Of Mice and…Gorillas? Mouse Gene Catalog as a Conservation Tool

Gorilla

Mice share a similar set of genes to humans and gorillas. A catalog of the functions of all mouse genes could help in conservation efforts for endangered species.

A new study from the International Mouse Phenotyping Consortium, which includes the UC Davis Mouse Biology Program, shows how the growing catalog of mouse genes could be applied to save endangered species. The paper was published May 24 in the journal Conservation Genetics.

Data Dump: 11,000 Donate Stool Samples to Gut Microbiome Project

By Greg Watry

The American Gut Project has just produced the largest study yet of microbial diversity in human poop. With “contributions” from more than 11,000 citizen scientists, the team led by researchers at UC San Diego has compiled a public reference database on the human gut microbiome, published May 15 in the journal mSystems. The study is a step forward in understanding how factors such as diet, antibiotics and mental health relate to the microbes living in the human gut.

Using DNA Databases to Track Down the Golden State Killer Suspect

It’s been widely reported that investigators got a break in the East Area Rapist/Golden State Killer case when they uploaded a DNA profile to a genealogy database, GEDmatch, and identified relatives of the suspect, Joseph DeAngelo. Did they get lucky, or did they have a good chance of finding him? UC Davis population biologists Graham Coop and M. D. “Doc” Edge have written a nice explainer of the science behind this search.

DNA overlap between first cousins and their common grandmother (GCBias.org)

Podcast: The Earth BioGenome Project

This month I talk to Professor Harris Lewin, one of the organizers of the Earth BioGenome Project. The ambitious project to sequence the genomes of all eukaryotic life on Earth within ten years is described in a paper published this week in the Proceedings of the National Academy of Sciences.

Listen: Three Minute Egghead: The Earth BioGenome Project

More information

Earth BioGenome Project Aims to Sequence DNA from All Complex Life on Earth (news release)

Earth BioGenome Project to Sequence All Life: Partnership Announced at World Economic Forum in Davos (news release)

Investigating the Seagrass Microbiome

By Karley Marie Lujan

Seagrass carpets the seafloor creating a unique and vital ecosystem in shallow marine environments. Sea turtles graze on seagrass leaves while smaller organisms seek refuge in the green fields but, on the microscopic level, seagrass is also home to microbial communities. Such microbes compose the seagrass microbiome and potentially play a role in seagrass ecology.

Turtle and seagrass

Sea turtles and other marine animals browse on seagrass meadows. (NOAA photo)

UC Davis graduate student Cassie Ettinger identifies and characterizes seagrass-associated microbial communities. A study published last year in the journal PeerJ suggests how understanding the role of these microbes could reveal new information about seagrass sulfur cycling and establish seagrass as a model organism.

Taking Cues From Speech Recognition, New Machine Learning Algorithm Finds Patterns in RNA Structures

By Greg Watry

Software inspired by speech recognition technology could help scientists understand the secret language inside cells. A machine learning algorithm called patteRNA, designed by UC Davis researchers, rapidly mines ribonucleic acid, commonly called RNA, for specific structures, providing a new method to establish links between structure, function and disease.

The study, co-authored by integrative genetics and genomics Ph.D. student Mirko Ledda and Assistant Professor Sharon Aviran, UC Davis Genome Center, appears in Genome Biology.

Deciphering the biological role of RNA structures

RNA is essential to all biological processes, from gene expression and regulation to protein synthesis. While DNA stores an organism’s genetic information, RNA puts that genetic information to use.

How Population Genetics Can Help Breed a Hardier Honey Bee

by Greg Watry

The western honey bee (Apis mellifera), the world’s most important pollinator for agriculture, is facing a crisis. Parasitic mites, colony collapse and climate change threaten hives. California, as the seasonal home of nearly half of the continental United States’ managed honey bee colonies, is a prime location for monitoring bee populations. And honey bee health, key to the nation’s largest fresh produce economy, is vital to the Golden State.

A foraging honeybee. Photo by Kathy Keatley Garvey.

One Place Like Home: Space Station Has Same Microbes as Your House

By Carole Gan

UC Davis microbiologists have analyzed swabs taken by astronauts on the International Space Station – and found pretty much the same types of microbes as in a home on Earth, according to an analysis published today (Dec. 5) in the journal PeerJ.

The International Space Station is interesting to scientists studying the microbial ecology of buildings because it is a “building” with very few ways to bring microbes in or out.

Citizen science and Project MERCURRI

The work was part of Project MERCCURI, a collaboration between UC Davis and other organizations including Science Cheerleader, a group of current and former professional cheerleaders pursuing careers in science and math.

Humans Gathered Grapes Long Before They Cultivated Them

By Diane Nelson

About 22,000 years ago, as the ice sheets that consumed much of North America and Europe began retreating, humans started to eat a fruit that today brings joy to millions of wine drinkers around the world: grapes.

People have been making wine from grapes for at least 8,000 years, but genetic evidence shows that humans influenced grape vines long before that (Gregory Urquiaga/UC Davis).

UC Davis Genome Researchers Facilitating NIH Data Commons Pilot

Researchers at the UC Davis School of Veterinary Medicine and Genome Center are taking part in an ambitious NIH initiative to make it easier for scientists to share research data and scientific tools online.

C. Titus Brown is associate professor in the UC Davis School of Veterinary Medicine and Genome Center.

“Harvesting the wealth of information in biomedical data will advance our understanding of human health and disease,” said NIH Director Francis S. Collins in a news release. “However, poor data accessibility is a major barrier to translating data into understanding. The NIH Data Commons Pilot Phase is an important effort to remove that barrier.”