texts: Conversion rate of topical Retinol to Retinoic Acid (Tretinoin)?

texts:
I'm wondering if someone out there has more information than me. Retinoids have well known metabolic pathways in vivo, and it's usually something like: Retinyl Palmitate --> Retinol --> Retinaldehyde (Retinal) --> Retinoic Acid (Tretinoin) which is the biologically active form of the Retinoids.

Retinoids are used in cosmetics all the time, and while Retinol is available OTC, Retinoic Acid (Tretinoin - a.k.a. "Retin-A" by brand) is available by prescription only since it is a 'stronger' version of Retinol. It's not difficult to find 1% Retinol creams or higher, but Retinoic Acid treatments top out at 0.1%.

However, I can't help but wonder 'why'? One study I was able to dig up was here: Retinoic Acid Biosynthesis and Metabolism PDF. The table on page 5 shows Physiological Concentrations - starting at 50 microM for Retinol and ending at "<50nM?" suggesting an ultimate conversion rate of a little less than 10% which would make the 1% Retinol treatments roughly equivalent to a 0.1% Retinoic Acid treatment (and a 2% Retinol treatment to a 0.2% Retinoic Acid treatment - double what's available by prescription).

Do other studies/other evidence support the rate of conversion of Retinol to Retinoic Acid to be roughly 10% or suggest than a 1% Retinol topical treatment is equivalent to a 0.1% Retinoic Acid topical treatment? Or are there some other interfering factors that reduce the utilization of Retinol to Retinoic Acid that I'm missing?


texts:
I need one bunsen and i have a friend that sells me a bunsen-meker burner.
I see that bunsen-meker burners have more flame diameter, so should have more diameter of sterile field, but i dont know XD
Is good for sterile field? or i should buy a typical bunsen?
thanks.


texts: If senescent cells are removed by the immune system, how can they contribute to ageing?

texts: It is said that senescent cells, also called zombie cells, can cause biological ageing.  These senescent cells are also killed by immune cells. It does not make sense as to how they cause ageing if they are removed?


texts: Which organs in the body are responsible for measuring temperature?

texts:
As an instrumentation engineer, I have designed temperature control systems
capable of measuring and controlling temperature with a precision of 0.001K over a
wide temperature range.  I have always wondered how the human body maintains its
temperature within a fraction of a degree; specifically, where and how is the
temperature measurement done?


texts: Toxoplasmosis modifies the rat's brain to make them love (and be eaten by) cats. It also infects ~30% of humans, and modifies traits in several bad ways (i.e. schizophrenia and increased reaction time). However, humans are thought to be a "dead end" for the parasite. Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance. If so, why are so many people infected?


texts: Why doesn't HDL cause diseases like LDL?

texts:
LDL particles pose a risk for cardiovascular disease when they invade the endothelium and become oxidized, since the oxidized forms are more easily retained by the proteoglycans. A complex set of biochemical reactions regulates the oxidation of LDL particles, chiefly stimulated by presence of necrotic cell debries and free radicals in the endothelium.

Why doesn't HDL cause diseases like LDL ? What's the reason?


texts: Normal position of Electrical axis only in the III lead?

texts:
I found this sentence in my notes which is not exact enough:

  Electrical axes

  Excitatory processes have definite direction and magnitude and could therefore be represented as vectors. At any moment there are two
  points in the heart with the biggest potential difference, which is
  called electrical axis, characterized by the angel α.
  Under normal conditions -> 30°< angel α < 90°
  Electrical axis gives information about the position of the heart, where the normal position ([arrow to south-east]) represents the
  biggest amplitude in the III lead

What is the exact electrical axis and of what they are talking about?


texts: Can we say the 'goal' of Mullerian mimicry is a 'decrease in the number of sacrificed indivials'?

texts:
Can we say that Mullerian mimicry allows two species to decrease their number of sacrifice individuals because:

Originally, one species needs to sacrifice some individuals to allow predators to recognize the warning signals (e.g., 10% of the population);
Another species, with a different set of warning signals, would also need this same population sacrifice (i.e., 10%);
Now, is the benefit of mimicry that, when two species share the same warning signals, each of those two species only loses half of the otherwise sacrificed number of individuals (i.e., 5% in the example)?


texts:
Small children and people in developing countries may take oral dosage forms of vaccines. Antigens passing through the GI tract will come into contact with Peyer's patches and be absorbed by microfold cells into lymphoid tissue, evoking an immune response.

Some of these vaccines are attenuated and can colonize in the small intestine, mimicking a natural infection. I am wondering why vomiting and diarrhea, which are common symptoms in many natural infections, aren't more prevalent.

To be even more specific: Serotonin is released in response to a cytokine release by immune cells. Serotonin activates 5-HT3 receptor to induce vomiting. Why is this response not provoked by an attenuated infection, which mimics an actual infection.


texts: How can I purify RNA after gel electrophoresis to remove residual acrylamide?

texts:
I sometimes use denaturing gel electrophoresis on a preparative scale to purify RNA produced by in vitro transcription. The major issue with this is that the sample after extraction from the gel still contains significant amounts of acrylamide, or acrylamide oligomers/polymers.

Exchanging the buffer using Vivaspins doesn't reliably remove it, precipitating the RNA also only reduces the amount, but can't remove the acrylamide entirely.

In some cases the acrylamide doesn't interfere much with the later experiments, but there are some experiments that won't work with acrylamide in the sample.

What are the options to purify the RNA after gel electrophoresis that would reliable eliminate acrylamide from the sample? Preferably they should be simple and fast, not something like a full FPLC/HPLC run.


texts: To define the total Resistance of Systemic Blood Circulation

texts:
Some systems are in parallel.
For instance, the resistance of lungs $R_{\text{lungs}}$.
Assume here for simplicity that these parallel systems can be handled linearly.
We also consider only Total Vascular Resistance for simplification.
So we have now only systems in series under consideration.

Linear system  for Systemic Vascular Resistance

Formula for the total resistance as mechanical definition as assuming linear connections between those systems:

$$R_{\text{total}}=R_A+R_a+R_c+R_V+R_v$$

where appropriate resistances are

$R_c$ capillaries,
$R_a$ arterioles,
$R_A$ Small artery,
$R_v$ venules and
$R_V$ vein.

Nonlinear system for Systemic Vascular Resistance

There are many factors involved in these locations:

permeability
vasoconstriction
...
growth factors (FGF) for renewal of the vessel wall
different channels (activated, deactivated - mostly potassium channels)

where I skip the consideration of vasoconstriction, growth factors and different channels.

Permeability is one which applies to all types of vessels.
Change in permeability of one location does not mean a linear change in permeability in another.
A change in the permeability of small arterioles does not lead to a similar change in the arteries or venules.

The vessel is permeable to gas and liquid.
Let's consider only these components.
I want to include these facts into the definition because, in the pathological situations, different state of inflammation for instance can apply to a vessel.
Let's call total permeability $S$ which is dependent on gas and liquid components, first on liquid component (so inner integral).

I could give you the nonlinear formula of the total resistance but I think it goes over the skills most here.
Let's call the nonlinear resistance dependent on permeability of the vessel, $W(x,y)(t,f)$ in time and space.
So consider only the nonlinear component of the permeability formula after parametrisation i.e. permeability, let's call it $T$, which is dependent on changes in water (w) and gas (g) components over a path integral.
The path covers all components in the vascular system that are in series.
So total resistance defined nonlinearly

$$W(x,y)(t,f) = \int_{\gamma} T(u) \frac{1}{u} \int_{t-u/2}^{t+u/2} T(w) \, S(x,y)(t,f) dw \, du$$

where the inner integral corresponds to the water component while the outer integral to the gaseous component.
There is only an averaging in the inner integral when the width of the window is $u$.
However, we do not any windowing here actually, just because of this averaging, so we lose no data and can handle the total resistance as a single process.

Notice that change in $T(u)$ leads to a change in $T(w)$ nonlinearly.
I skip the nonlinear definition of $S(x,y)(t,f)$ which stands for the energy in time in each instance - you can think it as the amount of permeability in each position of the vessel.
Actually, I also skipped the explicit definitions of the water and gaseous components too.

I have not found any work done on the nonlinear development of the resistance.
I think this is necessary for defining inflammation explicitly.

How can you describe the total resistance as an nonlinear operation better?


texts: Do cancer cells give off specific chemical signatures?   Are these signatures different from normal cells?


texts: What is (probably) the closest living relative of the trilobite?

texts: The trilobites vanished from the fossil record many millions of years ago, but they were obviously arthropods of some sort. Do we know which animals are their closest living relatives? I've heard both Armadillidiidae and horseshoe crabs. Can we tell which is right (or if there is a different answer), and how?


texts: DIY storing family DNAs' samples for future uses (eg medical)

texts:
I have a question I could not get an understandable reply from Google and I am no expert in the matter, so my plead to you is if you could give me practical and relatively easy to follow advice.

With the view of the breakthroughs in DNA research and all the anticipated applications to medicine in the near-future, I am willing to build a storage of the DNAs in my family (eg 20-30 people, some at a very old age). The use may not be for cloning :) but rather, for eg to map and trace specific hereditary genes when such services become more available to the wide public; and thus, probably help with a personalized medicine for someone, or find genome problems, and probably be able to 'turn them off' at some point.

Is there a way I can extract cells (ie from inside the cheek, or hairs), and store them for a few decades while preserving the DNA (eg put them in a freezer at -18C or in some solution)?
I have only common knowledge in this area so apologies if the examples are silly, but I assume you can understand my point.

I would be grateful if you provide practical instructions as: "you buy 500ml of the chemical xx"; or "mix 150ml of xx and 200ml of zz", so me and anyone who finds the idea appealing, can follow.
Ps-the lower the costs of the procedures, the better (I found some personal "dna vaults" costing several '000$).

