Phylogenomic evolutionary insights in the fern family Gleicheniaceae.

The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts.

miR-182 integrates apoptosis, growth, and differentiation programs in glioblastoma.

Glioblastoma multiforme (GBM) is a lethal, therapy-resistant brain cancer consisting of numerous tumor cell subpopulations, including stem-like glioma-initiating cells (GICs), which contribute to tumor recurrence following initial response to therapy. Here, we identified miR-182 as a regulator of apoptosis, growth, and differentiation programs whose expression level is correlated with GBM patient survival. Repression of Bcl2-like12 (Bcl2L12), c-Met, and hypoxia-inducible factor 2α (HIF2A) is of central importance to miR-182 anti-tumor activity, as it results in enhanced therapy susceptibility, decreased GIC sphere size, expansion, and stemness in vitro. To evaluate the tumor-suppressive function of miR-182 in vivo, we synthesized miR-182-based spherical nucleic acids (182-SNAs); i.e., gold nanoparticles covalently functionalized with mature miR-182 duplexes. Intravenously administered 182-SNAs penetrated the blood-brain/blood-tumor barriers (BBB/BTB) in orthotopic GBM xenografts and selectively disseminated throughout extravascular glioma parenchyma, causing reduced tumor burden and increased animal survival. Our results indicate that harnessing the anti-tumor activities of miR-182 via safe and robust delivery of 182-SNAs represents a novel strategy for therapeutic intervention in GBM.

A permineralized Early Cretaceous lycopsid from China and the evolution of crown clubmosses.

Lycopodiaceae are one of three surviving families of lycopsids, a lineage of vascular plants with a fossil history dating to at least the Early Devonian or perhaps the Late Silurian (c. 415 Ma). Many fossils have been linked to crown Lycopodiaceae, but the lack of well-preserved material has hindered definitive recognition of this group in the paleobotanical record. New, exceptionally well-preserved permineralized lycopsid fossils from the Early Cretaceous (125.6 ± 1.0 Ma) of Inner Mongolia, China, were examined in detail using acetate peel and micro-computed tomography techniques. The anatomy of extant Lycopodiaceae was analyzed for comparison using fluorescence microscopy. Phylogenetic relationships of the new fossil to extant Lycopodiaceae were evaluated using parsimony and maximum likelihood analyses. Lycopodicaulis oellgaardii gen. et sp. nov. provides the earliest unequivocal and best-documented evidence of crown Lycopodiaceae and Lycopodioideae, based on anatomically-preserved fossil material. Recognition of Lycopodicaulis in Asia during the Early Cretaceous indicates the presence of crown Lycopodiaceae at this time, and striking similarities of stem anatomy with extant species provide a framework for the understanding of the interaction of branching and vascular anatomy in crown-group lycopsids.

Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family.

PREMISE: The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. METHODS: We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. RESULTS: Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. CONCLUSIONS: Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

Effect of calcanean bone-tunnel orientation for teno-osseous repair in a canine common calcanean tendon avulsion model.

OBJECTIVE: To determine the influence of bone-tunnel anchoring technique on teno-osseous repair of the common calcanean tendon (CCT) in dogs. STUDY DESIGN: Randomized, ex vivo, biomechanical. POPULATION: Forty-two skeletally mature canine hindlimbs. METHODS: Canine hindlimbs were dissected to produce a model simulating avulsion of the CCT and accessory tendons from the calcaneus. Hindlimbs were randomized to 1 of 3 anchoring techniques (n = 14/group): a single transverse tunnel (TT), vertical tunnels (VT), or modified bone tunnels (MT) for teno-osseous repair in a 3-loop-pulley (3LP) pattern using 0 USP polypropylene. Yield, peak and failure loads, construct stiffness, loads to produce a 3 mm teno-osseous gap, and failure modes were compared between groups. RESULTS: The only difference detected consisted of TT constructs yielding at loads 25% higher than MT constructs (P = .027). CONCLUSION: Although yield loads were lower in MT constructs than other groups, the bone-tunnel anchoring techniques tested here did not appear to influence the biomechanical properties or gapping characteristics of teno-osseous repairs in this canine CCT avulsion model. CLINICAL SIGNIFICANCE: All drilling techniques and bone-tunnel orientations tested in the study reported here offer viable options to reattach the CCT to the calcaneus. Surgeons should evaluate how bone-tunnel orientation may affect placement of adjunctive fixation methods to stabilize the talocrural joint after primary CCT repair in dogs.

