texts: What data / tools exist for mapping of disease trends?

texts:
I was just looking at the Google Flu Trends map.  Google Insight could be used to gain similar information for other trends in disease keyword searches.

I started wondering how valid are keyword searches to represent the spread of diseases.  In some ways I think it could be a good representative, but in others I think it would be susceptible to influence by mass media.

Do maps of clinical data exist that could be compared to this Google data?  If so, where could I find some.  =)


texts: What does it mean to have different "metabolism"?

texts:
We hear talk of different body types, and that it is more difficult for certain people to lose weight than others. On the other hand, when my physician recommends that I lose weight, they say that it is really just as simple as "calories in, calories out". How can we reconcile these two?

Perhaps the "calories out" portion is different for different people? I.e. some people burn more calories than others do, doing the same activities, but their hunger level does not compensate for this?

Apologies if this is off-topic


texts: Statistical genetics: Allele frequencies that follow a Dirichlet distribution

texts:
From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population.

  We consider a set of $I$ loci and let $K_i$ be the number of alleles at the $i^{th}$ locus. The extent of differentiation at locus $i$ between subpopulation $j$ and the ancestral population is measured by $F^{ij}_{ST}$ and is the result of its demographic history. Let $p_i=\{p_{ik}\}$ denote the allele frequencies of the ancestral population at locus $i$, where $p_{ik}$ is the frequency
  of the allele $k$ at locus $i$ $\left(\sum_k p_{ik} = 1\right)$. We use $\mathbf {p} = \{\mathbf {p_i}\}$ to denote the entire set of allele frequencies of the ancestral population and $\mathbf {\tilde p_{ij}} = \{ \tilde p_{ijk}\}$ to denote the current allele frequencies at locus $i$ for subpopulation $j$. Under these assumptions, the allele frequencies at locus $i$ in subpopulation $j$ follow a Dirichlet distribution with parameters $\theta_{ij}\mathbf {p_i}$,

  $$\mathbf {\tilde p_{ij}}  \space \tilde \space\space  \text{Dir}(\theta_{ij} p_{i1}, ..., \theta_{ij}p_{iK_i})$$

  , where

  $$\theta_{ij} = \frac{1}{F^{ij}_{ST}}-1$$

(I don't have much experience with Dirichlet distributions but I understand its definition and its usefulness in bayesian statistics).

Can you please help me to understand why $\mathbf {\tilde p_{ij}}$ follows this Dirichlet distribution?

Calling the $j^{th}$ parameter of the Dirichlet distribution, $\alpha_j$, I typically don't understand why they "chose" $\alpha_j = \left(\frac{1}{F^{ij}_{ST}}-1\right) p_{ij}$ and not, say just $\alpha_j = F^{ij}_{ST} p_{ij}$ or anything else.


texts: How suddenly does lactose-intolerance onset?

texts:
How quickly can the loss of lactose tolerance onset in an adult?

Such as being able to process lactose normally to having notice symptoms associated with the inability to process lactose.

I am not asking how long it takes to digest food, but rather how long it takes for lactose intolerance to become noticeable (hours, days, weeks, months, years).


texts: What are these balls in meshopyll cells? [Plant biology]

texts: Anybody knows what are these small balls? The picture was collected with a confocal fluorescence microscope. These balls have a green epifluorescence and they are in mesophyll cells of rice leaves.


texts:
I was recently at a Leukemia and Lymphoma Society conference where a particular oncologist lecturer claimed that all antibodies are created in the bone marrow (I won't mention his name, as he was a great lecturer, and I don't wish to sully his name if he happened to be wrong on this particular point).

Wikipedia seems to indicate that antigens are produced in "Secondary Lymphatic Organs" or occasionally in the bone marrow, but I've been misled by Wikipedia before.  It seems to me that evolution would favor creating antibodies close to the infection, and not far away in the bone marrow or lymphatic organs (how would the antibodies "know" how to get back to the original infection?  It would be very inefficient to send antibodies all over the body if the infection is localized.)

My questions is: Could someone "map out" the travel of a typical B-cell throughout the body from the time the B-cell detects an antigen up to the time it produces antibodies (and if it later stops producing anti-bodies, please include that)?


texts:
I've accidentally touched pure glucose with my bare hands (fingers to be specific), which was intended for cell-culture.

I'm worried that bacteria from my skin may start to grow on the glucose and contaminate my animal-cell cultures.

Should I be worried about this really and get another glucose packet for it or just proceed to feed cells with that one?


texts: Do spinal cord reflexes (such as the knee-jerk reflex) continue to function under general anaesthesia?

texts:
The knee-jerk reflex (patellar reflex) is an example of a stretch reflex (myotatic reflex). Stretch reflexes are monosynaptic reflexes happening in the spinal cord without involvement of the brain.

Does it mean that this reflex will continue to function in an unconscious person, e.g. under general anaesthesia? Does it depend on the "deepness" of anaesthesia? Does it depend on a specific drug? I would also be interested to know if spinal reflexes keep working in unconscious states such as e.g. alcohol poisoning or a knockout.


texts:
Does a mould make a beetroot poisonous or inedible ?

Lemon's mould for instance, makes penicillin, but it's green there, and I'm allergic to penicillin, would the white mould produce penicillin too?


texts: If bortezomib, a cancer drug, inhibits cell proteasomes, wouldn't resulting protein aggregate in normal cells further increase the risk of cancer?

texts:
Bortezomib is an anti-cancer drug that inhibits the proteasomes of cancer cells, allowing proteins that stop cell growth to fold and perform their function.

However, wouldn't bortezomib also affect the proteasomes of normal cells? If the proteasomes of normal cells are inhibited, the major factor in the regulation of unfolded and damaged proteins is gone. The resulting protein aggregate would lead to cell damage and diseases such as cancer, Alzheimer's and Parkinson's.

What is stopping bortezomib from affecting normal cells? Does it?


texts: What species is this burrow-digging insect?

texts:
These are frames from a recent recording:

Location

Urban area in Central Europe.

Abiotic factors at the time of recording

Temperature = 27°
Humidity = 51%
Wind = 16 km/h

Description

Approximate size = 6 cm 4-5 cm
Elongated shape
Distinctive orange-ish abdominal segment near the end of the abdomen
6 legs
One pair of wings (I think it's very possible that it has two pairs of wings, though, hard to see on the video or pictures)

Observed behavior

The insect seemed to be digging burrows in one of my pots (so far there are 3 holes in one pot and I also saw another burrow in a second pot). Every time I've seen it, it was alone so I assume it's not a social species.

Internet search

I ran these images through google search images and the results were (in order):

hymenopteran
insect
pest
carpenter ant

I think the closest match was the first picture but I wasn't able to get a specific species so I would appreciate any insight from experts on the matter.


texts: When did vision evolve for the first time?

texts:
Today I wondered what the first organism to evolve vision would have been. I assume that it would have been kind of primitive and basic, but of course extremely innovative and eventually useful to a wide variety of beings.

It also makes sense that the evolution of vision would have accompanied the evolution of advanced brain functions in almost every case. So, do biologists have any idea as to what the first species to use vision would have been?

(By vision, I mean having some organ on your body that receives photons and has some signaling pathway that converts photons into a biochemical set of signals)


texts: Feedback affecting myocyte metabolism in humans

texts:
I understand that there are several reserves available to muscle that can be tapped for ATP, and that each reserve is being used to some degree at all times.

Are these reaction rates purely due to the presence of reactants which are products of myocyte activity?

Or are there other controlling reactants involved that determine the rate at which each reserve is consumed?


texts: Most examples of speciation describe a population splitting (via various mechanisms) into two or more populations that eventually become separate species from one another.  However, what if the population never splits? In other words, at some point in the evolution of a single species, an individual member would become (theoretically) unable to reproduce with its own ancestors--thereby becoming a distinct new species.  How can we say that this has happened, given the impossibility of the example?


texts:
What is the biological mechanism behind the variation within sexually reproducing species? Obviously, the children are combinations, to differing degrees, of their parents. But how does the variation originate in the parents to begin with?

I'm not referring to evolution or mutations rather I have in mind things like facial structure and personality in humans, or fur coloring in dogs. I just thought I vaguely remembered there was some kind of driver of variation... For example, does the parent produce a variety of germ cells that purposely differ from the parent's geneome?

I just think I'm missing something here.

(I'm familiar with DNA and genetics having taken a biology class in college and remembering much of it, I just can't seem to put my finger on this point...)


texts: Can anyone identify this locust / grasshopper in Florida, USA?


texts:
In biology I've learned that cells rapidly divide and can grow and split undefintely, and that certain parts of the body have to grow and evolve before growing, but I am tied up on the fact that the body produces hormones to have only grow up to a few feet tall and stops growing at a certain age.

Why does it stop in terms of height or physical mass when it can still keep on growing? Why do the hormones tell the body to stop growing when it can continue?


texts: What would bees be doing inside my furniture in the beginning of summer

texts:
I have an old chest of drawers in my garden shed. I've been noticing individual bees entering a closed drawer through the keyhole. Recently they've sealed that keyhole with a gray goo that's solidified and seems very hard to the touch at this point. I don't have anything terribly important in there but I'd have to break the goo if I wanted to pry the drawer open. What am I likely to find in there? If I don't disturb them should I be worried about a swarm of angry bees exiting at some point? It's currently the beginning of summer here in Europe.

EDIT:

I photographed 2 bee types that fly around in my garden (though another species might have been around a couple of months ago):


texts: Why do plants need oxygen through their roots?

texts:
I was asking myself why plants die from over-watering and the simple answer was that they can't get enough oxygen through their roots. But this made me ask myself why they need oxygen in their roots since oxygen is a product of photosynthesis and plants even release oxygen through their leaves.

With this seeming surplus of oxygen, how can plants "suffocate" when their roots dont get enough oxygen from the soil?


texts: Source of hydrogen in reduction of oxygen in electron transport?

texts:
What's the source of hydrogen in the reduction of oxygen to water in metabolism?

