qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
15,114 | <p>What modern insects are not flying or descended from flying ancestors?</p>
<p>(I read somewhere that 99% are, so of course I instantly became curious which <em>aren't</em>. xD )</p>
<p>EDIT: Sorry, I should have been clearer: I meant examples of modern insects with <em>no</em> flying ancestors.</p>
| [
{
"answer_id": 15124,
"pm_score": 4,
"text": "<p>Do you ask for examples of non-flying insects which ancestor were flying? In other words do you ask for examples of insect lineages that lost the ability to fly?</p>\n\n<p>The ability to fly arose with the clade called the <a href=\"http://tolweb.org/Pter... | [
{
"answer_id": 15116,
"pm_score": 3,
"text": "<p>Silverfish, also known as Lepisma (order Zygentoma), does not fly and does not descend from flying ancestors.</p>\n\n<p>It's close to Archeognatha, which don't fly either nor descend from flying ancestor.</p>\n\n<p><img src=\"https://upload.wikimedia.org/... |
15,144 | <p>Someone gives you a short DNA sequence that comes from the middle of a gene.</p>
<pre><code>5'- TCTAACTGATTAGC -3'
3'- AGATTGACTAATCG -5'
</code></pre>
<p>From this sequence, determine the following:</p>
<ol>
<li><p>Is the promoter located to the left or right as the sequence is written?</p></li>
<li><p>Is the sense strand the top or bottom strand?</p></li>
<li><p>What amino acids are encoded by this gene fragment?</p></li>
</ol>
<p>The only thing I have been able to come up with, is that since this is from the middle of a DNA sequence I need to choose a frame with no stop codons.</p>
| [
{
"answer_id": 15146,
"pm_score": 3,
"text": "<p>TCT AAC <em>TGA</em> TTA GC</p>\n\n<p>T CTA ACT GAT <em>TAG</em> C</p>\n\n<p>TC <em>TAA</em> CTG ATT AGC</p>\n\n<p>AGA TTG ACT AAT CG <<< this is the ORF</p>\n\n<p>A GAT <em>TGA</em> CTA ATC G</p>\n\n<p>AG ATT GAC <em>TAA</em> TCG</p>\n\n<p>If th... | [
{
"answer_id": 15145,
"pm_score": 2,
"text": "<p>On the sequence alone, you can answer neither of these questions because:</p>\n\n<ul>\n<li>from the sequence alone you don't know anything about the gene or the\npromoter.</li>\n<li>the same is true for the orientation</li>\n<li>and the codons, since you ... |
15,151 | <p>Lately, I've become a believer in the limits of reductionist explanations especially in areas like complex systems and biology. So, without wasting any more time, I'll get to my question..</p>
<p>Whenever we think of something like cooperation, the most common explanation that comes up is that of genetic fitness. It is said that evolution would have selected for psychological mechanisms of cooperation because it is beneficial in a society in which reciprocity is possible. You scratch my back, and I scratch yours. Add to the mix the ability to name names, and reputation becomes a kind of proxy signal for fitness.</p>
<p>Now, the major problem I have with this is <em>does it all have to boil down to fitness</em>? Can't it be a phenomenon that is culture-specific? Different cultures go to different lengths to help a stranger. Yet, we all share the same evolutionary history. This seems like a strong indicator that cooperation can't be reduced to one's genetic or reputational fitness alone. Should the study of cooperation be handed off to the anthropologists?</p>
| [
{
"answer_id": 15146,
"pm_score": 3,
"text": "<p>TCT AAC <em>TGA</em> TTA GC</p>\n\n<p>T CTA ACT GAT <em>TAG</em> C</p>\n\n<p>TC <em>TAA</em> CTG ATT AGC</p>\n\n<p>AGA TTG ACT AAT CG <<< this is the ORF</p>\n\n<p>A GAT <em>TGA</em> CTA ATC G</p>\n\n<p>AG ATT GAC <em>TAA</em> TCG</p>\n\n<p>If th... | [
{
"answer_id": 15145,
"pm_score": 2,
"text": "<p>On the sequence alone, you can answer neither of these questions because:</p>\n\n<ul>\n<li>from the sequence alone you don't know anything about the gene or the\npromoter.</li>\n<li>the same is true for the orientation</li>\n<li>and the codons, since you ... |
15,191 | <p>I am an electronic engineer so I am thinking about this from an electronics outlook.</p>
<p>How does the addressing system work, As I see it, the nervous system is small parallel branches attached to larger "serial" lines (spinal cord).</p>
<p>The serial line is then attached to the brain, but how does it then figure out where the message came from and then get the message back to the place it came from.</p>
<p>If I were to build a robot I would have an addressing system with each message and maybe some kind of error checking to make sure the messages don't become corrupted, but as it's not an electronic system I don't see how the brain could possibly do this. unless it is a fully parallel system and there is a single wire going from every sensor back to the CPU..</p>
| [
{
"answer_id": 15199,
"pm_score": 3,
"text": "<p>The brain knows where a sensory signal came from by what neuron is doing the signalling. The incoming neuron is dedicated to signals from one source and, since it is not shared by other sources, does not need to have an encoding as to what the source was... | [
{
"answer_id": 15192,
"pm_score": 1,
"text": "<p>your question is a little bit difficult to answer in the current forum format, however I'd suggest you reading about <a href=\"http://en.wikipedia.org/wiki/Reflex_arc\" rel=\"nofollow noreferrer\">Reflex arc</a> - from this you can understand consequence... |
15,195 | <p>Fulminant seems to mead rapid.
There is however some articles with both phrases: "fulminant meningococcecemia" (about 5000 Google matches) and "acute meningococcecemia" (about 3000 Google matches).</p>
<p>I am thinking Neisseria meningitidis and its pathogenesis</p>
<blockquote>
<p>Portal entry nasopharynx (pili)-> attach epithelium cells -> bloodstream (bacteremia); upper respiratory tract infection -symptoms; may be asymptomatic in transient flora; fulminant meningocococcemia (regardless of meningitis)</p>
</blockquote>
<p><strong>What is the difference between the two diseases?</strong></p>
| [
{
"answer_id": 15197,
"pm_score": 3,
"text": "<p>When we say \"Fulminant meningococcemia\" we mean failure of adrenal glands due to haemorrhage of infectious origin, or <a href=\"http://en.wikipedia.org/wiki/Waterhouse%E2%80%93Friderichsen_syndrome\" rel=\"nofollow\">Waterhouse–Friderichsen syndrome</a>... | [
{
"answer_id": 77398,
"pm_score": 1,
"text": "<p>Both fulminant and acute are adjectives that describe a disease course. The previous answer by @ilan is incorrect. Fulminant does not specifically refer to adrenal failure, despite the association between meningococcemia (which often has a fulminant cours... |
15,200 | <p>Sometimes when a person gets touched on one part of the body they feel it else where and may think it came from a different part of the body. What causes this? Other examples are similar to why you can trick your self into thinking your arms are heavier than they really are. another would be that you can close your eyes and move in circles up and down your arm slowly and then when you guess where u are touching your hand is higher or lower than expected. What causes these things?</p>
| [
{
"answer_id": 15197,
"pm_score": 3,
"text": "<p>When we say \"Fulminant meningococcemia\" we mean failure of adrenal glands due to haemorrhage of infectious origin, or <a href=\"http://en.wikipedia.org/wiki/Waterhouse%E2%80%93Friderichsen_syndrome\" rel=\"nofollow\">Waterhouse–Friderichsen syndrome</a>... | [
{
"answer_id": 77398,
"pm_score": 1,
"text": "<p>Both fulminant and acute are adjectives that describe a disease course. The previous answer by @ilan is incorrect. Fulminant does not specifically refer to adrenal failure, despite the association between meningococcemia (which often has a fulminant cours... |
15,214 | <p>Laplace law explains why the pressure is the same in aorta and arteries (100).
I am thinking why there is so big drop in pressure when going from arteries to arterioles (40-60).</p>
<p><strong>Why there is a great drop in pressure from arteries to arterioles?</strong></p>
| [
{
"answer_id": 15197,
"pm_score": 3,
"text": "<p>When we say \"Fulminant meningococcemia\" we mean failure of adrenal glands due to haemorrhage of infectious origin, or <a href=\"http://en.wikipedia.org/wiki/Waterhouse%E2%80%93Friderichsen_syndrome\" rel=\"nofollow\">Waterhouse–Friderichsen syndrome</a>... | [
{
"answer_id": 77398,
"pm_score": 1,
"text": "<p>Both fulminant and acute are adjectives that describe a disease course. The previous answer by @ilan is incorrect. Fulminant does not specifically refer to adrenal failure, despite the association between meningococcemia (which often has a fulminant cours... |
15,217 | <p>When searching for misprimings I have been told that an e value that is higher than 0.01 is ok and will produce no significant amounts of mispriming. Yet I searched some and it would seem that the e value threshold limit is dependent upon the "amount of information" in the database. Indeed I found that some papers cite as values lower than 0.07 to be significant already. </p>
<p>What are the criteria you use at times to judge this issue, and how do I know when to lower or increase my stringency when running a routine BLAST for the purposes of designing primers?</p>
| [
{
"answer_id": 15197,
"pm_score": 3,
"text": "<p>When we say \"Fulminant meningococcemia\" we mean failure of adrenal glands due to haemorrhage of infectious origin, or <a href=\"http://en.wikipedia.org/wiki/Waterhouse%E2%80%93Friderichsen_syndrome\" rel=\"nofollow\">Waterhouse–Friderichsen syndrome</a>... | [
{
"answer_id": 77398,
"pm_score": 1,
"text": "<p>Both fulminant and acute are adjectives that describe a disease course. The previous answer by @ilan is incorrect. Fulminant does not specifically refer to adrenal failure, despite the association between meningococcemia (which often has a fulminant cours... |
15,247 | <p>I am not a biology student, but just want to know if GULO gene are present only in mammals or all species possess it ?</p>
<p>And is GULO gene active in human fetus?</p>
| [
{
"answer_id": 15251,
"pm_score": 4,
"text": "<p>GULO encodes <a href=\"http://en.wikipedia.org/wiki/L-gulonolactone_oxidase\" rel=\"noreferrer\">L-gulonolactone oxidase</a> which catalyses a step in the biosynthetic pathway to ascorbic acid (vitamin C).</p>\n\n<p>I did a BLAST search at NCBI using the ... | [
{
"answer_id": 93441,
"pm_score": 0,
"text": "<p>De Tullio writes </p>\n\n<blockquote>\n <p>We know from other studies that pseudogenes are not inert, but can have a significant role in epigenetic control of gene expression (Poliseno et al. 2010). Could this also apply to the human gulonolactone oxidas... |
15,256 | <p>I could not spell the agar [gonoline-uroline] which I heard yesterday.
