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Everything posted by Dagl1

  1. An overexpression screen? You have a WT yeast, in which you knockout an essential gene, now this has become a lethal phenotype, if during this time you now add start overexpression of a random gene, and your yeast survives, then you have rescued said phenotype. One way to do this is to make a overexpression library, get your plate/plates with knockouts and just add the library. Then pick the clones that survive and genotype them (or if you added barcodes to your plasmid library, identify by barcodes). If the essential gene knockout leads to a lethal phenotype only under certain conditions (cold sensitivity, some amino acid or other substance auxotrophicity) it is easier, because if your essential gene kills the yeast in all conditions, it is much harder to make sure your initial plate has 100% knockouts (since they won't grow). hope something like this helps
  2. Could you not just design some primers for your specific genes, do PCR amplification and check on an agarose gel if the sizes are larger/smaller than expected? I am not entirely sure if that is the most feasible method, but at least I would assume you could see deletions, and duplications if they happened in the same region (of course if a duplication happened to be present in another chromosomal region, I would expect these to not be visible as the primers wouldn't lead to PCR amplification of 1 long transcript but just 2 equal sized ones, which I suppose you won't detect. Otherwise, can't you design some MLPA probes? I am not very familiar with qPCR MLPA validation, but if qPCR and sybr Green are used in this manner for duplication and deletion validation (even if it isn't the best way), then might just design the qPCR MLPA probe sets (I am not sure if that is feasible). I think you might find some information in: https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-13-55 Maybe someone with more knowledge of this particular subject can come along and give you some more useful answers, but I think with that paper and other papers you should find some way ("I searched for deletion and duplication validation of novel genes"). -Dagl
  3. I quoted only the relevant responses I want to discuss: 1. You say that each profile has its own specific pattern, and then you talk about gene expression and silencing, but that doesn't really answer my question: How did you determine what the boundaries are of 1 profile versus the next, if 2 people have the exact same gene expression except for 1 gene, are they the same profile? If so, at how much deviation do we find ourselves in another profile? How did you determine these boundaries? Have you considered alternatives? 2. So your profiles always match a trait, it never is wrong? What does 'to different degrees' mean when we are talking about matching. Either a profile associates with it or not right? Or have you scaled all the physical traits, so that one can get a score of 0 to x for 'long neckedness'? Please elaborate how they are matched, how things can be partially matched, and how is it possible that it matches always, you realise this is very unlikely with 26000 samples... 3. I am asking about how you chose to determine what physical phenotypes there were, you say it always matches, so how did you determine what a specific trait is. I don't care about why you chose these two to share, I am wondering about how you generated your list of total physical phenotypes, how you determined the boundaries and why not alternatives. 4. A list of people that I have to look up is not evidence, A I am a person, I can't quantify physical traits without significant amounts of bias, instead a computer should do this or a panel of people with very clear instruction. B Your list is going to be the definition of confirmation bias, I don't particularly doubt that these people from your dataset, for which you have produced epigenetic pattern definitions and physical trait definitions and which you then matched, will show the association that you are trying to tell us about. However, that doesn't mean anything; if I show you a bunch of pingpong balls that are all red, and I then tell you that I found red to be associated with pingpong balls, because, look all of the red pingpong balls that I am showing are red. Then this doesn't hold up. This is why we need frequency tables of the epigenetic patterns and of the physical traits, I would also love to actually see the statistics and the tests you have done to confirm your finding (again, you don't have to go showing everything, just of this one experiment). At the moment, I find it hard to believe that you have discovered anything, let alone came across an Nobel prize-winning discovery. This has little to do with the evidence, but a lot with your presentation and communication (skills). You might have discovered something really cool, but so far you have not provided evidence yet, and the lack in scientific rigour and the ease at which you apparently accept something to be evidence, makes it very hard for me to believe that you did actually find something. I think that regardless of what you have found, this is something you can improve on a lot! I am looking forward to hearing and seeing a bit more of the more methodical, quantitative and statistical side, since that is eventually how we can falsify information. Goodluck!
