Co-authored publications by UC Davis Genome Center Members or publications where UC Davis Genome Center or a GC Core is acknowledged for their technical support and services:
A paper titled, "Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements" by Tomkova et al. 2023 was recently published in Nucleic Acid Research.
Every modern mammal, from a platypus to a blue whale, is descended from a common ancestor that lived about 180 million years ago. We don’t know a great deal about this animal, but the organization of its genome has now been computationally reconstructed by an international team of researchers. The work is published Sept. 30 in Proceedings of the National Academy of Sciences.
This post summarizes the findings of the paper "Effects of pairing on color change and central gene expression in lined seahorses" by Mederos et al. published in Genes, Brain and Behavior (link).
A recent publication in MDPI Genes by Zhu et al. titled "Single-cell RNA-seq analysis reveals lung epithelial cell type-specific responses to HDM and regulation by Tet1" investigated house dust mite (HDM)-induced lung inflammation in mice using Tet1 knockout mice and wildtype mice.
Studies comparing animal genomes generally focus on the DNA sequence itself. A new study by researchers at the University of California, Davis shows how the three-dimensional scaffolding of chromosomes is related across several species of carnivores, offering a new approach of “comparative scaffotyping” that could be used to identify related genes across species and place them in context. The work, published the week of Feb.
Scientists are a step closer to breeding plants with genes from only one parent. New research led by plant biologists at the University of California, Davis, published Nov. 19 in Science Advances, shows the underlying mechanism behind eliminating half the genome and could make for easier and more rapid breeding of crop plants with desirable traits such as disease resistance.
A recent publication in Scientific Reports by Brydges et al. titled "Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature" investigated whether indoles in the gut microbiome are associated with depression and anxiety. The study found that abundance of indoles is correlated with anxiety, but anxiety treatment was not related to the modulation of indoles in the gut.
The first atlas of metabolites in the mouse brain has been published by a team led by UC Davis researchers. The dataset includes 1,547 different molecules across 10 brain regions in male and female laboratory mice from adolescence through adulthood and into advanced old age. The work is published Oct. 15 in the Nature Communications. The complete dataset is publicly available at https://mouse.atlas.metabolomics.us/.
The Vertebrate Genomes Project (VGP) today (April 28) announced their flagship study including high-quality, near error-free, and near complete reference genome assemblies for 16 species representing six major lineages of vertebrates, including mammals, reptiles, monotremes, amphibians and fish.
Blue coloring in nature is difficult to find; however, there is consumer demand for natural food coloring. Research conducted by Denish et al. (2021) in Science Advances describes the discovery of a cyan blue anthocyanin-based colorant. Synthetic biology and computational protein design tools were leveraged to develop an enzymatic transformation of red cabbage anthocyanins into the desired anthocyanin. This newly discovered cyan blue colorant could replace FD&C Blue No. 1.
Together, several Genome Center faculty have catalogued regulatory genes in chickens, cattle, and pigs that could lead to improvements in breeding these important farm animals.
Genome Sequence of Verticillium dahliae Race 1 Isolate VdLs.16 From Lettuce
This recent publication by Chen et al. in Molecular Plant-Microbe Interactions presented a high-quality reference genome sequence of Verticillium dahliae race 1 isolate VdLs.16, which is an important fungal pathogen of crop and ornamental plants. This resource is a building block for future research on pathogenicity and population diversity.
