texts: Does epigenetics suggest there is at least some element of truth to Lamarckism?

texts:
I am not a biologist. But googling "epigenetics lamarck", I find many different opinions:

For: Lamarck rises from his grave, Epigenetics: Lamarck’s Revenge?, Darwin’s theory ... is incomplete without input from evolution’s anti-hero: Lamarck;
Against: One more time: no, epigenetics is not Lamarckism, Why epigenetics is not a vindication of Lamarckism.

This is highly confusing to laypersons such as myself and I'm hoping an expert here can explain to me why there seem to be such vehement disagreements on this matter.

Here's my simplistic layperson understanding of the matter:

Lamarck: Variations transmitted from parent to child can be influenced by the experiences of the parent.
Darwin: Lamarck is wrong, variations transmitted from parent to child are purely random and cannot be influenced by the experiences of the parent.

Based on my above simplistic understanding (correct me if I've made any errors), it seems to me that epigenetics suggests that there is at least some element of truth to Lamarckism. Am I mistaken?


texts: spinal cord lesion and result in somatic sensation

texts:
Jimbo suffers a lesion to the entire right half of the spinal cord at the T6 level. A few weeks after his injury, his doctor tests his right and left legs for somatic sensation and tone.  fill out her chart concerning the absence or presence of different sensations and muscle tone in the lower limbs.
Mark a for absent, P for present

Right leg: Light touch, Pain, Proprioception, Temperature, Hypertonicity, Hypotonicity
Left Leg: Light touch, Pain, Proprioception, Temperature, Hypertonicity, Hypotonicity

what about if the lesion is in C1 or L5? where would it affect (leg/hand..) and fill out the above chart?


texts: If an antiserum was raised in a buffalo by injecting it with monkey red blood cells, what would be the full name for this antiserum?

texts: Im confused, i've attempted this & what i got is buffalo anti-monkey red blood cell antiserum. I'm not sure if this answer is right


texts: Can a non-disjunction event occur in meiosis II (in the paternal gametes) to result in an XXY male?

texts: My professor stated that non-disjunction in meiosis II of the father cannot produce an XXY male. However, a disjunction event in meiosis II of the mother can. I'm not understanding why this is (?)


texts: Identification of Bug/Insect (with picture)

texts:
What is this insect?

I’ve seen a lot of them indoors. The most distinctive characteristic is that single, orange dot in the middle of the back. The picture was taken in Louisiana, USA.


texts: Can a person die instantaneously from internal damage to the brain?

texts:
Given the human heart is autonomous, can a person die instantly from internal damage to the head/brain? I would expect the heart to continue to pulse until it ran out of energy ...

My contention is whether brain-injury can cause death, albeit Memming raised a deeper question - What is the biological definition of death?


texts: Does exhalation help us speak, and if so, how?

texts:
Everyone knows that we breathe in oxygen and breathe out carbon dioxide. That's how the respiratory system works. But we also use the respiratory system to produce sound and language. When we speak or emit sound, our glottis opens up, and depending on whether the sound is vocalized, our vocal chords vibrate. We then use articulators (tongue, lips, teeth) to shape the sound we produce.

But what kind of air is emitted in the first place? When our glottis opens up, what kind of air is passing through, and why does it pass through? The most obvious answer, which is my first guess, is that carbon dioxide is passing through our glottis and our trachea, and that we use this to create sound. In this way we would be using the product of respiration for a separate purpose: to create sound and communicate.

This is only a guess. But a logical one. The question, to put it most simply, would be, do we utilize our natural cycle of exhalation to produce sound and speak? Or is something else going on?


texts: How to find the age of a memory stored in the brain?

texts:
Is there any way to find how old one's memory is?

One can find the age of stones, plants, animals, etc. So why not find the age of a memory stored inside one's brain?


texts: Why are oxygen masks given to patients? Can't they take in the  atmospheric oxygen? Also, why do they die if the oxygen mask stops providing oxygen?


texts: how to change format of ent file into PDB format?

texts: whenever i download files from Protein Data Bank(PDB),they are downloaded in .ent format. How can i convert them into PDB format??


texts: I found it on my plant this morning while watering it. Location: Hyderabad, Telangana, India. Any ideas?


texts: Why is carbonylation added as a fixed modification in mass spectrometry peptide analysis?

texts: When using mass spectrometry analysis software we use carbonylation as a fixed modification. What is the significance of this modification and why doesn't it change?


texts: What's the state of the art in designing and creating your own life forms?

texts:
What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have a) a strong sense of smell, b) the ability to fly and c) a comfortable couch shaped saddle on its back. What's the sequence of steps you need to take so that you can create this life-form in the lab?

I realize that we are probably far away from solving this very general problem. But perhaps there are some smaller subproblems that we do know how to solve.

For example, as far as I gather, you can probably make any living being fluorescent green in color by inserting into its genome the gene responsible for expressing the Green Fluorescent Protein. So may be if we limit the set of features one is allowed to choose from, the above problem can be solved. So my first question of the set of questions is:

1)  What features can be easily inserted into almost any organism easily?

Next, I imagine that to design and create an artificial life-form will consist of three steps:

Figure out which proteins will give rise to those feaures,
Design a genome that will express those proteins in the right quantities and
Implant that genome into a cell and actually let the being grow.

2)  Is the above sequence of steps correct, or am I missing something?

3)  What is the state of the art for each of these steps?

Finally, in light of the recent spur in the open source biology groups and DIYbio enthusiasts, I feel that there might be some very simple but really cool things related to my question that you can already do in your garage. For example, may be there is some very simple single-cell life-form that's so well understood that you can add or subtract tons of features from it with a budget of a few hundred dollars. So my final question is:

4) What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)


texts: Training Data for Secondary Protein Structure prediction using neural network

texts: I am trying to find some training dataset for prediction of Secondary Structure of Protein. I am having problems finding them online.


texts: I am a private individual and I want my exomes sequenced, I don't know of any place that will keep my data confidential as I read reports of companies sharing this data with insurance companies. I tried looking into a number of university research centers but none of them sequence DNA of private individuals. Does anybody know of any university that does WES of individuals or a place which can keep my information confidential? Many thanks in advance for your replies!


texts: How could this fossil's soft tissue be preserved so well?

texts:
I found this article for non biologists like myself. It describes, how astounding fossils were found in China. They belong to a crustacean like animal that lived more than 500 Ma ago. The exciting thing about them is, that the nervous system -soft tissue - is fossilised in its finest detail. The article says:

  “Using fluorescence microscopy, we confirmed that the fibres were in fact individual nerves, fossilised as carbon films, offering an unprecedented level of detail. These fossils greatly improve our understanding of how the nervous system."

My question is: how can these soft tissues be so well preserved?

I managed to find the scientific publication   and attempted to identify the answer myself, but it seems to me, the question is not touched upon. Perhaps, being a layman, I overlooked it, or it is obvious to biologists?


texts: Why are certain aneuploidies more common?

texts:
Certain aneuploidies such as trisomy-21 (Downs syndrome), trisomy-18 (Edward syndrome), Turner syndrome (XO) etc are more common than others.

I had a vague thought that it is related to chromosome size: the chromosomes which are towards the extremes of size will be affected in an improper segregation event.

Chromosomes 13, 18, 21 and Y are among the smaller chromosomes in humans, and are commonly associated with aneuploidy (but 22 which is also small is not affected). The larger ones are unaffected (X is an anomaly).

I thought that longer ones should be more affected because more cohesin bridges have to be broken, but it seems that is not the case.

Is there any association of chromosome size and frequency of aneuploidy?

EDIT

If the difference is because of differential lethalities then does the length correlation still hold true? Smaller the chromosomes, lesser the genes and hence lesser would be the effect of extra copy on the cellular biochemical networks.


texts: Difference between facilitated diffusion and secondary active transport in cells

texts:
Specifically, what is the difference between facilitated diffusion carrier processes (passive transport) and secondary active transport co-transport processes (active transport)?

They seem to be the same thing - doesn't the passive process with the carrier transports substance $x$ against its gradient together with substance $y$ that is moving down its electrochemical gradient?

Similarly, in the active process, substance $x$ is transported against the gradient, and substance $y$ down its electrochemical gradient?

I don't see how energy differentiates the active transport in this case from the passive transport.


texts:
I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether it is in an intron variant, downstream gene variant, missions variant, etc...) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant,upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are "missense variants". The reason why I want to do so is that transcription factor binding sites (TFBS) might be located before gene and after it.

What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons,introns, 5' UTR etc?


texts: How does a veggie-less diet affect the human body?

texts:
I have some question, which I'm sure would fit better in the fitness section but proper answers should probably come from someone that knows biology.

My question is rather simple. How can a person that doesn't eat any vegetables at all be affected by such a diet? By no vegetables at all, I mean not eating any ever.


texts: Why increasing the vector concentration does not increase the effeciency of bacterial transformation?

texts:
I was reading some old description of the protocols used for the transformation of bacterial cells.

In the description I read that the transformation works best with low amount of DNA, and if we increase the amount of DNA used the amount of transformant cells does not increase proportionally.

I just wonder why, since in my eyes the process of entering the cell is mainly related to the diffusion principles, and therefore concentration dependent.


texts: Do all transmembrane proteins contain channels or tunnels?

texts:
In my book, there is written something like this.
The integral proteins pass into the lipid bilayer to different depths and establish hydrophobic bonds with lipid molecules. Some of the integral proteins run throughout the lipid bilayer. They are called tunnel proteins OR transmembrane proteins.
My question is do all the transmembrane proteins have to have channel or tunnel for transport of materials?


texts: How much is local blood non-Newtonian in Pathophysiology?

texts:
I am studying the Barus effect / Merrington effect / die swell / extrudate swell, which is a characteristic of non-Newtonian viscoelastic liquids (Introduction to the phenomenon in this video) i.e. the medium responds to the stress $\sigma$ of irritator with a strain $\epsilon (= \Delta l/l)$ that increases until the medium ultimately fails in a local pathology

blood has both viscous and elastic components which it can apply in pathophysiological condition
\begin{equation}
\gamma = \gamma_{v} + \gamma_{e}.
\end{equation}

#1 Maxwell material model

total shear stress if blood behaves like Maxwell material in local pathophysiological regions
\begin{equation}
\sigma = \sigma_{v} = \sigma_{E} = \eta \frac{d \gamma_{v}}{d t} = G_{M} \gamma_{E},
\end{equation}
implying $\sigma = \eta \, d\gamma_{v}/dt$ and $\sigma = G_{M} \gamma_{E}$.

