Stanford Medicine Develop RNA Blood Tests to Detect Cancer and More

 In a recent article by Kimberly D'Ardenne researchers at Sandford University have found a way to analyze the RNA molecules in a patients bloodstream called "cell-free RNA" to detect cancer treatment, resistance, and tissue injury from a single blood draw.

Unlike traditional DNA-based liquid biopsies this test focuses on mRNA fragments circulating in the bloodstream, offering a new way to monitor diseases that don't involve genetic mutations. It accurately detected lung cancer in 73% of patients, even in its early stages by analyzing about 5,000 genes not typically found in healthy blood. This test can also be used to identify non-genetic forms of treatment resistance giving doctors a chance to adjust treatment options before symptoms appear. Remarkably it works on both new and archived blood samples with the potential to to transform how we detect and treat diseases in the future. As co-author Dr. Maximilian Diehn put it, "We're reading the molecular history of the body - from just a blood sample."

Article: https://med.stanford.edu/news/all-news/2025/04/rna-blood-test-cancer-detection.html

Journal Article: https://www.nature.com/articles/s41586-025-08834-1

Breeding Plants with the Genes From One Parent to Attain More Desirable Traits

    The article, 'Breeding Plants with Genes From One Parent', discusses the research done at the University of California Davis College, when Simon Chan and colleagues, such as Ravi Maruthachalam, while breeding a lab plant known as Arabidopsis, accidentally stumbled across a way to completely omit one parent's genetic information from the offspring. This finding is exponential since plants are typically diploid, they inherit two sets of chromosomes one from each parent; if a trait is desirable, the plant will pass along the gene to its offspring. However, this process could take several generations to make its mark.  Eliminating half the genome, creating haploid crops, could aid in quickening the process of breeding crop plants for desirable traits easier, and creating true homozygous offspring faster. 

    Chan and Maruthachalam modified just one protein, CENH3, found in the centromere of the plant's chromosomes. When the plants with the modified CENH3 gene were crossed with wild-type Arabidopsis, the results were plants with half the normal number of chromosomes, making a haploid plant with only genetic information being passed down from one parent, completely eliminating the other parent's genome. 

    Once replicated by another researcher, Professor Comai, used a different plant species and manipulated the same CENH3 gene and also created plants with one set of chromosomes.  However,  Comai did state that the rules related to each species and the CENH3 gene are distinct from one another.  

    The true finding related to the CENH3 gene is when the CENH3 gene is altered, the centromere of the chromosome is weakened due to the gene being removed from the DNA inside the egg before fertilization. Thus, when embryonic division occurs, the centromeres lacking the CENH3 (female genome in the egg) fail to compete with the centromeres containing CENH3 (male genome in the sperm). Therefore, the female genome is eliminated, engendering the selective depletion of weak centromeres when CENH3 is eradicated. 

I chose this article since the idea is novel.  Typically, like other sexual organisms, plants are diploid and inherit two sets of chromosomes one from each parent.  However, in this article, researchers found a way to make the offspring haploid. This is a task that seems nearly impossible to accomplish.  Although more research is needed, I like this concept since these findings are applicable and useful in today's society, especially in breeding agricultural crops such as wheat, corn, beans, etc., with the potential to feed more people more quickly if bred desirably. 

A new look at Ozti the Iceman's DNA reveals new ancestry and other surprises

A new look at Ozti the Iceman's DNA reveals new ancestry 

and other surprises 

A new analysis of the Iceman's DNA, a 5,300-year-old mummy found in the Tyrolean Alps, challenges previous assumptions about his ancestry. Scientists had initially suggested that his ancestors came from the Caspian steppe, but this new research indicates that the steppe ancestry is entirely absent. Instead, about 90 percent of the Iceman's genetic heritage is traced back to Neolithic farmers, which is an unusually high proportion compared to other Copper Age remains. The study also reveals that the Iceman had male-pattern baldness and much darker skin than previously believed. This finding highlights that genetic changes for lighter skin tones in Europe occurred much later in human history, with the majority of people in Europe between 40,000 and 8,000 years ago having skin as dark as people in Africa.