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns.

Sex expression of homosporous ferns is controlled by multiple factors, one being the antheridiogen system. Antheridiogens are pheromones released by sexually mature female fern gametophytes, turning nearby asexual gametophytes precociously male. Nevertheless, not all species respond. It is still unknown how many fern species use antheridiogens, how the antheridiogen system evolved, and whether it is affected by polyploidy and/or apomixis. We tested the response of 68 fern species to antheridiogens in cultivation. These results were combined with a comprehensive review of literature to form the largest dataset of antheridiogen interactions to date. Analyzed species also were coded as apomictic or sexual and diploid or polyploid. Our final dataset contains a total of 498 interactions involving 208 species (c. 2% of all ferns). About 65% of studied species respond to antheridiogen. Multiple antheridiogen types were delimited and their evolution is discussed. Antheridiogen responsiveness was not significantly affected by apomixis or polyploidy. Antheridiogens are widely used by ferns to direct sex expression. The antheridiogen system likely evolved multiple times and provides homosporous ferns with the benefits often associated with heterospory, such as increased rates of outcrossing. Despite expectations, antheridiogens may be beneficial to polyploids and apomicts.

Site-Selective and Stereoselective O-Alkylation of Glycosides by Rh(II)-Catalyzed Carbenoid Insertion.

Carbohydrates are synthetically challenging molecules with vital biological roles in all living systems. Selective synthesis and functionalization of carbohydrates provide tremendous opportunities to improve our understanding on the biological functions of this fundamentally important class of molecules. However, selective functionalization of seemingly identical hydroxyl groups in carbohydrates remains a long-standing challenge in chemical synthesis. We herein describe a practical and predictable method for the site-selective and stereoselective alkylation of carbohydrate hydroxyl groups via Rh(II)-catalyzed insertion of metal carbenoid intermediates. This represents one of the mildest alkylation methods for the systematic modification of carbohydrates. Density functional theory (DFT) calculations suggest that the site selectivity is determined in the Rh(II)-carbenoid insertion step, which prefers insertion into hydroxyl groups with an adjacent axial substituent. The subsequent intramolecular enolate protonation determines the unexpected high stereoselectivity. The most prevalent trans-1,2-diols in various pyranoses can be systematically and predictably differentiated based on the model derived from DFT calculations. We also demonstrated that the selective O-alkylation method could significantly improve the efficiency and stereoselectivity of glycosylation reactions. The alkyl groups introduced to carbohydrates by OH insertion reaction can serve as functional groups, protecting groups, and directing groups.

The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae).

Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.

Photochemical Etching of Carbonyl Groups from a Carbon Matrix: The (001) Diamond Surface.

The surface of diamond is reported to undergo nonablative photochemical etching when exposed to ultraviolet (UV) radiation which allows controlled single and partial layer removal of lattice layers. Oxygen termination of surface dangling bonds is known to be crucial for the etching process; however, the exact mechanism of carbon ejection remains unclear. We investigate the interaction of UV laser pulses with oxygen-terminated diamond surfaces using atomic-scale surface characterization combined with first-principles time-dependent density functional theory calculations. We present evidence for laser-induced desorption (LID) from carbonyl functional groups at the diamond {001} surface. The doubly bonded carbonyl group is photoexcited into a triply bonded CO-like state, including scission of the underlying C─C bonds. The carbon removal process in LID is atom by atom; therefore, this mechanism provides a novel "top-down" approach for creating nanostructures on the surface of diamond and other carbon-containing semiconductors.

Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature.

The number of published materials science articles has increased manyfold over the past few decades. Now, a major bottleneck in the materials discovery pipeline arises in connecting new results with the previously established literature. A potential solution to this problem is to map the unstructured raw text of published articles onto structured database entries that allow for programmatic querying. To this end, we apply text mining with named entity recognition (NER) for large-scale information extraction from the published materials science literature. The NER model is trained to extract summary-level information from materials science documents, including inorganic material mentions, sample descriptors, phase labels, material properties and applications, as well as any synthesis and characterization methods used. Our classifier achieves an accuracy (f1) of 87%, and is applied to information extraction from 3.27 million materials science abstracts. We extract more than 80 million materials-science-related named entities, and the content of each abstract is represented as a database entry in a structured format. We demonstrate that simple database queries can be used to answer complex "meta-questions" of the published literature that would have previously required laborious, manual literature searches to answer. All of our data and functionality has been made freely available on our Github ( https://github.com/materialsintelligence/matscholar ) and website ( http://matscholar.com ), and we expect these results to accelerate the pace of future materials science discovery.

