DAVID GRUBER, PhD

Phillips, B.T., Becker, K.P., Kurumaya, S., Galloway, K.C., Whittredge, G., Vogt, D., Teeple, C., Rosen, M.H., Pieribone, V.A., Gruber, D.F., and R.J. Wood. 2018. A Dexterous, Glove-Based Teleoperable Low-Power Soft Robotic Arm for Delicate Deep-Sea Biological Exploration, Scientific Reports 8:14779.

The development and application of a soft robotic arm to enable delicate deep-sea exploration from submarines and remotely operated vehicles.

Tessler, M., Gaffney, J.P., Crawford, J.M., Trautman, E., Gujarati, N.A., Alatalo, P., Pieribone, V.A. and D.F. Gruber. 2018. Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens. PeerJ 6:e5506 https://doi.org/10.7717/peerj.5506

The identification of novel luciferases from the exceptionally bright copepod, Metridia lucens, and confirmation it makes its own coelenterazine.

Vogt, D.M., Becker, K.P., Phillips, B.T., Graule, M.A., Rotjan, R.D., Shank, T.M., Cordes, E.E., Wood, R.J. and D.F. Gruber. 2018. Shipboard design and fabrication of custom 3D-printed soft robotic manipulators for the investigation of delicate deep-sea organisms. PLoS ONE 13(8): e0200386. https://doi.org/10.1371/journal. pone.0200386

3D printing of bespoke/custom soft robotic manipulators at sea greatly increases a marine biologist's effectiveness in delicately investigating novel and fragile deep-sea marine life.

Teoh, Z.E., Phillips, B.T., Becker, K., Whittredge, G., Weaver, J.C., Hoberman, C., Gruber, D.F. and R.J. Wood. 2018. Rotary-actuated folding polyhedrons for midwater investigation of delicate marine organisms. Science Robotics, 3, eaat5276.

A new device to safely enclose delicate sea creatures, such as jellyfish, inside a folding polyhedral enclosure and lets them go without harm. This uses a novel, folding rotary design that only requires one motor to operate. 

Kurumaya, S., Phillips, B.T., Becker, K.P., Rosen, M.H., Gruber, D.F., Galloway, K.C., Suzumori, K., and R.J. Wood. 2018. A Modular Soft Robotic Wrist for Underwater Manipulation. Soft Robotics, 5:399-409. 10.1089/soro.2017.0097.

This paper presents the development of modular soft robotic wrist joint mechanisms for delicate and precise manipulation in the harsh deep-sea environment.

D.F. Gruber, Phillips, B.T., Marsh, L., and J.S. Sparks. 2018. In situ Observations of the Meso-Bathypelagic Scyphozoan, Deepstaria enigmatica (Semaeostomeae: Ulmaridae). American Museum Novitates, 3900, 1-14.

Observations of a rarely seen and unique jellyfish, Deepstaria enigmatica at 3,195 feet and evidence that jelly-falls of this species can impact deep-sea biodiversity.

D.F. Gruber, Gaffney, J., and V.A Pieribone. 2018. Method for detecting bilirubin from a marine eel fluorescent protein. US Patent # US 9,952,227.

A method for detecting bilirubin that could aid medical research in areas such as hemolysis.

Verdes, A. and D.F. Gruber. 2017. Glowing Worms: Biological, Chemical, and Functional Diversity of Bioluminescent Annelids. Integrative and Comparative Biology, 57 (1): 18-32.

A comprehensive review on bioluminescent worms.

Galloway, K.C., Becker K.P., Phillips, B., Kirby J., Licht S., Tchernov, D., Wood, R.J., Gruber, D. F.  2016.  Soft Robotic Grippers for Biological Sampling on Deep Reefs.
Soft Robotics. doi:10.1089/soro.2015.0019.
(2016_Soft Robotic Grippers for Biological Sampling on Deep Reefs w cover.pdf)
The first underwater use of soft robotics for marine biological applications.

