Compartment Syndrome of All Extremities in the Setting of COVID-19-Induced Systemic Capillary Leak Syndrome With Superimposed Myositis.

Three years following the pandemic's emergence, COVID-19 has continued to affect much of the symptomatic population with widely varied respiratory complaints, fevers, numerous unexpected prodromal manifestations, and unknown long-term consequences. Scattered cases involving myopathies, rhabdomyolysis, and compartment syndrome have also been reported throughout the pandemic. Some similar cases have been attributed to systemic capillary leak syndrome (SCLS). Here, we report the development of compartment syndrome involving all extremities in a 57-year-old vaccinated female known to have COVID-19. In retrospect, we believe the clinical severity and the patient's sudden deterioration can also be attributed to the lesser-known SCLS. Treatment required fasciotomies of both forearms, arms, and legs. This is the most significantly involved case, leading to survival reported thus far. Lab abnormalities, misleading imaging, and symmetric involvement of all extremities posed a significant challenge to proper diagnosis and treatment. This case serves as a reminder for providers to remain cognizant of neurovascular emergencies during the workup of critically ill patients when the presentation is unrecognized and usual treatments are refractory. Its purpose is also to contribute to the global understanding of and response to COVID-19.

The association between operating margin and surgical diversity at Critical Access Hospitals.

CONTEXT: Surgical volume is correlated with increased hospital profitability, yet many Critical Access Hospitals (CAHs) offer few or no inpatient surgical services. OBJECTIVES: This study aims to investigate the impact of the presence of different inpatient surgical services on CAH profitability. METHODS: The study design was a cross-sectional analysis of financial data from the most recent fiscal year (FY) of 1299 CAHs. Multiple linear regression was utilized to assess how the operating margin was affected by the number of different inpatient surgical services offered per hospital. Covariates known to be associated with hospital profitability included occupancy rate, case mix index (CMI), system affiliation, ownership status (public, private, or nonprofit), and geographic region. RESULTS: The regression model for the CAH operating margin returned an R2 value of 0.18. Each additional inpatient surgical service corresponded to a 1.5% increase in operating margin (p=0.0413). Each 10% increase in occupancy rate and 0.1 increase in CMI corresponded to a 0.9% increase in operating margin (p=0.0032 and p=0.0176, respectively). The number of surgical services offered per CAH showed positive correlations with occupancy rate (r=0.23, p<0.0001) and CMI (r=0.59, p<0.0001). CONCLUSIONS: A positive correlation exists between operating margin and the diversity of inpatient surgical specialties available at CAHs. Furthermore, providing surgery allows CAHs to accommodate higher occupancy rates and case mixes, both of which are significantly and positively correlated with CAH operating margin.

The Value Surgical Services Bring to Critical Access Hospitals.

Purpose Critical Access Hospitals (CAHs) serve rural populations and receive government subsidies to compensate for their relatively high overhead costs and low occupancy rates. Twenty-nine percent of all hospitalizations in the United States include a surgical procedure, and hospitalizations involving surgery accounted for nearly half of all hospital revenue in 2011. This study aims to determine the value surgical services bring to CAHs and their impact on the viability of these facilities.  Methods Public access data from the American Hospital Directory (AHD) was analyzed about each hospital's revenue and surgical services offered. Excel was utilized to randomly select 300 CAHs from a pool of 1350 CAHs based on a 95% confidence interval and a 5% margin of error. Linear regression models were fit to the data evaluating the association of net income with the number of surgical services offered per hospital and the association of total margin with the number of surgical services offered per hospital. Models were adjusted for location, occupancy rate, and case mix index.  Findings The linear regression model demonstrated that for every additional surgical service provided by a CAH, the hospital net income increased by $630,528 (p=0.0032). A similar trend was observed when modeling profitability. The total margin increased 0.73% for each additional surgical service added, albeit without statistical significance (p=0.1342). CAHs providing two or three surgical services showed tighter group variance than those not offering surgery or only offering one surgical service.  Conclusions Net income was significantly correlated to the number of surgical services offered at CAHs. Furthermore, CAHs offering more surgical services seem to have more predictable profits than those offering less surgical services. CAHs would financially benefit from offering more or expanding surgical services at their facilities.

