Phylogeny of Physarida (Amoebozoa, Myxogastria) Based on the Small-Subunit Ribosomal RNA Gene, Redefinition of Physarum pusillum s. str. and Reinstatement of P. gravidum Morgan.

Myxomycetes (also called Myxogastria or colloquially, slime molds) are worldwide occurring soil amoeboflagellates. Among Amoebozoa, they have the notable characteristic to form, during their life cycle, macroscopic fruiting bodies, that will ultimately release spores. Some 1,000 species have been described, based on the macroscopic and microscopic characteristics of their fruiting bodies. We were interested in Physarum pusillum (Berk. & M.A. Curtis) G. Lister, a very common species described with two variants, each bearing such morphological differences that they could represent two distinct species. In order to test this, we observed key characters in a large selection of specimens attributed to P.  pusillum, to its synonyms (in particular Physarum gravidum), and to related species. In addition, the small-subunit ribosomal RNA gene was obtained from seven of these specimens. Based on these data, we provide a comprehensive phylogeny of the order Physarida (Eukaryota: Amoebozoa: Conosa: Macromycetozoa: Fuscisporidia). Morphology and phylogeny together support the reinstatement of P. gravidum Morgan 1896 with a neotype here designated, distinct from P. pusillum, here redefined.

Impact of large industrial emission sources on mortality and morbidity in Chile: A small-areas study.

Chile suffers significant pollution from large industrial emitters associated with the mining, metal processing, paper production, and energy industries. The aim of this research was to determine whether the presence of large industrial facilities (i.e. coal- and oil-fired power plants, pulp and paper mills, mining facilities, and smelters) affects mortality and morbidity rates in Chile. For this, we conducted an ecological study that used Chilean communes as small-area observation units to assess mortality and morbidity. Public databases provided information on large pollution sources relevant to Chile. The large sources studied were oil- and coal-fired power plants, copper smelters, pulp and paper mills, and large mining facilities. Large sources were filtered by first year of production, type of process, and size. Mortality and morbidity data were acquired from public national databases, with morbidity being estimated from hospitalization records. Cause-specific rates were calculated for the main outcomes: cardiovascular, respiratory, cancer; and other more specific health outcomes. The impact of the large pollution sources was estimated using Bayesian models that included spatial correlation, overdispersion, and other covariates. Large and significant increases in health risks (around 20%-100%) were found for communes with power plants and smelters for total, cardiovascular, respiratory, all-cancer, and lung cancer mortality. Higher hospitalization rates for cardiovascular disease, respiratory disease, cancer, and pneumonia (20-100%) were also found for communes with power plants and smelters. The impacts were larger for men than women in terms of both mortality and hospitalizations. The impacts were also larger when the sources were analyzed as continuous (production volume) rather than dichotomous (presence/absence) variables. In conclusion, significantly higher rates of total cardiovascular, respiratory, all-cancer and lung cancer mortality and cardiovascular, respiratory, cancer and pneumonia hospitalizations were observed in communes with power plants and smelters.

Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia).

Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis.

In spite of the ecological importance of protists, very little data is available on their distribution in soil. This investigation is the first of its kind on what could be the major components of the soil protistan community, the Myxomycetes, or plasmodial slime-moulds, a monophyletic class in the phylum Amoebozoa. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour, which can be found in every terrestrial biome. Despite their prevalence, they are paradoxically absent from environmental DNA sampling studies. We obtained myxomycete SSU rRNA gene sequences from soil-extracted RNAs using specific primers. Soil samples were collected in three mountain ranges (France, Scotland and Japan). Our study revealed an unexpectedly high diversity of dark-spored Myxomycetes, with the recovery of 74 phylotypes. Of these, 74% had < 98% identity with known sequences, showing a hidden diversity; there was little overlap between localities, implying biogeographical patterns. Few phylotypes were dominant and many were unique, consistent with the 'rare biosphere' phenomenon. Our study provides the first detailed insight into the community composition of this ecologically important group of protists, establishing means for future studies of their distribution, abundance and ecology.

18S rDNA phylogeny of lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa).

The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa) challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU) ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (~600 bases) of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species.

Genetic structure of two protist species (Myxogastria, Amoebozoa) suggests asexual reproduction in sexual Amoebae.

