category stringclasses 107
values | title stringlengths 15 179 | question_link stringlengths 59 147 | question_body stringlengths 53 33.8k | answer_html stringlengths 0 28.8k | __index_level_0__ int64 0 1.58k |
|---|---|---|---|---|---|
cell signaling pathways | How do TLR1/TLR2 activate the MyD88 dependent pathway | https://biology.stackexchange.com/questions/15509/how-do-tlr1-tlr2-activate-the-myd88-dependent-pathway | <p>Recently, I've been reading about the MyD88 dependent signalling pathway, with particular reference to its activation in Macrophages and other cells of the immune system on recognition of a pathogen. I understand that when a PAMP (Pathogen Associated Molecular Pattern) binds with a PRR (Pattern Recognition Receptor)... | <p>The TLR are usually working as homodimers (<a href="http://www.sciencedirect.com/science/article/pii/S0960982211005975" rel="nofollow noreferrer">Toll-like receptors</a>), although TLR2 can cooperate with TLR1 or 6.
Upon binding of its ligand (this is called pathogen associated molecular pattern) the receptors chang... | 334 |
cell signaling pathways | Expression/Mechanism of ROR1 in healthy tissue | https://biology.stackexchange.com/questions/28464/expression-mechanism-of-ror1-in-healthy-tissue | <p>ROR1 is currently under investigation as a therapeutic target for cancer (1). A number of studies show different cancers may have their metastatic potential reduced, or become apoptotic through targeting or abrogation of ROR1 (1-3). ROR1 itself is show to have a number interactions (either through crosstalk or inter... | <p>Examining the literature it'd seem that the ROR pathways incl. ROR1 and ROR2 are critical for developing tissues in the majority of cases. We also see relevance in the expression of ROR1/2, more specifically ROR2, in cases where taxic cell types are required to migrate, branch, etc. Most of the literature determines... | 335 |
cell signaling pathways | How does formaldehyde/PBS or methanol fixation of cells affect lysosomal pH? | https://biology.stackexchange.com/questions/10476/how-does-formaldehyde-pbs-or-methanol-fixation-of-cells-affect-lysosomal-ph | <p><strong>The question</strong> is fairly simple - does formaldehyde or methanol fixation in preparation for immunocytochemistry/immunofluorescent staining affect the pH of the lysosomes?</p>
<p><strong>Some background:</strong> I'm trying to look at the intracellular trafficking of a fluorescently-labeled lysosomal ... | <p>In my opinion, cell fixation shouldn't change the pH. However unbuffered formalin will oxidize and lower the pH, but using PBS should buffer around pH 7.
Maybe Glutaraldehyde fixation would also be an option, if the others are not working...</p>
<p>I found this website by leica very useful, maybe it will also help ... | 336 |
cell signaling pathways | How does the phosphorylation state of 4E-BPs affect translation of nuclear-encoded mitochondrial transcripts? | https://biology.stackexchange.com/questions/104524/how-does-the-phosphorylation-state-of-4e-bps-affect-translation-of-nuclear-encod | <p><a href="https://www.nature.com/articles/s41580-019-0199-y" rel="nofollow noreferrer">A 2020 review paper about mTOR</a> (ref. 1) says:</p>
<blockquote>
<p>because biomass accumulation demands vast reserves of energetic currency, mTORC1 enhances translation of nuclear-encoded mitochondrial transcripts through 4E-BP1... | 337 | |
cell signaling pathways | Differences between synaptic connections | https://biology.stackexchange.com/questions/40144/differences-between-synaptic-connections | <p>Consider the following synaptic connections (<a href="http://www.apsubiology.org/anatomy/2010/2010_Exam_Reviews/Exam_3_Review/CH_11_Neuron-to-Neuron_Transmission.htm" rel="nofollow noreferrer">from here</a>):</p>
<blockquote>
<p><strong>axodendritic</strong> - A term pertaining to an excitatory or inhibitory synapti... | <p>Neurons are all about specialized structures having specialized roles. You've given a good justification for dendrites---an efficient way to fit lots of connections in a small space. A pyramidal neuron in cortex, for instance, will have tens of thousands of synapses. If you only had axosomatic connections, the soma ... | 338 |
cell signaling pathways | Reward pathway sequence of events | https://biology.stackexchange.com/questions/60294/reward-pathway-sequence-of-events | <p>So I've been reading a lot of papers on the reward pathway. But since I'm not schooled in any relevant knowledge I'm having trouble grasping the chain of events. Most papers detail just bits and pieces, but not the full sequence of events.</p>
<p>I'm trying to grasp how the error prediction signal works.</p>
<p>Th... | <p>Essentially that's what I remember, but there can be a lot more steps between A and C, i.e. more pathways interacting in different systems to produce an associative memory. Pavlov's dogs is the classic example:</p>
<p>1: Pavlov rings bell, dogs hear bell</p>
<p>2: Pavlov feeds dogs, (dogs rewarded)</p>
<p>3: Repe... | 339 |
cell signaling pathways | How does Sodium Valproate cause neural plasticity | https://biology.stackexchange.com/questions/19856/how-does-sodium-valproate-cause-neural-plasticity | <p>I have been reading a fascinating paper: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848041/">Valproate reopens critical-period learning of absolute pitch</a></p>
<p>18 individuals were given Sodium Valproate (VPA) for a fortnight during which they trained on a pitch-training game. Results suggest that VP... | <p>As far as I can see this paper is being a little misleading, by saying "VPA mimics Nogo-66 receptor deletion".</p>
<p>The action of VPA doesn't seem to be related to this receptor.</p>
<p>It seems that blocking this receptor and applying VPA both increase plasticity, but via different mechanisms.</p>
<p>VP... | 340 |
cell signaling pathways | Structure of RAP Antibodies (Specifically RAP-5) | https://biology.stackexchange.com/questions/1469/structure-of-rap-antibodies-specifically-rap-5 | <p><strong>[EDIT]</strong> - Have just found not <a href="http://www.uniprot.org/citations/7791872" rel="nofollow">one</a> but <a href="http://www.nature.com/nsmb/journal/v3/n8/abs/nsb0896-723.html" rel="nofollow">two</a> papers that address my structure problem. However they concern RAP-1A, so I guess my question is n... | <p>The confusion that you're facing is because RAP-5 is actually known as <a href="http://en.wikipedia.org/wiki/RAB5C" rel="nofollow">RAB5C</a> (<a href="http://www.ncbi.nlm.nih.gov/gene/5878" rel="nofollow">GENEID</a>). The <a href="http://en.wikipedia.org/wiki/Ras_superfamily" rel="nofollow">ras superfamily</a> (<a h... | 341 |
cell signaling pathways | Are there well studied examples of ERAD-mediated membrane insertion, especially from viruses? | https://biology.stackexchange.com/questions/45666/are-there-well-studied-examples-of-erad-mediated-membrane-insertion-especially | <p>Membrane insertion of transmembrane proteins typically requires highly hydrophobic alpha helixes at the N-terminus, N-terminal signal peptides, tail anchors, or a combination of the three.</p>
<p>Byun, H., Gou, Y., Zook, A., Lozano, M., & Dudley, J. (n.d). ERAD and how viruses exploit it. Frontiers In Microbiol... | 342 | |
cell signaling pathways | What are the factors affecting reaction time and/or reflex velocity? | https://biology.stackexchange.com/questions/112263/what-are-the-factors-affecting-reaction-time-and-or-reflex-velocity | <p>So there was this video of a cat killing a snake: <a href="https://youtube.com/shorts/ygJb5skuTPM?feature=share" rel="nofollow noreferrer">Cat reaction time</a><br>