This article just gives us another example of how many question marks we have in genetics. There are so many unanswered questions that leave us in the dark. There is a significant time period of ancestry missing between a few hundred years. There is always more work to be done in the field of genetics with all the research and data we can get together to eventually fill the gaps we have.

LINKS:

https://www.sciencenews.org/article/new-otzi-iceman-dna-ancestry-genome

https://www.scientificamerican.com/article/oetzi-the-iceman-gets-a-new-looks-from-genetic-analysis/

Africa's oldest human DNA helps unveil a 'ghost' group

 

Genes That Allow Rockfish to Live up to 200 Years

Living for more than 100 years are uncommon in fish. Fish are one of the few species that encapsulate the extremes of longevity. Greenland sharks can live for more than 500 years, whereas coral reef pygmy govies only live for 10 weeks. However, the fishes' longevity actually originates from their size and habitats. This is possible because bigger organisms have a slower metabolism and are less susceptible to predation. In addition, a colder environment could possibly slow down metabolism and make it possible for Greenland sharks to live for centuries. Nonetheless, rockfish grow in colder waters for that reason and live in deep water which allow for them to live a very long life. 

The DNA in rockfish allowed for genes that are less susceptible to certain cancers than their shorter-lived kin. In addition, they also have a way to regulate insulin and use butyrophilin, a group of genes which regulates the rockfishes' immune systems. These different genes are closely similar to suppressing inflammation in aging humans. However, this does not mean that it could allow for humans to live for a long time too.

Genomic Compatibility???

    Researchers from the University of Colorado at Boulder concluded that most people in their study of non-Hispanic white Americans were attracted to things they found in themselves, body type, age, race, income, and education to name a few. This isn’t a surprise to many of us as having a similar lifestyle in a relationship is usually ideal. They also found that after studying many genomes from an array of individuals in their study, those who had similarities in their genomic makeup were more likely to be attracted to each other. These researchers also begged the question of expanding the study to interracial couples and seeing if they could find genomic compatibility between couples from different backgrounds. This is an extremely interesting idea, similar to that of my previous post. If we can find certain genetic markers that are attracted to each other then scientists could potentially be creating “perfect matches.” Although I still think the idea of a perfect match is a little far-fetched for the time being. This type of matching could very well be something to look for in the year to come.

https://www.sciencedaily.com/releases/2014/05/140519160716.htm

https://blogs.scientificamerican.com/observations/the-illusion-of-genetic-romance/

https://www.healthline.com/health-news/the-new-science-of-matchmaking-091614

New Research and Studies Show Genetic Diversity in Corn

    Research and studies showed newly assembled genomes of 26 different genetic lines of corn, showing the crop’s rich genetic diversity. Detailed in an article published in the journal Science, first author of the study and an associate professor of ecology, evolution and organismal biology at Iowa State University, Matthew Hufford, says that these genomes as references can better help plant scientists select genes that lead to better crop yields or stress tolerance. The first corn genome, mapped in 2009 at Iowa State by Patrick Schnable and Doreen Ware and team, was the genetic line known as B73. Since then, B73 has served as the primary reference genome for corn, and scientists have a limited understanding of genetic sequences in corn genomes that are not in B73. The 26 genomes mapped in the new study, however, encompass a wide range of genetic diversity, including popcorn to sweetcorn to field corn from different geographical and environmental conditions. This genome mapping provides more reference data in order for scientists to combine maize genetics for targets that could lead to better crop performance. The large genetic diversity present in corn, however, creates major hurdles for the creation of new genomes, since 85% of the corn genome is composed of transposable elements. Hufford, comparing these elements to a jigsaw puzzle because the majority of pieces are one color. This repetition makes it harder to determine how the parts fit together. Technological advancements allow tools for researchers to overcome these hurdles, and allows for longer sequence reads, which make the pieces of the puzzle larger and more likely to be arranged properly by scientists.

