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► The genetic diversity of two threatened South African fossorial skinks was studied. ► Three mtDNA and two nDNA markers were used. ► They were found to be paraphyletic and ...genetically highly diverse. ► A molecular template is essential for planning their conservation.
We investigated the evolutionary relationships among populations of two threatened Red Data Book fossorial skinks, Scelotes gronovii and Scelotes kasneri, along the Western Cape Coast of South Africa. The genus Scelotes shows considerable variation in limb and digit reduction. We sampled four localities purported to contain S. gronovii and seven of S. kasneri, encompassing all of each species’ limited distribution. Each of these species lack forelimbs, and differ by the number of digits on the hind limbs, among other morphological characters; S. gronovii bears a single digit and S. kasneri bears two digits on the hind limbs. Sequence data obtained from three mtDNA (16S ribosomal RNA, cytochrome b, and nicotinamide adenine dinucleotide dehydrogenase 1 unit; 2035bp ttl.) and two nuclear (dynein axonemal heavy chain 3 and the natural killer tumor recognition; 1848bp ttl.) gene regions were used to reconstruct the evolutionary relationships among the two focal species and several other co-distributed species (Scelotes bipes, Scelotes montispectus, and Scelotes sexlineatus). Phylogenetic results (Bayesian and parsimony) revealed that several populations previously considered S. kasneri actually belong to other species, and others are paraphyletic with respect to one another. Additionally, populations of S. gronovii were also found to be paraphyletic, with populations south of the Berg River supported as sister to S. bipes, and populations north of the Berg River sister the remaining sampled species. Our results require a redefinition of S. sexlineatus to encompass populations morphologically convergent with S. kasneri and restrict the ranges of the already threatened S. kasneri and S. gronovii even further. The paraphyly of S. gronovii and the placement of each clade as sister to clades of species bearing two digits on the hind limbs suggests that digit loss has occurred at least twice in this group.
Kalk Bay, South Africa, has a typical south coast zonation pattern with a band of seaweed dominating the mid-eulittoral and between two molluscan-herbivore dominated upper and lower eulittoral zones. ...Encrusting coralline algae were very obvious features of these zones. The most abundant herbivores in the upper eulittoral were the limpet, Cymbula oculus (10.4 plus or minus 1.6 individuals m super(-2); 201.65 plus or minus 32.68 g.m super(-2)) and the false limpet, Siphonaria capensis (97.07 plus or minus 19.92 individuals m super(-2); 77.93 16.02 g.m super(-2)). The territorial gardening limpet, Scutellastra cochlear, dominated the lower eulittoral zone, achieving very high densities (545.27 plus or minus 84.35 m super(-2)) and biomass (4630.17 plus or minus 556.13 g.m super(-2)), and excluded all other herbivores and most seaweeds, except for its garden alga and the encrusting coralline alga, Spongites yendoi (35.93 plus or minus 2.26% cover). In the upper eulittoral zone, encrusting coralline algae were only present in the guts of the chiton Acanthochiton garnoti (30.5 plus or minus 1.33%) and the limpet C. oculus (2.9 plus or minus 0.34%). The lower eulittoral zone limpet, Scutellastra cochlear also had a large percentage of encrusting coralline algae in its gut with limpets lacking gardens having higher (45.1 plus or minus 1.68%) proportions of coralline algae in their guts than those with gardens (25.6 plus or minus 0.8%). Encrusting coralline algae had high organic contents, similar to those of other encrusting and turf-forming algae, but higher organic contents than foliose algae. Radula structure, grazing frequencies as a percentage of the area grazed (upper eulittoral 73.25 plus or minus 3.60% d super(-1); lower eulittoral 46.0 plus or minus 3.29% d super(-1)), and algal organic content provided evidence to support the dietary habits of the above herbivores. The data show that many intertidal molluscs are actively consuming encrusting coralline algae and that these seaweeds should be seen as an important food source.
