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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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What actually kills a plant that requires winter dormancy if it is kept indoors all year?

In bonsai practice, beginners will commonly purchase a juniper (often Juniperus procumbens 'Nana'), which is an outdoor tree, and keep it inside all year. The tree invariably dies. It is commonly ...
cape1232's user avatar
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8 votes
2 answers
792 views

How does LCR compare to Assembly PCR

The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction (...
bobthejoe's user avatar
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7 votes
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What are the additional considerations for primer design in ancient DNA?

I'm familiar with the principles of primer design and have previously designed primers for use in modern DNA. However, in my current project I am working with ancient DNA (nuclear gene) and need to ...
natb's user avatar
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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 ...
user3665690's user avatar
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Is there a name for this type of diagram?

Is there any commonly used name for this type of diagram / symbology? I have not been able to find them referred to by any name.
tsj's user avatar
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Does the molecules in nerve cell membrane change 100% during the life of the nerve cell?

In their lifespan nerve cells do not divide and so they stay the same. They do get damaged sometimes and require some maintenance and change their axons a bit. They also require a lot of energy so ...
Lauri's user avatar
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How much salt [NaCl] is too much in DNA precipitation?

In DNA extractions, how much is too much salt in a CTAB extraction buffer? Protocols hover around 2.5 molar; if you go over this (e.g. 25 molar), will you saturate your solution, and precipitate the ...
incertae_sedis's user avatar
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Is blood typing still useful for analysis of ancient tissues?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be extracted ...
James's user avatar
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Why am I getting a large horizontal band spreading across my native gel?

On every gel of this type that I've ran so far, I'm getting this large band interfering with my gel analysis no matter how much troubleshooting I've done. This is a Novex Wedgewell 6% Tris-Glycine Gel ...
novara's user avatar
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What happens exactly in the electron transport chain when there's no oxygen

what is the mechanism of hypoxia in the electron transport chain? It stops because there's no terminal electron acceptor so the IV complex become "stuck" with an electron? There's no other ...
lorga's user avatar
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Has there been a measurement of a stalling force for myosin molecular motors?

For processive molecular motors like kinesin, in vitro assays have allowed to measure directly a stalling force beyond which they do not progress anymore or detach. As far as I know, the literature ...
Joce's user avatar
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Use of plasmid pXen5 for transposon screening

I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen. It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409). ...
Julius's user avatar
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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 ...
naco's user avatar
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How do molecular biologists determine biochemical pathways?

I'm new to this community, so hopefully this is the right place to ask this question. I know my question is really general, but in all of my biology courses we are merely taught the chemical pathways ...
Sully Chen's user avatar
3 votes
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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 ...
J Thomas's user avatar
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Proteins folds: relation to splicing and post-translational modification?

Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?
L.Diago's user avatar
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What's the ratio of saturated to unsaturated fatty acids in human cell membrane?

It's well established that the fluidity of a cell is largely dependent upon the ratio of saturated to unsaturated fatty acids that exist within the membrane, but, what exactly are the values for this ...
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Why do I see so many kinetochores?

I am analysing RPE-1 cells from humans and I do not understand why I see so many kinetochores by immunofluorescence (more than 100 in many cells). They are in prometaphase.
Bio's user avatar
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27 views

How does DNA damage increase the activity of p53?

I understand the steps leading up to the halting of the S-cdK checkpoint from there, but I can't find the mechanism by which DNA damage actually increases the activity of p53.
ooakley's user avatar
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Why does a broad-leaved evergreen (Mahonia aquifolium) has red leaves?

To my knowledge, oregon grape (Mahonia aquifolium) is purportedly an evergreen shrub? Deciduous broadleaf plants lose their leaves in autumn usually and before that as the leaves die they oxidize and ...
Jaguar Domingo's user avatar
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147 views

Artificial reduction of NADP into NADPH by means of an electrical current

I've recently been attempting to artificially drive the formation of NADPH via the NADP reduction mechanism utilized by Ferredoxin-NADP Reductase in the Light-Dependent Reactions of Photosynthesis in ...
0fb1d8's user avatar
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L-tryptophan in mammalian cell culture

Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells? It's an essential amino acid, so I cannot fathom why low concentrations as opposed to ...
Hernandez's user avatar
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What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?

I want to know the trigger behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, it forms a relationship wherein ...
Adam Cat's user avatar
3 votes
0 answers
981 views

Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
wswr's user avatar
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291 views

How does estrogen influence collagen synthesis?

Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .
Boldeanu Elena's user avatar
3 votes
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618 views

How to prevent e coli from clumping (for FACS)?

I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells. I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run ...
Amanda's user avatar
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0 answers
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Gibson assembly using NeBuilder

I am supposed to construct a plasmid that contains features from two other plasmids. My strategy is to generate three fragments form the two other plasmids. I was encouraged to try Gibson assembly, ...
Flight505's user avatar
3 votes
0 answers
57 views

Adenosine metabolism

Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but ...
dutta's user avatar
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2 votes
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How did birds reduce their tail and fuse the last caudual vertebrae into a pygostyle?

