University of Hawai‘i at Manoa
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Last updated on Thursday, February 10, 2022     Make updates ->

Daniel  Jenkins

Name :

Daniel Jenkins

Title :

Dr.

Unit :

Department of Molecular Biosciences & BioEngineering

Address :

1955 East-West Rd. #218
                  Honolulu, HI 96822

Room :

St. John 511

Phone :

(808)781-1343

Fax :

(808)956-3542

E-mail :

danielje@hawaii.edu

Specialties :

Sensors and instrumentation, agricultural diagnostics; molecular testing; remote sensing for natural resource and invasive species management.

Professional Prep/Appointments :


Ph. D. Biological and Agricultural Engineering, University of California, Davis, CA, 2001.
M. Eng. Agricultural and Biological Engineering, Cornell University, Ithaca, NY, 1996.
B.S. Agricultural and Biological Engineering, Cornell University, Ithaca, NY, 1995.

Courses Taught:


BE 120 (Quantitative Biology; Spring 2011, Spring 2012)
BE 150 (Introduction to Biological Engineering; 2005 - 2010)
BE 350/350L (Modeling and Simulation of Dynamic Systems; 2003 - 2007)
BE 420 / EE 422 (Sensors and Instrumentation for Biological Systems; 2004 - present)
BE 606 (Instrumentation and Measurement; Spring 2016)
BE/MBBE 625 (Biological Instrumentation; 2005 - 2008, Spring 2018 - present)

Research Interests :


Portable Agricultural Diagnostics: Our laboratory has made significant impacts on developing technologies to facilitate low-cost agricultural diagnostics that can be applied in the field to detect plant disease and otherwise assess plant and animal health. These may also be useful for clinical diagnostics in developing countries operating under many of the resource constraints that generally face the agricultural industry- especially for highly contagious pathogens such as ebola (in humans) or foot and mouth disease (livestock) where transportation of infectious material away from the site of contamination is highly risky. Our lab has developed the first real-time molecular probe ("Assimilating Probes") for use in a truly single step molecular diagnostic reaction conducted under isothermal conditions. This technology has been licensed to the local start-up company Diagenetix Inc., which has also contracted our expertise to develop an extremely cost-effective handheld diagnostic device to conduct testing on-site, and information management software to manage and display the results intuitively. Our technologies are currently in use by a spectrum of agricultural industries for assessing disease risk as part of comprehensive management strategies to reduce pesticide use, control disease spread, and prevent introduction of contaminated materials into the food supply. We continue to work on technologies to integrate sample preparation on large statistically relevant agricultural and environmental samples for rapid enrichment and concentration into volumes suitable for rapid molecular assays.

Our lab has also been highly involved in several projects to develop tools to more effectively manage Hawaii's unique natural environment. For example, we have developed instrumentation and real-time map based interfaces to record critical data from manned aerial operations to find and eliminate incipient populations of weeds in extremely remote, rugged, and sensitive habitat in the Hawaiian islands, and are currently working on unmanned and distributed surveillance technologies to autonomously find invasive species to provide alerts of new introductions, or information to guide future control operations.

Recent Publications :


