Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms

Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.

Knowledge Based Planning for Lung SBRT: Model Transferability between Treatment Systems and Calculation Algorithms

PURPOSE/OBJECTIVE(S)

Knowledge based planning (KBP) is known to be effective and clinically feasible in achieving high quality treatment plans with less variability between planners and reduced planning time. A KBP model is highly dependent on characteristics of the training data. Our institution developed and validated a lung SBRT KBP model from plans treated with a C-arm linear accelerator (Linac). This study aims to evaluate the quality of lung SBRT plans with a KBP model when this model is used for an O-ring Linac with different MLC design, beam quality, and calculation algorithm.

MATERIALS/METHODS

Two academic hospitals in the same healthcare network were included in this study. One hospital trained a KBP model for five-fraction lung SBRT using 43 plans calculated using the Eclipse AcurosXB v15.6 algorithm for a C-arm Linac. The model was developed to prioritize dose gradient outside the PTV while satisfying institutional critical organ limits and validated using an additional set of 12 plans. A cohort of 10 patients (11 plans) previously treated with lung SBRT using the O-ring Linac at the second hospital was selected. These plans were calculated using the Eclipse AAA v15.6 algorithm with prescription doses of 30-50 Gy in five fractions. Each plan was re-optimized using the KBP model, without manual adjustment of the optimization objectives, using the same beam geometry as in the clinical plans. KBP plans were normalized to achieve the same PTV coverage as the clinical plans. Clinical and KBP plans were evaluated for ITV D98%, PTV conformity index (CI), R50 and maximum dose at 2 cm from the PTV (D2cm).

RESULTS

All clinical and KBP plans met critical organ dose constraints. The range of CI was 1-1.13 vs. 0.96-1.05 for clinical plans and KBP plans, respectively. R50 and D2cm were lower with KBP plans (p = 0.007 and p = 0.05, respectively). ITV D98% range was 105-120% vs. 117-122% of the PTV prescription dose for clinical plans and KBP plans, respectively, and higher with KBP plans (p<0.001). For plans where the PTV overlaps the chest wall (n = 7), the maximum chest wall doses (D0.03cc) from KBP plans were higher than the clinical plans (p = 0.16), with an absolute chest wall D0.03cc difference of 9 Gy (54 Gy vs 63 Gy). The KBP model includes an ITV SIB of 120% of the PTV prescription, whereas the clinical plans reduced the ITV SIB when the PTV overlapped the chest wall, highlighting a difference in clinical practice between the two hospitals in this study.

CONCLUSION

This study supports that a lung SBRT KBP model trained using plans for one Linac system and the AcurosXB algorithm can be used to generate clinically acceptable plans without manual planner intervention for a different Linac system and the AAA calculation algorithm, indicating the potential of a KBP model use for centralized planning process across different Linac systems and calculation algorithms.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding

Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'_bc), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

Selective zircon accumulation in a new benthic foraminifer, Psammophaga zirconia, sp. nov

Benthic foraminifera are single-celled eukaryotes that make a protective organic, agglutinated or calcareous test. Some agglutinated, single-chambered taxa, including Psammophaga Arnold, 1982, retain mineral particles in their cytoplasm, but the selective mechanism of accumulation is not clear. Here, we report the ability of a foraminiferal species to select and accumulate zircons and other heavy minerals in their cytoplasm. In particular, the use of Scanning Electron Microscope coupled with an Energy Dispersive X-ray microanalysis system (SEM-EDS) enabled a representative overview of the mineral diversity and showed that the analysed Psammophaga zirconia sp. nov. individuals contained dominantly crystals of zircon (51%), titanium oxides (27%), and ilmenite (11%) along with minor magnetite and other minerals. The studied specimens occur in the shallow central Adriatic Sea where the sediment has a content of zircon below 1% and of other heavy minerals below 4%. For that reason we hypothesize that: (i) P. zirconia may be able to chemically select minerals, specifically zircon and rutile; (ii) the chemical mechanism allowing the selection is based on electrostatic interaction, and it could work also for agglutinated foraminifera (whether for ingestion, like Xenophyophores, or incorporation in the test as in many other described taxa). In particular, this aptitude for high preferential uptake and differential ingestion or retention of zircon is reported here for the first time, together with the selection of other heavy minerals already described in members of the genus Psammophaga. They are generally counted among early foraminifera, constructing a morphologically simple test with a single chamber. Our molecular phylogenetic study confirms that P. zirconia is a new species, genetically distinctive from other Psammophaga, and occurs in the Adriatic as well as in the Black Sea.