Is this implying that half the hydrogen comes from NADH and the other half from lone protons?


texts: We know that most of the so called "Advanced" organisms are deuterostomes (i.e., development of gut starts from anus). Is there any evolutionary advantage of that? If not, why and how did it evolve?


texts: What percentage of twins has the same gender

texts: If 30% of all twins are identical twins, what percentage of twins has the same gender? I thought: all identical twins have the same gender so it’s at least 30%. And of the non-identical twins it’s about 50%. So 50+30=80%?? Correct me if I’m wrong..?


texts: How does bath application of KCl depolarize a neuron?

texts:
Increasing extracellular KCl is often a way to depolarize neurons in experiments.

My understanding is that increasing K+ extracellular concentration changes K+ reversal potential to more positive values and hence depolarises the neuron as the open leaky potassium channels will lead to influx of K+ into the neuron. Is this correct?

However, this explanation does not take into account Cl- ions.

How can this be explained in terms of Goldman equation?

Also, how does intracellular injection of KCl affect neuron membrane potential as compared to extracellular KCl application? In patch clamp experiments, often the pipette is loaded with KCl and injected into neurons that leads to depolarization. How can this be explained?


texts: How not to kill a spider while moving out of my flat?

texts:
About two weeks ago, when it started getting cold, a house spider (tegenaria domestica I believe) has chosen my flat for spending the winter. I like those spiders so it's not a problem for me. Only problem is, two weeks from now, I'm moving out. I don't know anyone around here who would want to take the spider in.

Would the spider die if I move it back outside now ? In the morning it's around 10°C / 50°F

Since I got a liking to the little guy, is it reasonable to try to take it with me ? There's going to be 5 days between moving out and moving in the new flat, if I go down this road how should I take care of it during those few days ?

What should I do to have the least chances to accidentally kill it ?

Thank you very much


texts: Is a set of chromosomes made up of many copies of DNA, or is one complete string of DNA broken up into one set of chromosomes?

texts:
I know technically the question isn't really accurate but hopefully it gives the essence of what I'm trying to ask.

By the way I was taught in school, I was under the impression that a chromosome was made out of multiple complete copies of DNA. But, what I'm reading online makes it sound like a single complete string of DNA is broken up into sections and those sections are wound into chromosomes (so that one complete set of chromosomes would make up one complete string of DNA).

I'm assuming neither are 100% correct, but could someone explain it in a way that I can understand?


texts: Mathematical model about the relationship between two animal species

texts:
I'd like to relate a mathematical model with  two animal species. This is the model:

$$
\begin{split}
\frac{dN}{dt} & =rN-\frac{rN(N+M)}{k} \\
\frac{dM}{dt} & =r'M-\frac{r'M(N+M)}{k'}
\end{split}
$$

The model means that there is competition within the population of the first species ($N$) and the population is also affected by the population of another animal species ($M$).

Something similar occurs with the population of species $M$.

My question is:

  What kind of animals would fit this model?

I was thinking about white sharks as $N$ and whales as $M$. Clearly the first equation would be correct but the second equation would be saying that the population of whales is affected by sharks, which I think is not true. Is it?


texts: It is a well-known phenomenon that sickness like the common flu is often accompanied by reduced appetite. Why do sick people stop eating?


texts:
I recently hiked in a swampy forest in the Yaroslavl region(Eastern Europe) near lake Plesheevo and came across a clearing. Although the area was swampy and verdant, there was a 5 meter wide "bald spot" on the ground which looked like sand. Near that spot there was a lot of buzzing (which I initially mistook for the buzzing of wasps), and soon I found myself covered in these black flies.

The flies clung to my fabric hoodie, at least one tried crawling in my hair, and one tried to find its way into my eye.
I tried shaking them off, but they seemed to be able to cling very firmly to my clothes. (later I discovered that even dead flies were really hard to remove from fabric)
At that point I panicked, quickly retreated, and spent a good 15 minutes extracting every single one of them from myself and my garb.

When I came back, I took a picture of the carcasses of two flies that found their way into my pocket and silently passed away there from unknown causes. Unfortunately, I didn't get to take a picture of a living fly because I was too agitated at the time.

Their length was approximately 0.3 inches and when squashed, they produced yellow spots on my clothes.

I tried identifying them, but didn't have much success. They seem to look like a variety of horse-fly (or a dear-fly), but I think none of them actually bit me. Also, strangely enough, my clothes were sprayed with insect repellent which they seemed to either completely ignore or were actually attracted by.


texts:
The mammalian cell line CHO-K1 has 24,383 genes. After 70 doublings (from a starting number of cells, 1) a
total of ~4,000 mutations have occurred in the overall population of cells (i.e. not all in one cell), due to incorrect DNA breakage repairs (non-homologous end joining), with the mutations randomly distributed throughout the genome. Assuming that 2% of CHO genome consists of crucial genetic information (1.5% coding and 0.5% regulatory). What number of genes will be affected by these mutations?

My attempt:

I was thinking that the mutations should be spread randomly and so 24383*70/4000 genes may be affected but doesn't that assume the mutations are one per gene and the affected areas are actually important to protein expression?


texts: Difference between Appendix and the Cecum?

texts: What's the difference between an appendix and a cecum, and what are their functions?


texts: What types of plants are Gibberellin used on?

texts:
On what type of plant (monocot/ eudicot? family? species?) is Gibberellin used on?

I searched through many sources but could not find whether Gibberellin works for all plants or just a specific type or family. I read that it works well for biennials, but what are some of the other plant families that it is useful for?


texts: Why does my corn appear to have perfect flowers?

texts:
Corn is said to be a synchronously monoecious plant with separate male and female flowers.

I am growing a cross between a Peruvian and heirloom variety which seems to be growing some perfect flowers on both main stems, and suckers. I have googled this and find nothing to suggest this happens.

Is this common? And did a corn ancestor also have perfect flowers?


texts: Identify this wild plant with brilliant scarlet red flowers

texts:
Location is Virginia, USA

They seem to last all summer


texts: What is the energy produced by the mitochondria?

texts:
I know that the mitochondria is basically the power house of the body,
it consumes amino acids, fatty acids, glucose, etc and oxygen.

When these molecules meet up in a enzyme, a series of reactions happen (Krebs
cicle) which end up in CO2, H20 and energy.

Then the enzyme and later mitochondria will release its energy which will be stored in ATP molecules.

My question is what is this energy?


texts:
A lot of things are claimed to cause cancer, eating red meat, eggs, smoking, using phones, deodorant, breathing.

Surely these can't all actually significantly contribute to the development of cancer.

I've heard smoking is a big one to lung cancer, with someone--I can't recall--saying that most patients with this cancer are smokers.

What kind of activities/foods are sure to, or have high chances to, lead to the development of cancerous cells and how do they cause them, at a molecular level?


texts: How long do fishes survive in a milk environment?

texts:
Suppose you placed a fish, a goldfish for example, into milk instead of water. How long could you expect the fish to survive?

Would it die due to lack of oxygen? Is there any other factor that could cause the death?


texts: Clarification of method notation in yeast cultivation method

texts:
I'm reading a paper about yeast culture and in the methods, it says:

  Then $5$ ml of sterile $M/15\ KH_2PO_4$, was added to the slant,

What is the meaning of $M/15$?


texts: How does the Pectoralis Major work when doing a bench press?

texts:
Disclaimer, I'm not a biology undergrad and I only know the basics about muscle movement.

I know that doing a bench press works the chest, and specifically the Pectoralis Major because, well, I feel muscle soreness. However, it is not obvious to me what the Pectoralis Major has to do with extending the arm.

Thinking about muscle contraction, I see clearly how, for example, the Bicep flexes the elbow when it contracts. In a similar way, when the Pectoralis Major contracts you get horizontal shoulder adduction.

But what about the bench press? The majority of the movement consists of raising the arms upwards from a tucked position, and the is little shoulder adduction.

Thanks!


texts:
Question:

In contrast to chemically-induced mutations, mutations induced by transposons are more likely to ...

be lethal
de dominant
be stable
revert to wild types
be a gain of function

The answer is 4; but I have no understanding of why this is the correct answer, or, why the others answers are not correct.  Could someone help to explain why this is the case?


texts:
Is it possible to get an infection by contact with a reservoir host ?

Can a reservoir host act as a vector ?

What is the distinction between these two concepts (reservoir host vs vector) ?


texts: Does darker skin color make it easier to live under sun?

texts:
I have always thought darker colors absorb more heat from the sun, so if you are wearing a white T-shirt you will be cooler under sun than wearing a darker T-shirt, or a black piece of steel will be hotter under the sun than a shiny silvery one.

If this is true, then why is the same not applicable to skin color? It seems to me like the more sun in an area the darker the people's skin has become, isn't that the case?


texts:
"The living state is a non-equilibrium steady state to be able to perform work."
I know that a "steady state" is the one in which the rate of energy gain is equal to rate of energy loss. Then how can living beings do work?  Can you simplify it?


texts: Most of the street/feral animals (cats, dogs, cows, some wild animals too) drink tap water or dirty water, but it doesnt seem to affect them. So, why do humans drink pure water?


texts: Is there a way for POPart to accept indels in chloroplastidial genes?

texts:
I need to construct a network concerning chloroplastidial genes using POPart. My problem is that POPart does not know how to deal with indels. I have already coded them using SeqState (simple indel coding) but unfortunately the nexus file does not work in POPart.
Is there any way that I can alter the nexus file in order to overcome this problem?


texts: Why does azithromycin not affect human mitochondria?

texts: Drugs like tetracyclines, macrolides and aminoglycosides bind to prokaryotic ribosomes. It is interesting that our body too having mitochondria, which have prokaryotic ribosomes, there is little(?) effect seen. It can not be ruled out that the effect may be lesser due to them being organelles. Azithromycin's effect on parasites like Toxoplasma and Plasmodium is due to its effect on the plastid that these Apicomplexans have (Castro-Filice et al. 2014).


texts: Which aspects of evolutionary biology are most relevant to medical practice?

texts:
I'm not pretty much sure if this question suites this forum. But I think its important.

In what aspects evolutionary biology can be seen to be very helpful in medical curricula?

Clearly infection and drug resistance seems to be relevant, also pointed are Cancer evolution.

