Jonathan Arnold

Professor
Ph.D. (1982) Yale University
  • Member, NIH study section (Genetic Variation and Evolution), 2005-2008
  • Fellow, American Association for the Advancement of Science
  • Grant Support -
    • "Collective Behavior of Cellular Oscillators", NSF
    • "Measuring and Modeling how Clocks in Single Cells Communicate: an Interdisciplinary Approach," NSF
    • "Systems Analysis of the Beneficial Associations of Sorghum with Arbuscular Mycorrhizal Fungi...," DOE
    • “Genomics and Computational Biology: an REU Site,” NSF
    • "Finding virulence genes as therapeutic targets in Covid-19", NSF
    • “ALICE, Adaptive Learning for Interdisciplinary Collaborative Environments," NSF
    • “Population-based Multidisciplinary Study of Centenarians,” NIH
  • Research Interests -
    • My research involves work on identifying gene regulatory and biochemical networks for fundamental biological processes in fungal systems and validating these biological circuits by fitting them to genomics data in single cells. Since the discovery of the structure of DNA, biologists have been taking apart living systems on a finer and finer scale until we have been able to determine the complete genetic blueprint of many organisms. The challenge of the new millennium is "reassembling the pieces", i.e., moving from genomes to life. One approach to reassembling the pieces is to borrow a metaphor from computer science: the entire chemical reaction network describing what a cell does is a biological circuit. The theme for the genomics and computational biology part of my research is “computing life”, i.e., identifying biological circuits for fundamental processes like fungal/plant symbioses and the biological clock and validating these biological circuits by fitting them to genomics data describing what the cell is doing (i.e., RNA and protein profiling data).
Research Areas:
Genomics and Bioinformatics
Research Interests:

Evolutionary genomics and systems biology: identifying gene regulatory and biochemical networks for biological processes

