The evolution of cnidarian stinging cells supports a Precambrian radiation of animal predators.

Cnidarians-the phylum including sea anemones, corals, jellyfish, and hydroids-are one of the oldest groups of predatory animals. Nearly all cnidarians are carnivores that use stinging cells called cnidocytes to ensnare and/or envenom their prey. However, there is considerable diversity in cnidocyte form and function. Tracing the evolutionary history of cnidocytes may therefore provide a proxy for early animal feeding strategies. In this study, we generated a time-calibrated molecular clock of cnidarians and performed ancestral state reconstruction on 12 cnidocyte types to test the hypothesis that the original cnidocyte was involved in prey capture. We conclude that the first cnidarians had only the simplest and least specialized cnidocyte type (the isorhiza) which was just as likely to be used for adhesion and/or defense as the capture of prey. A rapid diversification of specialized cnidocytes occurred through the Ediacaran (~654-574 million years ago), with major subgroups developing unique sets of cnidocytes to match their distinct feeding styles. These results are robust to changes in the molecular clock model, and are consistent with growing evidence for an Ediacaran diversification of animals. Our work also provides insight into the evolution of this complex cell type, suggesting that convergence of forms is rare, with the mastigophore being an interesting counterexample.

Sirtuin Evolution at the Dawn of Animal Life.

Sirtuins are a family of proteins that protect against cellular injury and aging; understanding their evolution should reveal fundamental mechanisms governing longevity. "Early-branching" animals such as sea sponges and jellyfish have been understudied in previous analyses of sirtuin diversity. These organisms not only hold important positions at the base of the evolutionary tree, but also have unique aging dynamics that defy convention, such as quasi-immortality and high regenerative capacity. In this study, we survey the evolution of sirtuin proteins in animals, with a focus on the oldest living lineages. We describe previously unrecognized expansions of "Class IV" and "Class I" sirtuins around the origin of animals, raising the number of sirtuin families in the last common ancestor to at least nine. Most of these undescribed sirtuins have been lost in vertebrates and other bilaterian animals. Our work also clarifies the evolution of PNC1 and NAMPT enzymes that carry out the rate-limiting step in sirtuin-related NAD+ biosynthesis. The genes for PNC1 and NAMPT enzymes were both present in the first animals, with the genes being lost a minimum of 11 and 13 times, respectively, over the course of animal evolution. We propose that species with these ancestral gene repertoires are ideal model organisms for studying the genetic regulation of animal longevity and will provide clues to increasing longevity in humans.

Paleoproterozoic sterol biosynthesis and the rise of oxygen.

Natural products preserved in the geological record can function as 'molecular fossils', providing insight into organisms and physiologies that existed in the deep past. One important group of molecular fossils is the steroidal hydrocarbons (steranes), which are the diagenetic remains of sterol lipids. Complex sterols with modified side chains are unique to eukaryotes, although simpler sterols can also be synthesized by a few bacteria. Sterol biosynthesis is an oxygen-intensive process; thus, the presence of complex steranes in ancient rocks not only signals the presence of eukaryotes, but also aerobic metabolic processes. In 1999, steranes were reported in 2.7 billion year (Gyr)-old rocks from the Pilbara Craton in Australia, suggesting a long delay between photosynthetic oxygen production and its accumulation in the atmosphere (also known as the Great Oxidation Event) 2.45-2.32 Gyr ago. However, the recent reappraisal and rejection of these steranes as contaminants pushes the oldest reported steranes forward to around 1.64 Gyr ago (ref. 6). Here we use a molecular clock approach to improve constraints on the evolution of sterol biosynthesis. We infer that stem eukaryotes shared functionally modern sterol biosynthesis genes with bacteria via horizontal gene transfer. Comparing multiple molecular clock analyses, we find that the maximum marginal probability for the divergence time of bacterial and eukaryal sterol biosynthesis genes is around 2.31 Gyr ago, concurrent with the most recent geochemical evidence for the Great Oxidation Event. Our results therefore indicate that simple sterol biosynthesis existed well before the diversification of living eukaryotes, substantially predating the oldest detected sterane biomarkers (approximately 1.64 Gyr ago), and furthermore, that the evolutionary history of sterol biosynthesis is tied to the first widespread availability of molecular oxygen in the ocean-atmosphere system.

