Design, construction, and functional characterization of a tRNA neochromosome in yeast.

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

Isolation and characterization of a californium metallocene.

Californium (Cf) is currently the heaviest element accessible above microgram quantities. Cf isotopes impose severe experimental challenges due to their scarcity and radiological hazards. Consequently, chemical secrets ranging from the accessibility of 5f/6d valence orbitals to engage in bonding, the role of spin-orbit coupling in electronic structure, and reactivity patterns compared to other f elements, remain locked. Organometallic molecules were foundational in elucidating periodicity and bonding trends across the periodic table1-3, with a twenty-first-century renaissance of organometallic thorium (Th) through plutonium (Pu) chemistry4-12, and to a smaller extent americium (Am)13, transforming chemical understanding. Yet, analogous curium (Cm) to Cf chemistry has lain dormant since the 1970s. Here, we revive air-/moisture-sensitive Cf chemistry through the synthesis and characterization of [Cf(C5Me4H)2Cl2K(OEt2)]n from two milligrams of 249Cf. This bent metallocene motif, not previously structurally authenticated beyond uranium (U)14,15, contains the first crystallographically characterized Cf-C bond. Analysis suggests the Cf-C bond is largely ionic with a small covalent contribution. Lowered Cf 5f orbital energy versus dysprosium (Dy) 4f in the colourless, isoelectronic and isostructural [Dy(C5Me4H)2Cl2K(OEt2)]n results in an orange Cf compound, contrasting with the light-green colour typically associated with Cf compounds16-22.

Dual-Hyperspectral Optical Pump-Probe Microscopy with Single-Nanosecond Time Resolution.

In recent years, optical pump-probe microscopy (PPM) has become a vital technique for spatiotemporally imaging electronic excitations and charge-carrier transport in metals and semiconductors. However, existing methods are limited by mechanical delay lines with a probe time window up to several nanoseconds (ns) or monochromatic pump and probe sources with restricted spectral coverage and temporal resolution, hindering their amenability in studying relatively slow processes. To bridge these gaps, we introduce a dual-hyperspectral PPM setup with a time window spanning from nanoseconds to milliseconds and single-nanosecond resolution. Our method features a wide-field probe tunable from 370 to 1000 nm and a pump spanning from 330 nm to 16 µm. We apply this PPM technique to study various two-dimensional metal-halide perovskites (2D-MHPs) as representative semiconductors by imaging their transient responses near the exciton resonances under both above-band gap electronic pump excitation and below-band gap vibrational pump excitation. The resulting spatially and temporally resolved images reveal insights into heat dissipation, film uniformity, distribution of impurity phases, and film-substrate interfaces. In addition, the single-nanosecond temporal resolution enables the imaging of in-plane strain wave propagation in 2D-MHP single crystals. Our method, which offers extensive spectral tunability and significantly improved time resolution, opens new possibilities for the imaging of charge carriers, heat, and transient phase transformation processes, particularly in materials with spatially varying composition, strain, crystalline structure, and interfaces.

Carbene Complexes of Plutonium: Structure, Bonding, and Divergent Reactivity to Lanthanide Analogs.

Organoplutonium chemistry was established in 1965, yet structurally authenticated plutonium-carbon bonds remain rare being limited to π-bonded carbocycle and σ-bonded isonitrile and hydrocarbyl derivatives. Thus, plutonium-carbenes, including alkylidenes and N-heterocyclic carbenes (NHCs), are unknown. Here, we report the preparation and characterization of the diphosphoniomethanide-plutonium complex [Pu(BIPMTMSH)(I)(µ-I)]2 (1Pu, BIPMTMSH = (Me3SiNPPh2)2CH) and the diphosphonioalkylidene-plutonium complexes [Pu(BIPMTMS)(I)(DME)] (2Pu, BIPMTMS = (Me3SiNPPh2)2C) and [Pu(BIPMTMS)(I)(IMe4)2] (3Pu, IMe4 = C(NMeCMe)2), thus disclosing non-actinyl transneptunium multiple bonds and transneptunium NHC complexes. These Pu-C double and dative bonds, along with cerium, praseodymium, samarium, uranium, and neptunium congeners, enable lanthanide-actinide and actinide-actinide comparisons between metals with similar ionic radii and isoelectronic 4f5 vs 5f5 electron-counts within conserved ligand fields over 12 complexes. Quantum chemical calculations reveal that the orbital-energy and spatial-overlap terms increase from uranium to neptunium; however, on moving to plutonium the orbital-energy matching improves but the spatial overlap decreases. The bonding picture that emerges is more complex than the traditional picture of the bonding of lanthanides being ionic and early actinides being more covalent but becoming more ionic left to right. Multiconfigurational calculations on 2M and 3M (M = Pu, Sm) account for the considerably more complex UV/vis/NIR spectra for 5f5 2Pu and 3Pu compared to 4f5 2Sm and 3Sm. Supporting the presence of Pu═C double bonds in 2Pu and 3Pu, 2Pu exhibits metallo-Wittig bond metathesis involving the highest atomic number element to date, reacting with benzaldehyde to produce the alkene PhC(H)═C(PPh2NSiMe3)2 (4) and "PuOI". In contrast, 2Ce and 2Pr do not react with benzaldehyde to produce 4.

