: Do organisms use detergents to fight off viruses?

It would be an interesting experiment to supplement growth medium with small amounts of detergent and see how that affects evolution in a model bacteria over successive generations (something like Lenski's LTEE). Keep in mind, however, that bacterial killing is a secondary effect of soap in handwashing. The primary effect is to get the bacteria off your hands.

But wouldn't the bacteria then just evolve to not "get off your hands"? Like - whatever mechanism the soap works by, it's creates evolutionary pressure to resist that (be functionally stickier, in this case).

I must be misunderstanding something about the boundary conditions, because the argument I'm making seems to be mechanisms-of-soap agnostic...

@NateRush I think it would be enlightening for you to review the excellent answers to the question Why do some bad traits evolve, and good ones don't?

To avoid clogging up the comments, please continue discussion in this chat room.


text:
Why does the time to reach equilibrium across a membrane decrease with concentration?
We're learning about flux and Fick's law and there's one point I'm having trouble understanding. Assuming we have a higher concentration of a species on one side of a membrane, I understand that increasing the concentration will increase the flux (net particle movement/(time*area)). We were told as well that increasing the concentration also decreases the time it takes to reach equilibrium. Why would that be?
Rephrased: If you have 10 particles on one side of the membrane and 0 on the other, it takes X amount of time to reach equilibrium (~ 5 particles on each side).
If you have 10 million particles, why would it take <X amount of time to reach equilibrium (~5M particles on each side).
Thanks

Considering Fick's first law, there must have been a misunderstanding between you and your teacher.

where

J is the diffusion flux, of which the dimension is amount of
substance per unit area per unit time. J measures the amount of
substance that will flow through a unit area during a unit time
interval.
D is the diffusion coefficient or diffusivity. Its dimension is area
per unit time.
φ (for ideal mixtures) is the concentration, of which the dimension
is amount of substance per unit volume.
x is position, the dimension of which is length.

As you can see, flux is proportional to concentration, meaning equilibrium time is not affected by concentration. Possibly, your teacher meant that either (1.) an absolute increase in concentration on both sides of the membrane (by the same offset) decreases the equilibrium time or (2.) that a proportional increase in concentration by down-scaling of the containers (x; length) would also shorten the equilibrium time.

+1, though this is relevant when you get closer to real world demonstrations: 1[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648224/]. Where absolute concentrations can effect your lattice walking. I agree that this is more likely a misunderstanding.

I agree; it's definitely more complicated than that, including considerations like viscosity or temperature and Boltzmann distribution of corresponding velocities.


text:
When recalling the same piece of memory in different times, are the brain activities different?
When we are thinking about the same piece of memory in multiple different times, would the corresponding brain activities always be the same? Or how similar/different can the corresponding brain activities be?

The term for the brain activity that corresponds to an experience is "neural representation".
Neural representations "drift" over time.  From https://elifesciences.org/articles/51121:

Similar ‘representational drift’ has been shown in other neocortical
areas and hippocampus (Attardo et al., 2015; Ziv et al., 2013; Levy et
al., 2019).

So that means that the brain activities corresponding to an experience can change over time.


text:
What evolutionary advantage do separate teeth have compared to a single piece of bone?
Humans and many animals have multiple teeth consisting of separate pieces of bone embedded in the jaw. For humans, this arrangement has some disadvantages:

teeth are quite fragile when impacted and break easily
gaps between teeth are difficult to clean and risk decay

Why don't we have a single piece of bone in our mouth (possibily with an uneven surface to aid crushing food)? Is there any evolutionary advantage to having multiple separate teeth, or does it simply not matter because by the time problems arise we have already reproduced?

teeth are used to crush bones,so they are significantly stronger than any of the bones in the body.

When discussing evolution, it's important to remember that forces of selection work by affecting reproductive fitness, i.e., the viability and number of offspring. So yes, as you point out in your last sentence, likely our teeth work well enough for us because their potential drawbacks don't significantly affect reproductive fitness. Also, as a matter of theoretical exercise, there is likely a redundancy benefit to having multiple teeth - if one is diseased, the others are still usable. I also wonder if there are any animals that do have one single bone as you describe.

Consider that many animals (sharks, for instance), have teeth that are continuously replaced.  So a better question might be to ask what caused humans (and I think most mammals) to lose this useful trait?

One broken tooth doesn't really affect the strength of the others.  A crack in a single long tooth would damage the structural integrity of the whole chewing surface.

There are significant differences between teeth and bone, for example teeth are much harder than bone, teeth are replaceable, teeth are directly exposed to the outside environment, not covered by tissue, and so forth. Perhaps some more research into teeth would be useful.

@Armand i know there are differences. My question was maybe a bit unclear. I didn't want to ask why there are teeth instead of bones, but why there are multiple teeth instead of one large spanning the entire jaw. Besides, parts of teeth (dentin, cementum) are not that different from bones. I never questioned the presence of the harder parts (enamel).

That would be a hell of a root canal...

@jamesqf Mammalian teeth are like mammalian hearing: sacrificing long term regeneration for short term performance because breeding is the only thing that matters,

You should check and see if an question has been asked before you post https://biology.stackexchange.com/questions/104682/what-evolutionary-advantage-do-separate-teeth-have-compared-to-a-single-piece-of/104721#104721 and https://biology.stackexchange.com/questions/8302/what-is-the-evolutionary-reason-behind-the-fragility-of-teeth/53692#53692

@DKNguyen: But it's difficult to see any short-term performance benefit from not replacing teeth.

@jamesqf I think I read somewhere it might have something to do with the specialization of teeth in mammals. They work better but their arrangement and alignment matters more.

It also has some advantages, although some of these have been mostly lost in humans.
In sharks for example teeth get continuously replaced, so losing one is much less of deal for them. This true in reptiles too, e.g. a lowly gecko can have 1,000 new teeth their lifetime. (The more technical term is polyphyodont.)
It is somewhat of a mystery why mammals lost most of this ability, but it is thought  to be related to the specialization in the shape of the teeth. Species that have little differentiation between teeth [types] are most prolific at replacing them. (I guess you're ware that humans get two sets, but this is driven by age rather than by a loss process.) There are few polyphyodont mammals as well: elephants, kangaroos, and "sea cows".
Being able to replace teeth in smaller increments (i.e. individual teeth) is probably an advantage as at any given time only a small proportion would be missing... although as with other things in evolution there are some exceptions. Piranhas actually have quadrant-fused teeth (which basically act like larger serrated knives)... and they replace them in whole quadrant increments. (They also grow the replacements in such a way that it takes only about a day for the new set to replace a lost quadrant.) However this is almost certainly energetically expensive, which is probably why few other species have this feature.

i know there are differences. My question was maybe a bit unclear. I didn't want to ask why there are teeth instead of bones, but why there are multiple teeth instead of one large spanning the entire jaw. Besides, parts of teeth (dentin, cementum) are not that different from bones. I never questioned the presence of the harder parts (enamel).

For one thing, multiple teeth can adjusted individually for wear and alignment.
However that clarification in the comments conflicts with with points in your question which could be construed intended as the argument against teeth of any kind, singular or multiple, especially singular.

teeth are quite fragile when impacted and break easily
gaps between teeth are difficult to clean and risk decay

Can you imagine what would happen if your ONE tooth broke or decayed?


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Do bacteria produce proteins other than ribosomal proteins when grown in wrong culture media?
Someone I know has done an experiment using pure culture and given it to me for rna-seq analysis.
But there are a few problems

the bacteria she gave me as reference was initially a Staphylococcus sp. but it turned out to be Bacillus sp. Upon my analysis.
upon analysis I could only find ribosomal RNAs for Bacillus sp.

So my question is does a bacteria that is grown on a wrong culture media produce any proteins even in small amounts?
Will it have a lot of rRNA transcripts? Because I see all the sequencing reads map to ribosomal region. Are those not dependent on growth conditions? Or is it that Bacillus can survive on different media in a vegetative state and thus have a large number of ribosomal RNA?

