Adelaide Rhodes | Nova Southeastern University (original) (raw)

Business Website by Adelaide Rhodes

Personal consultancy for researchers who need help with running ambitious bioinformatics projects... more Personal consultancy for researchers who need help with running ambitious bioinformatics projects with low-cost and free open science resources. I provide training, workflows and manuscript methods descriptions for researchers at low hourly rates.

www.zoologistic.com

Bioinformatic Scientist and Strategic Cloud Consultant Salem, MA I have more than 15 years of exp... more Bioinformatic Scientist and Strategic Cloud Consultant Salem, MA I have more than 15 years of experience in analyzing "big data" at the molecular, organismal, and ecological scales for environmental, metagenomic and human health data. I have experience with experimental design and advanced analytical software programs such as IPA as well as the ability to build bespoke scripts in R, Python, MATLAB, UNIX, and SAS to clean, interrogate and visualize data sets for multidisciplinary teams from the wet lab to the software engineers who maintain the pipelines. I enjoy speeding up and innovating data discovery using the FAIR best practices in test driven development of bioinformatics workflows on HPC and commercial cloud computing resources using advanced workflow tools such as Nextflow, Snakemake, Kubernetes, Cromwell and common workflow languages such as WDL and CWL.

Papers by Adelaide Rhodes

Additional file 6. LW opsin tuning site comparison.

Additional file 4 . Manually curated H. halys chemoreceptor protein sequences.

Additional file 1: Main Supplementary Information text file, including Tables S1-S17 and Figures ... more Additional file 1: Main Supplementary Information text file, including Tables S1-S17 and Figures S1-S18. Table S1. Sequencing, assembly, annotation statistics and accession numbers. Table S2. OrthoDB v10 comparison of five species for ortholog presence and copy-number in Hemiptera-level orthogroups. Table S3. Scaffolds present in the H. halys assembly (accession GCA_000696795.1) that may originate from contaminant sources. Table S4. Counts of repetitive DNA elements encountered in the H. halys genome assembly. Table S5. H. halys predicted protein products associated with the RNAi pathway. Table S6. Positional information for the annotated homeobox genes. Table S7. Nuclear receptors of H. halys. Table S8. Listing of candidate Y-linked genes. Table S9. Number of genes identified as putative cuticle proteins per family in the genome of H. halys. Table S10. Number of genes identified as putative cuticle proteins per species in the genomes of several insect orders. Table S11. Clusters of...

Additional file 2: Figure S2. Skeletal muscle lncRNA expression is consistent between beavers. Sk... more Additional file 2: Figure S2. Skeletal muscle lncRNA expression is consistent between beavers. Skeletal muscle gene expression of each of 187 known and novel lncRNA contigs in the present study and in the Lok et al. study [7]. Each mark corresponds to a single lncRNA contig

Table S4. List of DES on spreadsheets for the up- or down-regulated DES at 1, 2, and 6â h time po... more Table S4. List of DES on spreadsheets for the up- or down-regulated DES at 1, 2, and 6â h time points. These spreadsheets contain the identified nucleotide sequences, annotation, Reads Per Kilobase Million and log2 values for GLV treated samples and their corresponding untreated controls, p-values, FDR and GO terms are on separate spreadsheets for the up- or down-regulated DES at each time point. (XLSX 2883 kb)

Table S2. Table of sequence read counts and percent alignments, at 1, 2, and 6â h time points and... more Table S2. Table of sequence read counts and percent alignments, at 1, 2, and 6â h time points and their corresponding untreated controls. (XLSX 45 kb)

Genes, chromosomes & cancer, Apr 3, 2017

We investigated the correspondence between transcriptome and exome alterations in canine bladder ... more We investigated the correspondence between transcriptome and exome alterations in canine bladder cancer and the correspondence between these alterations and cancer-driving genes and transcriptional alterations in human bladder cancer. We profiled canine bladder tumors using mRNA-seq and exome-seq and used a comparative oncology approach to investigate: (i) the similarity of transcriptional alterations in bladder cancer vs. normal bladder, in humans and canines, at the levels of gene functions, pathways, and cytogenetic regions; and (ii) the extent to which genic mutations in canine bladder cancer are associated with known cancer mutations (from human) as well as alterations in transcript levels in the canine tumor. We found that the transcriptomes of canine and human bladder cancer are remarkably similar at the functional and pathway levels. We demonstrated that canine bladder cancer involves coordinated differential expression of genes within cytogenetic bands, and that these patte...

Nauplius

All content of the journal, except where identified, is licensed under a Creative Commons attribu... more All content of the journal, except where identified, is licensed under a Creative Commons attribution-type BY.

Scientific Data, 2020

Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. ... more Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. These sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

In January 2021, four teams of scientists, clinicians, and developers from around the world worke... more In January 2021, four teams of scientists, clinicians, and developers from around the world worked collaboratively in a virtual hackathon to create a framework for the automated analysis and interpretation of RNA sequencing data in the clinic. This preprint in BioHackrXiv describes SnpReportR: A Tool for Clinical Reporting of RNAseq Expression and Variants aimed for use by clinicians and others without in-depth knowledge of genetics.