My spelling is so wrong that I could not find it in Google.</p>
<p><strong>What is the right spelling for this agar?</strong></p>
| [
{
"answer_id": 15258,
"pm_score": 3,
"text": "<p>The first word is ok, there is agar called Gonoline, the second one is probably Euroline and there is an agar with this word too (Liver IgG Euroline).</p>\n\n<p>I've found both of them on the <a href=\"http://www.marigoitalia.com/public/reagenti.txt\" rel... | [
{
"answer_id": 15268,
"pm_score": 0,
"text": "<p>Looking at your two questions together, I think you mean gonoline media, followed by blood agar. To be honest, I feel like this question would be off topic. You may be referring to a specific blood agar, like Chocolate agar, but that would be wild specu... |
15,270 | <p>Animal -> bacterial gene transfer seems easier than bacteria -> animal (rotifers are an interesting exception); there are bacteria live in close contact to us but our germ-line cells are protected. Given enough time, even free-living bacteria would start to pick up some of our genes (once the introns were lost).</p>
<p>Is this true? If so, do we see animal/plant genes gradually spreading into single cell organisms as time goes on (although "seeing" this would be difficult)? Is this effect "significant" for evolution in microbes? </p>
| [
{
"answer_id": 15258,
"pm_score": 3,
"text": "<p>The first word is ok, there is agar called Gonoline, the second one is probably Euroline and there is an agar with this word too (Liver IgG Euroline).</p>\n\n<p>I've found both of them on the <a href=\"http://www.marigoitalia.com/public/reagenti.txt\" rel... | [
{
"answer_id": 15268,
"pm_score": 0,
"text": "<p>Looking at your two questions together, I think you mean gonoline media, followed by blood agar. To be honest, I feel like this question would be off topic. You may be referring to a specific blood agar, like Chocolate agar, but that would be wild specu... |
15,287 | <p>Life expectancy for human has significantly increased during the last century or so. We all know that there are many reasons that are not linked with "evolution", but I am wondering if such change in life expectancy has been observed "naturally" (not counting animals in zoos or domestic ones). Does evolution favor long lasting individuals?</p>
| [
{
"answer_id": 15311,
"pm_score": 3,
"text": "<p>As far evolution is concerned, there is no benefit whatsoever in having long lived individuals. Evolution only \"cares\" about individuals while they are capable of reproducing. Survival past the maximum age of reproduction is irrelevant from the evolutio... | [
{
"answer_id": 15288,
"pm_score": 1,
"text": "<p>The life expectancy of an animal (or anything) is just one aspect of how 'fit' they are to survive. having them live too long can be a detriment to the species. </p>\n\n<p>There is no simple 'better/worse' relationship of fitness to life expectancy. In... |
15,295 | <p>Succinate dehydrogenase is attached to the inner mitochondrial membrane. All the other enzymes of the Krebs cycle are located within the matrix of mitochondria, though. </p>
<p>In biological systems, there is often a relation between structural properties and function. For example, two enzymes that function sequentially in a metabolic pathway are sometimes held in close proximity to one another by a scaffold (e.g., in fatty acid synthesis). Is there a similar biochemical reason why succinate dehydrogenase is attached to the inner mitochondrial membrane, as opposed to being dissolved in the mitochondrial space?</p>
| [
{
"answer_id": 15296,
"pm_score": 2,
"text": "<p>The reason behind this lies in the properties of FAD+. Unlike NAD+, FAD+ is not free to diffuse within the mitochondrion, it is an integral part of the inner mitochondrial membrane. Its reduced form FADH2 contributes electrons directly to ETC.</p>\n"
}
... | [
{
"answer_id": 15298,
"pm_score": 0,
"text": "<p>Succinate dehydrogenase is also known as Complex II in the electron transport chain.</p>\n\n<p>Although textbooks often show Complex II as taking FADH<sub>2</sub> as a substrate, this is a little bit misleading. Succinate is the substrate, the oxidation o... |
15,299 | <p>Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a
patient with phenylketonuria revealed a mutation in the protein coding
region whose predicted effect would be to replace the amino acid aspartic
acid, with histidine. Nevertheless, no mutant protein could be found in the
patient’s cells.How this could be as mutation is in the protein coding region,can anyone explain?</p>
| [
{
"answer_id": 15318,
"pm_score": 3,
"text": "<p>In terms of the way that the question is worded, I imagine the most likely answer would be that the amino acid substitution D > H disrupts the folding of the protein so that it is recognised as being aberrant and is rapidly degraded.</p>\n"
}
] | [
{
"answer_id": 15310,
"pm_score": 2,
"text": "<p>There are many possible reasons for this, the two most obvious ones are:</p>\n\n<ol>\n<li><p><a href=\"https://en.wikipedia.org/wiki/Alternative_splicing\" rel=\"nofollow\">Alternative splicing</a>. Perhaps the mutation is indeed in the coding region but ... |
15,308 | <p>In molecular biology, what's the meaning of the terms "downstream signaling" and "upstream signaling"? What's the difference between them?</p>
| [
{
"answer_id": 15312,
"pm_score": 3,
"text": "<p>It simply means <em>after</em> and <em>before</em> with respect to the flow of information in a given pathway. For example, consider this schematic representation of a pathway:</p>\n\n<pre><code>TF1 ==activates==> gene1 ==produces==> Kinase1 ==phosp... | [
{
"answer_id": 15309,
"pm_score": 2,
"text": "<p>If you think of a transcription factor, than this factor needs to be regulated. This happens either by signalling pathways and also on the gene expression level (how much of the factor is available). So everything what regulates this factor is called upst... |
15,345 | <p>Are there "essential sugars"? Some have suggested that the 8 principal sugars found in glycoproteins are "essential sugars":</p>
<ol>
<li>Galactose</li>
<li>Glucose</li>
<li>Mannose</li>
<li>N-Acetylneuraminic acid</li>
<li>Fucose</li>
<li>N-Acetylgalactosamine</li>
<li>N-Acetylglucosamine</li>
<li>Xylose</li>
</ol>
<p>I realize the liver can convert glucose to many different sugars, so by "essential sugar" I mean a sugar that is difficult to obtain from diet or that the liver requires much energy to convert from glucose.</p>
<p>How difficult is it for the liver to convert glucose to the other sugars listed above?</p>
| [
{
"answer_id": 15347,
"pm_score": 3,
"text": "<p><strong>There are no essential sugars.</strong></p>\n\n<p>In the context of nutrition \"essential\" usually means \"must be obtained from the diet\". So for example the amino acid methionine is an essential amino acid (for humans).</p>\n\n<p>Within this d... | [
{
"answer_id": 15348,
"pm_score": 2,
"text": "<p>@AlanBoyd is right that the term 'essential sugar' is not a scientific or biologically defined term and is not true given the meaning of the word essential that is in use in biology. </p>\n\n<p>In alternative health and diet circles, the term 'essential s... |
15,365 | <p>What is the physiological mechanism behind the occurrence of orthostatic hypertension in the presence of hypovolemia?</p>
| [
{
"answer_id": 19349,
"pm_score": 2,
"text": "<p>The pathophysiology of orthostatic hypertension has not been elucidated. It is believed it involves activation of the sympathetic nervous system [1], vascular adrenergic hypersensitivity and diabetic neuropathy [2]. High levels of plasma atrial natriureti... | [
{
"answer_id": 15376,
"pm_score": 0,
"text": "<p>I presumed you meant orthostatic hypotension. </p>\n\n<p>Blood pressure falls on standing and is caused primarily by increased gravity causing blood pooling in the legs. This reduces venous return and subsequently cardiac output and therefore arterial blo... |
15,383 | <p>How do we know that everybody's DNA fingerprint is unique?</p>
<p>I know, I know, everybody's DNA is unique. </p>
<p>But when we do DNA fingerprinting, we're looking at very specific regions of high variability.</p>
<p>How do we know that just by chance, two people's DNA could be the exact same in the spot(s) we're observing. </p>
<p>With real fingerprints, uniqueness is (almost) guaranteed (I believe it's a 1 in 64 billion chance) because they are developed by physical stresses on the fetus in the womb. </p>
<p>Is there any similar mechanism/affect that acts on these non-coding/highly variable sections of DNA?</p>
<p>Thanks!</p>
<p>evamvid</p>
| [
{
"answer_id": 15385,
"pm_score": 4,
"text": "<p>First, remember that identical twins actually have the same genotype. So its not exactly true that everyone has a unique genome.</p>\n\n<p>But to get at the heart of it, you're asking how I can be sure that I have a different genome than you, or even than... | [
{
"answer_id": 15392,
"pm_score": 2,
"text": "<p>Possibly partly offtopic, but I'd like to add that when using dna fingerprint as evidence of identity in a legal investigation, the odds become smaller due to combination of human factors and reduced accuracy. There is the twin issue already mentioned, bu... |
15,386 | <p>In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)?</p>
<p><img src="https://i.stack.imgur.com/gnhLX.gif" alt="this">
<img src="https://i.stack.imgur.com/whngD.gif" alt="this"></p>
<p>(These images were samples that I took from an online activity we did for class)</p>
| [
{
"answer_id": 15391,
"pm_score": 4,
"text": "<p>These are sequencing gels (in the cases here even radioactive ones) - they are run a lot longer than ordinary agarose gels and they are made from polyacrylamide. Im my experience, the most likely cause for skewing of lanes (not only bands) are samples, wh... | [
{
"answer_id": 20963,
"pm_score": 2,
"text": "<p>@Chris's suggestion is very possible, high salt characteristically shows this towards the end of the gel. But there are additional suspects. This looks like it's just an agarose gel, Correct? I've seen a few things cause this including the gel not being l... |
15,431 | <p>I understand there are two kinds of active vaccination</p>
<ol>
<li><p>Injecting complete viruses that are weakened to not cause the disease being vaccinated against</p></li>
<li><p>Injecting only antigen particles of viruses that the body creates antibodies for. So the disease can't arise, not even in a weakened form.</p></li>
</ol>
<p>I am wondering how the viruses for vaccination are weakened. Is this simply a process where randomly parts of the virus DNA/RNA are taken out and tested on animals, and as soon as it is sufficiently weakened, it is considered suitable? Or is this an analytical and systematic process?</p>
<p>I am wondering because some popular vaccinations (including that against measles) can still (very rarely) cause fatal complications. Which made me think whether it's systematic or just "accelerated mutation and selection".</p>
<p>I'm interested in an answer for layman, if that is possible at all.</p>
| [
{
"answer_id": 15433,
"pm_score": 5,
"text": "<p>There is a Wikipedia page on the topic of <a href=\"http://en.wikipedia.org/wiki/Attenuated_vaccine\">attenuated vaccines</a>. </p>\n\n<p>Basically the idea is that the virus is grown on some sort of foreign host such as cells in culture, eggs or an anima... | [
{
"answer_id": 15434,
"pm_score": 3,
"text": "<p>There are basically three classical possibilies:</p>\n\n<ul>\n<li>Using an attenuated virus as Alan described in his answer</li>\n<li>use only parts of viruses (here mostly proteins, which are displayed\non the surface of the virus and which can be recogn... |
15,432 | <p>I think no, but I am not sure since Listeria is Gram-positive and probably has lipopolysaccharide (exception among Gram positive bacteria).</p>
<p><strong>Can Listeria monocytogenes' endotoxin act like exotoxin A-B?</strong>
(In which component B lets component A inside the cell and component A causes the toxicity.)</p>
| [
{
"answer_id": 15438,
"pm_score": 4,
"text": "<p>Considering great research we did after the answer was accepted, I should add important information about the topic. The old (and accepted) answer follows in \"\" marks for the sake of clarity.</p>\n\n<p>We found that in spite of the earlier reports, the ... | [
{
"answer_id": 15439,
"pm_score": 3,
"text": "<p>Just to add some important relevant information to the answer from @Ilan.</p>\n<p><strong>There is no evidence for the presence of <a href=\"http://en.wikipedia.org/wiki/Lipopolysaccharide\" rel=\"nofollow noreferrer\">endotoxin/lipopolysaccharide</a> in ... |
15,435 | <p>In order to initiate glycolysis, 2 ATP are necessary. In the glycolytic process, you generate an additional 4 ATP, which results in a net gain of 2 ATP.</p>
<p>If you don't undergo glycolysis, however, then you have an extra 2 ATP not being used. If you do glycolysis, you still got only 2 ATP. Am I missing something here?</p>
| [
{
"answer_id": 15437,
"pm_score": 3,
"text": "<p>Suppose the cellular pool has $x$ATP before starting glycolysis. In the initial phosphorylation steps, we use up two ATP to get the total tally at $(x-2)$ATP. The following steps yields $4$ ATP which brings the final total to $(x+2)$ATP.<br>\nAssuming the... | [
{
"answer_id": 15436,
"pm_score": 2,
"text": "<p>Remember that glycolysis yields 2 NADH as well as 2 net ATP. This NADH can be used to a terminal electron acceptor to produce an end product with a net gain of ATP. End-products of fermentation can include lactate, acetate, butyrate, propionate and ethano... |
15,469 | <p>I am thinking why hydrogen sulfide has its effects in the body.
For instance, it is one Salmonella's virulence factor.
I am not sure if such a balance equations holds</p>
<p><strong>H<sub>2</sub>O + H<sub>2</sub>S ←→ ...</strong></p>
<p>Actually, I miss here some factors because I am not understanding the biochemistry enough to answer this.
I think H<sub>2</sub>S can exists in some sort of ionic form.
Hydrogen sulfide reminds me of ammonia.
I think it inhibits some systems.
<strong>By which mechanisms?</strong> </p>
<p>It is mentioned in many places the empirical effects: signaling functions similar to NO and CO.
But I am interested in how this happens.
<strong>What is the rate of adhesion of H<sub>2</sub>S to hemoglobin for instance?</strong></p>
<p>H2S can change to sulfite and thiosulfate in mitochondria which are then excreted into urine.
I think most of the biological effects are done before these forms.
<strong>But in which forms?</strong></p>
| [
{
"answer_id": 23717,
"pm_score": 3,
"text": "<p>$H_2S$ is the end product of sulfur related respirations (like sulfate respiration, sulfur respiration, etc...).</p>\n\n<p>By aerob (oxygen) respiration the oxygen in $O_2$ has 0 <a href=\"http://en.wikipedia.org/wiki/Oxidation_state\" rel=\"nofollow\">ox... | [
{
"answer_id": 15999,
"pm_score": 0,
"text": "<p>Alan Boyd's answer</p>\n\n<blockquote>\n <p>Production of hydrogen sulphide is used as a convenient method for\n detecting the presence of pathogenic Salmonella, there is nothing to\n link this with virulence.</p>\n</blockquote>\n\n<p>which I agree wit... |
15,477 | <p>According to Invasive Species Advisory Committee (ISAC), the definition of the invasive species is “a species that is non-native to the ecosystem under consideration and whose introduction causes or is likely to cause economic or environmental harm or harm to human health.” </p>
<p>But considering the following facts, why is this species not categorized as an invasive species?