Thank you for your consideration!


texts: To which ungulate species does this tooth remainder belong?

texts:
Found on the beach in Çanakkale, Turkey.
I have found a lot of these, but this is the first one that has parts like long teeth. My other findings have sometimes 4, sometimes 6 tubes. Very solid, stone-like objects. Is this from a marine animal or is it a non-living formation, I wonder.
Below image is for scale in centimeters.

View from top and bottom

Other similar findings without teeth-like parts


texts:
After one year in college, I am quite surprised with the number of different abbreviations used in biology for the same thing.

I wonder if there are any rules for naming something new in biology, for example new genes, or if it is just up to the researchers without restriction?  If there are rules, how did the confusion arise?


texts: Interpretation of Pangenome: high number of accessory genes

texts:
I performed a pangenomic analysis on a collection of 52 strains belonging to the same genus (some 5-6 different species). All the strains were isolated from the same environment: interior compartment of surface-sterilized plant root.
Now, the results of my analysis (I used the R package FindMyFriends) indicated a total of 32911 gene groups divided as follow:

581 core (present in 95% or more of the genomes)
6116 shell (present in 15 to 95% of the genomes)
26214 cloud (present in up to 15% of the genomes)

This results are quite unexpected. Even though it is typical that most gene groups get labeled as cloud or accessory, it surprises me that the percentage is so high! Especially given the common origin of those strains.
Other software I tried (Roary, BPGA, microPAN) gave similar or more extreme results, so I can exclude a technical error.
Therefore, if anyone has some experience with pangenomic data, some input on how to interpret this data would be greatly appreciated.


texts:
I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp).

I have tried multiple assemblers (CLC, velvet, metavelvet, Meta-IDBA) but all produce few contigs (15 contigs, 1000bp average). The contig output is scarce considering the amount of raw data (5 Gpb).

Has anybody has any success in a task such as this?.

Thanks.


texts: Breeding laboratory mice with cancer; how does this work?

texts:
It has recently been brought to my attention that live laboratory mice with specific cancer strains can be readily purchased for medical research.  For example, the Jackson Laboratory sells mice with a wide range of strains of cancer (with price depending heavily on the type of cancer desired).

  Question: What is the general process behind breeding laboratory mice with specific cancers for medical research?


texts: Why are some housekeeping genes considered better?

texts:
Whenever a PCR is done, we have to use housekeeping genes like GAPDH, to self normalise the values to account for different starting cDNA/DNA. Now there are many different genes like GAPDH, ubiquitin, actin etc.

Now when dealing with cells, I can understand that due to their immortal nature and frankly shocking number of generations undergone by them, the expression of the housekeeping gene may change.

Assuming that I am not dealing with cells and instead with animal tissues, does it matter which house keeping gene I select? Or in other words is GAPDH going to give me the same consistency between samples as something like 18s Ribsomal RNA or am I missing something specific?


texts: Glycolysis step 5: isomerization by triose phosphate isomerase

texts:
On the 5th step in glycolysis, triose-phosphate isomerase converts dihydroxy-acetone-phosphate to glyceraldehyde-3-phosphate.
Now my question is: Why?

Most books and sites I've read only say that glyceraldehyde-3-phosphate has a direct pathway compared to dihydroxy-acetone-phosphate. Anyone with additional info on this would help much if they shared.


texts: Why can one swim longer underwater by blowing out air?

texts:
I am a human. I take a deep breath. I swim underwater... After some time, I need to blow out some air. I blow out some air... By doing so, I can swim underwater longer. Blowing out some air gives me more time underwater. Why?

Apparently, dolphins encounter this phenomenon too.


texts: What is the difference between a phosphotransferase, a phosphatase, a phosphorylase and a kinase?

texts:
I've looked in several sources, but I'm still confused. This is what I have so far:

A phosphotransferase catalyzes the addition of a phosphate group.
A kinase is a type of phosphotransferase that transfers a phosphate group from ATP to a substrate.
A phosphorylase is a type of phosphotransferase that catalyzes the addition of a phosphate group from an inorganic phosphate (HPO4) to a substrate.
A hydrolase catalyzes the hydrolysis of a chemical bond.
A phosphatase is a type of hydrolase that removes a phosphate group.

Is this right?

EDIT:
Also adding to the confusion is the enzyme Phosphorylase kinase, which is the kinase that phosphorylates the enzyme Glycogen phosphorylase, which hydrolyzes glycogen.


texts: How do plant cell divide without centrioles?

texts: Most plants do not have centrioles, so what organelle enables them to multiply?


texts: What is the function of the Moderator band?

texts: The moderator band in the right ventricle is a band sorts of muscle which consists of a significant branch of the AV bundle. Does it mean it delivers impulses to the anterior papillary muscle faster? If it does, how does this help? and why only the anterior papillary muscle? What makes it special to have a moderator band?


texts:
I Always thought that copper was toxic to the human body.
So how can it be safe to place a copper object (birth control spiral) into a uterus for a duration of 5 years?


texts: a biochemical pathway for evaluating the effect of 3' to 5' exonuclease on the proofreading activity of DNA synthesis

texts:
Can the following oversimplified biochemical pathway for DNA synthesis serve as a model for evaluating the degree of the effect that the 3' to 5' exonuclease affinity for mismatched base pairs can have on the degree of the fidelity of dsDNA synthesis? Is this idea basically correct to model the relationship?

Thank you for your attention


texts: What animal has fat with the highest energy density?

texts: Fat is more energy-dense than protein and carbohydrates, it is not only an energy deposit but also an organ with many functions such as cushioning and metabolism regulations. I want to know are animal fats similar across species (composition & function), specifically what animal has fat with the highest energy density?


texts: Evolutionary distance between Canidae, Felidae, and Rodentia

texts: Comparing the families Canidae and Felidae, which have the shorter evolutionary distance to the order Rodentia? Less sophisticatedly put, are cats or dogs more related to rodents?


texts: When is voltage generated across a membrane?

texts:
I'm very confused so bear with me please.

Electrogenic pumps are carrier proteins that generate voltage through the movement of ions, right ?

When is a voltage generated ? When there's a net movement of ions ?

Doesn't that mean that when any ion passes through a channel protein, voltage is generated ? And energy is released ? Doesn't that make them electrogenic too ?

We need energy to move ions against their concentration gradient but if energy is released when ions move then why do we need energy ?

Is it that a voltage is generated when an ion moves towards the env with the same charge ? So when the movement enhances the overall seperation of charge , a voltage is generated ? And energy is released ?

In other words, the movement of Na+ through the Na+ channel protein down a concentration gradient doesn't release energy because the Na+ is moving towards the -ve environment but it being pumped outside does ? See that doesn't make sense either, because we need energy to pump and ion.

I'm very very confused


texts:
I am a Biology novice so I apologize in advance if I state anything incorrectly....

My question is, are the DNA codon mappings arbitrary? I understand that the DNA code is made up of codons which each consist of 3 base pairs. There can be 64 codons which map to 20 amino acids (some are duplicated and others act as stop codons). So was there a reason why one particular codon mapped to one particular amino acid - or is the mapping completely arbitrary?

Thanks!


texts: What is immunopanning (vs. immunoprecipitation and FACS)?

texts: I had never heard the term before today. From what I can tell, it's using antibodies to purify a cell population of interest. I would appreciate more details, especially in how it differs from "immunoprecipitation" of cells via cell surface markers, and FACS.


texts: Is there an evolutionary advantage to crying when sad?

texts: It seems as though the act of crying when sad does nothing to relieve that sadness. Is there an advantage to crying from an evolutionary perspective, or is it the end result of a different process? Also, why is there the same physiological reaction of crying when in sadness or in pain?


texts: Does becoming martyr have an evolutionary advantage?

texts:
This is related to
How does "be altruist to those who are similar to you" evolve?

Altruism that is

Not reciprocal
Not familiar

has little explanation. One possible explanation is that the trait itself may correlate well with genetics. One great answer there is that often the cost of altruism is small anyway. It can explain why people vote. Here the expense is small anyway.

Still there seems to be some factors that are even bigger.

Let's take a look at people that die for their ideology. Christian martyrs, Muslim suicide bombers, or Communist guerilla fighters. They seem to get so little and well, die.

And that's pretty common. It seems pretty easy for a leader or pedagogue to rouse men to be soldiers. Of course, becoming a soldier is a pretty shitty job, yet most men don't mind.

These people make a huge sacrifice for the sake of their country, ideology, or people that are not even genetically related to them.

Why?


texts: Where to begin studying Biology in earnest, with preferably free sources?

texts:
I am a biology enthusiast and would like to study Biology in earnest. I have basic knowledge of biology (high school level) and some extended knowledge of small animals, mainly about mammals as I am naturally interested in them.

So I would like to start studying veterinary and Mammalogy first.
I would prefer free sources for studying since I have little money available.


texts: Which part of human body sustains most pressure when standing up straight?

texts:
Let's suppose a healthy fit barefoot young adult standing comfortably on a flat solid surface.

A reasonable guess is somewhere around the foot.
But is it the ankle, the heel, or the Metatarsus?


texts: how many times can a spitting cobra spit its venom?

texts:
exactly how many times can a spitting cobra spit its venom at a predator
it has a small venom sac, so I presume it can only spit once or twice only


texts: How the vaccine based on "non replicating viral vector" is produced?

texts:
As I understand, this kind of vaccine is a virus that can infect the cell, start synthesis of  proteins encoded by its genome, but cannot finish the replication cycle till the proper end. It can have extra genes in its genome, encoding proteins that cause the wanted immunity to develop. Some important vaccines against COVID-19 are based on this approach.
The question is, how such an "incomplete virus" could be produced in large amounts? It would be logical to assume that it was replicating during the manufacturing process, but then why does it cannot any longer? The only hint I found is the usage of the "helper virus" that infects the same cell, so the "incomplete virus" can borrow some parts from the healthy "coworker". However this raises another question: the helper virus obviously replicates also itself, and how to discard it later without inactivating the "non replicating" one? It would just cause infection without any use if not discarded.
I have done some search over web and article databases but was not able to find a short and clear explanation of this method. The main focus of the works I found is always somewhere else. I understand that exact technology may be secret, but it is likely at least remotely based on some research work anyway.
How is a "non replicating vector" replicated to produce enough of it, for making a vaccine out of it?


texts: We know that the nucleus of the cell is the White House of the cell and its DNA is the president and it commands to make protein. So my question when DNA only codes for protein and enzymes,after the birth of a new cell where does the cell get lipids and carbohydrates to make membranes, organelles, water, ions, plasma membrane etc ...?


texts: Richard Goldschmidt's “systemic mutations”?

texts:
[TLDR] I dont understand the fault people had/have with Richard Goldscmidt's concept of systemic mutations [/TLDR]

As a preface, I am a undergrad biology student, so sorry if this is a "Stupid question".

