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

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What is the best way to analyze quantitative mass spec hits from an immunoprecipitation pull down?

I am studying a nuclear protein and want to come up with a list of potential proteins that it interacts with. From the nuclear fraction of 293T cells, I did an IP (immunoprecipitation) to pull down my ...
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7 views

How do the chemical components of these spices prevent fungal growth?

I am doing an EE on how spices affect fungal growth for the following spices - oregano, garlic, cinnamon, cumin and turmeric. Its been hard to find any sites that say why or how they affect fungal ...
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43 views

Enzyme Inhibition in relation to Aspirin

I've been trying to learn a bit more about pharmacology, so bear with my ignorance. In short, I see that aspirin (in part) works by inhibiting cycloxygenase isoenzymes and that this inhibiting is ...
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1answer
61 views

What is the cause of the packaging capacity limit of recombinant adeno-associated viral (AAV) vectors?

I am working with recombinant AAV and I am puzzled by the limit of their packaging capacity (around 5Kb ssDNA), that is really a huge drawback for gene delivery. I have tried to look more in deep ...
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1answer
12 views

How do centrioles auto-locate to opposite sides of cell during mitosis?

I realize that centrioles are made of 9 triplets of microtubulin wound together with a hollow core, and that they are responsible for the configuration of the spindle during mitosis. The spindle ...
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71 views

RNA processing in eukaryotes

Why does post-transcriptional processing of eukaryotic mRNA involve addition of a 3' polyA tail, rather than one of polyU, -G, or -C?
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34 views

Function and expression of pseudogenes

Can pseudogenes be transcribed into mRNA and translated into functional proteins, or should they be regarded as functionless mutated genes?
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64 views

Codon tables and the wobble hypothesis

In E. coli, there are only 47 different tRNAs but 61 potential anticodons. This is because, from what I understand, the third base of the anticodon can pair by wobble rules. However, it is known that ...
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180 views

Redundancy of the genetic code

One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon UUU ...
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24 views

Good microscope? [duplicate]

Hi I am a teenager and I recently studied biology and found it very interesting. I want to get a microscope and study further into the microscopic world. What would be the best microscope for me? I ...
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1answer
34 views

How to prevent a old promoter region from attaching onto a plasmid instead of a new one during ligation?

What I am trying to do is take out a existing promoter region in a plasmid, and replace it with a new one. So first I use the appropriate restriction enzymes to get rid of the existing promoter region....
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1answer
93 views

Techniques to show a protein heterodimer-DNA interaction

It is known that c-Jun and fos dimerize to form AP1 factor that binds to a sequence on DNA containing PyPuGACGTCNNNNGAGGTCPyPU. In esophageal cancer cell lines there is no expression of the fos gene. ...
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31 views

Are all prokaryotic promotor regions the same, or do they differ depending on the product of the transcript?

Are all prokaryotic promotor regions the same or do they differ depending on the protein encoded by the mRNA being transcribed? What I am thinking is that if activator proteins are a method of ...
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30 views

Problems with housekeeping genes

I have tried several housekeeping genes to analise the relative expresion of a cytokine for measure the inflamatory local response in mice ears, all the housekeeping genes I have tried are not stable (...
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1answer
33 views

What legal possibilities exist to get access to articles behind paywalls? [closed]

Many publications, be it in high-profile journals, proceedings, book chapters or any other medium, cannot be accessed without subscription alongside substantial costs, even though most of the ...
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32 views
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42 views

Optimal pH of protein buffer? Basic principles to adjust buffers according method and analysis

Protein buffers such as PBST, which is used in western blotting, are normally adjusted to pH 7.4. When I try to find why, I find some information about optimal pKa for protein stability. Im not sure I ...
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2answers
364 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
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238 views

“X” in stock solutions

We prepare buffer solutions with concentration in terms of x, for example 50x TAE buffer. How do we come up with ...
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70 views

Do only one or both pairs of homologous chromatids exchange genetic material during the process of crossing over?

To be specific: Assume chromosomes A and B are homologous. They've both replicated into A1, A2 and B1, B2 and have formed a tetrad at the equator (synapsis). Most textbooks show either A1 and B1 OR A2 ...
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47 views

Deletion of codons at the start of a sequence in preparation for heterogeneous expression. Why?

I am reading a patent where they isolate a gene from cDNA constructed from RNA extracted from plant matter. The subsequent step (in preparation for heterogeneous expression in E Coli.) puzzles me: ...
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13 views

Are yeast plasmids methylated?

Do yeast plasmid have methylation? If they do have them, then what kinds of them?
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1answer
15 views

How do you obtain specific mRNA transcript levels for comparison from a Hi-Seq dataset?

I have HiSeq data from mice exposed to two conditions. I would like to answer the following question: "Is there a significant difference in mRNA transcript levels when comparing condition A to ...
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10 views

How can one measure the effect of a stem cell's matrix on the progeny of that stem cell?

A number of recent papers that have used hydrogels to alter the ECM of mesenchymal stem cells to quicken their development to cells used specifically for cartilage or really any other type of cell. ...
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Can LC-MS/MS and MRM act as a complementary to RT-PCR, Western blotting and ELISA?

I am working on protein quantification using Liquid Chromatography-tandom Mass Spectrometry with Multiple Reaction Monitoring (LC-MS/MS MRM), I am not sure if it can act as a complementary to RT-PCR, ...
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1answer
34 views

Can RNA be extracted from tissue suspended in formalin?