I was just looking at the phylogeny of Avialae and saw that birds go from having long tails made up of many caudal vertebrae (ex: Archaeopteryx, Jixiangornis, Jeholornis) to ones with very few ...
RenaMoon's user avatar
2 votes
0 answers
123 views

Immunoaffinity chromatography: avoiding damage to the antibodies from proteases

What are the possible methods to prevent the digestion of antibodies (mainly Polyclonal) by proteases during affinity chromatography? I read some papers about doing modifications to the anitbodies: ...
Alpha's user avatar
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39 views

chip sequencing

I understand the concepts of steps in Chip-seq up to DNA purification, but I don't get how one can then amplify the purified DNA samples that are once bound to the proteins.... Since sequence-specific ...
uwuwubread's user avatar
2 votes
0 answers
73 views

Rationale for two-components in feedback loop of circadian molecular clock

The circadian clock in humans and fruit flies involves a feedback loop in which the active components are protein heterodimers. This is illustrated for humans in the diagram below: The nuclear ...
yoshi's user avatar
  • 121
2 votes
1 answer
314 views

Is lactic acid build up the cause of muscle fatigue or only a symptom?

If your body could magically instantly remove lactic acid as it is produced, would that make you immune to muscle fatigue, or is the lactic acid only a symptom of muscle fatigue and instead exists, at ...
0xFFF1's user avatar
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2 votes
0 answers
50 views

What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?

From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011) The metabolic profile ...
CopperKettle's user avatar
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2 votes
0 answers
55 views

why does water go from high to low osmotic pressure to decrease the size of the nucleus?

I am reading this paper "Volume regulation and shape bifurcation in the cell nucleus" (linked below) https://jcs.biologists.org/content/joces/128/18/3375.full.pdf I am confused by this ...
veraxxarev's user avatar
2 votes
0 answers
206 views

What does it mean for a protein to be dominant-negative?

I am reading this journal paper, which investigates the interaction of the NCAM protein and the Pak1 protein. In this paper I have come across the term "dominant-negative Pak1" and "...
ceno980's user avatar
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2 votes
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40 views

What is the difference (if any) between an Intrinsically Disordered Protein and an Intrinsically Disordered Region

The wikipedia definition of an Intrinsically Disordered Protein is a protein that lacks a specific 3D structure. An Intrinsically Disordered Region is similarly defined. Why are they often listed ...
Joshua Morris's user avatar
2 votes
0 answers
86 views

design and assessment of qPCR primers for COVID19

I read the False Negative of qPCR test for COVID19 is high compare to CT scans. https://pubs.rsna.org/doi/10.1148/radiol.2020200642 I was curious if experts can comment on why and what makes it ...
user702846's user avatar
2 votes
0 answers
65 views

Fluorescence assays to identify protein concentration without adding a large peptide sequence?

I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. ...
Tal's user avatar
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2 votes
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68 views

ATP and Muscle Contraction

I have a question regarding how molecular interactions manifest in physical actions - such as hanging from a bar. To the best of my understanding, when it comes to the contraction of muscles, ATP is ...
Shayan Hemmati's user avatar
2 votes
0 answers
52 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 $x$ ...
Michael's user avatar
  • 129
2 votes
0 answers
68 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 ...
user3665690's user avatar
2 votes
0 answers
24 views

Using expression vector to express arsenite oxidase genes in E. coli

So I am trying to express a gene cluster that can oxidize arsenite into arsenite autotrophically. The arsenite oxidase gene cluster sequence is linked here: https://www.ncbi.nlm.nih.gov/nuccore/...
HLR's user avatar
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0 answers
78 views

Why does M1 RNA together with C5 protein in 100mM Mg(II) fail to cleave tRNA?

Sidney Altman discovered that RNA moeity of RNAse P (M1 RNA) alone is able to perform enzymatic cleavage of ptRNA, which won him the Nobel Prize of Chemistry in 1989. However, when I read the Nobel ...
user46857's user avatar
2 votes
0 answers
71 views

Molecular Docking Enzyme Inhibitor Biosensor?

I had some task to study Molecular Docking relations with Biosensor and I am really new with this discipline (beginner). I am docking C60 with Glucose Oxidase and my question is: what would happen if ...
Wawo Brown's user avatar
2 votes
0 answers
40 views

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 ...
Bio's user avatar
  • 227
2 votes
0 answers
178 views

Would I expect salt precipitate on fibres of DNA in a NaCl water solution?

I just recently conducted an experiment in my biochemistry class where we had to add DNA to distilled water, isotonic saline and 2.5M NaCl. I noticed different physical aspects depending on the ...
ro_the_electron's user avatar
2 votes
0 answers
232 views

How is the effect of proof-reading on error frequency during DNA replication determined?

An article in Nature Scitable on DNA Replication and the causes of Mutation states that: When an incorrect nucleotide is added to the growing strand, replication is stalled by the fact that the ...
Johnny Johnston's user avatar
2 votes
0 answers
164 views

E.coli fermentation - process flow

I have an engineering background and have been assigned a project to look into to failures during E.coli fermentation process using the data available before/during/after the process I have learnt ...
RTM's user avatar
  • 121
2 votes
0 answers
133 views

Can a phosphodiester bond form between RNA and DNA?

In the initiation of DNA synthesis: the RNA segments are first synthesized by primase and then elongated by DNA polymerase (Wikipedia). What does 'elongated' mean in this context? Is it possible ...
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