  4. How are epigenetic profiles defined, how are they measured or determined, where are there boundaries? What does this list tell us? Is the frequency at which epigenetic profiles and these features match higher than what would be expected from regular distributions? How often do these profiles and features match and how often do they not? Are there differences for particular features or profiles? What is the total sample size of the evidence? How are these features defined, why these features and not other ones? At the moment, I don't really see any evidence yet, nor explanation of your methods. It would be very useful if you could describe in a few paragraphs what you have done (in this or another particular experiment, you don't have to explain ALL your evidence, just start by explaining a single one very well), and also describe the results. This txt file is literally a bunch of names, there seems to be no evidence yet, nor does it give me any real idea of what the list describes or what we should interpret from it. I hope you can provide more explanations and answer our questions! Kind regards, Dagl
  5. This is a discussion forum, so people here would like to discuss things. You have stated you made some discoveries (and briefly and pretty vaguely described those discoveries), but what is there to discuss. I am interested in epigenetics, I would love to see and discuss your research, but then you need to post some of it. If you have so much evidence, what about sharing some of it HERE. Otherwise what is the point of this thread, without evidence there is nothing for us to discuss, so it seems like you are just (for a lack of a better term) gloating about discoveries made. Basically give us anything concrete, give us some evidence even if it is just a small part of all the discoveries you made. Or share the first 20(?) pages of your 'book' (not sure what to call it or how long it is). Things like 'causes of several epigenetic profiles' is pretty vague, it doesn't explain much and seems to be refuted by 'no', as that equals the amount of evidence provided. What tests did you to verify your discoveries, what alternatives exist to your explanation, did you test them. What about your general measurement methods, for what cells or organisms does this count? What is the difference between the epigenetic profiles? I assume you will have done some analyses of histone modifications, DNA methylation, residual RNA concentrations, and/or 3D genome structure. Just post any of those results, it could just be a bunch of pictures of Chip-seq analysis or whatever you have as evidence. Please note that I am not bashing you or your ideas, instead I hope to make you see why the current way of sharing your ideas may not be suitable for this forum. If you just want to let people know you made some discoveries, I think a profile message would be good. If you want to share your work, please do so! Me and others (probably) are interested in your discoveries, but with that must come the opportunity to review the evidence and doubt it. Right now it is similar to me saying that I have found a unifying theory of physics, or that I found novel protein functions, but that is all I tell anyone. Hope to hear more about your work soon! -Dagl
  6. The specific type of lipid may signal that a cell is undergoing apoptosis. Under normal conditions specific lipids are moved to either the outside or the inside of the cell, during apoptosis (and maybe other cell death inductions) a scrambling protein is activated. You may be interesting in those enzymes: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4613456/ for the more general mechanism https://pubmed.ncbi.nlm.nih.gov/28844836/ additional links that I just browsed through: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307283/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914033/ Hope that helps!