Are rates of species diversification and body size evolution coupled in the ferns?

PREMISE OF THE STUDY: Understanding the relationship between phenotypic evolution and lineage diversification is a central goal of evolutionary biology. To extend our understanding of the role morphological evolution plays in the diversification of plants, we examined the relationship between leaf size evolution and lineage diversification across ferns. METHODS: We tested for an association between body size evolution and lineage diversification using a comparative phylogenetic approach that combined a time-calibrated phylogeny and leaf size data set for 2654 fern species. Rates of leaf size change and lineage diversification were estimated using BAMM, and rate correlations were performed for rates obtained for all families and individual species. Rates and patterns of rate-rate correlation were also analyzed separately for terrestrial and epiphytic taxa. KEY RESULTS: We find no significant correlation between rates of leaf area change and lineage diversification, nor was there a difference in this pattern when growth habit is considered. Our results are consistent with the findings of an earlier study that reported decoupled rates of body size evolution and diversification in the Polypodiaceae, but conflict with a recent study that reported a positive correlation between body size evolution and lineage diversification rates in the tree fern family Cyatheaceae. CONCLUSIONS: Our findings indicate that lineage diversification in ferns is largely decoupled from shifts in body size, in contrast to several other groups of organisms. Speciation in ferns appears to be primarily driven by hybridization and isolation along elevational gradients, rather than adaptive radiations featuring prominent morphological restructuring. The exceptional diversity of leaf morphologies in ferns appears to reflect a combination of ecophysiological constraints and adaptations that are not key innovations.

Realizations of the Triple Point of Sulfur Hexafluoride in Transportable and Refillable Cells.

The Minamata Convention on Mercury has created a near-term need to develop alternative fixed points to replace the mercury triple point (Hg TP) for calibration of standard platinum resistance thermometers (SPRTs) on the International Temperature Scale of 1990 (ITS-90). The sulfur hexafluoride (SF6) TP is a good candidate to provide adequate "drop-in compatible" replacements for the lowest costs. We report our first results of SF6 TP realizations performed at the National Institute of Standards and Technology (NIST) using a new series of transportable and refillable triple-point cells. The melting curves are presented at various melted fractions F and compared to evaluate the reproducibility and overall uncertainty for the realizations. We obtained a TP temperature of 223.55587(33) K at F = 50 % and 223.55607(35) K at F = 100 % as a weighted average of realizations using two adiabatic-type cells and two immersion-type cells. (Unless otherwise stated, uncertainties are standard uncertainties corresponding to a 68 % confidence level.) Temperatures were derived using a combination of five different SPRTs as calibrated at NIST on the ITS-90. The data were evaluated over a region of the melting plateau for melted fraction F between 30 % ≤ F ≤ 80 % with a 0.2 mK wide melting range. The results from the immersion-type cells were used to derive an experimental value for the SF6 TP static head correction of -11.6(1.7) mK/m. This value implies an initial slope of the pressure-temperature (p-T) equilibrium melting line of 1.55 MPa/K, which is in agreement with the value predicted via the Clapeyron equation. The uncertainties of these initial SF6 TP realizations are limited by uncertainty in the realization of the ITS-90 (0.25 mK) and, to a lesser extent, static pressure head effects and chemical impurities.

The NIST Johnson Noise Thermometry System for the Determination of the Boltzmann Constant.

In preparation for the redefinition of the International System of Units (SI), five different electronic measurements of the Boltzmann constant have been performed using different Johnson noise thermometry (JNT) systems over the past seven years. In this paper, we describe in detail the JNT system and uncertainty components associated with the most recent National Institute of Standards and Technology (NIST) determination of the Boltzmann constant: k = 1.380642 9(69) × 10-23 J/K, with a relative standard uncertainty of 5.0 × 10-6 and relative offset of -4.05 × 10-6 from the Committee on Data for Science and Technology (CODATA) 2014 recommended value. We discuss the input circuits and the approach we used to match the frequency response of two noise sources. We present new measurements of the correlated noise of the 4 K on-chip resistors in the quantum-accurate, pseudorandom, voltage-noise source, which we used to estimate the correlated, frequency-dependent, nonthermal noise in our system. Finally, we contrast our system with those used in other measurements and speculate on future improvements.