A phase I/II dose-ranging open-label 28-day monotherapy study of the safety, pharmacokinetics, and antiviral activity of nelfinavir mesylate (Viracept), an inhibitor of human immunodeficiency virus ...(HIV)-1 protease, was done in 65 HIV-1-infected subjects. After 28 days, 54 responding subjects entered an open-label extension that allowed for the addition of nucleoside inhibitors of reverse transcriptase and dose escalation to maintain durability. The drug was well-tolerated and demonstrated robust antiviral activity, with demonstrable superiority of the 750 mg and 1000 mg three times daily regimens. Thirty subjects who continued to receive therapy at 12 months attained a persistent 1.6 log10 reduction in HIV RNA, accompanied by a mean increase in CD4 cells of 180–200/mm3 . Studies of viral genotype and phenotype after virus rebound revealed that the initial active site mutation allowing for nelfinavir resistance is mediated by a unique amino acid substitution in the HIV-1 protease D30N, which does not confer in vitro phenotypic cross-resistance to the currently available protease inhibitors.
Variable morphological characters have obscured genealogical relationships in the Cape fossorial skink Acontias meleagris meleagris species complex. Currently the species complex contains four ...dubious operational taxonomic units (A. meleagris meleagris, A. m. orientalis, A. percivali tasmani and the morph lineicauda) with poorly defined species boundaries. In the present study we examine the evolutionary relationships within the species complex by sampling 24 skink populations from the known geographical distribution in the Western and Eastern Cape provinces of South Africa, representing a total of 119 specimens. We used partial sequence data derived from two mitochondrial DNA genes, 16S rRNA and COI, and one nuclear DNA gene, intron β‐fibrinogen (β‐fibint 7), to examine evolutionary relationships. Phylogenetic relationships were determined using both Maximum Parsimony (MP) and Bayesian inference (BI) from the combined mtDNA, nDNA and the total evidence data. Additionally we employed Maximum likelihood (ML) analyses on the total evidence data that comprised ∼1.5 kb. Topologies derived from the combined mtDNA analyses were congruent with the total evidence analyses (mtDNA + nDNA) and retrieved five major clades with strong statistical support inferred from bootstrapping and posterior probabilities. The five clades were genealogically and geographically exclusive, diagnostic at both the mtDNA and nDNA level and characterized by pronounced sequence divergence, with no shared haplotypes between clades. Collectively these results suggest the presence of five putative cryptic operational taxonomic units within the A. meleagris meleagris species complex. Constraining the traditionally recognized taxa always retrieved a statistically worse topology suggesting that considerable taxonomic revision is required. Our results indicate that traditional morphological characters need to be reassessed to define the five novel lineages in the A. meleagris meleagris species complex. The phylogeographic pattern for the fossorial skinks we retrieved was novel compared to phylogeographic studies for codistributed above ground living taxa. These results suggest that the abiotic and biotic factors that impact subterranean taxa may differ from supraterranean taxa.
Abstract Objective Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is an aggressive tumor, with long term survival at ~ 30% in early stage disease. SCCOHT is caused by germline and ...somatic SMARCA4 mutations, but the effect of the mutation type on patients remains unknown. Furthermore, the rarity of SCCOHT has resulted in varied treatment, with no standardized protocols. We analyzed 293 cases to determine the effect of treatment modalities and SMARCA4 mutations on patient diagnosis and outcome. Methods In 293 SCCOHT patients we collected information on age and stage at diagnosis, treatment modality (surgery, chemotherapy, radiotherapy, and/or high-dose chemotherapy with autologous stem cell rescue (HDC-aSCR)), SMARCA4 mutation origin (germline/somatic), and overall survival. Cox analysis and log-rank tests were performed on 257 cases with available survival data. Results The strongest prognostic factors were stage at diagnosis ( p = 2.72e‐ 15) and treatment modality ( p = 3.87e‐13). For FIGO stages II–IV, 5-year survival was 71% for patients who received HDC-aSCR, compared to 25% in patients who received conventional chemotherapy alone following surgery ( p = 0.002). Patients aged ≥ 40 had a worse outcome than younger patients ( p = 0.04). Twenty-six of 60 tested patients carried a germline SMARCA4 mutation, including all patients diagnosed < 15 years; carriers presented at a younger age than non-carriers ( p = 0.02). Conclusions Stage at diagnosis is the most significant prognostic factor in SCCOHT and consolidation with HDC-aSCR may provide the best opportunity for long-term survival. The large fraction of SMARCA4 germline mutations carriers warrants genetic counseling for all patients.