From my experience, bacterial RNA-seq libraries derived from exponentially growing cells that have not been prepared using an rRNA depletion kit will result in >80% of reads mapping to 16S and 23S rRNA genes.
Ask your colleague if they used a bacterial rRNA depletion kit prior to RNA library preparation.
It is also my understanding that rRNA tends to be more stable than mRNA when exposed to ribonucleases given its structure and sequestration in ribosomal proteins. If your colleague performed rRNA depletion, my next hypothesis would be that the non-rRNA species were degraded due to poor technique during library preparation (samples too warm, contaminating RNase).

I will ask them and let you know the exact thing done. Thank you @acvill for your help.

If the cells are growing at all, then they are actively expressing a whole bunch of different proteins.
Ribosomal RNA, however, makes up the vast majority of all RNA in a typical cell, however.  There are also far fewer different rRNAs than there are mRNAs, so the relative concentration per rRNA is even greater.
As such, unless rRNA is excluded (e.g., using methods like those described in the linked paper), the mRNA reads will typically be swamped by rRNA reads.

I am getting very few reads for other proteins. Like you said they maybe getting swamped by rRNA reads. Thank you @jakebeal for your answer.


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Convert fasta to ascii?
Is there an algorithm or tool to convert a fasta sequence file (such as the file linked below) into an ascii file for the purpose of gene synthesis?
https://www.rcsb.org/fasta/entry/6EQJ
To the best of my knowledge, the fasta file contains the entire sequence of a protein, in which case there must be a way to convert it to a standard ascii formatted sequence, but I havent been able to find any tools to do so.

Why would gene synthesis require ascii format?

What do you mean with ascii? FASTA is plain text.

FASTA files are just text files, so you can open them up in your favorite text editor to see what they look like. The file you linked has a single entry. The first line begins with > and contains information about the sequence, delimited by | characters – the accession number, chain info, gene name, species, etc. Subsequent lines are just the protein sequence using the standard 20-letter alphabet for amino acids, or the nucleotide sequence from 5'-3' using ACTG. There can be multiple entries in a file, delineated by one or more blank lines.
If for whatever reason your instrument or vendor won't accept FASTA files, a very simple low-throughput solution is to just delete the first line of single-entry files, or delete any lines beginning with > for multiple-entry files. If you have many files to process, this can be automated using Unix/Linux command line tools or a scripting language like Python or Perl.


text:
How can I extract ligand with neighboring protein atoms from PDB with complex?
I'm not familiar with biology and coming from Data Science field, so please excuse me for the lack of knowledge. What I want is to create 3D voxel representation of ligand atoms with neighboring part of the protein (looks like it is called pocket) from PDB file which contains complex.
For example, let it be 10gs from RCSB (https://files.rcsb.org/download/10GS.pdb). For other example, it can be 4xit or 4wkc.
What I planned, was identify both protein and ligand atoms, compute the geometric center of the ligand, and then calculate proximity for each atom and fill some 3D surrounding cube.
When I open PDB for this complex (10gs) I see what I understand as two possible binding sites for ligand VWW, and another two - for MES:
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VWW A 210
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VWW B 210
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 211
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 211

How can I proceed from this point? Does this PDB contain atoms for ligand VWW, properly oriented, and how can I identify them along with neighboring ones of target protein?
Or my formulation of the problem is totally wrong?

You might find RCSB's Guide to Understanding PDB Data and the PDB file format documentation useful. I'll go over some of the information present in PDB files that seems relevant for you, using your example of 10GS.
Ligands are specified in the heterogen section:
HET    VWW  A 210      33
HET    MES  A 211      12
HET    VWW  B 210      33
HET    MES  B 211      12
HETNAM     VWW L-GAMMA-GLUTAMYL-S-BENZYL-N-[(S)-CARBOXY(PHENYL)
HETNAM   2 VWW  METHYL]-L-CYSTEINAMIDE
HETNAM     MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
FORMUL   3  VWW    2(C23 H27 N3 O6 S)
FORMUL   4  MES    2(C6 H13 N O4 S)

These records tell you the identity of the ligands that are bound to the protein (VWW and MES), how many are bound (4 in total), the chemical name (in the HETNAM record) and chemical formula (FORMUL record). The HET record also gives the number of associated HETATM records (33 for VWW and 12 for MES). Here are the first five HETATM records for VWW of chain A:
HETATM 3265  N   VWW A 210      15.088  10.798  23.547  1.00 14.90           N
HETATM 3266  CA  VWW A 210      15.010   9.987  24.792  1.00 20.92           C
HETATM 3267  C   VWW A 210      16.115   8.924  24.830  1.00 21.55           C
HETATM 3268  O   VWW A 210      16.520   8.515  25.940  1.00 17.16           O
HETATM 3269  CB  VWW A 210      13.635   9.327  24.908  1.00 14.23           C

Each HETATM record corresponds to an atom in the ligand and gives the chemical coordinates for each on the X, Y and Z axes. For example, the first record specifies a nitrogen atom at coordinates (15.088, 10.798, 23.547).
The connectivity (ie covalent bonding) between atoms in a ligand is specified in CONECT records. Here are the first five from the PDB file:
CONECT 3265 3266
CONECT 3266 3265 3267 3269
CONECT 3267 3266 3268 3273
CONECT 3268 3267
CONECT 3269 3266 3270

This tells you that atom 3265 (the first nitrogen in the HETATM records above) is bonded to atom 3266 (a carbon). Atom 3266 is bonded to atoms 3265, 3267, 3269. Et cetera...
The atoms of the protein are specified in ATOM records. Like the HETATM record, these records give some identifying information (atom serial number and type, residue name and number, etc) as well as the coordinates in 3D space. For your purposes, it sounds like you can just loop through the atoms of the protein and find the ones which are within some threshold distance of an atom in a ligand (or the geometric centre of the ligand). However, this PDB file does already contain some information about the binding sites for these 4 ligands in the SITE records (here are the first four corresponding to site AC1):
SITE     1 AC1 15 TYR A   7  PHE A   8  ARG A  13  TRP A  38
SITE     2 AC1 15 LYS A  44  GLY A  50  GLN A  51  LEU A  52
SITE     3 AC1 15 PRO A  53  GLN A  64  SER A  65  TYR A 108
SITE     4 AC1 15 HOH A 229  HOH A 303  ASP B  98

The SITE records also have corresponding REMARK 800 records (which are given in the question). For example, site AC1 is described as BINDING SITE FOR RESIDUE VWW A 210 as identified by SOFTWARE. So in this case, these SITE records are a list of residues that make up the binding site of their respective ligands.
You may want to be somewhat wary of these SITE records because (1) as far as I know they are not mandatory records in a PDB file and therefore may not always exist, and (2) it is not entirely clear how they are generated. In this case they are software generated... but which software... or what algorithm? I have previously looked through the SITE record of a binding site in a protein I am very familiar with and noted some conspicuous absences from the list of residues, so take that for what it's worth.

Thank you very much! I think I can proceed from this point. Yes, I've already found that SITE records are not mandatory while collecting ligand ids. For example, they are absent in 1f4x, 1hge, 4c4r, etc.

You have perfectly answered my question! But can I please ask you one more theoretic question which arises when I look into this data? There are two ligands for 10gs complex on RCSB, and there is affinity value (Ki) for only one of them - VWW. But even VWW is binded in two places already. How can I possibly understand it? I think it will be incorrect if I will completely forget about MES and will treat each of two binding sites of VWW with the same Ki value, right?

@Slowpoke MES is actually a buffer used during the crystallization of the protein. While it may bind the protein with some affinity, it isn’t really a ligand so much as an artifact of the experiment.

As for VWW binding sites: the protein is a homodimer and both binding sites are identical. Barring some kind of cooperative binding, the affinities should be the same.


text:
Was Darwin aware of the difficulties behind the concept of species?
Introduction
The concept of species is a very old concept that suffers from not being a natural category. There exists no single definition that would categorize living beings into groups and that would fit our intuitions of what a species should be.
Many of such problems in definitions are revealed in the field of evolutionary biology. For more information about the difficulties behind the definition of the concept of species, have a look at

How could humans have interbred with neanderthals if were a different species?
This post on ring species.