How does Richard Goldschmidt's concept of systemic mutations, reject the classical gene concept, why were biologists so against it?

From what I  understand he used the concept of systemic mutations and developmental macromutations in his lectures to explain how macromutations could cause speciation(macroevolution?). The results of the developmental macromutations, if I understand him correctly would be then the Hopeful Monsters?

And from what I have read on a timeline of his work, systemic mutations describe the "large rearrangments of the chromosome", with a new arrangement meaning a new phenotype?

How is that wrong though? Do chromosomes not have rearrangements via cross over events during meiosis or via transposable elements? Or is he referring to something else, since I understand at the time, meiosis and TE's were not understood well.

The source i was reading from was:
(Richard Goldschmidt: hopeful monsters and other 'heresies' by Michael R. Dietrich) Available from http://www.dartmouth.edu/~dietrich/NRG2003.pdf


texts: Which range are the Therapeutic Indices of Currently-Prescribed Benzodiazepines in?

texts:
A compound's therapeutic index is defined as:

$$TI = \frac{LD_{50}}{ED_{50}}$$

What range are the therapeutic indices of benzodiazepines in? For the method of administration I would prefer intravenous as with it one can estimate the therapeutic indices via other routes. Of course for humans it is difficult to find LD50's but a rat/mice LD50 will suffice provided the ED50 is for the same respective species. Such benzodiazepines I am interested in are (Although I will accept your answer if you just give me an estimate of the therapeutic indices of the drugs in bold, the others are just icing on the cake):

Alprazolam
Brotizolam
Clonazepam
Clorazepate
Diazepam
Estazolam
Flurazepam
Lorazepam
Lormetazepam
Midazolam
Nitrazepam
Temazepam


texts: Why do musk deer have the smallest red blood cells and amphibians have the largest?

texts: What is the reason that musk deer have the smallest red blood cells and amphibians have the largest? Should they not be proportionate to the size of the organism?


texts: How can I convert plate reader measurements of Pichia pastoris OD to cells per ml?

texts:
I am performing experiments with the yeast Pichia pastoris where it will be beneficial to calculate product yield per cell. I plan to use a plate reader to measure OD600 of my cultures and then somehow relate this to cell number.
The Pichia pastoris expression manual from ThermoFisher says that 1 OD600 is equivalent to 5x10^7 cells/ml, and Weis et al (2004) have a similar number of 1.5x10^8 cells per 1 OD.
However, there are now calibration protocols (Beal et al 2020) and packages (Fedorec et al 2020) for using absorbent beads to convert OD measurements to cell density in E.coli. These rely on the beads scattering the light in a way that is equivalent to cells, so that one can compare measurements of OD with a standard curve of known amounts of beads to estimate cell number. Pichia is about 5µm in size size, compared to E. coli which is about 1-2µm, therefore I do not believe that using the same protocol will work for me.
Is it necessary for me to develop a new protocol, or can I just convert by multiplying OD by the numbers given above? If it is necessary, how can I develop such a protocol? Can I just use the E. coli protocol that I linked with different size beads?
Refs:

Weis, Roland, Ruud Luiten, Wolfgang Skranc, Helmut Schwab, Marcel Wubbolts, and Anton Glieder. ‘Reliable High-Throughput Screening with Pichia Pastoris by Limiting Yeast Cell Death Phenomena’. FEMS Yeast Research 5, no. 2 (1 November 2004): 179–89. https://doi.org/10.1016/j.femsyr.2004.06.016.
Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Vishal Sanchania, Russell Buckley-Taylor, Geoff Baldwin, Natalie Farny, Richard Tennant, Paul Rutten 2020. Calibration Protocol - Plate Reader Abs600 (OD) Calibration with Microsphere Particles. protocols.io
https://dx.doi.org/10.17504/protocols.io.bgy6jxze
Fedorec, Alex J. H., Clare M. Robinson, Ke Yan Wen, and Chris P. Barnes. ‘FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data’. ACS Synthetic Biology, 27 August 2020. https://doi.org/10.1021/acssynbio.0c00296.


texts: What is contiguous premise culling and dangerous contact culling?

texts: I am reading this paper related to FMD (foot and mouth disease) epidemics which occurred in UK. It mentioned about terms like IP (infected premise culling), CP (contiguous premise) and DC (dangerous contact cull). IP is the mandatory slaughter of all livestock on an infected premise. But what is CP and DC?


texts: Would a stray ant re-home into a foreign colony (of the same kind) and will the colony accept an alien ant?

texts:
Let's say an ant got into my pocket as I was sitting in the park today. At home, I shook off my coat and the ant fell out and scurried out to my garden, which has ant colonies of the same kind.

Would the ant try to assimilate into that colony and would the colony accept it?
How would each know about the other's non-relation?

Thanks


texts:
How do the instinct to create a hive appeared in bees? Is there some evidence of
"intermediate" hives? With this questions i mean all the factors necessary to build a hive, including the social structure, the producing of beeswax and architecture.


texts: What are examples of genes succesfully reproducing in ways that is in conflict with helping the individual creating offspring

texts:
Most of the time, our genes have common interests with our "self".

We reproduce well if and only if our genes reproduce well.

In some cases, like in bees, the haploid bees can survive better if they help their queen reproduce.

In humans and other species, are there samples that give individuals "incentive" to help non family member to reproduce for the sake of their genes.

So

No filial altruism
No reciprocal altruism

So I need a sample between individual based evolution and gene base evolution.

For example, many genocide are done against the best and brightest. I wonder what sort of genes encode "kill the best and brightest" and how does that kind of gene survive well in the gene pool?


texts: Can you identify this insect (orange back, 6 legs)?

texts:
Found a couple of them in central europe on a zucchini plant (in august).

They are about a centimeter in size.

Tried looking for insect with orange back and 6 legs but no result.

[EDIT from comment]: The insect in this post looks pretty similar. There is a difference though - the one in my picture has orange legs not black ones. (maybe different stage of larvae or different species of ladybug or just random?)


texts: Quantifying DNA in a band on gel electrophoresis

texts:
I am a first year science undergraduate and I am just asking this as a more theoretical question rather than for carrying out a protocol, so I would appreciate if answers do not involve lots of complicated chemical names.

I was wondering how one would go about quantifying the amount of DNA in a given band on a gel electrophoresis. Some ideas I have had so far are:

Cut out the DNA band and extract the DNA. Quantify using some known method such as measuring the absorbance at 260nm of the DNA in solution to find the concentration.
When the DNA is stained with ethidium bromide, clearly there will generally be more stain uptaken in a band region if it has more DNA so it will fluoresce with greater intensity when illuminated with UV light. However I would have reservations to using this method because I would think that the amount of stain uptaken would depend also on the state of the DNA (i.e. if it is supercoiled or not), but then again I do not know how much of an impact this could have on how much stain is uptaken. Of course, if you know that all of your DNA is in the same state then there shouldn't be a problem with this method I think. Although here you would have to be aware that the concentration of ethidium bromide in a certain band depends on the concentration of nucleotides there, which depends both on the number of the DNA fragments and their size (which is known from the position of the band). Compare this with the final method...
Finally, if one is making the DNA for example using dideoxy chain termination/Sanger sequencing in PCR, then you can use a radioactively labelled primer. The intensity of the image on the radioautograph would then directly tell you the number of molceules of that DNA fragment present in the band.

I was wondering which of these are viable options to use in the lab, and why/why not.


texts:
On average, in a human being with no neurological deficits, how long does it take for a sound which is sensed in the ear to reach the cortex?

Which brainstem structures are most responsible for the delay?

(I'm interested in things like the effect of the Olivary n.)


texts:
Looking at the rules in the meta, it seems book-recs are a little on the iffy side for on-topic so I hope this is okay.

I am looking for a (graduate-level) textbook that has a thorough treatment of the molecular basis of learning and memory. The issue I am having is that a lot of textbooks seem to cover bits and pieces or just focus on one area. Usually, they just have a few small sections on the molecular events and the rest of the textbook covers channel properties, pharmacology, systems neuro, and behavior.

Synapses - This one comes close but is now quite dated (2003)
The Neurobiology of Learning and Memory - A significant section on the molecular aspect but is not particularly detailed. Very basic idea.

Review articles tend to be difficult because they are more specialized for specific kinases (mTOR, CaMKII etc), events, or channels.

I am trying to get a sense of the broader picture of the just the molecular side of all of this. Specifically the molecular and cell biology that underlies:

Early-phase LTP (receptor trafficking, signaling pathways)
Proteins expressed from local translation in dendritic spines, signaling pathways that control this
Details on synaptic tagging hypothesis
Late-phase LTP events, pathways, proteins, and regulation
Downstream effects of activation of different channels, how they control pathways below, how they all intersect and how this differs by brain area and cell type
LTD events
Events at the post-synaptic density (receptors, ion-channels, protein composition, scaffolding, actin network)
Synaptogenesis, plasticity, maintenance during long-term memory
Kinases in learning and memory
Transcriptional control
Post-translational modifications and consequences for learning and memory
Scaffolding proteins and their contribution to signal stability
Pre-synaptic events
Contributions of glia/auxiliary neuronal cells
Bonus: Disease focus - what pathways and proteins underlie various well-studied genetic diseases?
etc.