Homo sapiens:</p>
<ul>
<li><p>is non-native to the most of the ecosystem which it is inhabiting, since it originated from a certain area of Africa and spread quite recently.</p></li>
<li><p>has often caused environmental problems by decreasing the local species after its introduction, as it is known that the number of species in the planet is drastically decreasing ever since the advent of Homo sapiens.</p></li>
<li><p>is likely to cause the same problem after introduced to new environment where homo sapiens hasn't inhabited yet.</p></li>
</ul>
<p><a href="http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf" rel="noreferrer">http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf</a></p>
| [
{
"answer_id": 15537,
"pm_score": 3,
"text": "<p>Ignoring for the moment the question of politics, let's consider the various definitions of the term \"invasive species\" that are in use. Colautti and MacIsaac write in their discussion of invasive species terminology (<a href=\"http://www.esf.edu/efb/pa... | [
{
"answer_id": 84855,
"pm_score": 1,
"text": "<p>I don't think there is a good answer.</p>\n\n<ol>\n<li>Many people and organisations do not even consider Homo sapiens when making such lists. Why? Because we have been for millennia a narcissistic species (think about religious narrative). This is simil... |
15,478 | <p>I understand that the first BLAST yields almost the same results as blastp. The second time the iterated blast generates different results as it uses different matrix based on our first result.</p>
<p>But I don't understand how exactly the second matrix is generated. </p>
| [
{
"answer_id": 15537,
"pm_score": 3,
"text": "<p>Ignoring for the moment the question of politics, let's consider the various definitions of the term \"invasive species\" that are in use. Colautti and MacIsaac write in their discussion of invasive species terminology (<a href=\"http://www.esf.edu/efb/pa... | [
{
"answer_id": 84855,
"pm_score": 1,
"text": "<p>I don't think there is a good answer.</p>\n\n<ol>\n<li>Many people and organisations do not even consider Homo sapiens when making such lists. Why? Because we have been for millennia a narcissistic species (think about religious narrative). This is simil... |
15,479 | <p>I wonder if there are any benefits to eat earth. What I mean by earth is the topsoil that is sometimes on vegetable (I eat organic vegetables and some of them like spinach are full of topsoil).</p>
<p>I found this <a href="http://www.sciencedaily.com/releases/2011/06/110602162820.htm" rel="nofollow">article</a> (a study about why people, in certain culture, eat earth) but it doesn't clearly answer my question as it's about clay and not topsoil. Topsoil has a highest concentration of organic matter than clay.</p>
<p>I wonder if we can digest the soil nutrient (Phosphorus, Potassium, Calcium, Magnesium, Manganese, Zinc, Copper) just as we would if there were coming from vegetable and fruits. </p>
<p>What are the other pros and cons of eating earth (soil)? (I am aware of the cons about parasite and bacteria but my question is not about these risks. It's about nutritive value of earth.)</p>
| [
{
"answer_id": 15498,
"pm_score": 3,
"text": "<p>The article (a PDF can be found <a href=\"http://www.d.umn.edu/~pfarrell/Soils/Readings/geophagy.pdf\" rel=\"nofollow\">here</a>) suggests that this happens neither for feeding reasons (to get your belly filled, when anything else is available) nor that t... | [
{
"answer_id": 66609,
"pm_score": 0,
"text": "<p>A/ stronger immune system. children without soil environments are weaker, and the immune memory doesn't last forever across the decades, so it's good for adults too.\n<a href=\"http://www.npr.org/sections/health-shots/2017/07/16/537075018/dirt-is-good-why... |
15,486 | <p>I always wear gloves when I'm doing cell culture. Moreover, I always spray my gloves with ethanol to disinfect, so that I don't contaminate everything.</p>
<p>However, I recently heard the argument that EtOH could impair the integrity of the glove, making it an unsuitible barrier between your hand and the culture. According to this argument, the best idea is to not wear gloves during cell culture, but instead thoroughly spray your hands with EtOH to ensure decontamination.</p>
<p>I don't believe it, but I'm wondering if anyone else has heard a similar argument and if there is any truth to the claim.</p>
| [
{
"answer_id": 15489,
"pm_score": 4,
"text": "<p>In my opinion wearing gloves during cell culture is a good idea. It works both ways as a protection: For your cells since you are not loosing small danders from your hand and for you since you are not getting media or chemicals used in cell culture on you... | [
{
"answer_id": 15488,
"pm_score": 2,
"text": "<p>Assuming you use latex or nitrile, you're probably good. Nitrile does hold up better than latex in many situations, so if you're worried about it, switch to nitrile. <a href=\"http://amo-csd.lbl.gov/downloads/Chemical%20Resistance%20of%20Gloves.pdf\" re... |
15,493 | <p>In a <a href="http://p-gerlee.blogspot.ca/2014/02/the-role-of-mathematical-oncology.html" rel="noreferrer">recent post</a>, Philip Gerlee highlighted the two biggest contributions of mathematical oncology to cancer research: (1) increasing focus on the progress of cancer as an evolutionary process, and (2) looking at the importance of tumor heterogeneity.</p>
<p>For the first point, the standard historical reference is: Nowell, P. C. (1976). The clonal evolution of tumor cell populations. <em>Science</em>, 194(4260): 23-28.</p>
<p>However, for the second point, although I am vaguely familiar with <a href="http://www.pnas.org/content/110/10/4009.full" rel="noreferrer">modern work</a>, I don't know of a historical reference. <strong>When was tumour heterogeneity first recognized as important to cancer dynamics and treatment?</strong> Was this work related to mathematical or other modeling insights? If not, what is the first important mathematical (or computational) modeling work on tumour heterogeneity?</p>
| [
{
"answer_id": 15489,
"pm_score": 4,
"text": "<p>In my opinion wearing gloves during cell culture is a good idea. It works both ways as a protection: For your cells since you are not loosing small danders from your hand and for you since you are not getting media or chemicals used in cell culture on you... | [
{
"answer_id": 15488,
"pm_score": 2,
"text": "<p>Assuming you use latex or nitrile, you're probably good. Nitrile does hold up better than latex in many situations, so if you're worried about it, switch to nitrile. <a href=\"http://amo-csd.lbl.gov/downloads/Chemical%20Resistance%20of%20Gloves.pdf\" re... |
15,502 | <p>I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method?</p>
<p>I checked <a href="http://en.wikipedia.org/wiki/FASTQ_format" rel="noreferrer">wikipedia</a> and <a href="http://maq.sourceforge.net/fastq.shtml" rel="noreferrer">MAQ</a> but I want to know if is there a reliable document that describes all possible variants in sequence ID to check for single/paired end reads. </p>
<p>I am searching also for a library, better in Python, to achieve this.</p>
<p>Thanks </p>
| [
{
"answer_id": 15908,
"pm_score": 5,
"text": "<p>By now I got some interesting answers in <a href=\"http://www.biostars.org/p/95310/#95310\" rel=\"noreferrer\">this question on Biostars</a></p>\n\n<p>Basically what I did is the following:</p>\n\n<ul>\n<li><p>First of all, I checked if Sequence Id contai... | [
{
"answer_id": 97864,
"pm_score": 2,
"text": "<p><strong>This is complementary answer to <a href=\"https://biology.stackexchange.com/a/15908/63778\">what @gc5 provided</a>.</strong></p>\n<hr />\n<p>For cases that are using "the second notation" which looks like:</p>\n<pre><code>@EAS139:136:FC7... |
15,522 | <p><strong>Question:</strong></p>
<p>How does the telomeric repeating sequence vary in non-vertebrate Eukaryotes? If you know the repeating sequence of a given species I would appreciate hearing it.</p>
<p><strong>Background:</strong></p>
<p>Telomerase is a ribonucleoprotein enzyme that adds DNA sequence repeats to the 3' end of DNA strands in the telomere regions, which are found at the ends of eukaryotic chromosomes.</p>
<p>In vertebrates the conserved telomeric repeating sequence is "TTAGGG".</p>
| [
{
"answer_id": 15543,
"pm_score": 3,
"text": "<p>A database that answers the question, charting telomere repeat sequences for all known species, is: <a href=\"http://telomerase.asu.edu/sequences_telomere.html\" rel=\"nofollow noreferrer\">http://telomerase.asu.edu/sequences_telomere.html</a> </p>\n\n<p>... | [
{
"answer_id": 15534,
"pm_score": 2,
"text": "<ul>\n<li>TTAGG telomeric repeats have been found in several insects. From Sahara, Marek & Traut (<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/10560968/\" rel=\"nofollow\">1</a>):</li>\n</ul>\n\n<blockquote>\n <p>(TTAGG)n-containing telomeres were found... |
15,546 | <p>So, I saw a video on YouTube that says the banana we eat today is not what a banana looked like years ago. Since the banana has been genetically modified over the years, does that qualify as evolution?</p>
| [
{
"answer_id": 15547,
"pm_score": 4,
"text": "<p>Yes. Modern domesticated bananas have evolved from ancestral wild species under the influence of humans. Quoting D'Hont et al.: (<a href=\"http://www.nature.com/nature/journal/v488/n7410/full/nature11241.html\" rel=\"noreferrer\">1</a>)</p>\n\n<blockquote... | [
{
"answer_id": 15665,
"pm_score": -1,
"text": "<p>You could say it clasiffies as evolution only if you accept that the artificial things humans have done to bananas are actually natural occurences. I personally don't think they are, because intent is at play here, and evolution is a natural process with... |
15,577 | <p>The wikipedia page on <a href="http://en.wikipedia.org/wiki/Gestational_carrier" rel="nofollow">surrogacy</a> highlights two main forms of surrogacy: Traditional Surrogacy and Gestational Surrogacy. Traditional surrogacy inseminates the surrogate mother with sperm, while gestational surrogacy uses in vitro fertilization to form an embryo from egg and sperm, which is then transferred into the surrogate mother. </p>
<p>It does not discuss whether surrogacy is possible after a natural fertilization has already taken place, such as if a woman becomes pregnant and then wishes, for whatever reason, to have a surrogate take the baby to term. Is this biologically possible? If it is possible, what is the mechanism? Also, if possible, is heightened risk a major reason it is not more common?</p>
| [
{
"answer_id": 15579,
"pm_score": 3,
"text": "<p>No, it is not possible. The problem is the fertilization which takes place near the ovary. It takes the new forming blastocyst about 4-5 days to wander through the fallopian tube to reach the uterus and 8-9 days in total to implant itself into the uterine... | [
{
"answer_id": 80950,
"pm_score": -1,
"text": "<p>There are different types of surrogacy, but as you said the most common one are traditional and gestational surrogacy.</p>\n\n<p>Traditional surrogacy normally involves intrauterine insemination (IUI), so the eggs of the surrogate are used in the surroga... |
15,585 | <p>This question may seem illogical to some, but I seriously have this doubt. I searched google for some proofs but they were extremely complex and I couldn't understand anything.</p>
<p>I was just wondering whether we really have recessive allele or not? Is it like there are only dominant allele present, and when dominant allele isn't present we consider it recessive. </p>
<p>Is it like there is a place reserved for dominant allele and if that place is empty it turns out to be recessive.</p>
<p>Although this thought is vague but then if you take this example, it probably would make sense:
Let's say there are two allele : T and t for tall and short respectively. Now, because TT, Tt, tT are tall, they all lead to the formation of specific hormone due to the presence of dominant allele. But the plant with genotype tt is short, hence the "extra" hormone for "excessive" tallness is missing in tt plant because the dominant gene isn't present. Can we say that that place for two allele (dominant allele) is actually empty in the plant with genotype tt?</p>
| [
{
"answer_id": 15586,
"pm_score": 4,
"text": "<p>This is a good question. Firstly, let's get the terminology straightened out: The terms recessive and dominant are not actually used to describe genes, but rather <em>alleles</em>. The term allele is used for alternative forms of the same gene.(<a href=\"... | [
{
"answer_id": 15588,
"pm_score": 2,
"text": "<p>I'm having real difficulty understanding the original question. We know that a diploid organism has two copies of a gene because we can sequence them, and if they are different alleles we can point to the difference in their sequences. Then through geneti... |
15,589 | <p>Are there any commercially available fluorescent dyes that will bind only to double stranded DNA (not RNA, single stranded DNA etc.) for studying <em>in vitro</em> using confocal microscopy?</p>
| [
{
"answer_id": 15591,
"pm_score": 3,
"text": "<p>Most of the dyes used for visualization bind with a much higher affinity to dsDNA. This would be SybrGreen, EtBr (although this will bind RNA as well).\nThere is a pretty comprehensive website from Life Technologies about <a href=\"http://www.lifetechnolo... | [
{
"answer_id": 34107,
"pm_score": 2,
"text": "<p>You may also want to look at acridine orange. It binds both single stranded and double stranded DNA, but fluoresces green when bound to double sided DNA, and orange when bound to single stranded DNA/RNA, making it very easy to see both in the same image.... |
15,607 | <p>Methionine and Cysteine are the two amino acids containing sulfur. <a href="https://en.wikipedia.org/wiki/Cysteine" rel="nofollow">According to wikipedia, cysteine</a> is built from methionine. However, the wikipedia also claims that <a href="https://en.wikipedia.org/wiki/Methionine#Biosynthesis" rel="nofollow">methionine is synthesized from cysteine</a>.<br>
So, a chicken and egg problem (esp. since eggs are a rich source for those proteins). Where do living things get their sulfur to build these amino acids in the first place, in what forms is sulfur available biologically?</p>
| [
{
"answer_id": 15609,
"pm_score": 4,
"text": "<p>Microorganisms (and plants) make cysteine from serine using H<sub>2</sub>S as the sulphur source. Condensation of these two directly gives cysteine in some bacteria, but most often the reaction sequence is:</p>\n<blockquote>\n<p>serine + acetyl-CoA >&g... | [
{
"answer_id": 15608,
"pm_score": 2,
"text": "<p>First of all, the wikipedia article you quote states that methionine is synthesized from cysteine in <em>plants and microorganisms</em>, not in humans. In humans, both cysteine and methionine are <a href=\"https://en.wikipedia.org/wiki/Essential_amino_aci... |
15,612 | <p>After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it just falls off. However, since it is now outside of a cell, there are no protein-digesting enzymes -- or are there? </p>
<p>What happens to it now? I'm guessing it doesn't just float around for all eternity.</p>
| [
{
"answer_id": 15624,
"pm_score": 2,
"text": "<p>Interesting question and actually I haven't found a real answer here yet. The phages seem to bind rather hard, since the need to be blended (subjected to relatively high forces) to shear off. This was used in the <a href=\"http://en.wikipedia.org/wiki/Her... | [
{
"answer_id": 17962,
"pm_score": -1,
"text": "<p>I think the external protein coat is degraded as the virus releases it's nucleic acid into the Host' cell. This is due to the fact that a protein is lifeless without the activity of a gene(one gene-one enzyme hypothesis).Since the nucleic acid is compose... |
15,618 | <p>If we eat fat:</p>
<p>Does the fat go into heart, arteries and fat cells.</p>
<p>OR</p>
<p>Is the fat digested, following which our body creates fat that goes into heart, arteries and fat cells.</p>
<p>Which one is right?</p>
| [
{
"answer_id": 15628,
"pm_score": 4,
"text": "<p>Fat is, in molecular terms, triacylglcerol. In order to be absorbed in the small intestine triacylglycerol molecules are broken down by lipases into fatty acids and monoacylglycerols. Once these have got across the enterocyte membrane they are reassembled... | [
{
"answer_id": 15660,
"pm_score": 0,
"text": "<p>Fat is digested just like any other food you consume, and eventually the energy you do not expend ends up as an energy reserve in shape of fat cells.</p>\n\n<p>So, the second statement is right.</p>\n"
}
] |
15,637 | <p>Is it a viral vs. bacterial thing?