Are there some interesting output on Neurology in particular?


texts: Is chromosomal DNA more likely to interfere with restriction mapping or PCR analysis in E. coli?

texts:
We are characterizing YADH-1 in my biochemistry lab course. Over the course of the first weeks, we harvested E. coli cells, and isolated plasmid DNA via alkaline cell lysis. A previous exam for the course asked the following question concerning plasmid DNA and analysis:

"Is chromosomal DNA more likely to interfere with restriction mapping, with PCR analysis, or equally likely to interfere with both methods?"

Since we're using EcoRI and BamHI, my thought process is that while we can predict the cuts on a circular plasmid, we wouldn't be able to predict all of the cuts on high-molecular weight chromosomal DNA, and the resulting restriction map would be useless. However, PCR can work in a complex mixture of molecules, so even in chromosomal DNA, the primers should be able to find the target sequence. Is the answer therefore that chromosomal DNA is more likely to interfere with restriction mapping?


texts:
I have no expertise in biology, I'm a data scientist, and I would like to know if it makes sense, from the biological point of view, to analyze data (SNP data) coming from a single chromosome, and not all 22 chromosomes, to predict the risk of a certain disease.

Should I obligatorily use data from all chromosomes? Why?

Thank you very much. And sorry if it is a very basic question, but I really would like to understand this.


texts: Biophysically, how to change from a tonically firing neuron to an occasionally firing one?

texts:
In terms of membrane properties, size and neuronal biophysics (assuming no change in incoming excitation), how can a tonically firing neuron become (say during development) an occasionally bursting neuron?

Any references would be appreciated.


texts: Why is it advised to avoid bubble formation during mixing?

texts: I have been told not to vortex solution containing protein. The reason I was given is bubble formation. Here I am interested in the effect of bubble formation in general.


texts: What is the mechanism behind ventilatory acclimatization?

texts:
In my respiratory physiology lectures, my professor explained that hypoxia-induced hyperventilation occurs in 2 stages when people try to acclimate at high altitudes. My question is about the long-term 2nd stage, listed as #2 below:

there's an immediate increase in alveolar ventilation triggered by peripheral chemoreceptors, but this only leads to a small increase, and also decreases levels of $p_{CO_2}$.
over 8 hrs, there's a slow rise and 2 mechanisms are involved:
 a) bicarbonate ion ($HCO_3^-$) in cerebrospinal fluid is shuttled out and chemoreceptors increase their sensitivity to $p_{O_2}$
 b) kidneys excrete more $HCO_3^-$ to normalize blood pH

I get that the $HCO_3^-$ and $H^+$ comes from $H_2CO_3$ being broken down through carbonic anhydrase. But she never mentioned where the $HCO_3^-$ is shuttled to or which chemoreceptors are increasing their sensitivity to $p_{O_2}$ (I assume peripheral since it's mentioning sensitivity to $O_2$). She then says that because of this $H^+$ and $CO_2$ levels increase, stimulating central chemoreceptors to increase ventilation to help decrease the acidity/$CO_2$ levels. I don't understand how $H^+$ and $CO_2$ levels are even rising because I don't know where the $HCO_3^-$ is even going and what it's role is. This professor is terrible at explaining things, and I'm just so confused at this point! Any sort of direction would be so helpful! Thanks!


texts:
I am trying to determine the "translated" meanings (not seeking the common names) of different insects, (presently some bees and wasps).  Does anyone know of a printed or internet resource that defines the various names. I have one for plants, but not for animals.  Knowing the (English) meaning of the Latin / Greek/ etc. is often very informative -- IF I can find it.

I can give more specifics if you want.

Thanks.

Glen B
Olympia WA, USA


texts: what is the principle behind Allele Frequency Net Database

texts: I just wanted to know what is the basic principle of Allele*Frequency Net Database. How are the frequencies present in them calculated??


texts: Do people grow shorter as they age, how common is it, and what triggers it?

texts:
Is it true that people become gradually shorter as they age?

If it is, is it more common in one gender than the other?

And is it known what triggers this? (Considering that the "shortening" probably does not start immediately after the person stops growing?)


texts: minimum ratio of the shortest isoform to the longest one derived from one same parent gene

texts:
I want to know what is the minimum percentage of the shortest isoform/transcript to the longest one that derived from the same parent gene? Does it have organism specificity? What is the function of the shortest isoform?

Because I want to filter the gtf file from cuffmerge. One consideration is that the very short isoform maybe artificial or random transcripts that should be filtered.

From this page 1, the CREB gene has been manually annotated and included a processed transcripts only 84bp, while the longest transcript of this gene is 8532bp. So the ratio is < 0.01; However, this transcript is not coding sequences. I also plot the minimum ratio distribution in human GENCODE v22 data.

1 vega.sanger.ac.uk/Homo_sapiens/Transcript/Summary?g=OTTHUMG00000097081;r=7:28724300-28726731;t=OTTHUMT00000327948

Best,

Pengcheng


texts: Does DNA polymerase I require a $3^\prime$ end?

texts:
DNA polymerase III adds nucleotides in the $5^\prime \rightarrow 3^\prime$ direction because it can only add nucleotides to the $3^\prime$ end of the previous nucleotide. This is why it requires a primer. However, does DNA polymerase I operate by the same criterion? Does it require a $3^\prime$ end of a previous nucleotide in order to bind successive DNA nucleotides?

If it does, then how can it do so for Okazaki fragments when each Okazaki fragment is unbonded to each other? It is the DNA ligase that finally catalyzes the phosphodiester linkage between the $3^\prime$ end $5^\prime$ beginning of two Okazaki fragments, isn’t it?

If it does not, then what’s the deal with telomeres? After each DNA replication event, the DNA gets shorter and shorter at the very ends because that final primer can be removed but not replaced by DNA via DNA polymerase I, correct? This suggests to me that DNA polymerase I requires a previous nucleotide's $3^\prime$ end to work with, and it has confused me regarding its action on Okazaki fragments in conjunction with DNA ligase.


texts: What causes the development of antibiotic-resistant strains of bacteria?

texts: I understand bacteria have become resistant to antibiotics due to selection pressures, but how do resistant bacteria process antibiotics when exposed to it, compared to non-resistant bacteria. Also, what research is being conducted to combat bacteria resistant to antibiotics?


texts: How do cats survive falling from great heights?

texts:
Among mammals, cats are able to land safely when falling from great heights. For example, when compared to dogs or humans they can survive drops from relative large heights. How do they manage?

A 1987 study from the Journal of the American Veterinary Medical Association. Two vets examined 132 cases of cats that had fallen out of high-rise windows and were brought to the Animal Medical Center, a New York veterinary hospital, for treatment. On average the cats fell 5.5 stories, yet 90 percent survived.

See wiki on cats.

How can cats do this?


texts: Do prokaryotic chromosomes have centromeres?

texts:
I found this here.

Eukaryotic chromosomes are always linear. ... In contrast, prokaryotic chromosomes are either completely devoid of centromeres or carry the so-called “plasmid centromeres” which are not essential (with a few exceptions, such as Caulobacter) (57,–60).

What does it mean by prokaryotic chromosomes carry "plasmid centromers"?
Their chromosomes carry the centromeres of plasmids? Do they have centromeres or not?


texts:
How can we define ageing from a biological standpoint without making an appeal to chronological age?

Related, but less important, are there any metrics we can use to determine someone's biological age other than their chronological age?
Telomere length is an obvious candidate, but it is imperfect.


texts: What shows how healthy someone is by their heart rate?

texts:
What shows how healthy someone is by their heart rate - how low it is at resting pulse or how low it is during exercise or how large the difference is between the resting rate and rate with load? Any ideas?

Clarification:
Essentially, how does the heart rate reflect healthiness and in which ways (is it the resting pulse, pulse during exercise, differences, etc.)

Thank you for your time and effort


texts: How do steroids travel in the bloodstream?

texts: Cholesterol, which is hydrophobic, cannot simply travel in the bloodstream, and instead is enclosed in lipoprotein (LDL, HDL). Steroids, which are derived from cholesterol, are also hydrophobic (right?). So how do they travel in the bloodstream? If they are enclosed by anything, what is the molecular mechanism of their entering the target cell?


texts: Does the oxygen concentration equilibrate between red blood cells in the liver sinusoids?

texts:
In the sinusoids of the liver, venous blood from the hepatic portal system mixes with arterial blood from the hepatic arteries.

Do oxygen molecules move between oxygenated RBCs and non-oxygenated RBCs, so that the partial oxygen saturation of the blood in the sinusoids reflect partial saturation of the RBCs? Or do RBCs retain their initial oxygen saturation, so that the partial saturation of the blood in the sinusoids reflects a mixture of saturated and unsaturated RBCs?


texts: DNA fragments are known from bone fragments from the Mesozoic, but these don't count. I'm guessing the oldest DNA is recovered from permafrost, but how old exactly?


texts: Why do frogs and toads only appear when it is dark outside?

texts: I noticed outdoors how frogs and toads only appear when it is dark or cloudy. Such as only after it rains or during night time. Why is this?


texts: Does The Sympathetic Nervous System Increase or Decrease Urination?

texts:
According to my book:

Sympathetic nervous system stimulation, leads to the release of Norepinephrine(Noradrenaline), priming the body for the "Fight or Flight" response.

It is also stated that:

The effect of sympathetic stimulation is to maintain urinary continence.

But if sympathetic stimulation results in urinary continence, why do we urinate more when afraid or nervous?

I've read this quesion, but the accepted answer states that adernaline(epinephrine) is released (not norepinephrine) and doesn't provide evidence to support why does adernaline result in more urination.


texts: It's right to say coding sequence is part of exon sequence?

texts:
Some basic ambiguities making me confused. I downloaded 5'UTR, CDS, 3'UTR, and exon sequences, separately from Biomart for a gene P4HA2 (Homo sapiens) and found some simple sequence repeat (SSR) on them. While there is a repeat x on the exon sequence, it was not located on the 5'UTR, 3'UTR, and coding sequence (or CDS) of gene. As I remember, exon sequences is the same with coding sequence, except for the first and last exon, which are parts of 5'UTR and 3'UTR, respectively, am I right?. Could you please help me out to find how the mentioned event is possible?
Thanks


texts: What does it mean to use DMSO as a dissolvant in biology experiemnts?

texts:
In many biology publications, I saw that dimethyl sulfoxide (DMSO) is used to dissolve drugs. However, the cell-based assays are still performed in water-based medium such as RPMI or PBS.

