texts:
From an evolutionary perspective, why would anyone ever be sexually exited by small children who could not possibly have started puberty?

Is it a confusion between some combination of sexual and non-sexual systems?

Is it a evolutionary imperfection?

Or is Darwinian thinking not necessarily applicable to human behaviour?


texts: Statistical method for characterizing the relationship between body mass and metabolic rate

texts: There is a dataset that contains body mass ($x$) and metabolic rate ($y$) from many different organisms. It is common to fit the data to the model of the form $y=ax^b$ and estimate the parameters $a$ and $b$ (see Kleiber's law and The Metabolic theory of ecology). In doing so, it is also common to log transform $y$ and $x$ and create the linear relationship log($y$)=log($a$)+$b$log($x$) and perform linear regression analysis based on the log transformed data. Is this approach better than directly estimating $a$ and $b$ based on nonlinear regression for $y=ax^b$ (because results are different)?


texts: How can I differentiate between polysaccharide bands and protein bands on SDS-PAGE?

texts: I tried to extract bacterial polysaccharide but after running a SDS-PAGE I couldn't differentiate between the polysaccharide band and protein ones. I face a problem of moving up of the samples from the will and no clear bands. Any suggestions?


texts: What is the purpose of the outer mitochondrial membrane?

texts: The purpose of mitochondria is to generate ATP, utilising a chemiosmotic gradient across the inner mitochondrial membrane. Protons are pumped out of the mitochondria into the intermembrane space, but because the outer mitochondrial membrane is highly permeable to ions, the pH of the intermembrane space quickly equilibrates with the rest of the cell. As the outer membrane apparently does not contribute to maintaining this chemiosmotic gradient, what is its purpose? It seems to be doubly redundant in chloroplasts as H+ transport doesn't even occur across the inner membrane.


texts: Statistical Analysis of Protein Folding Problem

texts:
I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (Introduction to Protein Structure Prediction: Methods and Algorithms). Does anyone know whether I can find some code (say in C++, Java, or R) related to the prediction of protein structures? Or, do you know other good articles or books related to the statistics of the protein folding problem?

Thanks for the help.


texts: Confused about the calculation of BLOSUM matrix

texts:
I am trying to understand how the BLOSUM matrix is calculated.

I found a very nice tutorial here: http://www.cs.columbia.edu/4761/assignments/assignment1/reference1.pdf

Also i read through the wikipedia article, and a book "Understanding bioinformatics" from Marketa Zvelebim and Jeremy O. Baum

After i thought i understand the method i tried myself with this "alignment" (i will refer to the variable as they are at the link i provided)

Q
Q
S

So it has only one column, and 2 type of amino acids.

The Count pair frequencies (C) for Q -> Q substitution is 1 (2*1/2) and for Q -> S it should be 2 (2*1).

To normalise it T = 3 as 3*2/2

The q values then seem to be q(Q->Q) = 1/3, q(Q->S) = 2/3

The p(Q) is then 1/3 + 2/3/2 = 4/6

p(S) is 2/3+1/3/2 = 2/6

The e(Q->Q) = (4/6)^2 = 4/9

e(Q->S) = 4/6*2/6*2 = 4/9

Thus

S(Q->Q) = round(log2((1/3)/(4/9)) = -1

S(Q->S) = round(log2((2/3)/(4/9)) = 1

So from this alignment it is more likely to substitute a Q to an S rather then Q to Q? This makes no sense for me.

What am i missing?


texts: How was gene knock out done in pre CRISPR era?

texts:
I am trying to understand how CRISPR has made the gene knockout or gene editing process simpler to make transgenic animals. Here is an old (pre CRISPR) flowchart from Manis, 2007 that shows how knockouts can be made.

I assume much of this process remains the same even with CRISPR. But I want to understand what part of this flowchart has become easier with CRISPR? Is it that we do not need to wait for a random recombination event to occur? Is it that the yield has increased because we directly cut at the site and ask for HDR to happen rather than just sit and wait for it to happen?


texts: How does waking up from an alarm clock work?

texts:
During sleep, one's brain is shut down. All it can do is to see some dreams from the semi-conscious mind.

Then how does it hear when the alarm clock rings?


texts: How would the result of Hershey and Chase experiment been different if protein was the genetic material?

texts: Please answer in simple terms im only in 9th grade.


texts: To understand clearly extraintestinal diseases

texts:
Extradistestinal disease seems to prefer to "bowel" diseases, I think this is about diseases outside gastrointestinal tract so stomach.

Consider diseases ulcerative colitis and Crohn's disease (enteritis) as examples.
Colitis affects to colon, outside of small intestine, I think extraintestinal therefore.
Crohn's disease (enteritis) however affects to the small intestine so I would think intestinal disease (but this clause is wrong) - it should be at least have extraintestinal manifestations.

What is the exact definition of the word extra in intestinal diseases?


texts: Are there calcium channel blocking neurotoxins?

texts:
I am learning about calcium ion channel blockers (CCBs) and am confused whether there are neurotoxins that are CCBs.

If they exist, what is an example of a CCB neurotoxin?
What animals use CCB neurotoxins as a weapon / defense tool?


texts: Why does the mixture of infant formula with saliva provide an ideal breeding ground for disease-causing micro-organisms?

texts:
From: http://www.nal.usda.gov/wicworks/Topics/FG/Chapter4_InfantFormulaFeeding.pdf

  Discard any infant formula remaining after a feeding. The mixture of infant formula with saliva provides an ideal breeding ground for disease-causing micro-organisms.

Why is this so? Doesn't Saliva contain anti-bacterial properties?


texts:
I am working on a project for health center. It involves the creation of a database of all diseases. Currently I want to classify disease on the base of their category based on international standard.
Did anyone know where i can find one, I did a lot of research but was only able to come across this which seem not very useful to me: ICD


texts: How is histamine useful against allergies?

texts:
Histamine is a chemical produced and stored within the body. It is a part of our immune response and is released during an allergic reaction.

Often histamine is responsible for hypersensitive response of the body towards certain specific compounds(allergens). It causes nasal congestion and pollen allergy. Also it acts as a powerful vasodilator, and causes inflammation. But is it really helpful against allergies?

I was wondering why antihistamines would be required to inhibit normal functioning of histamine, then realised that if histamine was not there, then perhaps we would not have allergies..


texts: Why is it beneficial for bacteria to conjugate? (Horisontal gene transfer)

texts: Why is it beneficial for bacteria to conjugate? I would think it's more beneficial to take a plasmid from another cell, than to give yours away or "share". Not homework, I'm just curious.


texts: Are casein proteins in UHT milk digestable for infants or toddlers?

texts:
As a novice cheesemaker, I have read that Ultra High Temperature prosessed milk is unsuitable for cheesemaking, as casein proteins are denatured and cannot be curdled with rennet.
I have verified that claim experimentally. Although curd has formed, its quality was poor (I managed to make whey-like cheese after further heating though).

As casein is the majority of milk protein and curdling with rennet is important component of milk digestion, I started to worry if feeding UHT milk to toddlers is a good idea. (I also wonder, whether boiling milk may lead to a similar casein denaturation.)

Unfortunately, Wikipedia addresses only the cheesemaking aspect of UHT processing. I do not know whether it is possible to digest temperature-denatured casein (without proper curdling).
Moreover, after some more research I am not sure what is mechanism of milk digestion in infants: Which enzyme curdles milk in human infants?


texts: Evolution of the (phenotypic) facial features of the indigenous people of (west/central) Africa

texts:
I am not even remotely an expert in this field; I just got curious, so help me.

First of all, let us remove all human sentimental attributes from this question (such as connotations of scientific racism or emotional reactions thereof) and ask it from a purely scientific point of view. The typical facial feature of a West/Central African person (the so-called broad African type) exhibits a wide nose, a lack of nasal bridge projection (similar to many Asian noses) and a prognathous skull shape that resembles more closely to our ancestor Homo Heidelbergensis than many other indigenous phenotypes from other parts of the world do.

I agree that this claim sounds anecdotal, and is certainly not true of all Africans (for example, Ethiopians), but one cannot dismiss it simply on grounds of ethical policing. I cannot help but notice that many of my African friends remind me of our shared ancestry (with no disrespect meant whatsoever), as is clear from the photographs below, one of a supposed Homo Heidelbergensis and one of a random African Homo Sapiens of today.

My question is the following. What is the reason behind this seeming resemblance? Is this appearance an illusion and possibly a construct of a prejudiced mind, or does this have a valid scientific answer? For example, are most Africans closer to our ancestors than the rest of humanity is? How does evolution answer this question?

Thank you for your help.


texts: I'm just getting started out learning how to use the QTL package in R studio, and I'm trying to find additional datasets to practice with. I've already worked through the datasets here on the Rqtl website. Is there anywhere I can find similar datasets to work with? I'm specifically looking to work with autosomal data.


texts: What is the mechanism behind "acquired" alcohol tolerance?

texts:
I can understand natural variation in alcohol dehydrogenase (ADH) in a population leading to variation in rate of inebriation (after controlling for other variables -- e.g., mass, food consumption, etc.).

But what physiological (adaptive?) process leads to increased alcohol tolerance over the long term in a single individual?


texts:
Are there any carnivores with horns (whether extinct or currently alive)?

Do any flying creatures have horns?

By horns I mean horn like structure.


texts: Where can I download a list of all plant species of the world?

texts: Where can I download a complete list or dataset of every plant species in the world?


texts: How to find mutations related to disease for a protein?

texts: I have done research on the protein (CYP3A4). I have its function, purpose and diseases (breast cancer, prostate cancer, testicular cancer, lung cancer). I am however having trouble finding the mutations of the protein and how it correlates with the diseases, specifically breast and prostate cancer.


texts: Differences in structural target for LPS detection by LAL and MD-2/TLR4

texts:
I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte lysate (LAL) assay. However, I cannot seem to find a paper that indicated what structure on the LPS lipid A moiety is used for detection.

In humans, structure-and-function relationships exist between the phosphate groups of bisphosphorylated glucosamine disaccharide backbone as well as the six fatty acyl tails and the MD-2/TLR-4 co-receptor system.