Plasmodial slime molds (Myxogastria or Myxomycetes) are common and widespread unicellular organisms that are commonly assumed to have a sexual life cycle culminating with the formation of often macroscopic fruiting bodies that efficiently disseminate spores. However, laboratory studies based on mating compatibility revealed the coexistence of asexual as well as sexual strains. To test this hypothesis in natural populations, we investigated the genetic variability of two species of the genus Lamproderma. Detailed ecological relevés were carried out in 2007 and 2009 in several deep ravines in the Elbsandsteingebirge (Saxony, south-eastern Germany). Morphological characters of 93 specimens of Lamproderma were recorded and genetic analyses, based on the small subunit ribosomal gene, the internal transcribed spacer 1 and partial elongation factor 1α sequences were carried out for 52 specimens. Genetic analyses showed the existence of two major clades, each composed of several discrete lineages. Most of these lineages were composed of several identical sequences (SSU, ITS 1 and EF-1α) which is explained best by an asexual mode of reproduction. Detrended Correspondence Analysis of morphological characters revealed two morphospecies that corresponded to the two major clades, except for one genotype (Lc6), thus challenging the morphospecies concept. Genetic patterns were not related to the geographical distribution: specimens belonging to the same genotype were found in distinct ravines, suggesting effective long-distance dispersal via spores, except for the Lc6 genotype which was found only in one ravine. Implications for the morphological and biological species concept are discussed.

Two new species of nivicolous Lamproderma (myxomycetes) from the mountains of Europe and America.

As a result of the revision of European and American collections of genus Lamproderma two new nivicolous myxomycete species, Lamproderma argenteobrunneum and L. kowalskii, are described. The new species are characterized by the silvery-brown sporothecae, the areolate peridium and the ferruginous-brown spores in mass. They differ from one another mainly in spore size and ornamentation, the form of the capillitium and the stalk length and ratio of the stalk length to the total height of the sporocarp. The morphology of the new species was examined with light microscopy and scanning electron microscopy (SEM), and micrographs of relevant details are included. Lamproderma argenteobrunneum also was obtained in moist chamber culture, and the mature sporocarps displayed all features typical of field-collected samples. The known geographical distribution of L. argenteobrunneum includes the main ranges of the European alpine system (Alps, Carpathians, Pyrenees) as well as those of North America, while L. kowalskii has been recorded so far from several sites in California in the United States.

Association of reading disability on chromosome 6p22 in the Afrikaner population.

The genetic basis of reading disability (RD) has long been established through family and twin studies. More recently genetic linkage studies have identified genomic regions that appear to harbor susceptibility genes for RD. Association studies have been shown to have greater power for detecting genes of modest effect, particularly in genetically isolated populations. Hence, a case control study of RD was undertaken in the Afrikaner population in South Africa. Sixty-eight microsatellite markers in regions where linkages had been reported in previous studies were genotyped on 122 children with reading disability and 112 typically reading controls drawn from the same school population. A single allele of marker D6S299 showed a highly significant association with the RD phenotype (D6S299[229], P-value 0.000014). Other markers on other chromosomes also showed suggestive associations. Of particular interest were markers on chromosomes 1 and 15. These two regions have been implicated in studies of populations that formed the founding population in the Afrikaner population.

Evolution of dark-spored Myxomycetes (slime-molds): molecules versus morphology.

The Myxomycetes are a major component of soil amoebae, displaying a complex life cycle that terminates in the formation of often macroscopic fruiting bodies. The classification of Myxomycetes is controversial and strongly depends on the weight given by different authors to morphological and developmental characters. We used a molecular approach to establish the phylogenetic relationships in the dark-spored orders Stemonitales and Physarales. Twenty-five small subunit ribosomal RNA gene sequences were obtained, with focus on two Stemonitales genera, Lamproderma and Comatricha. Unexpectedly, our results show that Stemonitales are paraphyletic with Physarales arising from within a Lamproderma clade. The genus Lamproderma itself is polyphyletic and can be divided into two distinct clades. Additionally, we found that Comatricha nigricapillitia comprises two cryptic species, both related to Enerthenema. Our study allows the reappraisal of morphological and developmental characters in the light of molecular data and sets foundations for a new classification of Myxomycetes.

Breakthrough invasive pulmonary aspergillosis despite empirical voriconazole therapy for febrile neutropenia: case report and review of the literature.

We report the development of invasive pulmonary aspergillosis in a patient treated for acute myeloid leukaemia during empirical voriconazole therapy for febrile neutropenia. The patient failed to respond to the institution of salvage combination therapy with amphotericin B and voriconazole, but survived after adjunctive surgical resection.

Predictive assessment of reading.

