About

David Stern is an adjunct professor in the School of Integrative Plant Science, Plant Biology Section, at Cornell University. He is the former president of the Boyce Thompson Institute (BTI), a position he has held since 2004. Stern received his M. Phil. in Biochemistry from Cambridge University and his Ph.D. in Biological Sciences from Stanford University. Following postdoctoral training at the University of California, Berkeley, in plant molecular biology, he joined the Boyce Thompson Institute faculty as an Assistant Scientist in 1989. His research focuses on chloroplast biology, bioenergy, and nuclear-cytoplasmic interactions. Within his laboratory, he studies how chloroplast genes and metabolic activities are regulated by nuclear gene products, often at the transcriptional or post-transcriptional level. His areas of emphasis include the roles of ribonucleases and RNA-binding proteins, as well as the assembly of the carbon-fixing enzyme Rubisco. Additionally, he employs molecular and genetic techniques to modify chloroplast metabolism for the production of useful hydrocarbons.

Research topics

• Political Science
• Computer Science
• Biochemistry
• Horticulture
• Biology
• Agronomy
• Engineering ethics
• Botany
• Data science
• Engineering
• Geography

Selected publications

• The α form of Rubisco activase supports photosynthesis during heat stress in the absence of the β form in <i>Setaria viridis</i>

  Journal of Experimental Botany · 2025-06-26 · 1 citations

  articleSenior author

  Rubisco activase (RCA) facilitates the removal of inhibitors from the Rubisco active site and is essential for plant growth at atmospheric CO2. Here we report the phenotypes of gene-edited RCA mutants in the C4 grass Setaria viridis, which has two forms of RCA, RCAα and RCAβ, encoded by separate genes. In Setaria, only the β form accumulates at normal temperatures, with the α form being induced following exposure to heat. Inactivating the RCAβ gene (βKO) abolished accumulation of RCA at 25 °C and significantly reduced photosynthesis. These plants required elevated CO2 for survival. Inactivating the RCAα gene (αKO) did not affect RCAβ accumulation, photosynthesis, or growth. Neither mutant exhibited altered Rubisco content or activation when grown at 25 °C and elevated CO2. When βKO plants were transferred from elevated to ambient CO2 and 40 °C, RCAα induction supported growth for approximately 7 d, although plants were smaller with fewer tillers compared with WT and αKO plants. The ability of a small amount of RCAα to support growth in ambient CO2 at 40 °C is consistent with our results showing that its in vitro ATPase activity is more thermotolerant than RCAβ and suggests that RCAα may help C4 plants cope with certain heat stress conditions.

  PublisherDOI

• The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-15

  preprintOpen accessSenior author

  ABSTRACT RNase J is a ribonuclease found in bacteria, archaea, and plant chloroplasts, and plays diverse roles in RNA maturation and stability. Chloroplast RNase J is encoded by the nuclear RNJ locus and is essential for embryo maturation. Arabidopsis or tobacco plants depleted for RNase J accumulate massive amounts of double-stranded RNA, which interferes with translation and causes chlorosis. Land plant RNase J uniquely contains a C-terminal GT1 domain, a DNA- binding motif found in transcription factors. Here, we have used complementation of an Arabidopsis rnj mutant with versions of RNase J with a mutated or deleted GT1 domain to investigate its role in RNase J function. We show that in vitro , the recombinant GT1 domain binds both double-stranded RNA and DNA, but not single-stranded nucleic acids, with no sequence specificity. Furthermore, while RNase J lacking GT1 binding complements the rnj mutant, these plants accumulate high levels of dsRNA as detected by immunolocalization and RNA-Seq. GT1 mutations also change RNase J solubility in vivo , suggesting that the GT1 domain is involved in localization within the plastid. Taken together, our results suggest that the GT1 domain plays a key role in dsRNA removal through localizing the enzyme and/or selectively binding the dsRNA substrate. GRAPHICAL ABSTRACT

  PublisherOA PDFDOI

• Hybridization capture sequencing for <i>Vibrio</i> spp. and associated virulence factors

  mBio · 2025-06-25 · 4 citations

  articleOpen access

  ABSTRACT Proliferation of Vibrio spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundance Vibrio spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 Vibrio spp. and 162 Vibrio -specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic Vibrio spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific Vibrio spp., yielded significantly greater metagenomic insight, notably a variety of other Vibrio spp., including detection of Vibrio cholerae , Vibrio fluvialis , and Vibrio aestuarianus , in addition to Vibrio parahaemolyticus and Vibrio vulnificus , and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

