A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry.

Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) is a rapidly emerging tool for the investigation of nucleic acid structure and dynamics. IMS-MS determinations can provide valuable information regarding alternative topologies, folding intermediates, and conformational heterogeneities, which are not readily accessible to other analytical techniques. The leading strategies for data interpretation rely on computational and experimental approaches to correctly assign experimental observations to putative structures. A very effective strategy involves the application of molecular dynamics (MD) simulations to predict the structure of the analyte molecule, calculate its collision cross section (CCS), and then compare this computational value with the corresponding experimental data. While this approach works well for small nucleic acid species, analyzing larger nucleic acids of biological interest is hampered by the computational cost associated with capturing their extensive structure and dynamics in all-atom detail. In this report, we describe the implementation of a coarse graining (CG) approach to reduce the cost of the computational methods employed in the data interpretation workflow. Our framework employs a five-bead model to accurately represent each nucleotide in the nucleic acid structure. The beads are appropriately parameterized to enable the direct calculation of CCS values from CG models, thus affording the ability to pursue the analysis of larger, highly dynamic constructs. The validity of this approach was successfully confirmed by the excellent correlation between the CCS values obtained in parallel by all-atom and CG workflows.

A simple heated-capillary modification improves the analysis of non-covalent complexes by Z-spray electrospray ionization.

RATIONALE: The observation of intact non-covalent complexes by electrospray ionization mass spectrometry (ESI-MS) hinges on the ability to minimize in-source activation processes that take place during analyte desolvation. We explored the merits of replacing the sampling cone of a standard Z-spray source with a heated capillary that makes the desolvation process slower and more gradual. We employed well-characterized protein-RNA, RNA-RNA, and DNA-DNA assemblies to compare the alternative configurations. METHODS: Mass analysis evaluated the integrity of the complexes, whereas traveling wave ion mobility experiments assessed the stability of biomolecular structure. Analyses were performed back-to-back on the same samples on a Synapt G2 HDMS equipped with either the standard sampling cone or the heated-capillary apparatus. In each configuration, the source/capillary temperature was varied in controlled fashion, while keeping all other desolvation parameters constant to monitor the in-source dissociation of selected DNA duplexes. Ion mobility data were obtained from the same precursor by using the alternative configurations under the same settings. RESULTS: Monitoring the percentage of associated complex demonstrated that the heated capillary provided softer desolvation that was more conducive to the detection of intact non-covalent interactions. This configuration failed to produce complete dissociation of 14 bp and 24 bp duplexes, even when the source/capillary temperature was increased well above their solution melting points. Analyzed by IMS-MS, a selected construct displayed just one conformation with the heated capillary, but two with the standard sampling cone. CONCLUSIONS: The heated capillary minimizes in-source activation processes that can lead to unintended dissociation of complexes and perturbation of biomolecular structure, which rely on the integrity of non-covalent interactions. This effect can be attributed to the attenuation of the supersonic expansion typical of the Z-spray geometry and the greater ability to control the energy imparted to the system. This hardware modification will be expected to benefit the analysis of biomolecular structure performed on this particular instrumental platform.

Single-shot implementation of dispersion-scan for the characterization of ultrashort laser pulses.

We demonstrate a single-shot ultrafast diagnostic, based on the dispersion-scan (d-scan) technique. In this implementation, rather than translating wedges to vary the dispersion as in scanning d-scan, the pulse to be measured experiences a spatially varying amount of dispersion in a prism. The resulting beam is then imaged into a second-harmonic generation crystal and an imaging spectrometer is used to measure the two-dimensional trace, which is analyzed using the d-scan retrieval algorithm. We compare the single-shot implementation with the scanning d-scan for the measurement of sub-3.5-fs pulses from a hollow core fiber pulse compressor. We show that the retrieval algorithm used to extract amplitude and phase of the pulse provides comparable results, proving the validity of the new single-shot implementation in the near single-cycle regime.

Diffraction model for thermoreflectance data.

Thermoreflectance imaging provides the capability to map temperature spatially on the submicrometer scale by using a light source and CCD camera for data acquisition. The ability to achieve such spatial resolution and observe detailed features is influenced by optical diffraction. By combining diffraction from both the sample and substrate, a model is developed to determine the intensity of the thermoreflectance signal. This model takes into account the effective optical distance, sample width, wavelength, signal phase shift, and reflectance intensity, while showing qualitative and quantitative agreement with experimental thermoreflectance images from 1 and 10 µm wide gold lines at two wavelengths.

Clarifying the radiative decay of the Hoyle state with charged-particle spectroscopy.

