Anomalous Fragment Research Articles

Alpha-Thalassemia in Southern Italy: Characterization of Five New Deletions Removing the Alpha-Globin Gene Cluster.

α-thalassemia is characterized in about 80% of cases by deletions generated by the presence of duplications and interspersed repeated sequences in the α-globin gene cluster. In a project on the molecular basis of α-thalassemia in Southern Italy, we identified six families, showing an absence of the most common deletions, and normal α-globin gene sequences. Multiplex Ligation-dependent Probe Amplification (MLPA), qRT-PCR, and the sequencing of long-range PCR amplicon have been used for the identification and characterization of new deletions. MLPA analysis for the identification of α- and β-globin rearrangement revealed the presence of five new α-thalassemia deletions. The set-up of qRT-PCR allowed us to delimit the extent of the deletions ranging from about 10 kb to more than 250 kb, two of them being of the telomeric type. The long-range PCR generated a specific anomalous fragment in three deletions, and only several unspecific bands in the other two deletions. The sequencing of the anomalous amplicons revealed the breakpoints of two deletions: the --PA, 34 kb long, identified in two families, and the telomeric --AG, 274 kb long. The anomalous fragment containing the breakpoint of the deletion --FG was partially sequenced, and it was not possible to identify the breakpoints due to the presence of several repetitive Alu sequences. The analysis of the breakpoint regions of the --Sciacca and --Puglia, respectively, are about 10 and 165 kb long, and revealed the presence of repeats that most likely impaired the amplification of a specific fragment for the identification of the breakpoint. MLPA, in association with qRT-PCR and long-range PCR, is a good approach for the identification and molecular characterization of rare or new deletions. Breakpoint analysis confirms that Alu sequences play an important role in favoring unequal crossing-over. Southern Italy shows considerable genetic heterogeneity, as expected with its central position in the Mediterranean basin, favoring migratory flows.

Nanoparticle Fragmentation Below the Melting Point Under Single Picosecond Laser Pulse Stimulation.

Understanding the laser-nanomaterials interaction including nanomaterial fragmentation has important implications in nanoparticle manufacturing, energy, and biomedical sciences. So far, three mechanisms of laser-induced fragmentation have been recognized including non-thermal processes and thermomechanical force under femtosecond pulses, and the phase transitions under nanosecond pulses. Here we show that single picosecond (ps) laser pulse stimulation leads to anomalous fragmentation of gold nanoparticles that deviates from these three mechanisms. The ps laser fragmentation was weakly dependent on particle size, and it resulted in a bimodal size distribution. Importantly, ps laser stimulation fragmented particles below the whole particle melting point and below the threshold for non-thermal mechanism. We propose a framework based on near-field enhancement and nanoparticle surface melting to account for the ps laser-induced fragmentation observed here. This study reveals a new form of surface ablation that occurs under picosecond laser stimulation at low fluence.

Linkage Memory in Underivatized Protonated Carbohydrates.

Carbohydrates are among the most complex class of biomolecules, and even subtle variations in their structures are attributed to diverse biological functions. Mass spectrometry has been essential for large scale glycomics and glycoproteomics studies, but the gas-phase structures and sometimes anomalous fragmentation properties of carbohydrates present long-standing challenges. Here we investigate the gas-phase properties of a panel of isomeric protonated disaccharides differing in their linkage configurations. Multiple conformations were evident for most of the structures based on their fragment ion abundances by tandem mass spectrometry, their ion mobilities in several gases, and their deuterium uptake kinetics by gas-phase hydrogen-deuterium exchange. Most notably, we find that the properties of the Y-ion fragments are characteristically influenced by the precursor carbohydrate's linkage configuration. This study reveals how protonated carbohydrate fragment ions can retain "linkage memory" that provides structural insight into their intact precursor.

