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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Question Concerning Plasmid Transplant

Upon reading a report today, I discovered a interesting technic of plasmid transformation. Triparental Conjugation, a bacterial conjugation including three parts , a conjugative plasmid, a donor cell ,...
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Finding whether a DNA strand contains duplicate sequences

I know that using Hybridization Probes one can check if a nucleotide sequence complementary to the probe is present in a DNA strand by marking it and then verifying whether it attached the strand or ...
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156 views

number of chromatids seen in karyotype

The karyotype is performed on a cell whose cycle has been stopped in metaphase or pro metaphase, using colchicine or by other means. In the textbooks I read that during the S phase each of the 46 ...
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Structure of microscopic chromosomes

What is the characteristic of the microscopic structure of chromosomes? As an example, what are some types of chromosomes?
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2answers
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Is it ok to keep primers at 4 degrees?

I reconstitute my primers in nuclease free water ( no sterilised) this morning and I forgot them at 4 degrees, acording to the instructions, they should be storage at -20 after the reconstitution. I ...
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how Eukaryotic cell protect itself from RNAi , silencing mechanism?

RNAi- rna interference the siRNA can potentially bind to a part of coding rna strand having the complementary bases w.r.t siRNA. So how does cell protect essential coding rna from the RNAi mechanism ...
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Increasing my PCR efficiency to be able to better visualise my bands

I run an electrophoresis in agarose gel and my expected bands are extremely week, is even hard to see them. It looks I need to increase my PCR efficiency. I have read about a Hot start setp, which ...
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46 views

In centrioles, what type of fibers connect the triplet microtubules?

In a centriole, each "arm" (a triplet microtubule) is attached from its A-tubule to the C-tubule of the adjacent arm. What is the type of fiber that connects each arm ("connecting fibrils" in the ...
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Functional Difference between the Distal Promoter and Enhancer Region

According to the Wikipedia article on eukaryotic promoter regions, the distal promoter is: Anything further upstream (but not an enhancer or other regulatory region whose influence is positional/...
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222 views

Are microtubules in centrioles helical, like they are when in isolation?

Microtubules tend to be of a helical structure, do microtubules in centrioles also have a helical structure? The centriole is composed of nine circularly arranged triplet microtubules, one complete ...
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Experimental methods to demonstrate coupling of GPCRs [closed]

How would you experimentally demonstrate receptor coupling through each of the G proteins, Gs and/or Gi?
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1answer
31 views

how many spores are needed to “infect” a wall?

There's cardboard box in my room that used to be in another room that had mold all over the walls. and it still smells moldy ,it probably means the air in my room is polluted with mold spores.(right?) ...
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1answer
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What is an acceptable qPCR efficiency when adjust using the Pfaffl equation?

I have efficiencies of 76% and 85%. THis is clearly below what is normally acceptable. But the pfaffl equation corrects this, doesnt it? However is it acceptable to publish this data?
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Is Rh factor an evidence for human evolution from primates?

The Rhesus Factor is an important blood antigen that is found on Rhesus macaque and human being. So is this an evidence for human evolution from monkeys. ???
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Is tyrosine hydrophobic or hydrophilic?

I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does tyrosine actually ...
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28 views

how can I decrease noise in my staining and increase the signal?

I am trying to stain LN sections (from mice), for Madcam-1 using Madcam purified ab as primary and anti-Rat Cy3 ab as secondary. I have tried many times, very few times worked Ok but most of the times ...
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1answer
39 views

Oxygen in the earth’s atmosphere

If CO2 only makes up about 0.04% of the earth’s atmosphere how do trees and organisms in the ocean produce oxygen to 10% of the earth’s atmosphere?
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Isolation of Intact Granules from Mast Cells

How to isolate intact granules from mast cells without using sucrose and percoll?
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2answers
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Protein - one polypeptide molecule or a collection of molecules?

I'm struggling a bit in Bio 111 with confusing terminology between the terms "chain" and "molecule". I understand the primary structure of a protein is a chain of amino acids connected by peptide (...
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1answer
44 views

What is meant by “a codon codes for an amino acid”? [closed]

What is meant by "a codon codes for an amino acid"? Does it mean in order to build that amino acid you must combine those three nucleotides? Does it mean anything more than provides the instructions ...
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1answer
60 views

What is the meaning of “Rb is in the active state”?

I am reading about cyclins, cdks and Rb (Retinoblastoma) and some of the terminology is not clear to me. I understand that when CDK phosphorylates Rb, it disconnects from E2F, and E2F can act as a ...
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how can I get stronger staining for my lymph node sections

I am using the same protocol and same antibodies that the literature says but still I cannot get good staining for my lymph node sections, I tried to change the fixation method and I am using now ...
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1answer
238 views

Genotypes of gametes produced by an F1 individual?

I have an urgent question as I have an exam tomorrow. I was skimming some past exam papers and one question came up which has me completely confused. A cross was made between a pure breeding ...
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pcr troubleshoot for toxoplasma with GRA6

I did pcr for Toxoplasma genotyping with GRA6 gene. my primer sequences were forward 5-GTAGCGTGCTTGTTGGCGAC-3 reverse 5-TACAAGACATAGAGTGCCCC-3. PCR was done in a 25μl reaction mixture. I used 10pmol ...
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Do different transcription factors attract different kind of RNA polymerase?

Initiation step of transcription is simply binding of RNA polymerase on the DNA strand and its activation by addition of a phosphate group onto it. Different kind of promotors are present close to ...
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Is there recent info about the hypothetical ancient two-codon genetic code?

