Life Sciences Commons^™

Effects Of Cyanobacteria Harmful Algal Blooms On The Microbial Community Within Lake Okeechobee, Fl, Usa, Paisley S. Samuel

All HCAS Student Capstones, Theses, and Dissertations

The Lake Okeechobee (Lake O) watershed is a Floridian freshwater ecosystem that has been affected by the increased frequency and intensity of harmful cyanobacterial bloom (cyanoHAB) events occurring over recent decades. Lake O has several ecological and economic purposes such as providing habitats for various organisms and providing drinking water to urban communities surrounding the lake. Toxic cyanoHAB events are posing a threat to the ecosystem and economy of the lake due to the degradation of water quality. This study investigates how the microbial community structure within Lake O is affected by annual cyanobacterial harmful algal blooms over several years …

Acoustic Telemetry Provides Insights For Improving Conservation And Management At A Spawning Aggregation Site Of The Endangered Nassau Grouper (Epinephelus Striatus), Richard S. Nemeth, Elizabeth Kadison, Jonathan Jossart, Mahmood Shivji, Bradley Wetherbee, Jordan Matley

Biology Faculty Articles

Nassau grouper (Epinephelus striatus, Serranidae) were one of the most important fishery species in the Caribbean, but are now listed as critically endangered. Population collapse in most places occurred primarily by fishers targeting their spawning aggregation sites, where thousands of fish gathered during full moon periods from December to April. Identifying management options for protecting this vulnerable period is crucial for their survival. In the US Virgin Islands, we tagged 24 Nassau grouper with acoustic transmitters at a fish spawning aggregation (FSA) site called the Grammanik Bank, a 1.5 km2, marine protected area (MPA) closed each year from …

Genomes Of Endangered Great Hammerhead And Shortfin Mako Sharks Reveal Historic Population Declines And High Levels Of Inbreeding In Great Hammerhead, Michael J. Stanhope, Kristina M. Ceres, Qi Sun, Minghui Wang, Jordan D. Zehr, Nicholas J. Marra, Aryn P. Wilder, Cheng Zou, Andrea M. Bernard, Paulina D. Pavinski Bitar, Mitchell G. Lokey, Mahmood Shivji

Biology Faculty Articles

Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and 1 Mbp. Both these sharks experienced precipitous declines in …

Genetic Population Dynamics Of The Critically Endangered Scalloped Hammerhead Shark (Sphyrna Lewini) In The Eastern Tropical Pacific, Sydney P. Harned, Andrea Bernard, Pelayo Salinas-De-Leon, Marissa Mehlrose, Jenifer Suarez, Yolani Robles, Sandra Bessudo Lion, Felipe Ladino, Andrés López Garo, Ilena Zanella, Kevin A. Feldheim, Mahmood Shivji

Biology Faculty Articles

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single …

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …

Determination Of Atlantic Shortfin Mako Shark (Isurus Oxyrinchus) Population Genetic Structure And Comparison Of Mitogenomic Markers, Marissa Mehlrose

All HCAS Student Capstones, Theses, and Dissertations

This study provides the first genomics-level, population structure and genetic diversity assessment of the shortfin mako (Isurus oxyrinchus) shark. The assessments were based on mitogenome sequences from makos distributed throughout the Atlantic Ocean, with Pacific mako mitogenomes used as a comparative outgroup. In addition to complete mitogenome-based analyses, I assessed individual mitochondrial coding gene and non-coding (Control Region) sequences for their comparative resolution properties as markers for revealing matrilineal population structure and genetic diversity. Sequencing of 125 makos in the western and eastern Atlantic across northern and southern hemispheres yielded 92 complete mitogenomes (16,698-16,702 bp) and 33 partial …

A Decade Of Gigascience: A Perspective On Conservation Genetics, Stephen James O'Brien

Biology Faculty Articles

Wide interest in species conservation is young. To many it began early in 1903 when Teddy Roosevelt and John Muir set up a camp under the Grizzly Giant in the Mariposa Grove of California's Yosemite Valley. Over three days they decided to broaden the US National Park footprint across the USA. Conservationists were inspired in the coming decades by the writings of wildlife conservation pioneers—Osa Johnson (I Married Adventure), Karen Blixen (Out of Africa) and Rachel Carson (The Silent Spring). Countless crusaders developed a passion for preserving dwindling species in those early days, yet …

