texts: Cellulose acetate membrane filters vs. glass microfiber filters

texts:
At equivalent pore sizes and pressures, which exhibits faster flow rates, cellulose acetate membranes or glass microfiber filters?
I know cellulose acetate exhibits low protein binding, but what about glass microfibers? Would they be suitable when protein recovery is essential?


texts: Why are the genomes of some trees so large?

texts:
For example, the current largest known genome belongs to a tree: http://motherboard.vice.com/read/the-largest-genome-ever-sequenced-belongs-to-a-tree

I have heard that this could potentially be because trees require many duplicates of certain genes because they live their entire life exposed to direct sunlight.

Does anyone know of some specific scientific hypotheses for why this might be the case?


texts:
A seedling has popped up in one of my planters (acid soil; Toronto, Ontario).
What is it?

June 4, 2020:

June 20, 2020:


texts: The GUG start codon in E. coli: identity of initiating tRNA and efficiency of translation

texts: Translation in E. coli is usually initiated at an AUG codon, which encodes the amino acid methionine. In some cases, however, the start codon is GUG, which normally encodes valine. If GUG is used as the start codon, is a tRNA charged with methionine used or one charged with valine, and does the use of GUG as a start codon affect the efficiency of translation?


texts: What is this? I found it in tofino, Vancouver island

texts: I'm wondering what this sea creature is that I found washed up on McKenzie beach in Tofino, Vancouver Island? It wasn't dried up or anything. I've seen hundreds before but I cant find anywhere on the internet what they are!


texts: Recommendation of a comprehensive book on the history of medicine

texts: I was wondering if somebody could recommend a book on the history of medicine, be it comprehensive or an introduction to the history of medicine. I know there are a lot of medical books that cover this subject, but given that I have a limited amount of time for reading I was wondering which book would make the best use of my time.


texts: Why doesn't our immune system react to infused antibodies produced in a horse?

texts:
Calmette tried injecting horses with snake venom and then taking out the serum which has produced antibodies against the venom and injecting in the snake-bitten human.

Shouldn't our immune system recognize this exogenous protein and try to eliminate it as it's a non-self protein?


texts: How to generate protein graphics for illustrating articles?

texts:
The structure of insulin shown below appears in a Wikipedia entry.

What software was (or can be) used to create pictures of this type?


texts: What are the principles of stem cell engineering?

texts: Suppose you want to convert the skin cell into a pluripotent stem cell. I know there are a few genes that were identified for this purpose (a recent Nobel Prize). But apart from finding such genes, it also seems to involve maintaining the right environment, such that some critical receptor doesn't get triggered and alter the entire expression. It also seem to involve ensuring gene expression stability after the change has occurred. Could someone add to this? What are the broad paradigm ideas in stem cell engineering?


texts: How is nutrient uptake in humans measured?

texts:
There are many claims made about nutrient absorption, eg "Juicing helps you absorb all the nutrients from the vegetables".  I'm curious to know how nutrient uptake is measured.

Eg is it a pure nutrients in vs nutrients out equation?  Or are blood levels of nutrients measured before and after consumption?

What ever the methods, are they reliable enough to support claims made about relative absorption rates of certain diets or eating practices?


texts: How are bones growing, if bones are not connected to the brain?

texts:
If the bones are not connected to the brain, how is their growth controlled?

This question is not a duplicate of the question Mechanisms of bone growth, as this question deals with how bone growth is controlled, and not which bone structures or bone tissues are involved.


texts: Eukaryotic DNA polymerase in Leading and Lagging Strand

texts:
Different books say a different specifications on which eukaryotic DNA polymerase work in leading strand and which DNA polymerase work in lagging strand.

TL,DR: Which one is reality? and if there are multiple possibility, then which one is applicable for which organism (such as human mammal, yeast fungus, Arabidopsis plant etc.)?

Information greatly varying Such as,

According to book The Cell by G.M. Cooper (NCBI), in mammalian eukaryotic system, DNA polymerase δ works in both leading and lagging strand.

According to book Molecular biology by R. F. Weaver, ed-5; DNA pol- δ works in lagging strand and pol ε works in lagging strand and DNA pol ε work in leading strand.

Fundamentals of molecular biology, Lizabeth Allison (Semantic Scholar) says another thing, it says pol ε works on lagging strand.

The paper by Stillman B. , DNA polymerases at the replication fork in eukaryotes. (NCBI) (NCBI-PMC) (FIGURE) says in SV40 viral model the δ polymerase works in both strand but in cell chromosome, δ works on lagging and &epsilon works in leading strand.

Now which one is true? if all are true then does they applicable on different organism?


texts:
Why does looking at bright light trigger sneezing in some people?

Are there any recent studies that have found a cause for this Photic sneeze reflex? The Wikipedia article only references studies pertaining to the effect, stating that the cause is unknown. The article also states that "the condition affects 18–35% of the population", which seems to be quite a large percentage.

What could have lead to the development and persistence of such a genetic trait in humans? Are there any evolutionary advantages to this?


texts: Manifestations of open foramen ovale in adults

texts:
I read that foramen ovale opens in 30% of adults.
I do not know how much of these openings can then close again.
Probably, none.
It is not pathogenic if no symptoms.

It allows blood to enter from right atrium to left atrium (fetal), but from left atrium to right atrium in adults.
Assume that 50% of blood is doing so in adults.
This means that 50% of blood is not oxygenated.
Heart has to pump stronger to get some level of oxygenated blood as before.

Some thoughts about manifestations of open foramen ovale

hypertension
ischemic hypoxia
Clubbing
possible organ failures
higher risk for infections, SIRS and sepsis

Therefore, I think open foramen ovale can be a risk factor for myocardial infarction.

What are the manifestations of an open foramen ovale in adults?


texts: which of the two is the best method for presenting specimens in museum style?

texts:
A while back I had to preserve pieces of shrubs and trees then present them in a museum-style, for a course module at university.
A friend of mine opted in sticking them to a white A3 page with PVA glue, whilst I decided to tie them using string and needle, then knotting the string and taping over it with white tape.
It was my first time doing something like this and whilst we did fairly well, I was wondering, which of the two methods is better for preserving and presenting these species, overall?


texts: From inflammation to sickness and depression: when the immune system subjugates the brain

texts:
Recently, some research, for example this article has proposed that inflammation can cause innate immune cells to produce pro-inflammatory cytokines that act on the brain to cause sickness behaviour.

My questions are:

(1) What medication would potentially help to reduce the inflammation? I am not a biology expert so I do get a little confused reading the research articles.

(2) What are cytokines in laymen's terms? Are they the same as histamines which cause allergies?


texts: Can anyone please identify this plant and confirm if the species is Synsepalum dulcificum (Miracle fruit)? Pics were taken near my house in Bangalore. Because the miracle fruit plant is not native to India, I'm guessing it is a different species.


texts: Watermarks visible during DNA fingerprinting?

texts:
Let's say we have a human man that was somewhat genetically modified from the very beginning (conception?) by a team of scientists, and is also a product of careful selective breeding. They did this hoping to produce a specimen that would  certain physical characteristics such as superior size and strength, speed, vision, sense of smell, things like that that would result in a "perfect soldier" type of man.

Is it plausible that the team of scientists, like Craig Venter's team, could have installed Watermarks in this man's DNA that would show up on a DNA fingerprint? A DNA fingerprint done by the American FBI?

A user on this forum suggested this possibility in a former thread, so I mean no disrespect to that user by asking this question. I'm just interested in feedback from others. I am writing a novel and this is research for the story. Without getting too deep into specifics, I'm trying to find a way for the authorities to become alerted to the fact that this man is abnormal from other humans.

Any input greatly appreciated.

EDIT:

Basically, I am dipping my toe into the deep end of the pool. I know only the very basics of DNA fingerprinting and Genetic engineering, so technical language is hard for me to follow. I appreciate the answers very much but I'm still a little in the dark. Another user on this forum suggested that possibly "watermarks" might show up on the test, which is why I'm attempting to rephrase the question.

I have written a scene into my novel wherein my main character, a man that has been genetically engineered, unbeknownst to him, gets into a fracas with some bad guys and he wreaks havoc and escapes. The American FBI gets some of his DNA from the scene and works up a DNA Fingerprint on him, purely for the purposes of identification if they catch him. so, yeah, just like on CSI or whatever on TV. When the technicians complete the fingerprint, they recognize that something is different about this person and they contact the lead investigator to let him know. Perhaps they see some evidence of genetic modification or something that raises their eyebrows and they feel it's worth mentioning.

So, essentially all I'm asking is if that is at all possible, and what could they conceivably have seen in the fingerprint? If it's completely not plausible then I'll either delete the scene or rewrite it.

Thanks.


texts: Brain response frequencies while sleeping

texts:
I'm not sure if this is the right place to ask this but Biology seemed to fit best.

I'm trying to find out what frequencies the brain responds to best while sleeping.

The reason for this is recently I attended a lecture where it was stated that the brain hears low frequencies/deep noises better, meaning fire alarms for example might not be as effective as we think.

However I remember there was an episode of The Big Bang Theory where they said high pitch noises are heard better while sleeping as a built in response to, for example, a baby crying. Now I know this is just a TV show but I presume they must have some basis for the remark since they do have science advisors, it also just seems to make more sense.

Does anyone know which is correct or better yet can point me in the direction of some research to help.


texts: When giving blood, what is the specific Iron measurement they take?

texts:
I went to give blood the other day, and they take an "iron" measurement prior to actually drawing the blood. My level was 16.4 -- but what specific type of iron were they measuring?

I've heard of ferritin, transferrin, iron binding cap, total, etc., but when I asked what the upper limit was, she said 19, which didn't really fit within the healthy ranges I can find for the above types.

Thoughts?


texts: How many times did terrestrial life emerge from the ocean?

texts:
Evolution is often mistakenly depicted as linear in popular culture. One main feature of this depiction in popular culture, but even in science popularisation, is that some ocean-dwelling animal sheds its scales and fins and crawls onto land.

