Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins.

Genes encoding the RNA-binding proteins FUS, EWSR1, and TAF15 (FET proteins) are involved in chromosomal translocations in rare sarcomas. FET-rearranged sarcomas are often aggressive malignancies affecting patients of all ages. New therapies are needed. These translocations fuse the 5' portion of the FET gene with a 3' partner gene encoding a transcription factor (TF). The resulting fusion proteins are oncogenic TFs with a FET protein low complexity domain (LCD) and a DNA binding domain. FET fusion proteins have proven stubbornly difficult to target directly and promising strategies target critical co-regulators. One candidate is lysine specific demethylase 1 (LSD1). LSD1 is recruited by multiple FET fusions, including EWSR1::FLI1. LSD1 promotes EWSR1::FLI1 activity and treatment with the noncompetitive inhibitor SP-2509 blocks EWSR1::FLI1 transcriptional function. A similar molecule, seclidemstat (SP-2577), is currently in clinical trials for FET-rearranged sarcomas (NCT03600649). However, whether seclidemstat has pharmacological activity against FET fusions has not been demonstrated. Here, we evaluate the in vitro potency of seclidemstat against multiple FET-rearranged sarcoma cell lines, including Ewing sarcoma, desmoplastic small round cell tumor, clear cell sarcoma, and myxoid liposarcoma. We also define the transcriptomic effects of seclidemstat treatment and evaluated the activity of seclidemstat against FET fusion transcriptional regulation. Seclidemstat showed potent activity in cell viability assays across FET-rearranged sarcomas and disrupted the transcriptional function of all tested fusions. Though epigenetic and targeted inhibitors are unlikely to be effective as a single agents in the clinic, these data suggest seclidemstat remains a promising new treatment strategy for patients with FET-rearranged sarcomas.

Nanoscale Three-Dimensional Imaging of Integrated Circuits Using a Scanning Electron Microscope and Transition-Edge Sensor Spectrometer.

X-ray nanotomography is a powerful tool for the characterization of nanoscale materials and structures, but it is difficult to implement due to the competing requirements of X-ray flux and spot size. Due to this constraint, state-of-the-art nanotomography is predominantly performed at large synchrotron facilities. We present a laboratory-scale nanotomography instrument that achieves nanoscale spatial resolution while addressing the limitations of conventional tomography tools. The instrument combines the electron beam of a scanning electron microscope (SEM) with the precise, broadband X-ray detection of a superconducting transition-edge sensor (TES) microcalorimeter. The electron beam generates a highly focused X-ray spot on a metal target held micrometers away from the sample of interest, while the TES spectrometer isolates target photons with a high signal-to-noise ratio. This combination of a focused X-ray spot, energy-resolved X-ray detection, and unique system geometry enables nanoscale, element-specific X-ray imaging in a compact footprint. The proof of concept for this approach to X-ray nanotomography is demonstrated by imaging 160 nm features in three dimensions in six layers of a Cu-SiO2 integrated circuit, and a path toward finer resolution and enhanced imaging capabilities is discussed.

High-sensitivity electronic Stark spectrometer featuring a laser-driven light source.

We report developmental details of a high-sensitivity Stark absorption spectrometer featuring a laser-driven light source. The light source exhibits intensity fluctuations of ∼0.3% over timescales ranging from 1 min to 12 h, minimal drift (≤0.1%/h), and very little 1/f noise at frequencies greater than 200 Hz, which are comparable to or better than an arc-driven light source. Additional features of the spectrometer include balanced detection with multiplex sampling, which yielded lower noise in A, and constant wavelength or wavenumber (energy) spectral bandpass modes. We achieve noise amplitudes of ∼7 × 10-4 and ∼6 × 10-6 in measurements of single A and ΔA spectra (with 92 data points) taking ∼7 and ∼19 min, respectively.

Metastable Brominated Nanodiamond Surface Enables Room Temperature and Catalysis-Free Amine Chemistry.

