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gene expression | Bioinformatics : Drawbacks of using ORA(Overlap Analysis) | https://biology.stackexchange.com/questions/15058/bioinformatics-drawbacks-of-using-oraoverlap-analysis | <p>What do you think are the potential drawbacks/weakness of using ORA to explain distinction between two phenotypes.</p>
<p>I identified a few which were the dependencies of DE and the statistical method used to filter the starting DE list.</p>
<p>Any other weakness?</p>
<p>Thanks</p>
| <p>It really depends on the specific methods you're using. If you're using a pathway-based methodology, I'd strongly recommend reading Khatri et al (2012) (<a href="http://www.ploscompbiol.org/article/info%3adoi/10.1371/journal.pcbi.1002375" rel="nofollow" title="Khatri et al (2012)">1</a>), which provides a go... | 34 |
gene expression | Is the regulation of lactose operon different between Gram + and Gram -? | https://biology.stackexchange.com/questions/15125/is-the-regulation-of-lactose-operon-different-between-gram-and-gram | <p>I know that in E. coli the lactose operon is shut down by CAP protein when binding cAMP. Is this true also for Gram positive bacteria?</p>
| <p>I know it's stupid but I answer my own question, for those who are interested.
It is different. CAP protein regulates lactose operon only in Gram -. In Gram + the presence of glucose shuts down the operon with another mechanism: the TCRS that relies to concentration of fructose 1,6 phosphate.</p>
| 35 |
gene expression | What is the significance of and biological mechanisms demonstrated in lac operon? | https://biology.stackexchange.com/questions/15406/what-is-the-significance-of-and-biological-mechanisms-demonstrated-in-lac-operon | <p>I would appreciate it someone could explain clearly how the genes in the <a href="http://en.wikipedia.org/wiki/Lac_operon" rel="nofollow"><em>lac</em> operon of E coli</a> are activated to allow the bacteria to metabolize lactose? </p>
<p>The part that I really don't understand is the activation of the lac operon. ... | <p>The <em>lac</em> operon in E coli is a set of four genes which work together to allow the bacterium to make use of lactose for energy. An <a href="https://en.wikipedia.org/wiki/Operon" rel="nofollow noreferrer">Operon</a> is a set of genes which are co-transcribed on a single mRNA, controlled from a common promoter.... | 36 |
gene expression | Is it possible to elicit transient gene silencing by using virus induced gene silencing (VIGS) in plants? | https://biology.stackexchange.com/questions/15648/is-it-possible-to-elicit-transient-gene-silencing-by-using-virus-induced-gene-si | <p>I am looking for a molecular tech' which could result in transient gene silencing in plants. The objective is to not make transgenic plant, but to use these tech' to silence a gene of interest for a short time. From my limited knowledge, I found that virus induced gene silencing (VIGS) may be an option, I wonder how... | <p>Virus induced gene silencing (VIGS) is definitely an option. </p>
<p>The ease of using VIGS depends on a lot of factors. Current VIGS vectors have limited host ranges. Depending on the species of plant that you are working with, there may or may not be suitable, pre-made VIGS vectors available and published techniq... | 37 |
gene expression | Multi-modal distribution for gene expression data | https://biology.stackexchange.com/questions/27816/multi-modal-distribution-for-gene-expression-data | <p>Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly?</p>
<p>I'm referring to the expression distribution of a gene across different tissue samples. For example, if one was to download a bunch of data from NCBI GEO, and pinpoint one gene and ... | <p>One trivial situation in which this can happen is when the tissue used for expression studies is heterogeneous. Different cells express different levels of the gene. </p>
<p>Bimodality can be observed when the system can actually occupy two stable states; i.e. a gene can either have a high expression or a low expre... | 38 |
gene expression | Why are riboswitches mostly present in bacteria and not in eukaryotes? | https://biology.stackexchange.com/questions/27946/why-are-riboswitches-mostly-present-in-bacteria-and-not-in-eukaryotes | <p>Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation. </p>
<p>Most of the known riboswitches are found in bacteria, there are few examples of riboswitches in eukaryotes. There are no ... | <p>You get higher accuracy and more timely control at a post translational level (think about the time it takes to affect a pathway with cofactor stimulation compared to gene expression stimulation). You also have more points of control throughout the pathway if you affect activity post translationally allowing for a m... | 39 |
gene expression | IPTG and lac operator with e coli for foreign gene question | https://biology.stackexchange.com/questions/29751/iptg-and-lac-operator-with-e-coli-for-foreign-gene-question | <p>We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to the lac operator, which from what I've found just deals with lactose. Is there some other function that has? How can... | <p>The <a href="http://en.wikipedia.org/wiki/Lac_operon" rel="nofollow">lac operon</a> contains genes which are important for the metabolization of lactose as an energy source - normally glucose is used for this purpose. Usually the operon is tighly regulated and as long as there is another source of energy it is kept ... | 40 |
gene expression | Two heterozygote mice for skin color are reproduced. Find the probability that in 3 children 2 will be dark and one white | https://biology.stackexchange.com/questions/30028/two-heterozygote-mice-for-skin-color-are-reproduced-find-the-probability-that-i | <p>Two heterozygote mice for skin color are reproduced. Black is dominant to white color. Find the probability that in 3 children 2 will be dark and one white. How did you do the ordering. Well I found it that in F1: 1/4 are AA, 1/2 Aa, 1/4 aa or 3/4 black and 1/4 white.Now nI think I should multiply the chances: 3/4*1... | <p>You are on the right track, but you have to keep in mind there are multiple ways to have two dark and one child in a group of three. You have to add the probabilities of each unique outcome that results in two dark and one light child. So, the probability is (1/4) x (3/4) x (3/4) PLUS (3/4) x (1/4) x (3/4) PLUS (3/4... | 41 |
gene expression | What network motifs or other mechanisms can make the expression of a gene invariable to the environment? | https://biology.stackexchange.com/questions/30127/what-network-motifs-or-other-mechanisms-can-make-the-expression-of-a-gene-invari | <p>Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?</p>
| <p>This phenomenon of being insensitive to certain fluctuations is called robustness. The fluctuations can be of two kinds for an input-output device such as a gene that is activated by a signal:</p>
<ol>
<li>Fluctuations in the signal</li>
<li>Fluctuations in the intrinsic parameters</li>
</ol>
<p>Signal fluctuation... | 42 |
gene expression | Name two reasons why it is impossible to determine a gene's nucleotide sequence from the amino acid sequence of the polypeptide | https://biology.stackexchange.com/questions/30220/name-two-reasons-why-it-is-impossible-to-determine-a-genes-nucleotide-sequence | <p>I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason. </p>
| <p>I can think of at least 3 reasons in addition to the one you gave:</p>
<p>1: As mentioned in the comments, <a href="http://en.wikipedia.org/wiki/RNA_splicing">RNA splicing</a> takes place on most messenger RNA encoding proteins in eukaryotes. Sections of the mRNA may be spliced out, therefore multiple mRNAs with di... | 43 |
gene expression | Comparing gene expression levels between control and disease at different time points | https://biology.stackexchange.com/questions/30536/comparing-gene-expression-levels-between-control-and-disease-at-different-time-p | <p>I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group.</p>
<p>I want to identify the changes in expression between the two groups, however I'm having some trouble on formulating how best to do this. For... | <p>The gene expression profile may change at different time points between the two groups; you should decide what you actually want to measure. If you want to see if the diseased group is different from the control then you should compare them at every time point. For most situations you would need to compare just thei... | 44 |
gene expression | Is there a consensus on the CaMV 35S minimal promoter sequence? | https://biology.stackexchange.com/questions/34681/is-there-a-consensus-on-the-camv-35s-minimal-promoter-sequence | <p>We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely low. I heard this could be overcome by fusing it to a minimal 35S promoter fragment but I can't seem to find a clear se... | <p>In case anybody ever has the same question: I found the answer in this paper by Ow et al. 1987 (fig1)
<a href="http://www.pnas.org/content/84/14/4870.full.pdf" rel="nofollow">http://www.pnas.org/content/84/14/4870.full.pdf</a></p>
<p>Just to clarify, I did not want to boost expression of the enhancer element in my ... | 45 |
gene expression | Could fingerprints potentially be changed using a gene gun? | https://biology.stackexchange.com/questions/36738/could-fingerprints-potentially-be-changed-using-a-gene-gun | <p>Not to confuse with your "DNA fingerprint" I've read surgery is readily used to not just remove but even to change people's prints through employing very small grafts between opposing hands.</p>
