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Rationale: Ivacaftor's clinical effects in the residual function mutations 3849+10kb C →T and D1152H warrant further characterization. Objectives: Evaluate ivacaftor's effect in people with cystic fibrosis aged ≥6 years with 3849+10kb C→T or D1152H residual function mutations; explore the correlation between ivacaftor-induced organoid-based cystic fibrosis transmembrane conductance regulator function measurements and clinical response to ivacaftor. Methods: Participants were randomized (1:1) in this placebo-controlled crossover study; each treatment sequence included two 8-week treatments with an 8-week washout period. The primary endpoint was absolute change in lung clearance index2.5 from baseline through Week 8. Additional endpoints included lung function, patient-reported outcomes, and in vitro intestinal organoid-based measurements of ivacaftor-induced cystic fibrosis transmembrane conductance regulator function. Results: Of 38 participants, 37 completed the study. The primary endpoint was met; the Bayesian posterior probability of improvement in lung clearance index2.5 with ivacaftor vs placebo was >99%. Additional endpoints improved with ivacaftor. Safety findings were consistent with ivacaftor's known safety profile. Dose-dependent swelling was observed in 23/25 viable organoid cultures with ivacaftor treatment. Correlations between ivacaftor-induced organoid swelling and clinical endpoints were negligible to low. Conclusions: In people with cystic fibrosis aged ≥6 years with a 3849+10kb C →T or D1152H mutation, ivacaftor treatment improved clinical endpoints vs placebo; however, there was no correlation between organoid swelling and change in clinical endpoints. The organoid assay may assist in identification of ivacaftor-responsive mutations but in this study did not predict magnitude of clinical benefit for individual people with cystic fibrosis with these two mutations. Clinical trial registered with ClinicalTrials.gov (NCT03068312).

In previous work, participants with a G970R mutation in cystic fibrosis transmembrane conductance regulator (CFTR) (c.2908G>C) had numerically lower sweat chloride responses during ivacaftor treatment than participants with other CFTR gating mutations. The objective of this substudy was to characterize the molecular defect of the G970R mutation in vitro and assess the benefit of ivacaftor in participants with this mutation. This substudy assessed sweat chloride, spirometry findings, and nasal potential difference on and off ivacaftor treatment in three participants with a G970R/F508del genotype. Intestinal organoids derived from rectal biopsy specimens were used to assess ivacaftor response ex vivo and conduct messenger RNA splice and protein analyses. No consistent or meaningful trends were observed between on-treatment and off-treatment clinical assessments. Organoids did not respond to ivacaftor in forskolin-induced swelling assays; no mature CFTR protein was detected in Western blots. Organoid RNA analysis demonstrated that 3 novel splice variants were created by G970R-CFTR: exon 17 truncation, exons 13-15 and 17 skipping, and intron 17 retention. Functional and molecular analyses indicated that the c.2908G>C mutation caused a cryptic splicing defect. Organoids lacked an ex vivo response with ivacaftor and supported identification of the mechanism underlying the CFTR defect caused by c.2908G>C. Analysis of CFTR mutations indicated that cryptic splicing was a rare cause of mutation misclassification in engineered cell lines. This substudy used organoids as an alternative in vitro model for mutations, such as cryptic splice mutations that cannot be fully assessed using cDNA expressed in recombinant cell systems. ispartof: CTS-Clinical and Translational Science vol:14 issue:2 pages:656-663 ispartof: location:United States status: published

Primary ciliary dyskinesia (PCD) is a respiratory disease caused by dysfunction of the cilia with currently no approved treatments. This predominantly autosomal recessive disease is caused by mutations in any one of over 50 genes involved in cilia function; DNAI1 is one of the more frequently mutated genes, accounting for approximately 5-10% of diagnosed PCD cases. A codon-optimized mRNA encoding DNAI1 and encapsulated in a lipid nanoparticle (LNP) was administered to mice via aerosolized inhalation resulting in the expression human DNAI1 in the multiciliated cells of the pseudostratified columnar epithelia. The spatial localization of DNAI1 expression in the bronchioles indicate that delivery of the DNAI1 mRNA transpires the lower airways. In a PCD disease model, exposure to the LNP-encapsulated DNAI1 mRNA resulted in increased ciliary beat frequency using high speed videomicroscopy showing the potential for an mRNA therapeutic to correct cilia function in patients with PCD due to DNAI1 mutations.

Untreated sensorineural hearing loss (SNHL) has been linked to depression, social isolation, anxiety, and a reduction in health-related quality of life (QoL), and is independently associated with cognitive decline. Only one in five persons with SNHL pursues amplification; 76-97% of those having hearing aids report regular or occasional use. Although hearing aid use during all waking hours is advocated for children, recommendations for adults are not as clear. Treatment outcomes, including benefit, satisfaction, and self-efficacy with hearing aids, may be predictors of self-reported hearing aid use, which is useful in clinical practice.The aim of this study was to determine average hours of self-reported daily hearing aid use by adults and if treatment outcome measures of benefit, satisfaction, and self-efficacy with hearing aids can predict self-reported daily hearing aid use in adults.The present study was a prospective cross-sectional survey with retrospective chart review.The study sample consisted of 152 experienced adult advanced digital technology (ADT) hearing aid users between 18 and 90 years of age who were patients in a two-office private practice in California.A postal survey was sent to 500 experienced adult ADT hearing aid users. Participants completed the Visual Analog Scale for Daily Use of Hearing Aids (VASuse) and validated measures of (1) self-efficacy, (2) satisfaction, and (3) benefit. Retrospective data were collected for all respondents via chart review. Multivariable linear regression was used to explore relationships between treatment outcomes and hearing aid use.Experienced hearing aid users wore their hearing aids an average of 12.0 h/day. Daily hearing aid use was significantly associated with residual participation restriction (RPR) on the International Outcome Inventory for Hearing Aids (IOI-HA) item 5 (p = 0.02). The VASuse was significantly associated with the IOI-HA factor 1, "Me and My Hearing Aids" (p = 0.03), an aggregate measure of satisfaction, benefit, and QoL.Participants reported wearing their hearing aids an average of 12.0 h/day. Self-reported daily hearing aid use was associated with a combination of satisfaction, benefit, and increased QoL, and with RPR. The interconnectedness of satisfaction, benefit, and QoL positively affected hearing aid use, and greater levels of RPR seemed to discourage hearing aid use. If hearing aid owners are inconsistent or nonusers, then counseling and outcome measures should be used in the domains of satisfaction, benefit, and QoL. Future research should involve additional ADT hearing aid users with different experience levels across various study sites.