The Anomalous Fragmentation of Water Clusters at Ultrafast Impacts: An experimental and Theoretical Study

Abstract Experimental results for the hypersonic impact of singly charged, mass selected, water clusters at a hard surface demonstrate cooling of the heated cluster by sequential loss of a water molecule. The trends in the experiment are most simply summarized as an evaporation. This behavior is in contrast to the shattering phenomena observed for rare gas clusters. The same information theoretic approach that predicted the shattering transition is fully consistent with the results for the water clusters. It shows that the relatively high binding energy per water monomer is the key reason for the anomalous fragmentation. The tetra coordinated oxygen atom in a cluster does however imply that the fragmentation is not a pure evaporation but has residual elements of a shattering transition. For water clusters the transition is broadened to span the finite range in energy between the onset of boiling and the energy when the solvation of the hydronium ion is over and it is bare.

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

The gas-phase peptide ion fragmentation chemistry is always the center of attraction in proteomics to analyze the amino acid sequence of peptides and proteins. In this work, we describe the formation of an anomalous fragment ion, which corresponds to the selective deletion of the internal lysine residue from a series of lysine containing peptides upon collisional activation in the ion trap. We detected several water-loss fragment ions and the maximum number of water molecules lost from a particular fragment ion was equal to the number of lysine residues in that fragment. As a consequence of this water-loss phenomenon, internal lysine residues were found to be deleted from the peptide ion. The N,N-dimethylation of all the amine functional groups of the peptide stopped the internal lysine deletion reaction, but selective N-terminal α-amino acetylation had no effect on this process indicating involvement of the side chains of the lysine residues. The detailed mechanism of the lysine deletion was investigated by multistage CID of the modified and unmodified peptides, by isotope labeling and by energy resolved CID studies. The results suggest that the lysine deletion might occur through a unimolecular multistep mechanism involving a seven-membered cyclic imine intermediate formed by the loss of water from a lysine residue in the protonated peptide. This intermediate subsequently undergoes degradation reaction to deplete the interior imine ring from the peptide backbone leading to the deletion of an internal lysine residue.

Practical structure solution with ARCIMBOLDO

Since its release in September 2009, the structure-solution program ARCIMBOLDO, based on the combination of locating small model fragments such as polyalanine α-helices with density modification with the program SHELXE in a multisolution frame, has evolved to incorporate other sources of stereochemical or experimental information. Fragments that are more sophisticated than the ubiquitous main-chain α-helix can be proposed by modelling side chains onto the main chain or extracted from low-homology models, as locally their structure may be similar enough to the unknown one even if the conventional molecular-replacement approach has been unsuccessful. In such cases, the program may test a set of alternative models in parallel against a specified figure of merit and proceed with the selected one(s). Experimental information can be incorporated in three ways: searching within ARCIMBOLDO for an anomalous fragment against anomalous differences or MAD data or finding model fragments when an anomalous substructure has been determined with another program such as SHELXD or is subsequently located in the anomalous Fourier map calculated from the partial fragment phases. Both sources of information may be combined in the expansion process. In all these cases the key is to control the workflow to maximize the chances of success whilst avoiding the creation of an intractable number of parallel processes. A GUI has been implemented to aid the setup of suitable strategies within the various typical scenarios. In the present work, the practical application of ARCIMBOLDO within each of these scenarios is described through the distributed test cases.

Anomalous C-C bond cleavage in sulfur-centered cation radicals containing a vicinal hydroxy group.

1,3-dithianyl cation radicals having alpha-hydroxy-neopentyl or similar groups in position 2, which are generated via oxidative photoinduced electron transfer, undergo anomalous fragmentation necessitating refinement of the accepted mechanism. Experimental and computational data support a rationale in which proton abstraction from the hydroxy group in the initial cation radical does not cause a Grob-like fragmentation, but rather produces a neutral radical species, the alkoxy radical, that undergoes fragmentation in either direction, i.e., cleaving the C-C bond to dithiane or to the tertiary alkyl group.