and another of a bobcat killing a rattlesnake <a href="https://youtu.be/QUH3Sxcprws" rel="nofollow noreferrer">Bobcat kills rattlesnake</a><br>
And then... | 343 | |
cell signaling pathways | KRAS gene and K-Ras Mutations | https://biology.stackexchange.com/questions/89598/kras-gene-and-k-ras-mutations | <p>This question pertains to the <a href="https://en.wikipedia.org/wiki/KRAS" rel="nofollow noreferrer">KRAS wikipedia page</a>, and I just want to double check and clarify my own understanding of how this mutation works in cancer.</p>
<p>It states:</p>
<blockquote>
<p><em>K-Ras protein acts like a switch that is turne... | <p>NRAS is indeed a molecular switch, as part of the MAP-Kinase signaltransduction pathway it acts in controling the signal which goes downstream and finally will cause the expression of genes. In the case of NRAS this includes genes for proliferation, which is important for tumors. In principle, this looks like shown ... | 344 |
epigenetics | Defining paper(s) in epigenetics | https://biology.stackexchange.com/questions/264/defining-papers-in-epigenetics | <p>For someone who is interested in learning about the discovery of epigenetics, which are the foundational defining papers in the area?</p>
| <p>I understand that Robin Holliday was the first to discuss the possible role of DNA methylation
in the control of Gene expression. In his paper "<a href="http://www.ncbi.nlm.nih.gov/pubmed/3310230">The inheritance of epigenetic defects</a>"
he presents what is one of the first modern formulations of what we now rega... | 345 |
epigenetics | Gene regulation and epigenetics in specialized cells | https://biology.stackexchange.com/questions/101301/gene-regulation-and-epigenetics-in-specialized-cells | <p>Gene regulation is aided by epigenetics. Epigenetics determines which genes are turned off and which are switched on, and it varies throughout our lifetimes. Is it feasible that epigenetic modifications switch off the genes that determine whether a muscle cell or a neuron is a muscle cell or a neuron? I have searche... | <p>Correct me if I am wrong but it seems you are asking 'do epigenetic mechanisms influence cell fate/determination?'. If this is your question, the answer is yes. Epigenetic modifications play a key role in 'deciding' what type of cell a given stem cell will differentiate into. Here is some more information: <a href="... | 346 |
epigenetics | Quantitatively measure the impact of DNA vs epigenetics? | https://biology.stackexchange.com/questions/115592/quantitatively-measure-the-impact-of-dna-vs-epigenetics | <p><em><strong>Background:</strong></em> While classical genetics deals with how DNA sequences directly code for traits, epigenetics involves chemical modifications to DNA and associated proteins that can switch genes on or off without changing the underlying DNA sequence (including DNA methylation, histone modificatio... | <p>There is extensive work attempting to decompose phenotypic variance into genetic, epigenetic etc. terms. Here are just three random examples from the last 10 years that I got by googling this:</p>
<ul>
<li><a href="https://www.nature.com/articles/s41437-019-0261-8" rel="nofollow noreferrer">https://www.nature.com/ar... | 347 |
epigenetics | Do epigenetics determine the proteins a cell produces and therefore it's function? | https://biology.stackexchange.com/questions/80065/do-epigenetics-determine-the-proteins-a-cell-produces-and-therefore-its-functio | <p>I'm having trouble understanding what epigenetics is in a simple sense.</p>
<p>How I imagine it is that if we had 2 twins with identical DNA and we let them live we will see that they'll develop differently. Their DNA will stay the same (unless the DNA gains mutations, which could lead to cancer...) but their epige... | <p><strong>Short answer:</strong> Yes, epigenetics play a role in determining gene expression, therefore protein expression and function.</p>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3752894/" rel="nofollow noreferrer">Lifestyle factors</a> like diet, smoking, alcohol consumption, and stress can change... | 348 |
epigenetics | Can epigenetics have positive impact on the genes are development? | https://biology.stackexchange.com/questions/88325/can-epigenetics-have-positive-impact-on-the-genes-are-development | <p>I know that epigenetics have capacity to affect and degrade the genes thereby inducing problems/illness/degradation in body functions. </p>
<p>Can they also make better genes or have positive impact on genes or body? If yes, can someone give some examples?</p>
| <p>First, let me qualify the idea of "problematic" epigenetic modifications by saying that the impact of a modification on an organism is often dependent on the environment. That is to say that outcome is dependent on the interaction of genetics (or epigenetics) and the environment in which the associated genes are ex... | 349 |
epigenetics | DNA methylation and the validity of the definition of epigenetics | https://biology.stackexchange.com/questions/90676/dna-methylation-and-the-validity-of-the-definition-of-epigenetics | <p>I am currently studying a textbook that presents the following definition of <strong>epigenetics</strong>:</p>
<blockquote>
<p>Epigenetics is defined as heritable changes in gene expression without changes in the DNA sequence. </p>
</blockquote>
<p>The authors then claim the following:</p>
<blockquote>
<p>DNA... | <p>A methylated nucleotide is the same nucleotide, for the purposes of base-pairing events. The methylated base will be paired with its Watson-Crick opposite after replication, for instance (and methylation will even persist after replication).</p>
| 350 |
epigenetics | Role of epigenetics in evolution and transmission of defects caused by drugs | https://biology.stackexchange.com/questions/95332/role-of-epigenetics-in-evolution-and-transmission-of-defects-caused-by-drugs | <p>In a documentary, they were saying that epigenetics changes caused by the environment in an individual can be transferred to the following generations. I have some questions on that:</p>
<ol>
<li><p>How many generations are affected by an epigenetic change? can this be permanent?</p>
</li>
<li><p>Can drugs cause epi... | <p>Generally speaking, epigenetic modifications are not inherited as they are reset during embryogenesis. However, subsequent epigenetic modifications can be acquired during the period of pregnancy, which as a mechanism depends on the epigenetic state before the reset and on the physiological conditions of the mother i... | 351 |
epigenetics | Does epigenetics suggest there is at least some element of truth to Lamarckism? | https://biology.stackexchange.com/questions/94160/does-epigenetics-suggest-there-is-at-least-some-element-of-truth-to-lamarckism | <p>I am not a biologist. But googling "epigenetics lamarck", I find many different opinions:</p>
<ul>
<li>For: <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12322" rel="nofollow noreferrer">Lamarck rises from his grave</a>, <a href="https://www.acsh.org/news/2016/06/10/epigenetics-lamarcks-revenge" rel... | 352 | |
epigenetics | Epigenetic marks | https://biology.stackexchange.com/questions/101323/epigenetic-marks | <p>I was lately researching epigenetics and the current research on age reversal. Because epigenetic processes are influenced by the environment and can vary over time, I wanted to know if all epigenetic marks and mechanisms, including those that play a key part in cell differentiation, are reversible?