Peer Reviewed Publications

  1. Rodriguez, R., R. L. Perroy, J. K. Leary, and D. M. Jenkins. 2022. Direct Geolocation of Features by Humans and Artificial Intelligence in Unmanned Aircraft System Acquired Imagery for Operational Control of Invasive Plants in Sensitive Natural Habitats. Environmental Monitoring and Assessment (under review).
  2. Rodriguez, R., J. K. Leary, and D. M. Jenkins. 2022. Herbicide Ballistic Technology for Unmanned Aircraft Systems. Robotics. 11, 22 https://doi.org/10.3390/robotics11010022.
  3. Lee, B.-E., T. Kang, D. M. Jenkins, Y. Li, M. Wall, and S. Jun. 2022. A single-walled carbon nanotubes-based electrochemical impedance immunosensor for on-site detection of Listeria monocytogenes. Journal of Food Science. 87(1): 280-288. 10.1111/1750-3841.15996
  4. Rodriguez, R., R. L. Perroy, J. K. Leary, D. M. Jenkins, M Panoff, T. Mandel, and P. Perez. 2021. Comparing interpretation of high-resolution aerial imagery by humans and Artificial Intelligence to detect an invasive tree species. Remote Sensing 13(17):3503. 10.3390/rs13173503
  5. Jenkins, D.M., Watanabe, S., Haff, R.P., Melzer, M.J., Jackson, E., Liang, P.-S., 2021. Dose response of coconut rhinoceros beetle (Coleoptera: Scarabaeidae) to 92 kV x-ray irradiation. J. Appl. Entomol. 145, 1039–1049. https://doi.org/10.1111/jen.12930
  6. Domingo, R., C. Perez, D. Klair, H. Vu, A. Candelario-Tochiki, X. Wang, A. Camson, J. N. Uy, M. Salameh, D. Arizala, S. Dobhal, G. Boluk, J.-P. Bingham, F. Ochoa-Corona, M. E. Ali, J. P. Stack, J. Fletcher, J. Odani, D. M. Jenkins, A. M. Alvarez, and M. Arif, M. 2021. Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil. Sci. Rep. 11, 21948. https://doi.org/10.1038/s41598-021-01196-4
  7. Diaz, L. M., B. E. Lee, and D. M. Jenkins. 2021. Real-time optical analysis of a colorimetric LAMP assay for SARS-CoV-2 in saliva with a handheld instrument improves accuracy compared to endpoint assessment. Journal of Biomolecular Techniques. 32(3): 158–171. https://doi.org/10.7171/jbt.21-3203-011.
  8. Diaz, L. M., Y. Li, and D. M. Jenkins. 2021.  Chemical stabilization of Escherischia coli 25922 for enhanced recovery with a handheld electroflotation system and detection by loop-mediated isothermal amplification. PLoS One 16(1) e0244956. 10.1371/journal.pone.0244956
  9. McLamore, E. S., E. Alocilja, C. Gomes, S. Gunasekaran, D. M. Jenkins, Y. Li, Y. Mao, S. R. Nugen, J. Reyes-de-Corcuera, P. Takhistov, O. Tsyusko, J. P. Cochran, T-R. Tzeng, J-Y. Yoon, C. Yu, and A. Zhou. 2021. Feast of Biosensors: Food, Environment, Agriculture, Science, and Technology for Biosensing in North America. Biosensors and Bioelectronics 178:113011. 10.1016/j.bios.2021.113011
  10. McLamore, E., S. P. A. Datta, V. Morgan, N. Cavallaro, G. Kiker, D. M. Jenkins, Y. Rong, C. Gomes, J. Claussen, D. Vanegas, and E. Alocilja. 2019. SNAPS: Sensor Analytics Point Solutions for detection and decision support systems. Sensors 19(22): 4935. 10.3390/s19224935
  11. Jenkins, D. M., B. E. Lee, S. Jun, J. Reyes-de-Corcuera, and E. S. McLamore. 2019. ABE-Stat, a fully open-source and versatile wireless potentiostat project including electrochemical impedance spectroscopy. Journal of the Electrochemical Society 166(9): B3056-B3065. 10.1149/2.0061909jes
  12. Diaz, L., Y. Li, R. Kubota, and D. M. Jenkins. 2019. Characterization of a portable, non-instrumented incubator for enrichment of Escherischia coli O157:H7 and Salmonella  serovar Typhimurium and detection by Loop Mediated Isothermal Amplification (LAMP). Food Protection Trends 39(1): 40-50.
  13. Larrea-Sarmiento, A., U. Dhakal, G. Boluk, L. Fatdal, A. Alvarez, A. Strayer, M. Paret, J. Jones, D. M. Jenkins, and M. Arif. 2018. Development of a genome-informed loop mediated isothermal amplification assay for rapid and specific detection of Xanthomonas euvesicatoria. Scientific Reports 8:14298.  10.1038/s41598-018-32295-4
  14. Jenkins, D. M. and R. Kurasaki. 2018. ABE-VIEW: Android interface for wireless data acquisition and control. Sensors 18(8): 2647. 10.3390/s18082647