N-Heterocyclic Carbene to Actinide d-Based π-bonding Correlates with Observed Metal-Carbene Bond Length Shortening Versus Lanthanide Congeners.

Comparison of bonding and electronic structural features between trivalent lanthanide (Ln) and actinide (An) complexes across homologous series' of molecules can provide insights into subtle and overt periodic trends. Of keen interest and debate is the extent to which the valence f- and d-orbitals of trivalent Ln/An ions engage in covalent interactions with different ligand donor functionalities and, crucially, how bonding differences change as both the Ln and An series are traversed. Synthesis and characterization (SC-XRD, NMR, UV-vis-NIR, and computational modeling) of the homologous lanthanide and actinide N-heterocyclic carbene (NHC) complexes [M(C5Me5)2(X)(IMe4)] {X = I, M = La, Ce, Pr, Nd, U, Np, Pu; X = Cl, M = Nd; X = I/Cl, M = Nd, Am; and IMe4 = [C(NMeCMe)2]} reveals consistently shorter An-C vs Ln-C distances that do not substantially converge upon reaching Am3+/Nd3+ comparison. Specifically, the difference of 0.064(6) Å observed in the La/U pair is comparable to the 0.062(4) Å difference observed in the Nd/Am pair. Computational analyses suggest that the cause of this unusual observation is rooted in the presence of π-bonding with the valence d-orbital manifold in actinide complexes that is not present in the lanthanide congeners. This is in contrast to other documented cases of shorter An-ligand vs Ln-ligand distances, which are often attributed to increased 5f vs 4f radial diffusivity leading to differences in 4f and 5f orbital bonding involvement. Moreover, in these traditional observations, as the 5f series is traversed, the 5f manifold contracts such that by americium structural studies often find no statistically significant Am3+vs Nd3+ metal-ligand bond length differences.

Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features.

Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as "fission yeasts." As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.

Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast.

The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.

A novel role for gag as a cis-acting element regulating RNA structure, dimerization and packaging in HIV-1 lentiviral vectors.

Clinical usage of lentiviral vectors is now established and increasing but remains constrained by vector titer with RNA packaging being a limiting factor. Lentiviral vector RNA is packaged through specific recognition of the packaging signal on the RNA by the viral structural protein Gag. We investigated structurally informed modifications of the 5' leader and gag RNA sequences in which the extended packaging signal lies, to attempt to enhance the packaging process by facilitating vector RNA dimerization, a process closely linked to packaging. We used in-gel SHAPE to study the structures of these mutants in an attempt to derive structure-function correlations that could inform optimized vector RNA design. In-gel SHAPE of both dimeric and monomeric species of RNA revealed a previously unreported direct interaction between the U5 region of the HIV-1 leader and the downstream gag sequences. Our data suggest a structural equilibrium exists in the dimeric viral RNA between a metastable structure that includes a U5-gag interaction and a more stable structure with a U5-AUG duplex. Our data provide clarification for the previously unexplained requirement for the 5' region of gag in enhancing genomic RNA packaging and provide a basis for design of optimized HIV-1 based vectors.

Low-Loss Plasmonics with Nanostructured Potassium and Sodium-Potassium Liquid Alloys.

Alkali metals have low optical losses in the visible to near-infrared (NIR) compared with noble metals. However, their high reactivity prohibits the exploration of their optical properties. Recently sodium (Na) has been experimentally demonstrated as a low-loss plasmonic material. Here we report on a thermo-assisted nanoscale embossing (TANE) technique for fabricating plasmonic nanostructures from pure potassium (K) and NaK liquid alloys. We show high-quality-factor resonances from K as narrow as 15 nm in the NIR, which we attribute to the high material quality and low optical loss. We further demonstrate liquid Na-K plasmonics by exploiting the Na-K eutectic phase diagram. Our study expands the material library for alkali metal plasmonics and liquid plasmonics, potentially enabling a range of new material platforms for active metamaterials and photonic devices.