The use of transient electric birefringence to characterize the conformation of DNA in solution, the mechanism of DNA gel electrophoresis, and the structure of agarose gels

Abstract Two small, 153 base-pair (bp) DNA restriction fragments, one of which migrates anomalously slowly during electrophoresis in polyacrylamide gels, have been characterized by transient electric birefringence (TEB). The decay of the birefringence of the anomalously slowly migrating fragment is faster than that of the normal fragment under a variety of buffer conditions, suggesting that the anomalous fragment is stably bent or curved in free solution. Reversing field experiments suggest that both the anomalous and normal DNA fragments orient in the electric field by a slow induced dipole mechanism. Birefringence relaxation times have also been measured for three DNA molecules embedded in agarose gels of various concentrations. The embedded DNA molecules become oriented in the electric field, just as in free solution. If the median pore diameter of the gel is approximately twice as large as the apparent end-to-end length of the DNA in solution, the relaxation times of the embedded DNA molecules are unaffected by the presence of the gel, indicating that the DNA retains its usual wormlike coil conformation in the gel matrix. However, as the end-to-end length of the DNA approaches the median pore diameter of the gel, the DNA molecules become stretched out and elongated in the electric field, leading to a repetitive, or end-on, mode of migration during electrophoresis. The relaxation times of the stretched DNA molecules scale as the 2.8 power of molecular weight, in reasonable agreement with reptation theories. The structure of agarose gels has also been characterized by TEB. The long, low voltage electric fields used for pulsed field gel electrophoresis (PFGE) cause extensive orientation of the agarose gel fibers. A wide range of relaxation times is observed after the field is removed, corresponding to the orientation of gel fibers up to 22 μm in length. The sign of the birefringence is variable, indicating that the gel fibers can be oriented in different directions in different parts of the gel. Surprisingly, the sign of the birefringence reverses upon field reversal, suggesting that the gel fibers change their direction of orientation in reversing electric fields. This anomalous orientation behavior is not observed for chemically crosslinked polyacrylamide gels. The apparent orientation and reorientation of agarose gel fibers in rapidly reversing electric fields may lead to ‘dynamic pores’ in the gel matrix, facilitating the migration of very large DNA molecules during PFGE.

Anomalous Fragmentation of Hydrated Clusters of DNA Base Adenine in UV Photoionization

A multiphoton ionization study was carried out on hydrated clusters of DNA base adenine in supersonic molecular beams. Resonant two-photon ionization at 266 nm showed that the relative ion intensity between the hydrated clusters Am(H2O)n and the unhydrated ones was anomalously small, particularly for m = 1, in contrast to the case of electron impact ionization. The ratio was of the order of 10-2 for m = 1, 10-1 for m = 2, but about 1 for m ≥ 3. One-photon excitation to the first electronically excited state was found to be responsible for the extensive fragmentation of adenine monomer hydrates A1(H2O)n. The water acts as a proton-donating solvent whose hydrogen bonding with the solute becomes weakened in the nπ* excited state, thereby giving the excited state its repulsive nature. Hydrates of adenine complex Am(H2O)n (m ≥ 2) tend to better survive the rupture of the water cage at higher m, probably because the energy transfer between adenine molecules is not sufficiently fast. The fragmentation was found ...

On the dynamics of meteoroid streams

Zodiacal dust evolves from cometary debris through a stage called a meteoroid stream. Meteoroid streams produce meteor showers if a node of the stream is near 1 AU. On occasion, Earth encounters a stream of meteoroids that has not dispersed wide enough to be detected annually. A rare and often short lived enhancement of rates is observed during which the meteors typically have smaller radiant dispersion and sometimes anomalous fragmentation properties and end heights. Here, we summarize recent observations of these meteor outbursts and discuss how the results constrain our knowledge of the early stages of meteoroid stream formation. These stages tie meteoroid streams to cometary dust trails and are an important step in the dynamical evolution from cometary to zodiacal dust.

