Category: Genes

Posted on

Field Focus: High-Quality Genome Sequences Inform the Study of Human Evolution

by
1 comment

Leafing through my favorite biology textbook from a handful of years ago, I was struck by the relative brevity of the chapter on human evolution. While other fields of biological research have enjoyed a steady gallop of productivity over the last few decades due in part to advances in computing power, imaging technology and experimental methods, the study of human evolution can be seen as having lagged behind until recently due to an almost complete dependence on fossil evidence.

Fortunately, contemporary biology textbook chapters on human evolution are being primed for a serious upgrade thanks to the recent availability of high-quality genome sequences from diverse modern human populations as well as from ancient humans and other non-human hominids, including the Neanderthals and Denisovans (but, for purposes of this story, not the Great Apes).

Modern human skull (left) and Neanderthal skull (right), shown to scale. There are not enough Denisovan bone fragments to reconstruct its skull. Credit: Wikimedia Commons, hairymuseummatt.

What are the new resources for studying human evolution?

The cost of DNA sequencing has dropped precipitously in the last decade. As a result, more complete human genome sequences become available for analysis with each passing year.

For example, the 1000 Genomes Project Exit icon includes more than 1,000 full human genome sequences of individuals from European, Asian, American and Sub-Saharan African populations. Earlier this year, the Simons Genome Diversity Project Exit icon further increased the number of available human genomes by adding 300 individuals representing 142 populations around the globe.

Continue reading “Field Focus: High-Quality Genome Sequences Inform the Study of Human Evolution”
Posted on

On this Darwin Day, Evolutionary Geneticist Dr. Dan Janes Discusses the Scientific Contributions of Charles Darwin

by
3 comments

This Sunday, February 12, is Darwin Day—an occasion to recognize the scientific contributions of 19th-century naturalist Charles Darwin. In this video (originally posted on Darwin Day 2016), our own evolutionary geneticist, Dan Janes, answers questions about Darwin and the role of evolution in health and biomedicine.

Continue reading “On this Darwin Day, Evolutionary Geneticist Dr. Dan Janes Discusses the Scientific Contributions of Charles Darwin”

Posted on

There’s an “Ome” for That

by
1 comment
In the 13 years since the sequencing of the human genome, the list of “omes” has proliferated. Drop us a comment with your favorite ome—we may feature it in a follow-up post next month.

Have you ever collected coins, cards, toy trains, stuffed animals? Did you feel the need to complete the set? If so, then you may be a completist. A completist will go to great lengths to acquire a complete set of something.

Scientists can also be completists who are inspired to identify and catalog every object in a particular field to further our understanding of it. For example, a comprehensive parts list of the human body—and of other organisms that are important in biomedical research—could aid in the development of novel treatments for diseases in the same way that a parts list for a car enables auto mechanics to build or repair a vehicle.

More than 15 years ago, scientists figured out how to catalog every gene in the human body. In the years since, rapid advances in technology and computational tools have allowed researchers to begin to categorize numerous aspects of the biological world. There’s actually a special way to name these collections: Add “ome” to the end of the class of objects being compiled. So, the complete set of genes in the body is called the “genome,” and the complete set of proteins is called the “proteome.”

Below are three -omes that NIH-funded scientists work with to understand human health.

Genome

Illustration of the entire outer shell of the bacteriophage MS2. Credit: Wikimedia Commons, Naranson.

The genome is the original -ome. In 1976, Belgium scientists identified all 3,569 DNA bases—the As, Cs, Gs and Ts that make up DNA’s code—in the genes of bacteriophage MS2, immortalizing this bacteria-infecting virus as possessing the first fully sequenced genome.

Over the next two decades, a small handful of additional genomes from other microorganisms followed. The first animal genome was completed in 1998. Just 5 years later, scientists identified all 3.2 billion DNA bases in the human genome, representing the work of more than 1,000 researchers from six countries over a period of 13 years. Continue reading “There’s an “Ome” for That”

Posted on

Our Complicated Relationship With Viruses

by
9 comments
Illustration of Influenza Virus H1N1. Swine Flu.
Nearly 10 percent of the human genome is derived from the genes of viruses. Credit: Stock image.

