Observation of Rabi dynamics with a short-wavelength free-electron laser.

Rabi oscillations are periodic modulations of populations in two-level systems interacting with a time-varying field1. They are ubiquitous in physics with applications in different areas such as photonics2, nano-electronics3, electron microscopy4 and quantum information5. While the theory developed by Rabi was intended for fermions in gyrating magnetic fields, Autler and Townes realized that it could also be used to describe coherent light-matter interactions within the rotating-wave approximation6. Although intense nanometre-wavelength light sources have been available for more than a decade7-9, Rabi dynamics at such short wavelengths has not been directly observed. Here we show that femtosecond extreme-ultraviolet pulses from a seeded free-electron laser10 can drive Rabi dynamics between the ground state and an excited state in helium atoms. The measured photoelectron signal reveals an Autler-Townes doublet and an avoided crossing, phenomena that are both fundamental to coherent atom-field interactions11. Using an analytical model derived from perturbation theory on top of the Rabi model, we find that the ultrafast build-up of the doublet structure carries the signature of a quantum interference effect between resonant and non-resonant photoionization pathways. Given the recent availability of intense attosecond12 and few-femtosecond13 extreme-ultraviolet pulses, our results unfold opportunities to carry out ultrafast manipulation of coherent processes at short wavelengths using free-electron lasers.

Enthralling Anodic Protection by Molybdate on High-Entropy Alloy-Based Electrocatalyst for Sustainable Seawater Oxidation.

Efficient and sustainable seawater electrolysis is still limited due to the interference of chloride corrosion at the anode. The designing of suitable electrocatalysts is one of the crucial ways to boost electrocatalytic activity. However, the approach may fall short as achieving high current density often occurs in chlorine evolution reaction (CER)-dominating potential regions. Thereby, apart from developing an OER-active high-entropy alloy-based electrocatalyst, the present study also offers a unique way to protect anode surface under high current density or potential by using MoO4 2- as an effective inhibitor during seawater oxidation. The wide variation of d-band center of high-entropy alloy-based electrocatalyst allows great oxygen evolution reaction (OER) proficiency exhibiting an overpotential of 230 mV at current density of 20 mA cm-2. Besides, the electrocatalyst demonstrates impressive stability over 500 h at high current density of 1 A cm-2 or at a high oxidation potential of 2.0 V versus RHE in the presence of a molybdate inhibitor. Theoretical and experimental studies reveal MoO4 2- electrostatically accumulated at anode surface due to higher adsorption ability, thereby creating a protective layer against chlorides without affecting OER.

Dissociation and Isomerization Following Ionization of Ethylene: Insights from Nonadiabatic Dynamics Simulations.

Photoionized and electronically excited ethylene C2H4+ can undergo H-loss, H2-loss, and ethylene-ethylidene isomerization, where the latter entails a hydrogen migration. Recent pioneering experiments with few-femtosecond extreme ultraviolet pulses and complementary theoretical studies have shed light on the photodynamics of this prototypical organic cation. However, no theoretical investigation based on dynamics simulations reported to date has described the mechanisms and time scales of dissociation and isomerization. Herein, we simulate the coupled electron-nuclear dynamics of ethylene following vertical ionization and electronic excitation to its four lowest-lying cationic states. The electronic structure is treated at the CASSCF level, with an active space large enough to describe bond breaking and formation. The simulations indicate that dissociation and isomerization take place mainly on the cationic ground state and allow the probing of previous hypotheses concerning the correlation between the photochemical outcome and the traversed conical intersections. The results, moreover, support the long-standing view that H2-loss may occur from the ethylidene form. However, the ethylene-ethylidene isomerization time predicted by the simulations is considerably longer than those previously inferred from indirect experimental measurements.

Probing Photoionization Dynamics in Acetylene with Angle-Resolved Attosecond Interferometry.