  7. A few questions and maybe some suggestions (that you need to verify and check, or use as step off points). I am not a statistician, but I do have experience with statistics. Hopefully I don't say anything just blatantly wrong;/ So you have k keywords, and their averages on a single day. Do you put k keywords into a single variable KEYWORD or do you want to measure whether there is a difference for every k keyword? If you want to do k comparisons, please apply some type of multiple comparison correction as your p value (assuming 0.05 is used as cut-off) only means the type of for a type 1 error is 5%, so if you compare 100 times, we need to make sure that that chance doesn't actually go up, and we do this by reducing the acceptable p value. You will have to provide some more information about your data: Is the variance constant? Is the average of your data a function of time? (so can you make an y= aT +b graph, if so the ARIMA I talk about later can't be applied I think (according to a video about it)) How long are the measurement periods, is seasonality included in your analysis? Now depending on these questions and some other assumptions (that I don't know but you will need to test), and what exactly you want to know (you seem to be interested in a change in frequency, so one could of course take the average frequency of a keyword in a similar period before and after the pandemic, and then just test the two group (each group will have n datapoints (amount of days of each period) and so you can calculate SEM, SD, 95%CI and do regular T-tests (as Prometheus has said, t-tests have assumptions such as the distribution of your data, you will have to test each of these assumptions with a separate test. If you do not meet all the assumptions you can use a non-parametric alternative of the t-test (one for which your data does have all the required things)). With this approach, you measure frequency over almost a year, so seasonality is something to think of. Taking datapoints from the same days in the previous year or years could of course be a way around this seasonality problem. If you do want to analyse your data as a time series, there are several things you need to consider: What exactly do you want to analyze. Are the time series 'different' is really dependent on what you are particularly interested in. Are you interested in the total frequency over time (AuC), are you interested in a change in frequencies per week (a shift from monday to friday), are you interested in something else? From a quick google search, ARIMA seems to be one approach, but I am not entirely sure how to apply that to two datasets. I suppose you would do ARIMA for both and see if they predict similar things, if not then they are different. But if this is the case, then you would still need to find a way to define when the two predictions are 'statistically different'. Maybe someone more into this part of analysis could help out here. https://stats.stackexchange.com/questions/35129/how-to-compare-two-time-series https://stats.stackexchange.com/questions/19103/how-to-statistically-compare-two-time-series Another thing I found is a fixed-effects ANOVA, it seems that the dataset is similar to yours if you can overlay the data from the same days before and after the pandemic (note that ANOVA generally are for 3 or more groups, which is the case on this website, so there most likely is a t-test-like variant of this that you want to use) https://stats.stackexchange.com/questions/12902/comparison-of-time-series-sets Although not that important at the moment, I do wonder if overlaying march 1 2019 and march 1 2020 is actually the best option (as days of weeks change with such an approach) and it may be better to shift it to match days of the week instead of date). I am not sure if that is actually better, but I think it may be an interesting thing to note in your discussion. I hope this at least helps you a bit, but it is important to check yourself what you are and are not allowed to do! A lot of tests that you can perform on SPSS have nice documentation somewhere on the internet that includes the assumptions which need to be met, I like this website a lot: https://statistics.laerd.com/spss-tutorials/linear-regression-using-spss-statistics.php) Kind regards, Dagl
  8. Although you asked Markus, isn't there a lot of material on this? https://en.wikipedia.org/wiki/Heritability_of_autism Of course maybe you are just asking if there are other people in his family, regardless of how much it is inherited?
  9. I unfortunately am not of any help, but am curious to see how this advances and hope some people can hep you out! Well written account of what is up, although I do think you may need to elaborate more on what type of help you exactly want. The resources on various topics you ask for may be too broad (but you never know!). It would probably also help if you explain in more detail what you have done so far regarding the TensorFlow implementation and where you can't see a good way of doing it. Otherwise it may feel to some members that you are asking them to walk you through from start to finish (but as long as you continue providing well written posts that probably won't happen). Good luck!