I am extremely k... | 353 | |
epigenetics | How does epigenetics affect the birth conditions via alcohol? | https://biology.stackexchange.com/questions/46228/how-does-epigenetics-affect-the-birth-conditions-via-alcohol | <p><a href="http://www.ajsc.us/files/ajsc0030217.pdf" rel="nofollow">Recent study</a> has shown that epigenetics can play role in male-caused infertility and it cites for example studies which showed an enhancing of silent genes when drinking alcohol. Since the study argues this as a reason to the negative newborns' co... | 354 | |
epigenetics | Can epigenetic changes affect reproductive success? | https://biology.stackexchange.com/questions/3789/can-epigenetic-changes-affect-reproductive-success | <p>This is prompted by niallhaslam's answer to this question [<a href="https://biology.stackexchange.com/questions/3771/since-darwinian-times-has-there-been-any-striking-notable-effects-of-evolution">Since Darwinian times, has there been any striking/notable effects of evolution on humans?</a>]. A comment by Alan Boyd ... | <p><a href="http://rd.springer.com/static-content/0.5415/pdf/672/art%253A10.1186%252F1471-2164-13-59.pdf?token=1349547201563--df67f8e33c10393eeb2a5501673869cd27643eebc78b8e9ae9a8ba858d30b45062d36922685bb45cdc0fe9cfa3cbe814e638131409957240b1103900fa7df04a&doi=10.1186/1471-2164-13-59&contentType=article" rel="nof... | 355 |
epigenetics | Transmission of epigenetic regulation through surrogate mother | https://biology.stackexchange.com/questions/33/transmission-of-epigenetic-regulation-through-surrogate-mother | <p>I know the basics of epigenetics, but I do not know how epigenetic mechanisms are transmitted from parents to children (or if there is even enough literature to derive a consensus). My question is relates to surrogate motherhood, in which an egg is fertilized <em>in vitro</em> and then implanted in the womb of a wom... | <p>Epigenetic information is information that can be inherited through cell division that is not encoded in the DNA sequence. This includes, but is not limited to, DNA methylation and histone modifications (there is also non-chromatin based epigenetic information). A nice example is the centromere, the chromosomal regi... | 356 |
epigenetics | How do cells become differentiated using epigenetics despite having the same genome? | https://biology.stackexchange.com/questions/66370/how-do-cells-become-differentiated-using-epigenetics-despite-having-the-same-gen | <p>How is epigenetics used in the differentiation of cells and is this the only thing that is used? I've seen that transcription factors play a role but are these simply proteins that initially write the epigenetic code or something different altogether?</p>
<p>I've written this explanation of how I understand it curr... | 357 | |
epigenetics | Are epigenetic changes involved in evolution? | https://biology.stackexchange.com/questions/41192/are-epigenetic-changes-involved-in-evolution | <p>Evolution leads to phenotypic changes through changes in DNA such as mutations. Mutations are transmitted to offspring. Cumulative mutational changes across many generations may cause evolution and speciation. </p>
<p>As far as I know, <strong>epigenetic changes</strong> causes an individual to change in how it ap... | <p><strong>To start I will repost some of an answer I have previously posted, which will explain what evolution is:</strong></p>
<p>Evolution is simply <strong><a href="http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_02" rel="nofollow">a process of change</a></strong>. It is a change in trait values of pop... | 358 |
epigenetics | Semantics Question: epigenetic mark on a person's DNA? | https://biology.stackexchange.com/questions/77956/semantics-question-epigenetic-mark-on-a-persons-dna | <p>In an <a href="https://newatlas.com/child-abuse-dna-genetic-biomarker/56588/" rel="nofollow noreferrer">article on biomarkers of child abuse</a>, the author referred to an "epigenetic mark on a person's DNA". It's a popular science article, so the language may reflect a combination of the journalist's scientific com... | <p>We may restrict your definition of epigenetics as heritable changes in an organism's phenotype that occur without a change in the <em>sequence of DNA bases</em>. That is, changes to the DNA molecule itself is permitted, as long as the sequence of ATCGs are not affected.</p>
<p>In this sense, it would not be wrong t... | 359 |
epigenetics | Studying the epigenetic variability, can I use SNPs? | https://biology.stackexchange.com/questions/85168/studying-the-epigenetic-variability-can-i-use-snps | <p>So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region? I don't have environmental data, just the SNP information. </p>
<p>Since epigenetics refers to t... | <p>Starting from what appears to be your main question:</p>
<blockquote>
<p>Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region?</p>
</blockquote>
<p>I would strongly advise against using SNPs determine if genes are expressed (at all) ... | 360 |
epigenetics | Does the Jungian notion of collective unconsciousness have any legitimacy in the light of modern neurobiology and epigenetics? | https://biology.stackexchange.com/questions/21982/does-the-jungian-notion-of-collective-unconsciousness-have-any-legitimacy-in-the | <p>Carl Jung has long ago proposed a rather controversial notion of <em>collective unconsciousness</em><a href="http://www.britannica.com/EBchecked/topic/125572/collective-unconscious" rel="nofollow"> [1</a>, <a href="http://www.thefreedictionary.com/collective+unconscious" rel="nofollow">2</a>, <a href="http://en.wiki... | <p>Jung's premise is rather plausible: consciousness evolved rather than appeared suddenly, and therefore carries "pre-conscious" elements common to humans as a species. However, Jung goes very far in his interpretation of what may be hidden in subconscious, bordering on open mysticism - predicting accidents,... | 361 |
epigenetics | Determination of genes to be modified in epigenetics | https://biology.stackexchange.com/questions/46074/determination-of-genes-to-be-modified-in-epigenetics | <p>It seems that during reproduction particular genes are targeted for modification (mutation, deletion, insertion, etc.) given environmental inputs of either or both of the parents.</p>
<p>If a creature was fit given its environment, its <em>seems</em> there is little mutation. However, if the creature becomes less f... | <p>Mutations are not performed targeting a specific new phenotype. There is no way an organism can "know" the impact of a specific future mutation anyway. A mutation is just a mistake in the replication process. As a consequence the majority of mutations are deleterious and only a handful of mutations are beneficial.</... | 362 |
epigenetics | Are there epigenetic effects in the regulation of human height? | https://biology.stackexchange.com/questions/98516/are-there-epigenetic-effects-in-the-regulation-of-human-height | <p><strong>Development of human average height</strong></p>
<p>Human average height has fluctuated significantly throughout history. For instance, in the last 100 years or so, it has increased sharply by about 10cm. OWID (Our World in Data) has data and figures on, among other measures, the <a href="https://ourworldind... | 363 | |
epigenetics | Have researchers discovered how epigenetic information is passed down during cell division? | https://biology.stackexchange.com/questions/60218/have-researchers-discovered-how-epigenetic-information-is-passed-down-during-cel | <p>For example, how are histone code patterns passed down?</p>
<p>This question was asked a few years ago in this thread:</p>
<p><a href="https://biology.stackexchange.com/questions/5342/how-are-epigenetic-marks-transmitted-during-cell-division">How are epigenetic marks transmitted during cell division?</a></p>
<p>H... | 364 | |
epigenetics | epigenetic vs. environmental factors | https://biology.stackexchange.com/questions/71802/epigenetic-vs-environmental-factors | <p>I'm trying to understand the difference between epigenetic and environmental factors. For example, if gene A increases the risk of lung cancer by 50% and smoking increases the risk by another 75% when combined with gene A (just throwing out numbers) person X now has a higher chance of developing lung cancer. However... | <p>If I understand you correctly what you are saying is</p>
<blockquote>
<p>There is envrionmental variance and epigenetic variance underlying the phenotypic variance. There can even be a covariance between the envrionment and epigenetics.</p>
</blockquote>
<p>Yes, this is true. You might want to have a look at <a ... | 365 |
epigenetics | what causes epigenetic dysregulation in cancer? | https://biology.stackexchange.com/questions/84701/what-causes-epigenetic-dysregulation-in-cancer | <p>Do mutations in regulatory gene sequences lead to changes in epigenetic alterations in cancer, and if so which ones? I know abnormal hypermethylation of GCP islands occurs in promoters of tumour supressors, but what drives the abnormal methylation? Thanks </p>
| 366 | |
epigenetics | Can epigenetic structures carry a trait? | https://biology.stackexchange.com/questions/55298/can-epigenetic-structures-carry-a-trait | <p>Can epigenetic structures cause a trait to manifest in a person if the trait is not already in the DNA? In all my readings I have yet to find a definitive statement that it is impossible.</p>
| <p>Yes, epigenetic changes does affect the phenotype. This is here the whole interest behind epigenetic. Environmental variation (incl. parental care) affect epigenetics which in turn affect the phenotype (incl. behaviour) of an individual. It is pretty much clear from the <a href="https://en.wikipedia.org/wiki/Epigene... | 367 |
epigenetics | Can a gene-expression or epigenetic 'user-history' be found in the body? | https://biology.stackexchange.com/questions/52372/can-a-gene-expression-or-epigenetic-user-history-be-found-in-the-body | <p>(EDITED - a lot of what I am saying is implicit and simplified. I'm not looking to recreate the numerous textbooks and scientific papers on how DNA works). </p>
<p>As far as I can understand it, an organisms basic building blocks (proteins) are made up of DNA, Genes, and Chromosomes. The most basic form of this is ... | <h2>Main question</h2>
<blockquote>
<p>Does the body store a history of these expressions? Do the chromosomes
(or some other part) of an older organism store a 'user-history' of
which genes where previously activated when the organism was younger?</p>
</blockquote>
<p>Cells can sometimes have a "memory" of the ... | 368 |
epigenetics | Variance in epigenetic drift rate between different species | https://biology.stackexchange.com/questions/111946/variance-in-epigenetic-drift-rate-between-different-species | <p>My question relates to the prospect of (near?) future control of biological aging.