There are two tumor samples floating in a 10% formaldehyde solution (i.e formalin). Is there a protocol for RNA extraction under these circumstances? I am concerned that using the protocol for ...
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1answer
178 views

How is adrenaline (also known as “epinephrine”) a ligand?

I keep reading that adrenaline is a ligand, however, from what I understand a ligand is a molecule or ion which donates a pair of electrons to a central transition metal ion in a complex. If this is ...
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1answer
24 views

Can a cleaved plasmid “close” without exact matching “sticky ends”?

Say if you have a multiple restriction site and use two restriction enzymes on it to cleave a plasmid, can it recombine with ligase? My concern is that without the small sequence of nucleotides ...
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1answer
36 views

Is there a difference in the energy produced from the hydrolysis of GTP and ATP?

Is the energy produced from the hydrolysis of GTP greater than/less than or the same. I know that GTP can be converted to ATP through a pathway and so my thinking was that GTP would be less.
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19 views

What is a cognate enhancer sequence?

What is a cognate enhancer sequence? While reading a paper (1) presented at a journal class in graduate school, I encountered this sentence: HIF-1 binds to its cognate enhancer sequence, the ...
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1answer
22 views

For a recombinant pUC19 plasmid with cut sites at Hind III and EcoO109i, does lactose need to be present for the gene of interest to be expressed?

I am growing E. coli transformed with the plasmid pUC19 with an insert of an enzyme in rat brain between the mentioned cut sites (EcoO109i and HindIII). I have isolated and created the recombinant ...
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19 views

What is the molecule responsible of the yellow color of the Agave americana?

Does anybody know what is the molecule responsible of the yellow color at the edges of this plant? I noticed also that the new forming yellow part at the begging stage is soft green until it is ...
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6 views

Effector protein emission rate in host by pathogen

Is emission of effector protein a one-time process in the host, or does it emit effector multiple times in the same host? If effector proteins are emitted multiple times by the pathogen into the host, ...
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12 views

Rate of production of proteins in gram negative pathogenic bacteria

What is the rate of production of effector proteins in the gram-negative pathogenic bacteria, if any? The translocation unit that is present during secretion of effectors in the secretion system that ...
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1answer
16 views

Common Errors For Low R Value in Bradford Assay

I've recently started doing Bradford Assays for my samples and my standard curve has been non-linear and I have been getting low R values (.90-.95). I initially thought the error was in pipetting, ...
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157 views

Extending a small fragment of DNA

Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence? For example, I want a 1 ...
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24 views

How to specify a promoter in de novo gene synthesis service?

I am trying to use a de novo gene synthesis service (Genscript) and one part confuses me: Where do I pick the choice of promoter? Or is the promoter choice automatic based on my plasmid choice? e.g....
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30 views

Forgot to cool slides before washing

I just finished an immunofluorescence experiment and I'm wondering what went wrong. The tissues seem dimmer than they should be. One mistake I made was: I completed the antigen retrieval step, in a ...
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1answer
68 views

Forgot to vortex antibody before staining

Ugh. Did an immunofluorescence experiment last weekend, forgot to vortex both my primary and my secondary antibody solutions. And my final result looks dimmer than it should be. Is it possible that ...
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22 views

How does plant life obey the constraint that the change in Gibbs free energy in a reaction must be negative?

My understanding is that if a reaction takes place, either entropy of the system must rise, or energy must be released from the system as heat, or both. (Citation: paraphrasing from The Vital Question,...
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1answer
60 views

Difference between the P4 and P5 subtypes of P-type ATPases in plants

In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?
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72 views

Why is DNA Shuffling more efficient than Point Mutation?

In a related post on Biology-SE the following insightful comment was made: The advantage of DNA shuffling over introducing single mutations is that you have to screen fewer mutants and the ...
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1answer
38 views

Deducing protein sequence length from gene DNA sequence length

Is there a standard way to deduce protein sequence length from gene DNA sequence length of the gene coding for it? Naively I had assumed that ...
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1answer
31 views

How to put a gene under the control of a regulable promoter?

Suppose I have a hetrologous (eukaryotic, plant) gene sequence that I want to express in E Coli under the control of a regulable promoter (say the lac promoter induced by IPTG) how exactly does one ...
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1answer
586 views

Storing Taqman plates with polymerase in fridge before running

I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, ...
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129 views

In DNA repair, how is it determined which strand contains the error?

DNA replication is more accurate than transcription (or RNA replication) because mechanisms exist for proof-reading and repair of DNA, but not for RNA. Consider a segment of a DNA strand, AGTC. Its ...
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O-Group names of Salmonella serotypes?

What liposaccharides are represented by the O-group designations of Salmonalla serovars in the Kauffman-White classification scheme? I mean to ask, how do the numbers in a Sal serovar (1, 9, & 12 ...
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3answers
52 views

Needleman Algorithm for Optimal Alignment of two Amino Acid Sequences

I want to compute the optimal alignment of two amino acid sequences as per the following definition from a patent: "The percentage of identity between two peptidic or nucleotidic sequences is a ...
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13 views

Is there any technique other than restriction enzymes to introduce staggered cuts into DNA?

I'm curious about introducing staggered cuts into DNA, but wonder if there is a way to do this in vivo in E. coli, as I heard introducing restriction enzymes on a plasmid would end up just shredding ...
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34 views

Amount of variation between a canonical gene sequence in various samples

Suppose there is a GeneBank DNA sequence listed that produces a specific enzyme in a specific species of plant. e.g. A terpene Synthase. Now if someone samples various trees of the same species would ...