Is there just more variety among types of flu than other diseases, so that this year's vaccines don't cover next year's flu?</p>
| [
{
"answer_id": 15638,
"pm_score": 6,
"text": "<p>The flu virus changes rapidly so that the current vaccine doesn't work against the new strains. </p>\n\n<p>The way vaccines work is that they teach our immune system what to look out for. The vaccine contains bits of the virus but in a form that can't cau... | [
{
"answer_id": 15650,
"pm_score": 2,
"text": "<p>What you call influenza isn't a specific virus which is always the same, but a virus that has numerous different strains. Flu virus is constantly alive on this planet, and there are numerous different types, such as the ones which infect humans, the ones ... |
15,676 | <p>My question is:-<br>
<strong>Only liquid water supports almost every living organism's metabolism, neither the vapour nor the condensed form of water does so. What is the chemical & the biological reason behind this fact?</strong></p>
| [
{
"answer_id": 15638,
"pm_score": 6,
"text": "<p>The flu virus changes rapidly so that the current vaccine doesn't work against the new strains. </p>\n\n<p>The way vaccines work is that they teach our immune system what to look out for. The vaccine contains bits of the virus but in a form that can't cau... | [
{
"answer_id": 15650,
"pm_score": 2,
"text": "<p>What you call influenza isn't a specific virus which is always the same, but a virus that has numerous different strains. Flu virus is constantly alive on this planet, and there are numerous different types, such as the ones which infect humans, the ones ... |
15,726 | <p>According to this article, <a href="http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555" rel="nofollow">DNA has a half life of 512 years</a></p>
<p><a href="http://en.wikipedia.org/wiki/Oldest_viable_seed" rel="nofollow">Wikipedia</a> claims that there are seeds planted as old as 31000 years</p>
<p>Doing the basic math $100 / (2^{30000/512})$ we get that only about
$2.2989191*10^{-16}%$ of the DNA would be left</p>
<p>So how do these plants still grow when replanted?</p>
| [
{
"answer_id": 15728,
"pm_score": 5,
"text": "<p>That half-life was for temperatures of 13.1ºC. In more ideal conditions, such as for temperature of −5 ºC or drier conditions, the half-life would be longer. The Wikpedia article in fact states that the seeds that were 31,000 years old were frozen under p... | [
{
"answer_id": 15739,
"pm_score": 3,
"text": "<p>The source paper for the article is this one: <a href=\"http://rspb.royalsocietypublishing.org/content/279/1748/4724\">The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils</a> (available for free). The crux of their methodology is g... |
15,743 | <p>Linkage disequilibrium $\left(D\right)$ for two bi-allelic loci is defined as:</p>
<p>$$D=X_{11}X_{22} - X_{12}X_{21}$$</p>
<p>where $X_{11},\ X_{12},\ X_{21},\ X_{22}$ are the frequencies of the haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$ respectively (the subscript number correspond to the two different alleles and $A$ and $B$ correspond to the two different loci)</p>
<p><strong>My questions are</strong></p>
<ul>
<li><p>How is $D$ defined for more loci and a greater number of alleles?</p></li>
<li><p>How is $D$ defined when the number of alleles differ from locus to locus?</p></li>
</ul>
| [
{
"answer_id": 24072,
"pm_score": 3,
"text": "<p>LD describes the associations among alleles at different loci. For anything more than two bi-allelic loci, you need more than just one number to fully describe the associations. For instance, if we have three bi-allelic loci 1-3, we need the three pairwis... | [
{
"answer_id": 24012,
"pm_score": 1,
"text": "<p>Being a typical molecular biologist, I am a little uncomfortable with classical genetics terms. I might redefine some symbols (perhaps to mean the same) [<em>It is like talking to oneself while thinking</em>]. </p>\n\n<hr>\n\n<p>There are four DNA-blocks ... |
15,755 | <p>I read that proteins that have been highly conserved are non-immunogenic.</p>
<p>Why is it so ? What is the special thing that makes it non immunogenic(antibodies against them are hard to make) ?</p>
| [
{
"answer_id": 24072,
"pm_score": 3,
"text": "<p>LD describes the associations among alleles at different loci. For anything more than two bi-allelic loci, you need more than just one number to fully describe the associations. For instance, if we have three bi-allelic loci 1-3, we need the three pairwis... | [
{
"answer_id": 24012,
"pm_score": 1,
"text": "<p>Being a typical molecular biologist, I am a little uncomfortable with classical genetics terms. I might redefine some symbols (perhaps to mean the same) [<em>It is like talking to oneself while thinking</em>]. </p>\n\n<hr>\n\n<p>There are four DNA-blocks ... |
15,769 | <p>You need a solution containing 1000 buccal cells/mL. You count that you have 125 buccal cells in 50uL, from a total solution of 8 mL. How much of your stock solution should you take to make the 1000 cells/mL mixture? How much solvent if you would like a total volume of 5mL?</p>
<p>I don't even know how to approach this!!!
Help??</p>
| [
{
"answer_id": 24072,
"pm_score": 3,
"text": "<p>LD describes the associations among alleles at different loci. For anything more than two bi-allelic loci, you need more than just one number to fully describe the associations. For instance, if we have three bi-allelic loci 1-3, we need the three pairwis... | [
{
"answer_id": 24012,
"pm_score": 1,
"text": "<p>Being a typical molecular biologist, I am a little uncomfortable with classical genetics terms. I might redefine some symbols (perhaps to mean the same) [<em>It is like talking to oneself while thinking</em>]. </p>\n\n<hr>\n\n<p>There are four DNA-blocks ... |
15,800 | <p>When there is an error in copying DNA (a mutation), what exactly goes wrong?</p>
<p>If G goes with C and A goes with T, I don't see how that part can mess up.</p>
<p>Is the idea that when the double helix is split, an A gets ruined and replaced with a G by mistake, which then pairs with a C in one of the copies? So something that was <em>supposed</em> to be AT is now GC.</p>
| [
{
"answer_id": 15803,
"pm_score": 3,
"text": "<p>There are many way in which DNA can be damaged. As already pointed out in the comment by @skymninge, the <a href=\"http://en.wikipedia.org/wiki/DNA_repair\" rel=\"nofollow noreferrer\">Wikipedia page on DNA repair</a>, as well as the <a href=\"http://en.w... | [
{
"answer_id": 41792,
"pm_score": 0,
"text": "<p>Pyrimidine dimers are another example that cause errors is replication. Though this generally results in premature attenuation of replication, and not mispairing. Still a messup, and the primary cause of the skin cancer melanoma. Another is the incorporat... |
15,899 | <p>A friend used potassium permanganate solution to treat tinea on the hands/feet but after some initial success, the tinea seems to be making a comeback. Could the fungus develop resistance to potassium permanganate?</p>
| [
{
"answer_id": 15976,
"pm_score": 3,
"text": "<ol>\n<li><p>I don't think a fungus would develop resistance to something so quickly. </p></li>\n<li><p>As Chris suggested in the comments, it could be because \"<em>The disinfective effect is based on the production of reactive oxygen species. The problem i... | [
{
"answer_id": 20240,
"pm_score": 0,
"text": "<p>Fungi cannot develop resistance that quickly. Potassium permanganate is only used to clean wounds. Therefore, the reimmerging of the fungus may be because it wasn't killed in the first place. I suggest antifungal cream should be used generously to kill th... |
15,913 | <p>I am confused about relationship between isoelectric point and pH in context of ion exchange protein purification. Why we cannot use this method for protein with pI below 7? Thank you very much for any tips.</p>
| [
{
"answer_id": 15976,
"pm_score": 3,
"text": "<ol>\n<li><p>I don't think a fungus would develop resistance to something so quickly. </p></li>\n<li><p>As Chris suggested in the comments, it could be because \"<em>The disinfective effect is based on the production of reactive oxygen species. The problem i... | [
{
"answer_id": 20240,
"pm_score": 0,
"text": "<p>Fungi cannot develop resistance that quickly. Potassium permanganate is only used to clean wounds. Therefore, the reimmerging of the fungus may be because it wasn't killed in the first place. I suggest antifungal cream should be used generously to kill th... |
15,921 | <p>I know that <a href="http://en.wikipedia.org/wiki/BRCA2" rel="nofollow">BRCA2</a> interacts with RAD51 to repair DNA damage.</p>
<p>But how exactly does it function ? What are the other proteins that interact with it ? </p>
| [
{
"answer_id": 15923,
"pm_score": 3,
"text": "<p>I'm just skimming through it now, but <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/22193408\" rel=\"nofollow\">this 2011 review</a> in Nature Reviews Cancer looks like it has everything you could possibly want to know about the BRCA1/BRCA2 pathway. If you... | [
{
"answer_id": 15948,
"pm_score": 0,
"text": "<p><img src=\"https://i.stack.imgur.com/bwgpE.jpg\" alt=\"enter image description here\"></p>\n\n<p>Here is an image of BRCA2 and RAD51 oriented.( I produced this using PyMOL!)</p>\n\n<p>The chocolate coloured part is some BRCA repeats. You can see how BRCA ... |
15,927 | <p>Fibrosis is the formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process.
I used the word "fibrogenesis" as the outcome of acute inflammation (healing).
My colleges use the word "fibrosis".
The fibrogenesis seems to be used with the emphasises of the genetic part.</p>
<p><strong>What is the difference between fibrogenesis and fibrosis?</strong></p>
| [
{
"answer_id": 15923,
"pm_score": 3,
"text": "<p>I'm just skimming through it now, but <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/22193408\" rel=\"nofollow\">this 2011 review</a> in Nature Reviews Cancer looks like it has everything you could possibly want to know about the BRCA1/BRCA2 pathway. If you... | [
{
"answer_id": 15948,
"pm_score": 0,
"text": "<p><img src=\"https://i.stack.imgur.com/bwgpE.jpg\" alt=\"enter image description here\"></p>\n\n<p>Here is an image of BRCA2 and RAD51 oriented.( I produced this using PyMOL!)</p>\n\n<p>The chocolate coloured part is some BRCA repeats. You can see how BRCA ... |
15,940 | <p>Is inbreeding the same as interbreeding?</p>
<p>On this site <em>interbreeding</em> is defined as (<a href="http://www.thefreedictionary.com/interbreeding" rel="nofollow">http://www.thefreedictionary.com/interbreeding</a>):</p>
<blockquote>
<ol>
<li>To breed with another kind or species; hybridize.</li>
<li>To breed within a narrow range or with closely related types or individuals; inbreed.</li>
</ol>
</blockquote>
<p>But I am sure that interbreeding is not the same as inbreeding. Inbreeding would be between genetically related members of a species and interbreeding would be between genetically un-related members of the same or different species.</p>
<p>after looking at wikepedia pages for both terms as well as searching the english oxford dictionar I am certain they are different</p>
| [
{
"answer_id": 15941,
"pm_score": 3,
"text": "<p>You are basically correct. Most common usage in my experience:</p>\n\n<p><strong><a href=\"https://en.wikipedia.org/wiki/Inbreeding\" rel=\"nofollow\">Inbreeding</a></strong> refers to sexual reproduction between genetically closely related individuals, w... | [
{
"answer_id": 43432,
"pm_score": -1,
"text": "<p>interbreeding is a process in which same kind of species are breed together such as(male and female)but outer breeding is a process in which different kind of species are breed together such as(means horse is a specie it will breed with bitch those are d... |
15,987 | <p>I'm thinking in particular of wings on birds that would - I'm guessing - have to progress through stages during which they confer no particular advantage. Or is it that all evolved features must have followed a path of incremental benefit therefore imposing a fundamental limit on what evolution through natural selection can "achieve"? (features that are not beneficial while gradually appearing cannot be evolved)</p>
| [
{
"answer_id": 15989,
"pm_score": 2,
"text": "<p>Features can evolve (or change already present features) which have no negative effect under the current conditions. You can very well have neutral changes which have no purpose. They can then prove positive later (or in a different environment). Changes ... | [
{
"answer_id": 66433,
"pm_score": 2,
"text": "<p>There are some interesting hypotheses that wings initially evolved for display, not flight. Then at some point, the winged dinosaurs also had a locomotive advantage, at which point the wings could further evolve with selection for even better locomotion ... |
15,990 | <p>I am more or less familiar with the evolution theory based on mutations. </p>
<p>Now, starting with a nonsexual being, how did the first organism that reproduces sexually come to exist. </p>
| [
{
"answer_id": 16014,
"pm_score": 3,
"text": "<p>Big topic yes, but lets hit some high points. </p>\n\n<p>First, sexual reproduction is a no brainer in evolution. In its basis, sex only requires a segment of the chromosome to be heterogamous - that it will not be recombined. In male humans this is bo... | [
{
"answer_id": 16007,
"pm_score": 2,
"text": "<p>This is a very broad field, with many complementing, overlapping, and contrasting theories. I suggest that you read this part of the Wikipedia article on this topic:</p>\n\n<p><a href=\"http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction#Origin_... |
16,009 | <p>Why carbohydrates and lipids basically used as a sources of energy? Why only proteins are used as building blocks of all the creations? Yes there are some parts of cells like cell walls in which carbohydrates are used but 98% portion of cell is made up of proteins? Why it so? </p>
| [
{
"answer_id": 16010,
"pm_score": 3,
"text": "<p>First, it is a matter of the energy that food can provide. Here fat wins clearly (from the Wikipedia article on <a href=\"http://en.wikipedia.org/wiki/Food_energy\" rel=\"nofollow\">Food Energy</a>):</p>\n\n<ul>\n<li>Fat: 37 kJ/g</li>\n<li>Ethanol (drinki... | [
{
"answer_id": 16033,
"pm_score": 1,
"text": "<p>There can be many reasons for why proteins are chosen as building blocks. Apart from what Chris said, I would add some points:</p>\n\n<ol>\n<li>Amide bond in proteins is quite strong and thus provides a stable backbone</li>\n<li>Because of different amino... |
16,035 | <p>As blunt as possible: when performing real time PCR it is a routine step to run one PCR in order to plot a "standard curve" with several decreasing dilution ratios from your sample. what is the real purpose of this?