As I understand, it has been recently demonstrated by Prof. David Sinclair's group that epigenetic drift appears to be a major driver of aging, and demonstrated it may be reversed by applying a certain subset of Yamanaka factors. In p... | 369 | |
epigenetics | Are enhancers and silencers considered as epigenetic modifications? | https://biology.stackexchange.com/questions/51963/are-enhancers-and-silencers-considered-as-epigenetic-modifications | <p>Are enhancers and silencers considered as epigenetic modifications? I am confused as it seems like enhancers and silencers are sequences on the DNA and how they work is through binding with proteins, while epigenetic changes seem to be changes made to the bases for instance adding a methyl group.</p>
| <p>No. </p>
<p>Epigenetic information is (by definition) NOT included in the nucleotide sequence, but affects genetic expression.</p>
<p>Enhancers/silencers are themselves nucleotide sequences, and therefore not epigenetic information.</p>
<p>Methylation is an example of epigenetic information, but a DNA sequence it... | 370 |
epigenetics | How are epigenetic marks transmitted during cell division? | https://biology.stackexchange.com/questions/5342/how-are-epigenetic-marks-transmitted-during-cell-division | <p>As far as I know, this is one of the biggest questions in the epigenetic field: how are the epigenetic marks like histone modifications propagated through cell division? A lot is already known about DNA methylation (e.g. as in <a href="https://biology.stackexchange.com/questions/3450/how-does-inheritance-of-methylat... | <p>I can get the ball rolling..</p>
<p>Found a nice paper which looks at this phenomenon <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028980" rel="nofollow noreferrer">in yeast</a>.</p>
<p>So as a primer, 8 histone proteins come together to make a spool of sorts which DNA wraps around:</p>
<p>... | 371 |
epigenetics | Is there any biological basis for the emphasis on the value of the firstborn son? | https://biology.stackexchange.com/questions/64695/is-there-any-biological-basis-for-the-emphasis-on-the-value-of-the-firstborn-son | <p>Is the firstborn son biologically different in any way from the sons that follow?</p>
<p>Perhaps his epigenome is different? I have heard that a man's testosterone levels decrease when he becomes a father -- could this then have implications for the epigenetics of subsequent sons?</p>
| <p>There are lots of cases reported now that suggest that overall the firstborn child is usually more intelligent. The <a href="http://jhr.uwpress.org/content/early/2016/11/01/jhr.53.1.0816-8177.abstract" rel="nofollow noreferrer">articles supporting this</a> are based on behavioural and economic study though, so the b... | 372 |
epigenetics | How might IVF (and related technologies) alter epigenetic marks? | https://biology.stackexchange.com/questions/7691/how-might-ivf-and-related-technologies-alter-epigenetic-marks | <p>I was reading up on KCNQ1, which encodes a voltage-gated potassium channel, and I discovered that it happens to be only maternally expressed. This is regulated by KCNQ1OT1, a non-coding RNA, which is also epigenetically regulated (expressed only paternally). Mutations in KCNQ1OT1 are associated with Beckwith-Wiedema... | <p>I was at a talk last year where some geneticists were starting to look at the effect of IVF techniques on genetic issues. Because of the work being done and the inclinations of the clients involved, this has not been studied very much. One presumes that since zygotes are still used, there will not be much epigenet... | 373 |
epigenetics | What are the criteria for determining the influence of epigenetic factors? | https://biology.stackexchange.com/questions/202/what-are-the-criteria-for-determining-the-influence-of-epigenetic-factors | <p>Isolating a gene or sets of genes in diseases sometimes isn't enough to determine penetrance - epigenetic factors can have a significant effect. What are the criteria in determining whether epigenetic factors are significant?</p>
| <p>First of all, the nature of penetrance is almost entirely unknown. Likely it's a combination of epistasis and gene interactions, induced gene regulatory pathways, developmental noise, and other factors. Epigenetics (imprinting, etc) may have little to do with penetrance, while chromatin structure may be a conseque... | 374 |
epigenetics | Is post-transcriptional regulation of gene expression an epigenetic process? | https://biology.stackexchange.com/questions/50788/is-post-transcriptional-regulation-of-gene-expression-an-epigenetic-process | <p>Is post-transcriptional regulation of gene expression (for example regulation by microRNAs) a type of epigenetic gene expression regulation? </p>
<p>I think we can categorize it as epigenetic since the DNA sequence is not changed, but I have never come across that terming in any papers. Does someone have any idea, ... | <p>miRNAs and other post-transcriptional regulators are very well "genetic". They are encoded by genetic elements, are expressed and are affected by mutations. Just because this mode of regulation was not well known previously, it should not be classified as an epigenetic mechanism while the traditional protein based t... | 375 |
epigenetics | How can epigenetic changes be erased if they are inherited? | https://biology.stackexchange.com/questions/70090/how-can-epigenetic-changes-be-erased-if-they-are-inherited | <p>I’m a little bit confused about DNA methlyation reprogramming and about the nature of an epigenetic phenomenon. According to <a href="https://en.wikipedia.org/wiki/Reprogramming" rel="nofollow noreferrer">Wikipedia</a>:</p>
<blockquote>
<p>After fertilization the paternal and maternal genomes are once again demet... | <p>I have done a presentation in epigenetics and the main topic was imprinting.
This paper will answer all your questions <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941233/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941233/</a>
I am adding some glimpses from this paper here
Ma... | 376 |
epigenetics | What is wrong with this analogy: Individuals are to alleles what governments are to individuals | https://biology.stackexchange.com/questions/20020/what-is-wrong-with-this-analogy-individuals-are-to-alleles-what-governments-are | <p>I'm an amateur when it comes to genetics, I'm hoping to learn something from the corrections. I am taking epigenetics into account (kind of); all 3 entities are susceptible to external physical influences.</p>
<p>Kind regards,</p>
<p>Frank</p>
| <p>Alleles are passed down (to individuals) and created by individuals (although not fully under their control). But individuals are not passed out or created by the governments (I suppose), although individuals are influenced by the governments and they can influence governments, whereas individuals can not necessaril... | 377 |
epigenetics | Has lamarckism been discredited? | https://biology.stackexchange.com/questions/92317/has-lamarckism-been-discredited | <p>Lamarckism is a pre-darwinian theory according to which an organism's traits acquired to adapt to the environment are passed onto its offspring. A couple of years ago, I attended an event with Richard Dawkins and Jerry Coyne, both preeminent evolutionary biologists, in which I remember them agreeing that it is basic... | <p>The question is interesting at many levels. Of course, in biology and in any other science there is no absolute or 'objective' truth about some given phenomenon if we really care to look at the nuances. Lamarck seems to be vindicated mainly by a wave of empirical work on patterns of <a href="https://scholar.google.c... | 378 |
epigenetics | Can instincts disappear after a long period of non-usefulness? | https://biology.stackexchange.com/questions/114020/can-instincts-disappear-after-a-long-period-of-non-usefulness | <p>I recently dived into the topic of <strong>instincts</strong> and now I have a question, where I haven't found anything about.</p>
<p>There's this thesis (I think mentioned <a href="https://link.springer.com/article/10.3758/BF03200077" rel="nofollow noreferrer">here</a> amongst others) that, through epigenetics, lea... | <p>If it is like any other genetic trait, it will only be weeded out if there exists selective pressure that makes it counter-productive. Merely not being useful is not necessarily sufficient. Though I suppose over extremely long periods of time, it may get diluted out by mutation and propagation of those mutations if ... | 379 |
epigenetics | Are there any studies of epigenetic difference between twins during their lifespan? | https://biology.stackexchange.com/questions/7380/are-there-any-studies-of-epigenetic-difference-between-twins-during-their-lifesp | <p>Are there any studies of epigenetic difference between twins during their lifespan ? I ask because I wonder if there exist phases during lifespan, when environmental factors plays major role (expecially in early adulthood) - twins study should allow to distinguish between changes in epigenetic profile caused by ext... | <p>I would think there have to be, though do you mean collecting samples on a regular basis and plotting out the difference at each point? Or do you simply mean the total accumulated change. If it is the latter, the answer is certainly "yes". You have probably seen the Nova documentary "<a href="http://www.youtube.com/... | 380 |
epigenetics | Are epigenetic modifications the most stable mechanisms for cell differentiation? | https://biology.stackexchange.com/questions/84534/are-epigenetic-modifications-the-most-stable-mechanisms-for-cell-differentiation | <p>Wondering what the general take is on what are the molecular mechanisms that are mostly responsible for cell type differentiation stability; ie, for a cell's identity to actually become 'locked in' and progressively less susceptible to extracellular cues (for example, in heterotopic transplantation experiments such ... | <p>Epigenetic marks are reversible (you might be aware of <a href="https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell" rel="nofollow noreferrer">induced pluripotent cells</a>). Many animals can regenerate organs with high tissue complexity (such as a limb) and this involves de-differentiation in some species (... | 381 |
epigenetics | Data for Epigenetic Patterns of Human Tissue at the Gene Level | https://biology.stackexchange.com/questions/116212/data-for-epigenetic-patterns-of-human-tissue-at-the-gene-level | <p>Is anyone aware of a good data source to look at epigenetic patterns of human tissue at the gene level? I am trying to perform genetic mapping from DNA I am having sequenced. I want to be able to determine from which tissue, e.g., lung, the DNA sequence originates from.</p>
<p>Where might I find some good data?</p>
... | <p>Here's an atlas of <a href="https://www.nature.com/articles/s41586-022-05580-6" rel="nofollow noreferrer">whole-genome bisulfite sequencing</a> for sorted cell types. I haven't looked closely, but I think this one incorporated data from <a href="https://www.nature.com/articles/nature14248" rel="nofollow noreferrer"... | 382 |
epigenetics | Tree-pest coevolution | https://biology.stackexchange.com/questions/94661/tree-pest-coevolution | <p>Many trees first reproduce decades after germination. Many pests of trees reproduce in under a year. It would seem that the pests have an advantage in the evolutionary arms-race, as they can evolve a means of attack far faster than the tree can evolve a defense (<em>cf.</em> <a href="https://biology.stackexchange.... | 383 | |
