The Hazen Lab is set to move into the Life Science Laboratories in August 2013.

Our research cluster includes experts in Plant and Microbial Sciences and Engineering. This interdisciplinary team was design to address the challenges of establishing plant biomass derived renewable energy.

Undergraduate Brachypodium researcher Mike Veling wins prestigious Goldwater Scholarship Award.

Since his freshman year in 2009, Mike Veling has worked in the Hazen laboratory in the Biology Department at the University of Massachusetts Amherst. Mike, a Biochemistry and Molecular Biology junior, is interested in protein-DNA interactions that influence plant biofuel attributes. Recently he gave the inaugural presentation at the 4th Annual Northeast Undergraduate Research Development Symposium in Buddeford, ME. Mike’s efforts have been supported by research fellowships from the Commonwealth Honors College. Now he will enjoy up to $7,500 per year for up to two years support from the Goldwater Foundation.


Microbiologists and plant biologists teamed up to develop an assay to measure the feedstock quality of plant biomass.

Clostridium phytofermentans is a soil bacterium isolated from Harvard Forest in Massachusetts by Tom Warnick and Sue Leschine. Remarkable characteristics of this bacterium include the ability to degrade essentially all plant polysaccharides and produce copious amount of ethanol. The Hazen lab demonstrated that some mutants of the energy crop sorghum were converted to ethanol more quickly than normal varieties. They also showed similar differences in ethanol production in the energy crop shrub willow and among different accession of Brachypodium distachyon. This approach is now being used to characterize mutants and genetic mapping populations and potentially energy crop breeding programs.


US Department of Energy Joint Genome Institute and UMass initiate project to develop biofuel research tools.

This venture will create a collection of grass transcription factor genes to facilitate energy crop research using the model system Brachypodium distachyon. Transcription factors are proteins that regulate gene expression, and the B. distachyon transcription factors targeted in this project are implicated in grass cell wall biosynthesis and the regulation of growth and biomass accumulation. Samuel Hazen and collaborators Todd Mockler at the Donald Danforth Plant Science Center and Steve Kay at the University of California San Diego will use this project as the cornerstone of a new high-throughout platform for analyzing protein-DNA interactions for the purpose of understanding important traits in grass species.


The Donald Danforth Plant Science Center and UMass Amherst team up to improve biomass accumulation in energy crops.

Plants utilize light energy to create biomass, as well as process light signals to interpret the environment. A collaboration between Todd Mockler and Sam Hazen is among the ten awards from the DOE-USDA Plant Feedstock Genomics for Bioenergy Program. They seek to use genomics and genetics in the model grass system Brachypodium distachyon to identify genes involved in light perception and signaling that will increase the yield and improve the composition of bioenergy grasses

Read full press release


DOE grant to help study on boosting ethanol yields from energy crops.

The U.S. Department of Energy Office of Science announced today that 65 scientists from across the nation have been selected for five-year awards under the Office's Early Career Research Program. The five-year awards are designed to bolster the nation's scientific workforce by providing support to exceptional researchers during the crucial early career years, when many scientists do their most formative work. The proposed research project, "Plant‐Microbe Genomic Systems Optimization for Energy", will explore the genetics of feedstock digestibility.

Undergrads Mike Veling, Rebecca Lamothe, Jessica Sysopha, and Dominick Matos presented their research at the 5th Annual Undergraduate Life Science Research Symposium and the 17th Annual Massachusetts Statewide Undergraduate Research Conference.

Matos D, Lin L, Hazen SP (2011) Characterization of plants with loss-of-function mutations in proteins known to interact with cell wall biosynthetic genes.

Sysopha J, Lee SJ, Alvelo-Maurosa J, Warnick TA, Young NF, Pedersen JF, Leschine SB, Caicedo AL, Hazen SP (2011) Assaying natural variation for feedstock quality in accessions of Brachypodium distachyon.

Lamothe RC, Young NF, Lin L, Hazen SP (2011) Repression of plant vascular bundle development by the bHLH transcription factor PVB.

Veling MV, Handakumbura P, Trabucco GM, Hazen SP (2011) Analysis of Homeobox transcription factors in grass species.

Undergraduate lab assistant Mike Veling awarded a Commonwealth College Research Fellowship.

A sophomore majoring in Biochemistry and Molecular Biology, Mike Veling has provided key support in the laboratory since his freshman year. He is constructing a multifunctional B. distachyon transcription factor ORFeome. In addition to developing this valuable reagent, he is conducting a phylogenetic analysis of specific protein families believed to play a role in the regulation of cell wall biosynthesis.

