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Abstract Background Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. Results Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. Conclusion An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.

Myxozoans are a large group of poorly characterized cnidarian parasites. To gain further insight into their evolution, we sequenced the mitochondrial (mt) genome of Enteromyxum leei and reevaluate the mt genome structure of Kudoa iwatai. Although the typical animal mt genome is a compact, 13-25 kb, circular chromosome, the mt genome of E. leei was found to be fragmented into eight circular chromosomes of ∼23 kb, making it the largest described animal mt genome. Each chromosome was found to harbor a large noncoding region (∼15 kb), nearly identical between chromosomes. The protein coding genes show an unusually high rate of sequence evolution and possess little similarity to their cnidarian homologs. Only five protein coding genes could be identified and no tRNA genes. Surprisingly, the mt genome of K. iwatai was also found to be composed of two chromosomes. These observations confirm the remarkable plasticity of myxozoan mt genomes., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges., Results: We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinella (p) verrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals' mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns., Conclusions: The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated.

Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.

Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Multidrug resistance transporters (MDRs) are excellent candidates for molecular-level biomonitoring - they function in exporting xenobiotic compounds and their expression is inducible. However, currently available MDR sequence information from aquatic invertebrates is partial and mostly biased towards the conserved ATPase domain. In the present study, two genes belonging to the MDR/TAP (ABCB) family were cloned and characterized from the bivalve Brachidontes pharaonis, which thrives in rocky environments along the Israeli Mediterranean coast. One of these is a complete sequence of a 'half'ABCB, probably belonging to the ABCB10 subfamily, while the second is a 'full'ABCB1 transporter. A quantitative RT-PCR protocol for biomonitoring was tested in laboratory experiments. Bivalves exposed to diesel showed significant increase in B1 expression levels, while the expression of B10 was suppressed. These results suggest that B. pharaonis features an MDR1 homologue that is induced by pollution and may serve as a sentinel organism for routine biomonitoring programs. However, our findings also exemplify that not all MDRs are equally suitable for this purpose and sequence information must be expanded beyond the ATPase domain for correct classification of cloned genes.

A 14-month-old girl with chronic renal insufficiency received a massive overdose of vancomycin, resulting in worsened renal failure and ototoxicity. We report the use of combined charcoal hemoperfusion and dialysis to accelerate vancomycin removal in this patient.

Objective: The ketogenic diet is used in patients with intractable seizure disorders. To maintain a ketotic state, patients on this diet must maintain a strict low-carbohydrate intake. Because these patients often require medication, and because many pharmaceutical products (especially liquid formulations) contain significant quantities of carbohydrates, it is important that each drug product be evaluated before proceeding with the ketogenic diet. The purpose of this study was to compile the carbohydrate content of oral liquid products for patients on or considering a ketogenic diet., Methods: A list of 200 oral liquid drug products and their manufacturers was compiled using the Children's Health Care-Minneapolis pharmacy purchasing database, the Physicians' Desk Reference, and previously published lists of oral liquid medications. Manufacturers were contacted either by telephone or by letter and asked specifically about the sucrose, fructose, sorbitol, glycerin, and alcohol content of these liquid formulations., Results: The carbohydrate and alcohol content of 200 oral liquid products was determined and shown in an accompanying table., Conclusions: Many oral liquid medications contain significant amounts of carbohydrate. Tablet and capsule formulations are preferred when possible. To date, it has been difficult to quantify the carbohydrate content of liquid medications because of unavailability of this information. The carbohydrate content of 200 oral liquid medications is provided here to assist health care practitioners, patients, and care givers in designing drug regimens low in carbohydrates for patients on or considering a ketogenic diet.

High-dose acetaminophen (HDAC) produces hepatocellular necrosis and cytotoxic changes in other tissues that express mixed-function-oxidase (MFO) activity. N-acetylcysteine (NAC), administered within 8 hr of HDAC exposure, replenishes reduced glutathione and prevents these effects. Numerous cell culture and animal studies have demonstrated that NAC may differentially protect normal cells compared with malignant cells from the toxic effects of chemotherapeutic agents and radiation. It was therefore proposed that HDAC with NAC rescue may be effective in malignancies that express MFO activity. To test this hypothesis, a phase I trial of HDAC with NAC rescue was conducted on 19 patients with advanced cancer. HDAC was escalated from 6 to 20 g/m2 PO using a standard IV NAC rescue regimen. A total of 78 treatments were administered. Moderate fatigue, anorexia, and weight loss were the main toxicities observed. Transient grade 3 liver toxicity was noted following 1 treatment. Alopecia and renal and hematological toxicities were not observed. Responses after 4 courses administered weekly were as follows: response in at least 1 site-8 (partial 3, improved 3, mixed 2); stable disease-3; progressive disease-3; inevaluable-5. In conclusion, HDAC was tolerated with moderate fatigue, anorexia, and weight loss but few other effects using a standard IV NAC rescue regimen. A maximum tolerated dose was not reached at 20 g/m2. A 3/19 (15.8%) partial response rate was observed.

Objective: The American Academy of Pediatrics (AAP) recommends that ribavirin be reserved for infants who are severely ill and who are at high risk of morbidity and mortality, based on underlying clinical conditions. The purpose of this study was to evaluate current ribavirin use in our institution, implement hospital-specific guidelines for use, develop a prospective surveillance system to monitor ribavirin therapy, and evaluate the impact of these guidelines on subsequent use and cost of therapy., Methods: Ribavirin use was compared with the recommendations of the AAP. Results were presented to the professional staff, and hospital guidelines were implemented. Ribavirin therapy was reevaluated in a 2-year period after hospital guidelines were implemented., Results: In the initial evaluation period, only 67% of the ribavirin recipients met the AAP guidelines for use, and 19% received an inappropriate treatment regimen. The total cost and billed patient charges for ribavirin recipients who did not meet the guidelines for use in period 1 was $60,638 and $127,940, respectively. Over the next 2 years (period 2) after the implementation of hospital guidelines, the percentage of patients who received ribavirin decreased 35%, and approximately 96% of ribavirin recipients met the established criteria. Based on the decrease in the percentage of patients who received ribavirin in period 2 (41% versus 63%), the estimated cost avoidance and reduction in billed patient charges in period 2 was $55,540 and $117,334, respectively. This represents an estimated reduction in hospital costs and billed patient charges of $46,283 and $97,778 per 100 admissions for acute bronchiolitis., Conclusions: Before the implementation of hospital guidelines for use, a substantial percent of patients received ribavirin not consistent with the recommendations of the AAP. Following the adoption of a modified version of the AAP guidelines for our institution and the use of a multidisciplinary surveillance system for monitoring ribavirin therapy, we observed a substantial decrease in the overall ribavirin use. This has resulted in a significant savings in terms of cost avoidance and reduced billed patient charges.