Transcriptome Analysis Of The Entomopathogenic Fungus Culicinomyces Clavisporus, Dana E. Foresman

All HCAS Student Capstones, Theses, and Dissertations

Culicinomyces clavisporus is an entomopathogenic fungus that can infect mosquito larvae, such as Culex quinquefasciatus, Aedes aegypti, and Anopheles stephensi. Whereas most fungal entomopathogens infect hosts through the cuticle, C. clavisporus initiates infection through ingestion. This suggests that the C. clavisporus genome may be mined for novel pathogenicity factors with the potential for vector control. To this end, a transcriptome analysis was initiated. The strain C. clavisporus ARSEF 582 was grown in modified PYG liquid cultures that was supplemented with whole, insect larvae (Galleria mellonella) to elicit the expression of genes involved in host-pathogen relationships. Total RNA …

Population Genomic Dynamics Of Mesopelagic Lanternfishes Diaphus Dumerilii, Lepidophanes Guentheri, And Ceratoscopelus Warmingii (Family: Myctophidae) In The Gulf Of Mexico, Andrea Bernard, Kimberly A. Finnegan, Tracey Sutton, Ron Eytan, Max Weber, Mahmood Shivji

Marine & Environmental Sciences Faculty Articles

Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of …

Three Complete Mitochondrial Genomes Of Shortfin Mako Sharks, Isurus Oxyrinchus, From The Atlantic And Pacific Oceans, Marissa Mehlrose, Andrea Bernard, Kimberly A. Finnegan, Lauren E. Krausfeldt, Jose V. Lopez, Mahmood Shivji

Biology Faculty Articles

We present complete mitogenome sequences of three shortfin mako sharks (Isurus oxyrinchus) sampled from the western Pacific, and eastern and western Atlantic oceans. Mitogenome sequence lengths ranged between 16,699 bp and 16,702 bp, and all three mitogenomes contained one non-coding control region, two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. Comparative assessment of five mitogenomes from globally distributed shortfin makos (the current three and two previously published mitogenomes) yielded 98.4% identity, with the protein-coding genes ATP8, ATP6, and ND5 as the most variable regions (sequence identities of 96.4%, 96.5%, and 97.6%, respectively). These mitogenome sequences contribute resources …

The Earth Biogenome Project 2020: Starting The Clock, Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Katharine B. Baker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica Dipalma, Richard Durbin, Thankgod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill Sigurd Jakobson, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O'Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guojie Zhang

Biology Faculty Articles

No abstract provided.

Standards Recommendations For The Earth Biogenome Project, Mara K. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques-Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katherine J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose V. Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Françoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards

Biology Faculty Articles

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. …

Why Sequence All Eukaryotes?, Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A.M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin

Biology Faculty Articles

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes—about 2 million species—should be sequenced to high quality to produce a …

Genetic Population Dynamics Of The Critically Endangered Scalloped Hammerhead Shark (Sphyrna Lewini) In The Eastern Tropical Pacific Ocean, Sydney P. Harned

All HCAS Student Capstones, Theses, and Dissertations

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form large aggregations of mostly adult females, especially in the heavily-fished Eastern Tropical Pacific (ETP) Ocean. This species forms iconic, visually spectacular, seasonal aggregations in the northern Galápagos Islands, and it is hypothesized based on telemetry studies that pregnant females from these aggregations migrate to mainland coastal nurseries for parturition. This study investigated the population genetic dynamics of the scalloped hammerhead across most of its coastal and offshore distribution (Mexico to Ecuador) in the ETP, focusing on young-of-the-year animals sampled from nursery …

Commentary: Unbiasing Genome-Based Analyses Of Selection: An Example Using Iconic Shark Species, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Vincent P. Richards, Stephen J. O'Brien, Agostinho Antunes, Mahmood S. Shivji

Biology Faculty Articles

No abstract provided.

Genome-Wide Association Study Identifies New Loci Associated With Risk Of Hbv Infection And Disease Progression, Zheng Zeng, Liu Hankui, Xu Huifang, Lu Haiying, Yu Yanyan, Xu Xiaoyuan, Yu Min, Zhang Tao, Tian Xiulan, Xi Hongli, Guan Liping, Zhang Jianguo, Stephen James O'Brien

Biology Faculty Articles

Background: Recent studies have identified susceptibility genes of HBV clearance, chronic hepatitis B, liver cirrhosis, hepatocellular carcinoma, and showed the host genetic factors play an important role in these HBV-related outcomes.

