texts: How many generations between the first lifeform and humans are there?

texts:
I expect very large error bars, but what's the number of generations between the very first lifeform (that can be described as evolving in generations) and humans? Is it closer to a quadrillion or a trillion?

A related answer estimates that there were around 300,000 generations between us and the chimp/human common ancestor.


texts: How many nucleotides are there in the LMO1?

texts: Dr Maris at CHOP has linked the cause of high-risk neuroblastoma to a common SNP in  LMO1. How many nucleotides are there in the LMO1 gene?


texts: How do heredity and regression to the mean work with respect to intelligence?

texts:
I am trying to understand the heredity of intelligence between generations in general, and how regression to the mean works in detail in particular. The answer I'm looking for should preferably answer some of the following questions.

When looking at the genetic basis for intelligence, it seems to me that the additive contribution of the genes should not be subject to regression to the mean, and that regression to the mean should rather be due to recessive genes and emergenesis. Is this correct? If so, what do we know about the extents to which these two mechanisms contribute to intelligence?

Towards which mean will a specific child be expected to regress? I have seen various suggestions here, ranging from the mean of the racial groups of the parents, to that of the child's grandparents.

Is it even possible to write down an (approximate) equation for the expected intelligence of a child, in terms of for instance the intelligence of parents, siblings and gransparents?

If someone coould answer these questions, that would be awesome!


texts:
We are regularly doing bacterial transformation and subculture from plate to liquid media to extract DNA. This usually goes very well and is straightforward, but occasionally, the colonies that grew well on a plate, will not grow in liquid culture (with the same antibiotics that were in the plate). This has happened now to three persons on multiple plasmids.

For example, I was trying to ligate an ampicillin resistance gene (with its promoter) inside pENTR4 plasmid (already with Kanamycin resistance). My plate and LB both contained the two antibiotics, but the colonies only manage to get slightly turbid at a 16h timepoint.

Phage contamination is very unlikely, and the effect cannot be due to a toxicity of the inserted fragment, as both insert and vector have been grown in these same bacteria multiple times without problem.

Help?

EDIT1 - We use Carbenicillin in place of ampicillin in the plate, but not in the liquid media.

EDIT2 - After managing to grow some colonies in liquid, I managed to get a small amount of the plasmid (profile was good; concentration = 70ng/ul). The weird thing is that when I retransformed this DNA in Stbl3 bacteria, I had absolutely no trouble. Do you think the bacteria stock could be responsible?


texts: Explain a gene network to a first year undergrad

texts:
I have an adjacency matrix with list of genes connected to each other which signifies the gene network. How do you get this information that one gene is connected to other in the first place. Is it that you do a microarray analysis and find genes that are upregulated and downregulated and assume that all the genes that are upregulated, regulate each other. Kindly explain.

P.S The microarray example is what I assumed. Doesn't mean that it should be the way that a gene network is deduced. My network is an undirected one.


texts: identification of purposeful (engineered) genetic changes vs. random mutations

texts:
Okay, first - I'm not a proponent of intelligent design. I do not think it's a valid scientific theory (it has no mechanism of change/design). Second, I could be wildly off on what I think I know, in which case, my apologies for the question.

My question is, I know that scientists manipulate the genes of organisms (both animals and crops we use as food). I think this could be considered legitimate intelligent design (right? I'm talking as opposed to looking at an organism and saying that this couldn't have evolved naturally, therefore it was intelligently designed).

So, mankind has modified organisms - outside of knowing we did this, can we tell they were intelligently created? If so, how? Can we tell when a genome has been altered?

Also, if I'm totally off base, please correct me.


texts:
I am a student and I'm currently using the IB biology Oxford textbook. A few weeks ago I had a test on biochemistry. I studied on my textbook and it stated the following: "Mitochondrion: (…) fat is digested here if it is being used as an energy resource in the cell" (page 22) "The energy store from them (Triglycerides) can be released by aerobic cell respiration" (page 78). My teacher told me that I was wrong to write these statements in my test. Is there something wrong? Is the term 'fat' too generic? Do different kinds of fats undergo either aerobic or anaerobic respiration? I am currently confused as I do not know who is right and who is wrong… Can someone answer my questions?

Thank you


texts: Why don't macaws get selenium poisoning from brazil nuts

texts:
Google research has indicated macaws love or eat a lot of Brazil nut. These are highly toxic to humans in somewhat small quantities due to their selenium content.

Given the mass difference between a human and macaw, lets say 80kg and 2kg, if toxicity for humans 'starts' around 900micrograms or ~9 nuts, maths would indicate toxicity for a macaw might be around 20% of a nut?

These figures are all based on google and the margin of error I expect is quite large, nonetheless it seems quite disparate if a macaw could consume even a single nut a day on average, without consequence?


texts:
Is this a bee at all, is it just an albino Apis mellifera?

It is roughly the same size as regular honey bees, and was pollinating lavenders along with many of the latter. There was a couple of these white ones.

Here is a photo I took. Sorry for the bad quality.

The bees were seen (and the photo taken) on December 11 (late Spring), at about 1 pm in the eastern border of Santiago, Chile (South America), at the foothills of the Andes, at about 950$\,$m of altitude.

I'm aware that it is possible that the information I provide is not enough to identify the insect. If so, any advise on how to get more meaningful information will be appreciated.

Thanks in advance


texts: Why Hfr cells are called high frequency recombination cells?

texts: I understand that Hfr cells are formed when fragment of bacterial plasmid integrates itself in another bacteria's (host) genome through homologous recombination but my question is why do we call these cells as "high frequency recombination cells". Where is the term high frequency coming from?


texts:
I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant amount of interactors have only "Database" confirmation (mostly relaying on Reactome and KEGG data). Searching in these db's gives me neither article nor even the presence of these proteins in one pathway (what's weird). How can I obtain the data?
Thanks in advance!


texts: How do animals/plants change for each season?

texts:
The question pretty much sums it up. How do animals/plants change for each: Spring, Summer, Autumn, and Winter?

A detailed explanation on distinct behaviour and appearance changes would be nice.


texts:
I found that inducible enzymes can be regulated by many ways, but
I cannot find how constitutive enzymes are regulated...


texts: I know bees make honey from nectar, and I know they drink the juice of fallen fruit, but do they actually make honey from fruit, or do they only eat from it for themselves?


texts: How is it possible for a new species to evolve?

texts: Suppose a new species is created from a random mutation that happened during an instance of reproduction in an existing species. How can that new species survive and flourish if there only exists one of it's kind and therefore it's not able to reproduce? By definition a species can only reproduce with others of the same species, no? It seems to me the only way it could is if a mate is created due to a separate occurance of a similar mutation, and the chances of both mutations occurring at around the same point in timespace must be very close to zero. And even if it were to happen, it seems to me the offspring wouldn't be able to reproduce due to problems with inbreeding.


texts:
I found this insect today in front of my room.

I am just curious to know what kind of insect it is? And, is it poisonous?

Location: India


texts:
The male satin bowerbird builds a stick structure, known as a bower (distinct from a nest), where courtship and mating take place.  They curiously decorate their bowers using blue or shiny objects.

(Image source: Wikimedia commons.)

  When courting, the male satin bowerbird prances and struts around his bower. He offers the female items from his collection of blue objects, while making a series of hissing, chattering and scolding noises. Mating takes place in the avenue of the bower, and the male may mate with several females in a single season.  -- NSW Government Office Of Environment and Heritage

Question: Is the male satin bowerbird's bower-building behavior innate?

This is essentially a "nature vs. nurture" question.  E.g. If there were no other males around for him to learn it from, would he still build a bower?  If so, where did he get the idea from?  If there were no females around, would he still bother to build it?


texts: Photoreceptors and light with mixed frequencies

texts:
I am interested in how the activation of a, say, blue cone depends on the incident light. Wikipedia tells me this:

 ,
which describes how strong the activation of the blue cone is for light with a single wavelength and a given intensity. But what happens if the incident light has several frequencies?

My question is: given the intensity i(f) of the incident light at frequency f, what is the activation of the blue cone?

(A natural guess would be that if b(f) is the activation curve in the figure, then the activation of the blue cone should be the integral of b(f)*i(f) over f. But I have not found any confirmation of this guess. For example, in the reference for the picture above, only pure light was used in the experiments.)


texts: Humans, animals and birds all have two eyes. Why? In addition to why two instead of one, why aren't there more than two?


texts: Are left-handed people more likely to be colorblind?

texts:
My friend, uncle, and I are left handed and also suffer from Protan colorblindness. Is it more likely for left-handed people to be colorblind?

Disclaimer: I was originally Right handed and due to a physical handicap I developed left-handedness.

EDIT: We also suffer from either ADD or ADHD.


texts: Where are examples of Interspersed repeats?

texts:
Interspersed repeats are often defined as repetitive sequences dispersed throughout the genome.

However such definition (IMO) does not exclude Tandem Repeat Sequences.

So I started to search for examples of such sequences.

After checking many Bioinformatics and Genetics books, I found many examples of Microsatellites and Minisatellites. However, I couldn't find any examples of Interspersed Repetitive DNA out there, in any of its variants (LINEs: L1, L2, L3, SINEs, etc.).