Objective
To evaluate disease symptoms, and clinical and magnetic resonance imaging (MRI) findings and to perform longitudinal volumetric MRI analyses in a European multicenter cohort of pediatric ...anti–N‐methyl‐D‐aspartate receptor encephalitis (NMDARE) patients.
Methods
We studied 38 children with NMDARE (median age = 12.9 years, range =1–18) and a total of 82 MRI scans for volumetric MRI analyses compared to matched healthy controls. Mixed‐effect models and brain volume z scores were applied to estimate longitudinal brain volume development. Ordinal logistic regression and ordinal mixed models were used to predict disease outcome and severity.
Results
Initial MRI scans showed abnormal findings in 15 of 38 (39.5%) patients, mostly white matter T2/fluid‐attenuated inversion recovery hyperintensities. Volumetric MRI analyses revealed reductions of whole brain and gray matter as well as hippocampal and basal ganglia volumes in NMDARE children. Longitudinal mixed‐effect models and z score transformation showed failure of age‐expected brain growth in patients. Importantly, patients with abnormal MRI findings at onset were more likely to have poor outcome (Pediatric Cerebral Performance Category score > 1, incidence rate ratio = 3.50, 95% confidence interval CI = 1.31–9.31, p = 0.012) compared to patients with normal MRI. Ordinal logistic regression models corrected for time from onset confirmed abnormal MRI at onset (odds ratio OR = 9.90, 95% CI = 2.51–17.28, p = 0.009), a presentation with sensorimotor deficits (OR = 13.71, 95% CI = 2.68–24.73, p = 0.015), and a treatment delay > 4 weeks (OR = 5.15, 95% CI = 0.47–9.82, p = 0.031) as independent predictors of poor clinical outcome.
Interpretation
Children with NMDARE exhibit significant brain volume loss and failure of age‐expected brain growth. Abnormal MRI findings, a clinical presentation with sensorimotor deficits, and a treatment delay > 4 weeks are associated with worse clinical outcome. These characteristics represent promising prognostic biomarkers in pediatric NMDARE. ANN NEUROL 2020 ANN NEUROL 2020;88:148–159
Despite recent molecular systematic studies on the fossorial southern African skink subfamily Acontinae, evolutionary relationships among the three genera remain unresolved and disputed. Among these, ...the most recent study suggests that both Typhlosaurus and Acontias are paraphyletic, contrasting earlier results that suggest the presence of two divergent clades within Acontias. Here we further investigate the evolutionary relationships in the limbless fossorial southern African subfamily Acontinae with partial sequenced data derived from four mitochondrial loci (16S rRNA, 12S rRNA, cytochrome oxidase I and cytochrome b), as well as two nuclear protein coding loci (c‐mos and RAG‐1), in an attempt to clarify evolutionary relationships. Phylogenetic results derived from combined data analyses (comprising all six loci and totalling ∼3.1 kb) using maximum parsimony, maximum likelihood and Bayesian inferences converged on the same topology. The resulting phylogeny showed Typhlosaurus as monophyletic, while the monotypic genus Acontophiops was nested intermediate to two reciprocally monophyletic Acontias clades. These two Acontias clades can be distinguished on the basis of a number of morphological, morphometric and biogeographical characters, underscoring the presence of two distinct groups. In the present study, we propose the following taxonomic changes based on the multilocus phylogeny. We retain the genus name Acontias for the medium‐ and large‐bodied skinks in clade 2 comprising all taxa in the Acontias meleagris complex as well as Acontias plumbeus, Acontias gracilicauda gracilicauda, Acontias breviceps, Acontias percivali percivali and Acontias percivali occidentalis. We designate a new genus Microacontias gen. nov. for the reciprocally monophyletic taxa in clade 1 comprised of all the small‐bodied taxa that include Microacontias litoralis, Microacontias lineatus lineatus, Microacontias lineatus grayi and Microacontias lineatus tristis. We examine the evolution of characters used in the taxonomy of the Acontinae and suggest that symplesiomorphic morphological characters among fossorial taxa have been an impediment to understanding the evolution of this subfamily. This study underscores the importance of the application of multiple molecular markers (both nuclear and mitochondrial) in determining the taxonomic diversity among fossorial skinks and emphasizes the application of phylogenetics in defining synapomorphic (shared derived) features.