Does anyone have a paper, or a general lead, as to where I can find what area LAL uses for detection? I haven't had much luck with Google Scholar.


texts: Production of plant derivatives using genetic engineered micro-organisms

texts:
I saw a Thought Emporium video where spider silk was produced by genetically modifying yeast. I have also read about companies making vanillin (vanilla flavour) using this technique.
I am curious to know if plant derivatives like saffron (or its flavour), rubber, or even substances like quinine, tetrahydrocannabinol and cocaine, can also be produced by this same technique. From the information I have found, it seems that some plant derivatives are being manufactured in genetic engineered micro-organisms, but most are not.
Some of these derivatives are very expensive, so I would imagine such techniques could be used to mass-produce them more cheaply. If so, what is stopping industry from doing it? If not, what is the problem?


texts: Do symptoms of common cold infections correlate with the infectious agent?

texts:
The common cold - in summary, an acute upper respiratory tract viral infection - is one of the most frequent viral infections in humans and can be caused by about 200 viral types [Eccles (2005)]. Symptoms are thought to be caused by the immune response in the host, rather than by actual damage caused by the virus [(Hendley (1998)].

My question: is there a correlation between the symptoms observed during a common cold and the viral type that causes the infection? Of course, one can find out the cause of the infection diagnostically by taking samples and isolating DNA or setting up cultures, but that is not my question. My question is whether it is possible to predict the virus taxon causing the infection by symptoms.

My prediction from the information I have at hand is that it should, at least in tendency, be possible as different infections agents use different infection pathways that in return invoke different immune responses and, finally, symptoms [Eccles and Weber, ed. p. 107 - 147 (2009)]. However, I found a rather dated article by Tyrrell et al. (1993) that analyses infections caused by several rhinovirus strains, a coronavirus, and of the respiratory syncytial virus (virus taxa among the most common infectious agents for common colds). They conclude that the main difference between colds induced by different viruses is in duration of the incubation period, whereas patterns of symptom development were not substantially different with different viruses. So is this the current state-of-the-art?


texts: Why large snakes are mostly non-venomous?

texts:
Wikipedia has a list of largest snakes. In this table, there are 11 species of snakes, five of which are boidae and the rest are pythonidae. These two families of snakes are both non-venomous.
I understand that non-venomous snakes should typically be large to be able to suffocate their victims. But on the other hand, why venomous snakes are not as big? They both have a pretty similar body structure and food regime. So why venomous snakes don't grow as large as their non-venomous counterparts? Is there a specific evolutionary reason for this?
The question can be asked in two forms: why non-venomous snakes are bigger, and why venomous snakes are typically smaller? I don't know which one is more appropriate though.


texts: Why is blood drawn from veins? Is it because veins have a large lumen? Or is it because the blood is flowing at a lower pressure and makes discharge easier? Is it safer to draw blood from veins?


texts:
The Gateway cloning system utilizes what Life Technologies refers to as "Clonase enzyme mix" to catalyze the BP and LR reactions.

What is in this enzyme mix? Is there a sequence for them?


texts: Infer distance since duplication from tree?

texts:
Question
I have a really simple question, but I'm not able to figure it out.
I made a tree (using BLOSUM62). Here is a part of the tree:

How can I calculate the distance till the duplication event occured between HBD en HBB?

just for HBB 36.21 and for HBD 38.79
or 38.79 + 36.21 = 75

More info
I determined if this set of sequences follows a molecular clock, and indeed this was the case. So I determined the rate at which these sequences envolve. If I can determine the distance between HBD and HBB I can devide this by the rate to obtain the time since the duplication event happened.

How could you calculate this one?


texts:
I know that there are many hermaphrodite animals and plants. But many of them seem to still exchange genes by mating with another member of their species.

I now happened to read the Wikipedia article on Beef tapeworm, and it turns out that there normally is one worm per host, and it self-fertilizes. Which makes some sense - if I were a large internal parasite, I wouldn't want to wait around for my host to pick up a second member of my species before I can reproduce.

But this means that there is no gene exchange when taenia reproduce. Does it mean that they are all clones of each other, barring spontaneous mutations? How does evolution function in taenia when they don't mate? How comes there are different taenia species if they can't evolutionary adapt to new environments by producing offspring with mixed-up genes?


texts: If inhibiting S6 kinase decreases protein translation, then could inhibiting S6 kinase could possibly slow down long-term potentiation in neurons?

texts:
From http://en.wikipedia.org/wiki/P70S6_kinase...

  Phosphorylation of S6 induces protein synthesis at the ribosome.

  P70S6 kinase is in a signaling pathway that includes mTOR (the
  mammalian target of rapamycin). mTOR can be activated in distinct
  ways, thereby activating p70S6K. For example, branched chain amino
  acids such as leucine are sufficient to activate mTOR, resulting in an
  increase in p70S6K phosphorylation (and thereby activating it). mTOR
  is also in a pathway downstream of the kinase Akt. Akt is typically
  activated upon stimulation of a cell with a growth factor (such as
  IGF-1). Akt then activates mTOR (by inhibiting the Tsc complex),
  leading to p70S6K activation.

We also found a paper showing that downregulation of S6 kinase also results in a decrease in protein translation in yeast (but I'm waiting for Matt Kaeberlein to email me the slides from yesterday).


texts: What are the consequences of voluntary total celibacy?

texts: Psychologically this might be a tough question, but in means of biology, what are the effects of total celibacy on the gonads and the nervous system concerning both man and woman in short and long term? Has there any research made in medical terms and as a bonus question, is there anything similar on other animal kingdom like deliberate celibacy?


texts: I am looking for examples of colloids involved in digestion for a cross-curricular (bio-chem-physics) lesson plan.  Although I have found references implicating colloids in both lipid and protein digestion, I haven't been able to identify which colloids they are speaking of.  Can someone provide specific examples?


texts: Based on morphology alone, what type of claw does the Tyrannosaur have?

texts:
I understand that the exact use of Tyrannosaur Rex's claw is a mystery, or at least debated. I also understand that claws can be used for a variety of different purposes, selective pressure adapts their morphological to be better optimized for certain tasks. Some are used for hunting and killing, like large cats' claws, some are used for digging, like bear's claws, while others are used for climbing, like squirrel's claws.

My question is, all other clues and bits of information about if and how T. Rex might have used its arms, what 'type' of claws did it possess? I'm not asking, in this question, about its arm, the arm's musculature, its mouth or jaw, or about any of the rest of the animal. Based on the morphology of the claw alone, and comparing it to known uses of similarly shaped claws, what types of tasks were the claws geared towards?


texts:
I work in neuroscience, mostly Alzheimer's disease (AD), with some work in autism spectrum disorder (ASD). The work is in gene regulation and epigenomics. I'm familiar with monozygotic twin (MZ) discordance for AD and ASD and the methylome studies done in discordant MZ for those disorders. I began to become curious.

What disorders have never had MZ discordance reported in the literature? Even sickle cell has MZ discordant progression (Amin et al. 1991. Hemoglobin. 15:247-56). Do any disorders lack MZ discordance?


texts: Longest lived land mammal when subtracting sleeping time?

texts:
Recently, it has been found that wild elephants only sleep two hours per night. Wild elephants also live quite long, the median life span is 56 years. Now, 56 years lived with 2 hours sleep per day amounts to about 51 years spent being awake, while a human being who dies at the age of 80 who sleeps 8 hours a day will have spent about 53 years being awake (here we ignore the larger sleep requirement during infancy, taking that into account may put the elephants ahead of us).

So, we see that taking sleeping time into account greatly affects the comparison between waking lifespans of animals. The question is then what land mammal has the longest lifespan when subtracting sleeping time i.e only counting the waking hours. Some sea mammals like whales are known to live for a very long time, but that may be due to very peculiar features of such mammals who have adapted to living in the oceans.


texts: Is the promoter region of a gene transcribed?

texts:
If the RNA polymerase attaches to the promoter region of the gene, would it form the initial mRNA portion soon after attachment by reading the promoter region? Or should it slide across the DNA then form the initial mRNA portion?

Also, does the RNA polymerase read DNA base pairs one by one and add the RNA base pairs to the chain one by one? Or, does it read groups of base pairs just like tRNA which reads triplet of bases during translation?

Similarly, is the terminator region transcribed too and then the process of transcription ends, or does the process end immediately after the RNA polymerase reaches the terminator region? How does the process end just by reading the terminator region?

So, should the promoter and terminator region of a gene be considered parts  of the gene or separate entities?


texts: Stay young by reinserting own DNA from years ago?

texts:
As far as I know, the DNA sequence becomes shorter every time a cell divides.
A shorter sequence results in information loss and aging characteristics.

As a countermeasure, shouldn't one stay young and healthy at least longer, if the DNA in a cell is changed with a "better" DNA (from years ago... let's say your DNA was extracted with the age of 20 and you reinsert it every 10 years or so)?

If this is true, then (as for today's technology)
- is it already possible to perfectly reproduce the DNA? (I only found articles about XNA)
- is it possible to easily replace the DNA in all human cells? (I found articles about bacteria inserting pieces of DNA into human cells)


texts: Is Hemoglobin binding to oxygen the same as Adsorption

texts: I have recently been reading about Hemoglobin and came across how it binds to oxygen. This seems very similar to Adsorption. Is the process of Hemoglobin binding to oxygen through Adsorption ?


texts: Mithradates - Developing immunity to poison?

texts:
According to legend, Mithridates studiously researched and examined all known toxins and experimented with potential remedies by using prisoners as his guinea pigs. Supposedly, Mithridates’ toils paid off because numerous ancient authors, including Pliny the Elder, claimed that he created and regularly ingested a universal antidote for all identified toxins, and it became known as mithridate (mithridatium).

It was said that he was pretty much ingesting small amounts of poison to develop an immunity to it.

Whether universal poison or ingesting each type one by one, is this possible to build up your body to resist or be immune to poison/venom/toxins in general?


texts:
Since the precise amount of cells in each well of an MTT assay varies, how can I normalize the results by cell number/concentration?