<p>About 5 years ago a Chinese group identified SMARCAD1 as a key player in the development of fingerprints. this was d... | <p>Chimpanzees have fingerprints. Next all you have to do is find the homologue of SMARCAD1 and let the animal testing begin! But actually I doubt it will work. <a href="http://scienceline.ucsb.edu/getkey.php?key=2650" rel="nofollow">This</a> website goes into some depth and links some additional sources that show f... | 46 |
gene expression | Question about cutting gene in Plasmid | https://biology.stackexchange.com/questions/40140/question-about-cutting-gene-in-plasmid | <p>I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But because the plasmid already has a unc-54, I wonder if there a way that to cut the unc-54 out of the plasmid?</p>
| <p>Following the link you provided confirms that the <em>C. elegans</em> expression vector will express your insert of choice in the transgenic animals' pharyngeal muscle cells (driven by the <em>myo-3</em> promoter). </p>
<p>From examining the two images of the plasmid's restriction map on the page you linked to, I i... | 47 |
gene expression | How to Download the broadpeak files from the encode chip-seq experiment matrix? | https://biology.stackexchange.com/questions/43321/how-to-download-the-broadpeak-files-from-the-encode-chip-seq-experiment-matrix | <p>I have tried the SqlDatabase of Encode opened it trough R ,i have tried other packages in R, i have tried the ENCODExplorer package but none of them seems to do what i want. I have an app that asks the user which cell type and which antibody factor wants to choose in Shiny. These cell types and antibody targets are ... | 48 | |
gene expression | Genes that exist in old Affymetrix platform but not in the newer one | https://biology.stackexchange.com/questions/45393/genes-that-exist-in-old-affymetrix-platform-but-not-in-the-newer-one | <p>I am using two gene expression datasets from an Affy U95Av2 platform and an Affy U133 Plus 2.0 platform. When I map the Affy probe names to HUGO gene names, there are thousands of genes which exist in the newer Affy U133 Plus 2.0 dataset while not in the old Affy U95Av2 dataset, which is something expected. But ther... | <p>aI used to work at Affymetrix when most of these arrays were designed. I was not on the design team itself, but I can maybe talk about this a bit more. </p>
<p>RNA Array designs were built to cover anything that might possibly be real transcript in the mix of EST collections, cDNA, <em>in silico</em> gene detectio... | 49 |
gene expression | What do the intervals between groups of arrays in microarray gene expression data images mean? | https://biology.stackexchange.com/questions/52056/what-do-the-intervals-between-groups-of-arrays-in-microarray-gene-expression-dat | <p>This can be a dummy question, but I am not familiar with microarray experiments at all. In <a href="https://en.wikipedia.org/wiki/Binary_logarithm#/media/File:Mouse_cdna_microarray.jpg" rel="nofollow">this image</a>, what does each of 16 big squares mean, and what are the black intervals between them are? I know eac... | <p>The borders provide visual cues for the image analysis software to know which spot is which. The spots are also not printed all at once, but by a series of print heads, and the spaces allow for a small amount of error in the alignment of the print heads. It also allows for humans to more easily eyeball the results -... | 50 |
gene expression | Proteome patterns between treated and control cells | https://biology.stackexchange.com/questions/53669/proteome-patterns-between-treated-and-control-cells | <p>We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only one pair (one treated and one untreated) sample for each experiment. We want to see which proteins are differentiall... | <p>If I understand you did a treatment to some cells and compared them with non-treated ones. Instead of running the four experiments at the same time, you did one treated and one untreated at a time. Then you did proteomics for each sample. Is the treatment the same in all four experiments? </p>
<p>Edit after the fur... | 51 |
gene expression | Gene products of recessive/mutated alleles | https://biology.stackexchange.com/questions/53713/gene-products-of-recessive-mutated-alleles | <p>I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional enzyme that the dominant phenotype is present in heterozygous individuals. Will the individual have many uselessly n... | 52 | |
gene expression | Query for gene upregulation in cBioPortal | https://biology.stackexchange.com/questions/56265/query-for-gene-upregulation-in-cbioportal | <p>there! Could anyone help me with some biostatistical problems using cBioPortal.</p>
<p>We are looking for cell lines with upregulation of certain genes on cBioPortal. My supervisor is teaching me to use this website because I have no prior experience. She is using EXP >= 0.5 to define upregulation. Although I am of... | <p>Well, I have worked with expression patterns. Unfortunately there is no clear cut or magical numbers for cutoffs . I agree with you that 0.5 is not stringent. However, to explore data usually one can parse it using lower cutoffs and later on you can rise the bar to see what happens. </p>
| 53 |
gene expression | Validation of houskeeping genes in a mixture of cDNAs of two species | https://biology.stackexchange.com/questions/57867/validation-of-houskeeping-genes-in-a-mixture-of-cdnas-of-two-species | <p>I have a parasite sample (mixed with host blood) and I need to check gene expressions of parasite using relative quantification (RT_qPCR). For this, I need a good housekeeping gene. I chose 10 genes (suggested as housekeeping) that I need to validate and after choose the most stable one(s). My problem is that my par... | <p>Two possibilities:</p>
<ol>
<li><p>Design primers based on differences in the sequences of the gene for the same protein between the two organisms. (Suggested by @Artem)</p></li>
<li><p>Identify an aspect of the metabolism of your parasite that is not present in the host, then use enzymes from that pathway. If the ... | 54 |
gene expression | Overexpression by integration of an additional copy vs promoter exchange | https://biology.stackexchange.com/questions/68586/overexpression-by-integration-of-an-additional-copy-vs-promoter-exchange | <p>In <a href="http://www.sciencedirect.com/science/article/pii/S1096717611000048" rel="nofollow noreferrer">Becker et al (2011)</a>, the authors increase the expression of several genes through different methods. For some genes (e.g., <em>lysA</em>, <em>ddh</em>), they achieve overexpression by integrating an addition... | <p>Modifying promoters can give finer, more targeted control of expression than changing copy numbers. In the <a href="http://www.sciencedirect.com/science/article/pii/S1096717611000048" rel="nofollow noreferrer">paper you referenced</a>, for the <em>ddh</em> gene, it sounds like they just wanted to boost production of... | 55 |
gene expression | Question: What is CINWntUp and CINnormL? | https://biology.stackexchange.com/questions/78814/question-what-is-cinwntup-and-cinnorml | <p>What is CINWntUp and CINnormL?</p>
<p>I read a paper that uses this two things as classes but Im not sure what they represent. I imply that CIN is referring to Chromosomal instability but I don't know what WntUp & normL refer to. (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214593/" rel="nofollow nor... | <p>From the paper:</p>
<blockquote>
<p>The dataset contains six colon cancer subtypes: class 1 = CINImmune-Down (116 samples), class 2 = dMMR (104 samples), class 3 = KRASm (75 samples), class 4 = CSC (59 samples), class 5 = CINWntUp (152 samples), and class 6 = CINnormL (60 samples).</p>
</blockquote>
<p>CINWntUp ... | 56 |
gene expression | What are mutator genes which cause copying errors in other genes? | https://biology.stackexchange.com/questions/80205/what-are-mutator-genes-which-cause-copying-errors-in-other-genes | <p>Reading Dawkins' book "The Selfish Gene," I came across this line: "There are even genes--called mutators--that manipulate the rates of copying errors in other genes." (The context is his argument that such a gene is looking out for its best interest by killing off the competition.)</p>
<p>What are these "mutator" ... | <p>Most obvious examples are the genes directly involved in <a href="https://en.wikipedia.org/wiki/DNA_mismatch_repair" rel="nofollow noreferrer">DNA mismatch repair (MMR)</a> such as <a href="https://en.wikipedia.org/wiki/MSH2" rel="nofollow noreferrer">mutS</a>, <a href="https://www.uniprot.org/uniprot/P23367" rel="n... | 57 |
gene expression | Is there a difference between "genetic cross regulation" and "crosstalk"? | https://biology.stackexchange.com/questions/89607/is-there-a-difference-between-genetic-cross-regulation-and-crosstalk | <p>What is the difference between genetic cross regulation and crosstalk? I'm a physics major and learning about bioinformatics now. So it might seem trivial to many but from the article "<a href="https://jb.asm.org/content/jb/174/7/2053.full.pdf" rel="nofollow noreferrer">Wanner BL. Minireview. Is cross regulation by ... | 58 | |
gene expression | Mutated and unmutated PCR product | https://biology.stackexchange.com/questions/92719/mutated-and-unmutated-pcr-product | <p>If I have a mutated colony containing the fusion protein, mCherry instead of the stop codon TAA, and an unmutated colony which does not contain the protein. Why will the PCR products of the two colonies have the same size?</p>
<p>I thought that since the mutated colony contains the protein instead of the stop codon... | <p>If mCherry was successfully cloned replacing the stop codon, you would indeed expect a fusion protein that is about 27 kDa larger than the original protein.