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities.

Next-generation environmental diversity surveys of foraminifera: preparing the future

Foraminifera are commonly defined as marine testate protists, and their diversity is mainly assessed on the basis of the morphology of their agglutinated or mineralized tests. Diversity surveys based on environmental DNA (eDNA) have dramatically changed this view by revealing an unexpected diversity of naked and organic-walled lineages as well as detecting foraminiferal lineages in soil and freshwater environments. Moreover, single-cell analyses have allowed discrimination among genetically distinctive types within almost every described morphospecies. In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach. With the advent of high-throughput sequencing (HTS) technologies, these limitations disappeared in favor of exhaustive descriptions of foraminiferal diversity in numerous samples. Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation. Among the most controversial issues affecting the reliability of HTS diversity estimates are (1) the impact of technical and biological biases, (2) the sensitivity and specificity of taxonomic sequence assignment, (3) the ability to distinguish rare species, and (4) the quantitative interpretation of HTS data. Here, we document the lessons learned from previous HTS surveys and present the current advances and applications focusing on foraminiferal eDNA. We discuss the problems associated with HTS approaches and predict the future trends and avenues that hold promises for surveying foraminiferal diversity accurately and efficiently.

Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium

Recent palaeogenetic studies have demonstrated the occurrence of preserved ancient DNA (aDNA) in various types of fossilised material. Environmental aDNA sequences assigned to modern species have been recovered from marine sediments dating to the Pleistocene. However, the match between the aDNA and the fossil record still needs to be evaluated for the environmental DNA approaches to be fully exploited. Here, we focus on foraminifera in sediments up to one thousand years old retrieved from the Hornsund fjord (Svalbard). We compared the diversity of foraminiferal microfossil assemblages with the diversity of aDNA sequenced from subsurface sediment samples using both cloning and high-throughput sequencing (HTS). Our study shows that 57% of the species archived in the fossil record were also detected in the aDNA data. However, the relative abundance of aDNA sequence reads and fossil specimens differed considerably. We also found a limited match between the stratigraphic occurrence of some fossil species and their aDNA sequences, especially in the case of rare taxa. The aDNA data comprised a high proportion of non-fossilised monothalamous species, which are known to dominate in modern foraminiferal communities of the Svalbard region. Our results confirm the relevance of HTS for studying past micro-eukaryotic diversity and provide insight into its ability to reflect fossil assemblages. Palaeogenetic studies including aDNA analyses of non-fossilised groups expand the range of palaeoceanographical proxies and therefore may increase the accuracy of palaeoenvironmental reconstructions.

Clinical factors affecting engraftment and transfusion needs in SCT: a single-center retrospective analysis

Successful utilization of SCT modalities often requires utilization of both red cell and platelet transfusions. In this retrospective evaluation of clinical factors affecting transplant engraftment and transfusion utilization at a single transplant center in 505 patients from 2005 through 2009, we found that graft type, donor type and the conditioning regimen intensity significantly affected both the neutrophil engraftment time (P<0.001) and the platelet engraftment time (P<0.001). SCT patients required an average of 6.2 red cell units, and 7.9 platelet transfusions in the first 100 days with a wide s.d. Among auto-SCT patients, 5% required neither RBC nor platelet transfusions. Some reduced-intensity transplants were also associated with no transfusion need, and in allogeneic transplants, conditioning regimen intensity was positively correlated with platelet transfusion events as assessed by multivariate analysis. Other patient characteristics such as gender, graft type, donor type, underlying disease and use of TBI were all independently associated with transfusion needs in SCT patients. Further studies are required to understand the means to minimize transfusions and potential related complications in SCT patients.