  15. Diaz, L., D. M. Jenkins, Y. Li, T. McNealy, N. Walter, and R. Kubota. 2018. Electroflotation of Escherichia coli improves detection rates by Loop-mediated isothermal amplification. Transactions of the American Society of Agricultural and Biological Engineers  61(4): 1209-1220.
  16. Rodriguez, R., D. M. Jenkins, J. K. Leary, K. Nolan, and B. V. Mahnken. 2018. Performance analysis of different grades of handheld GPS units in manned helicopter operations. IEEE Aerospace and Electronic Systems 33(10): 14-20.
  17. Rodriguez, R., J. K. Leary, D. M. Jenkins, and B. V. Mahnken. 2016. Herbicide Ballistic Technology: spatial tracking analysis of operations characterizing performance of target treatment. Transactions of the ASABE 59(3): 803-809.
  18. Rodriguez, R., D. M. Jenkins, and J. Leary. 2015. Design and validation of a GPS logger system for recording aerially-deployed herbicide ballistic technology operations. IEEE Sensors 15(4): 2078-2086.
  19. Kubota, R. and D. M. Jenkins. 2015. Real-time multiplex applications of Loop Mediated AMPlification by Assimilating Probes. International Journal of Molecular Sciences. 16(3), 4786-4799.
  20. Keremane, M. L., C. Ramadugu, E. Rodriguez, R. Kubota, S. Shibata, D. G. Hall, M. L. Roose, D. M. Jenkins, and R. F. Lee. 2015. A rapid field detection system for citrus huanglongbing associated 'Candidatus Liberibacter asiaticus' from the psyllid vector, Diaphorina citri Kuwayama and its implications in disease management. Crop Protection 68:41-48.
  21. Jenkins, D. M., J. Jones, and R. Kubota. 2014. Evaluation of portable DNA-based technologies for identification of Ralstonia solanacearum race 3 biovar 2 in the field. 2014. Biological Engineering Transactions 7(2):83-96.
  22. Yasuhara-Bell, J. H., R. Kubota, D. M. Jenkins, and A. M. Alvarez. 2013. Loop-mediated amplification of the Clavibacter michiganensis subsp. michiganensis micA gene is highly specific. Phytopathology. 103(12):1220-1226.
  23. Marrero, G., K. L. Schneider, D. M. Jenkins, and A. M. Alvarez. 2013. Phylogeny and classification of Dickeya based on multilocus sequence analysis. International Journal of Systematic and Evolutionary Microbiology. 63(9):3524-3539.
  24. Kubota, R., P. LaBarre, B. H. Weigl, and D. M. Jenkins. 2013. Molecular diagnostics in a teacup: non-instrumented nucleic acid amplification (NINA) for rapid, low cost detection of Salmonella enterica. Chinese Science Bulletin. 58(1):1-7.
  25. Jenkins, D. A., P. E. Kendra, N. D. Epsky, W. S. Montgomery, R. R. Heath, D. M. Jenkins, and R. Goenaga. 2012. Antennal responses of West Indian and Caribbean fruit flies (diptera: tephritidae) to ammonium bicarbonate and putrescine. Florida Entomologist. 95(1):28-34.
  26. Jenkins, D. M., R. Kubota, J. Dong, Y. Li, and D. Higashiguchi. 2011. Low-cost handheld device for sequence-specific real-time LAMP-based detection of Salmonella enterica. Biosensors and Bioelectronics 30(1):255-260.
  27. Kubota, R., P. LaBarre, J. Singleton, A. Beddoe, B. H. Weigl, A. M. Alvarez, and D. M. Jenkins. 2011. Non-Instrumented Nucleic Acid Amplification (NINA) for rapid detection of Ralstonia solanacearum race 3 biovar 2. Biological Engineering Transactions. 4(2):69-80.
  28. Kubota, R., A. M. Alvarez, and W.-W. Su, and D. M. Jenkins. 2011. FRET-based assimilating probe for sequence specific real-time monitoring of Loop Mediated isothermal AMPlification. Biological Engineering Transactions. 4(2):81-100.
  29. Yang, K., D. M. Jenkins, and W.-W. Su. 2011. Rapid concentration of bacteria using submicron magnetic ion exchangers for improving PCR-based multiplex pathogen detection. Journal of Microbiological Methods. 86(1):69-77.
  30. Kubota, R., M. A. Schell, G. D. Peckham, J. Rue, A. M. Alvarez, C. Allen, and D. M. Jenkins.  2011.  In silico genomic subtraction guides development of highly accurate, DNA-based diagnostics for Ralstonia solanacearum race 3 biovar 2 and blood disease bacterium.  Journal of General Plant Pathology. 77(3):182-193.