I am thinking when blood is not non-Newtonian etc in muscular pathologies and muscular infections. I want to evaluate how much blood is non-Newtonian in particular situations.
I am interested in muscles and their supply with necessities.

How much is local blood non-Newtonian pathophysiologically?


texts: What are the ingredients of Pheromone Trap using for controlling Fruit flies of cucumber?

texts: Pheromone Traps are used for fruit fly control. But I have no idea which ingredients or chemicals are used for preparing Pheromone trap


texts: Is there any evidence contrary to the pheromone theory of bee washboarding?

texts:
I've heard beekeepers say they "don't know" what the function of washboarding is.
James F. Taulman suggested in a 2017 study that the primary function of bee washboarding is the application of pheromones to assist returning foragers in locating the hive.
Is there any evidence contrary to Taulman's theory?

For those interested: Taulman has a youtube channel with some videos of washboarding observations at wild hives.


texts: Could the Immune Gene HLA-B27 be gentically altered, snipped, switched off, replaced, edited within the body

texts:
Could the Immune Gene HLA-B27 be genetically altered, snipped, switched off, replaced, edited within the body.?

Thousands upon thousands suffer immune disease as do I from this highly implicated gene.

Is their a gene manipulation mechanism that 'could' work for this gene from within the body ?


texts: What is the defining characteristics of a Gap Species?

texts:
For the following competitive exam question: A road is constructed through a tropical rain forest, following which a population of a species of butterflies declines. Which of the following is NOT  a possible explanation for the road causing a decline in the forest butterfly population?
The answer: The Road facilitates immigration of gap-loving species which compete with the forest species
What is the defining characteristics of a 'gap' species?


texts: Some say that DNA is denatured only at basic pH. And some say at both acidic and basic pH. So I want to know clearly why and how if DNA is also denatured by basic pH.


texts: Why do left and right eyes can require different power of lenses?

texts: Both the eyes almost see the same things throughout our life. It is not like we use one eye more than other that it should become weaker. What causes requirement for different power of lenses for both eyes? Shouldn’t they be same?


texts: How often can you reuse coomassie stain?

texts: I usually heat to boil in the microwave, and stain for 12 minutes. How often can I reuse this buffer?


texts: Why the length constant of passive current flow isn't depend on the membrane capacitance?

texts:
I read that the equation for the length constant for passive conductance along a neuron depend on the resistance of the plasma membrane, the intracellular axoplasm and the extracellular medium. My question is why it's not dependent also on the membrane capacitance, since it can also affect how far the current can propagate (if for example the capacitance of the membrane is large, more negative charge will be on it's intracellular side, and will cause to the positive current to attract to the sides of the membrane).
Thanks!


texts:
So school has taught us that eukaryotes have DNA that is linear and inside of a membrane - called the nucleus. And that prokaryotes have circular DNA that is free floating inside of the cell.

We also know the pros and cons of both linear and circular DNA.

Are there organisms with circular DNA that also have a cell nucleus?
Are there organisms with linear DNA that is also free-floating within the cell?


texts: Is there a binding affinity metric for interactions not in equilibria?

texts:
I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the complex.
When I plot the collision energy against the proportion of bound and unbound proteins I get a curve that looks like a Kd curve.  However, as the interaction isn't in equilibria (i.e. it is in the gas phase) calculating the Kd value wouldn't be correct.

So is there another value I could calculate to describe the strength of the interaction?


texts:
I´m just starting my postdoctoral fellow and my new project involve sRNA Deep Seq. I´m having problems with the data normalization.
I´ve been reading papers about it and the variety of normalization method is huge!

The simplest one that I found is by TPM or RPM (transcript per millon or reads per millon), in which each raw read count is multipled by 1 millon and then divided by the total read count of the whole library.

The question is: which library?

I have 3 treatments. In one of them, the number of raw seq were 10 millons. After filtered of adaptor, length < 15nt, # <3 count, we generate 8 millons of mappable reads. Then, once we mapped against Arabidopsis genome, 3 libraries were generated. The mapped mRNA, tRNA, rRNA, RFAm, Repbase library (5.7 millon; 72%); the custom virus we sent library (20; 0%) and the miRNA (sRNA) library (2.3 millon; 28%). On the 3 treatments the numbers were diferent and always the miRNA library was smaller than the mRNA library.
In order to a direct compare between data set, we have to normalized the counts.

If I want to do it with RPM, which library do I have to use? The total mappable reads (including mRNA, tRNA, etc) or only the miRNA library?

I have noticed that the result is very different with one or the other, because the percentage of the libraries are not the same between treatments.

Any hint you can provide me will help me a lot.


texts: I was told in my microbiology course that blood agar can be put in GasPak system (anearobic) to grow strict anaerobes, but why would someone use blood-dependent bacteria in this experiment as these blood-dependent bacteria will be aerobes or at least facultative


texts: What is the difference between enrichment media and selective media?

texts:
Enrichment media

  These media are used to suppress commensal bacteria while allowing the pathogen to remain viable and grow.

  [Source: Ananthnarayan and Paniker's textbook of Microbiology.]

There is also an example of tetrathionate broth as enrichment media given in the book where tetrathionate inhibits coliforms while allowing typhoid-paratyphoid bacilli to grow.

For selective media it writes:

  As in the above case (of enrichment media), if inhibiting substance is added to a solid medium, it enables a greater number of the required bacterium to form colonies than the other bacteria.

For this selective media an example of Deoxycholate Citrate Agar (DCA) for fecal samples is given.

The question:

What's the difference between enrichment media and selective media? Some answers give quite contradictory statements to the statement of the book like stating that "...it is designed to stimulate growth of many different types of bacterial species" for enrichment media.

I am also not able to explain myself as to how selective medium enables a greater number of the required bacterium to form colonies than other bacteria since inhibitory substance is also present in enrichment media?


texts: Is existence of different alleles for a gene a result of mutation?

texts:
I would like to understand evolution. Here are a few questions

Why are there different alleles for a  gene?
Is the different alleles of a gene are mutated versions of a gene?
Why selection pressure favoured the existence of more than one alleles?


texts: Can cancer cells in the same person, organ, and origin have different DNA?

texts: Is it possible for cells from the same tumor to have different genetic material, and if so, to what degree is it possible (how fast do they mutate) ?


texts: What should be evaluated in food decomposition experiment?

texts:
Briefing
Some days ago I noted that 3 cookies left on my desk since 3 months ago are still "fresh", and by that I mean... not spongy like some cookies that get soft after some time outside.
However this particular brand of cookies do get spongy, I'm not sure why don't these do!
I also noted that there is a cockroaches/flies infestation in a home nearby, so these are getting in my house, but none of those insects dare to eat the cookies.
So, I decided to make an experiment inspired in the well known experiment of Watermelon vs McDonalds Burger where a watermelon decomposes extremely quick, and the burger does not. This article even mentions one that hasn't decomposed after two decades!
I understand that watermelon decomposes so fast mainly because of the sugar/water that it contains, but that is another story, let me tell you what I want to do.
Problem
In this experiment the only notable variables taken into account were: Visual appearance (picture), and time.
For my cookies I want to do a similar experiment, but I want to know which variables should I consider, so far I only have these in mind, but I want to know what else can be considered for food products:

Date of packaging
"Best before" date label
Visual appearance (daily pics)
Time gone by before going spongy
Humidity of room (3 daily measures across the day)
Temperature of room (3 daily measures across the day)

And the samples will be:

Being in a closed room (eg. my room)
Being in an open room (eg. dinning room)
Exposing to insects directly (eg. roaches, ants, flies)
Adding a drop of "morning saliva" (mainly for the bacteria)

Question is
In general, what do I need for food experiments? I think these are OK, but maybe I'm overdoing it on some, and maybe I need to consider some other parameters.
My experiment's objective is to see if it decomposes, why does it take X time to do so, or why doesn't it decompose at all, if it is safe to eat, or if it shenanigans like McBurgers.


texts: How are atoms in benzopyridines and benzopurines numbered?

texts:
I am well-aware of the numbering system used for the traditional bases, as seen below.

My question is how are the atoms in the size-expanded bases seen in xDNA and xRNA numbered?


texts: Are there specific features of birds that cats/small predators are attracted to?

texts:
I've recently heard a podcast, in which a professor describes one of the theories as to why we like abstract art. In his talk, he mentions an experiment with seagull chicks, in which the seagull chicks mistake a stick with a red dot for their mother's beak, and in the case of stick with 3 stripes actually preferred it to their mother's beak. When a stick like that is waved around a chick, it starts to peck at it, believing it is mother bird:

This experiment suggests that birds are imprinted to recognize specific patterns and interpret them as mother.

I'm in trying to create a similar experiment for cats. To do so I'm trying to understand if cats other small predators (ferrets,etc) are imprinted in a similar way - do cats recognize specific features of a bird to identify it as "bird", "prey" or "can hunt and eat"? I'm talking about stuff like - do they recognize eyes, beaks, wings or tail in a special way?

To paraphrase the question: If I'm to create a stick like above, but for cats, what features would be painted on the stick?