Selected Publications:
  • Montenegro, T. D. P., S. Kleindienst, A. E. Allen, A. M. Eren, J. McCrow, J. D. S. Calderon, J. Arnold, & S. B. Joye 2023. Species-specific responses of marine bacteria to environmental perturbation.  ISME Communications 3, 99, https://doi.org/10.1038/s43705-023-00310-z
  • Liu, Liang, Lili Yu, Shaoyuan Wu, Jonathan Arnold, Christopher Whalen, Charles Davis, & Scott V. Edwards (2023).  Short branch attraction in phylogenomic inference under the multispecies coalescent.  Frontiers Ecology and Evolution 11, doi:10.3389/fevo.2023.1134764  https://www.frontiersin.org/articles/10.3389/fevo.2023.1134764/full
  • Jialin Yang, J., Michael Skaro, M.,  Jiani Chen, J., Duna Zhan, D., Lyu, L., Gay, S., Ahmed Kandeil, A.,  Ali, M. A., Kayali, G., Stoianova, K., Ji, P., Alabady, M., Bahl, J., Liu, L.,  & J. Arnold (2023). The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic.  Scientific Reports 13: 5571 https://rdcu.be/c9dtc
  • Al-Omari, A. M., Tawalbeh, S. M.,  Akkam, Y. H., Al-Tawalbeh, M.  Younis, S. Abdullah A. Mustafa, A. A. & J. Arnold (2023).  Big Data Bot with a Special Reference to Bioinformatics. Computers, Materials & Continua 2023, 75(2), 4155-4173. https://doi.org/10.32604/cmc.2023.036956 
  • Wu, Y., M. T. Judge, A. S. Edison, & J. Arnold (2022).  Uncovering in vivo biochemical patterns from time-series metabolic dynamics.  PLoS ONE 17(5): e0268394. https://doi.org/10.1371/journal.pone.0268394.
  • Al-Omari, A. M., J. Griffith, A. Scruse, R. W. Robinson, H.-B. Schuttler, & J Arnold (2022). Ensemble methods for identifying RNA operons and Regulons in the Clock Network of Neurospora crassa.  IEEE Access 10: 32510-32524 , doi:10.1109/ACCESS.2022.3160481. https://ieeexplore.ieee.org/document/9737535
  • Cheong, J. W., X. Qiu, Y. Liu, A. Al-Omari, J. Griffith, H.-B. Schuttler, L. Mao, & J. Arnold (2022). The macroscopic limit to synchronization of cellular clocks in single cells of Neurospora crassa. Nature Scientific Reports 12, 6750, https://doi.org/10.1038/s41598-022-10612-2
  • Krach, E., M. Skaro, Y. Wu, & J. Arnold (2022).  Characterizing the gene-environment interaction underlying natural morphological variation in Neurospora crassa conidiophores using high-throughput phenomics and transcriptomics.  G3, https://doi.org/10.1093/g3journal/jkac050
  • Skaro, M.S., M. Hill, Y. Zhou, S. Quinn, M. Davis, L. Cai, A. Sboner, M. Murph, and J. Arnold (2021). Are we there yet? A machine learning architecture to predict organotropic metastases.  BMC Medical Genomics 14, 281, https://doi.org/10.1186/s12920-021-01122-7
  • Krach, E., Y. Wu, M. Skaro, L. Mao, & J. Arnold 2020. Wild isolates of Neurospora crassa reveal three conidiophore architectural phenotypes. Microorganisms 8: 1760 https://www.mdpi.com/2076-2607/8/11/1760
  • Caranica, C., A. Al-Omari, H.-B. Schuttler, & J. Arnold 2020.  A clock stochastic network with light entrainment is identified for single cells of Neurospora crassa by ensemble methods.  Nature Scientific Reports 10, 15168,  https://doi.org/10.1038/s41598-020-72213-1
  • Wu, Y., M. T. Judge, J. Arnold, S. M. Bhandarkar, & A. S. Edison 2020. RTextract: Time-series NMR spectra quantification based on 3D surface ridge tracking, Bioinformatics, https://doi.org/10.1093/bioinformatics/btaa631
  • Deng, Z., J. H. Cheong, C. Caranica, L. Wu, X. Qiu, M. Judge, B. Hull, C. Rodriguez, J. Griffith, A. Al-Omari, S. Arsenault, H.-B. Schuttler, L. Mao, & J. Arnold 2019.  Single cells of Neurospora crassa show circadian oscillations, light entrainment, temperature compensation, and phase synchronization.  IEEE Access 7, 49403-49417, DOI (identifier) 10.1109/ACCESS.2019.2910731
  • Judge, M. T., Y. Wu, F. Tayyari, J. Glushka, T. Ito, J. Arnold, & A. Edison 2019.  Untargeted, real-time metabolomics of single and multicellular organisms.  Frontiers Molecular Biosciences|Metabolomics 6, doi: 10.3389/fmolb.2019.00026
  • Al-Omari, A. D., J. Griffith, C. Caranica, T. Taha, H.-B. Schuttler & J. Arnold 2018.  Discovering regulators in post transcriptional control of the biological clock of Neurospora crassa using Variable Topology Ensemble Methods on GPUs.  IEEE Access 6, doi:10.1109/ACCESS.2018.2871876
  • Caranica, C, A D Al-Omari, Z Deng, J Griffith, R Nilsen, L Mao, J Arnold, and H-B Schuttler 2018.  Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa, PLoS ONE 13(5):e0196435
  • Deng, Z, S Arsenault, C Caranica, J Griffith, T Zhu, A Al-Omari, H-B Schuttler, J Arnold, & L Mao 2016. Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa, Scientific Reports 6, 35828, DOI: 10.1038/srep35828, www.nature.com/articles/srep35828
  • Al-Omari, A, J Griffith, M Judge, T Taha, J Arnold, & H-B Schuttler 2015. Discovering regulatory network topologies using ensemble methods on GPGPUs with special reference to the biological clock of Neurospora crassa, IEEE Access 3, 27-42, DOI 10.1109/ACCESS.2015.2399854, http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=7029612&queryText%3Ddiscovering+regulatory+network+topologies+with+ensemble+methods
  • Bouffier, A. M., J. Arnold, & H-Bernd Schuttler 2014. A MINE alternative to D-optimal designs for the linear model. PLoS ONE 9(10): e110234 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110234
  • Case, ME, J Griffith, W Dong, I Tigner, K Gaines, JC Jiang, SM Jazwinski & J Arnold for the Georgia Centenarian Study 2014. The aging biological clock in Neurospora crassa, Ecology & Evolution 4, 3494-3507, http://onlinelibrary.wiley.com/doi/10.1002/ece3.1202/full
  • Al-Omari, A., H.-B. Schuttler, J. Arnold and T. Taha. 2013. Solving nonlinear systems of first order differential equations using a Galerkin finite element method. IEEE Access 1(1): 408-417. DOI 10.1109/ACCESS.2013.2269192
  • Tang, X., W. Dong, J. Griffith, R. Nilsen, A. Mathes, K.B. Cheng, J. Reeves, H.-B. Schuttler, M.E. Case, J. Arnold and D.A. Logan 2011. Systems biology of the qa gene cluster of Neurospora crassa. PLoS ONE 6: e20671.