Investigation of fusionldistributions at near and sub-barrier energies through fission fragmentγray multiplicity measurements

Measurements of fission fragment gamma ray multiplicity distributions were carried out at near and sub-barrier energies in ${}^{12}$C, ${}^{16}$O + ${}^{232}$Th reactions. The results were analyzed to determine the average values of the total fragment spin, which were used to deduce the average spin of the compound nucleus $〈l{〉}_{\mathrm{CN}}.$ It is observed that $〈l{〉}_{\mathrm{CN}}$ decreases smoothly with decreasing bombarding energy and saturates as the energy falls through the barrier, thereby resembling features analogous to those predicted by various fusion models. The present results do not indicate any anomalous feature in the $〈l{〉}_{\mathrm{CN}\mathrm{}}$ at the sub-barrier energies, which imply that the recently observed anomalous fragment anisotropies in these systems are not due to anomalous broadening of fusion $l$ distributions but may result from the narrowing of $K$ distribution in the fission process.

Understanding the anomalous fragment anisotropies in heavyion induced fission in the dynamical trajectory model

Dynamical trajectory model has been used to calculate the fusion and non-fusion trajectories in 10B, 12C, 16O, 19F +232Th, 237Np reactions. It is seen that in some of the above systems, there exists an l-window (above fusion l-value) for which the trajectories are characterised by large mass exchange and energy relaxation (fission-like) before the system undergoes symmetric split, without formation of a shape equilibrated compound nucleus. These events would correspond to a small value of the variance of the K-distribution, thereby leading to large fragment angular anisotropies. The fission fragment angular distributions, calculated as an admixture of these two classes of events (fusion and non-fusion), are able to explain the anomalous angular anisotropies observed experimentally for some systems at the above barrier energies.

Reexamination of the nuclear orientation model of quasifission reactions to explain anomalous fragment anisotropies at sub-barrier energies.

In the present work we have measured fission fragment angular distributions and fusion excitation functions for the systems $^{12}\mathrm{C}$, $^{16}\mathrm{O}$+$^{232}\mathrm{Th}$ at energies around the Coulomb barrier. These results along with the results of our earlier measurements on $^{19}\mathrm{F}$ + $^{232}\mathrm{Th}$ system were analyzed following Hinde et al. [Phys. Rev. Lett. 74, 1295 (1995)] where it was pointed out that the anomalous fission fragment angular distributions seen in heavy ion reactions below the Coulomb barrier can be due to possible occurrence of quasifission events caused by the interaction of the projectile with the tip of the deformed target nucleus. The present data do not show the expected saturation behavior of the fission fragment anisotropy at sub-barrier energies for the $^{12}\mathrm{C}$+ $^{232}\mathrm{Th}$ system which exhibits different behavior of the fission fragment anisotropy in the sub-barrier region as compared to the other two systems. The present measurements using different projectiles on the same target nucleus do not seem to conform to the expected behavior of the quasifission mechanism to be caused by the interaction of the projectile with the tip of the deformed target nucleus.

Transient electric birefringence of two small DNA restriction fragments of the same molecular weight

The transient electric birefringence of two small DNA restriction fragments of the same molecular weight, one of which migrates anomalously slowly on polyacrylamide gels, has been investigated. Both fragments exhibit negative birefringence. The decay of the birefringence of the anomalously slowly migrating fragment is 8-9% faster than that of the normally migrating fragment. The faster birefringence decay of the anomalous fragment 12A persists under a variety of buffer conditions, suggesting that it is due primarily to static bending and/or curvature of fragment 12A. In reversing electric fields the absolute amplitude of the birefringence of fragments 12A and 12B decreased about 26% before returning to the steady state value. The minimum in the birefringence occurred faster than expected from the birefringence decay times and decreased with increasing electric field strength, suggesting that the minimum is due to a slow polarization of the ion atmosphere. For both fragments, the rise of the birefringence in the Kerr region is about 10% slower than the field-free decay. The buildup of the negative birefringence is preceded either by an interval when no birefringence is observed or by a small positively birefringent transient, suggesting that a small transverse ionic polarizability is also present. Both DNA fragments exhibit Kerr law behavior over most of the range of electric field strengths investigated. Analysis of the shapes of the saturation curves suggests that differences may exist in the polarization mechanisms of the two fragments.