How can I take into account the number of cells that have already disappeared due to the action of a toxin applied previously as part of this assay?


texts: Can humans transdermally absorb minerals from ocean water, and if so how much?

texts:
According to several studies quoted here, chemicals can be absorbed by the skin transdermally, at least under certain conditions.

When it comes to elements in seawater like sodium, magnesium, potassium and iodine, is it possible for a human to absorb them transdermally in this instance?

If it depends on various conditions, (such as length of time spent in the ocean, physiological factors (e.g. intense swimming vs. gentle bathing), temperature of the water and their respective effects on skin porousness or other factors affecting transdermal absorption), what would be they be?

And if it can indeed be absorbed (e.g. from open water swimming), are the amounts significant to even measure alongside that of recommended levels for human dietary intake by advisory bodies such as FDA for those mentioned elements, or is it an extremely small amount much smaller than dietary levels of mineral intake?


texts: What is the difference between Amino acids from blood and urine?

texts:
I would like to understand the difference between different tests for Amino Acids. Any blood laboratory offers amino acids tests using 3-4 methods

Blood serum
Urine Random
Urine 24 hour (all the urine samples collected in the last 24 hours)

After having tried Google and coming up empty, I have the following questions that I would like answered.

What would be the difference between testing it via each of the above methods?
What's the purpose of each of these different test methods?
Is one method better than the other? If so why?

Thank you.

Disclaimer: This question is for general knowledge purposes only. Please don't use the question or answers given as personal health advice.


texts: Can a single strand of mRNA form different polypeptide chains?

texts:
My book has a statement:

A single strand of mRNA is capable of forming a number of different polypeptide chains.

In my opinion this statement is wrong because a single strand of mRNA will have same sequence of codons. So, every time it gets translated, it produces same polypeptide chain. But, according to my book this statement is correct.

Am I wrong or is my book wrong?


texts: what kind of dinucleotides can be considered important from a mutational point of view other than CpG islands?

texts:
CpG islands are regions with an high frequency of CpG (Cytosine-phosphate-Guanine) sites. The usual formal definition is that of a region with at least 200 bp, a GC percentage greater than 50% and an observed to expected ratio grater than 60%. In colorectal cancer, these regions have been found drastically methylated with respect to the normal mucosa tissues surrounding the tumor (Illingworth et al. 2010). This brought to speculate a role in the cancer onset. My question is: are there any other kind of dinucleotide rich regions that represent important cases of study in literature?If yes, can you suggest me some papers and references?Than you
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP (2010). "Orphan CpG islands identify numerous conserved promoters in the mammalian genome". PLOS Genet. 6 (9): e1001134. doi:10.1371/journal.pgen.1001134. PMC 2944787. PMID 20885785.


texts:
When I was young, I was told never to put a fluorescent light in a hen house because it continuously turns on and off. Extra lighting is used, as far as I know, to 'extend' a chicken's day. Human eyes don't have the refresh frequency to notice that, but there are animals who have a frame-rate of up to 200 Hz (so they actually see the lights turn off and back on again). I was told chickens are among those animals and that they'd stop laying eggs when continuously exposed to interrupted lighting.

However, my neighbour has fluorescent lighting in his hen house. So either the above is bogus, or I have my facts mixed up. So, how (if at all) are chickens affected by light?


texts: Is it safe to use an egg incubator to grow bacterial cultures?

texts: I've been using a small egg incubator to grow environmental bacteria in petri dishes. I always wear gloves and glasses when I handle the plates and do Gram staining. How likely is it that bacteria grown on dish could become airborne when I open the incubator or the dishes themselves?


texts:
I have this so called "clubbed thumbs"also known as brachydactyly.

It is of D-type.

I searched for it on internet and found that it is a dominant inherited disease.

But to my surprise,none of my family members have such thumbs.Not even  my great grandfather/mother had this type of thumbs.

If it is a dominant trait then why didn't it show in any other family person. Is it that I have had any mutation in my genes?


texts: Why can cones detect color but rods can't?

texts: I don't know if this question applies to only humans but why can cones see much greater detail than rods? Is it possible to have a rod that can detect light intensity and color?


texts: How specimens are organized in a large biological specimens archive

texts:
In a library, (and I'm not totally sure about this, but from experience) books are organized by category/theme into sections, and then they are given a number so that, globally, the numbers are ordered sequentially. This way you can easily just look up a number and go right to it, but then you can also browse entire sections by a common theme. I'm not sure how exactly they do this, but this is roughly what I've seen how it works.

So I'm wondering how biological specimens are organized in a gigantic specimen archive like at a large museum or university collection, with hundreds of thousands or millions of specimens. I'm wondering if they just give them a random number, and then place them wherever that number falls in the sequence. Or if they do like the libraries and group them by category/theme, then by number. Or something different.


texts: What is the difference between conditional and inducible activation?

texts:
In the modern genetically modified animal models, there are not only constitutive mutations which start producing proteins already in the embryo, but also mutations which can be turned on later. I've seen the terms "conditional activation" and "inducible activation" used, especially in the context of Cre-Lox recombination.

Are they used interchangeably, or is there a difference? If they are different, what is the difference?

If I'm looking at a mouse name, like K-Ras+/G12V;Elas-tTA/tetO-Cre;p16Ink4a/19Arflox/lox, how can I recognize which of the two it is?


texts:
I am reading a journal paper about the association between NCAM2 and autism, and I have come across the following:

We performed microarray analysis and identified a 1.6-Mb deletion of
21q21.1-q21.2, containing the NCAM2 gene but no other functional gene.

I am not sure what the '-q21.2' after '21q21.1' in '21q21.1-q21.2' means. Does it mean that the deletion goes between band 21.1 to 21.2 on the long arm of chromosome 21 (21q)? Any insights are appreciated.


texts:
RELATED:

  Why does rabies cause hydrophobia?

  Agony, Hydrophobia and viruses in the light of evolutionary principles

Has hydrophobia been found outside of rabies?

I have only seen it being mentioned as a symptom of rabies.


texts:
HaCaT keratinocytes are described as "spontaneously immortalized "(see paper below) due to aneuploidy or chromosomal alteration.
From the paper I get that this is a literal term, that the cells just continued growing (?) in vitro and never went into senescence without any "human-induced" transformation.
Is this a common procedure for cell immortalization or a rather rare example?

[http://jcb.rupress.org/content/106/3/761.long][1]


texts: Can I figure out the identity of my grandparent from this information?

texts:
I know all my family up to my grandparents, with the exception of the grandfather on my mother's side. At the time my mother was conceived, my grandmother was having an affair so no one in my family knows for sure who the grandfather was.

In high school we learnt that blue eyes are a recessive trait and brown eyes are a dominant trait, as such I should be able to figure out who my grandfather is, but I only studied up to that level and I want to check with someone more knowledgeable than myself if it is correct.

So here's my reasoning:
I have blue eyes, meaning I have two blue eyed genes and got one from my father and one from my mother.
My mother has brown eyes, meaning that she has one brown eyed gene and one blue eyed gene to pass it on to me.
My grandmother has blue eyes, so she passed one on to my mother.
One of my potential grandfathers had blue eyes, so if it had been him my mother would have received two blue eyes genes and have blue eyes. But she has brown eyes so it must be the other potential grandfather (who's eyes I don't know the colour of).
Can someone tell me if this is correct, and if not, why not?


texts: What does irregular heartbeat mean in simple language?

texts: I bought a blood pressure monitor (A&D UA-851) which has the option to measure irregular heartbeat.  I do understand what 'irregular' means, but why do irregular heartbeats happen and what are it's implications short and long term?


texts: What species is this black, blue and white bird?

texts:
I think this species is native to Edmonton, Alberta, Canada, as I see it regularly, especially around the urban locality (Downtown Edmonton).

Season: Early Spring

Date: May 18, 2017

Basic Description: Medium sized bird, and I was not able to observe a characteristic chirp from the bird while I was taking a photograph. Most distinctive feature is the bright royal bluish gradient on the tail and tips of the wings.


texts: Comparison of humans and other primates in milk production amount

texts:
Do human females produce more milk (relatively to average child weight weight) than other primate females? Are human females more likely to feed several children through breastfeeding than other primates?

P.S. I am asking this, because it's what my antropologic hypothesis predicts: some women refused to nurse (and breastfeed) children born by them, so "nurses" - other women - fed those children. This, of course, would require those women to have extra (more than needed to feed their own children) amount of milk.


texts: Is swimming pool water actually a weak topical medication?

texts:
I was inspired by this question.

Given that the chlorine levels in swimming pool water are so high that they can seriously harm amphibians, it seems logical that the water should also kill various microorganisms, fungi or skin parasites.

Is the swimming pool water a weak disinfectant? Are there any illnesses for which a doctor would prescribe a full-body bath in a swimming pool for this reason?


texts: Difference between reciprocal inhibition and regular muscle movement?

texts:
I was looking into a condition I have, anterior pelvic tilt, quite a bit. I ran into a website describing part of the issue as reciprocal inhibition. This was my confusion:

Reciprocal inhibition, defined by just about everyone, is the relaxation of muscles antagonistic to muscles currently contracting, and vice versa. How is this different from regular muscular flex? When we flex a muscle, don't the antagonistic muscles relax to compensate, same as in reciprocal inhibition? Thanks.


texts: Does the body have a mechanism for cleaning plaque buildup in arteries?

texts: Is there a self synthesized substance in the body, or a mechanism that can break down plaque in arteries ?


texts:
What are mast cell membranes made out of?

What would weaken or strengthen them?

Web searches bring up a lot of information about mast cells but very little on the membrane. And the Wikipedia page is not clear as to whether or not additional calcium or sodium fluoride would improve/weaken mast cell wall strength.


texts: Is it true that scientists have disregarded their belief that there are five kingdoms and instead, they have theorized that there are multiple kingdoms?


texts:
The hazards of congenital insensitivity to pain (CIP) are well-known.

