Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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3
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1answer
53 views

Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
1
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1answer
41 views

Design rules for DNA linkers

I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism. I do not expect the ...
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0answers
13 views

Endocytic pathway: Macropinocytosis

So I'm trying to understand this phrase: Unlike other endocytic pathways, macropinocytosis is acutely induced by growth factors From the following paper The 4 endocytic pathways I know of are ...
7
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1answer
1k views

Can cysteine alone change pigmentation?

According to this graph (from here): cysteine contributes to pheomelanogenesis, and having a high enough concentration of cysteine makes the shift towards pheomelanin instead of eumelanin. So my ...
3
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4answers
277 views

How to find suitable qRTPCR reference gene for a inflammatory response experiment?

I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all ...
7
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2answers
2k views

Is NMDA produced in the body?

On the wiki page for NMDA it says that NMDA is a synthetic substance that mimics glutamate. So why does the body not use glutamate instead of NMDA? Also how is it possible that our body can produce ...
0
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1answer
36 views

Will DNA nanostructures be useful for medical applications?

There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA. I have heard researchers motivate this research with claims ...
0
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1answer
18 views

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?
3
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1answer
70 views

Emergence of novel protein interactions by mutation of amino acids

Are there any examples of proteins that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other protein ...
0
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1answer
26 views

Can Dpn1 digest hybrid PCR product with only one methylated strand?

In Site directed mutagenesis using PCR, after a cycle we obtain a hybrid molecule with one parental strand and other newly synthesized unmethylated strand. This is followed by Dpn1 digestion. Does ...
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2answers
37 views

Gene cluster of interest not being amplified in PCR

In a lab, I currently have a sample of Rhizobium sp. NT-26. This bacteria is a chemolithoautotrophic arsenite-oxidizer, and I want to clone the arsenite oxidase genes into another bacteria strain in ...
3
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1answer
2k views

Can mRNA be used by ribosomes more than once?

Can mRNA be used by ribosomes more than once? I mean can mRNA be translated more than one time? If not what will happen to it after translation?
1
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0answers
42 views

Does the molecular composition of human body change after a period of time?

I was discussing change in human biology over time and my two in-laws charged in saying, "we're molecularly different after x". I didn't pay attention to what time period they exactly mentioned (hence ...
6
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1answer
203 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 is ...
1
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1answer
41 views

When are neuropeptides loaded into vesicles?

It is well known that small neurotransmitters like monoamines (dopamine, serotonin, etc), acetylcholine, glutamate, etc are loaded into vesicles at the axon terminal. Stated differently, synaptic ...
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1answer
83 views

Why replication collapse but not stall leads to DNA break?

I have been looking into the concept of replication dynamics and was wondering why collapsing but not stalling leads to a DNA break.
0
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1answer
52 views

Is it possible to stop more/extra fat from being stored in the body?

I don't mean simply by restricting eating or upping the activities, but a way to basically stop the body from adding more fat on itself down on the bio level. For example, I'm not too knowledgeable on ...
19
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6answers
5k views

Why are some genes dominant over others? What is the mechanism behind it?

If I have a brown eye gene which encodes the protein that is responsible for the brown color and have a blue eye gene as well, what is the reason that my eye color is brown? How does one gene maintain ...
0
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1answer
25 views

Human Stem Cells and Disease

Can human stem cells be stored for use by future family members as a way to combat generational diseases like diabetes
3
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0answers
26 views

What phosphorylates tau protein & and what causes tau to be phosphorylated?

I want to know what phosphorylates tau protein and its 6 isoforms. I know kinases cause phosphorylation events, and in tau it can be phosphorylated in a healthy neuron in the trans conformation, but ...
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0answers
26 views

Techniques of molecular medicine/biology for aesthetic medicine?

Are there scientifically valid methods (possibly in the developmental stage) that can be used for aesthetic medicine. Usually surgical of physical therapies are used for aesthetic medicine, but ...
6
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1answer
206 views

Why did they expect Astronaut Scott Kelley's telomere shortening to accelerate? (they got longer!)

The NPR News article and podcast Scientists Share Results From NASA's Twins Study says: SCOTT KELLY (NASA Astronaut): You know, the symptomatic stuff is fine. I don't have any long-term negative ...
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0answers
28 views

Intein Splicing

Currently I am trying to read and understand this paper on intein splicing. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/22001202 However, I'm a little confused with Figure 4. Why do the ...
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0answers
18 views

RNAi termination

Can you stop an ongoing RNAi after transfection with a vector containing siRNA? I want to experiment on gene function loss effect, using RNAi, and gene function gain, using stopping the RNAi.
2
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2answers
376 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 ...
0
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1answer
35 views

Insertion Confirmation Cloning Strategy

So I am in a bit of a time constraint. Essentially, I inserted a DNA fragment via molecular cloning which contains a unique RE site. I need to confirm whether my colony has or does not have the ...
4
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2answers
96 views

How can you band wheat chromosomes using Giemsa dye?