Gruber DF, Loew ER, Deheyn DD, Akkaynak D, Gaffney JP, Smith WL, Davis MP, Stern JH, Pieribone VA, Sparks JS. 2016.  Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology. Scientific Reports. doi: 10.1038/srep24751.
(2016_Gruber Biofluorescence in Catsharks)
(2016_David Gruber National Geographic Magazine.pdf)
The development of a “shark-eye” camera to study what biofluorescence may mean to sharks.

Phillips B, Gruber DF,  Vasan G, Roman CN, Pieribone V, Sparks JS. 2016. Observations of in situ deep-sea marine bioluminescence with a high-speed, high-resolution sCMOS camera. Deep Sea Research Part I: Oceanographic Research Papers. 111:102-109.
(2016_Observations of in situ deep-sea marine bioluminescence with a high-speed high-resolution sCMOS camera)
The use of a extremly sensitive low-light camera to study deep sea bioluminescence.

Phillips, B.T., D.F. Gruber, G. Vasan, V.A. Pieribone, J.S. Sparks, and C.N. Roman. 2016. First evidence of bioluminescence on a “black smoker” hydrothermal chimney. Oceanography 29(2):10–11, http://dx.doi.org/10.5670/oceanog.2016.27.

(2016_First Evidence of Bioluminescence on a “Black Smoker” Hydrothermal Chimney.pdf)
The first observation of bioluminescence on a “Black Smoker” Hydrothermal Chimney

Einbinder, S., Gruber, D.F., Solomon, E., Keren, N., Tchernov, D. 2016. “Novel adaptive photosynthetic characteristics of mesophotic symbiotic microalgae within the reef-building coral, Stylophora pistillata.” Frontiers in Marine Science. doi: 10.3389/fmars.2016.00195.
(2016_Novel Adaptive Photosynthetic Characteristics of Mesophotic Symbiotic Microalgae within the Reef-Building Coral)
A new type of photosynthesis invented by algae on the deep coral reef.

Bhattacharya, D., S. Agrawal, M. Aranda, S. Baumgarten, M. Belcaid, J.L. Drake, D. Erwin, S. Foret, R.D. Gates, D.F. Gruber, B. Kamel, M.P. Lesser, O. Levy, Y.J. Liew, M. MacManes, T. Mass, M. Medina, S. Mehr, E. Meyer, D.C. Price, H.M. Putnam, H. Qiu, C. Shinzato, E. Shoguchi, A.J. Stokes, S. Tambutte, D. Tchernov, C.R. Voolstra, N. Wagner, C.W. Walker, A.P. Weber, V. Weis, E. Zelzion, D. Zoccola, and P.G. Falkowski. 2016. “Comparative Genomics Explains the Evolutionary Success of Reef-Forming Corals.” eLife 5. doi:10.7554/eLife.13288.
(2016_Comparative genomics explains the evolutionary success of reef-forming corals.pdf)

A comprehensive analysis of coral genomics.

Gruber, D.F. and J.S. Sparks. First Observation of Fluorescence in Marine Turtles. 2015. American Museum Novitates. 3845:1-8.

The discovery of a biofluorescent Hawsbill sea turtle made on a TBA-21 Academy Expedition in the Solomon Islands.

Dishon, G., Fisch, J., Horn, I., Kaczmarek, K., Bijma, J., Gruber, D.F., Nir, O., Popovich, Y. and D. Tchernov. 2015. A novel paleo-bleaching proxy using boron isotopes and high-resolution laser ablation to reconstruct coral bleaching events, Biogeosciences, 12, 5677-5687.
2015_Novel paleo-bleaching proxy using boron isotopes

A new method to look for coral bleaching events from thousands of years ago.

D. F. Gruber, J.P. Gaffney, S. Mehr, J.S. Sparks, J. Platisa, V.A. Pieribone. 2015. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment, PLoS ONE. 10(11): e0140972. doi:10.1371/journal.pone.0140972.