Of course, this showcases only one ancestral lineage for one specific species (Homo sapiens). My question is: Where else did life evolve out of water onto land?

Intuitively, this seems like a huge leap to take (adapting to a fundamentally alien environment) but it still must have happend several times (separately at least for plants, insects and chordates, since their respective most recent common ancestor is sea-dwelling). In fact, the more I think of it the more examples I find.


texts:
During the rainy season in India I see these miniature plants forming a light green mat over the green algae on my house's roof.

The interesting thing is they become very green and mushy after it rains. The rest of the year in dry winters and summers they go off green (kinda brown) and survive till the next rainy season.

I suspect them to be mosses/liverworts. What do you think?

Adding some more pics-

The small wood piece in the above photo is around 3 cm in length. (For comparing the size)

Temperature when these pics were taken was around 35°C and it was quite humid.


texts: Can it be said that proteins determine phenotypic traits?

texts:
I am not ignoring the function of genes, or the gene-environment interactions. What I want to know is if behind every "observable characteristic" we can find a protein -or a group of proteins- which is responsible for that trait. The idea comes from a school curriculum, and it is expressed as follows:

  In this unit the core topic is the central role of proteins as executors of fundamental biological functions and thus as responsible of an organism phenotype...

Thank you in advance.


texts: Ribosomal RNA amount in a Drosophila cell

texts: I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to get rid of rRNA. Thanks


texts: How did shellfish and coral survive acidic oceans in earlier eras?

texts: Throughout most of Earth's history, the planet has had more CO2 in its atmosphere, correct?  Therefore th pH of the oceans was even lower, right?  So how did CaCO3-using animals create their shells back then?


texts:
I've been living in my apartment for a year now, and noticed something lately. During spring and summer I have quite a lot of midges indoors, and even now there are some. But there are no spiders! So my question is a bit of the opposite of what all spider/house related articles are about: how do I get more spiders to my house?

Some info about my place: I live in a 40 year old apartment in Rotterdam, Netherlands on the second floor. It's always between 17 and 20°C, and the place is poorly isolated; plenty of cracks for visitors to crawl through. Also, I usually have a window open a bit. I have quite a lot of plants, and an aquarium, so I guess air humidity is relatively high. There is a large backyard with lots of weeds and some trees, however people use it for dumping old furniture so it is not a real garden (it's most likely the source of the midges).

Can I do something to stimulate spiders to come to my house?


texts:
We were studying butterflies in class and I asked my 7th grade teacher, but she deemed the concept "too complicated." I'm really curious now, not only about butterflies but insects in general...

Thank you!


texts: Evolutionary explanation to why we have such large memory capacities?

texts: The scientific consensus is that no one ever fills up their memory capacity by learning facts and so on, even in the information age.  My question is therefore, is there an evolutionary reason as to why we have evolved to have such large memory capacities, when we never come close to filling it up?


texts: How long does it take for a cell to synthesize an enzyme?

texts: Where can I find data regarding the times distinct cells take to synthesize distinct enzymes?


texts: How Incomplete dominance can be explained at molecular level?

texts: What is exactly happening at the molecular level when two alleles constitute incomplete dominance? Whether the protein formed from each of the alleles constitute a new protein having a different function or anything happens at the RNA level of the two alleles.


texts:
I am wondering how do genes become sex-biased? that is, how does a gene evolve expression which is regulated in a sex-specific manner (assuming no effect from sex-limited Y/W chromosomes).

I understand that gene duplication can lead to two sex-limited genes, the derived being expressed in one sex and the ancestral being expressed in the other.

Can the sex determining cascade cause sex-biased expression of a single locus? My thinking is that upstream differences between males and females might bring about regulatory opportunity to loci under sexually antagonistic selection over expression level. For example, if males favour upregulation in a locus, males who evolve some kind of transcription factor affecting that locus which responds to male-specific isoforms of DSX (in Drosophila), which could then cause the antagonistically selected locus to be more highly expressed in males without producing a negatively selected correlated response in females.

Is this correct? Are there other ways?

(Note: I'm looking for a clear explanation of the mechanics behind sex biased gene expression. Drosophila examples would be of particular worth)


texts: Why does evolution only involve heritable traits?

texts: If natural selection favors a certain behavior that is learnt, then wouldn’t that behavior be found more often among a population (as more offspring will learn that behavior from their parents or their peers)? Since the behavior is not encoded in the genes, it is not heritable, but it is transmitted through other means and will thus accumulate in the population. This, to me, seems a lot like the effects of evolution, yet this is not a heritable trait. So my question is why does evolution concern only heritable traits and not those that can be reproduced by learning?


texts: How exactly does symbolic language for apes work?

texts:
I'm talking about the panels with lots of colored symbols on them you sometimes see in documentaries and the like. Apes point at the symbols in a specific order and in this way can communicate with humans.

I already googled around a lot, but wasn't able to find any detailed explanation on how exactly the language works (meaning of all the symbols, grammatical structure of the language and so on). It might just be because I don't know what words to use for my search, so can anyone with more expertise in the field point me in the right direction?


texts: Serological assays not detecting native proteins

texts:
Is there anyone out there who has done much work with serological assays? We have antiserum for a manufactured viral protein but no luck so far getting it to detect native protein (unless today's attempt worked which we will find out tomorrow).

What are any common problems or possible considerations that we should bear in mind when testing?


texts: Why do changes in preload not cause changes in end systolic pressure?

texts: I am trying to understand why changes in preload do not cause concomitant changes in end systolic pressure. If you have preload enhancement than this should lead to an increase in cardiac output..increased cardiac output at a constant heart rate I would think would lead to increased end systolic pressure. Why doesn't this occur?


texts: How long will a vegetable live for after being harvested?

texts: I understand this might depend on the types of vegetables, but is there an average or studied specifics? Does it die immediately? Is there a way to precisely diagnose death in plants? If so, what are the conditions for it?


texts: How to interpret weighted Robinson-Foulds distance between phylogenies?

texts:
The Robinson-Foulds (RF) metric provides symmetric distance between two phylogenies as a sum of monophyletic groups present in one tree but not in the other. The normalised RF distance is given as $\frac{RF_i}{RF_{max}}$. Let's consider an example:

require(phangorn)
set.seed(123456)
tr = rtree(10, rooted = FALSE)
tr2 = rtree(10, rooted = FALSE)
RF.dist(tr, tr2)
# [1] 12
RF.dist(tr, tr2, normalize = TRUE)
# [1] 0.8571429

The last row would mean that the trees differ by 86 % of their maximum distance. But how does one interpret the RF distance if it is weighted on branch lengths?

wRF.dist(tr, tr2)
# [1] 13.20986
wRF.dist(tr, tr2, normalize = TRUE)
# [1] 0.7600115

Is it 76 % of maximum tree distance given the sum of tree lengths of the compared trees?


texts: What is the most detailed living-tissue scan available

texts: There are a lot of ways to scan living tissue. What is the most detailed one to date? What kinds of resolutions can it produce? Is there a different answer for 2D vs 3D?


texts:
Blebbistatin is a drug that specifically inhibits the assembly of myosin in the cytoskeleton. What effect would you expect blebbistatin to have on intracellular vesicles?

The formation of vesicles would cease.
The movement of vesicles within the cell would cease.
The vesicle membranes would fail and release their contents into the cytoplasm.
The vesicles would be unable to fuse with the plasma membrane.

I don't readily see how Blebbistatin would effect intracellular vesicles; I believe this ignorance comes from not knowing what myosin is and how it interacts in the cytoskeleton.


texts: Effects of X-ray exposure on upcoming pregnancies

texts:
Recently we had a little fight with my girlfriend about the risks of genetic diseases for our potential baby. The thing is that she had her medical check recently and it included an X-ray examination of her chest. The doctor performing the scan warned her that she should not get pregnant for 3-6 months after the examination.

A note on the wall also read similar to this (in Chinese):

  医生建议与X光射线接触的备孕期的女性朋友，最好在3个月后再进行怀孕，以降低胎儿畸形的风险。

Which translates roughly as:

  To reduce the risk of fetal malformations, doctors suggest that women who have had X-ray expose are better to avoid getting pregnant withing three months.

(I guess, this advice might come from the fact that an egg develops for about 150 days before being released to the ovary?)

However, since the average radiation dose of the X-ray chest exam is reported to be around 0.1 mSv (which is about the dose of radiation you get by a couple of round-trip flights: from the US to Paris and back), I have doubts that this piece of advice has any solid scientific foundation to it. (Otherwise, I guess, airline companies should be legally bind to warn any female clients of dangers of transoceanic travel.)

Are there any studies that show effects of X-ray exams on future pregnancies? Can the risk of "fetal malformations" for any pregnancy starting shortly after an X-ray exam really be assessed?


texts: Stockholm format to dot-brackets format?


texts: Why is venom more common in fish and snakes than other vertebrates?

texts:
Reading this question, I wondered why is it that we associate vertebrate venoms so often with snakes and fish, and more rarely with lizards, amphibians, mammals, and birds (apparently never, in birds?).

Are venoms more advantageous for snakes and fish, or more expensive or dangerous to produce for the other taxa? Or is it connected to evolutionary history – is venom somehow more 'evolvable' for snake and fish lineages?

