Find Out Why All Dentists are Having Trouble Falling Asleep

Teeth are well known to paleontologist for their prevalence and insight into the fossil record. Recently, geneticists are starting to starting to take notice as well.

Researchers at Trinity College Dublin have found two human teeth dating back some 4,000 years ago, and found that the microbiome of the mouth they came from was also remarkabley preserved. This allowed them to study the bacteria present and compare it to typical microbiomes of human oral cavities today. Not a huge surprise, but it was very different. The researchers were able to identify what bacteria was present from the perserved DNA profiles on the teeth.

The insights it gave them was that typical microbiomes in mouths 4,000 years ago may have been much more diverse than today. Although the teeth studied were over colonized by one bacteria S. mutans, demonstrating a pre-disease state, the fact that there was more biodiversity on the ancient teeth than our own is cause for concern. Like our guts, bacterial diversity is usually better and prevents overgrowth of disease causing strains. This pointed them to our changing diet, and the growing abundance of processed sugary foods some of us enjoy eating day to day. It is interesting to see Genetics having utility in archeology. Perhaps rock-lovers may soon be recruiting more DNA lovers for their specimen studies.

Posted by Michael Breslin

https://phys.org/news/2024-03-genetic-secrets-year-teeth-illuminate.html

https://www.sciencedaily.com/releases/2024/03/240327124735.htm

Only a Tiny Fraction of our DNA is Uniquely Human

 

Within this article, it discusses that there is only 1.5-7% of our DNA which is uniquely human and are scattered throughout a genome containing genes involved in brain development and function, leading to the conclusion that brain evolution was essential for making humans human. Researchers examined every spot of DNA in 279 peoples genomes to grasp a better image of the human genome and differ wether DNA came from Denisovans, Neandertals or was inherited from a common ancestor of humans and those long-lost relatives.About half of the human genome contains regions where people got DNA from Neandertals or Denisovans. This study highlights how interbreeding with other hominid species influenced the human genome several times. Only minor changes to DNA affecting one or more DNA bases — the molecule's information-carrying components  were analyzed. Given that humans and Neandertals split up relatively recently , including DNA that only humans have added to their genomes might result in a greater estimate of exclusively human DNA.  Researchers may learn that part of what appears to be distinctively human DNA was carried by those ancient cousins when more genomes from Neandertals, Denisovans, and other extinct hominids are decoded.

Most of Human DNA Is Not Actually "Human"

 

 (Harel, Maayan, and Ewen Callaway. “Portrait of a Denisovan Girl.” Nature.com, Nature, 19 Sept. 2019, www.nationalgeographic.com/science/article/dna-reveals-first-look-enigmatic-human-relative.)

    A study conducted by researchers at the University of Santa revealed that most "human" DNA is not human. The research team discovered that the percentage of distinctive human DNA ranged from only 1.5 to 7 percent of the entire human genome. The researchers are currently unsure what the distinct human DNA does yet, but the genes scattered throughout the genome typically had genes connected to brain development and function. This suggests that the evolution of the brain was critical in shaping modern humanity. Much of the DNA contained in the human genome appears to have come from ancient human ancestors, such as Neandertals, Denisovans, hybrids of ancient humans, and unknown human ancestors. The researchers emphasized that their results did not mean individuals are mostly Denosivan or Neandertal, but rather that individuals may contain Neandertal or Denisovan DNA in their genome. From the data collected, about half of the overall genome has regions where one or multiple individuals inherited DNA from Neandertals or Denoviosons. This makes sense considering humans and Neandertals and humans separated evolutionary-wise about 600,000 years ago. This is when the "evolutionary bursts" occurred when distinctly human DNA arose in the human genome. The second burst occurred only 200,000 years ago. This study demonstrates how greatly the human genome was affected by other hominid species. By understanding more about how human ancestors impact the genome, we can better understand our DNA.