Link to Study: https://www.sciencedaily.com/releases/2021/08/210805141202.htm

Link to Article: https://phys.org/news/2021-08-corn-genetic-diversity-genome.html

Lizard-like tuatara carry two distinct mitochondrial genomes

 

Lizard-like species tuatara has two distinct mitochondrial genomes. This revelation was reported recently in January 2021. Tuataras genomes are a very important discovery in nature today as they are the first vertebrate species that are found to have multiple copies of mitochondrial genomes. Mitochondria are tiny energy factories, and their genetic material is usually important in building the structures and keeping them running. Mitochondrial is essential in the development of aging, cancer, and many other biological diseases. 

Finding animals and other species that carry additional mitochondrial genomes can help advance the research of finding cures and diseases that stem from mitochondrial DNA. By studying animals' mitochondrial genomes, we may potentially be one step closer fully understanding how some human diseases work. Efforts to decode the tuatara’s genetic makeup began in 2012, with the launch of the Tuatara Genome Project led by Neil Gemmell, an evolutionary biologist at the University of Otago in Dunedin, New Zealand. His team discovered that the tuatara genome is 50 percent larger than the human genome. This led to a deeper exploration of the mitochondrial part of the genome which is where they discover that this species has two mt- genomes. The discovery raised concerns since mitochondrial DNA is usually inherited only from a mother’s egg, so the scientists expected to see a single copy of the mitochondrial genome, not two copies like they would see in nuclear DNA, which is inherited from both the mother and father. They believe that the purpose of the two mt- genomes are to provide flexibility in how their metabolisms respond to temperature extremes. This finding of the genetic basis for the animal’s metabolic feats can eventually help explain the mitochondrial genome’s function which will then help find treatments for human metabolic diseases. It is wild to me to think that a species can carry two distinct genomes.

Links

1. https://www.sciencenews.org/article/lizard-like-tuatara-mitochondrial-genomes-cold-tolerance

2.https://www.reptilesmagazine.com/tuataras-two-sets-of-mitochondrial-genome-may-help-it-withstand-cold-temperatures-better/#:~:text=Researchers%20have%20discovered%20that%20the,adaptive%20advantage%20to%20harsher%20weather

Lizard-like tuatara carry two distinct mitochondrial genomes

    

    

In this Science News article it states that researchers have discovered two distinct mitochondrial genomes in the Tuatara, these extra set of genes may be the reason why the Tuatara are tolerant to the cold which is very unique for a reptile. In Tuatara scientist discovered evidence of two distinct copies of genetic instruction manual for making mitochondria in a vertebrate. Mitochondria is important for building the structures and to keep them going. Finding this discovery could not only help other reptiles but humans as well when deal with different kinds of diseases. In 2012 the Tuatara Genome Project was created to decode the Tuatara's genetic makeup which was led by Neil Gemmell. The team was provided a sample of the reptiles blood and what they found was that the Tuatara's genome is 50 percent larger than the human genome.

    Further investigation of decipher the DNA which they compared by chopping it into small pieces with the overall structure they found differences in the mitochondrial DNA which appeared to have striking differences in their gene sequences. This created many of the people working on the project to be stunned because usually mitochondrial DNA is inherited by the mother's egg resulting in a single copy of mitochondrial genome not two copies. They conclude that the genomes were different by 10.4 percent so when comparing it to humans and chimpanzee mitochondrial genomes differ 8.9 percent. 

    I think this discover is very important because if we could find the genetic basis of what causes them to have two distinct mitochondrial genomes we can help find treatments for human metabolic diseases. The picture use above is from Neil Gemmell own experiment article where you can also find a little bit more about the Tuatara. 