  • Aleman-Meza, B., Y. Yu, H.-B. Schuttler, J. Arnold and T.R. Taha. 2009. KINSOLVER: a simulator for computing large ensembles of biochemical and gene regulatory networks.  Computers and Mathematics with Applications, doi:10.1016/j.camwa.2008.10.086.
  • Tewari, S., J. Arnold and S.M. Bhandarkar. 2008.  Likelihood of a particular order of genetic markers and the construction of genetic maps. Journal of Bioinformatics and Computational Biology 6: 125-162.
  • Dong, W., X. Tang, Y. Yu, R. Nilsen, J. Griffith, R. Kim, J. Arnold, and H.-B. Schuttler. 2008. Systems biology of the clock in Neurospora crassa. PLoS ONE 3: e3105.
  • Dai, J., L. Li, S. Kim, B. Kimball, M. Jazwinski, and J. Arnold. 2007. Exact sample size needed to detect dependence in 2 x 2 x 2 tables. Biometrics 63: 1245-1253.
  • Tewari, S., S.M. Bhandarkar and J. Arnold. 2007. Design and analysis of an efficient recursive linking algorithm for constructing likelihood based genetic maps for a large number of markers. Journal of Bioinfomatics and Computational Biology 5: 201-250.
  • Yu, Y., W. Dong, C. Altimus, X. Tang, J. Griffith, M. Morello, L. Dudek, J. Arnold, and H.-B. Schuttler. 2007. A genetic network for the clock of Neurospora crassa. PNAS USA 104: 2809-2814.
  • Cushion, M.T., A.G. Smulian, B.E. Slaven, T. Sesterhenn, J. Arnold, C. Staben, A. Porollo, R. Adamczyk and J. Meller. 2007. Transcriptome of Pneumosystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite. PloS ONE 2: e423.
  • Tewari, S., J. Arnold and S.M. Bhandarkar. 2006. "Efficient Recursive Linking Algorithm for Computing the Likelihood of an Order of a Large Number of Genetic Markers" Proc. of the IEEE LSS Computational Systems Bioinformatics Conference (CSB 2006), Aug. 14-18, 2006, Stanford University, Palo Alto, CA., P. Markstein and Y. Xu (eds), Imperial College Press, London, pp. 191-198.
  • Sanchez, M.S., C.J. Basten, A.M. Ferrenberg, M.A. Asmussen, and J. Arnold. 2006. Exact sample sizes needed to detect dependence in 2 x 3 tables. Theoretical Population Biology 69: 111-120.
  • Icenhour, C.R., J. Arnold, M. Medvedovic, and M.T. Cushion. 2006. Competitive coexistence of two Pneumocystis species. Infection, Genetics, and Evolution 6: 177-186.
  • Dai, J., A. Davey, I.C. Siegler, J. Arnold, and L.W. Poon. 2006. GCSDB: an integrated database system for the Georgia Centenarian Study. Bioinformation 1: 214-219.
  • Bhandarkar, S.M., J. Huang, and J. Arnold. 2006. An Information theoretic approach to genome reconstruction. Chapter 11 in Handbook of Computational Molecular Biology. 11-1-11-26 CRC Press, Boca Raton, FL.
  • Arnold, J., W. Dong, J. Griffith, D. Choi, J. Baldwin, L. Hilton, K. Kelps, J. McGuire, R. Morgan, M. Smith, Q. Wang, J. Liu, J. Reeves, D.A. Logan, M.E. Case, and H.-B. Schuttler. 2006. Systems Biology of the Biological Clock. IEEE Proceedings of the First International Conference on Computational Systems Biology (ICCSB-2006), pp. 119-125.
  • Xiong, M. and J. Arnold. 2006. Do genetic networks obey Kirchhoff’s and Ohm’s Laws? Proc. IASTED International Conf. on Comp. & Systems Biology, Dallas, TX, November 13-14, 2006, pp. 13-19.
  • Lott, T.J., R.E. Fundyga, R.J. Kuykendal, and J. Arnold. 2005. The human commensal yeast, Candida albicans, has an ancient origin. Fungal Genetics and Biology 42: 444-451.
  • Strobel, G.L. and J. Arnold. 2004. Essential eukaryotic core. Evolution 58: 441-446.
  • Arnold, J. H.-B. Schuttler, D. Logan, D. Battogtokh, J. Griffith, B. Arpinar, S. Bhandarkar, S. Datta, K.J. Kochut, E. Kraemer, J.A. Miller, A. Sheth, G. Strobel, T. Taha, B. Aleman-Meza, J. Doss, L. Harris and A. Nyong. 2004. Metabolomics. In: Handbook of Industrial Mycology. Marcel Dekker, NY, NY.
  • Xu Z., B. Lance, C. Vargas, B. Arpinar, S. Bhandarkar, E. Kraemer, K.J. Kochut, J.A. Miller, J.R. Wagner, M.J. Weise, J.K. Wunderlich, J. Stringer, G. Smulian, M.T. Cushion and J. Arnold. 2003. Mapping by sequencing the pneumocystis genome using the ordering DNA sequences V3 tool. Genetics 163: 1299-1313.
  • Battogtokh D., D.K. Asch, M.E. Case, J. Arnold and H.-B. Schuttler. 2002. An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa. Proc. Natl. Acad. Sci. USA 99: 16904-16909.
  • Hall, R. D., J. Miller, J. Arnold, K. Kochut, A. Sheth and M.J. Weise. 2002. Using workflow to build an information management system for a geographically distributed genome sequencing initiative. In: Genomics of Plants and Fungi. R.A. Prade and H.J. Bohnert (eds). Marcel Dekker, NY.
  • Fang, X., J.A. Miller and J. Arnold. 2002. J3DV: a Java-based 3D database visualization tool. Software – Practice and Experience 32: 443-463.
  • Kochut, K.J., J. Arnold, A. Sheth, J. Miller, E. Kraemer, B. Arpinar and J. Cordoso. 2002. INTELLIGEN: a distributed workflow system for discovering protein-protein interactions. Parallel and Distributed Databases 13: 43-72.
  • Fundyga, R., T.J. Lott and J. Arnold. 2002. Population structure of Candida albicans, a member of the human flora, as determined by microsatellite loci. Infection, Genetics, and Evolution 2: 57-68.
  • Kelkar, H.S., J. Griffith, M.E. Case, S. Covert, R.D. Hall, C. Keith, J.S. Oliver, M.J. Orbach, M.S. Sachs, J. Wagner, M.J. Weise, J. Wunderlich and J. Arnold. 2001. The Neurospora crassa genome: cosmid libraries sorted by chromosome. Genetics 157: 979-990.
  • Hoyer, L.L., R. Fundyga, J.E. Hecht, J.C. Kapetyn, F.M. Klis and J. Arnold. 2001. Characterization of ALS genes from non-albicans Candida and phylogenetic analysis of the ALS family. Genetics 157: 1555-1567.
  • Hall, R.D., S.M. Bhandarkar, J. Arnold and T. Jiang. 2001. Physical mapping with automatic capture of hybridization data. Bioinformatics 17: 205-213.
  • Kraemer, E., J. Wang, J. Guo, S. Hopkins and J. Arnold. 2001. An analysis of gene-finding approaches for Neurospora crassa. Bioinformatics 17: 901-912.
  • Sanchez, M.S., J. Arnold and M.A. Asmussen. 2000. Symbiont survival and host-symbiont disequilibria under differential vertical transmission. Genetics 154: 1347-1365.