Link to article: https://www.sciencenews.org/article/only-a-tiny-fraction-of-our-dna-is-uniquely-human

Link to supporting study: https://advances.sciencemag.org/content/7/29/eabc0776

Variability with polygenic risk scores

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    With increased popularity in companies such as 23andme and the ability to assess a person's DNA for a "polygenic risk scores", preventative health decisions are becoming more and more popular. The polygenic risk score is basically an overall assessment of an individuals DNA using a small piece of DNA from saliva and generate an estimation based on large-scale genomic studies. While a large majority of the consumers can be accurately assessed for risk, other users may find themselves in the wrong category. This has lead to a study to be conducted, in which coronary heart disease, atrial fibrillation, type 2 diabetes, Alzheimer's disease, glaucoma, and breast cancer, were used in order to calculate risk scores. The data had shown that regardless of what control is used for the risk factor, due to the scale of population-level genetics, there is always introduced variability. In order to reduce this randomness the researchers had to run the tool multiple times to eliminate the random elements and create an average to assist in a computational process that strives for accuracy. 
    Based on the information provided by the article, it has created a sense of yes and no debate with regards to these polygenic tests. Essentially the information is saying that the more they sequence the snippet of DNA the more the results are accurate. The question is how many times are these companies actually doing these sequences as well as how radical are these overall results? Of course this research is evidentially useful to those who are prone to these risks, but if the inaccuracies are substantial in certain groups is the information really that useful on a global scale? It is all interesting regardless, just more curious in terms of information that is actually gathered by these tests versus what is generally assumed by the test itself based on these population level pools.

https://medicalxpress.com/news/2020-12-highlights-strategies-boosting-accuracy-personal.html

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00801-x

DNA Origami Reveals Molecular Motor Movements

A recent study from Harvard University produced the first recording of the rotational steps of a molecular motor as it moved from one DNA base pair to another. These researchers created ORBIT, origami-rotor-based imaging and tracking, to see molecular motors in action. Molecular motors are crucial in the human body for events such as muscle contraction and repair, replication or transcription of DNA. 

Photo from Irish Times - Why did I risk my privacy with home DNA testing

To study the molecular motors in motion, researchers wanted to focus on the twisting movement of a strand of DNA. First, they glued a DNA interacting motor to a strong support. The motor then had to rotate the helix of DNA in order to travel from one base pair to the next. However, every time a motor moves across one base pair, the rotation of the helix shifts the DNA. This shift is so tiny, it can’t be observed under a light microscope. 

Pens lying in the shape of helicopter propellers sparked a genius idea. If the spinning DNA could move at the same rate as the helix and the molecular motor, researchers could capture the movement on camera. DNA origami was used to construct such propellers. More specifically the team wove approximately 200 pieces of DNA into a propeller shape that was 160 nanometers in length. The propeller was attached a standard double helix on one end and a molecular motor that unzips DNA (RECBCD) at the other end.

“No one had seen this protein actually rotate the DNA because it moves super-fast,” Pallav Kosuri from the Zhuang Lab admitted. The molecular motor can travel across hundreds of base pairs of DNA in just a few seconds. With the origami propellers and a high speed camera, the team could finally record the movements. The technology that ORBIT will allow and inspire is astonishing. Finally, researchers are able to study such tiny processes that are so important. I think ORBIT and further studies, can allow scientists, especially geneticists, to study specific pieces of DNA or genes. In my opinion, this process can allow researchers to be more accurate in concluding the cause of many diseases and disorders. 

Have Mental Disorders Developed Through Human Evolution?

Human Evolution has caused the human genome to change over time. A new study has found that the genes that are involved in bad backs and impacted wisdom teeth have changed over many years to make people more susceptible to several mental disorders such as, schizophrenia and many others. The evolution of the human family tree, humans begin to walk upright which contributes to many common aches in the lower back and knees that we currently suffer from today. Many of the evolutionary changes that have happened over time contribute to more than just our outside appearance. Mental disorders effects many individuals worldwide. 3% of the world population is affected by bipolar disorder and schizophrenia. It is believed that due to evolutionary changes, the structure of the human brains size and structure is now different.

