Research: Rare genes in halophilic communities; Evolution of early life on Earth

Research: Functional analysis of marine microbialites to investigate carbon utilization processes

Research: Examining the infection host range of Sinorhizobium meliloti

Department of Molecular and Cell Biology, Storrs, CT USA

• Analyzing rare genes in halophilic communities using High-Throughput Sequencing Techniques
  • Identify CRISPR-Cas gene arrays, transposons, and genomic islands
  • Examine horizontal gene transfer of niche adapting genes within each population/community
  • Apply novel tools and methods for analyzing rare genes at the community level
• Haloferax volcanii whole transcriptome data analysis
  • Differential expression analysis of multiple experiments to examine active functional genes, e.g. quorum sensing, biofilm formation, restriction modification systems, DNA uptake
• Genome and Pangenome analyses of Archaea isolated from hypersaline environments
  • Combine existing pipelines with novel methods to identify the core and unique genes
  • In depth analysis of niche adapting genes with focus on horizontal gene transfer and evolution
• Additional responsibilities include day to day lab management, mentoring graduate, undergraduate, and high school aged students, purchases and procurement card management, all initial training in coding

Space Life Sciences Lab, Kennedy Space Center, Merritt Island, FL USA

• Metatranscriptome, metagenome, and 16S rRNA extractions from microbialites for sequencing
• Bioinformatic analysis of metatranscriptome, metagenome, and 16S rRNA data
• Performed draft genome assemblies from metagenomic sequences
• Completed secondary ion mass spectrometry (SIMS) on stable isotopes – oxygen and carbon

USDA APHIS CPHST PPQ Otis Laboratory, Buzzards Bay, MA USA

• Molecular analysis of Lepidoptera species and the nematode, Deladenus siricidicola
• DNA barcoding of Lymantria dispar and unknown Lepidoptera, D. siricidicola, and woodborer species
• Statistical analysis of microsatellite data for Lymantria dispar global populations
• Developed lab protocol for statistical methods and trained coworkers in system use
• Hybridization of two strains of D. siricidicola for analysis as a biocontrol agent

• Makkay, A. M.*, Louyakis, A. S.*, Ram-Mohan, N., Gophna, U., Gogarten, J. P., & Papke, R. T., 2020. Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon. Scientific Reports
• Mickol, R. L., Louyakis, A. S., Kee, H. L., Johnson, L. K., Dawson, S. C., Hargreaves, K. R., Chadwick, G. L., Newman, D. K., Leadbetter, J. R., and Brown, C. T., 2020. Draft Genome Sequence of the Free-living, Iridescent Bacterium Tenacibaculum mesophilum strain ECR. Microbiology Resource Announcement
• Fullmer, M.S.*, Ouellette, M.*, Louyakis, A.S.*, Papke, R.T., and Gogarten, J.P., 2019. The patchy distribution of restriction-modification system genes and the conservation of orphan methyltransferases in halobacteria. Genes
• Feng, Y.*, Louyakis, A.S.*, Makkay, A.M., Guerrero, R.O., Papke, R.T., and Gogarten, J.P., 2019. Complete genome of Halorubrum ezzemoulense strain Fb21. Microbiology Resource Announcement 
• Louyakis, A.S., Gourlé, H., Casaburi, G., Bonjawo, R.M., Duscher, A.A. and Foster, J.S., 2018. A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles. Environmental microbiology, 20(2), pp.842-861.
• Babilonia, J., Conesa, A., Casaburi, G., Pereira, C., Louyakis, A. S., Reid, R. P. and Foster, J. S., 2018. Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia. Frontiers in Microbiology, 9, 1359. 
• Louyakis A.S., Mobberley J.M., Vitek B.E., Visscher P.T., Hagan P.D., Reid R.P., Kozdon R., Orland I.J., Valley J.W., Planavsky N.J., Casaburi G., and Foster J.S., 2017. A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses. Astrobiology 17:5, pp.413-430.
• Wu, Y., Molongoski, J.J., Winograd, D.F., Bogdanowicz, S.M., Louyakis, A.S., Lance, D.R., Mastro, V.C. and Harrison, R.G., 2015. Genetic structure, admixture and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae). Molecular ecology, 24(6), pp.1275-1291.

The Unix Shell; Programming with R; R for Reproducible Scientific Analysis, Git, Python, Data management

MCB 5472 Computer Methods in Molecular Evolution Graduate Course

Head TA – Provided guidance and structure to GTA’s, UTA’s, and students

Microbiology Laboratory instructor – Undergraduate Intermediate and Advanced Labs

Character of Service: Honorable; multiple awards received

• ASM Peggy Cotter Award, 2020
• ASM Peggy Cotter Award, 2019
• ISME Symposium Travel Award, 2016
• University of Florida Graduate School Travel Award, 2016
• ASM General Meeting Travel Award, 2014
• National Science Foundation Graduate Research Fellowship, 2013
• Graduate Student Teaching Award nomination, 2013