Study 1 retrospectively analyzed neuropsychological and psychoeducational tests given to N=220 first graders, with follow-up assessments in third and eighth grade. Four predictor constructs were derived: (1) Phonemic Awareness, (2) Picture Vocabulary, (3) Rapid Naming, and (4) Single Word Reading. Together, these accounted for 88%, 76%, 69%, and 69% of the variance, respectively, in first, third, and eighth grade Woodcock Johnson Broad Reading and eighth grade Gates-MacGinitie. When Single Word Reading was excluded from the predictors, the remaining predictors still accounted for 71%, 65%, 61%, and 65% of variance in the respective outcomes. Secondary analyses of risk of low outcome showed sensitivities/specificities of 93.0/91.0, and 86.4/84.9, respectively, for predicting which students would be in the bottom 15% and 30% of actual first grade WJBR. Sensitivities/specificities were 84.8/83.3 and 80.2/81.3, respectively, for predicting the bottom 15% and 30% of actual third grade WJBR outcomes; eighth grade outcomes had sensitivities/specificities of 80.0/80.0 and 85.7/83.1, respectively, for the bottom 15% and 30% of actual eighth grade WJBR scores. Study 2 cross-validated the concurrent predictive validities in an N=500 geographically diverse sample of late kindergartners through third graders, whose ethnic and racial composition closely approximated the national early elementary school population. New tests of the same four predictor domains were used, together taking only 15 minutes to administer by teachers; the new Woodcock-Johnson III Broad Reading standard score was the concurrent criterion, whose testers were blind to the predictor results. This cross-validation showed 86% of the variance accounted for, using the same regression weights as used in Study 1. With these weights, sensitivity/specificity values for the 15% and 30% thresholds were, respectively, 91.3/88.0 and 94.1/89.1. These validities and accuracies are stronger than others reported for similar intervals in the literature.

Utility of the lateral chest radiograph in the evaluation of patients with a positive tuberculin skin test result.

STUDY OBJECTIVES: In the United States, chest radiographs are performed on patients with positive tuberculin skin test (TST) results. It is not known whether, in addition to a single posteroanterior radiograph, a lateral chest radiograph is clinically indicated or cost-effective. We sought to determine the utility of the lateral chest radiograph in evaluating TST-positive adults. DESIGN: Cross-sectional study. SETTING: Tertiary-care hospital. PATIENTS: Adults with positive TST results. MEASUREMENTS: Findings on posteroanterior radiographs alone were compared to posteroanterior and lateral chest radiographs. RESULTS: In 2 of 535 cases (0.4%), lateral chest radiographs revealed a calcified granuloma not visible on posteroanterior radiographs. This finding did not alter patient management. In all other cases, lateral radiographs only confirmed findings seen on posteroanterior chest radiographs. CONCLUSION: Treatment altering findings were always visible on posteroanterior radiographs alone. These results suggest that lateral chest radiographs are not useful in evaluating adults with positive TST results.

Continuing the search for dyslexia genes on 6p.

This study is a continuation and extension of the work with Orton Developmental Dyslexia (DD) pedigrees [Grigorenko et al., 1997; 2000, Grigorenko et al., 2001]. This study utilized an extended sample (N = 176) and a well-saturated map of chromosome 6p (30 markers). Six phenotypes were constructed to span a range of dyslexia-related cognitive processes. These phenotypes were: (1) Phonemic Awareness (of spoken words); (2) Phonological Decoding (of printed nonwords); (3) Rapid Automatized Naming (of colored squares or object drawings); (4) Single Word Reading (orally, of printed real words); (5) Phonemic Awareness/Decoding/Single-Word Reading pathway; and (6) Phonemic Awareness/Rapid Naming/Single-Word Reading pathway. The study resulted in two major findings. First, considering the distributions of the genetic linkage indicators across all phenotypes examined, there appear to be three regions of interest (around markers D6S109, D6S1261, and in the D6S105-D6S265 region). Any of these regions could serve as a starting point in the search for specific gene candidates contributing to the manifestation of DD, yet they all might be echo peaks of a single peak, the boundary of which is difficult to establish due to the limited power of this sample. Second, the DD-related linkage in 6p21.3 appears to be most closely related to the manifestations of DD through phonemic awareness and single-word reading deficits.

Repeat bedside percutaneous dilational tracheostomy is a safe procedure.

OBJECTIVE: Previous tracheostomy has been considered a relative contraindication for percutaneous dilational tracheostomy. The objective of this study was to assess the safety of percutaneous dilational tracheostomy in critically ill patients with a history of previous tracheostomy. DESIGN: Retrospective, single-center case series of all consecutive patients requiring repeat tracheostomy for continued mechanical ventilatory support. SETTING: Intensive care unit of a tertiary-care referral center. SUBJECTS: Fourteen patients (eight female, six male) with a median age of 70 yrs (range, 33-94). All patients had previously undergone tracheostomy. INTERVENTION: Bedside percutaneous dilational tracheostomy. MEASUREMENT AND MAIN RESULTS: Subjects' previous tracheostomies dated back between 10 days and 8 yrs. Present intubation time before percutaneous dilational tracheostomy varied between 4 and 30 days. Bedside percutaneous dilational tracheostomy was performed successfully in all 14 patients by trained pulmonologists and surgeons. Eleven patients received an 8-mm and three received a 7-mm tracheostomy tube. There were no significant periprocedural complications, and no patient required surgical revision. The only postprocedural complication was accidental decannulation in one patient, which was managed with repeat percutaneous dilational tracheostomy. CONCLUSIONS: Trained physicians can safely perform bedside percutaneous dilational tracheostomy after previous tracheostomy. Percutaneous dilational tracheostomy offers an alternative to surgical tracheostomy in this particular patient population and should not be considered contraindicated.