Norris Armstrong

Professor
Ph.D. (1993) Duke University
  • Using Sandy Beaver Teaching Professorship, University of Georgia, 2013-2015
  • National Academies Education Mentor in the Life Sciences, 2012-2014
  • Disability Resource Center Outstanding Faculty Member Award, 2009-2010
  • Sandy Beaver Excellence in Teaching Award, Franklin College, University of Georgia, 2006
  • National Academies Education Fellow in the Life Sciences, 2004-2005
  • Grant Support -
    • “Promoting inquiry and scientific literacy in non-science major undergraduate biology”, NSF
    • “Using technology to engage students more effectively during lectures.”, CAIT-Learning Technologies Grant
    • “Measuring Scientific Literacy as a Function of Inquiry in Non-Science Major Undergraduate Biology Labs.”, Georgia PRISM Mini-Grant
    • "Peer mentoring in Introductory Biology", UGA V.P. for Instruction
    • “Using Peer-Evaluation and Web-Based Software to Enhance Student Writing and Learning ”, Georgia PRISM Mini-Grant
    • "Reliability and Validity of Short Answer Exam Scoring" UGA STEM Initiative Grant
  • Research Interests -

    • My research concentrates on developing and evaluating approaches to improve instruction in large classes. In the past decade, our understanding of how students learn and of practices that can facilitate this process has grown rapidly. However, significant work still needs to be done translating these findings into approaches that can be readily adapted in the classroom, in particular in large enrollment courses. Towards this end, my work currently examines three issues.  

      Improving assessment. Research has shown that using a variety of assessments helps to inform instructional practices and to improve student learning. However, large enrollment courses often rely primarily on multiple-choice exams because of logistical and resource issues. I am investigating how to effectively incorporate additional assessment types into large classes.

      Active classrooms. Students learn concepts and develop skills best when they actively apply and practice them. However, in most large science classes, students passively listen to lecture and often delay working with the topics being taught until shortly before an exam. I am investigating ways to adapt new (technology) and old (collaborative learning) approaches to encourage students to actively practice skills and apply concepts on a regular basis in and out of class in large enrollment courses.

      Peer Mentoring. To learn concepts and skills being taught in a class effectively, students need frequent, timely, and personalized feedback on their efforts. Unfortunately, it is very difficult for an instructor to provide this type of feedback in a large enrollment course. I am investigating ways to encourage students to take advantage of another underutilized, and often unappreciated, source of feedback, other students. In particular, cooperative learning groups and facilitated study-sessions led by advanced undergraduates are being adapted for use in large classes. 