Official repository for the Bridging Genomics Data to the Clinic Hackathon hosted virtually in Ja... more Official repository for the Bridging Genomics Data to the Clinic Hackathon hosted virtually in January 2021 by DNAnexus, the OpenCravat Group at Johns Hopkins University, and Carnegie Mellon University Libraries.

Wellcome Open Research

We present a genome assembly from an individual Trachurus trachurus (the Atlantic horse mackerel;... more We present a genome assembly from an individual Trachurus trachurus (the Atlantic horse mackerel; Chordata; Actinopteri; Carangiformes; Carangidae). The genome sequence is 801 megabases in span. The majority of the assembly, 98.68%, is scaffolded into 24 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 25,797 protein coding genes.

Wellcome Open Research , 2022

BioHackrXiv, 2021

With the increasing availability of next-generation sequencing (NGS), patients and nonspecialist ... more With the increasing availability of next-generation sequencing (NGS), patients and nonspecialist health care professionals are obtaining their genomic information without sufficient bioinformatics skills to analyze and interpret the data. In January 2021, four teams of scientists, clinicians, and developers from around the world worked collaboratively in a virtual hackathon to create a framework for the automated analysis and interpretation of RNA sequencing data in the clinic. Here, we present SnpReportR: A Tool for Clinical Reporting of RNAseq Expression and Variants aimed for use by clinicians and others without in-depth knowledge of genetics.

Lockdowns and "stay-at-home" orders, starting in March 2020, shuttered bench and field dependent ... more Lockdowns and "stay-at-home" orders, starting in March 2020, shuttered bench and field dependent research across the world as a consequence of the global COVID-19 pandemic. The pandemic continues to have an impact on research progress and career development, especially for graduate students and early career researchers, as strict social distance limitations stifle ongoing research and impede in-person educational programs. The goal of the Bioinformatics Virtual Coordination Network (BVCN) was to reduce some of these impacts by helping research biologists learn new skills and initiate computational projects as alternative ways to carry out their research. The BVCN was founded in April 2020, at the peak of initial shutdowns, by an international group of earlycareer microbiology researchers with expertise in bioinformatics and computational biology. The BVCN instructors identified several foundational bioinformatic topics and organized hands-on tutorials through cloud-based platforms that had minimal hardware requirements (in order to maximize accessibility) such as RStudio Cloud and MyBinder. The major topics included the Unix terminal interface, R and Python programming languages, amplicon analysis, metagenomics, functional protein annotation, transcriptome analysis, network science, and population genetics and comparative genomics. The BVCN was structured as an open-access resource with a central hub providing access to all lesson content and hands-on tutorials (https://biovcnet.github.io/). As laboratories reopened and participants returned to previous commitments, the BVCN

Nature - Scientific Data, 2020

Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. ... more Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. these sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

www.zoologistic.com

Additional file 6. LW opsin tuning site comparison.

Additional file 4 . Manually curated H. halys chemoreceptor protein sequences.

Genes, chromosomes & cancer, Apr 3, 2017

Nauplius

Scientific Data, 2020

Wellcome Open Research

Wellcome Open Research , 2022

BioHackrXiv, 2021

Nature - Scientific Data, 2020

Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. ... more Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. these sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

Nature: Behind the Paper, 2020

An organism known since the inception of Linnaean taxonomy still has more to reveal in its geneti... more An organism known since the inception of Linnaean taxonomy still has more to reveal in its genetics and in its partnership with a drug-producing bacterial symbiont.

BMC Genomics, 2020

Background: Long noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecul... more Background: Long noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations. However, for many mammalian species, the absence of a genome assembly precludes the comprehensive identification of lncRNAs. The genome of the American beaver (Castor canadensis) has recently been sequenced, setting the stage for the systematic identification of beaver lncRNAs and the characterization of their expression in various tissues. The objective of this study was to discover and profile polyadenylated lncRNAs in the beaver using high-throughput short-read sequencing of RNA from sixteen beaver tissues and to annotate the resulting lncRNAs based on their potential for orthology with known lncRNAs in other species. Results: Using de novo transcriptome assembly, we found 9528 potential lncRNA contigs and 187 high-confidence lncRNA contigs. Of the high-confidence lncRNA contigs, 147 have no known orthologs (and thus are putative novel lncRNAs) and 40 have mammalian orthologs. The novel lncRNAs mapped to the Oregon State University (OSU) reference beaver genome with greater than 90% sequence identity. While the novel lncRNAs were on average shorter than their annotated counterparts, they were similar to the annotated lncRNAs in terms of the relationships between contig length and minimum free energy (MFE) and between coverage and contig length. We identified beaver orthologs of known lncRNAs such as XIST, MEG3, TINCR, and NIPBL-DT. We profiled the expression of the 187 high-confidence lncRNAs across 16 beaver tissues (whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovary, placenta, castor gland, tail, toe-webbing, and tongue) and identified both tissue-specific and ubiquitous lncRNAs.