Ecological network analysis of traits reveals variable response capacity to stress.

Response diversity increases the potential 'options' for ecological communities to respond to stress (i.e. response capacity). An indicator of community response diversity is the diversity of different traits associated with their capacity to be resistant to stress, to recover and to regulate ecosystem functions. We conducted a network analysis of traits using benthic macroinvertebrate community data from a large-scale field experiment to explore the loss of response diversity along environmental gradients. We elevated sediment nutrient concentrations (a process that occurs with eutrophication) at 24 sites (in 15 estuaries) with varying environmental conditions (water column turbidity and sediment properties). Macroinvertebrate community response capacity to nutrient stress was dependent on the baseline trait network complexity in the ambient community (i.e. non-enriched sediments). The greater the complexity of the baseline network, the less variable the network response to nutrient stress was; in contrast, more variable responses to nutrient stress occurred with simpler networks. Thus, stressors or environmental variables that shift baseline network complexity also shift the capacity for these ecosystems to respond to additional stressors. Empirical studies that explore the mechanisms responsible for loss of resilience are essential to inform our ability to predict changes in ecological states.

Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini).

The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the âˆ¼ 30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to âˆ¼ 5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.

Stabilization of Pu(IV) in PuBr4(OPCy3)2 and Comparisons with Structurally Similar ThX4(OPR3)2 (R = Cy, Ph) Molecules.

The pursuit of a trivalent plutonium halide phosphine oxide compound, e.g., "PuBr3(OPR)3," instead led to the isolation of the tetravalent trans-PuIVBr4(OPCy3)2, PuBr/Cy, compound by spontaneous oxidation of PuIII. The donating nature of phosphine oxides has allowed the isolation and characterization of PuBr/Cy by crystallographic, multinuclear NMR, solid state, and solution phase UV-vis-NIR spectroscopic techniques. The presence of a putative plutonyl(VI) complex formulated as "trans-PuVIO2Br2(OPCy3)2" was also observed spectroscopically and tentatively by single-crystal X-ray diffraction as a cocrystal of PuBr/Cy. A series of trans-ThX4(OPCy3)2 (X = Cl, ThCl/Cy; Br, ThBr/Cy; I, ThI/Cy) complexes were synthesized for comparison to PuBr/Cy. The triphenylphosphine oxide, OPPh3, complexes, trans-AnI4(OPPh3)2 (An = Th, ThI/Ph; U, UI/Ph), were also synthesized for comparison, completing the series trans-UX4(OPPh3)2 (X = Cl, Br, I), UX/Ph. To enable the synthesis of ThI/Cy and ThI/Ph, a new nonaqueous thorium iodide starting material, ThI4(Et2O)2, was synthesized. The syntheses of organic solvent soluble ThI4L2 (L = Et2O, OPCy3, and OPPh3) are the first examples of crystallographically characterized neutral thorium tetraiodide materials beyond binary ThI4. To show the viability of ThI4(Et2O)2 as a starting material for organothorium chemistry, (C5Me4H)3ThI was synthesized and crystallographically characterized.

Documenting the microbiome diversity and distribution in selected fleas from South Africa with an emphasis on the cat flea, Ctenocephalides f. felis.

The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysis of 107 flea samples collected from 8 distinct sampling sites in South Africa. Pooled DNA samples mostly comprising of 2 or 3 individuals sampled from the same host, and belonging to the same genetic cluster, were sequenced using the Ion PGM™ Hi-Q™ Kit and the Ion 316™ Chip v2. Differences were detected in the microbiome compositions between Ctenocephalides felis, Ctenocephalides canis and Ctenocephalides connatus. Although based on a small sample, C. connatus occurring on wildlife harboured a higher bacterial richness when compared to C. felis on domestic animals. Intraspecific differences in the microbial OTU diversity were detected within C. f. felis that occurred on domestic cats and dogs. Different genetic lineages of C. f. felis were similar in microbial compositions but some differences exist in the presence or absence of rare bacteria. Rickettsia and Bartonella OTU's identified in South African cat fleas differ from those identified in the USA and Australia. Intraspecific microbial compositions also differ across geographic sampling sites. Generalized dissimilarity modelling showed that temperature and humidity are potentially important environmental factors explaining the pattern obtained.