I know this is a tall order but with 1000+ page textbooks out there on other neuroscience topics, surely someone has written something? Review article are great too, perhaps I just haven't found the right one yet.


texts: Measuring Bioluminescent Algae Intensity

texts: For a science project, I am required to measure the intensity of the light given off by the Algae, Pyrocystis lunula. Can a photometer with a range of 1-50000 lux be able to pick it up? If not, what are some tools to measure the intensity(without costing to much money.)?


texts: Can the apparent drop in insect population be explained by local insects evolving to avoid traps?

texts:
In this widely reported Plos One article, it is stated that, after roughly 3 decades of placing Malaise traps in a set of predetermined locations (counting and replacing them regularly), a sharp decline (roughly 75%) of insect population is observed. The idea is that the amount of insects caught in the traps is a proportionate representation of the insect population.

This seems to be a very important publication. It is getting reported in many popular articles as the most compelling evidence for a massive recent decline in insect biomass.

Maybe I didn't read the article thoroughly enough, but I saw no mention of the possibility that the local population (around where the traps are set) are adapting to avoid the traps. Since getting caught in a Malaise trap is lethal, genes that promote the behavior of avoiding those traps would thrive, in a local population of flies, at a higher proportion than their competitors. And since flies reproduce very quickly, 27 years seems (intuitively, to me) like a lot of time for this new local selection pressure, created by the experimenters, to make notable changes in a local fly population--particularly, their tendency to avoid Malaise traps.

Could the result of the linked article be explained by local flies adapting to the new selection pressure of Malaise traps?

When I first read about the methods with which the insect population drop was measured, this was the first possibility that came to my mind. But I can't find anywhere where this possibility is discussed. Could that be because it's so ridiculous that it's not even worth considering?


texts: How do poiklotherms survive at different temperatures even though enzymes work at specific temperature?

texts: Since enzymes have an optimum temperature at which they are able to catalyze the reaction best and increasing the temperature above optimum can even damage them, how do poikilotherms survive as they change their body temperature according to environment unlike homeotherms. Also wouldn't their metabolism stop with increased temperature?


texts: How many paraphyletic groups can be formed from a phylogeny?

texts:
How many paraphyletic groups can theoretically be created from this phylogeny?

I found (2n)-2. Is this correct?
This is not homework nor exam, just a question about paraphyletic groups.


texts: What would the RBCs of someone heterozygous for sickle cell anemia look like?

texts:
Would half of the RBCs look normal, and the other half sickled?
Or would all of the RBCs have slight deformation/sickling?

Thanks!


texts: I do understand that the female has to prepare for possible fertilization and make sure that the egg is of the best quality, so they try to remove aged egga from the uterine. However why cant the body just simply get rid of the egg not the uterine lining?  Maybe like reabsorb the egg or pass them out as waste? I mean its extremely energy consuming etc and it would be an evolutionary disadvantage since many other mammals dont go through menses.


texts: Which method of gene amplification for toehold switches?

texts:
My team and I are from a high school and are planning to carry out some research investigating some toehold switch riboregulators which we have designed in silico. However, we have little experience in wet lab work. We plan to order 3 genes containing an arabinose inducible promoter, a riboswitch, a leuciferase CDS and a terminator. These genes are each ~3kb in length.
We plan to order our genes from IDT, but we're not quite sure which strategy to deploy to amplify these genes before adding them to a cell free extract for characterisation.
The four methods we have narrowed it down to are as follows:

Order the genes in plasmids, linearise, PCR,  ligate, add to cell
free extract for characterisation.
Order genes in plasmids, transform straight into E. coli, culture, mini prep, add to cell free extract for characterisation.
Order genes in plasmids, linearise, PCR, ligate, transform into E. coli, culture, mini prep, add to cell free extract for characterisation.
Order genes as gBlocks (not in plasmids), amplify with PCR, ligate into plasmid backbone, transform, culture, mini prep, add to cell free extract for characterisation.

We'd ideally like to use the method which is most simple as we will not have a lot of time in the lab, and we don't have much experience.
Any advice on choosing between these strategies would be much appreciated!


texts: Species diversity in cheese and yoghurt?

texts:
There have been studies on the number of species on humans and in various other environments. I was wondering how many species including: viruses, bacteria, yeasts, and fungi inhabit ordinary farm yoghurt, supermarket yoghurt, and cheeses like parmesan, edam, and blue.

I can find some studies, but not an actual count of species diversity in living dairy products.


texts: Impact of Natural Selection on Population Size

texts: I have conducted a lab with my IB Biology 11 class, regarding changes in allele frequencies within generations overseeing the natural selection of an advantageous phenotype. We were looking to conclude some sort of link between the changing allele frequencies and an overall changing population number of the species. Lab results saw, that as the frequency of the advantageous phenotype increased, the total population dipped and then increased after the 3rd generation. Can anyone point out any possible reasons as to why this occurred - regarding any factors at all? The image below depicts frequency of the advantageous allele vs total population.


texts:
Hi! I'm trying to make sense of this illustration (from the textbook Biological Science by Scott Freeman).

The general question is: How do point mutations arise from mistakes in DNA replication?

If you don't mind, however, I'd like to explain how I interpret the illustration so you can see the confusion. As the original molecule of DNA is replicated (in gray), a mistake occurs in the synthesis of the bottom strand in the new molecule (the noncomplimentary bases G and T have been paired together). Now, it seems like a second replication is required for the mutation to arise: the defective molecule is replicated resulting in two new molecules, one free of mistakes (because it takes as its template the top strand) and one "wrong" where the mutation is present.

But my doubt is, wouldn't the middle molecule already constitute a mutation? If a mRNA were to transcribe that sequence, the codon is already different from the original molecule. Must a DNA molecule be replicated two times for a mutation to arise (where the first time a mistake is made and a second where such mistake is, let's say, "consolidated")?

Thank you very much in advance.


texts: is there a way to do batch download for all gene pathways?

texts: I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package.


texts:
I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process.

So far..

I retrive pairs of orthologous DNA sequences from genbank using Biopython package.
I translate the orthologous pairs into peptide sequences and then align them using EMBOSS Needle program.

I wish to..

Transfer the gaps from the peptide sequences into the original DNA sequences.

Question

I would appreciate suggestions for programs/code (called from Python) that can transfer gaps from aligned peptide sequence pairs onto codons of the corresponding nucleotide sequence pairs. Or programs/code that can carry out the pairwise codon alignment from scratch.


texts: What is the reasoning behind the Drake Equation?

texts:
I've read a bunch on how the Drake Equation is constructed, but I'm not able to understand some of the reasoning behind it.

$$
N = R_* \cdot f_p \cdot n_e \cdot f_l \cdot f_i \cdot f_c \cdot L \cdot f_d
$$

Why does $f_c$ represent the fraction of intelligent life able to communicate? Isn't communication (in some form) part of what defines intelligent life itself? Or is this term included just to break the number down further?

I'm asking this here and not elsewhere because I'm wondering specifically about this term and not the entire equation.


texts:
These two spiders were found at the Fairchild Gardens in Miami, FL.
What spiders are these?


texts: Is there any kind of "unintended consequence" in evolutionary systems?

texts:
In the social sciences, unintended consequences is a term used to describe an unexpected positive or negative effect of a particular action. This is obviously the wrong word to use in the context of evolutionary systems but I am looking for something that has a similar concept. It may be related to concepts in dynamical systems theory.

For example, if we look at one trait or a group of traits, we may be able to see how this adaptation benefited a population. However, the mutations that occurred along the way would no doubt alter other systems/properties of the organism. In many cases these effects would be negligible. I am looking for any cases where the effect of one set of adaptation leads to another comparably impactful (either positive or negative) effect for the population.

The following is more theoretical and controversial but I am particularly interested in larger, more complex traits such as behavior (which may be considered the product of many different evolutionary adaptations and molecular changes) and any "unintended consequences" that could occur as a result of such a behavior. For example, empathy may be considered a very complex trait that has an evolutionary advantage (post hoc we might say it evolved because it allows specific kinds of communication in social groups) but it may also cause populations to react incorrectly (with regards to survival) in threatening situations when an empathetic response is not the most optimal response. I realize I am treading in vague territory here and it may be controversial to reduce empathy down to the molecular level as I have done in this example. But if there is any work at least related to this idea on a basic level I would be interested.

In summary, I am looking for either the term that describes this sort of analysis, if it exists, or some major examples that may help me do further research on the topic.


texts: Did Darwin explain why he believed that domestic dogs descend from several distinct species of ancestor?

texts:
Charles Darwin begins his book Origin of the Species (1859), in which he argues that species evolve as a result of variations caused by natural selection, with a chapter about variations that have occurred not naturally but under domestication. There he writes

  I may, without here entering on any details, state that, from
  geographical and other considerations, I think it highly probable that
  our domestic dogs have descended from several wild species.

The ancestry of the subspecies Canis lupus familiaris is a controversial topic, but I have not found any papers which argue that it descends from several wild species. When the view is that the subspecies descends from two separately domesticated strands of ancestral wolf - East Eurasian and West Eurasian - the strands are not, as far as I am aware, referred to as separate species, but even if they were, two is not "several".

I appreciate that in a book on natural selection Darwin does not wish to spend more than a chapter on selection under domestication, but does he explain elsewhere his detailed reasons for his conclusion?


texts: How can I perform virus neutralization assay for influenza?

texts: How can I perform a Virus Microneutralization assay for influenza virus using serum from mice vaccinated with this virus?


texts: Does one neurotransmitter travel all the way through the nervous system?

texts:
Nerve impulses of course go really fast, but the neurotransmitters have to travel through millions of nerves, so how can it go that fast?