When viruses infect us, they can embed small chunks of their genetic material in our DNA. Although infrequent, the incorporation of this material into the human genome has been occurring for millions of years. As a result of this ongoing process, viral genetic material comprises nearly 10 percent of the modern human genome. Over time, the vast majority of viral invaders populating our genome have mutated to the point that they no longer lead to active infections. But they are not entirely dormant.

Sometimes, these stowaway sequences of viral genes, called “endogenous retroviruses” (ERVs), can contribute to the onset of diseases such as cancer. They can also make their hosts susceptible to infections from other viruses. However, scientists have identified numerous cases of viral hitchhikers bestowing crucial benefits to their human hosts—from protection against disease to shaping important aspects of human evolution, such as the ability to digest starch.

Protecting Against Disease

Geneticists Cedric Feschotte, Edward Chuong and Nels Elde Exit icon at the University of Utah have discovered that ERVs lodged in the human genome can jump start the immune system.

For a virus to successfully make copies of itself inside a host cell, it needs molecular tools similar to the ones its host normally uses to translate genes into proteins. As a result, viruses have tools meticulously shaped by evolution to commandeer the protein-producing machinery of human cells.

Continue reading “Our Complicated Relationship With Viruses”
Posted on

Interview With a Scientist: Janet Iwasa, Molecular Animator

by and
0 comments

The world beneath our skin is full of movement. Hemoglobin in our blood grabs oxygen and delivers it throughout the body. Molecular motors in cells chug along tiny tubes, hauling cargo with them. Biological invaders like viruses enter our bodies, hijack our cells and reproduce wildly before bursting out to infect other cells.

To make sense of the subcutaneous world, Janet Iwasa, a molecular animator at the University of Utah, creates “visual hypotheses”—detailed animations that convey the latest thinking of how biological molecules interact.

“It’s really building the animated model that brings insights,” Iwasa told Biomedical Beat in 2014. “When you’re creating an animation, you’re really grappling with a lot of issues that don’t necessarily come up by any other means. In some cases, it might raise more questions, and make people go back and do some more experiments when they realize there might be something missing.”

Iwasa has collaborated with numerous scientists to develop animations of a range of biological processes and structures Exit icon. Recently, she’s undertaken an ambitious, multi-year project to animate HIV reproduction Exit icon.

Posted on

Interview With a Slime Mold: Racing for New Knowledge

by
1 comment
Dictyostelium discoideum
Credit: Wikimedia Commons, Usman Bashir.
Dictyostelium discoideum
Natural habitat: Deciduous forest soil and moist leaf litter
Favorite food: Bacteria
Top speed: 8 micrometers per minute

Like the athletes in Rio, the world’s most highly advanced microbial runners recently gathered in Charlestown, Massachusetts, to find out which ones could use chemical cues to most quickly navigate a maze-like microfluidic racecourse. The winners’ prize: credit for helping scientists learn more about how immune system cells navigate through the human body on their way to fight disease.

The finalists were a group of soil-dwelling slime molds called Dictyostelium that were genetically engineered by a pair of Dutch biochemists to detect minuscule chemical changes in the environment. The racers used their enhanced sense of “smell” to avoid getting lost on their way to the finish line.

While researchers have been racing the genetically souped-up microbes at annual events for a few years—another competition is scheduled for October 26—scientists have been studying conventional Dictyostelium for decades to investigate other important basic life processes including early development, gene function, self/non-self recognition, cell-type regulation, chemical signaling and programmed cell death. Continue reading “Interview With a Slime Mold: Racing for New Knowledge”

Posted on

CRISPR Serves Up More than DNA

by
0 comments
Marine bacterium Marinomonas mediterranea
The marine bacterium Marinomonas mediterranea uses a CRISPR system to spot invading RNAs and store a memory of the invasion event in its genome. Research team member Antonio Sanchez-Amat was the first to isolate and characterize this bacterial species. Credit: Antonio Sanchez-Amat, University of Murcia.