Or, perhaps, is it just chance?


texts: What type of distribution should binding affinities fit?

texts: I've been averaging Ki values from the PDSP Ki Database, and I can't help but to wonder: how I can determine p values for the binding affinities, so I can exclude anomalies in the data if need be?


texts: High frequency tone/ringing in movies/music and its effects

texts: I was watching a horror movie and I noticed during a scene that there was a high pitched noise playing in the background. It had been playing for a while before I noticed it and when I took notice it started to irritate my ears, however this isn't my concern. I noticed that while this noise played during the scene I was in a trance-like state almost felt like I was hypnotized, so my question is can these high pitched sounds be used put the viewer/listener into a trance-like state or hypnotize them and if so are there any scientific studies that prove or debunk my theory?


texts: How can antibodies in rapid antibody tests be kept at room temperature without denaturing?

texts: The normal temperature for long term antibody storage is around -20 degrees Celsius. However, when developed into rapid antibody tests, they can be kept at room temperature for prolonged periods. How is that possible?


texts: Can you please identify these yellow dot parasites which grow on non-living surface?

texts:
Little yellow dot parasites have screwed me for years and I still don't know how to fight back as I don't know what they are. I just know that they are living beings because they grow in number.
Images:

(Click the images to enlarge)
Location: North India
Size: Visible to naked eyes (one dot is approx 0.25 mm in diameter; their colony is upto 5 mm in length or diameter; their colonies aren't perfect circles as seen in the images)
Behavior: They grow on any plastic, metal and glass surfaces (but not on clothes, walls or wood) if they are stored in open (the surface is in contact with oxygen)
Can you please identify it?


texts: What do we mean by distribution of species?

texts:
What is meant by distribution of species in the following context?

  density-independent factors tend to limit the distribution of individuals and therefore of species.


texts: Once clonal selection is done, B cells would start dividing and producing antibodies. So, after an antigen is eliminated, what stops the division of B cells and antibody production?


texts: Quantifying the Genetic Basis of Complex Diseases

texts:
In general, there are 2 types of diseases for which we understand "causality" very well:

Infectious disease, where there is some etiological agent that causes the disease and
Monogenic genetic diseases (e.g. cystic fibrosis), where there are a set of mutations that make specific proteins that are very important non-functional.

My question is not about these diseases. Rather it's about the diseases like T2D (type two diabetes mellitus). Simply put, are complex, chronic diseases like this always traceable to genetic causes? For a given complex disease state, is there always a set of genotypes that leads to the disease? Large-scale GWA (genome-wide association) studies of course have upturned tons of disease-associated variants in complex conditions like T2D, most with tiny effect sizes.

But is it possible to get the disease with none of the disease associated variants (even assuming that you had a list of all disease associated variants; of course you don't actually have this list, but I'm just trying out an intellectual exercise)? If yes, what is the causal pathway for this way to 'get' the disease?

EDIT: To clarify my question as per comment suggestions: Do all (complex) diseases have a genetical background/causative mutation or can they arise for other reasons?


texts:
eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia).

There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly proportional to the level of protein coded by that mRNA.[1]

It means that even if the abundance of mRNA is high, we cannot be sure that the abundance of protein is high as well. Why do we still need eQTL if we cannot derive abundance of protein from mRNA transcripts? In the end, the abundance of protein influences the disease rather than the abundance of a transcript.

Does a pQTL implement the idea of a relationship between a genetic variance and the abundance of a protein? I do not understand how a genetic variance can influence the protein level. I assume it is related with a post-transcriptional modification but how?


texts:
Is there any mathematical model to predict the behaviour and long-term consequence of counter-acting selection at different time scale?

For example, let's consider the bi-allelic gene A, with alleles A1 and A2. During a long period of n1 generations A1 is slightly beneficial (differential of selection: s1). After this period, follows a short period of n2 generations when A2 is highly beneficial (differential of selection: s2).

What mathematical model describes the frequency fluctuations of alleles and which allele will get fixed at the long term given the initial frequency ( f0 ), assuming infinite population size and random mating.


texts:
Hello everyone.
I have been seeing tiny critters like this one in bed and I started to worryif they are bed bugs. Although they seem different in appearance as well as the fact that they don't seem to bite, I wanted to be sure.
Sorry if the pic is a bit hazy, they are only about 1mm long.
I also did have a bit of a humidity issue since the roof was leaky.
Does anyone know how to get rid of them. I tried different insecticides around the bed and on wooden part of the bed but nothing works.
Could they have settled in my new mattress? :(


texts: Half-life and production rate of ion channels

texts:
There are "not millions, not a few hundred...somewhere in between (some tens of thousands)" of ion channels in a neuron.

Given the number of ion channels per neuron, knowing the  half-life of ion channels allows to calculate the production rate of ion channels, and vice versa.

I am looking for estimates of tpyical half-lifes of ion channels, somehow like this: "not years, not seconds... somewhere in between" but with better upper and lower bounds: months, weeks, .... minutes, hours.

Alternatively: estimates of production rates: "not thousands per second, not one per second ... somewhere in between".

[I know, that all numbers - number of ion channels, production rates, effective half-lifes - can change over time for a given neuron - this may have to do with long-term potentation. So I am talking about neurons in steady-state over a period in which no long-term potentation takes place. But I guess this won't change the rough estimates I asked for too much.]


texts: What would be the membrane's form if phospholipid tail lengths vary?

texts:
I was trying to visualize and draw the situation if the membrane lipid chain length varies.
I assume so many possible conditions if in a membrane some taller or shorter components mixed:
Such as:

etc.
But which one of this is correct? or all / some from them could be applicable?


texts: Is a haploid essentially half of a homologous pair? I understand that a haploid consists of only one set of each chromosome, so does that mean that if that chromosome was replicated the cell would become diploid and have homologous pairs?


texts: How to evaluate the efficacy of an antibody for fluorescence microscopy?

texts:
I'm trying to evaluate data taken from fluorescence microscopy with antibody staining, and am wondering whether there is any standard way to evaluate the specificity of the antibody for such measurements? In particular, I am interested in evaluating whether there is specific binding of the antibody to the cells in the experiment, or only unspecific binding.

By leaving out the primary antibody or taking a control antibody without specific binding, I can compare fluorescence intensity, and an increase in intensity in the actual experiment towards this control will indicate qualitatively that the antibody binds specifically. But I wonder whether there is a standard statistical test or something to get such a result in a more quantitative way?


texts: Which enzymes degrade dynorphins and what drugs inhibit these enzymes?

texts: Which enzymes degrade dynorphins and what drugs are there available to inhibit said enzymes?


texts: Interdependency between organsims on our planet and its relation to ecosystem?

texts:
I am not a biologist but I just wonder if all species are interdependent. I mean if the tiger becomes extinct does it affect the ecosystem? If the mosquito or mouse become extinct does it affect the environment and us?

I am asking because this question was raised by one of my friends when I was in favor of protecting tigers, lions but I had no answer to "tiger extinction will not affect humans".

So, is it true that the extinction of any species will affect all other species?


texts: List of proteins by number of amino acids / chain length

texts:
Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino acid sequences?

I'd like to start from the short & simple protein structures to see how their particular sequences of amino acids translate into their folding shape, and what those short chains are capable of doing in organisms. (I heard about the LILs, but they are artificially-generated and consist of just two amino acids, Lysine and Isoleucine, so not much variety to study in there :q )

But I'm quite new to these databases, they present a lot of details, but usually not the one I'm looking for, and one has to know what too look for first to get any meaningful information :q


texts: Does this recording sound like the pulses emitted by bats?

texts:
Out of curiosity, I recorded sounds in an area with lots of bats, hoping to be able to "hear" the bats communicating by lowering the ultrasound to a level down to the frequency which can be heard by a human.
After a bit of post-processing, I actually hear interesting sounds, but I'm not sure about the origin. It seems that the frequency of the pulses is too low compared to bats.
The final audio is available on YouTube.
Are those actual sounds emitted by bats? If not, what other animal could be the source of those sounds?
About the audio
The sound was recorded at 10 p.m. at 46°34'32.0"N, 0°20'45.4"E near a river, with more of a dozen bats flying in this zone. There is a bridge nearby, and the sides of the river are flat concrete, which means that there are a lot of opportunity for sound reflection (although high frequency sounds don't reflect well).
Zoom H5 with the default XY directional microphone was used. The bitrate was set to 24-bit. Unfortunately, I used the sampling frequency of 48 kHz instead of the maximum 96 kHz.
The following transformations were made to the original audio:

The pitch was shifted by -12 semi-tones, which means that the 20 kHz sound becomes 10 kHz, and 15 kHz becomes 7.5 kHz.

All sounds below 6 kHz were removed.

The sound was amplified.

Severe noise reduction was applied to eliminate everything but the actual sounds emitted by the bats.

The empty parts of the audio were removed.

The sound was amplified once again.

Frequency
The frequency analysis of the transformed audio a peak around 9 kHz (18 kHz in the original audio), slowly fading to suddenly drop at 16 kHz (32 kHz in the original audio).

hypertextbook contains many sources with different indications about the frequency range of the sounds emitted by bats, only a few referencing the frequencies low enough to be heard by a human:

Frequency Produced 10kHz-120kHz
Ramsey, Gabriel, McGuirk, Phillips, Watenpaugh. Holt Physical Science. New York: Holt, Rinehart and Winston Publishers, 1986.

while most agreeing on the fact that bats use frequencies higher than 20 kHz.

Most bats use frequencies in the range 20-80 kHz, only a few bats use frequencies less than 20 kHz.
Long, M.R. & Savage, J.G. Mammal Evolution. New York: Harper, 1976: 108.

The observed range of 18..32 kHz seems too low compared to the sources, but I have an impression that the frequencies vary a lot between different species of bats.
Pattern
When viewing the audio track (see below), each cry consists of several pulses in two to three sub-groups which are in turn in two groups. Each peak is a bit less than 1 ms. The second group occurs from 40 to 200 ms. after the end of the first one. Each sub-group is separated by 5 to 10 ms.
The frequency of every pulse doesn't vary, except the very first pulse. The first cry starts by a more quiet pulse at 6 kHz (12 kHz in the original audio). The second and third cries don't follow this pattern.
Hyperphysics indicates that there are three categories of sounds emitted by the bats:

Short clicks,

Frequency-swept pulses,

Constant frequency pulses.

It looks like it's still the third category which we are observing here, and the overall pattern looks similar to the one described for the bats.
The gap between the left and the right track is mostly irrelevant: at higher frequencies, microphones become more and more directional, and the sound is reflected less, which leads to such difference.

Note: this question was considered to be on-topic at Biology.SE on Meta.


texts: Is there a difference between polarity and hydrophobicity?

texts:
From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms?