Is it a sort of relay with lots of neurotransmitters taking over at each nerve cell, or do the neurotransmitters go all the way from A to B?


texts: Book recommendation on mammal (or just primate) behaviour, especially in relation to child-rearing

texts:
I have a growing frustration with the lows 'new-age' parenting is reaching, along with asininity of so much of our public schools' (and summer camps') philosophies and policies in relation to our kids. Whatever the implications, this has continually lead me to the thought of

  what the natural precedent is for how primates (or other mammals) raise their young, collectively or otherwise -- how they're guided, rewarded, chastised, and conditioned.

May someone please recommend a book that delves in to some of this? (Humans don't necessarily have to enter the picture, but something that does compare and contrast with the human condition would be a bonus.) (Preferably not a text book, but, by all means, please recommend those too.)


texts: Metrics to analyze branch lengths in phylogenetic trees

texts: I'm interested know about some basic metrics that could be used to discriminate trees based on their branch lengths. I know of branch length unaware topological/tree shape-based methods such as Colless and Sackin's indices and am curious whether there are similar metrics that utilize branch length to discriminate. For example, the two trees below have an identical topology but are very different.


texts: What are all the elements affecting human reaction time?

texts:
I'm helpless at biology/science-y stuff in general. But, as a writer, for the sake of story research, I often have to delve into it. I make use of the Worldbuilding Stack Exchange, but this question didn't seem like it would be a good fit for that site, because it's more about clarifying my understanding of certain scientific concepts than about anything specifically worldbuilding related.

I am looking to create a character with high-speed reflexes and reaction time. However, my question is not about how to accomplish this (scientifically dubious) feat, as this would belong on the worldbuilding forum, but rather whether I have properly identified the elements necessary to do so.

From the research I've done, it seems that the most basic steps regulating how quickly someone reacts to something are a) sensory neurons recognize a stimulus b) they send a signal to the brain/spinal cord and c) this signal is processed and another signal is sent to the muscles, resulting in whatever physical reaction observably occurs.

Hypothetically, then, no matter how fast any single element in this chain (if given a brain that could process signals 10x faster than normal or nerve signals that traveled 10x faster (bear with me)), the speed with which the final action was triggered and completed would still be limited by, say, the eyes' tracking speed and the speed with which the eye converted light into electrical signals on one end, or the speed the muscles were capable of contracting at the other end of the chain.

How am I doing so far?

So, by my estimation potential limiters of reaction speed are as follows:

the speed the eye moves (or would speeding up other things, such as muscles and nerve signals, also increase this?)
the speed the eye converts light into signals
the speed that signals can travel from sensory neurons to the brain/spinal column
the speed with which the brain can process these signals (and potentially its ability to handle multiple tasks/stimulus simultaneously)
similar to (3), the speed that signals from the brain (or spinal cord) can travel to the muscles
the speed with which muscles can contract

Am I confused about or missing anything? Thank you!


texts: How does one calculate the amount of oxygen produced by trees?

texts:
I'm currently working on a project to measure the impact of tree planting.
Calculating the amount of oxygen seems harder than I imagined.

Of-course there's the type and size of the tree and the environment (soil and air consistency), but there are plenty of other variables in play of which I have no knowledge of (being an engineer, not a biologist).

From a computational standpoint I'm looking for rough and finer methods of calculation for the amount of oxygen the following produce:

A tree
A large forest
Multiple countries with their forest

The one tree can be calculated exact, given enough variables. Oxygen during the day, during the night, tracked over it's age, etc.

A large forest will be calculated more approximate. Extra relevant would be how growth and oxygen production are influenced by tree density (trees per square mile).

Calculating multiple countries would be a whole other problem. It looks like it's very hard to prevent estimations from completely destroying the accuracy of calculations.

Basically I've written down some concerns and now I'm looking for a way of actually calculating these numbers and preferably some real numbers to validate against. The internet is crawling with estimates ((1)(2)(3)(4) and many, many more), but finding decent sources to compare your calculations seems hard.

How does one usually tackle this calculation problem?


texts: Do primate RGCs have overlapping receptive fields?

texts:
According to this link,

http://hubel.med.harvard.edu/book/b10.htm

retinal ganglion cells (RGCs) receive input from overlapping receptive fields (RFs). This is also an idea used in convolutional neural networks for deep learning of images.

On the other hand, this one, for the primate retina, states that there is no such overlap:
http://www.sciencedirect.com/science/article/pii/0042698995001670

So do primate RGCs have overlapping RFs? If not, how does the primate visual system deal with this sparse input? How does it fill in the blanks?


texts: Are viruses more common due to modernity?

texts:
Is there any evidence to say whether in the past viruses like the cold virus were less common?  I wonder if high density living and globalisation mean that the cold virus mutates and spreads much more than in the past.

Perhaps in the past, owing to lower population density, slower and less frequent transport, viruses were effectively localised and isolated from the general population?  Of course that might not be true, as perhaps those things have been offset by improvements in sanitation and nutrition?  Perhaps virus frequency is always proportional to population size?


texts: Why does botulinum toxin cause only NMJ symptoms?

texts: Botulinum toxin acts by preventing release of ACh by cleaving SNARE proteins. But if it is acting on snare proteins shouldn't all vesicle releases be effected? Why is it limited only to the acetylcholine vesicles in the motor neuron bat the end plate? Why not some other neurotransmitter at some other place like GABA in the brain?


texts: Finding confidence level of miRNA disease associations

texts: I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence of miRNA disease relationships. Let me make more clear my question with an example. For instance, in one of the bioinformatics related databases( HMDD) it is said that, miRNA X is related with disease Y. I want to find that what is the confidence. I mean  you're 100% sure about such releationship? Do you know any database for that purpose? In HMDD I can only find miRNA - disease name couples it does not give any statistics.


texts:
I am part of an undergraduate research group and we are trying to produce a protease in an E.coli gene circuit. We are not sure where to place the His tag in our circuit. The sequence is
...OmpA(gene)->linker->his tag->protease->Terminator->res site
Should the His tag be in this position, before the linker, or after the protease? OmpA is a outer membrane protein that will allow a protein to be taken to, and linked to, the outer membrane of the E.coli. Our fear is that the protease will not fold correctly and will be nonfunctional.


texts: Organism with the greatest amount of gold as percentage of body mass

texts:
I've read that the human body contains trace amounts of gold:

http://www.tellmehowmuch.net/how-much-gold-is-found-in-the-human-body.html
http://web2.airmail.net/uthman/elements_of_body.html

Are there other species that are known to have significantly higher ratios of gold to body mass?

And while there seems to be no definitive answer about the benefit of gold being in the human body, are there any species for which gold has demonstrative bodily uses or benefits?


texts: Mathematical Modelling of Natural Selection

texts:
I'm a math undergrad looking for some papers on modelling the process of natural selection. The only paper I've been able to find is by the pre-eminent mathematician Herbert Wilf from 2010,

There's Plenty of Time for Evolution

Unfortunately, Wilf's model is extremely simplistic - he calculates the number of 'generations' required to spell out a 'word', if we allow each letter to 'mutate' with certain probability every generation, and we stop mutating a letter once it is correct (this is the 'selective' feature of the model). So to spell the word 'Evolution' by randomly placing scrabble tiles would require 5.4 trillion generations, but if we keep the correctly placed letters each generation and only allow incorrect letters to 'mutate', Wilf calculates we'd only need about 57 generations on average.

Wilf's model is a good first step towards modelling natural selection, but it's clearly only a first step. In particular, the fact that nature seems to know in advance exactly what letters it needs to keep in particular places and what it needs to throw out to construct a complex genetic 'word' is dubious at best.

As a young maths student the idea of the incredible complexity and diversity of life developing by a directed stochastic process gets me shamelessly excited :) I have been very surprised at just how little mathematical literature there seems to be on this topic, as I say, Wilf's one super-simplistic model is all I've been able to find. Can someone direct me to any other theoretical analyses of the power of natural selection?

Thanks


texts: Is there a way to derive Bazett's formula to correct QT interval in ECG?

texts:
As we know that QT interval in ECG is a function of heart rate (HR) and to comment on the pathology associated with altered QT interval, we must neutralise the effect of HR. For this Bazett's formula is broadly accepted, i.e. $QT_c=\dfrac{QT}{\sqrt{RR}}$.
Is it purely based on experimental data? Or, there is some mathematical logic behind it?
Here, $QT_c$ = correcred QT interval; $QT$ = measured in original ECG; $RR$ = RR interval.


texts:
Given a fix volume of water saturated with dissolved oxygen through aeration. Suppose that ammonium, Nitrosomonas, and Nitrobacter are always available in the water. We know that some of the ammonium will eventually be oxidized, by the bacteria, to nitrate. We also know that under anaerobic condition, some of the nitrate, through many steps, will be broken down into Nitrogen by denitrifying bacteria.

Question: Are there any bacteria, in our environment, able to break down nitrate under aerobic conditions? If there aren't, will the nitrate continue to accumulate?


texts: Why does HPV Infect Squamous Epithelial Cells and Not Others?

texts:
I've seen this question about HPV and the reference therein. The link states "Human papillomavirus (HPV) is a DNA virus that presents tropism for epithelial cells, causing infections of the skin and mucous membranes. Replication of HPV occurs in the nuclei of squamous cells and its life cycle is directly related to the differentiation program of the host cell. "

Why does HPV infect squamous epithelial cells and not others, what are the major differences? And why can't that difference be used to provide medication?


texts: How does sodium in one's diet affect blood pressure?

texts:
Due to high blood pressure, my doctor has recommended I go on a low-sodium diet.  So, that got me wondering what it is about sodium that drives this recommendation?

What does sodium do to a body that, by its presence or absence, affects blood pressure in humans?


texts: In some microscopic images, there is a bar scale at one of the corners or near a specific object. How are they added to the images? Does the slide have some markers, or are they digitally added? If so, how are they computed? I am planning to buy a microscope and wondering is there something I should look for. Thanks for any help!


texts: How do we sweat immediately after drinking water on a hot day?

texts: On hot summer days, when I drink water to quench my thirst, my body immediately responds by sweating in 5 to 10 seconds or maybe less. How does our body detect the presence of water in the stomach so fast. Does our body detect the sudden decrease in temperature of the stomach or is it by some other mechanism. Why do we sweat after drinking water in the first place. Is it to remove the excess water or to cool the body down on a hot day?


texts: Will new proteins incorporating new amino acids trigger an immune response?

texts:
This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done were able to produce new proteins using the newly added bases. The article quotes the scientists as saying that the extra amino acids “might become building blocks for new drugs and novel materials”.