However, with a PCR you are not testing for the full length protein, but rather for a part of the target gene sequence. </p>
<p>The length of the PCR product ... | 59 |
gene expression | What is a good book to start with if I'm interested in Gene clustering analysis? | https://biology.stackexchange.com/questions/100285/what-is-a-good-book-to-start-with-if-im-interested-in-gene-clustering-analysis | <p>As a beginner, I would like to learn more about gene clustering analysis, namely discovering groups of correlated genes potentially coregulated or associated to some conditions or finding patterns in gene expression data, identification of coexpressed genes from microarray data.</p>
<p>I was looking up for some book... | 60 | |
gene expression | Relative abundance of transcription factors and protein kinases | https://biology.stackexchange.com/questions/101511/relative-abundance-of-transcription-factors-and-protein-kinases | <p>Are transcription factors and protein kinases only expressed at low levels in eukaryotes?</p>
<p>As regulatory proteins, I would expect their abundance to be lower than most other proteins, but I cannot find any published research to support that.</p>
| <p><strong>Summary</strong>
<br>
The abundance of protein kinases and transcription factors vary among and between these broad classes of protein.</p>
<p><strong>General Considerations</strong>
<br>Let us first think what might be expected for the abundance of transcription factors and protein kinases.<br>
<em>Protein ... | 61 |
gene expression | Can proteins structure change depending of alimentation of an organism? | https://biology.stackexchange.com/questions/67565/can-proteins-structure-change-depending-of-alimentation-of-an-organism | <p>In my understanding protein are built using information caring by RNA. So a given protein should always have the same structure in a given organism has the DNA of this organism does not change.</p>
<p>I'm asking this question because peoples told me that "cow milk protein become longer because how we feed them ... | <p>While it is theoretically possible for a protein to change size (based on length) because of nutrition, I don't think that's happening here. </p>
<p>You are right-- DNA encodes information that is transcribed to RNA which is translated into proteins. Proteins are made of a finite number of amino acids, which are th... | 62 |
gene expression | What does it mean that the transcript is enriched? | https://biology.stackexchange.com/questions/89180/what-does-it-mean-that-the-transcript-is-enriched | <p>I think I don't get the meaning of "enriched" in the context of genes.
What's the difference of gene being "enriched" and "expressed" in the cell?</p>
| <p>In the context of transcriptomics the term 'enrichment' is usually connected to differential analysis:</p>
<ul>
<li>If a transcript (or some/all transcripts of a gene) are detected in a given sample that transcript is <em>expressed</em></li>
<li>If a transcript is detected at (statistically significant) higher leve... | 63 |
gene expression | PCR for gene expression | https://biology.stackexchange.com/questions/109015/pcr-for-gene-expression | <p>Could somebody please explain the basic principle behind how qPCR can detect if a gene is expressed or not? I tried looking at literature on ScienceDirect and other websites but I could not find any information. I understand what qPCR is supposed to do - amplify a target DNA and provide numbers for the resulting DNA... | <h2>What is qPCR? What's the central concept?</h2>
<p>qPCR (or more stringently, qRT-PCR, a term that is less ambiguous) usually refers experiments which use <strong>quantitative polymerase chain reactions</strong> to quantitate (measure) gene expression in real time ("RT"), and when the source material is RN... | 64 |
gene expression | One flybase gene number (FBgn), many Affymetrix Id's | https://biology.stackexchange.com/questions/7646/one-flybase-gene-number-fbgn-many-affymetrix-ids | <p>I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the <a href="http://flybase.org/static_pages/downloads/bulkdata7.html" rel="nofollow">Flybase file</a> required to do so (as described <a href="http://flybase.org... | <p>I can answer this - I may not have time to dig though the file you are pointing to... but here's some explanation - lmk if you need more. </p>
<p>The shorter names (123456_at) are the original names for the probe sets that Affymetrix gave. The file you area asking about has been extended for FlyBase's purpose and... | 65 |
gene expression | water stress expression markers in arabidopsis thaliana | https://biology.stackexchange.com/questions/14980/water-stress-expression-markers-in-arabidopsis-thaliana | <p>So far I found papers that show studies using RNA arrays on whom they categorized water stress gene markers in root. Water stresses were reproduced by different protocols (manitol...) but always on several week old plants. Does anyone know any study carried on young (6 days more or less) arabidopsis thaliana plants?... | 66 | |
gene expression | Word denoting genetic state | https://biology.stackexchange.com/questions/23822/word-denoting-genetic-state | <p>Is there a single word, or brief phrase, that denotes the state of the total genetic machinery (genome + transcriptome + proteome + ...) of a cell or organ or organism at a particular point in time?</p>
| 67 | |
gene expression | Why people fear GMOs? Can't we map a plant composition? | https://biology.stackexchange.com/questions/29875/why-people-fear-gmos-cant-we-map-a-plant-composition | <p>My main question is can we map what a fruit is made of? For instance apples are made of 0.0002% of protein X, 0.00001 of protein Y, 0.001% of amino acid Z... etc...</p>
<p>If we can, then my next question would be why do people fear eating GMOs?