A detailed knowledge of the decay properties of the so called Hoyle state in the 12 C nucleus ( E x = 7.654 MeV, 0 + ) is required to calculate the rate at which carbon is forged in typical red-giant stars. This paper reports on a new almost background-free measurement of the radiative decay branching ratio of the Hoyle state using advanced charged particle coincidence techniques. The exploitation, for the first time in a similar experiment, of a bidimensional map of the coincidence efficiency allows to reach an unitary value and, consequently, to strongly reduce sources of systematic uncertainties. The present results suggest a value of the radiative branching ratio of Γ rad / Γ tot = 4.4 ( 6 ) · 10 - 4 . This finding helps to resolve the tension between recent data published in the literature.

Laboratory tests of low density astrophysical nuclear equations of state.

Clustering in low density nuclear matter has been investigated using the NIMROD multidetector at Texas A&M University. Thermal coalescence modes were employed to extract densities, ρ, and temperatures, T, for evolving systems formed in collisions of 47A MeV (40)Ar+(112)Sn, (124)Sn and (64)Zn+(112)Sn, (124)Sn. The yields of d, t, (3)He, and (4)He have been determined at ρ=0.002 to 0.03 nucleons/fm(3) and T=5 to 11 MeV. The experimentally derived equilibrium constants for α particle production are compared with those predicted by a number of astrophysical equations of state. The data provide important new constraints on the model calculations.

Experimental determination of in-medium cluster binding energies and Mott points in nuclear matter.

In-medium binding energies and Mott points for d, t, 3He and α clusters in low-density nuclear matter have been determined at specific combinations of temperature and density in low-density nuclear matter produced in collisions of 47A MeV 40Ar and 64Zn projectiles with 112Sn and 124Sn target nuclei. The experimentally derived values of the in-medium modified binding energies are in good agreement with recent theoretical predictions based upon the implementation of Pauli blocking effects in a quantum statistical approach.

X-ray fluorescence from the element with atomic number Z=120.

An atomic clock based on x-ray fluorescence yields has been used to estimate the mean characteristic time for fusion followed by fission in reactions 238U + 64Ni at 6.6 MeV/A. Inner shell vacancies are created during the collisions in the electronic structure of the possibly formed Z=120 compound nuclei. The filling of these vacancies accompanied by a x-ray emission with energies characteristic of Z=120 can take place only if the atomic transitions occur before nuclear fission. Therefore, the x-ray yield characteristic of the united atom with 120 protons is strongly related to the fission time and to the vacancy lifetimes. K x rays from the element with Z=120 have been unambiguously identified from a coupled analysis of the involved nuclear reaction mechanisms and of the measured photon spectra. A minimum mean fission time τ(f)=2.5×10(-18) s has been deduced for Z=120 from the measured x-ray multiplicity.

Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions.

Non-ergodic as well as ergodic activation methods are capable of maintaining the integrity of base pairs during the top-down analysis of nucleic acids. Here, we investigate the significance of this characteristic in the investigation of higher-order structures of increasing complexity. We show that cognate fragments produced by typical backbone cleavages may not be always detected as separate sequence ions, but rather as individual products that remain associated through mutual pairing contacts. This effect translates into unintended masking of cleavage events that take place in double-stranded regions, thus leading to the preferential detection of fragments originating from unpaired regions. Such effect is determined by the stability of the weak non-covalent association between complementary stretches, which is affected by base composition, length of the double-stranded structure, and charge of the precursor ion selected for analysis. Although such effect may prevent the achievement of full sequence coverage for primary structure determination, it may provide the key to correctly differentiate double- versus single-stranded regions, in what could be defined as gas-phase footprinting experiments. In light of the critical role played by base pairs in defining the higher-order structure of nucleic acids, these approaches will be expected to support an increased utilization of mass spectrometry for the investigation of nucleic acid structure and dynamics.

MS analysis of nucleic acids in the post-genomic era.

Alternative approaches complementing the existing technologies for analysis of nucleic acids and their assemblies are necessary to take on the new challenges posed by the postgenomic era. The versatility of MS in biopolymer analysis and its ability to reach beyond sequence information are the basis of ever expanding applications aimed at the elucidation of nucleic acid structure-function relationships. This Feature summarizes the current state of MS-based approaches devised to overcome the limitations of traditional techniques and to advance different facets of nucleic acids research.

Optical properties and pulse shape discrimination in siloxane-based scintillation detectors.