Results: In order to discover new susceptibility genes for HBV-related outcomes, we conducted a genome-wide association study in 1031 Chinese participants, including 275 HBV clearance subjects, 92 asymptomatic persistence infection carriers (ASPI), 93 chronic hepatitis B patients (CHB), 188 HBV-related decompensated cirrhosis patients (DC), 214 HBV-related hepatocellular carcinoma patients (HCC) and 169 healthy controls (HC). In the case-control study, we observed novel locus significantly associated with CHB …

Genomic Adaptations And Evolutionary History Of The Extinct Scimitar-Toothed Cat, Homotherium Latidens, Ross Barnett, Michael V. Westbury, Marcela Sandoval-Velasco, Filipe Garrett Vieira, Sungwon Jeon, Grant Zazula, Michael D. Martin, Simon Y.W. Ho, Niklas Mather, Shyam Gopalakrishnan, Jazmín Ramos-Madrigal, Marc De Manuel, M. Lisandra Zepeda-Mendoza, Agostinho Antunes, Aldo Carmona Baez, Binia De Cahsan, Greger Larson, Stephen J. O'Brien, Eduardo Eizirik, Warren E. Johnson, Klaus Peter Koepfli, Andreas Wilting, Jörns Fickel, Love Dalén, Eline D. Lorenzen, Tomas Marques-Bonet, Anders J. Hansen, Guojie Zhang, Jong Bhak

Biology Faculty Articles

Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1–4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6–8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread …

Ultracontinuous Single Haplotype Genome Assemblies For The Domestic Cat (Felis Catus) And Asian Leopard Cat (Prionailurus Bengalensis), Kevin R. Bredemeyer, Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody E. Roelke-Parker, Stephen James O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy

Biology Faculty Articles

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the …

Karyotype Evolution In 10 Pinniped Species: Variability Of Heterochromatin Versus High Conservatism Of Euchromatin As Revealed By Comparative Molecular Cytogenetics, Violetta R. Beklemisheva, Polina L. Perelman, Natalya A. Lemskaya, Anastasiya A. Proskuryakova, Natalya A. Serdyukova, Vladimir N. Burkanov, Maksim B. Gorshunov, Oliver A. Ryder, Mary Thompson, Gina Lento, Stephen James O'Brien, Alexander S. Graphodatsky

Biology Faculty Articles

Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, Erignathus barbatus), and Otariidae (Eumetopias jubatus, Callorhinus ursinus, Phocarctos hookeri, and Arctocephalus forsteri). Structural and functional chromosomal features were assessed with telomere repeat and ribosomal-DNA probes and by CBG (C-bands revealed by barium hydroxide treatment followed by Giemsa staining) and CDAG (Chromomycin A3-DAPI after G-banding) methods. We demonstrated diversity of heterochromatin among pinniped karyotypes in terms of localization, …

Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain

All HCAS Student Capstones, Theses, and Dissertations

Symbionts within marine sponges are actively participating in the biogeochemical cycles. Among them, the role of symbiont microbes in the sulfur cycle remains a mystery. This study measured the abundance of microbes within the genus Cinachyrella before and after exposure to hydrogen sulfide. A four-part study was conducted: a) five-hour drop experiments, b) vertical distribution experiments, c) five-hour uptake experiments, and d) long-term exposure experiments. The five-hour drop experiment utilized a microsensor to measure sulfide levels, which was lowered 1.0 mm every thirty minutes for a total of 5 hours. Three trials were performed, each with one sponge and a …

A Shark Conservationists Toolbox: Current Dna Methods And Techniques Aiding In The Conservation Of Sharks, Arianna N. Nixon

All HCAS Student Capstones, Theses, and Dissertations

Elasmobranchs are important members of their community. Many sharks are important apex predators that help maintain the health of their ecosystem. However, shark populations are globally declining. This is partially due to the fact that sharks are highly targeted for their fins, meat, liver oil, teeth, and skin. However, they are also killed from anthropogenic effects such as habitat destruction and pollution. Most shark species have life history characteristics that also make them more vulnerable to overfishing. Sharks are also difficult to study due to their elusive nature and identification issues. That is why molecular tools are increasingly becoming important …

Linking Crude Oil And Dispersant Effects To Gene Expression Of Marine Sponge Cinachyrella, Yvain Desplat