Here is the latest I have found. link This is the basic idea: Evolution does not look ahead and make plans. It would not create a system of mRNA with giant ribosomes to create proteins, until ...
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How do Wikipedia users create the structure of proteins and peptides?

Recently I saw the structure of insulin on Wikipedia. And my question is that which software(s) or application(s) (I don't know the proper way to name it) do they use to create that picture of the ...
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Compare affinity to potency h1 receptor

This quote from Miller (2004) makes it clear that the affinity of drugs for the H1 receptor does not correlate to sedation: Although both dosage and affinity for histamine H1 receptors play a part ...
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1answer
197 views

Relative rates of migration of circular, linear and supercoiled DNA in agarous gel electrophoresis

I have read the supercoiled plasmid DNA migrates fastest when subjected to agarose gel electrophoresis and this makes sense to me because it is small and experiences the least friction because of its ...
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1answer
62 views

what is CpG coverage? DNA starting material?

referring to this quote from an article about predicting methylation states: "Because of the small amounts of genomic DNA starting material per cell, single-cell methylation analyses are ...
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26 views

How to perform TUNEL Assay for yeast?

Currently, I am working on yeast strain CEN PK and I want to carry out TUNEL Assay to detect the amount of damage upon treatment with some damaging agent. We have a kit in the name of TUNEL Assay Kit -...
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1answer
29 views

Expected bands in polyacrylamide gel

I have something in my notes that doesn't seem right. If I use restriction enzymes on a PCR product how many bands should I see provided I know the restriction enzimes will cut the DNA? If I use two ...
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45 views

Antibody staining

I am staining tissue sections and I did a mistake, I was supposed to have mixed 3 primary antibodies but I stained only with one of them. After the 1h incubation I washed 10 min with PBS and then I ...
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Lifelong Immunity Question Regarding Erysipelas And Scarlet fever

So my question is after you carry on Scarlet fever you develop lifetime immunity. But with Erysipelas you might develop recurrence type. What is the mechanism behind it? Both diseases are caused by ...
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1answer
29 views

Calculation of extinction coeffcient of GFP

I want to convert the absorption of a protein into concentration. Hence ı need to calculate the extinction coefficient of the protein (GFP). ı found the formula (nTrp)5500+(nTyr)1490 on the internet ...
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Gases from breathing

It was brought to my attention my question isn't direct and simply written enough. Ok in an effort to simplify this question: Can I resuse exhaled nitrogen and supplement it with new oxygen only? ...
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How are siRNAs introduced to cells for RNAi experiments?

Specifically, can somebody explain how in-vitro transcription can synthesize siRNAs to conduct RNAi? I have been reading a number of research papers that discuss how to use siRNA and shRNA to conduct ...
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Can Programmable Cell Death (PCD) be engineered in a bacterium like E. coli?

I am reading a paper which says : Messages not received after a certain time can be considered lost, as bacteria carrying them will suicide. I even read some paper which says about PCD like this, but ...
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1answer
37 views

How do I reverse my insert within a plasmid?

I have a plasmid with: ...T7pro. -- RBS -- XBa1 cut site -- ProDpro. -- RBS -- AmilCP -- T -- Spe1 cut site -- T... How do I design primers to reverse the portion in bold, such that the T7 and ProD ...
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Advanced books about molecular biology and genetics

I'm finishing my third year of biochemistry and doing gene therapy practicals during the summer. I'd like to buy a book that describes flow of genetic information (transcription, translation, ...
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Preparation of DNA ladder

how to prepare working stocks of 100 bp and 1 kb DNA ladder supplied by promega? the pack that we purchased contains a 6X loading dye. thanks!
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63 views

Significance of Nissl bodies

What is the significance of Nissl bodies? How are Nissl bodies different from any other RER seen in any other cell of the body?
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Does vesicles fragmantation (fusion) during endocytosis require energy?

In the process of endocytosis, does the stage of fragmanting of the vesicle membrane to the cell membrane requires energy? I know that the disconection of the Vsnare and t-snare from the membrane ...
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1answer
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What are the types of interactions in biological network (protein networks)?

In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, ...
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Are longer and shorter DNA similarly charged?

A longer DNA molecule would have more phosphate groups, so it should have a greater negative charge, right? It was taught in my class that only terminal ends of DNA are charged and all the phosphates ...
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1answer
346 views

Why do bacteria use formylated methionine in the initiator tRNA, while eukaryotes do not?

Could anyone suggest an explanation for the evolution of this trait in bacteria? Does it confer any advantage? It is also exploited by immunity receptors of some eukaryotes for the recognition of ...
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1answer
76 views

What would be the fate of protein made from D-amino acids after ingestion by humans?

There are some natural peptides made of D-amino acids, rather than the L-amino acids normally found in nature. It is now possible to chemically synthesize artificial proteins made of D-amino acids. ...
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24 views

Highest yielding protein in E coli culture

Which protein can be isolated or over-expressed to the highest possible yield per liter of E coli culture. Or in other words, what is the easiest possible protein to express in a typical E coli ...
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1answer
120 views

We know archea and eukarya are more closely related but endosymbiotic theory says eukarya have evolved from prokaryotes, justify the statements?

I am confused if eukaryotes have evolved from prokaryotes then how are they more closely related to archea?
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Gene located on Which strand? Want reference. [duplicate]

Update: Initially my question (below) was appropriately marked as duplicate/overlapping with two other questions; This and this ; among them a specific part of an answer of the second duplicate/...