Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa.
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ABSTRACT:
SUBMITTER: Redmond AK
PROVIDER: S-EPMC9918546 | biostudies-literature | 2023 Feb
REPOSITORIES: biostudies-literature
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Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa.
Redmond Anthony K AK McLysaght Aoife A
Nature communications 20230210 1
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Project description: Not available
| S-EPMC9918479 | biostudies-literature
Project description:Choanoflagellates are single-celled aquatic flagellates with a unique morphology consisting of a cell with a single flagellum surrounded by a "collar" of microvilli. They have long interested evolutionary biologists because of their striking resemblance to the collared cells (choanocytes) of sponges. Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. However, molecular phylogenetic studies within choanoflagellates are still extremely limited. Thus, little is known about choanoflagellate evolution or the exact nature of the relationship between choanoflagellates and Metazoa. We have sequenced four genes from a broad sampling of the morphological diversity of choanoflagellates including most species currently available in culture. Phylogenetic analyses of these sequences, alone and in combination, reject much of the traditional taxonomy of the group. The molecular data also strongly support choanoflagellate monophyly rejecting proposals that Metazoa were derived from a true choanoflagellate ancestor. Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor.
| S-EPMC2575473 | biostudies-literature
Project description:Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.
| S-EPMC4426464 | biostudies-literature
Project description:Replacement of mRNA 5' UTR sequences by short sequences trans-spliced from specialized, noncoding, spliced leader (SL) RNAs is an enigmatic phenomenon, occurring in a set of distantly related animal groups including urochordates, nematodes, flatworms, and hydra, as well as in Euglenozoa and dinoflagellates. Whether SL trans-splicing has a common evolutionary origin and biological function among different organisms remains unclear. We have undertaken a systematic identification of SL exons in cDNA sequence data sets from non-bilaterian metazoan species and their closest unicellular relatives. SL exons were identified in ctenophores and in hydrozoan cnidarians, but not in other cnidarians, placozoans, or sponges, or in animal unicellular relatives. Mapping of SL absence/presence obtained from this and previous studies onto current phylogenetic trees favors an evolutionary scenario involving multiple origins for SLs during eumetazoan evolution rather than loss from a common ancestor. In both ctenophore and hydrozoan species, multiple SL sequences were identified, showing high sequence diversity. Detailed analysis of a large data set generated for the hydrozoan Clytia hemisphaerica revealed trans-splicing of given mRNAs by multiple alternative SLs. No evidence was found for a common identity of trans-spliced mRNAs between different hydrozoans. One feature found specifically to characterize SL-spliced mRNAs in hydrozoans, however, was a marked adenosine enrichment immediately 3' of the SL acceptor splice site. Our findings of high sequence divergence and apparently indiscriminate use of SLs in hydrozoans, along with recent findings in other taxa, indicate that SL genes have evolved rapidly in parallel in diverse animal groups, with constraint on SL exon sequence evolution being apparently rare.
| S-EPMC2844618 | biostudies-literature
Project description:See https://www.cancerresearchuk.org/about-cancer/find-a-clinical-trial/a-study-looking-at-a-new-test-called-fit-to-look-for-signs-of-bowel-cancer-nice-fit
| 2418716 | ecrin-mdr-crc
Project description:The concern for diverticulitis often leads to the use of computed tomography (CT) scans for diagnosis. We aim to develop an ultrasound-based clinical decision rule (CDR) to confidently rule-out the disease without requiring a CT scan. We analyzed data from a prospective study of adult emergency department (ED) patients with suspected diverticulitis who underwent both bedside ultrasound (US) and CT. Patient history, physical examination, laboratory findings, and US results were used to create a CDR via a recursive partitioning model designed to prioritize sensitivity, with a loss matrix heavily penalizing false negatives. We calculated the test characteristics for this CDR (TICS-Rule) and assessed the potential reduction in CT scans and ED length of stay. Data from 149 patients (84 female; mean age 58 ± 16) were used to develop the TICS-Rule. The final model integrates US diagnosis of simple and complicated diverticulitis, along with variables of heart rate, age, history of diverticulosis, vomiting, and leukocytosis. Negative US results and a heart rate below 100 effectively excluded diverticulitis. The sensitivity increased from 54.5% (32.2-75.6) in the US alone to 100% (84.6-100%) for complicated diverticulitis in the model. The TICS-Rule missed no cases of complicated diverticulitis but one case of simple diverticulitis. The median time from ED greeting to US interpretation was 103 min (IQR 62-169), compared to 285 min (IQR 229-372) for CT. The TICS-Rule uses a combination of negative US and heart rate less thanQ1 100 to exclude diverticulitis without the need for a CT scan. Integration of the TICS-Rule offers a promising enhancement to clinical decision-making while reducing both CT use and ED length of stay.
