Biology subjects

Benedict, C.

Publications and source records attributed to Benedict, C..

4 recordsLinked to original sources

bioRxiv2026

The Curious Case of the Golden Orb -- Relict of Relicanthus daphneae (Cnidaria, Anthozoa, Hexacorallia), a deep sea anemone

The discovery and collection of the enigmatic Golden Orb by the NOAA Ship Okeanos Explorer and ROV Deep Discover in deep Alaskan waters during 2023 has yielded substantial interest by the scientific and public communities alike. Initial field identifications of the specimen collected at 3,250 meters depth ranged from an egg mass to sponge to microbial biofilm. Here we characterize the biology and ecology of the Golden Orb, as well as other specimens of similar appearance identified since the collection of the original material. Through an integrative taxonomic approach including morphological analysis and genomic characterization of the Golden Orb, we identified the presence of cnidocytes of the spirocyst type (restricted to Hexacorallia), as well as metazoan DNA, from which we were able to derive complete mitochondrial genomes and Ultra Conserved Elements. These results indicate that the Golden Orb and a similar specimen from deep equatorial waters represent remnant cuticles belonging to the geographically widespread deep-sea anemone ally Relicanthus daphneae. We also document the presence of cuticle from a collected specimen of R. daphneae from the Southern Ocean and in situ photographic evidence of similar cuticles beneath living individuals. These findings underscore the extent to which the biodiversity and organismal biology of obscure deep sea fauna broadly remain unresolved and highlight the value of whole-specimen collections and rigorous taxonomic follow-up in telepresence-enabled ocean exploration.

zoology↗

bioRxiv2019

An epigenetic clock for skeletal muscle

BackgroundAgeing is associated with DNA methylation changes in all human tissues, and epigenetic markers can estimate chronological age based on DNA methylation patterns across tissues. However, the construction of the original pan-tissue epigenetic clock did not include skeletal muscle samples, and hence exhibited a strong deviation between DNA methylation and chronological age in this tissue. MethodsTo address this, we developed a more accurate, muscle-specific epigenetic clock based on the genome-wide DNA methylation data of 682 skeletal muscle samples from 12 independent datasets (18-89 years old, 22% women, 99% Caucasian), all generated with Illumina HumanMethylation arrays (HM27, HM450 or HMEPIC). We also took advantage of the large number of samples to conduct an epigenome-wide association study (EWAS) of age-associated DNA methylation patterns in skeletal muscle. ResultsThe newly developed clock uses 200 CpGs to estimate chronological age in skeletal muscle, 16 of which are in common with the 353 CpGs of the pan-tissue clock. The muscle clock outperformed the pan-tissue clock, with a median error of only 4.6 years across datasets (vs 13.1 years for the pan-tissue clock, p < 0.0001) and an average correlation of {rho} = 0.62 between actual and predicted age across datasets (vs {rho} = 0.51 for the pan-tissue clock). Lastly, we identified 180 differentially methylated regions (DMRs) with age in skeletal muscle at a False Discovery Rate < 0.005. However, Gene Set Enrichment Analysis did not reveal any enrichment for Gene Ontologies. ConclusionsWe have developed a muscle-specific epigenetic clock that predicts age with better accuracy than the pan-tissue clock. We implemented the muscle clock in an R package called MEAT available on Bioconductor to estimate epigenetic age in skeletal muscle samples. This clock may prove valuable in assessing the impact of environmental factors, such as exercise and diet, on muscle-specific biological ageing processes.

bioinformatics↗

bioRxiv2019

Phylogenetic relationships among the clownfish-hosting sea anemones

The clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test 1) the monophyly of each clownfish-hosting family and genus, 2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and 3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly-and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Sticodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.

evolutionary biology↗

bioRxiv2017

Methomyl Injury To Carbon Exchange Rates And Related Processes In Cotton

Some insecticides have the potential to cause varying levels of phytotoxicity. This study examined 1) the time courses of photosynthetic injury in cotton (Gossypium hirsutisms L.) leaves treated with methomyl [S-methyl-N-[(methyl carbamoyl)oxy]-thioacetimidate] and 2) the relationships between carbon exchange rate (CER), stomatal conductance, the chlorophyll fluorescence parameter FX/FP, and ribulose-1,5-bisphosphate carboxylase/ oxygenase (rubisco) activity. Plots were sprayed with either 0 or 0.84 kg methomyl{middle dot}ha-1 when cotton was in mid-reproductive growth. Starting on the day of spraying, CER, stomatal conductance, FX/FP, and rubisco activity were measured daily for five consecutive days [4, 28, 52, 76 and 100 hours after spraying (HAS)]. In methomyl-treated leaves, CER decreased within hours after spraying, reached their lowest point at 28 HAS in experiment I and 76 HAS in experiment II, then recovered near-control levels by 100 HAS. At their lowest points, CER of methomyl-treated leaves decreased from 20 to 50% compared to controls. Stomatal conductance, FX/FP, and rubisco activity followed similar patterns to CER. Stomatal conductance was more closely related to CER than were FX/FP and rubisco activity. Chlorophyll fluorescence recovered more quickly than did CER. Rubisco activity did not decrease till after CER. From the parameters measured in this study, stomatal conductance appeared to be the major factor influencing methomyl-induced changes in CER, although all three parameters may be involved in the process of CER change.\n\nAbbreviations

plant biology↗