Waksman Funded Projects

A list of currently funded research projects as reported by various funding sources.

Areas of Research

More than a few Model organisms at work: Maize, Drosophila, C. Elegans, Mice, Tobacco, Yeast, E.coli, Algae and more.

SpirodelaBase

Methods and Tools to aid researchers.

In the News: High School Student Makes Duckweed Discovery

Old Bridge Student Finds Unknown Gene in Duckweed During a Student Scholar Program at Rutgers University

High-throughput Sequencing Services Available from the Waksman Genomics Core Facility

Genomics Facility's High-Throughput, Next Generation Systems offers major advancements in throughput and maximum savings with new technology.

Located on Busch Campus of Rutgers, The State University of New Jersey, the Waksman Institute of Microbiology is an interdisciplinary research institute devoted to excellence in basic research. Focus areas include developmental biology, cell biology, biochemistry, structural biology, genetics, and genomics.

To support the educational mission of Rutgers, Waksman faculty members hold appointments in academic departments throughout the university. Our researchers train undergraduate students, graduate students, and post-doctoral fellows, as well as engage high school students in research through an outreach program.

Latest News

“Once I entered Rutgers in 2013, I felt like I need to be involved in research because it was calling me,” he said.

Rutgers Today Media Contact: Todd B. Bates

Ten Rutgers professors have been named fellows of the American Association for the Advancement of Science (AAAS), an honor conferred on 381 other experts in the U.S. and abroad.

The fellows were chosen by their AAAS peers for efforts to advance science applications that are deemed scientifically or socially distinguished, according to the AAAS.

Andrea Gallavotti, Assistant Professor in the Department of Plant Biology at the Waksman Institute, is a Co-PI of a recently awarded five-year collaborative grant. The project, sponsored by the National Science Foundation and titled “Genomic and Synthetic Approaches Linking Auxin Signaling Modules to Functional Domains in Maize”, seeks to understand how auxin signaling regulates the formation of specific functional domains in maize inflorescences (http://www.nsf.gov/awardsearch/showAward?AWD_ID=1546873).

With generous support from Chancellor of Rutgers New Brunswick, we are pleased to announce the acquisition of a PacBio Sequel DNA sequencer. The Sequel uses Single Molecule Real Time (SMRT) technology to produce long reads, uniform coverage, and high consensus accuracy. The Sequel long 10-15kb reads are ideal for whole genome sequencing, full-length transcript sequencing, or sequencing of long amplicons. Additionally, its SMRT sequencing technology can also be used to directly detect DNA base modifications.

By Deborah Walsh, Suburban Trends
Although some students might relish a respite from the most challenging of school work over the summer months, a couple of Kinnelon High School (KHS) students seized an opportunity to conduct high level scientific research at the Waksman Student Scholars Program (WSSP) Summer Institute at Rutgers University.
 

Madelaine Travaille, the school district's science supervisor, said a science research club was started at KHS in the 2015-16 school year.

Recent Publications

Zhang, W, Messing J.  In Press.  PacBio RS for gene family studies. Methods in Molecular Biology. Haplotyping.
Wu, Y, Messing J.  In Press.  Understanding and improving protein traits in maize seeds. Achieving Sustainable Maize Cultivation.
Bartlett, A, O'Malley R, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR.  2017.  Mapping genome-wide transcription factor binding sites using DAP-seq. Nature Protocols. 12(8):1659-1672. AbstractWebsite
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro-expressed TF, and TF–DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be derived. A researcher with molecular biology experience should be able to follow this protocol, processing up to 400 samples per week.
Chatterjee, M, Liu Q, Menello C, Galli M, Gallavotti A.  2017.  The Combined Action of Duplicated Boron Transporters Is Required for Maize Growth in Boron Deficient Conditions. Genetics. AbstractWebsite
The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) cause severe developmental defects and sterility. RTE is part of a small gene family containing five additional members (RTE2-RTE6) that show tissue specific expression. The close paralogous gene RTE2 encodes a protein with 95% amino acid identity with RTE and is similarly expressed in shoot and root cells surrounding the vasculature. Despite sharing similar functions with RTE, mutations in the RTE2 gene do not cause growth defects in the shoot, even in boron deficient conditions. However, rte2 mutants strongly enhance the rte phenotype in soils with low boron content, producing shorter plants that fail to form all reproductive structures. The joint action of RTE and RTE2 is also required in root development. These defects can be fully complemented by supplying boric acid, suggesting that diffusion or additional transport mechanisms overcome active boron transport deficiencies in the presence of an excess of boron. Overall, these results suggest that RTE2 and RTE function are essential for maize shoot and root growth in boron deficient conditions.