Question

Did Charles Darwin comment on this problem?
If yes, did Charles Darwin comment on the reason why he chose to keep using the term "species" instead of simply "lineage"?

On the contrary, species seems a fairly natural and obvious categorization.  The problem is with people who insist on rather too narrow a definition, e.g. deciding that Neandertals should be a different species from modern humans, when the evidence shows otherwise.

I did not think a debate on the question remained. I assumed it was given the overall agreement on the Sapiens and Neanderthals question. I don't think there is a subjective threshold for how low should the fitness of the hybrid (unless we chose sterility). There is also no objective way to solve ring species problems. Also the concept of species based on reproductive isolation fits only sexually reproducing lineages.

I don't think we can comment about whether Darwin was aware of this problem, unless he documented it.  Since we don't have a rigourous definition of species,  we can parsimoniously assume that he didn't. In that case the other two questions would have no meaning.

@WYSIWYG I slightly rephrased to ensure the questions are not opinion-based. Does it seems better to you?

Yep but still it is quite easy to assume that Darwin didn't comment. If he did, we would probably have known.

Sure.... "Not that I am aware of" could well be the best answer. As I never read through any of his books, I would not be confident enough to say such thing.

As this is not really a biology question I think it would be better suited for History of Science and Mathematics SE.

There is a history tag on Biology.SE though. But I agree that HS&M.SE could eventually be an even better place for this post. Thanks

The whole point of Darwin's theory was that transition from one species to another is extremely slow and gradual. There are plenty of quotes in "Origin of Species" stating this, and also affirming that there is no clear boundary between species and subspecies, or "races".
Quotes from Origin of Species > Variation under Nature (Chapter 2)
Quote 1

Nevertheless, no certain criterion can possibly be given by which variable forms, local forms, sub species and representative species can be recognised

Quote 2

Several experienced ornithologists consider our British red grouse as only a strongly marked race of a Norwegian species, whereas the greater number rank it as an undoubted species peculiar to Great Britain. A wide distance between the homes of two doubtful forms leads many naturalists to rank them as distinct species; but what distance, it has been well asked, will suffice if that between America and Europe is ample, will that between Europe and the Azores, or Madeira, or the Canaries, or between the several islets of these small archipelagos, be sufficient?

Quote 3
It is here the most definitive quote I managed to find and partially answers to your second question.

From these remarks it will be seen that I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, for convenience sake.

Great answer. +1 Thanks. I edited the post to change the format. Feel free to roll back if you don't like it. It'd be great if you could add the book/chapter/paragraph/page at which these quotes were taken.

Thanks, your edits made the response easier to read. As for the quotes, I gave a link to the book available online. There are no pages as such, but anyone may search it by text. These quotes are the first relevant ones it took me literally a minute to find.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Transformation of coordinates found in PDB
According to the PDB guide there are some coordinate translation matrices found in PDB file:
ORIGXn                  Transformation from orthogonal  coordinates to the
                        submitted coordinates (n = 1, 2, or 3).
SCALEn                  Transformation from orthogonal coordinates to fractional
                        crystallographic coordinates  (n = 1, 2, or 3).
MTRIXn                  Transformations expressing non-crystallographic symmetry
                        (n = 1, 2, or 3). There may be multiple sets of these records.

For example, in 10gs complex from RCSB I see:
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.012543  0.000000  0.001805        0.00000
SCALE2      0.000000  0.011055  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014557        0.00000
MTRIX1   1  0.945333  0.099229  0.310644       -5.48795    1
MTRIX2   1  0.099832 -0.994906  0.013998       21.83043    1
MTRIX3   1  0.310451  0.017779 -0.950423       27.67516    1

I want to do 3D voxel reconstruction of some part of the complex stored in PDB. What is the purpose of those matrices, do I need to apply any of those translations to the coordinates stored in PDB to "standartize" the data and obtain the same coordinate system and same grid for different PDBs? Or they are just related to the data which was submitted by authors and are needed for inverse translation? Or something else? Thank you very much!

The purpose of these matrices is to reconstruct the crystal lattice from the coordinates, which only contain one copy of the repeating structural unit found in the crystal. In other words, they represent the affine transformations required to convert one copy of the repeating unit to its neighbors.
To a biologist (as opposed to a crystallographer), these are not useful except if one of the crystallographic symmetry axes happens to also be a biological dimer (or other multimer) axis. However, in this case, the PDB usually gives an option to download the "biological unit", which includes the coordinates for all neighboring copies that associate in the cell with the copy specified by the original coordinates. I should point out that sometimes the biological unit is in fact smaller than the crystallographic unit, if multiple copies of a monomer or dimer or whatever occur in non-equivalent spatial contexts within the crystal. There is no substitute for biological knowledge to know what the relevant structural unit in the cell is.

Thanks! So, it means that generally I can forget about them and treat different PDBs from RCSB as represented in the same coordinate system and use spatial representation of those different proteins as data points for training a machine learning model (e,g, classifier) without any recalculation?

Different PDBs from RCSB? There is no way to relate the coordinates frames of entirely different proteins that are not bound to each other in the same crystal, their rotational and translational positions are arbitrary because they aren't relative to anything. There is no such thing as the "top", "bottom", "back", or "front" of a protein. Only distances and angles, i.e. measures within the internal coordinate system of a molecule, are meaningful. If you mean the length scale, then yes that's the same across all PDB files (it's always in units of Angstroms).

Okay, so we may consider that coordinate system across PDBs is the same up to orthogonal transformation (rotation, swap of axes, etc). Scale is always the same and is represented in angstroms, angles are preserved. Thank you!


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Why, when someone eats food, and he/she directly checks his body weight, why it seems to be no changes in body weight?
Why, when someone eats food, and he/she directly checks his body weight on balance, why it seems to be no changes in body weight and there wasn't any execration, I want to know where did food weight went?

How accurate is your scale? How big is the meal?

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This question is wrong. If you eat some food, that extra mass goes straight into your belly and has to show up on the scale. Conservation of mass.

Compared to their body weight, humans don't really eat that much
Where I live, the typical serving at a restaurant is 150g or 200g of meat, plus about the same amount of side dish. Even if your test subject is a big eater, that's just 300 + ~200g of biomass. Eating that much food without drinking is difficult, so you allow your subject one beer, or about 500g of liquids.
Even with generous assumptions, an intake of more than half a kilogram of food in one go is unusual.
If you live in a country where this specific figure is higher than that, please adjust the value accordingly, and the next figure in the same ratio.
I could perform a scientific measurement of an average human mass based on a sample size of two people, but the more rigorous way to do it is to open a random web page on the topic and use the number stated there, up to 80kg for a healthy male.
Therefore, a person's weight after one meal will typically increase by, Fermi estimate, 1% of their body weight. Compare that to the common shrew, which eats 125% of its body weight per day. Source: Google
A scale I have available at home is graded at 5kg, so an increase of 0.5 kg is difficult to notice. The only scientifically valid test would be to have two different people read the scale reading and only communicate their values after the experiment. A single person taking two readings is likely to introduce a bias.
A typical digital scale, however, should be able to pick up the difference.
Be sure the "no excretion" criterion is met. A human body is able to dispose of just as much mass in one go.
The other answer beat me to this figure, but the amount of perspiration cited by Wikipedia is up to 2-4 liters per hour. So, if you've just been working out or if your AC is broken, You can actually sweat faster than you eat. That's the maximum rate of perspiration, though, and far from the typical situation.
Finding the typical rates is much more difficult. Every article I've checked boils down to "how much you sweat varies wildly, and if you think you sweat too much, go find a doctor".
For perspiration, Science Alert suggests 2.3 lb (1 kg) of carbon dioxide per day as the usual amount. If your meal takes 15 minutes, that amounts to about 10 grams of mass loss due to breathing while eating.

