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.


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.

Chris Wakim’s odyssey took him from Alexandria, Egypt, to Bergen Community College to Rutgers University-New Brunswick, where he will graduate next month with a double major in microbiology and the biotechnology concentration in bioinformatics.

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.


Karl Maramorosch, 101, professor emeritus, Department of Entomology, School of Environmental and Biological Sciences, Rutgers University–New Brunswick, passed away of natural causes on May 9, 2016, during a visit to Poland.

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).

Discovered in bacteria as viral defense mechanism, researchers program C2c2 to manipulate cellular RNA using CRISPR

Recent Publications

Lin, W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M et al..  2018.  Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).. Molecular cell. 70(1):60-71.e15. Abstract
Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.
Sosio, M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S.  2018.  Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.. Cell Chemical Biology. Abstract
Pseudouridimycin (PUM) is a selective nucleoside-analog inhibitor of bacterial RNA polymerase with activity against Gram-positive and Gram-negative bacteria. PUM, produced by Streptomyces sp. ID38640, consists of a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 5'-aminopseudouridine. We report the characterization of the PUM gene cluster. Bioinformatic analysis and mutational knockouts of pum genes with analysis of accumulated intermediates, define the PUM biosynthetic pathway. The work provides the first biosynthetic pathway of a C-nucleoside antibiotic and reveals three unexpected features: production of free pseudouridine by the dedicated pseudouridine synthase, PumJ; nucleoside activation by specialized oxidoreductases and aminotransferases; and peptide-bond formation by amide ligases. A central role in the PUM biosynthetic pathway is played by the PumJ, which represents a divergent branch within the TruD family of pseudouridine synthases. PumJ-like sequences are associated with diverse gene clusters likely to govern the biosynthesis of different classes of C-nucleoside antibiotics.
Yu, Q, Lutz KA, Maliga P.  2017.  Efficient plastid transformation in Arabidopsis. Plant Physiology. 175:186-193.
Ge, Z, Bergonci T, Zhao Y, Zou Y, Du S, Liu M-C, Luo X, Ruan H, García-Valencia LE, Zhong S et al..  2017.  <em>Arabidopsis</em> pollen tube integrity and sperm release are regulated by RALF-mediated signaling. Science. 358(6370):1596. AbstractWebsite
In plants, sperm cells travel through the pollen tube as it grows toward the ovule. Successful fertilization depends on the pollen tube rupturing to release the sperm cells (see the Perspective by Stegmann and Zipfel). Ge et al. and Mecchia et al. elucidated the intercellular cross-talk that maintains pollen tube integrity during growth but destroys it at just the right moment. The signaling peptides RALF4 and RALF19, derived from the pollen tube, maintain its integrity as it grows. Once in reach of the ovule, a related signaling peptide, RALF34, which derives from female tissues, takes over and causes rupture of the pollen tube.Science, this issue p. 1596, p. 1600; see also p. 1544In flowering plants, fertilization requires complex cell-to-cell communication events between the pollen tube and the female reproductive tissues, which are controlled by extracellular signaling molecules interacting with receptors at the pollen tube surface. We found that two such receptors in Arabidopsis, BUPS1 and BUPS2, and their peptide ligands, RALF4 and RALF19, are pollen tube–expressed and are required to maintain pollen tube integrity. BUPS1 and BUPS2 interact with receptors ANXUR1 and ANXUR2 via their ectodomains, and both sets of receptors bind RALF4 and RALF19. These receptor-ligand interactions are in competition with the female-derived ligand RALF34, which induces pollen tube bursting at nanomolar concentrations. We propose that RALF34 replaces RALF4 and RALF19 at the interface of pollen tube–female gametophyte contact, thereby deregulating BUPS-ANXUR signaling and in turn leading to pollen tube rupture and sperm release.