  31. Paret M. L., R. Kubota, D. M. Jenkins, and A. M. Alvarez. 2010. Survival of Ralstonia solanacearum race 4 in drainage water and soil, and detection with immunodiagnostic and DNA-based assays. HortTechnology.  20(3):539-548.
  32. Jenkins D. M.,  Song, C., S. Fares, H. Cheng, and D. Barrettino.  2009.  Disposable thermostated electrode for temperature dependent electrochemical measurements.  Sensors and Actuators, B- Chemical. 137(1):222-229.
  33. Kutin, R., A. Alvarez, and D. M. Jenkins.  2009.  Detection of Ralstonia solanacearum in natural substrates using phage amplification integrated with real-time PCR assay.  Journal of Microbiological Methods.  76(3):241-246.
  34. Teruel, M. J., D. M. Jenkins, and J. I. Reyes de Corcuera.  2009.  Crystallization of b-D-glucose and analysis with a simple glucose biosensorJournal of Chemical Education. 86(8):959-961.
  35. Fares, A., M. Safeeq, and D. M. Jenkins. 2009. Adjusting temperature and salinity effects on single capacitance sensors. Pedosphere. 19(5):588-596.
  36. Jenkins, D. M., M. J. Teruel, J. I. Reyes de Corcuera, and O. Young.  2008.  Simultaneous determination of hydrolysis and mutarotation rates during the enzymatic hydrolysis of lactose.  Journal of Agricultural and Food Chemistry. 56(18):8303-8308.
  37. Kutin, K., D. M. Jenkins, and D. Borthakur.  2008.  Characterization of a Corynebacterium strain that can grow in medium containing up to 2 M nitrate.  Bioremediation Journal.  12(3):168-172.
  38. Kubota, R., D. M. Jenkins, B. Vine, and A. Alvarez.  2008.  Detection of Ralstonia solanacearum by Loop-mediated isothermal AMPlification method (LAMP).  Phytopathology 98(9):1045-1051.
  39. Jenkins, D. M., C. Zhu, and W. Su.  2008.  A simple hybrid circuit for direct detection of fluorescence lifetimes.  Applied Engineering in Agriculture. 24(2):259-263.
  40. D. A. Jenkins, E. Diaz, R. Goenaga, and D. M. Jenkins.  2008.  Solar sterilization of abscised fruit: a cultural practice to reduce infestations of Anastrepha spp. around orchards.  The Journal of Agriculture of the University of Puerto Rico. 92:197-206.
  41. Fares, A., H. Hamdhani, and D. M. Jenkins.  2007.  Temperature Dependent Scaled Frequency to Improve the Accuracy of Multisensor Capacitance Probes.  Soil Science Society of America Journal.  71(3):894-900.
  42. Jenkins, D. M., B. Chami, M. Kreuzer, G. Presting, A. Alvarez, and B. Y. Liaw.  2006.  Hybridization probe for femtomolar quantification of selected nucleic acids on a disposable electrode.  Analytical Chemistry.  78(7):2314-2318.
  43. Jenkins, D. M.  2004.  Desorption as a rate limiting step for gas permeation through a polymer membrane.  Journal of Physical Chemistry, B.  108(50):19,325-19,329.
  44. Jenkins, D. M. & D. A. Jenkins.  2003.  Digital detector array for the study of non-specifically tagged bees and wasps.  Biosystems Engineering.  86(3):295-303.
  45. Jenkins, D. M. and M. J. Delwiche.  2003.  An immersible manometric sensor for measurement of humidity and enzyme mediated changes in dissolved gas.  Biosensors & Bioelectronics.  18(9):1085-1093. dfsd
  46. Jenkins, D. M. and M. J. Delwiche.  2003.  Adaptation of a manometric biosensor to measure glucose and lactose.  Biosensors & Bioelectronics.  18(1):101-107.
  47. Jenkins, D. M., M. J. Delwiche, E. J. DePeters, and R. H. BonDurant.  2002.  Factors affecting the application of on-line milk urea sensing.  Transactions of the ASAE.  45(5):1687-1695.
  48. Jenkins, D. M., M. J. Delwiche and R. W. Claycomb.  2002.  Electrically controlled sampler for milk component sensors.  Applied Engineering in Agriculture.  18(3):373-378.
  49. Jenkins, D. M. and M. J. Delwiche.  2002.  Manometric biosensor for on-line measurement of milk urea.  Biosensors & Bioelectronics.  17(6-7):557-563.
  50. Jenkins, D. M., M. J. Delwiche, E. J. DePeters, and R. H. BonDurant.  2000.  Refinement of the pressure assay for milk urea nitrogen.  Journal of Dairy Science.  83(9):2042-2048.
  51. Jenkins, D. M., M. J. Delwiche, E. J. DePeters, and R. H. BonDurant.  1999.  Chemical assay of urea for automated sensing in milk.  Journal of Dairy Science.  82(9):1999-2004.