I know that butterflies, caterpillars and other insects have evolved to mimick "eyes" on non-vital organs to confuse birds. I'm interested if same stuff exists for small mammal predators.


texts: Is it possible to make synthetic olfactory receptors?

texts: Are there any electronic engineering technologies that allow people to make synthetic olfactory receptor that generate electrical impulses when exposed to certain proteins or molecules? If not, what are the primary challenges of creating such a device?


texts: A chromonemata is composed of two chromonema. Which are again composed of chromatin fibre. Thus my question is chromonemata is composed of how many chromatin fibre ?


texts: What determines a successful protein expression in E. coli?

texts: Some proteins express well in a heterologous host; others- don't. A few requirements are known to determine the protein expression, like a strong promoter (like T7) for transcription and a strong ribosome binding site for translation. I am working with a protein, which consists of 2 subunits - alpha and beta. Both of them are on a plasmid with T7 promoter in front of the beta subunit (i.e. the construct is T7 promoter, CDS for beta subunit, CDS for the alpha subunit). The beta subunit expresses well, but the alpha doesn't. Do you thing this has something to do with the local environment (promoters, RBSs, etc) and how much does it depend on that? How can I increase the protein expression?


texts: Does the body prioritise the use of available sugar before fat?

texts:
Let's say you eat a very unhealthy snack that contains 90% sugar and 10% fat. Would somatic cells not start using the fat for energy until all the sugar is used up?

Does the body not use fat at all if there is more bio-available sugar to be used? Or is there always a proportion of fat being used for energy?


texts:
I am looking for recommendations to good textbooks introducing modern immunology. Review articles, preferably modern (post 2000) would also be useful.

Please, include a brief comment with each book recommendation.

About book listing questions on SE: I understand that SE sites in general have adopted in the last year a policy against book listing questions. Instead, book lists should be moved to tag wikis. However, since BiologySE is still beta and young and the tag-wiki for immunology is mostly empty, I believe we would benefit from a question listing good introductory books to modern immunology, at least temporarily. Eventually, when Biology.SE matures, this question should be closed or locked, and the book recommendations herein moved to the tag-wiki for immunology. Moreover, for most other SE sites I have seen, the tag-wikis usually gather information that first appeared in questions like this, even if the question is eventually closed or locked. That's why I think this question will be useful to the community, at least temporarily.


texts: Has aloe vera been proven to help heal burned skin areas?

texts:
I don't like buying into "natural remedy" type things without seeing scientific proof behind them. There's an almost universal belief that aloe vera helps to heal burned skin, and whether that includes assisting in cell regrowth, preventing inflamation, or something else, I haven't bedn able to find any real scientific evidence.

Can anyone cite legitimate scientific evidence that aloe vera has any helpful effect for burned skin? If so, how does it work?


texts: Is the deep ocean fish look ugly because due to darkness there is no visual sexual selection? If so, is there a common notion of beauty between humans and animals?


texts: How are fMRI responses to auditory stimuli measured?

texts: How can fMRI experiments be conducted which measure the response to auditory stimuli (e.g. music) when the apparatus makes such loud, nasty, and distracting noises? Are there quieter MRI tomographs in the meanwhile, or must the stimuli (transfered by earphones) be louder than the noise of the machine? How to measure the effect of a whishper then?


texts: Does vitamin C decrease after reacting with oxygen free radicals?

texts:
From the research that I have done, I know that antioxidants such as vitamin c donate electrons to oxygen free radicals and effectively neutralize them. They themselves do not become free radicals as they are stable in both forms.

So, would it be correct to say that after the vitamin C is oxidized(giving electrons to free radicals) so much that it can no longer give any more electrons(not sure what the actual limit is):

What happens to vitamin C (does it get broken down and therefore
decrease)
Is it any useful in destroying free radicals?


texts: Why do I always close my eyes when someone takes a photo of me using a flash?

texts:
Everytime some tries to take a photo of me with a flash I manage to close my eyes (blink).

It's not intentional and it's quite annoying.

Why am I doing it?


texts: Does my brain have limited learning capacity or memory?

texts: Lately in my free time I like to read books, articles etc etc.. What I have discovered, or maybe it is an illusion(lack of concentration or something), is that I usually forget most of the material that I read about, and have lost my ability to remember names of objects, planets or whatever I read about. Does that mean that I am over-reading or that my brain has limited memory/learning capacity? I should also mention that I have an IT job, which you know requires high concentration throughout the day.


texts: Are there COVID-19 citizen science projects to compare habits and outcomes?

texts:
I've seen some "citizen science" projects for coronavirus that are not really collaborations, but simply requests for processing time.  Are there any "real" projects where people who have gotten their diagnoses could go, chat with one another, volunteer to publicly disclose their virus status, test results such as O2 perfusion, and daily self-rating of symptoms, and agree on group surveys to profile what they eat and other activities they do?

I would like to see ordinary people work together toward answers to basic questions.  For example:
a) does salt intake affect symptoms?  [re: blood pressure]
b) does drinking coffee affect symptoms? [re: type II diabetes risk]
c) does exercise affect symptoms? [re: HIFs]
d) do dietary supplements such as flax, curry, and elderberry affect symptoms?
e) does the overall intake of calories, or ratio of carbohydrates/protein/fat, affect symptoms?

Of course, trying to correlate actions by a patient with immediate self-reported changes in symptoms is fraught, as is a comparison of subsequent hospitalization or death between groups of online survey respondents.  Yet such disorder on an informal basis is where ideas often come from, and citizen science might mark out candidate factors for formal validation by professionals.  Is there anything like this going on?


texts:
I know myopia is caused by elongation of the eyeball. When the eye is too long, light entering the eye balls falls in front of the retina instead of on it.

However I do not quite understand how this leads to the "blur" we observe. If part of the light entering the eyeball "misses" the retina shouldn't the observed effects simply be a reduction in the brightness of the object - as if I were standing in a less illuminated place? For example, if I take off my glasses in broad daylight my retina is getting a far greater dose of light than when I'm indoors (wearing my glasses) under artificial lighting. Yet the world still looks blurry outside (without glasses) and clear indoors (with glasses).

What causes the blur effect? If less light is hitting the retina it should simply look less illuminated, not blurry.


texts: How does a drastic change to the genome persist and spread?

texts:
I just read the article on songbirds in the November, 2019 Scientific American. The article explains that songbirds have an extra chromosome, called GRC (germ-line restricted chromosome) that other bird species don't have, and there's a hypothesis that this may have been partially or wholly responsible for the diversity of this group of species.

The following line caught my attention:

  Once the GRC originated in the last common ancestor of songbirds, members of that ancestral species that carried the GRC could produce fertile offsping only with mates that also had the GRC.

But when the mutation that created the GRC occurred, who did that bird mate with in the first place?

My belief is that most genetic changes are relatively minor, so they don't immediately result in incompatible mating. Speciation occurs as genetic changes accumulate over time. But the above quote implies that an entirely new chromosome is too drastic to allow interbreeding at all.

Wouldn't there need to be a whole bunch of birds who all had this extra chromosome at the same time to allow it to spread through the population? That seems unlikely to occur.

Am I just reading the line too literally? Could early birds with the extra chromosome mate with other birds, until the new chromosome accumulated too many changes?


texts:
I am attempting to perform metatranscriptomics analysis of a cleanroom. The DNA input is known to be rather low (<1pg). Despite this, I want to still attempt to try it. I am thinking it might be best to perform extraction trials before hand where certain parameters are manipulated. I can then determine from these extraction trials which values for which parameters are best.

As an example, I am reading a peer-reviewed paper called "Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics" where they used the Illumina Nextera XT DNA library preparation kit on low biomass samples. Two of the parameters they manipulated were:

1) PCR cycle numbers (Values = 12, 14, 16, 18, 20)
2) ATM dilution (Values = undiluted, 1:5, 1:10, 1:20, 1:50)

I am hoping to use the same type of extraction trials to determine which combination of values from these two parameters is best for a clean room. My first question is: How can I determine which combination is best (as there are 25 combinations)? I have two ideas (but am open to others):

1) Check the amount of RNA derived
2) Check some quality metric on RNA

As I hope to do triplets of each of the 25 combinations, I will have 75 samples. I am hoping not to have to do sequencing as it is time consuming and possibly expensive in order to chose the best combination. Is there a way to chose which combination works best without having to sequence?

My second question is: Are there any other parameters in this workflow that I can also test for if I am not getting decent results in these low-biomass cleanrooms?

(As you can tell, I do not have too much direct molecular biology experience, so feel free to correct or question any of my post and/or "dumb down" your response). Thank you for sharing advice (for either question)!


texts: Did Carl Linnaeus ever name a species he never saw?

texts:
According to this post Carl Linnaeus named more than 13,000 species which is definitely quite impressive. If we consider a 50 years career it makes about 5 species per week! It would feel impressive that he could actually take time to find, observe and describe that many species.

Apparently Linnaeus named species from outside Europe such as the Wild Turkey (Meleagris gallopavo, Linnaeus, 1758). This surprised me a little bit as travelling accross the atlantic wasn't all that common in the middle of the eighteenth century. Also, the wiki article on Carl Linneaus says:

  Boerhaave offered him a journey to South Africa and America, but Linnaeus declined, stating he would not stand the heat.

It made me realize that there are actually many non European species that have been described by Linnaeus such as the Llama (Lama glama, Linnaeus, 1758).

I heard of Linnaeus trip to Lapland and I always pictured Linnaeus as a field naturalist but now I am wondering

Where did he get his specimens from? Did he have an army of graduate students exploring the world for him?
What fraction of the species he named did he really see in the wild?
What fraction of the species he named did he really see alive? (has he ever seen a Llama and a Narwhal?
Did he name species based on other people description but without ever seeing one dead or alive?


texts: I need help identifying a perculiar species of mushroom found in my yard today. Color is orange-yellow, around 3-4 inches total radius, its a cluster of tiny to medium mushrooms. They were found near an oak tree. Location is southern Georgia, USa.


texts:
I want to 3D print the skull of the newly discovered Homo naledi.

The printing data can be found here: http://morphosource.org/index.php/Detail/MediaDetail/Show/media_id/7300

Where can I find the exact size of the skull so that I get a 1:1 copy? Google was of no help.


texts: Would a person live longer, if such a person lived in a planet with lower gravity? (say, Mars)

texts:
I was wondering: some companies plan to colonize Mars, many of us know.

But if one were to live on Mars, would this person live longer?

