Doctor of Philosophy

dissertationLipids, including fats, waxes and sterols, are a group of naturally occurring cellular molecules that perform a diverse array of vital functions within every organism. Broadly, lipids directly or indirectly participate in signaling, act as building blocks within membranes, and function as highly efficient sources of energy. In all these roles, lipids can heavily influence the chemical activities that sustain life-processes collectively known as metabolism. Lipids are composed of fatty acids and particularly, the lipids that constitute biological membranes are composed of long chain fatty acids. Long chain fatty acids, in order to be used for energy generation, membrane biogenesis, or signaling within the cell, need to be activated by esterification to Coenzyme-A. Long chain Acyl CoA Synthase enzymes catalyze this important esterification reaction and hence act as key metabolic regulators of fatty acid metabolism within the cell. The membrane fatty acid composition of a cell determines the protein composition of biological membranes and can thus define the developmental fate of a cell as well as its membrane bending and migratory abilities. In this regard, Acyl CoA Synthases can also act as key developmental regulators. In the current study, we present evidence for the role of Long chain Acyl CoA Synthases (ACSL): Bgm and Dbb in Drosophila embryogenesis. Particularly, maternally deposited bgm transcript is required for the processes of iv cellularization and neurogenesis during Drosophila embryonic development. Rab-5 tagged endocytic vesicles are critical sources of membrane components during cellularization, and Bgm is required for the proper subcellular targeting of these vesicles. Neurogenesis also requires maternal expression of bgm, and abnormal neurogenesis in bgm mutants appears to be related to the early defect in cellularization. In addition, we also demonstrate that bgm and dbb are duplicated genes with partially diverged developmental expression patterns and are transcriptionally regulated by dorsoventral patterning genes. Lastly, we provide evidence for behavioral abnormalities in bgm and dbb mutant flies, thus making them attractive models of neurodegenerative disorders, which can be potentially used in large scale screens for diet and drug therapies

The pandemic push: can COVID-19 reinvent conferences to models rooted in sustainability, equitability and inclusion?

The COVID-19 pandemic necessitates a change in conference formats for 2020. This shift offers a unique opportunity to address long-standing inequities in access and issues of sustainability associated with traditional conference formats, through testing online platforms. However, moving online is not a panacea for all of these concerns, particularly those arising from uneven distribution of access to the Internet and other technology. With conferences and events being forced to move online, this is a critical juncture to examine how online formats can be used to best effect and to reduce the inequities of in-person meetings. In this article, we highlight that a thoughtful and equitable move to online formats could vastly strengthen the global socio-ecological research community and foster cohesive and effective collaborations, with ecology and society being the ultimate beneficiaries

Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations

Mitochondrial genome of the Smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean

We present the first mitogenome sequence of the Smoothnose Wedgefish, Rhynchobatus laevis obtained through field sequencing on the MinION handheld sequencer. The mitochondrial genome of R. laevis is 16,560 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 867 bp in length. Whole mitochondrial genome sequence of R. laevis will enable improved understanding of distribution, abundance, catch and trade rates of the Critically Endangered species

Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area

We present the first mitochondrial genome of Trianenodon obesus from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area. The mitogenome was 16,702 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 38.9%. The control region was 1064 bp in length. This mitogenome for the BIOT MPA T. obesus differed from the previously published T. obesus genome by 15 bp and the differences include a 2 bp insertion and 13 single nucleotide polymorphisms distributed across the mitogenome in the BIOT MPA sequence. Whole mitogenome sequence of T. obesus from the Chagos archipelago presented here fills existing gaps in genetic information on marine species from the BIOT MPA and provides additional tools for species specific assessments as to the effectiveness of MPA management. In addition, methods presented here lay the framework for genetic studies in remote locations with limited infrastructure

Mitochondrial genome of the silky shark Carcharhinus falciformis from the British Indian Ocean Territory Marine Protected Area

We present the first mitochondrial genome of Carcharhinus falciformis from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area (MPA). The mitochondrial genome of C. falciformis is 16,701 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 1063 bp in length. The complete mitogenome sequence of C. falciformis from the BIOT MPA will enable improved conservation measures of the CITES listed species through studies of species distribution, population abundance, fishing pressure and wildlife trade