Bromination of high-pressure, high-temperature (HPHT) nanodiamond (ND) surfaces has not been explored and can open new avenues for increased chemical reactivity and diamond lattice covalent bond formation. The large bond dissociation energy of the diamond lattice-oxygen bond is a challenge that prevents new bonds from forming, and most researchers simply use oxygen-terminated NDs (alcohols and acids) as reactive species. In this work, we transformed a tertiary-alcohol-rich ND surface to an amine surface with ∼50% surface coverage and was limited by the initial rate of bromination. We observed that alkyl bromide moieties are highly labile on HPHT NDs and are metastable as previously found using density functional theory. The strong leaving group properties of the alkyl bromide intermediate were found to form diamond-nitrogen bonds at room temperature and without catalysts. This robust pathway to activate a chemically inert ND surface broadens the modalities for surface termination, and the unique surface properties of brominated and aminated NDs are impactful to researchers for chemically tuning diamond for quantum sensing or biolabeling applications.

Design of a 3000-Pixel Transition-Edge Sensor X-Ray Spectrometer for Microcircuit Tomography.

Feature sizes in integrated circuits have decreased substantially over time, and it has become increasingly difficult to three-dimensionally image these complex circuits after fabrication. This can be important for process development, defect analysis, and detection of unexpected structures in externally sourced chips, among other applications. Here, we report on a non-destructive, tabletop approach that addresses this imaging problem through x-ray tomography, which we uniquely realize with an instrument that combines a scanning electron microscope (SEM) with a transition-edge sensor (TES) x-ray spectrometer. Our approach uses the highly focused SEM electron beam to generate a small x-ray generation region in a carefully designed target layer that is placed over the sample being tested. With the high collection efficiency and resolving power of a TES spectrometer, we can isolate x-rays generated in the target from background and trace their paths through regions of interest in the sample layers, providing information about the various materials along the x-ray paths through their attenuation functions. We have recently demonstrated our approach using a 240 Mo/Cu bilayer TES prototype instrument on a simplified test sample containing features with sizes of ∼ 1 µm. Currently, we are designing and building a 3000 Mo/Au bilayer TES spectrometer upgrade, which is expected to improve the imaging speed by factor of up to 60 through a combination of increased detector number and detector speed.

Fluorescence and Metal-Binding Properties of the Highly Preorganized Tetradentate Ligand 2,2'-Bi-1,10-phenanthroline and Its Remarkable Affinity for Cadmium(II).

The metal-ion-complexing properties of the tetradentate ligand 2,2'-bi-1,10-phenanthroline (BIPHEN) in 50% CH3OH/H2O are reported for a variety of metal ions. BIPHEN (with two reinforcing benzo groups in the backbone) was compared to other tetrapyridyls, 2,9-di(pyrid-2-yl)-1,10-phenanthroline (DPP; with one benzo group) and 2,2':6',2″:6″,2‴- quaterpyridine (QPY; with no benzo groups), with levels of preorganization BIPHEN > DPP > QPY. Formation constants were determined by following the variation of the intense π → π* transitions in the absorbance spectra of BIPHEN in the presence of metal ion as a function of the pH. The log K1 values show that the increased level of preorganization produced by the two benzo groups, reinforcing the backbone of the BIPHEN ligand, leads to increased complex stability with large metal ions (an ionic radius greater than 0.9 Å) compared to the less preorganized tetrapyridines DPP and QPY. In particular, the large CdII ion [log K1(BIPHEN) = 12.7] shows unusual selectivity over the small ZnII ion [log K1(BIPHEN) = 7.78]. The order of levels of preorganization BIPHEN > DPP > QPY leads to enhanced selectivity for SmIII over GdIII with increased preorganization, which is of interest in relation to separating AmIII from GdIII in the treatment of radioactive waste. AmIII is very close in ionic radius to SmIII, so that the size-based selectivity produced by the enhanced preorganization of BIPHEN should translate into enhanced AmIII/GdIII selectivity. The chelation-enhanced fluorescence (CHEF) effect in BIPHEN complexes is discussed. The CHEF effect in the ZnII complex is somewhat smaller than that for CdII, which is discussed in terms of decreased overlap in the Zn-N bonds formed by the too small ZnII, leading to a partial photoinduced-electron-transfer quenching of fluorescence. The structure of the complex [Cd(BIPHEN)2](ClO4)2 is reported and shows that the Cd-N bonds are largely normal for the unusual 8-coordination observed, except that steric clashes between the terminal pyridyl groups of each of the BIPHEN ligands, and the rest of the orthogonal BIPHEN ligand, lead to some stretching of the outer Cd-N bonds.