The Link Between Your Genes and COVID-19

 

        According to this article it is possible that genes can determine one's risk factor for COVID-19. If scientists discover ways to link genetics and COVID-19 together then finding cures and drugs to treat the virus will become much easier. Simple genetics testing founded from universal healthcare can help detect genes that cause people to be more susceptible to COVID-19. The genes can also tell us when and how to fight the virus. In my opinion genetic testing can help us find COVID cures faster.

https://elemental.medium.com/genetics-could-explain-why-some-people-with-covid-19-get-sicker-than-others-d8b28aa915b1

https://www.nejm.org/doi/full/10.1056/NEJMoa2020283

The Cross Link Between Genetics and Suicide

 

         Suicide has been a rising cause of death in America. One reason many people feel suicidal is because of their family history with mental health. Not only has family history contributed to suicidal tendencies, it also can cause depression, bipolar disorder, anxiety, schizophrenia, and more mental health issues. Genome wide association study (GWAS) was used to study different families to cross check their genomes. Approximately 22 genes were discovered that indicated elevated risk of suicide death. Although family history is just one factor of the many environmental factors such as childhood, trauma, and poverty; it still increases a person's likelihood. With that being said I believe more people and families should seek therapy. Suicidal thoughts will never truly go away, you learn to live with it and become the bigger person. However not many people can afford therapy which is why better FREE counseling services should be provided at schools and colleges as well as better education to children and adults about suicide and how to prevent it.

https://medicalxpress.com/news/2020-11-genetic-discovery-suicide-families.html

https://ajp.psychiatryonline.org/doi/10.1176/appi.ajp.2020.19101025

Genetic Variations in Africa

 

        Since Africa has always had a large population there has been a theory that all human have descended from the continent. However not many individuals from Africa have been asked to participate in genetic studies to see if this is true. Zane Lombard and his colleagues studied 426 individuals from 13 African countries to see if their genomes could show any signs of variations that would help prove this theory. They ended up discovering over 3 million new variations as well as many regions of Africa that have shown signs of natural selection. Studying genomes of these individuals is important because it helps to see how past individuals migrated to different places around the world. According to this study, Zambia was a very popular migrant place. In my opinion it's quite obvious that Africa was a big pool of human descendants and hopefully more individuals from different African countries participate willingly so scientists can discover more about humanity.

https://mg.co.za/opinion/2020-11-24-africa-study-finds-three-million-new-genetic-variations/

https://www.nature.com/news/2000/001207/full/news001207-8.html#:~:text=Researchers%20led%20by%20Ulf%20Gyllensten,about%20170%2C000%20years%20ago1.

Genome of Birds

In this article Scientist report on the genomes of 363 species of birds which includes 267 that have been sequenced for the first time. The study have was done in this article represent more than 92 percent of the world's avian family. Avian family is a bird family that have warm blooded egg-lying vertebrates characterized by feather and forelimbs modified as wings. Since the first bird evolved more than 150 million years ago , its decedent have adapted to vast range of ecological niches. On November 11 scientist from the Smithsonian institution, the university of Copenhagen, BGI- Shenzhen, the university California Santa Cruz and about 100 other institute reported on the genomes of 363 species of birds, including 267 that have been sequenced for the first time. About 40 % of the genomes were obtained from the tissue samples preserved in the National Museum of Natural History's avian genetic resources collection.  

https://www.sciencedaily.com/news/plants_animals/genetics

https://www.technologytimes.pk/2020/11/12/scientists-release-genomes-of-birds-representing-nearly-all-avian-families/

Ancient dog DNA introducing more theories

 

In this New York Times article, it introduced 27 new genomes of ancient dogs. This study brings a lot more findings as well. The study suggests dogs were domesticates around 20,000 years ago. Another idea it suggests in ancient dogs being more genetically diverse than modern dogs. This all provides new information and new thoughts on dog domestication. They also talk about dogs coming from an extinct form of wolves, and how fast dogs spread all across the globe. This brings up a lot of interesting theories on these dogs. Some scientists think humans have an effect on this, and humans and dogs migrated together, but in some areas this in not true. I believe some dogs where probably taken to travel with humans resulting in the migration. These specific dog breeds were probably pasted on from generations resulting in only certain populations of dogs migrating. I agree with most of the theories presented in this article, like humans and dog migration interacting intentionally.  I also believe the theory dogs came from an extinct form of wolves. They have many similarities, but so many differences from the current wolves that dogs could be from an extinct version of wolves.