My question is that if new proteins are made from amino acids that don’t naturally occur, won’t the body reject them?


texts: Help in identifying crusty formation on Eucalyptus leaves

texts: I am working with the plant species Eucalyptus perriniana (spinning gum) for one of my research projects. A few days into the experiment, I noticed some crusty deposits forming on several leaves (as shown in the attached photographs). I was wondering if anyone here might be able to identify it. I am not sure if the deposits are biological in nature, or if they are some kind of chemical precipitate.


texts: Which came first in hominid evolution: language or bipedalism?

texts:
I suspect both language-use and upright-posture have anatomical consequences. So does the fossil record show which came first?

NOTE: To the folks who marked this question "homework": This is certainly not an actual homework question. I have been an accomplished biologist for over 30 years and I am genuinely interested in the evidence for the timing of these critical human attributes. If you feel that the answer is so trivially obvious, that I should have been able to find out with only modest research, could you please leave a comment explaining, as if to a child, exactly how it is so obvious?


texts: Cancer history on environment-cancer relationship

texts:
I am interested to know how environment-cancer relationship knowledge has developed.
I know that all began when Muller first proved that mutation could be induced via ionizing radiation, X rays in the case, and hypothesized for the first time the role that this could have on carcinogenesis. Do you know further data and the main or most significant events that leaded from that point until the current state of the art? (like when smoking and cancer were proved related)

(all factors enhancing risk would be included in the query, as human behavioral aspects (such as diet), work environment...)


texts: I know it's kind of hard to see but can anyone tell what it is?


texts: Can life forms exist from simple structures not made of the four bases?

texts:
I understand that all life forms on the planet are made from adenine, gauatine, cytosine and thymine, which chemically joined together to form RNA or DNA (correct me if I'm wrong). This goes on to form all complex life as we know it.

I was wondering if it was possible- even studied theoretically- that other life forms could exist made of different elements and compounds, perhaps let's say iron, cobalt or tungsten? Or are the 4 bases the only possible way of life as we currently know it?


texts: Fraction of channels open at equilibrium

texts:
I found the formula for the fraction of channels open at equilibrium for a three-state mechanism (Colquhoun's paper in the microelectrode book http://www.utdallas.edu/~tres/microelectrode/me.html)

k1 and beta are forward rate constants. k-1 and alpha are backward rate constants.

p1(equilibrium) = (Xa/Ka)(beta/alpha) / (1+ ((Xa/Ka)(1+beta/alpha)))

Can someone show me how to arrive at this by derivation. I tried and I got it wrong (obviously!!!).

Xa is the concentration of the agonist and Ka is the equilibrium constant k1/k-1


texts:
The small intestine has villi for increased surface area for absorption but does the large intestine also have villi?
I searched this and some sources say large intestine has villi while others say the large intestine does not have villi.
What is the correct answer??


texts:
A lot of people live in a 7 day cycle, where 5 days of work are followed by 2 days of "rest". Vacations and holidays can increase the time available for resting.

Is there any biological reason for humans to rest after x days of work? Can this be explained by the buildup of by-products of metabolism, like Homocysteine?


texts:
Googling leads to results such as this:

  DIET
  Eagles primarily eat fish, carrion, smaller birds and rodents. Eagles are also known to prey on large birds and large fish.

  POPULATION
  Bald eagle numbers in the U.S. were estimated to be between 300,000-500,000 in the 1700s. Numbers were once as low as 500 nesting pairs in the lower 48 states. Bald eagle numbers have rebounded since and now the lower 48 states boast over 5,000 nesting pairs. There are a total of about 70,000 bald eagles in the whole of North America (Including Alaska and Canada).

  RANGE
  Bald eagles live near bodies of water in Canada and Alaska, and in scattered locations all throughout the lower 48 states and Mexico.

I would like to find something like this but with more detail, perhaps scholarly papers or such like that, like you might find on a synopsis/summary article for a specific protein. Wondering if anything like this exists.

Examples of "facts" I would like to look up:

food sources
habitat
range
color
sound
population size
lifespan range

Stuff you see like this has few if any citations where they get the info from.


texts: Is it impossible to increase skeletal bone mass, as opposed to just bone density?

texts:
I've heard exercise and resistance/strength training increases the density, but doesn't increase mass. So basically, experimentally or theoretically possible at least, can modern science do this/is it feasible?

Density is just how "packed" the current bone is on the micro-level -- i.e., doesn't affect total mass potential. Filling or adding "density" is just like putting water in a fixed-size bucket until it fills. By "adding mass" I want the bone's bucket to be able to hold more density, i.e., a larger potential of density along with an overall greater weight to the bones themselves. I can't find any evidence that this is possible with long and flat bones alike, AKA the spine, leg and arm bones, clavicles and etc. -- or any bone.

I've heard facial bones are more malleable, but their bone mass cannot change with diet/training either.

So to make this as easy to understand as possible: Can bone mass in an adult be significantly changed somehow? Can I make my whole skeletal set heavier somehow, rather than just dense? Like for example, say I am considered "small framed." Rather than just density, could I make my frame bigger? Could I make my entire frame base more robust through some possible bio/drugs/etc. means?

And since I know someone will come along and claim this is a "medical/personal question," explain to me how this would be possible to ask in a non-medical/personal way then to enlighten me. Go ahead.


texts: How to determine the evolution of a dimension of fitness that has high variability of selection intensity?

texts: How can one determine the evolution of a dimension of fitness that has high variability of selection intensity (low in some generations, high in others) compared to other dimensions of fitness?


texts: Do domesticated animals necessarily live longer than wild animals? counterexample wanted!

texts:
Generally domesticated animals do not need to worry about their food and other predators, and they have a lower probability of getting sick.

However, it seems there is no sharp difference between the life expectancy of wild pigs and domesticated pigs. Both can survive more than ten years if they are not killed.

Is it normal for domesticated animals to have a longer life span? Is it necessarily so?

Is there an example of a wild animal that statistically lives longer than its domesticated counterpart?


texts: phylogenetics and substitution ratios for positive selection

texts:
So very new to phylogenetics!. I've been scrambling and reading so much to get this done!!.

I would like to see if one or more of the sequences I have (from a gene family) are under positive selection using the dN/dS ratio. The conceptual parts are clear to me, however, practically speaking i have found several problems/questions along the way.

My most important question would be: I have four related organisms (insects), and their full sets of genes in a gene family. I have reconstructed trees to delineate their evolutionary story (duplications and losses). What would be the input for the calculation of dN/dS ratios when a single gene has several possible orthologs in the other organisms?, like gene A in species 1 has gene B and C and D in species 2 and E, F, G, H in species 3 etc... Do I need to align only the orthologs for each species? all of them?, or just align all the sequences form the subfamily including all paralogs and orthologs?, wouldnt that overestimate the ratio?

I have tried PAML yn00 package and got a result for a small "test" set of sequences, which were not codon aligned. Results are pairwise, how can I interpret this?, do I want to get "overall" omega values instead of pairwise? what would be the most interpretation on each case?

Second question is how I get codon alignments for these sequences?. I saw a couple of free software on th internet but they wouldn't work.

thanks a lot!


texts: What is Growing on These Tree Leaves? (Image)

texts: I found a seemingly diseased tree when I was out playing tennis yesterday... What is growing on this tree leaf? Is this a disease? If so, is it contagious? I have zero knowledge in botany, but I'm curious about what is happening to these trees. :)


texts: How does mad cow disease evade immune system?

texts:
The mad cow disease is caused by prions right?

So how do prions avoid white blood cells and antibodies?


texts: Resources for similarity between embryos

texts:
Is there a scientific paper/reputable image resource out there which I can use that the embryos of different organisms (vertebrata) are similar in their early developmental stages(without falling into the ontogeny recapitulates phylogeny trap) ?

All I am able to find are the haeckel drawings or somethings that suspiciously look like haeckel drawings and after that debacle, I do not want to be using that.


texts: Are there any types of cancer that cause neurons to divide?

texts: After birth neurons generally do not divide. But is there any specific type of rare cancer or tumour where neurons divide? And if there is such a cancer, then how is it possible for a neuron to regain the division power?


texts: I want to know what makes the balance of the Prolactin abnormal. Is that related to the presence of a nodule near the pituitary?


texts: Why not use lactase to aid the break down of lactose when making biofuels?

texts: I did an experiment using nine different substrates (Lactose + lactase, corn, sugar cane, glucose control, wood, grass, no yeast control and yeast control) and observed their fermentation rates. Lactose + lactase had the highest fermentation rate. So now my question is: is there a usage of lactase in aiding the break down of lactose to make biofuels? I did a web search and all I could find was that lactase was used for helping lactose-intolerant people,etc.  And that the current whey-ethanol industry used special species of yeast that break down lactose directly instead of the enzyme lactase. There are other methods too, including the Carbery and the Bio-process Innovation (BPI) processes; all of which use yeast that can directly break down lactose. Does lactase play no role in the biofuel industry? And why don't people use lactase to aid them in making biofuels?


texts: Can the spinal cord contain an "epileptic focus"?

texts:
I was wondering, is there a possibility of an something similar to an epileptic focus to exist within the spinal cord?

Note I am using the terminology "epileptic" loosely here, principally for the lack of a better name for it. When I say epileptic focus I mean an excitable area capable of sustaining a pathological rhythmic electrical activity which may or may not extend to other areas of the central nervous system.

I believe it is due to the connection types that occur within the spinal chord (closed loops that exist there are resistant to this) and as such this might be true for other CNS areas (epileptogenic susceptible tissue might be specific of cortex areas). But I did some research on the topic and couldn't find any data on this.