For example what is the difference in these sentences:

Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues.
Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.


texts: Flowers in Arachis hypogea, are they clestogamous or chasmogamous?

texts: I have seen the flowers of groundnut, they open and remains open for one day, so they should be chasmogamous, but in my school book, they mentioned it as clestogamous, and I searched for it in wikipedia but it wasn't clear. So how to classify it?


texts: Do women experience more bonding hormones than men after sex?

texts:
Does Oxytocin (or any other bonding hormone) increase more so for women than for men after sex?

Someone told me that it increases 4-fold for men and 12-fold for women (unconfirmed).

Is there any observable or scientific relationship between sex, Oxytocin and the desire for a monogamous relationship with a sexual partner?


texts: What is meant by [protein name]+/- (ie "Myod+" and "Myod-")

texts:
I have read a paper where this notation for protein names is used:

Myod+ and Myod-

(or another example, Myog+, Myog-).
What does this indicate?  In the paper I'm reading, and some brief googling, it seems that Myog is itself a protein, and not that there are two kinds called Myog+ and Myog-.
Examples are here (the one I'm reading) (Figure 6c), or here (page 3, pdf page (journal page 958)).


texts: Relationship between small and large fast-twitch motor units

texts:
When large fast-twitch motor units are temporarily fatigued, non-fatigue small motor units in the same muscle are impaired for small delicate tasks. Why?

When impulses from the brain comes down, the impulses from interneuron goes to small diameter motor neuron, which are associated with non-fatigue motor units, and large diameter motor neurons, which are associated with fast-twitch motor units. More impulse is necessary to activate the fast twitch-muscles because the larger neurons have higher leak current and capacitance. Thus, we have an ascending activation of muscle units, from least forceful units to most forceful. Now my question is, if the fast-twitch muscle units are fatigued, why cant we perform delicate movement/ task?

Fatigue is mainly caused when the motor unit runs out of ATP. So, is that the bridge between these to things, or is it something else?

Or, is it related to how motor units are used is a fixed ascending order for completing tasks? If so, how?

Thanks for all the help!


texts: Do action potentials cause the neuron to heat up as well as its environment?

texts: I have read that we might be yawning to cool our brains down, so then a thought occurred to me. If we need to cool down our brain, then our brain but heat up for some reason. The only reason I could see would be the action potential causing some sort of temperature increase. My query is how exactly would a neuron heat up, if it does do so in the first place?


texts:
Compared to a tardigrade, the cockroach seems fragile.

But can tardigrades survive the acidic environment of being eaten by most animals?


texts: Identifying a beetle from northern California

texts: Just found this organism crawling across my wall on the second story at around 12:30 AM. We're in Sonoma County in California. Our best guess so far is a soldier beetle, but the coloration doesn't seem to match any images we can find online. It's body was about 1.5 inches long and was a uniform brownish-tan color with black eyes. It may be worth noting we're in the middle of the worst heat wave we've seen in 15 years of living here.


texts: Is taking a shower unnecessary if good bacteria surround our skin?

texts:
David Whitlock, a scientist, has not taken a shower for 12 years. Instead, he sprays a bacterial mist containing live bacteria to remove odor and maintain the number of good bacteria.

It is because using soap can remove good bacteria on our skin. So he chose not to take a shower but to spray the mist.

This kind of behavior sounds strange to me. But can it be very effective to maintain good bacteria and prevent disease?

I cannot do like him but I am just curious.
Thanks.


texts: How do the chemical components of these spices prevent fungal growth?

texts:
I am doing an EE on how spices affect fungal growth for the following spices -
oregano,
garlic,
cinnamon,
cumin and turmeric. Its been hard to find any sites that say why or how they affect fungal growth, as far as I can tell I am pretty sure they affect the Krebs (TCA) cycle and inhibit the production of ATP. It would be great if someone could help me explain why :)


texts: What is the name of cellular respiration that Prokayotic cells use?

texts:
Eukaryotic cells use mitochondria using anaerobic or aerobic respiration. Prokayotic cells lack mitochondria but are bacteria. Mitochondria originated from bacteria and can be used in the same way. Bacteria produce ATP the same way that Mitochondria do.

So, what is that kind of cellular respiration called?


texts: What are some examples of animals who return to their group when threatened?

texts:
Based on my (limited) understanding, some types of animals use the power of numbers for protection. I assume, then, some species instinctively respond to threat by immediately seeking out and joining their group/hive/pack, not just to hide or get lost within the group (eg., school of fish), but to also take advantage of the power of the organized group (eg., swarm of bees).

Is this correct? If so, what are some examples?

[Note: It is my understanding that bees don't flee to their hive in response to threat, but rather sting and release a pheromone to draw the other bees to the area and create a swarm.]


texts: Specific activity vs turnover number of enzymes in BRENDA

texts:
From my understanding, the specific activity (A, units: umol/min/mg protein) can be derived from the turnover number (k, units: 1/seg) and the molar mass of an enzyme (MW, units: g/mol):

A = k / MW / 60000

When I try to do this for several entries in the BRENDA database, I don't get an agreement, sometimes the equality is off by an order of magnitude.
However I understand that there can be experimental errors involved, or I might be using the wrong MW (sometimes it is not clear what specific protein the value refers to).

Am I doing something wrong in this calculation?


texts:
Different types of cell cyclins are designated as a to y

Why are some letters like m, n, p, q.. etc. skipped?

Source: https://en.wikipedia.org/wiki/Cyclin


texts: How can Haemophilus influenzae survive and grow alone in the human body?

texts:
Haemophilus influenzae gets its name from the fact, that it requires nutrients from blood in order to grow. More specifically, I see it mentioned that in vitro they often exhibit the pheomenon that they don't really grow in plates with blood alone. They do, however, grow when other bacteria are added that causes haemolysis (like Staphylococcus aureus).

H. influenzae is known to cause otitis media, meningitis and pneumonia. How does it get its nutrients in these places? Is there a coinfection with other bacteria that do haemolysis?


texts: Is it possible to remove one strand of double stranded DNA in vivo?

texts:
Assume we do have a double stranded DNA sequence in human cells, say

...ATCGATATCGATATTGCAGAGCATAGCTATAA...
...TAGCTATAGCTATAAGCTCTCGTATCGATATT...

Now I want to cleave one strand, such that I do have

...ATC..........................TAA...
...TAGCTATAGCTATAAGCTCTCGTATCGATATT...

The distance is not so important to me, so it can be 20 bp I remove or 1000s. Hence, if I need some PAM or so and it is not nearby the target deletion site, I will simply move in 5' resp. 3' direction until I find it and cleave there, as long it is ensured that I have the target site single stranded then.

I would be very grateful I you could help me here!


texts: How many times have the cells in a human body divided?

texts:
Every single cell in a multicellular organism can in principle trace its "ancestry" back to the zygote through a continuous chain of cell divisions. How many divisions have occurred in a typical cell in an adult human body since the zygote was fertilized?

Obviously the answer depends on the organism's age and on the type of cell (as different types of cells divide at different rates). To be concrete, what is the average number of cell generations from the zygote across all the cells in, say, a typical 25-year-old human?

(Or any other age, if that's more convenient to estimate. I'd also be curious about the approximate minimum and maximum number of divisions, and which types of cells they occur in. If it's too difficult to estimate these statistics over the whole organism, I'd be interested to know if there are any specific types of specialized cells for which it's possible to estimate the "generation number".)

To be clear, I'm not asking about the maximum number of times that a cell can divide. I'm asking about the average number of times it has divided at a given point in time.


texts:
Well, I've not any biological background but I feel interested towards it. Can you biologists suggest me how to start? Like, from where I can start learning it, from the basic level.
I'm from engineering and physics background.

Edit- I was advised to add the fields of biology that interest me.
I would like to learn microbiology, genetics and plant biology. I should mention that I've very little to no knowledge in biology. So, advise me how to get started from basics. I really have no idea how and from where to start.


texts: Are microsatellites viable markers for GWAS?

texts:
I'm just reading some papers on genome-wide association studies and find that most of them use SNPs as a marker. I understand that they're the most polymorphic and thus the best for accurate correlations, but would microsatellites provide another viable method to check for genetic correlation?
They're highly polymorphic and small enough to showcase differences, while maybe allowing for more statistical significance.


texts: DNA is charged negative. Where is all the positive charge in my body?

texts: DNA is charged negative because of its phosphate backbone. Since charges need to be balanced (so that there are no charges building up somewhere), what is the positive charge which neutralizes this negative charge?


texts: Is a wet-mount needed to use Immersion Oil?

texts:
When I prepare my slide to use immersion oil, do I really need to wet-mount the specimen?  Can I do it with just the coverslip?

I am preparing fungus spores.

Using water for the wet-mount gives you a sort-of time limit.  You have to do your work before the water evaporates else you get little rivers at x100.


texts:
What kind of insect is this, and is this venomous, or dangerous? Don't need full species name just common name will do, color is red. Grandma always warned me of this, they usually are seen in monsoon season during heavy rains. They coil upwhen disturb .
Location: Country: India, lower himalayas
Google Map :Exact location
A miniature version of this also exist in my area don't have pic though.


texts: Can two proteins activate/inhibit the same gene at the same time?

texts:
Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right?
So if one protein has already inhibited that gene before the other protein, what is left for the other protein to inhibit this gene? It has already been inhibited right? What more does the other protein inhibit?


texts: How does translational immunotherapy work?

texts: I skimmed an article on a recent experiment which suggested that it was effective to inject induced colon cancer tumors with an attenuated salmonella variant. According to the article, this stimulated an immune response which suppressed metastasis of the cancer. How exactly does this work?


texts: Why do parasites sometimes kill their hosts?

texts:
It's bothered me for a while now. I understand why a parasitoid would do this, as it only temporarily requires the host, and that not all parasites kill their hosts.

There seems to be no evolutionary advantage in killing a host, because the parasite relies on the host for resources. Yet some organisms, usually microscopic pathogens, seem to fatally damage the host with no immediate benefit to themselves. Why is this?

I know this is asking for a broad soft answer, but I don't want the question to get bogged down by a specific species, although bonus points for using examples.


texts: Which organs do cats not eat on their prey?

texts:
My female cat is a very active hunter and brings me her prey daily. Except for shrews and birds, she always eats them entirely.