Infections in patients with rheumatoid arthritis receiving tofacitinib versus tumour necrosis factor inhibitors: results from the open-label, randomised controlled ORAL Surveillance trial.

OBJECTIVES: To characterise infections in patients with rheumatoid arthritis (RA) in ORAL Surveillance. METHODS: In this open-label, randomised controlled trial, patients with RA aged≥50 years with ≥1 additional cardiovascular risk factor received tofacitinib 5 or 10 mg two times per day or a tumour necrosis factor inhibitor (TNFi). Incidence rates (IRs; patients with first events/100 patient-years) and hazard ratios (HRs) were calculated for infections, overall and by age (50-<65 years; ≥65 years). Probabilities of infections were obtained (Kaplan-Meier estimates). Cox modelling identified infection risk factors. RESULTS: IRs/HRs for all infections, serious infection events (SIEs) and non-serious infections (NSIs) were higher with tofacitinib (10>5 mg two times per day) versus TNFi. For SIEs, HR (95% CI) for tofacitinib 5 and 10 mg two times per day versus TNFi, respectively, were 1.17 (0.92 to 1.50) and 1.48 (1.17 to 1.87). Increased IRs/HRs for all infections and SIEs with tofacitinib 10 mg two times per day versus TNFi were more pronounced in patients aged≥65 vs 50-<65 years. SIE probability increased from month 18 and before month 6 with tofacitinib 5 and 10 mg two times per day versus TNFi, respectively. NSI probability increased before month 6 with both tofacitinib doses versus TNFi. Across treatments, the most predictive risk factors for SIEs were increasing age, baseline opioid use, history of chronic lung disease and time-dependent oral corticosteroid use, and, for NSIs, female sex, history of chronic lung disease/infections, past smoking and time-dependent Disease Activity Score in 28 joints, C-reactive protein. CONCLUSIONS: Infections were higher with tofacitinib versus TNFi. Findings may inform future treatment decisions. TRIAL REGISTRATION NUMBER: NCT02092467.

Screening for subjective cognitive decline in the elderly via subjective cognitive complaints and informant-reported questionnaires: a systematic review.

BACKGROUND: Subjective cognitive decline may represent at-risk persons progressing to mild cognitive impairment (MCI), which can be exacerbated by effects of anesthesia and surgery. The objective of this systematic review is to identify the most common questions in subjective cognitive complaint and informant-reported questionnaires used in assessing cognitive impairment of elderly patients that are correlated with standardized tests for cognitive impairment screening. METHODS: We searched Medline, PubMed, Embase, Cochrane Central Register of Controlled Trials, Cochrane Database, Emcare Nursing, Web of Science, Scopus, CINAHL, ClinicalTrials.Gov, and ICTRP between September 20, 2005 to August 31, 2020. We included studies that evaluated subjective cognitive complaints and informant-reported questions in elderly patients. RESULTS AND CONCLUSION: A total of 28,407 patients were included from 22 studies that assessed 21 subjective complaint questionnaires and nine informant-reported questionnaires. The most common subjective cognitive complaints were those assessing anterograde memory, closely followed by perceptual-motor function and executive function. The most common informant-reported questions were those assessing executive function, temporal orientation, and anterograde memory. Questions assessing learning and memory were most associated with results from standardized tests assessing cognitive impairment. Assessing learning and memory plays a key role in evaluating subjective cognitive decline in elderly patients. Delivering subjective cognitive complaints questions to elderly patient preoperatively may aid in screening for those exhibiting cognitive signs, and in turn are at risk of postoperative complications. Thus, the results from this review contribute to knowledge for healthcare professionals regarding the use of subjective cognitive complaints and informant-reported complaints in preoperative settings.

Cognitive behavioral therapy in 22q11.2 deletion syndrome: A case study of two young adults with an anxiety disorder.

BACKGROUND: The prevalence of anxiety disorders is high in 22q11.2 deletion syndrome (22q11.2DS), an under-recognized multisystem condition. Prominent features include an array of somatic, cognitive, and neuropsychiatric disorders. This case study reports for the first time on the application of individual cognitive behavioral therapy in 22q11.2DS. METHOD: Two young adults with 22q11.2DS and an anxiety disorder received cognitive behavioral therapy based on standard protocols. Feasibility and efficacy were assessed through clinical interviews, clinical observations by the therapist, and questionnaires. RESULTS: Both participants were engaged in the therapy and showed understanding of basic cognitive behavioral therapy principles. However, they did not show a clear clinical improvement. Adjustments to the protocol were required, including increased flexibility and a proactive approach by the therapist, additional time per session, written information, and significant involvement of the family and multidisciplinary team. CONCLUSIONS: Our findings may help identify required adaptations to cognitive behavioral therapy protocols for this and similar genetic conditions.

