The study of the molecular processes of the nucleus and cell function.

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Does Cas9 require a nuclear localization signal (NLS) for it to work in a Eukaryote?

I'm trying to establish if it's required to add a NLS to Cas9 when expressed (or transfected) in a Eukaryotic cell. Several papers report using a viral NLS, but is it absolutely necessary? Could ...
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38 views

Does depolymerisation take place at the minus end of microtubule?

Wikipedia says that Dynamic instability refers to the coexistence of assembly and disassembly at the 'ends' of a microtubule. but Karp's Cell Biology, 7th edition says Dynamic instability ...
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33 views

Artificial reduction of NADP into NADPH by means of an electrical current

I've recently been attempting to artificially drive the formation of NADPH via the NADP reduction mechanism utilized by Ferredoxin-NADP Reductase in the Light-Dependent Reactions of Photosynthesis in ...
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32 views

Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
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32 views

In the life-cycle of the HIV virus, how does the created DNA enter the nuclear membrane?

I am in a high school biology class, so I cannot truly attest to how accurate the information I am given is, but as far as I know only RNA and very small molecules can enter the nuclear membrane ...
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60 views

What is the advantage of using plant-derived antibacterials rather than bacteria-derived antibacterials?

So obviously we have a big problem with antibiotic resistance. Most of our antibiotics originate from bacteria themselves (or are synthetic variations on scaffolds which originate from bacteria). I ...
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271 views

How much salt [NaCl] is too much in DNA precipitation?

In DNA extractions, how much is too much salt in a CTAB extraction buffer? Protocols hover around 2.5 molar; if you go over this (e.g. 25 molar), will you saturate your solution, and precipitate the ...
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93 views

L-tryptophan in mammalian cell culture

Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells? It's an essential amino acid, so I cannot fathom why low concentrations as opposed to ...
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58 views

What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?

I want to know the trigger behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, it forms a relationship wherein ...
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160 views

Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
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336 views

E. coli not growing in liquid medium

We are regularly doing bacterial transformation and subculture from plate to liquid media to extract DNA. This usually goes very well and is straightforward, but occasionally, the colonies that grew ...
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70 views

How does estrogen influence collagen synthesis?

Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .
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223 views

How to prevent e coli from clumping (for FACS)?

I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells. I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run ...
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191 views

Gibson assembly using NeBuilder

I am supposed to construct a plasmid that contains features from two other plasmids. My strategy is to generate three fragments form the two other plasmids. I was encouraged to try Gibson assembly, ...
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41 views

Adenosine metabolism

Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but ...
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28 views

Lifeforms concentrations of the categories of macromolecules, and Lipids

Lifeforms are formed of large, modular, organic molecules called macromolecules, large organic molecules called Lipids, and simpler molecules such as H2O. Macromolecules are commonly grouped into the ...
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45 views

PCR that worked previously is now only showing primer dimers and a smear on gel

PCR amplification of a promoter sequence for gel extraction worked beautifully using Phusion HF enzyme with GC (higher error but less picky) buffer. However, DNA concentration from the gel extraction ...
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31 views

Gel Electrophoresis

we add Etbr within the agarose gel but we do not add Etbr directly in native PAGE ?when we make agarose gel, we add Etbr before its solidification but we do not add Etbr when the native PAGE gel is in ...
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49 views

Why is there a size limit on inserts that a plasmid can accept?

Throughout my undergraduate education I have been taught that plasmids can't carry very large inserts, but I have never been told why. Any insight would be greatly appreciated.
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474 views

Why does supercoiled DNA run faster?

The DNA exists in linear and cirular forms. The latter form has interesting feature called Supercoiling. The more number of writhe makes it more supercoiled because of which it gets more compact. ...
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18 views

Why are multiple copies of the 35S enhancer used for overexpression in plants?

I know that the CaMV 35S promoter is widely used for transgenic plants, and I also know that it can be used as an enhancer element for overexpression. I noticed that it is always used as a ...
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65 views

PAGE gel in EtBr

I have been using TBE-PAGE gel to see small fragments of DNA by post-staining that means gel is stained with EtBr after electrophoresis. Someone told me that you can add EtBr before polymerizing ...
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26 views

Can mutation rate be increased for instance by mutagenesis targeting the DNA polymerase?

I am studying a non-cultivable bacterium living in an insect host, and I would like to generate some random mutants of this bacteria while preserving the insect. I am wondering if one way to do so ...
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31 views

BSA for trouble shooting failed PCRs?

I am using PCR to amplify a 1000bp region of the CytB mt gene. Some of the samples had not amplified and I wish to change the reaction components (or use additives like BSA) to attempt at getting ...
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31 views

Does blood typing still provide a use for ancient tissue analysis?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be ...
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26 views

Can encoding of miRNAs in introns not cause dysregulation of gene expression?