A certain gene that was discovered for a protein called CACNA1C. In the process of neurotransmitters communicating with neurons is all happening because of the CACNA1C gene by control the flow of calcium inside and outside of the cell. CACNA1C is linked to issues regarding mental disorders such as bipolar disorder, anxiety, depression etc., in earlier studies. The main focus on this gene was the "non-coding" element that don't have what they need to build the CACNA1C  rotein.  After comparing different human genomes around the globe, they saw that there was variation in a certain region of the gene. This discovery of the CACNA1C gene could be playing a role in the development of mental disorders across all humans. Over the next however many years, this could change the development of mental disorders all over the world. I strongly believe that this could work if studied more thoroughly. This discovery can help with developing medicines and determine any risk factors that could be present in someone's DNA.

Article: http://blogs.discovermagazine.com/d-brief/2018/08/09/human-evolution-changes-caused-mental-disorders/#.W7QOCy_Mz-Y

Related Article: https://www.news-medical.net/news/20160427/Study-reveals-new-function-for-CACNA1C-gene-in-psychiatric-diseases.aspx

We are more genetically similar to our dogs than we thought

A study done by Dr Luis Pedro Coelho suggests that the genes of the gut micro biomes in dogs is genetically similar to the gut micro biome in humans. In fact more genetically similar than the micro biomes found in mice and pigs. The results of this study has revealed that dogs are a better model for nutrition studies than mice and pigs. The experiment showed that changes in carbohydrates and proteins has nearly the same effect on humans and dogs. The micro biomes in obese dogs were more receptive to high protein diets than in lean dogs. This same pattern can be seen in humans too. Dogs are becoming more and more obese and this is most likely because humans feed their pets food from the dinner table all the time. They are not getting fat because they can not eat human food, they are getting fat because they are eating more than they should for their size. If dogs were fed human food in a balanced diet they would not become obese because they have very similar gut micro biomes. I find this study very interesting because as a pet owner, I look at my dogs are being apart of my family. I have never been one to feed my dog food from the table because I do not want him begging every time I eat, but I may start feeding him more carbohydrates and proteins that humans would eat. There are also many different diets out there made for dogs using only "human food", the link is attached below to one of these diets.

Article: https://www.sciencedaily.com/releases/2018/04/180419131136.htm
Additional Information: https://www.whole-dog-journal.com/issues/15_7/features/Home-Prepared-Dog-Food-Nutritional-Information_20568-1.html

Who Cares, He Is Just A Dog They Said, That Dog Remembers What You Did!

People frown upon animals, they think they are just animals and they shouldn't be treated as well as people. Why people have that mindset, I will never know and nor would I want to know. People have the ability to remember and recall things from the past, even if they aren't important. What if I told you that dogs also have that ability as well? Researchers have proof that dogs do have that "episodic memory" too.

Claudia Fugazza is a researcher at the Comparative Ethology Research Group in Budapest, Hungary. She said,"dogs are among the few species that people consider 'clever,' and yet we are still surprised whenever a study reveals that dogs and their owners may share some mental abilities despite our distant evolutionary relationship." In this study, the researchers used the trick "Do as I Do." The dogs that were trained using the "do as I do" trick,  can watch their owners perform an action and then do that same thing themselves. For instance, if the owner rolls over on the floor and gives their dog the "do it!" command, their dog will roll over on the floor too.  Researchers trained 17 dogs to imitate things humans do with the "do as I do" training method. Next their did another part of training in which dogs were trained to lay down on the floor after the human action, no matter what it was.
When the dogs learned to lie down, the researchers then surprised them and said "DO IT", and the dogs did it. Amazingly, the dogs remembered what they saw the person doing even though they did not have a reason to think they would need to remember that, they showed episodic-like memory.

In easier words, the dogs remembered what their owner did even when they had no reason to remember it, just like us humans. I think this is a great discovery, dogs are a humans best friend, they are one of the most loyal animals, and one benefit we can get from this discovery with dogs is safety. They can be trained to remember specific things in order to protect someone, in order to help someone.

What's the Longest Humans Can Live?