I understand the argument that if you introduce a new compound to your... | <p>People are not always rational when it comes to what they eat, especially when the compounds that make up the food have long, arcane-sounding names. </p>
<p>It is indeed possible to analyse the amino acid composition of a food substance. However, this has no bearing whatsoever on the safety of the food product. </p... | 68 |
gene expression | Expression of an ancestral gene | https://biology.stackexchange.com/questions/3225/expression-of-an-ancestral-gene | <p>Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity?</p>
<p>Update:
By ancestral gene I mean a gene which was used by an ancestor but than changed slightly through evolution, though it still serves the same purpose. And by the mislea... | <p>Your updated question is still very vague, but I'm going to assume it is basically: "Why would the ancestral version of a gene be mistaken for a more recent version than the modern gene?"</p>
<p>If this is incorrect, please let me know and modify your question to clarify.</p>
<p>The simple answer to that question ... | 69 |
gene expression | Mutating a protein without mutating the gene? | https://biology.stackexchange.com/questions/46507/mutating-a-protein-without-mutating-the-gene | <p>Is it possible to mutate a region of a protein (says about 300 amino acids long) without actually mutating the gene?</p>
<p>One possible way that I can think of is to use RNAi and specifically block that region of the mRNA which codes for the 300 amino acids in the protein?</p>
<p>But then wouldn't it cause a prob... | <p>I assume that you mean changing the amino acid sequence in a single protein in an organism to one that no longer reflects the sequence predicted from the DNA sequence. In that case, I would suggest using ADAR (Double-stranded RNA-specific adenosine deaminase) or similar enzymes. ADAR deaminates adenosine to inosin... | 70 |
gene expression | Negative value on linear gene expression in microarrays | https://biology.stackexchange.com/questions/10797/negative-value-on-linear-gene-expression-in-microarrays | <p>I am starting to use microarrays and maybe this is a dumb question:</p>
<p>Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?</p>
<p>And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value) or floor... | <p>I'm not personally familiar with Illumina arrays, but I can give some notes here. This link is a <a href="http://res.illumina.com/documents/products/technotes/technote_gene_expression_data_quality_control.pdf" rel="nofollow noreferrer">paper which describes the array quality controls specifically</a>. This presenta... | 71 |
gene expression | why should someone study mRNAs instead of miRNAs as a biomarker | https://biology.stackexchange.com/questions/59514/why-should-someone-study-mrnas-instead-of-mirnas-as-a-biomarker | <p>why should someone study mRNAs instead of miRNAs as a biomarker from liquid cell-free biopsy like from exosomes? Is it wrong to do it? Does it offer you something different? Thank you in advance</p>
| 72 | |
gene expression | How to preprocess htseq counts for gene expression (TCGA) | https://biology.stackexchange.com/questions/56841/how-to-preprocess-htseq-counts-for-gene-expression-tcga | <p>I want to prepare a matrix of gene expression to analyse TCGA LAML data.</p>
<p>The required data is available at <a href="https://gdc-portal.nci.nih.gov/search/s?facetTab=files&filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22v... | 73 | |
gene expression | Can Blood Types Change? | https://biology.stackexchange.com/questions/58562/can-blood-types-change | <p>I recently heard a radio show where two callers claimed that their blood types had changed. One caller claimed that he was born O-, but recent tests said he was A+. Another caller claimed to change from AB- to AB+. Both callers claim that they had multiple tests before and after the change.</p>
<p>What I noticed is... | <p>Blood group antigens are either sugars or proteins found attached to the red blood cell membrane. ABO blood group antigens are the most clinically important antigens because they are the most immunogenic. As red blood cell antigens are inherited traits, they are usually not altered throughout the life of an individu... | 74 |
gene expression | Is there a resource to query gene expression similarity? Stratified by sex? | https://biology.stackexchange.com/questions/78265/is-there-a-resource-to-query-gene-expression-similarity-stratified-by-sex | <p>We developed such a resource. The editors of "Bioinformatics" (at OUP) rejected the paper on the grounds that we did not run a comparison with "state-of-the-art" [similar] resources. Can someone help me find similar resources?
Link to our own resource, <a href="http://unmtid-shinyapps.net/exfiles/" rel="nofollow nor... | <p>There are some similar resources, which at the same time do not mix the ingredients in the same way as your tool. Hope that pointing out the respective differences will help your rebuttal or resubmission! e.g.:</p>
<ul>
<li>A similar web service is part of <a href="https://www.flyrnai.org/tools/dget/web/similar_gen... | 75 |
gene expression | How are oncogenes targeted for therapy? | https://biology.stackexchange.com/questions/58472/how-are-oncogenes-targeted-for-therapy | <p>How would oncogenes be targeted for therapy and are there any examples of existing therapies for such cancers if the gene was upregulated (i) as a result of copy number variation and (ii) due to increased promoter activity?</p>
| 76 | |
gene expression | Are there any papers that give examples of what is a "high" and "low" TPM expression value for given gene types? | https://biology.stackexchange.com/questions/114653/are-there-any-papers-that-give-examples-of-what-is-a-high-and-low-tpm-expres | <p>My question relates to how to interpret TPM gene expression values, and what might be considered as "high" and "low" expression values, based on the gene type. For example, a receptor tyrosine kinase or an enzyme can catalyse many reactions and so only needs a relatively low gene expression to ha... | <p>No.</p>
<p>High and low gene expression are not absolute concepts, as the poster himself would seem to recognize in his speculations about different types of protein. In science you can only talk about “high” and low in relation to some reference <strong>normal</strong> situation, and this means making a measurement... | 77 |
gene expression | In which phenomena does one gene pair hide the effect of other unit? | https://biology.stackexchange.com/questions/37450/in-which-phenomena-does-one-gene-pair-hide-the-effect-of-other-unit | <p>This question was asken in an exam,</p>
<p><img src="https://i.sstatic.net/dm32D.png" alt="image"></p>
<p>The answer they are saying is "Epistasis". But I think "Dominance" fits better, because it is not mentioned whether genes of same allele are to be considered or different allele. Also it is not told whether g... | <p>The definition of "gene", according to <a href="http://dictionary.reference.com/browse/gene" rel="nofollow">The American Heritage Science Dictionary</a> is:</p>
<p>"A segment of DNA, occupying a specific place on a chromosome, that is the basic unit of heredity. Genes act by directing the production of RNA, which d... | 78 |
gene expression | How do I read an RNA expression pattern? | https://biology.stackexchange.com/questions/57138/how-do-i-read-an-rna-expression-pattern | <p>When reading about diseases one can find links to proteins and their associated genes, an example of which is <a href="https://en.wikipedia.org/wiki/LMNA" rel="nofollow noreferrer">here</a>.</p>
<p>I'm wondering how to decode/read the following graph as a non-specialist in this area:</p>
<p><a href="https://i.ssta... | <p>This image shows the expression of a gene (in your case Lamin A/C) in various tissues. A picture with a higher resultion for mouse looks like this (from <a href="http://biogps.org/#goto=genereport&id=4000" rel="nofollow noreferrer">here</a>):
<a href="http://biogps.org/#goto=genereport&id=4000" rel="nofollo... | 79 |
gene expression | Is there a mechanism of timing or delaying the expression of gap genes? | https://biology.stackexchange.com/questions/79805/is-there-a-mechanism-of-timing-or-delaying-the-expression-of-gap-genes | <p><strong>Summary</strong></p>
<blockquote>
<p>Gap genes are expressed in presence of the right combination and amount of
transcription factors. But is there any additional mechanism of timing the expression of the gap genes to ensure that they are expressed at the right time?</p>
</blockquote>
<p><strong>Contex... | 80 | |
gene expression | Can we change the Eye/Hair color by knocking out the OCA2, HERC2 and MC1R genes using CRISPR in an adult human? | https://biology.stackexchange.com/questions/96043/can-we-change-the-eye-hair-color-by-knocking-out-the-oca2-herc2-and-mc1r-genes | <p>This paper seems to describe the use of a plasmid delivered by a gene gun to depigment rat skin;</p>
<blockquote>
<p><a href="https://www.nature.com/articles/3302264" rel="nofollow noreferrer">https://www.nature.com/articles/3302264</a>
Published: 27 May 2004
Seeing the gene therapy: application of gene gun techniqu... | <p>Let's first breakdown this question</p>
<blockquote>
<p><strong>What is CRISPR?</strong></p>
</blockquote>
<ul>
<li>CRISPR is a group of DNA sequences that play a key role in the antiviral defense system of prokaryotic organisms such as bacteria and archaea.</li>
<li>They are derived from DNA fragments of bacterioph... | 81 |
gene expression | How to choose a method for upregulating an endogenous protein? | https://biology.stackexchange.com/questions/113282/how-to-choose-a-method-for-upregulating-an-endogenous-protein | <p>What factors affect the method that should be chosen to engineer a cell line that upregulates an endogenous protein? I am mostly asking permanent or long-term expression of nuclear proteins in mammalian cell lines, but more selection criteria for more applications would be appreciated too.</p>
<p>As I understand it,... | <p>This is one of those questions that needs to be determined <a href="https://en.wikipedia.org/wiki/Empirical_research" rel="nofollow noreferrer">empirically</a>, as it is highly dependent on the protein in question. For any one system, the best method to use needs to be determined by trial and observation. Upregulati... | 82 |
gene expression | Does penetrance depend in a regular way on zygosity? | https://biology.stackexchange.com/questions/116076/does-penetrance-depend-in-a-regular-way-on-zygosity | <p>I'm doing some self-directed study in genetics and microbiology. For example, I've viewed most of the videos from <a href="https://www.youtube.com/playlist?list=PLF83B8D8C87426E44" rel="nofollow noreferrer">the MIT OpenCourseWare series 7.01SC <em>Fundamentals of Biology</em></a> by Eric Lander and others. I have al... | <p>Yes, penetrance would "vary in a somewhat consistent way between heterozygous and homozygous genotypes". Some genes may usually show that (for a phenotype) one particular allele shows 0% penetrance in the heterozygous genotype and 100% (complete) penetrance in the homozygous genotype. Such an ideal allel... | 83 |