The Allied Genetics Conference, 2020

The advent of the “personal genome” is revolutionizing how we derive medical insight from whole-g... more The advent of the “personal genome” is revolutionizing how we derive medical insight from whole-genome DNA sequencing for individuals. Sequencing millions of personal genomes integrated with phenotype (observable (BMI) versus inherited (eye color) characteristics) and personal medical data creates data storage and analytical challenges on an unprecedented scale. Researchers are developing a new generation of algorithms to overcome limitations of approaches that rely on mapping sequences to one consensus human reference genome, which is not a “one-size-fits-all” solution to medical research, as it was built from few individuals - resulting in missing data and large discrepancies when applied to diverse populations. Having reference genomes that are customized for ancestry, phenotype and disease state can provide more specific insights that lead to effective treatments. The ability to store and analyze multiple reference genomes on the cloud will be a fundamental building block in this new research paradigm.

This poster describes a journey from the familiar to the possible by deep-diving into some of the latest tools available in the cloud stratosphere to support data-driven discovery for “personal genomics” by optimizing the use of new and existing analytics tools for researchers. This demonstration provides best practices to get the most out of databases for genomics applications and simple ML to examine cohorts and populations using pan-genomes, a compilation of a representative genome for a given population. We’ll also explore the potential of AI and ML high-throughput data analysis tools to speed up research insights from personal genomes.

F1000 Research for Open Science, 2019

The lack of readily accessible large scale public genomic data sets currently limits the reproduc... more The lack of readily accessible large scale public genomic data sets currently limits the reproducibility of published biomedical research to a subset of authorized users. Tool developers, educators, journal editors and researchers alike are affected by the lack of open access genomic datasets appropriate for reproducing biologically meaningful analysis at scale. We will present a prototype pipeline that promotes reproducible analysis by making it easy to generate publicly shareable custom synthetic datasets. The prototype workflow links existing tools into a consolidated community resource for generating synthetic data cheaply and efficiently. We will demonstrate how to use this workflow on Broad Institute's open access Terra platform, to reproduce someone else's analysis and make your own work reproducible. The workflow, as written, is portable to any cloud platform that runs the Cromwell Engine, an open source scientific Workflow Management System.

This presentation was given as part of the Earth BioGenome Project's joing meeting with the V... more This presentation was given as part of the Earth BioGenome Project's joing meeting with the Vertebrate Genome Project in the Fall of 2019 at Rockefeller University in New York City. The Earth BioGenome Project is a collaboration among partner institutions that have the common goal of sequencing and annotating the genomes of all 1.5 million known eurkaryotic species (animals, plants, fungi, protozoa and other microbes). There are 25 member institutions and more than 20 large-scale projects affiliated with the organization since its official launch in November 2018 in London. The members of EBP hope to create a new foundation for biology to drive solutions for preserving biodiversity and sustaining human societies.<br>I am a member of the Arthropod i5K and Global Invertebrate Genomics Alliance groups and have delivered training to the Conservatoin Genomics group (Vertebrate 10K). I wanted to speak to how the students of the world can participate in our conferences using the ...

The academic job market is rapidly filling with low-wage, low-security positions. According to th... more The academic job market is rapidly filling with low-wage, low-security positions. According to the Department of Education, more than 40% of teaching staff at universities are part-time faculty without tenure or adjunct faculty. This has left an entire generation of talented scientists with poor academic employment prospects. Students and post-docs who want to prepare for a career in industry must pursue those skills independently. To the recent graduate who has spent the past 10 years thinking about an academic career, the prospect of retraining for the private sector may seem daunting.

We aim to provide students and scientists information about 1) What they can do now to prepare for a career in the private sector, 2) How to start their own science-based company, and 3) The many misconceptions about industry. This workshop will focus on resources and best practices for transitioning from academia to industry including, but not limited to 1) Interview and resume skills, 2) Differences and similarities between academia and industry, 3) Discovering your value proposition, 4) Navigating SBIR and STTR, and 5) Finding resources for starting your own company.

Co-convened this workshop with Anne Thessen at the Coastal and Estuarine Research Foundation meeting 2015

In April 2010, the Deepwater Horizon blowout resulted in the largest oil release in American his... more In April 2010, the Deepwater Horizon blowout resulted in the largest oil release in American history. The release was two incidents: the common surface slick, and a subsurface deep water plume depositing oil to sediments. In fall 2010, benthic cores were collected in the deep sea at depths from 76 m to 2767 m. Stations ranged from < 1 km to approximately 200 km from the DWH wellhead. Annelid and crustacean assemblages were analyzed and compared. These taxa were chosen because of their differing feeding strategies (deposit vs. suspension feeders), habits (burrowing vs. crawling) and different sensitivity to pollution (generally greater for crustaceans). Abundance, family diversity and annelid:crustacean ratios were examined as possible bioindicators of spill effects. Community composition was analyzed at various distances from the spill using multivariate statistical analyses. This study presents results for over two years of work performed to assess potential impacts of the blowout to deep sea benthos.

