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Question: <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... | https://biology.stackexchange.com/questions/15509/how-do-tlr1-tlr2-activate-the-myd88-dependent-pathway |
Question: <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 crosstal... | https://biology.stackexchange.com/questions/28464/expression-mechanism-of-ror1-in-healthy-tissue |
Question: <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 ... | https://biology.stackexchange.com/questions/10476/how-does-formaldehyde-pbs-or-methanol-fixation-of-cells-affect-lysosomal-ph |
Question: <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 thro... | https://biology.stackexchange.com/questions/104524/how-does-the-phosphorylation-state-of-4e-bps-affect-translation-of-nuclear-encod |
Question: <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 inhibito... | https://biology.stackexchange.com/questions/40144/differences-between-synaptic-connections |
Question: <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.<... | https://biology.stackexchange.com/questions/60294/reward-pathway-sequence-of-events |
Question: <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 sugge... | https://biology.stackexchange.com/questions/19856/how-does-sodium-valproate-cause-neural-plasticity |
Question: <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 que... | https://biology.stackexchange.com/questions/1469/structure-of-rap-antibodies-specifically-rap-5 |
Question: <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... | https://biology.stackexchange.com/questions/45666/are-there-well-studied-examples-of-erad-mediated-membrane-insertion-especially |
Question: <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... | https://biology.stackexchange.com/questions/112263/what-are-the-factors-affecting-reaction-time-and-or-reflex-velocity |
Question: <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 tha... | https://biology.stackexchange.com/questions/89598/kras-gene-and-k-ras-mutations |
Question: <p>For someone who is interested in learning about the discovery of epigenetics, which are the foundational defining papers in the area?</p>
Answer: <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="htt... | https://biology.stackexchange.com/questions/264/defining-papers-in-epigenetics |
Question: <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 ha... | https://biology.stackexchange.com/questions/101301/gene-regulation-and-epigenetics-in-specialized-cells |
Question: <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 m... | https://biology.stackexchange.com/questions/115592/quantitatively-measure-the-impact-of-dna-vs-epigenetics |
Question: <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 t... | https://biology.stackexchange.com/questions/80065/do-epigenetics-determine-the-proteins-a-cell-produces-and-therefore-its-functio |
Question: <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>
Answer: <p>First, let me qualify the idea of... | https://biology.stackexchange.com/questions/88325/can-epigenetics-have-positive-impact-on-the-genes-are-development |
Question: <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... | https://biology.stackexchange.com/questions/90676/dna-methylation-and-the-validity-of-the-definition-of-epigenetics |
Question: <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... | https://biology.stackexchange.com/questions/95332/role-of-epigenetics-in-evolution-and-transmission-of-defects-caused-by-drugs |
Question: <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-re... | https://biology.stackexchange.com/questions/94160/does-epigenetics-suggest-there-is-at-least-some-element-of-truth-to-lamarckism |
Question: <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 e... | https://biology.stackexchange.com/questions/101323/epigenetic-marks |
Question: <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 ne... | https://biology.stackexchange.com/questions/46228/how-does-epigenetics-affect-the-birth-conditions-via-alcohol |
Question: <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 ... | https://biology.stackexchange.com/questions/3789/can-epigenetic-changes-affect-reproductive-success |
Question: <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 wom... | https://biology.stackexchange.com/questions/33/transmission-of-epigenetic-regulation-through-surrogate-mother |
Question: <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 understa... | https://biology.stackexchange.com/questions/66370/how-do-cells-become-differentiated-using-epigenetics-despite-having-the-same-gen |
Question: <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... | https://biology.stackexchange.com/questions/41192/are-epigenetic-changes-involved-in-evolution |
Question: <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 scie... | https://biology.stackexchange.com/questions/77956/semantics-question-epigenetic-mark-on-a-persons-dna |
Question: <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 r... | https://biology.stackexchange.com/questions/85168/studying-the-epigenetic-variability-can-i-use-snps |
Question: <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... | https://biology.stackexchange.com/questions/21982/does-the-jungian-notion-of-collective-unconsciousness-have-any-legitimacy-in-the |
Question: <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 beco... | https://biology.stackexchange.com/questions/46074/determination-of-genes-to-be-modified-in-epigenetics |
Question: <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://o... | https://biology.stackexchange.com/questions/98516/are-there-epigenetic-effects-in-the-regulation-of-human-height |
Question: <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>... | https://biology.stackexchange.com/questions/60218/have-researchers-discovered-how-epigenetic-information-is-passed-down-during-cel |
Question: <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 cance... | https://biology.stackexchange.com/questions/71802/epigenetic-vs-environmental-factors |
Question: <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>
Answer: | https://biology.stackexchange.com/questions/84701/what-causes-epigenetic-dysregulation-in-cancer |
Question: <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>