epigenetics | Does parental conflict lead to genes combining important functions with functions only advantageous for one of the parents? | https://biology.stackexchange.com/questions/98869/does-parental-conflict-lead-to-genes-combining-important-functions-with-function | <p>In a sitation of a mother-father conflict of interests, the mother <a href="https://www.researchgate.net/publication/5985782_Parental_conflict_does_not_necessarily_lead_to_the_evolution_of_imprinting" rel="nofollow noreferrer">might use</a> epigenetics to turn off some genes only advantageous for the father's genes ... | 384 | |
epigenetics | What is an aromatic cage and what does it do? | https://biology.stackexchange.com/questions/52664/what-is-an-aromatic-cage-and-what-does-it-do | <p>Epigenetics, 2. ed, Chapter 3.6:</p>
<blockquote>
<p>Similarly, methylated lysine residues embedded in histone tails can be
read by “aromatic cages” present in chromodomains, or similar domains
(e.g., MBT, Tudor) contained within complexes that facilitate
downstream chromatin modulating events (see Ch. 7 [P... | <p>It refers to the structures in the <a href="https://en.wikibooks.org/wiki/Structural_Biochemistry/PHD_Finger" rel="nofollow noreferrer">PHD-finger domain</a> and chromodomains. The aromatic amino acid residues form a cage like structure which covers and interacts with the methylated ammonium of lysine via a cation-p... | 385 |
epigenetics | Can the brain influence gene expression? | https://biology.stackexchange.com/questions/50441/can-the-brain-influence-gene-expression | <p>A neuroscientist told me (according to my hazy memory) that the brain/nervous system can have an epigenetic function, ie directly regulate gene expression. </p>
<p>I'm not a biologist, but she talked me through how it worked, and I know enough of the basics to follow along and think it sounded reasonable. I think... | <p>As has been pointed out in comments, the brain can certainly affect gene expression; but so can <em>anything</em> in our bodies, because the blood stream is super good at carrying stuff around the body to wreak havoc.</p>
<p>But I'm going to take a somewhat uncharitable view of this question<sup>1</sup>; and assume... | 386 |
epigenetics | Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli | https://biology.stackexchange.com/questions/3432/literature-about-putative-epigenetic-state-changes-in-mammal-sequences-after-clo | <p>I would like you to point me out some literature about putative epigenetic state changes in mouse/mammal sequences after cloning steps in <em>Escherichia coli</em>.</p>
<p>This are the last search details I used in NCBI PubMed:</p>
<blockquote>
<p>"epigenomics"[MeSH Terms] AND "cloning, molecular"[MeSH Terms] OR... | <p><em>E.coli</em> strains that have <em>dam</em> or <em>dcm</em> methylases can methylate plasmid at adenines or cytosines respectively. See <a href="https://www.neb.com/tools-and-resources/usage-guidelines/dam-and-dcm-methylases-of-e-coli" rel="nofollow">here</a> — It is a NEB web page but has links to the cited refe... | 387 |
epigenetics | Do identical twins have the same metabolism rate at birth? | https://biology.stackexchange.com/questions/95066/do-identical-twins-have-the-same-metabolism-rate-at-birth | <p>Will monozygotic twins defecate at the same time if fed at the same time during the first weeks of life?</p>
<p>They should have the same genetics (and epigenetics) since they are monozygotic and the same environment since they live in the same house and they are just born.</p>
<p>I looked if metabolism (assuming it... | <p>I like admire your interest.</p>
<p>Organisms in development rely not only on their <a href="https://en.wikipedia.org/wiki/Nature_versus_nurture" rel="nofollow noreferrer">genetic make-up but also: their environment and epigenetics</a> (no matter how early in development).</p>
<p>In addition to variables other than ... | 388 |
epigenetics | Can sealed epiphyseal growth plates theoretically be restored via epigenetic or genetic methods? | https://biology.stackexchange.com/questions/23153/can-sealed-epiphyseal-growth-plates-theoretically-be-restored-via-epigenetic-or | <p>I know that epiphyseal growth plates seal up once people become young adults and that it is currently impossible to restore them to actively produce new bone growth but, is it theoretically possible via genetic or epigenetic means to reactivate them to produce new bone?</p>
| 389 | |
epigenetics | Are all genes capable of being switched on or off? | https://biology.stackexchange.com/questions/108155/are-all-genes-capable-of-being-switched-on-or-off | <p>Are all genes capable of being switched on or off or only some genes? Are there some genes that permanently do not have the functionality that enables them to be switched on or off?</p>
<p>Everything I have found in response to this question seems to assume that ALL genes are capable of being switched on or off.</p>... | <p>I cannot think of a mechanism that would entirely <em>prevent</em> a gene from being regulated. For example, consider mechanisms like <a href="https://en.wikipedia.org/wiki/Histone#Modification" rel="nofollow noreferrer">histone modification</a>: there is very little about the sequence of a single underlying gene th... | 390 |
epigenetics | Did operon evolve after endosymbiosis and specialisation of mitochondria? | https://biology.stackexchange.com/questions/114042/did-operon-evolve-after-endosymbiosis-and-specialisation-of-mitochondria | <p>We know that all extant bacteria use the operon system as their mode of regulating gene expression, in contrast to eukaryotes, which use individual gene promoters as well as epigenetic mechanisms, supporting the idea that the first eukaryotes came from archaea as the 'host' in endosymbiosis, not bacteria [2]. Howeve... | 391 | |
epigenetics | Genetic Imprinting and Cell differentiation | https://biology.stackexchange.com/questions/31186/genetic-imprinting-and-cell-differentiation | <p>It does not seem possible that these two processes can coexist: </p>
<p>1) Genetic imprinting is the phenomenon where genes are expressed differently depending on the parent of origin: </p>
<p>1a. Methylated stretches of DNA are not transcribed. </p>
<p>1b. If the gene copy originating with mom is methylated but ... | <p>What if imprinted regions are immune to being wiped? Also, you may be confusing DNA methylation, and histone methylation (?). Classical biochemistry posits that DNA methylation states can be transmitted from a dividing mother cell to both daughter cells because after DNA replication the two daughter chromosomes will... | 392 |
epigenetics | How correlated are proximally related CpG sites in human DNA? | https://biology.stackexchange.com/questions/10365/how-correlated-are-proximally-related-cpg-sites-in-human-dna | <p>Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together. </p>
<p>I can only find one paper that states this empirically (1), that 90% of CpG sites within 50bp of one another are in the same methylation sta... | <p>I've got to dash off so I won't be able to give a fully in-depth answer today, but this basically boils down to the concept of CpG islands. Something like 70-80% of CpGs are methylated in humans, so if they were randomly scattered around the genome there is already a pretty high chance nearby CpGs are in the same s... | 393 |
epigenetics | Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods? | https://biology.stackexchange.com/questions/82878/computational-approaches-for-making-hypotheses-about-the-effects-of-genetic-engi | <p>Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some CRISPR-like tools? I guess, that extensive databases of already performed experiments are available and human mind is re... | <p>I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769084/" rel="nofollow noreferrer">just entering clinical trials for a very few, well studied diseases</a>. Almost all the work with CRISPR-CAS9 is sti... | 394 |
epigenetics | What determines the differences between differentiated cells? | https://biology.stackexchange.com/questions/67642/what-determines-the-differences-between-differentiated-cells | <p>Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their <em>different DNA</em>.</p>
<p>However two types of cells in an adult organism may have clearly different phenotypes (e.g. morphology), but the <em>same DNA</em>, with a different set of gene... | 395 | |
epigenetics | Can diet, supplementation and/or drugs affect sexual dimorphism? | https://biology.stackexchange.com/questions/79868/can-diet-supplementation-and-or-drugs-affect-sexual-dimorphism | <p>After puberty, can certain diets, exercise, and/or possible drugs affect masculine/feminine dimorphism in adults? We know dimorphism and/or morphology is a product of genes, but to what extent can this be altered through environment? Like, can chewing more give a more masculine jaw shape/angle? Can talking a certain... | <p>There is a slight inaccuracy in your title question. Let's clarify to begin with:</p>
<p>I think you are asking whether environmental factors can affect sexually dimorphic <strong>traits</strong>. I don't think you are aiming to ask about dimorphism itself (i.e. the presence of apparent differences between the sexe... | 396 |
epigenetics | Is the mutation rate in organisms in general consistent over the genome? | https://biology.stackexchange.com/questions/21145/is-the-mutation-rate-in-organisms-in-general-consistent-over-the-genome | <p>Coming from computer science with an interest in genetic programming (a process emulating evolution) I'm curious about whether the rate of mutation is homogeneous across the whole genome, or if some parts of the genome differ in the rate of mutation.</p>
<p>For example we could imagine, without going to into detail... | <p>Well, for start, there are "mutational hot spots", regions that are more prone to mutation than others.</p>
<p>As for immune system genes, first of all, lung cells and heart cells and retina cells don't need to mutate those genes, because they don't use them.</p>
<p>But you are right that in immune cells there is ... | 397 |
epigenetics | How does comparing shuffled proteomes to the unshuffled ones help us understand independent protein adaptation? | https://biology.stackexchange.com/questions/113390/how-does-comparing-shuffled-proteomes-to-the-unshuffled-ones-help-us-understand | <p>From '<strong>Protein and DNA Sequence Determinants of Thermophilic Adaptation</strong>', by Konstantin B Zeldovich, Igor N Berezovsky and Eugene I Shakhnovich (Published: January 12, 2007 | <a href="https://doi.org/10.1371/journal.pcbi.0030005" rel="nofollow noreferrer">https://doi.org/10.1371/journal.pcbi.0030005<... | 398 | |
epigenetics | Can the environment affect genes and adaptation in offspring? | https://biology.stackexchange.com/questions/74035/can-the-environment-affect-genes-and-adaptation-in-offspring | <p>I recently read several articles that believe that environment can affect gene expression and this change will transfer down to the children. Some theorists believe that random mutations are more rare and time consuming than a mutation that develops as a response to change of the environment the organism is in.