DNA fingerprinting of tilapia, Oreochromis niloticus, and its application to aquaculture genetics

DNA fingerprinting has proven to be an extremely powerful tool for the identification of individuals and pedigrees. Here we report that the Jeffreys' 33.6 and 33.15 multilocus probes produce complex yet informative DNA fingerprints in tilapia, Oreochromis niloticus. With the exception of one anomalous fragment, presumably the result of mutation in the tandem array, each hypervariable fragment in the fingerprint could be attributed to one or other of the parents, thereby indicating Mendelian inheritance of these loci. The results of these studies suggest applications in aquaculture genetics including assessment of inbreeding rates, as genetic markers to identify individuals and family groups, and the labelling of broodstocks to secure ownership of property.

Entrance-channel dependence of fission-fragment anisotropies: A direct experimental signature of fission before equilibration.

Fission-fragment angular distributions in reactions of $^{10}\mathrm{B}$, $^{12}\mathrm{C}$, $^{16}\mathrm{O}$${+}^{232}$Th and $^{237}\mathrm{Np}$, and $^{19}\mathrm{F}$${+}^{237}$Np have been measured. While the measured anisotropies in B- and C-induced fission are found to be in agreement with the predictions of the standard Halpern-Strutinsky theory, they are anomalously large in the case of O- and F-induced fission. Such a discontinuous behavior in angular anisotropy with respect to the entrance-channel mass-to-charge asymmetry provides an experimental verification of the predictions of the preequilibrium fission model proposed earlier to explain the anomalous fragment angular distributions.

Anomalous fragmentation in the electron-impact ionization of SF 6 and SiF 4 in Ar clusters

Anomalous fragmentation in the electron-impact ionization of molecules has been observed under conditions in which the molecules would be in van der Waals clusters with argon. This is interpreted as evidence for the Penning transfer of excitation energy within clusters from the inert gas atom to the molecular species. The effect may have important implications for the interpretation of mass spectra of molecular beams.

Search for a nucleon-participant multiplicity effect on a possible anomalous fragment production

Momentum spectra of projectile fragments from 1.1 A GeV20Ne interactions with a Fe target have been measured with associated charged-particle multiplicity of participant nucleons. We also measured fragment absorption by introducing a Fe absorber. We searched for enhanced anomalous fragment production for fragments of charge 6≦Z≦ 10 as a function of multiplicity. To the possible exception of18Ne, a negative result is reported.

Novel electron impact-induced hydrogen rearrangements in the mass spectra of organorhenium hydrides and alkyls

The electron impact-induced hydrogen rearrangement of an organorhenium hydride is described, in which the remote hydrogen is identified to be the hydride hydrogen by deuterium-labelling experiments. Rearrangement accompanies intra-ligand cleavage of the triphenylphosphine ligand, an unusual event in itself, resulting in neutral loss of benzene from the molecular ion. Closer examination of the electron impact mass spectra of a series of organorhenium alkyl compounds indicates that another rearrangement of a beta hydrogen from the alkyl ligand onto the metal center produces the rhenium hydride, which then undergoes rearrangement and neutral loss. These two rearrangements serve to explain the heretofore anomalous fragment peaks in the spectra of the organorhenium alkyl compounds.

Monte Carlo simulations of anomalon experiments

Computer simulations of low statistics track detector heavy ion collision experiments on projectile fragmentation are presented. We find a non-negligible probability to obtain the recently observed anomalous fragmentation component also with normal fragmentation processes. We discuss the significance of the expected mean-free-path behaviour when an anomalous component is included.