Bipolar gene flow in deep-sea benthic foraminifera

Despite its often featureless appearance, the deep-ocean floor includes some of the most diverse habitats on Earth. However, the accurate assessment of global deep-sea diversity is impeded by a paucity of data on the geographical ranges of bottom-dwelling species, particularly at the genetic level. Here, we present molecular evidence for exceptionally wide distribution of benthic foraminifera, which constitute the major part of deep-sea meiofauna. Our analyses of nuclear ribosomal RNA genes revealed high genetic similarity between Arctic and Antarctic populations of three common deep-sea foraminiferal species (Epistominella exigua, Cibicides wuellerstorfi and Oridorsalis umbonatus), separated by distances of up to 17, 000 km. Our results contrast with the substantial level of cryptic diversity usually revealed by molecular studies, of shallow-water benthic and planktonic marine organisms. The very broad ranges of the deep-sea foraminifera that we examined support the hypothesis of global distribution of small eukaryotes and suggest that deep-sea biodiversity may be more modest at global scales than present estimates suggest.

Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny

Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia's genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. Phylogenetic analyses of S. savaglia mitochondrial sequences show Zoantharia branching closely to other Hexacorallia, either as a sister group to Actiniaria or as a sister group to Actiniaria and Scleractinia. The close relationships suggested between Zoantharia and Actiniaria are reinforced by strong similarities in their gene order and the presence of similar introns in the COI and ND5 genes. Our study suggests that mitochondrial genomes can be a source of potentially valuable information on the phylogeny of Hexacorallia and may provide new insights into the evolution of early metazoans.

Psychological distress in Brazilian caregivers of relatives with dementia

The authors evaluated stress, anxiety, depression, and feelings of hopelessness in caregivers of relatives with dementia. One hundred and twenty-nine caregivers and 145 non-caregivers who lived in metropolitan Porto Alegre, Brazil completed Lipp's Inventory of Stress Symptoms for Adults, (ISSL), and Beck's Anxiety (BAI), Depression (BDI), and Hopelessness (BHS) scales. Caregivers showed higher levels of anxiety, depression, hopelessness, resistance/pre-exhaustion stress than controls. This study indicates that constant caregiving may significantly increase the risk of physical and mental health problems for caregivers in Brazil.

Constrictive bronchiolitis obliterans in patient with Castelman’s disease

A 37-year-old woman with hialin- vascular type Castelman’s disease (CD) localised in the retroperitoneal region, incompletely resected, developed progressive dyspnoea. The chest radiograph taken 3 months before the operation was normal. The chest CT scan revealed diffused bronchiectases, hyperinflation and air trapping. Pulmonary function tests disclosed severe obstructive impairment with hyperinflation. The bronchoscopic examination of the bronchial tree was normal. Cultures of sputum, bronchial washing and blood were negative. No pemphigus antibodies were found. Mycoplasmal, chlamydial and viral infections were excluded. Histological examination of specimens obtained by open lung biopsy revealed bronchiolar inflammation, submucosal bronchial fibrosis with obliteration of bronchiolar lumen. Constrictive bronchiolitis obliterans (CBO) was diagnosed. Despite slight clinical and spirometric improvements that were achieved due to corticosteroid therapy, one year later she died as a result of respiratory failure. It is widely known that patients with CD develop CBO during the course of paraneoplastic pemphigus. However we present the case of CBO and CD but without any symptoms of this condition.

SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited

Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for the amoeboid lineages and an extraordinary diversity of amoebae species. Molecular data, however, exist only for a few species of the numerous taxa belonging to this group. Here, we present the small-subunit (SSU) rDNA sequences of four species of typical large gymnamoebae: Amoeba proteus, Amoeba leningradensis, Chaos nobile, and Chaos carolinense. Sequence analysis suggests that the four species are closely related to the species of genera Saccamoeba, Leptomyxa, Rhizamoeba, Paraflabellula, Hartmannella, and Echinamoeba. All of them form a relatively well-supported clade, which corresponds to the subclass Gymnamoebia, in agreement with morphology-based taxonomy. The other gymnamoebae cluster in small groups or branch separately. Their relationships change depending on the type of analysis and the model of nucleotide substitution. All gymnamoebae branch together in Neighbor-Joining analysis with corrections for among-site rate heterogeneity and proportion of invariable sites. This clade, however, is not statistically supported by SSU rRNA gene sequences and further analysis of protein sequence data will be necessary to test the monophyly of gymnamoebae.

Severity of airway hyperreactivity associated with laryngeal mask airway removal: correlation with volatile anesthetic choice and depth of anesthesia

STUDY OBJECTIVE

To compare the influence of anesthetic depth and choice of volatile anesthetic drug on the incidence and severity of airway hyperreactivity associated with Laryngeal Mask Airway (LMA) removal.

DESIGN

Randomized observer-blinded study.

SETTING

Ambulatory Surgical Center at a University Medical Center.

PATIENTS

123 ASA physical status I and II children undergoing infraumbilical procedures.

INTERVENTIONS

Patients were randomly assigned to one of four treatment groups: Group 1 = anesthetic induction with halothane, maintenance with isoflurane, nitrous oxide (N(2)O), and oxygen (O(2)), LMA removed when child awakened; Group 2 =anesthetic induction and maintenance as in Group 1, LMA removed while child anesthetized with age adjusted 2 minimum alveolar concentration (MAC) end-tidal concentration of isoflurane; Group 3 = anesthetic induction and maintenance with sevoflurane, N(2)O, and O(2), LMA removed when child awakened; Group 4 = anesthetic induction and maintenance as in Group 3, but LMA removed while child anesthetized with age-adjusted 2 MAC end-tidal concentration of sevoflurane.

MEASUREMENTS AND MAIN RESULTS

Severity of airway hyperreactivity was graded as mild, moderate, or severe. A significant difference was not found amongst the four groups with respect to mild and moderate airway hyperreactivity. Severe airway hyperreactivity leading to a critical event [partial or complete laryngospasm with oxygen saturation (SPO(2)) < 85%] was only encountered in Group 1 patients (incidence 13%). Adverse airway events (SPO(2) < 90%, vomiting and bronchospasm) were also significantly higher in Group 1 (p < 0.05). Isoflurane use was independently associated with significantly higher airway hyperreactivity when compared with sevoflurane (p < 0.05).

CONCLUSIONS

Depth of anesthesia during LMA removal does not appear to affect the incidence or severity of airway hyperreactivity when sevoflurane is the maintenance anesthetic. However, awake LMA removal during isoflurane anesthesia results in a higher incidence of adverse airway events and carries the risk of severe airway hyperreactivity.

Morphological and molecular characterization of a new terrestrial allogromiid species: Edaphoallogromia australica gen. et spec. nov. (Foraminifera) from Northern Queensland (Australia)

The foraminiferal family Allogromiidae occurs mainly in marine environments, although some genera are described from brackish and freshwater habitats. We report here the occurrence of a terrestrial allogromiid foraminiferan. Phylogenetic relationships were investigated by sequencing part of the SSU rDNA. DNA sequence analysis confirms a close relationship of the new species to the genus Allogromia. Morphological studies corroborate the affiliation to the family Allogromiidae but the lack of an entosolenian tube and an internal septum as well as the different ecology do not allow a classification into a known genus of this family. Taking the molecular, morphological and ecological differences into account, a new genus Edaphoallogromia with the type species E. australica is erected.