  10. Note: While writing this, and putting my thoughts on paper, I changed my mind, I am keeping my reasoning because the questions I want to ask still follow from them. Well I do personally hope that we may have a bunch of people there at that point 😛, because what if these aliens try really hard to use microexpressions or are mimicking the general human expressions in order to convey meaning. Anyway that is kind of off topic and more a joke than anything else. Thank you Markus for sharing this, whenever you explain things about how your brain and that of other people on the autistic spectrum works, I feel I get a lot of insight, and your posts are always very well structured! I really like this type of thinking, but I do catch myself not always thinking in this way, although I know I should rationally (this is what I changed my mind on after finishing writing). I have known two people (in high-school) whose thinking and way of doing things was so different from that of others that it seemed to hurt and hamper them a lot. It feels to me that at least the current environment and culture (especially during school years) makes life (seem) miserable for these people. Of course these feelings are not exclusive to any group of people, but it is hard to not think of their neurodivergent thinking as at least a partial cause of these problems. You mention that there are also strong points, which I don't doubt, but I suppose I haven't been around those two long enough to see the strong points come to light: I didn't know them that well, so I might just be only seeing what I saw in school, but from the few talks I did have about how they experienced these things, I didn't get the feeling that they felt their way of thinking was beneficial, it seemed they at the time viewed it as something net negative (Two people do not represent the whole of the spectrum, but because of these cases I find it difficult to not see it is a disability, at least in those people that themselves view it that way (again, we are talking 15-17 year old kids here.)) @Markus Hanke, in your opinion/experience, is this common, and if it is, people later in their lives come to see their neurodivergence as a benefit? I suppose now that I am thinking about these things and analysing my thoughts, it could also be that the kids were bullied and the reason 'given' was their autism, and that this made them feel that 'without autism these people wouldn't bully me" or "if I wasn't autistic, I could be friends with them". I am still interested in what you think, but I see now that these two examples can't or shouldn't be the only thing that I think of, especially with the fact that we were teenagers at the time. -Dagl
  11. I suppose 'plenty' is not a right word, but just so I do understand correctly (and understand the other people's responses as well): The sol system sun (our sun), contains radioactive isotopes, its not a first generation star, so supernovea have happened already. There is fission in stars, regardless if that contributes (or not) significantly to anything within the sun? When you say 'basically' no fission, do we mean: no fission, or fission happens but is basically irrelevant? I am asking because MigL says the following (so I assume that we just mean there is little fission compared to all the fusion going on, not none?) I was wondering if you mistaked me for someone else, but wasn't sure, anyway no problem!
  12. You inherit them from your father and mother, maybe some combinations make very similar phenotypes, maybe just like with eye color, there can be some genes that are dominant or co-dominant. We inherit DNA (and maybe some epigenetic stuff), DNA leads to protein production, and all the proteins together will determine the phenotype (together with the environment). It is really difficult to predict emerging properties, especially when so many genes interact with each other. Thus by just inheriting the right combination, you may get phenotypes that are very similar.
  13. Ehh? He didn't say anything very controversial I think, so ye I think those other criticisms are valid? Like I don't think I have ever heard of anyone describing light as anything other than always being at c? The big bang thing seems pretty much how I have heard and seen it explained, the whole of space time expanding, no consuming anything. Am I missing anything? I was just interested in his statement about fission in stars?
  14. Oh, I thought there was. But maybe I am being a little pedantic, and you may mean there fission doesn't contribute to much in the star? It seems strange to me if there is no fission in stars , there are plenty of radioactive isotopes and it feels logical (I say feel because I don't know) to think that a place full of particles moving at high speed around and towards fissionable elements would also lead to fission?)
  15. Isn't this the same question? We don't know (or at least I don't) which parts of autism are reprogammable at age 10, we can only speculate about it. If the gut micriobiome can affect it THAT MUCH, then you could of course argue that even if you change the DNA of the whole head (or even the gut) you may not be changing the gut microbiome, therefore actually having less effect. But again, at this point is really speculative and I think the question is answered by (bold added by me for clarification)
  16. Pretty sure if you would that in an embryo, and you knew what to tweak then most likely. If you do it in an adult or a 10 year old, maybe, it depends on how much of those things are reversible, but maybe.
  17. Thank you! I would be careful with saying things like: The schizophrenia article is about a model for schizophrenia, which requires the loss of a single allele of SETD1A. The risk of getting schizophrenia increases from SETD1A mutations, but that doesn't mean that by fixing this mouse model we can also fix scihizophrenia, especially if someone has a SETD1A unrelated type of schizoprhenia? The paper regarding autism talks about how autism related symptons will be lessened in mice by correcting SHANK3, but also that SHANK3 is really rare (aprox 2% of autistic people have mutations in SHANK3). So we are again looking at a mouse model where problems are simulated and fixed. I would say that that is a far way off from reversing autism by just switching a gene off. "In mice, we can reduce autism- and schizophrenia-like symptoms, caused by specific mutations that are not the only risk factors in autism/schizophrenia in humans." I would feel pretty confident that if we find someone with SHANK3 mutations, or too little or too much expression of SHANK3, and this person is showing autism-like symptoms, it may be helpful to (once we are good enough at it) gene edit SHANK3, but that isn't going to just fix 'autism' in general.)