To make a proper evaluation of the immediate effect of food on your weight you need to:

Have a sensitive (optimally: digital) and properly working scale that shows the same value when you weigh yourself few times in a row
Wear the same clothes during the pre- and post-meal measurement
Not vomit, urinate, defecate or sweat significantly between the 2 measurements

How much weight you can GAIN by having a meal?
An average main meal for an adult consisting of a soup, potatoes, steak, sauce, salad and compote could weigh, let's say 500 grams (0.5 kg). Such a meal should contribute about 500 grams to your weight (let's say in 30 minutes between your pre- and post-meal measurement), because no significant weight of food is lost during digestion and absorption of nutrients and because no significant metabolism that "burns" the nutrients occurs within 30 minutes of starting a meal.
How much weight you can LOSE during a meal?
If there is no vomiting, defecation and urination between the pre- and post-meal weight measurements, you can lose  a significant amount of weight only by sweating. In one study, the sweat rate of athletes during training was 1.2 liters/hour in average, but up to 5.7 liters/hour (see Fig 1). In another study, young males sitting in the sauna at 95 °C 2 x for 10 minutes with a 5 minute break resulted in 0.2-1.1 kg loss of weight (check Table 1, the BML column). So, it might be theoretically possible that a person with a very high sweat rate would lose 500 mL of sweat (and hence 500 g of body weight) just by sweating when eating for 30 minutes in a hot environment. This seems to be the only possible explanation for "no weight gain after a meal" when the measurements have been done properly.


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Is APOE present in Lipid Rafts?
What evidence is there that APOE is present in lipid rafts (neurons or glial cells)?
I would be interested in any comparison between the APOE gene variants as well, but that is not required. I've looked around quite a bit for this but could only find apparently the background for a conference presentation (https://alz-journals.onlinelibrary.wiley.com/doi/abs/10.1002/alz.054511). The link is very vague on details.
However, I'm sure someone somewhere has looked at this question...


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Can blood vessels be weakend
Lets say everyday you fall off your bike and your leg starts bleeding at the same spot everytime. Do the bloodvessels at this spot get weakend and if yes, does less blood reach your foot because the bloodvessels are weakend?

So blood vessels in the human transport (circulatory) system are of three types: capillaries, arteries and veins.
Capillaries: Even if you get a slight cut or scratch, capillaries will get affected.
Veins: If you get a moderate (intensity) cut or scratch on a place on the skin where veins are close, veins will get affected and you will need immediate first aid eg bandage, etc.
Arteries: If the cut is deep enough to reach arteries, then arteries will be affected and this is a pretty risky situation as high pressure blood flows through the arteries which gushes out upon rupture.
As the intensities of cuts increase, and depending on the type(s) of blood vessels affected, healing times will differ.
I don't know what you mean by 'weakened'. If this refers to permanent damage, then yes it is possible. However, in most cases, given urgent medical treatment, the affected blood vessels eventually heal.
Hope it helps.


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Why do fish and marine mammals need special low density adaptations for buoyancy?
When one reads about fish and marine mammals, it is always said that for example blubber of marine mammals helps them with buoyancy because it is so low density and similarly for example sharks have large low density liver (possibly up to 30% of their body mass) and mainly cartilage that is about half the density of a normal bone (and it is implied this is necessary for buoyancy).
However, many terrestrial mammals like humans are already positively buoyant when having lungs filled with air (most humans in their normal weight), so it is not obvious why any kind of adaptions for marine animals are necessary as their body density composition could a priori be essentially just that of humans. There thus has to be a factor which makes it beneficial for e.g. marine mammals to have more something denser in relation to humans (like bigger muscles in relation to lower density tissue) which then needs to be compensated with such things as blubber. I am looking for what that factor is exactly.

The answer is that air in the lungs of a diving mammal is compressed, meaning that it takes up less volume than air at the surface. This phenomenon is called "Thoracic squeeze". The deeper the dive, the smaller volume the lungs and air occupy.
Because the air takes up less volume, the buoyancy of the lungs is decreased once the diver reaches a certain depth below the surface. You can experience this for yourself in a diving pool - take a deep breath and pointing your toes to the bottom, submerge yourself to about 1-2 m (3-7 feet) below the surface and you will start to sink as the volume of your lungs has decreased to a point where their buoyancy is counteracted by your density.
Positive buoyancy in a diving animal is a plus - it means that they don't need to expend (as much, if any) energy to reach the surface, they can rely on their body to take them up, no matter what.
I have no idea why sharks and fish that don't rely on lungs need low density tissues, other than to make them neutral buoyancy so that they don't need to expend energy to maintain their place in the water column.


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Alzheimer's drug Aduhelm causing viral encephalitis
Over 40% of patients who received Biogen's anti-amyloid beta drug Aduhelm had "brain swelling or bleeding." (See, https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2792897) Could these reports of swelling/bleeding include viral encephalitis? I haven't been able to find any sources indicating that this is what patients had, but there is reason to believe that removing amyloid beta from the brains of Alzheimer's patients could increase viral encephalitis (see, https://www.cell.com/neuron/pdf/S0896-6273(18)30526-9.pdf). Is there a reason that the clinical trial monitors/sponsors would not have to publicly report it as such?

Why do you think it is viral encephalitis?

Hey @Chris, thanks for your message. The second link is to a paper published in Cell - it shows that when herpes simplex virus 1 (HSV1) infects a transgenic Alzheimer's Disease mouse model, the infection leads to increased amyloid beta deposits. These increased amyloid beta deposits (specifically Aβ42 oligomers) protect mouse models from herpesvirus encephalitis and inhibit several types of herpesviruses. This indicates that when Aduhelm clears amyloid plaques from the brain, it could inadvertently let herpesviruses go wild...

... Many papers have shown that herpesviruses, including HSV1, HHV-6A, and HHV7 (and others) are consistently found in the brain, specifically in the parts of the brain most ravaged by Alzheimer's Disease (see, Readhead et al., 2018 - https://www.cell.com/neuron/pdf/S0896-6273(18)30421-5.pdf)

I suggest that SE Medical Sciences would be a better fit for this question. The examples of appropriate questions for this site in the [Tour] do not suggest clinical trials or disease are part of the SE Biology remit.

This is a very interesting question. I think this site is correct for the question because it falls under "questions about the biological mechanisms behind medical conditions."


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Predicting protein folding with Alphafold
I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ website for downloading it and using it but there’s one part I don’t understand (see the sections mentioned in the link below), and because a mistake here could be costly, I would like to understand it before I make a mistake. To me, the website seems to be saying that I have to download the software, and then also download the two terabytes worth of data that the model was trained on, and that having both the sotware and the training data will allow me to predict the folding of new amino acid sequences (kind of like if I’d have to train the model myself). This seems odd to me because although I don’t know much about modelling software, it was my understanding that the software creators use data to train a model, find what model would best predict new inputs, and then give you that pre-set model.
My question - do I have to download both the Alphafold model and all that data in order use the software to predict the folding of new amino acid sequences? In particular, if I really only just want a visualization of the folding and accompanying statistics, is this the simplest way for someone with little background in programming (although my university does have the storage capacity for the data if need be)?
(See the Model Parameters and Running Alphafold sections of this github link: https://github.com/deepmind/alphafold)

I’m voting to close this question because it is asking for details concerning the installation and use of software. Re: "do I have to download both the Alphafold model and all that data in order use the software to predict the folding of new amino acid sequences?"

@acvill thanks for your comment. I disagree, I think it’s about the best way to analyze the folding of specific protein sequences

Because the focus of my question, and my untimate focus, is on analyzing the folding of protein sequences, I do strongly believe that falls within the scope of allowed questions on this site. In addition, because Alphafold is a groundbreaking method and its source code was only released recently, this question will be relevant to current and future researchers who will analyze protein folding using the software

Your question consists of two parts: (1) do I have to download 2+ TB of model and data to use the software? Their github page makes it clear that, yes, you do, if you want to run it AF locally. Domen gives a alternative, but this question is outside the scope of the site. (2) is AF the simplest way to predict the folding of new amino acid sequences? Similar general questions about coding recommendations for protein modeling have been asked and closed in the past.