For example, consider a gene X which has an intron which encodes a miRNA that downregulates expression of another gene Y. When the gene X is translated, this miRNA will appear as a byproduct of ...
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59 views

CRISPR Knock in

Using the CRISPR/Cas9 technology, it is possible that after inducing a DSB with the Cas9 endonuclease guided with an RNA designed by the user and using a template DNA, get a desired Knock-In (KI) by ...
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57 views

What is NK-cell compartments?

with respect to the paper: Adaptive reconfiguration of the human NK-cell compartment in response to cytomegalovirus: A different perspective of the host-pathogen interaction What is meant by ...
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60 views

Zinc and brewer's yeast

I'm hoping for some information relating to yeast nutrition (specifically Saccharomyces cerevisea) in beer fermentation. Zinc is well-known to be necessary for yeast cultures to perform successful ...
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26 views

Gene expression for mouse feeder cells (inactivated MEFs)

I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there ...
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20 views

Resource for finding Repressive/Inhibitory factors for a given gene?

I have a list of genes for each of which I'd like to find: A list of transcription factors that up-regulate the gene A list of inhibitory factors that down-regulate it. I used this tool on ...
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363 views

Image Processing Suite for bacterial microscopy: Schnitzcells or MicrobeTracker?

I am looking to start doing some work tracking the size and growth of individual bacterial cells in the microscope. In order to analyze the images I need software that can segment the cells, ...
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307 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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14 views

Why are there so many regulatory mechanisms in gene expression?

first time posting here, apologies if this is a stupid question. I am a layman, so I might be ignorant to some already well-known or obvious concepts in biology. From what I understand, gene ...
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51 views

Genomic DNA extraction protocol by salting out with NaCl, how to improve yield

In these papers A rapid non-enzymatic method for the preparation of HMW DNA from blood for RFLP studies A simple salting out procedure for extracting DNA from human nucleated cells Modified ...
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25 views

UV light-induced mutagenesis during gel extraction

this is a very short question I did not find the answer for online, neither on this nor other fora. At the beginning of my cloning protocol, I extracted the band with the sequence of interest directly ...
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17 views

de novo gene synthesis vs cDNA library creation from plant RNA: Pros & Cons

What are the relative pros & cons of the following two approaches when one wants to insert a known, sequenced plant gene into a target host organism: de novo gene synthesis vs plant matter ...
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172 views

Construct a restriction map of a linear fragment of DNA using the following data?

I've attempted to do the single digests, and the double digests, but cannot complete the map.... I've attached what I've done so far DNA Sizes of Fragments (bp) uncut DNA 900 DNA cut with EcoRI ...
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19 views

Enzyme immobilization: Factors that help or hurt success

Are there any factors to consider that can help / hurt the chance to get a successful immobilized enzyme catalyst? i.e. The relative attractiveness of a live host synthesis vs an immobilized enzyme. ...
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22 views

Computer Models of E Coli / Saccharomyces cerevisiae metabolite pathways

Are there mathematical models one can use to predict the expression levels of a foreign gene inserted into a well studied host organism like E Coli or S cerevisiae? I'm not, obviously, looking for ...
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18 views

codon optimization / enzyme active site improvement

Does one necessarily have to use de novo synthesis of DNA when attempting protein expression improvement by codon optimization? Or are there other ways? e.g. Say the gene coding for the enzyme needed ...
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26 views

Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes

In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as ...
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17 views

Problem with phosphorylated and total forms of antibodies

Antibodies are available that can detect both phosphorylated and total endogeneous levels of the given protein. I have a question here, why is it necessary to have equal amounts of total protein? This ...
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35 views

How to cut out a specific named gene from plant DNA

Suppose one has extracted RNA from a plant, converted it to the corresponding cDNA & amplified it but now wants to cut out a particular, already-sequenced gene out from it, how does one proceed? ...
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25 views

mRNA extraction from mice ears.

I am trying to extract RNA from mice ears and for some reason I don't have RNA when I perform the electrophoresis. I directly cut the ears and I put it in a tube with a bead and trizol. then I place ...
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27 views

Dogs recognize eachother on sight. How come?

Is it possible that the fact that dogs regonize eachother on sight is caused in the developing embryo, wich is to say that the developing map from wich the motorcells conect to the motorsystem somehow ...
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16 views

How is “fine mapping of pelvic regulatory region” done in the stickleback PitX1 paper?

I'm working through this paper for a class. I'm a bit confused by the methods they used in one experiment. So the researchers are studying spine development in stickleback fish. They noticed some ...
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57 views

Which of the three is true for insulin receptors?

I have seen the following question in a Cell Biology exam: Which of the following is true" Insulin has an hydrophobic Signal Peptide and the insulin receptor does not have an hydrophobic ...
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17 views

Ions in different cell compartments

I would like to understand the distribution of metal ion concentrations (such as Mg2+) in the different cell compartments. I tried very hard but still couldn't find such information. Could anyone ...
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final control prior to transfecting an expression vector into a mammalian cell?

I have been asked a general question: Once I have cloned a full-length cDNA into an expression vector, what final important control must I do before I transfect this into an embryonic stem cell line? ...