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Microbiology at William Paterson University

William Paterson University in Wayne, NJ is home to 10,000 students and 400 faculty. WPU offers a B.S. in Biology, Biotechnology and an M.S. in Biotechnology. There are seven microbiologists on the Biology Department faculty, a full a third of the department: Professor Kendall Martin [1–6], Professor Pradeep Patnaik [7, 8], Professor Miryam Wahrman [9–14], Associate Professor Carey Waldburger [15, 16], Associate Professor Emily Monroe [17–22], Assistant Professor James Arnone [23–25] and Assistant Professor Kelley Healey [26–29]. With such critical mass of eminently qualified and talented microbiologists, one wonders if a microbiology major (or at least a minor) is not far in the future!

With publications that include 12 William Paterson undergraduate students, Dr. James Arnone is a stand out faculty member. It’s not easy doing research at universities mainly devoted to undergraduate education. Tenure and promotion packages customarily demand a research component, but teaching aptitude usually counts more. Involving undergrads in research is difficult and very few professors attempt it. Undergrads have limited time, experience and attention span. Their competing priorities such as course study, outside work, and social are significant obstacles. It’s usually quicker and easier for faculty to work with past associates from their post-doc and graduate days or with local faculty colleagues.

Professor Arnone and his Chemistry Dept. colleague Professor Jonathan Foley shaped the 12 undergraduate students into a community of research and engaged them in scholarly activities that included performing experiments, testing hypotheses, reading scientific literature and communicating findings. Their efforts went well beyond standard lecture and laboratory course training. They provided an authentic undergraduate research experience that enlighten students on the nature of science and increased their confidence in doing science. The projects produced peer reviewed data and analysis, improved the student’s critical thinking skills, increased their understanding of the nature of scientific research, engaged and excited the students and left a lasting record of their work well beyond course entries on a transcript. The 12 students now have something significant and instantly recognizable on their resumes that will impress future employers. It would be interesting to follow the long-term impact of the research projects on the careers of the students involved.

Eldabagh et al. [24] investigated the spatial positioning of genes throughout the yeast (Saccharomyces cerevisiae) genome. Genes that arrange into clusters had altered expression in comparison to un-clustered (singleton) genes during environmental and nutritional perturbation. They found gene clustering represented a level of transcriptional control that helped maintain coordinated levels of gene expression. They also found that many fungal species exploit this phenomenon to help regulate functionally related gene sets and adjacent-gene coregulation by functional clustering may be much more widespread than has been previously appreciated.

Remarkably, the research team used extensive data mining of already published data sets to test their hypotheses; they performed no wet-lab experiments of their own in the work. As microarray and sequence datasets become more readily available, repurposing the data becomes more feasible. Arnone’s team used this attractive research strategy when funding for reagents and experimental infrastructure were lacking but when bioinformatics skills were at hand.

In Cera et al. [25] the team again used Saccharomyces cerevisiae to test the mechanism

underlying adjacent gene coregulation. They continued to extensively use data mining but also performed wet lab experiments using yeast strains provided by Harvard Medical School to perform qRT-PCR and yeast growth experiments. They establish promoter distance variations in a multi-gene locus disrupt transcript levels in the region and the amount of disruption varied depending on the loci. They learned neighboring genes tend to be correlated in transcript abundance genome-wide and the correlation decayed exponentially with increasing intergenic distance. This occurred at the level of transcriptional activation, growth phenotype and in the degree of disruption surrounding the integration locus - the distance a promoter can activate a gene varies based on both its proximity to a gene and the site of integration. They also identified a putative role for chromatin remodeling in the coregulation of functional clusters and identify several chromatin remodeling complexes that are necessary.

Dr Arnone told me he received outstanding support from his department and from the WPU Provost who provided release time from teaching duties to conduct the research. The investment has paid dividends in advancing not only his own career but in the careers of his students. We all look forward to seeing more innovative research from the microbiologists at William Paterson University!

I plan on attending the 14th Annual Undergraduate Research Symposium hosted by the College of Science & Health at WPU on Saturday, April 18th, 2020. It’s a forum for undergrads around the state to present their original research to their peers and professors. Abstracts are due March 27th, 2020. Check out the symposium website for more information. See you there!