Answer: <p>Yes, epigenetic changes does affect the phenotype. This is here the whole interest behind epigenetic. E... | https://biology.stackexchange.com/questions/55298/can-epigenetic-structures-carry-a-trait |
Question: <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 o... | https://biology.stackexchange.com/questions/52372/can-a-gene-expression-or-epigenetic-user-history-be-found-in-the-body |
Question: <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 fac... | https://biology.stackexchange.com/questions/111946/variance-in-epigenetic-drift-rate-between-different-species |
Question: <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>
Answ... | https://biology.stackexchange.com/questions/51963/are-enhancers-and-silencers-considered-as-epigenetic-modifications |
Question: <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-o... | https://biology.stackexchange.com/questions/5342/how-are-epigenetic-marks-transmitted-during-cell-division |
Question: <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>
Answer: <p>There ar... | https://biology.stackexchange.com/questions/64695/is-there-any-biological-basis-for-the-emphasis-on-the-value-of-the-firstborn-son |
Question: <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 Beckwi... | https://biology.stackexchange.com/questions/7691/how-might-ivf-and-related-technologies-alter-epigenetic-marks |
Question: <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>
Answer: <p>First of all, the nature of penetrance is almost entirely unknown... | https://biology.stackexchange.com/questions/202/what-are-the-criteria-for-determining-the-influence-of-epigenetic-factors |
Question: <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 ... | https://biology.stackexchange.com/questions/50788/is-post-transcriptional-regulation-of-gene-expression-an-epigenetic-process |
Question: <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 a... | https://biology.stackexchange.com/questions/70090/how-can-epigenetic-changes-be-erased-if-they-are-inherited |
Question: <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>
Answer: <p>Alleles are passed down (to individuals) and crea... | https://biology.stackexchange.com/questions/20020/what-is-wrong-with-this-analogy-individuals-are-to-alleles-what-governments-are |
Question: <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 i... | https://biology.stackexchange.com/questions/92317/has-lamarckism-been-discredited |
Question: <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 epigen... | https://biology.stackexchange.com/questions/114020/can-instincts-disappear-after-a-long-period-of-non-usefulness |
Question: <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 cau... | https://biology.stackexchange.com/questions/7380/are-there-any-studies-of-epigenetic-difference-between-twins-during-their-lifesp |
Question: <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 experim... | https://biology.stackexchange.com/questions/84534/are-epigenetic-modifications-the-most-stable-mechanisms-for-cell-differentiation |
Question: <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 ... | https://biology.stackexchange.com/questions/116212/data-for-epigenetic-patterns-of-human-tissue-at-the-gene-level |
Question: <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.stac... | https://biology.stackexchange.com/questions/94661/tree-pest-coevolution |
Question: <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 fathe... | https://biology.stackexchange.com/questions/98869/does-parental-conflict-lead-to-genes-combining-important-functions-with-function |
Question: <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 (se... | https://biology.stackexchange.com/questions/52664/what-is-an-aromatic-cage-and-what-does-it-do |
Question: <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... | https://biology.stackexchange.com/questions/50441/can-the-brain-influence-gene-expression |
Question: <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... | https://biology.stackexchange.com/questions/3432/literature-about-putative-epigenetic-state-changes-in-mammal-sequences-after-clo |
Question: <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 (a... | https://biology.stackexchange.com/questions/95066/do-identical-twins-have-the-same-metabolism-rate-at-birth |
Question: <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>
Answer: | https://biology.stackexchange.com/questions/23153/can-sealed-epiphyseal-growth-plates-theoretically-be-restored-via-epigenetic-or |
Question: <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 o... | https://biology.stackexchange.com/questions/108155/are-all-genes-capable-of-being-switched-on-or-off |
Question: <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 [... | https://biology.stackexchange.com/questions/114042/did-operon-evolve-after-endosymbiosis-and-specialisation-of-mitochondria |
Question: <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 methy... | https://biology.stackexchange.com/questions/31186/genetic-imprinting-and-cell-differentiation |
Question: <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 methy... | https://biology.stackexchange.com/questions/10365/how-correlated-are-proximally-related-cpg-sites-in-human-dna |
Question: <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 ... | https://biology.stackexchange.com/questions/82878/computational-approaches-for-making-hypotheses-about-the-effects-of-genetic-engi |
Question: <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 s... | https://biology.stackexchange.com/questions/67642/what-determines-the-differences-between-differentiated-cells |
Question: <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... | https://biology.stackexchange.com/questions/79868/can-diet-supplementation-and-or-drugs-affect-sexual-dimorphism |
Question: <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 i... | https://biology.stackexchange.com/questions/21145/is-the-mutation-rate-in-organisms-in-general-consistent-over-the-genome |
Question: <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.pcb... | https://biology.stackexchange.com/questions/113390/how-does-comparing-shuffled-proteomes-to-the-unshuffled-ones-help-us-understand |
Question: <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 i... | https://biology.stackexchange.com/questions/74035/can-the-environment-affect-genes-and-adaptation-in-offspring |