gene expression | Time scale for cAMP-dependent pathway cascades | https://biology.stackexchange.com/questions/94262/time-scale-for-camp-dependent-pathway-cascades | <p>What is the time scale for cAMP-dependent pathway cascades that start at the level of ligand binding to a G-protein receptor and finish at the level of gene transcription regulation?</p>
<p>For example, when corticotropin releasing hormone binds to CRH receptor 1, a cAMP-dependent pathway cascade is initiated, which... | 84 | |
gene expression | Limits of gene editing | https://biology.stackexchange.com/questions/94862/limits-of-gene-editing | <p>I was reading some articles about CRISPR and the world of gene editing, but then a lot of questions for which I couldn't find any answer online came into my mind. Those are all about how far can we edit an organism. So here is the general question, followed by some other to narrow down a little bit this broad subjec... | <p>Your question is very broad, but I'll try to address each of your points briefly.</p>
<ol>
<li><p>It would be nearly impossible to edit the genes in every cell of a human being or other complex organism simply due to the number (and accessibility) of cells. A full-grown human has in the neighborhood of 30 <em>trilli... | 85 |
gene expression | Are the controls for RT-PCR the same as those for RT-qPCR? | https://biology.stackexchange.com/questions/96115/are-the-controls-for-rt-pcr-the-same-as-those-for-rt-qpcr | <p>I am searching for negative and positive controls for RT-PCR but all the results seem to point towards RT-qPCR. Are the controls the same for both?</p>
<p>I have found</p>
<ol>
<li>-RT control</li>
<li>No template control</li>
<li>exogenous control</li>
<li>endogenous control</li>
<li>no amplification control</li>
<... | 86 | |
gene expression | Meaning of “gene expression heterogeneity” of embryonic stem cells | https://biology.stackexchange.com/questions/96118/meaning-of-gene-expression-heterogeneity-of-embryonic-stem-cells | <p>What does it mean if a gene has a heterogeneous expression? Does it describe the differences of patterns of expression of that particular gene in a population of cells that are identical? The papers I have found did not really elaborate on what it meant, and I do not know where else to find the definition.</p>
<p>In... | <p><strong>Heterogeneity</strong> is a noun meaning:</p>
<blockquote>
<p><a href="https://dictionary.cambridge.org/dictionary/english/heterogeneity" rel="nofollow noreferrer">the fact of consisting of parts or things that are very different from each other</a></p>
</blockquote>
<p>In scientific use the context determin... | 87 |
gene expression | variation in expression accounted for a SNP -- what's a usual percent? | https://biology.stackexchange.com/questions/2767/variation-in-expression-accounted-for-a-snp-whats-a-usual-percent | <p>I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the variation in the nearby gene expression. 55% sounds like a lot to me, what is the usual percent accounted for a signif... | <p>eQTLs (expression quantitative trait loci) are variants that affect the expression of one or more genes.</p>
<p>There have been several 'genome-wide' studies of SNPs that directly affect expression. The actual effect sizes are hard to pin down in most of them, but in the supplementary data for <a href="http://dx.do... | 88 |
gene expression | Where can I find histograms and tables of prevalence of mutations in cancer? | https://biology.stackexchange.com/questions/3090/where-can-i-find-histograms-and-tables-of-prevalence-of-mutations-in-cancer | <p>At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was presented in various pleasantly coloured interactive histograms and you could search per-gene or per-disease. </p>
<p>How... | <p>Perhaps you mean <a href="http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=bygene&ln=BRCA1&start=1&end=1864&coords=AA%3aAA" rel="nofollow">COSMIC</a>? The <a href="http://www.ebi.ac.uk/gxa/gene/ENSG00000012048" rel="nofollow">EBI Gene Expression Atlas</a> also has pretty charts, but now mutati... | 89 |
gene expression | Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)? | https://biology.stackexchange.com/questions/3404/where-can-i-find-the-tissue-specific-protein-expression-levels-for-htert-telome | <p>I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as is possible) lists the various tissues and hTERT's protein expression levels?</p>
<p>Any similar resource for gene ... | <p>I have found that biogps.org has all expression data I need:</p>
<p><a href="https://biogps.org" rel="nofollow">https://biogps.org</a></p>
<p><a href="https://biogps.org/#goto=genereport&id=7015" rel="nofollow">https://biogps.org/#goto=genereport&id=7015</a></p>
| 90 |
gene expression | What do breeders call the effect when a breed resists modification? | https://biology.stackexchange.com/questions/5037/what-do-breeders-call-the-effect-when-a-breed-resists-modification | <p>It is impossible to breed a blue rose or a cat with a bulldog shape. This is because breeding is limited by gene variations in the population. </p>
<p>What do breeders call this effect?</p>
<p><strong>UPDATE</strong></p>
<p>I guess this term is from medieval and/or handicraft breeders, not modern and hi-tech.</p>... | <p>I'm honestly not sure if one exists. They simply lack the gene/allele - the only specific term I can think of when it comes to <em>lacking</em> a gene is referencing <strong>Knockout</strong> variations where a researcher purposefully removes a gene from a subject in order to observe the effect.</p>
<p>However, "Kn... | 91 |
gene expression | How to determine the direction of regulation of a gene by comparing gene expressions? | https://biology.stackexchange.com/questions/6885/how-to-determine-the-direction-of-regulation-of-a-gene-by-comparing-gene-express | <p>I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease. </p>
<p>I am confused about how people can determine whether a gene is down-regulated or up-regulated b... | <p>If you have control expression values $c$ and e.g. disease expression values $d$, you take the ratio: $\frac{d}{c}$. If this is greater than one, it's up-regulated. Usually, the log-ratio is computed: $log\frac{d}{c}$. Now, if this is positive, the gene is up-regulated. </p>
<p>Gene expression values are usually me... | 92 |
gene expression | What is the mechanism of regulation of PER /CRY genes? | https://biology.stackexchange.com/questions/8137/what-is-the-mechanism-of-regulation-of-per-cry-genes | <p>I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate each other. <strong>Do these genes encode proteins that once created bind to the DNA and cover the transcription sit... | <p>Wikipedia gives a very good explanation of this, on the page for the suprachiasmatic nucleus.</p>
<blockquote>
<p>For example, in the fruitfly Drosophila, the cellular circadian rhythm
in neurons is controlled by two interlocked feedback loops.</p>
<p>In the first loop, the bHLH transcription factors clock... | 93 |
gene expression | How is gene expression estimated? | https://biology.stackexchange.com/questions/8153/how-is-gene-expression-estimated | <p>I'm reading <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509173/pdf/10111227.pdf" rel="nofollow">this fantastic article on estimating body time: Molecular-timetable methods for detection of body
time and rhythm disorders from single-time-point
genome-wide expression profiles</a> and one of the things that is... | <p>The technique described here is called microarray. Your question has given me an opportunity to put forth one of my opinions about certain problems of gene expression studies.</p>
<p>Gene expression is a measure of the activity of any gene. If the gene performs its activity in the form of a protein, then its expres... | 94 |
gene expression | Root hair formation in Arabidopsis | https://biology.stackexchange.com/questions/10355/root-hair-formation-in-arabidopsis | <p>In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells.</p>
<p>The immature epidermal cells that are in contact with 2 underlying cells of root cortex differentiate into root hair cells whereas the immature epidermal cells having contact with only one cortical cell d... | 95 | |
gene expression | Shine-Dalgarno sequence and expressing proteins | https://biology.stackexchange.com/questions/14242/shine-dalgarno-sequence-and-expressing-proteins | <ul>
<li>Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in initiation of translation.</li>
<li>We often try to express a eukaryotic gene in a prokaryote. For example : expressi... | <p>Eukaryotes have an analogous sequence called the Kozak sequence. cDNA is easily expressed in prokaryotes by substitution of the Kozak sequence for the Shine-Dalgarno sequence, using standard molecular biology techniques. A caveat is that not all eukaryotic protein will be properly expressed in bacteria because of th... | 96 |
gene expression | Constitutive mutation in operator gene | https://biology.stackexchange.com/questions/14681/constitutive-mutation-in-operator-gene | <p>If a constitutive mutation happens in the operator of an inducible operon, does that mean that repressors won't be able to bind them ? Or does it mean that even if repressors are bound, they will not have any effect on the gene ?</p>
<p>I am specifically talking about lac operon.</p>
| <p>For the lac operon there are two possibilities for constitutive expression mutations:</p>
<ol>
<li>The operator is never closed.</li>
</ol>
<p>Reason: Mutation of the repressor, so its not present, doesn't bind or binds only with very low affinity for the operon.</p>
<ol>
<li>The repressor can not bind.</li>
</ol... | 97 |
gene expression | regarding genetic disorders related to protein production | https://biology.stackexchange.com/questions/19526/regarding-genetic-disorders-related-to-protein-production | <p>I am not completely familiar with biology, but i had a genetics course in college along with practicals. Forgive me if there is something wrong with my question.</p>
<p>Is there a genetic disease which results in partially functioning or complete non functioning of genes resulting in little or no production of prot... | <p>There are many protein deficiency issues caused by genetic mutation for eg: Protein C whose deficiency causes abnormal blood clots. This protein is controlled by the PROC gene whose mutation causes Type I Protein C deficiency (<a href="http://ghr.nlm.nih.gov/condition/protein-c-deficiency" rel="nofollow">reference</... | 98 |
gene expression | How to identify the genes that distal enhancers pair? | https://biology.stackexchange.com/questions/20799/how-to-identify-the-genes-that-distal-enhancers-pair | <p>I am writing a project proposal and I have to talk about this problem: <strong>how to identify the genes that distal enhancers pair</strong>?</p>
<p>I am really new to this topic and I don't know what it is all about. I have been searching the literature but I did not find anything useful. Can someone explain to me... | <p>Check this technique called Chromosome Conformation Capture (3C). Its variants exist such as 4C, Hi-C etc.</p>
<p>Basically, the principle of this technique is based on the physical interaction between the enhancer and promoter that is bridged by a transcriptional modulator(protein). </p>
<ol>
<li>The chromatin is... | 99 |
protein folding | Protein folding | https://biology.stackexchange.com/questions/88978/protein-folding | <p>I've two questions