Chemical control of competing electron transfer pathways in iron tetracyano-polypyridyl photosensitizers.

Photoinduced intramolecular electron transfer dynamics following metal-to-ligand charge-transfer (MLCT) excitation of [Fe(CN)4(2,2'-bipyridine)]2- (1), [Fe(CN)4(2,3-bis(2-pyridyl)pyrazine)]2- (2) and [Fe(CN)4(2,2'-bipyrimidine)]2- (3) were investigated in various solvents with static and time-resolved UV-Visible absorption spectroscopy and Fe 2p3d resonant inelastic X-ray scattering (RIXS). This series of polypyridyl ligands, combined with the strong solvatochromism of the complexes, enables the 1MLCT vertical energy to be varied from 1.64 eV to 2.64 eV and the 3MLCT lifetime to range from 180 fs to 67 ps. The 3MLCT lifetimes in 1 and 2 decrease exponentially as the MLCT energy increases, consistent with electron transfer to the lowest energy triplet metal-centred (3MC) excited state, as established by the Tanabe-Sugano analysis of the Fe 2p3d RIXS data. In contrast, the 3MLCT lifetime in 3 changes non-monotonically with MLCT energy, exhibiting a maximum. This qualitatively distinct behaviour results from a competing 3MLCT → ground state (GS) electron transfer pathway that exhibits energy gap law behaviour. The 3MLCT → GS pathway involves nuclear tunnelling for the high-frequency polypyridyl breathing mode (hν = 1530 cm-1), which is most displaced for complex 3, making this pathway significantly more efficient. Our study demonstrates that the excited state relaxation mechanism of Fe polypyridyl photosensitizers can be readily tuned by ligand and solvent environment. Furthermore, our study reveals that extending charge transfer lifetimes requires control of the relative energies of the 3MLCT and the 3MC states and suppression of the intramolecular distortion of the acceptor ligand in the 3MLCT excited state.

Soft X-ray spectroscopy with transition-edge sensors at Stanford Synchrotron Radiation Lightsource beamline 10-1.

We present results obtained with a new soft X-ray spectrometer based on transition-edge sensors (TESs) composed of Mo/Cu bilayers coupled to bismuth absorbers. This spectrometer simultaneously provides excellent energy resolution, high detection efficiency, and broadband spectral coverage. The new spectrometer is optimized for incident X-ray energies below 2 keV. Each pixel serves as both a highly sensitive calorimeter and an X-ray absorber with near unity quantum efficiency. We have commissioned this 240-pixel TES spectrometer at the Stanford Synchrotron Radiation Lightsource beamline 10-1 (BL 10-1) and used it to probe the local electronic structure of sample materials with unprecedented sensitivity in the soft X-ray regime. As mounted, the TES spectrometer has a maximum detection solid angle of 2 × 10-3 sr. The energy resolution of all pixels combined is 1.5 eV full width at half maximum at 500 eV. We describe the performance of the TES spectrometer in terms of its energy resolution and count-rate capability and demonstrate its utility as a high throughput detector for synchrotron-based X-ray spectroscopy. Results from initial X-ray emission spectroscopy and resonant inelastic X-ray scattering experiments obtained with the spectrometer are presented.

Vincristine and bortezomib use distinct upstream mechanisms to activate a common SARM1-dependent axon degeneration program.

