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A Shevchenko

Publications and source records attributed to A Shevchenko.

At least 19 recordsLinked to original sources
PubMed2006

Gamow-Teller strengths in the A = 14 multiplet: a challenge to the shell model.

A new experimental approach to the famous problem of the anomalously slow Gamow-Teller (GT) transitions in the beta decay of the A=14 multiplet is presented. The GT strength distributions to excited states in 14C and 14O were studied in high-resolution (d,2He) and (3He,t) charge-exchange reactions on 14N. No-core shell-model calculations capable of reproducing the suppression of the beta decays predict a selective excitation of Jpi=2+ states. The experimental confirmation represents a validation of the assumptions about the underlying structure of the 14N ground state wave function. However, the fragmentation of the GT strength over three 2+ final states remains a fundamental issue not explained by the present no-core shell model using a 6homega model space, suggesting possibly the need to include cluster structure in these light nuclei in a consistent way.

Journal Article↗
PubMed2006

Fine structure of the Gamow-Teller resonance in 90Nb and level density of 1+ states.

The fine structure of the Gamow-Teller resonance in a medium-heavy nucleus is observed for the first time in a high-resolution 90Zr(3He,t)90Nb experiment at the Research Center for Nuclear Physics, Osaka. Using a novel wavelet analysis technique, it is possible to extract characteristic energy scales and to quantify their relative importance for the generation of the fine structure. This method combined with the selectivity of the reaction permits an extraction of the level density of 1+ states in 90Nb.

Journal Article↗
PubMed2004

Fine structure in the energy region of the isoscalar giant quadrupole resonance: characteristic scales from a wavelet analysis.

Fine structure in the energy region of the isoscalar giant quadrupole resonance in nuclei is observed in high-resolution proton scattering experiments at iThemba LABS over a wide mass range. A novel method based on wavelet transforms is introduced for the extraction of scales characterizing the fine structure. A comparison with microscopic model calculations including two-particle two-hole (2p2h) degrees of freedom identifies the coupling to surface vibrations as the main source of the observed scales. A generic pattern is also found for the stochastic coupling to the background of the more complex states.

Journal Article↗
PubMed2002

Nature of low-energy dipole strength in nuclei: the case of a resonance at particle threshold in 208Pb.

A high-resolution (gamma,gamma') study of the electric dipole response in 208Pb at the S-DALINAC reveals a resonance structure centered around the neutron emission threshold. Microscopic quasiparticle phonon model calculations in realistic model spaces including the coupling to complex configurations are able to describe the data in great detail. The resonance is shown to result from surface density oscillations of the neutron skin relative to an approximately isospin-saturated core. It also forms an integral part of a toroidal E1 mode representing an example of vortex collective motion in nuclei.

Journal Article↗
PubMed2002

Degree of polarization for optical near fields.

We investigate an extension to the concept of degree of polarization that applies to arbitrary electromagnetic fields, i.e., fields whose wave fronts are not necessarily planar. The approach makes use of generalized spectral Stokes parameters that appear as coefficients, when the full 3 x 3 spectral coherence matrix is expanded in terms of the Gell-Mann matrices. By defining the degree of polarization in terms of these parameters in a manner analogous to the conventional planar-field case, we are led to a formula that consists of scalar invariants of the spectral coherence matrix only. We show that attractive physical insight is gained by expressing the three-dimensional degree of polarization explicitly with the help of the correlations between the three orthogonal spectral components of the electric field. Furthermore, we discuss the fundamental differences in characterizing the polarization state of a field by employing either the two- or the three-dimensional coherence-matrix formalism. The extension of the concept of the degree of polarization to include electromagnetic fields having structures of arbitrary form is expected to be particularly useful, for example, in near-field optics.

Journal Article↗
PubMed2002

Deuteron breakup in the 2H(e,e' p) reaction at low momentum transfer and close to threshold.

