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Metagenomics in 'Everyday' Life
Metagenomics in 'Everyday' Life
Finding Alien Metagenomes
Finding Alien Metagenomes
The rise of next generation sequencing has matched the age of space travel. Two great scientific achievements that have to potential to advance to the quest to find extraterrestrial life. "...Integrated nucleic acid extractors for studying “Martian metagenomics”..." are just some of the proposed options to directing future efforts of identifying past or present life on Mars. There remains the question of how to implement the technology and more importantly where, and at what scale, to begin the new sampling efforts.
The rise of next generation sequencing has matched the age of space travel. Two great scientific achievements that have to potential to advance to the quest to find extraterrestrial life. "...Integrated nucleic acid extractors for studying “Martian metagenomics”..." are just some of the proposed options to directing future efforts of identifying past or present life on Mars. There remains the question of how to implement the technology and more importantly where, and at what scale, to begin the new sampling efforts.
Original article: The Search for Life on Mars Is about to Get Weird by Leonard David on May 9, 2017
Quick DNA Test Diagnoses a Boy's Illness
Quick DNA Test Diagnoses a Boy's Illness
This New York Times article follows the treatment of a young boy who is suffering from encephalitis cause by an unknown pathogen. After various tests came back negative and the boy's condition worsened, the doctors decided to try a cutting edge technique in order to find the culprit pathogen.
This New York Times article follows the treatment of a young boy who is suffering from encephalitis cause by an unknown pathogen. After various tests came back negative and the boy's condition worsened, the doctors decided to try a cutting edge technique in order to find the culprit pathogen.
"The researchers latest method is called unbiased next-generation sequencing. To identify a pathogen, the researchers extract every scrap of DNA in a sample from a patient, which might be blood, cerebrospinal fluid or stool. Then they sift the genetic fragments for those belonging to pathogens."
"The researchers latest method is called unbiased next-generation sequencing. To identify a pathogen, the researchers extract every scrap of DNA in a sample from a patient, which might be blood, cerebrospinal fluid or stool. Then they sift the genetic fragments for those belonging to pathogens."
After overnighting the boy's sample to another state, and sequencing and analyzing the results by comparing them to a database, the results showed that the lethal Leptospira pathogen was to blame. Luckily, Leptospira is treated with penicillin.
After overnighting the boy's sample to another state, and sequencing and analyzing the results by comparing them to a database, the results showed that the lethal Leptospira pathogen was to blame. Luckily, Leptospira is treated with penicillin.
Because of the speed and proficiency of this technique, the doctors and scientists were able to diagnose and treat the boy
Because of the speed and proficiency of this technique, the doctors and scientists were able to diagnose and treat the boy
before his state had a chance to worsen more, saving him.
before his state had a chance to worsen more, saving him.
Ana Remis + Joshua D
Athletes’ Microbiomes Differ from Non athletes
Athletes’ Microbiomes Differ from Non athletes
A girl ~14 year old girl had chronic lime disease throughout her childhood. She was an athlete in mountain bicyclist and received extensive antibiotic treatments. Since the disease continuously came back she was given a daily dosage of antibiotics for an entire year to fight off the lime disease completely. This task was successful in curing the disease however she then suffered with chronic fatigue and bad stomach aches. She became a PhD student and studied pathogenic biology when she learned about Microbiome, and how it might affect the health as well as kill the required good bacteria in the body along with the bad. She began to believe that something was wrong with her microbiome.
A girl ~14 year old girl had chronic lime disease throughout her childhood. She was an athlete in mountain bicyclist and received extensive antibiotic treatments. Since the disease continuously came back she was given a daily dosage of antibiotics for an entire year to fight off the lime disease completely. This task was successful in curing the disease however she then suffered with chronic fatigue and bad stomach aches. She became a PhD student and studied pathogenic biology when she learned about Microbiome, and how it might affect the health as well as kill the required good bacteria in the body along with the bad. She began to believe that something was wrong with her microbiome.
She attended a Microbiome research conference which welcomed people to submit stool samples for analysis. The samples was accompanied with survey Q&A on lifestyles & diets.
She attended a Microbiome research conference which welcomed people to submit stool samples for analysis. The samples was accompanied with survey Q&A on lifestyles & diets.
https://www.the-scientist.com/?articles.view/articleNo/49450/title/Athletes--Microbiomes-Differ-from-Nonathletes/
Eugenia K Beache & Charlene Mcintosh
The connection between DNA and hair loss
The connection between DNA and hair loss
Baldness always troubles many people. Everyone wants their hair thick. But unfortunately, people can’t control it because the research found that the baldness is actually related to the genetic makeup of each person. And the DNA inheritance decides that if a parent have the losing hair problem, then the children will have a big probability to have the baldness too. It’s says that there is no special way to cure baldness.