My question is: If a compound is not soluble in water, what is the purpose of using DMSO? Although the drug can be dissolved in pure DMSO, won't it precipitate after putting the DMSO-dissolved compound into culture medium?


texts: How is there no limit to a human lifespan again?

texts:
It's probably just misconstrued pop science, but I thought a read an article recently that said there's no known limit on how long humans can live. I could have sworn though that there were a few automatic processes that took place though, like that the chromosomes all shorten in length every time they're copied (is there any limit to that? Also, why does that matter?), the retinas in the eyes harden, the metabolism slows down, the heart muscles wears out, etc.
So, how could it be true?


texts: Is process, opposite for growth, known for mammals?

texts:
Every animal born small, then grow larger and larger.

The same is true for parts of the animal bodies.

Is there any cases, when body or part of the body diminishes in size and mass, while staying healthy?


texts:
I know, that the CRISP/Cas approach for "cutting" the human genome is not completely suitable if we can't say not suitable at all. Because we have many repeats and this approach can bring to our genome additional breaks in DNA and after DNA-repair it causes unwanted mutations. If so, why scientist still continue to play with it (See the link, only 16% success chinese scientist got) ? And what other DNA-editing mechanisms we have? I might be wrong, so correct me please.

Thanks for explanation.

Chinese Scientists Defy Ethics, Double Down on Editing Human Embryos


texts:
Hi
My friend and I get 2 different answers to this question. I would like to know how to calculate the value of q. My friend says that 500/1500=q because there are 500 recessive alleles in the population and there are 1500 alleles in total. I say that p2= 500/1500 and P is the square root of that value and  q+p=1 but we both get different answers.  Please let me know which way is correct. Thank you guys in advance


texts: How can Valonia ventricosa cells get so big?

texts:
Valonia ventricosa are single-celled algae that range between one and few centimetres. In rare cases, they can reach sizes exceeding 5cm. They range from grass-green to dark green, and some are even a blackish colour.

Weirdly, a lot of the literature covering these organisms seems to be pre-1950. This X-ray crystallography project in 1937 identified key structures in the cell wall of V. ventricosa:

It is found to consist of layers in which the cellulose chains in any
one layer are inclined to those in the preceding and subsequent layers
at an angle which is on the average rather less than a right angle.
The two sets of striations on the layers of the wall correspond closely to the
meridian and spiral directions of cellulose chains, while the
extinction directions, being defined both by the directions and by the
relative proportions of the two sets of cellulose chains, lie in
variable positions between. The development of the rhizoids has been
investigated and found to be associated with regions of the wall
adjacent to the poles of the spiral.

Although the authors hesitate to speculate on their function, has any progress in the field suggested the fibres identified in this 1948 Nature paper be involved in sustaining such a massive cell (Figure below)?

So it seems like the cell wall structure has been categorised long ago. But what allows these single-celled organisms to get so big? Is it the plant-like cell wall, or something else? I was under the impression that cells would burst or collapse well before reaching this size.


texts: What is the human species divergence time

texts: How far back along the evolutionary tree do we have to go to find divergence to a completely different species to Hom. sapiens? I don't count Neanderthals because it seems that part of our genome contains fragments of Neanderthal DNA, and therefore, according to the species definition, Humans and Neanderthals could not have been an entirely different species. What about Denisovans? Is enough known about their DNA to consider them a completely different species? In fact, is it even possible to distinguish 'a species' from the DNA alone?


texts: Where would the majority of the Indoleacetic acid (IAA) be in the shoot and what would the effect be?

texts:
If I propose that a plant is 2D and then a light source was shone on both horizontal side of the shoot, in which direction would positive phototropism occur (or would positive phototropism occur at all?).

I am presuming that light intensity is the same and there has been no modification of the tip.


texts: Are bFGF and/or EGF necessary in NSC expansion medium?

texts: My understanding is that it isn't necessary since it appears that the idea behind a feeder layer is that the stem cells produce their own bFGF & EGF along with other growth factors. Yet I've still seen some papers (e.g. this one which I am trying to reproduce), use it in mediums used for NSC maintenance (their neural progenitor culture contains both). This paper seems to suggest that a feeder layer for NSCs is unnecessary which would make sense but I wanted to know what is common practice and the most robust method and how it is related to these findings. Because of that I would like to hear from personal experience but references are also obviously useful.


texts: Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common sec. structure/shape.


texts: Is the heart more relaxed when stretched or contracted, and how does it affect cross-bridge interactions?

texts: In the heart, are stretched muscles during the diastole more relaxed or are the contracted muscles more relaxed? Depending on the answer, are there then more cross-bridge interactions in cardiac muscle cells when the heart is stretched or contracted?


texts: Is there any standard of notation for ecological diagrams?

texts:
General Question

Is there any convention of how to express different types of relations (e.g., eats, turns into, is beneficial to) and agents (e.g., species, nutrient) in an ecological diagram? I know that inhibitory relationships are indicated by barred arrows, but I failed to find anything going beyond this.

Example

Suppose, I want to express that Species A excretes Nutrient X, which in turn is metabolised by Species B. Naïvely, I would sketch this as follows:

However, this it not necessarily clear:

I here arbitrarily used squares and circles to distinguish species and nutrients.
If you do not know this, you could not immediately distinguish them.
(Of course, I may just use specific examples like tree instead of A, but then for my theoretical cases, a tree is too concrete.)
The arrows mean different things.
The left arrow means excretes, the right arrow means is metabolised by.
Moreover, the arrows could be mistaken for something like turns into or a general is beneficial to.

How would I denote the above relation unambiguously in a diagram?


texts: Do multiple axons innervate a single skeletal muscle fiber?

texts: The typical text-book illustration of innervation of muscle fibers shows branches at a single position along the fiber. Does any given muscle fiber have more axons that innervate it though, given that muscle cells can be quite long, up to half a meter in Sartorius?


texts: When in the cell cycle is the number of chromosomes normally reduced?

texts:
Page 96 of the Study Guide for Campbell Biology, 11th Edition has the following question:

  A reduction in the number of chromosomes per cell occurs

  a. During meiosis I

  b. During meiosis II

  c. During mitosis

  d. During the S phase of interphase

Page 451 states that the answer is a.

I thought that the number of chromosomes at the end of meiosis I per cell equals the number of chromosomes in the parent cell (although sister chromatids remain attached), whereas the number of chromosomes at the end of meiosis II per cell equals half the number of chromosomes of the parent cell. If so, isn't the answer b?


texts: Species identification - what kind of worm is this?

texts:
I am finding these worms in my bathroom since summer arrived. I have been finding these on floor, walls and damp towel I left hung overnight in bathroom couple of times. When these worms are squished, a bang like sound is produced. Can you help me identifying this, is it something to be taken seriously & requires immediate action? Average length of these worms is ~ 1-1,5 inches.  Please find a closeup picture I managed to capture with mobile camera.

I moved into this house last winter so don't know previous summer history. Anyways I think I should get bathroom drain cleaned.

Edit: Just noticed it has very tiny hair thin, white/ transparent legs, many of them. These legs are barely seen with naked eye. May be they are just hair like things not legs (I don't know proper terminology).

Edit2: origin is Lahore, Pakistan. It's far from sea, open agricultural terrain. Climate is hot.

About movement, no they don't move like earth worms (shortening in length and then stretching). Neither it's snake like. It kinda straight. They also don't have legs as centipedes do, on their sides.


texts: How much genomic variation one usually find within a given bacterial species?

texts: If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to find the same position in a different member of the same species?


texts: Detrimental effects of fructose in fruit on the liver?

texts:
Fructose is mostly broken down by the liver. During this breakdown, the liver also creates fats (by the process of lipogenesis) which over time can get accumulated in the liver and give rise to nonalcoholic fatty liver disease.

Now, fruits contain fructose. So, here is my question: "Will eating lots of fruit lead to fatty liver disease?" If yes, how much fruit consumption is too much? If no, why not? What about lipogenesis, then?

I got the above information from this article by Harvard Medical School.


texts: Is a variable domain in immunoglobulin's heavy chain different from the one in light chain?

texts: I guess yes, there is difference in amino acid sequences of $V_L$ and $V_H$. And so we have 6 different complementarity determining regions (CDRs) per monomeric immunoglobulin as two heavy chains are identical, and two light chains are the same. Is that correct?


texts: What's the difference between a free chromosome fragment and an extrachromosomal array?

texts:
This is reference to a review on C. elegans mosaic analysis by Yochem and Herman, in which the authors make a distinction between free chromosome fragments and extrachromosomal arrays.

For the former, they reference Herman 1984.
For the latter, they reference Lackner et al 1994 and Miller et al 1996, but these are studies that use extrachromosomal arrays, not papers defining them as a technique, per se.

I am curious to know what the distinction is - I am under the impression that extrachromosomal arrays are fragments with many copies of the gene of interest + a marker.


texts:
Why can't we (human, or even unicellular organisms) withstand low (body) temperatures (5 - 25°C). I have a limited background in chemistry and biology, so this might be obvious, but not to me.

I know that low temperature reduce the speed of chemical reactions, so any creature cold enough should just perform slower? Or are there any other cold-induced effects that prevent certain reactions? (a reaction requiring more energy to happen, would still happen, but at a lesser rate, right?)

And, supposing a bacteria/virus/small&simple organism was subjected to low temperature (above freezing, but low enough to stop working), what would prevent this organism from booting up again when subjecting to "normal" temperature?


texts: Does increased physical activity increase the rate of cell division?

texts:
Ever since learning that the shortening of telomeres is linked to aging I've tried to figure out what causes cells to divide, and if it's possible to slow down the rate of cell division through life style changes.

How would, for example, increased or decreased metabolism affect the cell cycle? If we exercise a lot, would it tear on the cells in any way, forcing faster cell division?


texts: To what extent does the distribution of nerual transmiters in the brain vary human to human?

texts:
Suppose $x$ is a position in the brain, and $n_i(x)$ is the density of neuro recepter $i$ around that point. Any given human will have some distribution of neruo recepters $n_i(x)$ through out there brain.