how should results be used/interpreted?</p>
| [
{
"answer_id": 16038,
"pm_score": 3,
"text": "<p>You can use 3 or 4 dilutions- 1:1, 1:5, 1:25, 1:125</p>\n\n<p>Purpose of doing this is to calculate the primer efficiency. Ideally primer efficiency should be 2 i.e. two molecules of DNA are formed in a round of PCR. So after n-rounds of PCR there should ... | [
{
"answer_id": 16037,
"pm_score": 1,
"text": "<p>Because the purpose of the standard curve (which actually results in a standard line) needs to be linear. If it is not linear (because of not enough values which are not linear distributed), then you quantification will be wrong.\nIdeally the line should ... |
16,042 | <p>If you injected a tumor with epithelial cells infected with the Rhinovirus, would this still evoke an immune response as it would with the respiratory system? Secondly, what is the specific reason the Rhinovirus is only attracted to the epithelial cells in the respiratory system. Do these cells give off a specific chemical signature in which the virus is attracted to?</p>
| [
{
"answer_id": 16053,
"pm_score": 3,
"text": "<p>Infecting tumor cells with viruses to provoke an immune response used to be termed (tumor / immune ) 'xenogenization'. The approach may now fall under the general headings of tumor immunology, immune modifiers or <a href=\"http://en.wikipedia.org/wiki/C... | [
{
"answer_id": 16044,
"pm_score": 1,
"text": "<p>The virus has some molecules on it surface, which fit to receptors on the surface of their host cells. In the case of rhinoviruses there are three receptors possible. The viruses of the so called major group (or HRV-A species) dock to ICAM1, the minor gro... |
16,049 | <p>Does our DNA adapt by human lifetime? Or do we have the same genetic information from birth to death?
I mean: What is usually called "evolution" means "natural selection" like this:
<a href="http://www.youtube.com/watch?v=hOfRN0KihOU&list=UUsXVk37bltHxD1rDPwtNM8Q" rel="nofollow">http://www.youtube.com/watch?v=hOfRN0KihOU&list=UUsXVk37bltHxD1rDPwtNM8Q</a>
-stronger animals have more descendants, so they make bigger percent of strong animals.
But does evolution work by some primitive genetics-engineering too? Thank you.</p>
| [
{
"answer_id": 16050,
"pm_score": 3,
"text": "<p><strong>Lewontin's recipe</strong></p>\n\n<p>A very nice way to consider natural selection is through the lense of Lewontin's recipe. Evolution of a given trait (tail length for example) through natural selection occurs whenever the three following condit... | [
{
"answer_id": 16055,
"pm_score": 1,
"text": "<p>The concept that the environment directly <em>changes</em> DNA and alters the characteristics of the offspring falls under the heading of <a href=\"http://en.wikipedia.org/wiki/Lamarckism\" rel=\"nofollow\">Lamarkism</a>. In the context of DNA the Lamark... |
16,069 | <p>What happens when two sperm fertilize an egg? This can be either naturally or by experiment.</p>
| [
{
"answer_id": 16070,
"pm_score": 3,
"text": "<p>This phenomenon is called <a href=\"http://en.wikipedia.org/wiki/Polyspermy\" rel=\"nofollow\">polyspermy</a> and results in an embryo which is not viable. This is because it has more than the usual two sets of chromosomes (one from each parent), but one ... | [
{
"answer_id": 94689,
"pm_score": 0,
"text": "<p>Although the results are fatal in animals, as Chris' answer explains, recent research has demonstrated that plants can produce viable offspring with three parents. E.g.:</p>\n<ul>\n<li><a href=\"https://www.nature.com/articles/s41467-017-01044-y\" rel=\"n... |
16,144 | <p>Is there any measurement I could perform after RT that allows me to check the efficiency that the procedure had? Nanodrop cannot be used as remnants of RNA and poly T primers mask measure, or? </p>
| [
{
"answer_id": 16164,
"pm_score": 2,
"text": "<p>Nanodrop may be fine for the volumes but as you rightly guessed it is not so easy to distinguish DNA from RNA (and primers). <a href=\"http://wetlab.izzid.com/2008/Feb/Review_of_Qubit/\" rel=\"nofollow\">Qubit</a> (invitrogen) is a sensitive, dye based qu... | [
{
"answer_id": 16178,
"pm_score": 0,
"text": "<p>Treat with RNAse and spec at 260.</p>\n\n<p>A spec can definitely be used. The extinction coefficient (Beers Lamberts Law) will not be calculating measuring NTPs, just intact dsDNA.</p>\n"
}
] |
16,147 | <p>My question is dealing with how many ancestors it took to produce <strong>me</strong>:</p>
<ul>
<li>--> to produce me it took 2 people (my parents) = ($2^1$) people = 2</li>
<li>--> one generation further included = ($2^1 + 2^2$) people = 6</li>
<li>--> in the past 500 years my pedigree chart contains 15 generations, so $2^{16}$ people = 65.532 people to produce <strong>me</strong> (-2 to be completely correct)</li>
<li>--> when i calculate back to 35.000 year ago I get a larger number *)</li>
<li>--> when i calculate to all humans 2.400.000 ago I get a ridiculous large number *)</li>
<li>--> when i include up to all mammal grandfathers and grandmothers 60.000.000 years ago the total number takes pages to scroll *)</li>
</ul>
<p>*) see: <a href="http://ed.je/2L6" rel="nofollow">http://ed.je/2L6</a> for the actual numbers did not want to clutter here.</p>
<p>*) I took 3 generations per 100 years to let the numbers be small as possible.</p>
<p>So, I think I'm making a mistake somewhere. Only I don't know where: to create a child you need 2 parents. And to create a parent you need 2 further parents. But somehow calculating back to "all mammals" just related directly to me would mean $2^{1.800.001}$ mammals walking around 60 millions years ago being my direct predecessor back then. </p>
<p>So where am I going wrong? Somehow I can't figure out where my error lies (I've not studied Biology though).</p>
<p>I visualize a pedigree tree (reverse pyramid) starting with me and then logically each parent needs to be born out of 2 other parents just calculating my way up.</p>
| [
{
"answer_id": 16149,
"pm_score": 4,
"text": "<p>Your calculations are the following. Assuming non-overlapping generations, the number of ancestors you have in the last $t$ generation is given by:</p>\n\n<p>$$\\sum_{i=1}^t 2^t$$</p>\n\n<p>This sounds correct. But there are some very strong assumptions:<... | [
{
"answer_id": 16160,
"pm_score": 2,
"text": "<p>An easy way to visualize the mistake in your thought experiment is to consider a <a href=\"http://en.wikipedia.org/wiki/Population_bottleneck\" rel=\"nofollow noreferrer\">bottleneck event</a>, when the ancestral population was very small, maybe just a fe... |
16,181 | <p>This may be anecdotal. </p>
<p>At the pharmacy earlier, the prescription called for a drug with X mg of the target chemical. The pharmacy however only had stock of a higher potency of the same brand. </p>
<p>E.g. A prescription may call for 25mg of a particular chemical, whereas the pharmacy could only service a request for 50mg of that chemical in the <strong>same brand</strong>.</p>
<p><em>According to the pharmacist, and the medic - a proportional fraction of higher potency drug of the same brand may be substituted for the lower potency. Thus in the example above, half-a-tablet of 50mg may serve in lieu of a single tablet of 25mg.</em></p>
<p>For a given brand </p>
<ul>
<li>Is half-a-tablet of X a substitute for a full tablet of X/2? </li>
<li>Does the corollary scale upwards too?</li>
</ul>
| [
{
"answer_id": 16149,
"pm_score": 4,
"text": "<p>Your calculations are the following. Assuming non-overlapping generations, the number of ancestors you have in the last $t$ generation is given by:</p>\n\n<p>$$\\sum_{i=1}^t 2^t$$</p>\n\n<p>This sounds correct. But there are some very strong assumptions:<... | [
{
"answer_id": 16160,
"pm_score": 2,
"text": "<p>An easy way to visualize the mistake in your thought experiment is to consider a <a href=\"http://en.wikipedia.org/wiki/Population_bottleneck\" rel=\"nofollow noreferrer\">bottleneck event</a>, when the ancestral population was very small, maybe just a fe... |
16,183 | <p>What if cellular growth and repair is 'forced' to occur repeatedly in a region where it wouldn't normally happen , if the biological area was 'healthier'. Could this more aggressive cellular growth and repair cause any apoptosis mechanisms to shut down permanently?</p>
| [
{
"answer_id": 16149,
"pm_score": 4,
"text": "<p>Your calculations are the following. Assuming non-overlapping generations, the number of ancestors you have in the last $t$ generation is given by:</p>\n\n<p>$$\\sum_{i=1}^t 2^t$$</p>\n\n<p>This sounds correct. But there are some very strong assumptions:<... | [
{
"answer_id": 16160,
"pm_score": 2,
"text": "<p>An easy way to visualize the mistake in your thought experiment is to consider a <a href=\"http://en.wikipedia.org/wiki/Population_bottleneck\" rel=\"nofollow noreferrer\">bottleneck event</a>, when the ancestral population was very small, maybe just a fe... |
16,217 | <p><a href="http://de.wikipedia.org/wiki/H%C3%BChnerei" rel="nofollow">http://de.wikipedia.org/wiki/Hühnerei</a> says it takes up to 24 h for a chicken to produce an egg.</p>
<p>Is that dependent on the chickens nutrition, i.e., if it does not get enough food or the wrong kind, meaning it can survive on the food but it does not have everything to produce an egg?</p>
<p>Do we have data on this?</p>
| [
{
"answer_id": 16219,
"pm_score": 3,
"text": "<p>In short; yes. It depends on the breed (not all lay up to 1 egg/day), the age of the bird and on nutrition. High yielding breeds of chicken are e.g. dependent on supplements of calcium to be able to produce new shells rapidly (e.g. in the form of ground-u... | [
{
"answer_id": 60726,
"pm_score": 1,
"text": "<p>every 24 hours they can lay an egg new young chickens that are for the first time laying eggs could possibly but there is no breed that lays two eggs a day. and note it might be about a year for some to start so don't think if there not producing eggs th... |
16,228 | <p>When performing normalization of real time PCR results, I found two ways of doing it:</p>
<ol>
<li><p>In my lab they follow the next layout: $\text{Efficiency}^{-(CT\ _{\large\text{interest gene}} - CT _{\large\text{ housekeeping}})}$ each time controls with controls and treatments with treatments. Then they divide the all values (treated and controls) each with controls.</p></li>
<li><p>On the other hand I found another way to normalize that follows this steps: $\text{Efficiency}^{(CT_{\large\text{control}} - CT_{\large\text{treated}})}$. Then you make the same for the normalizing gene and divide the first by the last.</p></li>
</ol>
<p>The values obtained are similar but not exact. Also I noticed that first algorithm gives rather different values for most diluted when performing a standard curve.
