4

A methylated nucleotide is the same nucleotide, for the purposes of base-pairing events. The methylated base will be paired with its Watson-Crick opposite after replication, for instance (and methylation will even persist after replication).


3

Starting from what appears to be your main question: Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region? I would strongly advise against using SNPs determine if genes are expressed (at all) in a given tissue.For one thing SNPs that affect expression (then often called eQTLs)...


3

Yes, Agrobacterium is indeed a very widely used vector in plants. So it wouldn't be wrong to consider bacteria as vectors. Just to add, it's worth noting that in recent times, bacterial vector options have been explored in the case of humans also, especially in the case of gene therapy for cancer treatment, though its success hasn't been demonstrated yet. ...


2

Transcription factors generally bind to promoters, enhancers, silencers, and other regulatory regions that lie outside coding regions, through there are "duons" which code for amino acids and also bind TFs to regulatory effect. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967546/ One paper suggests GC content helps balance recombination events with genetic ...


2

The answer to your general question is 'it depends': A lot of RNA localisation to the ER and mitochondria happens co-translationally (based on the protein targeting sequences), so these mRNA actually depend on translation to be localised. However, RNA localisation to mitochondria can also happen due to targeting sequences in the mRNA 3'UTR - in these cases ...


2

There are technologies available for inducing higher (or lower) gene expression in cultured mammalian/human cells as well as in bacteria. The state of the art is CRISPR-mediated gene activation/repression, where you fuse a transcription activation domain to a Cas gene in a CRISPR-Cas system (usually Cas9), and provide a guide RNA to target genes of interest. ...


1

A sequence is executed with transcriptase. To double amount of signaling or some protein production try doubling the sequence occurrence.


1

If you are after large amounts of a particular protein, search "recombinant protein production". It is a huge field.


1

Agrobacterium tumefaciens and Agrobacterium rhizogenes are soil-based plant pathogenic bacterial strains containing plasmid. This plasmid is known as Ti plasmid and is responsible for inducing tumor. Part of this plasmid called T-DNA can be integrated into the host chromosomes. So, this bacterium plasmid act as vector, but not the whole bacterial cell. (...


1

The Methylation will change the individual nucleotide(s) and persist after replication. However the order of the base pairs does not change, so the information in the DNA will still remain , and the base pairs remain with their same partners.For an analogy consider a hardcover book as the DNA . Then the author of the book signs the cover. The signature is ...


1

In the context of transcriptomics the term 'enrichment' is usually connected to differential analysis: If a transcript (or some/all transcripts of a gene) are detected in a given sample that transcript is expressed If a transcript is detected at (statistically significant) higher levels in sample (or condition) A compared to another sample B, that ...


1

In most cases (i.e. assuming there is no aneuploidy) a gene won't be enriched, however, the transcript from a gene may be enriched. A synonym in this case would be overrepresented. In other words, you find relatively more of the transcript compared to other transcripts. Since you seem to confused about the difference between transcripts and genes, I highly ...


1

So, would it be possible to engineer a CRISPR gene editing tool to prevent Vibrio Cholerae from getting into our cells? Vibrio Cholerae doesn't get into our cells. Did you observe that your paper has no in vitro experiments? It's going to be tough to get a cell to transcribe and translate something so small, and will the peptide work if it needs a ...


1

Submit your ensembl IDs to biomart, and get the "gene biotype". "protein-coding" is one of the options there.


1

bambara groundnut does not have a reference genome This is your biggest problem if you want to do any sequencing based analysis. Neither GWAS nor RNAseq data analysis are possible without a reference genome (or at least transcriptome). Depending on the availability, quality & similarity of reference genomes from related species it may however be ...


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