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

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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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0answers
10 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
14 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, ...
2
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3answers
155 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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0answers
23 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
28 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 ...
3
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1answer
59 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 ...
0
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0answers
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,...
2
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1answer
58 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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2answers
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
37 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 ...
1
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1answer
25 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 ...
3
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1answer
546 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, ...
4
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2answers
128 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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0answers
15 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 ...
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0answers
33 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: ...
3
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3answers
49 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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0answers
12 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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1answer
32 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 ...
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1answer
18 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: ...
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1answer
71 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 ...
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1answer
47k views

Why do we add salt when precipitating DNA?

All the DNA extraction protocols I have seen involve adding salts to the extraction buffer. What is the purpose of the salts? What happens if they aren't included?
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2answers
65 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 ...
2
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1answer
87 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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1answer
375 views

Why should phospholipid non-polar tails be “protected” in the membrane bilayer?

lipids are arranged within the membrane with polar head towards the outer side and non polar tails towards inner side, this ensures that the non polar tail is protected from aqueous environment. My ...
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0answers
30 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 ...
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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 ...
4
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2answers
65 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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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 ...
3
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1answer
132 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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0answers
40 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
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 ...
8
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2answers
96 views

How do we find antibiotics?

So the last class of antibiotics were made in 1984 (I think), which makes it appear as though they are hard to find(/design maybe). How is it then they were discovered? Was it by chance? I know some ...
0
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1answer
29 views

How do normal cell division chance into a tumor forming cell division? [closed]

Or its better to say what happens at molecular level that tumors are formed? I tried normal google search and google books but couldn't find any appropriate explanation. I am trying to understand why ...
2
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1answer
12 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 pUC19 with an enzyme in rat brain in between the mentioned cut sites. I have isolated and created the recombinant molecule with custom gene synthesis so that the ...
4
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2answers
163 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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0answers
12 views

Similarity between lncRNA and Enhancers

Please read it carefully. Question below is purely based on computational experiments: I have been running an analysis algorithm (pretty new one) on lncRNAs and its showing pretty much the same ...
1
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1answer
45 views

Lifetime of secondary messengers such as Calcium or IP3

Can anyone suggest me literature on the lifetime of secondary messengers such as calcium or IP3? A book would be preferred. What I am specifically looking for is a validation that secondary messengers ...
0
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1answer
36 views

How to isolate two plasmids from E. Coli strand?

I have an E. coli cell line I use to express a protein using a two plasmid system. One confers AmpR and one KanR. For mutagenesis I would like to separate the plasmids to increase efficiency of the ...
2
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1answer
75 views

Programs/software to graph biological data [closed]

I am curious about what sort of programs people in my field of academia are using to graph their data. I am a master student in biochemistry, and have more or less only used excel (on rare occasions I ...
5
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2answers
2k views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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0answers
23 views

Why are there so many regulatory mechanisms in gene expression? [closed]

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 ...
3
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1answer
87 views

How does a protein reach its substrate within the cell?

After a protein has been synthesized and its the final tertiary/quartenary adopted, how does it reach its substrate within the cell and what causes it to interact with it? The transcription factors ...
0
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1answer
30 views

Why is tRNA called an adaptor molecule?

All I know about adaptor is that it is a device that converts attributes of one electrical device or system to those of an otherwise incompatible device or system. Thank you.
5
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1answer
63 views

Do two compatible tRNA codons bond together?

Can two tRNA with complementary anti-codons link together? For instance UUU with AAA. If not, why not?
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2answers
352 views

What is the importance of urea in mass spectrometry?

What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?
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2answers
61 views

Material recommendation: molecular biology for mathematicians and computer scientists [closed]

I am wondering if there are some introductory learning resources on molecular biology designed specifically for scientists with heavily math-oriented curricula (math/physics/computer science). They ...
7
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2answers
7k views

What is the difference between transformation and transfection?

What is the difference between transformation and transfection? How do both of these methods work?
4
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0answers
83 views

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 ...
4
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0answers
41 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 ...