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Creators/Authors contains: "Anthony, J"

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  1. Free, publicly-accessible full text available February 1, 2027
  2. Methane is a potent greenhouse gas, largely produced by methanogenic archaea, contributing to Earth’s dynamic climate and biogeochemical cycles. In the past decade, metagenomics revealed that lineages outside of the Euryarchaeota superphylum encode genes for methanogenesis. This was recently confirmed through the cultivation of two classes of methanogenic Thermoproteota. Thus far, all methanogens within the Thermoproteota are predicted or were shown to be methylotrophic. The only exception to this are the Nezhaarchaea, for which metagenomic predictions suggest they are CO2-reducing methanogens. Here, we demonstrate methanogenic activity in a third class of Thermoproteota, the Methanonezhaarchaeia. Contrary to genomic predictions for this class, we cultivated a methylotrophic species,CandidatusMethanonezhaarchaeum fastidiosum YNP3N, highlighting the importance of testing metagenomic hypotheses through experimentation. We investigate the metabolic diversity of Methanonezhaarchaeia, including metabolic modifications accompanying frequent loss of methanogenesis in this class. This highlights gaps in our understanding of the biochemistry, diversity, and evolution of thermoproteotal methanogens and their contributions to carbon cycling. 
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    Free, publicly-accessible full text available December 12, 2026
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  4. CRISPR-associated transposons (CASTs) are RNA-guided mobile genetic elements that are widespread in bacterial genomes. Here, we describe the UltraCAST, a suicide vector with the Vibrio cholerae Type I-F CAST system and Golden Gate assembly sites with fluorescent protein gene dropouts for guide RNA and a mini-transposon cargo cloning. We show an example of UltraCAST genome editing by disrupting a gene in the chromosome of Serratia symbiotica CWBI-2.3T, a culturable relative of aphid endosymbionts. The UltraCAST can be used to flexibly insert DNA into specific genomic sites and facilitates testing this genome editing platform in non-model bacterial species that lack genetic tools. 
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    Free, publicly-accessible full text available August 2, 2026
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  7. The issue of fairness in decision-making is a critical one, especially given the variety of stakeholder demands for differing and mutually incompatible versions of fairness. Adopting a strategic interaction of perspectives provides an alternative to enforcing a singular standard of fairness. We present a web-based software application, FairPlay, that enables multiple stakeholders to debias datasets collaboratively. With FairPlay, users can negotiate and arrive at a mutually acceptable outcome without a universally agreed-upon theory of fairness. In the absence of such a tool, reaching a consensus would be highly challenging due to the lack of a systematic negotiation process and the inability to modify and observe changes. We have conducted user studies that demonstrate the success of FairPlay, as users could reach a consensus within about five rounds of gameplay, illustrating the application's potential for enhancing fairness in AI systems. 
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    Free, publicly-accessible full text available May 2, 2026
  8. Abstract Despite the organic molecule inventory detected in the Orion Kleinmann–Low Nebula (Orion KL), acetaldehyde (CH3CHO)—one of the most ubiquitous interstellar aldehydes—has not been firmly identified with millimeter-wave interferometry. We analyze extensive Atacama Large Millimeter/submillimeter Array archival data sets (142–355 GHz) to search for acetaldehyde, revealing two distinct acetaldehyde emission peaks and one component with more complex kinematic structures. One peak aligns with MF10/IRc2, where emissions of other O-bearing complex organic molecules are rarely reported, while the other is coincident with the ethanol peak in the southwest region of the hot core. The MF10/IRc2 detection suggests unique chemistry, possibly influenced by repeated heating events. In contrast, codetection with ethanol indicates an ice origin and suggests a potential chemical relationship between the two species. We determine acetaldehyde column densities and kinetic temperatures toward these two peaks under local thermodynamic equilibrium assumptions and compare its distribution with ethanol and other molecules that have an aldehyde (HCO) group, such as methyl formate, glycolaldehyde, and formic acid. Toward the ethanol peak, the observed abundance ratios between HCO-containing species are analyzed using a chemical model. The model suggests two key points: (1) the destruction of ethanol to form acetaldehyde in the ice may contribute to the observed correlation between the two species; and (2) a long cold-collapse timescale and a methyl formate binding energy similar to or lower than water are needed to explain the observations. The relative abundance ratios obtained from the model are highly sensitive to the assumed kinetic temperature, which accounts for the high spatial variability of the aldehyde ratios observed toward Orion KL. 
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    Free, publicly-accessible full text available July 1, 2026
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  10. Free, publicly-accessible full text available March 10, 2026