Biological diversity, on average, increases community stability by harboring a variety of or... more Biological diversity, on average, increases community stability by harboring a variety of organisms that can respond to environmental fluctuations and maintain ecosystem function after a perturbation. However, when using traditional multivariate analyses to assess ecological integrity, occurrences of rare species are often transformed and removed. Even though biodiversity is a standard measure for assessing ecosystem integrity, the debate is not settled on whether rare species can be removed from data sets without having an impact on ecological assessment. It is possible that the property of rarity itself (proportion of rare species over various temporal and spatial scales) could improve ecological assessments of biodiversity. The signal of rare species occurrence may also contain additional information on the resilience and recovery rate of ecosystems.
This presentation will compare common measures of ecological integrity utilizing various long-term data sets of macrobenthos
in Texas Bays and Estuaries to investigate how rare organisms complement patterns of ecosystem stability. For example, are rare organisms observed more frequently in certain seasons? Does the proportion of rare organisms at a given site or time correlate with other measures of ecosystem health? Does the inclusion/exclusion of rare species in multivariate analyses impact the relative assessment of ecosystem health between sites and times?

Hydrothermal vents, cold seeps and whale falls are unique ecosystems found in the deep benthos ar... more Hydrothermal vents, cold seeps and whale falls are unique ecosystems found in the deep benthos around the world. A common food web structure is found at each location type, even though species composition differs between vents and seeps, which have different components for chemosynthesis. Utilizing presence/absence data and known environmental factors, we found abiotic and biotic correlations that may determine the distribution of the most common organisms inhabiting these specialized environments. Using general linear models, we found significant relationships between the most widely distributed genera and environmental factors. The most commonly found species, the polychaete Amphisamytha galapagensis, was found to be negatively correlated with oxygen concentrations. The ability to persist in anoxic conditions may allow Amphisamytha galapagensis to become widely distributed. The bivalve Bathymodiolus was found to be positively correlated and the bivalve Calyptogena was found to be negatively correlated to phosphate concentrations. Differing biogenic pathways may lead to slightly varying ecological niches that also correlate with phosphate concentrations. Members of the most common crustacean genus encountered, the squat lobster Munidopsis, were found to be positively correlated with the presence of the two most common bivalve genera, Bathymodiolus and Calyptogena. This significant correlation could indicate a common food source.

The parasitic crustacean taxon Tantulocarida contains 36 species in 23 genera known from eastern ... more The parasitic crustacean taxon Tantulocarida contains 36 species in 23 genera known from eastern Atlantic, Indo-West Pacific and Antarctic waters. To date, none have been reported from the western Atlantic Ocean. We report here on a new species of tantulocarid, apparently a species of Microdajus based on light microscopy observations, collected at 684 m on a new species of Typhlotanaidae (Crustacea: Tanaidacea) in the Gulf of Mexico. 75% (6/8) of these tanaid host specimens in a single core were infested. The unique and complex life cycle of tantulocarids is reviewed and additional evidence provided based on this new material. The biogeographic and bathymetic implications of the new species discovery are discussed: Tantulocarida is postulated to have a global distribution where suitable tanaid hosts (all currently known to belong to Paratanaoidea) are present and a wide depth range from 20 to nearly 3000 m. Tantulocarids are often found on locations on hosts (antennae, chelipeds) where the likelihood of mechanical removal is high, suggesting that the host behavior is modified to prevent parasite removal.

A striking color polymorphism exists in diaptomids inhabiting adjacent alkaline lakes in the Gran... more A striking color polymorphism exists in diaptomids inhabiting adjacent alkaline lakes in the Grand Coulee area of Eastern Washington. These highly alkaline lakes were formed following the last Ice Age, when the Columbia River became channelized. Copepods isolated from Soap Lake exhibit higher levels of red pigmentation at all times of the year in comparison to copepods from Lake Lenore. Nutrients, salinity, light and predation pressure have all been proposed to explain the difference in pigmentation between the lakes. Copepods from Lake Lenore cannot be induced to express the bright red coloration of Soap Lake copepods, even though Soap Lake copepods can lose their color in the lab. An alternative hypothesis to explain the difference in coloration between the populations of diaptomid copepods is genetic adaptation to the more stressful environment of Soap Lake. It is possible that copepods from Soap Lake and Lake Lenore represent parapatric groups formed by dispersal from allopatric Pleistocene refugia during the formation of the Grand Coulee. Soap Lake is deeper, saltier and more alkaline than Lake Lenore, and the lakes are not connected. These unique mineral and geological conditions could have led to a genetic divergence in coloration, enhanced by the more extreme alkalinities experienced by Soap Lake diaptomid copepods. Carotenoid biosynthesis might be increased in Soap Lake copepods due to a shared pathway for lipid desaturation utilizing oxidoreductase. The production of carotenoids increases antioxidant activity and allows for lipid storage and utilization in highly alkaline conditions. It is possible that intense red color is a byproduct of basic metabolic functions involving lipid storage and utilization in copepods. The function of carotenoid genes in Soap Lake diaptomids could provide clues as to why so many species of copepods in extreme environments are bright red.

