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

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14 views

Why do we need to replicate incomplete DNA fragments by PCR from crime scene?

If the DNA from crime scene is damaged ,why would it be helpful to replicate it by PCR(polymerase chain reaction)? I mean even we get billions of that copies ,it is still incomplete,isn't it ? How ...
3
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0answers
40 views

What is the source of the electrons generated in the Krebs cycle?

In the Krebs cycle where do the hydrogens and electrons that NAD+ and FAD accept come from? It seems that citric acid only loses two hydrogens because it starts out with six hydrogens and becomes ...
2
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2answers
63 views

Crick’s Central Dogma — Counter Cases

I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks! UPDATE - Reference of lncRNAs ...
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16 views

house keeping gene variation under treatment

I am injecting BCG in mice ears to measure the local inflamation response in the infection side, one ear in the same mouse is kept as control by injecting PBS, in the other one, BCG is injected. When ...
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25 views

Do users of CRISPR/Cas iterate or parallelize to try multiple guide sequences?

I've read about on-target efficiency and off-target effects in use of CRISPR/Cas9, and about tools that suggest good guide sequences. I am wondering: how many guide sequences do typical CRISPR users ...
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1answer
34 views

What is the best way to analyze non-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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18 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 ...
4
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1answer
15 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 ...
6
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2answers
73 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?
3
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2answers
66 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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2answers
28 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 ...
0
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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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32 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
32 views

Can you knockout a gene specifically in the dorsal root ganglion in adult mammals?

Since the dorsal root ganglion is so small, would that be easier than the entire body?
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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 ...
6
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1answer
62 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 ...
4
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1answer
241 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 ...
0
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2answers
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 ...
6
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0answers
45 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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13 views

Are yeast plasmids methylated?

Do yeast plasmid have methylation? If they do have them, then what kinds of them?
0
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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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0answers
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. ...
1
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1answer
36 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 ...
3
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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 ...
0
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1answer
37 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.
0
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1answer
20 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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0answers
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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0answers
7 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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13 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 ...
0
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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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0answers
25 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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0answers
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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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
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 ...
0
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1answer
39 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 ...
3
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1answer
70 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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0answers
16 views

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 ...
1
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1answer
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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0answers
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 ...
3
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3answers
53 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 ...
1
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1answer
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 ...
0
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1answer
22 views

Are the subordinate genes of a repressed operon really “turned off”?

Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says: ...
1
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1answer
80 views

What exactly are genes, DNA and chromosomes. How do they relate to each other and what is their function? [closed]

So I am new to biology and I have been reading, and searching the web, but I couldn't understand the whole framework of a cell. So as I understood: A DNA, is a double chain of Nucleotides (A,T,G,C ...
1
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2answers
73 views

Relationship between DNA strands and mRNA

Does the sense strand or antisense strand of DNA code for the polypeptide product? I'm confused because I know the antisense strand is the template for mRNA but it has anti codons so I do not know how ...
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1answer
50 views

Can we infect with “bad” genes other organisms? [closed]

We know that some organism's DNA stay with human for life (Herpes) and we also can, i think, design such "gene" that can interact with human's DNA-polymerase very intensive. If we attached this gene ...
3
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1answer
134 views

how to quantify toxicity

When going through this link, Table 1, what are the numbers mentioned there? How is one quantifying toxicity?
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31 views

Question related to pathogen population [closed]

Does only one pathogen of one species enter the host and cause harm to the host or is a certain number of pathogen populations of the same species needed inside the host to disrupt the functionality ...
2
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0answers
41 views

Has a restriction enzyme ever been tagged?

As part of an experiment that I am preparing, it would seem necessary for me to tag a restriction enzyme (HaeIII to be exact) with GFP. I began researching its domains to determine whether to tag the ...
0
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1answer
31 views

Quantity of toxin release by pathogen in host

I came across these lines from this paper: Pathogenic microbes exert a broader sphere of influence by releasing a bolus of toxin that can act upon many cells within a given tissue and/or diffuse ...
0
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1answer
22 views

Using exogenous genes to reduce the set of essential amino acids?

Various organisms have sets of essential amino acids that they cannot synthesize themselves, but rather that they must obtain from food. Humans have 9 of these amino acids. However, obviously certain ...