Experience with tofacitinib in Canada: patient characteristics and treatment patterns in rheumatoid arthritis over 3 years.

OBJECTIVES: To describe characteristics, treatment patterns and persistence in patients with RA treated with tofacitinib, an oral Janus kinase inhibitor, in Canadian clinical practice between 1 June 2014 and 31 May 2017. METHODS: Data were obtained from the tofacitinib eXel support programme. Baseline demographics and medication history were collected via patient report/special authorization forms; reasons for discontinuation were captured by patient report. Treatment persistence was estimated using Kaplan-Meier methods, with data censored at last follow-up. Cox regression was applied to analyse baseline characteristics associated with treatment discontinuation. RESULTS: The number of patients with RA enrolled from 2014 to 2017 was 4276; tofacitinib utilization increased during that period, as did the proportion of biologic (b) DMARD-naïve patients prescribed tofacitinib. Of patients who initiated tofacitinib, 1226/3678 (33.3%) discontinued, mostly from lack of efficacy (35.7%) and adverse events (26.9%). Persistence was 62.7% and 49.6% after 1 and 2 years of treatment, respectively. Prior bDMARD experience predicted increased tofacitinib discontinuation (vs bDMARD-naïve, P < 0.001). Increased retention was associated with older age (56-65 years and >65 years vs ⩽45 years; P < 0.05), and time since diagnosis of 15 to <20 years (vs <5 years; P < 0.01). In bDMARD-naïve, post-1 bDMARD, post-2 bDMARD and post-⩾3 bDMARD patients, median survival was >730, 613, 667 and 592 days, respectively. CONCLUSION: Since 2014, tofacitinib use in Canadian patients with RA increased, especially among bDMARD-naïve/post-1 bDMARD patients. Median drug survival was ∼2 years. Likelihood of persistence increased for bDMARD-naïve (vs bDMARD-experienced) patients and those aged ⩾56 (vs ⩽45) years.

Mechanisms of cnidocyte development in the moon jellyfish Aurelia.

Stinging cells called cnidocytes are a defining trait of the cnidarians (sea anemones, corals, jellyfish, and their relatives). In hydrozoan cnidarians such as Hydra, cnidocytes develop from interstitial stem cells set aside in the ectoderm. It is less clear how cnidocytes develop outside the Hydrozoa, as other cnidarians appear to lack interstitial stem cells. We addressed this question by studying cnidogenesis in the moon jellyfish (Aurelia) through the visualization of minicollagen-a protein associated with cnidocyte development-as well as transmission electron microscopy. We discovered that developing cnidoblasts are rare or absent in feeding structures rich in mature cnidocytes, such as tentacles and lappets. Using transmission electron microscopy, we determined that the progenitors of cnidocytes have traits consistent with epitheliomuscular cells. Our data suggests a dynamic where cnidocytes develop at high concentrations in the epithelium of more proximal regions, and subsequently migrate to more distal regions where they exhibit high usage and turnover. Similar to some anthozoans, cnidocytes in Aurelia do not appear to be generated by interstitial stem cells; instead, epitheliomuscular cells appear to be the progenitor cell type. This observation polarizes the evolution of cnidogenesis, and raises the question of how interstitial stem cells came to regulate cnidogenesis in hydrozoans.

Prospects for continuous-wave molecular modulation in Raman-active microresonators.

We propose the extension of existing molecular modulation techniques for continuous-wave optical modulation to Raman-active microresonators. Intense pump and Stokes modes inside a microresonator prepare a high coherence of the Raman transition between two ro-vibrational states. With the coherence prepared, any laser in the optical region can be coupled to the microresonator and be modulated. We perform numerical simulations which predict that these "microresonator-based molecular modulators" could have modulation efficiencies on the order of 1% at 10 THz-scale frequencies for any optical wavelength.