For this study, historic data from research cruises composed of more than 8,000 biogeographic obs... more For this study, historic data from research cruises composed of more than 8,000 biogeographic observations were compared to data gathered during research cruises led by Texas A&M University-Corpus Christi, Harte Research Institute (TAMUCC-HRI) and the US Geological Survey. The depths targeted by these monitoring cruises (below 1000 m) have been historically undersampled for tanaidacean diversity. New observations from these expeditions have increased total bathyal tanaidacean observations in the Northern Gulf of Mexico (GOM) by 12% (more than 1,000 observations) over previous sampling efforts. Of the approximately 1200 global species of tanaidaceans, 109 were found in the bathyal GOM. More than 10 genera and at least 1 family of tanaidaceans were new records for this region. Minimum and maximum depth ranges of several known families have been expanded. Diversity estimates based on these new observations indicate that tanaidacean diversity is significantly higher than previously reported (e.g. a 72% increase in species richness between 1000 m and 1500 m and a 216% increase in species richness between 1500 m and 2000). These new observations demonstrate that diversity estimates of tanaidaceans in the bathyal region of the GOM have been historically underestimated and are sensitive to sampling effort. Our results suggest that diversity estimates will increase as our expertise and sampling effort increases not only for tanaidaceans, but in other deep-sea taxa as well.

Meiobenthic harpacticoid copepod abundance and diversity were compared among three sites tha... more Meiobenthic harpacticoid copepod abundance and diversity were compared among three sites that differ in impact from freshwater releases from an inland lake. These manmade releases from Lake Okeechobee increase soft sediments and lower the salinity in the coastal Indian River Lagoon. Understanding the effects of these releases on the benthos may assist managers in planning the timing and duration of freshwater inputs to minimize impacts.
Copepod abundance ranged from 60 to 413 in the cores and from 7 to 126 in the core water. The site furthest away from the mouth of the river and considered to be the most pristine did
have the highest summer abundance (322), but the lowest winter abundance (106). The site between the river and ocean inlet had a mix of species at both times of the year, with increasing abundance from summer (184) to winter (304). The site closest to the mouth of the river and presumed to be the most disturbed had comparable abundances in summer (183) and winter (226) comprised mainly of Longipedia americana (59% in summer, 31% in winter). Longipedia americana has been described as an emergent species, which allows it to disperse in limited geographic areas. However, L. americana has not been previously noted in such high abundance in benthic core samples in other estuarine or coastal systems. Due to the shifting densities among the sites, L. americana does not appear to have a seasonal
pattern. The high abundance in the sediment and core water at the most disturbed location at both times of the year and in the sediment at the other sites in the winter may indicate that L.
americana is an opportunistic species in the Indian River Lagoon.

Differences in abundance and diversity of benthic invertebrates were measured at three sites in t... more Differences in abundance and diversity of benthic invertebrates were measured at three sites in the Indian River Lagoon using two different sampling methods. Three sampling sites were chosen in relation to the St. Lucie Estuary: near the mouth, in the middle of the lagoon, and at Peck’s Lake near the inlet. These sites are part of the Comprehensive Everglades Restoration Plan (CERP) quarterly monitoring program, funded by the Army Corps of Engineers and South Florida Water Management District. Three grabs using a petite Ponar (232 cm2) and eight cores using an Ogeechee core device (17.9 cm2) were taken at each site in summer 2010. Petite Ponar grabs were sieved in the field through a 500 micron metal mesh screen (1810 cm2) and preserved in 5% formalin stained with Rose Bengal. Core samples from 0-2 cm were also taken, preserved and stained. Upon return to the lab, core samples were passed through a 500 micron NitexTM mesh screen (71.6 cm2) and sorted. In the cores 2,713 specimens were sorted into 18 taxonomic groups. The Ponar grabs contained 4,543 specimens in 19 taxonomic groups. Fifteen groups were shared by both methods. Two biotic diversity indices were calculated: Shannon-Weiner (H’) and AMBI. While all sites were ranked as “slightly disturbed” by AMBI, the estimates from the core data were significantly higher, and hence, more disturbed than the estimates for the Ponar data for the mid-Lagoon and Peck’s Lake sites (p < 0.05). Conversely, the Shannon-Weiner index indicated a significantly higher (and healthier) value for the Peck’s Lake site (p < 0.05) and no differences among sites when the core data were used.