1. Bull, C.T.; Goldman, P.H. and Martin, K.J. Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ. Molecular and Cellular Probes 2014, 28, 211-217

2. Martin, K.J. Introduction to molecular analysis of ectomycorrhizal communities. Soil Science Society of America Journal 2007, 71, 601-610

3. Martin, K.J. and Bull, C.T. Novel primers for detection and quantification of Myxococcusspecies in situ. Molecular Ecology Notes 2006, 6, 773-775

4. Rygiewicz, P.T.; Monleon, V.J.; Ingham, E.R.; Martin, K.J. and Johnson, M.G. Soil life in reconstructed ecosystems: initial soil food web responses after rebuilding a forest soil profile for a climate change experiment. Applied Soil Ecology 2010, 45, 26-38

5. Wu, T.; Chellemi, D.O.; Martin, K.J.; Graham, J.H. and Rosskopf, E.N. Discriminating the effects of agricultural land management practices on soil fungal communities. Soil Biology and Biochemistry 2007, 39, 1139-1155

6. Wu, T.; Chellemi, D.O.; Graham, J.H.; Martin, K.J. and Rosskopf, E.N. Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microbial Ecology 2008, 55, 293-310

7. Mota, M.M.; Jarra, W.; Hirst, E.; Patnaik, P.K. and Holder, A.A. Plasmodium chabaudi-infected erythrocytes adhere to CD36 and bind to microvascular endothelial cells in an organ-specific way. Infect. Immun. 2000, 68, 4135-4144

8. Espinal, A.; Quijano, J.; Hunt, C.; Lorenzo, R.; Mulligan, C.; Sampson, M.; Sauchelli, M. and Patnaik, P.K. A 10 base-pair sequence within Domain III of the GPEET procyclin promoter is essential for the autonomous replication of a plasmid in procyclic Trypanosoma brucei. Molecular and Biochemical Parasitology 2007, 151, 224

9. Basch, C.H.; Wahrman, M.Z.; Shah, J.; Guerra, L.A.; MacDonald, Z.; Marte, M. and Basch, C.E. Glove changing when handling money: observational and microbiological analysis. Journal of community health 2016, 41, 334-339

10. Basch, C.H.; Wahrman, M.Z.; MacLean, S.A.; Quisido, A.; Ponsica, C. and Patel, N. Glove changing practices of mall food vendors in New Jersey. Journal of community health 2018, 43, 4-10

11. Basch, C.H.; Wahrman, M.Z.; MacLean, S.A. and Garcia, P. Escherichia coli on the internet: The power of YouTube to educate and influence consumer behavior regarding pathogenic bacteria. Infection, disease & health 2019, 24, 107-112

12. Sahni, M.K.; Spanos, S.; Wahrman, M.Z. and Sharma, G.M. Marine corrinoid-binding proteins for the direct determination of vitamin B12 by radioassay. Anal. Biochem. 2001, 289, 68-76

13. Wahrman, M.Z. The hand book: surviving in a germ-filled world. 2016,

14. Wahrman, M.Z. and Basch, C.H. Hands-on research: reaching across disciplines. The American Biology Teacher 2019, 81, 412-415

15. Cheung, J.; Bingman, C.A.; Reyngold, M.; Hendrickson, W.A. and Waldburger, C.D. Crystal structure of a functional dimer of the PhoQ sensor domain. J. Biol. Chem. 2008, 283, 13762-13770

16. Goldberg, S.D.; Soto, C.S.; Waldburger, C.D. and DeGrado, W.F. Determination of the physiological dimer interface of the PhoQ sensor domain. J. Mol. Biol. 2008, 379, 656-665

17. Kleigrewe, K.; Almaliti, J.; Tian, I.Y.; Kinnel, R.B.; Korobeynikov, A.; Monroe, E.A.; Duggan, B.M.; Di Marzo, V.; Sherman, D.H.; Dorrestein, P.C.; Gerwick, L. and Gerwick, W.H. Combining mass spectrometric metabolic profiling with genomic analysis: a powerful approach for discovering natural products from cyanobacteria. J Nat Prod 2015, 78, 1671-1682, doi:10.1021/acs.jnatprod.5b00301

