Genome sequencing to identify Corona virus SARS-Cov-2 (COVID-19)

COVID-19, a disease caused by the coronavirus, SARS-CoV-2, will forever be linked to one of the most devastating outbreaks the world has ever known. As the virus is highly infectious, it has rapidly spread across the globe, and as a result, the World Health Organization (WHO) on March 11, 2020 declared the COVID-19 outbreak as a pandemic. As of April 30, 2020, over 3.23 million people are infected, and over 230 thousand people have died as a result. Understanding the genetic constitution of the virus is vital to the identification and development of treatment and control strategies against the disease.

A group of scientists in Korea has reported that they have sequenced the complete genome of the SARS-Cov-2 virus

 

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NGS Digs up Ancient Mummy DNA

It was previously believed that ancient Egyptian mummies did not have any viable DNA available for sequencing.  Possibly due to the hot climate or the chemicals used in mummification, several attempts to extract DNA were unsuccessful.  However a team of ancient DNA specialists has successfully sequenced genomes from 90 ancient Egyptian mummies.  Until now, the most recent success was a 2010 study that performed polymerase chain reaction on 16 mummies.  However, PCR cannot always distinguish between ancient DNA and modern contamination.

Johannes Krause, a geneticist at the Max Planck Institute for the Science of Human History in Jena, Germany, used next generation sequencing to read stretches of DNA and identify any that resemble human DNA.  The complete reads allowed the team to piece together data that had tell tale markers of ancient DNA.  The results were more reliable than the previous PCR study.

The mummy’s soft tissue contained almost no DNA, but the bones and teeth were full of genetic material.  Ninety of the mummies yielded mitochondrial DNA, but this left out the DNA inherited from the father.  The nuclear genome, which contains DNA from both parents, is far more informative.  Unfortunately, only a small number of mummy nuclear genome was viable, and even fewer passed strict contamination tests.  The team ended up with only three nuclear genomes from mummies of different time periods.

 

 

 

 

 

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DNA in My Garden: What is that bug that keeps eating my cantaloupes?Or maybe you are having issues with some aphids that have been attacking grandma’s blue ribbon county fair roses that seem almost post-apocalyptic in their resistance to every method you have tried to wipe them out, including throwing the proverbial kitchen sink at them. Maybe you have discovered something that needs further elucidating, something slightly different that can either change your approach in your gardening arsenal or something as big that a thesis is begging to be researched and written.

So you have a strange insect that has been poking holes in the bottom of all those luscious cantaloupes you have been tending to. You cut that cantaloupe open and something vibrantly colored and slightly vicious looking locks eyes with you, something that stumps even the precursory Internet search. Instead of calling the fire brigade, pull out some tweezers and drop the little guy into a sterile container. Then take some deep breaths and remind yourself it is all for the good of science.

 

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Are Mental Disorders Genetic?

Mental disorders, also known as mental illnesses are health condition that involves changes in behavior, emotion, thinking, or combination of all of these. Some of the examples of such disorders include attention deficit hyperactivity disorder (ADHD), autism, bipolar disorder, major depression, substance use disorder, and schizophrenia. Mental disorders can lead to trouble in normal personal behavior, and social functioning of an individual.  According to World Health Organization about 25% of the world population will develop at least one mental disorder at some stage of their life. According to the NIMH, currently, there are about 450 million people worldwide living with mental disorder. In the US, about 20% (46.6 million) adults have some kind of mental disorder . The mental disorder was higher among women (22.3%) than men (15.1%).  When it was compared among different age groups, mental disorder was observed highest (25.8%) among young adults (18-25 years) as compared to adults aged 26-49 years (22.2%) and adults aged 50 years and above (13.8%).

 

 

 

 

 

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Decomposition and eDNA: Good for the Environment

Have you ever considered that roadkill might be beneficial to the environment such as providing growth factors for the soil? For most that is not the first thought that comes to mind, nevertheless it’s been backed up by scientific research.