Chemotherapy-induced peripheral neuropathy is one of the most prevalent dose-limiting toxicities of anticancer therapy. Development of effective therapies to prevent chemotherapy-induced neuropathies could be enabled by a mechanistic understanding of axonal breakdown following exposure to neuropathy-causing agents. Here, we reveal the molecular mechanisms underlying axon degeneration induced by 2 widely used chemotherapeutic agents with distinct mechanisms of action: vincristine and bortezomib. We showed previously that genetic deletion of SARM1 blocks vincristine-induced neuropathy and demonstrate here that it also prevents axon destruction following administration of bortezomib in vitro and in vivo. Using cultured neurons, we found that vincristine and bortezomib converge on a core axon degeneration program consisting of nicotinamide mononucleotide NMNAT2, SARM1, and loss of NAD+ but engage different upstream mechanisms that closely resemble Wallerian degeneration after vincristine and apoptosis after bortezomib. We could inhibit the final common axon destruction pathway by preserving axonal NAD+ levels or expressing a candidate gene therapeutic that inhibits SARM1 in vitro. We suggest that these approaches may lead to therapies for vincristine- and bortezomib-induced neuropathies and possibly other forms of peripheral neuropathy.

Surface-to-Bulk Redox Coupling through Thermally Driven Li Redistribution in Li- and Mn-Rich Layered Cathode Materials.

Li- and Mn-rich (LMR) layered cathode materials have demonstrated impressive capacity and specific energy density thanks to their intertwined redox centers including transition metal cations and oxygen anions. Although tremendous efforts have been devoted to the investigation of the electrochemically driven redox evolution in LMR cathode at ambient temperature, their behavior under a mildly elevated temperature (up to ∼100 °C), with or without electrochemical driving force, remains largely unexplored. Here we show a systematic study of the thermally driven surface-to-bulk redox coupling effect in charged Li1.2Ni0.15Co0.1Mn0.55O2. We for the first time observed a charge transfer between the bulk oxygen anions and the surface transition metal cations under ∼100 °C, which is attributed to the thermally driven redistribution of Li ions. This finding highlights the nonequilibrium state and dynamic nature of the LMR material at deeply delithiated state upon a mild temperature perturbation.

L-edge spectroscopy of dilute, radiation-sensitive systems using a transition-edge-sensor array.

We present X-ray absorption spectroscopy and resonant inelastic X-ray scattering (RIXS) measurements on the iron L-edge of 0.5 mM aqueous ferricyanide. These measurements demonstrate the ability of high-throughput transition-edge-sensor (TES) spectrometers to access the rich soft X-ray (100-2000 eV) spectroscopy regime for dilute and radiation-sensitive samples. Our low-concentration data are in agreement with high-concentration measurements recorded by grating spectrometers. These results show that soft-X-ray RIXS spectroscopy acquired by high-throughput TES spectrometers can be used to study the local electronic structure of dilute metal-centered complexes relevant to biology, chemistry, and catalysis. In particular, TES spectrometers have a unique ability to characterize frozen solutions of radiation- and temperature-sensitive samples.

Glycogen synthase from the parabasalian parasite Trichomonas vaginalis: An unusual member of the starch/glycogen synthase family.

Trichomonas vaginalis, a parasitic protist, is the causative agent of the common sexually-transmitted infection trichomoniasis. The organism has long been known to synthesize substantial glycogen as a storage polysaccharide, presumably mobilizing this compound during periods of carbohydrate limitation, such as might be encountered during transmission between hosts. However, little is known regarding the enzymes of glycogen metabolism in T. vaginalis. We had previously described the identification and characterization of two forms of glycogen phosphorylase in the organism. Here, we measure UDP-glucose-dependent glycogen synthase activity in cell-free extracts of T. vaginalis. We then demonstrate that the TVAG_258220 open reading frame encodes a glycosyltransferase that is presumably responsible for this synthetic activity. We show that expression of TVAG_258220 in a yeast strain lacking endogenous glycogen synthase activity is sufficient to restore glycogen accumulation. Furthermore, when TVAG_258220 is expressed in bacteria, the resulting recombinant protein has glycogen synthase activity in vitro, transferring glucose from either UDP-glucose or ADP-glucose to glycogen and using both substrates with similar affinity. This protein is also able to transfer glucose from UDP-glucose or ADP-glucose to maltose and longer oligomers of glucose but not to glucose itself. However, with these substrates, there is no evidence of processivity and sugar transfer is limited to between one and three glucose residues. Taken together with our earlier work on glycogen phosphorylase, we are now well positioned to define both how T. vaginalis synthesizes and utilizes glycogen, and how these processes are regulated.

Beating Darwin-Bragg losses in lab-based ultrafast x-ray experiments.