If it isn't possible to have this problem on the spinal chord then, why is that?


texts: DNA is always shaped like a double helix. But could you flatten the double helix (which is essentially just a twisted ladder) and would DNA still be able to duplicate and control cells?


texts: Is the water transpired by plants pure H₂O, or does it contain trace minerals?

texts:
I'm considering the idea of drinking water that I trap from what is transpired by trees.

Interestingly, is this water a fairly (or maybe even extraordinarily) pure form of H₂O, a remarkably pure by-product of the respiration / evapotranspiration processes - so does the process give off a fairly distilled form of water into the atmosphere - or is there actually a fairly measurable amount of trace elements that also are transpired in that water through the leaves?

A second complication which would be good to clarify, is that even if minerals / other chemicals are excreted along with the H₂O, would condensing that water in a water trap still only collect the pure H₂O anyway?


texts:
I took the pictures today in Cusco Peru. It is the third insect of its class in a month. I never see it before. I thought that it is a wasp, but I think it's really thin to be a wasp. It's about 4 or 5cm.

I want to know what kind of insect is and if it's dangerous. Thanks!


texts: How do near sightedness, farsightedness, and normal sightedness work? If the eye is accustomed to one small focal point, how can it manage a wall of light? And also, how does it process the small pinpoint that it normally does?


texts: Effect of angle of light on flowering of plants

texts:
I understand that the angle of light changes the direction of growth in plants (phototropism), but would the angle of light have any effect as such on the flowering of plants?

Thank you!


texts: I was wondering, why V. Cholera synthesize toxins which induce in humans diarrhea? I know that diarrhea is protective mechanism for humans, to get rid of bacteria. But why V. Cholera just stop producing it? What is its function in bacteria? In which bacterial metabolism it is involved?


texts: quantification of glucose utilization in different metabolic processes

texts:
Glucose is commonly associated with ATP production. However, only a small fraction of glucose is utilized this way.

The intermediates of glycolysis, TCA cycle, etc. are precursors to various anabolic pathways and are ultimately involved in amino acid synthesis, nucleotide synthesis, fatty acid synthesis, etc.

Has glucose utilization in different pathways been quantified? What approximate percentage of glucose is used in different pathways?

Certainly, the numbers could vary between organisms, different cell types, cell microenvironment, etc. It helps to have an intuition of how much glucose is used where.


texts: Why swordfish aren't put in the same family as Marlins?

texts:
Why Swordfish (Xiphias gladius), which are very similar to Marlins, do not belong to the same family as Marlin - Istiophoridae?

Both has long bill or a sword in the upper jaw, both has (at least in some stage of life) a long sail along the back, both are predators and fast swimmers and both are of similar overall shape and size.

Moreover, as cladistics is prevailing over Linnean taxonomy, the ranks of family or superfamily are not essentially different, can we say that swordfish and marlins belong to the same clade which includes the two families Xiphiidae and Istiophoridae?


texts: In myosin II are regulatory and essential light chains calcium binding proteins or sites of phosphorylation?

texts:
According to my medical physiology by Rhodes and Bell their description is as follows:

  the essential light chain is necessary for myosin stability, and the other chain called the regulatory light chain is phosphorylated during muscle activity and serves to modulate muscle function*

However, according to molecular biology 4th edition:

it states that the light chains both exert their function via Calcium binding, they make no mention of phosphorylation.

So do light chains regulate myosin by calcium binding, phosphorylation or both ?


texts: How does the hypothalamus get the information out of the blood?

texts: The hypothalamus is a very important nervecentre which checks continuously how many hormones neurotransmittors and other molecules and information (like temperature) are there present, so it can keep a kind of balance in our body. But how does the hypothalamus do this? Does he has so much different receptors on his membrane for each type of molecule one or does it do that in a different way?


texts: Did not understand a small excerpt from a research paper

texts:
Was going through this paper, among multiple things that i did not understand, I came across this part:

  Each amino acid residue of a single
  window was encoded into a unitary bit string of length 20, where a
  bit was set (value = 1) if its position in the string corresponds to the position of the amino acid residue and zero otherwise

Did not understand this line. Someone please explain what position they are talking about


texts: Which organism has the sharpest vision in terms of distance and spectrum. Please propose any other useful measure.


texts: About The Selfish Gene Book - How Replicators Molecules forms duplicates?

texts:
I was reading The Selfish Gene. In the 2nd chapter - "Replicators" I read:

  Think of the replicator as a mold or template. Imagine it as a large molecule consisting of a complex chain of various sorts of building block molecules.

  The small building blocks were abundantly available in the soup
  surrounding the replicator. Now suppose that each building block has
  an affinity for its own kind. Then whenever a building block from out
  in the soup lands up next to a part of the replicator for which it has
  an affinity, it will tend to stick there. The building blocks that
  attach themselves in this way will be automatically arranged in a
  sequence that mimics that of the replicator itself.  It is easy then to
  think of them joining up to stable chain just as in the
  formation of the original replicator. This process could continue as a
  progressive stacking up, layer upon layer.

  This is how crystals are formed. On the other hand, the two chains
  might split apart, in which case we have two replicators, each of
  which can go on to make further copies.

I don't get the part in bold.

If these molecules joins the replicator then the replicator wouldn't change?
To what refers with "The building blocks that attach themselves in this way will be automatically arranged in a sequence mimics that of the replicator itself"? A new sequence? The same sequence?
In the part "It is easy then to think of them joining up to stable chain just as in the formation of the original replicator", what is it joined? replicator with this building block? these building blocks with other building blocks in the soup to form a copy of replicator?
Why you can infer that is how the crystals are formed?

Take into account that I don't have a solid biology background, so it would be great if you can answer it in detail. I really appreciate your help!.


texts: Sequencing a specific region of a genome

texts:
First off, I'm new to bioinformatics and I am learning about DNA sequencing.

Let's say that I knew that a specific region of a genome which contained information about a disease (whether it a person had the disease or not).

It would make sense that we would only want to sequence that part of the genome in order to make a detector for this disease.

Would it be possible to 'cut-out' this region of the genome and only sequence that part (so we don't have to sequence the entire thing)? If not, how would we sequence only this part of the genome (it doesn't make sense to sequence the other parts as they don't give us information).

Thanks in advance.


texts: What factors should I consider when selecting a reference genome for mapping?

texts: I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular reason not to go with the most recent reference genome when aligning short reads from RNAseq?


texts:
I was reading about earthworms and came to know that they have 4 hearts.

Why is there a need for a 4 heart system? What advantages would it have over a 1 heart circulatory system except for pumping more blood obviously.


texts: How does MEME compute the background frequency of nucleotides?

texts:
I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested.

I would like to know how MEME estimates the background frequency of nucleotides, as it does the conversion from position-specific probability matrices to log-odds matrices when you choose to run MAST on MEME output.  Is it simply counting frequencies in the sequences supplied, or is there some sort of modeling going on to correct for sample size and whatnot?

EDIT: Another possibility that occurred to me is that MAST is capable of converting position-specific matrices to log-odds matrices.  I'd appreciate it if someone could clarify this point for me (and I'm still interested in how the background frequencies are calculated).  Also, I am specifically looking for answers with links to supporting documentation.

EDIT 2 (05/07/13): Alexander has answered the original question.  Does anyone have an answer to the first edit (re: MAST)?

EDIT 3: MAST doesn't like PSPMs; it will accept the job but crash.


texts: Why is chronic lymphocytic leukemia (CLL) most common leukemia in the West but so rare in Asia?

texts:
In "Advances in Chronic Lymphocytic Leukemia" (2013, Edited by Sami Malek), several times it is stated that CLL is very common in Western countries.

However, it is quite rare in Asia. (I do not have data regarding other regions in the world.)

Why would this be? I am familiar with cancers being related to lifestyle, which varies by country. (The obvious example would be how countries with high rates of smoking have higher rates of lung cancer.)

Do we have any reasons why this is? Thanks for any help.


texts: Is hydrochloric acid suitable for pickling food?

texts: I was wondering whether it is possible to pickle food using hydrochloric acid (HCl), rather than acetic acid. I am not very familiar with the biology of the fermentation process involved in pickling and I do not know if HCl would give rise to a suitable environment. Is HCl-based pickling possible? What percentage of HCl should be used?


texts: Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome?

texts:
Case: I am writing a summary for a class in protein structure and function, and was asked to describe some different ways that peptides are synthesized (that does not involve the ribosome). I understand that glutathione is a tri-peptide consisting of L-cystine with a "gamma" bond to L-glycine which is then bound to glutamic acid.

Problem: Why is it that the ribosome cannot produce this peptide? What is special about the peptide-gamma-bond?

My reasoning: The peptide is too short, meaning that the large ribosome complex cannot bind to mRNA of this length as it need many different binding spots in order for the large and small subunit to come together. Also, the "gamma" bond is very special, and the ribosome can only produce peptides with the "Standard" peptide bonds.

Is this correct, and is there something else I am missing?
Does the "gamma" bond relate to the fact the glutathione is not that easily degraded by peptidases in the cytosol?


texts: Non-radioactive nucleotide labeling compatible with reverse transcriptase?

texts: Are there any methods for nucleotide labeling which are compatible with use for reverse-transcription, besides radiolabeling, and for which the regulatory framework in the EU / USA are permissive ? Regulatory obligations around radionucleides being too strict.


texts: What happens when we re-start a PCR reaction?

texts: Recently when my PCR reaction was running there was power fluctuation and the entire lab was blacked out for a few minutes and unfortunately PCR that I was running got switched off. So, would it be okay to restart the PCR? What would happen if the same PCR program was run again?


texts:
The hills around Santa Fe are covered in a particular xeric tree which is quite small and looks like some kind of juniper which I have been unable to identify:

What is this species?


texts: Can dissolved aluminium from centrifuge tank deactivate enzymes?

texts: I extract an enzyme called diamine oxidase with a tubular centrifuge. The centrifuge uses an aluminium tank to collect the liquide after centrifugation. I asked myself what would happen if some aluminium particles pell of from the tank due to the collision of liquid and got into the solution. Could this deactivate the enzyme?


texts: Question about Autosomal Recessive Alleles

texts:
I had a homework question that I could not figure out.