1. Is free ATP available in the cytoplasm of the cell?
2. In the protein folding funnel, prions and other misfolded proteins are located at the local minima of the graph. If ATP was freely available, it could possibly give a kick to the misfolded structure to cross the energy barrier and this sho... | <ol>
<li>Yes</li>
<li>The energy released by ATP hydrolysis must be coupled, by enzymes, to some other reaction or process in order to be useful. It isn’t magic. There are <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814418/" rel="nofollow noreferrer">ATP-dependent chaperones</a> that assist in protein foldin... | 100 |
protein folding | When does protein folding begin? | https://biology.stackexchange.com/questions/78477/when-does-protein-folding-begin | <p>I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds <strong><em>as</em></strong> they exit the ribosome, while translation is still occuring. </p>
<p>This leads me to a... | <h2><strong>When does protein folding begin?</strong></h2>
<p>With reference to time you have asked, it can be after the translation has occurred (called <strong>Translational protein folding</strong>) or while translation is still occuring (called <strong>Co-Translational protein folding</strong>). Here is the <a hre... | 101 |
protein folding | Statistical Analysis of Protein Folding Problem | https://biology.stackexchange.com/questions/8871/statistical-analysis-of-protein-folding-problem | <p>I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (<a href="http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470470593.html" rel="nofollow">Introduction to Protein Structure Prediction: Methods and Algorithms</a>). Does anyone know whether I can find... | <p>One of the quickest ways to get oriented on what is going in the world of protein folding and modeling is to look at the proceedings of the <a href="http://www.predictioncenter.org/casp10/" rel="nofollow">Critical Assessment of Structure Prediction</a> (CASP). CASP is basically a contest, held every 2 years where a... | 102 |
protein folding | Could AI be applied to protein folding? | https://biology.stackexchange.com/questions/67115/could-ai-be-applied-to-protein-folding | <p>Two years later, there is a follow up question to the one asked here: <a href="https://biology.stackexchange.com/questions/30240/how-do-we-know-if-the-foldinghome-project-results-are-right">How do we know if the folding@home project results are right?</a>
Since we are quite sure F@H is working right and following <a... | <p>Yes, and no :-)</p>
<p>In the meantime many protein structures can be predicted quite accurately - even those for which no reference fold had been known before. </p>
<p>In this case the important buzz word is "big data": co-mutations (of charged amino acids) that can be found when sequencing many independent genom... | 103 |
protein folding | Thermodynamics of spontaneous protein folding: role of enthalpy changes | https://biology.stackexchange.com/questions/51295/thermodynamics-of-spontaneous-protein-folding-role-of-enthalpy-changes | <p>I'm trying to get clear why protein folding occurs spontaneously.</p>
<p>$$\ce\Delta G=\Delta H-T\Delta S$$</p>
<p>According to thermodynamics the ΔG should be negative for a process to occur spontaneously.
When a protein folds the ΔS (Entropy) is decreasing, because the protein gets more ordered. However I think ... | <p><strong>Summary</strong></p>
<ul>
<li>The first explanation is commonly encountered.</li>
<li>The second explanation cannot be correct, <em>as it stands</em>, as it ignores the free energy change in the protein.</li>
<li>A modification of the second explanation (perhaps what was intended) is that it is necessary to ... | 104 |
protein folding | Verifying Protein Folds | https://biology.stackexchange.com/questions/19974/verifying-protein-folds | <p>I have recently begun using <a href="http://folding.stanford.edu/home/" rel="nofollow">Folding@Home</a> and I am curious how people are prevented from cheating the system. It seems to me that unless the final result is easily verifiable users could submit bogus folds in order to quickly gain credits. Is it in fact t... | <p>Besides duplication as verification there are numerous other computational methods to ensure that the result is valid. Proprietary software is used for folding at home so one can safely assume that they check <a href="http://en.m.wikipedia.org/wiki/Md5sum" rel="nofollow">hashes</a> on processors and files regularly.... | 105 |
protein folding | Any good website/book to understand protein folding and enzymes? | https://biology.stackexchange.com/questions/30810/any-good-website-book-to-understand-protein-folding-and-enzymes | <p>I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. </p>
<p>I understand that the protein is a polypeptidic chain, I know its composition, but the part that I really can't figure out is "the folding of proteins", I mean "... | <p>Okay, so for introduction the 4 levels of protein structure (each level influences the levels after it):</p>
<ul>
<li>primary (1st): the order of amino acids.</li>
<li>secondary (2nd): alpha-helicies and beta-sheets</li>
<li>tertiary (3rd): complex 3d structure</li>
<li>quaternary (4th) : 3rd+ non-protein elements ... | 106 |
protein folding | Relation of conformational entropy and protein folding | https://biology.stackexchange.com/questions/51230/relation-of-conformational-entropy-and-protein-folding | <p>I'm trying to figure out the relation between conformational entropy and protein folding.