A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector.

The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe-animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm Hydroides elegans is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium Pseudoalteromonas luteoviolacea. Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the mif1 gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe-animal interactions in diverse contexts.

Efficient genome editing using CRISPR-Cas-mediated homology directed repair in the ascidian Ciona robusta.

Eliminating or silencing a gene's level of activity is one of the classic approaches developmental biologists employ to determine a gene's function. A recently developed method of gene perturbation called CRISPR-Cas, which was derived from a prokaryotic adaptive immune system, has been adapted for use in eukaryotic cells. This technology has been established in several model organisms as a powerful and efficient tool for knocking out or knocking down the function of a gene of interest. It has been recently shown that CRISPR-Cas functions with fidelity and efficiency in Ciona robusta. Here, we show that in C. robusta CRISPR-Cas mediated genomic knock-ins can be efficiently generated. Electroporating a tissue-specific transgene driving Cas9 and a U6-driven gRNA transgene together with a fluorescent protein-containing homology directed repair (FP-HDR) template results in gene-specific patterns of fluorescence consistent with a targeted genomic insertion. Using the Tyrosinase locus to optimize reagents, we first characterize a new Pol III promoter for expressing gRNAs from the Ciona savignyi H1 gene, and then adapt technology that flanks gRNAs by ribozymes allowing cell-specific expression from Pol II promoters. Next, we examine homology arm-length efficiencies of FP-HDR templates. Reagents were then developed for targeting Brachyury and Pou4 that resulted in expected patterns of fluorescence, and sequenced PCR amplicons derived from single embryos validated predicted genomic insertions. Finally, using two differentially colored FP-HDR templates, we show that biallelic FP-HDR template insertion can be detected in live embryos of the F0 generation.

Electroporation in Ascidians: History, Theory and Protocols.

Embryonic development depends on the orchestration of hundreds of regulatory and structural genes to initiate expression at the proper time, in the correct spatial domain(s), and in the amounts required for cells and tissues to become specified, determined, and ultimately to differentiate into a multicellular embryo. One of the key approaches to studying embryonic development is the generation of transgenic animals in which recombinant DNA molecules are transiently or stably introduced into embryos to alter gene expression, to manipulate gene function or to serve as reporters for specific cell types or subcellular compartments. In some model systems, such as the mouse, well-defined approaches for generating transgenic animals have been developed. In other systems, particularly non-model systems, a key challenge is to find a way of introducing molecules or other reagents into cells that produces large numbers of embryos with a minimal effect on normal development. A variety of methods have been developed, including the use of viral vectors, microinjection, and electroporation. Here, I describe how electroporation was adapted to generate transgenic embryos in the ascidian, a nontraditional invertebrate chordate model that is particularly well-suited for studying gene regulatory activity during development. I present a review of the electroporation process, describe how electroporation was first implemented in the ascidian, and provide a series of protocols describing the electroporation process, as implemented in our laboratory.

Do all adult orthopaedic injuries seen in emergency departments need to attend fracture clinic? A Queensland multicentred review.