Multi-phase volcanic resurfacing at Loki Patera on Io.

The Jovian moon Io hosts the most powerful persistently active volcano in the Solar System, Loki Patera. The interior of this volcanic, caldera-like feature is composed of a warm, dark floor covering 21,500 square kilometres surrounding a much cooler central 'island'. The temperature gradient seen across areas of the patera indicates a systematic resurfacing process, which has been seen to occur typically every one to three years since the 1980s. Analysis of past data has indicated that the resurfacing progressed around the patera in an anti-clockwise direction at a rate of one to two kilometres per day, and that it is caused either by episodic eruptions that emplace voluminous lava flows or by a cyclically overturning lava lake contained within the patera. However, spacecraft and telescope observations have been unable to map the emission from the entire patera floor at sufficient spatial resolution to establish the physical processes at play. Here we report temperature and lava cooling age maps of the entire patera floor at a spatial sampling of about two kilometres, derived from ground-based interferometric imaging of thermal emission from Loki Patera obtained on 8 March 2015 ut as the limb of Europa occulted Io. Our results indicate that Loki Patera is resurfaced by a multi-phase process in which two waves propagate and converge around the central island. The different velocities and start times of the waves indicate a non-uniformity in the lava gas content and/or crust bulk density across the patera.

Molecular magnetic hysteresis at 60 kelvin in dysprosocenium.

Lanthanides have been investigated extensively for potential applications in quantum information processing and high-density data storage at the molecular and atomic scale. Experimental achievements include reading and manipulating single nuclear spins, exploiting atomic clock transitions for robust qubits and, most recently, magnetic data storage in single atoms. Single-molecule magnets exhibit magnetic hysteresis of molecular origin-a magnetic memory effect and a prerequisite of data storage-and so far lanthanide examples have exhibited this phenomenon at the highest temperatures. However, in the nearly 25 years since the discovery of single-molecule magnets, hysteresis temperatures have increased from 4 kelvin to only about 14 kelvin using a consistent magnetic field sweep rate of about 20 oersted per second, although higher temperatures have been achieved by using very fast sweep rates (for example, 30 kelvin with 200 oersted per second). Here we report a hexa-tert-butyldysprosocenium complex-[Dy(Cpttt)2][B(C6F5)4], with Cpttt = {C5H2tBu3-1,2,4} and tBu = C(CH3)3-which exhibits magnetic hysteresis at temperatures of up to 60 kelvin at a sweep rate of 22 oersted per second. We observe a clear change in the relaxation dynamics at this temperature, which persists in magnetically diluted samples, suggesting that the origin of the hysteresis is the localized metal-ligand vibrational modes that are unique to dysprosocenium. Ab initio calculations of spin dynamics demonstrate that magnetic relaxation at high temperatures is due to local molecular vibrations. These results indicate that, with judicious molecular design, magnetic data storage in single molecules at temperatures above liquid nitrogen should be possible.

Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early- and late-replicating euchromatin.

A eukaryotic chromosome relies on the function of multiple spatially distributed DNA replication origins for its stable inheritance. The spatial location of an origin is determined by the chromosomal position of an MCM complex, the inactive form of the DNA replicative helicase that is assembled onto DNA in G1-phase (also known as origin licensing). While the biochemistry of origin licensing is understood, the mechanisms that promote an adequate spatial distribution of MCM complexes across chromosomes are not. We have elucidated a role for the Sir2 histone deacetylase in establishing the normal distribution of MCM complexes across Saccharomyces cerevisiae chromosomes. In the absence of Sir2, MCM complexes accumulated within both early-replicating euchromatin and telomeric heterochromatin, and replication activity within these regions was enhanced. Concomitantly, the duplication of several regions of late-replicating euchromatin were delayed. Thus, Sir2-mediated attenuation of origin licensing within both euchromatin and telomeric heterochromatin established the normal spatial distribution of origins across yeast chromosomes important for normal genome duplication.

Toward a network perspective in coastal ecosystem management.