I read the following in Lehninger, <em>Principles of Biochemistry</em> (6th edition): </p>
<blockquote>
<p>Most of the net change in free energy as weak interactions form within a protein is therefore derived from the increa... | <p>This question is an example of an important general problem in chemical biology: “How does an ordered system arise without violating the second law of thermodynamics?” Berg <em>et al.</em>, <em>Biochemistry</em>, addresses this in the following manner:</p>
<blockquote>
<p>The Second Law of Thermodynamics states that... | 107 |
protein folding | Protein folding, extra dimensions and bio-mathematics | https://biology.stackexchange.com/questions/36740/protein-folding-extra-dimensions-and-bio-mathematics | <p>One metaphor that I have found to explain how proteins fold so quickly to a native shape is that of <a href="http://www.funtrivia.com/en/SciTech/Biochemistry/Question2795680_51649F.html" rel="nofollow">the blind golfer</a>.</p>
<p>I have made <a href="http://openspark.com/foldit/lowest_energy/" rel="nofollow">a vid... | <h2>Short Answer</h2>
<blockquote>
<p>What mathematical work is currently being done in this area?</p>
</blockquote>
<p>A... lot?</p>
<h2>Longer Answer</h2>
<p>The "n-dimensional slope" thing that you're talking about shows up in the modern theory of protein dynamics as the "landscapes" concept. The... | 108 |
protein folding | Why is statistical mechanics relevant to RNA and protein folding? | https://biology.stackexchange.com/questions/45459/why-is-statistical-mechanics-relevant-to-rna-and-protein-folding | <p>This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding environment (so basically a many body problem). So I don't understand how statistical mechanics, such as Boltzmann's ... | <p>I’m no physicist, but your statement “To my knowledge statistical mechanics and thermodynamics exist when we have an ensemble of particle such as in a liquid or a gas” is surely incorrect. The problem of protein folding is one of thermodynamics — finding the structure of lowest free energy, and the path by which it ... | 109 |
protein folding | How can predicting protein folding speed up drug discovery? | https://biology.stackexchange.com/questions/97114/how-can-predicting-protein-folding-speed-up-drug-discovery | <p>I'm asking this as a layperson without much knowledge in biology, so please correct me if my understanding is wrong.</p>
<p>Recently DeepMind's AlphaFold managed to predict protein structure from acid amino sequence with stunning accuracy. We are being told that this could "<strong>pave ways toward advances in ... | <p>Firstly protein structures are not infinite. Most proteins adopt specific structure.<br />
Drugs carry out their function by binding to its target protein. Structure prediction helps drug discovery process in two ways -</p>
<ol>
<li>it allows identification of pockets in target proteins (where drugs can bind) whose ... | 110 |
protein folding | What is protein folding and how is it relevant to disease? | https://biology.stackexchange.com/questions/54739/what-is-protein-folding-and-how-is-it-relevant-to-disease | <p>I am trying to understand what is protein folding and how it could help cure some diseases.</p>
<p>When reading articles about it, it looks like the goal is to find perfect folds for proteins because some diseases are due to proteins that don't fold correctly. I don't understand why do we need to find them in the f... | <p>Protein folding is a complex thing. There are huge computer algorithms and huge mainframes which are trying to predict the final 3D structure of a protein. </p>
<p>Knowing the tertiary and the quaternary structure of a protein, allows us to understand why diseases happen. In many cases a mutation of the gene provok... | 111 |
protein folding | What characteristics of the protein folding process ensure that the energy landscape is a funnel? | https://biology.stackexchange.com/questions/60289/what-characteristics-of-the-protein-folding-process-ensure-that-the-energy-lands | <p>The folding funnel hypothesis states that the energy landscape that proteins observe when they fold is funnel shaped with a single global optima. This ensures that no matter what sequence of folds the protein follows, it should eventually end up in the same folded configuration thanks to the laws of thermodynamics.<... | <p>Naturally occurring proteins are evolved such that this is the case</p>
<p>Natural proteins only occupy a very small amount of sequence space. For a 200 aa protein, there are $20^{200} \approx 10^{260}$ possible sequences. There are nowhere near that many naturally occurring protein sequences, even if you take into... | 112 |
protein folding | Why does protein folding not depend on the order in which it is synthesized? | https://biology.stackexchange.com/questions/88137/why-does-protein-folding-not-depend-on-the-order-in-which-it-is-synthesized | <p>I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:</p>
<blockquote>
<p>Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the ribosome to prot... | <blockquote>
<p>how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein?</p>
</blockquote>
<p>The quote by the researcher says that the form is unrelated to the direction of synthesis (N->C rather than C->N). It implies th... | 113 |
protein folding | Why is it thought that protein folding is determined solely by amino acid sequence? | https://biology.stackexchange.com/questions/86264/why-is-it-thought-that-protein-folding-is-determined-solely-by-amino-acid-sequen | <p>It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein with two different functional foldings (possibly with different functions) is known, or is there some theoretical reaso... | <p>This question is, in my opinion, based on an incorrect premise but nevertheless throws up a number of points about protein folding and protein structure that can be addressed, albeit briefly.</p>
<p><strong>The False Premise</strong></p>
<blockquote>
<p>“it is a generally accepted idea that protein folding <stro... | 114 |
protein folding | Predicting protein folding with Alphafold | https://biology.stackexchange.com/questions/103194/predicting-protein-folding-with-alphafold | <p>I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ website for downloading it and using it but there’s one part I don’t understand (see the sections mentioned in the link... | <p>If you have little experience with programming, I strongly suggest using the <a href="https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb" rel="nofollow noreferrer">official Google Colab notebook</a> for AphaFold. It really involves only some button clicks and pasting the ... | 115 |
protein folding | How can computer predictions of protein folding be verified computationally? | https://biology.stackexchange.com/questions/34344/how-can-computer-predictions-of-protein-folding-be-verified-computationally | <p>Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, <a href="https://fold.it/portal/">https://fold.it/portal/</a>, etc.).</p>
<p>The question that I have is: How do you know when you get it right? Is there some way of verifying, <em>in silico</em... | <h2>Overview</h2>
<p>Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures.</p>
<blockquote>
<p>How do you know when you get it right? </p>
</blockquote>
<p>Ultimately, one still <strong>needs expe... | 116 |
protein folding | What proportion of proteins require chaperone-assisted folding? | https://biology.stackexchange.com/questions/76165/what-proportion-of-proteins-require-chaperone-assisted-folding | <p>I am new to the field of biochemistry (I am a chemist, actually).</p>
<p>I have long known the process of folding as the process that leads to the minimum energy conformation of a protein.</p>
<p>Now, I am introduced to the chaperones, that I didn't know before.</p>
<p>What I am wondering is: my previous view of ... | <p>I'm reminded of a lovely <a href="https://www.ncbi.nlm.nih.gov/pubmed/9538692" rel="nofollow noreferrer">review in Trends in Biochemical Sciences</a> that discusses chaperone independent, partially dependent, and fully dependent proteins in prokaryotes. The conclusion was that smaller polypeptides are less likely t... | 117 |
protein folding | What is Genome Folding? | https://biology.stackexchange.com/questions/57195/what-is-genome-folding | <p>Why does <a href="https://openi.nlm.nih.gov/detailedresult.php?img=PMC3102647_2046-1682-4-8-1&req=4" rel="nofollow noreferrer">genome folding</a> have such great interest? </p>
<p>For protein folding I could say that's important because protein's functionality closely depends on its folded state, since it affec... | 118 | |
protein folding | Proteins folds: relation to splicing and post-translational modification? | https://biology.stackexchange.com/questions/71358/proteins-folds-relation-to-splicing-and-post-translational-modification | <p>Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?</p>
| 119 | |
protein folding | How to obtain a list of proteins sorted by the ~1400 unique protein folds? | https://biology.stackexchange.com/questions/44162/how-to-obtain-a-list-of-proteins-sorted-by-the-1400-unique-protein-folds | <p>The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data.</p>
<ol>
<li><p>A list of each of the 1400 folds (just an id number, and/or a descriptor)?</p></li>
<li><p>For each individual fold (of the 1400... | <p>If there is a simple way provided to do this it is very well hidden. The tedious and stupid way to do 1 (get a list of folds) would seem to involve rolling your own:</p>
<ol>
<li><p>Go to <a href="http://scop.berkeley.edu/ver=2.07" rel="nofollow noreferrer">http://scop.berkeley.edu/ver=2.07</a> (or whatever is the l... | 120 |
protein folding | Is protein folding symmetric with respect to reversing the sequence order? | https://biology.stackexchange.com/questions/73105/is-protein-folding-symmetric-with-respect-to-reversing-the-sequence-order | <p>Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A.</p>
<p>For example (these are made-up proteins):</p>
<pre><code>protein A = [G,A,L,G,M,F,R]
protein B = [R,F,M,G,L,A,G]
</code></pre>
<p>Will th... | <p>No! Although there is a relationship, the protein would not fold properly since the C and N terminals are reversed consider the following: </p>
<p>H(NH)-A-C(=O)(NH)-B-C(=O)(NH)-C-C(=O)(NH)-D-C(=O)(NH)-E-(C=O)OH</p>
<p>as appose to :</p>
<p>HO(C=O)-A-(NH)(C=O)-B-(NH)(C=O)-C-(NH)(C=O)-D-(NH)(C=O)-E-(NH)H</p>
<p>Th... | 121 |
protein folding | What does 'kinetically accessible' mean in protein folding? | https://biology.stackexchange.com/questions/77790/what-does-kinetically-accessible-mean-in-protein-folding | <p>The <a href="https://en.wikipedia.org/wiki/Hydrophobic_collapse" rel="nofollow noreferrer">hydrophobic collapse model</a> discusses this term in the energetics section. What does this actually mean?</p>
| <p>At some point during protein folding, there may exist lower energy states from a thermodynamic perspective (lower ΔG free enegy) which are actually unreachable in a given environment, because the required <a href="https://en.wikipedia.org/wiki/Activation_energy" rel="nofollow noreferrer">activation energy</a> is too... | 122 |
protein folding | Is it possible to isolate and analyse intermediates of protein folding? | https://biology.stackexchange.com/questions/30277/is-it-possible-to-isolate-and-analyse-intermediates-of-protein-folding | <p>I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form.
