Christopher E. Lane
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Let’s Jettison Some Executive Perks: Exploring the SEC and IRS Approaches to Personal Use of Corporate Aircraft Open
In 2023, 46% of the S&P 500 companies provided personal use of corporate aircraft to their chief executive officers, and 31% provided this perk to other named executive officers. This type of executive compensation has notoriously garnered…
View article: DNA Barcoding and Phylogenetic Analysis of Commercially Important Groupers (Serranidae) in Raja Ampat using gene marker Cytochrome c Oxidase I (COI)
DNA Barcoding and Phylogenetic Analysis of Commercially Important Groupers (Serranidae) in Raja Ampat using gene marker Cytochrome c Oxidase I (COI) Open
Groupers are one of the most important and commercial fishes; many of the species are classified as Life Reef Fish Trade (LRFT). The number of grouper species in these locations may be more diverse than at other sites. Identifying the spec…
Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics Open
Ochrophyta is a vast and morphologically diverse group of algae with complex plastids, including familiar taxa with fundamental ecological importance (diatoms or kelp), and a wealth of lesser-known and obscure organisms. The sheer diversit…
Rubble fields shape planktonic protist communities in Indonesia at a local scale Open
The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fi…
Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding Open
Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodini…
Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida) Open
Previous work, using morphological characters, identified a generalist copepod parasite (Pharodes tortugensis) at high prevalence on two common gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin Islands (BVI). DNA bar…
View article: One-Stop Serum Assay Identifies COVID-19 Disease Severity and Vaccination Responses
One-Stop Serum Assay Identifies COVID-19 Disease Severity and Vaccination Responses Open
SARS-CoV-2 has caused over 100,000,000 cases and almost 2,500,000 deaths globally. Comprehensive assessment of the multifaceted antiviral Ab response is critical for diagnosis, differentiation of severity, and characterization of long-term…
Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Background Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidi…
View article: Mitochondrial gene dataset files for: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Mitochondrial gene dataset files for: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Datasets and trees for inferring mitochondrial metabolism. The directory for each gene includes the initial dataset of all potential sequences considered, and the final dataset and aligned dataset used for tree reconstruction, the tree use…
View article: Additional file 15 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Additional file 15 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Additional file 15: Table S6. Presence-absence table for genes involved in apicomplexan mitochondrial metabolism.
View article: Additional file 1 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Additional file 1 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Additional file 1: Table S1. Sources, uses, and BUSCO completeness for data used in this study.
View article: Additional file 10 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Additional file 10 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Additional file 10: Table S4. Genes unique and overlapping between phylogenomic datasets A and B.
View article: Additional file 11 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Additional file 11 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Additional file 11: Table S5. Maximum likelihood topologies produced by unique and shared genes from datasets A and B.
View article: Phylogenomic log files for: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Phylogenomic log files for: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
Log Files from Phylogenomic analyses
Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States Open
Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher pric…
View article: Raw nucleotide assemblies for: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Raw nucleotide assemblies for: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
SPAdes v13 assemblies for newly generated data in this study
View article: Protein assemblies used in: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
Protein assemblies used in: Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans Open
All protein assemblies, in fasta format, used in this study for phylogenomics and/or mitochondrial metabolism analyses. Fasta headers include the original naming scheme and our abbreviated version as: ">TaxonA__0@OriginalHeader"; ">TaxonA_…
Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae Open
Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces , was describe…
Author Correction: Roadmap for naming uncultivated Archaea and Bacteria Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Resistance-Conferring Mycobacterial Mutations and Quantification of Early Bactericidal Activity
Resistance-Conferring Mycobacterial Mutations and Quantification of Early Bactericidal Activity Open
"Resistance-Conferring Mycobacterial Mutations and Quantification of Early Bactericidal Activity." American Journal of Respiratory and Critical Care Medicine, 203(5), pp. 635–637
Metabolic contributions of an alphaproteobacterial endosymbiont in the apicomplexan <i>Cardiosporidium cionae</i> Open
Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces , was describe…
Codependence in the <i>Nephromyces</i> species swarm depends on heterospecific bacterial endosymbionts Open
The phylum Apicomplexa encompasses 6000 ubiquitous animal parasites, including Plasmodium , the most deadly human parasite on Earth. Anciently parasitic lineages, like apicomplexans, lose core metabolic pathways over time, as they evolve l…
Response to Preuss and Zuccarello (2020): biological definitions that can be unambiguously applied for red algal parasites Open
In response to a comment in this issue on our proposal of new terminology to distinguish red algal parasites, we clarify a few key issues. The terms adelphoparasite and alloparasite were previously used to identify parasites that infected …
Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts Open
A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to…
View article: Recruitment tolerance to increased temperature present across multiple kelp clades
Recruitment tolerance to increased temperature present across multiple kelp clades Open
Kelp systems dominate nearshore marine environments in upwelling zones characterized by cold temperatures and high nutrients. Worldwide, kelp population persistence and recruitment success generally decreases with rising water temperatures…
Molecular phylogenetics supports a clade of red algal parasites retaining native plastids: taxonomy and terminology revised Open
Parasitism is a life strategy that has repeatedly evolved within the Florideophyceae. Historically, the terms adelphoparasite and alloparasite have been used to distinguish parasites based on the relative phylogenetic relationship of host …