I am working with wheat chromosomes and trying to stain the chromosomes. However, during staining with Giemsa dye chromosomes appear totally dark. I'm not sure why this might be. Anyone have any ideas?...
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2answers
176 views

What is a “pan-specific” antibody?

I am new to biology. I searched a lot to find an article that explains what "pan-specific" antibody is but I could not find anything substantial that would help me understand what it is. An example ...
11
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4answers
12k views

Why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon? Can’t translation start with different codons?
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0answers
10 views

Rhodamine 123 Staining Function

How does Rhodamine 123 act as a probe for Mitochondrial Staining? What is the Exact Biochemical Basis? and can it Stain Chloroplast as well? Thanks in Advance
3
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0answers
27 views

Can sperm cells penetrate the cell membrane of non-ovum cells?

Sperm cells have tiny bags of enzymes on their tip (the acrosome) which allow them to penetrate the ovum. My question is whether or not the process that allows sperm cells to penetrate the cell ...
0
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0answers
5 views

What is a secretion target family protein?

I came across this link: https://www.genome.jp/dbget-bin/www_bget?btw:BF38_3398 What is this protein, is it a secreted effector protein or is it something else? What is the difference between type ...
0
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1answer
34 views

Approximate Cell Doubling Time?

If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the ...
3
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0answers
25 views

Why are Barr Bodies usually seen along the edge of the nucleus under the light microscope?

We do a typical class exercise of aceto-orsein staining of buccal epithelial cells from female students to visualize Barr bodies under the light microscope. All the illustrations and pictures in the ...
10
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3answers
31k views

What's the difference between shotgun sequencing and clone based sequencing?

In a lecture during my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera ...
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3answers
112 views

Why are there three stop codons but only one start codon?

I was wondering whether there is any specific reason that there are three stop codons but only one start codon in prokaryotic and eukaryotic cytoplasmic mRNAs.
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1answer
1k views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
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0answers
36 views

How to detect specific mRNA dsRNA by Northern analysis?

I silenced a gene by RNAi method, for that i chose the gene and the size of the gene is 1.5kb and my insert size is 500nts. i did the transfection and i want to confirm the silencing by northern ...
15
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2answers
8k views

Why is there more variation in proteins than genes?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
0
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0answers
5 views

What is the frequency of AUG near-cognates (as start codon) in ‘Leaderless’ mRNA?

In typical bacteria that use SD-dependent translation initiation, the AUG start codon may sometimes be replaced by near-cognates (GUG, UUG, etc.). The frequency of these near-cognates is somewhat ...
2
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1answer
53 views

Relationship between the ambiguity (wobble) at codon position 3 in elongation and codon position 1 in initiation

In prokaryotes the usual observed start codon frequency is AUG > GUG > UUG. An explanation for this is that AUG is the most common initiator codon because it forms the most stable interaction with ...
2
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0answers
35 views

Is there other unknown-compound in Blood?

Blood is made of red blood cells, platelets, plasma etc. Let's say, then, there are these $x$ known compounds in blood. But how can one be sure that there is no other compound other than those $x$ ...
1
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1answer
148 views

What is the difference between a signal peptide and a transit peptide?

From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal ...
2
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1answer
56 views

How are primary monoclonal antibodies for screening mutant cells made, physically?

I'm working with a fairly common protein expressed in a large numbers of organisms, let's say a keratin-associated beta-protein. I'm trying to develop a process which requires primary-secondary ...
2
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1answer
80 views

What is meant by “heads” and “tails” in the context of gene orientation?

I have a hard time understanding what this paper is talking about when it says: We observed maximal cleavage at sites oriented tail-to-tail and separated by -10 bp to +30 bp (Fig. 2d). Finally, ...
2
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0answers
45 views

What regulates cyclic AMP?

After reading a textbook chapter on GPCRs I am still confused by what regulates cAMP. I took in my notes that cAMP is made by adenylyl cyclase and destroyed by cAMP phosphodiesterases (also another ...
6
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2answers
140 views

Why is Turner syndrome a problem?

Turner syndrome is a chromosomal disorder where one of the X chromosomes is missing. For more details visit the Wikipedia page I don't understand why missing one X chromosome would be harmful. In ...
0
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2answers
51 views

identification of differentially expressed genes in RNA-seq analysis [closed]

I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream ...
2
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1answer
39 views

Storage DNA Condition

It is possible to store a digestion of cells with lysis buffer several days at -20 degrees and then proceed with the phenol chloroform isoamyl purification?
1
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1answer
162 views

When should you use a stringent plasmid?

I was wondering if anyone had good examples of when you would want to use a stringent plasmid vs. a relaxed plasmid in a research setting.