Undergraduate lab assistant, Scott Lee, receives a Plant Biology 2010 Travel Grant and a 2009-2010 Gerald F. Scanlon Student Employee of the Year Award.

Using the well-developed microbial system, Clostridium phytofermentans, Scott has developed a robust bioassay for biomass digestibility and conversion to biofuels. The bioassay can be used to measure the impact of plant genetic diversity on digestibility, and thereby determine the potential effects of altered energy crop traits. Visit his poster in Montreal!

Team maps genome for potential fuel source.

It took the work of more than 100 researchers, including Samuel Hazen, assistant professor of Biology, for the journal Nature last week to be able to publish the entire genome of the model grass commonly known as purple false brome.

It is the first member of this economically important grass family – which is being eyed as potential fuel source – to have its DNA fully sequenced.......

Brachypodium distachyon genome published in Nature.

The International Brachypodium Initiative describes the genome sequence of Brachypodium distachyon, a wild grass. The consortium suggests that their genome sequence, along with the grass’ rapid life cycle and ease of cultivation, will help brachy to become a model system for the development of novel energy sources and food crops.

Undergraduate lab assistants, Torie Carroll and Gina Trabucco, receive Honors College Research Awards.

Gina and Torie are both conducting their senior year honors thesis research in the Hazen Lab.

Gina has quickly become proficient in grass transformation and is working to silence various candidate genes using artificial microRNA technology. Only after she has identified some of the important genes can we move forward with cell wall systems biology in grasses.

Some regulatory regions will cause a gene to be expressed constitutively in all cell types. Torie is exploring just what makes this phenomenon occur. Specifically, what proteins bind to these regions to dictate downstream gene expression behavior. 12/18/09

Undergraduate lab assistant, Rebecca Lamonthe, awarded HHMI Research Intership and a Commonwealth College Research Fellowship.

Having recently completed a very competitive NSF supported Research Experience for Undergraduates in Integrative and Evolutionary Biology summer program at UMass Boston, she will continue her research in our laboratory with the support of the Howard Hughes Medical Institute and the Honors College at UMass Amherst. Rebecca will functionally characterize noncoding RNAs predicted to target genes involved in cell wall biosynthesis. 10/15/2009.

The Brachypodium genome is now available.

Version 4.0 of Phytozome is now available and includes JGI v1.0 8x assembly of strain Brachypodium Bd21 with JGI/MIPS PASA annotation. 5/13/2009.

Sam Hazen presents at Dartmouth College 

Sam Hazen will present a seminar entitled 'Transcriptional Landscape of Plant Circadian Rhythms' at the Department of Biological Sciences, Dartmouth College on April 22.

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.

This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known. View at Genome Biology

Biologists Identify Genes Controlling Rhythmic Plant Growth. 
The University of California San Diego, The Salk Institute for Biological Studies and Oregon State University has identified the genes that enable plants to undergo bursts of rhythmic growth at night and allow them to compete when their leaves are shaded by other plants. They reported that that these genes control the complex interplay of plant growth hormones, plant light sensors and circadian rhythms that permit plants to undergo rhythmic growth spurts at specific times of the day or year in response to varying levels of light and other environmental conditions.   9/15/2008. View at PloS Biology

DOE and USDA Announce More than $10 Million in Bioenergy Plant Feedstock Research.

Agriculture Under Secretary for Research, Education and Economics Gale Buchanan and Energy Department (DOE) Under Secretary for Science Raymond Orbach and today announced plans to award 10 grants totaling more than $10 million to accelerate fundamental research in the development of cellulosic biofuels.  8/7/2008. View summary

Network discovery pipeline elucidates conserved time of day specific cis-regulatory modules.

Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study we describe a hypothesis driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility we applied the pipeline to a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition tested and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover we show that the three transcription modules are conserved across Arabidopsis, poplar and rice. These results confirm the complex interplay between thermocycles, photocycles and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.  View at PLoS Genetics

The DOE Joint Genome Institute has selected Brachypodium distachyon as a target for resequencing.

Energy-rich Portfolio of New Genome Sequencing Targets for DOE JGI. 
Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects to be tackled by the U.S. Department of Energy Joint Genome Institute (DOE JGI) over the next year.   7/11/2006

Why sequence Brachypodium?