It seems to me that a lower gravity would mean less overall damage to the body cells, so they could last longer: resulting in a longer lifespan.

Or maybe lack of gravity = lack of exercise = lesser lifespan?

I'd like the opinion of some expert in the matter. Thanks.


texts: Cultivate snails and maintaining them alive

texts:
I found snails in my garden, I want to create a good house for them. I don't really know how to do. Sorry if this is not the good site to ask that but I don't want them to die so I'm trying to be quick.

This is a temporary terrarium for them, is it good ? What do I need to keep them in good health ? What do I need to put in the box ? Is it too small ? I will inquire all about later, I want them first in a safe place.

Thank you :)


texts:
Just spotted this fruit while walking to school. It's the size of a small coin.The taste is almost sour and tangy and somewhat sweet (I only tried one of them and very little of it).  I admit, I've never seen it before. Does anyone know what this is?

Update: Location is two or three blocks north of UC Berkeley (Berkley, CA, USA).


texts: If eating 100% fat 2 times more worth the energy I spend during the day, will I store body fat?

texts:
So in theory, insulin hormone is the one that tells the body "eat more. don't burn body fat". Alongside with glucose blood level regulation and turning excessive glucose into liver (which later goes into muscles as glycogen or into fat cells). Fats are the only thing that do not provoke insulin secretion. 0 glycemic index.

So in theory, if I eat 2 or 3 times more worth the energy I spend during the day, I'll never store body fat because of 0 glycemic index?

Or will I still gain because such huge fat intake will make liver into making glucose from fats & proteins?

Surely u'll never find a sustainable product to eat that is 100% fat, but just a few examples are butter, lard, heavy cream. This is just a theoretical question, where the proteins/carbs intake is so low that it is not count.

Could you please clarify it since I got lost.


texts: Standard practice for generating rarefaction curves from Next Generation Sequencing data

texts:
We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database.

To generate a rarefaction curve, my understanding is that one randomly samples $n$ reads where $n$ ranges (with some step size) from 0 to the total number of reads, and counts the number of OTUs observed at each such sub-sampling.

Which of these two ways, as implemented by sequence analysis suites such as QIIME and mothur, is standard practice? Which would be best to use with the above situation?

Treat the original assignments of reads to OTUs as truth, and when resampling $n$ reads, just count the number of "original" OTUs observed in this sub-sample.
Re-cluster the sub-sampled reads, and then count the number of "new" OTUs in the sub-sample.

My sense from reading through the QIIME documentation is that method 1 is the standard, but I am not sure. I also do not quite understand why method 2 wouldn't be the better way to go, though it would be computationally more expensive.


texts: Is there production of TDF in birds? If so which gene produces it?


texts: Flow cytometric counting of apoptotic adhering cells

texts: I have been trying to measure rates of apoptosis in epithelial cells by marking apoptotic cells with annexin V conjugated with phycoerythrin (PE) and sorting using flow cytometry. Unfortunately, the cells are adherent, and have been cultured in a collagen coated plate. Thus, to suspend them for flow cytometry, I have been using a trypsin treatment. Unfortunately, my results have been quite poor. I believe that there are several problems. First, the trypsin treatment is likely to induce the disruption of integral membrane proteins, potentially causing the externalization of phosphatidylserine (PS) (to which the annexin binds) on the outer plasma membrane of cells. Since the cells were incubated with the annexin V following suspension with trypsin, this could have led to a substantial increase in apparent rates of apoptosis, and masked real differences between rates of apoptosis in WT and KO cells. Furthermore, I was informed that epithelial cells, in order to maintain their structural integrity, have a relatively large ratio of cytoplasm to nucleus, and a prominent cytoskeleton resulting in increased background noise (greenish in color). In order to solve these problems I was considering several alternatives, such as changing the fluorescent marker that annexin V is conjugated with to reduce autofluorescent interference, using a different marker of apoptosis (in the place of annexin V), or, if I were to continue using annexin V, I think that incubating with annexin V followed by washing off of excess annexin, followed only then by trypsin treatment could potentially solve one of my various problems (or then again, it might not). Please help me find a suitable protocol for flow cytometric analysis of apoptotic markers in adherent epithelial cells. Additionally, if you know of any studies which utilize such methods, please direct me to them. Thanks in advance.


texts: Could a person become physically transgender through artificial means?

texts:
Let's say there's a girl who carries a few masculine traits not normal in most girls, such as a high level of testosterone; we know there are countless reasons why something like this could happen, but could that girl have actually been concieved as a boy but modified before birth to become almost fully female, with only slight traces of male traits left? Is that possible through any sort of technology, or does biology even work that way?

For instance, if a male baby was injected with high amounts of female hormones before his birth, or really, anything else that could alter his gender, in any case could he start morphing into a girl, even if not fully? (Say, to the extent where he became more of a girl but still possesed a few common but not very specific/clear/exclusively male traits such as excessive body hair, etc.?)


texts: Organ cloning - possible to make a non-antigenic organ?

texts:
From a J. Neil Schulman article on Organ Cloning:

  Cannibalizing organs from other people also entails the risk of
  rejection because of incompatibilities, not only for tissue-typing but
  also for gross anatomical mismatches. Cloning organs [...] has the
  potential of taking a human being's own genetic material and growing
  perfect replacement organs which are fully compatible with their
  genetic makeup.

The reason for using a person's own DNA, is obviously to avoid an allergic reaction to the antigen markers on a strange organ. But in the blood typing system, there exist types which don't have any trouble-making antigens (such as type O-negative, called a "Universal Donor").

Would it be possible to grow an analogous "universal" internal organ, which didn't have any antigens indicating it was a foreign body? (By editing a DNA sample to remove certain expressed proteins, then growing it into an organ.)

I realize this is technically a science-fiction question :) But - A: it may not be in the near future, and B: I can rephrase it to remove the SF component:

In the blood-typing system, the AB antigens don't appear necessary for proper functioning of red blood cells - are the antigens on a person's own cells, actually needed for any essential functions, or could they be removed, without affecting that person's health?


texts: Why are two-winged animals much more common than four-winged?

texts:
In flying vertebrates, almost all have only two wings (with the exception of Microraptor and its close relatives). This makes some sense because you need some way to walk also, and a wing isn't very good as a leg, hence why bats are so bad at walking. Of course, bats do demonstrate that being able to walk well is not necessary to be a successful clade.

As far as insects are concerned this might seem like an odd question, since most insects technically have four wings. But among the four largest insect orders (which together make up a sizeable majority of insects), Coleoptera, Lepidoptera, Diptera, and Hymenoptera, all of them functionally have two wings. In Diptera and Coleoptera, only one pair of wings is used to fly. In Hymenoptera and Lepidoptera the two pairs are attached and don't move indepedently.

So my question is, why is two-winged flight so much more common than four-winged? If two-wingedness is advantageous, why do other insects retain four-winged flight (most notably Odonata)?


texts: Why do some texts say that noncompetitive antagonist dose no change in ED50 of agonist in Dose-respond curve?

texts:
Competitive antagonists increase the ED50 while the Emax remains the same. Non-competitive antagonists do not change the ED50 while decreases the Emax.

I wonder how does this happen as Non-competitive has no effect on ED50.


texts: What if we inject rabies virus into an insect body, like spider or a bee, will it contract rabies as humans, cats, dogs, racoons or bats do?


texts: I found this sitting on my window, could not understand what it is. Any help would be appreciated.


texts: If only dicots have pith, what is the foam in the middle of cornstalks?

texts: I've heard that the only plants that have pith are dicots, because of the shape of their vascular bundle. If that is true, what is the foam inside of the corn plants, which are monocots?


texts: How can TMS induce enough depolarization to cause an action potential?

texts:
Creating an action potential needs at least tens of mV potential difference across the membrane to occur.
But the membrane is really thin, surely less then 0.01µm (some reference give 25A).

Then the potential gradient, that is to say the electric field E, must be very strong :
The order of magnitude of the needed electric field is much greater than 10mV/0.01µm = $10^{6}$ V/m

But TMS produces E of the order of 200 V/m on the scalp, which is even less inside the brain. Then how can TMS induces neurons depolarization ?


texts:
What is accumulation and release centre of neurohormones?

Is it hypothalamus?


texts:
Found in a waterway in Butte County, CA. First thought it was a beaver kit, but it has no
tail.
What aquatic mammal has no tail?


texts:
I was pondering about the genetics of siblings. It occured to me that a pair of biological brother and sister (not brothers or sisters) could inherit completely distinct sets of chromosomes from their parents, the mathematical probability being $\frac{1}{2^{46}}$.
This calculation is based on the assumption that each pair of chromosomes, upon meiosis, get separated independently of other pairs. Do you think I’m right about that? Has anyone looked into this matter? Could it be that a chromosome prefers to be accompanied by a specific chromosome (in a pair other than its own) during meiosis?

Edit: I only have a high school level understanding on this matter and I just realized that my speculation directly contradicts Mendel’s law of segregation. But as pointed out in the comment on the answer, some wiggly interaction might interfere with the assortment with some peculiar genes, although it doesn’t mean that some chromosomes are more fond of each other. Close the case.


texts: What is the difference between transcriptional activator and general transcription factors? Are they same or different, and do the transcriptional activators first attract general transcription factors or the RNA-polymerase also, at the same time?


texts: What information does the KEGG Module statistics page show?

texts:
While browsing through the home page of KEGG Module, I clicked the button named Module statistics.
Can someone tell me what does these numbers signify? What are they the statistics of?


texts: I would like help Identifying this insect

texts: We found this in our house after coming in from outside but we are unsure if it came in on one of us (riding our coat) or was in our house before. We live in Massachusetts if that helps. We would like to know if anyone can ID these poor quality images.


texts: Can anyone (urgently) tell me if this is a bed bug

texts:
We just arrived in a place where a lot of people were living before.