Photoionization of acetylene by extreme ultraviolet light results in a stand-alone contribution from the outermost valence orbital, followed by well-separated photoelectron bands from deeper molecular orbitals. This makes acetylene an ideal candidate for probing the photoionization dynamics in polyatomic molecules free from the spectral congestion often arising after interaction with an attosecond pulse train. Here, using an angle-resolved attosecond interferometric technique, we extract the photoionization time delays for the outermost valence orbital in acetylene relative to an atomic target, namely argon. Compared to argon, the photoemission from the acetylene molecule is found to be advanced by almost 28 attoseconds. The strong variation of the relative photoionization time delays as a function of the photoemission angle was interpreted using an analytical model based on semiclassical approximations to be the interplay between different short-range potentials along and perpendicular to the molecular axis. Our results highlight the importance of using attosecond time-resolved measurements to probe the nonspherical nature of the molecular potential, even in the case of relatively small, linear systems.

Controlling photoionization using attosecond time-slit interferences.

When small quantum systems, atoms or molecules, absorb a high-energy photon, electrons are emitted with a well-defined energy and a highly symmetric angular distribution, ruled by energy quantization and parity conservation. These rules are based on approximations and symmetries which may break down when atoms are exposed to ultrashort and intense optical pulses. This raises the question of their universality for the simplest case of the photoelectric effect. Here we investigate photoionization of helium by a sequence of attosecond pulses in the presence of a weak infrared laser field. We continuously control the energy of the photoelectrons and introduce an asymmetry in their emission direction, at variance with the idealized rules mentioned above. This control, made possible by the extreme temporal confinement of the light-matter interaction, opens a road in attosecond science, namely, the manipulation of ultrafast processes with a tailored sequence of attosecond pulses.

Few-Femtosecond Isotope Effect in Polyatomic Molecules Ionized by Extreme Ultraviolet Attosecond Pulse Trains.

Following ionization by an extreme ultraviolet (XUV) attosecond pulse train, a polyatomic molecule can be promoted to more-than-one excited states of the residual ion. The ensuing relaxation dynamics is often facilitated by several reaction coordinates, making them difficult to disentangle by the usual spectroscopic means. Here, we show that in atto-chemistry isotope labeling can be an efficient tool for unraveling the relaxation pathways in highly excited photoionized molecules. Employing an XUV pump pulse and a near-infrared probe pulse, we found the nuclear as well as coupled electron-nuclear dynamics in ethylene to be almost 40% faster compared to that of its deuterated counterpart. The findings, which are supported by advanced nonadiabatic dynamics calculations, led to the identification of the relevant nuclear coordinates controlling the relaxation. Our experiment highlights the relevance of ultrashort XUV pulses to capture the isotopic effect in few-femtosecond molecular photodynamics.

CRISPR-Cas9 a boon or bane: the bumpy road ahead to cancer therapeutics.

Genome editing allows for the precise manipulation of DNA sequences in a cell making this technology essential for understanding gene function. CRISPR/Cas9 is a targeted genome-editing platform derived from bacterial adaptive immune system and has been repurposed into a genome-editing tool. The RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, making this technology easier, more efficient, scalable and an indispensable tool in biological research. This technology has helped genetically engineer animal models to understand disease mechanisms and elucidate molecular details that can be exploited for improved therapeutic outcomes. In this review, we describe the CRISPR-Cas9 gene-editing mechanism, CRISPR-screening methods, therapeutic targeting of CRISPR in animal models and in cancer immunotherapy. We also discuss the ongoing clinical trials using this tool, limitations of this tool that might impede the clinical applicability of CRISPR-Cas9 and future directions for developing effective CRISPR-Cas9 delivery systems that may improve cancer therapeutics.

Fano's Propensity Rule in Angle-Resolved Attosecond Pump-Probe Photoionization.

In a seminal article, Fano predicts that absorption of light occurs preferably with increase of angular momentum. We generalize Fano's propensity rule to laser-assisted photoionization, consisting of absorption of an extreme-ultraviolet photon followed by absorption or emission of an infrared photon. The predicted asymmetry between absorption and emission leads to incomplete quantum interference in attosecond photoelectron interferometry. It explains both the angular dependence of the photoionization time delays and the delay dependence of the photoelectron angular distributions. Our theory is verified by experimental results in Ar in the 20-40 eV range.

Multi-slit-type interference in carbon 2s photoionization of polyatomic molecules: from a fundamental effect to structural parameters.