  18. They have? Links please, I am interested. I would say that memory formation potential and hormone related stuff will become different the most, other stuff almost by definition as well but I don't know how much of the initial neuron paths/connections will be able to change, that feels kind of structural. I don't think you will suddenly get Neil, but there will certainly be things that change in how it works in that person, and then many years later those differences and different behaviours will manifest more (I imagine that from the moment that you change this person's genes, him and what he would have become will start diverging a lot).
  19. Probably some bone structures will be set, but I suppose (ignoring the full on immune response this would probably elicit) skin colour and any other thing that is dependent on regenerating/remodelling tissue, will at least change a bit. Significant is more a measure of how sure we are, I think could definitely notice the difference, but how extreme those differences would be are hard to predict.
  20. Yes, it seems this is a possibility in black are my comments: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696326/ Communication between the systemic immune system and the brain and its consequence on microglia is a critical poorly understood component of the inflammatory response to systemic disease (78). Systemic infections activate neural and humoral pathways that communicate with the brain and initiate a coordinated set of metabolic and behavioral changes (79). However, these adaptive responses may become maladaptive when microglia have been “primed” by an ongoing pathology and respond to a systemic inflammatory challenge by switching their phenotype to an aggressive pro-inflammatory state (47), adversely affecting neuronal function and potentially leading to a psychotic decompensation through modulating effects of pro-inflammatory cytokines on neurotransmitter function (47). https://minerva-access.unimelb.edu.au/handle/11343/234029#:~:text=Accumulating evidence indicates that inflammation,of structural deficits in psychosis. Peripheral markers of inflammation As described above microglial activation can have pro- or anti-inflammatory effects. Determining which pathway predominates in psychotic disorders in vivo is currently not possible as the available radioligands do not distinguish between M1 and M2 states.117 Nevertheless, evidence that there may be an imbalance in favor of the M1 pathway comes from studies examining peripheral cytokine levels.118 This suggests that medication-naive first-episode psychosis patients have increased expression of the M1 associated pro-inflammatory cytokines: IL-1B, IL-6 and TNFa.119, 120 Moreover, one of the triggers of M1 activation, S100B, is present at higher levels in individuals with schizophrenia.121 A parallel is seen here with childhood trauma in which raised levels of pro-inflammatory IL-6 and TNF-a,122 and reductions in brain-derived neurotrophic factor expression (a product of the M2 pathway) have been observed.118, 120 But the next paragraph indicates the possibility that inflammation may actually be present before the onset of psychosis, in which case it is still possible that psychosis furthers this inflammatory phenotype, but it does not have to be that way. There is also evidence that alterations in inflammatory markers may exist well before the onset of psychosis, and may predict progression to psychosis.123 Post-mortem and neuroimaging studies in individuals with schizophrenia provide support for a link between immune activation and damage to both gray and white matter.94, 118, 124, 125, 126 In individuals with schizophrenia, an increase in peripheral cytokines associated with the M1 pathway has been shown to correlate with reductions in both hippocampal,118 and prefrontal cortex volumes.124, 126 A link between cytokine levels and TSPO binding, however, has not been demonstrated,108 which could be because cytokine levels fluctuate.
  21. I don't know of evidence that there is a single gene or set of genes responsible for having 'wide eyes'. So whether 'wide eyes' are dominant, I don't know and don't think we know, but wide eyes are probably at least partially going to be hereditary, like most body features I think.