So my conclusion is Interspersed Repeats DNA Sequence looks like any other type of repeat (such as STRs or Minisatellites), the only real difference is they are flanked by Open Reading Frames (ORFs 1 and 2 for LINEs) or specific tandem duplications (like GC for SINEs)

Do anyone have one or two examples of concrete Interspersed Repeat DNA Sequences?


texts: How are Raunkiær's plant life forms viewed today?

texts:
At the beginning of the 20th century, Raunkiær proposed a typology of plant life-forms based on where they bear their buds, roughly as:

cryptophytes: belowground

hemicryptophytes: at the surface

chamaephytes: close to the surface

phanerophytes: projected above the surface

Are these still held to be useful / biologically meaningful categories? Is there a different typology preferred (eg. tree/shrub/subshrub)? Or are people moving toward gradients of quantified traits instead of typologies (eg. measuring plant height, specific leaf area, etc.)?


texts: What's the difference between the *types* of tissue dissociation enzymes?

texts:
I'm trying to dissociate a tumor, and most protocols like NCI/NIH recommend a 10X triple enzyme digestion stock consisting of: collagenase type IV, DNase I type IV and hyaluronidase type V in HBSS. This goes all the way back to the 90s, and the recipe varies between papers (dispase, papain, neutral protease, elastases, etc.). The so-called official recipe that I've been tasked to use is composed of the above, however, mostly from Sigma-Aldrich (C5138, D5025, H6254)

I can't really find anything that says what the real differences are between these types of enzyme are, however. Or why for example type IV DNase works better than type II, and so forth. Is it perhaps that the recipe just happened to stick?


texts: Can a heterozygous allele show non-heterozygous expression in a family?

texts:
I'm doing a family study looking for novel cancer-associated variants in germ-line samples; the goal is to find candidate biomarkers which might be used for early detection. At an earlier step our analysis, we eliminated a family that showed a heterozygous mutation known to be associated with our cancer under the premise that this known mutation better explained the presence of the disease than any novel variant we may have found.

I've now found another mutation, strongly associated with out cancer, which we does not appear to be heterozygous. 2 out of 3 family members share this mutation with a within-family allele frequency of 0.5.

Trying to decide whether this means I need to discard this family from further consideration, adjust my thinking, or not worry about it. My current thinking is that it'd be safest to eliminate the family from consideration because the mutation pathogenic and found in the germline but I can't wrap my head around how the lack of a heterozygous pattern affects things. Does it absolutely mean the variant was not inherited? Can anyone help me get my thoughts straight?


texts: Could an animal with an open circulatory system survive in a near-zero gravity environment?

texts: An animal such as a crayfish relies on gravity to keep its circulatory system running. If it is turned upside down, the gravity works against the system, suffocating the animal. Now if, instead of placing the animal on it's back, we were to take take it to a space station, gravity would not be working against it, and random blood flow plus capillary action should get some blood flowing. Would the animal survive this?


texts: What signal processors comprise an Event-Related Potential system for EEG?

texts:
So my 30,000 ft. understanding of the EEG signal processing data flow is:

Capture raw EEG data ("raw waveforms")
Run these raw waveforms through a Signal Processing Framework that consists of 1+ "nodes"/processors, where each processor is doing some kind of transform on the raw waveform. In doing so, new information is unlocked from the raw waveform that was previously hidden
Perform individual analyses on this unlocked data based on what suits your research/application

So first off, if the above understanding is misled in any way, please begin by correcting me!

Assuming I'm more or less correct, my specific application at hand is that I want to correlate certain raw waveforms with events (such as "thinking of a turtle", "moving head up and down", etc.). I believe Event-Related Potentials are what I'm looking for, but...

What I'm struggling with is: what does my "Signal Processing Network" need to look like in order to implement ERP? From an architectural perspective, I'm looking for this "network" to take raw waveforms in as input, and to output events, like the few I mentioned above.

Is FFT a player here? Some kinds of filters? What processors comprise an ERP system, and what does their respective "network" (data flow pipeline) look like?


texts: Distribution of fitness in wild populations

texts:
If I get out in the wild observe wild populations and measure the distribution of fitness $f(w)$ in a given population. What will I find out? Will I observe a Gaussian distribution, a Poisson distribution, an exponential distribution, ….?

It probably depends on the species under consideration, typically it may depend on whether there is an sexual selection in this species. I welcome any insights!


texts: Is there a resource to query gene expression similarity? Stratified by sex?

texts:
We developed such a resource. The editors of "Bioinformatics" (at OUP) rejected the paper on the grounds that we did not run a comparison with "state-of-the-art" [similar] resources. Can someone help me find similar resources?
Link to our own resource, ExFiles.


texts: Where does reverse transcriptase come from?

texts:
I can't figure out whether the viruses provide reverse transcriptase, or their RNA has the code for it, or the host cell normally contains it.
Multiple sources just introduce the enzyme without explaining who provides it / where it comes from. Apparently, both the host cell and viruses have processes that are dependent on reverse transcriptase, so I guess the answer is all of above / case-dependent?


texts: How many mitotic divisions do haploid cells undergo before fertilization?

texts:
Background

This question is about human physiology and gametogenesis. A spermatozoid is not necessarily the direct "offspring" of a diploid cell. Stated differently, a spermatozoid cell can be the offspring cell of another haploid cell. I am saying "can be" and "is not necessarily", but the correct formulation might be "always is". A given spermatozoid might eventually be the descendent of 1000 generations of haploid cells before (going back in time) finding the diploid ancestor (the one who underwent meiosis II). I'd expect the same to be true for ovules although I'd expect that a given ovule have fewer haploid descendent before (going back in time) finding the diploid cell.

Question

How many haploid generations preceded a typical spermatozoid/ovule that could eventually fertilize an egg?
How does this answer vary with age and sex?

In its most beautiful form, the question is:

What is the distribution of the number of mitotic divisions that happened in the father/mother of a given individual?

Any answer that would offer a step toward answering these questions are welcome!


texts: flavivirus virus genome, methylated guanine

texts:
I'm looking at the sequence of a flavivirus virus genome (mRNA). Kindly see the link MH900227.1. How can I identify the Guanine nucleotide that is methylated in the capping process?

Thanks,


texts: Can 'hardware' thermalization explain memory decay?

texts:
Often we are able to memorize very precise bits of information (exact addresses, birthdays of inlaws, number of dirty socks under the bed), but over time our recollection tends to become fuzzy. We no longer recall the day and month a certain president was killed, only the year, or maybe the decade (despite being straight A students in junior high). Like the smoothing out of a delta function under the heat equation, instead of a pin-sharp value we're left with a range of values where the correct one is likely situated. However, most of the time we are perfectly satisfied with such approximate information and can work with them just fine (except in some extreme cases of function impairment, such as Alzheimer's or the aftermath of binge drinking).

Discrete data must be stored in low entropy structures in the brain that over time spontaneously shift to a higher entropy state. Meanwhile, our biology tries incessantly to slow down the decay by expending energy (with the frequently utilized neural pathways being better maintained than the abandoned ones). Even processes analogous to error correction take place, e.g. when we arrive at a certain lost piece of information by lateral thinking and piecing together available data.

My question is whether the fading of memory exactitude can be explained in terms of the thermalization of the digital-like structures where discrete information is stored, and if anyone can point me to studies in this direction.


texts: Are some animals, like dogs and cats, color-blind and how do we know that?

texts: I have heard that some animals, including dogs, cats and donkeys, are color-blind. They cannot recognize any color. Is that true? And how can humans verify that animals are color-blind, or not? During evolution, has color-blindness not bothered them at all?


texts: What allows for no selection pressure against non-coding DNA?

texts:
Genomes of prokaryotes tend to have a higher proportion of coding DNA to non-coding DNA in their sequence than eukaryotes.
This means that either eukaryotes accumulated lots of non-coding DNA, much of which is regulatory, in the course of evolution — or that prokaryotes lost this proportion of non-coding DNA.

In order for transcription of a particular gene to occur, it seems that there must be some search performed on the DNA sequence to find the gene to be transcribed.
This search seems to be independent of the sequence length — if it weren't, that could act as a selection pressure, inducing loss of DNA that doesn't do anything. Therefore, it seems that the method by which this search is done must be O(1) — that is, it takes a constant amount of time to complete the search, regardless of the length of the sequence.
Such a method would be most welcome in computational sequence searches (in place of BLAST for example).

My question is, what, if anything, is currently known about the process of transcription that could explain this constant search time?
Or, if I am completely wrong in my assumptions, what are more reasonable assumptions?


texts: How do I view the simulated protein structure along with ligand in VMD?

texts: I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot see the ligand. How do I select the heteroatom in the graphical representation window? My complex has 1129 + 50(ligand atoms) but while loading it just shows the protein molecule(1129).


texts:
I wrote the following phrase in my scientific text:

X is ubiquitous in life of Y. On some occasions X might be detrimental, resulting, for example, in so so phenomena. But is it plausible that a function that takes 50% of organism resources would have only negative effects? The answer is likely "no" because such a function would have likely not survived the evolution.

But I was suggested that there a bug in my logic because if an adaptation is neutral and has no effect on reproductive fitness, it can be preserved. Would you agree with this critique? If so, how should I rephrase so that it become more correct?

Many thanks


texts: What is the mass of a pigeon tail feather?

texts:
There is question at Space.SE If I drop a feather from orbit, would it burn up or “hit” the ground? there is an attempt to answer the question, but the mass of pigeon tail feather and possibly the drag coefficient is required to complete the answer.

I have looked around on the web and if there is an answer it is not jumping out at me.

What is the mass & drag coefficient of a pigeon tail feather?


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


texts: Is the variance of a trait related to its rate of evolution?

texts:
Posed with a question that has me stuck:

  Is increased variance of a phenotypic trait in a population associated with slower evolution of that trait?

I have to either 'disagree or agree' and argue my point. And I disagree. For this question, I think that if the variance of phenotypic trait has a genetic basis (additive genetic variance =/= 0) then increased additive genetic variance should speed up it's evolution. The greater the additive genetic variance, the greater the response to selection in the next generation. So increased additive genetic variance should increase the rate of evolution of that trait.

However, at the same time, if there is variation in a phenotypic trait but it does not have a genetic basis (narrow sense heritability is zero) and the basis for variation is due to an environmental, dominance, or interactive effect, then increased variation would have no effect in the rate of evolution. Or so I think. I'm not too sure how the rate of evolution would be affected in the case of a non-genetic basis of variation.


texts: DNA polymerases have proof-reading ability, but RNA polymerase does not. Does the use of RNA as a primer affect the accuracy of DNA replication in E.coli? Explain


texts: where can I find estimated costs of laboratory equipment?

texts:
Often when I am curious about purchasing new laboratory equipment I cannot find a ballpark figure for the price.  Companies that sell expensive lab equipment prefer if you contact their customer service or sales teams to inquire about prices.  I don't want to go through all of that hassle, as well as exposing myself to  potential marketing emails.  Is there any website that lists ballpark figures for lab equipment?  The type of equipment I am talking about are things like PCR thermal cyclers, Flow cytometers, nucleofection devices, centrifuges, etc.