Extra reference

New Virus Detecter Helps Identify Any Virus

An article by Science Daily describes a new disease surveillance tool that can help detect any human-infecting virus. One of the problems during the Zika outbreak in 2015 was that there weren't many Zika virus particles in the blood of an infected patient. This made it difficult to obtain clinical samples and to study the genetics of the virus. Broad Institute developed CATCH, a new computational method that can be used to design molecular baits for any human-infecting virus. This approach enables small sequencing centers to conduct disease surveillance more efficiently and without spending as much money. Instead of metagenomic sequencing, which loses viral material among the other patient's DNA, scientists "enrich" clinical samples for a particular virus. This uses genetic bait to immobilize the virus's genetic material. The baits are "short strands of DNA or RNA that pair with bits of viral DNA", Susanna Hamilton writes. CATCH (Compact Aggregation of Targets for Comprehensive Hybridization) allows users to design custom sets of bait probes to capture genetic material of any combination of viruses. Previously, scientists could only target a few viruses at a time. Users easily input genomes from forms of human viruses that are on the National Center for Biotechnology's database. The program produces the best set of probes based on what the user is targeting. The CATCH software is publicly accessible on GitHub.

I think the CATCH software is very adaptive because it can pull any information from the Biotechnology database, which is always being updated. So when new virus strains are discovered, CATCH will already be able to access the genetic information of the strain and produce the best genetic probes for the job. This is a good thing because it makes obtaining clinical samples of the virus much easier, it will take less time, and it will save money. Hopefully this allows for more studying of the virus and better treatments for the illness.

How Evolution Genetically Connects us to All Animals, Including the First One

Two scientists in England have recently done work to study and reconstruct the genome of whatever the very first animal was, though it lived over 600 million years ago. All animals currently on earth (including us) stemmed from this very first animal, and those genes remain in animals; 55% of human genomes that are present in us now were present in that animal all those years ago. 65 species were studied closely during this testing in order to determine how and if we are all related by means of this mysterious creature, and the construction of an animal family tree has enabled these scientists to put together ways that we are believed to be connected with each other and with the very first animal.

This article is incredibly interesting and some of the findings are remarkable. Though they studied 65 of the millions of species on earth, they found that we are most closely genetically related to starfish of invertebrates (though we are of course in the vertebrate category). I’m not sure why I never really thought of this possibility before, but I really like the thought that all species on earth, no matter how different, likely share at least some type of gene that link us together. To me, it makes it even more dire that the human race be more conscious of how we treat our environment and the other animals who inhibit it.

Scientists May Have Just Connected Suicide Risk to Genetics

A new research study suggests that four different genetic variants may increase the risk of suicide, disregarding environmental factors. The World Health Organization suggests that 800,000 people die from suicide each year and is the second leading cause of death among people ages 15-29. There are many environmental factors that can increase risk of death due to suicide, but it seems that genetics could play a major role. In fact, older suicide research suggests that heritability of suicide could be up to 50%.

The article in Molecular Psychiatry used genomic techniques to identify genetic factors that may affect the risk of cancer. Scientists looked at 43 families that were at a higher risk for suicide, and by doing this they reduced the affect of environmental factors on individuals. Analysis of 1,300 DNA samples from people that died by suicide suggests that specific variants in SP110, AGBL2, SUCLA2 and APH1B could be responsible for raising suicide risk. The team also identified 207 genes that could influence suicide risk.

Suicide Statistics in the United States

I find this research article particularly interesting because suicide is not usually looked at in this light. Typically, suicide is seen as mainly a mental health issue not a genetic health issue. Although it do agree with how his study was performed, I do see other limitations to the study. The article highlights that the study was only conducted in one area of Utah, where the residents were mainly of Northern European descent. I think that further research needs to be done in other areas of the world and with other ethnicities to see if these same conclusions apply. This research is a step into understanding individuals that we think are “troubled” and perhaps with some genetic counseling, they can improve the health of these individuals.