OBJECTIVE: Musculoskeletal injuries account for a significant proportion of ED presentations annually, with a large percentage being referred to the fracture clinic (FC). A literature review found that many referrals could be safely managed outside the traditional model of care. The present study aims to review all adult presentations to FCs at two Queensland metropolitan hospitals, finding low-risk injuries that can safely and appropriately be managed by their general practitioner (GP) or allied health professionals (AHPs), potentially affording significant savings to the health system. METHODS: A retrospective study at Logan and Redland Hospitals was undertaken, reviewing all adult patients (≥16 years) referred to FCs over an eight week period. Injuries were categorised into those requiring FC care supervised by an orthopaedic surgeon (fracture clinic pathway) and those that could be safely managed by GPs or AHPs, with the aid of evidence-based, protocol-driven guidelines known as the primary care pathway (PCP). RESULTS: A total of 1367 patients were referred to FC over the study period, of whom 546 (40%) were assessed as suitable candidates for PCP. Redland Hospital accounted for 65% of all PCP-suitable patients, whereas Logan Hospital accounted for 35%. Failure-to-attend rates were significantly higher (P < 0.001) in the PCP patients compared to other patients attending FCs. CONCLUSION: Adopting the PCP could potentially reduce fracture clinic referrals by 40%. Having a structured pathway has the potential to empower primary health professionals, which could result in a more streamlined process that aids in significant time and financial savings and maintains good patient satisfaction and outcomes.

Properties and kinetics of microRNA regulation through canonical seed sites.

MicroRNAs are a fundamental class of small RNAs involved in post-transcriptional gene regulation; however, the mechanism by which microRNAs regulate their gene targets in animals remains poorly understood. Practically, a mechanistic understanding of microRNA binding and regulation is crucial for the rational design of microRNA-based vectors for RNA interference. In this report, we focus on the largest known class of microRNA targets, the canonical seed targets, and explore the factors involved in modulating target downregulation in vivo at the protein level. Using an in vivo sensor assay in the ascidian Ciona intestinalis, we quantify miR-124-mediated downregulation of 38 canonical seed targets cloned from the Ciona genome as well as 10 control non-targets. Supporting previous findings, we observed that the seed type and number of seed sites are correlated with downregulation. However, up to a 50% variation in downregulation levels was observed for targets within the same seed class, indicating a role of non-seed factors in modulating downregulation. Although we did not observe a significant correlation of previously reported non-seed determinants with downregulation levels at saturation in our assay, our data suggest that two previously identified factors, secondary structure and 3'end complementarity, may play a role in the initial kinetics of microRNA-target binding. Importantly, using different concentrations of miR-124 we show that dose-dependent target downregulation profiles follow Michaelis-Menten kinetics. In summary, our findings emphasize the importance of non-seed factors as well as the importance of cellular concentrations of microRNAs relative to their targets when studying the mechanisms of endogenous microRNA regulation.

An expanded Notch-Delta model exhibiting long-range patterning and incorporating MicroRNA regulation.

Notch-Delta signaling is a fundamental cell-cell communication mechanism that governs the differentiation of many cell types. Most existing mathematical models of Notch-Delta signaling are based on a feedback loop between Notch and Delta leading to lateral inhibition of neighboring cells. These models result in a checkerboard spatial pattern whereby adjacent cells express opposing levels of Notch and Delta, leading to alternate cell fates. However, a growing body of biological evidence suggests that Notch-Delta signaling produces other patterns that are not checkerboard, and therefore a new model is needed. Here, we present an expanded Notch-Delta model that builds upon previous models, adding a local Notch activity gradient, which affects long-range patterning, and the activity of a regulatory microRNA. This model is motivated by our experiments in the ascidian Ciona intestinalis showing that the peripheral sensory neurons, whose specification is in part regulated by the coordinate activity of Notch-Delta signaling and the microRNA miR-124, exhibit a sparse spatial pattern whereby consecutive neurons may be spaced over a dozen cells apart. We perform rigorous stability and bifurcation analyses, and demonstrate that our model is able to accurately explain and reproduce the neuronal pattern in Ciona. Using Monte Carlo simulations of our model along with miR-124 transgene over-expression assays, we demonstrate that the activity of miR-124 can be incorporated into the Notch decay rate parameter of our model. Finally, we motivate the general applicability of our model to Notch-Delta signaling in other animals by providing evidence that microRNAs regulate Notch-Delta signaling in analogous cell types in other organisms, and by discussing evidence in other organisms of sparse spatial patterns in tissues where Notch-Delta signaling is active.