Subspecies in the limbless, endemic African fossorial skink genus
Acontias constitute ill-defined operational taxonomic units, consequently considerable systematic debate has lingered on the ...systematic diversity within
Acontias. In the present study, the systematic affinities among acontine taxa are explored with the utility of partial sequence data from two mitochondrial gene loci (16S rRNA and cytochrome oxidase subunit 1 (COI)) for all taxa, while two additional loci (12S rRNA, cytochrome
b) were used to investigate relationships within the
Acontias meleagris complex. Phylogenetic results, derived from the combined analysis, revealed two monophyletic clades. Clade 1 is comprised of small-bodied skinks while clade 2 comprised the medium bodied skinks. Within clade 2 none of the traditionally recognized subspecies formed reciprocally monophyletic groups. Furthermore, constraining the topology and enforcing sister taxa relationships between the assumed subspecies, consistently recovered a topology that was statistically significant worse, indicating that the traditionally designated subspecies groupings probably represent invalid taxonomic units, thus clearly reflecting considerable discord with current taxonomy. The burrowing life style of these lizards has probably led to marked convergent evolution and constrained the development of diagnostic morphological characters among these species. Morphological similarities in color as well as scale architecture within
Acontias are labile and highly homoplaseous and do not reflect the evolutionary history of the group. Taxonomic implications of these results are discussed.
Non-fission nuclear reactions were investigated by NASA as part of efforts to develop long-lasting electric power systems for space applications where solar energy is weak or unavailable. Key to ...investigation of nuclear reactions is spectroscopy of the neutron energies produced in such reactions. In addition to employing a standard scintillating-type neutron spectrometry system, the NASA team investigated the application of a moderating-type neutron spectrometer in a high-radiation environment as a parallel approach. The unfolded log-scale and linear-scale spectra of well-known calibration neutron sources are presented along with the ISO standard spectra for comparison. This new technology shows promise as a compact instrument capable of neutron spectroscopy in laboratory settings, and in particular, space applications where small size, low data rate and no onboard computation are advantages.
Sea ice is a dynamic biogeochemical reactor and a double interface actively interacting with both the atmosphere and the ocean. However, proper understanding of its annual impact on exchanges, and ...therefore potentially on the climate, notably suffer from the paucity of autumnal and winter data sets. Here we present the results of physical and biogeochemical investigations on winter Antarctic pack ice in the Weddell Sea (R. V. Polarstern AWECS cruise, June–August 2013) which are compared with those from two similar studies conducted in the area in 1986 and 1992. The winter 2013 was characterized by a warm sea ice cover due to the combined effects of deep snow and frequent warm cyclones events penetrating southward from the open Southern Ocean. These conditions were favorable to high ice permeability and cyclic events of brine movements within the sea ice cover (brine tubes), favoring relatively high chlorophyll‐a (Chl‐a) concentrations. We discuss the timing of this algal activity showing that arguments can be presented in favor of continued activity during the winter due to the specific physical conditions. Large‐scale sea ice model simulations also suggest a context of increasingly deep snow, warm ice, and large brine fractions across the three observational years, despite the fact that the model is forced with a snowfall climatology. This lends support to the claim that more severe Antarctic sea ice conditions, characterized by a longer ice season, thicker, and more concentrated ice are sufficient to increase the snow depth and, somehow counterintuitively, to warm the ice.
Key Points
Winter Weddell Sea pack ice (Antarctica) remains warm and permeable due to large snow depth and frequent occurrence of warm cyclonic events
These conditions trigger brine dynamics and associated sea ice biogeochemical processes
Of the limited number of winter Weddell Sea pack ice studies (3), this one reveals higher snow depth, negative freeboard, and higher Chl‐a
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