I am wondering what do we know about the statistics of these densities, or how they vary from person to person?

For example, is there a variance in the amount of serotonin receptors in the brain between healthy or unhealthy people?

How does one go about measuring this?


texts:
When it is in the body, does it matter if vitamin C has peviously been heat-treated? Can the body still use it?

For instance, if vitamin C is added to 90 degree celsius water does it matter if you drink all of the water? Will you still gain the vitamin C?


texts: What is the end-point of material from an apoptotic cell, after phagocytosis?

texts:
Apoptosis occurs. The organelles and interior material form apoptotic bodies that are packed in vesicles. The cell membrane breaks apart (cell no longer exists) and apoptotic bodies enter the extracellular space. Phagocytes "eat" the apoptotic bodies.

What happens then?

Is the material processed again and effluxed into the blood, sent to other cells, ...?


texts: Rosetta - What score does RosettaDock use for I_sc?

texts:
I want to get a score using Rosetta for how well a protein binds to a ligand. I understand RosettaDock has a score called I_sc which will give me a number to indicate that.

I found documentation in https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring about how Rosetta scores structures, but not sure what scoring function RosettaDock uses and whether it is the talaris2014 score.

So the question is what scoring function is used in RosettaDock for calculating I_sc.

Cheers


texts: How Does Green Tea Increase Metabolic Rate?

texts:
According to the article "Green Tea Supplementation Affects Body Weight, Lipids, and Lipid Peroxidation in Obese Subjects with Metabolic Syndrome", Green tea increases metabolism and fat loss:

  Green tea beverage consumption (4 cups/d) or extract supplementation
  (2 capsules/d) for 8 weeks significantly decreased body weight and
  BMI. Green tea beverage further lowered lipid peroxidation versus age-
  and gender-matched controls, suggesting the role of green tea
  flavonoids in improving features of metabolic syndrome in obese
  patients.

Is there any information available concerning the mechanism of that metabolic increase?


texts: Which part of human eyes is getting tired?

texts:
It's a thing of common sense that if you read, drive or look at computer screen for too long your eyes will get tired. They burn, itch and try to close all the time.

But I was wondering which part(s) of them need rest so much... Blinking muscles? Lense muscles? Or the eyeball is drying out?


texts: What are some places where biofilms could develop?

texts: I'm trying to think of places where a biofilm could develop other than on medical equipment or food processing equipment such as stainless steel mechanized blades or knives. I'm thinking more along the lines of biofilms on typical house hold things such as the bottoms of shower curtains


texts: Use of restriction endonucleases to analyse Variable Number Tandem Repeats (VNTRs)

texts:
The textbook I’m using states that “Ends of VNTR have conserved sequences. These can easily be cut by restriction endonucleases.”
But restriction endonucleases cleave palindromic sequences. Does this mean that the repeated DNA and conserved sequences together form a palindromic sequence?


texts: Can/Have cancer cells be/been used in stem cell culture lines?

texts:
Since Cancer cells have unlimited growth potential, can they be induced towards totipotency and pluripotency?
If so, can cancer cells be used in stem cell culture because of similar properties of unlimited replication?
Can they be used in cell lines to culture viruses even?


texts: Do the simplest bacteria have ribosomes and helicase?

texts: I find it interesting that all life on earth use DNA. I've seen video on how helicase and ribosomes work together to copy DNA sequences (to RNA) with helicase then recreate them using ribosomes. Does this process work the same way in the simplest life forms? Bacteria and other unicellular life that reproduce through mitosis, for example?


texts: As far as I know, people suffer from the cold since ever. Why didn't and don't we evolve to resist it?


texts:
What nutritious insects exist to farm that require the least attention? I'm looking to automate simply, in a self regulating way.

Edit: To add detail, I imagine the insects would live densely in a large tank and be isolated from the outside. They would be able to breed and would co-exist with a plant that is also able to propagate, that could if needs be even be an air plant, that is eaten by the insects, dead insects either return to nourish the plant, or leave through a funnel, water also evaporates and falls as rain inside the tank.

The idea is to produce food without human effort. This could be in the form of a very cheap to use coin operated vending machine. The insects could be compressed and dry fried into a block to be dispensed, maybe like a bar, the machine could be solar powered.


texts:
MEN 2A is a dominant inherited disease caused by a mutation in the RET proto-oncogene.
The probability of being sick when you have the mutation of the RET proto-oncogene varies with age and is assumed to be 40% at 40 years of age.

With autosomal dominant inherited diseases, this formula can be used, where p indicated penetration and D is the sick allele:

P(II inherits D given that II is healthy) = $\frac{1-p}{2-p}$

The uncle of the son III1 in the tree has the disease so he assumes it comes from I1 or I2. The father of the son II2 is 40 years old with no symptoms.

What are the odds of the father having the mutation?

What are the odds of the son having the mutation knowing the % in the first question?

I just used the formula above as so for the first question: $$\frac{1-0.4}{2-0.4} = 37.5\%$$

I'm having problems with the second though and I assume to use Bayes formula.

I've tried as so:

$$P(\text{son mut given dad mut}) = \frac{P(\text{Dad mut given son mut}) \cdot P(\text{son mut)}}{P(\text{Dad mut})}$$

I know the probability of the dad having the mutation is 37,5% and the probability of the dad having the mutation given that his son has the mutation is 100%. However I can't seem to know what to put in the probability of the son having the mutation? Any help appreciated, thanks! Sorry for a long question.


texts: Can we detect the origin of a 1000 year old dead body after grave excavation?

texts:
I recently read an article saying DNA analysis has shown some of the people buried in Viking graves in Scandinavia originated from places like Persia and it is talking about something around 1000 years ago.

How accurate could this analysis be based on our DNA and the fact that we have 99.9%  DNA similarity?


texts: Needleman Algorithm for Optimal Alignment of two Amino Acid Sequences

texts:
I want to compute the optimal alignment of two amino acid sequences as per the following definition from a patent:

  "The percentage of identity between two peptidic or nucleotidic
  sequences is a function of the number of amino acids or nucleotide
  residues that are identical in the two sequences when an alignment of
  these two sequences has been generated. Identical residues are defined
  as residues that are the same in the two sequences in a given position
  of the alignment. The percentage of sequence identity, as used herein,
  is calculated from the optimal alignment by taking the number of
  residues identical between two sequences dividing it by the total
  number of residues in the shortest sequence and multiplying by 100.
  The optimal alignment is the alignment in which the percentage of
  identity is the highest possible. Gaps may be introduced into one or
  both sequences in one or more positions of the alignment to obtain the
  optimal alignment. These gaps are then taken into account as
  non-identical residues for the calculation of the percentage of
  sequence identity."

The Needleman and Wunsch implementation at NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) mostly works but not exactly. Thanks to @David & @WYSIWIG from a related SE Thread that suggested this (Computing Percent Identity between DNA / Amino Acid Sequence)

I want to know if there is a way to fix the mismatch.

e.g. My test case is:

Seq1: ABDE
Seq2: AAAAAAAAAAABCDE

The NCBI implementation yields the following alignment which has only 3 identical residues:

But shouldn't an optimal alignment  with 4 identical residues be possible like so:

Seq1: ----------AB-DE
Seq2: AAAAAAAAAAABCDE

Thoughts? Any way to tweak the implementation to give the result I want? Alternatively any other algorithm that can be coerced into getting this alignment? BLAST or a variant?


texts: Determination of a chemical compound in a non-homogeneous sample

texts:
This is a more generalized question of my other question here.

I want to know if it is possible to determine a chemical compound in a non-homogeneous sample. I am asking this because we are aiming to create a device that will detect histamine level in fish without homogenizing the samples. In all the journals we've read (which are a lot), fish samples are homogenized (blended + chemically-treated) before histamine is determined.

I am a computer engineering student with basic knowledge on biochemistry. I'm researching on this because this is our thesis topic (which our adviser has forced recommended to us).

Any help/recommendation regarding this is appreciated. Thank you!


texts: My son studies genetics at school right now and they have been covering gender. It's well known that slightly more boys are born than girls. However, originally there's an equal number of sperm cells with X and Y chromosomes. From what I've read it sounds that fertilization is affected by different factors but it seems that on average it's about equally likely? At school, they told them that more fertilized female "embryos" die than male?? Could it be true? Question: Do you know how it happens that there is an equal number of X, Y-carrying sperm cells, but more boys are born?


texts:
This is a figure summarising the quorum sensing mechanism in Vibrio cholerae.

In this video by Bonnie Bassler, she explains how quorum sensing can be targeted to control infections.

At 15:09 she explains why cqsA- mutants show more dramatic effect when external CAI1 is added - because we are not fighting against the endogenously produced autoinducer1.

My question : But won't endogenously produced autoinducer help in controlling virulence, as the more the auto inducer lesser the virulence ? Why should we be fighting against endogenously produced autoinducer 1 ?


texts: Do cockroaches eat their shells after moulting?

texts: I recently witnessed a cockroach eat its shell after it moulted. Do cockroaches always do this?


texts: What is the mechanism behind the F-Wave?

texts:
Can someone explain the actual mechanism behind the F-wave? Is it really different from a H-reflex response or does it just have another name for historical reasons?
The H-reflex (Hoffmann's reflex) is a reflex motor response triggered by a afferent sensory nerve signals.
As far as I could find, the literature describes the F-Wave as a motor response elicited by "backfiring" motor fibres that were antidromically activated by stimulation. It is unclear to me how such backfiring is coherent with the concepts of refractory periods and normal axonal signal transmission.


texts:
Birds and mammals are both endothermic, meaning they metabolically generate the heat they need to keep their body within a certain temperature ranger.

But birds are closer relatives to reptiles than they are to mammals, and reptiles are not endothermic. Thus birds and mammals developed endothermy independently; and here is the question:

How does thermal regulation differ in birds and mammals?


texts: Database of Multicellular and Unicellular organisms?

texts:
I'm trying to annotate a list of organisms taken from NCBI for cellularity (unicellular or multicellular). Does any of you ever found a database with association between an organisms' name or taxa and whether it is unicellular or multicellular? Desirably, I would like to get information both on species level and on higher taxonomic level (phyla, classes, etc.), but any information on this is welcomed.