Optimization of a method for chromatin immunoprecipitation assays in the marine invertebrate chordate Ciona.

Chromatin immunoprecipitation (ChIP) assays allow the efficient characterization of the in vivo occupancy of genomic regions by DNA-binding proteins and thus facilitate the prediction of cis-regulatory sequences in silico and guide their validation in vivo. For these reasons, these assays and their permutations (e.g., ChIP-on-chip and ChIP-sequencing) are currently being extended to several non-mainstream model organisms, as the availability of specific antibodies increases. Here, we describe the development of a polyclonal antibody against the Brachyury protein of the marine invertebrate chordate Ciona intestinalis and provide a detailed ChIP protocol that should be easily adaptable to other marine organisms.

Transcriptional regulation of the peripheral nervous system in Ciona intestinalis.

The formation of the sensory organs and cells that make up the peripheral nervous system (PNS) relies on the activity of transcription factors encoded by proneural genes (PNGs). Although PNGs have been identified in the nervous systems of both vertebrates and invertebrates, the complexity of their interactions has complicated efforts to understand their function in the context of their underlying regulatory networks. To gain insight into the regulatory network of PNG activity in chordates, we investigated the roles played by PNG homologs in regulating PNS development of the invertebrate chordate Ciona intestinalis. We discovered that in Ciona, MyT1, Pou4, Atonal, and NeuroD-like are expressed in a sequential regulatory cascade in the developing epidermal sensory neurons (ESNs) of the PNS and act downstream of Notch signaling, which negatively regulates these genes and the number of ESNs along the tail midlines. Transgenic embryos mis-expressing any of these proneural genes in the epidermis produced ectopic midline ESNs. In transgenic embryos mis-expressing Pou4, and MyT1 to a lesser extent, numerous ESNs were produced outside of the embryonic midlines. In addition we found that the microRNA miR-124, which inhibits Notch signaling in ESNs, is activated downstream of all the proneural factors we tested, suggesting that these genes operate collectively in a regulatory network. Interestingly, these factors are encoded by the same genes that have recently been demonstrated to convert fibroblasts into neurons. Our findings suggest the ascidian PNS can serve as an in vivo model to study the underlying regulatory mechanisms that enable the conversion of cells into sensory neurons.

Detection of copy-number variation in AUTS2 gene by targeted exonic array CGH in patients with developmental delay and autistic spectrum disorders.

Small genomic rearrangements and copy-number variations (CNVs) involving a single gene have been associated recently with many neurocognitive phenotypes, including intellectual disability (ID), behavioral abnormalities, and autistic spectrum disorders (ASDs). Such small CNVs in the Autism susceptibility candidate 2 (AUTS2) gene have been shown to be associated with seizures, ID, and ASDs. We report four patients with small CNVs ranging in size between 133-319 kb that disrupt AUTS2. Two patients have duplications involving single exons, whereas two have deletions that removed multiple exons. All patients had developmental delay, whereas two patients had a diagnosis of ASDs. The CNVs were detected by an exon-targeted array CGH with dense oligonucleotide coverage in exons of genes known or hypothesized to be causative of multiple human phenotypes. Our report further shows that disruption of AUTS2 results in a variety of neurobehavioral phenotypes. More importantly, it demonstrates the utility of targeted exon array as a highly sensitive clinical diagnostic tool for the detection of small genomic rearrangements in the clinically relevant regions of the human genome.

Randomized Phase III evaluation of the efficacy and safety of a novel glycopyrrolate oral solution for the management of chronic severe drooling in children with cerebral palsy or other neurologic conditions.

