Microbial Genomics Gold Found in Old Data

By Scott Edmunds

There’s gold in those old databases. Analyses of genomic data often miss a large amount of information, but genome scientists at UC Davis have now created an automated analysis pipeline to dig out this hidden information. 

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

In a new study published in the journal GigaScience the researchers mine a huge marine microbial dataset from the Microbial Transcriptome Sequencing Project (MMETSP) to find new results.

Uncovering How Dengue, Zika Viruses Manipulate Hosts

A new, holistic approach to biology is giving researchers new insights into how the Dengue and Zika viruses attack their hosts and, in the case of Zika, affect brain development. Published Dec. 13 in the journal Cell, the work may open up new ways to think about treating virus infections or mitigating their effects.

Priya Shah in lab

Priya Shah’s work in systems biology spans the Colleges of Engineering and of Biological Sciences. The approach is giving new insight into how dengue and Zika viruses attack human cells. Credit: David Slipher, College of Biological Sciences

Rapid Genetic Evolution Linked to Lighter Skin Pigmentation in a Southern African Population

By Karen Nikos-Rose

Populations of indigenous people in southern Africa carry a gene that causes lighter skin, and scientists have now identified the rapid evolution of this gene in recent human history.

The gene that causes lighter skin pigmentation, SLC24A5, was introduced from eastern African to southern African populations just 2,000 years ago. Strong positive selection caused this gene to rise in frequency among some KhoeSan populations.

Brenna Henn

UC Davis anthropologist Brenna Henn and colleagues have shown that a gene for lighter skin spread rapidly among people in southern Africa in the last 2000 years.

The Whole Tooth: New Method to Find Biological Sex From a Single Tooth

A team led by UC Davis researchers have come up with a new way to estimate the biological sex of human skeletal remains based on protein traces from teeth.

Tooth of a European-American buried in San Francisco in the 1850s. A new technique developed at UC Davis allows archaeologists
to find a person’s biological sex based on a single tooth. (Jelmer Eerkens)

Estimating the sex of human remains is important for archaeologists who want to understand ancient societies and peoples. Researchers can measure features of bones that differ between males and females, usually the pelvis. But skeletons of children and adolescents don’t show these structural changes, and often sites may only yield a few pieces of bone.

Detecting E.coli Strains Using Molecular Electronics

New technology developed by Josh Hihath and colleagues at UC Davis uses atomically fine electrodes to suspend a DNA probe that binds target RNA. The device is able to detect as little as a one-base change in RNA, enough to detect toxic strains of E. coli.

By Aditi Risbud Bartl

Finding a fast and inexpensive way to detect specific strains of bacteria and viruses is critical to food safety, water quality, environmental protection and human health. However, current methods for detecting illness-causing strains of bacteria such as E. coli require either time-intensive biological cell cultures or DNA amplification approaches that rely on expensive laboratory equipment.

From Lab Fruit Flies to Mosquito Extermination in 30 Years

Louis Pasteur famously compared science and its application to a tree and it’s fruit. The path from a fundamental discovery to application can be a long and winding one, but rewarding none the less.

Mosquito

Discoveries in basic genetics have now enabled scientists to wipe out lab populations of the malaria mosquito, Anopheles gambiae. (Anthony Cornel)

Professor Ken Burtis, faculty advisor to the Chancellor and Provost, recently came across an exciting example. Burtis was looking for a study for his first year seminar class when he found a paper from Andrea Crisanti’s lab at Imperial College London. Crisanti’s team was able to wipe out a lab population of Anopheles gambiae mosquitoes by introducing a disrupted gene for sex determination and using CRISPR “gene drive” technology to spread it through the population. Within eight generations, there were no female mosquitoes left for breeding.

Physics Nobel for Optical Tweezers, Enabled Single Molecule DNA Work

The 2018 Nobel Prize for Physics has been awarded to Arthur Ashkin of Bell Labs, Gérard Mourou, École Polytechnique, Palaiseau, France
and the University of Michigan, Ann Arbor and Donna Strickland, University of Waterloo, Canada for work on laser pulses that led to the development of “optical tweezers” that use lasers to manipulate small objects. 

The invention of optical tweezers made it possible for UC Davis biologists led by Professor Stephen Kowalczykowski and the late Professor Ron Baskin to design experiments where they could manipulate and observe single DNA molecules being copied in real time. In 2001, they used optical tweezers to move a tiny bead with a piece of DNA attached under a microscope, where they could watch a helicase enzyme unwind the DNA — the first step to copying or repairing it.

Study Challenges Evolution of How Humans Acquired Language

By Karen Nikos-Rose

A gene implicated in affecting speech and language, FOXP2, is held up as a “textbook” example of positive selection on a human-specific trait. But in a paper in the journal Cell on Aug. 2, researchers challenge this finding. Their analysis of genetic data from a diverse sample of modern people and Neanderthals saw no evidence for recent, human-specific selection of FOXP2 and revises the history of how we think humans acquired language.

Brain graphic

What makes us human? The FOXP2 gene has been associated with uniquely human language abilities. But a new study with a wider variety of people shows no evidence of selection for FOXP2 in modern humans. (Image by Brenna Henn, UC Davis)

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.