In molecular photoemission, the analogue of the celebrated Young's double slit experiment is coherent electron emission from two equivalent atomic centers, giving rise to an interference pattern. Here multi-slit interference is investigated in inner-valence photoionization of propane, n-butane, isobutane and methyl peroxide. A more complex pattern is observed due to molecular orbital delocalization in polyatomic molecules, blurring the distinction between interference and diffraction. The potential to extract geometrical information is emphasized, as a more powerful extension of the EXAFS technique. Accurate reproduction of experimental features is obtained by simulations at the static Density Functional Theory level.

A theoretical and experimental benchmark study of core-excited states in nitrogen.

The high resolution near edge X-ray absorption fine structure spectrum of nitrogen displays the vibrational structure of the core-excited states. This makes nitrogen well suited for assessing the accuracy of different electronic structure methods for core excitations. We report high resolution experimental measurements performed at the SOLEIL synchrotron facility. These are compared with theoretical spectra calculated using coupled cluster theory and algebraic diagrammatic construction theory. The coupled cluster singles and doubles with perturbative triples model known as CC3 is shown to accurately reproduce the experimental excitation energies as well as the spacing of the vibrational transitions. The computational results are also shown to be systematically improved within the coupled cluster hierarchy, with the coupled cluster singles, doubles, triples, and quadruples method faithfully reproducing the experimental vibrational structure.

Auger electron angular distributions following excitation or ionization of the I 3d level in methyl iodide.

Auger electron spectra following excitation or ionization of the I 3d level in CH3I have been recorded with horizontally or vertically plane polarized synchrotron radiation. These spectra have enabled the Auger electron angular distributions, as characterized by the ß parameter, to be determined. The I 3d photoionization partial cross section of CH3I has been calculated with the continuum multiple scattering approach, and the results show that in the photon energy range over which Auger spectra were measured, the I 3d cross section exhibits an atomic-like behavior and is dominated by transitions into the εf continuum channel. In this limit, the theoretical value of the alignment parameter (A20) characterizing the core ionized state in an atom becomes constant, independent of photon energy. This theoretical value has been used to obtain the Auger electron intrinsic anisotropy parameters (α2) from the ß parameters extracted from our normal (non-resonant) molecular Auger spectra. The resulting anisotropy parameters for the M45N45N45 transitions in CH3I have been compared to those calculated for the corresponding transitions in xenon, and the experimental and theoretical results are in good agreement. Anisotropy parameters have also been measured for the M45N1N45, M45N23N45, and M45N45O23 transitions. For the M45N1N45 and M45N23N45 Auger decays in CH3I, the experimentally derived angular distributions do not exhibit the strong dependence on the final ionic state that is predicted for these transitions in xenon. Resonantly excited Auger spectra have been recorded at 620.4 and 632.0 eV, coinciding with the I 3d5/2 → σ* and 3d3/2 → σ* transitions, respectively. The resulting Auger electron angular distributions for the M4N45N45 and M5N45N45 decays were found to exhibit a higher anisotropy than those for the normal process. This is due to the larger photo-induced alignment in the neutral core excited state. For a particular Auger transition, the Auger electron kinetic energy measured in the resonantly excited spectrum is higher than that in the normal spectrum. This shift, due to the screening provided by the electron excited into the σ* orbital, has been rationalized by calculating orbital ionization energies of I 3d excited and I 3d ionized states in CH3I.

Photoionization of the iodine 3d, 4s, and 4p orbitals in methyl iodide.