Decomposition plays a major role in the carbon cycle of any given ecosystem. It is organic recycling at its finest: the carbon travels from the atmosphere to be absorbed by plants via photosynthesis, plants get eaten by animals, and animals that eat other animals get carbon through their meal as well. When animals and plants die, their carcasses, leaves and wood are broken down by the process of decay. This process couldn’t be performed without the involvement of decomposers that are made up of communities of bacteria and fungi with the capability to transform the dead plants and animal remains into nutritional elements for the soil to promote growth. Some of the carbon in the soil can also turn into fossil fuel. There are several pathways via which carbon could return back to the atmosphere:

 

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Next Generation Sequencing and Athletics

It is unusual to see those two topics merging into one title. What’s the common ground, you ask? Bacteria. Next generation sequencing has become a revolutionizing tool in the knowledge and use of microbiomes. One such example is an idea by Jonathan Sheiman Ph.D., a former postdoctoral fellow at the Wyss Institute for Biologically Inspired Engineering at Harvard University, which was brought to George Church, Wyss Institute Core Faculty member, to see if bacterial gut flora of elite athletes affects their physical performance. They recruited a cohort of Boston marathon runners for the study and sampled them every day the week before and after the marathon. Once the sample retrieval of the athletes was complete, the sample processing began with DNA extraction, leading into 16s PCR amplification of the V4 variable region which then underwent sequencing on Illumina’s MiSeq or HiSeq 2500 platforms. After sequencing, the data from the samples underwent bioinformatic analysis to discover down to the genus level, the community of bacteria residing in each individual’s microbiome. The human gut flora houses vast complex communities of microorganisms that affect human health with the capability of adapting to the host’s lifestyle.

 

 

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What Diet Is The Most Beneficial for Our Microbiome?

It feels like every week there’s a new fad miracle diet that promises to cure diseases.  One week certain foods that are labeled “bad” can be suddenly considered a key element to nutrition.  From the Cabbage Soup Diet to the Atkins Diet, supporters usually claim that their ailments were healed by simple substitutions or restrictions, but how do these diets affect our intestinal microbiome?  More importantly, does the diversity and health of our microbiome affect our overall health? And what is the microbiome anyway?

A research team from the University of California had a few of these same questions and decided to delve deep into recent microbiome literature in order to further investigate what sort of impact the bacteria living in our intestines can have on our overall health. The intestinal microbiome is the microorganism ecosystem that resides in your gut, and it is comprised of not only bacteria, but viruses, fungi, and protozoa as well.  As more and more research studies are being published, there is an increasing amount of evidence linking a healthy diet and a healthy gut to positive overall health. A great number of microbiome studies are completed using 16s rRNA amplicon sequencing.  16s rRNA sequencing is the most common method used to study the microbiome due to its low cost.  However, it only provides microbial identification, not function.  Although more expensive, shotgun metagenomic sequencing sequences the whole bacterial genome.  Through shotgun metagenomic sequencing, microbial identification and gene composition can be analyzed.  This in turn allows researchers to draw conclusions of the functionality of different genes.

 

 

 

 

 

 

 

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A high sugar diet acutely promotes the predisposition to colitis in mice

Researchers at the University of Alberta discovered that a high sugar diet promotes chemically induced colitis with more severe symptoms in mice after only two days compared to those with a balanced diet. Previous studies have shown that one’s diet determines the susceptibility of disease. With that in mind, the research team wanted to see just how quickly would an onset change in the diet affects health. The study involved two groups of mice: a group fed with chow and a group that was fed with high sugar diet (50% sucrose) over a two day period. After two days of different treatments, the mice were introduced to a low concentration of dextran sodium sulfate (DSS) to induce colitis.  After 10 days, cecum samples were collected and underwent 16s rRNA sequencing method and placed to run on Illumina’s MiSeq platform.

 

 

 

 

 

 

 

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Mucins Attacking and Regulating Biofilms

In a recent study published in Nature magazine, a group of scientists researched and developed a hypothesis that the body’s production of mucins helps with the regulation and diffusion of Pseudomonas aeruginosa based biofilms. A biofilm, very simply defined, is a group of cells clustered together that have adhered to a surface. Biofilms can and do exist in the human body on many different surfaces (such as in the lungs or the intestines), forming a community of bacteria that can consist of one type of bacteria or many different genus and species co-existing in symbiosis. When the human body becomes exposed to a toxic element or becomes immunocompromised, biofilms can become unregulated and cause or further the side effects of disease. So what method of attack does the human body utilize for the regulation of biofilms to keep from essentially waging biological warfare and harming their host?

In a paper titled “Mucins trigger dispersal of Pseudomonas aeruginosa,” Julia Co et al. developed a study that supported the hypothesis that the body’s production of a material called mucin is one way the human body is able to accomplish such a task. Mucus is vital to the many of the body’s functions, such as keeping the surface of the lungs clear of pathogens, and mucins are a structural part of mucus. Mucins are the parts of mucus that resemble “bottle-like structures with dense O-linked glycosylation” (1) and this structure of the mucins is what compromises the “gel-forming polymers” (1) of mucus. Basically, mucins are what give mucus its consistency.