Thanks in advance.


texts: According to this news, scientists can use stem cells to print objects. So say theoretically, is there any possibility to print human beings?


texts: Why are there only two unique semi-independent organelles? Why are there no others, symbiogenesis seems like it should be a relatively common thing. So do most organelles just lose all their DNA? Or is it something that occurs fairly rarely?


texts:
I came across an article about flavodiiron proteins that are responsible for reducing ${\rm O}_2$ to ${\rm H}_2{\rm O}$ thereby protecting the anaerobic prokaryotes and some eukaryotes from oxidative stress. However, I am confused about the structure of that protein and its relation to heme proteins. Is this a heme protein?

The article I am reading is:

  Di Matteo et al., The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J Biol Chem. 2008 Feb 15;283(7):4061-8. Epub 2007 Dec 12.


texts: Extract protein sequences from a GBK(GenBank) file without scripting

texts:
How to extract protein sequences from a GBK(GenBank) file without scripting?
I know that writting a script using BioPerl or Biopython can do this, but it is not elegant and daunting to beginners and biology persons. Any thing like

$ SOME_PKG_MANAGER install PKG
$ CMD ab.1234.gbk > ab.1234.faa


texts: Staying underwater: would mutual rebreathing help?

texts:
If two people want to stay underwater for as long as possible, could they last longer if they exchange breaths in turns (ie: through a simple tube or mouth-to-mouth) than if they simply hold their breaths alone?

Would there be any dangers in doing this somewhat regularly?


texts: What kind of larve is this? Found in shed on terracotta pot in Northwest Oregon

texts: Found this on a terracotta pot in my shed


texts: Can restriction sites be used as PCR primers?

texts: I have a DNA fragment that contains the gene of interest sandwiched by restriction enzyme sites. Then, can PCR amplify the entire fragment, recognizing the restriction enzyme sites?


texts:
I read that Huntington's is a disorder caused by dynamic mutations in the DNA, which means that a triplet sequence of DNA changes from generation to generation. Say we have the sequence ATGATGATGATG. The child of this person with have ATTATGATGATG and the grandchild will have ATTATTATGATG etc.
This means that Huntington's will be worse (debut earlier) the longer the generation lasts.

My questions are: Is my understanding of dynamic mutation correct? Is there no MINIMUM age where Huntington's will debut? In other words, if a generation is very long and has Huntington's, can a baby have symptoms at birth?


texts: Are there verbs for "undergo mitosis" and "undergo meiosis"?

texts:
From my experience on SE sites, I believe this is the right site to ask this question under "terminology".

I've been trying to find out whether English has one-word verbs for "undergo mitosis" and "undergo meiosis". I haven't been able to find confirmation on Google, but my linguistic imagination is limited, and I may have failed to google the right things.

Could you tell me if there are such verbs in common use in biology? I mean, if such verbs exist, can I find them in modern biology books or papers?


texts: White resin or powder on conifer needles

texts: I often notice that certain conifers often have a whitish powder on what seems to be their youngest needles, giving them a blue green tint. Does anyone know what this is? Is it something excreted by the trees themselves, is it a yeast or some other endophytic microorganism? Very curious and unfortunately I don't have a microscope.


texts: How is RNA of retrovirus converted into cDNA?

texts:
The retrovirus (oncovirus) contains RNA. It also has a molecule called reverse transcriptase. This molecule transcribes RNA into cDNA. This cDNA is the DNA copy of viral RNA genome

RNA has Uracil instead of thymine and DNA has thymine instead of uracil. So, how can RNA be converted into DNA? Where does Uracil go and where does thymine come from?


texts: What is the upper limit of number of SNP based mutation in any protein?

texts: I want to know if there is any upper limit of, how many point mutation a protein can have because of disease or nsSNPs? The general studies only focus mostly on a single or double site mutation of any protein structure.


texts: If the xylem and phloem of the bamboo is not in the hollow center than where is it located/situated? cannot get clear cut answers from the above discussions


texts: Do fruit juices have a diuretic effect & what governs this?

texts:
Was just contemplating this.

Juices tend to contain a lot of sugar.

Does the body absorb all the sugar in juices?
If the body does not, that sugar must be excreted by the kidneys alongside water thereby causing a diuresis, right?

NB I realise even if there is a diuretic effect that is outweighed by the large proportion of water in juices. But my question is whether there still is a small diuretic effect


texts: Which Darwin book (and today edition) is illustrated by his own drawings?

texts: I am interested in buying Charles Darwin books and mostly drawings (nowadays editions, I am not a collector). Please, can you advise in which book and which edition I can find the most of his drawings? I found some books as On the Origin of Species ad the Geology of The Voyage of The Beagle but I am not sure if there are his drawings too. I am a student so I couldn't spend too much money on it, but I was interested in his texts and drawings, supporting each other in one book/journal/publication. Thank you !


texts: Meaning of "external demands" in a paper describing the gut-brain axis

texts:
From "Brain Gut Microbiome Interactions and Functional Bowel Disorders":

  In response to external and bodily demands, the brain modulates individual cells (ECC – enterochromaffin cells; SMC – smooth muscle cells; ICC – interstitial cells of Cajal) within this network via the branches of the autonomic nervous system (ANS) (sympathetic and parasympathetic/vagal efferents) and the hypothalamic pituitary adrenal (HPA) axis.

What is the meaning of "external demands"? What other possible demands can the brain strive to meet by modulating the activity of the neural network of the gut?


texts: Can cognitive functioning of the human brain change the physical state of the brain? E.g. does self-awareness, self-reflection change the number of neurons or synapses among neurons? I.e. I am trying to develop self-modifying neural networks as described in my other question https://ai.stackexchange.com/questions/7966/dynamic-self-improving-self-modifying-neural-networks-which-can-simulate-goede and I am interested in the biological process that can be analogues of self-modifying neural networks. What determines the physical structure of the brain - number of neurons and synapses and are the cognitive functions among the determinants? I guess that generally the brains can be less developed matter comparing to the artificial neural networks that humans can invent or that can self-evolve in silica after sufficient period of time and that is why human brain can be more restricted in its self-improving capabilities than in silica ANNetworks. Similar situation is with genetic algorithms which can allow unrestricted number of sexes while biology has at most two sexes.


texts: What's the smallest organism that can produce voice?

texts: What's the smallest organism (animal, insect, or any living creature) that can produce voice. And not just make sound, but has an organ to specifically to create sound, like how us mamals have vocal chords.


texts: Recycling and storage of nitrogen from breakdown of macromolecules?

texts: If nitrogen is so important (it's a constituent of both proteins and nucleic acids), why are animals still throwing them out, and needing to eat it again? Is it true that in almost a billion years of evolution, life still haven't found a way to recycle nitrogen inside the cells or inside the body of multi-cellular organisms? Why does this seem so hard to achieve? Or are there animals that don't need to excrete nitrogen compounds (like ammonia, urea and uric acid), and instead reuse them?


texts: Blood pressure in various blood vessels and heart

texts:
What are the typical systolic and diastolic blood pressure in arteries,capillaries, veins and the heart?

I know it must be highest in the arteries. arteries>capillaries>veins

Arteries: 120-80mmHg (systolic - diastolic). I also found mean values for capillaries (30mmHg) and veins (10mmHg) but not able to find systolic and diastolic pressure specifically.


texts:
I have been clearing brush by a lake in northwest Missouri and seen a lot of dragonflies. It's hard to get decent pictures because my phone camera sucks and they fly away before I get close. But here is one I managed to get:

I got one other picture of another species, but it's much lower quality.


texts:
I am having a bit of trouble interpreting flow charts given in my biology question sets.

Given the following stimulus

The Question is :

In which of the following options does each substance play two different roles in the series of events from plaque ruprture to MI?

ADP and collagen
Collagen and Fibrinogen
Antithrombin III and collagen
Fibrinogen and antithrombin III

The answer is:

"Fibrinogen binds to the glycoprotein (GO) IIb/IIIa leading to the cross-linking of platelets. It is also converted into fibrin which stabilises these cross-links and leads to aggregation. Antithrombin III inhibits the activation of the coagulation cascade and also inhibits the production of thrombin. The answer is D.

My issue is:

This answer doesn't make sense to me.

The fibrinogen square connects to the "Cross links-platelets via GPIIb/III receptor" square, which THEN connects to the "Platelet cross-links stablised" square (i.e. "Fibrinogen" doesn't directly connected to "Platelet cross-links stablised").

Why does this count as "two different roles" yet e.g. "Exposure of collagen" connecting to "platelets adhere to collagen" which connects to "Platelet activation release of TXA2 and ADP" not count as "two different roles".


texts: Are prosauropods ancestors of all sauropods?

texts: My daughter, while reading a book about dinosaurs, asked me if prosauropods are ancestors of all sauropods. Are they? From the name ("pro-sauropods"), I guess that they are, but am I right?


texts:
I come from Physics, not biology. My understanding is that without sufficient oxygen present, the Krebs cycle terminates in lactic acid formation for the body to later continue the reaction when oxygen becomes more available for oxidation.

If I understand correctly, for a period of time there will be an excess of Lactic acid in the body which will change the pH of the cell. How does that translate into the perception of pain?

I was taught in a Cognitive Science class that pain is cause my a neurotransmitter (Substance P) which is released due to bodily damage. This might not be entirely true, please correct this if wrong.

So my thinking is:

Lack of Oxygen => Lactic Acid production => ... (?) => Substance P => Pain

Thus possibilities for the "..." would be, bodily damage => Substance P, or Lactic Acid signals Substance P release without a need for bodily damage.