This is what we found on the mattress and we are curious to see if this is a bedbug, or some harmless species; To know if we go out right away or not :)

Location: Poland. ;  Size: ~13mm long

Here is a photo with a measuring tape next to it:

Closeup:


texts: What differentiates neurons in different parts of the brain?

texts:
For example: what makes a neuron in the hippocampus of the brain different from a neuron in, say, the amygdala, or the frontal lobe, or anywhere else in the brain? Do neurons in different parts of the brain have different structures, or are they differentiated solely by location?
By "different structure", I mean things like receptors that other neurons don't have and things like that.


texts: Is magnetic resonance microscopy appropriate for investigating ion-channel flow?

texts:
I've been looking into ways to characterize the elecrophisiology of neurons for cell signaling and I came across magnetic resonance microscopy as a tool for gaining images of neuronal activiy at a large scale.
This made me question, is it possibly to take a timeseries video of an active neuron and view the actual signal flow through and outside of it?


texts: Is there a taxonomy of species with emergence and extinction dates?

texts:
I know the NCBI has a list of each species and their place in the evolutionary tree. But do they have the dates that these species existed? Does any such database (partial or complete) exist anywhere?
For example, Adelobasileus on Wikipedia says "about 225mya", so that would be one example date. Obviously they aren't super exact, but it would be cool if this has already been collected somewhere.


texts:
I am trying to predict the secondary structure of certain predicted pre-miRNAs through mFOLD which is the generally accepted technique for structure prediction in most studies. I am finding it hard to interpret the result and accept if the pre-miRNA which I have picked and the miRNA I have can be accepted and included in my result.

This is one predicted pre-miRNA structure with the predicted miRNA position shown in green.

Is this a good/bad structure and if so, can anyone give me a reason why. Thank you.

edit: I understand that energy levels are also something that is looked for in the prediction. In this particular figure, ΔG = -75.00 kcal/mol which I think is fine.

Sequence used for folding is

AAAAATAAAAAACAGAACCATGAGGCAGCGCACCAAGAGCGTCGTGAACGTCCGCGAATA CTTCCGCATGGACGGCAGTGGCGCCCCCGAGCAGGAGGACGACGATGACAACGATGACTG GATGGCCATCGCCATGCAGGGCGCACCGCGTAAGGTCAGCGTGGAAGTCGTTAAGCCTGG CAAGAAGGCACGCGCTCGTACGTCGACGTGTGACTCAC

and the highlighted match area is

ACGATGACAACGATGAC

So this structure should be fine because the sequence lies along a stem-loop structure.

I am worried about that bulge on the left top corner though. That doesn't affect the predictability of this structure does it?


texts: Does the harvesting time of broccoli sprouts change their glucoraphanin content and sulforaphane formation capacity?

texts: Does anybody know if the harvesting time affects glucoraphanin content and sulforaphane formation of broccoli sprouts? Do they also get affected by light exposure or lack of it?


texts: Introductory biology text for an outsider

texts: I'm a maths major and I have an interest in learning biology. I know very, very little; I know how babies are made and that's about it. Could anyone recommend a stimulating text to read for its own sake and also to use to learn biology?


texts: It seems impossible to have reptiles the size of dinosaurs, just because they are really big! Did they have different systems of maintaining body temperature or maybe they weren't the exact type of animals that we today call reptiles?


texts: How can biologists rule out multiple early organisms that went through conjugation?

texts: The current idea is that all life evolved from a single cell. Analysis indicates the probability of two different origins being very unlikely, given shared DNA. However, why couldn't numerous organisms have evolved and then conjugated, with a few lineages surviving? It would vastly increase the odds of modern organisms sharing the DNA that they do.


texts: Do SSRIs downregulate or upregulate the 5-HT3 receptor?

texts: What effect do SSRIs have on the expression of the ligand-gated ion channel, the 5-HT3 receptor?


texts: Why can Toll-like receptors be found either inside and outside the cell?

texts: Innate immune cells may present Toll-like receptors either inside (TLR3 and TLR9, for instance) or outside (TLR4 and TLR5, for instance) the cell, but is there any beneficial reason for this? If so, what is it?


texts: Calculating Protein Concentration from Kilo Units (KU)

texts:
I am looking to purchase Pyruvate Kinase from the Sigma Website, they state the volume in Kilo Units (KU) i.e. 1, 5 or 25 KU. It also states there are 350-600 units / mg protein.

Does this mean one unit is one protein? so 1KU is 1000 units of protein?
What is the relationship between the KU and mg? and how can I use this relationship to calculate my concentration in um or mg.

EDIT

In this paper (look at the methods section) they calculated the concentration of 25,000 units of calmodulin in 0.5 ml to be approximately 75um which is 40,000 units/mg. How did they calculate this?


texts: Is there a specific suffix for "within a cell"? i.e. in a similar manner to how -aemia refers to within the blood

texts: Words like hyperglycemia and hyponatremia refer to the relative level of each component in the blood, not in the cell. Is there a suffix for within the cell? For reference I would like one word as an alternative to "hyperglycemic cell".


texts: As DNA is organized in a double-helix, a change in one strand must be accompanied by a corresponding change in the other strand. Let's say an original sequence CATCAT mutates into CATGAT. The other strand must change from GTAGTA to GTACTA - or, more precisely, as the other strand is read in the opposite direction, from ATGATG to ATCATG, possibly in a completely different gene. Has the effect of this pairing of mutations been explored mathematically?


texts: What is this beautiful pink flower plant seen at Bodnant Gardens?

texts: Seen at Bodnant Gardens, North Wales UK.


texts: Is it possible to have sleep paralysis while sleepwalking?

texts:
At least from a conceptual level, these two disorders don't conflict. The effect of sleep paralysis is being conscious while having the inability to consciously direct motor functions. Sleepwalking is the unconscious direction of motor functions. So combining the two, the effect would be that you are consciously aware of yourself and your surroundings while you are also unconsciously moving about, outside of your conscious control.

Therefore the only way the two wouldn't be possible together is if their activation conditions were mutually exclusive.

From wikipedia

  Sleepwalking occurs during slow-wave sleep (N3) of non-rapid eye movement sleep (NREM sleep) cycles. It typically occurs within the first third of the night when slow-wave sleep is most prominent. Usually, it will occur once in a night, if at all.

https://en.wikipedia.org/wiki/Sleepwalking#Causes

  The first of these stems from the understanding that sleep paralysis is a parasomnia resulting from dysfunctional overlap of the REM and waking stages of sleep.

https://en.wikipedia.org/wiki/Sleep_paralysis#Pathophysiology

So from a small amount of searching it seems it is not possible, unless SWS, REM, and the waking stages of sleep can all be overlapped.


texts: What is the role of lactic acid bacteria (such as L. acidophilus and L. bulgaricus) in glycolysis during yogurt fermentation?

texts:
I am trying to prove that an increase in monosaccharides (glucose, fructose, galactose) that have been added to milk during fermentation will result in a decreased pH. My current argument is:

"The increase in the concentration of Phoenix Dactylifera is representative of an increase in the disaccharide, sucrose, and the monosaccharides, glucose and fructose — the primary sugars in date palm. This source of sugars adds to the natural sugar content already found in low-fat milk, which are lactose molecules composed of glucose and galactose. As such, more energy from these carbohydrates are available in the process of glycolysis, where LAB facilitate the conversion of six-carbon sugars like glucose, fructose, and galactose into pyruvate. This creates a greater frequency of glycolysis reactions, resulting in a greater overall yield of pyruvate molecules which can be converted into lactic acid. Hence, the increase in overall production of lactic acid increases acidity in the yoghurt and, thus, the pH."

What can I fix with my answer?


texts: Can proteins structure change depending of alimentation of an organism?

texts:
In my understanding protein are built using information caring by RNA. So a given protein should always have the same structure in a given organism has the DNA of this organism does not change.

I'm asking this question because peoples told me that "cow milk protein become longer because how we feed them today". But I don't understand how a protein can become longer or shorter.

Info: I have no background in biology.


texts: Can someone identify this stinging plant?

texts:
I have no idea where this plant came from, or what it is. What I do know is its leaves are covered in little hairs, there's little thorns growing all over it, and just by rubbing its leaf it burns you and leaves a red mark as well as blisters. It stung my mother and I would like to know what it is so I can find a remedy.

larger image:

http://i1094.photobucket.com/albums/i449/cupcaketurtle1/20150714_225505_zpskr24gklq.jpg


texts: Does a certain tumor type being invasive mean that it is highly metastatic?


texts:
Found this in my room and haven't seen anything like it before. It was about 4-5cm long and has wings. Flew away before I could get a better picture.
Photo taken from the Midlands, UK


texts: Could bacteria and phages be found in tissues?

texts:
in the literature, there are several studies of the gut virome and microbiome, for instance Reyes et al. on Nature (https://www.nature.com/articles/nature09199?error=cookies_not_supported&code=f5201dbe-3cda-4e09-ba17-688d0352ef81).
Now, it makes sense to find bacteria (hence phages) in stools. However, there are other studies reporting bacteria from tissue, for instance Kostic et al. on Genome res (
Article Genomic analysis identifies association of Fusobacterium wit...
). In this specific case, the identified bacterium (Fusobacterium nucleatum) is an endocellular parasite and has virulence factors that allows it to penetrate tissues. But my question is more general:
Would be normal to identify bacteria and bacteriophages INSIDE human tissues?
In particular, would whole genome sequencing metagenomic experiments be likely to identify bacteria genome from human tissues? And if yes, how can we explain the presence of bacteria inside loci that are supposed to be sterile?
Thank you


texts: The Lotka–Volterra equations describe how predator–prey interactions affect population growth. Do these equations describe parasite-host interactions? If not, how would they change by adding these interactions as well?


texts: A non human adaptive behaviour with a spandrel

texts:
Is there any adaptive behaviour in non humans which, when it is functioning as it was selected to do, creates a spandrel behaviour?

  In evolutionary biology, a spandrel is a phenotypic characteristic
  that is a byproduct of the evolution of some other characteristic,
  rather than a direct product of adaptive selection


texts: Origin of the biochemical term, Pi (inorganic phosphate)

texts:
I would like to know when the term Pi (inorganic phosphate) was introduced in the representation of biochemical reactions, how it was originally defined, and the justification given then for using it rather than an individual species of phosphate.