The discovery of a new family of fluorescent proteins from marine eels

Mehr, S.F.M., Verdes, A., DeSalle, R., Sparks, J., Pieribone, V. and D. F. Gruber. 2015. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)”, BMC Genomics, 16:445.

The most comprehensive genomic analysis of the Bearded Fireworm. This is also the first report of biofluorescence in this stinging species.

Sparks, J. S., Schelly, R. C., Smith, W. L., Davis, M. P., Tchernov, D., Pieribone, V. A., and D. F. Gruber. 2014. The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon. PLoS ONE 9(1): e83259.

The discovery of over 180 new species of biofluorescent fish and sharks.

Gruber, D.F., Kao, H-T and V.A. Pieribone. 2014. Isolated australian coral reef fluorescent proteins and cell-based kinase or phosphatase platforms for cancer drug development, US Patent # US 8,709,981.

A patent based on a novel fluorescent protein from the Great Barrier Reef that can be developed into a sensor to find better cancer drugs.

Nir, O., Gruber, D.F., Glasser, E., Shemesh, E. and D. Tchernov. 2014. Seasonal mesophotic coral bleaching of Stylophora pistillata in the northern Red Sea, PLoS ONE 9(1): e84968. doi:10.1371/journal.pone.0084968.

A study showing that the deep reef undergoes seasonal coral bleaching events.

Tchernov, D., Irwin, A. and D. F. Gruber. 2014. Isotopic fractionation of carbon in the coccolithophorid Emiliania huxleyi, Marine Ecological Progress Series 508:53-66.

A study that assists with paleo-reconstruction of ocean climate data.

Olden, K., Lin, Y-S, D. F. Gruber and B. Sonawane. 2014. Epigenome: Biosensor of Cumulative Exposure to Chemical and Nonchemical Stressors Related to Environmental Justice, American Journal of Public Health, 104(10):1816-1821.

A summary of how environmental quality impacts the human epigenome.

Rubin-Blum, M., Tsadok, R., Shemesh, E., Goodman-Tchernov, B. N., Austin, J. A., Coleman, D. F. Gruber. (2014). Distribution of the Lamellibrachia spp. (Siboglinidae, Annelida) and their trophosome endosymbiont phylotypes in the Mediterranean Sea. Mar. Biol. 161, 1229–1239. doi:10.1007/s00227-014-2413-y.

This study used the Hercules Remotely Operated Vehicle to show how a deep sea tube worm is distributed along the bottom of the Mediterranean Sea.

Mehr, S.F.M., DeSalle, R., Kao, H-T, Narechania, A., Han, Z., Tchernov, D., Pieribone, V. and D. F. Gruber. 2013. De novo RNA-seq assembly and clustering of expressed proteins from uncharacterized corals, BMC Genomics 14:546.

The use of transcriptomics to discover several new fluorescent proteins from a mesophotic coral.

Sparks, J. S., Gruber, D.F. 2012. A new mesophotic clingfish (Teleostei: Gobiesocidae) from the Bahamas. Copeia. 2:251-256.

A new species of clingfish found at 286 feet deep.

Gruber, D.F, Mass, T., Tchernov, D. 2012. Symbiotic Transition of Algae-Coral Triggered by Paleo-Climatic Events? Trends in Ecology and Evolution, 27(4), 194-195.

A hypothesis that low oxygen concentrations following a major mass extinction event helped forge the symbiotic relationship between coral and algae.

Nir, O., Gruber, D.F., Einbinder, S. Kark, S., and D. Tchernov. 2011. Changes in scleractinian coral Seriatopora hystrix morphology and its endocellular Symbiodinium characteristics along a bathymetric gradient from shallow to mesophotic reef, Coral Reefs. 30:1089-1100.

How the composition of algal inside a coral shifts as they descend into the deep reef.

Ilagan, R. P., Rhoades, E., Gruber, D. F., Kao, H.-T., Pieribone, V. A., and Regan, L. 2010. A new bright green-emitting fluorescent protein – engineered monomeric and dimeric forms. FEBS J. 277: 1967-1978.