My question is then, how do I get from Lactic Acid to Pain?


texts: Can HBV pseudotyped oncolytic viruses be used to treat hepatocellular carcinoma?

texts:
Chronic hepatitis B is the leading cause of hepatocellular carcinoma (HCC). Oncolytic virotherapy (OV) is an emerging tool to treat cancer. However, one challenge of OV is that our immune system may produce neutralizing antibodies, which impaired its efficacy.

While on the other hand, antibody production against surface glycoprotein of HBV is inhibited in chronic hepatitis B. So can we use the HBV glycoprotein to pseudotype OV (e.g. VSV, measles, MLV), thereby circumvent the host humoral immunity? Can such viruses be used to treat HCC caused by chronic hepatitis B?


texts: Order of arrangement of tissue layers in dicot Stem and roots due to secondary growth

texts:
While studying about the Secondary Growth in Dicot Roots and stems I came to know that due to the secondary growth the peripheral layers i.e. the epidermis and primary cortex.. these two layers get gradually crushed and need to be replaced and cork cambium does that job by the formation of Periderm.
Now due to the secondary growth the order of tissues should be in these way (which I think)

From inner to outer

Primary Xylem
secondary Xylem
vascular cambium
secondary phloem
primary phloem
pericycle
Periderm
primary cortex
epidermis

Please let me know if I'm right.Thanks.


texts: Evolutionary motivation behind number of neurons in DCMMP

texts: I'm studying neuro-anatomy right now and I was surprised to learn that there are only three neurons along the Dorsal Column Medial Lemniscal Pathway (DMLP) which relays mechanical sensations from the limbs to the brain. Is this the same across all mammals? Is there an evolutionary motivation behind having exactly three neurons, instead of 4 or 2?


texts: What is this strange flower which I found on an upheaval in Rhodes (Greece) in July?

texts: It looks like it carries berries instead of blossoms. Is it actually a flower or rather a baby tree? I found it in a Google image search (see here: https://goo.gl/images/vfBDSP), but there was no description with the picture.


texts: Could tumor cells have normal genomic profiles?

texts:
I have thawed primary tumor cells and performed FACS. They were EpCAM positive cells. Then, I expanded them as organoids in 3D and did another FACS analysis. Again, they were EpCAM positive. I also sent organoids to pathology for IHC. Results showed they expressed EpCAM, EGFR, and panCK. But to my surprise, the Ampli LowPass sequencing results showed they had a balanced profile like normal cells. How could that be explained? Any help (comments, papers, ...) is appreciated.
Thank you.


texts: what is the exact definition of entdothelial cell fenestrae?

texts: In fact, I want to know that are fenestrae 1.holes which exist between cells or 2.they are holes in a cell( for example, a cell is like a paper we have punched it and the holes are called fenestrae). which one is true?


texts: Mutation-immunity in Luria-Delbruck experiment

texts:
If experiments like those of Luria and Delbruck on E. coli and T1 phage are the main source of our confidence in the mutation-immunity model, is it then highly unlikely that there are other types of bacteria for which an encounter with a phage is the mutagenic (or immunity-conferring) event?

Are the two possibilities in principle mutually exclusive?


texts: Why does high blood pressure not damage the body during exercise?

texts:
Exercise is commonly understood to lower blood pressure by making the heart stronger. Mayo Clinic says,

Regular physical activity makes your heart stronger. A stronger heart can pump more blood with less effort. If your heart can work less to pump, the force on your arteries decreases, lowering your blood pressure.

While exercising, though, systolic blood pressure will often go up significantly.
Why does this dramatic increase in blood pressure not damage the cardiovascular system? Stress, for example, can damage the blood vessels,

Increases in blood pressure related to stress can be dramatic. But when your stress goes away, your blood pressure returns to normal. However, even frequent, temporary spikes in blood pressure can damage your blood vessels, heart and kidneys in a way similar to long-term high blood pressure. (Mayo Clinic)

Does daily exercise, for example, not cause "frequent, temporary spikes in blood pressure"?
Why does a blood pressure increase from exercise not damage the cardiovascular system as a similar blood pressure increase from stress (or other sources)?


texts: How does MSMA kill crabgrass with only minimal damage to lawn grasses?

texts:
I use MSMA (Monosodium methyl arsenate) to kill crabgrass in lawns. I am not certain of the mode of action.

How does this chemical work? How does it target the annual grassy weeds, without damaging the lawns much?


texts: Why does post-transcriptional  processing of eukaryotic mRNA involve addition of a 3' polyA tail, rather than one of polyU, -G, or -C?


texts:
I have read somewhere that a butterfly might be two animals that combined together. One animal was a worm-like creature and the other an insect.

And the insect basically hatched inside the worm. Somehow they combined into one creature.

Is there any truth in this? Wouldn't this mean a catterpillar and a butterfly would have different DNA?

But in that case why would a butterfly lay eggs that turned into caterpillars?


texts:
I remember being told as a child that dogs stick their tongue out to stay cool, because they can't sweat like us. This made sense to me.

But only a couple of days ago I suddenly thought: What about all the other animals?! I mean, I don't see a cat or a horse putting their tongues out, and yet I don't see them sweating either. How do they lose heat? How do different kinds of animals lose heat?


texts: How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

texts:
GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions.

However it has been shown that in certain cases, GTP and water can mimic ATP (Niefind et al., 1999).

Are there examples where ATP has acted as a mimetic of GTP? Or in other words, are there any proteins that can't discriminate between GTP and ATP very well?


texts:
I cannot find a reliable way to kill fleas after removing them from my cats with a flea comb.  Soap and water does not do the job and they climb back out of the drain.
Will cooking oil  suffocate fleas?  If so how long of time until the flea expires?


texts: (Soft) Lay Survey of human natural history

texts:
I am looking for an introduction to the natural history of humans. I had originally thought Sapiens until I found out it is more a history and archeology book of dubious scientific accuracy. The Sorts of things I am interested in are: Neanderthal interbreeding, human canine bond, comparison of human with other primates.

If this is off topic, I am sorry. There was a similar question already posted some time ago, but the answers seems outdated.


texts: How did Shulgin take cognizance of the dosage of a new substance?

texts: We know that Alexander Shulgin synthesized MDMA, 2C compounds and several other tryptamine derivatives and phenethylamines. But how did he find out that the average dosage of an unknown compound is X mg? For instance, if I synthesized a new psychoactive compound, how could I find out the dosage?


texts: Do omnivore mammals vary food preferences based on dietary needs?

texts:
I'm wandering if mammals that can eat many different kinds of food (omnivores) vary their preference for food not only based on the availability, but also based on dietary needs?

I'm looking at this site Food nutritional content and see that "not all foods are created equal" - the vitamin/mineral and amino acid contents can vary dramatically. Is there some part of an omnivore brain/digestive system that "monitors" the micronutrient density of digested food and adjusts food preferences towards foods that make the diet more complete?


texts: Do birds have quadriceps and thighs fused into their hips?

texts: I'm looking at 3D modeling a large bird like an emu or ostrich, but I don't know how the muscles surrounding the femur connect to the hips/back. It seems weird that the entire thigh and quadriceps would be fused into the hip because that would greatly reduce the range of motion of the femur which affects how I animate it, but I can't find any reference that shows it either way.


texts: DNA synthesis companies: cost per base, turn-around time, codon-optimization algorithms

texts:
I would like to synthesize a 3.4kb gene (originally isolated from soil bacteria) and transform it into E. coli. There are several companies (DNA2.0, GeneScript, BlueHeron) which will synthesize the gene for you. I would like to know how these companies (or others) compare with each other in terms of:

Codon optimization - most of the companies are going to codon optimize the sequence and thus increase the protein expression in the desired host. Recently I learned that there are different algorithms that can be applied. I am mostly interested in how the codon-optimization is performed in the different companies and whether there are some direct comparisons of protein expression between them.
cost per base - I would like to find the cheapest one. In general, the cost of gene synthesis usually depends on the size of the fragment, as well as the complexity of the sequence. But on the other hand, DNA2.0 can synthesize 1kb fragment and 5kb fragment for the same price.
Turn-around time - which company will synthesize the fragment the fastest? I think that this mainly depends on size. Of course I have an option of ordering 3 x 1.1kb fragments and joining them myself, but then I have to sequence-verify the final product. So, I need to find the trade-off.

Please, keep in mind that I am not asking about your favorite company, but about specific characteristics of the companies.


texts: How is it thought that phosphine is synthesized by living organisms on Earth?

texts:
The recent (Sept. 2020) report of “Phosphine gas in the cloud decks of Venus” states that phosphine (PH3) is only known to occur on Earth due to anaerobic life. Quoting from a report in the New York Times:

But scientists have yet to explain how Earth microbes make it.
“There’s not a lot of understanding of where it’s coming from, how it forms, things like that,” said Matthew Pasek, a geoscientist at the University of South Florida in Tampa. “We’ve seen it associated with where microbes are at, but we have not seen a microbe do it, which is a subtle difference, but an important one.”

What are the current hypotheses about how phosphine is formed?


texts:
Is glycolysis the beginning part of fermentation, or does fermentation follow glycolysis?

I see conflicting information from different sources

https://honchemistry.wikispaces.com/Lactic+Acid+and+Alcohol+Fermentation+in+Humans

  "..Alcohol fermentation follows glycolysis, just like lactic acid
  fermentation..."  <-- So glycolysis is preceding fermentation, not part of fermentation

and

  " The Actual Fermentation Part

  Glycolysis and fermentation are two separate processes. Glycolysis was
  explained briefly to give the reader an idea of the events leading up
  to fermentation and the starting conditions in terms of molecules
  available for reaction.....Going into the fermentation, the molecules NADH and pyruvic acid are present. "  <---  so glycolysis is preceding fermentation, not part of fermentation.

Whereas these two links put glycolysis as part of fermentation, not a preceding stage before fermentation.

https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/variations-on-cellular-respiration/a/fermentation-and-anaerobic-respiration

  "Fermentation and cellular respiration begin the same way, with
  glycolysis" <-- glycolysis is part of fermentation, not preceding it.

and

http://study.com/academy/lesson/anaerobic-respiration-lactic-acid-alcoholic-fermentation.html

  "fermentation, which is a process that anaerobically generates ATP by
  performing glycolysis..." <-- fermentation includes glycolysis,  so glycolysis is part of fermentation, not preceding it.