The possibility to detect fast neutrons as a distinct signal from that one of γ-rays background is surely of great importance for several topics, spanning from homeland security to radiation monitoring in nuclear physics research plants. Nowadays, Helium-3 based detectors are extremely expensive, while the use of large volume liquid scintillators presents serious concerns related to spillage risks and waste disposal. A very attractive alternative is the use of commercially available solid scintillators, which exploits an aromatic polymer matrix entrapping very high loadings of primary dye, thereby enabling the use of pulse shape analysis (PSA) to discriminate between fast neutrons and γ-rays. In this work, we analyse in detail the optical features of a solid scintillator composed by polymethylphenylsiloxane (PMPS) as base polymer loaded with moderate amounts of 2,5-diphenyloxazole (PPO). Furthermore, fluorescence decay kinetics have been correlated to the observed pulse shape discrimination capabilities of this radiation and thermally resistant scintillator, whose performances have been discussed in terms of conformational features and excimers formation revealed by the optical analyses.

Monitoring metal ion flux in reactions of metallothionein and drug-modified metallothionein by electrospray mass spectrometry.

The capabilities of electrospray ionization mass spectrometry are demonstrated for monitoring the flux of metal ions out of and into the metalloprotein rabbit liver metallothionein and, in one example, chlorambucil-alkylated metallothionein. Metal ion transfers may be followed as the reactions proceed in situ to provide kinetic information. More uniquely to this technique, metal ion stoichiometries may be determined for reaction intermediates and products. Partners used in these studies include EDTA, carbonic anhydrase, a zinc-bound hexamer of insulin, and the core domain of bacteriophage T4 gene 32 protein, a binding protein for single-stranded DNA.

High-energy collision-induced dissociation of multiply charged polypeptides produced by electrospray.

The recent commercial implementation of an electrospray source on a four-sector mass spectrometer has allowed the study of high-energy collisional activation of multiply charged cations. With this configuration, higher mass-to-charge ratios can be accommodated in both precursor ion selection and fragment ion detection. Good mass accuracy facilitates analysis of fragment ions and allows more reliable mechanistic correlation of these fragments. A convenient scheme was devised to permit the use of kilovolt potentials in both MS-I and MS-II, with precursors of varying charge states. Algorithms were devised to assign masses of different types of multiply charged fragment ions. Nine polypeptides were studied in the mass range 2000-5000 Da. Through this entire mass range, fragment ions were observed to be amply formed by cleavages in both the backbone and side chains, analogous to high-energy collisional activation of singly charged ions. This stands in sharp contrast to the patterns reported with low-energy, multiple collisions. Abundances of sequence ion series are influenced by the positions of basic residues. Analysis of charge distributions in fragment ions also indicates that the charges tend to be spread out across the peptides.

Investigation of Zinc Chelation in Zinc-Finger Arrays by Electrospray Mass Spectrometry.

The chelation of zinc by consensus zinc-finger arrays of the CCCC, CCHC, and CCHH type has been investigated by electrospray ionization mass spectrometry. Accurate mass measurements of the most abundant isotopic species have demonstrated that two protons are lost for each Zn(II) ion chelated. Methylation of zinc-finger peptides has revealed that two thiolate anions from cysteine side-chains are necessary to maintain chelation. The other cysteine(s) retain the thiol proton(s) and can be methylated without loss of chelating ability.

Surgical treatment of severe L5-S1 spondylolisthesis in children and adolescents. Results of intraoperative reduction, posterior interbody fusion, and segmental pedicle fixation.

STUDY DESIGN: A retrospective study was done in 12 teenagers with severe L5-S1 spondylolisthesis surgically treated with a single-stage posterior procedure for reduction, posterior interbody fusion, and segmental instrumentation. OBJECTIVE: To evaluate the effectiveness and reliability of intraoperative reduction and posterior interbody fusion in severe lumbosacral spondylolisthesis in children. SUMMARY OF BACKGROUND DATA: Twelve young patients (age, 13-18 years; mean = 16 +/- 1.5) with severe L5-S1 spondylolisthesis (slip, 59%-85%; mean = 70.4 +/- 8.8%) were available for follow-up evaluation (6-24 months after surgery). All presented with serious preoperative clinical signs (tight hamstrings, waddling gait, lumbosacral pain, radiated leg pain). METHODS: The patients underwent surgery using a single posterior surgical procedure. After removal of the loosened arch and complete discectomy, a temporary device placed bilaterally between L1 and the sacral wings was used to achieve reduction by distraction. This was followed by a posterior interbody strut graft and pedicle segmental fixation. No postoperative casting was used. Clinical examination was done, and radiographic measurements were taken after surgery and at follow-up evaluation. Patients were evaluated for fusion rate, stability of reduction, clinical outcome, and possible complications. RESULTS: All patients underwent solid fusion without loss of reduction. No intraoperative or postoperative complications were observed. Mean correction of the initial slipping was 79.5 +/- 7% of the initial deformity. No clinical signs were present at follow-up evaluation. CONCLUSIONS: Intraoperative distraction appears to be truly effective in reducing severe lumbosacral olyshtesis in children. Posterior interbody fusion (and eventual sacral dome osteotomy) successfully combines the goals of solid fusion with the requirements of root decompression. No neurologic problems were seen as a consequence of distraction. The solidity of the posterior segmental pedicle instrumentation combined with the anterior strut graft eliminate the need for postoperative casting.