In case it matters, I'm using Perl to do this annotation.

Thanks in advance


texts: Does inhaling glue (glue sniffing) reduce appetite?

texts:
I have heard from many homeless people that they sniff glue just to reduce appetite, as it comes cheap and is more affordable than actual food.

Is this true, and if yes, why? This is totally opposite to the effects of marijuana where people feel hungry.

  GLUE SNIFFING : Involves inhaling the fumes from domestic and
  industrial products (glue etc.).


texts: How does mutation cause natural selection? and is it common in protists or prokaryotes?

texts: Why is it inevitable that evolution by mutations alone should be a common cause of evolutionary change in most natural populations? And do you expect mutation-driven evolution to be more common in typical protists or typical prokaryotes? Why?


texts: I left outside a piece of wax few weeks ago and each day I saw lots of bees "eating" it. Why do they do this when they can create new wax? (it seems a really hard work considering how little was taken in the course of few weeks).


texts: How much energy does a neuron use for information processing as opposed to just surviving?

texts: That is, as part of a neural network in a brain.


texts:
A neurotropic virus is a virus which capable of infecting nerve cells.

Herpes simplex virus (HSV) has low neuroinvasivesess and high neurovirulence. HSV is transmitted in vesicle fluid, saliva and vaginal secretions. So the site of infection determines the disease - "mixing and matching of mucous membranes".

Source: Murray 2013, Medical Microbiology.

Why is herpes virus neurotropic?


texts:
It's a lizard that has the ability to burst blood vessels in it's eyes and shoot blood as self defense.

How can this behavior be explained evolutionary? Wouldn't it mean that there had to be some intermediate evolutionary step where the lizard could bleed from it's eyes only slightly? How did that not cause it's extinction?

To generalize more, how does a specific trait evolve when it seems the intermediate traits are detrimental to survival?


texts: What theories exist as to how self-replicating molecules organised into the first cells?

texts:
When I was a biology student in the early 90's, what I learned and read seemed to indicate a gap in theories around the origins of life. There was, of course, no real evidence about how the first self-replicating macromolecules came about, but there were plenty of reasonable theories. One that particularly stuck in my head was Graham Cairns-Smith's idea that replication began with effective competition for space between slow-growing crystal structures, for example.

Once you have something which loosely resembles a cell then, of course, we can invoke our understanding of Darwinian evolution to explain how those early cells differentiated and developed into the diversity of life we see today. But as a student there seemed a paucity of ideas as to how we could have got from macromolecules to cells. This isn't a small step: it requires our macromolecules to be localised, enclosed in a membrane and to begin to work with each other to form basic metabolic chains.

I left academia after a few years of bench work but I was struck again by this question the other day and wondered whether there were any theories or evidence about this transition that had arisen in the meantime? A quick search on Google didn't turn up anything but the same vague platitudes about enclosures of self-replicating RNA, with little explanation of how this might have happened. It also found this question on Biology SE - How did the first self replicating organism come into existence? - but that deals with initial abiogenisis, not early cells.

Are there any more up to date ideas?

EDIT: Clarification was requested. The linked question - and information elsewhere - tend to focus on the broad question of abiogenisis and seek evidence. I'm asking about a very specific step of the process, that between replicating molecules and the first cell-like structures. I am also aware evidence is unlikely, and I'm asking for plausible theory.

Not entirely sure why this isn't clear, or why I'm getting close votes.


texts: Can jellyfish improve the Black Sea ecosystem?

texts:
According to this study, cited by many popular science magazines, jellyfish and other, smaller animals can contribute to the vertical ocean stir as much as currents do.

Black Sea chemistry and biodiversity is highly coupled with the lack of vertical currents, present in oceans or bigger seas. Some of the effects are low salinity in the top layers - many ocean fish species cannot tolerate the Black Sea salinity, and limited space for life (below 50 meters there is no oxygen)

Can the jellyfish population (which is exploding now) change the stratification of water layers enough that the highly saline waters from bottom go up, and oxygen goes to the deeper layers, allowing a completely new ecosystem here?

If yes, what are the outcomes of such prospects? Besides the potentially catastrophic release of hydrogen sulphide form the bottom, can it be an improvement for the biodiversity here?


texts: Where can I find the pMON7124 plasmid sequence?

texts: I need the map of the pMON7124 plasmid. As this is not easy to find, I welcome any hints.


texts: confusion regarding degrees of flexion and a goniometer

texts:
I have read

https://en.wikipedia.org/wiki/Anatomical_terms_of_motion#Flexion_and_extension

"Flexion ... decreases the angle...Extension is the opposite of flexion, describing a straightening movement that increases the angle between body parts"

I am clear on the directions of flexion and extension

So all agree on direction, but if I look up degrees of flexion, for example

and videos showing usage of a goniometer to measure shoulder flexion, which echo that picture, so 180 degrees is the arm up, and 0 degrees is the arm down.

What I don't quite understand, is that flexion according to wikipedia, should decrease the angle.  Whereas looking at the degrees in that diagram, and in videos of usage of a goniometer, the more flexion you have, the higher the degree.

I can think of two possible resolutions

A) that wikipedia has missed out that in fact, for the case of the arm,  flexion increases the angle. Whereas for bending movement, it decreases it.

or

B) the planes that describe degree of flexion, are different to the ones shown on a goniometer, perhaps, one field uses a gynometer, the other uses a measure with the angles going the other direction

I'm guessing that it's "A" , that wikipedia is misleading and in the case of the "shoulder"(the arm movement considered shoulder flexion and extension), flexion doesn't decrease the angle, it increases it(though wikipedia doesn't say that). But i'd be interested if that can be confirmed.


texts: Presence of Aromatase enzyme in males : Result of Natural Selection

texts:
Males have increased chances of getting cardiovascular diseases than females ; one of the reasons might be less level of oestrogen ( which decreases deposition of low density lipoprotein LDL in blood vessels).

I know that Aromatase enzyme is produced by sertoli cells in males. It converts androgen into oestrogen.

Now ,
today my teacher said that the presence of Aromatase enzyme in males is the result of natural selection against increased chances of heart attack in males.

My question is-

1. Is the amount of oestrogen produced significant to decrease cardiovascular diseases that it can lead to natural selection?

2. Are there any evidences for the same? please enlist them.

Any help is appreciated.  Thank you!  :)


texts: Are there any organisms with larva more advanced than adult form?

texts: Usually adult organisms are more sophisticated than corresponding larva, i. e. frogs, mosquitoes, fish. Are there species where the opposite is true?


texts: Pedigree analysis : autosomal or mitochondrial

texts:
I have tried a to decide if this is a autosomal dominant, recessive or a mitochondrial disorder.

Is it possible to know for sure, or do you have to use probability?

(English is not my native language)

No other pedigrees have had carriers marked so I did not expect this one had it either.

Auto dominant.

I:1 aa I:2 A-
II:1 aA II:2 aa II:3 aa II:4 aA
II:1 children could have got a from him and a from her the the disorder would be gone.
III:9 children got her dominant A

Recessive
I:1 A- I:2 aa
II:1 aa II:2 A- II:3 A- II:4 aa

Mitochondrial disorder
I read "transmission only accours through females"


texts:
I'd like to know whether it is possible to convert from RU/ml to AEU/ml.
I work in the ELISA department in our laboratory. We need to validate some kits by comparing results between our lab and another lab. They reported their values using the AEU/ml unit whilst ours are in RU/ml.
Is it possible to convert between AEU/ml and RU/ml?
RU: Relative Unit   AEU: Arbitrary Elisa Unit. The plates are read on a Biotek microplate absorbance reader via UV-VIS detection at a wavelength of 450.
Thanks in advance!


texts:
While reading this article about tardigrades that had been previously frozen, I came across some verbiage I wasn't sure of and couldn't find any real explanation given the context. The article kept making mention of the tardigrades "in tun form", yet the only references I could find to the meaning of tun dealt with weight or casks (like for holding liquid).

So does tun mean cask (like a casing) in this context?


texts: Hela live cell confocal laser scanning - reccommendations for good fluorophore that will show good movement

texts:
I've been doing a lot of live cell imaging lately mostly using hela cells expressing some EYFP based chimeric proteins. I'm building a video library for an art student here at the university who is going to create an exposition using the videos. I need a lot of content to make this sucessful and rather than requiring much scientific merit these videos need to be "busy" and look good. I'm looking for suggestions as to any dyes or fluorophores, drug treatments or conditions someone has worked with that will show significant movement/change of/in the cell, change in intracellular localization....doesn't matter it just needs to be a significant alteration for the cell.

I'm still really optimizing the system with the CO₂ etc.. and the longest aquisition i have taken is about 8 hours - after that either the cells are dead or the focal drift becomes too much of a problem. I am hoping to see some division once I can get the system recording long enough. Until then was looking for some suggestions as to other possibilities.

The various dyes I have been using include:  hoechst, dapi, mito-tracker, draq5, er-red, rox-red. also eyfp/tubulin, eyfy/mito, eyfp/golgi, draq5. These dyes aren't cheap and I'm only one i know doing this so I'm checking here.


texts: Location of nucleotide synthesis and transport

texts:
I couldn't find this question directly asked so I thought I would ask it

In Fundamentals of Biochemistry 3e (Voet et al), it has a small small little comment about pyrimidine synthesis:
(In a diagram showing UMP synthesis)
"In the eukaryotic enzyme, which contains FMN and nonheme Fe, is located on the outer surface of the inner mitochondrial membrane where quinones supply its oxidizing power. The other five enzymes of pyrimidine biosynthesis are cytosolic in animal cells."

So it seems for the most part pyrimidine synthesis occurs in the cytosol??

When the book talks about purine synthesis no mention is made of where this is actually happening in the cell.

Also, if nucleotides are being made in the cytosol, I suspect there must be some kind of membrane protein that allows nucleotides to cross the nuclear and mitochondrial membranes... what are they??

I'm a visual person, and knowing where and how these things are happening in the cell helps me understand it better than just following what's happening after each synthesis step.