(I would also be interested in the current justification, but that’s probably another question.)

Let me provide some background to my question. Phosphoric acid (H3PO4) has three ionizations, which produce successively the species: dihydrogen phosphate (H2PO4–), monohydrogen phosphate (HPO42–) and orthophosphate (PO43–). At pH 7.4, according to the Wikipedia entry on phosphate, the main species are the mono- and di-hydrogen phosphates (61% and 39% respectively). The term Pi must have been introduced in the 1950s at latest (perhaps before the war), at a time when there would have been little knowledge of the nature of the species involved in reactions involving phosphate — certainly not at the active sites of enzymes.

One of the reasons I am curious to know how the term was introduced is the extent to which it persists in 21st century biochemical text books, where it would seem that many authors either do not know or do not care to explain to their readers why they are still using it at a time when much more is known about the reaction mechanisms. Neither of two well-known texts explain the different ionizations of phosphate, and give only parenthetical definitions in terms of a single species — different in each case: Berg et al. referred to Pi as orthophosphate, whereas Nelson and Cox’s, Lehninger  Principles of Biochemistry referred to it as HPO42–.

Acknowledgement: This question was provoked by the SE-Biology question — Where is the H+ ion in this step of glycolysis coming from?


texts: What is the most heat-tolerant organism?

texts: What is the most heat-tolerant (or heat loving - hyperthermophile) organism so far identified? What adaptations does this organism have in order to endure such high temperatures?


texts: Trade-offs between phage and yeast displays?

texts:
If you wanted to test a peptide you designed, you can do a phage display or a yeast display experiment to assess binding affinity.

What are the trade-offs between these two methods?

I've heard anecdotally that yeast display is more sensitive and closer to human cells?


texts:
What factors must be taken into account for the maintenance of the immunogenicity of ovalbumin antigen?

If the ovalbumin is aggregated, could we inject it for induction of immune reponse?


texts: Why were the earliest humans hunter gatherers instead of fruit eaters living on trees?

texts: How is it that the earliest humans who evolved from primates (who live on trees and mostly eat fruit) became hunter-gatherers (which seems like a harder, more stressful and more dangerous way to find food)?


texts: what do I need to use for protein protein interaction network

texts:
I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with another protein and a relationship

YAL011W YBR231C 0.804967
YAL011W YDR190C 0.790977
YAL011W YDR334W 0.840367
YAL011W YDR485C 0.815874
YAL011W YJL081C 0.574536

or sometimes I only see this

YAL011W YBR231C
YAL011W YDR190C
YAL011W YDR334W
YAL011W YDR485C
YAL011W YJL081C

what do I need to make a network ? and which structures normally used for making these networks.


texts: Identify bee in photo (found in Utah, USA)

texts: A friend took this photo of a bee in his back yard in central Utah (© Jon Mott, CC-BY 3.0). I have no formal training in systematics or entomology, so to me everything looks like the bees' poster child Apis mellifera. Can someone with a bit more experience confirm or refute this?


texts: Since humans and apes share up to 99% of their DNA, can they interbreed? For example, a horse and a donkey seem to be just as distantly related and produce offspring. Mules, however, are sterile. Would ape-human interbreds be sterile?


texts: RNA-seq Data on domestic animal with different environment

texts: I want to find the RNAseq data available on domestic animals in different environments. If microarray data is available, it would be more useful. If you know I would appreciate to inform me.


texts: Breakdown of functional human genome by organ/What fraction of the functional human genome is devoted specifically to brain functioning?

texts:
Of course, there won't be a precise known answer to the question, as it is not even known precisely what percentage of the genome is functional in the first place - but I am still looking for research.

The book "Principles of Neural Design" claims that "20% of our genome is devoted to coding neural signaling molecules". This seems not only vague, but also suspect to me, as that is more than the fraction of DNA that is known to have a function in the first place - maybe they meant only protein-coding genes?

One hears a lot about the human brain as "the most complicated object in the universe" etc., but I would like to put a number of that and compare the genetic complexity needed to express it to that needed for other body parts.


texts: What is the smallest pressure differential that humans can detect?

texts:
While cooking dinner under an extractor on its lowest setting, I noticed that none of the steam (referenced by the amount of fogging on a nearby window, compared to the absence of the fan, was effectively zero) was going anywhere else but through it.

However, placing my hand under the hood, I couldn't feel a difference in pressure. This is most likely due to two things: my hand smoothly transitioned from "normal" atmospheric pressure to the "adjusted" pressure near the hood, and the hood area is quite wide, so that extraction is done over the significant area not covered by my hand and hence less pressure applied.

But it got me thinking, and a literature check revealed nothing helpful so far, as to what is the smallest pressure differential detectable by the skin of the human body?

I would prefer to exclude anything related to hearing, as this is a well-researched area but tells us nothing about the other 99.9% of what is directly exposed to atmospheric pressure changes. Answers that cover particular parts of the body beyond skin and ears (for example, the eyes) are appreciated but only additional.


texts:
I just came back home a few hours ago from the airport and my aunt had peaches in her car full of ants. This made me wonder if the ants had joined us from the plane?

This leads to the question can ants can survive at high altitude?


texts: How does imbibition and turgor pressure generate much force?

texts: Both imbibition and turgor pressure together create a large force in plants such as force required to burst the seed coat open?


texts: Could Racemic Epinephrine be used to Treat Anaphylaxis?

texts:
To be clear, this question is not a personal health question nor a question seeking health advice, it is only a theoretical question born of a curiosity for the pharmacology and biochemistry of adrenalin/epinephrine... I have never in my life had any kind of allergic reaction and your answer bears no effect on my health or anyone else's health.  The answer will only serve to help a fictional story be as scientifically accurate as possible.

My question is: In theory, is racepinephrine (the active ingredient in Asthmanefrin) compatible as an emergency replacement for epinephrine to combat anaphylaxis?

As a side question, what effect if any, does benzyl alcohol have on epinephrine?

Thank you for your time I certainly appreciate it!


texts: What other cognitive behaviors in bees, outside of navigation, are affect by neonicotinoids

texts:
It is conclusive that neonicotinoids alter navigation in bees when locating food sources. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091364

But if so, shouldn't cognition also be affected? And if it is affected, then wouldn't the effect on the hive be even more pronounced due to inaccurate bee dances and an overall delay/inability in finding food source? Shouldn't this be conclusive in explaining neonicotinoids to be a contributor to colony collapse disorder?


texts: What is this row of pits along the "upper lip" of theropod skulls?

texts:
Consider the row of pits visible in the "upper lip" area (and to some extent, the "lower lip" too) of this T-Rex skull at the Palais de la Découverte, Paris (picture from Wikipedia):

I noticed similar pits in a Deinonychus skull a few weeks ago when I visited the American Museum of Natural History in New York:

What are they?


texts: Are there any animals that are unable to hear the human voice?

texts:
Humans and animals have different hearing ranges. The frequency range of a human, for example, is stated with 20 Hz to 20 kHz, whereas the fundamental voice frequency is stated with 125 Hz for men, 250 for women and 440 for children.

Now if I understand correctly, the hearing range of bats, for example, is commonly stated with 1 kHz to 200 kHz (depending on species). The hearing range of mice is stated with 1 kHz to 70 kHz.

Are there (apart from those with no sense of hearing at all) any animals that are unable to hear human voices at all?

(Edited in reaction to the first and the second comment below. Humans can obviously realise speech with energy at much higher frequencies. My examples are in this respect misleading.)


texts: How to identify the genes that distal enhancers pair?

texts:
I am writing a project proposal and I have to talk about this problem: how to identify the genes that distal enhancers pair?

I am really new to this topic and I don't know what it is all about. I have been searching the literature but I did not find anything useful. Can someone explain to me what it is all about?
Maybe suggest some papers to me.


texts: Why do we get tunnel vision during fight or flight response?

texts:
I have a question regarding tunnel vision during the fight or flight response. I believe that during fight or flight high levels of adrenaline are released which causes the pupils to dilate allowing more light to enter which allows us to be more aware of our surroundings. Why is it that sometimes we suffer from tunnel vision then? I know it allows us to focus on the main threat but if our pupils are dilated and more light is entering and hitting our retina how is it that we have tunnel vision? Shouldn't we see more now with a dilated pupil?
Thank you for reading my question!


texts: Behavior of plant guard cells: open or closed stomata

texts:
On an exam of mine, I had the following question:

  The interaction between the guard cells and stomata in a plant leaf can be seen in the diagram below.

  In which scenario could the guard cells and stomata be in situation 2?

  (A) High humidity

  (B) High light intensity

  (C) Low temperatures

  (D) Nighttime

The answer choices aside, I was thinking the answer should be along the lines of "a scenario in which the temperature is really hot", since an open stomata on a very hot day would cause a plant to lose a lot of water. The only answer choice that seems to fit this is "high light intensity" (although I'm not sure if high light intensity would necessarily cause high temperatures, but this seems to be the closest thing to what I predicted). However, the exam key is saying that "D", nighttime, is the correct answer. My teacher explained that since plants don't need to do the light reactions during the night, they apparently close their stomata because they don't need to intake CO2. But this doesn't make sense to me: why would a plant close its stomata during the night instead of keeping it open to stockpile CO2 for use in the day? If I'm not mistaken, this is precisely what CAM plants do (although there's no mention of whether the plant in question is a CAM plant).


texts: BWA-MEM single strand or doublestrand alignment

texts: In whole genome secondary analysis does BWA-MEM use a double stranded fasta reference or are reads aligned to only one, single stranded fasta reference?


texts: Why are there no complex hermaphrodite land animals?

texts:
The title says it all.  I know that 'complex' is a pretty ambiguous term to use, but I can't think of a more scientific term/definition for my meaning.  I can't think of any large (larger then a small rodent) hermaphrodite species, or any that we tend to think of as having complex structures; hermaphrodite species all seem pretty boring really.

