Human pathogenic viruses are responsible for nearly all recent pandemic diseases. We set out to search for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (pulmonary, gastrointestinal, etc.) — irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed a customized amino acid sequence alignment program to speed up protein-sequence comparisons and alignments in each viral category. We identified the conserved seven amino acid motif, VAIVLGG, in both Old World and New World alphaviruses. Our further analysis localized the VAIVLGG consensus sequence on the adherence spikes of the chikungunya virus (CHIKV), a well-known mosquito-borne arthrogenic member of the Old World alphaviruses which caused a recent chikungunya fever outbreak in Florida. Our further search revealed that this sequence is located within the viral region involved in its binding to the newly-discovered human CHIKV receptor. In light of the fact that several ongoing clinical trials are aimed at developing vaccines against CHIKV, it is tempting to entertain the idea that our identified VAIVLGG consensus sequence might potentially be used to serve as a single-antigen for producing a pan-vaccine effective not only against CHIKV but also the following alphaviruses: Onyong-nyong, Semiliki Forest, Ross River, Mayaro, VEEV, WEEV, EEEV, and Sindbis.

The sensory mechanisms by which organisms orient towards potential food prior to initiating movement are well-researched. However, behavioral mechanisms in stimulus-poor environments which determine foraging through seemingly stochastic movement variability or random-walk models remain poorly understood. Existing literature describe analyses of a variety of single-organism emergent movement patterns but do not appear to offer comparative analysis between single- and multi-individual environments nor within degrees of resource availability. We introduce a new analysis of observed fluctuations in spontaneous movement by Caenorhabditis elegans exposed to diverse conditions of competition and resource abundance. We describe a sequence of experiments which quantify the movement patterns of C. elegans through video imaging pattern recognition codified by run-length-time and turn-angle-time in comparison to recursively updating algorithmic position estimation. We expect to observe movement patterned on optimized explore-exploit strategies—such as simple random walk or Lévy flight—with frequency of implementation influenced by both population and resource density.

Secondary nucleotide messengers are used by all domains of life to sense and respond to the changes in their environment. In bacteria these secondary nucleotide messengers play a role in regulating several signaling pathways such as cell wall homeostasis, motility, and the expression of virulence genes. The nucleotide cyclic di- 3, 5’ adenosine monophosphate (c-di-AMP) was recently added to the list of secondary nucleotides. C-di-AMP is found in many bacteria such as S. aureus, S. pneumoniae, B. subtilis, and L. monocytogenes (Lm). C-di-AMP has been best characterized in Lm, a well-studied intracellular pathogen. Lm has adapted to survive and replicate in the host cell cytosol by evading host cell defenses through use of key virulence factors. In Lm, synthesis of c-di-AMP is catalyzed by the diadenylate cyclase dacA and degradation is coordinated by the phosphodiesterases, pdeA and pgpH. Studies using Lm mutants that lack both pdeA and pgpH contain abnormal c-di-AMP levels that cause growth and virulence defects of about four logs compared to wild type Lm. This highlights the importance of c-di-AMP regulation for bacterial virulence and growth, but we still know very little about c-di-AMP regulation and toxicity. Our goal is to further understand the toxicity of high levels of c-di-AMP during bacterial infection. We aim to create a transposon library in the double phosphodiesterase KO (ΔΔ Pde) background to identify suppressor mutations. Previous approaches to analyzing suppressor mutations in the ΔΔ Pde strain has not been thorough or cannot be utilized in vivo. Therefore, we have created an amenable phosphodiesterase mutant that knocks out the phosphodiesterases in Lm (pdeA and pgpH) to grow in vivo successfully to investigate c-di-AMP regulation. Understanding the regulation of c-di-AMP could result in targets for novel treatments against Lm and allow for ways to investigate regulation methods of c-di-AMP in other organisms.