Sterol and genomic analyses validate the sponge biomarker hypothesis.

Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650-540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta, Capsaspora owczarzaki, Sphaeroforma arctica, and Creolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C30 sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, or SMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C30 sterol biosynthesis through clade-specific SMT duplications. Using a molecular clock approach, we demonstrate that the relevant sponge SMT duplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algal SMT duplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.

Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck.

Chendytes lawi, an extinct flightless diving anseriform from coastal California, was traditionally classified as a sea duck, tribe Mergini, based on similarities in osteological characters. We recover and analyze mitochondrial genomes of C. lawi and five additional Mergini species, including the extinct Labrador Duck, Camptorhynchus labradorius. Despite its diving morphology, C. lawi is reconstructed as an ancient relictual lineage basal to the dabbling ducks (tribe Anatini), revealing an additional example of convergent evolution of characters related to feeding behavior among ducks. The Labrador Duck is sister to Steller's Eider which may provide insights into the evolution and ecology of this poorly known extinct species. Our results demonstrate that inclusion of full length mitogenomes, from taxonomically distributed ancient and modern sources can improve phylogeny reconstruction of groups previously assessed with shorter single-gene mitochondrial sequences.

Cell tracking supports secondary gastrulation in the moon jellyfish Aurelia.

The moon jellyfish Aurelia exhibits a dramatic reorganization of tissue during its metamorphosis from planula larva to polyp. There are currently two competing hypotheses regarding the fate of embryonic germ layers during this metamorphosis. In one scenario, the original endoderm undergoes apoptosis and is replaced by a secondary endoderm derived from ectodermal cells. In the second scenario, both ectoderm and endoderm remain intact through development. In this study, we performed a pulse-chase experiment to trace the fate of larval ectodermal cells. We observed that prior to metamorphosis, ectodermal cells that proliferated early in larval development concentrate at the future oral end of the polyp. During metamorphosis, these cells migrate into the endoderm, extending all the way to the aboral portion of the gut. We therefore reject the hypothesis that larval endoderm remains intact during metamorphosis and provide additional support for the "secondary gastrulation" hypothesis. Aurelia appears to offer the first and only described case where a cnidarian derives its endoderm twice during normal development, adding to a growing body of evidence that germ layers can be dramatically reorganized in cnidarian life cycles.

The early expansion and evolutionary dynamics of POU class genes.

The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class, these studies have been limited by a small number of representative taxa, and a lack of sequences from basally branching organisms. In this study, we performed comparative analyses on available genomes and sequences recovered through "gene fishing" to better resolve the topology of the POU gene tree. We then used ancestral state reconstruction to map the most likely changes in amino acid evolution for the conserved domains. Our work suggests that four of the six POU families evolved before the last common ancestor of living animals-doubling previous estimates-and were followed by extensive clade-specific gene loss. Amino acid changes are distributed unequally across the gene tree, consistent with a neofunctionalization model of protein evolution. We consider our results in the context of early animal evolution, and the role of POU5 genes in maintaining stem cell pluripotency.

Ancestral state reconstruction of ontogeny supports a bilaterian affinity for Dickinsonia.

Despite numerous attempts, classification of the Precambrian fossil Dickinsonia has eluded scientific consensus. This is largely because Dickinsonia and its relatives are structurally simple, lacking morphological synapomorphies to clarify their relationship to modern taxa. However, there is increasing precedence for using ontogeny to constrain enigmatic fossils, and growth of the type species Dickinsonia costata is well understood. This study formalizes the connection between ontogeny in Dickinsonia-which grows by the addition of metameric units onto one end of its primary axis-with terminal addition, defined as growth and patterning from a posterior, subtermial growth zone. We employ ancestral state reconstruction and stochastic character mapping to conclude that terminal addition is a synapomorphy of bilaterian animals. Thus, terminal addition allies Dickinsonia with the bilaterians, providing evidence that large stem- or crown-group bilaterians made up a significant proportion of the Precambrian biota. This study also illustrates the potential for combining developmental and phylogenetic data in constraining the placement of ancient problematic fossil taxa on the evolutionary tree.

Naturalistic Action Performance Distinguishes Amnestic Mild Cognitive Impairment from Healthy Aging.