Nitokra lacustris Shmankevich, an epibenthic, coastal harpacticoid copepod species, is shown to p... more Nitokra lacustris Shmankevich, an epibenthic, coastal harpacticoid copepod species, is shown to provide several advantages for use as a live feed in the aquaculture of marine fish. This study addresses culture methods, population growth rate prediction, fatty acid composition and carotenoid content of N. lacustris. The highly consistent growth rate and the high proportion of highly unsaturated fatty acids (HUFA) and astaxanthin indicate that this species also has potential as a fish oil replacement in the animal feeds industry. Nitokra lacustris was chosen as the test organism because of its small size, short generation time, high reproductive rates, and potential to contain substantial concentrations of long-chain HUFA and ketocarotenoid pigments. The ability of harpacticoid copepods to synthesize HUFA and ketocartenoids may be related to the highly variable coastal habitats of theses species. HUFA and carotenoids are important in energy storage and protection from cell membrane degradation for many marine plants and animals. Nitokra lacustris contains a high amount of the essential fatty acids DHA and EPA as well as the essential carotenoid pigment astaxanthin, when compared to other live feeds (rotifers and Artemia). N. lacustris is also able to convert HUFA and astaxanthin from a diet that is deficient in these nutrients. The ability of N. lacustris to bioconvert essential fatty acids and carotenoid pigments without the addition of fish oil represents a potential new source of HUFA and astaxanthin for the animal feeds industry as well as for human health supplements.

Please pay attention to the comments section for a full list of credits. The camera cut off some... more Please pay attention to the comments section for a full list of credits. The camera cut off some of the credits in place in the slides.

Copepods-TR-Ep69 ReleasedSep 01, 2006 Copepods, you think you know them? well in this show im... more Copepods-TR-Ep69
ReleasedSep 01, 2006

Copepods, you think you know them? well in this show im joined by Dr. Adelaide Rhodes, a world recognized expert on Copepods. Adelaide will take us though the in's and out's of copepods and what they mean to out tanks today, and in the future. In this show we discuss - What are copepods - Identifying copepods - What are copepods good for - How to get copepods in your system - Breeding copepods in and out of your tank - And much more

In today’s data-heavy research environment, wet-lab scientists can benefit from new computational... more In today’s data-heavy research environment, wet-lab scientists can benefit from new computational skills.

PLoS Biology (in press), Nov 25, 2014

I presented on free biogeographic tools and taxonomy resources on that can be used to construct i... more I presented on free biogeographic tools and taxonomy resources on that can be used to construct individual species distributions. This work is important for developing quality data on the distribution of any endangered species. Some of the challenges my talk presented solutions to included: updating synonymy with WoRMs web service tools, adding ocean depths to coordinate data using Google Earth API applications and free mapping tools such as Google Fusion Tables.

Nature Communications, 2021

About 20–25% of dengue virus (DENV) infections become symptomatic ranging from self-limiting feve... more About 20–25% of dengue virus (DENV) infections become symptomatic ranging from self-limiting fever to shock. Immune gene expression changes during progression to severe dengue have been documented in hospitalized patients; however, baseline or kinetic information is difficult to standardize in natural infection. Here we profile the host immunotranscriptome response in humans before, during, and after infection with a partially attenuated rDEN2Δ30 challenge virus (ClinicalTrials.gov NCT02021968). Inflammatory genes including type I interferon and viral restriction pathways are induced during DENV2 viremia and return to baseline after viral clearance, while others including myeloid, migratory, humoral, and growth factor immune regulation factors pathways are found at non-baseline levels post-viremia. Furthermore, pre-infection baseline gene expression is useful to predict rDEN2Δ30-induced immune responses and the development of rash. Our results suggest a distinct immunological profile for mild rDEN2Δ30 infection and offer new potential biomarkers for characterizing primary DENV infection.

Aimee Massey Ph.D. dissertation. Thank you for the acknowlegement!

Ecosphere, 2021

DNA metabarcoding has become a powerful technique for identifying the species present in a bulk e... more DNA metabarcoding has become a powerful technique for identifying the species present in a bulk environmental sample. The application of DNA metabarcoding to wildlife diet analysis is a particularly promising tool for exploring trophic interactions. The extent to which molecular approaches agree with traditional approaches, and how this varies with the quality of field-collected scats, is unknown. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were to (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear were the primary prey species, but metabarcoding revealed a more diverse diet with greater occurrence of rare species. However, there was a large discrepancy in the occurrence of beaver in scats (52% and 25% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. While the number of wolf sequence reads for fresh scats was nearly eight times higher than in degraded scats, neither the number of prey sequence reads nor the quantity of DNA to be sequenced varied between fresh and degraded scats suggesting that metabarcoding is sensitive enough to determine prey assemblages in degraded scats. Even using scats from extremely wet conditions hostile to DNA preservation, we found that metabarcoding was more effective than mechanical sorting in describing diet.

Journal of Fisheries and Aquatic Science, 1997

This study aims to introduce diets that are more affordable and applicable, compared to algal die... more This study aims to introduce diets that are more affordable and applicable, compared to algal diet, which is time consuming and costly in maintenance.
Methodology:
The present study was designed for 15 days to observe the effects of different diets on population growth of marine tropical harpacticoid copepod, Stenhelia stephensoni under laboratory condition. The constant value of salinity was at 28 PSU and temperature at 27° C.