AIM: To evaluate the efficacy of glycopyrrolate oral solution (1 mg/5 mL) in managing problem drooling associated with cerebral palsy and other neurologic conditions. METHOD: Thirty-eight patients aged 3-23 years weighing at least 27 lb (12.2 kg) with severe drooling (clothing damp 5-7 days/week) were randomized to glycopyrrolate (n = 20), 0.02-0.1 mg/kg three times a day, or matching placebo (n = 18). Primary efficacy endpoint was responder rate, defined as percentage showing ≥3-point change on the modified Teacher's Drooling Scale (mTDS). RESULTS: Responder rate was significantly higher for the glycopyrrolate (14/19; 73.7%) than for the placebo (3/17; 17.6%) group (P = 0.0011), with improvements starting 2 weeks after treatment initiation. Mean improvements in mTDS at week 8 were significantly greater in the glycopyrrolate than in the placebo group (3.94 ± 1.95 vs 0.71 ± 2.14 points; P < 0.0001). In addition, 84% of physicians and 100% of parents/caregivers regarded glycopyrrolate as worthwhile compared with 41% and 56%, respectively, for placebo (P ≤ 0.014). Most frequently reported treatment-emergent adverse events (glycopyrrolate vs placebo) were dry mouth, constipation, and vomiting. INTERPRETATION: Children aged 3-16 years with problem drooling due to neurologic conditions showed a significantly better response, as assessed by mTDS, to glycopyrrolate than to placebo. CLINICALTRIALS.GOV IDENTIFIER: NCT00425087.

Safety and efficacy of glycopyrrolate oral solution for management of pathologic drooling in pediatric patients with cerebral palsy and other neurologic conditions.

BACKGROUND: The purpose of this study was to assess the safety and efficacy of oral glycopyrrolate solution 1 mg/5 mL for 24 weeks in pediatric patients with chronic moderate-to- severe drooling associated with cerebral palsy and other neurologic conditions. METHODS: In this multicenter, open-label, 24-week study, males and females aged 3-18 years weighing at least 27 lb received oral glycopyrrolate solution, starting at 0.02 mg/kg three times daily and titrated in increments of 0.02 mg/kg every 5-7 days for 4 weeks to an optimal maintenance dose or a maximum dose of 0.1 mg/kg, but not exceeding 3 mg three times daily. Safety was assessed by description and tabulation of all adverse events. The primary efficacy endpoint was response, defined as at least a three-point change from baseline to week 24 on the modified Teacher's Drooling Scale. RESULTS: Of 137 intent-to-treat participants, 10 (7.3%) received the maximum dose of 0.1 mg/kg three times daily; 122 (89%) had at least one treatment-emergent adverse event, 47% related to oral glycopyrrolate solution, with most being mild-to-moderate in intensity. The most commonly reported treatment-emergent adverse events were constipation (20.4%), vomiting (17.5%), diarrhea (17.5%), pyrexia (14.6%), dry mouth (10.9%), flushing (10.9%), and nasal congestion (10.9%). Nineteen patients (13.9%) discontinued treatment due to an adverse event, but no adverse event was specifically associated with discontinuation. Two patients had clinically significant toxicity grade shifts, one each in platelet count and calcium concentration. No deaths occurred on treatment; deaths of three patients (multisystem organ failure, anoxic encephalopathy, and aspiration pneumonia) within 30 days of their last dose were not considered to be treatment-related. At 24 weeks, 52.3% (95% confidence interval 43.7-60.9) of patients were responders, with at least a three-point decrease in modified Teacher's Drooling Scale from baseline, with 83.5% of parents/caregivers and 85.8% of investigators rating oral glycopyrrolate solution as being worthwhile. CONCLUSION: Oral glycopyrrolate solution 1 mg/5 mL for chronic moderate-to-severe drooling associated with cerebral palsy or other neurologic conditions was well tolerated over 24 weeks by pediatric patients aged 3-18 years.

miR-124 function during Ciona intestinalis neuronal development includes extensive interaction with the Notch signaling pathway.