  22. Not entirely sure if exactly what you are asking, but potentially relevant: DNA positioned relatively close to the nuclear lamina also undergoes inhibited gene regulation, but you could of course argue that that still is chromatin remodeling (eventually histones, cohesins, and other proteins will still be involved in the actual gene regulation). I feel lately more and more research is also looking into phase separation as an part of gene regulation, that is generally difficult to sequence as well: Lamina-associated Domains: https://www.biorxiv.org/content/10.1101/464081v1.full Phase separation: https://www.cell.com/cell/fulltext/S0092-8674(18)31649-0
  23. @Capiert Could you do the calculations people ask you to? If you want to convince people here that your ideas are valid, show it with numerical examples. Show the formulas you use and the numbers you put in. Words are great, but eventually you will need to show math, and I really think this is that moment (or it was a few posts ago already). You make many claims, so why not just do the simple thing, use your own formulas/ideas to calculate some stuff, showing what you do and why. It shouldn't be hard. Oh and, if your answer is different from that of standard physics, please don't you know.... claim that all the regular physics must therefore be wrong, because we use the regular physics to make basically everything work, and it would be honestly absurd and extremely ignorant if you do do the calculations, find that your answer differs from that of regular formulas, and then just refute the regular formulas. I of course am sure that you won't do that, but I thought it would just say it anyway! Goodluck!
  24. Hey everyone, hope you are doing fine in these tumultuous times! Edit: I found my mistake: I used 'if' instead of 'elif', therefore the code executes: is r larger than 2, if not, ArrayB = Array (which is the original array of length 10). I have the following code, what I don't understand is that without the 'if r > 2:' part of the code, len(ArrayB) will be 20 in both cases (r =2) but with this piece of code, which is not running, len(ArrayB) becomes 10 (= losing False variables). I don't understand how why this piece of code affects the rest of my code, when r is not larger than 2? I am running python 3.8 in Pycharm r = 2 Array = [0,1,2,3,4,5,6,7,8,9] if r < 1: ArrayB = [1] * int(r*len(Array)) Const = len(Array)/len(ArrayB) for i in range(len(ArrayB)): ArrayB[i] = Array[int(i*Const)] if r > 1 and r <= 2 : ArrayB = [False]*int(r*len(Array)) for i in range(len(Array)): ArrayB[int(i*r)] = Array[i] print(len(ArrayB)) # First len(ArrayB) print(ArrayB) # First print(ArrayB) # if r > 2: #Uncomment this part and len(ArrayB) afterwards becomes 10 # print('r is bigger than 2') # ArrayB = [False] * int(r * len(Array)) # for i in range(len(Array)): # ArrayB[int(i*r)] = Array[i] else: ArrayB = Array print(len(ArrayB)) # Second len(ArrayB) print(ArrayB) # Second print(ArrayB) output with all code active: 20 [0, False, 1, False, 2, False, 3, False, 4, False, 5, False, 6, False, 7, False, 8, False, 9, False] 10 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9] output without if r >2: code: 20 [0, False, 1, False, 2, False, 3, False, 4, False, 5, False, 6, False, 7, False, 8, False, 9, False] 20 [0, False, 1, False, 2, False, 3, False, 4, False, 5, False, 6, False, 7, False, 8, False, 9, False Thank you for your time! Edit: problem found, if statements should be elif - Dagl
  25. Other people will give you much better answers (or provide more information). Have you looked at https://www.w3schools.com/php/php_arrays_multidimensional.asp (first link that came up, the language (PHP) does not matter to understand multi dimensional arrays)? An array contains a collection of elements, such as integers, strings and booleans. Let's say we have: Array = [1,2,3,4] Then Array[0] = 1 and Array[2] = 3 A multidimensional array contains arrays as its elements. MultiDimensionalArray = [ [1,2,3,4], [5,6,7,8], [9,10] ] (this array has 2 dimensions) Then the first position of this MultiDimensionalArray will be MultiDimensionalArray[0] = [1,2,3,4] if we want to access one of the numbers in this array, we would specify a second dimension: MultiDimensionalArray[0][1] = 2. Does this help? Other people will be able to help you further, but I highly recommend reading/searching about these things yourself first and explain the parts that you do not understand, that way people can help you more and you will learn faster. Good luck!
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