Pathways to justice, equity, diversity, and inclusion in marine science and conservation

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johri, S., Carnevale, M., Porter, L., Zivian, A., Kourantidou, M., Meyer, E. L., Seevers, J., & Skubel, R. A. Pathways to justice, equity, diversity, and inclusion in marine science and conservation. Frontiers in Marine Science, 8, (2021): 696180, https://doi.org/10.3389/fmars.2021.696180.Marine conservation sciences have traditionally been, and remain, non-diverse work environments with many barriers to justice, equity, diversity, and inclusion (JEDI). These barriers disproportionately affect entry of early career scientists and practitioners and limit the success of marine conservation professionals from under-represented, marginalized, and overburdened groups. These groups specifically include women, LGBTQ+, Black, Indigenous, and people of color (BIPOC). However, the issues also arise from the global North/South and East/West divide with under-representation of scientists from the South and East in the global marine conservation and science arena. Persisting inequities in conservation, along with a lack of inclusiveness and diversity, also limit opportunities for innovation, cross-cultural knowledge exchange, and effective implementation of conservation and management policies. As part of its mandate to increase diversity and promote inclusion of underrepresented groups, the Diversity and Inclusion committee of the Society for Conservation Biology-Marine Section (SCB Marine) organized a JEDI focus group at the Sixth International Marine Conservation Congress (IMCC6) which was held virtually. The focus group included a portion of the global cohort of IMCC6 attendees who identified issues affecting JEDI in marine conservation and explored pathways to address those issues. Therefore, the barriers and pathways identified here focus on issues pertinent to participants’ global regions and experiences. Several barriers to just, equitable, diverse, and inclusive conservation science and practice were identified. Examples included limited participation of under-represented minorities (URM) in research networks, editorial biases against URM, limited professional development and engagement opportunities for URM and non-English speakers, barriers to inclusion of women, LGBTQ+, and sensory impaired individuals, and financial barriers to inclusion of URM in all aspects of marine conservation and research. In the current policy brief, we explore these barriers, assess how they limit progress in marine conservation research and practice, and seek to identify initiatives for improvements. We expect the initiatives discussed here to advances practices rooted in principles of JEDI, within SCB Marine and, the broader conservation community. The recommendations and perspectives herein broadly apply to conservation science and practice, and are critical to effective and sustainable conservation and management outcomes.The Society for Conservation – Marine Section provided partial funding to support publication costs of this manuscript

Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome

Abstract Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos–Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant ‘core’. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health

What Can Professional Scientific Societies Do to Improve Diversity, Equity, and Inclusion: A Case Study of the American Elasmobranch Society

Scientific professional societies are reviewing diversity, equity, and inclusion (DEI) practices and policies in response to recent calls for much-needed change. Organizations like scientific professional societies contribute to establishing disciplinary norms, and can influence the diversity of disciplinary workforces in multiple ways through both action and inaction. This paper examines these issues using the American Elasmobranch Society (AES), a medium-sized professional scientific society, as a case study. It consists of three parts: (1) an analysis of the demographics of AES members, leaders, and award winners; (2) an evaluation of a diversity initiative created by the society which includes a survey of program alumni focusing on potential improvements to the program; and (3) a synthesis of recommendations of steps that AES and similarly sized societies can take to better support DEI goals. AES’s membership in recent years is more than half women, but 71.5% of all leadership positions in the Society’s history (including all but two Presidents) have been held by men since the society was founded in 1983. AES’s membership has significantly fewer Black/African-American members than the United States scientific workforce overall, with just 1 member out of over 400 identifying as Black in 2019, and 86.6% of Society leadership positions have been held by white-presenting members. The Society’s diversity initiative has led to some limited professional benefits for awardees, but could benefit from additional resources and support to enact suggested expansions and improvements. We provide a series of actionable recommendations that will make the annual meetings of societies like AES, and the field of chondrichthyan science, safer and more inclusive