Nicolai
  • Member for 4 years, 8 months
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Can DNA methylation induce breast cancer?
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Okay I'll try to put together a quick answer. First: 'How do you analyze DNA methylation data generated from the EPIC array from Illumina' The most common method to analyse DNA methylation is based ...

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Zygosity and Strands
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The directionality of the strands matters, because genes can be encoded on both strands of a chromosome (each strand can be read in 3'-5' direction by RNA polymerase). Therefore someone with the A-T ...

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Are transcription factors some kind of eQTLs?
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No, eQTLs and transcption factor are very different things. Like you described TFs are proteins that control the expression level of genes. eQTLs are nothing that is physically present in the cell. ...

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Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins?
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There a few things you have to take care of with chirality in biological systems: First note, that for amino acids we usually use L and D instead of r and s nomencalture. In chemistry the ...

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Analyzing Messy Data Files
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The answer of David explains most of the common/general problems you encountered and how to tackle them. In case you don't have anyone more experienced to consult, I'll try to give suggestions for the ...

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Is there a reliable estimate of the number of cells on Earth?
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Okay so I looked around a bit, and there are surprisingly few papers related to this question. This paper is the best I cold find, but it's almost 20 years old. There's also this one, which slightly ...

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What goes wrong in the immune system that leads to autoimmune diseases
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Your understanding of the process is basically correct. There are of course a lot more details to it, but that wouldn't be in the scope of the question. Do note that only T cells mature in the thymus (...

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Can neutrophils kill bacteria inside other cells?
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Are neutrophils able to get inside epithelial cells in order to kill bacteria. Therefore, even if a bacteria gets inside the epithelial cells can the neutrophils get inside the epithelium to kill ...

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Can I do an MS in biotechnology after a bachelors degree in chemical engineering?
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This will probably to a high degree depend on the (exact) curriculum and prerequisites of your chosen bachelor and master. Also note that I'm not from the US and judging from the terms you are using, ...

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How to analyze phosphorylation shift by western blot?
1 votes

The run length of bands in an SDS-PAGE (which your western is probably based on) depends - at least in theory - only on the size of the protein: SDS binds to proteins with a fixed size ratio and ...

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It there any experimental approach to determine the electronic structure of a given aminoacid inside a protein?
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The two most often used methods used to determine protein structures are X-Ray crystallography and NMR (nuclear magnetic resonance spectroscopy). Both of these allow some deductions of electron ...

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DNA described somewhere?
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This question is both easy and hard to answer: DNA and its (known) functions have been described in scientific literature, textbooks and databases for the last few decades, but because this is a ...

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What is the substance that tumors release that stimulates growth of blood vessels but suppresses its release from other tumors?
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One very important signal for angiogenesis are the Vascular endothelial growth factors (VEGF) (a small group of ~5 similar proteins). They generally promote generation of new blood vessels & ...

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Which one is better to use for water stress experiment GWAS or RNASeq?
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bambara groundnut does not have a reference genome This is your biggest problem if you want to do any sequencing based analysis. Neither GWAS nor RNAseq data analysis are possible without a ...

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What do we mean by MHC molecule diversity? Does each human have a variety of MHC molecule isoforms?
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You're right that both polygeny and polymorphism contribute to the diversity of a given gene in the population correctly described what they mean individually. However, you missed that the polygeny ...

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How could pharmaceutical metabolizing bacteria be used to synthesize them?
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In principle yes, because almost all reactions exist in an equilibrium and enzymes are catalysts (meaning they affect mainly the activation energy for a specific reaction). The best approach is to ...

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How does bonding between non-complementary bases occur?
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How do the two bases that aren't complementary remain bonded? Non complementary bases can only form non-Watson-Crick bonds, which are very unstable and noticeably different. Therefore any mismatch in ...

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From refseq ids to Go term Ids
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1 votes

So, I've looked a bit into this and the way you want to do your analysis won't work as you planned it. The main reason for this is that the GO database does not contain any virus species (as fas as I ...

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Can someone help me interpret these charts on fluorescent polarization?
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These charts are flow cytometry graphs, something not explicitly stated in the figure description, but obvious to everyone who has seen similar graphs before (and I assume it's at least mentioned in ...

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Do green algae form obligate symbioses with fungi?
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1 votes

Yes, Lichen are composite organisms of green algae (or cyanobacteria) living togther with fungi. In most cases the fungi-part is completely dependent on that symbioses and is completely dependent ...

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Michaelis Menten kinetics - Plotting to find V-max and Km
1 votes

The order of magnitude for your intercept value depends on the axis of your graph, which in turn depends on the values / units of your input values. As an example if your substrate concentrations are ...

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Why does photosynthesis occur even in blue light when the photocentres are activated in red light
1 votes

While it is true that strongest activity of Photosystem I and II happens with 700nm and 680nm light, these are not the only wavelengths that can be used for photosynthesis. The green color of plants ...

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List of genes across species (or just for humans)
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In principle there are a LOT of these databases and depending on your specific questions you may want to look into different ones. Like already mentioned NCBI hosts basically all of the available ...

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Tree of Life in Text Format
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The NCBI taxonomy database contains an (as far as I know most complete/up-to-date) database with information about all classified species. I haven't tested it, but I would guess that its accessible ...

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Basic questions about human genome project
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Okay, a quick answer since I don't have time to go into all the details: 1) As correctly mentioned in the comments already the human genome project had multiple DNA donors, however up 70% of the ...

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How does collaboration on reconstructing metabolic networks work?
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A bit of a preface: A lot of this large scale collaboration (which I would maybe rather describe as the work of a whole [sub]field over a given time frame) often ends up in some sort of database. ...

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Is there a publically available database of microbes that details what their wastes and food sources are
1 votes

You could try to look into the kegg database. It's main purpose is to describe biochemical pathways, but it also has information on which species actually have these pathways (not sure how well this ...

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qPCR : Cross-contamination while sealing plate
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1 votes

I can't say this happened to me before (but also don't do qPCR all the time). In principle it should be fine to add the template to the side of the well, since this also lets you visually confirm ...

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Biological validation of computationally determined gene-gene interaction
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I'm gonna try to cover as many scenarios as I can think of: Gene interaction ( = co-expression): This is probably the easiest to validated (e.g. by western blot like you mentioned) but the hardest to ...

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Why are there multiple sequences for the same segment for an individual "strain" of influenza?
1 votes

It looks to me that the website you're looking at is mostly taking publicly available data from Genebank (the NCBI repository for sequence data) an collects it to form an overview. For your question ...

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