Molecular identification of algal endosymbionts in large miliolid Foraminifera: 2. Dinofiagellates

Large miliolid foraminifers of the subfamily Soritinae bear symbiotic dinoflagellates morphologically similar to the species of the "Symbiodinium" complex, commonly found in corals and other marine invertebrates. Soritid foraminifers are abundant in coral reefs and it has been proposed that they share their symbionts with other dinoflagellate-bearing reef dwellers. In order to test this hypothesis, we have analysed partial large subunit ribosomal DNA sequences from dinoflagellates symbionts obtained from 28 foraminiferal specimens, and compared them to the corresponding sequences of Symbiodinium-like endosymbionts from various groups of invertebrates. Phylogenetic analysis of our data shows that all soritid symbionts belong to the "Symbiodinium" species complex, within which they form seven different molecular types (Frl-Fr7). Only one of these types (Fr1) branches within a group of invertebrate symbionts, previously described as type C. The remaining six types form sister groups to coral symbionts previously designed as types B, C, and D. Our data indicate a high genetic diversity and specificity of Symbiodinium-like symbionts in soritids. Except for type C, we have found no evidence for the transmission of symbionts between foraminifers and other symbiont-bearing invertebrates from the same localities. However, exchanges must have occurred frequently between the different species of Soritinae, as suggested by the lack of host specificity and some biogeographical patterns observed in symbiont distribution. Our data suggest that members of the subfamily Soritinae acquired their symbionts at least three times during their history, each acquisition being followed by a rapid diversification and independent radiation of symbionts within the foraminiferal hosts.

Molecular identification of algal endosymbionts in large miliolid foraminifera: 1. Chlorophytes

Large miliolid foraminifers bear various types of algal endosymbionts including chlorophytes, dinoflagellates, rhodophytes, and diatoms. Symbiosis plays a key role in the adaptation of large foraminifera to survival and growth in oligotrophic seas. The identity and diversity of foraminiferal symbionts, however, remain largely unknown. In the present work we use ribosomal DNA (rDNA) sequences to identify chlorophyte endosymbionts in large miliolid foraminifera of the superfamily Soritacea. Partial 18S and complete Internal Transcribed Spacer (ITS) rDNA sequences were obtained from symbionts of eight species representing all genera of extant chlorophyte-bearing Soritacea. Phylogenetic analysis of the sequences confirms the previous fine structure-based identification of these endosymbionts as belonging to the genus Chlamydomonas. All foraminiferal symbionts form a monophyletic group closely related to Chlamydomonas noctigama. The group is composed of seven types identified in this study, including one previously morphologically described species, Chlamydomonas hedleyi. Each of these types can be considered as a separate species, based on the comparison of genetic differences observed between other established Chlamydomonas species. Several foraminiferal species share the same symbiont type, but only one species, Archaias angulatus, was found to bear more than one type.

Phylogeny of the genus Scathophaga (Diptera: Scathophagidae) inferred from mitochondrial DNA sequences

Scathophaga stercoraria has been used for a large number of studies in animal ecology and evolution. Morphological phylogenetic work on the relationships among flies of the family Scathophagidae in general, and the genus Scathophaga in particular, has led to limited or incomplete conclusions. We addressed these relationships by sequencing 810 base pairs (bp) from the mitochondrial cytochrome oxidase subunit I (COI) gene and 738 bp of the mitochondrial cytochrome b (Cyt b) gene in 16 species of Scathophagidae. Phylogenetic analysis of these two protein-coding genes allows us to resolve relatively well the relationships within the genus Scathophaga, using both separate and combined (COI + Cyt b) data. Most of the phylogenetic trees generated by our data support the following relationships: (((S. analis + S. inquinata) + S. lutaria) + S. cineraria + (S. taeniopa + S. suilla + S. incola) + S. furcata + S. tropicalis). The most noteworthy findings are that (i) S. obscura and S. tinctinervis, which were formerly placed in the genus Coniosternum, form a sibling species cluster; (ii) S. taeniopa and S. suilla, which are morphologically very similar species, are clearly distinct taxa; (iii) S. analis, considered a doubtful species in the Catalogue of Palearctic Diptera, could be a synonym of S. inquinata; and (iv) the South American S. tropicalis and the Old World S. stercoraria are not sister-species.