We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing.

Background The phase 3 studies of telaprevir (T) in combination with peginterferon α-2a and ribavirin (PR) in treatment-naive genotype 1 chronic hepatitis C virus-infected patients (ADVANCE/ILLUMINATE) were not designed a priori to assess the effect of race and ethnicity on treatment response. However, these factors are important given the lower sustained virologic response (SVR) rates observed in black and Hispanic/Latino patients treated with PR. Goals This retrospective pooled analysis evaluated the effect of race or ethnicity on treatment-naive patient response to telaprevir-based therapy and assessed resistant variant profiles. Materials and methods This analysis comprised patients enrolled in ADVANCE (N=363) and ILLUMINATE (N=540) who received 12 weeks of telaprevir in combination with PR followed by 12 or 36 weeks of PR alone and patients in ADVANCE (N=361) who received 48 weeks of PR alone. Race and ethnicity were self-reported and not mutually exclusive. Results Higher SVR rates were observed with telaprevir-based therapy compared with PR in blacks [n=99 (62%) vs. n=28 (29%), respectively] and in Hispanics/Latinos [n=89 (72%) vs. n=38 (39%)]. The SVR was lower in telaprevir-treated blacks [n=99 (62%)] compared with nonblacks [n=791 (78%)] and in Hispanic/Latinos compared with non-Hispanics/Latinos [n=89 (72%) vs. n=801 (76%)]. Low discontinuation rates due to adverse events, including rash and anemia, were observed across subgroups. Resistance profiles were similar among the subgroups. Conclusions Treatment-naive black and Hispanic/Latino patients with genotype 1 chronic hepatitis C virus infection may benefit from telaprevir-based therapy, an important finding given the lower SVR rates observed in these patients when they are treated with PR alone.

Understanding hepatitis C virus (HCV) replication has been limited by access to serial samples of liver, the primary site of viral replication. Our understanding of how HCV replicates and develops drug-resistant variants in the liver is limited. We studied 15 patients chronically infected with genotype 1 HCV treated with telaprevir (TVR)/pegylated-interferon alpha/ribavirin. Hepatic fine needle aspiration was performed before treatment and at hour 10, days 4 and 15, and week 8 after initiation of antiviral therapy. We measured viral kinetics, resistance patterns, TVR concentrations, and host transcription profiles. All patients completed all protocol-defined procedures that were generally well tolerated. First-phase HCV decline (baseline/treatment day 4) was significantly slower in liver than in plasma (slope plasma: −0.29; liver, −0.009; P

Background Population sequencing (PS) has shown that telaprevir-resistant variants are not typically detectable at baseline (prevalence, ≤5% of patients), and most variants present at the time of treatment failure are no longer detectable at the end of the study. Methods To gain insight into the evolution of telaprevir-resistant variants, their baseline prevalence and persistence after treatment was investigated using a more sensitive, deep-sequencing (DS) technique in a large number of treatment-experienced patients from the REALIZE study who were infected with hepatitis C virus genotype 1. Results Before treatment initiation, telaprevir-resistant variants (T54A, T54S, or R155K in 1%-2% of the viral population) were detected by DS in a fraction (2%) of patients for whom PS failed to detect resistance; these variants were not necessarily detected at the time of treatment failure. Of 49 patients in whom telaprevir-resistant variants were detected by PS at the time of treatment failure but not at the end of the study, DS revealed the presence of variants (V36A/L/M, T54S, or R155K in 1%-36% of the viral population) in 16 patients (33%) at the end of the study. Conclusions Similar to PS findings, DS analysis revealed that the frequency of telaprevir-resistant variants before treatment was also low, and variants detected at the time of treatment failure were no longer detectable in the majority of patients during follow-up.

Background Telaprevir (TVR), a hepatitis C virus (HCV) NS3/4A protease inhibitor, has been approved to treat genotype 1 HCV. To understand the clinical impact of TVR-resistant variants, we analyzed samples from patients in phase 3 clinical trials to determine the frequency and retention of TVR-resistant variants in patients who did not achieve sustained virologic response (SVR). Methods A total of 1797 patients were treated with TVR. Resistant variants (V36A/G/I/L/M, T54A/S, I132V [subtype 1a only], R155G/K/T/M, A156F/N/S/T/V, and D168N) were identified after treatment failure and at visits thereafter, by direct (population) sequencing of the NS3/4A region. Kaplan-Meier analysis was used to determine median time to loss of these variants. Results Resistant variants were observed in 77% (299/388) of patients who did not achieve SVR. Resistance occurred more commonly in subtype 1a (86%; 232/269) than subtype 1b infections (56%; 67/119). After treatment failure, 355 patients had at least 1 follow-up visit (median follow-up period: 9.6 months). Of patients with resistance at time of failure and at least 1 follow-up visit, 60% (153/254) lost resistance. Kaplan-Meier analysis, including all patients with any sequence data after treatment failure, indicated that median time to wild type was 10.6 months (95% confidence interval [CI], 9.47-12.20) in subtype 1a and 0.9 months (95% CI, 0.00-2.07) in subtype 1b infections. Conclusions After failure to achieve SVR with TVR-based treatment, resistant variants are observed in most patients. However, presumably due to the lower fitness of those variants, they tend to be replaced with wild-type virus over time.