Which is correct? </p>
| [
{
"answer_id": 16247,
"pm_score": 3,
"text": "<p>First step is the calculation of efficiency, denoted by lets say $E_{gene}$. See <a href=\"https://biology.stackexchange.com/questions/16035/real-time-pcr-standard-curve/16038#16038\">this post</a> for calculation of primer efficiency.</p>\n\n<p>So the fo... | [
{
"answer_id": 16235,
"pm_score": 2,
"text": "<p>This topic could probably have it's own StackExchange, there is so much info and trial and error done with rtPCR. Here's my 2 cents:</p>\n\n<p>Your adjusted calculation does not normalize your data, it just subtracts the 'background' or control. For expre... |
16,233 | <p>Melatonin regulates the wake-sleep cycle by causing drowsiness and lowering body temperature, but which specific chemical pathways lead to this drowsiness?</p>
| [
{
"answer_id": 16552,
"pm_score": 3,
"text": "<p>This is a quite complicated question, as melatonin has quite a range of effects on the cells. First, melatonin binds to three different melatonin receptors, which are found in a wide variety of tissues or organs including brain and retina, cardiovascular ... | [
{
"answer_id": 16545,
"pm_score": 0,
"text": "<p>From wikipedia article on <a href=\"http://en.wikipedia.org/wiki/Melatonin_receptor\" rel=\"nofollow\">melatonin receptors</a> (with some modifications) :</p>\n\n<blockquote>\n <p>In mammals, melatonin receptors, which are G protein coupled receptors, ar... |
16,236 | <p>How many ways can an Apoptosis mechanism be made disfunctional or irreparably damaged? If a cell has damaged Apoptosis mechanisms and it divides will its daughter cells have such damage?</p>
| [
{
"answer_id": 16552,
"pm_score": 3,
"text": "<p>This is a quite complicated question, as melatonin has quite a range of effects on the cells. First, melatonin binds to three different melatonin receptors, which are found in a wide variety of tissues or organs including brain and retina, cardiovascular ... | [
{
"answer_id": 16545,
"pm_score": 0,
"text": "<p>From wikipedia article on <a href=\"http://en.wikipedia.org/wiki/Melatonin_receptor\" rel=\"nofollow\">melatonin receptors</a> (with some modifications) :</p>\n\n<blockquote>\n <p>In mammals, melatonin receptors, which are G protein coupled receptors, ar... |
16,251 | <p><strong>What is the distribution/probability density function (<a href="http://en.wikipedia.org/wiki/Probability_density_function" rel="nofollow noreferrer">PDF</a>) of impacts on fitness of new mutations?</strong></p>
<hr>
<p>I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution. Information of the kind: "If we consider only beneficial mutations, then the PDF is $P(X=x) = f(x)$" are also welcome.</p>
<p>When I say mutations, one might have want to reduce the concept of mutations only to indels and point mutations.</p>
<p>Of course the answer will depend on the species under consideration and from population to population but I welcome any answer that could give some insights. Eventually, some information according to what is generally assumed to be the PDF of effects on fitness of new mutations might be useful.</p>
<p><a href="https://biology.stackexchange.com/questions/16250/dominance-recessivity-of-new-mutations">Here</a> is a related question</p>
<p><a href="http://www.genetics.org/content/163/4/1519.short" rel="nofollow noreferrer">Here</a> is an article that assumes an exponential distribution of effects on fitness of beneficial mutations.</p>
| [
{
"answer_id": 16257,
"pm_score": 3,
"text": "<p>To a good first approximation $\\overline{\\Delta f} = 0$. Where $\\overline{\\Delta f}$ is the mean change in fitness down to any point or indel mutation. The reasons for this are as follows:</p>\n\n<ol>\n<li>In the genome of higher organisms, most of th... | [
{
"answer_id": 16252,
"pm_score": 1,
"text": "<p><em><strong>[This is purely speculative]</em></strong></p>\n\n<p>Assumptions: </p>\n\n<ul>\n<li>impact on fitness is measured by survival chance</li>\n<li>impact is because of protein coding genes</li>\n</ul>\n\n<p>Probability of a mutation at position $i... |
16,319 | <p>I've recently had a blood test and the results displayed elevated levels of erythrocytes as well as hemoglobin. (As a result my hematocrit levels were also above average)</p>
<p>At my workplace there is a water cooler which also has an option to dispense carbonated water (this is just regular ol' carbonated tap water) and usually over the course of the day I tend to drink quite a lot of the stuff.</p>
<p>Since erythrocytes/hemoglobin deals with O<sub>2</sub> and CO<sub>2</sub> transport, I was wondering if my daily consumption of carbonated water is a plausible cause for the additional erythrocytes that are being pumped out?</p>
| [
{
"answer_id": 16322,
"pm_score": 3,
"text": "<p>The main regulatory input into erythrocyte production is hypoxia. The response to elevated CO<sub>2</sub> levels in the blood (<a href=\"http://en.wikipedia.org/wiki/Hypercarbia\" rel=\"nofollow\">hypercapnia</a>) is mainly to increase ventilation (i.e. m... | [
{
"answer_id": 16320,
"pm_score": 1,
"text": "<p>Answer: No. How should the CO<sub>2</sub> from you stomach get into your blood? \nAnd: Most of the CO<sub>2</sub> is removed (by burping) from the solution in your stomach anyway due to the conditions there.</p>\n"
}
] |
16,357 | <p>What are mast cell membranes made out of? </p>
<p>What would weaken or strengthen them?</p>
<p>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.</p>
| [
{
"answer_id": 16359,
"pm_score": 3,
"text": "<p>Cell membranes (not cell walls) are composed of a double layer of phospholipids. The lipids are orientated in the way, that the hydrophilic part of the molecule is oriented to the outside and the inside of the cell and the hydrophobic tail to the inside o... | [
{
"answer_id": 16366,
"pm_score": 2,
"text": "<p>Although the Wikipedia page on <a href=\"http://en.wikipedia.org/wiki/Dermatographism\" rel=\"nofollow\">dermatographism</a> refers to \"weak membranes\" it cites no source for this, and like Chris, I haven't found any mention of this in a quick look at t... |
16,365 | <p>Please feel free to construe this question broadly--I don't see why the question would not apply to branches of biology other than mycology. </p>
<p>If the goal of taxonomy is to create classification of fungi that reflect evolutionary relationships, and if this results in a more or less unmanageable proliferation of names, might it not be a good idea to use a numeric or alpha-numeric system instead of a verbal one? One author estimates there may be as many as 5 million species of fungi (and it may take 1000 years to catalog them). If we did manage to note them all would the result really be useable? The ease of storage and retrieval alone would seem to commend a numerical approach. </p>
<p>I assume someone has thought of this before and I guess viral taxonomy does this to some extent. Are there any proposals like this afoot?</p>
<p>Thanks for any insights. </p>
| [
{
"answer_id": 16369,
"pm_score": 2,
"text": "<p>(First of all the term <a href=\"http://en.wikipedia.org/wiki/Numerical_taxonomy\" rel=\"nofollow\">numerical taxonomy</a> has a completely different meaning. Here you are talking about nomenclature.)</p>\n\n<p>(To make it clear: you are talking about spe... | [
{
"answer_id": 16368,
"pm_score": 2,
"text": "<p>This is actually already done in some contexts.</p>\n\n<p>For instance: yeast (a fungus) is a pretty extensively studied organism, and this means that there are a vast number of yeast strains which are know/used by biologists. Many of these strains are r... |
16,372 | <p>I read in the book "Why we get sick." by Nesse and Williams that:</p>
<blockquote>
<p>Steady detective work and fabulous luck have enabled geneticists to
pinpoint the Huntington's gene on the short arm of chromosome 4.</p>
</blockquote>
<p>I want to know what was the "detective" work and the fabulous luck - the whole story of the discovery of the location of the gene.</p>
| [
{
"answer_id": 16375,
"pm_score": 4,
"text": "<p>A Google search for \"Huntingtons disease gene discovery\" yielded <a href=\"http://www.nature.com/scitable/topicpage/huntington-s-disease-the-discovery-of-the-851\" rel=\"noreferrer\">this page</a> at the Nature Education Scitable website. The following ... | [
{
"answer_id": 16374,
"pm_score": 1,
"text": "<p>It was fascinating because Huntington himself described what we now call genetics before the field existed. Then to locate the gene scientists used essentially trial and error. They took enzymes that cut different parts of the DNA and looked at which of t... |
16,385 | <p>Although farmers appear to be able to tell their cows apart, cows look very much alike to me. And this similarity in appearance seems to be a general trait across the animal kingdom: one individual of one animal species looks much like another.</p>
<p><strong>Why do human facial and body shapes vary so much?</strong></p>
<p>I understand that human beings live in many different environments (e.g. hot and cold) and have adapted to these (e.g. through lighter or darker skin color), but there seems to be much variation that has no apparent evolutionary purpose. So does the difference have a purpose in itself? That is, did we evlove to vary in appearance, and what is the purpose of this variation?</p>
| [
{
"answer_id": 16387,
"pm_score": 4,
"text": "<p>There is a substantial variation in some human traits: hair colour, eye colour, height, weight, skin colour, build etc. etc. <strong>HOWEVER</strong> there is also considerable variation within other species, to suggest otherwise is naive (though quite co... | [
{
"answer_id": 51272,
"pm_score": 1,
"text": "<p>The answer by rg255 suggests that individual differences are the result of adaptation or genetic drift. That is, humans look different, because they lived in different circumstances.</p>\n<p>While this may explain different skin colors (adaptation to diff... |
16,404 | <p>There are reactions with large Delta G negative values. Why these reactions are irreversible? As in: out of 10 steps of Glycolysis, 3 are irreversible steps. I need an explanation for why they are irreversible.</p>
| [
{
"answer_id": 16405,
"pm_score": 4,
"text": "<p>The term \"irreversible\" means that the reverse reaction occurs so rarely that it is considered negligible. This means that you do not have to consider equilibrium, as you have to for reversible reactions. Instead, you can assume that all of the reactant... | [
{
"answer_id": 21368,
"pm_score": 1,
"text": "<p>Whether a reaction is reversible or irreversible, in the presence or absence of an enzyme, is not related to activation energy. An enzyme lowers activation energy in both directions.</p>\n\n<p>A reaction is reversible or irreversible depending on the cond... |
16,410 | <p>Antioxidants reduce damage to tissue (by scavenging the free radicals) and thus may reduce ageing.It is known that Uric acid is a very good antioxidant.</p>
<p>People with gout have excess accumulation of uric acid.</p>
<p>Considering the above information the authors of the book "Why we get sick?" put up an interesting question : Do people with gout live longer ?</p>
<p>I would like to know if there are any studies done to answer the question.</p>
| [
{
"answer_id": 16413,
"pm_score": 4,
"text": "<p>In men, gout is associated with a higher risk of death from all causes. This would imply that their life expectancy is shorter. From a review by Kim et al. (<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/19026153\">1</a>):</p>\n\n<blockquote>\n <p>Among me... | [
{
"answer_id": 43334,
"pm_score": 1,
"text": "<p>The reason some gout patients live longer is beacuse they often get treated with xanthine oxidase inhibitors like allopurinol which have beneficial effects regarding vascular oxidative stress: \n<a href=\"https://www.youtube.com/watch?v=v7DL24uca_I\" rel=... |
16,418 | <p>In common lab sessions to extract DNA from strawberry or cheek cells, will there be protein contaminating the DNA extract in alcohol? If so, how can we prevent protein from precipitating out of the solution?</p>
| [
{
"answer_id": 16420,
"pm_score": 3,
"text": "<p>Yes, Ethanol can precipitate proteins during a DNA precipitation as well, although Acetone will be more efficient. Usually you do a proteinase K digest or a proteinase K digest followed by a Phenol/Chloroform extraction to avoid this problem. I was usuall... | [
{
"answer_id": 16419,
"pm_score": 0,
"text": "<p>A proteinase eg.proteinase K is usually added when extracting dna.</p>\n"
}
] |
16,431 | <p>Step 7 of the glycolysis pathway is the conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate by the action of the enzyme phosphoglycerate kinase, resulting in the production of 2 ATP molecules (per glucose). </p>
<p>This reaction has a large negative value of ΔG (-18.5 kJ/mol). If reactions having large negative value of ΔG are classed as being irreversible, then why is Step 7 of Glycolysis reversible?</p>
| [
{
"answer_id": 16434,
"pm_score": 4,
"text": "<p>The free energy change that you quote for the phosphoglycerate kinase (PGK) forward reaction is, of course, the <strong>standard free energy change</strong> (ΔG<sup>0</sup>') for the overall reaction. The standard free energy change is defined for a... | [
{
"answer_id": 16433,
"pm_score": 2,
"text": "<p>You have to look at the complete reaction including the cofactors. In general, you can drive a chemical reaction into directions which are not favorable by:</p>\n\n<ul>\n<li>removing products from the environment (if they are gaseous for\nexample or react... |
16,491 | <p>Assume a patient with previous cardial infaction which SA node not possible to activate action potential anymore.
However, SA trying to beat unsuccessfully repeatedly waisting energy.
Therefore, I thought in <a href="https://biology.stackexchange.com/questions/16490/laser-surgery-to-stop-damaged-sinus-node-from-beating">this discussion</a> about the possibility to stop Sinus node from trying to start action potential; which was deleted but the <a href="http://www.jafib.com/published/webFormat/Fisher/fisher.pdf" rel="nofollow noreferrer">article</a> about the SSS (sick SA) and remodelling is about its goal. The proposed treatment (laser ablation) of AF/AFL can backfire and cause SN (Sick Node) through remodeling. Assume there is no bypass of impulses through SA node.</p>
<ul>
<li>Can the heart still beat through AV node and bundle? Yes. </li>
<li>Do you have any evidence that [heart] can "beat" properly on just the AVN? Yes, see <a href="http://www.jafib.com/published/webFormat/Fisher/fisher.pdf" rel="nofollow noreferrer">article</a>. Short-term mechanisms where electrical/metabolic remodeling. Long-term mechanisms where irregular rhythms and complete heart block can occur because of anatomical remodeling. </li>
</ul>
<p>I want to know if these pacemakers are in series or parallel.
If they are in series, then laser operation can be dangerous to the SA node.