 

 

 

 

 

 

 

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Whole Genome Sequencing Used in Human Trait Prediction

Scientists from Human Longevity Inc. and Craig Venter Institute report that they have developed methods for predicting human traits by using whole-genome sequencing data. The traits they used are 3D facial structure, skin color, eye color, height, weight, biological age, and body mass index (BMI). For the study, they collected samples from 1,061 ethnically diverse populations from San Diego, California. The ethnic groups included African, Latino, East Asian, and South Asian. The study also included individuals from 18 years to 82 years of age with an average age of 36 years. Genomes of those 1,061 individuals were sequenced, and phenotypic data from all individuals were also collected. They used a two-step approach to match the genomic data to phenotypic data by first mapping of the phenotypes and genomes followed by using the statistical functions i.e. learning embeddings and learning similarity functions to create matches between the phenotype and genomic data.

 

 

 

 

 

 

 

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Nature vs Nurture

Dr. Eric J. Nestler, Director of Friedman Brain Institute at the Mount Sinai Medical Center in New York City discussed with Scientific American how environmental stresses that we encounter everyday play a role in our genetic makeup. Dr. Nestler describes throughout the interview how through the process of genetic modifications, the expression of genes in the human genome can be regulated as a result of certain environmental pressures experienced by the individual. In certain cases, these genetic modifications can be passed down to our offspring via epigenetic inheritance. While the idea of epigenetic inheritance may sound daunting to the general population, it is a concept that most people have become familiar with. Dr. Nestler provides a great example in the case of a female mouse who is fed a high-fat diet. The progeny of this mouse, before they are ever exposed to any diet, are likely to be more vulnerable to becoming obese due to the inherited genetic modifications as a result of their mother's high-fat diet. Whether we are discussing an individual who is more prone to becoming obese or has a greater risk to becoming addicted to drugs and alcohol, through the study of epigenetics, researchers are discovering that it is not Nature or Nurture, but Nature and Nurture that play a vital role in our genetic makeup. But are these changes permanent? Why should I have to pay for the experiences of my parents?

 

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Ancient mtDNA and Migration  During the Iron Age

Genome sequencing studies involving ancient human DNA have played a crucial role in uncovering ancient human migration events, processes, and history in Europe and Asia continent. One example of how next generation sequencing technology is of exquisite help to apprehend human history is the genetic studies revealing initial colonization of Europe by modern humans from Romania. However, the human history of Northeastern Europe isn't properly studied due to the shortage of preserved human samples and the lack of genetic statistics from those sites. This is primarily because of the annual repeated freeze-thaw cycles that degrade the DNA present in the bone material. A recent study by the Onkamo group, published in Scientific Reports, involving mitochondrial DNA sequencing revealed the presence of diverse populations and migration of farmers from east of Finland in the closing duration of Iron-Age

 

 

 

 

 

 

 

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Algae and its effects on aging

Spirulina is a blue - green spiral shaped algae that are rich in antioxidants, protein, has anti-inflammatory agents that minerals and vitamins. It is claimed that it also might have anticancer properties. Sounds like a magic algae that cure all ailments, right? In 2017, a study has been conducted by a group of researchers out of Belgium to see if Spirulina has an effect on aging and if gut microbiota is somehow involved. Mice of 3 months and 24 months of age were used for the study that was categorized into three groups: young mice standard diet (3 months), old mice standard diet (24 months), and old mice with 5% Spirulina infused diet. After a six week dietary implementation, fecal samples were harvested to undergo 16S rDNA profiling of the V1-V3 hypervariable region and were sequenced on the Illumina Miseq platform. They reported that the mice with Spirulina infused diet had an increased diversity, richness, and evenness of the bacterial microbiota when compared to the other two groups. The Spirulina fed mice also had a positive effect on their intestinal innate immune system by seeing an increase of antimicrobial molecule secretion that is involved in shaping the composition of the gut bacteria. Furthermore, it has been shown that the composition of the gut microbiota does affect homeostasis and immunity function of the whole organism. So implementing Spirulina into the diet can help you stay young health wise and keep disease away by strengthening the immune system.

 

 

 

 

 

 

 

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