bluuebunny/crossref_metadata_2025_split huggingface dataset:
End3p-Mediated Endocytosis Is Required for Spore Wall Formation in Saccharomyces cerevisiae
Authors: Morishita Masayo , Engebrecht JoAnne 
Published: June 2005

Abstract
During sporulation in Saccharomyces cerevisiae, vesicles transported to the vicinity of spindle pole bodies are fused to each other to generate bilayered prospore membranes (PSMs). PSMs encapsulate the haploid nuclei that arise from the meiotic divisions and serve as platforms for spore wall deposition. Membrane trafficking plays an important role in supplying vesicles for these processes. The endocytosis-deficient mutant, end3Δ, sporulated poorly and the spores produced lost resistance to ether vapor, suggesting that END3-mediated endocytosis is important for sporulation. End3p-GFP localized to cell and spore peripheries in vegetative and sporulating cells and colocalized with actin structures. Correspondingly, the actin cytoskeleton appeared aberrant during sporulation in end3Δ. Analysis of meiosis in end3Δ mutants revealed that the meiotic divisions occurred with wild-type kinetics. Furthermore, PSMs were assembled normally. However, the levels of proteins required for spore wall synthesis and components of the spore wall layers at spores were reduced, indicating that end3Δ mutants are defective in spore wall synthesis. Thus, END3-mediated endocytosis is important for spore wall formation. Additionally, cytological analyses suggest that trafficking between the plasma membrane and PSMs is important earlier during sporulation.
Epistasis in Monkeyflowers
Authors: Kelly John K 
Published: June 2005

AbstractEpistasis contributes significantly to intrapopulation variation in floral morphology, development time, and male fitness components of Mimulus guttatus. This is demonstrated with a replicated line-cross experiment involving slightly over 7000 plants. The line-cross methodology is based on estimates for means. It thus has greater power than the variance partitioning approaches historically used to estimate epistasis within populations. The replication of the breeding design across many pairs of randomly extracted, inbred lines is necessary given the diversity of multilocus genotypes residing within an outbred deme. Male fitness is shown to exhibit synergistic epistasis, an accelerating decline in fitness with inbreeding. Synergism is a necessary, but not sufficient, condition for a mutational deterministic hypothesis for the evolutionary maintenance of sexual reproduction. Unlike male fitness measures, flower morphology and development time yield positive evidence of epistasis but not of synergism. The results for these traits suggest that epistatic effects are variable across genetic backgrounds or sets of interacting loci.
A Duplication in the Canine β-Galactosidase Gene GLB1 Causes Exon Skipping and GM1-Gangliosidosis in Alaskan Huskies
Authors: Kreutzer Robert , Leeb Tosso , Müller Gundi , Moritz Andreas , Baumgärtner Wolfgang 
Published: June 2005

Abstract
GM1-gangliosidosis is a lysosomal storage disease that is inherited as an autosomal recessive disorder, predominantly caused by structural defects in the β-galactosidase gene (GLB1). The molecular cause of GM1-gangliosidosis in Alaskan huskies was investigated and a novel 19-bp duplication in exon 15 of the GLB1 gene was identified. The duplication comprised positions +1688–+1706 of the GLB1 cDNA. It partially disrupted a potential exon splicing enhancer (ESE), leading to exon skipping in a fraction of the transcripts. Thus, the mutation caused the expression of two different mRNAs from the mutant allele. One transcript contained the complete exon 15 with the 19-bp duplication, while the other transcript lacked exon 15. In the transcript containing exon 15 with the 19-bp duplication a premature termination codon (PTC) appeared, but due to its localization in the last exon of canine GLB1, nonsense-mediated RNA decay (NMD) did not occur. As a consequence of these molecular events two different truncated GLB1 proteins are predicted to be expressed from the mutant GLB1 allele. In heterozygous carrier animals the wild-type allele produces sufficient amounts of the active enzyme to prevent clinical signs of disease. In affected homozygous dogs no functional GLB1 is synthesized and GM1-gangliosidosis occurs.
Multiple Roles of a Heterotrimeric G-Protein γ-Subunit in Governing Growth and Development of Aspergillus nidulans
Authors: Seo Jeong-Ah , Han Kap-Hoon , Yu Jae-Hyuk 
Published: June 2005

