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Here is an answer from Bard:
The Species Hypothesis as Operational Taxonomic Unit (OTU) is a relatively recent approach in ecology and environmental studies that uses DNA sequences to group organisms into putative species. Here’s how it works:
– DNA Sequencing: Researchers collect environmental samples, such as soil or seawater, and extract DNA from all the organisms present (without necessarily knowing what they are).
– Clustering: They then sequence a specific DNA region (often a “barcode” gene) for each organism and use computer algorithms to cluster these sequences based on their similarity.
– OTU Definition: A threshold of similarity is chosen (e.g., 97% for bacteria, 95% for fungi). Sequences that are more similar than this threshold are grouped into the same OTU, which is assumed to represent a single species under the species hypothesis.
– Species Inference: While acknowledging limitations, researchers interpret each OTU as a potential species, even if it hasn’t been formally described or confirmed through traditional taxonomic methods.This approach has several advantages:
– Speed and Scalability: It allows researchers to quickly and efficiently assess species diversity in complex environments with many unknown organisms.
– Standardization: OTUs provide a standardized way to compare data across different studies and ecosystems, even when dealing with unidentified species.
– Hypothesis Generation: By identifying distinct OTUs, the species hypothesis can guide further research efforts to formally describe and characterize these potential new species.Here is the answer from Bard:
Microbiota and microbiome are two terms that are often used interchangeably, but they have slightly different meanings.
Microbiota refers to the community of microorganisms that live in a particular environment. These microorganisms can include bacteria, archaea, fungi, viruses, and protozoa. The microbiota of a particular environment is unique and is shaped by a variety of factors, including the environment itself, the host organism (if there is one), and the host’s diet.
Microbiome refers to the collective genomes of the microorganisms in a particular environment. This includes the genes of all the bacteria, archaea, fungi, viruses, and protozoa in the environment. The microbiome is a complex system that is constantly changing in response to changes in the environment.
In other words, the microbiota is the community of microorganisms that live in a particular environment, while the microbiome is the genetic material of those microorganisms.
Here is a table that summarizes the key differences between microbiota and microbiome:
Feature Microbiota Microbiome Definition The community of microorganisms that live in a particular environment The collective genomes of the microorganisms in a particular environment What it includes Bacteria, archaea, fungi, viruses, protozoa Genes of bacteria, archaea, fungi, viruses, protozoa How it changes Changes in response to changes in the environment Changes in response to changes in the environment I hope this helps!
Spatial transcriptomics is a method for assigning cell types (identified by the mRNA readouts) to their locations in the histological sections and can also be used to determine subcellular localization of mRNA molecules. First described in 2016 by Ståhl et al., it has since undergone a variety of improvements and modifications.
Spatial transcriptomics – Wikipedia
RNA editing (also RNA modification) is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase. It occurs in all living organisms and is one of the most evolutionarily conserved properties of RNAs.
RNA editing may include the insertion, deletion, and base substitution of nucleotides within the RNA molecule. RNA editing is relatively rare, with common forms of RNA processing (e.g. splicing, 5′-capping, and 3′-polyadenylation) not usually considered as editing. It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases.
The diversity of RNA editing phenomena includes nucleobase modifications such as cytidine (C) to uridine (U) and adenosine (A) to inosine (I) deaminations, as well as non-template nucleotide additions and insertions. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence.
The following answer was generated using Bard:
The term “empty DNA” can refer to a few different things in the context of biology.
– Noncoding DNA: This is DNA that does not encode proteins or RNA molecules. It makes up about 98% of the human genome, and its function is still being actively researched. Some scientists believe that noncoding DNA may play a role in gene regulation, while others believe that it may be evolutionary junk DNA.
– Empty vector DNA: This is a type of DNA plasmid that has been engineered to not contain any genes. It is often used as a carrier for gene therapy vectors or as a negative control in molecular biology experiments.
– Empty DNA columns: These are specialized columns that are used to synthesize DNA molecules. They are typically empty when they are first used, and the user then packs them with the necessary reagents and DNA precursors.
It is important to note that the term “empty DNA” is not always used in a strictly scientific sense. For example, some people may use it to refer to DNA that is not being used by a cell, or to DNA that is damaged or has been deleted.