Deuteron breakup has been studied in a 2H(e,e' p) coincidence experiment at low momentum transfer and for energies close to threshold. The longitudinal-plus-transverse ( L+T) and longitudinal-transverse ( LT) interference cross sections are deduced. Nonrelativistic calculations based on the Bonn potential and including leading order relativistic contributions, meson exchange currents, and isobar configurations describe the ( L+T) data well. Surprisingly, large deviations of 30% to 45% are observed for the LT contribution.

Journal Article↗
PubMed2001

Prospore membrane formation linked to the leading edge protein (LEP) coat assembly.

In yeast, the differentiation process at the end of meiosis generates four daughter cells inside the boundaries of the mother cell. A meiosis-specific plaque (MP) at the spindle pole bodies (SPBs) serves as the starting site for the formation of the prospore membranes (PSMs) that are destined to encapsulate the post-meiotic nuclei. Here we report the identification of Ady3p and Ssp1p, which are functional components of the leading edge protein (LEP) coat, that covers the ring-shaped opening of the PSMs. Ssp1p is required for the assembly of the LEP coat, which consists of at least three proteins (Ssp1p, Ady3p and Don1p). The assembly of the LEP coat starts with the formation of cytosolic precursors, which then bind in an Ady3p-dependent manner to the SPBs. Subsequent processes at the SPBs leading to functional LEP coats require Ssp1p and the MP components. During growth of the PSMs, the LEP coat functions in formation of the cup-shaped membrane structure that is indispensable for the regulated cellularization of the cytoplasm around the post-meiotic nuclei.

Fluorescent Antibody Technique↗
PubMed2001

The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4.

The SET domain proteins, SUV39 and G9a have recently been shown to be histone methyltransferases specific for lysines 9 and 27 (G9a only) of histone 3 (H3). The SET domains of the Saccharomyces cerevisiae Set1 and Drosophila trithorax proteins are closely related to each other but distinct from SUV39 and G9a. We characterized the complex associated with Set1 and Set1C and found that it is comprised of eight members, one of which, Bre2, is homologous to the trithorax-group (trxG) protein, Ash2. Set1C requires Set1 for complex integrity and mutation of Set1 and Set1C components shortens telomeres. One Set1C member, Swd2/Cpf10 is also present in cleavage polyadenylation factor (CPF). Set1C methylates lysine 4 of H3, thus adding a new specificity and a new subclass of SET domain proteins known to methyltransferases. Since methylation of H3 lysine 4 is widespread in eukaryotes, we screened the databases and found other Set1 homologues. We propose that eukaryotic Set1Cs are H3 lysine 4 methyltransferases and are related to trxG action through association with Ash2 homologues.

Amino Acid Sequence↗
PubMed2001

The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program.

Set3 is one of two proteins in the yeast Saccharomyces cerevisiae that, like Drosophila Trithorax, contains both SET and PHD domains. We found that Set3 forms a single complex, Set3C, with Snt1, YIL112w, Sif2, Cpr1, and two putative histone deacetylases, Hos2 and NAD-dependent Hst1. Set3C includes NAD-dependent and independent deacetylase activities when assayed in vitro. Homology searches suggest that Set3C is the yeast analog of the mammalian HDAC3/SMRT complex. Set3C represses genes in early/middle of the yeast sporulation program, including the key meiotic regulators ime2 and ndt80. Whereas Hos2 is only found in Set3C, Hst1 is also present in a complex with Sum1, supporting previous characterizations of Hst1 and Sum1 as repressors of middle sporulation genes during vegetative growth. However, Hst1 is not required for meiotic repression by Set3C, thus implying that Set3C (-Hst1) and not Hst1-Sum1, is the meiotic-specific repressor of early/middle sporulation genes.

Amino Acid Sequence↗
PubMed2001

Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome.

SCF ubiquitin ligases control various processes by marking regulatory proteins for ubiquitin-dependent proteolysis. To illuminate how SCF complexes are regulated, we sought proteins that interact with the human SCF component CUL1. The COP9 signalosome (CSN), a suppressor of plant photomorphogenesis, associated with multiple cullins and promoted cleavage of the ubiquitin-like protein NEDD8 from Schizosaccharomyces pombe CUL1 in vivo and in vitro. Multiple NEDD8-modified proteins uniquely accumulated in CSN-deficient S. pombe cells. We propose that the broad spectrum of activities previously attributed to CSN subunits--including repression of photomorphogenesis, activation of JUN, and activation of p27 nuclear export--underscores the importance of dynamic cycles of NEDD8 attachment and removal in biological regulation.

