IM students and faculty have bee busy! Below are recent publications by IM students, faculty, and affiliates. Would you like your research showcased? Send your paper to firstname.lastname@example.org in time for the next edition!
Bold Indicates ISU faculty and affiliates
^Indicates publications by IM students
1. Nguyen, H. N., Jain, A., Eulenstein, O., & Friedberg, I (2019). Tracing the Ancestry of Operons in Bacteria. Bioinformatics. Jan 24. doi: 10.1093/bioinformatics/btz053
Relevance of this work: In this work, we developed a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We describe several ancestral states that are plausible functional intermediate forms leading to the full operon.
2. Hamid, M. N., & Friedberg, I. (2018). Identifying antimicrobial peptides using word embedding with deep recurrent neural networks. Bioinformatics. 2018 Nov 10. doi: 10.1093/bioinformatics/bty937
Relevance of this work: Here we use word embeddings of protein sequences to represent bacteriocins, and apply a word embedding method that accounts for amino acid order in protein sequences, to predict novel bacteriocins from protein sequences without using sequence similarity. Our method predicts, with a high probability, six yet unknown putative bacteriocins in Lactobacillus.
3. Hamid, M. N., & Friedberg, I.(2018). Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics. Machine Learning for Health (ML4H) Workshop at NeurIPS 2018 arXiv:1811.07216
Relevance of this work:In this paper, we introduce a deep learning model trained with Stochastic Gradient Langevin Dynamics (SGLD) to classify antibiotic resistant genes. The model provides bet- ter uncertainty estimates when tested against OoD data compared to traditional optimization methods such as Adam.
4. Kraft, J.J., Peterson, M.S., Cho, S.K., Wang, Z., Hui, A., Rakotondrafara, A.M., Treder, K,. Miller, C.L., Miller, W.A.(2019) The 3’ untranslated region of a plant viral RNA directs efficient cap-independent translation in plant and mammalian systems. Pathogens 8, 28. https://www.mdpi.com/2076-0817/8/1/28.
Relevance of this work:Viruses must have ways to take over the host’s translational machinery. Many plant RNA viruses do this by having a structure in the 3’ untranslated region that binds translation initiation factors and facilitates efficient cap-independent translation. No mRNA of animal viruses or their hosts are known to have such a sequence. Here we describe a plant viral RNA that translates efficiently in mammalian cells and extracts, leading us to propose that some animal viral or host mRNAs may have such sequences, but they have not been discovered yet.
5. Dolezal, A., Carrillo-Tripp, J., Judd, T., Miller, W.A., Bonning, B., Toth, A. (2019) Interacting stressors matter: Diet quality and virus infection in honeybee health. Royal Society Open Sci. 6: 181803. http://dx.doi.org/10.1098/rsos.181803
Relevance of this work: Collapse of honeybee colonies has been a crisis in American agriculture. Here we show that one contributor to this may be the lack of availability of good and diverse sources of pollen in the honeybee diet. We show that a low-quality pollen diet (typical in the corn belt) makes honeybees more susceptible to the widespread and abundant Israeli acute paralysis virus.
6. Santoscoy, M. C., & Jarboe, L. R.(2019). Streamlined assessment of membrane permeability and its application to membrane engineering of Escherichia coli for octanoic acid tolerance. Journal of industrial microbiology & biotechnology, 1-11.
Relevance of this work: The economic viability of bio-production processes is often limited by damage to the microbial cell membrane and thus there is a demand for strategies to increase the robustness of the cell membrane. Damage to the microbial membrane is also a common mode of action by antibiotics. Membrane-impermeable DNA-binding dyes are often used to assess membrane integrity in conjunction with flow cytometry. We demonstrate that in situ assessment of the membrane permeability of E. coli to SYTOX Green is consistent with flow cytometry, with the benefit of lower experimental intensity, lower cost, and no need for a priori selection of sampling times.
7. ^Naditz, A. L.,Dzieciol, M., Wagner, M., & Schmitz-Esser, S. (2019). Plasmids contribute to food processing environment–associated stress survival in three Listeria monocytogenes ST121, ST8, and ST5 strains. International Journal of Food Microbiology.
Relevance of this work: Our data revealed that L. monocytogenes ST5, ST8, and ST121 plasmids contribute to tolerance against elevated temperature, salinity, acidic environments, oxidative stress and disinfectants.