Thanks!


texts: Why are bees "committing suicide" in my house?

texts:
There is a beehive about 500-1000 meters away from my house.
During the last years, almost every day, one or more bees enter from the window, "dance" for an hour or two, and then drop dead on the floor. Some more details:

The bees may come in every hour of the day, but most of them come just before sunrise. This morning about 20 of them came in; now they are all dead on the floor near the window:

Often, the bees prefer to make their "dance" near the lamp. But this is not always the case.
They usually do not sting me; I was stung only twice, the bee died immediately afterwards, I took the sting out with tweezers, and it did not hurt too much.
I did not use pesticides or any other stuff that could kill the bees.

Why are they doing this? How can I stop them from coming?

I read that bees are disappearing; maybe it's because they all come to my house to die? :-)


texts: What Software could I use to create Diagrams of Biochemical Processes like these?

texts:
Cross-posted at GraphicDesign.SE here

Is there any software software that I could use to (closely) create pathways as depicted in these diagrams?

Or does anyone happen to know what software was used for these diagrams specifically? [Sourced from Harper's Illustrated Biochemistry (31e) and Murray's Medical Microbiology (8e) respectively]

I would like to be able make alterations such as adding extra steps, changing color, including newer pieces of data and such-like for the purpose of making my own notes.
I assume that knowing which software was (or can be) used to create these, I'd have greater versatility making the edits I need, or creating something in similar from scratch for other processes/pathways.


texts: How is the enzyme glycogen synthase regulated?

texts: How is the enzyme glycogen synthase regulated in regards to glycogen synthesis? I think I understand that phosphorylation decreases its activity (through glycogen synthase kinase?), but what role do molecules like insulin, glucagon (or epinephrine), protein kinase A, and Protein phosphatase 1 (PP1) play? Do they activate or inhibit glycogen synthesis, and how so?


texts: Using only one antibody to detect COX-2 enzyme

texts: If I wanted to detect COX-2 from a western blot test, would only a primary antibody work? I'm on a budget so does anyone know of relatively cheap COX-2 antibodies?


texts: Identification of a spider from my basement

texts:
It's a little over 1" long including legs, and I found it in my basement in Pennsylvania. My guess is a funnel weaver, which would be nice since then I can free it (right?) from the tin can it's currently sitting in.

Thanks!


texts:
Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. A summary of the protocol for ChIP is here. Briefly, the steps are:

DNA and associated proteins on chromatin in living cells or tissues are crosslinked;
The DNA-protein complexes are  sheared into ~500 bp DNA fragments by sonication or nuclease digestion;
Cross-linked DNA fragments associated with the protein(s) of interest are selectively immunoprecipitated from the cell debris using an appropriate protein-specific antibody;
The associated DNA fragments are purified and their sequence is determined.

After step 3 (immunoprecipitation of the protein-DNA complex), it is my understanding that the protein–DNA cross-link is reversed and proteins are removed by digestion with proteinase K.

Can anyone tell me if during this step the DNA at site of cross-linking is included in further sequencing step or is washed away with the protein itself?


texts: Are there more/less favourable phases of menstrual cycle to donate blood?

texts:
I was wondering whether it makes a difference when during the menstrual cycle a female is donating blood in terms of:

Blood quality (iron or hormones levels)
Her health/safety

I am aware that females can donate blood during menstruation as the blood they lose does not directly come from circulatory system and the amount is not that big after all. As for the hormones - their levels do change considerably during the cycle and can affect a whole range of things. Can they also affect the blood quality or are such fluctuations rather negligible?


texts: How do red blood cells obtain energy without mitochondria?

texts: RBCs don't have mitochondria so there is no Respiratory chain in them. But how does they get energy from Lactate. Because Lactate produce NADH which gives energy only in respiratory chain.


texts: Why can action potentials not be initiated at dendrites?

texts:
Why are action potentials not initiated at dendrites, although dendrites are the first to receive input from the presynaptic cell?

In fact, excitatory postsynaptic potentials (EPSPs) at the dendrites are smaller than in the cell body and axon.

Considering the fact that dendrites have enough voltage gated ion channels, why is it that cation influx through these channels is not able to depolarize the dendrite above threshold and generate an action potential?


texts:
I have a Chamaerops humilis in my apartment and in there is these small plants growing. I live in Denmark, Europe and my palm tree has only been inside my apartment since i got it.

Can anyone identify this plant?

Click on photos for full size


texts: Is this a form of *LaetIporous sulfurous*? Tree is in north central Virginia

texts: I found this while walking our dogs. Is this "chicken of the woods"?


texts: What's the smallest animal with hemoglobin running in its veins?

texts:
What's the smallest known animal with hemoglobin running in its veins?

Here I mean an animal that on its own is able to produce the hemoglobin that is running in its veins. For that reason this excludes mosquitoes that have filled themselves with blood from another creature, for example.

With smallest I mean either by mass or by spatial dimensions. Either would be interesting.


texts: Species of dinosaur with longest fossile record (no birds!)

texts: There were many species of dinosaurs and many got extinct long before the whole clade disappeared. I am wondering which species has shown the longest fossile record. Since birds descend from dinosaurs, I excluded that case to preclude the easy answer! I fully understand the vagueness of my question, stemming from the uncertainties associated with the definition of species but I would think that at least some ballpark could be estimated?


texts: Which of this 2 affirmations is more close to the explanation of evolution?

texts:
I am almost secure that this affirmation aren't exactly true but I want to know which of these statements is more near to a description of how evolution works:

The evolution has an exactly target and always progress to it, each generation the childs are more close to make complete a certain task, that is beacuse evolution is like "directional".
For example: The task is be 10cm taller. Each generation the race become 1mm taller up to complete the task.
The evoultion is random but the specie (or natual selection) try to reach a target, each generation has random traits but only benefical traits tends to "survive" and get offpring.
For example: In order to survive the task is be 10cm taller. Some childs are half cm taller and other childs are half cm smaller, the last ones die naturally and only the taller ones survive enough to get offspring.


texts: Creating a cell, not from another cell. Will it be possible?

texts:
If some time in the future, we can know exactly what a cell (for example simple prokaryote bacteria) contains, (I mean, exactly which molecules, the shape of them, the density of each, everything), Then can we create a new cell (not from another cell)?

I mean, if we have such technology, then create a soup just like what that cell contains, and a DNA exactly same as that bacteria cell, and then put some of it inside a Cell membrane, will it start living?


texts:
I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. For example, cis-acting sex-specific modifiers can affect gene expression.

What other mechanisms can create a gene*sex interaction?


texts: Is it possible to sort droplets inside an oil phase with a FACS

texts:
In a nutshell, is it possible to FACS a sample that is in oil rather than in a buffer (water based solution)?
I would greatly appreciate any help with this.
Thank you


texts: Many hormones released by endocrine organs travel down in the blood and bind to specific receptors on the target cells. What then breaks that binding of the molecule with the receptor ? ( thus inactivating further stimulation of the target cell )


texts: I read about "topological crossover" in this paper, Table 1. What does this refer to?


texts:
As far as I understand, evolution is nowadays pretty much analyzed through phylogenetic trees, that is cladograms. These are constructed using the available records and taking some key structures and deduce whether species acquired or lost it, thereby generating a node. By  this approach, chronology is of utmost importance, but chronological time is not. Hence, cladograms are not 'Darwinian' evolutionary trees as the latter are based on chronological time.

However, I cannot help myself when analyzing a cladogram and interpreting the accumulation of various nodes along a branch as moving through time. Isn't evolution all about time? At the risk of pitfalling myself into a 'this is a primarily opinion based question':

Isn't it just so that along a certain branch, each successive node has taken time to develop? Would it not be plausible to determine and assign a certain 'standard evolutionary time unit (a SETU if you like) representing the average time it takes for any organism to loose or acquire a certain trait, thereby allowing each node to be interpreted as time? Of course, the SETU would be a gross estimate, but could still potentially re-animate the Darwinian look on modern-day evolution.


texts: It looks like a wolf spider, but I've not seen these exact markings.


texts: How is the Guide RNA created for Crispr?

texts:
It seems that to modify DNA a guide RNA and Cripr are introduced.

But I'm unable to understand how the Guide RNA is made or created.

Is it a simple method which can be done with simple lab equipment or is it complicated?

What is the equipment need to create it?


texts: Why is Leptospirosis so difficult to catch?

texts:
I was on a small mammals training course and the professor was warning of the dangers of Leptospirosis. Apparently 5-40% of Rats have it and an unknown proportion of other animals. The warning sheet they handed out listed farmers, gardeners, etc as 'at risk' groups. I looked it up on the NHS website out of interest but it said there were only about 25 cases a year in the UK, even of the mild form.

I understand that it dies when it's dried out, but still, in notoriously rainy Britain, I can't seem to make sense of the numbers. There are at least half a million farmers in our country, probably a similar amount of gardeners, at least several thousand homeless and poverty stricken who must live in very close proximity to the huge urban Rat population, not to mention the potential for rodents to get into domestic water tanks. In rainy weather everything can stay wet for days. Also, if I remember rightly, an Olympic athlete recently died from it, so it obviously doesn't require a weak physiology to get in.

So, the question is, given what seems to me to be a massive prevalence (40% of all Rats), vast contact opportunities (all land workers during spells of wet weather), and seemingly a tough little organism (can kill an Olympic athlete), why is it so rare (25 cases in 70,000,000 people)?


texts:
I hope this is the right place to ask. I subscribe to several Stack Exchange threads, and regard them as the best internet forum for genuine and credible answers.

I spent last evening talking to friend, at an Amateur Radio Club, who told me he has recently recovered from the norovirus. I was demonstrating an oscilloscope to him, and he also handled the handbook. All this is now in the holdall I used to carry it to the Club. I took all the precautions I could, like washing my hands and not getting them near my lips, nose etc. So, my question is: how long should I wait before opening my holdall, to be sure any infection there is dead?


texts:
I see that UV-C is the best to kill bacteria generally. We are interested in using to kill off odor in shoes.

What illuminance is needed to kill most bacteria with UV-C?