Research Areas:
Biology Education
Selected Publications:
  • Glynn, S.M., Bryan, R. R., Brickman, P., and Armstrong, N. (2015) Intrinsic Motivation, Self-Efficacy, and Interest in Science In: Interest and K-16 Mathematics and Science Learning In and Out of School. American Educational Research Association. Washington, DC
  • Herreid, C.F., Terry, D., Lemons, P., Armstrong, N., Brickman, P., Ribbens, E. (2014) Emotion, Engagement and Case Studies. Journal of College Science Teaching 44(1):86-95
  • Glynn, S.M., Brickman, P., Armstrong, N., and Taasobbshirazi, G. (2011) Science Motivation Questionnaire II: Validation With Science Majors and Nonscience Majors. J. Res. Sci. Teach. 48(10): 1159-1176.
  • Lundeberg, M. A., Kang, H., Wolter, B., DelMas, R., Armstrong, N, Borsari, B., Boury, N., Brickman, P., Hannam, H. C., Horvath, T., Knabb, M., Platt, T., Rice, N., Rogers, B., Sharp, J., Ribbens, E., Maier, K. S., Deschryver, M., Hagley, R., Goulet, T., Herreid, C. F. (2011) Context Matters: Increasing Understanding with Interactive Clicker Case Studies. Education Tech. Research Dev., 59(5): 645-671
  • Gormally, C., P. Brickman, B. Hallar and N. Armstrong. 2011. Lessons learned from developing and assessing an inquiry-based college science curriculum. Journal of College Science Teaching.
  • Brickman, M., C. Gormally, N. Armstrong and B. Hallar. 2009. Effects of Inquiry-based Learning on Students’ Science Literacy Skills and Confidence. International Journal for the Scholarship of Teaching and Learning 3.
  • Armstrong, N., C.S. Wallace and S. Chang. 2008. Learning from Writing in College Biology. Res. in Sci. Ed. 38: 483-499.
  • Armstrong, N., S. Chang and P. Brickman. 2007. Cooperative learning in industrial sized biology classes. CBE-Life Sciences Education 6: 163-171.
  • Armstrong, N. and S. Chang. 2007. Location, Location, Location: Does seat location affect performance in large classes: Journal of College Science Teaching 37: 54-58.
  • Armstrong, N. 2007. An inquiry based enzyme laboratory. In: Tested Studies for Laboratory Teaching: Proceedings of the 29th Workshop/Conference of the Association for Biology Laboratory Education. Vol. 29. (Peer evaluated educational materials.)
  • Armstrong, N. 2003. Writing assignments in large classes with minimal support. In: Tested Studies for Laboratory Teaching: Proceedings of the 25th Workshop/Conference of the Association for Biology Laboratory Education. Vol. 24.
  • Thorn, M.J., N.A. Armstrong, L.A. Cantrell and B.K. Kay. 1999. Identification and characterization of Xenopus moesin, a Src substrate in Xenopus laevis oocytes. Zygote 7: 113-122.
  • Hardin, J.D. and N.A. Armstrong. 1997. Short-range cell-cell signals control ectodermal patterning in the oral region of the sea urchin embryo. Dev. Biol. 182: 134-149.
  • Armstrong, N., N.B. Adey, S.J. McConnell and B.K. Kay. 1996. Vectors for Phage Display. In: Phage Display of Peptides and Proteins: A Laboratory Manual. Kay, B.K., J. Winter and J. McCafferty (eds). Academic Press, New York.
  • McClay, D.R., J.R. Miller, C.Y. Logan, P.L. Hertzler, E.S. Bachman, J.C. Matese, D.R. Sherwood and N. A. Armstrong. 1995. Cell adhesion and cell signaling at gastrulation in the sea urchin. Theriogenology 44: 1145-1165.
  • Armstrong, N.A. and D.R. McClay. 1994. Skeletal pattern is specified autonomously by the primary mesenchyme in sea urchin embryos. Dev. Biol. 162: 329-338.
  • Armstrong, N.A., J.D. Hardin and D. R. McClay. 1993. Cell-cell interactions regulate skeleton formation in the sea urchin embryo. Development 119: 833-40.

David Brown

IT Professional Specialist (Retired)

EDUCATION

Virginia Polytechnic Institute and State University, Blacksburg, VA. Microbiology, 1975-1978,

Marine Biological Laboratory, Woods Hole, MA. Microbial Ecology Training Program, Summer 1975,

University of West Florida, Pensacola, FL. Estuarine Ecology 1972-1975,

University of Michigan, College of Natural Resources. Ann Arbor, MI. Fisheries Biology/Biological Oceanography 1968-1972

 

EXPERIENCE

IT PROFESSIONAL SPECIALIST - Department of Genetics, University of Georgia, Athens, GA 1997-PRESENT

LABORATORY COORDINATOR - Department of Genetics, University of Georgia, Athens, GA 1991-1997

MOLECULAR BIOLOGIST. Corporate Molecular Biology, Abbott Laboratories, Abbott Park, IL., 1983 -1991

LABORATORY SPECIALIST -  Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 1979-1983

FIELD TEAM LEADER - U.S. Antarctic Research Program, 1976 & 1977 Austral Summers

Selected Publications:

Ravagnani, A., K. C. B. Jennert, E. Steiner, R. Grünberg, J. R. Jefferies, S. R. Wilkinson, D. I. Young, E. C. Tidswell, D. P. Brown and P. Youngman (2000). "Spo0A directly controls the switch from acid to solvent production in solvent‐forming clostridia." Molecular microbiology 37(5): 1172-1185.