Question: <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 sa... | https://biology.stackexchange.com/questions/112507/how-long-does-it-take-for-a-gene-to-be-switched-on-or-off-through-the-process-of |
Question: <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 inv... | https://biology.stackexchange.com/questions/16861/psychological-database-with-sequenced-dna-records |
Question: <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... | https://biology.stackexchange.com/questions/93075/can-untargeted-metabolomics-detect-epigenomic-changes-such-as-methylation |
Question: <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 ther... | https://biology.stackexchange.com/questions/101284/higher-order-evolutionary-adaptations |
Question: <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 i... | https://biology.stackexchange.com/questions/43608/molecular-cellular-biology-textbook-to-consolidate-what-i-know-about-molecular-c |
Question: <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, ... | https://biology.stackexchange.com/questions/74959/what-is-the-relationship-between-induction-of-cell-differentiation-and-dna-methy |
Question: <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 im... | https://biology.stackexchange.com/questions/92906/is-this-trial-that-reversed-aging-in-humans-worth-taking-seriously |
Question: <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... | https://biology.stackexchange.com/questions/78447/is-there-any-example-of-genetic-mechanism-of-delayed-onset-toxic-effects |
Question: <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 environmen... | https://biology.stackexchange.com/questions/113229/searching-for-reference-regarding-the-impact-of-famine-on-a-womans-grandchildre |
Question: <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" heig... | https://biology.stackexchange.com/questions/37208/function-and-mechanism-of-height-genes |
Question: <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. ... | https://biology.stackexchange.com/questions/2680/dna-methylation-and-genome-size |
Question: <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#Em... | https://biology.stackexchange.com/questions/98898/do-stem-cells-have-no-epigenome |
Question: <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 ade... | https://biology.stackexchange.com/questions/98143/why-are-adenoviral-vector-vaccines-safe-in-terms-of-insertion-mutagenesis-due-to |
Question: <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 vi... | https://biology.stackexchange.com/questions/45268/can-one-talk-about-deacetylation-of-a-promoter-rather-than-associated-histone |
Question: <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 ... | https://biology.stackexchange.com/questions/80561/why-nucleosome-spacing-is-longer-in-heterochromatin-than-euchromatin |
Question: <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>
Answer: <p><a href="https://www.nature.com/articles/s41467-018-04836-y"... | https://biology.stackexchange.com/questions/104546/can-the-same-histone-tail-have-both-h3k4me3-and-h3k27me3 |
Question: <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.c... | https://biology.stackexchange.com/questions/1130/are-prions-an-important-driver-in-evolution |
Question: <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>
Answer: | https://biology.stackexchange.com/questions/85563/what-causes-cellular-differentiation |
Question: <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 suck... | https://biology.stackexchange.com/questions/45295/can-the-restless-leg-syndrome-may-have-been-caused-due-to-natural-selection |
Question: <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 develo... | https://biology.stackexchange.com/questions/7543/if-a-receptor-is-inhibited-throughout-embryogenesis-could-there-be-observable-p |
Question: <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 D... | https://biology.stackexchange.com/questions/103005/what-s-so-remarkable-about-position-effect-variegation |
Question: <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>
<... | https://biology.stackexchange.com/questions/52184/spermatogenesis-in-humans-timing-of-phases-and-chromatin-modifications |
Question: <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 environmen... | https://biology.stackexchange.com/questions/95369/what-type-of-factor-is-practice-of-motor-skills |
Question: <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 perfect... | https://biology.stackexchange.com/questions/71807/does-anyone-know-if-there-is-a-term-to-describe-the-following-process |
Question: <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... | https://biology.stackexchange.com/questions/116198/are-hormones-the-main-factor-for-determining-sexual-orientation |
Question: <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 i... | https://biology.stackexchange.com/questions/82869/techniques-of-molecular-medicine-biology-for-aesthetic-medicine |
Question: <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 physi... | https://biology.stackexchange.com/questions/5295/cell-growth-conditions-for-preparing-electrocompetent-cells |
Question: <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_com... | https://biology.stackexchange.com/questions/20277/x-inactivation-in-ovaries |
Question: <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... | https://biology.stackexchange.com/questions/40963/prader-willi-syndrome-and-angelman-syndrome |
Question: <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 intr... | https://biology.stackexchange.com/questions/8204/detecting-introns-and-exons |
Question: <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>
Answer: <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... | https://biology.stackexchange.com/questions/7424/is-it-possible-to-do-chip-seq-on-a-specfic-region |
Question: <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 ther... | https://biology.stackexchange.com/questions/10880/why-do-i-have-a-lot-in-common-with-my-mother |
Question: <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>
Answer: <p>The genome is... | https://biology.stackexchange.com/questions/30652/is-there-a-genomic-code-for-nucleosome-positioning |
Question: <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 latt... | https://biology.stackexchange.com/questions/48641/allele-specific-bisulfite-sequencing |
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