That said, general questions about computational protein structure prediction are on-topic and well-received. I suggest taking a look at the ongoing discussions on biostar concerning the use and accessibility of AlphaFold.

Questions regarding analytical methods, such as those related to bioinformatics or biological simulation, that do not ask explicitly about the underlying biology are considered off-topic. One place where this is covered in the [help] is the page "What topics can I ask about here?".

In addition to the other comments, these sorts of software are usually run on high performance computing clusters, which have large numbers of CPUs/GPUs as well as the storage needed. Most computers would struggle to run this locally without a specialist build.

If you have little experience with programming, I strongly suggest using the official Google Colab notebook for AphaFold. It really involves only some button clicks and pasting the amino acid sequence.
This notebook folds without templates, but there is another unofficial notebook that uses the template generation.


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Coinfecting oncolytic viruses - first virus carrying the receptor for the second
One challenge to using oncolytic viruses as a treatment for cancer is that the viruses may cause off-target effects. I'm curious to know how useful it would be to create an oncolytic virus that has the receptor for another virus encoded into its genome (kind of like a viroreceptor)? It would probably be best if the encoded receptor is a receptor not present in humans, so maybe a receptor present on the surface of another animal's cells. If the first virus replicated to a higher degree in cancer cells than normal cells, and/or if the first virus was largely cleared from the normal cells before the second virus was administered, then it seems the cancer cells would differentially express the receptor for the second virus, and that could limit the off-target effects of the second (perhaps more potent) virus. (Of course, there are other ways of limiting off-target effects - injecting the viruses intratumorally, using viruses that the host would mount a memory response against, etc. - feel free to include these in your answer if you'd like.)
I'm sure there may be challenges in practice (one that comes to mind is whether a given first virus would have the genomic space to carry a receptor for the second, in addition to other desired genes) but I'm curious to know what people about this idea in the spirit of a thought experiment, or if you could point me to any relevant papers etc.

From the [help/dont-ask], If your motivation for asking the question is “I would like to participate in a discussion about ______”, then you should not be asking here. In addition, this is an opinion-based question (and thus off-topic) because it is asking about a hypothetical situation. From the [help/dont-ask], avoid asking subjective questions where … you are asking an open-ended, hypothetical question: “What if ______ happened?” We expect answers to be based on verifiable facts and references, along with subject-related expertise. Please see the [tour] and other [help] for details.

Short answer: No.
Longer - No. Why would you do this? - if you can get the first virus to replicate to high levels in a manner that is specific to cancer, then why not use that first virus alone rather than run the risk with two separate viruses.
Don't forget that for the virus to reach all parts of the tumour it will need some cell to cell transmission, which means that it exits the cell (possibly in a lytic manner) in the first case, so there probably isn't any need for the second virus.
The second point is that the immune system (innate and adaptive) will recognize the virus infected cells and start to clear them (that's the whole point of oncolytic therapy), probably before the second virus is administered.
Thirdly, not all cell types support viral replication efficiently. This may or may not be the case for the specific virus(es) and cancer types you target, but it is something to be considered.


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Why does cucumber skin kill ants?
I recently read that cucumber skin is an effective repellent for some ants:

Set out cucumber peels or slices in the kitchen or at the ants' point of entry. Many ants have a natural aversion to cucumber. Bitter cucumbers work best.
Source: Natural Insect Pest Control

See also: How to Use Cucumbers to Prevent Ants from Entering the Home
But when I tried it out they died instead. What made this happen?

Please include the source of your information. Where did you read this?

There you go @OneFace

It's always good to include the source, especially when asking about things that are not commonly known.

Under what circumstance did the ants die? If possible, post a photo of the dead ants near the cucumber skin.

@MarchHo Sorry , cant post a photo since this was done a few days back .

Was an edit necessary ?

I think the ants aren't killed but they are forced to move out because the Cucumber slices are just disabling the ants pheromone tracking system there by forcing them to withdraw from the location.

Cucumber contains a compound called trans-2-nonenal (reference 1 and reference 2) that repels insects. This particular compound (reference) has can also be used in insecticide foams for repelling ants (reference)

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Transpiration and Water Uptake
I know that water moves into the root hair cells from the soil via Osmosis down the water potential gradient and then this water travels through diffusion and osmosis through the symplast pathway reaching the base of the xylem vessels. But there isn't any movement of water through the apoplast pathway. So I am thinking that the water also moves in between the cell walls of root hair cells without crossing the cell membrane and hence by diffusion and then takes up the apoplast pathway. Am I correct? Because in my book, it is mentioned that water goes in by osmosis and nothing is mentioned regarding diffusion. Someone please clarify this.
Thank you

Investigate tight junctions...

water goes in by osmosis and nothing is mentioned regarding diffusion. Someone, please clarify this.

You'll need a good understanding of the difference between osmosis and diffusion for this.
Osmosis is a special kind of diffusion.
The only difference between the two is the molecules that are carried. Diffusion is used to transport solute molecules, whereas osmosis is used to transport solvent molecules (in most cases water). In both situations, until equilibrium is reached, the movement is from a higher concentration gradient to a lower concentration gradient.

Regarding the movement of water through the various pathways.

I'm quoting this directly from the Plant Physiology book (Taiz and Zeigner). Please refer to the same for more information.

In the soil, water is transported predominantly by bulk flow.
However, when water comes in contact with the root surface,
the nature of water transport becomes more complex.
From the epidermis to the endodermis of the root, there are
three pathways through which water can flow:
the apoplast, transmembrane, and symplast pathways.
In the apoplast pathway, water moves exclusively
through the cell wall without crossing any membranes.
The apoplast is the continuous system of cell
walls and intercellular air spaces in plant tissues.
The transmembrane pathway is the route followed
by water that sequentially enters a cell on one side,
exits the cell on the other side, enters the next in the
series, and so on. In this pathway, water crosses at
least two membranes for each cell in its path (the
plasma membrane on entering and on exiting).
Transport across the tonoplast may also be involved.
In the symplast pathway, water travels from one cell
to the next via the plasmodesmata. The symplast consists of the entire network of cell cytoplasm interconnected by plasmodesmata.

Please follow the three pathways in the image to get the insights.

Thank you so much!!


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Monoclonal antibody mass production
There is a long conversation taking place these days about monoclonal antibodies against COVID-19. From a few biology courses I had a long time ago, I remember that the process of creating mAbs was a very complex and delicate one, with relatively small yields, something that contributed to the reduced availability and the high price of such treatments.
I wanted to ask because after my research I got even more confused and I couldn't conclude: what is the current, "modern" procedure of mAb production? What are the yields and eventually how logical is to expect a mAb treatment to become widely accessible? Especially though, when "common" mAb therapies like adalimumab and infliximab cost a few thousand euros/year.

What recent reviews have you consulted? That is the way to find out the current status of technology, rather than expecting someone here to write a pale imitation.

Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure. Please see our homework policy for more information.

I am going to edit my question and list the papers I have already read. So please wait before delete/downvote! :) On top of that please keep in mind that I'm not related in any way to Biology other than having an extra interest from childhood. My studies and expertise are lying in a completely unrelated field.


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Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015
I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others.
However, as this book was published 6 years ago (2015) I wonder if there's a newer and better book on the topic of genome-scale algorithms?
Thanks in advance!

A suggestion if you get no satisfaction here is our sister site [bioinformatics.se].

Please read the description of the purpose of this site o the [Tour]. It is a question and answer site about problems in biology. Subjective opinions of a book are not that.

The book I ask about is on topic to this site. If you cannot offer to help or answer my question, please refrain from commenting/posting.


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What is an example of a benign or beneficial de novo copy number variation?
Duplication events in particular. In any species. Have enough genomes been sequenced and studied to identify any? It is rather easy to find studies which identify them with diseases but have they ever looked for benign or beneficial instances?

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. This will also allow you to clarify and focus your question — as written it sounds like you haven't read this relevant wikipedia page. Please take the [tour] and consult the [help] starting with [ask] for details.

