The utility of marine neogastropod Californiconus californicus as a model system for investigation of the venom microbiome

The primary question of my dissertation is, “Does venom possess a microbiome specific to it as an ecosystem, and why?” Given the limited amount of literature on venom microbiomes, I selected the California Cone Snail, Californiconus californicus as a proposed, wild model system for studying venom-microbe interactions in the process of investigating hypothesized microbial interactions with host venom. First, I present a data-driven approach for how sampling sites of venomous animals of interest can be selected in conjunction with the current trend to rely on anecdotal information. This work integrates curated museum collections, crowd-sourced data through digital mediums, knowledge through scientific literature, and personal research. This segment delves deeper into our understanding of C. californicus across space and time, dating back to the Pleistocene. We identify relationships between shell morphology and temperature, contributing foundational knowledge for this species and prospective context of venom microbiome coevolution. Second, I characterize the seawater and sediment coastal microbial ecology of the initial known sampling site (Puerto Nuevo, Mexico) in which this species is commonly found. We sampled several sites along a gradient of exposure to urbanization (0.45 km) and characterized the core microbial communities for archaea, bacteria, and microbial eukaryotes using 16S and 18S amplicon sequencing. While only representing one time point and location, our experimental design allows us to demonstrate consistency in the literature in that we identify functionally relevant microbial taxa specific to different environmental types and distance. This work contributes as a preliminary example for the determination of how and where microbes in the venom may be sourced from the wild. Third, I outline the main findings of the venom microbiome for C. californicus. Model organisms used today are common, simplified points of reference for downstream application. The California Cone Snail is a commonly found neogastropod along the California-Baja coast by the 100s. It can be cultured and maintained in a laboratory, acting well for experiments in the wild and in vivo or in vitro. We sampled C. californicus for three major sites for geographical variation: Puerto Nuevo, San Diego, and Monterey. We sampled summer, winter, and summer again, as well as three consecutive days in Puerto Nuevo for temporal variation. We sampled adult and eggs to compare microbial communities across life stage. We then compared venom microbial communities in a lab setting by testing for different hydrostatic pressures, axenic conditions, and exposure to prey. In summary, we find a specific microbial community (16S and 18S) found in and along the venom gland when compared to other environments, tissues, and conditions. Finally, I tie extensions of science outreach together with scientific practice through communication, education, policy, and the first venom-microbe consortium. These initiatives act as proof-of-concept for strengths in democratically practiced open-source, interdisciplinary research through inclusion across demographics and educational and professional stages

The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP)

Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, endoparasites, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date and the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remain unknown. We highlight the potential for the discovery of venom-microbiomes within the adaptive landscape of venom systems. The considerable number of known, convergently evolved venomous animals juxtaposed with the comparatively few studies to identify microbial communities in venom provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics to which we refer to as venom-microbiomics. We also introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing consortium for interested parties to contribute and collaborate within this subdiscipline. Our consortium seeks to support diversity, inclusion and scientific collaboration among all researchers interested in this subdiscipline

The utility of marine neogastropod Californiconus californicus as a model system for investigation of the venom microbiome