Ionization of the I 3d, 4s, and 4p orbitals in methyl iodide (CH3I) has been studied by using synchrotron radiation to measure the total ion yield and by recording photoelectron spectra with linearly polarized radiation in two polarization orientations. The complete photoelectron spectrum of CH3I has been recorded at several photon energies, and bands due to the C 1s, I 3d, 4s, 4p, and 4d atomic-like orbitals, as well as the molecular orbitals, have been observed and assigned. In the vicinity of the I 3d5/2 and 3d3/2 ionization thresholds at 626.8 and 638.3 eV, respectively, the ion yield displays weak structure in the pre-edge region due to transitions into valence or Rydberg states, and, at higher energies, a shoulder and a broad maximum attributed to the I 3d5/2 → εf and the I 3d3/2 → εf shape resonances, respectively. The absorption spectrum calculated using time-dependent density functional theory, within the Tamm-Dancoff approximation, has allowed assignments to be proposed for the valence and Rydberg states. The Stieltjes imaging technique has been used to simulate the absorption spectrum above the ionization threshold and indicates that transitions into the f(l = 3) continuum channel dominate. This conclusion has been corroborated by a Continuum Multiple Scattering-Xα (CMS-Xα) calculation. The asymmetric broadening of the photoelectron bands associated with the I 3d orbital, due to post collision interaction, is taken into account in our experimental analysis. Experimentally derived photoelectron anisotropy parameters for the I 3d orbital are in good agreement with the theoretical predictions obtained with the CMS-Xα approach. The I 3d shake-up/shake-off photoelectron spectrum has been recorded, and assignments have been proposed for several of the satellites. The M4N45N45 and M5N45N45 Auger electron yields have been measured, and that for the M5N45N45 decay exhibits a maximum due to interchannel coupling between the 3d5/2 and 3d3/2 continua. The photoelectron band associated with the I 4p orbital has an unusual appearance. Based upon previous theoretical work for the analogous Xe 4p orbital, it appears that the initial I 4p-1 hole state decays rapidly through Coster-Kronig and super-Coster-Kronig transitions. This leads to a redistribution of the spectral intensity associated with the I 4p orbital and results in a photoelectron spectrum containing a single structured band together with an extended continuum. Another continuum is observed on the high binding energy side of the peak due to the 4s orbital, and we assign this to super-Coster-Kronig transitions into the 4p-14d-1 continuum.

Synthetic lethality in DNA repair network: A novel avenue in targeted cancer therapy and combination therapeutics.

Synthetic lethality refers to a lethal phenotype that results from the simultaneous disruptions of two genes, while the disruption of either gene alone is viable. Many DNA double strand break repair (DSBR) genes have synthetic lethal relationships with oncogenes and tumor suppressor genes, which can be exploited for targeted cancer therapy, an approach referred to as combination therapy. DNA double-strand breaks (DSBs) are one of the most toxic lesions to a cell and can be repaired by non-homologous end joining (NHEJ) or homologous recombination (HR). HR and NHEJ genes are particularly attractive targets for cancer therapy because these genes have altered expression patterns in cancer cells when compared with normal cells and these genetic abnormalities can be targeted for selectively killing cancer cells. Here, we review recent advances in the development of small molecule inhibitors against HR and NHEJ genes to induce synthetic lethality and address the future directions and clinical relevance of this approach. © 2017 IUBMB Life, 69(12):929-937, 2017.

DNA damage response and cancer therapeutics through the lens of the Fanconi Anemia DNA repair pathway.

Fanconi Anemia (FA) is a rare, inherited genomic instability disorder, caused by mutations in genes involved in the repair of interstrand DNA crosslinks (ICLs). The FA signaling network contains a unique nuclear protein complex that mediates the monoubiquitylation of the FANCD2 and FANCI heterodimer, and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. FA proteins act at different steps of ICL repair in sensing, recognition and processing of DNA lesions. The multi-protein network is tightly regulated by complex mechanisms, such as ubiquitination, phosphorylation, and degradation signals that are critical for the maintenance of genome integrity and suppressing tumorigenesis. Here, we discuss recent advances in our understanding of how the FA proteins participate in ICL repair and regulation of the FA signaling network that assures the safeguard of the genome. We further discuss the potential application of designing small molecule inhibitors that inhibit the FA pathway and are synthetic lethal with DNA repair enzymes that can be used for cancer therapeutics.

Photoelectron diffraction in methane probed via vibrationally resolved inner-valence photoionization cross-section ratios.

Vibrationally resolved photoionization of the 2a1 orbital in methane has been studied both experimentally and theoretically, over a wide range of photon energies (40-475 eV). A vibrational progression associated with the symmetric stretch mode of the 2a1(-1) single-hole state was observed in the experimental photoelectron spectra. Individual vibrational sub-states of the spectra were found to be best modeled by asymmetric line-shapes with linewidths gradually increasing with the vibrational quantum number. This indicates the occurrence of a pre-dissociation process for the involved ionic state, discussed here in detail. Finally, diffraction patterns were observed in the vibrational branching ratios for the first three vibrational sub-states ("v-ratios") of the experimental photoelectron spectra. They are found to be in excellent qualitative agreement with those obtained from ab initio models. Compared with previous studies of the 1a1(-1) core-shell photoionization of methane, the period of oscillation of the v-ratios is found to be very different and the phases are of opposite signs. This suggests a strong interplay between the electron diffraction and interference effects inside the molecular potential.