The nervous system-enriched microRNA miR-124 is necessary for proper nervous system development, although the mechanism remains poorly understood. Here, through a comprehensive analysis of miR-124 and its gene targets, we demonstrate that, in the chordate ascidian Ciona intestinalis, miR-124 plays an extensive role in promoting nervous system development. We discovered that feedback interaction between miR-124 and Notch signaling regulates the epidermal-peripheral nervous system (PNS) fate choice in tail midline cells. Notch signaling silences miR-124 in epidermal midline cells, whereas in PNS midline cells miR-124 silences Notch, Neuralized and all three Ciona Hairy/Enhancer-of-Split genes. Furthermore, ectopic expression of miR-124 is sufficient to convert epidermal midline cells into PNS neurons, consistent with a role in modulating Notch signaling. More broadly, genome-wide target extraction with validation using an in vivo tissue-specific sensor assay indicates that miR-124 shapes neuronal progenitor fields by downregulating non-neural genes, notably the muscle specifier Macho-1 and 50 Brachyury-regulated notochord genes, as well as several anti-neural factors including SCP1 and PTBP1. 3'UTR conservation analysis reveals that miR-124 targeting of SCP1 is likely to have arisen as a shared, derived trait in the vertebrate/tunicate ancestor and targeting of PTBP1 is conserved among bilaterians except for ecdysozoans, while extensive Notch pathway targeting appears to be Ciona specific. Altogether, our results provide a comprehensive insight into the specific mechanisms by which miR-124 promotes neuronal development.

Ascidians: an invertebrate chordate model to study Alzheimer's disease pathogenesis.

Here we present the ascidian Ciona intestinalis as an alternative invertebrate system to study Alzheimer's disease (AD) pathogenesis. Through the use of AD animal models, researchers often attempt to reproduce various aspects of the disease, particularly the coordinated processing of the amyloid precursor protein (APP) by alpha-, beta- and gamma-secretases to generate amyloid beta (Abeta)-containing plaques. Recently, Drosophila and C. elegans AD models have been developed, exploiting the relative simplicity of these invertebrate systems, but they lack a functional Abeta sequence and a beta-secretase ortholog, thus complicating efforts to examine APP processing in vivo. We propose that the ascidian is a more appropriate invertebrate AD model owing to their phylogenetic relationship with humans. This is supported by bioinformatic analyses, which indicate that the ascidian genome contains orthologs of all AD-relevant genes. We report that transgenic ascidian larvae can properly process human APP(695) to generate Abeta peptides. Furthermore, Abeta can rapidly aggregate to form amyloid-like plaques, and plaque deposition is significantly increased in larvae expressing a human APP(695) variant associated with familial Alzheimer's disease. We also demonstrate that nervous system-specific Abeta expression alters normal larval behavior during attachment. Importantly, plaque formation and alterations in behavior are not only observed within 24 hours post-fertilization, but anti-amyloid drug treatment improves these AD-like pathologies. This ascidian model for AD provides a powerful and rapid system to study APP processing, Abeta plaque formation and behavioral alterations, and could aid in identifying factors that modulate amyloid deposition and the associated disruption of normal cellular function and behaviors.

High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates.

Pre-mRNA 5' spliced-leader (SL) trans-splicing occurs in some metazoan groups but not in others. Genome-wide characterization of the trans-spliced mRNA subpopulation has not yet been reported for any metazoan. We carried out a high-throughput analysis of the SL trans-spliced mRNA population of the ascidian tunicate Ciona intestinalis by 454 Life Sciences (Roche) pyrosequencing of SL-PCR-amplified random-primed reverse transcripts of tailbud embryo RNA. We obtained approximately 250,000 high-quality reads corresponding to 8790 genes, approximately 58% of the Ciona total gene number. The great depth of this data revealed new aspects of trans-splicing, including the existence of a significant class of "infrequently trans-spliced" genes, accounting for approximately 28% of represented genes, that generate largely non-trans-spliced mRNAs, but also produce trans-spliced mRNAs, in part through alternative promoter use. Thus, the conventional qualitative dichotomy of trans-spliced versus non-trans-spliced genes should be supplanted by a more accurate quantitative view recognizing frequently and infrequently trans-spliced gene categories. Our data include reads representing approximately 80% of Ciona frequently trans-spliced genes. Our analysis also revealed significant use of closely spaced alternative trans-splice acceptor sites which further underscores the mechanistic similarity of cis- and trans-splicing and indicates that the prevalence of +/-3-nt alternative splicing events at tandem acceptor sites, NAGNAG, is driven by spliceosomal mechanisms, and not nonsense-mediated decay, or selection at the protein level. The breadth of gene representation data enabled us to find new correlations between trans-splicing status and gene function, namely the overrepresentation in the frequently trans-spliced gene class of genes associated with plasma/endomembrane system, Ca(2+) homeostasis, and actin cytoskeleton.