The series connection is however the idea which I get from many schematic drawings:</p>
<p><img src="https://i.stack.imgur.com/0XV3r.png" alt="enter image description here"></p>
| [
{
"answer_id": 16494,
"pm_score": 3,
"text": "<p>The SA node is not necessary for contraction of the heart.</p>\n\n<p>The reason that this works is exactly what you mentioned: schematics.</p>\n\n<p>They are in sequence, but within that sequence, there are multiple <strong>autonomous</strong> signal gene... | [
{
"answer_id": 16499,
"pm_score": 1,
"text": "<p><strong>Extension to Doctor Whom's clear answer.</strong></p>\n\n<p>Clearer problem</p>\n\n<blockquote>\n <p>It is debated whether the pathophysiology of IST and POTS results from\n abnormal autonomic regulation or abnormal sinus node function.</p>\n</b... |
16,531 | <p>At 10.000 BC (12 ka), we became the last of the <em>Homo</em> species on Earth. In evolutionary terms this is a very little time range to something happen, but I'm wondering anyway, in this meantime which are the most significant changes in our species? Were there any?</p>
<p>Also, I've heard something about how our body hair and nails will be gone 'soon', there's any estimation of when such a thing could happen?! </p>
| [
{
"answer_id": 16538,
"pm_score": 3,
"text": "<p><strong>Background</strong></p>\n\n<p>I'd like to start by saying that <a href=\"http://en.wikipedia.org/wiki/Phenotype\" rel=\"nofollow\">phenotypic</a> (loosely speaking phenotypic mean morphological) traits evolve because their variance in the populati... | [
{
"answer_id": 16566,
"pm_score": 1,
"text": "<p>One example of an active selection pressure's effect on human phenotype is in areas where malaria is endemic, the prevalence of sickle cell anemia is higher. Sickle cell anemia is highly protective against malaria, and less people die from sickle cell th... |
16,542 | <p>When learning about the immune response, my teacher mentioned that all the bodies B cells are present at birth, and there is one to counter every disease. But if this is the case, why should the primary response take a long time? </p>
<p>As far as I know, the primary response involves the non-specific response followed by the specific response, where APCs cause the activation of T cells resulting in clonal selection and expansion of T and B cells. The B cells then differentiate into plasma cells and produce antibodies. It results in the memory cells being produced, which can quickly reengage the specific response the next time the pathogen enters.</p>
<p>Why doesn't the body just make memory cells to begin with? As if it has already encountered every possible pathogen. I presume it is just a lack of specificity in the A level teaching, but I am curious to know what I am missing here.</p>
<p>Thanks,
Jamie</p>
| [
{
"answer_id": 16543,
"pm_score": 4,
"text": "<p>These so called virgin B-cells (becase they never had contact with their antigen) which are present in your body only have random B-cell receptors (when secreted, these are the antibodies), mostly of a relatively low binding affinity. These B-cells underg... | [
{
"answer_id": 36792,
"pm_score": 2,
"text": "<p>This is a great question, Jamie. And Chris gave an excellent answer above, describing how antibodies go through 'germinal center reactions' that improve the affinity of responding cells. However, Jamie actually brings up several concepts that are worth di... |
16,611 | <p>I'm reading <a href="http://www.jbioleng.org/content/6/1/9" rel="nofollow noreferrer">a paper</a> where the authors constructed a toggle switch that uses bidirectional <span class="math-container">$P_R/P_{RM}$</span> promoter found in the <span class="math-container">$\lambda$</span> phage. There are 3 binding sites - <span class="math-container">$O_{R1}$</span>, <span class="math-container">$O_{R2}$</span>, <span class="math-container">$O_{R3}$</span> - located between the two promoters. CI is expressed by <span class="math-container">$P_{RM}$</span> and CI dimers bind to these binding sites:</p>
<p><img src="https://i.stack.imgur.com/R3NZt.png" alt="Bidirectional lambda phage promoters" /></p>
<p>What I don't get is that <strong>CI seems to function as both an activator and a repressor of <span class="math-container">$P_{RM}$</span></strong>.</p>
<p>First, my understanding was that <span class="math-container">$P_{RM}$</span> is an inducible promoter activated by CI which also represses a constitutive promoter <span class="math-container">$P_R$</span>:</p>
<blockquote>
<p>CI is a transcriptional activator of <span class="math-container">$P_{RM}$</span>, thus producing positive feedback.</p>
<p>CI preferentially binds to <span class="math-container">$O_{R1}$</span> and <span class="math-container">$O_{R2}$</span>, repressing the constitutive promoter, <span class="math-container">$P_R$</span>.</p>
</blockquote>
<p>However, it is also stated:</p>
<blockquote>
<p>In high concentrations, CI binds to <span class="math-container">$O_{R3}$</span> and acts as a repressor to <span class="math-container">$P_{RM}$</span>.</p>
</blockquote>
<p>This seems to suggest that the CI can function either as an activator or as a repressor depending on the binding site bound; specifically, CI dimer binding to <span class="math-container">$O_{R1}$</span> and <span class="math-container">$O_{R2}$</span> will repress <span class="math-container">$P_R$</span> and at the same time activate <span class="math-container">$P_{RM}$</span>, while CI dimer binding to <span class="math-container">$O_{R3}$</span> will repress <span class="math-container">$P_{RM}$</span>. Is this correct?</p>
<p>I (a computer scientist by training) was always given the impression that a transcription factor is either inherently a repressor or an activator of a promoter, but this doesn't seem to be the case here. I would expect that e.g. CI would act as a repressor to <span class="math-container">$P_R$</span> and an activator to <span class="math-container">$P_{RM}$</span> regardless of the binding site. So why does CI binding to <span class="math-container">$O_{R2}$</span> (and <span class="math-container">$O_{R1}$</span> as well?) activate <span class="math-container">$P_{RM}$</span>, while binding to <span class="math-container">$O_{R3}$</span> represses it - why the inconsistency? Note that I'm primarily interested in this from the modeling perspective.</p>
<p>What I also don't understand is whether or not <span class="math-container">$P_{RM}$</span> promoter is inducible or constitutive (e.g. in the absence of bound transcription factors, how leaky is it)?</p>
| [
{
"answer_id": 16616,
"pm_score": 4,
"text": "<p>There's no rule that says a transcription factor must be either a repressor or an activator. The lambda repressor (CI) is in fact a repressor and activator of transcription, depending on where it is bound and to what promoter you are referring to. I know ... | [
{
"answer_id": 16613,
"pm_score": 3,
"text": "<p>I'm tempted to say, \"It's complicated.\"</p>\n\n<p>CI does indeed act as both a repressor and activator. Transcription regulation in the lambda bacteriophage is quite complex for such a small system, so some confusion is understandable. Lewis et al. give... |
16,643 | <p>This is mostly a question about usage. </p>
<p>There is a probability-related idea that has been used in at least two biological contexts. The idea is that if something happened, it was <em>probably</em> likely to do so. </p>
<p>This has been used in discussions about evolution, in which it is said that while we have trouble imagining circumstances in which self-replicating forms arise, the odds were probably in favor of their emergence when it actually occurred. And in discussions of the existence of intelligent life--it may be prevalent if we make the somewhat natural assumption (among others) that our own emergence was not highly improbable, given the existence of a suitable planet and so on. </p>
<p>Is there a name for this principle? I am familiar with the idea in the context of probability but have thought of it as an 'argument from likelihood' in biology. Also if there is a good description of the idea in a biological context a reference would be appreciated. </p>
<p>The tag is a little arbitrary. Thanks for any suggestions. </p>
| [
{
"answer_id": 16656,
"pm_score": 3,
"text": "<p>It may also be called as Idea of maximum parsimony. It is used in phylogenetics to construct phylogenetic trees which require the least number of evolutionary events.</p>\n"
}
] | [
{
"answer_id": 16653,
"pm_score": 1,
"text": "<p>The principle of least effort / path of least resistance fit pretty well: animals, people, and systems (like evolution or a mechanical system like a machine) will naturally choose the path of least resistance or effort. The principal applies to chemistry ... |
16,673 | <p>I keep reading about how primers are useful in pcr -- they allow you to select a specific dna region. Similarly, in NGS or Sanger sequencing they give you a starting point. The primers I see are about 20-30 bases long.</p>
<p>However, how were the first primers developed? Somewhere, someone needed to come up with a 20-base sequence that bound to a specific part. Aren't there 4^20 such combinations? That's a lot of potential options to test.</p>
<p>How was that done?</p>
| [
{
"answer_id": 16677,
"pm_score": 5,
"text": "<p>The MIT synthetic chemist <a href=\"https://en.wikipedia.org/wiki/Har_Gobind_Khorana\" rel=\"noreferrer\">Gobind Khorana</a> won the 1968 Nobel Prize in Chemistry for his work which successfully was able to make chains of Ribonucleic acids. The chemistry... | [
{
"answer_id": 16714,
"pm_score": 2,
"text": "<p>The process of sequencing was, and can be, assisted by cloning a DNA fragment into a known site in a plasmid designed to help sequencing. That cloning site is flanked by a known sequence(s) that can use standard primers<br>\n<img src=\"https://i.stack.img... |
16,700 | <p>I'm using Alconox powder detergent to clean my laboratory glassware, the powder is a pain to store near the sink and to use. Would like to make a concentrated liquid to use in its stead. </p>
<p>I have tried a few things, obviously just water and mixing, even up to overnight. It really doesn't go into solution very well, even at seemingly low concentrations. Ive got it up to about 20% w/v but I've tried heat, glycerin, adjusting pH to ~8.8, adding EDTA. I have not added these things in any scientific way, just kind of pouring glycerol or EDTA in. </p>
<p>Wondering if anyone in here has experience with detergents like this , or has done something like this before. Thanks in advance!</p>
| [
{
"answer_id": 57873,
"pm_score": 3,
"text": "<p>If you're just using it for hand washing, you probably don't need an ultra-concentrated solution. A very small amount of detergent goes a long way. (Think about it - what would you do with an ultra-concentrated solution? Probably squirt a small amount on ... | [
{
"answer_id": 21581,
"pm_score": 2,
"text": "<p>In our labs we just use something like palmolive or bleach followed by a 95% EtOH rinse and finally rinsing with DI water.</p>\n"
}
] |
16,701 | <p>I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've been looking at Chip Seq data. But to make sense of the Chip Seq data I wish to understand how the experiment is first performed. </p>
<p>Basically my question relates to step 1 of the following diagram:
<img src="https://i.stack.imgur.com/ocBEJ.jpg" alt="enter image description here"></p>
<p>Now my main question is <strong>how come the reads are overlapped?</strong> Where did we get so many of the (almost the) same reads? </p>
<p>My "understanding" is that:</p>
<p>1) They take a DNA sequence and crosslink the protien of interest. Then they get rid of the DNA sequence surrounding this area of interest so now we have a "small" sequence of DNA and in this small DNA is somewhere where our TF binds. Now we make copies of this small DNA seq and run it through a sequencing machine. Is this correct?</p>
<p>2) They take a bunch of cells = bunch of DNA sequences. Then they do the same procedure above (by crosslinking and getting a "smaller" DNA sequence of interest). Since they had many cells to begin with, this means they had many DNA seq to begin with. Now they shear the DNA seq and we have fragments. Then we align these up with the reference genome.</p>
| [
{
"answer_id": 16706,
"pm_score": 4,
"text": "<p>The basic steps of ChIP-Seq are:</p>\n\n<ol>\n<li>Crosslinking proteins to DNA - this fixes the proteins in their natural positions</li>\n<li>Nuclease digestion - this removes regions that are unbound to protein; nucleases are sterically hindered from dig... | [
{
"answer_id": 16702,
"pm_score": 3,
"text": "<p>So that's not quite how ChIP-Seq (Chromatin ImmunoPrecipitation and Sequencing) works. First, you start out with a large number of cells per sample (preferably on the order of 10<sup>7</sup> or more - the more sample, the more <a href=\"http://en.wikipedi... |
16,715 | <p>I understand that when naive B cells are exposed to antigens, they become memory B cells, but what is the functional difference between the two? I've looked at the quite a few article on B cells, but none of them stated the difference clearly enough for me to understand.</p>
| [
{
"answer_id": 16716,
"pm_score": 3,
"text": "<p>The main difference is that memory B cells start an immune reaction much more effective and faster than naive B cells. The reaction is also specific towards the antigen.</p>\n\n<p>The memory B cell has a specific membrane receptor for an antigen. It produ... | [
{
"answer_id": 17894,
"pm_score": 0,
"text": "<p>Naive B cells have not yet been trained by the immune system to recognize specific antigens -therefore the term \"naive\". Prior to antigen exposure, they must be trained in the bone marrow to recognize certain antigens.</p>\n\n<p>Memory B cells, on the o... |
16,721 | <p>I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package. </p>
| [
{
"answer_id": 16716,
"pm_score": 3,
"text": "<p>The main difference is that memory B cells start an immune reaction much more effective and faster than naive B cells. The reaction is also specific towards the antigen.</p>\n\n<p>The memory B cell has a specific membrane receptor for an antigen. It produ... | [
{
"answer_id": 17894,
"pm_score": 0,
"text": "<p>Naive B cells have not yet been trained by the immune system to recognize specific antigens -therefore the term \"naive\". Prior to antigen exposure, they must be trained in the bone marrow to recognize certain antigens.</p>\n\n<p>Memory B cells, on the o... |
16,731 | <p>This is from SAT subject biology test practice question. The answer it gave me was both chiasmata and centromeres. I can understand they are held by chiasmata but why also centromeres? I looked it up, I didn't find anywhere mentioned that they are held by centromeres also, only synaptonemal complex and chiasmata. </p>
<p>tetrads are truly held by spindle fibers on centromeres too, but isn't the question asking what hold them together? Even without spindle fibers, they can still be held by chiasmata I guess.</p>
| [
{
"answer_id": 16716,
"pm_score": 3,
"text": "<p>The main difference is that memory B cells start an immune reaction much more effective and faster than naive B cells. The reaction is also specific towards the antigen.</p>\n\n<p>The memory B cell has a specific membrane receptor for an antigen. It produ... | [
{
"answer_id": 17894,
"pm_score": 0,
"text": "<p>Naive B cells have not yet been trained by the immune system to recognize specific antigens -therefore the term \"naive\". Prior to antigen exposure, they must be trained in the bone marrow to recognize certain antigens.</p>\n\n<p>Memory B cells, on the o... |
16,749 | <p>What feature of rabies pathophysiology causes hydrophobia? Why is hydrophobia unique to this one particular type of viral infection? </p>
| [
{
"answer_id": 16750,
"pm_score": 5,
"text": "<p>Rabies causes hydrophobia in the encephalitic stage which means when it affects the brain and causes swelling and inflammation of multiple areas of the brain. Hence, it affects the complex areas in the brain needed for swallowing. Initially into the cours... | [
{
"answer_id": 57437,
"pm_score": 3,
"text": "<p>No doubt, the selected answer is sufficient for the question. But for the ones more interested in citations, here is a more credible answer.</p>\n\n<p>When the rabies virus attacks someone, it begins with muscle cells, so that it is not detected by the ho... |
16,776 | <p>I'm programming an implementation of an algorithm for pattern matching in RNA structures.