Epig... | <p><strong>Generalities</strong></p>
<p>You have misread the articles (or read misleading articles). </p>
<p>Epigenetic modifications are, by definition, any modification to the DNA and proteins attach to DNA that does not affect the nucleotidic sequence (note that I here ignore some of the difficulties defining the ... | 399 |
epigenetics | How long does it take for a gene to be switched on or off through the process of epigenetic expression? | https://biology.stackexchange.com/questions/112507/how-long-does-it-take-for-a-gene-to-be-switched-on-or-off-through-the-process-of | <p>I understand that in our lifetime, our experiences affect the expression of our genes. Some get switched on, while others switched off. Our experiences, diet, lifestyle etc. determines this expression of genes, but my question is, how long does it roughly take for such an expression to take place? Let's say you are ... | 400 | |
epigenetics | psychological database with sequenced DNA records | https://biology.stackexchange.com/questions/16861/psychological-database-with-sequenced-dna-records | <p>I'm looking for an epigenetic database which includes for each example the psychological history of the persons DNA. Right now I can only find DNA and epigenetic databases. Sadly none of the databases provide "thick data" (qualitative data eg. history of person) to the sequenced DNA. </p>
<p>I want to investigate t... | <p>You might want to look at the Danish Data archive: </p>
<p><a href="http://www.sa.dk/content/us/about_us/danish_data_archive" rel="nofollow">http://www.sa.dk/content/us/about_us/danish_data_archive</a></p>
<p>I have never used their data and I don't know what barriers there might be to accessing it, but the impres... | 401 |
epigenetics | Can untargeted metabolomics detect epigenomic changes such as methylation? | https://biology.stackexchange.com/questions/93075/can-untargeted-metabolomics-detect-epigenomic-changes-such-as-methylation | <p>My main focus is transcriptomics analysis and very recently I have also started working on metabolomics. From my transcriptomic data it looks like there is a gene/protein that could potentially generate epigenetic modifications. I also have untargeted metabolomics data of equivalent experimental conditions that I pl... | <p>This is a fascinating question, and I spent a fair amount of time looking into it. From what I've been able to find regarding the relationship between metabolics and epigenetics, it seems that metabolites drive epigenetic changes, not the other way around.
This can be shown quite well by looking at cell differentia... | 402 |
epigenetics | higher-order evolutionary adaptations | https://biology.stackexchange.com/questions/101284/higher-order-evolutionary-adaptations | <p>Most adaptations are what I'd call first-order. Cats evolve better eyesight; redwoods evolve to grow taller; male cardinals evolve attractive bright feathers. All of these changes were selected for because they directly make the organisms and their offspring more likely to reproduce. But it seems like there is a fun... | <p>I think that you are talking about evolvability (as I see it).</p>
<p>Sex is indeed a sort of a meta-adaptation, see e.g. <a href="https://books.google.com/books/about/The_Evolution_of_Sex.html?id=SbI5AAAAIAAJ" rel="nofollow noreferrer">The Evolution of Sex by John Maynard Smith</a>. The math for this is rather well... | 403 |
epigenetics | Molecular/cellular biology textbook to consolidate what I know about molecular/cell biology | https://biology.stackexchange.com/questions/43608/molecular-cellular-biology-textbook-to-consolidate-what-i-know-about-molecular-c | <p>I'm a medical student (who is halfway through med school) looking for a textbook that will <strong>consolidate</strong> some of the biology I already know. While I've read a lot of books that go into great detail about genetics, immunology and cell signaling, I've not found many books that focus on clear insights.</... | <p>Campbell's Biology is, I quote my biology teacher, "the Bible of AP Biology". I know you're a medical student and therefore far past that introductory college level, but Campbell's does quite a good and thorough job of explaining a plethora of biology topics. It's a fairly reliable textbook, I think you might like i... | 404 |
epigenetics | What is the relationship between induction of cell differentiation and DNA methylation status? | https://biology.stackexchange.com/questions/74959/what-is-the-relationship-between-induction-of-cell-differentiation-and-dna-methy | <p>This may sound like a broad question to ask, but I am working on interpreting a review article for my epigenetics course and I'm having trouble reconciling two seemingly contradictory things this review is saying.</p>
<p>Ehrlich, M., & Lacey, M. (2013). DNA methylation and differentiation: Silencing, upregulati... | <p>This is a good question. I'm not as steeped in this literature as I'd like, but here is my understanding of the process:</p>
<p>Methylation is one of the key methods by which cell fate is restricted. The review you're reading is giving specific examples of cell lines that are at least partially restricted into cell... | 405 |
epigenetics | Is this trial that reversed aging in humans worth taking seriously? | https://biology.stackexchange.com/questions/92906/is-this-trial-that-reversed-aging-in-humans-worth-taking-seriously | <p>In September 2019 Fahy et al. <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/acel.13028" rel="nofollow noreferrer">published</a> results from the TRIIM (Thymus Regeneration, Immunorestoration, and Insulin Mitigation) trial. Their stated goals were to investigate whether they could restore the immune syste... | 406 | |
epigenetics | Is there any example of genetic mechanism of delayed onset toxic effects? | https://biology.stackexchange.com/questions/78447/is-there-any-example-of-genetic-mechanism-of-delayed-onset-toxic-effects | <p>We know that exposure to many toxic chemicals during embryonic development may show toxic effects later in life. It is called Developmental Origins of Health and Disease (DOHAD). Most of the mechanisms reported behind these kind of toxic effects are epigenetic. I could not find any genetic mechanism in the literatur... | 407 | |
epigenetics | Searching for reference regarding the impact of famine on a woman's grandchildren | https://biology.stackexchange.com/questions/113229/searching-for-reference-regarding-the-impact-of-famine-on-a-womans-grandchildre | <p>I was once told that if a woman experiences a famine, her grandchildren will show epigenetic changes because the egg that the intervening mother came from also experienced the famine.</p>
<p>In other words, the grandchild would be more susceptible to obesity, due to the grandmother's nutritional environment, even th... | <p>Here's an article in Science about the phenomenon:</p>
<p><a href="https://www.science.org/content/article/moms-environment-during-pregnancy-can-affect-her-grandchildren" rel="nofollow noreferrer">https://www.science.org/content/article/moms-environment-during-pregnancy-can-affect-her-grandchildren</a></p>
<p>It ref... | 408 |
epigenetics | Function and Mechanism of Height Genes | https://biology.stackexchange.com/questions/37208/function-and-mechanism-of-height-genes | <p>I have an inquiry regarding the exact function of height genes.</p>
<p>To my knowledge, although they are heavily regulated by epigenetic factors, height genes can have either an "on" or an "off" allele, and the probability of the person being "tall" shows positive correlation with the number of "on" height genes a... | 409 | |
epigenetics | DNA methylation and genome size | https://biology.stackexchange.com/questions/2680/dna-methylation-and-genome-size | <p>Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability in <em>Drosophila melanogaster</em> and yeast, both genomes much smaller than mammalian or plant genomes. Could it b... | <blockquote>
<p>Is there any relationship between DNA methylation as a level of