This question is about the obverse: what selective advantage, if any, does the normal sensation of pain confer? I'm thinking of severe pain such as that associated with back injury, burns, and some intestinal problems in which the pain seems to serve no function other than to incapacitate.

A related question is whether there is a spectrum of sensitivity to pain, ranging from CIP to heightened sensitivity, what the distribution looks like, and whether this is a genetically plastic trait (like color perception)? If the distribution were sensitive to selective pressure then naively I would guess it serves our needs well, but we spend a lot of our collective time trying to dial it back, hence my question.


texts:
From the picture it can be seen that Bicarbonate is secreted into lumen of duct of salivary glands by exchanging Cl- ions.

So if flow rate of saliva is increased then its obvious that less Cl- is taken in the cells and less bicarbonate is secreted out.

  At high flow rates, there is less time for reabsorption and secretion, and therefore the saliva is most like the initial secretion by the acinar cells. Thus, with the increase in flow rate the concentration of ions changes2

But it is also said that when flow rate increases the bicarbonate concentration also increases and when flow rate decreases bicarbonate concentration also decreases.

Doesn't this contradict the former fact?


texts:
What are the differences between cancer and tumour? I mean is it in the DNA or shape or something else... And how can a benign tumour turn into a malignant tumour? The body has a lot of tumours all the time, however not all of them become cancerous, why is this so?

So my main question is: What is so special about cancer cells that they can get out of control unlike an ordinary benign tumour?


texts:
So I was solving some biology questions, and this question left me confused. The response is supposed to be 22% according to the answers, but all the methods that I used did not lead me to it. I really hope that somebody can help me with it, the question sounds as follows:
Human ABO blood type is determined by two genes (H and I). First, the H gene codes
for the antigen precursor. The dominant allele (H) leads to expression of the precursor; the recessive
allele (h) does not. Second, the I gene has three allele forms, IA, IB and i, and determines blood type
(A, B, O or AB).
A male with blood type A and a female with blood type B marry. Each of them is heterozygous for
both the H gene and the I gene. What is the probability of having a son with blood type O? Give your
answer as a percentage (%) rounded to an integer (without any decimals).


texts: Why are there so many species of large predator on the African savanna?

texts:
On the tropical grasslands of Africa, there are loads of large carnivores. Lions, cheetahs, leopards, hyenas and wild dogs are all found, sometimes, in the same place. I was wondering, why is it that there are so many species of large predator in the same place? Wouldn't competition drive all but one species to extinction?

Obviously, this means that each of the predators fills a special niche. So, could anyone tell me what these ecological niches are? What makes the position in the food web of lions, leopards, cheetahs, hyenas and wild dogs different to eachother?


texts:
I'm planning to test the antimicrobial activity of endophytic fungi (their secondary metabolites) against Gram-positive bacteria, Gram-negative bacteria, and one fungus (Candida).

I was wondering what could be a suitable positive control for them? One kind of control each for the Gram (-), Gram (+), and the fungus? If yes, what kind? Or is there one kind of substance that would work against them all?


texts: Why use RRBS (reduced representation bisulfite sequencing) instead of general BiSeq?

texts:
My understanding is that RRBS is used for certain cases. For example, WGBS (whole genome bisulfite sequencing) is limited by repeated sequences.

However, many papers seem to use both techniques.

What are the reasons researchers would use RRBS instead of WGBS?


texts: I am trying to visualize biradial symmetry. I have read the section in the Wiki entry on Symmetry in Biology but it is quite brief and there is no example to illustrate it. I haven’t been able to find one anywhere else on the internet.


texts: Methods for microbial identification in soil

texts: I'm trying to perform a survey of the life in a soil sample. I want to know what species of bacteria, fungi, and other organisms are in it. I've heard that ITS sequencing and 16S rRNA sequencing are both possible ways of doing this, but I don't know enough about these techniques to understand which (if either) I should use, or how you interpret the resulting sequence file delivered by the lab. Will these techniques do what I want? How do I choose one over the other? And how do I interpret the results?


texts:
Why do we ignore all imperfections in people we fall in love with for a couple of months, but after a certain period we start noticing imperfections?

Can hormones - or any chemical - be used to influence someone to fall in love with you?


texts: What are the exceptions to Mendel's laws?

texts:
What are the exceptions to the $-$

Law of dominance
Law of independent assortment
Law of segregation

My knowledge:

Exception of law of dominance:

Incomplete dominance

In incomplete dominance when a red snapdragon flowered plant is crossed with a white flowered plant an intermediate phenotype appears in the F1 hybrid instead of a parental phenotype.
Codominance

Unlike dominance in codominance when a A ($I^AI^A$) blood group individual mates with B ($I^BI^B$) blood group individual the offsprings have blood group AB ($I^AI^B$) instead of A or B.

Exception of law of segregation:

Nondysjunction

During meiosis homologous chromosomes/sister chromatids and hence genes may move to a common gamete violating law of segregation.

Exception of law of independent assortment:

Linkage

When genes are present on the same chromosome they tend to remain together and enter into the same gamete. This is the reason behind deviation of dihybrid test cross ratio from 1:1:1:1 and occurrence of parental combination in high frequencies.

Am I correct? Are there any more exceptions to these laws?


texts: How can space travel affect women’s fertility?

texts:
From Time:

  The reasoning behind the prerequisite, according to officials, is that
  spaceflight could potentially harm the women's fertility.

How can space travel affect a woman’s fertility?


texts:
What determines speciation at a molecular level?

At what point does a scientist determine two lineages are different enough to be considered separate species?

Does it have a margin of error?


texts: Why does the high consumption of saturated fats lead to more risk of cardiovascular diseases and increased cholestrol levels?

texts: People with higher consumption of saturated fats are more at risk of developing cardiovascular diseases as compared to people who mostly consume unsaturated fat. The only structural difference is a saturation bond. Then why are saturated fats increase cholesterol and are bad for our health whereas the unsaturated ones are comparatively a lot safer? What difference does that one structural difference make?


texts: Can anyone tell me what species this baby bird this is? He or she is less than two weeks old. Fell out of nest. He is doing well. I live in Sacramento Ca, Thank you.


texts: Downstream analysis after in vivo pathogen RNAseq

texts:
We performed RNA-Seq of in vivo bacterial samples and identified some key up- and down-regulated pathways.

We compared bacteria during infection with conventional agar plate.

Which could be the next steps to validate our findings? We are interested in antibiotic and vaccine developemnt.


texts:
I was walking down to my mailbox when I saw this tree:

And by the looks of the branches, the tree seems to be dying because it has no leaves.  What is happening to the tree?


texts:
I'm not a biologist so bear with me. I know that the DNA molecule carries extremely large amounts of information. If the process of evolution is driven by completely random process .I think about it as the complex interactions between environment and random genetic mutations that leads to natural selection.
I've two questions:

What's the probability of evolution of intelligent human beings within this scenario? I've heard that the probability of spontaneous generation of a good protein molecule should be nil in our universe: is this correct ?


texts: How can predicting protein folding speed up drug discovery?

texts:
I'm asking this as a layperson without much knowledge in biology, so please correct me if my understanding is wrong.
Recently DeepMind's AlphaFold managed to predict protein structure from acid amino sequence with stunning accuracy. We are being told that this could "pave ways toward advances in drug discovery."
But I fail to see how it can happen. From my understanding the combination of protein structure is infinite, and if we tweak a protein structure that works good to fight against a virus, it will either work better or worse, but the key point is we don't know until we try. So essentially this is still a hit-and-miss thing, depending purely on dumb luck.
So how can the fast, accurate prediction of protein folding help in drug discovery?


texts: why does the score matrix influence the E value (BLAST)

texts:
When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results.
I noticed that the bit score is higher when I used PAM30 instead of BLOSUM62, which makes sense because PAM30 is based on more closely related species.
However I don't understand why the E-values differs from each other:

PAMP62: Bit score: 251, E value: 8 * 10^91
PAM30: Bit score: 258, E value: 6*10^82

Question: I don't understand why the E-value changes when using an other scoring matrix?
thankyou,


texts: Why is DNA double stranded and RNA single stranded?

texts: Why is DNA present as a double helix structure and RNA as a single helix? What causes the difference between them? What are the practical physiological differences between dsDNA and ssRNA? How are the key biophysicochemical features responsible for those differences? What is the role of these differences? Also, why is DNA preferred over RNA as the genetic material?


texts: Identify this dragonfly with orange body and orange wings?

texts:
The photo shows a red dragonfly on top (in front of some hot pink snail eggs) but an orange dragonfly with orange and perhaps translucent(?) wings near the bottom. This is the best resolution I could get. While the red one is easy to photograph (see Identify these two big, beautiful dragonflies in Taiwan?) this orange species is really jittery and difficult to approach.
I believe I have seen dozens of them in an isolated grassy patch in a parking lot, but they never landed and I could not capture a photo or see them clearly, but today this one was "available" for a photoshoot.
The orange dragonfly's body is about 4 to 5 cm long, the location is Hsinchu county Taiwan. That's all I've got, except that the last centimeter or so of the wings appear to be almost transparent.


texts:
I understand the difference between cladograms and phylograms; the latter can show the evolutionary linkage over time. However, I am having trouble finding out which two organisms are most closely related.

In the image above for example:

Referring to the cladogram, would these following statements be correct

-Bacteria 1 is least related to Eukaryote 4 (the furthest branch is always the least related as there common node is furthest away, correct?)

-The most related organisms are Bacteria 2 and 3, and Eukaryote 2 and 3

Referring to the phylogram

-Is Eukaryote 2 the least related to Bacteria 1 as its branch is the furthest away? Or is it Eukaryote 4 as it is the furthest away (bottom of list)?

-Is Eukaryote 1 most closely related to Eukaryote 3?


texts:
I was reading the etymology of the Latinate English verb 'inoculate' which contains the following part that generated the question entitled above:

  [...] inoculare "graft in, implant a bud or eye of one plant into another," from in- "in" (see in- (2)) + oculus "bud," originally "eye" (see eye (n.)).