So, which is it?

Is it a)like khanacademy and study.com,  or b)like honchemistry.wikispaces.com

I have heard the idea that glycolysis is independent, in that it can produce some (not much, but some), energy on its own, and it can happen without fermentation or cellular respiration following. Though when would glycolysis occur without fermentation or respiration following? And even if glycolysis is that independent, it may still be at the beginning of respiration and fermentation and not preceding it.

Wikipedia speaks in a contrary way..

https://en.wikipedia.org/wiki/Fermentation

  "Before fermentation takes place, one glucose molecule is broken down
  into two pyruvate molecules. This is known as glycolysis." <-- so glycolysis is preceding fermentation, not part of it.

so the above quote from wikipedia suggests that glycolysis is not the beginning part of fermentation, but a step preceding it

whereas still on the fermentation wikipedia page, it says

  "Fermentation is a metabolic process that converts sugar to acids,
  gases, or alcohol....The first step, glycolysis" <-- so glycolysis is part of fermentation.

Links on respiration are more unambiguous that glycolysis is part of respiration.. the links on fermentation vary a bit on whether glycolysis precedes fermentation or is part of it.


texts: What is the difference between rheobase and threshold?

texts: Neuronal tissues can be excited by electrical stimulation. Two commonly encountered characteristics for electrically stimulating nerve cells is the threshold and the rheobase. My question is what the difference is between rheobase and threshold? In the definitions I've read it's described as almost the same thing. The threshold, or minimal stimulus, is defined as "the electrical stimulus whose strength (or voltage) is sufficient to excite the tissue. Rheobase is defined as "the minimum strength (voltage) of stimulus which  can  excite  the  tissue". What is the difference?


texts: Why does sequencing virus proteins take time?

texts:
According to the below paper, the coronavirus spike protein sequence was available to scientists by end of february 2020 - the begin of march 2020 timeline. I had this question that why does sequencing of a virus protein take so much time (I am a software engineer, currently studying molecular biology to better understand the pandemic, hence I am seriously unaware!) ? The reason of asking is because, in case of another epidemic, we might need to spend again a lot of time to sequence the protein. This might be a real concern!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151553/#:~:text=At%20the%20time%20of%20the,remain%20identical%20or%20almost%20so.


texts: What negative effects can pinhole glasses have on the body?

texts:
While shopping in the local supermarket yesterday, I was surprised to find this display on one of the shelves.

I also realize that I should have taken a pamphlet with me, as well as a picture of the boxes for the glasses, as seen in the picture to read more about it.

This answer at Skeptics.SE shows that there are in fact probably no long-term benefits of wearing pinhole glasses, but my question is...

What potential harm/side effects can be caused in the short and long-term from wearing this type of eyewear?


texts:
I am reading a journal paper about the relationship between NCAM2 and autism. I have come across the following statement in the paper:

Based on analysis utilizing the UCSC Genome Browser (hg18, build 36),
there are a total of 19 genes deleted (Table I). The proximal deletion
breakpoint falls within the NCAM2 gene, deleting 17 out of 18 exons,
and the distal deletion involves 16 out of 17 exons of the GRIK1 gene.

I am not sure what is meant by a 'proximal deletion breakpoint'. I have tried searching for the definition online but I have not found anything useful. Any insights are appreciated.


texts: Origins of transcription factors and RNA Polymerase

texts:
I was learning about transcription factors and RNA polymerase from Khan Academy to supplement Dr. Robert Sapolsky's lectures on Human Behavioral Biology. As I understand:

RNA Polymerase transcribes DNA to RNA
Transcription factors are proteins that help the RNA Polymerase bind or inhibit it from binding to the DNA and transcribe it to RNA
Transcription factors called activators help RNA Polymerase bind to the DNA
Transcription factors called repressors prevent RNA Polymerase from binding to the DNA

It seems like we need transcription factors and RNA Polymerase to express genes and produce their corresponding proteins. But transcription factors and RNA Polymerase are proteins themselves. Thus, they must have come from their own respective genes. This seems like a "chicken and egg" problem.

How did early organisms with genetic material get around this problem?


texts: How do cells relocate transmembrane proteins from one side of the cell to the other? Is it possible?

texts:
Is there a process by which cells can relocate proteins residing on the cell membrane in areas of low demand to that of a high demand location somewhere else in on the cell? What's that process called?

Through protein catabolism, cells can break down the proteins into their individual amino acids and then reuse these resources to build new proteins in needed locations. This process seems inefficient if the cell simply needs to move a transmembrane protein (for example integrin or cadherin) from one side of the cell to the other.

I hope the question is clear. I haven't taken a biology course since early high school (8 years ago) so if there's something i need to clarify let me know!


texts:
I am looking for any database about pacemakers with the leads

atria A
right ventricle VR
left ventricle VL

I did not find any in Physionet.

Is there any anonymous data about different situations online or accessible by request?


texts: If I am going to transform a plasmid into a bacterium, which will then be fed to a C. elegans, the expression vector needs to be bacterial correct? The other option is to have a worm expression vector, but I just wanted to make sure that I was correct in my thinking. Thank you.


texts:
For the planning of an experiment I would like to know the binding kinetics (kon and koff) of a 6x-His-tag to a Ni-NTA surface.

I know they should differ due to surface quality and position of the His-tag in the protein. But maybe there is some literature out there (that someone of you knows) from which one could get at least a rough estimate of the kinetics.


texts: Hummingbirds travel to Alaska during summer. If global warming continue, allow birds stay longer in Alaska, can hummingbirds cross Bering Strait to Russia, then spread in Asia?


texts: Reference to hypothesis about breast sexual attractiveness?

texts: Some time ago there was a hypothesis published,suggesting evolution made breasts mimic buttocks for either primitive men being attracted to women when they started to walk on two legs, or to discourage sexual intercourse from behind for other reasons I can’t remember. I can find many posts about this online, but I can’t find any reference to the original idea. Can anyone provide information about this?


texts: From where does the oxygen in glucose come in photosynthesis?

texts: Is it carbon dioxide or water? I'm talking about the oxygen present in glucose and not the oxygen that is released after photolysis of water.


texts:
I am working on an assay for phenol products created by a colony of bacteria. I have searched up a paper that involves gibbs reageant but the protocol is kind of unclear.

Does any of you know where I can look for a detailed protocol for a gibbs reagent colormetric assay (preferably one that uses cell medium)

Thanks


texts: What is the best color for a PPG signal (photoplethysmography)?

texts:
What is the best color for a PPG signal?
Red, green, blue or infra-red?

I'm asking because commercial oximeter sensors usually use a pair of red and infra-red LEDs. But recently, I've seen a lot of sensors using green LEDs.

Thanks.


texts: Do there exist enzymes that can take up multiple cofactors to do different reactions?

texts: I was thinking about enzyme catalysis, and it seems like enzymes can only catalyse one kind of forward/reverse reaction (please correct me if I am wrong). Does there exist an enzyme that can catalyse multiple reactions with different cofactors? For example, an oxidoreductase that has $Fe(III)$ as a cofactor for one reaction and $H_2O_2$ as a cofactor for another reaction.


texts:
The Wikipedia-article about Inflammation says

  The five classical signs of inflammation are heat, pain, redness, swelling, and loss of function (Latin calor, dolor, rubor, tumor, and functio laesa).

What does 'loss of function' mean? And how does it occur?


texts: What is the biggest facultative anaerobic metazoan known to science?

texts:
Related: What's the biggest obligate anaerobic organism discovered till now?

I had always assumed that the Riftia tube worms were obligately anaerobic since they lived next to anoxic volcanic vents, but a quick literature search showed it to be a facultative anaerobe, being able to survive at least 60 hours without oxygen.

If "facultative anaerobe" is defined as being able to survive at least 24 hours in the absence of molecular oxygen in an otherwise normal environment, are there any metazoal organisms larger than Riftia (which are up to 1.5m long)?


texts: Snail species identification from the United Kingdom

texts:
Can anybody identify the species of this snail?

From this website, it looks like a Common Snail.

Could it be the dextral type of Cornu aspersum?

These snails have been found in a garden, have survived a month on lettuce in a home environment, retreat in their shell sometimes. Their shell measures about 2 cm diameter.


texts: Which pair of primers should be used to amplify the ORF in PCR?

texts:
So I want to choose the correct set of pair of primers to amplify the ORF of the gene that corresponds to amino acids in a protein. The start and stop codons are underlined. (I know that these need to be synthesised by the primer also for correct PCR technique)

The boxed sets of nucleotides are the primer options I have at hand. I know that the DNA synthesis can only carry out from 5' to 3' and there is a forward and reverse primer. The forward primer should be easy enough but non of the options seem acceptable? Could someone please explain to me how to go about this problem?


texts: What physiological processes within a muscle cause the latent period in a muscle fiber?

texts:
This is a lab question I cant find the answer in the lab manual or in the text book.
What physiological processes in a muscle cause the latent period in a muscle fiber?
Please help.

Edit:
The latent period is the short delay between the muscle action potential and the beginning of muscle tension development. This is what I'm talking about. I'm sorry I didn't make that clear.


texts: What is the name if this glittery fly seen in Pittsburgh?

texts:
I have photographed the following fly which is iridescent green in Pittsburgh, PA.
I guess it was about 0.5-1.5cm long.

Can you help me to identify it?


texts: How do I read an RNA expression pattern?

texts:
When reading about diseases one can find links to proteins and their associated genes, an example of which is here.

I'm wondering how to decode/read the following graph as a non-specialist in this area:

What does it all mean?


texts:
I'm coming across an increasing number of papers that use trait-based approaches for risk assessment, like this one . This paper defines a trait as follows:

  Traits are the physiological, morphological, and ecological attributes
  of species or other taxonomic entities, which describe their physical
  characteristics, ecological niche, and functional role within an
  ecosystem.