It states:

  A woman has cystic fibrosis in her family and did not want to have a
  child that suffered from the disease. She and her spouse went for
  genetic testing and counselling. She tested positive as a carrier and
  her spouse tested negative, and their first child was born with cystic
  fibrosis. Explain how this could happen.

This doesn't make sense because the punnet square would be:

$$
\begin{array}{c|c|c}
  & A  & A  \\
\hline
A & AA & AA \\
\hline
a & Aa & Aa
\end{array}
$$

This says there are no two recessive alleles which can cause  cystic fibrosis.


texts: Why is funnel web spider venom so lethal to humans and not so much for other mammals?

texts:
According to the information from this article,

  People and other primates are exquisitely sensitive to funnel web venom but, intriguingly, other mammals such as mice, rabbits, guineapigs, dogs and cats are relatively immune and often survive 100 times the human lethal dosage.

Why is the funnel web spider venom so much more lethal for humans and primates than other mammals?


texts:
Can anyone explain me if there is a difference in amplitude of signals between extracellular recording and intracellular recording. I know that the amplitude of neural signals when an action potential occurs is from -70mV to 45mV for intracellular recording. The same results are for extracellular recording?Can someone help me?

Also, I have read a paper that refers:

  Neural signals from extracellular recording are very weak (typically between 10 μV and 500 μV). As a result, amplification is needed before such signals can be processed further."

So my question is why neural signals are so weak (maybe author when he says 10μV refers to amplitude) when we know that an action potential has amplitude approximately 75mV(-70mV to 45mV)?


texts:
Can phylocode classify viruses? Based on what I found this system began in 2019, so there is not much information about it.
I know that the Linnaean classification system cannot classify viruses, but what about this new classification system (phylocode)?


texts: Why and how do red bone marrow concentrations in humans change during traditional aging?

texts: I have found several pictures that suggest this is the case.  As for peer reviewed papers I've found plenty of papers hypothesizing and testing as to the why of changes in populations of HSCs, a few on quantitative changes in MSCs, but none explaining why red bone marrow would become less active hematopoietically in long bones before flat bones.


texts: What is the average volume of the hippocampus?

texts:
I'm trying to find any information on sizes of the hippocampus?
Ideally in the average adult male & female brain


texts: Is the amount of dNTPs rate limiting for very long PCR products?

texts:
I'm using the Q5 system and I'm PCRing a product that will have a final length of around 9500 bases. I have noticed that the product is there but very faint. The primer seems to be used up.

So my question is, can the dNTPs be rate limiting in a long reaction? That is, can all the dNTPs be used up in the first PCR cycles and maybe not be available for the later exponential rounds?

It seems you have about 1000 times the amount of dNTPs to the amount of primer (200 µM compared to 0.2 µM). So maybe...or is my basic chemistry off. Any precedence?


texts: Why largest cats so much larger than canids?

texts: It is striking to me that there is no dog-like creature larger than a wolf while there are at least two species, tigers and lions, many (at least twice and probably 3 or 4) times the size of the largest wolves. I would guess it has something to do with hunting style, packs vs individual hunters although lions do sometimes attack in groups. I am not saying I would like one to exist, but why is there nothing like a 400-500 pound wolf?


texts: How much mechanical stress can a skeletal muscle bear?

texts:
In the movie- Saw, for the last trap Bobby was told to insert metallic hooks into his pectoralis major muscle. In his fake story Bobby has raised himself successfully, but when he was "really" trapped, his muscles were broken under his own weight.

Is it true, that muscles can be broken so easy? When human is pulling up on the bar, aren't these muscles undergo much more tension, because of lever effect made by his arms?

Also, what if Bobby insert hooks under his ribs, would he die immediately due to pneumothorax?

The question is biological, no interest of how it was possible to overcome trap with mechanical means.


texts:
$R_0$ is the average number of secondary cases arising from a single infectious individual in a fully susceptible population.

In many of the compartmental models for epidemiology, the parameter $\frac{1}{R_0}$ appears frequently.

In particular, in an SIS model, the non-trivial steady state is $(S^*, I^*) = \left(\frac{1}{R_0}, 1 - \frac{1}{R_0} \right)$.

  Is there any intuitive interpretation one can give to the reproductive ratio's reciprocal?

I'm thinking some sort of average rate of secondary cases, but this doesn't feel right since $S^*$ is a number.


texts: How do pBAD and T7 promoter strengths compare when pBAD is induced under conditions which would lead to its highest strength? Are there any papers that compare the two inducible promoter systems?


texts: Why do the major and minor groove exist in DNA?

texts:
So I know that the major/minor groove arise from the offset pairing of the two strands in the helix.  All my textbook tells me is that "pitch causes the off-set pairing of DNA and this gives rise to the major and minor grooves."

I'm not too sure what this is saying.  What exactly is pitch and how does it give rise to the grooves?


texts: Need some good resources to learn about Protein function and structure

texts:
I'm taking a course on biochemistry at edx.
Since I'm a computer science student, I'm having some trouble in understanding many biochemical concepts. While the first module was just fine, I found the second module really hard to understand. I have problems to learn and understand about amino acids and proteins, so I would like to study apart from some good resources.

Which is a good resource to learn about amino acids and macromolecules?
Also, please let me know if this book is up to date?


texts: What are good sources of free-to-use images and diagrams

texts:
I am looking for good image repositories for biology teaching. Photos and textbook-like diagrams.

I am interested  in images that can be used commercially without payment, or, at least, that require a small one-time payment. They would be used in videos, not only on lectures, hence the worry about copyright.


texts:
This is a question I posted on Cross Validated few weeks ago but no response has been given so far.

I am looking for a book that would cover a lot of different ordinations techniques (indirect gradient analysis e.g. PCA, CA, DCA, MDS, nMDS but also direct gradient analysis e.g. CCA, CCorA, RDA) with applications in ecology (with R would be better) and mostly focusing on these methods.

I think " Numerical Ecology " by Legendre & Legendre (https://www.elsevier.com/books/numerical-ecology/legendre/978-0-444-53868-0#) would be relevant but it seems to cover a very extensive number of topics. Any other idea ?


texts: How is the blood volume of a living organism measured without killing it?

texts:
How is the blood-volume of an organism measured without killing it?

Note:The blood-volume of an organism is defined as the total volume of blood present inside that organism.


texts:
I understand that puberty begins when hormones are released from the pituitary gland as instructed by the hypothalamus, but why does the hypothalamus instruct this to occur?

How is this process timed by the body?


texts: Identify a large wasp (?) from southern Poland

texts:
This insect has appeared "out of nowhere" in one of my rooms. Can you help me identify it?

Details:

location: Katowice, Upper Silesia, southern Poland, eastern Europe (46.42 N, 17.78 E),
date: April 3rd, 2021 (early Spring, approx. 3:10 pm).

At first I was more than sure that this is large male bee / wasp / Apidae family member. But I was surprised to see absolutely no signs of yellow or orange strips, only gray ones, if I am not mistaken.
The windows were closed tightly at the moment of its appearance and were not open too many times in the days before, as we still have kind of cold early Spring here, in Poland right now. Though I must admit that we had a very warm previous weekend (March 27th/28th) with temperatures of up to 19°C / 66°F. But, I am still unsure, if it appeared just "these days", or if it was able (in some magical way) to survive somewhere behind wardrobe since past Autumn (very not likely?).
It was very weak at the moment of finding it. It was certainly unable to fly though its wings seemed OK. It was looking like it had at least one leg broken. He was moving very slowly and attaching itself to any surface it found (piece of paper, ruler etc.). I moved it gently to my balcony / piece of grass and let the nature do the rest.


texts: I understand that apoptosis and necroptosis share the same upper part of the pathway, but I cannot seem to distinguish when is each one activated? From my readings, it seems that when procaspases 8 or 10 are unavailable, the cell will shift to necroptosis. What makes these procaspases unavailable and why does a cell second the necropotosis?


texts: I don't know the name of the plant. It's a common house plant in Bangladesh. What interests me about its flower is the colorful leaflike structure that probably functions as a petal. What is this structure homologous to? Petal, sepal, bract or leaf?


texts: Why do chickens not try to get up if laid on their backs?

texts:
I've seen a few videos about chickens being laid on their backs for a few seconds after which the chickens stay in that position until they are turned over. Comments around the video suggested that lying on their backs is a very unnatural position for most birds and so they don't have any reflexes or instincts that would help them get back up. But this is only speculation. Why is that really happening?

Here's one video demonstrating the effect:
https://youtu.be/R9mzz9jxNsM

I've been told Chicken hypnotism is related to this.


texts: Function of heparin and dextran sulfate for removing proteins

texts:
From this article :

  The reaction was terminated and the histones, and most nonhistones,
  were removed by adding the nuclease-treated chromosomes to a solution
  containing dextran sulfate (2 mg/ml) (Pharmacia), heparin (0.2 mg/ml)
  (Sigma), 10 mM Tris (pH 9.0), 10 mM EDTA, 0.1% Nonidet P40, and 1 mM
  phenylmethylsulfonyl fluoride (PMSF) at a ratio of 1 volume of
  chromosomes to 3 volumes of solution.

What is the function of  dextran sulfate and heparin in removing the proteins ?


texts: Cockroach-like insect identification (India)

texts:
I just saw an insect in my room, and I have never seen anything like it ever before. I captured a photo, please see if you can identify it. It has got quite unique colours on its exodermis and it has 2 pairs of wings ( I was not able to get a picture of them) which are very similar in structure and position to those of a cockroach. In addition to that, it is able to fly, albeit for short distances.

I live in Kolkata, India and the length of the insect is approx. 6-8 cm.