The OED confirms 'eye' as a synonym of 'bud,' but I doubt that 'potato buds' generated this meaning because it already existed in Classical Latin that (I am assuming) South Americans did not speak in the 1500s when they introduced potatoes to the Spaniards.


texts:
I was wondering why dogs shouldn't eat chocolate. Can't dogs just excrete the indigestible component in their droppings?

It's common knowledge that dogs shouldn't eat chocolate. What I don't know is why chocolate would kill them, from a specifically biological perspective.


texts: Can we study all the genes of one human being?

texts:
Considering the fact that a new-born child gets 23 chromosomes containing DNA and genes from each of his parents and then 23 chromosomes from those 46 chromosomes of the new-born child will be transmitted to his child, I am wondering do all the people have the same 46 chromosomes or all have different chromosomes ( that's another thing that some genes present in the DNA of chromosomes don't express themselves. Of course, they are present there, no? )

If all of us have same chromosomes then can we study those genes present in 46 chromosomes to find out ALL the characters one person can have?


texts:
Mutation rate is a phenotypic trait that evolves. The process of evolution of such kind of traits are often referred to as evolvability. I am wondering about the evolution of the mutation rates in viruses. For the purpose of this question, I'll focus only on viruses that do not possess DNA polymerase. Because the replication of the viral DNA is performed by the molecular machinery of the host cell (eukaryote or not) it seems rather impossible to me for a virus to evolve its mutation rate. Is it correct?

Do we have any evidence of adaptive mutation rate in viruses?
Is there a correlation between the mutation rate of the host and the mutation rate of the virus?
Could the virus evolve some structure (or codon bias) of their DNA/RNA in order to adapt their mutation rate?
Is there another mechanism allowing a virus lineage to adapt their mutation rate?


texts:
Excluding situations where you die from accidents, the main reason for death is -generaly- diseases.

And usually it is about an organ which becomes "tired" after many years. These results are all from experience and statistics:

But I've never heard of any study that said: "people can't live longer than x age because the heart can't live longer than that".

From my point of view, I think it's us who control the way we live and consequently someone can live longer than the other. For example, smokers die at an early age.

But even the oldest person in the world, lived for 122 years and 164 days. For me this isn't enough. It seems that someone can't control his age after all.

Basically my question is: Does science provide any limit that a person isn't able to live more than it? For instance can someone live more than 1000 years?

Note: I don't think someone is able to do this because simply even our healthiest habits are not "so" healthy. But imagine someone who doesn't live like any of us as humans, i.e. Can have a very healthy and natural life


texts: How to predict the top microRNAs that bind to 3`UTR of a specific gene

texts:
I would like to know whether someone could tell me

1) some of the online programs that will predict the top microRNAs that bind to 3`UTR of a specific gene (for eg-GAPDH).

I am relatively new to the field.

thanks


texts: How does the body make sure that Vasoactive Intestinal Protein reaches only the target tissue?

texts:
Vasoactive Intestinal Protein (VIP) is a 28 amino acid neuropeptide that has several effects in several systems. These include the cardiovascular system, respiratory systerm, urinary system, immune system, etc. Furthermore, some of the effects appear to clash with each other. For example, studies have shown that VIP can have an antidipsogenic effect, while some have shown that it induces the secretion of vasopressin. Vasopressin is usually secreted when there is not enough water in the body. Thus, it seems contradictory that the hormone would induce cessation of thirst and secretion of vasopressin.

The hormone is  a paracrine mediator. This makes sense since limiting the distance that VIP travels allows for the hormone to only reach the intended tissues. However, it is also a neurohormone. Which means that it travels through blood and I would assume that it causes a myriad of effects. My question is, how does the body make sure that VIP does what is intended to do?


texts: What is the length of tunnels puffins dig in the Farne Islands?

texts: I was watching this video and the host said that the puffins dig over 80km of tunnels in the Farne Islands. Is that true? I couldn't find a source to confirm that number.


texts:
I have found that many studies use the mRNA concentration as a “proxy” for protein activity because there should be correlation between mRNA levels and proteins expression levels. How is protein activity quantified? Which quantity is used? What are protein expression levels?
I am doing some statistical data analysis using this dataset. I would like to understand why they have been interested in measuring mRNA concentration after the cells gamma irradiation (and in general it seems to me that biologists in many experiments are interested in that). I found in this site that discussion about correlation between mRNA concentration (so gene expression level)  and "protein expression level". Therefore I wanted to know what the latter is. Moreover, in the article related to my dataset is written

Very few DNA repair genes displayed significant differential expression in P. furiosus following gamma
irradiation.

And then

the data we reported here suggest that DNA repair proteins in P. furiosus and several other archaea are constitutively expressed and that they may be present in the cell at a level sufficient to maintain the integrity of the cell’s genetic material.

So putting together what the scientists conclude with what MattDMo has answered to me and what is discussed here , I think that I can conclude that "protein expression level" is a measure of the amount of protein actually translated from the mRNA, that then (in this case) will effectively act to repair DNA. Therefore, "protein expression level", as well as "protein activity", indicates the proteins translated from mRNA and that will actively act to repair DNA damages (in this case that we are talking about DNA repair proteins and DNA repair genes).
I have to say that I do not really know well what "DNA repair proteins are constitutively expressed" means, but I think that is that DNA repair proteins have already been translated from the mRNA and therefore they are "present in the cell at a level sufficient to maintain the integrity of the cell’s genetic material" (as they say soon after).
All this makes sense to me if I think about my first objective that was to understand the reason for measuring mRNA concentration. We are interested in it because there should be correlation between mRNA concentration (gene expression level) and the proteins actually translated from mRNA from that specific gene, in order to know which kind of proteins will effectively act in the DNA repair processes (in this case).
I wonder if all this interpretation is correct...


texts: Looking for raw cell videos from a light microscope

texts:
First off, I'm not looking for online lectures.

I am trying to find creative commons licensed videos of live cells moving around without annotation or anything extra. I would prefer a few minutes of video of tumorous somatic cultures of eukaryotes in vitro and at a few different magnifications but it doesn't really matter. I don't have a microscope or I'd just get some pond water and look at multicellular organisms. The license must be creative commons or public domain, the author must be citable, and the subject organism should be known.

Any ideas where to find such video? Thanks!


texts: Co-dependency between carbohydrates, fats and protein in the mammalian diet?

texts:
Following up from the question Are carbohydrates an essential component of human diet? I am interested in knowing more specifically how carbohydrates, fats and proteins are linked in the mammalian diet.

For example, cats and other obligate carnivores eat mostly protein, so I imagine that protein has to be converted first to fat and then to glucose and other carbohydrates that the body needs. Does that mean cats are in a state of ketosis constantly? Do cats have special metabolic tuning to optimize on this metabolic pathway?

Human variations seem to suggest that such tuning exists. For example, (historic) eskimoes when fed carbohydrates tend to be especially likely to suffer from obesity and diabetes. This would suggest that their bodies are tuned to exist on protein and fat. What is this tuning?


texts:
My biology teacher used to show us videos (actually animations) on the human immune system. What I remember is that one video was on a virus (represented as a purple colored sphere with spikes) that a woman (who is a part of a music band) inhales in an elevator when a man sneezes.

The documentary shows how the virus travels to her throat and enters one cell, multiplies, and spreads. Then the video shows how white blood cells and T-cells defend the body. In the end, when she drinks coffee, she leaves the virus on a coffee mug and her friend takes on that virus when he drinks from the same mug.

Other videos of the same series include a documentary on fractures, another one on obesity, another one on a disease transmitted when one eats chicken, etc. Can someone tell me what is the name of that series?

I think (not sure) it is a national geographic series?


texts: Help understanding the word 'glycosaminoglycan'?

texts:
In my biochemistry course I have to know about various polysaccharides and variants, and I am struggling with remembering them. I think it would help if I could break down their names.

For 'glycosaminoglycan' i think

-glycan just refers to the fact that it is a polysaccharide. Some, but not all polysaccharides have glycan in their name, e.g. glycogen vs amylase and amylopectin

-amino means there is an amino group somewhere in there?

That's all I can think of...


texts: Are there animal species in which the females expend more energy attracting males than in their offspring?

texts:
In general, males of a species expend a lot of energy attracting females.  There are many instances where males utilize much of their nutrient intake to produce antlers, tusks, horns, etc. to either attract females or compete with other males for potential mates.  Are their any instances in animals in which the females do this to attract males or to compete with other females?  If so, what features have the females evolved to win over potential mates and fight off competitors and what advantage is there for the species?

I'm aware of a few animals, such as the seahorse and jacana where the males invest more energy in the offspring, but I'm not sure that the females of these species expend some of the energy saved in the offpring and put it into attracting males or competition with other females.


texts: What do we know about the Last Universal Common Ancestor (LUCA)?

texts: All life on Earth (bacteria, archaea, eukarya) is thought to have evolved from a common ancestor, or last universal common ancestor (LUCA). What do we know about the characteristics of LUCA based upon extant life?


texts: What organism has the longest Hayflick Limit?

texts:
Assuming I am understanding the concept correctly, Hayflick Limits are reflective of a cells capacity for stable division. Additionally, the Hayflick Limits of various organisms differs.

My question is, what organism has the longest Hayflick Limit? I know humans have one ranging from 40-60, just to give a bit context.


texts: Is there any current knowledge of how DNA polymerase is "motivated" to perform error corrections during transcription?

texts:
I was trying to understand the process of how polymerase performs error corrections on DNA. Every paper on this topic mentions what happens during the process, but there's no mention of how it happens. I even looked up the page on enzymes and it only explains enzyme binding sites, enzymes acting as catalysts and the types of reactions the enzymes perform.

It'd be reasonable to theorize that codons on DNA would have chemical properties that can attract certain enzymes to them to start the transcription process. But during transcription when the enzyme makes an error, what incentive does the enzyme have, to move backward to correct the error? I know that sometimes the error correction is performed only after the transcription, but the question is the same: How does the enzyme know what to do? Moreover, if enzymes were mere catalysts, does this mean that even without an enzyme, the DNA would get transcribed at an extremely slow rate? Could this mean that the "software code" that contains instructions of what to do during a transcription, is in the DNA itself?


texts: What neurophysiological process keeps reflex arcs in check? For example, the withdrawal reflex causes the hand to jerk back when the fingers touch something painfully hot incidentally. However, that reflex can be voluntarily suppressed when one deliberately touches that same hot object on purpose. What neural process is involved in conscious suppression of reflexes?


texts: How do leafcutter ants choose what plants to cut?

texts:
I know that leafcutter ants don't actually eat plants and only use them to harvest fungi. How do they choose what plants to cut?