Individuals with amnestic mild cognitive impairment (aMCI) show minor decrements in their instrumental activities of daily living (IADL). Sensitive measures of IADL performance are needed to capture the mild difficulties observed in aMCI groups. Routine naturalistic actions (NAs) are familiar IADL-type activities that require individuals to enact everyday tasks such as preparing coffee. In the current study we examined the extent to which NAs could be used to help facilitate differential diagnosis of aMCI relative to composite measures of episodic memory, semantic knowledge, and executive function. Healthy older adults (n=24) and individuals with aMCI (n=24) enacted two highly familiar NAs and completed tests of episodic memory, semantic knowledge, and executive function. Binary logistic regression was used to predict group membership (aMCI vs. control participants). The regression analyses indicated that NA performance could reliably predict group membership, over and above measures of cognitive functioning. These findings indicated that NA performance can be used to help facilitate differential diagnosis of healthy aging and aMCI and used as an outcome measure in intervention studies.

Shear-driven aggregation of SU-8 microrods in suspension.

A non-Brownian suspension of micron scale rods exhibits reversible shear-driven formation of disordered aggregates resulting in dramatic viscosity enhancement at low shear rates. Aggregate formation is imaged using a combined rheometer and fluorescence microscope. The size and structure of these aggregates are found to be a function of shear rate and concentration, with larger aggregates present at lower shear rates and higher concentrations. Quantitative measurements of the early-stage aggregation process are modeled by collision driven growth of porous structures which suggest that the aggregate density increases with shear rate. This result is combined with a Krieger-Dougherty type constitutive relationship and steady-state viscosity measurements to estimate the intrinsic viscosity of complex structures developed under shear. These results represent a direct, quantitative, experimental demonstration of the association between aggregation and viscosity enhancement for a rod suspension, and demonstrate a way of inferring microscopic geometric properties of a dynamic system through the combination of quantitative imaging and rheology.

Clinical trial simulation to assist in COPD trial planning and design with a biomarker-based diagnostic: when to pull the trigger?

Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous disease with a wide range of clinical phenotypes that vary from predominantly airway disease (chronic bronchitis) to predominantly parenchymal disease (emphysema). Current advances for the treatment of COPD are increasingly focused on targeted treatments and development of novel biomarker-based diagnostics (Dx)'s to select the patients most likely to benefit. Clinical trial planning and design with biomarkers includes additional considerations beyond those for conventional trials in un-selected populations, e.g., the heterogeneity of COPD phenotypes in the population, the ability of a biomarker to predict clinically meaningful phenotypes that are differentially associated with the response to a targeted treatment, and the data needed to make Go/No Go decisions during clinical development. We developed the Clinical Trial Object Oriented Research Application (CTOORA), a computer-aided clinical trial simulator of COPD patient outcomes, to inform COPD trial planning with biomarkers. CTOORA provides serial projections of trial success for a range of hypothetical and plausible scenarios of interest. In the absence of data, CTOORA can identify characteristics of a biomarker-based Dx needed to provide a meaningful advantage when used in a clinical trial. We present a case study in which CTOORA is used to identify the scenarios for which a biomarker may be used successfully in clinical development. CTOORA is a tool for robust clinical trial planning with biomarkers, to guide early-to-late stage development that is positioned for success.

A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration.

Molecular studies of animal regeneration typically focus on conserved genes and signaling pathways that underlie morphogenesis. To date, a holistic analysis of gene expression across animals has not been attempted, as it presents a suite of problems related to differences in experimental design and gene homology. By combining orthology analyses with a novel statistical method for testing gene enrichment across large data sets, we are able to test whether tissue regeneration across animals shares transcriptional regulation. We applied this method to a meta-analysis of six publicly available RNA-Seq data sets from diverse examples of animal regeneration. We recovered 160 conserved orthologous gene clusters, which are enriched in structural genes as opposed to those regulating morphogenesis. A breakdown of gene presence/absence provides limited support for the conservation of pathways typically implicated in regeneration, such as Wnt signaling and cell pluripotency pathways. Such pathways are only conserved if we permit large amounts of paralog switching through evolution. Overall, our analysis does not support the hypothesis that a shared set of ancestral genes underlie regeneration mechanisms in animals. After applying the same method to heat shock studies and getting similar results, we raise broader questions about the ability of comparative RNA-Seq to reveal conserved gene pathways across deep evolutionary relationships.