Baldness always troubles many people. Everyone wants their hair thick. But unfortunately, people can’t control it because the research found that the baldness is actually related to the genetic makeup of each person. And the DNA inheritance decides that if a parent have the losing hair problem, then the children will have a big probability to have the baldness too. It’s says that there is no special way to cure baldness.
Yanyan Chen
Phylogenetics Informed by Metagenomics
Phylogenetics Informed by Metagenomics
Zika Virus Genomes Elucidate Disease Spread in Central America, Mexico
Zika Virus Genomes Elucidate Disease Spread in Central America, Mexico
In 2015, the first Zika virus was reported in America. It has infected more than 100 million people. Researchers have reconstructed the spread of the Zika virus in Central America and Mexico using the genomes of viruses collected from patients in the region.
The researchers took a combined metagenomic next-generation sequencing and spiked primer enrichment strategy to tease out Zika viral genomes from their samples. From this, they identified sequencing reads that matched the Zika virus in 71 samples, with an average consensus coverage of 64 percent. For the remaining samples, all of which were from Nicaragua, the researchers used a different metagenomic approach that relied on bait probe capture.
Pybus and his colleagues constructed a phylogenetic tree using these and 298 published Zika virus genomes. Their tree placed 102 of the 107 Zika virus genomes from Central America and Mexico into a single monophyletic clade, dubbed clade B, which was closely related to viruses from Brazil. Four other Zika virus genomes from Panama and Mexico formed clade C, suggesting multiple introductions of the virus to the region, though only one has dominated.
"What we found was not what we expected," said first author Julien Thézé from Oxford. "There is usually only one breeding season per year, but we found two separate outbreaks in a relatively small country like Honduras."
Bacterial Diversity Illustrates the Potential Diversity Across the Universe
Bacterial Diversity Illustrates the Potential Diversity Across the Universe
Metagenomics has expanded the tree of life by facilitating the inclusion of unculturable bacteria! Since 1837 we have learned much about life, building upon the foundation Darwin built for the relationship among organisms (top photo) and the discovery & diversity of bacteria! This diversity has been explored as the computational power has improved our ability of detection and identification. The creation of the field of bioinformatics pairs well with astrobiology and the search for extraterresterial life.
Metagenomics has expanded the tree of life by facilitating the inclusion of unculturable bacteria! Since 1837 we have learned much about life, building upon the foundation Darwin built for the relationship among organisms (top photo) and the discovery & diversity of bacteria! This diversity has been explored as the computational power has improved our ability of detection and identification. The creation of the field of bioinformatics pairs well with astrobiology and the search for extraterresterial life.
Original Article: "Alien Life on Earth" --New Tree of Life Foreshadows the Amazing Potential Diversity of Life in the Cosmos
The Daily Galaxy via NASA /Astrobiology - March 14, 2017
Viruses Would Rather Jump to New Hosts Than Evolve With Them:
Viruses Would Rather Jump to New Hosts Than Evolve With Them:
This article discuses Co divergence of host and viruses and Cross species transmission. Researchers in Australia conducted the first study of the long-term evolution of thousands of diverse viruses. Cross species transmission has been more relevant than anyone realized while co divergence was less common than was previously believed.
This article discuses Co divergence of host and viruses and Cross species transmission. Researchers in Australia conducted the first study of the long-term evolution of thousands of diverse viruses. Cross species transmission has been more relevant than anyone realized while co divergence was less common than was previously believed.
With the two paths to viruses evolution the which one is more common to occur?
With the two paths to viruses evolution the which one is more common to occur?
Co divergence and hosts and virus is when a part of a host population splinter off to become a new species, viruses can go with them.
Co divergence and hosts and virus is when a part of a host population splinter off to become a new species, viruses can go with them.
Cross species transmission is when viruses evolved mostly by jumping into a new host species
Cross species transmission is when viruses evolved mostly by jumping into a new host species
In the above illustration is a comparison of the family tree of the adenoviruses (Adenoviridae) with the branching evolution of their host species shows that the viruses jumped to completely different hosts more than they co-diverged with emerging host species. The same was true of all 19 major families of virus examined in a long-term study
In the above illustration is a comparison of the family tree of the adenoviruses (Adenoviridae) with the branching evolution of their host species shows that the viruses jumped to completely different hosts more than they co-diverged with emerging host species. The same was true of all 19 major families of virus examined in a long-term study
Original Article:https://www.quantamagazine.org/viruses-would-rather-jump-to-new-hosts-than-evolve-with-them-20170913/
Eugenia K Beache & Charlene Mcintosh
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