Flatworm Transcriptomes Reveal Widespread Parasitism by Histophagous Ciliates.

Unicellular ciliates like Tetrahymena are best known as free-living bacteriovores, but many species are facultative or obligate parasites. These "histophages" feed on the tissues of hosts ranging from planarian flatworms to commercially important fish and the larvae of imperiled freshwater mussels. Here, we developed a novel bioinformatics pipeline incorporating the nonstandard ciliate genetic code and used it to search for Ciliophora sequences in 34 publicly available Platyhelminthes EST libraries. From 2,615,036 screened ESTs, we identified nearly 6,000 high-confidence ciliate transcripts, supporting parasitism of seven additional flatworm species. We also cultured and identified Tetrahymena from nine terrestrial and freshwater planarians, including invasive earthworm predators from the genus Bipalium and the widely studied regeneration models Dugesia japonica and Schmidtea mediterranea. A co-phylogenetic reconstruction provides strong evidence for the coevolution of histophagous Ciliophora with their Platyhelminthes hosts. We further report the antiprotozoal aminoglycoside paromomycin expels Tetrahymena from S. mediterranea, providing new opportunities to investigate the effects of this relationship on planarian biology. Together, our findings raise the possibility that invasive flatworms constitute a novel dispersal mechanism for Tetrahymena parasites and position the Platyhelminthes as an ideal model phylum for studying the ecology and evolution of histophagous ciliates.

FLATWORM TRANSCRIPTOMES REVEAL WIDESPREAD PARASITISM BY HISTOPHAGOUS CILIATES.

Unicellular ciliates like Tetrahymena are best known as free-living bacteriovores, but many species are facultative or obligate parasites. These 'histophages' feed on the tissues of hosts ranging from planarian flatworms to commercially important fish and the larvae of imperiled freshwater mussels. Here, we developed a novel bioinformatics pipeline incorporating the nonstandard ciliate genetic code and used it to search for Ciliophora sequences in 34 publicly available Platyhelminthes EST libraries. From 2,615,036 screened ESTs, we identified nearly 6,000 high-confidence ciliate transcripts, supporting parasitism of seven additional flatworm species. We also cultured and identified Tetrahymena from nine terrestrial and freshwater planarians, including invasive earthworm predators from the genus Bipalium and the widely studied regeneration models Dugesia japonica and Schmidtea mediterranea. A cophylogenetic reconstruction provides strong evidence for coevolution of histophagous Ciliophora with their Platyhelminthes hosts. We further report the antiprotozoal aminoglycoside paromomycin expels Tetrahymena from S. mediterranea, providing new opportunities to investigate the effects of this relationship on planarian biology. Together, our findings raise the possibility that invasive flatworms constitute a novel dispersal mechanism for Tetrahymena parasites and position the Platyhelminthes as an ideal model phylum for studying the ecology and evolution of histophagous ciliates.

Quantitative Analysis of Planarian Pigmentation.

The ommochrome and porphyrin body pigments that give freshwater planarians their brown color are produced by specialized dendritic cells located just beneath the epidermis. During embryonic development and regeneration, differentiation of new pigment cells gradually darkens newly formed tissue. Conversely, prolonged light exposure ablates pigment cells through a porphyrin-based mechanism similar to the one that causes light sensitivity in rare human disorders called porphyrias. Here, we describe a novel program using image-processing algorithms to quantify relative pigment levels in live animals and apply this program to analyze changes in bodily pigmentation induced by light exposure. This tool will facilitate further characterization of genetic pathways that affect pigment cell differentiation, ommochrome and porphyrin biosynthesis, and porphyrin-based photosensitivity.

Defined diets for freshwater planarians.

BACKGROUND: Planarian flatworms are popular invertebrate models for basic research on stem cell biology and regeneration. These animals are commonly maintained on a diet of homogenized calf liver or boiled egg yolk in the laboratory, introducing a source of uncontrolled experimental variability. RESULTS: Here, we report the development of defined diets, prepared entirely from standardized, commercially sourced ingredients, for the freshwater species Schmidtea mediterranea, Dugesia japonica, and Girardia dorotocephala. These food sources provide an opportunity to test the effects of specific nutritional variables on biological phenomena of interest. Defined diet consumption was not sufficient for growth and only partially induced the increase in stem cell division that normally accompanies feeding, suggesting these responses are not solely determined by caloric intake. Our defined diet formulations enable delivery of double-stranded RNA for gene knockdown in a manner that provides unique advantages in some experimental contexts. We also present a new approach for preserving tissue integrity during hydrogen peroxide bleaching of liver-fed animals. CONCLUSIONS: These tools will empower research on the connections between diet, metabolism, and stem cell biology in the experimentally tractable planarian system.

Augmented Intelligence to Identify Patients With Advanced Heart Failure in an Integrated Health System.

BACKGROUND: Timely referral for specialist evaluation in patients with advanced heart failure (HF) is a Class 1 recommendation. However, the transition from stage C HF to advanced or stage D HF often goes undetected in routine care, resulting in delayed referral and higher mortality rates. OBJECTIVES: The authors sought to develop an augmented intelligence-enabled workflow using machine learning to identify patients with stage D HF and streamline referral. METHODS: We extracted data on HF patients with encounters from January 1, 2007, to November 30, 2020, from a HF registry within a regional, integrated health system. We created an ensemble machine learning model to predict stage C or stage D HF and integrated the results within the electronic health record. RESULTS: In a retrospective data set of 14,846 patients, the model had a good positive predictive value (60%) and low sensitivity (25%) for identifying stage D HF in a 100-person, physician-reviewed, holdout test set. During prospective implementation of the workflow from April 1, 2021, to February 15, 2022, 416 patients were reviewed by a clinical coordinator, with agreement between the model and the coordinator in 50.3% of stage D predictions. Twenty-four patients have been scheduled for evaluation in a HF clinic, 4 patients started an evaluation for advanced therapies, and 1 patient received a left ventricular assist device. CONCLUSIONS: An augmented intelligence-enabled workflow was integrated into clinical operations to identify patients with advanced HF. Endeavors such as this require a multidisciplinary team with experience in design thinking, informatics, quality improvement, operations, and health information technology, as well as dedicated resources to monitor and improve performance over time.

The exon junction complex is required for stem and progenitor cell maintenance in planarians.

Named for its assembly near exon-exon junctions during pre-mRNA splicing, the exon junction complex (EJC) regulates multiple aspects of RNA biochemistry, including export of spliced mRNAs from the nucleus and translation. Transcriptome analyses have revealed broad EJC occupancy of spliced metazoan transcripts, yet inhibition of core subunits has been linked to surprisingly specific phenotypes and a growing number of studies support gene-specific regulatory roles. Here we report results from a classroom-based RNAi screen revealing the EJC is necessary for regeneration in the planarian flatworm Schmidtea mediterranea. RNAi animals rapidly lost the stem and progenitor cells that drive formation of new tissue during both regeneration and cell turnover, but exhibited normal amputation-induced changes in gene expression in differentiated tissues. Together with previous reports that partial loss of EJC function causes stem cell defects in Drosophila and mice, our observations implicate the EJC as a conserved, posttranscriptional regulator of gene expression in stem cell lineages. This work also highlights the combined educational and scientific impacts of discovery-based research in the undergraduate biology curriculum.