They won't touch anything in my garden, but if I plant roses, they'll completely wipe all the leaves and petals in a single day.

If some plants are better suited than others for their "farming", how do they know them?


texts:
In Fullmetal Alchemist when Ed goes to disprove to Rose the Sun God's "miracle" to bring humans back to life by proving that science (in the form of Alchemy) can create people by saying

  Water (35 L), Carbon (20 kg), Ammonia (4 L), Lime (1.5 kg), Phosphorous (800 g), Salt (250 g), Saltpeter (100 g), Sulfur (80 g), Fluorine (7.5 g), Iron (5 g), Silicon (3 g) and trace amounts fifteen other elements.

I am wondering, is this composition true in real life? if so what are fifteen trace elements?


texts: Exclusive microtubule minus-end labeling

texts: Like the title explains I am looking for a way to exclusively label microtubule minus end in vivo. Looking through the literature I could not find any techniques yet. Do you have an idea?


texts: What is causing my problem with very low yields when isolating a 42kb yeast plasmid?

texts:
I have to isolate a large plasmid from yeast and transform it in E. coli. After transformation, I often get no colonies. One reason for that is the yeast mini prep hasn't worked or the DNA concentration is too low. I tried two different isolation protocols:

Zymoprep I yeast plasmid prep kit

From the doc: "based on the old E.  coli alkaline lysis method with our Zymolyase added in the first  solution."
Phenol chloroform YAC isolation protocol

used by Dan Gibson et. al] for their huge constructs (>100kb)

They use an expensive Qiagen large-construct column at the end, in order to purify and visualize the yeast extract on a gel, but I skip that step because the Qiagen column cost $40 per yeast clone which doesn't scale if we do many of these.

How can I troubleshoot and optimize the above-mentioned protocols? Are there any other protocols that might be more suitable for a large plasmid and don't use too expensive materials?


texts: How to identify genes required for biofilm formation

texts:
This is just a homework question:

Q: Let’s assume that there is an unknown set of E. coli genes that are required for biofilm formation. Describe a genetic experiment you could perform to try to identify those genes.

The one idea that I can think of is:

Compare strains that produce biofilm against strains that do not produce biofilm. Sequence genes, find differences, interrupt genes in biofilm producing strains and confirm biofilm ability is impaired.

Is there a better approach than this?


texts: How long before robin no longer needs the nest on my porch?

texts:
A robin has made a nest on my porch. Unfortunately, the nest is on my weed wacker which I might want to use at some point this summer. Currently, there are two eggs in the nest.

How long will it be before the robin is done needing the nest?

Location is Eastern Massachusetts.

-- Update May 13 --

I think one of the eggs must have hatched. The robin no longer sits in the nest, she just stands on it constantly.


texts: Why is blood pressure different in different parts of our blood vessels?

texts: Why does it change throughout our circulatory system ?


texts: What is positive and negative supercoiling?

texts:
Is the following correct?

Positive supercoiling  = the coiling of DNA helix (B-DNA) on itself during intesified coiling of the two DNA stands in right handed direction

negative supercoiling  = the coiling of DNA helix(B-DNA) upon itself during uncoiling of the two DNA strands performed in left handed direction?

I'm a little confused.


texts: Can any organism possibly have the capability to create a new species every time it reproduces?

texts:
There are lots of different kinds of living organism in our planet. So i was wondering if such an organism could possibly exist?

Can any organism possibly exist, that would have the capability to acquire some genetic information of the organism it consumes, and pass that along with its own genetic information, forming a new species every single time it reproduces.


texts: Does lack of adaptations for sperm competition necessarily shows the species are monogamous/serially monogamous/polygynous?

texts:
On the one hand adaptations for sperm competition, such as large testes, mate guarding, etc. are used to support that female in species are promiscuous.
On the other hand we know multiple eusocial species where most inidividuals don't reproduce letting their kin (e.g. the bee queen) reproduce. Which means that in some cases it is more beneficial to let your kin reproduce than to do it yourself.
For that matter, would not there be intermediate states, where multiple indivuduals reproduce, females are promiscuous, but since reproducing as much as possible yourself is not necessarily good, sperm competition adaptations would not get developed? Are there any candidates for such species?


texts:
Plants and animals have the following distinct properties:

Plants live from solar energy by photosynthesis, they use solar energy to make sugar and oxygen out of carbon dioxide, which gives them energy. Animals live from the sugar and oxygen plants created and produce carbon dioxide for their energy.
Animals can move across the planet while plants are tied to the ground.

Clearly, animals have a harder time to survive with no plants within their reach than plants have without animals coming close. This is logical because solar energy is always there while plants are not.

So my question is: Are there animals that can do photosynthesis? It's obvious that an animal with plant-like stateliness would be non-beneficial since it relies on eating other plants for it's energy and there may not always be plants within reach from it's spot.

But animals using the sun and carbon dioxide for energy production does not sound so stupid.

Night animals could also gather energy in their sleep.
Much easier than plants, animals could make sure nothing blocks their sunlight.
Many animals go through periods of hunger because food is scarce, for some of them this period is paired with high sunlight levels. (the dry season f.e.) (EDIT: This is just an idea, of course photosynthesis requires water, which is absent in the dry season. But still, in warm period with enough water, there's sometimes too much animals to feed from the available vegeation.)

Some things I already took into consideration:

I know that plants, because they are small in mass (compared to the area with which they can collect sunlight) and static, don't need nearly as much energy as animals do. Is this the main reason?
I know that f.e. reptiles, but in fact all cold-blooded animals, already use the sun's energy. But they only use the heat from the sun to warm their bodies, they don't photosynthesize.


texts: Genetic engineering for experimenting at home?

texts:
I am just wondering whether it is possible to carry out small scale genetic engineering at home, without any sophiscated tools.
Ive searched google and found this http://explorebiotech.com/the-7-important-molecular-tools-used-in-genetic-engineering/
So i am wondering whether these tools are easily acquirable and how feasible it is to be done at home maybe as a hobby.
Also my budger is probably about 200 USD so my hopes arent that high.


texts: Question related to L-arginine biosynthesis

texts:
With respect to the L-arginine Biosynthesis pathway, the very first reaction converts L-glutamate to N-acetyl L-glutamate.

In the linked reaction scheme, why are only L-glutamate and N-acetyl glutamate considered, and not acetyl-CoA or the coenzyme? Is this because L-glutamate and N-acetyl L-glutamate are the main compounds to be considered? Why are they the main compounds being considered? Are these two compounds (L-glutamate and N-acetyle L-glutamate) the ligands?


texts: What type of animation software is used to create these molecular motor motions?

texts: Recently, I came across this video on molecular motor motion. Can someone suggest software that can do similar animations? I am not sure what they (at Harvard Medical School) used but the animations are really cool.


texts:
I have some questions regarding Satellite chromsomes which could not be resolved by a google search.

Does the satellite consist of telomeric sequences ?
If not, What is the function of a satellite ? And where will the telomeric sequences be present - in the main body ? On the secondary constriction ?
Satellite chromosomes are also known as SAT chromosome which stands for Sino Acid Thymidine. I read in some sources that SAT means without thymidine. But how is that possible, if there is A then obviously there has to be T ? ( in dsDNA)


texts:
Out of curiosity, I got this question whether knocking out (deletion) of a gene on one side and knocking down (RNAi) of the same gene on the other side will affect the cell in a similar manner or not.

If not why?
If yes, is it applied to every gene?

Knock out of a gene will correspond to no expression (gene deletion) in the cell, which can be appropriate to confirm the functional specificity, to observe processes which are affected in its absence and some other processes which are compensating the absence of the gene.

Knockdown of a gene will result in expression defect by decreasing the level of the transcript (mRNA silencing).

Now, the points which I am wondering upon are:

no mRNA presence and silenced mRNA will create two different environments for the cell to deal with or not.
whether the whole amount of transcript should be targeted to have the same phenotype as of gene knockout.


texts: How has the use and subsequent ban of DDT affected insect populations?

texts:
Living in Australia there were less ticks for example during the use of DDT, now there are more ticks prevalent here. I am wondering if any insect species have declined permanently as the result of the DDT use, and if some have repopulated disproportionately (compared to populations prior to the use of DDT- if there is such data) since it's cessation of use.

How has the use and subsequent ban of DDT (dichlorodiphenyltrichloroethane) affected insect populations?

Are there any studies on this?


texts: Would a shark whip into a frenzy from smelling its own blood?

texts: Sharks normally respond very quickly to the scent of blood in up to a mile radius, but what if the shark itself simply got injured? Would it respond to its own blood at all?


texts: I am looking into SRAP markers and I have realized I am not sure if I need a reverse complement of the sequence given in the article or they are "ready to use" primers?


texts: I know why phototaxis happens but why did those bees die?

texts:
There is a tube light in front of my veranda. This is just spring. So at night when I turn on the tube light many bees gather around the tube for phototaxis. But in the morning I see many of them are lying dead on the floor.

Why does this happen?


texts:
The Varicella zoster virus causes chickenpox in children and shingles in adults.

It appears after the initial infection, it can go dormant in the nerve, and reactivate itself decades later.

My question is: What is the name of the property of viruses that can go dormant in the host for 30 years?


texts: How do genes code for differences in arms and legs?

texts:
So to me it seems like arms and legs are pretty similar that they almost have the same blueprint. And if you change part of it like the number of digits, you will have 12 fingers and 12 toes.

But at the same time there are differences.

So my question is, are arms and legs encoded with the same piece of DNA? Or two very similar pieces. But in that case why would a change in the arm blueprint to give you 12 fingers also give you 12 toes?