This is the answer generated by by Bard:
Exclusome is a newly discovered organelle in mammalian cells. It is made up of DNA rings known as plasmids. It is located within the cell plasma. This discovery is significant because eukaryotic cells (cells with nuclei) usually keep most of their DNA in the cell nucleus, where it is organized into chromosomes. However, in the exclusome, the DNA is organized into plasmids – small, circular DNA strands that can replicate independently of chromosomes and are usually found in bacteria and other microscopic organisms.
The function of the exclusome is still under investigation, but researchers believe it may play a role in gene expression and cell differentiation. It is also possible that the exclusome is involved in the immune response, as it has been found to contain proteins that are known to be involved in fighting infection.
The discovery of the exclusome is a reminder that there is still much we don’t know about the inner workings of cells. It is also a testament to the power of scientific research, as it was only through careful observation and experimentation that scientists were able to identify this new organelle.
A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism. A haplotype is a group of alleles in an organism that are inherited together from a single parent. Thus, a haplogroup is a combination of alleles at different chromosomal regions that are closely linked and that tend to be inherited together, from one parent.
In human genetics, the haplogroups most commonly studied are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups, each of which can be used to define genetic populations. Y-DNA is passed solely along the patrilineal line, from father to son, while mtDNA is passed down the matrilineal line, from mother to offspring of both sexes. Neither recombines, and thus Y-DNA and mtDNA change only by chance mutation at each generation with no intermixture between parents’ genetic material.
For more information, go to Wikipedia: https://en.wikipedia.org/wiki/Haplogroup#:~:text=More%20specifically%2C%20a%20haplogroup%20is,a%20single%20line%20of%20descent.
CRISPR gene drive is used for production of malaria-resistant mosquitoes:
https://bioinformaticshub.net/genetically-modified-mosquitoes-fighting-malaria/
CRISPR/Cas9 technology is used to insert new genes in the mosquito egg. The insert contains not only the new gene sequences, but also sequences of Cas9 and its guide RNA. When a homozygous transgenic mosquito mates with a wild-type mosquito, the offspring should be heterozygous. However, one chromosome having the insert will work to edit the other one, making a homozygous offspring. This way, the new gene is not diluted, but rather driven in the population against Mendelian rules of heredity.
The aforementioned cases are examples of tetragametic chimerism. An embryo is formed from two different ova and two different sperms, with two cell lines.
Chimerism most commonly occurs when a pregnant woman absorbs a few cells from her fetus, or a fetus absorbs a few cells from its mother. These cells may travel into the mother’s or fetus’s bloodstream and migrate to different organs. They may remain in a mother’s body or a child’s body for a decade or more following childbirth. This condition is called microchimerism. The cause, physiology, and consequent pathology of this phenomenon are not well-settled.
Do you mean the 3’→5′ exonuclease activity?
The answer is yes, sure.
This activity is also the cause why many nucleoside analogue antiviral drugs do not work with the corona virus.
Base editing is a new method of gene editing.
The traditional CRISPR-Cas9 editing technique depends on making a targeted (using a guide RNA) double-strand DNA break (DSB). This DSB is repaired by the error-prone non-homologous end joining, causing disruption of the gene, or homology-directed repair using a template DNA. Correction of faulty genes by this technique proved to be difficult and of low efficiency. See applications described in this site here and here.
DNA base editing also uses a guide RNA to find the target sequence, then makes a transition mutation in DNA. Cytosine base editing (CBE) uses a cytosine deaminase to convert cytosine to uracil, which is recognized as thymine during DNA replication. Thus, the C-G base pair becomes T-A. Adenosine base editing (ABE) uses an adenosine deaminase to convert adenosine to inosine, which is recognized as guanosine. Thus, the A-T base pair becomes G-C by replication.
Base editing has a potential application in treating diseases caused by single nucleotide mutation. The continuous developing of new techniques carries the hope of treating such diseases with a high efficiency.
You can find a 2020 review of this subject here
You are asking about nucleic acid aptamers, which you probably encountered while reading about a product that required specific binding.
An aptamer is a short segment of DNA, RNA, or peptide that binds to a specific ligand like antibodies do. The ligand may be a small molecule or may be a protein or even a cell.
Aptamers are usually synthesized and isolated by repetitive screening of large pools of randomized molecules for those that bind best to the target ligand. They are used in basic research and in various applications, e.g., diagnostics and therapeutics.
I agree with Y Soun.
Besides the ease and convenience for the patient, Liquid biopsy can detect cancer very early before the appearance of any signs and before any imaging technique can do. This is of utmost importance when we are concerned with monitoring the efficacy of treatment and testing for relapses.