Muchova, K., R. J. Lewis, J. A. Brannigan, W. A. Offen, D. P. Brown, I. Barak, P. Youngman and A. J. Wilkinson (1999). "Crystallization of the regulatory and effector domains of the key sporulation response regulator Spo0A." Acta Crystallographica Section D: Biological Crystallography 55(3): 671-676.

Milenbachs, A. A., D. P. Brown, M. Moors and P. Youngman (1997). "Carbon‐source regulation of virulence gene expression in Listeria monocytogenes." Molecular microbiology 23(5): 1075-1085.

Barak, I., J. Behari, G. Olmedo, P. Guzman, D. P. Brown, E. Castro and D. Walker (1996.). "Structure and function of the Bacillus SpoIIE 181 protein and its localization to sites of sporulation septum assembly." Molecular microbiology 182(19): 1047-1060.

Barák, I., J. Behari, G. Olmedo, P. Guzmán, D. P. Brown, E. Castro, D. Walker, J. Westpheling and P. Youngman (1996). "Structure and function of the Bacillus SpoIIE protein and its localization to sites of sporulation septum assembly." Molecular microbiology 19(5): 1047-1060.

Gutierrez, J. A., P. J. Crowley, D. P. Brown, J. D. Hillman, P. Youngman and A. S. Bleiweis (1996). "Insertional mutagenesis and recovery of interrupted genes of Streptococcus mutans by using transposon Tn917: Preliminary characterization of mutants displaying acid sensitivity and nutritional requirements." Journal of bacteriology 178(14): 4166-4175.

Brown, D. P., L. Ganova‐Raeva, B. D. Green, S. R. Wilkinson, M. Young and P. Youngman (1994). "Characterization of spo0A homologues in diverse Bacillus and Clostridium species identifies a probable DNA‐binding domain." Molecular microbiology 14(3): 411-426.

Brown, D. P., K. B. Idler, D. M. Backer, S. Donadio and L. Katz (1994). "Characterization of the genes and attachment sites for site-specific integration of plasmid pSE101 in Saccharopolyspora erythraea and S  i." Molecular and General Genetics MGG 242(2): 185-193.

Metzger, R., D. P. Brown, P. Grealish, M. J. Staver, J. Versalovic, J. R. Lupski and L. Katz (1994). "Characterization of the macromolecular synthesis (MMS) operon from Listeria monocytogenes." Gene 151(1): 161-166.

Taylor, A., D. P. Brown, S. Kadam, M. Maus, W. E. Kohlbrenner, D. Weigl, M. C. Turon and L. Katz (1992). "High-level expression and purification of mature HIV-1 protease in Escherichia coli under control of the araBAD promoter." Applied microbiology and biotechnology 37(2): 205-210.

Katz, L., D. P. Brown and S. Donadio (1991). "Site-specific recombination in Escherichia coli between the att sites of plasmid pSE211 from Saccharopolyspora erythraea " Molecular and General Genetics MGG 227(1): 155-159.

Brown, D. P., K. B. Idler and L. Katz (1990). "Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea." Journal of bacteriology 172(4): 1877-1888.

Brown, D. P., S. J. Chiang, J. S. Tuan and L. Katz (1988). "Site-specific integration in Saccharopolyspora erythraea and multisite integration in Streptomyces lividans of actinomycete plasmid pSE101." Journal of bacteriology 170(5): 2287-2295.

Brown, D. P., J. S. Tuan, K. A. Boris, K. B. Idler, J. P. Dewitt, S. J. D. Chaing and L. Katz (1988). "Plasmid− chromosome interactions in Saccharopolyspora erythraea and Streptomyces lividans." Developments in industrial microbiology 29: 97-105.

Baron, S. F., D. P. Brown and J. G. Ferry (1987). "Locations of the hydrogenases of Methanobacterium formicicum after subcellular fractionation of cell extract." Journal of bacteriology 169(8): 3823-3825.

Katz, L., D. P. Brown, K. A. Boris and J. S. Tuan (1987). "Expression of the MLS resistance methylase gene ermE from Streptomyces erythreus in Escherichia coliresults in N6,N6-dimethylation of ribosomal RNA." Gene 55: 319-325.

McAlpine, J. B., J. S. Tuan, D. P. Brown, K. D. Grebner, D. N. Whittern, A. Buko and L. Katz (1987). "New antibiotics from genetically engineered actinomycetes. I. 2-Norerythromycins, isolation and structural determinations." The Journal of antibiotics 40(8): 1115-1122.

Nelson, M. J. K., D. P. Brown and J. G. Ferry (1984). "FAD requirement for the reduction of coenzyme F 420 by hydrogenase from Methanobacterium formicicum." Biochemical and biophysical research communications 120(3): 775-781.

Schauer, N. L., D. P. Brown and J. G. Ferry (1982). "Kinetics of formate metabolism in Methanobacterium formicicum and Methanospirillum hungatei." Applied and environmental microbiology 44(3): 549-554.