Single-nucleotide polymorphisms (SNPs) can be used to study the nucleotide diversity both within and between species. Furthermore, as some SNPs impact organismal phenotype, characterizing SNPs can provide insights into the relationship between genotype and phenotype and the adaptive evolution of populations. Model systems that combine a large quantity of available sequence data (e.g., large-scale expressed sequence tag (EST) sequencing projects) with diverse natural environments provide potent opportunities to investigate the evolution of adaptive nucleotide polymorphism in the wild. We developed a relational database of SNPs from 17,108 ESTs for the estuarine sea anemone Nematostella vectensis ( www.stellabase.org/SNP ). In these ESTs, we identified 20,063 candidate SNPs in 3,233 assembled contigs. Of these SNPs, 555 can be regarded with a high degree of confidence because the nucleotide variants occurring at that position were observed in at least two different ESTs. All 555 of these high-confidence SNPs were scored with respect to their location in coding or noncoding regions. Three hundred forty-three SNPs were within coding regions, 78 of which were nonsynonymous polymorphisms. We sequence-confirmed and analyzed the distribution of three nonsynonymous polymorphisms—one that occurs in the highly conserved homeodomain of the transcription factor tlx and two that occur in a deiodinase gene.

The ability to measure body composition is critical for studying the physiological ecology of animals. This is particularly true for small mammals that have a high metabolic rate. We evaluated a nondestructive method of body composition analysis that would allow accurate assessment of body fat, body water, and lean mass. We used total body electrical conductivity (TOBEC) to estimate body composition in the little brown myotis (Myotis lucifugus). In a sample of 46 individuals, TOBEC was both accurate and precise in estimating total body water and lean mass but was less effective at estimating total body fat. Mass-independent or whole-body compartments (i.e., total body water, total body fat, lean dry mass, and lean body mass) were more accurately estimated than mass-dependent or mass-specific body composition compartments (i.e., water content, fat index, and % lean dry mass). The TOBEC measurements we made using an SA-3000 analyzer were influenced by extremes in body temperature, as well as by aluminum and incoloy wing bands. Our study also presents a new method of restraint especially suited for small mammals and birds that increases precision of TOBEC measurements. This study shows that TOBEC is a potentially valuable tool for studying changes in body composition of small mammals and may provide insight into the physiological impacts of various life history stages such as postnatal growth, reproduction, and hibernation.

The evolution of parasitism is often accompanied by profound changes to the developmental program. However, relatively few studies have directly examined the developmental evolution of parasitic species from free-living ancestors. The lined sea anemone Edwardsiella lineata is a relatively recently evolved parasite for which closely related free-living outgroups are known, including the starlet sea anemone Nematostella vectensis. The larva of E. lineata parasitizes the ctenophore Mnemiopsis leidyi, and, once embedded in its host, the anemone assumes a novel vermiform body plan. That we might begin to understand how the developmental program of this species has been transformed during the evolution of parasitism, we characterized the gross anatomy, histology, and cnidom of the parasitic stage, post-parasitic larval stage, and adult stage of the E. lineata life cycle. The distinct parasitic stage of the life cycle differs from the post-parasitic larva with respect to overall shape, external ciliation, cnida frequency, and tissue architecture. The parasitic stage and planula both contain holotrichs, a type of cnida not previously reported in Edwardsiidae. The internal morphology of the post-parasitic planula is extremely similar to the adult morphology, with a complete set of mesenterial tissue and musculature despite this stage having little external differentiation. Finally, we observed 2 previously undocumented aspects of asexual reproduction in E. lineata: (1) the parasitic stage undergoes transverse fission via physal pinching, the first report of asexual reproduction in a pre-adult stage in the Edwardsiidae; and (2) the juvenile polyp undergoes transverse fission via polarity reversal, the first time this form of fission has been reported in E. lineata.

Sea anemones use an arsenal of peptide neurotoxins accumulated in special stinging cells (nematocytes) for defense and predation. Intriguingly, genomic analysis of Nematostella vectensis revealed only a single toxin, Nv1 (N. vectensis toxin 1), encoded by multiple extremely conserved genes. We examined the toxic potential of Nv1 and whether it is produced by the three developmental stages (embryo, planula, and polyp) of Nematostella. Nv1 was expressed in recombinant form and, similarly to Type I sea anemone toxins, inhibited the inactivation of voltage-gated sodium channels. However, in contrast to the other toxins, Nv1 revealed high specificity for insect over mammalian voltage-gated sodium channels. Transcript analysis indicated that multiple Nv1 loci are transcribed at all developmental stages of N. vectensis, whereas splicing of these transcripts is restricted to the polyp stage. This finding suggests that regulation of Nv1 synthesis is posttranscriptional and that the embryo and planula stages do not produce the Nv1 toxin. This rare phenomenon of intron retention at the early developmental stages is intriguing and raises the question as to the mechanism enabling such differential expression in sea anemones.