The algorithm assumes the following types of base pairs:</p>
<ul>
<li><em>Plain</em>: No base pairs (just the primary structure of the RNA)</li>
<li><em>Single</em>: Each base can be connected to at most one other base</li>
<li><em>Multiple</em>: Each base can be maximally connected to a number of other bases (where 'number' can be constant or infinite)</li>
</ul>
<p>Although there is no problem with the implementation of the above types of base pairs (apart from the probable high computation complexity), I wonder if all of them were observed in real RNAs?</p>
<p>In particular, I'm interested in the following cases:</p>
<ul>
<li>A base pair between two <strong>adjacent</strong> bases i,j.</li>
<li>One base (i) which connected to two different bases (j,k) (i is not adjacent to j or/and k).</li>
<li>One base (i) which connected to more than two different bases, all of them not adjacent to i.</li>
</ul>
<p>Can these exist? Some of them?
If they can, how common is their existence?</p>
| [
{
"answer_id": 16796,
"pm_score": 2,
"text": "<blockquote>\n <p>A base pair between two adjacent bases i,j.</p>\n</blockquote>\n\n<p>It is not possible. To form an intramolecular hydrogen bond, the RNA has to bend. The persistence length i.e. the minimum length of the chain required for bending, is aro... | [
{
"answer_id": 16777,
"pm_score": 2,
"text": "<p>By far the most common type of base pair is the Watson-Crick base pair in an RNA helix. Those are comparably easy to predict, e.g. Mfold and the Vienna RNA package can do this.</p>\n\n<p>Base triples, three nucleobases that form hydrogen bonds to each oth... |
16,813 | <p>As I know evolution comes bit by bit mutation by mutation</p>
<p><strong>How sex evolved which requires a major change in at least two individuals one to become male and one to become female ?</strong></p>
<p>When that happened as we can see sex in all animals and most plants? </p>
| [
{
"answer_id": 16878,
"pm_score": 3,
"text": "<p>Sex (depending on how you define it), evolved very early (more than a billion years ago). Even species like yeast have a type of \"sex\" (see below).</p>\n\n<p>Also, this doesn't mean there is necessarily a big difference between the two sexes.</p>\n\n<p>... | [
{
"answer_id": 16988,
"pm_score": 2,
"text": "<p>The oldest evidence we have of sex comes from the fossil record which shows it was present more than <a href=\"http://paleobiol.geoscienceworld.org/content/26/3/386.abstract\" rel=\"nofollow\">one billion years ago</a> - it could be even longer (it would ... |
16,821 | <p>I recall reading about a 20th century scientist who made a life-saving drug that could have patented it and made millions. He chose not to and saved the lives of millions around the globe. </p>
<p>I thought it was <a href="http://www.scienceheroes.com/index.php?option=com_content&view=article&id=80&Itemid=115" rel="nofollow">Frederick Banting</a> - but it doesn't sound quite right. </p>
<p>None of the others <a href="http://www.scienceheroes.com/index.php?option=com_content&view=article&id=258&Itemid=232" rel="nofollow">in this list</a> seem quite right. </p>
<p>My question is: <strong>What is the name of scientist who discovered lifesaving drug and chose not to patent it?</strong></p>
| [
{
"answer_id": 16823,
"pm_score": 4,
"text": "<p>Dr Jonas Salk or Dr Albert Sabin who did not patent their respective polio vaccines. There are some more such researchers so I am not sure who exactly you are looking for but this would be a start. </p>\n"
}
] | [
{
"answer_id": 16829,
"pm_score": 2,
"text": "<p>You could've been thinking correctly. Banting did patent insulin but felt it was unethical to profit from such a critical drug. He sold the patent for a dollar to a (now nonexistent) pharmaceutical company.</p>\n"
}
] |
16,844 | <p>As far as I know, roots of plants grow to the direction of Earth's gravity - this is called gravitropism.</p>
<p>But what happens if plants are in space? Are they able to perceive gravity in state of weightlessness? Either way, where do they grow their roots in those circumstances?</p>
<p><em>Note: this question may fit better either to Space.SE or to Astronomy.SE, but I was not sure about it.</em></p>
| [
{
"answer_id": 16853,
"pm_score": 3,
"text": "<p>Astronomers on the International space station have done exactly that and grown Arabidopsis Thaliana in space. You can read the whole article <a href=\"http://news.nationalgeographic.co.in/news/2012/121207-plants-grow-space-station-science/\" rel=\"nofoll... | [
{
"answer_id": 16884,
"pm_score": 0,
"text": "<p>Roots are negatively phototropic in addition to being positively gravitropic. Both growth patterns are mediated by the same hormone, auxin. Removing one factor or the other will not prevent roots from growing \"down.\"</p>\n"
}
] |
16,870 | <p>I was wondering if a neuron can make a synapse to itself? I suspect that it would be extremely unusual for a neuron to do this. Anyway, has anyone seen even a single instance of this?</p>
<p>Is the process by which a neuron 'knows' not to make a synapse onto itself is known?</p>
| [
{
"answer_id": 16875,
"pm_score": 5,
"text": "<p>A synapse from a neuron unto itself is called an <a href=\"http://en.wikipedia.org/wiki/Autapse\">Autapse</a>. Not a whole lot is known about them. Tamas et al. (<a href=\"http://en.wikipedia.org/wiki/Autapse\">1</a>) give a summary:</p>\n\n<blockquote>\n... | [
{
"answer_id": 16909,
"pm_score": 3,
"text": "<p>There isn't enough research out there to explain the role of autapses however having read a selection of the latest research I can perhaps explain some of the proposed theory. Autapses may self inhibit or self excite. In the latter, one of their roles is ... |
16,887 | <p>I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. Any explanation is appreciated. </p>
| [
{
"answer_id": 17336,
"pm_score": 3,
"text": "<p>Chimeric sequences show up in sequencing projects a lot and you always have to watch for them. They show up a lot for a couple of reasons.</p>\n\n<p>Firstly, sequencers are not perfect and generate sequences with errors. Also they produce a lot of data b... | [
{
"answer_id": 17314,
"pm_score": 0,
"text": "<p>My understanding of chimeric sequences is that they are produced as the result of inserting two different cDNAs (usually from different species) into a backbone such as pUAST to make a protein that is partly from one species and partly from another specie... |
16,905 | <p>I have noticed that if you look directly at tubelight (I have only white ones in my home) and close your eyes little, you see little random shaped colourless things sometimes with slow speed and sometimes with falling down. </p>
<p>They are shaped like circles with something in between and in chains of random length. </p>
<p>My father has also seen them. So, I am sure I am not imagining things. What the hell are they?</p>
| [
{
"answer_id": 16906,
"pm_score": 5,
"text": "<p>Those are <a href=\"http://en.wikipedia.org/wiki/Floater\" rel=\"noreferrer\">floaters</a>. These are objects floating in the vitreous humour that fills the eyeball. They typically look like:</p>\n\n<p><img src=\"https://i.stack.imgur.com/c4K1H.png\" alt=... | [
{
"answer_id": 55131,
"pm_score": 1,
"text": "<p>In <a href=\"https://en.wikipedia.org/wiki/Blue_field_entoptic_phenomenon\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wiki/Blue_field_entoptic_phenomenon</a> this phenomenon is explained with white blood cells in your retina.</p>\n"
}
] |
16,953 | <p>How are two species with similar phenotypes identified as different? Have two different individuals that were thought to be different species ever been determined to be from the same species ( or one a subspecies of the other's species ) ?</p>
| [
{
"answer_id": 16960,
"pm_score": 4,
"text": "<p><strong>Species are difficult to define.</strong> This is because they form over a gradual continuous spectrum via evolution, one species does not suddenly become two, but lineages diverge (perhaps because there is some kind of barrier - like a mountain r... | [
{
"answer_id": 16954,
"pm_score": 1,
"text": "<p>Genotypes are used to differentiate when phenotypes are identical. In Bacteria the 16S rRNA sequence is particularly useful in helping to identify which population is present in what percentage. In fungal its ITS and in mammals its 18S. </p>\n"
}
] |
16,972 | <p>A friend told me, during a 3 minute discussion, that viruses that are endemic in host $A$ and make repeated jumps to host $B$ but can't be transmitted between individuals of species $B$, may slowly adapt (through these repeated jumps) to be able to be transmitted between individuals of host $B$ and become epidemic.</p>
<p>I don't know much about epidemiology. I don't understand how a virus population that is endemic to host $A$ may adapt to host $B$ with repeated jumps while the viruses that jump to host $B$ are dead end because they cannot be transmitted further more. Or Are these viruses able to jump back to host $A$ to bring back their newly acquired adaptations to host $B$?</p>
<p>Also, I might misunderstand the meaning of "repeated host jumps transmission". I first thought it meant repeated jumps from a reservoir population in host $A$ to host $B$, but it is also possible that it describes the dynamic of a virus population that is adapted to jump from species to species and they actually gain this ability by keeping jumping and jumping. But then, how could a virus species get adapted to jump from species to species? I'm a bit confused…. Can you give me some hints about this process of cross-species transmission through repeated jumps?</p>
| [
{
"answer_id": 17004,
"pm_score": 3,
"text": "<blockquote>\n <p>A friend told me, during a 3 minute discussion, that viruses that are\n endemic in host A and make repeated jumps to host B but can't be\n transmitted between individuals of species B, may slowly adapt\n (through these repeated jumps) t... | [
{
"answer_id": 16980,
"pm_score": 2,
"text": "<p>A quick answer for now (I'll add details as I find):</p>\n\n<p>The infection of <strong>B</strong> from <strong>A</strong> would be zoonosis. This transfer may not have followed a classical route of infection. For example the case of hantavirus pulmonary ... |
16,987 | <p>How does the ebola virus attack and how do some people get away with it? Normally any virus would attack a cell with some kind of receptors and some kind of lock and key mechanism entering the cell and then multiplying.</p>
<p>What happens to the virus if a person manages to live through it, does the virus die and is thrown out or still remains inside the host?</p>
<p>I am not sure about a normal virus attack i tried to explain please correct on that also.</p>
| [
{
"answer_id": 16989,
"pm_score": 5,
"text": "<p>It is known that Ebola uses at least one cholesterol transporter called \"Niemann-Pick C1\" (NPC1) to enter its host cells. Cells with a mutated form of this transporter were not infected by the virus (this extends to other viruses from the Filovirus grou... | [
{
"answer_id": 23479,
"pm_score": 2,
"text": "<p>Ebola enters the cells most probably using the <a href=\"http://en.wikipedia.org/wiki/NPC1\" rel=\"nofollow\">NPC1 receptor</a>, which is expressed by all cells. That receptor is important by other viruses as well e.g. by <a href=\"http://en.wikipedia.org... |
17,001 | <p><a href="http://en.wikipedia.org/wiki/Virophage">Wikipedia</a> states "Virophages are satellite viruses that inhibit or impair the reproduction of the auxiliary virus." </p>
<p>Is it theoretically possible for a virophage that doesn't hurt the human body to attach itself to a more serious virus like the AIDS virus for example and be used to wipe out the virus, or at least inhibit it's reproduction? I'm completely ignorant of the virophage relationship, so feel free to inform me as needed. </p>
| [
{
"answer_id": 17003,
"pm_score": 4,
"text": "<p>There are few enough virophages occurring in nature that I don't know if there's a clear and compelling case for them being potentially therapeutic.</p>\n\n<p>In <em>principle</em> however, the answer is yes, though they may suffer from the same problems ... | [
{
"answer_id": 17006,
"pm_score": 2,
"text": "<p>In theory it should be possible, though this approach seems to be limited by the nature of the virophages known today. They seem to \"infect\" (this is actually wrong, since they take use of some of the proteins produced by the mama virus and do not infec... |
17,026 | <p>Has there ever been incidences of one or more cancerous cells having all it's cell-death pathways and apoptosis mechanisms intact and functional?</p>
| [
{
"answer_id": 17028,
"pm_score": 4,
"text": "<p>Usually the cell death mechanisms are overridden and therefore oncogenesis. The pathway components themselves are not mutated. One classical case I can cite is that of Ras-oncogene. See this <a href=\"http://cancerres.aacrjournals.org/content/72/10/2457.l... | [
{
"answer_id": 17027,
"pm_score": 2,
"text": "<p>This is pretty unlikely, since one of the most important steps for cancer cells is to shut off apoptosis and proteins which control it (like p53, BCL2 and so on). Cancer cells (especially when they are genetically unstable) acquire so much mutations and m... |
17,041 | <p>I have a question, maybe a naive one.</p>
<p>Let's assume that we isolated some RNA from a tissue. Do RNA molecules can bind each other if they have the complementary sequence? I know that some small RNA molecules can bind other RNAs and regulate them but I do not know it is possible in this case? It is like 2 different mRNA can bind each other or not?</p>
| [
{
"answer_id": 17042,
"pm_score": 3,
"text": "<p>The difference between RNA and DNA is rather small, and both can form a double-helix structure. So if you had two sequences of RNA complementary to each other they would basepair and form a helix.</p>\n\n<p>There were also some ideas to use this for thera... | [
{
"answer_id": 17043,
"pm_score": 2,
"text": "<p>@MadScientist answer is very good. I just want to add a detail that could not fit in a comment.</p>\n\n<p>Double stranded RNA is nothing exceptional. You can see an RNA strand that binds to its antisense in <a href=\"http://en.wikipedia.org/wiki/Transfer_... |
17,055 | <p>Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome?</p>
<p>How much of this is 'junk-DNA' (non-coding)?</p>
| [
{
"answer_id": 17069,
"pm_score": 3,
"text": "<p>You asked about eukaryotes. The genome of the yeast <em>Saccharomyces cerevisiae</em> is 12.2 Mb.</p>\n\n<p>The genome of the smallest free-living eukaryote, <em>Ostreococcus tauri</em> (a unicellular green alga) <a href=\"http://www.pnas.org/content/103/... | [
{
"answer_id": 17066,
"pm_score": -1,
"text": "<p>According to this:\n<a href=\"http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html\" rel=\"nofollow\">http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html</a>\nThe shortest DNA of a individually living cell is th... |
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