Environmental management in coastal ecosystems has been challenged by the complex cumulative effects that occur when many small issues result in large ecological shifts. Current environmental management of these spaces focuses on identifying and limiting problematic stressors via a series of assessment techniques. Whilst there is a strong desire among managers to consider complexity in ecological responses to cumulative effects, current approaches for assessing risk focus on breaking down the issues into multiple cause and effect relationships. However, uncertainty arises when data and information for a place are limited, as is commonly the case, and this creates decision paralysis while more information is generated. Here, we discuss how ecological understanding of network interactions in coastal marine ecosystems can be used as a lens to bring together multiple lines of evidence and create actions. We list and describe four characteristics of marine ecosystem interaction networks including the possibility for; 1) indirect effects, 2) effects that emerge as stressor magnitude increases the number of network components implicated, 3) network interactions that amplify these indirect effects, and 4) feedbacks that reinforce or stabilise against indirect effects. We then link these four characteristics to three case studies of common coastal environmental issues to demonstrate how a general understanding of ecological interaction networks can enhance priorities for stressor management that can be applied even when specific data is limited.

Tos4 mediates gene expression homeostasis through interaction with HDAC complexes independently of H3K56 acetylation.

Saccharomyces cerevisiae exhibits gene expression homeostasis, which is defined as the buffering of transcription levels against changes in DNA copy number during the S phase of the cell cycle. It has been suggested that S. cerevisiae employs an active mechanism to maintain gene expression homeostasis through Rtt109-Asf1-dependent acetylation of histone H3 on lysine 56 (H3K56). Here, we show that gene expression homeostasis can be achieved independently of H3K56 acetylation by Tos4 (Target of Swi6-4). Using Nanostring technology, we establish that Tos4-dependent gene expression homeostasis depends on its forkhead-associated (FHA) domain, which is a phosphopeptide recognition domain required to bind histone deacetylases (HDACs). We demonstrate that the mechanism of Tos4-dependent gene expression homeostasis requires its interaction with the Rpd3L HDAC complex. However, this is independent of Rpd3's well-established roles in both histone deacetylation and controlling the DNA replication timing program, as established by deep sequencing of Fluorescence-Activated Cell Sorted (FACS) S and G2 phase populations. Overall, our data reveals that Tos4 mediates gene expression homeostasis through its FHA domain-dependent interaction with the Rpd3L complex, which is independent of H3K56ac.

Carbene Complexes of Neptunium.

Since the advent of organotransuranium chemistry six decades ago, structurally verified complexes remain restricted to π-bonded carbocycle and σ-bonded hydrocarbyl derivatives. Thus, transuranium-carbon multiple or dative bonds are yet to be reported. Here, utilizing diphosphoniomethanide precursors we report the synthesis and characterization of transuranium-carbene derivatives, namely, diphosphonio-alkylidene- and N-heterocyclic carbene-neptunium(III) complexes that exhibit polarized-covalent σ2π2 multiple and dative σ2 single transuranium-carbon bond interactions, respectively. The reaction of [NpIIII3(THF)4] with [Rb(BIPMTMSH)] (BIPMTMSH = {HC(PPh2NSiMe3)2}1-) affords [(BIPMTMSH)NpIII(I)2(THF)] (3Np) in situ, and subsequent treatment with the N-heterocyclic carbene {C(NMeCMe)2} (IMe4) allows isolation of [(BIPMTMSH)NpIII(I)2(IMe4)] (4Np). Separate treatment of in situ prepared 3Np with benzyl potassium in 1,2-dimethoxyethane (DME) affords [(BIPMTMS)NpIII(I)(DME)] (5Np, BIPMTMS = {C(PPh2NSiMe3)2}2-). Analogously, addition of benzyl potassium and IMe4 to 4Np gives [(BIPMTMS)NpIII(I)(IMe4)2] (6Np). The synthesis of 3Np-6Np was facilitated by adopting a scaled-down prechoreographed approach using cerium synthetic surrogates. The thorium(III) and uranium(III) analogues of these neptunium(III) complexes are currently unavailable, meaning that the synthesis of 4Np-6Np provides an example of experimental grounding of 5f- vs 5f- and 5f- vs 4f-element bonding and reactivity comparisons being led by nonaqueous transuranium chemistry rather than thorium and uranium congeners. Computational analysis suggests that these NpIII═C bonds are more covalent than UIII═C, CeIII═C, and PmIII═C congeners but comparable to analogous UIV═C bonds in terms of bond orders and total metal contributions to the M═C bonds. A preliminary assessment of NpIII═C reactivity has introduced multiple bond metathesis to transuranium chemistry, extending the range of known metallo-Wittig reactions to encompass actinide oxidation states III-VI.

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.

Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git .