A new study has added another twist to the CRISPR story. As we’ve highlighted in several recent posts, CRISPR is an immune system in bacteria that recognizes and destroys viral DNA and other invading DNA elements, such as transposons. Scientists have adapted CRISPR into an indispensable gene-editing tool now widely used in both basic and applied research.

Many previously described CRISPR systems detect and cut viral DNA, insert the DNA pieces into the bacterial genome and then use them as molecular “mug shots” to flag and destroy the virus if it attacks again. But various viruses use RNA, not DNA, as genetic material. Although research has shown that some CRISPR systems also can target RNA, how these systems can archive harmful RNA encounters in the bacterial genome was unknown. Continue reading “CRISPR Serves Up More than DNA”

Posted on

Another Piece to a Century-Old Evolutionary Puzzle

by
0 comments
After mating about 55,000 pairs of fruit flies and sifting through 333,000 daughter flies, a research team found six sons that each had mutations in the same gene that helped make two fruit fly species unique from each other. Credit: Jim Woolace, Fred Hutch News Service.

Nitin Phadnis and Harmit Malik set out to conduct an experiment that could solve a century-old evolutionary puzzle: How did two related fruit fly species arise from one? Years after they began their quest, they finally have an answer.

The existence of a gene that helps make each of these fruit fly species unique and separate from each other had been guessed at since 1940, following experiments decades earlier in which geneticists first noticed that the two types of flies, when mated, had only daughters—no sons.

Scientists had previously discovered two other genes involved in driving the fruit fly species apart, but they knew those two genes weren’t the full story.

Continue reading “Another Piece to a Century-Old Evolutionary Puzzle”
Posted on

Finding Adventure: Blake Wiedenheft’s Path to Gene Editing

by
1 comment
Blake Wiedenheft
Blake Wiedenheft
Grew up in: Fort Peck, Montana
Fields: Microbiology, biochemistry, structural biology
Job site: Montana State University
Secret talent: Being a generalist; enjoying many different subjects and activities
When not in the lab, he’s: Running, biking, skiing or playing scrabble with his grandmother

Scientific discoveries are often stories of adventure. This is the realization that set Blake Wiedenheft on a path toward one of the hottest areas in biology.

His story begins in Montana, where he grew up and now lives. Always exploring different interests, Wiedenheft decided in his final semester at Montana State University (MSU) in Bozeman to volunteer for Mark Young, a scientist who studies plant viruses. Even though he majored in biology, Wiedenheft had spent little time in a lab and hadn’t even considered research as a career option. Continue reading “Finding Adventure: Blake Wiedenheft’s Path to Gene Editing”

Posted on

Cool Image: A Circadian Circuit

by
1 comment
Clock neurons (middle right, right corner and edge), leucokinin (LK) neurons (top left, top right and bottom middle), leucokinin receptor (LK-R) neurons (top left, top right and bottom middle)

This image, taken with a confocal microscope, shows how time-of-day information flows through the fruit fly brain. Clock neurons (stained in blue) communicate with leucokinin (LK) neurons (stained in red at the top left, top right and bottom middle), which, in turn, signal to leucokinin receptor (LK-R) neurons (stained in green). This circuit helps regulate daily activity in the fly. Credit: Matthieu Cavey and Justin Blau, New York University.

Feeling sleepy and dazed after the switch to daylight savings time this weekend? Your internal clocks are probably a little off and need some time to adjust.

Researchers have been studying biological clocks for decades to figure out how they control circadian rhythms, the natural 24-hour pattern of physical, mental and behavioral changes that affect sleep, appetite and metabolism. Knowing more about what makes our clocks tick could help researchers develop better therapies for sleep problems, metabolic conditions and other disorders associated with mistimed internal clocks. Continue reading “Cool Image: A Circadian Circuit”