The use of low temperature thermal detectors for avoiding Darwin-Bragg losses in lab-based ultrafast experiments has begun. An outline of the background of this new development is offered, showing the relevant history and initiative taken by this work.

Ultrafast Time-Resolved X-ray Absorption Spectroscopy of Ferrioxalate Photolysis with a Laser Plasma X-ray Source and Microcalorimeter Array.

The detailed pathways of photoactivity on ultrafast time scales are a topic of contemporary interest. Using a tabletop apparatus based on a laser plasma X-ray source and an array of cryogenic microcalorimeter X-ray detectors, we measured a transient X-ray absorption spectrum during the ferrioxalate photoreduction reaction. With these high-efficiency detectors, we observe the Fe K edge move to lower energies and the amplitude of the extended X-ray absorption fine structure reduce, consistent with a photoreduction mechanism in which electron transfer precedes disassociation. These results are compared to previously published transient X-ray absorption measurements on the same reaction and found to be consistent with the results from Ogi et al. and inconsistent with the results of Chen et al. ( Ogi , Y. ; et al. Struct. Dyn. 2015 , 2 , 034901 ; Chen , J. ; Zhang , H. ; Tomov , I. V. ; Ding , X. ; Rentzepis , P. M. Chem. Phys. Lett. 2007 , 437 , 50 - 55 ). We provide quantitative limits on the Fe-O bond length change. Finally, we review potential improvements to our measurement technique, highlighting the future potential of tabletop X-ray science using microcalorimeter sensors.

Hyperglycemic hyperosmolar state associated with low-dose quetiapine treatment in a patient with bipolar disorder.

There is increasing concern about the development of diabetes mellitus and associated complications in patients administrating second-generation antipsychotics. Previous reports indicate that the risk of quetiapine, although relatively lower, is not negligible. We report a patient with bipolar disorder who, after treating with low-dose quetiapine, develops newly-onset diabetes and hyperglycemic hyperosmolar state. Clinical manifestations and managements of quetiapine-associated diabetes are addressed, and we recommend routine monitoring of serum glucose after initiating quetiapine treatment at any given dose.

Insensitivity of sub-Kelvin electron-phonon coupling to substrate properties.

We have examined the role of the substrate on electron-phonon coupling in normal-metal films of Mn-doped Al at temperatures below 1 K. Normal metal-insulator-superconductor junctions were used to measure the electron temperature in the films as a function of Joule heating power and phonon temperature. Theory suggests that the distribution of phonons available for interaction with electrons in metal films may depend on the acoustic properties of the substrate, namely, that the electron-phonon coupling constant Σ would be larger on the substrate with smaller sound speed. In contrast, our results indicate that within experimental error (typically ±10%), Σ is unchanged among the two acoustically distinct substrates used in our investigation.

Dynamics and spectroscopy of vibrational overtone excited glyoxylic acid and 2,2-dihydroxyacetic acid in the gas-phase.

The early time dynamics of vibrationally excited glyoxylic acid and of its monohydrate 2,2-dihydroxyacetic acid are investigated by theoretical and spectroscopic methods. A combination of "on-the-fly" dynamical simulations and cavity ring-down spectroscopy on the excited O-H stretching vibrational levels of these molecules observed that conformers that possess the correct structure and orientation react upon excitation of Deltaupsilon(OH)=4,5, while the structurally different but near isoenergetic conformers do not undergo unimolecular decay by the same direct and fast process. Experiment and theory give a femtosecond time scale for hydrogen atom chattering in the vibrationally excited glyoxylic acid. This process is the precursor for the concerted decarboxylation of the ketoacid. We extrapolate the results obtained here to suggest a rapid subpicosecond overall reaction. In these light-initiated reactions, relatively cold hydroxycarbenes, stable against further unimolecular decay, are expected products since most of the excitation energy is consumed by the endothermicity of the reaction. Glyoxylic acid and its monohydrate are atmospherically relevant ketoacids. The vibrational overtone initiated reactions of glyoxylic acid leading to di- and monohydroxycarbenes on subpicosecond time scales are potentially of importance in atmospheric chemistry since the reaction is sufficiently rapid to avoid collisional dissipation.