18. Kleigrewe, K.; Almaliti, J.; Tian, I.Y.; Kinnel, R.B.; Korobeynikov, A.; Monroe, E.A.; Duggan, B.M.; Di Marzo, V.; Sherman, D.H. and Dorrestein, P.C. Discovery of novel chlorinated acyl amides from a marine cyanobacterium using integrated technologies. Planta Medica 2015, 81, IL13

19. Boudreau, P.D.; Monroe, E.A.; Mehrotra, S.; Desfor, S.; Korobeynikov, A.; Sherman, D.H.; Murray, T.F.; Gerwick, L.; Dorrestein, P.C. and Gerwick, W.H. Expanding the described metabolome of the marine cyanobacterium Moorea producensJHB through orthogonal natural products workflows. PLoS One 2015, 10, e0133297, doi:10.1371/journal.pone.0133297

20. Bertin, M.J.; Vulpanovici, A.; Monroe, E.A.; Korobeynikov, A.; Sherman, D.H.; Gerwick, L. and Gerwick, W.H. The phormidolide biosynthetic gene cluster: a trans-AT PKS pathway encoding a toxic macrocyclic polyketide. ChemBioChem 2016, 17, 164-173, doi:10.1002/cbic.201500467

21. Kinnel, R.B.; Esquenazi, E.; Leao, T.; Moss, N.; Mevers, E.; Pereira, A.R.; Monroe, E.A.; Korobeynikov, A.; Murray, T.F.; Sherman, D.; Gerwick, L.; Dorrestein, P.C. and Gerwick, W.H. A maldiisotopic approach to discover natural products: cryptomaldamide, a hybrid tripeptide from the marine cyanobacterium Moorea producens. J Nat Prod 2017, 80, 1514-1521, doi:10.1021/acs.jnatprod.7b00019

22. Leao, T.; Castelão, G.; Korobeynikov, A.; Monroe, E.A.; Podell, S.; Glukhov, E.; Allen, E.E.; Gerwick, W.H. and Gerwick, L. Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea. Proc. Natl. Acad. Sci. U S A 2017, 114, 3198-3203, doi:10.1073/pnas.1618556114

23. Arnone, J.T. Ribosome biogenesis: streamlining the genome for the efficient production of this biological nanomolecular machine. Nanomedicine and Nanotechnology Journal 2018, 2, e118

24. Eldabagh, R.S.; Mejia, N.G.; Barrett, R.L.; Monzo, C.R.; So, M.K.; Foley, J.J. and Arnone, J.T. Systematic identification, characterization, and conservation of adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiae. mSphere 2018, 3, doi:10.1128/mSphere.00220-18

25. Cera, A.; Holganza, M.K.; Hardan, A.A.; Gamarra, I.; Eldabagh, R.S.; Deschaine, M.; Elkamhawy, S.; Sisso, E.M.; Foley, J.J. and Arnone, J.T. Functionally related genes cluster into genomic regions that coordinate transcription at a distance in Saccharomyces cerevisiae. mSphere 2019, 4, doi:10.1128/mSphere.00063-19

26. Healey, K.R. and Perlin, D.S. Fungal resistance to echinocandins and the MDR phenomenon in Candida glabrata. Journal of Fungi 2018, 4, 105

27. Healey, K.R.; Kordalewska, M. and Ortigosa…, C.J. Limited ERG11 mutations identified in isolates of Candida auris directly contribute to reduced azole susceptibility. Antimicrobial agents … 2018,

28. Hou, X.; Healey, K.R.; Shor, E.; Kordalewska, M.; Ortigosa, C.J.; Paderu, P.; Xiao, M.; Wang, H.; Zhao, Y. and Lin, L.-Y. Novel FKS1 and FKS2 modifications in a high-level echinocandin resistant clinical isolate of Candida glabrata. Emerging microbes & infections 2019, 8, 1619-1625

29. Shields, R.K.; Kline, E.G.; Healey, K.R.; Kordalewska, M.; Perlin, D.S.; Nguyen, M.H. and Clancy, C.J. Spontaneous mutational frequency and FKS mutation rates vary by echinocandin agent against Candida glabrata. Antimicrob. Agents Chemother. 2019, 63, e01692-18

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