One of the brightest fluorescent proteins discovered from coral.

Kao, H.-T., Buka, S.L., Kelsey, K.T., Gruber, D.F., Porton, B. 2010. The correlation between rates of cancer and autism: an exploratory ecological investigation. PLoS One. Feb 23; 5: e9372.

One of the first studies to form a connection between mutations associated in reproductive cancers and autism.

Kuguru, B., Achituv, Y., Gruber, D.F. and D. Tchernov. 2010. Photoacclimation mechanisms of corallimorpharians on coral reefs: Photosynthetic parameters of zooxanthellae and host cellular responses to variation in irradiance, J. Exp. Mar. Biol. Ecol. 394:53-62.

How algae and corals coral respond changes in sunlight.

Gruber, D.F., DeSalle, R., Lienau, E.K., Tchernov, D., Pieribone, V.A. and H-T Kao. 2009. Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns, Molecular Biology and Evolution. 26(12):2841-2848. (Highlighted in: Oct 1, 2009 Nature 461:572)

The discovery of 18 new fluorescent proteins – and the finding that an internal region of the fluorescent protein molecule has undergone divergent evolution.

Gruber, D.F. 2009. Three’s Company: The Tripartite Synapse, Nature Medicine 15:232-235.

Glia, once a backwater of neuroscience, takes center stage.

Gruber, D.F., Tuorto, S. and G.L. Taghon. 2009. Growth Phase and Elemental Stoichiometry of Bacterial Prey Influences Ciliate Grazing Selectivity, Journal of Eukaryotic Microbiology. 56(5):466-71.

The use of fluorescent proteins to show that protozoa preferentially consume slower growing bacteria

Gruber, D. 2008. Preliminary studies find DNA erosion in mental disorders, Nature Medicine 12:1295.

elomere erosion rates are associated with schizophrenia. This may help find a biological test for certain mental disorders.

Gruber, D.F., Kao, H.-T., Janoschka, S., Tsai, J., and V.A. Pieribone. 2008.  Patterns of fluorescent protein expression in Scleractinian corals.  Biol. Bull. 215:143–154.

Biofluorescence reported in 28 new species of coral; and correlations drawn between patterns.

Gruber, D.F., Pieribone, V.A., Porton, B., Kao, H.-T. 2008. Strict regulation of gene expression from a high-copy plasmid utilizing a dual vector system.  Protein Expr. Purif. 60:53-57.

A new molecular biology technique for those looking to regulate gene expression in high copy plasmids.

Kao, H.-T., Sturgis, S., DeSalle, R., Tsai, J., Davis, D., Gruber, D. F., Pieribone, V.A. 2007. Dynamic regulation of fluorescent proteins from a single species of coral.  Mar. Biotechnol. 9: 733-746.

Real-time PCR draws correlations of fluorescent protein expression with depth of the coral.

Gruber, D.F., Simjouw, J-P. Seitzinger, S.P. and G. L. Taghon. 2006. Dynamics and Characterization of Refractory Dissolved Organic Matter Produced by a Pure Bacterial Culture in an Experimental Predator-Prey System. Applied and Environmental Microbiology 72(6): 4184-4191.

How the predator-prey relationship of bacteria and protozoa impacts the production of refractory carbon in the ocean.

Pieribone, V., and D. F. Gruber. 2006. Aglow in the Dark: The Revolutionary Science of Biofluorescence.  Harvard University Press, Cambridge, MA.  288 pp.
NO PDF AVAILABLE
A journalistic narrative of the discovery of fluorescent proteins. Those profiled in the study were awarded the Nobel Prize for Chemistry two years after publication.

Nasar, S. and Gruber, D. 2006. Manifold Destiny. The New Yorker, Aug. 28 issue, p. 44-57. (Also included in The Best American Science Writing 2007, Harper Perennial).

A 10,000 word investigative piece on the solution to the Poincare Conjecture by Gregori Perelman. This article led to the retraction of a compering article that claimed to provide the complete proof.