I've provided an answer, but I'm not sure whether it actually addresses the question, given "de novo" in the title. I assume you're looking for examples of nonpathogenic CNV mosaicism in somatic tissues? Clarifying edits would be appreciated.

Copy number of the human salivary amylase gene (AMY1) varies across populations and is positively correlated with the starch content of traditional diets.1,2 Amylase gene copy number expansions are common in the evolutionary histories of several mammals.3

References

Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007 Oct;39(10):1256-60.
Carpenter D, Mitchell LM, Armour JA. Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity. Hum Genomics. 2017 Feb 20;11(1):2.
Pajic P, Pavlidis P, Dean K, Neznanova L, Romano RA, Garneau D, Daugherity E, Globig A, Ruhl S, Gokcumen O. Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife. 2019 May 14;8:e44628.


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Does bone resorption cause alkalosis?
The phosphate in hydroxyapatite Ca5(PO4)3(OH) is a strong base, PO4^3-, and the hydroxide is also a base, OH-. I was talking with a biologist the other day about if bone resorption (at a level that causes elevated calcium and phosphate) also causes alkalosis. He did not think so, but mentioned that it might be buffered or compensated for. In general, does bone resorption cause alkalosis?

I'm not sure if this helps but Metabolic alkalosis decreases bone calcium (in general).


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Why do humans need pillow to sleep better?
As far as I know, no animal sleeps with a pillow/support under their heads. Why then do we need to keep a pillow?

Many, many animals make beddings and nests. Not unique to humans at all.

Yes agreed. But specifically do they have to use a support for their necks?

humans can sleep fine without pillows.

Our cat does it all the time ;-)

This is because the pillows keep the head align with body making it easier for the spine to maintain its natural curve. It reduces the tension in the lower dorsal region of neck. Many animals are found to be using pillow like substitutes for the same reason.

Which animals  .?

@YasirSadiq mamals in general use pilows most often their front legs/paws humans too putting our arm under our head while we sleep.


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Mariana Trench fish "how they can thrive under that extreme water pressure is still a mystery"
New Mariana Trench species is the deepest-dwelling fish in the ocean

Exactly how they can thrive under that extreme water pressure is still a mystery for now, but these creatures have been sighted regularly at depths of around 26,200 ft (8,000 m) and down to a record-breaking depth of 26,830 ft (8,178 m), as captured on video by Japanese researchers earlier this year.

I often see comments like this, but I have not seen any explanation why extreme water pressure would be a problem. Is there a reason?


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Are self pollinated plants genetically different?
Gametes in pollen grain are formed during meiosis in the anther. And meiosis produces genetically different gametes. When the pollens grains are carried to the stigma to fertilise the egg cell of the different/same flower from the same plant, doesn't it produce genetically different flowers even though it is self pollinating because of the variation in gametes?

Yes, it does.
In Meiosis there is genetic recombination (by recombinase) in the Meiosis-1. So even though it is self pollination, there is significant genetic variation.
Still for higher degree of variation cross pollination is exhibited.
It should be noted that cross pollination has greater evolutionary significance.
Few plants exhibit self-incompatibility to supress self pollination (in monoecious flowers/plants).


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Using serotonin for relief from allergies
When someone suffers from an allergy, due some allergens they are given drugs like anti-histamine, adrenaline or serotonin. How does serotonin affects the body to give a relieve from the action of allergents?
What is the physiology behind this?

Welcome to the Biology commmunity. Please improve your question by citing sources of the information used (in particular, that serotonin is useful in relieving allergies).

Also, please mention in your question body what attempts you made to answer it yourself. This will enable users to post helpful answers.


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Cancer in cardiac cells
We were recently taught that  cancer occurs only in those cells which undergo cell division so, cancer is not possible in cardiac cells and neurons.
But we know that till a certain age our heart grows in size so that means it goes under cell division. So doesn't that mean that cancer can also occur in heart cells?

Though very rare, primary cardiac tumours do exist.
Most of the 1° cardiac tumours are benign, malignancy occurence is pretty much low.
Give it a read—
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113129/

As the other answer has already stated, there are cases of heart cancer. Just to expand on that answer further, according to this article, the rate of heart tumors is a mere 1.38 in 100,000 people per year and of that only around 10% are malignant (truly cancerous tumors) in nature. Just to put this into perspective of how low of a rate this is, the overall rate of cancer in the U.S. for both men and women combined is 352.2 per 100,000.[source]
Doing some rudimentary calculations, if the rate of malignant tumors is one tenth of 1.38 in 100,000, that means the rate of heart cancer is around 0.14 per 100,000! Just to add to how rare this is, the Mayo Clinic on average only sees around one case of heart cancer per year.[source]
Also, to clarify your statement about what types of cells can have cancer, it is not only dividing cells that can have cancer (even though the majority of cancer originates from cells undergoing a lot of cell division such as the skin and GI tract). While cell division by its nature causes a vast number of the mutations which would potentially lead to cancer, other environmental factors such as toxins and radiation could cause also cause similar mutations in cells that might not even be dividing.


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Can viruses be deformed?
Viruses are created in their fully-formed state and do not grow. But one thing has been bugging me lately:
can a virus be deformed, e.g. in order to fit into an opening slightly smaller than itself? Say you were to apply a force to the virus perpendicular to the smaller hole; would the virus merely break, or is it possible for it to deform and retain its structure on the other side?

It would depend upon the virus.

Most viruses of human concern are "enveloped", that is, they are surrounded by a lipid membrane. This membrane is usually what determines the shape of the outer layer, and is intrinsically flexible, so most human viruses would be able to deform a bit to fit through a hole. Additionally, the size of individual enveloped virus particles tends to vary quite a bit as seen in this image from a previous answer:
You can also see that biologically active proteins stick out of the membrane. These are likely to break off if the virion experiences any significant forces. My experience with coronaviruses has been that even relatively mild purification procedures remove the spikes from most particles, let alone forcing them to deform through a hole. So, while they might pass through a small hole without rupturing, it's likely their ability to infect cells would be greatly reduced.
In the case of non-enveloped viruses such as adenoviruses or picornaviruses, their outer layer is composed of many copies of a "capsid protein", linked together according to quasi-equivalence. The capsid proteins need to join together over a range of angles, so they should be able to tolerate some flexing. Again, though, any extra proteins that stick out for biological functions (such as the adenovirus' fibers) will likely be damaged or detached, which would remove the virus' ability to infect cells.


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Looking to understand the difference between (Fibroblast Growth Factor) FGF-2 and FGF-5
Non-biologist nor medically trained person here, but still nonetheless interested in the functioning of the human body, and more specifically, hair growth cycles.
I've read in several sources that FGF-2 is potentially a hair growth 'stimulant' (source), whereas FGF-5 is a potential hair growth inhibitor (source) and I was looking to better understand the differences between the two?
According to a basic definition, and the bounds of my current knowledge, FGF's are signalling proteins that are involved in a whole host of bodily functions including but not limited to wound healing.
What are the potential differences between '2 and '5 that makes them appear to affect hair in opposite ways, as I would have thought that the general FGF family would act in a similar way if anything.

Growth factors and other signaling molecules are often grouped into families based on sequence and structural similarity, not necessarily by function. It's actually rather common to have this scenario, where one family member promotes an effect opposite that of another family member. All that means is they probably bind to their receptor(s) in a similar manner, with one being an agonist and the other an antagonist.