This afternoon she brought me this:

It was quite large (maybe between half and two thirds of the length of a mole), and I couldn't identify it (I'm in Europe if that matters).

The prey was already dead when my cat brought it to me, and she quickly started eating it. I noticed that she didn't eat this part:

I'm not a biologist, but I guess this is the stomach of an herbivorous animal?  What's inside looked like wasabi.

Why didn't she eat it? She is not so picky with smaller animals. Is it because of the size of this one?

Are there some organs or parts of the prey that cats usually don't eat ?


texts: Cationic lipid mediated transfection optimization for 150mm dishes

texts:
I need to optimize a transfection protocol to transiently express a plasmid encoding a chimera of  eyfp attached to the c term of a Golgi apparatus signaling molecule) in hela cells and hepg2 cells and get as high expression as I can get.

I need enough protein for about 100 wb's. I've seeded hela cells to 12 150mm dishes. And the same with the hepg2. I've prepped mg's of plasmid.

I'm using invitrogens original lipofectamine reagent; not the 2000, or ltx or any of that stuff.

Any suggestions on a protocol here for hela and hepg2 plasmid dna and lipofectamine mediated transfection on such a large plate size.

I figure just scaling up should work but there's some pitfalls here. Look at this table for example when you go from 60 to 100 mm you about double the area, so you also about double the culture volume. However when you go from 100 to 150mm you triple the area, but only increase the culture volume two fold about. This is making my scale-up calculations for transfection look really off:


texts: If a hand was suddenly chopped off while holding something, would the severed hand still hold a grip?

texts:
This question was inspired by Star Wars Episode V: The Empire Strikes Back. In it, Luke Skywalker is battling Darth Vader in a lightsaber duel. Vader manages to win out and chops off Luke's hand, which is holding the lightsaber.

My question is: would his severed hand still hold a grip on the lightsaber? Or would it fall slack and lose grip, likely separating as it falls into the pit?

While this question is from a sci-fi series with a fantasy means of dismemberment, it might apply to other real-world situations (for instance, an industrial worker holding a tool while a piece of machinery accidentally severs his hand).


texts:
I have noticed the droppings below, quite visible on snow, next to an inner-town building situated next to this place in Luxembourg, central Europe. There are quite a few, but I have not noticed them anywhere else. What animal creates these and why do they have this red color which stains the surrounding snow? Is it a cat being fed colored food?

Local wildlife is mostly city pigeons (with digestive tracts of steel), huge flocks of crows (inhabiting parks and occupying the construction cranes at nightfall), maybe a few stray foxes and rabbits. House dogs and cats of course although these don't run around unattended.


texts:
When I search for this online I get answers such as substitutions, deletions, insertions etc. But I mean in the sense that I have been reading different terms infront of the word SNP such as: lead SNP, tag SNP, sentinel SNP, indirect SNP, direct SNP, secondary SNP, imputed SNP etc.

From my understanding lead/tag/sentinel are all the same (SNP with lowest P value in a locus, representing the variance in that section). An indirect SNP is also a lead/tag/sentinel SNP and indirect because these have not been genotyped but are in LD with the genotyped SNP + having that they have the lowest P value. Also a secondary SNP is a indepedently correlating SNP, and is specifically independent from the tag SNP? Is there a resource defining these sort of categories? Apologies if this is misinformed, I have been trying to learn about GWAS from different studies, and would appreciate any help to clarify this.


texts: Have there been studies done to test Immortality of cancer cells in culture?

texts:
This website on cultured cancer cells () says cancer cells may be immortal.

I am wondering if there has been any research done to find if cancer cells are really immortal.

How old is the still maintained living oldest culture of cancer cells?
Has there been any research done on replicative senescence of Cancer Cells invitro?

Edit 1:

If there is some data relating to the number of replications the cells have undergone, it will be very useful


texts: Pain perception in animals with nerve nets

texts:
Are animals with nerve nets, like sea urchins and jelly fish, theoretically able to feel pain? They have output and input organs which would make them "vulnerable" to feel pain but on the other hand, they don't have brains. I was wondering if they show any signs of "pain" when they are attacked or eaten?
And if they don't show any signs of pain is there the possibility to measure something that could be interpreted as pain?
Edit:
The word pain is here meant in a way, that it responds to an outer force with behavior which one could interpret as an inner-process that shows discomfort. The important parts are here the words "interpret" and "show signs of".
Pain is here thus meant as a behavioural response that could lead to an interpretation of an inner-process


texts: Is there a preferred sleeping position for humans?

texts:
I remember hearing various sleep related advice as a child, like "sleep on your right side", or " have your head pointed in X direction".

Is there any biological reason why sleeping on one side versus another, or with a head pointed in some direction is beneficial for humans?


texts:
I live in a semi-rural area in Germany, close to a park which trains go through every 20 minutes.

Today, I saw something that left me perplexed.

There is a large population of birds that look like crows or ravens, yet fatter. They seem to be quite social and move around in large groups. Today, I spotted one carefully laying sticks from a nearby tree on the train track while the others seemed to spectate.

What exactly was that bird doing? Is this common? Did it have a purpose, or was it just coincidental?


texts:
For some ELISA based antibody tests (e.g. h-tTg antibody test), labs report units as RU/mL or U/mL. Also different labs have different cut off (normal range) values.

I understand that different kit manufacturers recommend different ranges because the units are not standardized (e.g. IU/mL) for enzyme activity concerned. But I didn't understand the difference between RU, U and AU

Question
Is there a difference between RU/mL, AU/mL and U/mL? Are the figures comparable across reports from different labs (which may be using different kits)?


texts:
As B-cells undergo affinity maturation, their BCR sequences change. Are they still considered to be part of the same clone?

I couldn't find a clear answer in response to this very similar question:

What is meant by clones of B-cells?


texts:
I was researching mutations and came across an interesting question:
Do mutations occur in the DNA or mRNA of an organism? Is this more opinion that science?

Thanks in advance!


texts: How does DNA determine all of our hereditary traits?

texts: It's my understanding that DNA codes only for protein synthesis. Does that mean that hereditary traits, like the shape of our nose, are determined only by the proportions in which various proteins are synthesised in various parts of our body ?


texts: What is the molecular mechanism of cystine bond formation?

texts: My bioinorganic and redox chemistry isn't up to par and I'm having a very difficult time understanding the chemical mechanism behind cystine bond formation. Most reactive environments are actually reductive whereas an oxidative environment is important for cystine bond formation. How does the oxidative environment oxidize the thiols, rearrange the orbitals and form a disulfide bond?


texts: Check on 23andme what type of CYP2D6 substrate metabolizer I am

texts:
CYP2D6 is responsible for the metabolism and elimination of approximately 25% of clinically used drugs. Which SNPs do I need to check on 23andme in order to determine if I'm a poor or ultrarapid metabolizer of CYP2D6 substrates, and how reliable would the results be?

I've found one article on this topic, but I'm not sure how accurate it is, and it doesn't cite sources.

PS: why isn't this information more readily accessible to 23andme users, given the relatively large risks incurred by not knowing one's reaction to a large number of drugs?


texts: True examples of common variation due to Mendelian Inheritance

texts:
Classic examples of mendelian inheritance are genetic diseases such as sickle-cell anemia, Tay-Sachs, cystic fibrosis, and xeroderma pigmentosa. For some of these diseases, it is believed that they evolved because the genes gave a beneficial effect that outweighed the rare occurrence of the disease (e.g sickle cell and protection against malaria).

However, all of these are examples of uncommon phenotypes, usually less than 1% of the relevant population (where it is most common) has those diseases. I'm interested in examples of mendelian inheritance where variation is common (all of the relevant phenotypes have, say, >5% frequency or something like that).

Consider eye color. In European populations both blue and brown eyes are common phenotypes. Many people have probably experienced a typical high-school class of biology, where this was introduced as an example of mendelian inheritance with brown eyes being dominant and blue eyes being recessive. However, modern studies (for example, genome-wide association studies) show that things like eye, hair and skin color are all polygenic traits. See for example (Sulem, ..., Stefansson, 2007).

Throughout the years I've heard of other traits that some said were examples of mendelian inheritance. Being able to roll the tongue, for example. This question was inspired by this recent question where absence of teeth (Hypodontia) was taught to the OP as an example of a dominant trait. The current answer says that hypodontia is probably an example of a polygenic trait that interacts with certain environmental effects. This got me wondering whether there even are examples of common mendelian variation.

I don't quite know the best way to phrase it, but my question is the following:

  Are there any examples of human phenotypes that are due to mendelian inheritance where all of the phenotypes are common?

Take eye color as an example again. By common, I mean that both blue eyes and brown eyes are common (over, say, 5% in for example Sweden). On the other hand, for example Tay-Sachs disease occurs only about 1 in 3,500 among Ashkenazi Jews where it is most common, according to Wikipedia. Way less than even 1%.

Preferably I want it to be verified by modern genomic studies (such as GWAS) that it is an example of mendelian inheritance. If such an example does not exist, then I will accept any answer that provides modern, relevant scientific literature that explores this topic. For example, it might explain why we would not expect to see common variation due to mendelian inheritance.


texts:
I was doing a protein prep and I made a mistake. After sonicating my cells, I was supposed to centrifuge and collect the supernatant (my protein is soluble and comes in the supernatant). I however, forgot to centrifuge and loaded the entire solution after sonication (debris and all) onto a Ni-NTA column.

Is there any way to dissolve the cell debris so that I may be able to recover the NTA beads?


texts: Gel electrophoresis after RNAse treatment

texts:
I do not understand how to solve this question. I know that RNAse will cut smaller pieces of RNA.

The answer given is A


texts: Why do the RNAseq reads map to only a certain region of a viral genome?

texts:
I am looking at RNAseq data and mapping them to 3 RNA segments from Cucumber Mosaic Virus.

I trimmed the adapters from the fastq files and converted them to fasta, which I searched against a virus database using BLASTN.