Gene families, which encode toxins, are found in many poisonous animals, yet there is limited understanding of their evolution at the nucleotide level. The release of the genome draft sequence for the sea anemone Nematostella vectensis enabled a comprehensive study of a gene family whose neurotoxin products affect voltage-gated sodium channels. All gene family members are clustered in a highly repetitive approximately 30-kb genomic region and encode a single toxin, Nv1. These genes exhibit extreme conservation at the nucleotide level which cannot be explained by purifying selection. This conservation greatly differs from the toxin gene families of other animals (e.g., snakes, scorpions, and cone snails), whose evolution was driven by diversifying selection, thereby generating a high degree of genetic diversity. The low nucleotide diversity at the Nv1 genes is reminiscent of that reported for DNA encoding ribosomal RNA (rDNA) and 2 hsp70 genes from Drosophila, which have evolved via concerted evolution. This evolutionary pattern was experimentally demonstrated in yeast rDNA and was shown to involve unequal crossing-over. Through sequence analysis of toxin genes from multiple N. vectensis populations and 2 other anemone species, Anemonia viridis and Actinia equina, we observed that the toxin genes for each sea anemone species are more similar to one another than to those of other species, suggesting they evolved by manner of concerted evolution. Furthermore, in 2 of the species (A. viridis and A. equina) we found genes that evolved under diversifying selection, suggesting that concerted evolution and accelerated evolution may occur simultaneously.

The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.

Distinguishing natural versus anthropogenic dispersal of organisms is essential for determining the native range of a species and implementing an effective conservation strategy. For cryptogenic species with limited historical records, molecular data can help to identify introductions. Nematostella vectensis is a small, burrowing estuarine sea anemone found in tidally restricted salt marsh pools. This species’ current distribution extends over three coast lines: (i) the Atlantic coast of North America from Nova Scotia to Georgia, (ii) the Pacific coast of North America from Washington to central California, and (iii) the southeast coast of England. The 1996 IUCN Red List designates N. vectensis as “vulnerable” in England. Amplified fragment length polymorphism (AFLP) fingerprinting of 516 individuals from 24 N. vectensis populations throughout its range and mtDNA sequencing of a subsample of these individuals strongly suggest that anthropogenic dispersal has played a significant role in its current distribution. Certain western Atlantic populations of N. vectensis exhibit greater genetic similarity to Pacific populations or English populations than to other western Atlantic populations. At the same time, F-statistics showing high degrees of genetic differentiation between geographically proximate populations support a low likelihood for natural dispersal between salt marshes. Furthermore, the western Atlantic harbors greater genetic diversity than either England or the eastern Pacific. Collectively, these data clearly imply that N. vectensis is native to the Atlantic coast of North America and that populations along the Pacific coast and in England are cases of successful introduction.

The lined sea anemone Edwardsiella lineata has evolved a derived parasitic life history that includes a novel body plan adapted for life inside its ctenophore hosts. Reputedly its sole host is the sea walnut, Mnemiopsis leidyi, a voracious planktivore and a seasonally abundant member of many pelagic ecosystems. However, we have observed substantially higher E. lineata prevalence in a second ctenophore species, the ctenophore predator Beroë ovata. The interplay among these 3 species has important conservation consequences as M. leidyi introductions are thought to be responsible for the severe depletion of numerous commercial fisheries in the Mediterranean basin, and both E. lineata and B. ovata have been proposed as biological controls for invasive M. leidyi. Over a 3-yr period (2004-2006), we collected 8,253 ctenophores from Woods Hole, Massachusetts, including M. leidyi, B. ovata, and a third ctenophore, Pleurobrachia pileus, and we recorded E. lineata infection frequencies, parasite load, and parasite location. We also conducted laboratory experiments to determine the likely mechanisms for parasite introduction and the effect of each host on parasite development. We observed peak E. lineata infection frequencies of 0% in P. pileus, 59% in M. leidyi, and 100% in B. ovata, suggesting that B. ovata could be an important natural host for E. lineata. However, in laboratory experiments, E. lineata larvae proved far more successful at infecting M. leidyi than B. ovata, and E. lineata parasites excised from M. leidyi exhibited greater developmental competence than parasites excised from B. ovata. Although we show that E. lineata is efficiently transferred from M. leidyi to B. ovata when the latter preys upon the former, we conclude that E. lineata larvae are not well adapted for parasitizing the latter species and that the E. lineata parasite is not well adapted for feeding in B. ovata; these developmental and ecological factors underlie the host specificity of this recently evolved parasite.

Invertebrate animals have provided important insights into the mechanisms of, and treatment for, numerous human diseases. A surprisingly high proportion of genes underlying human disease are present in the genome of a simple, evolutionarily basal invertebrate animal, Nematostella vectensis , including some genes that are absent in established invertebrate model organisms. This, together with the laboratory tractability and regenerative capability of N. vectensis, recommends the species as an important new experimental model for the study of genes underlying human disease.

The Rel/NF-kappaB and NFAT families of transcription factors are related through an N-terminal DNA-binding domain called the Rel Homology domain (RHD). Neither the RHD nor the NF-kappaB pathway has been identified in a basal (i.e., nonbilaterian) animal phylum. Using genomic and cDNA databases, we have identified two RHD domain-containing proteins from the cnidarian Nematostella vectensis: an NF-kappaB-like protein (Nv-NF-kappaB) and an NFAT-like protein (Nv-NFAT). The gene structure and RHD predicted amino acid sequence of Nv-nfkb are similar to those of the vertebrate NF-kappaB p50/p52 proteins, whereas the sequence of Nv-NFAT allows only ambiguous assignment to the NFAT family. Nv-NF-kappaB lacks the C-terminal IkappaB-like sequences present in all other NF-kappaB proteins. There are, however, two IkappaB-like genes in Nematostella encoded by loci distinct from Nv-nfkb. The separate nfkb and ikb genes of Nematostella may reflect the ancestral metazoan condition, suggesting that a gene fusion event created the nfkb genes in Drosophila and vertebrates. Nematostella also has genes that encode upstream and downstream components of the vertebrate NF-kappaB signaling pathway. Upstream components include Toll- and tumor necrosis-like receptors and ligands, adaptor proteins (Trafs, Myd88), caspases, and a TBK-like kinase. Downstream components include the NF-kappaB coactivator protein Bcl-3 and several NF-kappaB target genes. These results demonstrate that RHD-containing transcription factors and associated pathways are evolutionarily more ancient than previously known. Moreover, they suggest models for the evolutionary diversification of the insect and vertebrate Rel/NF-kappaB/IkappaB and NFAT gene families and suggest that cnidarians possess an NF-kappaB-regulated developmental or stress response pathway.

