Don’t be fooled by the sessile nature of plants, for these botanical beauties actively respond to their surroundings, competing with their neighbors for resources. And in the plant world, the most precious resource is sunlight.
“Plants have mechanisms to sense their neighbors and if they sense that there’s a neighbor near them, then they compete with that neighbor by changing their growth,” said Professor Julin Maloof, Department of Plant Biology.
This biological phenomenon, called “shade avoidance,” is the focus of Maloof’s research. For years, he’s investigated this behavior and the genes underlying it, trying to understand the mechanisms that allow plants to allocate their resources for growth to reach the sunlight.
For nearly two decades, Maloof has also shined a light on biological knowledge for UC Davis students.
He played a pivotal role in the establishment of the genomics track in the Genetics and Genomics undergraduate major, developing and teaching courses that introduced computational biology methods to the undergraduate curriculum. For his dedication to his students, Maloof received the 2018-2019 Faculty Teaching Award.
“Top-tier teaching is an integral part of the Aggie experience," said College of Biological Sciences Dean Mark Winey. "To prepare the next generation of biologists, we need educators who are innovating curriculum to introduce the latest technologies and techniques in the life sciences to our students. Since joining UC Davis, Professor Maloof has done just that.”
Mentors of mentors
Maloof didn’t cut his science teeth with plants. As an undergraduate at Haverford College, located in Haverford, Pa., he studied development in nematodes (Caenorhabditis elegans, known commonly as a roundworm) in the lab of Professor of Biology Kaye Edwards.
In Edwards’ lab, Maloof focused on how mutations to collagen genes affect nematode development. These genes govern the development of the nematode’s body. Mutations to these genes can lead to different phenotypes. The research swallowed Maloof’s attention, and he could often be found working in the lab.
After graduating from Haverford College in 1989 with a B.A. in Biology, Maloof continued experimenting with nematodes while studying for his Ph.D. at UC San Francisco with now Professor Emeritus of Biochemistry and Biophysics Cynthia Kenyon.
This time Maloof and his colleagues were investigating the genetic factors that govern neuron distribution throughout the nematode’s nervous system. Maloof recalled that Kenyon’s insight when it came to hypotheses consistently awed him. For this project, Kenyon hypothesized that this area of the worm’s development would be governed by the Wnt signaling pathway.
“This is a specific biology pathway that was known from fruit flies and had started to be studied in mammalian cells,” said Maloof. “I was like, ‘What? Why does she think that?’ Because I could not connect what we were seeing in the worm with what I expected a Wnt pathway mutant might look like.”
“But she was right,” he added.
Today, Maloof works tirelessly to ensure his students and mentees understand the latest computational tools in biology.
UC Davis alum Ciera Martinez, ’16 Ph.D. in Plant Biology, recalled that Maloof organized a weekly programming teaching module for graduate students.
“This module introduced us gently and early to programming, and proved to greatly impact all of our research,” said Martinez. “I can also speak highly of this initiative to teach us on a personal level because it unlocked a passion for programming in me.”
Today, Martinez is a data science fellow at the Berkeley Institute for Data Science.
Finding the (sun)light
By the time graduation rolled around in 1998, Maloof felt the need to branch out. A friend shared with him an article about how light affects plant development. The article, written by Distinguished Professor Johanna (Annie) Schmitt, Department of Evolution and Ecology, stuck with Maloof.
“I read it and I was totally fascinated,” he said, noting it was the first time he really considered the plasticity of plants.
As a postdoc at the Salk Institute for Biological Studies, Maloof started studying how shaded plants compete for sunlight. He was mentored by Professor Joanne Chory, director of the Plant Molecular and Cellular Biology Laboratory, and Detlef Weigel, now a director at the Max Planck Institute for Developmental Biology. About two years into the position, Maloof attended a few talks about vacant junior faculty positions at the Salk Institute. While he didn’t apply for those jobs, the talks convinced Maloof he could be a competitive candidate. He started applying to faculty positions.
“As soon as I saw there was an ad at Davis, I was very excited,” he said. “It’s a really great school for plant biology.”
In 2002, Maloof joined the UC Davis faculty.
Teaching at the command line
Currently, Maloof teaches BIS 181 Comparative Genomics during the fall quarter and BIS 180L Genome Biology Lab during the spring quarter, both of which he co-designed. Maloof’s goal is to outfit the next generation of biologists with the skills necessary to be competitive in the life sciences fields. When it comes to the genomics that means processing and analyzing large swaths of data.
“The reality is bioinformatics is done on the command line,” he said, noting students learn programming languages like R and Python.
“His teachings made complex subjects, such as genome-wide association studies and genomic methods for reconstructing evolutionary history, digestible and memorable,” said Leslie Herrera, ’15 B.S. in Genetics and Genomics. He “also used alternative teaching methods that encouraged critical thinking.”
Herrera said Maloof used real-life examples in his teachings. During the 2014-2016 Ebola epidemic, Herrera’s class analyzed the evolution of the virus by reading the primary literature, which utilized genomic techniques Maloof taught in class. “The discussion of this literature challenged us to think about the applications and assumptions of certain modern techniques,” she said.
Maloof hopes to instill in his undergraduates the skills he’d expect from a new graduate student joining his lab.
“I’m really trying to teach the students science and skills that I think are important and exciting, so to be recognized for that is fantastic,” Maloof said of receiving the award. “It’s a real honor.”