Molecular and morphological differentiation between species of the Plagiorchis vespertilionis group (Digenea, Plagiorchiidae) occurring in European bats, with a re-description of P. vespertilionis (Müller, 1780)

The taxonomic history of the species of Plagiorchis Lühe, 1899 occurring in European bats has been very confused because of high morphological similarity between different forms/species and the inadequate initial description of P. vespertilionis (Müller, 1780). As morphological data alone have not provided enough convincing arguments to solve the problem, the sequences from the nuclear rDNA ITS region (ITS1, 5.8S and ITS2) of three species of the P. vespertilionis group (P. vespertilionis, P. muelleri Tkach & Sharpilo, 1990 and P. koreanus Ogata, 1938) occurring in European bats were used to test the validity of these species and evaluate some of the morphological characters used for the species differentiation within this group. P. elegans from birds was used as the outgroup in the analysis. All three ingroup species were clearly distinguishable using ITS sequences. Among them, P. koreanus occupied a basal position, while P. vespertilionis and P. muelleri appeared as a cluster of two closely related, derived species. ITS sequences of the specimens obtained from different hosts and/or geographical areas did not exhibit any intraspecific variability. Morphological study of the material in collections revealed characters which enable the species of Plagiorchis from bats in Europe to be distinguished. Taking into account that the type-material of P. vespertilionis. described during the 18th Century, has been lost, for nomenclatural stability, a neotype is established and described. An amended description of the type-material of P. muelleri and keys for the determination of Plagiorchis spp. from European bats are presented.

The anesthetic and recovery profile of two doses (60 and 80 mg) of plain mepivacaine for ambulatory spinal anesthesia

Reports of transient neurological symptoms with the use of subarachnoid lidocaine has generated interest in alternate local anesthetics of intermediate duration, such as mepivacaine. This prospective randomized, double-blinded, dose-response study examined the anesthetic and recovery profiles of 60- and 80-mg doses of preservative-free plain mepivacaine for ambulatory spinal anesthesia. Sixty patients undergoing ambulatory anterior cruciate ligament repair of the knee under spinal anesthesia were randomized into two groups; Group 1 (29 patients) received 4 mL of 1.5% (60-mg dose) and Group 2 (31 patients) received 4 mL of 2% (80-mg dose) of plain mepivacaine. All patients received a combined spinal-epidural anesthetic technique. The epidural catheter was used only in the event the surgery outlasted the duration of surgical anesthesia with subarachnoid mepivacaine. Epidural supplementation was administered in three patients (12%) in Group 1 and one patient (3%) in Group 2 when the sensory block regressed to L-1 with surgery expected to last longer than 15 min. The cephalad dermatome level of the block and degree of motor block was comparable in the two groups. Times to two-segment and T-10 regression were comparable in the two groups (112 +/- 26 min in Group 1 versus 122 +/- 28 min in Group 2). Time to L-1 regression was significantly longer in Group 2 (146 +/- 28 min in Group 1 versus 159 +/- 19 min in Group 2). All of the ambulatory milestones were significantly faster in Group 1. Side effects, such as hypotension and emesis were negligible, severe bradycardia and urinary retention did not occur, and none of the patients in the two groups reported transient neurological symptoms over 24 h. In conclusion, plain mepivacaine in a 60- or 80-mg dose is a suitable local anesthetic choice for ambulatory spinal anesthesia with respect to anesthetic, as well as recovery profiles.