Synopsis Direct development lies at 1 end of a continuum that encompasses various degrees of indirect development. Indirect development exists where a larval stage is interposed between the embryo and the adult and undergoes metamorphosis, though the ecological and morphological distinctiveness of the larval stage relative to the adult stage can vary tremendously. There are numerous empirical examples where direct development has evolved from indirect development, but little empirical evidence describing a recent transition from direct to indirect development. Here, we suggest 4 criteria for defining indirect, and therefore metamorphic, life histories. We then apply these criteria to address the planula–polyp transition in cnidarians, focusing on 2 species in the anthozoan family Edwardsiidae. The lined sea anemone, Edwardsiella lineata, has made a qualitative shift towards indirect development that coincides with, and was potentially facilitated by, the evolution of endoparasitism. We compare E. lineata’s development with that of a closely related sea anemone, Nematostella vectensis, where the nonfeeding planula gradually develops the morphology of the adult polyp. In E. lineata, a novel parasitic life history stage is interposed between the planula and the polyp. We discuss how the evolution of endoparasitism could facilitate the evolution metamorphic life histories.

Stable isotopes can be used to evaluate trophic relationships, nutrient state, and temporal and spatial variation in diet, food webs, and behaviour both within and between species. Here we describe the development and application of models to predict habitat use of a common insectivorous bat (Eptesicus fuscus) based upon δ13C and δ15N signatures of skin tissue. We used a 42-specimen sample collected from three well-characterized ecogeographic regions, disparate both in photosynthetic mechanism and fertilizer use, to generate the models. Significant univariate differences between these three sites in terms of δ13C (F2, 39 = 112.92, P < 0.0001) and δ15N (F2, 39 = 97.06, P < 0.0001), and multivariate significance of both variables (Wilk's λ = 0.032, F4, 76 = 87.02, P < 0.0001), made it possible to develop three predictive models using Fisher's linear discriminant functions: 1) a model predicting if bats forage in C3 or mixed C3/C4 sites, 2) a model predicting if bats forage in agricultural areas, an...

In recent years, a handful of model systems from the basal metazoan phylum Cnidaria have emerged to challenge long-held views on the evolution of animal complexity. The most-recent, and in many ways most-promising addition to this group is the starlet sea anemone, Nematostella vectensis. The remarkable amenability of this species to laboratory manipulation has already made it a productive system for exploring cnidarian development, and a proliferation of molecular and genomic tools, including the currently ongoing Nematostella genome project, further enhances the promise of this species. In addition, the facility with which Nematostella populations can be investigated within their natural ecological context suggests that this model may be profitably expanded to address important questions in molecular and evolutionary ecology. In this review, we explore the traits that make Nematostella exceptionally attractive as a model organism, summarize recent research demonstrating the utility of Nematostella in several different contexts, and highlight a number of developments likely to further increase that utility in the near future.

We have investigated the leaching behavior of actinides from simulants of tank waste sludges derived from the BiPO4, Redox, and PUREX processes, the principal chemical separations processes that operated at the Hanford site during 40+ years of plutonium production. Fundamental investigations of the speciation of uranium and neptunium in solutions representative of proposed alkaline sludge washing liquors have also been completed. Correlation of the results from sludge leaching indicate that, while Am and Pu are generally not appreciably dissolved from the sludges into alkaline solutions in the absence of oxidants, Np and U can be mobilized during alkaline sludge washing. Leaching of sludges with acidic solutions and strong complexing agents indicate considerable association of all actinide ions with Cr, Fe, and Mn oxides in the sludge simulants. Electrochemical experiments conducted in strongly alkaline solutions have defined the formal potentials of Np in strong base and reveal that mononuclear hydrolysi...

VX-222, a thiophene-2-carboxylic acid derivative, is a selective nonnucleoside inhibitor of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase. In phase 1 and 2 clinical studies, VX-222 demonstrated effective antiviral efficacy, with substantial reductions in plasma HCV RNA in patients chronically infected with genotype 1 HCV. To characterize the potential for selection of VX-222-resistant variants in HCV-infected patients, the HCV NS5B gene was sequenced at baseline and during and after 3 days of VX-222 dosing (monotherapy) in a phase 1 study. Variants with the substitutions L419C/I/M/P/S/V, R422K, M423I/T/V, I482L/N/T, A486S/T/V, and V494A were selected during VX-222 dosing, and their levels declined over time after the end of dosing. Phenotypic analysis of these variants was conducted using HCV replicons carrying site-directed mutations. Of the 17 variants, 14 showed reduced susceptibility to VX-222 compared with the wild type, with the L419C/S and R422K variants having higher levels of resistance (>200-fold) than the rest of the variants (6.8- to 76-fold). The M423I and A486S variants remained susceptible to VX-222. The 50% effective concentration (EC 50 ) for the L419P variant could not be obtained due to the poor replication of this replicon. The majority of the variants (15/17) were less fit than the wild type. A subset of the variants, predominately the L419S and R422K variants, were observed when the efficacy and safety of VX-222- and telaprevir-based regimens given for 12 weeks were investigated in genotype 1 HCV-infected patients in a phase 2 study. The NS3 and NS5B variants selected during the dual combination therapy showed reduced susceptibility to both telaprevir and VX-222 and had a lower replication capacity than the wild type. The phase 1b study has the ClinicalTrials.gov identifier NCT00911963, and the phase 2a study has ClinicalTrials.gov identifier NCT01080222.