I'd suggest looking at this article on the FGF family. You will find a lot of information there about comparative analysis of the different proteins therein. For example (FGFR = FGF receptor, which binds FGF to transmit signals):

FGF–FGFR binding specificity is regulated both by primary sequence differences between the 18 FGFs and the 7 main FGFRs (FGFR1b, FGFR1c, FGFR2b, FGFR2c, FGFR3b, FGFR3c and FGFR4) and by temporal and spatial expression patterns of FGFs, FGFRs and HSGAGs. The alternative splice isoforms of FGFRs are generally tissue specific: the b isoform is usually expressed in epithelial tissue, whereas the c isoform is usually expressed in mesenchymal tissue23. Ligands are produced in either epithelial or mesenchymal tissue and generally activate receptors of the opposite tissue specificity: in normal physiology, a ligand produced in the epithelium will activate a mesenchymal receptor and vice versa. Several ligands, including FGF1 in particular, pose an exception to this general understanding by promiscuously binding to both b and c isoforms of certain FGFRs. Pathological states can result from a breakdown in binding specificity, as is common in cancers in which FGFs are overexpressed24. Structural studies of FGF1, FGF2, FGF8 and FGF10 with their cognate FGFRs show that sequence diversity at FGF N termini, variation in β1 strand length (FIG. 1b) and the alternatively spliced regions in D3 dictate their binding specificities (FIG. 2b, c).

So it's rather complex. Differences in FGF function are at least in part due to small biochemical differences that may give them differential affinity for different FGFRs, which then go on to transmit the FGF signals down the line. But at the same time the FGFs/FGFRs are expressed in different tissues, meaning that they may have relatively narrow spheres of influence.
If you look here you will see that different FGFs actually have relatively low similarity at the amino acid sequence level, and in some cases quite significant differences in gene structure (though they don't talk about 2 and 5 specifically). One notable difference there:

Most FGFs (FGFs 3-8, 10, 15, 17-19, and 21-23) have amino-terminal signal peptides and are readily secreted from cells. FGFs 9, 16 and 20 lack an obvious amino-terminal signal peptide but are nevertheless secreted [25,26,27]. FGF1 and FGF2 also lack signal sequences, but, unlike FGF9, are not secreted; they can, however, be found on the cell surface and within the extracellular matrix.

For some work on this topic specifically targeted towards FGF2 and FGF5, you can see this paper, which has this table about the location of FGF expression in follicle cells, showing that they are expressed in different places:

apologies to people with screen readers, I didn't have the motivation to copy it out into text. Here is a summary figure that they give:


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Data repositories for data on the Tumor Microenvironment?
Does anyone know of any data repositories for data on the Tumor Microenvironment? I know of the The Cancer Gene Atlas and the Gene Expression Omnibus databases but I'm more curious about data on the (molecular) composition of the TME. (I'm also curious about any databases with data less specific.)

Have you seen the St Jude Children's Research Hospital Pediatric Cancer data repository PeCan?
They have a bunch of data on a wide range of different types of pediatric cancers. These are all in the form of genomes and RNA-seq. However, they also have a bunch of visualizations set up so that you can see how these profiles work from a perspective of mutations and RNA in tumours of all sorts.


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PCR markers for C57B6
Do you know any primers that can be used to genotype mice and check if they are still C57B6? I'm concerned about genetic drift in my colony. I bought a breeding pair 3 years ago and expanded. I wanna make sure my animals still retain genetic markers of c57b6. Thanks

Why not buy more mice? Breeders have schedules to make them as homogeneous as possible. Spontaneous mutations that are maintained in your colony won't show an association with any sort of markers.

Welcome to Biology.SE! The only way to check for genetic drift would be to sequence the entire genome of your mice — in all likelihood any pair of primers would give you the same result even if you had a significant accumulation of point mutations. As @BryanKrause says, buying more mice is much more practical. ——— You may also benefit from taking the [tour] and then going through the help pages starting with [Ask] questions effectively on this site. Thanks!

Jackson Labs offers a service for this for what looks like a reasonable price. I have no experience with the service other than general good feelings about Jackson.

We have a unique selection of mouse single nucleotide polymorphism (SNPs) panels useful for a diverse set of mouse research applications.
Applications of SNP scanning services

Development of congenic mouse lines
Confirmation of C57BL/6 substrain background

[...]
Available custom designed SNP panels specifically tailored for your needs
The right panel for your needs - $179/sample
[...]
C57BL/6 substrain characterization panel distinguishes between C57BL/6J (B6J) and C57BL/6N (B6N) or C57BL/6NTac (B6NTac) genetic backgrounds

--GENOME SCANNING SERVICE
Edit to include some points raised in comments:

"These panels [i.e. the ones Jackson labs offers, noted above] seem to be intended for comparing between known strains, like when you make a transgenic strain and are in the process of backcrossing. It would not be as useful for monitoring drift, or for comparing an unknown C57BL-derived line to a standard one." – Bryan Krause
Any mouse colony will diverge from other colonies, especially if there are relatively few founders.

The identification of two CNVs in the small portion of the genome screened demonstrates that individual mice of highly inbred strains are not isogenic and suggests other CNVs may be segregating within C57BL/6J as well as other carefully maintained inbred strains.

--Genomic copy number and expression variation within the C57BL/6J inbred mouse strain

At the very least, intermittent back-crossing to a mouse from a different source is recommended.

With time, isolation and a little spontaneous genetic drift, a founder pair can produce a new substrain in as little as three generations (something to bear in mind if you're breeding mice in-house without “refreshing” the gene pool with an intermittent backcross to a bona fide C57BL/6J ... Clearly, substrains of C57BL/6 (and other inbred strains) are not all the same.

--All (C57BL/6) Mice are not Created Equal

Simply buying new mice as needed, from the same (reliable and standard) source each time, gives you a better chance of consistency, since a large breeder is less likely to see on-going founder effects.

If you have a solid reason for keeping your own colony, talking to the experts at Jackson Labs would be a good starting point; presumably monitoring strain consistency is something they think about as an ongoing issue, and they can give better advice than we can.


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Book request: biology of sensation and perception
I’m interested in learning about the biological and chemical basis of human sensation and perception (on both a microscopic and macroscopic level). This includes

The mechanisms underlying our “five senses,” i.e. the eye, inner ear, tongue, nose, and nervous system, and how (chemically/physically) they are triggered
How our brain makes inferences from the raw sensory data we receive, e.g. using our depth perception to infer distance from a two-dimensional projection onto each of our eyes
Comparison with other species of animals
Experimental results relating to the three points above
An evolutionary perspective hypothesizing about why these sense-detecting organs were important for human survival

There is plenty of information about these ideas scattered throughout Wikipedia, but I was wondering if anyone knows of a single book (or perhaps another online resource) that covers most/all of the points above in an accessible and interesting way.
Any suggestions?

"An evolutionary perspective hypothesizing about why these sense-detecting organs were important for human survival" is going to be pretty tough since as far as we can tell human sense are identical to a chimps senses. the exception appears to be in proprioception which is not among the classic five senses.

Foundations of Perception from George Mather covers three of your 5 requested bullet points, namely:

The mechanisms underlying our senses;
How our brain makes inferences from the raw sensory data we receive, including depth perception;
Experimental results.

I can highly recommend the book; it's clearly written, richly illustrated and complete, yet it is concise, interesting and highly readable.


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Understanding entropy and the second law of thermodynamics as involved in metabolic processes
My AP biology textbook, (the 10th edition of Campbell Biology) states entropy as being the disorder or randomness of the atoms involved in any matter, but Khan Academy says that this example isn't quite right, and is too simplistic of a way of explaining the concept. And the TedED video I watched goes on talking about quanta and stuff ...
The online definition I was able to find of entropy on Wikipedia states the "The entropy of an object is a measure of the amount of energy which is unavailable to do work. Entropy is also a measure of the number of possible arrangements the atoms in a system can have. "
I'm confused how it's both at the same time and how they're related. And how does this even relate back to Biology again???

check this video https://youtu.be/8N1BxHgsoOw?t=63 and this: https://youtu.be/tFmJ4uVNX44?t=36 and https://youtu.be/Svvr5uF_FZ8?t=187 and some other vids :D https://youtu.be/9PGNeFmEFa8?t=1523 and https://www.youtube.com/watch?v=Ntdqft89_e4

If you want the concept of entropy explained, this is not on-topic for this site. In the general sense this is physics, but as it relates to chemical reactions, would be suitable for our sister site SE Chemistry. I would also suggest you read the account in Berg's Biochemistry. There are specific areas of biology and biological chemistry — not metabolic reactions, which are just chemistry — that raise particular problems in relation to the second law, but it does not seem that you are asking about these and that your question is off-topic.