stability to epigenetic states and genome size?</p>
</blockquote>
<p>I would say yes, because methylation is used to disable genes in differentiated cells. Disabled genes in differentiated cells generally need to stay disabled to maint... | 410 |
epigenetics | Do stem cells have no epigenome? | https://biology.stackexchange.com/questions/98898/do-stem-cells-have-no-epigenome | <p>Till now I thought that embryonic stem cells have no epigenome as they are pluripotent. (I thought that since epigenome is what gives a cell its identity, no cellular identity means no epigenome) I saw something similar to this on this Wikipedia page. <a href="https://en.wikipedia.org/wiki/Reprogramming#Embryonic_de... | <p>So there are a couple of things to bear in mind.</p>
<ol>
<li><p>pluripotent does not mean that all genes are active. It means that the stem cells have the ability to form different cell types. However, it still needs to keep the cellular programme of a neuron for example silent. So the epigenome is still present to... | 411 |
epigenetics | Why are adenoviral vector vaccines safe in terms of insertion mutagenesis due to genome integration and E4 region's proteins effects? | https://biology.stackexchange.com/questions/98143/why-are-adenoviral-vector-vaccines-safe-in-terms-of-insertion-mutagenesis-due-to | <p><strong>Disclaimer</strong>: I'm neither a genetics professional nor an anti-vax fanatic, I just tried to compare COVID-19 vaccine types currently available on the market and got some questions that I'd like to answer rationally.</p>
<p>Some of the vaccines that are being actively used now are based on adenoviral ve... | <p>This question envisages putative harmful changes arising in host tissue cells infected with the replication-defective virus of a 'vectored' vaccine.</p>
<p>The scenarios of the question leave out of account a significant factor that opposes such putative harms. That is, one of the main purposes and effects of such v... | 412 |
epigenetics | Can one talk about deacetylation of a promoter rather than associated histone? | https://biology.stackexchange.com/questions/45268/can-one-talk-about-deacetylation-of-a-promoter-rather-than-associated-histone | <p>I am confused on a detail in a paper I am reading and am not sure whether I am misunderstanding the wording or misunderstanding the concept. I am including the whole abstract of this paper for background:</p>
<blockquote>
<p><strong>Epigenetic regulation of uterine biology by transcription factor KLF11 via posttran... | <p>The authors obviously meant to write that the histones associated with the promoter become deacetylated. They cannot mean the promoter itself as that is DNA.</p>
<p>What they wrote is not shorthand or acceptable alternative usage, but just a mistake — published papers often contain typos and mistakes of this sort. ... | 413 |
epigenetics | why nucleosome spacing is longer in heterochromatin than euchromatin | https://biology.stackexchange.com/questions/80561/why-nucleosome-spacing-is-longer-in-heterochromatin-than-euchromatin | <p>Heterochromatin is defined as tightly packed form of DNA. But some experiments show that the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are longer than those with euchromatin marks. why packed DNA has longer spacing?</p>
<p>e.g in article :Genome-Wide Nucleosome... | 414 | |
epigenetics | Can the SAME histone tail have both H3K4me3 and H3K27me3? | https://biology.stackexchange.com/questions/104546/can-the-same-histone-tail-have-both-h3k4me3-and-h3k27me3 | <p>I'm studying bivalent promoters and enhancers. I understand that the same region of genome can have both H3K4me3 and H3K27me3.
But can they occur on the same histone tail?
Please provide me with a reference to support your answer.</p>
| <p><a href="https://www.nature.com/articles/s41467-018-04836-y" rel="nofollow noreferrer">This paper</a> suggests that people have tested if two proteins can bind on a histone tail that contains both epigenetic marks. This implies that indeed both markings can be on the same tail.</p>
<p>"Next, we investigated if ... | 415 |
epigenetics | Are prions an important driver in evolution? | https://biology.stackexchange.com/questions/1130/are-prions-an-important-driver-in-evolution | <p>I understand that prions have been implicated in the passing on of epigentic information<sup>[<a href="http://dx.doi.org/10.1016/j.cell.2009.02.044" rel="nofollow">1</a>]</sup>. Are prions thought to play a significant role in the evolution of organisms?</p>
<ol>
<li><a href="http://dx.doi.org/10.1016/j.cell.2009.0... | <p>It is proposed that prions are a good mechanism for "testing" phenotypic variation.</p>
<p>There are many identified proteins with prion-determining domains (PrD) in the yeast genome that can spontaneously switch between conformations with some low probability (eg: check <a href="http://www.yeastgenome.org/cgi-bin/... | 416 |
epigenetics | What causes cellular differentiation? | https://biology.stackexchange.com/questions/85563/what-causes-cellular-differentiation | <p>Each cell in our body contains identical dna. And, yet some cells become liver cells, some become brain cells etc. How this happens , when all of them has same dna? Is it because of epigenetic control of gene expression?</p>
| 417 | |
epigenetics | Can the restless leg syndrome may have been caused due to natural selection? | https://biology.stackexchange.com/questions/45295/can-the-restless-leg-syndrome-may-have-been-caused-due-to-natural-selection | <p><strong>Disclaimer</strong>: I don't know how much restless the leg has to be, in order to be considered a syndrome. </p>
<p>RLS runs not only in my family but also several people in the locality. My hypothesis is that RLS is a genetic/epigenetic adaptation to prevent mosquitoes or other insects from sucking blood.... | 418 | |
epigenetics | If a receptor is inhibited throughout embryogenesis, could there be observable phenotypic differences in the adult? | https://biology.stackexchange.com/questions/7543/if-a-receptor-is-inhibited-throughout-embryogenesis-could-there-be-observable-p | <p>So I read a journal article entitled <a href="http://www.ncbi.nlm.nih.gov/pubmed/22612345" rel="nofollow">"Maternal hypoxia and caffeine exposure depress fetal CV function during primary organogenesis</a>" (Momoi, et al., 2012) and in essence the article speaks of the period of time in embryological development when... | 419 | |
epigenetics | What’s so remarkable about position effect variegation? | https://biology.stackexchange.com/questions/103005/what-s-so-remarkable-about-position-effect-variegation | <p>I am reading Albert et. al’s Molecular Biology of the Cell and at one point the authors discuss the idea of “position effect variegation.” They mention that through events of DNA relocation, it’s possible for portions of echromatic DNA to become heterochromatic by being positioned next to heterochromatic DNA. They s... | <p>Re:</p>
<blockquote>
<p>In particular, if the underlying DNA structure is changing, then
wouldn’t we expect the progeny to inherit these epigenetic changes?
Why is it so remarkable?</p>
</blockquote>
<p>Given the context of the quote, the "variegation" part of the phrase refers to gene expression sometimes... | 420 |
epigenetics | Spermatogenesis in humans - timing of phases and chromatin modifications | https://biology.stackexchange.com/questions/52184/spermatogenesis-in-humans-timing-of-phases-and-chromatin-modifications | <p>I'm interested in the timing of events during <em>human</em> spermatogenesis, ideally with some references I can build off of. Specifically, I am trying to pin down the number of days for:</p>
<ul>
<li>Spermatogenesis, beginning to end (I have come across 65, 75, and 100). </li>
<li>Leptotene stage</li>
<li>Zygoten... | <h2><strong>Spermatogenesis (Beginning to end):</strong></h2>
<pre><code>64 +- 8 days (range 42 to 76)
</code></pre>
<p>There is considerable individual variation. This includes time in epididymis.</p>
<p>Amann 2008 argue for 74 days based on early study by Clermont 1972.