A continuously mixed series of microbial communities inhabits various points of the respiratory tract, with community composition determined by distance from colonization sources, colonization rates, and extinction rates. Ecology and evolution theory developed in the context of biogeography is relevant to clinical microbiology and could reframe the interpretation of recent studies comparing communities from lung explant samples, sputum samples, and oropharyngeal swabs. We propose an island biogeography model of the microbial communities inhabiting different niches in human airways. Island biogeography as applied to communities separated by time and space is a useful parallel for exploring microbial colonization of healthy and diseased lungs, with the potential to inform our understanding of microbial community dynamics and the relevance of microbes detected in different sample types. In this perspective, we focus on the intermixed microbial communities inhabiting different regions of the airways of patients with cystic fibrosis.

Consecutive washing of simulant sludges from the BiPO4 (Cycle 3), Redox, and PUREX processes shows less than 4.5% of sorbed Pu(III/IV) or Pu(VI) is mobilized during CrO4 2− dissolution by the 0.01 M NaOH + 0.01 M NaNO2 sluice or 3.0 M NaOH leach solutions to be used for sludge pretreatment at Hanford. Experimental sludge washing with 2.0 M HNO3 results in 5.8-65.5% dissolution of Pu(III/IV) or Pu(VI) from all simulants and dissolution of Nd(III), Cr(III), and Fe(III) (where present) from BiPO4 simulants. The dissolution of Pu(III/IV) and Pu(VI) from BiPO4 sludge simulants by strongly chelating media is accompanied by dissolution and reduction of Mn(IV) to a Mn(III) complex. Details of radioanalytical and spectroscopic investigations of sludge simulant washing are discussed in the context of understanding actinide behavior during alkaline leaching of radioactive sludge wastes.

The kinetics of ligand exchange between bulk solution TBP and uranyl nitrate bound TBP in o-xylene has been investigated by 31P dynamic NMR spectroscopy. First order ligand exchange rate constant, k, and the activation energy for the uranyl nitrate-TBP system were determined from plots of transverse relaxation rates (In (l/τ)) versus reciprocal temperature (1/T). Using the Eyring equation, the average values of activation enthalpy, δH* (30.8±5.1 kJ-mole−1), and activation entropy, δS* (-109±19 J/mol-K) have been calculated. The negative entropy of activation value indicates an increase in order on proceeding from the reactants to the activated complex. Therefore, an associative mechanism may be proposed for the ligand exchange reaction between UO2(NO3)2 TBP2 and TBP. Equilibration of the extractant phase with 1.0 M HC1 did not change the ligand exchange rate constants or the activation parameters appreciably. These results are discussed in comparison with previous reports on TBP exchange rates fo...

The rates of hydrogen ion exchange on phosphonic acid ligands and that of phosphonate ligand exchange on selected uranyl-phosphonate complexes have been investigated by dynamic NMR spectroscopy. The spin-spin relaxation time (ln(1/T{sub 2})) for H{sup +} exchange on the fee ligands exhibits a parabolic dependence on reciprocal temperature (1/T (K{sup {minus}1})). The empirical fit parameters are correlated with the activation parameters ({Delta}H{sup *}, {Delta}S{sup *}, {Delta}C{sub p}{sup *}) by adapting the statistical mechanical framework developed by Braibanti et al. to the Eyring activated complex theory. The correlation of the apparent activation enthalpy with temperature indicates that 6--11 water molecules participate in the transition from reactants to activated complex for ligand proton exchange reactions, depending on the ligand. Mechanistic details of ligand exchange reactions of phosphonic acid complexants onto the corresponding uranium(VI) complexes are not fully developed, but the negative values for {Delta}S{sup *} imply increased order in the transition to the activated complex. Though {Delta}H{sup *} for ligand exchange covers a range of 15 kJ/mol, the free energy of activation ({Delta}G{sup *}) is nearly constant for the series of ligands, implying substantial entropy compensation in the activation process. Application of the Marcus relationship defines a correlation between {Delta}G{sup *} andmore » the thermodynamic stability ({Delta}G{degree}) for the 1:2 uranyl complexes with methanediphosphonic acid and 1-hydroxyethane-1,1-diphosphonic acid.« less

We report herein a summary of what is known about actinide complexation kinetics. The systems include actinide ions in the four principal oxidation states (III, IV, V, and VI) and complex formation and dissociation rates with both simple and complex ligands. Complex formation reactions tend to be rapid, accessible only to rapid-scan and equilibrium perturbation techniques. Complex dissociation reactions exhibit a wider range of rates and are generally more accessible using standard analytical methods. Literature results are described and correlated with the known properties of the individual ions.