IMPLICATIONS

We evaluated the anesthetic and recovery profiles of 60- and 80-mg doses of plain mepivacaine for ambulatory spinal anesthesia. Both doses produced comparable sensory and motor block. Sensory and motor regression and ambulatory milestones were 20-30 min longer with the 80-mg dose. Side effects were negligible and transient neurological symptoms were not reported during a 24-h follow-up.

Phylogeny of the scathophagidae (Diptera, calyptratae) based on mitochondrial DNA sequences

The family Scathophagidae constitutes, together with members of the families Muscidae, Fannidae, and Anthomyiidae, the Muscoidea superfamily. The species Scathophaga stercoraria has been used extensively to investigate questions in animal ecology and evolution, particularly as a model system for studies of sperm competition and life history evolution. However, no phylogenetic studies have ever been performed on the Scathophagidae and the relationships within this family remain unclear. This study represents a molecular approach aimed at uncovering the phylogenetic relationships among 61 species representing 22 genera of Scathophagidae. A fragment of the terminal region of the mitochondrial gene COI (subunit I of the cytochrome oxidase gene) was sequenced in scathophagid species covering a wide geographic area, as well as a diverse spectrum of ecological habitats. Several clades grouping different genera and species have been identified, but the resolution power of the COI was insufficient to establish the exact relationships between these clades. The molecular data confirm the existence of a group consisting of the genera Delina, Chylizosoma, and Americina, which could represent the subfamily Delinae. Concerning the controversial position of the genus Phrosia, our data clearly suggest that it should be removed from the Delinae and placed within the genus Cordilura. Monophyly of most genera was confirmed, except for the genus Scathophaga, which should be divided into several different taxa.

Elongation factor 1-alpha sequences do not support an early divergence of the Acoela

The phylogenetic position of the Acoela is a key problem in the understanding of metazoan evolution. Recent studies based on 18S ribosomal DNA (rDNA) sequences have placed the Acoela in an extremely basal position as the sister group to all other extant triploblastic animals, suggesting that the phylum Platyhelminthes is polyphyletic. In order to test the results obtained with 18S rDNA, we sequenced elongation factor 1-alpha (EF1a) for the acoel Convoluta roscoffensis and five species of Turbellaria (two polyclads, Leptoplana tremellaris, and Prostheceraeus vittatus, and three triclads, Crenobia alpina, Schmidtea polychroa, and Girardia tigrina). Phylogenetic analyses of EF1a sequences show that the acoel sequences branch within the Platyhelminthes, in opposition to the 18S rDNA data. Moreover, comparison of the central variable region of EF1a shows similar sequence signatures between C. roscoffensis and the three triclad species. Although EF1a sequences fail to prove the monophyly of the phylum Platyhelminthes, they do not confirm the early divergence of the Acoela.

Evolution of Antp-class genes and differential expression of Hydra Hox/paraHox genes in anterior patterning

The conservation of developmental functions exerted by Antp-class homeoproteins in protostomes and deuterostomes suggested that homologs with related functions are present in diploblastic animals. Our phylogenetic analyses showed that Antp-class homeodomains belong either to non-Hox or to Hox/paraHox families. Among the 13 non-Hox families, 9 have diploblastic homologs, Msx, Emx, Barx, Evx, Tlx, NK-2, and Prh/Hex, Not, and Dlx, reported here. Among the Hox/paraHox, poriferan sequences were not found, and the cnidarian sequences formed at least five distinct cnox families. Two are significantly related to the paraHox Gsx (cnox-2) and the mox (cnox-5) sequences, whereas three display some relatedness to the Hox paralog groups 1 (cnox-1), 9/10 (cnox-3) and the paraHox cdx (cnox-4). Intermediate Hox/paraHox genes (PG 3 to 8 and lox) did not have clear cnidarian counterparts. In Hydra, cnox-1, cnox-2, and cnox-3 were not found chromosomally linked within a 150-kb range and displayed specific expression patterns in the adult head. During regeneration, cnox-1 was expressed as an early gene whatever the polarity, whereas cnox-2 was up-regulated later during head but not foot regeneration. Finally, cnox-3 expression was reestablished in the adult head once it was fully formed. These results suggest that the Hydra genes related to anterior Hox/paraHox genes are involved at different stages of apical differentiation. However, the positional information defining the oral/aboral axis in Hydra cannot be correlated strictly to that characterizing the anterior-posterior axis in vertebrates or arthropods.