All HCAS Student Capstones, Theses, and Dissertations

Because of their filter-feeding lifestyle, sponges (Phylum Porifera) have shown to be bio-accumulators of heavy metals, and bio-monitors for polychlorobiphenyl (PCB) contaminants. Furthermore, marine sponges have been shown to be regulators of reef ecosystems by fulfilling many ecological functions. However, very little is known about their behavior in the face of environmental changes. Consequently, our lab has developed the reef sponge Cinachyrella spp. as novel experimental model. We have designed an experiment to study the effects of WAF (Water Accommodated Fraction), Corexit 9500 dispersant, and CE-WAF (Chemically Enhanced Water Accommodated Fraction)mixtures, in an effort to mimic the conditions of the …

Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

Biology Faculty Articles

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that …

Genome-Wide Sequence Analyses Of Ethnic Populations Across Russia, Daria V. Zhernakova, Vladimir Brukhin, Sergey Malov, Taras K. Oleksyk, Klaus Peter Koepfli, Anna Zhuk, Pavel Dobrynin, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Anna Gorbunova, Ekaterina Chernyaeva, Andrey Shevchenko, Sofia Kolchanova, Alexei Komissarov, Serguei Simonov, Alexey Antonik, Anton Logachev, Dmitrii E. Polev, Olga A. Pavlova, Andrey S. Glotov, Vladimir Ulantsev, Ekaterina Noskova, Tatyana K. Davydova, Tatyana M. Sivtseva

Biology Faculty Articles

The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show …

Characterization Of Bacterial Communities In Biscayne Bay Through Genomic Analysis, Eric Fortman

HCNSO Student Theses and Dissertations

Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. This study examined the bacterial community at 14 stations throughout Biscayne Bay —6 stations were located at the mouths of canals; 1 upstream-canal station; 6 stations in the center of the bay; and one ocean influenced station, located near the entrance to the bay. One liter, surface water samples were …

Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani

HCNSO Student Theses and Dissertations

Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …

Characterization Of The Microbiome And Bioluminescent Symbionts Across Life Stages Of Ceratioid Anglerfishes Of The Gulf Of Mexico, Lindsay L. Freed, Cole Easson, Lydia Baker, D. Fenolio, Tracey Sutton, Yasmin Khan, Patricia Blackwelder, Tory Hendry, Jose Lopez

Biology Faculty Articles

The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities (‘microbiomes’) and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA. Transmission Electron Microscopy was used to characterize the location of symbionts in adult light organs (esca). Whole larval microbiomes, and adult skin and gut microbiomes, were dominated by bacteria in the genera Moritella and Pseudoalteromonas genera. 16S rDNA sequencing results from adult fishes corroborate …

Precision Nomenclature For The New Genomics, Harris A. Lewin, Jennifer A. Marshall Graves, Oliver A. Ryder, Alexander S. Graphodatsky, Stephen James O'Brien

Biology Faculty Articles

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images …

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

Integrated Analysis Of Competing Endogenous Rna Network Revealing Potential Prognostic Biomarkers Of Hepatocellular Carcinoma, Xiwen Liao, Xiangkun Wang, Ketuan Huang, Chuangye Han, Jianlong Deng, Tingdong Yu, Chengkun Yang, Rui Huang, Xiaoguang Liu, Long Yu, Guangzhi Zhu, Hao Su, Wei Qin, Xianmin Zeng, Bowen Han, Quanfa Han, Zhengqian Liu, Xin Zhou, Yizhen Gong, Zhengtao Liu, Jianlv Huang, Cheryl A. Winkler, Stephen J. O'Brien, Xinping Ye, Tao Peng

Biology Faculty Articles

Objective: The goal of our study is to identify a competing endogenous RNA (ceRNA) network using dysregulated RNAs between HCC tumors and the adjacent normal liver tissues from The Cancer Genome Atlas (TCGA) datasets, and to investigate underlying prognostic indicators in hepatocellular carcinoma (HCC) patients. Methods: All of the RNA- and miRNA-sequencing datasets of HCC were obtained from TCGA, and dysregulated RNAs between HCC tumors and the adjacent normal liver tissues were investigated by DESeq and edgeR algorithm. Survival analysis was used to confirm underlying prognostic indicators. Results: In the present study, we constructed a ceRNA network based on 16 …