The results were confusing:

The reads align to one RNA segment (RNA 1 segment) of this virus but not the other segments. I looked in my BLAST result file the qseqid of this RNA segment of this virus and compared with the ids in my fasta file.

I copied this sequence and I did a NCBI BLAST which gave to me the same result. These 3 segments are in the capsid together, so they should be together. I am sure that they are in this NGS file.

What parameters should do I change?


texts: Dextrocardia is displacement of human heart to the right side. Does it occur during the life span of a human being or right from birth?


texts: What is the difference between the glycolate pathway and photorespiration?

texts:
I came across the definition of photorespiration as a process that forms CO2 from O2 in the presence of light. However, the CO2 is released only when the plant cell undergoes the conversion of glycolate to PGA, i.e in the glycolate pathway.

Most textbooks seem to use the term photorespiration and glycolate pathway interchangeably, but then they seem to say that the glycolate pathway evolved to regain the energy lost in the formation of glycolate, whereas photorespiration is wasteful. How is this possible?

Shouldn't photorespiration be a conservation pathway as well? It is trying to regain lost energy from glycolate, isn't it? or Have I got the two terms completely confused?

Please Explain


texts: I received this cactus as a gift and I'd love to know the family/scientific name. Only one flower has bloomed since, it was between orange and yellow. At first it was perfectly spherical, but in one month it has become almost pear-shaped.


texts: How does the brain fake itself into hearing our own sounds even when we are not speaking?

texts: Typically When we are talking to our own selves at any time in the day,the Brain thinks that it's me who's speaking , how does it create illusion of speaking ?


texts:
I was watching Nosferatu, and this dog-like animal appeared, with very curious stripes. I was wondering if this is clearly a specific animal, and which one it is, or if it's too mixed up and low resolution to tell. You can see in this video, at 11:43 and 12:22 (close up) to 12:33.
https://www.youtube.com/watch?v=PH7L4V-3VxA&t=703
Sorry about my lack of a more scientific research, but I couldn't be farther from being a biologist. This is all I got: from the stripes, it immediately brought to my mind a Thylacine (which is what caught my attention), but even though it would not me an anacronism (it was extinct in 1936, the movie is from 1922), the movie is European (filmed in Germany, Slovakia and Romenia) and the story happens in Europe too, so it wouldn't make sense to be a Thylacine (not to mention that in 1922, you wouldn't find them right around the corner ;) ). Further investigation confirmed the already almost obvious, the stripes are too in the front in their body to be a Thylacine. My second thought, from the apparent big head and the way it moves (hips lowered), it resembled a hyena to me. But it doesn't seem to have ears big enough, they also wouldn't make sense in context of the movie, and hyenas usually have spots instead of stripes. A quick search showed me that there are striped hyenas, and from pictures it looks kind of similar, but the snout doesn't seem to match. Also, they don't occur in Europe, according to Wikipedia.
So at this point I'm in doubt if it's a striped hyena (that doesn't seem to make sense to me), another real animal that I don't know, or if it's a fictional creature, some animal "modified" specifically for the movie (painted, extra/less fur, artificial modifications in height, body size, ear size, etc). Although that also doesn't make sense.
Any pointers appreciated, sorry if this should belong in scifi or another SE.


texts: What is the representation for Sulfur in organic matter?

texts:
We often represent organic matter with the following equation:
$$
(CH_2O)_x(NH_3)_y(H_3PO_4)_z \tag{0}
$$
For example, the organic matter with the Redfield ratio has the form of $(CH_2O)_{106}(NH_3)_{16}(H_3PO_4)_1$.
But if we want to put inside the element Sulfur ($S$), which form below should we use?
$(CH_2O)_x(NH_3)_y(H_3PO_4)_z(H_2S)_m \tag{1}$
$(CH_2O)_x(NH_3)_y(H_3PO_4)_z(S)_m \tag{2}$
$(CH_2O)_x(NH_3)_y(H_3PO_4)_z(SO_4)_m \tag{3}$.
These different forms assume the different covalency of sulphur (-2, 0, or +6). Which form above should we take to describe the composition of organic matter with S?
I guess maybe Eq.(2) $(CH_2O)_x(NH_3)_y(H_3PO_4)_z(S)_m$? Because in this way, sulfur has the covalency of zero, which is the same as carbon (0).
I asked this question because I found many papers use the Eq.0 to build the mineralization of organic matter (e.g., O2 oxidation, [R1] in Table 2 here. See Fig.1 below). The amount of O2 depends on the assumption that carbon in OM has the covelency of zero (then, 1 mole of C corresponds to 1 mole of O2).
Since I didn't find a paper that put S into the OM compositon to balance the similar equation like [R1] in Fig.1, I am curious about which covalency value is "more common" for such an equation (because Sulfur's covalency can affect the amount of O2 needed).


texts:
Wild bees decided to build their hive in my shed, right above the table where I work on occasion.

The image is rotated 90 degrees left.

It started out as a single bee from what I could see two weeks ago. I thought fine, we won't bother each other and I like the company. But now two weeks later the bees are busily constructing and it is quickly growing larger. It started with a smallish dome, and new layers are being added from the outside. Every now and then a drop of some fluid falls out of the hive, and also small black grains, perhaps bee poop? Any ideas what these are?

Anyway, I have no idea how big this hive will become, so it is is probably a good idea to move it (it is around 15 inches from my head ;-)). Any suggestions?


texts: Do animal muscles atrophy slower than humans?

texts:
Suppose I consider the silver back gorilla as an example.  I cannot imagine ever seeing one in the wild intentionally doing something akin to weightlifting like humans solely for the purpose of getting stronger (if I'm wrong about this, that would be fascinating to know as well).  However, last I checked a male silver back can easily lift several times its own body weight.  I used to workout heavily and used to hold my high school bench press record (330 lbs in the 160-171 lb weight class).  However, even then I would have struggled to do more than a few pull ups with a 170 lbs strapped to my waste.  Meanwhile, I've watched various types of monkeys and apes do handfuls of seemingly effortless pull ups at zoos as part of their play.
So do animals like gorillas have muscles that either start and stay stronger than humans or just atrophy much more slowly?  Or is it just a matter of constant use?  Or is it just a different proportion of fast vs slow twitch muscles as this study suggests?
I am skeptical of this last part because some estimates of gorilla strength suggest they can lift upwards of 10 times their body weight [e.g., https://storyteller.travel/how-strong-is-a-gorilla/].  I also recall reading a study in grad school of an orangutan pulling over 600 lbs with one arm clearly not straining according to the article (though I failed to find the reference while searching today, unfortunately).
If anyone has some useful references with quantitative data, that would be great as well.


texts: Amplified Fragment Length Polymorphism (AFLP) primers

texts:
I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome.

For example, in the paper "AFLP fingerprinting of the human genome", Human Genetics,  108(1):59-65, Table 1 reports 100's of location of each primer pair:

Now the MseI primer is GATGAGTCCTGAGTAA. So the M-CAA primer should be GATGAGTCCTGAGTAACAA. When I blast this on the reference human genome at NCBI, the results show the best alignment only covers 6-21 of the query:

Homo sapiens chromosome 7, GRCh38.p2 Primary Assembly
Query  6          TGAGTCCTGAGTAACA  21
                  ||||||||||||||||
Sbjct  148723256  TGAGTCCTGAGTAACA  148723241

However, there should be close to a thousand matches for MseI-CAA across the genome according to the table. Does AFLP not require the whole primer to be matched?

According to the original AFLP paper, "AFLP: a new technique for DNA fingerprinting", NAR 1995, the figure 1, the whole primer is being aligned.

Cross-posted to Biostars.

Update: One needs to use the digestion enzyme recognition site to map the AFLP markers. Example: http://insilico.ehu.es/AFLP/info.html


texts:
I was just reading the sleep threads, and I wondered, why is the body so constructed so that sleep is necessary? (Is it just a design error?) But then, how do things come to be awake at all? How did this happen? Yes, I can see the advantages, but how did it happen? What is "awake"? Are single-cell animals awake?

The question I want to ask is, how did things progress from just sitting around ingesting and growing, like plants, to being something more? Is it more? What do "wakers" have that the rest don't?

Sorry, I'm not a biologist, this may be a foolish question, or in the wrong place.


texts: What's a good reference for choosing histological staining chemicals?

texts:
It's often difficult to find the appropriate or best stain to use when I want to examine a new type of tissue. I think that's partly because many histological techniques were developed a long time ago, so the papers don't turn up in Google Scholar. Is there a standard reference which links tissues, cell types or states and their corresponding best stain?

I'm mostly interested in a reference text or website covering plant histology, but general references are welcome too.


texts: Examples of alkali metal and halogens covalently bonded in biological molecules?

texts: Divalent and monovalent ions are often non-covalently bonded in biological molecules, they are primary building blocks of the machinery of biology. Iodine, the halogon in period 5, is covalently bonded in thyroxide. What are other examples of covalently bonded monovalent ions, alkali metals and halogens? Are there molecules that covalently bond Flourine, Chlorine, Sodium and Potassium?


texts: Why arent mosquitoes found near neem trees?

texts:
I read an article yesterday that wherever neem trees or spices are cultivated mosquitoes are not seen there. So why arent  mosquitoes seen near these places (neem trees , spices, etc).
What is it that prevents mosquitoes from living near these places?


texts: Are there cases when genus name is equal to the name of a higher taxon?

texts: Are there any cases when the name of a genus equal to the name of a higher taxon: family, order, class, etc. in botany and zoology?


texts:
Does it make ANY difference to which strand of DNA double helix base pair heads? I mean, could base pair AT and base pair TA makes any difference when interpreted by biochemical mechanisms which use DNA?

Double helix has two strands, right? So does pair Adenine on the first and Thymine on the second strand make any difference with Adenine on the second and Thymine on the first?

I am a novice in biochemistry, so please excuse me my ignorance if the question is ridiculous.


texts:
Please apologies if this has been answered somewhere else, but I couldn't find an answer to this problem.