Simmons, G., B. C. Parker, T. A. Allnutt, D. P. Brown and K. G. Seaburg (1979). "Ecological comparisons of oasis lakes and soils." Antarctic Journal U.S. XIV: 181-183.

Moshiri, G. A., D. P. Brown and W. G. Crumpton (1977). "An inexpensive and easily fabricated sampler for collecting sediment cores to measure Eh potentials." Florida Scientist 40(2): 203-205.

Moshiri, G. A., W. G. Crumpton, D. P. Brown, P. R. Barrington and N. Aumen (1976). "Interrelationships tetween certain microorganisms and some aspects of sediment-water nutrient exchange in two bayou estuaries." Fla. Water Resources Research Center publ. no 37

Moshiri, G. A., D. P. Brown, P. Conklin, D. Gilbert, M. Hughes, M. Moore, D. Ray and L. Robinson (1974). "Nitrogen-Phosphorus budget for Bayou Texar, Pensacola, Florida." Fla. Water Resources Research Center publ.no. 29.

Moshiri, G. A., D. P. Brown, R. S. Engert and P. H. Crittenden (1973). "Certain nutrient-primary productivity relations in a bayou Estuary." Quart. J. Fla. Acad. Sci 36(suppl no. 1).

           

Tessa Andrews

Josiah Meigs Distinguished Teaching Professor
Ph.D. (2012) Montana State University

ANDREWS LAB WEBSITE

Research Interests

The Andrews Lab specializes in college biology education research. We are trained as both biologists and social scientists and are always recruiting individuals passionate about improving undergraduate STEM education through research. We study how college biology faculty can be best supported to help students learn in undergraduate STEM courses, especially at research institutions. Our research takes a systems approach to studying undergraduate teaching. That means that means that we consider multiple levels and interrelated factors that influences teaching that occurs in college classrooms. We consider cognitive, affective, social, cultural, and structural factors that influence how college instructors teach. Our ultimate goal is to improve learning and diversity in undergraduate STEM, and especially the life sciences.

 

Grant Support

  • National Science Foundation Improving Undergraduate STEM Education (IUSE)

 

Of note

  • Senior Advisor to Bill & Melinda Gates Foundation Convening about promoting the adoption of evidence-based teaching in colleges and universities
  • Lilly Teaching Fellow & CTL Innovative Teaching Fellow
  • Member of the Steering Committee for the Society for the Advancement of Biology Education Research
  • Manuscripts selected for Highlights Issue of CBE-Life Sciences Education in 2010 and 2012

 

Research Areas:
Biology Education
Selected Publications:
  • Ziadie MA, Andrews TC (2018) Moving evolution education forward: A systematic analysis of literature to identify gaps in collective knowledge for teaching. CBE-Life Sciences Education 17(1), ar11.
  • Auerbach AJ, Higgins M, Brickman P, Andrews TC (2018) Teacher knowledge for active-learning instruction: Expert-novice approach reveals differences. CBE-Life Sciences Education, 17(1), ar12.
  • Andrews TC, Conaway EP, Zhao J, Dolan EL (2016) Colleagues as change agents for undergraduate teaching. CBE-Life Sciences Education, 15 (2), 1-17.
  • Andrews TC, Lemons PP (2015) It’s personal: Biology instructors prioritize personal evidence over empirical evidence in teaching decisions. CBE-Life Sciences Education, 14(1), 1-18.
  • Leonard MJ, Kalinowski ST, Andrews TC (2014) Misconceptions yesterday, today, and tomorrow. CBE-Life Sciences Education, 13(2), 1-8.
  • Price RM, Andrews TC, McElhinny TL, Mead LS, Abraham JK, Thanukos A, Perez KE (2014) The Genetic Drift Inventory: A tool for measuring what advanced undergraduates have mastered about genetic drift. CBE-Life Sciences Education, 13(1), 65-75.
  • Kalinowski ST, Leonard MJ, Andrews TM, Litt AR (2013) Six classroom exercises to teach natural selection to undergraduate biology students. CBE-Life Sciences Education, 12(3), 483-793.
  • Andrews TM, Price RM, Mead LS, McElhinny TL, Thanukos A, Perez KE, Herreid CF, Terry DR, Lemons PP (2012) Biology undergraduate’s misconceptions about genetic drift. CBE-Life Sciences Education, 11(3), 248-259.
  • Andrews TM, Leonard MJ, Colgrove CA, Kalinowski ST (2011) Active learning not associated with student learning in a random sample of college biology courses. CBE-Life Sciences Education, 10(4), 394-405. 
  • Andrews TM, Kalinowski ST, Leonard MJ (2011) ‘Are Humans Evolving?’ A classroom discussion to change students’ misconceptions about natural selection. Evolution: Education and Outreach, 4(3), 456-466.