An improved electronic determination of the Boltzmann constant by Johnson noise thermometry.

Recent measurements using acoustic gas thermometry have determined the value of the Boltzmann constant, k, with a relative uncertainty less than 1 × 10-6. These results have been supported by a measurement with a relative uncertainty of 1.9 × 10-6 made with dielectric-constant gas thermometry. Together, the measurements meet the requirements of the International Committee for Weights and Measures and enable them to proceed with the redefinition of the kelvin in 2018. In further support, we provide a new determination of k using a purely electronic approach, Johnson noise thermometry, in which the thermal noise power generated by a sensing resistor immersed in a triple-point-of-water cell is compared to the noise power of a quantum-accurate pseudo-random noise waveform of nominally equal noise power. The experimental setup differs from that of the 2015 determination in several respects: a 100 Ω resistor is used as the thermal noise source, identical thin coaxial cables made of solid beryllium-copper conductors and foam dielectrics are used to connect the thermal and quantum-accurate noise sources to the correlator so as to minimize the temperature and frequency sensitivity of the impedances in the connecting leads, and no trimming capacitors or inductors are inserted into the connecting leads. The combination of reduced uncertainty due to spectral mismatches in the connecting leads and reduced statistical uncertainty due to a longer integration period of 100 d results in an improved determination of k = 1.380 649 7(37) × 10-23 J K-1 with a relative standard uncertainty of 2.7 × 10-6 and a relative offset of 0.89 × 10-6 from the CODATA 2014 recommended value. The most significant terms in the uncertainty budget, the statistical uncertainty and the spectral-mismatch uncertainty, are uncorrelated with the corresponding uncertainties in the 2015 measurements.

On the widespread capacity for, and functional significance of, extreme inbreeding in ferns.

Homosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been a subject of debate for decades. We cultured gametophytes in the laboratory and quantified the relative frequencies of sporophyte production from isolated and paired gametophytes, and examined associations between breeding systems and several ecological and evolutionary traits. The majority of fern species studied show a capacity for gametophytic selfing, producing sporophytes from both isolated and paired gametophytes. While we did not follow sporophytes to maturity to investigate potential detrimental effects of homozygosity at later developmental stages, our results suggest that gametophytic selfing may have greater significance for fern evolution and diversification than has previously been realized. We present evidence from the largest study of mating behavior in ferns to date that the capacity for extreme inbreeding is prevalent in this lineage, and we discuss its implications and relevance and make recommendations for future studies of fern mating systems.

Dynamics of asymmetrical hybridization in North American wood ferns: reconciling patterns of inheritance with gametophyte reproductive biology.

Hybridization is an important evolutionary force in plants, but the mechanisms underlying it have not been well studied for many groups. In particular, the drivers of non-random patterns of interspecific gene flow (asymmetrical hybridization) remain poorly understood, especially in the seed-free vascular plants. Here, we examine patterns of asymmetrical hybridization in two widespread fern hybrids from eastern North America and study the role of gametophyte ecology in the determination of hybridization bias. We characterized the maternal parentage of > 140 hybrid sporophytes by sequencing a c. 350-bp region of chloroplast DNA (cpDNA). To identify factors contributing to patterns of asymmetrical hybridization, we cultured gametophytes of the parental species and evaluated critical aspects of their reproductive biology. We found that asymmetrical hybridization was prevalent across the populations of both hybrids. Reproductive traits varied across species and suggest that selfing potential, antheridiogen responsiveness, sperm dispersal capacity and gamete size all contribute to the mediation of the direction of hybridization in this group. Our findings suggest that asymmetrical hybridization in ferns is driven by an array of reproductive traits. This study helps to sharpen and define a mechanistic understanding of patterns of hybridization in this group and demonstrates the importance of considering gametophyte biology when studying evolutionary processes in ferns.

Bistable Magnetism and Potential for Voltage-Induced Spin Crossover in Dilute Magnetic Ferroelectrics.

A first-principles investigation into the magnetic ferroelectric PbTi(1-x)Co(x)O(3) has revealed a bi-stable magnetic system with strong spin-lattice coupling. The local distortions induced by the low-spin to high-spin crossover are ferroelectric in nature, and are characterized by the displacement of the dopant ion with respect to the surrounding O(6) octahedral cage. We demonstrate how this spin-lattice effect could mediate magnetoelectric coupling and possible electric field induced spin-crossover, indicating a promising route to voltage manipulation of isolated spins in a solid-state system.