Patents

  1. Sensor for components of a fluid (US Patent No. 6,287,851, awarded September 2001).
  2. Sensor for analyzing components of fluids(US Patent No. 6,733,984, awarded 2004).
  3. Disposable Electrode for Detection of Selected Nucleic Acid Sequences (disclosure, September 2005; utility patent filed September 2006).
  4. A simple, rapid, and inexpensive circuit for direct measurement of luminescent lifetimes (disclosure, October 2006).
  5. Automatic flush trigger for toilet-trained cats (utility patent filed January 2010).
  6. Real-time isothermal sequence specific detection of DNA with non-contact temperature controller (disclosed January 2010 - Utility patent filed June 2011/ PCT/US2011/041540).
  7. Sequence specific real-time monitoring of Loop Mediated Isothermal Amplification (LAMP). Disclosed June 2010. US application US61/357,428, international patents pending application WO2011163425A1)
  8. Real-time microalgae harvesting efficiency monitoring system(disclosed September 2013).
  9. Integrated global position system logging system for electro-pneumatic delivery applications (utility patent filed May 2014).
  10. Hardware and mobile software for operation of portable instruments for nucleic acid amplification (2019, US Patent 10,203,284).
  11. Method of detecting amplified nucleic acid molecules (2020, US Patent 10,830,702)
  12. Point-of-care electroflotation of dispersed, low tolerance pathogens (disclosed July 2018; utility patent application filed July 2019 206339-0007-00WO; US Patent App. 17/259,647 2021).


Languages :


English, Spanish