  PublisherDOI

• The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-22 · 1 citations

  preprintOpen access

  RNA Covalent Modifications (RCMs) are post-transcriptional chemical alterations that influence RNA stability and translation efficiency, thus play critical roles in eukaryotic growth and development. However, their role in regulating plant performance under abiotic stress remain largely unexplored. Here, we integrated multi-omics data in six Sorghum bicolor accessions under water-limiting conditions in the field to explore the relationship between RCMs and drought response. Within a stress and photosynthesis-associated gene co-expression module, we identified SbDUS2, a member of family of enzymes, conserved across eukaryotes, which catalyzes the reduction of uracil to dihydrouridine (DHU) on RNA molecules. DHU-modified transcripts in this module were enriched for photosynthetic functions and showed strong correlation with photosynthetic traits. To elucidate the function of this RCM, we characterized loss of function dus2 mutants in the genetic model, Arabidopsis thaliana. Under control conditions, these DHU-deficient mutants exhibited impaired germination and delayed development. Furthermore, when exposed to heat or water-limiting conditions, these mutants showed significantly reduced net CO2 assimilation and survival. Using multiple transcriptome-wide RNA stability assays, we demonstrated that transcripts associated with lower DHU level in a dus2 background generally exhibited increased stability compared to Col-0 controls. Particularly, lack of DUS2 led to the hyperstability of photosynthesis-related transcripts, impeding their turnover and likely preventing proper photosynthetic acclimation during stress. We propose a model based on these data where DHU acts as a critical post-transcriptional regulator marking mRNAs for rapid turnover under stress, highlighting an overlooked regulatory layer contributing to plant resilience.

  PublisherDOI

• Transgenic expression of Rubisco accumulation factor2 and Rubisco subunits increases photosynthesis and growth in maize

  Journal of Experimental Botany · 2024-05-02 · 18 citations

  articleSenior author

  Carbon assimilation by Rubisco is often a limitation to photosynthesis and therefore plant productivity. We have previously shown that transgenic co-expression of the Rubisco large (LS) and small (SS) subunits along with an essential Rubisco accumulation factor, Raf1, leads to faster growth, increased photosynthesis, and enhanced chilling tolerance in maize (Zea mays). Maize also requires Rubisco accumulation factor2 (Raf2) for full accumulation of Rubisco. Here we have analyzed transgenic maize lines with increased expression of Raf2 or Raf2 plus LS and SS. We show that increasing Raf2 expression alone had minor effects on photosynthesis, whereas expressing Raf2 with Rubisco subunits led to increased Rubisco content, more rapid carbon assimilation, and greater plant height, most notably in plants at least 6 weeks of age. The magnitude of the effects was similar to what was observed previously for expression of Raf1 together with Rubisco subunits. Taken together, this suggests that increasing the amount of either assembly factor with Rubisco subunits can independently enhance Rubisco abundance and some aspects of plant performance. These results could also imply either synergy or a degree of functional redundancy for Raf1 and Raf2, the latter of whose precise role in Rubisco assembly is currently unknown.

  PublisherDOI

• Revolutionizing academic hiring: a faculty cluster hire emphasizing teamwork

  Trends in Plant Science · 2024-08-01

  article1st authorCorresponding
  PublisherDOI

• Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop “Inclusivity in the Plant Sciences”

  Plant Direct · 2022-08-01 · 11 citations

  articleOpen accessSenior authorCorresponding

  A future in which scientific discoveries are valued and trusted by the general public cannot be achieved without greater inclusion and participation of diverse communities. To envision a path towards this future, in January 2019 a diverse group of researchers, educators, students, and administrators gathered to hear and share personal perspectives on equity, diversity, and inclusion (EDI) in the plant sciences. From these broad perspectives, the group developed strategies and identified tactics to facilitate and support EDI within and beyond the plant science community. The workshop leveraged scenario planning and the richness of its participants to develop recommendations aimed at promoting systemic change at the institutional level through the actions of scientific societies, universities, and individuals and through new funding models to support research and training. While these initiatives were formulated specifically for the plant science community, they can also serve as a model to advance EDI in other disciplines. The proposed actions are thematically broad, integrating into discovery, applied and translational science, requiring and embracing multidisciplinarity, and giving voice to previously unheard perspectives. We offer a vision of barrier-free access to participation in science, and a plant science community that reflects the diversity of our rapidly changing nation, and supports and invests in the training and well-being of all its members. The relevance and robustness of our recommendations has been tested by dramatic and global events since the workshop. The time to act upon them is now.