Jeanne Calment set the record for the longest living person after she died on August 4, 1997 at 122 years old. Humans have been progressively living for longer over the last few centuries, but it is likely that we have reached our limit, at about 115 years, according to Dr. Jan Vijg from Albert Einstein College of Medicine. Other experts agree with him, but some disagree strongly, basing their arguments on the fact that life expectancies have been increasing rapidly since the early 1900s. However, studies have been done which look at the growth of the population of a given age from year to year. For example, in France in the 1920s, 85 year olds were the fastest growing group of people. This trend shifted to even older people as the average life expectancy grew but about a decade ago, the peak stopped shifting. This is likely due to the stall in life expectancy. The International Database on Longevity also points to the same conclusion- people are not living as long as they used to decades ago, and besides the rare case like Jeanne Calment's, no one is living longer than about 115 years.

It is predicted that 115 will be the highest age that anyone reaches in the foreseeable future. It has been an ongoing argument for years whether or not there is a limit to lifespans, and because people have been steadily reaching the same age for decades now, it seems that there are only so many years that a body can live and work and continue repairing itself before it collapses.
I agree that there is a certain ceiling for age that humans can reach. The body is simply not able to continue repairing itself after a certain point. Because of the advancements in medicine and quality of life that have been improving over the past few centuries, life span has been increasing steadily, but at this point in time we have most likely reached the limit to how old we can get. 

I Got It From My Mama - or Maybe a Protist?

In a new study from the University of Cambridge , researchers are finding that not all human genes are ancestrally inherited. While there is no doubt that bacteria partake in horizontal gene transfer, it's been thought that complex animals only receive their genes from their parents. This new study, however, challenges the established idea that there is no horizontal gene transfer in more highly developed animals. In the study, the genomes of four nematode species, twelve fruit fly species, and ten primate species (including humans) were examined and then compared with that of the other species. The researchers then estimated how long ago the similar genes were acquired, and how likely it was that these genes were foreign in origin. Almost 150 human genes were identified as foreign, and thus acquired through horizontal gene transfer, and nearly all of them related to enzymes involved in metabolism. Along with identification, the researches were also able to determine where the genes most likely came from, finding that most of the genes were transferred from bacteria and protists, while some were from viruses and fungi. While some of the other species involved in this study continue to receive genes from outside sources, it's likely that humans and other primates haven't procured genes through horizontal transfer since the common ancestor species  - probably around 5-8 million years ago. The researchers of this study hope that their findings lead to a better understanding of the genomes of complex animals, and hope that bacterial sequences in DNA shouldn't always be written off as bacterial contamination in genomic studies.

Thousands of Never-Before-Seen Human Genome Variations Uncovered

     A new genome sequencing process known as Single-Molecule, Real-Time sequencing (SMRT) has been developed and used to discover thousands of genetic variants and close numerous mapping gaps in the human genome. Through this sequencing method, it is possible to determine which genetic mutations are responsible for certain conditions, most of which have yet to be discovered. According to what scientists call the “missing heritability problem”, the genetic cause for only about half of the inherited conditions has been determined. However, the main reason for this problem is the fact that the standard methods of genome sequencing are not as precise as SMRT. These methods analyze millions segments of DNA that are approximately 100 bases long and use this information to create a genome map. By looking for the replacement of a single nucleotide base, known as a single-nucleotide polymorphism or SNP, genetic variations in the human genome can be identified.

     Due to the limitations in technology, DNA sequences of 5,000 bases or more were unable to be sequenced using the standard methods of genome sequencing. However, through the use of SMRT, DNA sequences of more than 5,000 base pairs can be analyzed and sequenced. Therefore, through the use of this new sequencing technology, much more detailed genome maps can be created. A study was conducted upon a hydatidiform mole, which is when an egg that lacks the DNA of the mother is fertilized by a sperm and only carries one copy of each gene. Due to this, the search for genetic variation becomes easier when analyzing the hydatidiform genome. It was concluded that 26,079 segments differed from a reference human genome when using the SMRT method, 22,000 of which had never been reported before. 

     I thought this article was interesting because it shows how quickly genome research is advancing and how more detailed maps of the human genome can be used to determine the causes of hereditary conditions. In the future it may be possible to sequence a patient’s genome at the doctor’s office and tell him that the presence of particular SNPs or variations may make him more susceptible to a specific disease. Advances like these will make it easier to not only cure diseases and conditions that occur in the human body, but also prevent them before they arise.