Site-specific fluorescence labelling of RNA using bio-orthogonal reaction of trans-cyclooctene and tetrazine.

This communication describes a general approach for site-specific fluorescence labelling of RNA using a cytidine triphosphate (CTP) analogue derivatized with a trans-cyclooctene group. The analogue was efficiently incorporated into a model RNA strand using in vitro transcription. Bio-orthogonal reaction with fluorescein-labelled tetrazine was utilized to fluorescently tag the synthetic RNA strand.

A new facility for non-destructive assay using a 252Cf source.

A new laboratory facility for non-destructive analysis (NDA) using a time-tagged (252)Cf source is presented. The system is designed to analyze samples having maximum size of about 20 × 25 cm(2), the material recognition being obtained by measuring simultaneously total and energy dependent transmission of neutrons and gamma rays. The equipment technical characteristics and performances of the NDA system are presented, exploring also limits due to the sample thickness. Some recent applications in the field of cultural heritage are presented.

Possible effects of clustering structure in the competition between fast emission processes and compound nucleus decay / Posibles efectos de estructura de agrupamiento en la competencia entre los procesos de emisión rápida y desintegración del núcleo compuesto

Abstract The attention to nuclear clustering has been renewed due to the study of weakly bound nuclei at the drip lines. In particular, clustering structural properties in medium-mass systems have been studied by looking at the competition between the evaporation and pre-equilibrium particle emission in central collisions. Although for light nuclei at an excitation energy close to the particle separation value there are experimental evidence of such structure effects, this is still not the case for heavier systems since the determination of pre-formed clusters within nuclear matter is less obvious. Two systems, leading to the same 81Rb* compound nucleus, have been studied at the same beam velocity 16 AMeV: 16O + 65Cu and 19F + 62Ni. The experiment has been performed using the GARFIELD + RCo detection system installed at the Legnaro National Laboratories.Light charged particles energy distributions and multiplicities have been compared with different statistical and dynamical model calculations. From the first comparison between the two systems a difference in the fast α-decay channel has been evidenced, which can be related to the difference in the projectile structure. Recent data analysis results and comparisons with model calculations are presented in this contribution.

Resumen La atención a la agrupación nuclear se ha renovado debido al estudio de núcleos débilmente unidos en las líneas de goteo. En particular, se han estudiado las propiedades estructurales del agrupamiento en sistemas de masa media al observar la competencia entre la evaporación y la emisión de partículas de preequilibrio en colisiones centrales. Aunque para núcleos ligeros a una energía de excitación cercana al valor de separación de la partícula hay evidencia experimental de tales efectos de estructura, este no es el caso para sistemas más pesados ya que la determinación de agrupamientos preformados dentro de la materia nuclear es menos obvia. Se han estudiado dos sistemas, que conducen al mismo núcleo compuesto 81Rb *, a la misma velocidad de haz 16 AMeV: 16O + 65Cu y 19F + 62Ni. El experimento se ha realizado utilizando el sistema de detección GARFIELD + RCo instalado en los Laboratorios Nacionales Legnaro. Las distribuciones de energía y las multiplicidades de partículas de carga ligera se han comparado con diferentes cálculos de modelos estadísticos y dinámicos. Desde la primera comparación entre los dos sistemas, se ha evidenciado una diferencia en el canal de desintegración α rápida, que se puede relacionar con la diferencia en la estructura del proyectil. En esta contribución se presentan los resultados del análisis de datos recientes y las comparaciones con los cálculos del modelo.

Light output of EJ228 scintillation neutron detectors.

The light output of neutron detectors based on the plastic scintillator EJ228 is studied as a function of neutron energy using a time tagged (252)Cf source. Calibration of the light output scale is performed by fitting the experimental distribution of Compton scattering events of photons from a (22)Na source with a response function obtained by Gaussian smearing of the predicted line-shape. The light output curve as well as the pulse height resolution for the EJ228 scintillators is very close (within 5%) to those recently reported for NE213 type organic liquid scintillators.