  PublisherDOI

• Rubisco production in maize mesophyll cells through ectopic expression of subunits and chaperones

  Journal of Experimental Botany · 2021-04-26 · 7 citations

  articleOpen accessSenior authorCorresponding

  C4 plants, such as maize, strictly compartmentalize Rubisco to bundle sheath chloroplasts. The molecular basis for the restriction of Rubisco from the more abundant mesophyll chloroplasts is not fully understood. Mesophyll chloroplasts transcribe the Rubisco large subunit gene and, when normally quiescent transcription of the nuclear Rubisco small subunit gene family is overcome by ectopic expression, mesophyll chloroplasts still do not accumulate measurable Rubisco. Here we show that a combination of five ubiquitin promoter-driven nuclear transgenes expressed in maize leads to mesophyll accumulation of assembled Rubisco. These encode the Rubisco large and small subunits, Rubisco assembly factors 1 and 2, and the assembly factor Bundle sheath defective 2. In these plants, Rubisco large subunit accumulates in mesophyll cells, and appears to be assembled into a holoenzyme capable of binding the substrate analog CABP (carboxyarabinitol bisphosphate). Isotope discrimination assays suggest, however, that mesophyll Rubisco is not participating in carbon assimilation in these plants, most probably due to a lack of the substrate ribulose 1,5-bisphosphate and/or Rubisco activase. Overall, this work defines a minimal set of Rubisco assembly factors in planta and may help lead to methods of regulating the C4 pathway.

  PublisherOA PDFDOI

• Plant Summit 2019

  2020-02-25

  reportOpen access1st authorCorresponding

  The Plant Science Research Network organized the Plant Summit 2019, which took place February 10-13, 2019 at Biosphere 2 (Oracle, AZ). The Summit brought together plant scientists from many quarters, including stakeholders from academic institutions, government, nonprofits, and private industry with a broad range of experience in plant science research and education. Participants were guided through a facilitated workshop to review and assess the outcomes from previous PSRN workshops on cyberinfrastructure, postgraduate training, broadening participation, and future scenarios. An outcome of the Summit is the development of a report, “The Plant Science Decadal Vision (2020-2030): Reimagining the Potential of Plants for a Healthy Future.” The Decadal Vision frames societally vital, exciting and far-reaching research challenges as being necessary and deeply interwoven with human and technical resources. An Executive Summary of that report is provided.

  PublisherOA PDFDOI

• CFM1, a member of the CRM‐domain protein family, functions in chloroplast group II intron splicing in <i>Setaria viridis</i>

  The Plant Journal · 2020-11-03 · 9 citations

  articleOpen accessSenior authorCorresponding

  The chloroplast RNA splicing and ribosome maturation (CRM) domain is a RNA-binding domain found in a plant-specific protein family whose characterized members play essential roles in splicing group I and group II introns in mitochondria and chloroplasts. Together, these proteins are required for splicing of the majority of the approximately 20 chloroplast introns in land plants. Here, we provide evidence from Setaria viridis and maize that an uncharacterized member of this family, CRM Family Member1 (CFM1), promotes the splicing of most of the introns that had not previously been shown to require a CRM domain protein. A Setaria mutant expressing mutated CFM1 was strongly disrupted in the splicing of three chloroplast tRNAs: trnI, trnV and trnA. Analyses by RNA gel blot and polysome association suggest that the tRNA deficiencies lead to compromised chloroplast protein synthesis and the observed whole-plant chlorotic phenotypes. Co-immunoprecipitation data demonstrate that the maize CFM1 ortholog is bound to introns whose splicing is disrupted in the cfm1 mutant. With these results, CRM domain proteins have been shown to promote the splicing of all but two of the introns found in angiosperm chloroplast genomes.

  PublisherOA PDFDOI

Recent grants

• Gene-specific and General RNA Regulators in Chloroplasts

  NSF · $432k · 2007–2011

• Activation of an Endoribonuclease by Non-intein Protein Splicing

  NSF · $445k · 2013–2016

• NIH Grant R01GM052560

  NIH · $380k · 1999

• RCN: The Coordinated Plant Science Research and Education Network

  NSF · $902k · 2015–2021

Frequent coauthors

• Amber M. Hotto

  Ithaca College

  44 shared

• Arnaud Germain

  Cornell University

  39 shared

• Benoît Castandet

  Université Paris Cité

  35 shared

• Zhangjun Fei

  Cornell University

  27 shared

• Katia Wostrikoff

  Sorbonne Université

  26 shared

• Gadi Schuster

  Technion – Israel Institute of Technology

  26 shared

• Karen L. Kindle

  Cornell University

  24 shared

• Thomas Bollenbach

  19 shared

Labs

• Stern LabPI

Education

• Ph.D., Biological Sciences

  Stanford University

• Other, Biochemistry

  Cambridge University