I get why sex is a huge advantage, but by that regard hermaphrodites seem quite powerful.  The ability to both produce your own young and impregnate others allow for more young.  Plus, it provides the opportunity for a species to choose to self fertilize if no mate is available.  I realize sexual reproduction is preferable, by it's nice to have Autogamy as a backup option just in case.

I understand why there are advantages to two sexes, particularly in terms of sexual dimorphism which allows male to be better at potentially reproducing with many females by specializing in it.  I completely understand how two genders would evolve and be successful.

What I find odd is that nearly all larger or complex species seem to have genders.  I would have thought that, like many other mating strategies, there would be variance across species; with some choosing to be hermaphrodites to increase the maximum children they can produce as a species, by having twice the child bearers, and others choosing to go the sexual dimorphism route by having roles that they are best at.   I mean even Obligate parthenogenesis has evolved separately many larger specie like lizards, despite it arguably being an evolutionary dead end in the long term due to the lose of the advantages of sexual reproduction.  If adaptations that completely toss away the power of sex evolve all over the place why do new hermaphrodite species never seem to evolve, and existing hermaphrodite species never seem to grow bigger or more diverse?

In particular sequential hermaphrodite, like many aquatic fish use, seems a pretty effective strategy.  When your young, and small, play a female role to have guaranteed offspring, only once your big and at your most fit bother competing as a male for access to multiple mates.

A related question, associated with my own attempt to explain why existing hermaphrodite species don't seem to take as many varied forms; but which I'm not really sure I buy.  Is it possible that the lack of sexual conflict (primarily, but not limited to, competition between males for mates, driven from the fact that males would have more drive to compete then hermaphrodites since it's their only reproductive strategy), would mean there was less of a drive towards adaptation in hermphrodite species?  A sort of red-queen scenario, where your own species is the red queen?


texts: Are boat-tailed grackles efficient flyers?

texts: The boat-tailed grackle's deep-V tail would seem to cause a great deal of drag or even downward deflection (like an airplane's elevators). How much does this actually affect the bird's flight?


texts: Why are the results of local BLAST and miRbase BLAST different?

texts:
I am trying to reproduce locally on my computer what I get running mirbase on their website using BLAST. The search sequences is: mature miRNAs which I had downloaded on my computer and make it as a BLAST database with command:

./makeblastdb -in /home/marianoavino/Downloads/mature.fa -dbtype 'nucl' -out /home/marianoavino/Downloads/mature

then on mirbase I see they use an e-value of 10, which I leave locally.
On mirbase at the end of the analysis they give you these parameter setting:

Search parameters

Search algorithm:
    BLASTN
Sequence database:
    mature
Evalue cutoff:
    10
Max alignments:
    100
Word size:
    4
Match score:
    +5
Mismatch penalty:
    -4

and this is the command line I use on my computer for BLAST

./blastn -db /home/marianoavino/Downloads/mature -evalue 10 -word_size 4 -query /home/marianoavino/Downloads/testinputblast.fasta -task "blastn" -out /home/marianoavino/Downloads/testBLast.out

The results of the two analysis are different, with mirbase finding much more stuff than local BLAST.

Do you have any idea on which parameters I should use on local blast command line to match those listed mirbase parameters in order to get the same answer?


texts:
I am seeing C to T transitions in my sequencing data, but also some strange signatures that follow along with that. I am trying to understand the biology of what is occurring. In the data I see more C to T changes than G to A changes, when it would be expected that these numbers would be relatively the same.

So, in vivo when a C to T transition occurs, does the complementary base get changed to ensure watson and crick binding, or will you end up with a T-G pair? This would explain the phenomenon that I am seeing but I don't know if this happens. (Andy references would also be super helpful. Thanks.)


texts: What would cause E. coli to change from filamentous growth to normal growth?

texts:
In my lab we've observed a phenomenon in which a culture of E. coli is found to shift from normal rod growth to filamentous growth and then back to normal rod growth again several times over the course of 400 hours. This was shown by an OD600 graph which oscillates from high values (~5) to low (~0.5) (the culture was also viewed directly).

The shift to filamentous growth is usually associated with an SOS response in E. coli and this makes sense (the media is M9 supplemented with 0.2% casamino acid and 0.1mM thiamine hydrochloride), however we don't know why it switches back from filamentous to normal growth.

Has anyone observed a similar phenomenon? Does anyone have any suggestions why this might be happening?


texts: Why do we suddenly forget things, like PIN or phone numbers, that we've known for years?

texts:
Is it common to forget a 4 or 5 numeric code which has been used extensively for months and well remembered?

There's an article on the guardian describing this phenomenon and by the number of comments it seems quite common yet no scientific aspect trying to solve the mistery.

Is it some common phenomenon of the brain? Some erasing of irrelevant numeric things happening during sleep?


texts: How long can Legionella survive at 60°C?

texts:
I'm coding some stuff for water heaters and one of the functions is anti-Legionella.

Anyway, I've read on wikipedia that 90% Legionella dies in first two minutes if the water temperature is 60°C, but I'm interested in how long should the temperature be 60°C for 99.99999% of Legionella to die? (I guess I can never get to 100%)

Follow-up question: On what intervals should this be done so that the water isn't contained? Should it be one week, two weeks, several days?

Final question: If the water in a water heater has 60°C for 30 minutes every 2 weeks, would the water be safe?


texts: What is the name of this plant with small, 5-leaved divided pink blooms?

texts:
I found this in a forest in Karlsruhe (Germany).

The blooms are pink and have 5 leaves. Each leave is divided into two parts. It is pink and has a diameter of about 1-2cm.


texts: Barcode exchange between neighbouring cells

texts:
I am currently interested in equipping animal cells in a tissue with individual barcodes. These barcodes should get amplified in the cells (not to a cell degrading extent, of course), and also transmitted to neighbouring cells.

The question is now, how do I a) insert these barcodes into the cells and b) how do I transmit them to the neighbouring cells.

In the Zador et al. paper "Sequencing the connectome" (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001411), it was proposed to use a transsynaptic virus like as rabies or pseudorabies, for making that exchange possible between neurons that are synaptically linked. Here, however, I am interested in the directly neighbouring cells and I am insecure whether it makes sense to use transsynaptic virus here.

If so, it would be great, but if not, do you know some alternatives?


texts: What are "intrinsic hypothalamic fibers"? (From an article on neuronal mechanisms of sexual desire)

texts:
I came across the phrase intrinsic hypothalamic fibers which I cannot understand. What is meant by intrinsic - that these fibers (long myelinated axons?) start in the hypothalamus? Or that they start and end in hypothalamus? Or something else?
The article is "Pathways of Sexual Desire" by James Pfaus (2009).

Figure 8 Brain opioid systems overlaid on opioid binding regions (high density of receptors indicated by red to yellow, lower density in green to blue). Three systems exist: the pro-opiomelanocortin (POMC)-derived opioids such as р-endorphin, which arise from the same population of projection neurons that produce the melanocortins; the interneurons in the cortex, limbic system, hypothalamus, and brain stem, which produce enkephalins and dynorphins; and the intrinsic hypothalamic fibers, which contain endo- morphins. These systems are activated at orgasm in humans, at ejaculation in male rats, and during paced copulation in female rats. They shut down hypothalamic regions associated with sexual arousal and desire, thereby inducing refractoriness. However, opioids are also released in the VTA during phases of sexual arousal and desire and help to disinhibit DA neurons and, thereby increasing DA release in mesolimbic terminals. This is an important mechanism by which experience with sexual rewards sensitizes sexual excitement once the inhibitory effects of refractoriness and satiety wear off. VTA = ventral tegmental area; DA = dopamine; mPOA = medial preoptic area; mPFC = medial prefrontal cortex; NAcc = nucleus accumbens; PIR = piriform cortex; MeA = medial amygdala.


texts: In the future, it is plausible that we can change the physical appearance of a living animal by editing DNA?

texts:
http://www.independent.co.uk/news/science/revealed-scientists-edit-dna-to-correct-adult-genes-and-cure-diseases-9273555.html

This article explains that scientists managed to change the DNA of adult laboratory mice with an inherited liver disease, thereby curing them of the disease.

The change in the liver is not be a change in physical size and shape, instead it was a change in the liver metabolism.

If we used this same method to edit our hair follicles, could we alter our hair color? The new hairs would have altered DNA, and come out a different color depending on what the cells have been altered to.

And then, is it possible to change the physical size and shape of a living animal by editing DNA? For example, if an animal has porous and small bones, is it plausible that we could edit its DNA so that its bones start to become more dense and thick? The physical appearance of the living animal would be changed, since the bones are larger than before.

Along these lines, could we then edit DNA of an adult human to change bone structure so that we have sharper noses? Larger eyes?


texts: Pharmacokinetics and cell-membrane permeability of Adenosine triphosphate disodium hydrate

texts:
【My Question】
(1) Please tell me the pharmacokinetics of this ATP (or Adenosine triphosphate disodium hydrate) when it is administered orally or intravenously. In particular, Does this material has permeability to the Blood-Brain Barrier?
(2) When human cells (for example, fibroblast, MSC,…,) are cultured in a medium supplemented with this material, how much ATP is taken into the cells. (Please tell me about the cell-membrane permeability of this material.)

The known effects of Adenosine triphosphate disodium hydrate are as described below.

【Effects of this medicine】
This medicine increases the blood flow by its vasodilatory effect and activates the metabolism of the body to improves the functions of the organs.
It is usually used to improve symptoms accompanied by aftereffects from head injury; to treat heart failure or chronic gastritis associated with dysfunction of the digestive tract, Meniere's disease, dizziness based on inner ear disorder; to stabilize the accommodative function in accommodative asthenopia.

【References】
http://www.rad-ar.or.jp/siori/english/kekka.cgi?n=1808#

P.S.
P.S. I'm not very good at English, so I'm sorry if I have some impolite or unclear expressions. I welcome any corrections and English review. (You can edit my question and description to improve them)


texts: Does the Peptide bond produce water in our organism?

texts:
According to Wikipedia http://en.wikipedia.org/wiki/Peptide_bond , when a peptide bond is made a water molecule is released as a secondary product.