Computational identification of Ciona intestinalis microRNAs.

MicroRNAs (miRNAs) are conserved non-coding small RNAs with potent post-transcriptional gene regulatory functions. Recent computational approaches and sequencing of small RNAs had indicated the existence of about 80 Ciona intestinalis miRNAs, although it was not clear whether other miRNA genes were present in the genome. We undertook an alternative computational approach to look for Ciona miRNAs. Conserved non-coding sequences from the C. intestinalis genome were extracted and computationally folded to identify putative hairpin-like structures. After applying additional criteria, we obtained 458 miRNA candidates whose sequences were used to design a custom microarray. Over 100 of our predicted hairpins were identified in this array when probed with RNA from various Ciona stages. We also compared our predictions to recently deposited sequences of Ciona small RNAs and report that 170 of our predicted hairpins are represented in this data set. Altogether, about 250 of our 458 predicted miRNAs were represented in either our array data or the small-RNA sequence database. These results suggest that Ciona has a large number of genomically encoded miRNAs that play an important role in modulating gene activity in developing embryos and adults.

Computational analysis of Ciona intestinalis operons.

Operons are clusters of genes that are co-regulated from a common promoter. Operons are typically associated with prokaryotes, although a small number of eukaryotes have been shown to possess them. Among metazoans, operons have been extensively characterized in the nematode Caenorhabditis elegans in which ∼15% of the total genes are organized into operons. The most recent genome assembly for the ascidian Ciona intestinalis placed ∼20% of the genes (2909 total) into 1310 operons. The majority of these operons are composed of two genes, while the largest are composed of six. Here is reported a computational analysis of the genes that comprise the Ciona operons. Gene ontology (GO) terms were identified for about two-thirds of the operon-encoded genes. Using the extensive collection of public EST libraries, estimates of temporal patterns of gene expression were generated for the operon-encoded genes. Lastly, conservation of operons was analyzed by determining how many operon-encoded genes were present in the ascidian Ciona savignyi and whether these genes were organized in orthologous operons. Over 68% of the operon-encoded genes could be assigned one or more GO terms and 697 of the 1310 operons contained genes in which all genes had at least one GO term. Of these 697 operons, GO terms were shared by all of the genes within 146 individual operons, suggesting that most operons encode genes with unrelated functions. An analysis of operon gene expression from nine different EST libraries indicated that for 587 operons, all of the genes that comprise an individual operon were expressed together in at least one EST library, suggesting that these genes may be co-regulated. About 50% (74/146) of the operons with shared GO terms also showed evidence of gene co-regulation. Comparisons with the C. savignyi genome identified orthologs for 1907 of 2909 operon genes. About 38% (504/1310) of the operons are conserved between the two Ciona species. These results suggest that like C. elegans, operons in Ciona are comprised of a variety of genes that are not necessarily related in function. The genes in only 50% of the operons appear to be co-regulated, suggesting that more complex gene regulatory mechanisms are likely operating.

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.

BACKGROUND: The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly. RESULTS: We have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models. CONCLUSION: Using these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.