Chimps and bonobos had flings—and swapped genes—in the past

There has been a lot of evidence in recent years of species that have interbred with closely related species in their past.  A study was performed in order to compare the genomes of chimpanzees and bonobos in Africa in order to determine their evolutionary relationship.  Chimps and bonobos are closely related species that fall into the Great Apes group that humans are also a part of. This study was started due to the findings in 2010 that humans and Neandertals actually interbred in the past, causing genes to be shared and passed between species.

Picture of African Chimpanzee

Chimps and bonobos in Africa are mostly separated by the Congo River, so these species don't interact very often.  The Congo River may be a large factor that led to the speciation and split of these two animals and caused them to evolve independently.  However, genome tests concluded that the chimps actually had 1% of bonobo DNA in them.  This led the scientists to conclude that these two species had two separate interbreeding events in the past that led to the shared DNA.  These findings along with the discovery of Neandertal DNA in humans is helping to change the classical definition of a species.  More and more evidence has been showing that different species can in fact interbreeed to produce fertile offspring, and is changing the way that evolutionary relationships are being viewed between species.

Animal hybrids may hold clues to Neandertal-human interbreeding

It has long been thought that lineages between species were rigid lines that do not connect with other living species and that mating between species is impossible.  Recent studies show that human evolution may have been a river stream of  inter connected lineages that interbred rather than the conventional theory that our lineage was a tree with individual lines leading to each species.  After comparing modern day non-African human DNA with DNA from Neandertal fossils, it was found that 1.5 to 4 percent of Neandertal DNA still exists in our genome.  There is also evidence of interbreeding between humans and another ancient hominid known as the Denisovans.  Evidence of these interbreeding relationships can be found in human skulls that have been found in caves that share a resemblance to the skulls of our ancient hominid relatives.

Drawing comparing human skull to Neandertal skull.

Some scientists believe that these ancient skulls may be the evidence of hybrids that are the product of human and hominid mating.  Species that diverged from a common ancestor within a few million years still have the capacity and similar DNA to still be able to reproduce.  To further observe this, scientists have experimented with hybridizing species that exist today and comparing the results they get with those of the cave skulls they have found.  Yellow and olive baboons were interbred to see how the resultant generations would appear and what traits would be exhibited.  The results showed that hybridization blurs the lines between species and makes it harder to detect differences among the species.  Due to this, a theory has come up that Neandertals were not physically pushed to extinction by being out-competed by humans, but rather they slowly began to fade away by interbreeding with humans and leaving their mark in our DNA. 

Non-Coding DNA May Not be as Useless as We Think

Non-Coding DNA May Not be as Useless as We Think

DNA is the genetic material that makes everything that's living unique and similar at the same time.  All living things share at least a small percentage of their DNA with all other organisms, and this is due to the idea that all life on earth came from a single common ancestor.  DNA calls for the production of amino acids, and these chains of amino acids form to become more complex proteins.  DNA is made up of a 4 letter alphabet, GTCA, and is read in groups of 3, however, not all DNA calls for the production of proteins. Start and stop codons call for what parts of the DNA are to be transcribed and then translated into the basic building blocks that create us and all other life.  The genes that do not fall between these codons are called non-coding DNA, simply because they do not code for the production of protein.  For years, scientists have questioned the importance of these non-coding regions, and many thought that they were completely useless. A team led by Moises Mallo from Portugal explored what may happen if the non-coding regions were altered.

Picture of a snake's backbone and vertebrae, retrieved from here

The team looked into why snakes have ribs that extend out of each vertebra all the way down to their tails.  This is uncommon among vertebrates because for most vertebrates there is a distinguished head, neck, rib cage, and tail region, even though the sizes for each region vary between species.  For snakes it seems just like all one long region.

The scientists examined the specific genes that slow down the rib production in mice, and actually found that it was the same in snakes too.  The difference was in the non-coding DNA that was surrounding those certain genes.  This has led scientists to believe that the non-coding sequences may have some important evolutionary stems and that they are related to the body size of the organism.

Link to article