Co-Authors: M Fatimah Atirah, ML Shabdin, AR Khairul Adha, MT Zakirah, N Awangku Shahrir, JG Stottrup, NH Norsker, JO Evjemo, KI Reitan, Y Olsen, G Drillet, S Frouel, MH Sichlau, PM Jepsen, JK Hojgaard, AK Joarder, BW Hansen, K Zaleha, I Busra, LA Copeman, CC Parrish, JA Brown, M Harel, J Sargent, L McEvoy, A Estevez, G Bell, M Bell, J Henderson, D Tocher, T Benitez-Santana, R Masuda, EJ Carrillo, E Ganuza, A Valencia, CM Hernandez-Cruz, MS Izquierdo, MS Izquierdo, B Sun, JW Fleeger, CJ Cutts, JW Fleeger, P Pepin, RW Penney, I Olivotto, F Capriotti, I Buttino, AM Avella, V Vitiello, F Maradonna, O Carnevali, C Rajthilak, P Santhanam, A Anusuya, A Pazhanimuthu, R Ramkumar, N Jeyaraj, P Perumal, M Gee, D Delbare, P Dhert, P Lavens, R Huys, RL Herman, C Heip, BA Abdullahi, A Rhodes, L Boyd, AC Puello-Cruz, S Mezo-Villalobos, B Gonzalez-Rodriguez, D Voltolina, JNC Whyte, N Bourne, CA Hodgson, Q Zhang, G Uhlig, N Jeyaraj, P Santhanam, P Raju, S Ananth, K Jothiraj, R Gaudy, JP Guerin, M Moraitou-Apostolopoulou, GRF Hicks, BC Coull, HM Matias-Peralta, FM Yusoff, M Shariff, S Mohamed, WA Wurts, EJ Ansa, J Jiya, F Fiers, V Ghenne, HA Meyer, SS Bell, T Mascart, G Lepoint, S Deschoemaeker, M Binard, F Remy, M de Troch, CJ Corkett, IA McLaren, HG Dam, RM Lopes

Journal of Experimental Marine Biology and Ecology, 2014

ABSTRACT Many investigators need to determine whether individuals belong to the same species. DNA... more ABSTRACT Many investigators need to determine whether individuals belong to the same species. DNA-sequence data have helped with this task, but current procedures of DNA isolation from millimeter-scale crustaceans, such as harpacticoid copepods, leave little to no voucher material for morphological analysis, and many procedures yield only enough DNA for a single amplification reaction. We therefore developed a DNA-isolation procedure that yielded essentially intact exoskeletons and sufficient DNA for multiple polymerase chain reactions. DNA-amplification success of our DNA-isolation procedure was relatively insensitive to (1) the length of preservation time from sample collection to DNA isolations and (2) the length of time the DNA was stored at − 20 °C after isolation. An additional benefit of our procedure is therefore that the DNA isolated is relatively stable. Primers available for the nuclear 18S rRNA gene and the mitochondrial cytochrome oxidase b (cytb) gene are known not to work for many harpacticoids. We therefore designed primers that would amplify and sequence an ~ 750-base-pair fragment of the 18S rRNA gene and others that would amplify and sequence an ~ 450-base-pair fragment of the cytb gene. Both primer sets worked for at least 12 harpacticoid families.

Journal of Heredity, 2013

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles ... more Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.

PLOS and the PLOS ONE editorial team would like to express our tremendous gratitude to all those ... more PLOS and the PLOS ONE editorial team would like to express our tremendous gratitude to all those individuals who participated in the peer review process this past year at PLOS ONE. 2014 was an amazing year for PLOS ONE; during the year, over 80,000 reviewers from around the world and across disciplines provided their expert input that led to publication of over 30,000 articles.
The names of our 2014 PLOS ONE reviewers are listed in S1 Reviewer List. It’s a lengthy list rivaled only by the depth of our gratitude. Thank you to all our reviewers for generously sharing your time, insight and expertise with PLOS ONE authors in the evaluation of their work.
Your efforts are a key reason PLOS ONE is a successful publication and continues to be a force for positive change in scientific and medical publishing.

Journal of Experimental Marine Biology and Ecology, Jun 30, 2014

Journal of Experimental Marine Biology and Ecology, Dec 21, 2011

Recent advances in robotic technologies provide new opportunities to conduct high-resolution samp... more Recent advances in robotic technologies provide new opportunities to conduct high-resolution sampling of patchily distributed zooplankton and associated environmental variables. We used two robots and molecular probes to assess the temporal and spatial variability of zooplankton in water samples obtained from Monterey Bay, California. The Autonomous Underwater Vehicle (AUV) Dorado is a mobile platform that carries ten, 1.8-L bottles ("Gulpers") capable of rapidly acquiring discrete seawater samples, and an extensive sensor suite for gathering contextual environmental data during day-long expeditions. Molecular assays were conducted ex situ at a shore-based laboratory. In contrast, the Environmental Sample Processor (ESP) was deployed as a stationary (moored) device capable of repeatedly "sipping" water to conduct in situ molecular assays and record environmental data during month-long deployments. Molecular analyses were conducted with the sandwich hybridization assay (SHA), which employed 18S ribosomal RNA oligonucleotide probes designed to detect calanoid and podoplean copepods, and the larvae of barnacles, mussels, polychaete worms, brachyuran crabs, and invasive green crabs (Carcinus maenas). Both the stationary and mobile sampling protocols revealed the greatest zooplankton diversity and abundance in relatively warm waters, higher in chlorophyll and lower in salinity and nitrate. Diversity and abundance were least in recently upwelled waters with the inverse conditions. High-resolution sampling revealed that while calanoid copepods were generally associated with elevated chlorophyll, they were most abundant in upwelling fronts, in some cases. These narrow features appear to provide favorable conditions for the growth and aggregation of certain zooplankton.