So, my question is simple (perhaps silly). Considering that proteins are being made every time in our organisms and this water molecule is being released in every peptide bond, why our bodies are not flooded of water?

Thanks!


texts: Can a mathematical function be assigned to ECG diagram?

texts:
This is a 12 lead electeocardiogram of a 26 year old male:

This is the graph of function $5sin(7x)sin(.5x)cos(3.25x)$
 This graph look quite similar to the ECG diagram.After sketching this graph, I thought whether ECG diagram could be assigned roughly to a mathematical function.

Question: Has anyone ever tried to even roughly assign the diagram to a mathematical function? Is it even possible?


texts: How to determine whether a newly discovered dinosaur is not a young one and not an entirely different species?

texts:
Every once in a while, there is an official announce that a new species has been discovered. For example, paleontologists have recently discovered a dinosaur they named Nanuqsaurus hoglundi, which really resembles Tyrannosaurus Rex, but in a smaller version. It also lived during the same era. Is there something that indicates it's a cousin of the T-Rex, and not Mr. Rex's son?

Other small dinosaurs include the Compsognathus, the Microraptor and others. Why were they classified as new species when they were discovered?

Considering evolution over a few million years, my guess is that some earlier species may have been smaller and evolved into more complex animals, bigger bodies, horns, frills, etc.


texts: Does boiling or frying fish make Omega3 be denatured?

texts: I read some articles about omega-3, and I found there are two different opinions about how sensitive omega-3 is to heat. one is Applying heat to omega-3 make omega-3 become trans-isomer which is very bad for the body. and the other is Applying heat to omega-3 doesn't make omega-3 become any bad compound. I want to know which is true. I think maybe Applying heat to omega-3 make trans-fatty acid, but I want to know exact temperature. and what about boilling or frying fish? Wiil applying heat to fish make trans-fatty acid too?


texts: What are the migratory patterns of Orcas in the Pacific Northwest? Do they pass by Vancouver in the Fall?

texts:
What are the migratory patterns of Orcas in the Pacific Northwest? Do the pass by Vancouver in the Fall?

I know you can never predict the sightings of a wild creature, but I was wondering what the migratory patterns of orca pods are in October in the Pacific Northwest, and what the possibilities are that they may be passing through Vancouver?

How large is the population of the migratory orca pods passing in the fall (if one can even know that)?

Thanks!


texts:
I just received a small plant as a gift from a friend.

Here is its leaf:

I tried looking it up on flowers of India, but their database is too much to read manually.

Physical description:

It's short, around 5 inches, probably a flowering plant as per my experience (She says it is a cactus but I don't think so). The leaf is around 1.5 cm and has a cone+cylinder like structure.

Which species is this plant, and is it a flowering one?

Any help would be great.


texts: Why are (some) cats attracted by bleach?

texts:
(Sorry if this question is only partly biological)
I have noticed that several cats (including the one that keeps sleeping in my house), are fond of the odor of bleach (eau de Javel) and chlorine.

Among examples, chlorine is used in small quantities in tape water and the cat is fond of licking the faucet in acrobatic positions even if there is mineral freshwater nearby.
I was one day not careful enough using a bleach based gel cleaning product and some of it got on my hand. Even after cleaning my hands, they still had a bleach "perfume" and my cat cling to me and even cleaned my hands with his tongue for minutes.

Why is this so ? Are there other animals known to have this taste ?
Might it be in fact acquired through living with humans ?
Is this potentially detrimental to their physiology ?


texts: Balancing selection can maintain polymorphisms in natural populations for extended periods of evolutionary time. However, in this paper, Dannemann et al. 2016 identify three archaic haplotypes in the modern human genome that are due to adaptive introgression. Why can we exclude that haplotypes III, IV and VII (the introgressed haplotypes) have remained in the human gene pool since the split between modern humans and Neanderthals because of balancing selection?


texts: What species is this blue and white bird?

texts: I want to know what kind of species this bird is


texts: Chromosome and chromatid numbers during cell cycle phases

texts:
A diploid cell in G1 has 6 chromosomes. How many chromosomes and how many chromatids are present in each of the following stages?

Here is what I am guessing

G1: 6 chromosomes ; 6 chromatids
G2: 6 chromosomes ; 12 chromatids
Prophase: 6 chromosomes; 12 chromatids
Metaphase: 6 chromosomes; 12 chromatids
Anaphase: 12 chromosomes; 12 chromatids
Telophase: 12 chromosomes; 12 chromatids


texts: I have read that the furniture beetle (Anobium punctatum) has larva that will burrow for three to four years in wood before emerging and pupating. How do they obtain water during that time if they are just eating wood?


texts:
A couple of years ago I saw a BBC Horizon television documentary about sugar and fat. One section mentioned three experiments in which rats were given their ordinary rat food plus and unlimited supply of:
Experiment A. Unlimited sugar
Experiment B. Unlimited fat
Experiment C. Unlimited sugar&fat mixed together (50:50)
The stated results were that in experiment A the rats did not put on any weight, in experiment B the rats put on weight but not much and in experiment C they put on loads of weight and would eat the 50:50 mixture to the exclusion of their ordinary food. I also remember the documentary said the 50:50 ratio was critical and if the ratio was shifted too far in either direction then the weight gain effect reduced sharply.
I have two questions. 1. What was the original research paper. and 2. Have there been any related new results with other mixtures like sugar/salt fat/salt?
EDIT: I have just found this related paper. I don't know if its the exact one relied upon by the documentary, but it's certainly close... perhaps the documentary employed the results from multiple papers.
EDIT: You can see the whole documentary here: https://www.dailymotion.com/video/x1arpze - the rat experiment discussion begins around 46 minutes in.
EDIT: years later... I found this and this.


texts:
I'm hoping to do a clonal expansion of Jurkat, expressing my construct which is currently transduced virally. From the FACS data I currently have roughly 30-40% expression in my culture but I need it to be close to 100% as the effect I'm looking for I believe to get diluted by the reduced presence of my molecule of interest in the total culture. I can do cell sorting but usually what happens is that the 5% cell population that do not express the construct eventually take over after a few passages.

I'm planning to do a 96 well plate format single cell seeding and expansion of Jurkats but it has been done before by another member of our lab and the person suggests that single cell Jurkats (unlike CHO cells) do not survive a single cell state although they are suspension cells and do not necessarily require contact to survive although they clump. Hence I'm wondering if anyone has any protocols they could suggest such as contents of the media (e.g. conditioned media) or any other recommendations for Jurkat single cell clonal expansion.

P.S. I am fully aware that there might not be a single right answer to this and the answer requires a degree of experience/opinion on the working method but I would fully appreciate any helpful suggestions/responses.

Many thanks


texts:
I have two different papers. One claims that gut motility is reduced by stimulation of the Opioid κ and δ receptors. The receptors are activated by Morphine and certain derivatives, specifically Codeine, Fentanyl, Hydromophone, Methadone, and Oxycodone.

The second paper claims that gut motility is reduced by blocking the 5-HTb3 receptors.  Antagonists or competitors to the 5-HTb3 receptors being Morphine and certain derivatives.

Are these two different theories, two different action mechanisms, or am I missing something?


texts:
When the DNA replicates, it first attaches RNA since the DNA polymerase can't attach DNA in the 3' end. Why the replication is happened this way?
If the DNA polymerase can attach DNA from the 3', the replication process will be much simpler.
Is there a special reason for this?


texts: How does a heat-ratio sap flow sensor work and how invasive is it?

texts:
The Gizmodo article Undead Tree Stump Is Being Kept Alive by Neighboring Trees says:

Leuzinger and Bader stumbled upon the stump while out for a hike. The woody stub caught their eye because callus tissue could be seen growing over its dead and rotting parts. It was also producing resin, which indicated the presence of living tissue. This prompted a more thorough investigation in which the researchers measured water flowing through the tissues of the stump, and also its rate of respiration, which matched those seen in the surrounding trees.
“We measured water flow with ‘heat-ratio sap flow sensors’,” Leuzinger told Gizmodo. “They detect water movement in tissue by sending out very small heat pulses and measuring how quickly that heat dissipates.”
These measurements indicated that the kauri stump is inactive during the day when living trees transpire. But during the night and on rainy days, the tree stump becomes active, circulating water—and presumably carbon and nutrients—through its tissues. As the authors write in the new study, these results

"...indicate that such symbioses may be much more complex than previously assumed: by physiologically exploiting ‘‘downtimes’’ of transpiring trees during the night or rainy days with high water potentials in the root network living stumps seem to act partially autonomously, strategically tapping into resources rather than simply becoming part of the neighboring trees’ extended root networks."

I can get a general feeling for the principle. After a thermal pulse the local temperature of a probe will decay due to heat diffusion, but if there is movement of water (or sap) in and out of the area the decay will be faster...
But I have a few questions:

How exactly would you analyze a temperature decay curve $T(t)$ in order to determine if there was water, sap, or any material moving in and out of the volume or not? Is there a distinctly different shape to the curve that rules out thermal diffusion alone, demonstrating that there must be mass flow as well?
When used on trees, how is this instrument applied to the tree? Does it need to penetrate into live tissue to work, or can it work by proximity, perhaps using radio frequency or microwaves for heating and a surface contact thermometer?


texts:
Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI.

Specifically, I am not sure if NCBI includes the mass spectrometry data / datafiles in their FTP server related to any of their chemicals. So I am just wondering if there is an open database of mass spec datafiles out there somewhere.


texts: Follow-up to The Red Queen by Matt Ridley?

texts: I just finished reading The Red Queen: Sex and the evolution of human nature by Matt Ridley. Since this book is over 20 years old, I was wondering if more recent research made part of the book obsolete or inaccurate in some way. If so, would you have a recommendation for a recent book that would be a good complement to it?


texts: What's the use of DNA sequencing results?

texts:
Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA "string" - the sequence of nucleotides.

What's the use of that? It's just a "string" where nucleotides encode something but I have no idea what they encode specifically. So to me it looks like some raw data, just represented as a sequence of elements.

How is having the entire DNA sequenced useful?