I've wondered about using this sort of approach during some analyses of invasiveness potential in vector insects before and it's likely to come up during a systematic literature review I'm coordinating, but I'm concerned that devising my own trait classification system is likely to introduce confirmation bias into a study. Is there either a recognised methodology for trait definition, or alternatively some sort of accepted list or classification of traits that I could use, to minimise the chances of this? Is there a generally-accepted method to correct for phylogenetic correlation?

I've tried Google but the results mostly appear to be about trait theory, which is an approach used in psychology to study human personality.


texts: How many co-expressed genes would be expected in a tissue?

texts:
I am working with gene expression microarrays of tumor tissues and I want to use a program to find the clusters of co-expressed genes in order to know if some particular genes are co-expressed with another genes and which genes are those.

As I must do this for many microarray experiments and I have read that there are a lot of genes that have constant expression in a tissue, I ranked the gene by its variability (coefficient of variation) that they had in the experiments and keep the first 3000 genes to search their co-espression. Then I employed a program (a bioconductor package) to find co-expression.

Now, I was expecting to find several clusters of genes (no particular reason for this) in the experiment that I was using as example, but instead of that, I only find one cluster of co-expressed genes of about one hundred, and the others genes didn't were co-expressed.

My question is: this result could have a biological sense, or I'm making a terrible mistake in some place?, Thanks in advance.


texts:
This basic evolution theory question has been haunting me since childhood and I'm kind of embarrassed that I can't explain it yet:

Consider a butterfly. It's wings have evolved to look like the eyes of an owl, so to prevent it's predators who are themselves preys of the owl to attack it.

From what I've learned (and feel free to indulge me in the very basics if I get this wrong), natural selection suggests that the butterflies that didn't have the owl's eyes in their wings would be eaten, leaving the ones with the eyes to survive, right?

But that implies that this useful trait appeared in the butterfly's wings by chance. Now, I know trillions of butterflies have been born before this, but trying to figure out the possibility of this to happen by chance doesn't look like it's plausible. Let's go through the things that have to work right before this trait is passed over:

For a butterfly to be born in a different wing colour, it should be a genetic mutation which doesn't happen this often, for what I know.
The wings are composed of micro-scales. For every scale to compose an image so similar that confuses even us, the margin of error is very slim. It could be anything. It could be a picture of Tom Selleck for all we know. The scales must be in the correct spectrum of colour by a small margin of error. So that is already a very unlikely thing to happen.
Then, this butterfly cannot be eaten out of bad luck (mind you, the wings don't guarantee it will not be eaten, just enlarge her chances).
It has to mate, which also is not a guarantee to happen, since nature deals with competition. If this butterfly we are considering is a male, the female must find the wings hot, instead of being afraid of those creepy eyes.
The genes of this mutations must also be dominant, so when it mates and generates offspring, at least part of the new butterflies inherit this trait.

And this is a simple example. There are animals that evolved so smartly I can't even start to think of the possibilities.

My question is, more precisely, how likely is it for a species to evolve into complex solutions?


texts: Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?

texts:
Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some CRISPR-like tools? I guess, that extensive databases of already performed experiments are available and human mind is required to select candidate genes for experiments. But maybe there are some methods, that allow computational select, planning of experiment, e.g. using: 1) already known biological pathways for different biological processes or incomplete pathways for the process under consideration; 2) protein-protein interaction models to predict some pathways and to select genes from them. Etc.

I am complete novice for this field, coming from computer science and only starting to read books about molecular cell biology, epigenetics and protein-protein interaction. Maybe there are special terms that allow me to Google for the subject of this question


texts: Do PC-12 cells have to be stored in nitrogen?

texts: My lab has been storing their PC 12 cells in the -80 freezer... upon arriving here and investigating a new project I see that it specifically stated to be stored in nitrogen vapor? Is this the absolute case or is -80 for short term storage okay as well?


texts: Did birds descend from a single or multiple species of dinosaur?

texts: It seems like there are mixed results because sometimes I read about a single missing link, like an archaeopteryx that somehow single-handedly explains all modern-day birds, but then I see conflicting articles about how different birds are descended from different dinosaurs like a t-rex or a velociraptor and so on. Which theory is correct? Did birds all descend from one common ancestor or multiple?


texts: I heard that the Earth's atmosphere is opaque at most wavelengths and only allows visible light and radio waves through, so why have plants evolved to only absorb visible light?


texts: Why Rh conflict happen but no ABO conflicts?

texts: I wonder why Rhesus conflict can happen during pregnancy and mother can make antibodies against Rh protein (I think the correct name is D protein), but it doesn't happen if mother has different ABO type than the child?


texts:
What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR?

I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used 25 cycles because I was hoping to see a difference between an endogenous level and an overexpression. However, I detected no band at the expected height of 500 bp but a diffuse band at 100 bp. What can this 100 bp represent? primer dimer? I switched to 35 cycles and I used either the same amount of cDNA or add 3 times more cDNA. In both cases I got bands at the expected height (but stronger when I put more cDNA) and still big bands at 100 bp.


texts: What gives researchers a reason to test the Radiation Resistance of organisms?

texts:
I was reading about the Thermococcus Gammatolerans and its absurdly high radiation resistance, when something occurred to me.

What reason did anyone have in the first place to subject this thing to this level of radiation?

I'm very curious to find out about the process behind deciding which organisms to test the radiation resistance of. Is there an ongoing effort to test the resistance of every species yet discovered? Or are there other factors in determining which species should be subjected to this kind of testing?


texts: Would a vial of anticoagulated, warm blood attract mosquitoes?

texts:
Would mosquitoes feed on free blood as an easy source of nutrients? They home in on veins by means of infrared light (heat detection). Also, blood needs to be in liquid form. So would they feed on anticoagulant-treated blood kept at 37oC? Or is there some physiological phenomenon that mosquitoes necessarily need to pierce something to draw in blood?

I am asking this, because just keeping a vial of blood at the end of a room might save us from mosquito bites.


texts: Could a large constrictor kill a small animal?

texts:
According to this article there was a python whose body circumference was 85cm.  This means its diameter was 27cm.

Would it be possible for this snake to constrict animals that are about the same size as its diameter?  It is hard to imagine it having enough flexibility to constrict a swamp rat, for example, whose size is less than 27cm.  Could it kill such animals by another method, say with its jaws or by crushing them by rolling over them?  Or are such small animals simply off its target list?


texts: About which cells in the human body do we know most?

texts:
Are there model cells (in the sense of model organisms) in the human body (other than E.coli) about which is known most (with respect to structure, function, metabolism, gene expression, ...) and to which I can refer when asking questions about "typical cells" (which per se don't exist). The other way around:

  About which cells (added: normal and mature) in the human body do we know most?

(Maybe there's a cell in the rat we know more about, but also know/believe that it is very similar to a human cell? Which one, then?)

Having asked this, I'd also like to know, about which neurons in the human brain is known most, e.g. about "pyramidal cells in cortical layer IV"?

Related question: Are all functions of a human cell known?


texts: Do Black Pepper and Black Nightshade share specific characteristics?

texts: In my textbook, I read that two organisms of the same species share specific or fundamental characters. Piper nigrum (Black pepper) and solanum nigrum (Black nightshade) share the same specific epithet despite belonging to different families. Is this because they share common fundamental characters ?


texts:
There are a lot of these little bugs in my backyard. The floor, walls, the bbq island.

Are they hurtful to my dogs ?

What are these ?


texts: Does this leaf belong to carissa macrocarpa?

texts:
I have a picture of a leaf and I am trying to find it's scientific name. The closer I got is Carissa Macrocarpa based on thorns alignment. If I am wrong, I need help in identifying correct species.. Thank you very much in advance!

Edit: Adding some more images


texts: Why certain COGs appears more often in Humans Bacteria but not in plants Bacteria

texts:
I'm doing a Bioinformatic project from the university where I  got a DB of COGS from Human & Plants Bacteria genomes and I need to find distinguishing sets in this DB and explain the biological reason behind these results. Unfurtinly my Biologi knowledge is very basic and I do not know how to explain the results so maybe someone here could help me.
Here are some of the distinguishing COGs I found and the known info about them:
Results for FreqItem: ['0049', '4465']
IG of FreqItem:  0.6682341035127484
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG4465;K;INFORMATION STORAGE AND PROCESSING;Transcription;GTP-sensing pleiotropic transcriptional regulator CodY;
Number of occurrences in Human Bacteria genomes: 63
percentage of genomes that carry it in Human Bacteria genomes: 25.0%
Number of occurrences in Plant Bacteria genomes: 4
percentage of genomes that carry it in Plant Bacteria genomes: 5.56%

Results for FreqItem: ['0049', '3833']
IG of FreqItem:  0.6952252521930348
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG3833;G;METABOLISM;Carbohydrate transport and metabolism;ABC-type maltose transport system, permease component;
Number of occurrences in Human Bacteria genomes: 109
percentage of genomes that carry it in Human Bacteria genomes: 43.25%
Number of occurrences in Plant Bacteria genomes: 8
percentage of genomes that carry it in Plant Bacteria genomes: 11.11%

Results for FreqItem: ['0049', '1847']
IG of FreqItem:  0.7334916442185917
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1847;R;POORLY CHARACTERIZED;General function prediction only;Predicted RNA-binding protein Jag, conains KH and R3H domains;
Number of occurrences in Human Bacteria genomes: 122
percentage of genomes that carry it in Human Bacteria genomes: 48.41%
Number of occurrences in Plant Bacteria genomes: 9
percentage of genomes that carry it in Plant Bacteria genomes: 12.5%

Results for FreqItem: ['0049', '1115']
IG of FreqItem:  0.6323046964671385
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1115;E;METABOLISM;Amino acid transport and metabolism;Na+/alanine symporter;
Number of occurrences in Human Bacteria genomes: 161
percentage of genomes that carry it in Human Bacteria genomes: 63.89%
Number of occurrences in Plant Bacteria genomes: 15
percentage of genomes that carry it in Plant Bacteria genomes: 20.83%

Results for FreqItem: ['4585']
IG of FreqItem:  0.3643909812004458
COG_INFO semantic description per each COG in the itemSet if exist:
COG4585;T;CELLULAR PROCESSES AND SIGNALING;Signal transduction mechanisms;Signal transduction histidine kinase;
Number of occurrences in Human Bacteria genomes: 118
percentage of genomes that carry it in Human Bacteria genomes: 46.83%
Number of occurrences in Plant Bacteria genomes: 49
percentage of genomes that carry it in Plant Bacteria genomes: 68.06%

Results for FreqItem: ['0049', '1006']
IG of FreqItem:  0.8034282332952798
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1006;P;METABOLISM;Inorganic ion transport and metabolism;Multisubunit Na+/H+ antiporter, MnhC subunit;
Number of occurrences in Human Bacteria genomes: 50
percentage of genomes that carry it in Human Bacteria genomes: 19.84%
Number of occurrences in Plant Bacteria genomes: 23
percentage of genomes that carry it in Plant Bacteria genomes: 31.94%

Thank you for your time!


texts: Why does human chromosome 19 have the second highest number of protein-coding genes?

texts:
While chromosome 19 only is the 19th largest autosomal chromosome, it contains 1440 protein-coding genes, and thus has the second highest number of protein-coding genes of any human chromosome.