The primary question of my dissertation is, “Does venom possess a microbiome specific to it as an ecosystem, and why?” Given the limited amount of literature on venom microbiomes, I selected the California Cone Snail, Californiconus californicus as a proposed, wild model system for studying venom-microbe interactions in the process of investigating hypothesized microbial interactions with host venom. First, I present a data-driven approach for how sampling sites of venomous animals of interest can be selected in conjunction with the current trend to rely on anecdotal information. This work integrates curated museum collections, crowd-sourced data through digital mediums, knowledge through scientific literature, and personal research. This segment delves deeper into our understanding of C. californicus across space and time, dating back to the Pleistocene. We identify relationships between shell morphology and temperature, contributing foundational knowledge for this species and prospective context of venom microbiome coevolution. Second, I characterize the seawater and sediment coastal microbial ecology of the initial known sampling site (Puerto Nuevo, Mexico) in which this species is commonly found. We sampled several sites along a gradient of exposure to urbanization (0.45 km) and characterized the core microbial communities for archaea, bacteria, and microbial eukaryotes using 16S and 18S amplicon sequencing. While only representing one time point and location, our experimental design allows us to demonstrate consistency in the literature in that we identify functionally relevant microbial taxa specific to different environmental types and distance. This work contributes as a preliminary example for the determination of how and where microbes in the venom may be sourced from the wild. Third, I outline the main findings of the venom microbiome for C. californicus. Model organisms used today are common, simplified points of reference for downstream application. The California Cone Snail is a commonly found neogastropod along the California-Baja coast by the 100s. It can be cultured and maintained in a laboratory, acting well for experiments in the wild and in vivo or in vitro. We sampled C. californicus for three major sites for geographical variation: Puerto Nuevo, San Diego, and Monterey. We sampled summer, winter, and summer again, as well as three consecutive days in Puerto Nuevo for temporal variation. We sampled adult and eggs to compare microbial communities across life stage. We then compared venom microbial communities in a lab setting by testing for different hydrostatic pressures, axenic conditions, and exposure to prey. In summary, we find a specific microbial community (16S and 18S) found in and along the venom gland when compared to other environments, tissues, and conditions. Finally, I tie extensions of science outreach together with scientific practice through communication, education, policy, and the first venom-microbe consortium. These initiatives act as proof-of-concept for strengths in democratically practiced open-source, interdisciplinary research through inclusion across demographics and educational and professional stages

Academic Twitter v3.0

This figure has been developed as a resource for academics, with a lean towards scientists, interested in building their digital presence on Twitter and beyond. The quality of this resource has been enhanced by a number of well-versed academics on Twitter. <br><br

The impact of host dispersal on parasite biogeography

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Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance—the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the leading global cause of multidrug-resistant bacterial infections, and overexpression of multidrug efflux (MEX) transport systems has been identified as one of the most critical mechanisms facilitating the evolution of multidrug resistance in ESKAPE pathogens. Despite efforts to develop efflux pump inhibitors to combat antibiotic resistance, the need persists to identify additional targets for future investigations. We evaluated evolutionary pressures on 110 MEX-encoding genes from all annotated ESKAPE organism genomes. We identify several MEX genes under stabilizing selection—representing targets which can facilitate broad-spectrum treatments with evolutionary constraints limiting the potential emergence of escape mutants. We also examine MEX systems being evaluated as drug targets, demonstrating that divergent selection may underlie some of the problems encountered in the development of effective treatments—specifically in relation to the NorA system in S. aureus. This study provides a comprehensive evolutionary context to efflux in the ESKAPE pathogens, which will provide critical context to the evaluation of efflux systems as antibiotic targets

Towards Convergence of IoT and Blockchain for Secure Supply Chain Transaction

Supply chain management (SCM) is essential for a company’s faster, efficient, and effective product life cycle. However, the current SCM systems are insufficient to provide product legitimacy, transaction privacy, and security. Therefore, this research proposes a secure SCM system for the authenticity of the products based on the Internet of Things (IoT) and blockchain technology. The IoT-enabled Quick Response (QR) scanner and the blockchain-integrated distributed system will allow all the SCM stakeholders to begin secure and private transactions for their products or services. Resulting, the consumer will receive an authentic and genuine product from the original producer. A lightweight asymmetric key encryption technique, i.e., elliptic curve cryptography (ECC) and Hyperledger Fabric-based blockchain technology with on-chain smart contracts are applied for distributed IoT devices to make the authentication process faster and lighter. Each SCM stakeholder is registered by the service provider and receives corresponding public and private keys, which will be used for the authentication process of the participants and IoT devices. The authenticated QR scanner records all transactions on the blockchain. Consequently, there will be no human intervention for the SCM transactions. The security and scalability analysis demonstrates that the proposed system is more secure and robust than other state-of-the-art techniques