It seems to me that the question you have that it relevant to this site, is not the definition of entropy, but why it appears in biology book in a section on metabolism. I do not own a copy of Campbell  so cannot check the section, but I can explain why it appears in the section of Berg et al. that I quoted in my other comment. It may be this is the reason it is mentioned in the less chemical Cambell. If you wish an explanation, could you please read through the section, accepting his definition of entropy, and tell us where it leads. Does it lead to the Gibbs Free Energy of coupled reactions?

2nd law of thermodynamics states that the overall entropy of the universe cannot decrease at any time. This can also be stated as the fact that the universe naturally falls towards the lowest energy state, or equilibrium. This becomes important in metabolic reactions. Reactions which seem to increase the state of energy, or perhaps the 'order' of the universe, have done so at the expense of another part of the universe, usually through the conversion of energy from molecules such as ATP or NADPH.
Think of the ATP Synthase on the cell membrane. It is creating ATP (Adenine tri-phosphate) molecules from ADP (adenine di-phosphate) and a phosphate group. This too seems like a system changing molecules from a low energy state to a high energy state. It is, but it can only do so by the natural flow of H+ ions which have accumulated on one side of the cell membrane and naturally flow from their high concentration to their low concentration on the other side. So while the ATP synthase molecule is making higher energy molecules (decreasing entropy) it is doing so as H+ naturally flows towards equilibrium, which increases the overall entropy in the universe.
In essence: things are always going towards a low energy state, i.e. equilibrium, i.e. maximum entropy. If any system goes against this, it does so via an outside energy source which has increased the entropy of the universe somewhere else.

+1 for describing entropy without using the word "random" and avoiding usage of "disorder".

I don't understand why you have to use the complex ATP synthase as an example. Surely any metabolic reaction would do, or indeed any chemical reaction as enzymic catalysis has no effect on the energetics.

(Pt. 1) I think I have a better idea of entropy now, my definition and example in my notes are as follows: Entropy is the measure of thermal energy in a system, thermal energy referring to the concentration of energy in bonds between molecules, this concentration naturally falls twords reaching equalibrium or the equal dispersion of energy between all bonds, when something is closer to equalibrium it cannot be used for work and carries less information.

(Pt. 2) For example, water is free flowing with energy bouncing between its molecules and is more stable then say, ice, which is structured and carries the information of it's structure, has fewer degrees of freedom for it's energy to flow, and want to melt into water to become more stable (spontaneously) It takes work to freeze water into ice (it's most natural ordered state) but work cannot be applied to water to make it anything more than plasma.

(Pt. 3) This is why it requires work (ATP) to create complex biological molecules, however life still increases the overall entropy of the universe because of the citric cycle and being "wirlpools" of moving matter becoming simpler forums

As tax money is no longer available for you payments, entropy is the tax of nature in that it is the energy taken (leaked) from your system, be it supplied or produced, that is no longer available for work.
You have to pay the tax (entropy) for every activity involving energy (money) other wise your activity will not be possible. If your activity involves lots of properties (number of particles or large size of the system, therefore higher degrees of freedom) you have to pay a higher tax ( termed entropic penalty). If your activity involves fancy properties (not so large number of particles but a highly flexible molecules in themselves, hence again higher degrees of freedom) again you have to pay a higher tax.
Carnot realized the concept of entropy when he was trying to design a perpetual motor.
He concluded that as long as the motor is made of material that consists of particles there will be leakage of some energy to the particles by means frictional dissipation and you cannot convince the particles not to do so. You can only minimize this leakage by choosing a system that has the least possible degrees of freedom.
This applies to literally every thing (every energy-involving activity or process) from biochemical reactions to electromagnetic radiation too (their particles are termed photons), and so it is a universal principle.

I am afraid this answer does not relate the concept of entropy to metabolism or even biology in general, so does not address the part of the question that is on-topic for this site.

Is it nearer to the topic now ? @David

By inserting “biochemical” in front of “reactions”?

Maybe, however, do you have any technical criticism for the answer?

My main concern with this question and answers to it is the relation to biology in general and metabolism in particular, as laid out in my detailed comment to the poster. This is so things remain appropriate for SE Biology. I will comment on answers if I think they are factually incorrect, especially if they have been upvoted, but otherwise I would not wish to discourage new contributors to the site. As for "technical criticism": you present a "tax" analogy that you think may help the poster. Only the poster can say whether or not it does so, although I personally would doubt it.

You doubt it because how much it relates to the question or because something in its essence?

The fact that I doubt it is unimportant here because it is a personal subjective opinion. I was just being honest with you. The basis of my doubt is a lifetime’s experience of teaching in higher education, together with my guess at the poster’s educational stage and requirements. I may be wrong.

I asked you for your honest opinion, so thank you.


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What's the role of bromelain in pineapple?
Bromelain refers to one of two proteases found in pineapple and its relatives. Like other proteases, many believe it has therapeutic uses and it's the subject of a lot of research. But what role does it play in the pineapple itself? Why does pineapple (or papaya, for that matter) generate large quantities of protease when other plants do not?

Antifungal properties? as tested in below article.
López‐García, B., Hernández, M. and Segundo, B.S., 2012. Bromelain, a cysteine protease from pineapple (Ananas comosus) stem, is an inhibitor of fungal plant pathogens. Letters in applied microbiology, 55(1), pp.62-67. Available here

Please cite scientific papers fully using a formal citation guide. (Google Scholar does all the work for you if you want): see here

Citing is absolutely necessary here, so thank you for pointing toward a reputable study (though see my comment above and my edits). However, posts citing other's work need to summarize, quote, or otherwise explain the rationale for including the citation (especially if no further explanation is provided as part of the answer). Answers on SE need to be complete in and of themselves -- as in someone 5 years from now should be able to view your answer and feel like they had the question adequately answered without needing to leave the site. External links and citations can be for further reading

I thought the name of the paper was a good answer already, didn't want to waste peoples time reading long answers.

@PolypipeWrangler Please reread theforestecologist's comment, this is site policy not one person's opinion. Link only answers are frowned upon and decrease the quality of StackExchange. An answer doesn't need to become "long" to include more than just a link.


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Is it fair to say that the majority of alleles of a typical diploid organism are homologous at each locus?
I'm trying to get an overview of when zygosity actually comes to bear in regard to the entire genome, the following statement represents my understanding so far...

In a typical diploid organism, most of the genes/alleles on each locus are identical/homologous (say in the order of 95-99%) with the corresponding gene/allele on the other chromosome.
  When compared to the overall genome, it is only on a relatively small number of genes/alleles where the degree of similarity of the alleles for a trait becomes an issue.

So in other words would it be fair to say that, for a typical diploid organism, most of the genes on each chromosome are identical to their counterpart, it is only on a relatively small number where differences occur. e.g. most of the genes/alleles in a pea plant are the same and the resulting traits can be easily predicted. It is only a relatively small number of genes e.g. the genes responsible for flower color in a pea plant, or eye color in humans that the issue of zygosity, and using statistical techniques like Punnet squares etc comes play?

Please cite some evidence that supports your assertion. SNPs are incredibly common and widespread, so that would seem to rule out your hypothesis right away, as any two alleles would not have 100% nucleotide identity.

@MattDMo thanks, its of course possible my statement was wrong, it was not something I had derived from a credible source I could site it was my intuitive "guess" at the role zygosity played in the larger overall context of the genome. Something that has been omitted from any biology lessons I have studied. It wouldn't surprise me that the answer to my question is there is alot more going on and its more complicated than can be explained in a single statement


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How are cardiac cells connected by intercalated discs?
I understand that intercalated discs run transversely across the longitudinal axis of the muscle. But what I don't understand is how this same disc binds the cardiac cells together.
Are the cells joined end-to-end (in series) or side-to-side (in parallel) by the disc?

Does this answer your question: https://www.britannica.com/science/cardiac-muscle?

This helps a lot.