The FANCM ortholog Fml1 promotes recombination at stalled replication forks and limits crossing over during DNA double-strand break repair.

The Fanconi anemia (FA) core complex promotes the tolerance/repair of DNA damage at stalled replication forks by catalyzing the monoubiquitination of FANCD2 and FANCI. Intriguingly, the core complex component FANCM also catalyzes branch migration of model Holliday junctions and replication forks in vitro. Here we have characterized the ortholog of FANCM in fission yeast Fml1 in order to understand the physiological significance of this activity. We show that Fml1 has at least two roles in homologous recombination-it promotes Rad51-dependent gene conversion at stalled/blocked replication forks and limits crossing over during mitotic double-strand break repair. In vitro Fml1 catalyzes both replication fork reversal and D loop disruption, indicating possible mechanisms by which it can fulfill its pro- and antirecombinogenic roles.

The ATPase activity of Fml1 is essential for its roles in homologous recombination and DNA repair.

In fission yeast, the DNA helicase Fml1, which is an orthologue of human FANCM, is a key component of the machinery that drives and governs homologous recombination (HR). During the repair of DNA double-strand breaks by HR, it limits the occurrence of potentially deleterious crossover recombinants, whereas at stalled replication forks, it promotes HR to aid their recovery. Here, we have mutated conserved residues in Fml1's Walker A (K99R) and Walker B (D196N) motifs to determine whether its activities are dependent on its ability to hydrolyse ATP. Both Fml1(K99R) and Fml1(D196N) are proficient for DNA binding but totally deficient in DNA unwinding and ATP hydrolysis. In vivo both mutants exhibit a similar reduction in recombination at blocked replication forks as a fml1Δ mutant indicating that Fml1's motor activity, fuelled by ATP hydrolysis, is essential for its pro-recombinogenic role. Intriguingly, both fml1(K99R) and fml1(D196N) mutants exhibit greater sensitivity to genotoxins and higher levels of crossing over during DSB repair than a fml1Δ strain. These data suggest that without its motor activity, the binding of Fml1 to its DNA substrate can impede alternative mechanisms of repair and crossover avoidance.

Generation of entanglement using a short-wavelength seeded free-electron laser.

Quantum entanglement between the degrees of freedom encountered in the classical world is challenging to observe due to the surrounding environment. To elucidate this issue, we investigate the entanglement generated over ultrafast timescales in a bipartite quantum system comprising two massive particles: a free-moving photoelectron, which expands to a mesoscopic length scale, and a light-dressed atomic ion, which represents a hybrid state of light and matter. Although the photoelectron spectra are measured classically, the entanglement allows us to reveal information about the dressed-state dynamics of the ion and the femtosecond extreme ultraviolet pulses delivered by a seeded free-electron laser. The observed generation of entanglement is interpreted using the time-dependent von Neumann entropy. Our results unveil the potential for using short-wavelength coherent light pulses from free-electron lasers to generate entangled photoelectron and ion systems for studying spooky action at a distance.

Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine.

Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.

Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer.

Development requires the careful orchestration of several biological events in order to create any structure and, eventually, to build an entire organism. On the other hand, the fate transformation of terminally differentiated cells is a consequence of erroneous development, and ultimately leads to cancer. In this review, we elaborate how development and cancer share several biological processes, including molecular controls. Transcription factors (TF) are at the helm of both these processes, among many others, and are evolutionarily conserved, ranging from yeast to humans. Here, we discuss four families of TFs that play a pivotal role and have been studied extensively in both embryonic development and cancer-high mobility group box (HMG), GATA, paired box (PAX) and basic helix-loop-helix (bHLH) in the context of their role in development, cancer, and their conservation across several species. Finally, we review TFs as possible therapeutic targets for cancer and reflect on the importance of natural resistance against cancer in certain organisms, yielding knowledge regarding TF function and cancer biology.