Thanks!


texts: I saw these fish in a video at an art exhibition, I'd like to find out what kind they are.


texts: The correlation between a leaf's age and its length in the initial stage of growth

texts: I am building a machine learning algorithm which predicts the age of a leaf before its maturity period based on its measured length or area. I would like to know whether there is a mathematical relation to describe this or a repository of data on this topic.


texts: Are there any (chemical) processes occuring inside a seed while it's in a dormant state?

texts:
If a seed were in a glass jar without a chance of germination, are there any (chemical) processes occurring inside the seed while it sits there?

My intuition tells me no since my understanding of seed dormancy tells me that dormancy serves as a delay mechanism to increase the chances of survival of the plant.

I deductively reason that dormancy prevents germination by pausing all reactions (processes) in a seed until a combination of conditions triggers the process that initiates germination.

I've done some research online but I can't find anything to support the "pausing all reactions” portion of my statement which would answer my question.


texts: Trial pre-registration service that accepts non-clinical trials, or specifically ecology?

texts:
I'm in the early stages of designing a trial in ecology. I'm interested in pre-registering the trial, as suggested here.

My concern is that all of the registries (that I can find) deal specifically with clinical trials, not ecological or general natural-sciences research. Does anyone know of a service that would accept pre-registration of non-clinical biological trials?


texts: Why can't we feel pain when the eye lid touches the eye ball?

texts:
When I press a finger on a closed eye lid it means the eye lid touches eye ball, then I didn't feel any pain.

Now I open my eye lid, then I small touch(not press) the eye ball, it gives me pain, why so?


texts: Help with histological cell identification in colon

texts:
I have scans of a histology slide of tissue of colorectal cancer and its surrounding tissue. This slide has been stained with the typical Hematoxylin & Eosin (HE) staining then unstained and stained again with two immunehistochemical markers, one for each B- and T-Lymphocytes. Those markers are CD3 for T-cells (which appears red) and CD20 for B-cells (which appears brown). The two scans were then aligned so that it is easy to identify a lymphocyte on the immunehistochemical stain (IHC stain) and find that exact cell in the HE stain.
After looking at these scans for some time I noticed, that there was a cell type that, to me, looks indistinguishable from a lymphocyte on the HE stain but clearly expresses neither CD3 nor CD20 when referencing the IHC stain. These cells are mostly found inside colon epithelium or cancer. Below are two images (one in the HE stain and one in the IHC stain) with two example cells marked with red arrows.
My question is what type of cell this is? Could it be some sort of precursor cell or sub-class of T- or B-cells, that expresses neither CD3 nor CD20? Is it even an immune cell at all?


texts:
I don't know what I am asking is silly or not, but I have always heard that eating a banana after a meal helps in digestion.

Some people says before food while others say after.

Is it a fact or some silly myth?


texts:
I have tried pretty hard to get a detailed description of what exactly the median eminence and the tuber cinereum are but to no avail. I am very familiar with their anatomical relationships (spatially) with the hypothalamus, 3rd ventricle, mammillary bodies, etc; however, I still do not quite understand what they are or what cell types comprise them.

Are they areas of grey matter? Are they some sort of modified ependymal cell layer of the 3rd ventricle floor?

Or are they areas of connective tissue that merely "house" white matter projections from the hypothalamus to the pituitary? So, to repeat the inquiry from above:

What cell types comprise the median eminence and the tuber cinereum?

And, moreover, what's the actual function of the cell types that comprise them?


texts:
In a PCR type protocol, the high temperature stage of the cycle will cause dsDNA to denature, as well as any annealed primers. At the lower temperature the denatured dsDNA will remain denatured. As far as I understand, though, the primers are re-annealed.

My question is this: are there any enzymes that catalyses this re-annealing, or does this happen by chance?


texts: Are more molecules of ADP than inorganic phosphate returned to the light reaction in photosynthesis?

texts: During the dark reaction, 9 molecules of ATP are consumed for every 3 carbon dioxide molecules, yet only 6 molecules of inorganic phosphate ultimately leave the cycle. Does that mean that there is a greater concentration of ADP than inorganic phosphate returning to the light reactions?


texts: What did Francis Crick and James Watson discover that Rosalind Franklin didn't?

texts:
I've recently been introduced to the history of DNA research from Miescher to Franklin, Crick, and Watson, and I've found that Franklin had figured out a great many number of things out that Crick and Watson are popularly credited for when they 'acquired' her photo, including that:

DNA has a helical shape
The distance between two base pairs is 0.34nm, and each helical turn is made up of 10 bases at 3.4nm
Nitrogenous bases protrude inwards and the sugar-phosphate backbone is on the outside

On that note, did the paper written by Crick and Watson in 1953 result in any information that Franklin herself hadn't figured out? Or were Crick and Watson redundant when it comes to the current model of DNA?


texts:
I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes through the color of each reaction in the map.

I have tried using tools like Mathematica and Cytoscape, but it is very hard to get a nice layout of the metabolic network. I have seen maps of E.coli metabolism which look very nice on paper. What I need is a map like these, but where I can define the colors of the reactions.

For example, see the image below for an example. Forget about the yellow bounding boxes delimiting compartments. I can spare those.


texts: an umbrella term for homeolog and ohnolog?

texts:
Is there a word that refer to homologous chromosomes within a polyploid species? If I have AABB species, what is A to B?

The words "homeolog" and "ohnolog" are reserved for the cases if the homologous chromosomes have diverged via speciation or whole genome duplication event. But what if we just don't know?

I hesitate to use word "homologous chromosomes" since they do not for a choromosome pair anymore, they are homologous in sense of an recent common chromosome ancestor.


texts: What is the effect of surfactant deficiency on dead space (of lung volumes)?

texts:
Surfactant deficiency in adults with acute respiratory distress syndrome has long been recognized. This deficiency causes decrease in lung volumes (tidal volume or redisual volume for example).
Dead space is the portion of each tidal volume that does not take part in gas exchange.
So this deficiency cannot cause decrease in the volume of dead space, right?
I am asking this question because our teacher told us that this deficiency causes decrease in all lung volumes, without exception.


texts: What's the difference between the neuroendocrine system vs endocrine system?

texts:
This is what I have understood so far:

Neuroendocrine system involved neuroendocrine cells (also known as neurosecretory cells) that receive nerve impulses by a sensory neuron to release neurohormones into the blood stream. The endocrine system releases hormones by endocrine cells into the blood stream when a receptor protein senses a stimulus.

Here are my questions:

When it comes to the brain, are the neurosecretory cells located in
the hypothalamus or the posterior pituitary gland or both?
Is the hypothalamus and the posterior pituitary gland classified as
    neuroendocrine glands and is the anterior pituitary classified as an
    endocrine gland?
If the posterior pituitary gland is indeed a neuroendocrine gland,
    is ADH and Oxytocin, which are both released by the posterior
    pituitary gland, classified as "neurohormones", not just the classic
    hormones?


texts: Do repetitive movements on EEGs show up as discernible patterns?

texts:
Here is a typical EEG reading:

(source: frontalcortex.com)
If I am connected to an EEG, and am sitting perfectly still, and then begin doing some repetitive motion, say, 10,000 times, will we see discernible patterns emerge in the output?
In other words, would it be possible to categorize a particular pattern in the output and say "Waves with this signature correspond to the subject wiggling his left pinky"?
I would imagine that, over time (and many trials) wave patterns converge to predictable signatures for a given movement.


texts:
I have a list of Refseq accession numbers such as :

YP_009448812
YP_009448725
YP_009448701
NP_659591
around 10 000 acc_numbers...

and I'm looking for a tools in R or Python in order to get the corresponding Go term ids.

I tried the packages (org.Mm.eg.db) and (GO.db) but it does not work.

> Term(names(get(get("YP_009165174", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "YP_009165174" not found
> Term(names(get(get("YP_009448701", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "YP_009448701" not found
> Term(names(get(get("NP_659591", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "NP_659591" not found
> Term(names(get(get("YP_009448812", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "YP_009448812" not found

Does anyone have an idea? Thank you for your time. I cannot find a egREFSEQ2EG for viruses.


texts:
I'm trying to get my head around what a pseudoknot is and how I can identify them given some RNA string. For example, suppose I have a string s = CGUUGUGUACACGAUAGUACAU. Suppose the two longest substring inversions are identified in bold CGUUGUGUACACGAUAGUACAU, which form the stack of the hairpin and everything after the first substring and before the start of the last substring make up the hairpin as illustrated below.

                                  U G U
                                G       A
                                 U     C
                                  C - A
                                  G - C
                                  U - G A U A G U A C A U

By definition, a pseudoknot is defined as a secondary structure formed by pairing between a loop and a region located outside of the stem flanking the loop. In this example, we would start the pairing using some substring of the outer tail and start matching bases around the hairpin. My question: is the pseduoknot the alignment of these base pairs, and what is the significance of this alignment?


texts: Do squids or octopus suffer from myopia(hyperopia)? Do other vertebrates get myopia(hyperopia)?

texts:
Both vertebrates and cephalopods evolved very sophisticated camera-type eyes, and both are capable of focus. But it also pose a risk of inability of focusing, such as myopia in human. So is myopia a common problem of vertebrate eyes or just occurred in a few vertebrate species?

Cephalopods also have the ability of focusing, but they focus in a different way. They focus by changing the distance between lens and retina, instead of contracting the lens like human. So are cephalopod eyes more flexible and less prone to get myopia?


texts: Possible to remove accumulated haze on fluorescence interference filters?

texts:
I have a few different fluorescent microscopes, the two that use Mercury  lamps are older than 7 years. I notice on those that the thin film filters in the filter cubes (green, red, blue) have accumulated this haziness. Both the excitation and barrier filters seem to have this, more so on the ex filter and it's not present on the dichroic.

I've always referred to this as the filter being "burned" and my rational is that it's from the heat & intensity & low wavelengths from the Mercury lamp.  But in all honesty I don't know what it is or if it's removable and if so how? I would like to see if removing it improves my image clarity.

I know a picture would help here and I'm having trouble showing it but will keep attempting and add it to an edit for this question. However I have seen this on many microscopes if you have one with a merc arc lamp and it's getting up there in age take a look at the filters on it. Let me know if you see this too.