3T3 Cells↗
PubMed2001

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.

MALDI-quadrupole time-of-flight mass spectrometry was applied to identify proteins from organisms whose genomes are still unknown. The identification was carried out by successively searching a sequence database-first with a peptide mass fingerprint, then with a packet of noninterpreted MS/MS spectra, and finally with peptide sequences obtained by automated interpretation of the MS/MS spectra. A "MS BLAST" homology searching protocol was developed to overcome specific limitations imposed by mass spectrometric data, such as the limited accuracy of de novo sequence predictions. This approach was tested in a small-scale proteomic project involving the identification of 15 bands of gel-separated proteins from the methylotrophic yeast Pichia pastoris, whose genome has not yet been sequenced and which is only distantly related to other fungi.

Algorithms↗
PubMed2001

Ephrin B1 is expressed on neuroepithelial cells in correlation with neocortical neurogenesis.

To identify molecules involved in neurogenesis, we have raised monoclonal antibodies against embryonic day 12.5 mouse telencephalon. One antibody, monoclonal antibody 25H11, stains predominantly the ventricular zone of the anterior and lateral telencephalon. Purification of the 25H11 antigen, a 47 kDa integral membrane protein, from approximately 2500 mouse telencephali reveals its identity with ephrin B1. Ephrin B1 appears at the onset of neocortical neurogenesis, being first expressed in neuron-generating neuroepithelial cells and rapidly thereafter in virtually all neuroepithelial cells. Expression of ephrin B1 persists through the period of neocortical neurogenesis and is downregulated thereafter. Ephrin B1 is present on the ventricular as well as basolateral plasma membrane of neuroepithelial cells and exhibits an ventricular-high to pial-low gradient across the ventricular zone. Expression of ephrin B1 is also detected on radial glial cells, extending all the way to their pial endfeet, and on neurons in the mantle/intermediate zone but not in the cortical plate. Our results suggest that ephrin B1, presumably via ephrin-Eph receptor signaling, has a role in neurogenesis. Given the ventricular-to-pial gradient of ephrin B1 on the neuroepithelial cell surface and its known role in cell migration in other systems mediated by its repulsive properties, we propose that ephrin B1 may be involved in the migration of newborn neurons out from the ventricular zone toward the neocortex.

Animals↗
PubMed2001

The budding yeast proteins Spc24p and Spc25p interact with Ndc80p and Nuf2p at the kinetochore and are important for kinetochore clustering and checkpoint control.

Here, we show that the budding yeast proteins Ndc80p, Nuf2p, Spc24p and Spc25p interact at the kinetochore. Consistently, Ndc80p, Nuf2p, Spc24p and Spc25p associate with centromere DNA in chromatin immunoprecipitation experiments, and SPC24 interacts genetically with MCM21 encoding a kinetochore component. Moreover, although conditional lethal spc24-2 and spc25-7 cells form a mitotic spindle, the kinetochores remain in the mother cell body and fail to segregate the chromosomes. Despite this defect in chromosome segregation, spc24-2 and spc25-7 cells do not arrest in metaphase in response to checkpoint control. Furthermore, spc24-2 cells showed a mitotic checkpoint defect when microtubules were depolymerized with nocodazole, indicating that Spc24p has a function in checkpoint control. Since Ndc80p, Nuf2p and Spc24p are conserved proteins, it is likely that similar complexes are part of the kinetochore in other organisms.

Amino Acid Sequence↗
PubMed2001

Archived polyacrylamide gels as a resource for proteome characterization by mass spectrometry.