Phylogenetic analysis of the suborder plagiorchiata (Platyhelminthes, Digenea) based on partial lsrDNA sequences

The phylogenetic relationships and systematic position of the members of the suborder Plagiorchiata, one of the derived and most diverse groups of Digenea, have always been controversial. Here, we present a phylogeny of this group based on the analysis of partial sequences of the lsrDNA in 28 species representing 13 families of Plagiorchiata, as well as four outgroups. Our results show that the Plagiorchiata, as considered by most authors, is not monophyletic, and that the superfamilies Opecoeloidea, and most probably Dicrocoelioidea and Gorgoderoidea, may have to be removed from this suborder. According to our results, the Plagiorchiata includes only parasites of terrestrial vertebrates. We find the Plagiorchiata to be composed of two well-supported clades which can be ranked as superfamilies: (1) Plagiorchioidea, including the Plagiorchiidae, Haematoloechidae, Telorchiidae, Brachycoeliidae and Leptophallidae; and (2) Microphalloidea containing the Microphallidae, Prosthogonimidae, Lecithodendriidae and Pleurogenidae. The genetic analysis also allowed revision of the position of several taxa of Plagiorchiata, including: (1) a confirmation of the position of the Brachycoeliidae within the Plagiorchiata; (2) a close phylogenetic relationships of Macrodera with Paralepoderma, Leptophallus and Metaleptophallus; (3) the grouping of Opisthioglyphe and Telorchis within a distinct and strongly supported clade; and (4) the placement of Allassogonoporus amphoraeformis within the Pleurogenidae, and not close to Lecithodendriidae. Some systematic changes, corresponding to these results, are proposed.

Molecular identification of developmental stages in Opecoelidae (Digenea)

Nuclear ribosomal DNA sequences represent a useful tool for distinction of poorly differentiated developmental stages, such as trematode cercariae or metacercariae. Here, the complete internal transcribed spacer region of the ribosomal DNA (ITS 1 + 5.8S + ITS 2) was sequenced for 29 specimens of the digenean family Opecoelidae, including 16 adult specimens and 13 undescribed larval stages (nine cercariae and four metacercariae) occurring in various marine host organisms. Six cercariae and three metacercariae were found to match their corresponding adult form. This work also revealed that cercariae of the same species are able to infect more than one gastropod host species, suggesting that the specificity for the first intermediate host within the Digenea may be lower than previously thought.

Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer

Reticulomyxa filosa is a freshwater protist possessing fine granular, branching and anastomosing pseudopodia and therefore traditionally placed in the class Granuloreticulosea, order Athalamida, as a sister group to the order Foraminiferida. Recent studies have revealed remarkable similarities in pseudopodial motility and ultrastructure between R. filosa and foraminifera (e.g. Allogromia laticollaris), prompting us to conduct a molecular phylogenetic analysis of these seemingly disparate organisms. We sequenced the complete small-subunit of the ribosomal DNA of the cultured strain of R. filosa and compared it to the corresponding sequences of other protists including 12 species of foraminifera. We also sequenced and analyzed the actin coding genes from R. filosa and two species of foraminifera, Allogromia sp. and Ammonia sp. The analysis of both data sets clearly shows that R. filosa branches within the clade of foraminifera, suggesting that R. filosa is in fact a freshwater naked foraminiferan.