The prevalence of naturally occurring hepatitis C virus (HCV) variants that are less sensitive to direct-acting antiviral (DAA) inhibitors has not been fully characterized. We used population sequence analysis to assess the frequency of such variants in plasma samples from 3,447 DAA-naive patients with genotype 1 HCV. In general, HCV variants with lower-level resistance (3- to 25-fold increased 50% inhibitor concentration [IC 50 ]) to telaprevir were observed as the dominant species in 0 to 3% of patients, depending on the specific variant, whereas higher-level resistant variants (>25-fold-increased IC 50 ) were not observed. Specific variants resistant to NS5A inhibitors were predominant in up to 6% of patients. Most variants resistant to nucleo(s/t)ide active-site NS5B polymerase inhibitors were not observed, whereas variants resistant to non-nucleoside allosteric inhibitors were observed in up to 18% of patients. The presence of DAA-resistant variants in NS5A, NS5B, or NS3 (including telaprevir-resistant variants), in baseline samples of treatment-naive patients receiving a telaprevir-based regimen in phase 3 studies did not affect the sustained viral response (SVR). Treatment-naive patients with viral populations containing the telaprevir-resistant variants NS3 V36M, T54S, or R155K at baseline achieved a 74% SVR rate, whereas patients with no resistant variants detected prior to treatment achieved a 76% SVR rate. The effect of specific resistant variant frequency on response to various DAA treatments in different patient populations, including interferon nonresponders, should be further studied.

Defective DNA damage repair, leading to genomic instability, is a common event during tumorigenesis. Despite enabling the persistence of mutations, any of which can confer a growth advantage to the nascent tumor, these defects place an Achilles Heel reliance on remaining repair pathways for survival from DNA damage. The protein kinases ataxia telangiectasia mutated (ATM) and ATM and Rad3 related (ATR) are key mediators of a DNA damage response activated by DNA damage during the S and G2 phases of cell cycle. Together they signal a series of cellular responses including activation of checkpoints and repair by homologous recombination. Loss of ATM pathway function frequently occurs in cancer, commonly from loss of function mutations in the tumor suppressor, p53, a substrate of ATM. This leads to a reliance on ATR that can be exploited for therapeutic benefit. Activation of ATR, by generation of S-phase DNA damage (replication stress, [RS]), can arise from treatment with DNA damaging drugs and certain targeted therapies such as inhibitors of poly ADP ribose polymerase (PARP). PARP is an enzyme involved in several DNA repair pathways, including base excision repair. Some PARP inhibitors have been shown to form an irreversible complex with DNA, potentially generating a direct RS lesion. While initial data indicates that inhibition of ATR and PARP is synergistic in some cancer cells, a comprehensive assessment has not been reported. Inhibition of ATR was cytotoxic in combination with PARP inhibitors against many cancer, but not non-cancer, cells. This effect was observed with multiple PARP inhibitors irrespective of their potential to form a DNA complex. In large cell panels of over 100 cancer cell lines, greater synergy was observed for the combination of an ATR and PARP inhibitor in cell lines with mutation of the TP53 gene. This was confirmed in isogenic cell lines depleted for ATM or p53, and is consistent with the profile of ATR and DNA damaging drug combinations. Furthermore, a triple combination of a PARP inhibitor, ATR inhibitor and the DNA damaging drug, cisplatin, retained cancer cell specific cytotoxic activity. In vitro dose-scheduling studies with the doublet of a PARP and ATR inhibitor showed optimal activity was achieved with transient concurrent exposure to both agents. This schedule contrasts with that for ATR inhibitors in combination with DNA damaging drugs where sequential dosing was optimal. In a mouse xenograft model concurrent dosing on a twice-weekly schedule was effective and well-tolerated. These data demonstrate the potential of combining ATR and PARP inhibitors in patients with p53 defective tumors. An optimal dose schedule was defined from cell and mouse studies. Together the data support clinical evaluation of ATR and PARP inhibitor combinations. Citation Format: John Pollard, Phil Reaper, Adele Peek, Stuart Hughes, Hakim Djeha, Steven Cummings, Karen Larbi, Marina Penney, Jim Sullivan, Darin Takemoto, Chris DeFranco. Pre-clinical combinations of ATR and PARP inhibitors: Defining target patient populations and dose schedule. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3711.

Background Development of compensatory mutations within the HIV p7/p1 and p1/p6 protease cleavage site region has been observed in HIV-infected patients treated with protease inhibitors. Mechanisms of fitness compensation may occur in HCV populations upon treatment of HCV protease inhibitors as well. Findings In this study, we investigated whether substitutions in protease cleavage site regions of HCV occur in response to a treatment regimen containing the NS3/4A protease inhibitor telaprevir (TVR). Evaluation of viral populations from 569 patients prior to treatment showed that the four NS3/4A cleavage sites were well conserved. Few changes in the cleavage site regions were observed in the 159 patients who failed TVR combination treatment, and no residues displayed evidence of directional selection after the acquisition of TVR-resistance. Conclusions Cleavage site mutations did not occur after treatment with the HCV protease inhibitor telaprevir.

BackgroundIn patients with genotype 1 chronic hepatitis C infection, telaprevir (TVR) in combination with peginterferon and ribavirin (PR) significantly increased sustained virologic response (SVR) rates compared with PR alone. However, genotypic changes could be observed in TVR-treated patients who did not achieve an SVR.MethodsPopulation sequence analysis of the NS3•4A region was performed in patients who did not achieve SVR with TVR-based treatment.ResultsResistant variants were observed after treatment with a telaprevir-based regimen in 12% of treatment-naïve patients (ADVANCE; T12PR arm), 6% of prior relapsers, 24% of prior partial responders, and 51% of prior null responder patients (REALIZE, T12PR48 arms). NS3 protease variants V36M, R155K, and V36M+R155K emerged frequently in patients with genotype 1a and V36A, T54A, and A156S/T in patients with genotype 1b. Lower-level resistance to telaprevir was conferred by V36A/M, T54A/S, R155K/T, and A156S variants; and higher-level resistance to telaprevir was conferred by A156T and V36M+R155K variants. Virologic failure during telaprevir treatment was more common in patients with genotype 1a and in prior PR nonresponder patients and was associated with higher-level telaprevir-resistant variants. Relapse was usually associated with wild-type or lower-level resistant variants. After treatment, viral populations were wild-type with a median time of 10 months for genotype 1a and 3 weeks for genotype 1b patients.ConclusionsA consistent, subtype-dependent resistance profile was observed in patients who did not achieve an SVR with telaprevir-based treatment. The primary role of TVR is to inhibit wild-type virus and variants with lower-levels of resistance to telaprevir. The complementary role of PR is to clear any remaining telaprevir-resistant variants, especially higher-level telaprevir-resistant variants. Resistant variants are detectable in most patients who fail to achieve SVR, but their levels decline over time after treatment.