Source: Thousands of Never-Before-Seen Human Genome Variations Uncovered

New view of mouse genome finds many similarities, striking differences with human genome

Link to the Article

A group of scientists that are a part of the Mouse ENCODE Project studying the mouse genome have not only found many similarities in the systems that control gene activity between humans and nice, but they have also found differences between these systems. They found that many of the similarities in these systems have been either conserved or continued through evolutionary time.  Through this research, they were able to discover a lot of information on just how the mouse genome works. The researches have found that some DNA sequence differences linked to human diseases also have counterparts in mice. The differences that were found appeared in specific tissue and cell types. It was found that although the mouse and human genomes have a common language during the regulatory process, there is a great amount in "flexibility in evolution".

This could be a huge determining factor in decided what exactly is tested for/on a mouse and what needs another test subject that is possibly closer to the human in ways the mouse is not. Although the genomes do have similarities, they still have a lot of differences which means some experiments that might work on mice won't necessarily work on the human genome.  This could effect how often mice are used when attempting to find cures or other medical discovers by first testing them on mice.

Fast-Mutating DNA Sequences Shape Early Development; Guided Evolution of Uniquely Human Traits

Researchers at Gladstone Institutes, University of California have looked at the connection between humans and chimps and what regions of dna they differ in. They had found that there are regions where the mutation rate for humans and chimps vary. These sites are called human accelerated regions (HARs). In humans, there were over 2600 of these sites, of them, it was deemed that about 100 of them had a very fast mutation rate in comparison to the other regions. They have decided that these 100 will be watched closely in future research. This technology has the posibility to pave the way for controlling human evolution.

http://www.sciencedaily.com/releases/2013/11/131110204417.htm

http://www.genome.gov/10001177

John A. Capra, Genevieve D. Erwin, Gabriel McKinsey, John L. R. Rubenstein, and Katherine S. Pollard. Many human accelerated regions are developmental enhancers. Phil. Trans. R. Soc. B., 2013 368 20130025 DOI: 10.1098/rstb.2013.0025

Humans Develop Faster than Chimpanzees

     It is apparent that humans and primates are compared genetically. 98% of the DNA from humans and chimpanzees are the same; therefore the difference remains in the 2% left. It is thought that Alu DNA (also known as junk DNA) make up various mutations and rearrangements. Although these can be helpful in discovering new proteins, they can also be harmful in creating a cancerous tumor and other defects. A team of scientists has found 2,200 new human Alu DNA, which are not found in chimpanzees. It is due to this that the development of humans has occurred at a much faster pace than the development in chimpanzees.

     This Alu DNA has also shown that it has been written into the human chromosomes. Achilles Dugaiczyk, professor of Biochemistry at UCR, comments that it is not due to natural selection. He also comments that this expansion of DNA was due to a chemical process within the human chromosomes.

    When determining the genetic difference between humans and other animals, it is an important process because it can lead to many other things. This can enhance our knowledge base on how life began on earth. It also allows us to compare our DNA with other DNA to find a link to a possible genetic disease. 

Original Article: http://www.sciencedaily.com/releases/2004/08/040831090221.htm

Zebrafish Important Model For Understanding How Genes Work In Health And Disease

An article found on Medical News Today along with another article talks about how the Zebra Fish can be used to understand how genes work in health and disease. The zebra fish shares 70% of its protein coding genes with humans, and 84% of its overall genome. Due to this astonishing fact, the zebra fish's genome is one of three that has been sequenced in great depth. The other two are the human and the mouse. This genome will be crucial to studying diseases in humans in ways that cannot be studied. Zebra fish research has already been used to understand cancer, heart disease and muscular dystrophy. Scientists are hoping to use the genome to undertand the function of specific genes and develop medicines.

The zebra fish is unlike most other vertebrates. They have the highest repeat content in their genome sequences as well as genes that code for sex determination. The zebrafish also has very few pseudogenes,  or genes that have lost function through evolution, compared to the human genome.

"Armed with the zebrafish genome, we can now better understand how changes to our genomes result in disease," said Professor Christiane Nüsslein-Volhard, author and Nobel laureate from the Max Planck Institute for Developmental Biology.