On the other hand if arms and legs are encoded by the same piece of DNA. How do legs develop heals and arms develop wrists?

Are arms and legs only different by their shape (morphology?).

Equally if a thumb is encoded by the same DNA as encodes fingers, (i.e. all are similar and have fingernails), why are thumbs different?


texts: Absorption rate of Infrequently eating animals?

texts:
Clearly, creatures such as us humans, after vastly increasing the entropy of our food, expel most of the mass that we consume.

Some creatures, however, do NOT get the opportunity to eat nearly as often, even though these creatures are if anything more competitive (and perhaps cannibalistic!) than we are - snakes come to mind here, as do spiders.

Such a lifestyle implies that growing large - or at least to adult form - quickly has a huge advantage evolutionary.

So the awkward question that arises is thus: do such animals have a higher "absorption rate", if you will, then humans and other frequent feeders?

In other words, do such animals maximize their diet by incorporating more of the mass of their food and expelling less of it, or is there some physics/chemistry which makes this difficult?

Thanks!


texts: What is the fibre axis in the Watson and Crick paper?

texts: I was reading Watson and Crick’s original article on DNA structure in Nature 171, 737–738 (1953). The accompanying diagram (shown below) has something called the “fibre axis” going through the DNA. This axis isn’t shown in modern models of DNA, so what is it?


texts: Unable to identify a muscle of the anterior thorax

texts:
I was watching an YouTube Anatomy Video which goes over the major muscles of the anterior superficial thorax. There is a structure present throughout the video which goes unmentioned, and I can't seem to identify.

It is shown as a pair of structures, each running from the manubrium to the xiphisternal junction along the lateral margin of the anterior sternum, perhaps with a second head attaching to the costal cartilage.

I'm probably missing something obvious, but for the life of me I can't think of what that could be.


texts:
For each inhibitory synapse, how many excitatory synapses are in the brain?
It is the same ratio along the animal kingdom or nervous system areas?


texts: What kind of experiments could you do to see which end of a microtubule is most dynamic?

texts:
I'm stuck between two ideas. Not sure which one of them would be best.

Do a FRAP on the middle of a MT. If it grows from the + end, that section will remain dark. If it grows from the - end, existing fluorescent tubulin will be pushed into the photobleached area. However, how would I be able to tell if the middle region is dynamic using a FRAP?
Introduce GFP-Tubulin into a cell. See where existing microtubules begin to fluoresce as new subunits are added.

Do either of these sound reasonable? Any better ideas?


texts:
Yew seeds have very long dormancy when artificially planted.
They are also adapted to passage through digestive systems of animals that eat/transport them.

But could the dormancy be shorter (or the viability higher) if the seed passes through a birds digestive tract first? (An explanation: the seed's outer layers can get worn down that way, signalling that it is ready to start the process leading to germination.)
That would imply that the dormancy could also be artificially shortened by eg. dipping the seeds in acid and then alkaline solutions, which would be great.


texts: Please give information about this insects

texts: I took this photo of a small insect which I found near to my house (Maharashtra state, India). What insect is this?


texts: How many species did Carl Linnaeus classify?

texts: How many species did Carl Linnaeus (senior) classify?


texts: Is transplantation of neurons between species possible?

texts:
Can brain tissue from one species be implanted into the brain of another species? Because the brain is tolerant to the introduction of antigens (it is said to be immuno-privileged), I was wondering whether neurons would be subject to graft rejection?

If neurons from another species survive in their new host, would they create functional connections?


texts:
From Wikipedia:

  For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, while introns are rare within the nuclear genes of some eukaryotic microorganisms,[8] for example baker's/brewer's yeast (Saccharomyces cerevisiae). In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of eukaryotic microorganisms may contain many introns. Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.

In my biochemistry course we learned that bacteria have no introns and eukaryots nearly always have them. What's correct?

Do viruses have introns as the Wikipedia article claims?


texts: What do you call clearly different sub-groups within a species?

texts: If you look at species of bees and ants, you can clearly see there are drastically different specialized ants, like queen ants and workers. They're both part of the same species, yet are still obviously different. What is the proper name for that phenomena?


texts: How does a polymerized TruSeq adapter affect sequencing reads?

texts:
I am trying to build a NGS library on enriched DNA (DNA length = 93 bp).  I am using PCR amplification with two overhanging primers, both containing Illumina adapter sequences (Universal Adapter & TruSeq Adapter w/ barcode).  My final library should be (~182 bp):

Universal Adapter (-), Enriched DNA (+), TruSeq Adapter(=)

------------------++++++++++++++++++++++==================

After PCR amplification and QC by gel, I am seeing fragments of larger size.  Analysis by Bioanalyzer indicates that I am might be getting some polymerization of the TruSeq adapter on the library.  This is most likely due to bad primer design, with the primer containing two recognition sequences (21-nt), one at the 3' end and one at the 5' end of the TruSeq adapter

My question is:

How would the NGS analysis be affected if a library is submitting for sequencing, containing a mixture of single and dbl TruSeq adaptors?

Single:

Universal Adapter (-), Enriched DNA (+), TruSeq Adapter(=)

------------------++++++++++++++++++++++==================

Double:

Universal Adapter (-), Enriched DNA (+), TruSeq Adapter 1(=),  TruSeq Adapter 2(=)

------------------++++++++++++++++++++++==================\==================

Would the sequencing info from the "double library" be lost or would those fragments be read, just fine?

Thanks,


texts: What is/are the effect(s) of altering the Tris concentration on polyacrylamide gels?

texts: Why do we use two different concentrations of Tris (i.e. 1.5M Tris in resolving gel and 1.0M Tris in stacking gel)? For the gel to run properly there needs to be a different pH, but that can be done with with same Tris concentration and altering the HCl concentration.


texts: Do we have enough diversity of antibodies to overcome almost any antigen?

texts:
I always wonder about the capability of diversity of our antibodies. Do we have enough antibodies to fit to every kind of molecule? Wont't it be easier if our antibodies are like clay and can be molded to any form by antigens? Why to waste energy producing so many types of antibodies?

If some pathogen makes its antigens just like antibodies of our body, (I think) they won't ever be detected. So what would our body do?


texts:
I was wondering why, when you are cold, scar tissue turns bluish or purple while original skin stays the same color.

The only thing I can think of, is that maybe scar tissue gets less circulation than regular skin, so when it gets cold it restricts circulation.


texts: Streamlined flattened worm identification

texts:
These streamline shaped tiny shells are sticking around on dark untouched corners, hanging by one end .Or one of their flat sides is touching a wall. Some are reddish brown in color, others are pale grey.

I have seen a little worm like thing peep out of the two openings on the tips and start crawling very slowly .If disturbed ,they go right back in ,like a tortoise. They can even poke their head out from the opposite hole and reverse their direction of crawling. Otherwise ,they are almost inert.
I live in South India.


texts: Reporting observation of a bird outside its seasonal presence

texts:
Last summer I saw this bird in the countryside of Bulgaria (Dobrich area) and I think this is a specimen of Great Grey Shrike (Lanius excubitor).

By looking more in detail the distribution of that bird (I checked in few books including the Collins Bird Guide in French edition), I noticed it is present in Bulgaria but only in winter season. However I took this pictures in August 2017.

First, is it really a specimen of Lanius excubitor?

And if yes, should it be reported in some way?

I know some other countries have reporting tool on Internet but I have no clue about observations in Bulgaria.


texts: Did humans evolve the ability to swim? Or is it just luck that we are able to swim?

texts: Many animals like ducks have evolved features to be able to swim. Even not so aquatic animals like a tiger evolved so that its feet can act as paddles. In humans I don't see any direct feature that has specifically evolved for the purpose of swimming. So is it just luck that we are able to swim and some of our cousins like gorillas are not able to swim? Or did we evolve in some way to be able to swim


texts: Stupid question perhaps but what does happen if one completely removes DNA from a single cell organism? As far as I know DNA is only needed for propagating information to descendants doing it's removed from a grown up cell and put some artificial source of protein there will it just lose ability to mate or will it die immediately?


texts: What is the Importance of Acid Alcohol and Sodium Bicarbonate during staining?

texts:
I've just learnt about staining during a histology class and I'm confused.
Why do we have to add acid alcohol and sodium bicarbonate to the tissue during Hematoxylin & Eosin staining? Is there any difference if we don't add them at all and just skipped to eosin instead?


texts: How to get smallest subtree containing a set of nodes from BioPhylo?

texts:
I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and efficient in dendropy and ete2:

newick = '((raccoon, bear),((sea_lion,seal),((monkey,cat), weasel)),dog);'
taxa = ['raccoon', 'sea_lion']

import ete2
tree = ete2.Tree(newick)
pruned = tree.prune(taxa)

import dendropy
tree = dendropy.Tree.get_from_string(newick, 'newick')
pruned = tree.prune_taxa_with_labels(taxa)

I'm trying but failing to find equivalent functionality in the Bio.Phylo package. Trees do have a "prune" method, but it prunes a single node from the tree.


texts: Figuring out an honest indicator in intrasexual selection

texts:
In the first picture, the parameter $r$ seems to compare the direction and strength of two variables. In the second picture, $R^2$ seems to describe the variation of proportion of independent and dependent variables.

With this being said, are honest indicators determined by $R^2$?
Why is it a positive number for both graphs if we refer to the second picture?


texts: Possible to get Furniture carpet beetle specimen for collection?

texts:
I was wondering if anyone knows how it'd be possible to get a Anthrenus flavipes (or furniture carpet beetle) specimen for my collection?

I can't find a source anywhere online, only the dermestid beetles used to clean skulls and such. Any help would be appreciated!

Bump


texts: How were (many) dinosaurs' brains so small?

texts:
Brain size (or its proxy, encephalization quotient) usually varies allometrically with mass -- larger creatures need larger brains to control their larger bodies, apparently.