Drought stress, plant water status, and floral trait expression in fireweed, Epilobium angustifolium (Onagraceae).

In a controlled environment, we artificially induced drought during flowering of Epilobium angustifolium, an animal-pollinated plant. Leaf water potential (ψ(l)) and floral traits were monitored over a 12-d period of soil moisture depletion. Soil moisture depletion induced drought stress over time, as revealed by significant treatment × day interactions for predawn and midday ψ(l). Nectar volume and flower size showed significant negative responses to drought stress, but nectar sugar concentration did not vary between treatments. Floral traits were more buffered from drought than leaf water potentials. We used path analysis to examine direct and indirect effects of ψ(l) on floral traits for plants in well-watered (control) vs. drought treatments. According to the best-fit path models, midday ψ(l) has significant positive effects on flower size and nectar volume in both environments. However, for controls midday ψ(l) also had a significant negative effect on nectar sugar concentration. Results indicate that traits influencing floral attractiveness to pollinators in E. angustifolium vary with plant water status, such that pollinator-mediated selection could indirectly target physiological or biochemical controls on ψ(l). Moreover, under mesic conditions selection for greater nectar sugar reward may be constrained by the antagonistic effects of plant water status on nectar volume and sugar concentration.

Down the tube: pollinators, predators, and the evolution of flower shape in the alpine skypilot, Polemonium viscosum.

We address how a conflict between pollinator attraction and avoidance of flower predation influences the evolution of flower shape in Polemonium viscosum. Flower shape in P. viscosum is the product of an isometric relationship between genetically correlated (rA = 0.70) corolla flare and length. Bumblebee pollinators preferentially visit flowers that are more flared and have longer tubes, selecting for a funnel-shaped corolla. However, flower shape also influences nectar-foraging ants that sever the style at its point of attachment to the ovary. Surveys of ant damage show that plants having flowers with flared, short corollas are most vulnerable to ant predation. Consistent with this result, the ratio of corolla length to flare is significantly greater in a krummholz (high predation risk) population than in a tundra (low predation risk) population. To explicitly test whether the evolution of a better defended flower would exact a cost in pollination, we created tubular flowers by constricting the corolla during development. Performance of tubular flowers and natural controls was compared for defensive and attractive functions. In choice trials, ants entered control flowers significantly more often than tubular ones, confirming that the evolution of tubular flowers would reduce the risk of predation. However, in a bumblebee-pollinated population, tubular flowers received significantly less pollen and set fewer seeds than controls. A fitness model incorporating these data predicts that in the absence of the genetic correlation between corolla length and flare, intermittent selection for defense could allow tubular flowers to spread in the krummholz population. However, in the tundra, where bumblebees account for nearly all pollination, the model predicts that tubular flowers should always confer a fitness disadvantage.

Life on the edge: adaptation versus environmentally mediated gene flow in the snow buttercup, Ranunculus adoneus.

We used experimental transplant studies to understand how dispersal and habitat-specific selection interact to influence plant populations occupying heterogeneous environments. The snow buttercup (Ranunculus adoneus) occupies a steep ecological and flowering time gradient caused by persistent snowmelt differences within its snow bed habitat. We transplanted seeds, seedlings, and adults to learn about the potential interactions between dispersal and selection. We found that adaptive differentiation is not occurring along the snowmelt gradient, despite striking differences in microhabitat conditions and reproductive phenology between early- and latemelting sites. Instead, our results imply that environmentally based differences in seed quality are contributing to directional gene flow from early-melting locations toward latemelting locations. Emergence and early survival of seedlings is greater in late-melting sites in some years, but the larger seeds produced by maternal plants in early-melting locations consistently have a fitness advantage in all parts of the snow bed. Larger seeds survive longer in the soil and have a second peak of seedling emergence in their third year, but these late-emerging seedlings are successful only if dispersed to less vegetated, late-melting destinations. The longer growing season in earlymelting sites enhances vegetative growth at all life-history stages and increases fecundity of seedling transplants but also limits the opportunity for establishment from seed. Our demographic analysis suggests that maternal environmental effects on propagule quality can lead to directional gene flow from benign to marginal sites in populations occupying heterogeneous habitats.