Jill Anderson

Associate Professor
Ph.D. (2009) Cornell University
  • Grant Support -
    • National Science Foundation, CAREER award
  • Research Interests -
    • Anthropogenic climate change has already influenced the ecological dynamics of species, through elevational and latitudinal shifts in geographic ranges, altered phenology, and disrupted species interactions. Owing to the rapid pace of climate change, species might not have the dispersal abilities needed to track preferred climates, nor the traits necessary to survive in novel conditions. Climate change will likely impose considerable selection for stress tolerance. Nevertheless, the evolutionary consequences of contemporary climate change remain essentially unresolved.

      We are investigating constraints on adaptation in the context of global change using a species of mustard (Boechera stricta) native to the U.S. Rocky Mountains. We conduct large-scale field and growth chamber/greenhouse experiments to examine how climate influences patterns of trait expression, natural selection, and local adaptation. We test whether phenotypic plasticity could enable population persistence in the short term and whether fluctuating conditions associated with climate change actually favor plasticity. Our studies also evaluate whether local populations maintain sufficient genetic variation to respond to novel selection. Finally, we are using ecogenomic techniques to examine patterns of gene expression under varying climatic regimes, and ultimately to dissect the genetic basis of local adaptation to climate.

      Our lab also investigates seed dispersal by frugivorous fish in tropical South America. Seed dispersal is a critical stage in the life history of plants. It determines the initial pattern of juvenile distribution, and influences community dynamics, species diversity and gene flow among populations. One major group of vertebrates has been largely overlooked in studies of seed dispersal: fruit-eating fishes. During the lengthy annual flooded season, hundreds of species of frugivorous fish move into South American floodplain forests and consume fallen fruits and seeds.

      Large fruit-eating fish species are highly overexploited throughout their ranges. Overfishing has likely biased the age structure of populations to younger fish, with unknown implications for plant community dynamics and the maintenance of diversity in Amazonian floodplains. We are interested in the ecological and evolutionary consequences of overexploitation of fruit-eating fish in the Brazilian Pantanal and the Colombian Amazon. Our current studies integrates data on fish behavior, plant ecology and fisheries to test whether commerical fisheries target the best seed dispersers (generally larger, older fish).

Research Areas:
Evolutionary Genetics
Selected Publications:
  • For full publication list, please see: http://andersonlab.genetics.uga.edu/Publications.html
  • For Google Scholar page, please see: http://tinyurl.com/mdbvose
  •  
  • Wadgymar, S., S.C. Daws and J.T. Anderson, 2017. Integrating temporal viability and fecundity selection to illuminate the adaptive nature of genetic clines. Evolution Letters. 1: 26-39.
  •  
  • Wadgymar, S., D. Lowry, C. Byron, B. Gould, R. Mactavish, and J.T. Anderson, in press. Identifying targets and agents of selection: Innovative methods to evaluate the environmental and genetic factors that contribute to local adaptation. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12777
  •  
  • Correa, S., J. K. Arujo, J. Penha, C Nunes da Cunha, K. E. Bobier, J.T. Anderson, 2016. Stability and generalization in seed dispersal networks: A case study of frugivorous fish in Neotropical wetlands. Proceedings of the Royal Society of London B: Biological Sciences. DOI: 10.1098/rspb.2016.1267
  •  
  • Anderson, J.T., 2016. Plant fitness in a rapidly changing world. New Phytologist. 210: 81-87.
  •  
  • Anderson, J.T. and Z. Gezon, 2015. Plasticity in functional traits in the context ofclimate change: A case study of the subalpine forb Boechera stricta (Brassicaceae). Global Change Biology. 21(4): 1689-1703
  •  
  • Anderson, J.T., N. Perera, B. Chowdhury T, T. Mitchell-Olds, 2015. Microgeographic patterns of genetic divergence and adaptation across environmental gradients in Boechera stricta (Brassicaceae). The American Naturalist. 186 (S1): S60-S73.
  •  
  • Correa, S., R. Costa-Pereira, T. Fleming, M. Goulding, J.T. Anderson, 2015. Neotropical fruit-fish interactions: eco-evolutionary dynamics and conservation. Biological Reviews. 90: 1263-1278.
  •  
  • Correa, S., J. Araujo, J. Penha, C. Nunes Da Cunha, P. Stevenson, J.T. Anderson, 2015. Overfishing disrupts an ancient mutualism between frugivorous fish and plants in Neotropical wetlands. Biological Conservation. 191: 159-167

CSCI 2150

Introduction to Computational Science

This course fulfills Area III (Quantitative Reasoning) requirements. Introduction to Matlab and other software packages for numerical and symbolic manipulation, computer arithmetic, solutions of systems of equations, differentiation and integration, root finding, interpolation and curve fitting.

Prerequisites: 

http://bulletin.uga.edu/CoursesHome.aspx

Semester Offered:
Fall
Spring
Level:
Undergraduate
Course Information File:
CIS_CSCI_2150.pdf (178.2 KB)
Subscribe to

Support Genetics at UGA

Thank you for your support to the Genetics Department and the University of Georgia. Contributions from alumni and friends are critical to maintaining our core missions of teaching and research. Gifts are tax deductible.

Click here to learn more

Every dollar contributed to the department has a direct impact on our students and faculty.