Dinosaurs are popularly known as small-brained. While this certainly doesn't hold in general -- theropods and especially birds were particularly intelligent -- but sauropods and thyreophorans (ankylosaurs and stegosaurs) seem to have preposterously small brains. How were they able to control their large bodies with such small brains? Are there modern animals with similar proportional brain size, and if so does that give any clues as to how these dinosaurs functioned?


texts:
I am hoping to mutate the active site of the enzyme I am researching that has 5 residues in proximity with the substrate. I am wondering how many colonies I'll have to assess to theoretically sample all the possible mutant combinations?
I am guessing that just screening the number of possible combinations will not be very successful because I am likely to sample a particular mutant more than once?
I have been looking at 'NNK Saturated Mutagenesis' which uses the redundancy in the genetic code to be able to create all residue encodings where N = A/G/C/T and K = G/T, while limiting the number of repeated residues from synonymous codons.
Are there any other ways of performing this sort of mutagenesis with better codon compression?


texts: Learning tensors for evolutionary or developmental biology

texts:
I'm looking for book recommendations on tensor algebra for use in biology.

Tensors are being used increasingly in evolutionary biology and developmental biology, it seems.  For example, here is an example of an empirical study that makes use of tensors in its analysis of data: http://rspb.royalsocietypublishing.org/content/282/1819/20151119

There are lots of books on the mathematics of tensors, and many introductions online.  So far, what I have found is that either (a) the presentation is heavily oriented toward physics applications, or (b) the presentation begins from an abstract algebra (or category theory?) point of view.

I'm willing to work through physics-style or abstract algebra presentations of tensor concepts and methods, but I am wondering whether there are any textbooks or other introductions that someone would recommend for biological applications.

(I have read the brief appendix on tensors in Sean Rice's book Evolutionary Theory.  Although I've found his other mathematical appendices and most of the mathematics in the book accessible, the tensor material in the book is too brief for me--I need more.)


texts: Why don't most life forms show uniqueness in progeny?

texts:
I guess everyone must have observed this. Dogs, cats, and most of all insects (including mosquitoes) appear more or less the same.

Why is there so little variation in their offspring, unlike humans, where you rarely find two humans showing even a little resemblence.

Is it the large size of the human genome that allows infinite combination of traits? (seems unlikely, as even small flies like drosophila melanogaster have somewhat large genomes, but show very little variation).


texts:
Could someone help with identification of this small mammal? Is it a possum? A dormouse?

It was photographed in Sukhumi botanical garden, in Abkhazia (west of Georgia, on the shores of the black sea).


texts: Does anyone know of any resources that detail an extensive number of receptor types, their effects, and signalling pathways?

texts:
In a similar manner to this Wikipedia page, although I am not too concerned about the localisation of the receptor, or any known ligands, as I can already access this knowledge easily.

https://en.m.wikipedia.org/wiki/Alpha-2_adrenergic_receptor


texts: Where I can download the genome sequence of various species of Fusarium?

texts:
I'm looking for genome sequence of various species of Fusarium (a kind of fungus!) on net, but I found no suitable information. Could you please help me out for this purpose?
Thanks in advance


texts:
I noticed that in my hand the index and middle finger are aligned in one direction and the next two fingers somewhat in the opposite direction. My question is, why are our fingers aligned in that way?
Moreover, is it of any evolutionary significance?

For clarity, I am posting a picture of my hand.


texts: How do non-human apes cool their body temperature in warm climates?

texts:
Humans have sweat and we all know how that provides cooling along with the remaining vellus hairs acting as wicks.

So how do hominids, our close relatives (some of which are more massive than humans) regular their body temperature, given that they are completely covered in fur like typical mammals?

I’m specifically interested in how a human who had an atavism※ that’s like generalized hypertrichosis terminalis would fare and get by.

※ in my story, it’s due to a repaired chromosome 17 that didn’t turn out the way that was intended.


texts:
What does U mean in Viral protein U?

  Viral protein U (Vpu) is a unique gene product of human immunodeficiency virus (HIV) type 1 (HIV-1) with two well-described functions...

So does U in this case mean unique?

Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC114397/


texts: If coelocanths are more related to humans than groupers -does a Coelocanth's DNA literally have more sequences in common with a human than a grouper?

texts: Would a coelocanth and a human still have more sequences in common than a coelocanth and a grouper? Would the coelocanth and human dna basically "look" more similar than either would to a ray-finned fish based on sequences?


texts: How to Download the broadpeak files from the encode chip-seq experiment matrix?

texts:
I have tried the SqlDatabase of Encode opened it trough R ,i have tried other packages in R, i have tried the ENCODExplorer package but none of them seems to do what i want. I have an app that asks the user which cell type and which antibody factor wants to choose in Shiny. These cell types and antibody targets are drawn from chip-seq matrix here https://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html. I want to download the .broadpeak file from the experiment that was made using the two selections of the user . I cant find where the data from this matrix are stored and for sure they are not stored in the new website database of ENCODE.
Does anyone has an idea ??
These are some notes not all  from a what i searched

1)https://www.bioconductor.org/packages/3.3/bioc/vignettes/ENCODExplorer/inst/doc/ENCODExplorer.html
New portal of ENCODE https://www.encodeproject.org/
#Load the ENCODExplorer
suppressMessages(library(ENCODExplorer))
#Find all the files from the experiment with biosample from A549 human cell using H2AFZ as antibody target
query_results <- searchEncode("a549 chip-seq homo sapiens h2afz") or
search_results <- searchEncode(searchTerm = "a549 chip-seq h2afz", limit = "all")
//downloadEncode(resultSet = search_results, resultOrigin = "searchEncode", format = "bed_broadPeak")
cant find any broadpeak files

2)Connect to an Oracle database(Encode sql Database) using R
http://rprogramming.net/connect-to-database-in-r/
channel <- odbcConnect("genome-mysql.cse.ucsc.edu", uid="genomep", pwd="password", believeNRows=FALSE)
http://stackoverflow.com/questions/15420999/rodbc-odbcdriverconnect-connection-error
#Database schema
install.packages("RMySQL")
library(RMySQL)
drv = dbDriver("MySQL")
con = dbConnect(drv,host="genome-mysql.cse.ucsc.edu",user="genomep",pass="password")
album = dbGetQuery(con,statement="show tables")
Tables_in_hgcentral
1          blatServers
2                clade
3                 dbDb
4             dbDbArch
5            defaultDb
6               gbNode
7          genomeClade
8            geoIpNode
9            hubPublic
10           jorgetest
11       liftOverChain
12       liftOver_bkup
13           sessionDb
14   tableDescriptions
15            targetDb
16              userDb
17           wikiTrack
3)Not working-->https://www.simple-talk.com/sql/reporting-services/making-data-analytics-simpler-sql-server-and-r/


texts: Cell evolution: immortality vs reproduction

texts:
Many sci fi movies produce interesting ideas and technologies that we seem to be able to realize in real life at some point. "Lucy" was not one of those movies.

But Morgan Freeman's speech in the movie on cell evolution did interest me.

The speech claimed that cells in harsher environments evolve towards immortality, while cells in favorable environments evolve toward reproduction.

Is this idea accurate?


texts:
can anyone help me with this?

It shows two gene sequences for a sheep and a goat.

   5’------C C T G A G G A G C A T G T T------3’
   3’------G G A C T C C T C G T A C A A------5’
               5         6         7         8        9
   5’------C C T G A G G G G C A T G T T------3’
   3’------G G A C T C C C C G T A C A A------5’
               5         6         7         8        9

I hope u can see it.

number 1 = goat
number 2 =sheep

what differences are there between the two gene sequences?
Decide the amino acids 5-9 for both gene sequence?


texts: DIfference between diversification and differentiation

texts:
In Adaptive dynamic :

what is the difference between Ecological Differentiation and Ecological Divergence ?


texts: We use creatine phosphate as an energy storage to resupply ADP with a phosphate group as our muscle cells only contain about 2-5 mM ATP. But why doesn't the muscle cells just keep 20-30 mM ATP instead of 20-30 mM creatine phosphate?


texts: How do neuroblastoma cells divide? Is it via mitosis?

texts: My name is Daniel and I'm 17 years old. I am currently designing a study to investigate compounds that potentially increase the replication of neural cells. I will be using neuroblastoma cells and creating different water based media to apply to these cells. I don't however understand how they divide. Is it via mitosis or do they replicate in a different way as they are essentially, cancer cells.


texts: Rationale behind different classification of nerve fibres

texts:
Two main types of classification of nerve fibres are numerical and Erlanger-Gasser classification, based on diameter and conduction properties.

In numerical classification group Ia and Ib both have same conduction velocity and diameter, then on what basis are they different ,is it just because they are innervating different structures, then why this criteria is not followed further?

Also in Erlanger and Gasser classification both A and B types are myelinated and C is unmyelinated, then why is B not clubbed as subgroup of A? How is B different from A(delta) even though both are myelinated and have same conduction speed?

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


texts: Is there any organism that is born with all the nutrients and resources needed for their entire lifetime?

texts:
I understand that adult mayflies have no mouth, but they do take in oxygen through openings in their exoskeleton.

Is there any organism that does not need to ingest any type of nutrition and does not need to take in something for cellular respiration?


texts: What is the life of cell-free genetic circuits?

texts:
Can genetic circuits be tested in a cell-free environment? What would be their life if we keep them at room temperature?
The circuits which are composed of DNA-based components are commonly referred to as genetic circuits. By testing, I meant to say to test its behavior i.e. applying input signals (perhaps proteins) to see if it generates an output signal (another protein, may be fluorescent protein).
By life, I meant to say, for how long such a circuit (containing strings of dna) can survive at normal room temperature.


texts: Why FgenesH and Genscan don't give good results as I have prdicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and only 47 genes predicted by GenScan. why they have done missed predictions. Kindly help me to know the reason?


texts: How do normal cell division chance into a tumor forming cell division?

texts:
Or its better to say what happens at molecular level that tumors are formed?

I tried normal google search and google books but couldn't find any appropriate explanation.
I am trying to understand why p53 or Rb genes are called tumor suppressor genes.I'm acquainted with the pathway through which p53 protein cause checkpoint arrest if the DNA is damaged and the pathway through which pRb protein cause G1 arrest.