Mass spectrometry was applied to identify protein spots excised from an archived two-dimensional polyacrylamide gel that had been dried and stored for eight years at room temperature. All proteins were successfully identified. Detailed characterization of protein digests by matrix-assisted laser desorption/ionization (MALDI) peptide mapping, nanoelectrospray tandem mass spectrometry and MALDI-quadrupole time-of-flight mass spectrometry revealed no evidence of protein degradation or modifications that could hamper identification of proteins in a sequence database. The experiment with a model protein demonstrated that the pattern of tryptic peptides and the yield of individual peptides were not noticeably changed in the in-gel digest of the archived protein spot compared to the digest of the spot excised from a fresh gel. Thus, the characterization of "archived proteomes" has the potential to advance proteomic research without repeating "wet" biochemistry experiments, that had been perfected in the laboratory years ago.

Acrylic Resins↗
PubMed2001

Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly.

SCF ubiquitin ligases are composed of Skp1, Cdc53, Hrt1 and one member of a large family of substrate receptors known as F-box proteins (FBPs). Here we report the identification, using sequential rounds of epitope tagging, affinity purification and mass spectrometry, of 16 Skp1 and Cdc53-associated proteins in budding yeast, including all components of SCF, 9 FBPs, Yjr033 (Rav1) and Ydr202 (Rav2). Rav1, Rav2 and Skp1 form a complex that we have named 'regulator of the (H+)-ATPase of the vacuolar and endosomal membranes' (RAVE), which associates with the V1 domain of the vacuolar membrane (H+)-ATPase (V-ATPase). V-ATPases are conserved throughout eukaryotes, and have been implicated in tumour metastasis and multidrug resistance, and here we show that RAVE promotes glucose-triggered assembly of the V-ATPase holoenzyme. Previous systematic genome-wide two-hybrid screens yielded 17 proteins that interact with Skp1 and Cdc53, only 3 of which overlap with those reported here. Thus, our results provide a distinct view of the interactions that link proteins into a comprehensive cellular network.

Cell Cycle Proteins↗
PubMed2000

Euplotes telomerase contains an La motif protein produced by apparent translational frameshifting.

Telomerase is the ribonucleoprotein enzyme responsible for the replication of chromosome ends in most eukaryotes. In the ciliate Euplotes aediculatus, the protein p43 biochemically co-purifies with active telomerase and appears to be stoichiometric with both the RNA and the catalytic protein subunit of this telomerase complex. Here we describe cloning of the gene for p43 and present evidence that it is an authentic component of the telomerase holoenzyme. Comparison of the nucleotide sequence of the cloned gene with peptide sequences of the protein suggests that production of full-length p43 relies on a programmed ribosomal frameshift, an extremely rare translational mechanism. Anti-p43 antibodies immunodeplete telomerase RNA and telomerase activity from E.aediculatus nuclear extracts, indicating that the vast majority of mature telomerase complexes in the cell are associated with p43. The sequence of p43 reveals similarity to the La autoantigen, an RNA-binding protein involved in maturation of RNA polymerase III transcripts, and recombinant p43 binds telomerase RNA in vitro. By analogy to other La proteins, p43 may function in chaperoning the assembly and/or facilitating nuclear retention of telomerase.

Amino Acid Motifs↗
PubMed2000

MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research.

A MALDI QqTOF mass spectrometer has been used to identify proteins separated by one-dimensional or two-dimensional gel electrophoresis at the femtomole level. The high mass resolution and the high mass accuracy of this instrument in both MS and MS/MS modes allow identification of a protein either by peptide mass fingerprinting of the protein digest or from tandem mass spectra acquired by collision-induced dissociation of individual peptide precursors. A peptide mass map of the digest and tandem mass spectra of multiple peptide precursor ions can be acquired from the same sample in the course of a single experiment. Database searching and acquisition of MS and MS/MS spectra can be combined in an interactive fashion, increasing the information value of the analytical data. The approach has demonstrated its usefulness in the comprehensive characterization of protein in-gel digests, in the dissection of complex protein mixtures, and in sequencing of a low molecular weight integral membrane protein. Proteins can be identified in all types of sequence databases, including an EST database. Thus, MALDI QqTOF mass spectrometry promises to have remarkable potential for advancing proteomic research.

Amino Acid Sequence↗