While studying structural biology, I only came to know the forces that stabilize the structure, but not the gap between the original random coil and the protein in its native form.</p>
| <p>Theoretically by <strong>molecular modeling</strong> -- see the works by Harold Scheraga:
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Harold+Scheraga%5BAuthor%5D" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/?term=Harold+Scheraga%5BAuthor%5D</a></p>
<hr>
<p>Note: An unfolded protein is not... | 123 |
protein folding | Can a bacterium survive without GroEL protein? | https://biology.stackexchange.com/questions/55599/can-a-bacterium-survive-without-groel-protein | <p>In prokaryotes, GroEL protein (together with GroES) is required for protein folding. </p>
<p>Question: Can a bacterium survive without GroEL protein?</p>
| <p>In E. coli, GroEL/GroES is found to interact with about 10% of all soluble proteins (Kerner et al. Cell 2005) and is the only chaperone essential to the bacterium under all tested conditions (Horwich et al. Cell 1993).</p>
| 124 |
protein folding | why do chaperones bring protein into mitochondria? why would mitochondria need protein? | https://biology.stackexchange.com/questions/64442/why-do-chaperones-bring-protein-into-mitochondria-why-would-mitochondria-need-p | <p>Sounds trivial? Please help to sort out. I saw this picture while looking at dehydration reactions and cell revision. </p>
<p><a href="https://i.sstatic.net/LiI6U.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/LiI6U.jpg" alt="enter image description here"></a></p>
<p>And proceeded to the <a href="h... | <p>As you probably know, mitochondria (together with chloroplasts) are a very interesting organelle: they are a result of an <a href="https://www.nature.com/scitable/topicpage/the-origin-of-mitochondria-14232356" rel="nofollow noreferrer">endosymbiotc relationship</a> that took place more than 1 billion years ago.</p>
... | 125 |
protein folding | How does the shape of a protein determine its function? | https://biology.stackexchange.com/questions/101805/how-does-the-shape-of-a-protein-determine-its-function | <p>There is currently much interest in protein folding and the problems in predicting how the sequence of amino acids determines how proteins fold into specific shapes. Accounts of this generally mention in passing that the shape of a protein determines its function.</p>
<p>How, in fact, does the shape of a protein det... | <p>Determining function and predicting function are two separate things. For example, a screwdriver's shape determines its function, but it might be hard to predict that function unless you also see some screws.</p>
<p>There are obviously a zillion different other molecules a protein might interact with, so just from i... | 126 |
protein folding | Are Hsp70 proteins only activated in response to heat shock? | https://biology.stackexchange.com/questions/89224/are-hsp70-proteins-only-activated-in-response-to-heat-shock | <p>Hsp70 proteins are chaperones that assist in protein folding in my plant physiology textbook it says the Hsp70 proteins were discovered by inducing heat shock. But do they only work in response to heat shock stress? </p>
<p>I know these types of proteins are found in many organisms but I am interested in how they a... | 127 | |
protein folding | What I can do in order to improve the folding of the protein? | https://biology.stackexchange.com/questions/19151/what-i-can-do-in-order-to-improve-the-folding-of-the-protein | <p>I am struggling with the expression of the certain protein. It seems that it is not properly folded and thus, it is not active. I tried to express it at the lower temperature and for the longer time, but it did not help. Can anyone give me a clue what I can try to do?</p>
<p>The size of the protein is around 55 kDa... | <p>If you have over-expressed an eukaryotic full length protein or the enzymatic part, then <em>E. coli</em> does not necessarily provide a good environment for its folding so you need to express it in the same system which the original protein came from, e.g. mammalian or Drosophila etc. <em>E. coli</em> over expressi... | 128 |
protein folding | how long do chaperone proteins take to fold a protein? | https://biology.stackexchange.com/questions/74779/how-long-do-chaperone-proteins-take-to-fold-a-protein | <p>how long do chaperone proteins take to fold a protein?</p>
| 129 | |
protein folding | Kinetics and de novo protein prediction | https://biology.stackexchange.com/questions/49019/kinetics-and-de-novo-protein-prediction | <blockquote>
<p>De novo conformation predictors usually function by producing candidate conformations (decoys) and then choosing amongst them based on their thermodynamic stability and energy state. Most successful predictors will have the following three factors in common:</p>
<p>1) An accurate energy function ... | <p>Generally speaking, structure prediction programs look only at the thermodynamic minimum, without consideration of the kinetic trajectory of folding. </p>
<p>The main reason for this is mostly time considerations. It's very difficult to accurately model the true folding pathway of even a moderately sized protein. W... | 130 |
protein folding | Solution based measurement of Solvent-Accessible Surface Area of macromolecules | https://biology.stackexchange.com/questions/1909/solution-based-measurement-of-solvent-accessible-surface-area-of-macromolecules | <p>The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA from a solved (and generally static) structure.</p>
<p>Chemical probes like diazirine and hydroxyl radicals show some b... | <p>I only know of one method, but here it is. You create a sphere the diameter of the <a href="http://jmol.sourceforge.net/docs/surface/" rel="nofollow noreferrer">VdW radius of water, and then 'roll' it along the surface</a>. I know this as a Richards-Lee surface, wikipedia has another name for it. </p>
<p><img src... | 131 |
protein folding | How to manufacture different sized micelles in nano -scale? | https://biology.stackexchange.com/questions/2343/how-to-manufacture-different-sized-micelles-in-nano-scale | <p>I am trying to answer <a href="http://tenttiarkisto.fi/exams/9605.1.pdf" rel="nofollow">q5</a>:</p>
<blockquote>
<p><strong>"How can you manufacture micelles in A) nanometerer -scale B) and in ten nanometer -scale?"</strong></p>
<p><strong>My Thinking</strong></p>
<blockquote>
<p><strong>Observation... | <p>A key factor that determines the radii of a micelle is the <a href="http://en.wikipedia.org/wiki/Critical_micelle_concentration" rel="nofollow noreferrer">critical micelle concentration</a>. The other is the the hydrophobicity of the micelles which can be measured using the <a href="http://en.wikipedia.org/wiki/Cont... | 132 |
protein folding | Why is translation so much faster in prokaryotes than eukaryotes? | https://biology.stackexchange.com/questions/70202/why-is-translation-so-much-faster-in-prokaryotes-than-eukaryotes | <p>Prokaryotes perform transcription and translation much faster than eukaryotes. If memory serves, a single 70S prokaryotic ribosome can incorporate around 20 amino acids per second, whereas the 80S eukaryotic counterpart is much slower, at around 2 amino acids per second. Is the reason for this known? The only possib... | <p>Unless the poster can cite more recent papers to support the assertion regarding a difference in rates of prokaryotic and eukaryotic protein synthesis, I would say that this is incorrect.</p>
<p><a href="https://www.sciencedirect.com/science/article/pii/S0022283668800440" rel="nofollow noreferrer">Lacroute and Sten... | 133 |
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