| S-EPMC11531591 | biostudies-literature
Project description:Genome duplication is temporarily coordinated with sister chromatid cohesion and DNA damage tolerance. Recently, we found that replication fork-coupled repriming is important for both optimal cohesion and error-free replication by recombination. The mechanism involved has implications for the etiology of replication-based genetic diseases and cancer.
| S-EPMC4845193 | biostudies-other
Project description:ObjectivesNon-fatal drownings confer significant morbidity and mortality in the United States. Chest radiograph (CXR) is typically used as a screening modality for interstitial edema but lacks sensitivity early after submersion. No study has evaluated lung ultrasound in assessing for pulmonary edema after submersion events and we hypothesized that lung point-of-care (POC) ultrasound can identify interstitial edema in patients presenting after non-fatal drownings.MethodsPatients presenting to the emergency department after a submersion event were eligible if a CXR was obtained as part of their care. Emergency medicine residents performed a lung POC ultrasound and provided a "novice" interpretation of "normal" or "abnormal," which was independently reviewed by a blinded expert sonographer. Patients were contacted 2 weeks after presentation to assess for late sequela.ResultsA prospective convenience sample of 59 patients included 21 adults (36%) and 38 children (64%) enrolled over 17 months with a median age of 6. Twenty-four (41%) patients had abnormalities on CXR. Of these, 20 patients had a positive ultrasound per novice interpretation. Compared to CXR, ultrasound had an overall sensitivity of 83% and a specificity of 66% for detecting pulmonary edema in non-fatal drownings. Notably, out of 35 subjects with a negative CXR, there were 12 (34%) cases with a positive lung ultrasound, 10 of which required hospital admission.ConclusionLung POC ultrasound has a moderate sensitivity and specificity when performed by novice sonographers to detect pulmonary edema presenting to an ED setting after a non-fatal drowning event.
| S-EPMC10363851 | biostudies-literature
Project description:Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
| S-EPMC4687580 | biostudies-other
Project description:AimsWhether a single cardiac troponin measurement can safely rule out myocardial infarction in patients presenting within a few hours of symptom onset is uncertain. The study aim was to assess the performance of troponin in early presenters.Methods and resultsIn patients with possible myocardial infarction, the diagnostic performance of a single measurement of high-sensitivity cardiac troponin I at presentation was evaluated and externally validated in those tested ≤3, 4-12, and >12 h from symptom onset. The limit-of-detection (2 ng/L), rule-out (5 ng/L), and sex-specific 99th centile (16 ng/L in women; 34 ng/L in men) thresholds were compared. In 41 103 consecutive patients [60 (17) years, 46% women], 12 595 (31%) presented within 3 h, and 3728 (9%) had myocardial infarction. In those presenting ≤3 h, a threshold of 2 ng/L had greater sensitivity and negative predictive value [99.4% (95% confidence interval 99.2%-99.5%) and 99.7% (99.6%-99.8%)] compared with 5 ng/L [96.5% (96.2%-96.8%) and 99.3% (99.1%-99.4%)]. In those presenting ≥3 h, the sensitivity and negative predictive value were similar for both thresholds. The sensitivity of the 99th centile was low in early and late presenters at 71.4% (70.6%-72.2%) and 92.5% (92.0%-93.0%), respectively. Findings were consistent in an external validation cohort of 7088 patients.ConclusionIn early presenters, a single measurement of high-sensitivity cardiac troponin I below the limit of detection may facilitate the safe rule out of myocardial infarction. The 99th centile should not be used to rule out myocardial infarction at presentation even in those presenting later following symptom onset.
| S-EPMC10406338 | biostudies-literature