I would like to retrieve all the predicted coding sequences on the NCBI ftp for a given species. Let's say my interest species today is Stegastes partitus and that I go here. I know how to get all the predicted mRNAs (./RNA/Gnomon_mRNA.fsa) or all the predicted proteins (./protein/protein.fa) but I cannot find how to get the CDS... if ever it's possible? This can be done on the Ensembl FTP.

Thanks for any insight!

EDIT: The output would ideally be a multifasta file like this:

>Stegastes_partitus_gene1_cds
ATG(.................................)TAA
>Stegastes_partitus_gene2_cds
ATG(.............................)TGA
>Stegastes_partitus_gene3_cds
...


texts: Why haven't environmentally-reactive bodies developed as an evolutionary advantage?

texts:
Regardless of region, earth's tilt results in yearly seasonal changes, which organisms deal with through processes like migration/hibernation. Both seem like attempts to avoid the extreme fluctuations... so why haven't certain organisms developed environmentally-reactive bodies, changing with the seasons throughout the year (based on measures like temperature- I.E., additional fur growth during the winter), and why hasn't this continued as an evolutionary advantage to allow organisms to thrive in longer
environmental ranges (like staying in place instead of migrating) or even go a step beyond and take advantage of the qualities specific to each season?


texts: Does a pregnant female body treat the fetus based on gender?

texts:
I have seen on a youtube video that the female body produces antigenes and antibodies when she is pregnant with a boy. But this behaviour is not produced when she is pregnant with a girl. These means that the more antigenes she produces, the more femminin the next child will be. More antigenes are produced when she is pregnant with a boy.

Is this correct? if yes, then why does the female body produce antibodies and antigenes when the fetus is a boy and not a girl?
What other pregnancy actions or behaviours are gender based?


texts: Can someone link me to resources on the efficiency of sticky end ligation?

texts: I really would like to know if sticky end ligation could potentially be performed with very high efficiency, and which factors influence that.  However, I can't find any papers on the subject, even though I'm sure they exist.  I was hoping someone would know of some literature.


texts: Finding intensity of selection against dominant homozygotes

texts:
I was looking at some Olympiad questions and came across the following:

  If the frequency of a completely recessive allele is $0.2$ and it remains unchanged from generation to generation due to superior fitness of heterozygotes, then find the intensity of selection against the dominant homozygotes.

As far as I know, selection intensity is a quantitative measure of the superiority of the individuals selected for breeding. However, I am not really aware of how to compute its numerical value.

The best I could do was to assume that the frequency would be a ratio of the selection coefficient of recessive homozygotes ($s$) to that of the sum of selection coefficients of both recessive ($s$)and dominant homozygotes ($t$), i.e. $\frac{s}{s+t}$, but that doesn't seem to lead me anywhere. Also, I can't think of a concrete reason as to why the frequency would be of this form if it is actually.

Any suggestions/pointers would be much appreciated.


texts:
How likely is a lack of DNA match with a distant relative?
I have recently gotten interested in ancestry research and have had a DNA analysis performed by a prominent commercial provider.
I've been working on my family tree for a few months now and have gotten into contact with a lot of distant relatives of mine, which has generally been quite delightful. In one particular case, we discovered that we actually have a double-relationship about 5-7 generations back in time, depending on how you count (common links go back to about ~1790).
We found this quite interesting, and this distant relative had a DNA analysis performed on their own genome as well.
Much to our surprise, however, we didn't find any commonalities in our DNA, which seems odd given the double-relation, and the fact that we have what we believe to be original and authentic documents of all the relatives forming the link.
Of course, we began speculating about the possible reasons for this. Maybe a misattributed child somewhere in the family tree? However, this seems unlikely, given the double nature of the link - most likely, we would need two misattributed children to explain the lack of any commonalities.
The other explanation would of course be that the DNA analysis provided by these companies is less reliable than we think, and that just by random mutations and "unlucky" inheritance, any common DNA might have been lost or scrambled beyond recognition.
I would like to calculate the probabilities of this happening in order to judge whether it makes sense to dig further into the original documents to try and clear up this mystery, or whether a mismatch by chance alone is sufficiently likely to explain this oddity. Of course, I don't need super precise numbers, but a back-of-the-envelope estimation would be nice - are we talking a few percent, or one in a billion? Also, I would be curious anyway on how to calculate probabilities like this, given the publicly available data on these tests.
What are the relevant quantities for this calculation (number of SNPs, I suppose), and how would one define and calculate a probability like this?
About myself
I'm a physicist with a strong background in data analysis with some basic understanding of biology and genetics. Don't be afraid to hit me with those numbers and probabilities, but please explain any genetics jargon you're going to use!


texts: What is the most appropriate way to normalize gene expression data?

texts:
This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for microarrays.

For RNA-Seq data, there are methods of normalization which adjust for GC-content effect or other gene-level effects. It make sense consider these effects in the normalization of microarray gene-expression data?


texts: Why does increased humidity decrease coronavirus "survival"?

texts:
All news I can see scientist telling that the SARS-CoV-2 virus survive more in cold and dry weather. I can understand cold as hot weather will desiccate virus, but why dry  weather.

Would not dry weather dry droplets of saliva sooner also desiccate virus, would not humid weather support virus?


texts:
Most organisms depend on water for metabolisms. Even the higher organisms need to maintain their daily water intake.
Why water and not something else (for example like H2S)?
I know H2S is poisonous for our body but isn't that just because our body is not compatible with it?
Is there a possibility that we could have been compatible with H2S and not H2O?
What are the factors that prevent this?


texts: Stochastic parameters in population growth equations

texts:
I'm more of a mathematician than a biologist, so I had a question about an application of the population growth equation to real-life models, and thus would like to ask biologists for their insights. The equation I'm looking at is the following (in reality, I have n-species but it's just an extension of this two dimensional problem):

$$ \frac{dx_1}{dt} =x_1\Big(b_1-a_{11}x_1-a_{12}x_2 \Big) $$
$$ \frac{dx_2}{dt} =x_2\Big(b_2-a_{21}x_1-a_{22}x_2 \Big) $$

where the $b$ are growth parameters, and the $a$'s are all parameters describing interactions among the species (and carrying capacity). The papers I've looked at for stochastic perturbations with these equations have primarily dealt with stochastically perturbing either the $b$ parameters while holding the others constant, or perturbing the $a$ parameters while holding $b$'s constant. However, these papers are written by mathematicians with no biological experience, so the decision on which sets of parameters to perturb are somewhat arbitrarily decided without any biological basis.

For the biologists, can someone suggest some cases for where it would be more biologically reasonable to perturb the growth parameters and some cases were it would make more biological sense to perturb the interacting parameters? I ask because I'm a part of some interdisciplinary neuroscience project which is using equations of this form to study interacting neuron clusters, but since I'm a math person and not a biologist, I am trying to understand reasonable explanations for what stochastic perturbations mean biologically for these parameters.


texts: Why are hard boiled eggs so homogeneous?

texts:
A eukaryotic animal cell is a complicated piece of biological machinery.  Some major structures inside of the cell (see the image below) include: the nucleus, mitochondria, Golgi vesicles, and various tubular structures.  Why then is the single-celled, unfertilized chicken egg so homogeneous when it is cooked (or before)?  The only major structure I can recognize is the cell nucleus.

*Image Credit: "Animal cell structure en" by LadyofHats (Mariana Ruiz) - Own work using Adobe Illustrator. Image renamed from Image:Animal cell structure.svg. Licensed under Public domain via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Animal_cell_structure_en.svg#mediaviewer/File:Animal_cell_structure_en.svg


texts:
In a separate question I've described my general experimental setup where I need to measure the number of live cells in a growing bacterial culture in a fairly rapid and high-throughput manner. In that question I'm asking if there are any alternatives to the gold standard of CFU plating for making this measurement. As I wrote that question, it occurred to me that if I could just make CFU plating easier to do with lots of samples (esp. using fewer plates), then this method could work just as well. So my question here is if there is a way to make CFU serial dilution plating easier when I have to measure the number of live cells in 7+ different growth conditions every hour of growth?

Thanks!


texts: ‘Inoculum’ vs ‘inoculant’ – which one is it?

texts: I’m currently writing the report of a study which looked at commercial soil inoculants (Rhizobium sp.). However, I’m confused about the differences between the words inoculum and inoculant and when to use which.


texts: definition of tempo and mode in evolution

texts:
I am reading Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered, which mentions the "tempo" and "mode" of evolution. I'm not familiar with the related literature and when I google the concept, what I got is something like:

  One general topic, suggested by the word "tempo," has to do with "evolutionary rates..., their acceleration and deceleration, the conditions of exceptionally slow or rapid evolutions, and phenomena suggestive of inertia and momentum." A group of related problems, implied by the word "mode," involves "the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo''

This is as elusive as a definition can be. A clear definition should be something like "tempo is ...."

So what are the definitions of mode and tempo in evolution?


texts: Web making seems like a fairly complex behavior built from a pretty strong material.  So how exactly did it evolve? Do we have any clues about what kind of features/behaviors preceded web making and made it possible? Are there any examples of convergent evolution?


texts: Difference between aerosol and droplet transmission for airborne diseases

texts:
I've been doing some pandemic reading and can't find why there is a distinction between transmission by aerosols and by droplets. Some articles give a size cutoff of 5 microns; how is that important?