For comparison: If one would naively assume the same density of protein-coding genes as on chr1, which has the highest absolute number of protein coding genes (2109), the anticipation for chr19 would be ~540 protein-coding genes.

The x-axis of this graph highlights the increased density of protein-coding genes on chromosome 19;


texts: RT-qPCR of selected differential expressed genes: which dilutions in calibration curve?

texts:
I've seen in MIQE guidelines that calibration curves a needed when performing RT-qPCR. I'll use genomic DNA to perform these calibration curves.

My question is that I don't know the range of concentrations to test.

The genes I will check for differential expression have logFC between 2-8 (base 2 log).

50 ng/μL is the sample concentration I will have when performing the Comparative CT Experiment, but 98% is ribosomal RNA.

Please let me know you suggestions and possible reference books/papers to revise.


texts: Why did whales end up larger than most sauropods and what is a whale's limits?

texts:
I understand that due to the square-cube law (when something grows 2 times but its volume grows 4 times and it goes on) sauropods were massive but not enough when compared to whales because whales got around the square-cube law by using the buoyant force to balance their bodies in the water. In addition, being mammals allowed them to breathe, oxygen-rich air while fish were limited to oxygen-poor water, this thenceforth allowed whales to grow many times more than the largest fish. So my question is what is the limit to whale size and if there is one what is their true potential?
A question presented by the scientific community and given to the public.


texts: Why and when did the misconception about the Panther being a species came to be?

texts:
People usually call Panther to any big black cat, I did so until I watched Apocalypto and saw they were calling the black cat Jaguar which confused me. (I have no biology knowledge)

It was kind of a shock to discover that Tigers and Lions, among other species, where Panthers too, and it surprises people when I tell them.
Does anybody know why and when this started to happen?

* I realize this might not be related to biology but actually to popular culture, but I couldn't find a stackexchange site about that.


texts: Do we have evidence of heritable personality traits in chimpanzees?

texts: I have read that chimpanizees have distinct personalities. Do we have evidence of heritable personality traits in them?


texts: Why does brain invert the image formed on retina?

texts: I have been studying about the human eye and it's working in school for some time. I came across something. I have been taught that the image formed on the retina of the eye by the lens is inverted and the image is made erect by the brain so as for correct perception. But how does the brain know what is erect or inverted? Why doesn't it just keep the image as it is? Please note that I am asking why the brain reverses the image and not about the nature of image formed on retina.


texts: Shouldn't evolution have taken care of baldness already?

texts:
It is my understanding that the hair on the head is there to protect us from sunburn.  I've never seen a bald animal, so isn't evolution in charge of addressing these type of things?

How is it that evolution gave us a thumb, but hasn't found a way to keep the hair on our heads?


texts: Change in synthesis rate of a molecule changes equilibrium concentration

texts:
I was reading the topic of 'The concentration of the molecule can be adjusted quickly only if the lifetime of a molecule is short' from Molecular Biology of the Cell by Alberts.

At the end of pg-837 (this part can also be found here), the author says -

  "In fact, after a molecule's synthesis rate has been either increased
  or decreased abruptly, the time required for the molecule to shift
  halfway from its old to its new equilibrium concentration is equal to
  its normal half-life—that is, equal to the time that would be required
  for its concentration to fall by half if all synthesis were stopped."

What do they exactly mean by 'shift halfway'? I am not able to understand quite clearly what the above sentence means. I hope some of you may be able to help me. Thanks.


texts: Detection of bacteria to measure quality of water

texts:
I have been working on a science project were I have built a water filter.

To prove that it works I would need to test if there are bacteria in a sample which has been treated vs a sample that hasn't been treated.

I really just need to know if there are bacteria not how many. I looking to do this at home.


texts: What reason that land vertebrate evolve keratin while other animal use chitin

texts: I don't know why there are evolutionary split in material. Why we evolve keratin and lose chitin? What the advantage and disadvantage for each material? Is it because the size or there are other biological reason?


texts: Why is Carbon Dioxide a Greenhouse Gas whereas Ammonia is not?

texts:
Why are some gases Greenhouse gases while some are not?

I did search this on the net but didn't get any clearcut/credible answers.

What exactly is the property that is common among Ozone, Water Vapour, CFC and Methane?


texts: When two amoeba cells form from one amoeba, does spindle fibers form? Some sources say that spindle fibers do not form while an amoeba cell is undergoing cell division. If spindle formation does not occur, than how are the chromosomes pulled apart? Which intracellular transport mechanisms are used?


texts: Get protein annotation from Uniprot out of protein mappings

texts:
Having a file of for about 10k mapping identifiers how can I get the annotations of the proteins from Uniprot  ? As it is not possible to do It manually

My mappings are contained in a .csv file
They are from STRING database Example 9606.ENSP00000387699


texts: Does the order of amino acids matter in making up a protein?

texts: For instance, if a protein is made of 2 amino acids, that is, AB, would the same protein form if the order of combination of amino acids become BA? If yes, would the behavior of interaction of that protein change? For instance, if AB interacted with another protein XY, would BA interact with XY in the same way?


texts: If my brain lost all of its activity for a moment, would my memory be gone too?

texts:
I can't remember which question it was, but in the past here, it was explained to me that memory is actively stored in the brain, rather than "physically". Meaning, memories are made up of the brain's activity, not its physical cell structure.

I'm not sure I have that right though. I mean, that, for one thing seem inefficient and overly complex. It seems like a vast amount of energy would be required to store so much information in the form of activity patterns. Maybe I misunderstood. So I'm asking. If my brain lost all of its energy (activity) for a moment (for example, one second), would my memory be gone too?


texts:
I'm reading some urology papers and came across one involving penis growth (Kim & Song, 2008); here's an intro passage that I'm confused about:

A total of 58 patients with constitutionally small penises, without chromosomal anomalies and gene-associated syndromes, intersex, and hypospadias, were included in this study. The average patient age at their first visits was 10 years and the average follow-up period was 2.2 years.

What's a "constitutionally small penis"?
Edit:
I've read the paper in detail and I don't see where the authors distinguish between a small penis and a "constitutionally small" penis.
Would a "constitutionally small penis" be the same thing as a "micro-penis"?  If not, then where do we draw the line?
References
Kim, K. S., & Song, G. G. (2008). Penile Growth After Puberty in Patients with a Constitutionally Small Penis. Journal of Pediatric Urology, 4, S63. doi: 10.1016/j.jpurol.2008.01.174


texts:
A popular "well-known fact" is that all creatures on Earth consist mostly of water (i.e. H2O). Indeed, a liquid called "normal saline solution" is just a solution of 0.9% sodium chloride in distilled water. It is generally considered the "safe" liquid to be injected into human body in relatively high volumes without any bad effects.

I know that the same 0.9% solution is also used in vet practice for at least cats and dogs. As far as I understand, that's because blood circulation structure and basic blood regeneration specs are more or less the same for cats and dogs as for humans.

But what about other animals? My wild guess is that same 0.9% solution would be ok for all mammals (probably because their blood tract is similar), but what about others? Birds? Fish? Vertebrae? Invertebrae? Animals? Plants?

If 0.9% solution is not universal, what are the other possible variants? (i.e. could you provide examples of other compositions for some other species?)

If 0.9% is indeed universal, I'd be glad to hear any pointers on why does it happen (i.e. is it related to evolution of life in Earth history, is it related to chemical composition of bodies, related to some specific cells, etc).


texts: Finding a easy and cheap method for dyeing dNTP

texts: I want to measure OD to know the concentration of dNTP. Any idea for dyeing dNTP at cheapest price and easiest way ?


texts: What is the difference between polar and charged amino acids?

texts:
Chemically polar amino acids have an uneven (AKA  polar) distribution of electrons over their surface.

Charged amino acids have a charged ion in their structure. This is probably where my knowledge is a little shaky!

I guess I am confused at this point. Does this just mean that charged amino acids are really polar amino acids? If that is correct that would explain why I have seen histidine categorised as a charged amino acid, but has no clear ions.


texts:
Staphylococcus aureus, Streptococcus pyogenes, and Clostridium perfringens all produce hyaluronidase.
Each of these bacteria are pathogens (use hyaluronidase as a virulence factor to destroy the polysaccharide that holds animal cells together, making it easier for the pathogen to spread through the tissues of the host organism)

  The role of hyaluronidases in cancer is controversial, however there is substantial evidence of increased hyaluronidase activity in malignancies.