In the Phase 3 REALIZE study, 662 genotype 1 hepatitis C virus (HCV)-infected patients with prior peginterferon/ribavirin treatment failure (including relapsers, partial, and null responders) were randomized to 12 weeks of telaprevir given immediately (T12/PR48) or following 4 weeks of peginterferon/ribavirin (lead-in T12/PR48), or 12 weeks of placebo (PR48), combined with a total of 48 weeks of peginterferon alfa-2a/ribavirin. Sustained virologic response (SVR) rates were 64% (T12/PR48), 66% (lead-in T12/PR48), and 17% (PR48). This analysis aimed to characterize treatment outcomes and viral variants emerging in telaprevir-treated patients not achieving SVR. HCV NS3·4A population sequencing was performed at baseline, during treatment, and follow-up. Telaprevir-resistant variants were classified into lower-level (3- to 25-fold 50% inhibitory concentration [IC50] increase: V36A/M, T54A/S, R155I/K/M/T, and A156S) and higher-level (>25-fold IC50 increase: V36M+R155K and A156T/V) resistance. Resistant variants were uncommon at baseline. Overall, 18% (52%, 19%, and 1% of prior null and partial responders and relapsers, respectively) of telaprevir-treated patients had on-treatment virologic failure, with no significant difference with or without a lead-in. Virologic failure during the telaprevir-treatment phase was predominantly associated with higher-level resistance; virologic failure during the peginterferon/ribavirin-treatment phase was associated with higher- or lower-level, or wildtype variants, depending on genotype. Relapse occurred in 9% of patients completing assigned treatment and was generally associated with lower-level resistant variants or wildtype. Resistant variants were no longer detectable by study end (median follow-up of 11 months) in 58% of non-SVR patients. Conclusion: In REALIZE, variants emerging in non-SVR, telaprevir-treated patients were similar irrespective of the use of a lead-in and were consistent with those previously reported. In most patients, resistant variants became undetectable over time. (HEPATOLOGY 2012;56:2106–2115)

Background & Aims Telaprevir, a hepatitis C virus NS3/4A protease inhibitor has significantly improved sustained viral response rates when given in combination with pegylated interferon alfa-2a and ribavirin, compared with current standard of care in hepatitis C virus genotype 1 infected patients. In patients with a failed sustained response, the emergence of drug-resistant variants during treatment has been reported. It is unclear to what extent these variants persist in untreated patients. The aim of this study was to assess using ultra-deep pyrosequencing, whether after 4 years follow-up, the frequency of resistant variants is increased compared to pre-treatment frequencies following 14 days of telaprevir treatment. Methods Fifteen patients from 2 previous telaprevir phase 1 clinical studies (VX04-950-101 and VX05-950-103) were included. These patients all received telaprevir monotherapy for 14 days, and 2 patients subsequently received standard of care. Variants at previously well-characterized NS3 protease positions V36, T54, R155 and A156 were assessed at baseline and after a follow-up of 4±1.2 years by ultra-deep pyrosequencing. The prevalence of resistant variants at follow-up was compared to baseline. Results Resistance associated mutations were detectable at low frequency at baseline. In general, prevalence of resistance mutations at follow-up was not increased compared to baseline. Only one patient had a small, but statistically significant, increase in the number of V36M and T54S variants 4 years after telaprevir-dosing. Conclusion In patients treated for 14 days with telaprevir monotherapy, ultra-deep pyrosequencing indicates that long-term persistence of resistant variants is rare.

Background: Telaprevir is a selective inhibitor of the hepatitis C virus NS3 center dot 4A serine protease. Treatment with telaprevir resulted in a rapid HCV-RNA decline in chronic hepatitis C genotype 1 patients. Objectives: To report the clinical and viral course of a patient treated with telaprevir in combination with pegylated interferon-alpha-2a and ribavirin in a Phase 2 clinical trial (PROVE3). Study design: This previous non-responder to interferon based therapy was treated for 40 weeks with a telaprevir, pegylated interferon alpha-2a, and ribavirin regimen. Viral sequencing and phylogenetic analysis were performed before, during and after therapy. Results: The patient, a 54 years old male patient, experienced a viral relapse 4 weeks post-treatment and HCV-RNA levels continued to increase 14 weeks post-treatment (150,000 IU/mL). The viral population, which was wild type at baseline, consisted of only V36A variants at both of these post-treatment time-points. Subsequently, this patient had a transient disappearance of HCV-RNA for more than 1 year in the absence of antiviral therapy. Thereafter, HCV-RNA reappeared again with a viral population consisting of only wild type virus. Phylogenetic analysis of NS3 center dot 4A corresponded with a viral population bottleneck resulting in changes in viral quasispecies. Conclusion: In this case report, significant viral load reductions resulted in a genetic bottleneck leading to a reduction of variability in the hepatitis C viral population. We hypothesize that the reduction in viral heterogeneity potentially led to a reduced viral capacity to adapt to a host immune response leading to a transient loss of detectable HCV-RNA. (C) 2011 Elsevier B.V. All rights reserved