Also argue that biopsies are still needed on... | 421 |
epigenetics | What type of factor is practice of motor skills? | https://biology.stackexchange.com/questions/95369/what-type-of-factor-is-practice-of-motor-skills | <p>I recently asked a question about the cause of motor laterality: <a href="https://biology.stackexchange.com/questions/95291/what-causes-motor-laterality-side-dominance">What causes motor laterality/ side dominance?</a></p>
<p>I understand that there can be genetic factors, epigenetic factors, or environmental factor... | 422 | |
epigenetics | Does anyone know if there is a term to describe the following process? | https://biology.stackexchange.com/questions/71807/does-anyone-know-if-there-is-a-term-to-describe-the-following-process | <p>I'm actually currently studying physics but this came up in my textbook (taken from Giancoli 7th edition section 16-10):</p>
<p>The random (thermal) velocities of molecules in a cell affect cloning. When a bacterial cell divides, the two new bacteria have nearly identical DNA. Even if the DNA were perfectly identic... | <p><strong>The two terms of main interest to you</strong></p>
<p><a href="https://en.wikipedia.org/wiki/Cellular_noise" rel="nofollow noreferrer"><strong>Cellular noise</strong></a></p>
<blockquote>
<p>Cellular noise is random variability in quantities arising in cellular biology. For example, cells which are genetical... | 423 |
epigenetics | Are hormones the main factor for determining sexual orientation? | https://biology.stackexchange.com/questions/116198/are-hormones-the-main-factor-for-determining-sexual-orientation | <blockquote>
<p>First off, it's not "we don't know," it's "they don't know." Just because some sources are uncertain doesn't mean the answer isn't out there. Consensus doesn’t determine truth. Look at how many still believe in astrology, miracles, or gods. Answers emerge over time, usually in pocket... | <h3>Possibly yes, but <em>not the way you think</em>!</h3>
<p>The use of hormones to influence sexual orientation has a terrible history, which illustrates that it is not very simple to change sexual behavior. <a href="https://en.wikipedia.org/wiki/Alan_turing" rel="nofollow noreferrer">Alan Turing</a> was involuntari... | 424 |
epigenetics | Techniques of molecular medicine/biology for aesthetic medicine? | https://biology.stackexchange.com/questions/82869/techniques-of-molecular-medicine-biology-for-aesthetic-medicine | <p>Are there scientifically valid methods (possibly in the developmental stage) that can be used for aesthetic medicine. Usually surgical of physical therapies are used for aesthetic medicine, but actually all the problems of aesthetic appearance should be traceable to the genetic/epigenetic causes and that is why the ... | 425 | |
epigenetics | Cell growth conditions for preparing electrocompetent cells | https://biology.stackexchange.com/questions/5295/cell-growth-conditions-for-preparing-electrocompetent-cells | <p>Usually the protocol for preparing electrocompetent E. coli cells calls for growing the cells at 37deg and 225rpms until they reach OD of 0.3. I was wondering, is there any reason they should grow at optimal conditions for growth, instead of at suboptimal, for example at 30 degrees? Also, what is the physiological/e... | <p>I'm new so I can't make this a comment, and I don't think the other commenter addressed your questions so here it goes: I don't think there will be much difference, if any, between 0.2 and 0.3 OD. Once you get higher and the cells start transitioning into a stationary phase is a different story. Did you mean to ask ... | 426 |
epigenetics | X-inactivation in ovaries | https://biology.stackexchange.com/questions/20277/x-inactivation-in-ovaries | <p><strong>Background</strong></p>
<p>In all <a href="http://en.wikipedia.org/wiki/Eutheria" rel="nofollow">eutherian</a> (mammals excluding the marsupials), the female (who is $XX$ for the pair of sexual chromosomes) inactivates one of her $X$. This is called <a href="http://en.wikipedia.org/wiki/Dosage_compensation"... | <p>See these two papers:</p>
<ul>
<li><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000860#abstract0" rel="nofollow">Early Loss of Xist RNA Expression and Inactive X Chromosome Associated Chromatin Modification in Developing Primordial Germ Cells</a></li>
<li><a href="http://www.plosgene... | 427 |
epigenetics | Prader-Willi Syndrome and Angelman Syndrome? | https://biology.stackexchange.com/questions/40963/prader-willi-syndrome-and-angelman-syndrome | <p>On the website <a href="http://www.whatisepigenetics.com/fundamentals/2/" rel="nofollow">http://www.whatisepigenetics.com/fundamentals/2/</a> it states that </p>
<blockquote>
<p>the imprint disorders Prader-Willi syndrome and Angelman syndrome, display an abnormal phenotype as a result of the absence of the pater... | <p>In a wild-type human, you will inherit one paternal chromosome and one maternal chromosome, in this case, chromosome 15.</p>
<p>The paternal chromosome which is packaged into the sperm will be methylated in such a way that the <a href="http://omim.org/entry/601623" rel="nofollow">Ubiqitin-Protein Ligase E3A</a> (<e... | 428 |
epigenetics | Detecting Introns and Exons | https://biology.stackexchange.com/questions/8204/detecting-introns-and-exons | <p>I know that when RNA is transcribed from the original strand of DNA it contains introns and exons, and that the introns are spliced out of the strand to provide genetic diversity. However, what I don't understand is, how does whatever is doing this splicing know whether the section it is reading is an intron or an e... | <p>Quick answer: we don't really know.</p>
<p>As WYSIWYG said, splice sites <em>do</em> have a sequence signature. The image below (taken from <a href="http://dx.doi.org/10.1016/j.sbi.2004.05.007" rel="nofollow noreferrer">[1]</a>) shows the consensus for human acceptor and donor sites:</p>
<p><img src="https://i.sstat... | 429 |
epigenetics | Is it possible to do chip-seq on a specfic region? | https://biology.stackexchange.com/questions/7424/is-it-possible-to-do-chip-seq-on-a-specfic-region | <p>Is it possible to do Chip-Seq on specific region of the genome. The idea is to enrich before the sequencing step to have more sensitivity.</p>
| <p>If the question here is to perform an assay that only sequences from a specific set of segments of the genome, you probably could, but it would be a lot of work and you'd need a good reason to want to go through that trouble.</p>
<p>Not sure how you would limit the nucleotides you get back to a specific region of t... | 430 |
epigenetics | Why do I have a lot in common with my mother? | https://biology.stackexchange.com/questions/10880/why-do-i-have-a-lot-in-common-with-my-mother | <p>I have not spoken to my mother in 15 years but recently connected with her and her side of the family. I was primarily raised in a different sub-culture after the age of 4. As it turns out I "accidentally" have a lot in common with my maternal relatives. We like and dislike many of the same things. Is there some dom... | <p>In this answer I mainly repeat the comments!</p>
<p>There are several reasons why you might share some traits with your mother.</p>
<ul>
<li>genetic (see below)</li>
<li>epigenetic</li>
<li>environmental influence while being in the womb</li>
<li>environmental influence up to the time you were 4 years old</li>
<li... | 431 |
epigenetics | Is there a genomic code for nucleosome positioning? | https://biology.stackexchange.com/questions/30652/is-there-a-genomic-code-for-nucleosome-positioning | <p>What does a genomic code for nucleosome positioning in eukaryotes actually mean? By the code is it right to think that specific DNA sequences favour nucleosomes and others don't? I see that there for and against arguments on this topic. What is the current view on this topic? </p>
| <p>The genome is the complete set of DNA in an organism, including genes and non-gene sequences of base pairs (bp).1 Each codon of three base pairs in a DNA sequence specifies one of twenty different amino acids. There are four available bases in DNA; Adenine (A), Thymine (T), Guanine (G), and Cytosine (C). Four lette... | 432 |
epigenetics | Allele-specific bisulfite sequencing | https://biology.stackexchange.com/questions/48641/allele-specific-bisulfite-sequencing | <p>When evaluating methylation status at various CpG sites after sequencing, how much consideration should one give to random single base pair insertions and deletions. Suppose there is a CA dinucleotide; can we assume that the CA is native to the sequence or results from a G deletion especially when the latter is susp... | <p>I agree with Vance, we need a little more detail to better answer your question. From what I can tell, you are asking whether a single nucleotide polymorphism (SNP) that results in the addition of a cytosine base to your sequence is of concern when examining the methylation signature of that sequence. </p>
<p>I wou... | 433 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.