Journal of Heredity, Jul 15, 2013

In business since 2003….. 2020 --- we are on hiatus indefinitely Ocean Pods is a unique produc... more In business since 2003…..

2020 --- we are on hiatus indefinitely

Ocean Pods is a unique product for the hobbyist. It is a combination of 3 species of copepods for starting or restocking your live rock copepod populations.

Ocean Pods are 100% aquacultured copepods that have been field-tested with multiple species of fish and invertebrates to ensure that there are not harmful interactions with your tank inhabitants.

They can be added directly to your tank and make a great live food for mandarin gobies, seahorses, pipefish, yellow tangs, clownfish, scooter blennies, corals, ornamental shrimp and many more species enjoyed by reef enthusiasts.

2020 --- we are on hiatus indefinitely

The Deepwater Horizon (DWH) accident in the northern Gulf of Mexico occurred on April 20, 2010 at... more The Deepwater Horizon (DWH) accident in the northern Gulf of Mexico occurred on April 20, 2010 at a water depth of 1525 meters, and a deep-sea plume was detected within one month. Oil contacted and persisted in parts of the bottom of the deep-sea in the Gulf of Mexico. As part of the response to the accident, monitoring cruises were deployed in fall 2010 to measure potential impacts on the two main soft-bottom benthic invertebrate groups: macrofauna and meiofauna. Sediment was collected using a multicorer so that samples for chemical, physical and biological analyses could be taken simultaneously and analyzed using multivariate methods. The footprint of the oil spill was identified by creating a new variable with principal components analysis where the first factor was indicative of the oil spill impacts and this new variable mapped in a geographic information system to identify the area of the oil spill footprint. The most severe relative reduction of faunal abundance and diversity extended to 3 km from the wellhead in all directions covering an area about 24 km2. Moderate impacts were observed up to 17 km towards the southwest and 8.5 km towards the northeast of the wellhead, covering an area 148 km2. Benthic effects were correlated to total petroleum hydrocarbon, polycyclic aromatic hydrocarbons and barium concentrations, and distance to the wellhead; but not distance to hydrocarbon seeps. Thus, benthic effects are more likely due to the oil spill, and not natural hydrocarbon seepage. Recovery rates in the deep sea are likely to be slow, on the order of decades or longer.

PLoS biology, 2014

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to oth... more Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolv...

Ag Data Commons U.S. Ag Data Commons, DEPARTMENT OF AGRICULTURE, 2021

Additional file 3: Supplementary Data 1. [SuppData1.txt] Text file of 9528 potential lncRNA trans... more Additional file 3: Supplementary Data 1. [SuppData1.txt] Text file of 9528 potential lncRNA transcript contigs, in FASTA format. These contigs have no known orthologs (by BLASTn) and low coding potential scores (CPAT p

Additional file 5: Table S1. Manual curation of the 40 known lncRNAs. Columns are as follows: Con... more Additional file 5: Table S1. Manual curation of the 40 known lncRNAs. Columns are as follows: Contig, the query contig's identifier; Category, the classification of the contig ("probable lncRNA" or "possible lncRNA", as per Methods Sec. "BLASTn-based classification of noncoding transcript contigs"); Matching Sequence (subject), the subject sequence identifier(s) as per BLASTn; Species, the species of the subject from the previous column; Description, the BLASTn descriptor of the subject sequence; E-value, BLASTn provided E-value for the query-subject pair; %ID, BLASTn provided percent identity between the contig and matching query sequence; length of match, BLASTn provided length, in nucleotides, of query-subject alignment. Only those subject-query pairs that were retained after steps 1 and 2 of curation, as described in the Methods Section, "BLASTn-based classification of noncoding transcript contigs", are included in the table. Contigs a...

Table S3. Table describing the GLV transcriptome values, contig length range and # of unique sequ... more Table S3. Table describing the GLV transcriptome values, contig length range and # of unique sequences (XLSX 40 kb)

Table S5. List of DES on spreadsheets for the up- or down-regulated DES Venn comparisons at 1, 2,... more Table S5. List of DES on spreadsheets for the up- or down-regulated DES Venn comparisons at 1, 2, and 6â h time points. These spreadsheets contain the locus designations, annotation and GO terms, and log2 values for GLV treated samples and their corresponding untreated controls, for the up- or down-regulated DES for each related group shown in the Venn diagrams (Fig. 3). (XLSX 884 kb)

Additional file of Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpi... more Additional file of Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Additional file 2. H. halys gene expression omnibus (per RNA-Seq data).

Additional file 3. H. halys transcription factor details.

Additional file 7. Y-linked gene sequences.