We know, human sperm also produces hyaluronidase (for penetration of ovum),
So what would happen if sperm enters blood (Like:via cuts or wounds on genitals)?


texts: Why do children not have the Acid Mantle?

texts: Post puberty humans begin to secrete a substance called Sebum which changes the neutral PH of our skin from ~7 to 4.5-5.5. This has that advantage of serving as a protective line against pathogens and discourages larger organism like lice. My question is given these benefits, why are children not born with these advantages?


texts: Can Alzheimer's disease be caused by Slow Prion infection?

texts:
I found this claim in my study materials with explanation of amyloi plaques, in comparison to CJD (Creutzfeldt-Jakob Disease).

Its characteristic are

Long doubling time of at least 5.2 days (I think this means the time it takes to double the amount of prions in the target organ)
NO Cypopathic Effect (CPE) in vitro
Long incubation period (about 30 years)
Vacuolation of neurons, amyloid-like plaques
Deficient immunity
Deficient immunoresponse
Deficient Interferen (IFN) production

so this suggests me that the person with infection at a young age can have the disease then at an old age.
Other possible agent could be virus, but it seems that prion is the major one.

Can Alzheimer's disease be caused primarily by Slow Prion infection?


texts: How does consumption of vinegar affect food chemistry?

texts: For example: does consumption of vinegar somehow change digestion of flour (bread, cakes, pasta, puffs) ? May be there are some benefits to eat flour meal with vinegar ?


texts: Why can't I smell things that aren't there?

texts:
I can close my eyes and imagine a red cube with a yellow star on it. Although I don't literally see it -- if there was a red cube with a yellow star on the inside of my eyelids, I'd know the difference -- I can experience it in much the same way as if I was seeing it.

I can do much the same thing with sound, imagining (say) the sound of a bird, or of a bell ringing.

But I can't imagine any tastes, or smells. I know what cinnamon smells like: if several spices were placed in front of me, I could readily identify the cinnamon. But I can't call a familiar smell or a taste to mind in the same way I can call a familiar sight or sound to mind.

I don't think it's merely a memory thing. Even if I've never seen the box, I can still imagine it. I can imagine the sound of a bird tweeting in a large echoing hall, even though I've never heard it. But I can't synthesize unknown smells or tastes in my imagination in the same way I could unknown sights or sounds. I don't think I'm unusual in this respect (correct me if I'm wrong).

Are there any theories as to why this is?


texts: Is it possible for a prey to become its main predator's predator?

texts:
This is actually for a worldbuilding project, but I thought I'd just ask it here as it is solely about biology.

Anyway, would it be possible for a herbivore, let's call him X, that is predated by a predator, or Y, to evolve to become a specialized hunter of Y?
For example, wolves hunt deer. Imagine that in millions of years, the deer has evolved into the main predator of wolves.

If that's not possible, is it at least possible for X to evolve adaptations for fighting/killing Y (Not for food)?

If you require any further context or clarification, please let me know.


texts: Is serine considered an acid in the catalytic triad involved in the mechanism of action of serine proteases? It is donating a proton to His but I am not sure if this really qualifies as an acid?


texts: My dog and I are wondering: is this a biting midge, or another bug?

texts:
A week or two ago, my dog started scratching, and it only increased. Not long after, I started getting bit by something that itches something awful. I thought it was fleas so got some medication and moved my dog out of my room. He stopped scratching immediately. After deep cleaning, I let him back in my room the next day. He shortly thereafter scratched again, but not intensely or frequently. My bites have continued.
I set out a flea trap (water, dish soap, flashlight on the water) and it caught the bug you see in the pic (it has only caught four of them).
Is that a biting midge, or something else?
Also, I'm in New York City.

https://i.stack.imgur.com/GC0iL.jpg -- close-up pic, color and pattern
https://i.stack.imgur.com/CVgnl.jpg -- several from a distance to show size
https://i.stack.imgur.com/rQqp4.jpg -- same one as in the first pic

The size is maybe as big as the hole a small nail makes in the wall, a very small ant, or a freckle.


texts: Do conservation oriented genetic database exist?

texts: Are there any projects for the creation of the international genetic database of all endangered species, so we, at least, have a chance to clone them in the future if our current conservational efforts fail?


texts: Can I use TBE to elute a plasmid shipped on filter paper?

texts:
I'm receiving a plasmid shipped to me dried on sterile filter paper, as described in this question. This protocol and many others like it call for eluting the DNA from the paper using TE buffer.
My question is can I also use TBE to elute, as I already have a bunch on-hand? And in general, what concentration should the buffer be as I never see that mentioned in any of the protocols (including the AddGene version).


texts: New evidence about the beginning of life?

texts:
The cover story of the August Scientific American is about new evidence suggesting "volcanic pools" as the location for "first life" as opposed to deep sea smokers like "The Lost City".

I was under the impression that one of the strong arguments for the deep sea vents is that the DNA of the life there is some of the "oldest DNA" on the planet. I'm wondering how the authors would explain that. (Maybe life spread to every "nook and cranny" in a geological blink of an eye?)


texts: How is the appropriately-stratified gut microbiome acquired in organisms performing horizontal transmission?

texts: I am studying horizontal transmission of primary symbionts in insect reproduction. This reminded me of an earlier question I had asked, in which I learned that humans analogously acquired their particular microbiomes. It is also known how the human gut can be stratified in microbial content along the digestive tract. My question is what mechanisms are employed in ensuring that organisms acquiring their microbiomes from outside sources via horizontal transmission acquire the correct microorganisms in the correct parts of the gut? As the human gut metagenome does show "homology" between individuals, it can be safely assumed that the process can't be due to random chance.


texts:
I came through this pic while scrolling through facebook, and it was a bit strange to me.

As far as I know apples have a corymbose type of inflorescence, in which a single pedicel ends in a single thalamus.

And I am totally sure that the edible part, which is fleshy in the apple, is thalamus. How did this fruit came into existence?

I want a biological answer for this query.


texts: Are there animals / mammals which only have one eye?

texts:
Do all animals (of a certain size and not thinking about worms) have the possibility to perceive depth?

Do all mammals have at least two eyes? Are there mammals with more than two eyes?


texts: Technical term for a mutation that only occurs after a preceding one

texts:
Consider a hypothetical population of 1000 organisms.

(a) 300 of these 1000 have a T to G substitution at a specific position 1.

(b) 200 of these 1000 have an A to T substitution at a second position 2.

(c) All of the 200 with the substitution at position 2 (b) also have the substitution at position 1 (a).

As a non-geneticist, I would call the second mutation a refinement of the first mutation. Would that seem reasonable, or is there a specific technical term for this phenomenon?


texts: Why are there no known animals with an odd number of legs?

texts:
In my 6th grade science book it is said that there are no three legged animals, and that no animal with an odd number of limbs exists. I checked Wikipedia and could confirm this:

  There are no known naturally occurring three-legged animals

On yahoo it is said that

  When an embryo is developing, it grows by cell division - the first single cell divides into two, then four, then eight etc. It doesnt' divide into odd numbers - each cell divides in half. So, this means that every creature develops the same on each side of it's body - same number of limbs per side.

It seems to be a valid explanation. So is it true that any organ in any living organism is either one in amount or is in even number? And the explanation of yahoo.com is fine?

I am a beginner in Biology. Please explain in simple terms.


texts: Filamentous algae - what exactly am I looking at?

texts:
I have just taken some images with my light microscope at 400x of  (what I think is) some form of filamentous algae from a local pond.

Now, I think I am looking at a single cell (centre) with some sort of arrangement of chloroplasts. Is this correct? Can anyone give me some more information on these structures?

I also have included a higher-constrast image of the specimen.


texts: Is genome recurrence possible like in Jupiter Ascending?

texts:
I have watched Jupiter Ascending many times now and I was wondering if genome recurrence, like what happened to Jupiter Jones, is possible.

Is it possible to find two unrelated people, possibly several generations apart, that cannot be distinguished between by DNA sequencing?

Taking the example of Jupiter Ascending: in the movie Seraphi Abrasax they show the "genetic recurrence" of Jupiter Jones, which means the same sequence of DNA has repeated after several thousand years from Seraphi to Jupiter.


texts: Why dogs move their noses when smelling?

texts:
I read on Wikipedia that:

  The wet nose, or rhinarium, is essential for determining the direction of the air current containing the smell. Cold receptors in the skin are sensitive to the cooling of the skin by evaporation of the moisture by air currents.

That explains why their noses are wet. Why they're slightly moving them when smelling, like on this video (see the close-up in the second part)? Could this very little movement create enough air currents around the nose to determine what smells are coming from what directions? Or is there another reason?


texts: How do I know which molecular structure is glycine's "base state"?

texts:
I was looking up the chemical structure of glycine, and I found the following two images:

and

.

My question is, what is the "base state", or the "natural state" of glycine? Under what scenarios does glycine become oxidized/reduced?

Also, I know that amino acids contain a carboxyl group, an amino group, a lone hydrogen atom, and a side chain. What is the formula for the amino group? Is it $\ce{-NH_2}$ or $\ce{-NH_3^+}$?


texts: Are humans the only animal that requires "clean water"?

texts:
I've seen a number of animals - dogs, cats, squirrels, ducks and geese, etc drink from puddles, some of them were muddy, others had green flora growing under water. Same goes for lakes and rivers. A human would not drink that. Do animals experience gastrointestinal discomfort or can they die from drinking water like that?

At the same time I hear about the problem of "clean water" in 3rd world countries and how diarrhea is the #1 killer of children under 5.

Are humans the only animals that require a certain purity of their drinking water? Why is it that a dog can drink from a puddle, but a human is likely to get sick from doing the same? Do baby animals get sick from drinking "dirty" water?


texts: Is starch and glycogen digestion intra or extracellular?

texts:
Do humans have the enzyme for starch intracellular digestion?
Also, do plants have the ability to digest Glycogen? Intra or extracellular, or both?


texts: What are good practices with reusing desalting columns

texts:
At least according to a few sources Prozyme and Protocols-Online, it is possible to reuse desalting columns and since I'm cheap I would like to also.

Key things seem to be washing with several column volumes of your buffer of choice. Also certain columns like crosslinked desalting columns are not amenable to regeneration. I'm curious about other factors.

I'm mainly using Bio-Rad micro-spins