Aerosols were also mentioned to be either wet (small droplets) or dry (dry remains from an evaporated droplet). Does that mean droplets can evaporate enough to count as an aerosol?


texts: What does `knee atlas` means in an IEEE's paper?

texts:
I am referring an IEEE's paper for my project which has a term called knee atlas, I am not getting the exact meaning of this term, does they mean it a processed image or something else? I am working in matlab and here is the paragraph of IEEE's paper:

    Six atlases were derived from 3-D DESS WE series from six subjectswith visually normal knee images ... The series for three of these atlases were selected from the public release OAI image dataset 0.D.1 and three were from the baseline pilot study. Trained human observers created the knee MRI atlases using manual segmentation.


texts: Are new blood vessels able to deliver oxygen to hypoxic tissue before the establishment of blood circulation?

texts:
Sprouting angiogenesis - the growth of new blood vessels from a preexisting vasculature - can be triggered by cells in hypoxia in order to re-stablish the oxygen and nutrients supply to the tissue.
The formation of a new vessel is a multistep process starting by the activation of the Endothelial Tip Cell (ETC) phenotype that migrates through the tissue guided by chemotactic cues, such as the Vascular Endothelial Growth Factor (VEGF) concentration. The cells near to the ETC gain the Endothelial Stalk Cell (ESC) phenotype and start to follow the ETC and proliferate in order to form the new branch.
The Endothelial Cells (ECs) re-arrange in the new branch, forming the lumen. Thus Smooth Muscle Cells (SMC) and pericytes are recruited to maturate the new vessel. Consequently the vessel is filled with blood from the main branch.
My question is: when does the new vessel starts to deliver oxygen to the surrounding tissue? Can it occurs before the anastomosis formation where the circulation is stablished, even for a short period of time due to the plasma that filled the new branch? (See the following picture where they represent the cells near to the new branch with a high concentration of oxygen even without anastomosis/blood circulation)

Image Source: Peter Fraisl et al. Regulation of Angiogenesis by Oxygen and Metabolism. DOI 10.1016/j.devcel.2009.01.003


texts:
I know Meoisis involves a reductional division and an equational division.Say if I am asked a question to find the no. of divisions an egg mother cell undergoes in a Polygonum type division to form the 7 celled 8 nucleate stage, would the Meoisis2 be counted as a mitosis?
Then would it be said to have undergone 1 reduction division and 2 equational division(1Meoisis +2Mitosis).
Or is it just 1Meoisis +1Mitosis ?


texts: Is there a reliable source for storage and stability of reducing agents like DTT?

texts:
Reading the literature on DTT, one is confronted with a confusing mass of papers; some claim that a 1M solution in water is stable, other papers say it is not. I use the reaction with DTNB to show that the DTT is still good, but that is cumbersome.

Is there some source of reliable (as in data driven) information on how to store compounds like DTT and other reducing agents?


texts: How interrelated are computational biology and biophysics?

texts:
I am considering applying to Ph.D. programs, and am not sure what direction to take. I'm hoping you all can help me out.

I have a background in both biology (molecular focus) and physics (condensed matter and math, heavy on theory). Several years industry experience working in labs doing molecular biology and genetics research.

My primary interest is in mathematical modeling of biological systems, and taking this knowledge to then engineer function. Essentially, what I view as a combination of biophysics, systems biology, and synthetic biology.

Here is the dilemma. It is important for me, should I pursue a Ph.D., to have a solid foundation and training in fundamental principles in physics and math, because I want to be able to derive new theories, models, and methods when needed. This leads me to think biophysics or applied math is the "right" area to do my Ph.D in. But biophysics is very broad and systems biology is only a small part. It is also removed from applications in bioengineering.

I know computational and systems biology intermingles biophysics, applied math, genetics, computer science, and various other fields. It also seems like the type of research I am interested in is typically done in computational and systems biology groups. But I'd like to know if computational biologists, aside from doing simulations, also commonly do work in deriving new models/theories in biophysics. Or do they generally apply this knowledge to build simulations and understand data sets (i.e. removed from fundamental biophysics research)? I don't want to be a programmer -- I want to be a theorist who uses computational tools (and only programs when it's needed to simulate something) to solve problems that can't be solved analytically.

Is computational and systems biology an appropriate "umbrella term" for what I'd like to do? Or would I be better suited in a physics Ph.D. program, and attempt to bridge that training towards systems biology research?

Also, how difficult is it to change to a related field if the opportunity arises? Can computational biologists, who are also interested in engineering work, build a model of a system and then work with others to help engineer it?

My overall concern is pigeonholing myself into a field that I don't want to spend decades working in. I want to maintain flexibility along the range of biophysics to bioengineering, and work on problems when the need arises. Also, what field do my research interests actually fall under? I find it often depends on the university and specific department, so it's a hard question for me to answer myself....

Thanks in advance for any input.


texts: What is this white/translucent with brown back, larva/worm creature I found, in the UK, on my lettuce?

texts:
I'm in United Kingdom, East Anglia. I've just started to grow lettuce in my back garden, taking my first harvest today, I found one of these creatures:

They have a distinctive brown/white mark along the top of their behind. The black dot appears to be its front, as it scouts with that, and moves in that direction most of the time. This is about 10mm long, give or take 50% depending on how stretched out it is.

They appear to have transparent skin, as I think we can see its organs in there. It moves almost peristaltically (similar to a worm), but with direction, not just flapping around, and seems to like the undersides of things.

They're not particularly segmented, though they have those tiny, tiny ridges as you can see. And there are no legs or meaningful features to speak of on its underside. They were also slightly sticky, with a white-ish secretion.

I have since looked and found a few amongst the other lettuce, which all look incredibly similar to this. Usually hiding inside the outer leaves, but not exactly an infestation (yet!). They don't seem to be on any other plants at the moment. There's no evidence that they've eaten any leaves, or anything, currently.

I have done a lot of searching and attempts to identify, but I can't for the life of me find this online. My amateur guess is some sort vermiform fly larva, but it could be anything from a baby caterpillar to a worm, for all I know. Any help in narrowing it down, or especially in finding out if I should be worried for the plants, would be helpful.


texts: Why can't two different genetically species reproduce to give a viable offspring?

texts: What is the reason that only organisms belong to same species can produce a viable and reproductively healthy offspring but organisms of two different species cannot?


texts: Name of neurons affecting or being affected by a neuron?

texts:
This question is about terminology:

  By which established and catchy terms are the sets of neurons with
  respect to a given neuron $N$ called which

  directly affect $N$ synaptically
  are directly affected by $N$ synaptically?

These terms came to my mind, but I am not sure which ones are most commonly used:

the presynaptic/postsynaptic neurons of $N$
the afferent/efferent neighbours of $N$
the afferents/efferents of $N$
the incoming/outgoing neurons of $N$
the neurons projecting on/to $N$ vs. the neurons projected on/to by $N$

Or is there no such established term, and anything goes, depending on the context?


texts: Why is traditional rank based taxomomy considered by some as logically inconsistent with phylogenetic knowledge?

texts:
Following is from wikpedia:

  Under the traditional nomenclature codes, such as the International
  Code of Zoological Nomenclature and the International Code of
  Nomenclature for algae, fungi, and plants, taxa that are not
  explicitly associated with a rank cannot be formally named, because
  the application of a name to a taxon is based on both a type and a
  rank. The requirement for a rank is a major difference between
  traditional and phylogenetic nomenclature. It has several
  consequences: it limits the number of nested levels at which names can
  be applied; it causes the endings of names to change if a group has
  its rank changed, even if it has precisely the same members (i.e. the
  same circumscription); and it is logically inconsistent with all taxa
  being monophyletic.

  Especially in recent decades (due to advances in phylogenetics),
  taxonomists have named many "nested" taxa (i.e. taxa which are
  contained inside other taxa). No system of nomenclature attempts to
  name every clade; this would be particularly difficult in traditional
  nomenclature since every named taxon must be given a lower rank than
  any named taxon in which it is nested, so the number of names that can
  be assigned in a nested set of taxa can be no greater than the number
  of generally recognized ranks. Gauthier et al. (1988)[6] suggested
  that, if Reptilia is assigned its traditional rank of class, then a
  phylogenetic classification has to assign the rank of genus to
  Aves.[7] In such a classification, all ~12,000 known species of extant
  and extinct birds would then have to be incorporated into this genus.

What is the precise meaning of "it is logically inconsistent with all taxa being monophyletic"?


texts:
In this figure out of the two heteroduplexes formed one is considered to be non-recombinant product(left) and the other recombinant product(right). My question is despite the exchange of middle DNA segment why is the right heteroduplex considered a non-recombinant product or patch. I've been reading two books:

Molecular Biology: Principles of Genome Function
By Nancy Lynn Craig, Rachel Green, Orna Cohen-Fix, Carol Greider, Gisela Storz, Cynthia
Molecular Biology
By Burton E. Tropp

both had the same illustration and descrpition.


texts: Which is the tissue damaging agent in krokodil (street desomorphine)

texts:
I've just read about krokodil and saw some quite hideous pictures about what it does to the human body. I guess just desomorphine alone wouldn't have this effect.
Which ingredient(s) causes the damage to the tissue?


texts: Common genes and enzymes involved in pathogen entry into host

texts: Many microbes like Salmonella, E.coli, Legionella pneumophila etc. enter host cells via cystoskeleton remodeling of the host cell. Do all microbes follow the same path or there are any other ways for the microbe to enter the host cell. What are the most prominent and significant enzymes involved in these and what are the genes involved in the same. It's a general question as I am looking for the common genes and enzymes that most microbes employ the mechanism of cytoskeleton remodeling.


texts: Is metastatic cancer always lethal if uncured?

texts: Can matastases spread in different parts of the body of an animal suffering from cancer grow in a limited way, such as not to cause much more harm that a benignant tumor in those parts of the body would, or are metastases guaranteed to eventually cause death, if left uncured?


texts:
If a species has a vestigial anatomical
structure that it no longer uses, would
you expect this structure to disappear
over many generations through the action
of natural selection? Always, sometimes,
or never? Explain your answer.

I'm having a hard time with this question. I don't know what should I do


texts: Is blunt end repair and A-tailing necessary when adaptors can be custom made?

texts:
I'm planning on creating a RADseq library, which naturally involves digesting genomic DNA following P1 adaptor ligation. I've read a few protocols that require any over-hangs resulting from restriction enzyme activity (e.g MspI or Nlaiii) need to be repaired (blunt-end repair) followed by adding a single A nucleotide at the end so as to make the DNA fragments "sticky". But is this really necessary? Wouldn't it be more efficient to custom make P1 adaptors so that they have a complimentary 3 or 4 bp overhang specific to the restriction enzyme used instead?

What I want to ask is what are the practical advantages of having a single nucleotide overhang vs. 3 or 4 nucleotides?

Thanks in advance.