Abstract
Vegetative growth signaling in the filamentous fungus Aspergillus nidulans is primarily mediated by the heterotrimeric G-protein composed of FadA (Gα), SfaD (Gβ), and a presumed Gγ. Analysis of the A. nidulans genome identified a single gene named gpgA encoding a putative Gγ-subunit. The predicted GpgA protein consists of 90 amino acids showing 72% similarity with yeast Ste18p. Deletion (Δ) of gpgA resulted in restricted vegetative growth and lowered asexual sporulation. Moreover, similar to the ΔsfaD mutant, the ΔgpgA mutant was unable to produce sexual fruiting bodies (cleistothecia) in self-fertilization and was severely impaired with cleistothecial development in outcross, indicating that both SfaD and GpgA are required for fruiting body formation. Developmental and morphological defects caused by deletion of flbA encoding an RGS protein negatively controlling FadA-mediated vegetative growth signaling were suppressed by ΔgpgA, indicating that GpgA functions in FadA-SfaD-mediated vegetative growth signaling. However, deletion of gpgA could not bypass the need for the early developmental activator FluG in asexual sporulation, suggesting that GpgA functions in a separate signaling pathway. We propose that GpgA is the only A. nidulans Gγ-subunit and is required for normal vegetative growth as well as proper asexual and sexual developmental progression.
Systematic Segregation to Mutant Mitochondrial DNA and Accompanying Loss of Mitochondrial DNA in Human NT2 Teratocarcinoma Cybrids
Authors: Turner Carrie J , Granycome Caroline , Hurst Rachel , Pohler Elizabeth , Juhola M Katariina , Juhola Martti I , Jacobs Howard T , Sutherland Lesley , Holt Ian J 
Published: June 2005

Abstract
In this study a well-characterized pathological mutation at nucleotide position 3243 of human mitochondrial DNA was introduced into human ρ0 teratocarcinoma (NT2) cells. In cloned and mixed populations of NT2 cells heteroplasmic for the mutation, mitotic segregation toward increasing levels of mutant mitochondrial DNA always occurred. Rapid segregation was frequently followed by complete loss of mitochondrial DNA. These findings support the idea that pathological mitochondrial DNA mutations are particularly deleterious in specific cell types, which can explain some of the tissue-specific aspects of mitochondrial DNA diseases. Moreover, these findings suggest that mitochondrial DNA depletion may be an important and widespread feature of mitochondrial DNA disease.
Mutational Analysis of the pH Signal Transduction Component PalC ofAspergillus nidulansSupports Distant Similarity to BRO1 Domain Family Members
Authors: Tilburn Joan , Sánchez-Ferrero Juan C , Reoyo Elena , Arst Herbert N , Peñalva Miguel A 
Published: June 2005

AbstractThe alkaline ambient pH signal transduction pathway component PalC has no assigned molecular role. Therefore we attempted a gene-specific mutational analysis and obtained 55 new palC loss-of-function alleles including 24 single residue substitutions. Refined similarity searches reveal conserved PalC regions including one with convincing similarity to the BRO1 domain, denoted PCBROH, where clustering of mutational changes, including PCBROH key residue substitutions, supports its structural and/or functional importance. Since the BRO1 domain occurs in the multivesicular body (MVB) pathway protein Bro1/Vps31 and also the pH signal transduction protein PalA (Rim20), both of which interact with MVB component (ESCRT-III protein) Vps32/Snf7, this might reflect a further link between the pH response and endocytosis.
The initial oxidation of beryllium by water vapor
Authors: Zalkind Shimon , Polak Micha , Shamir Noah 
Published: June 2005

AbstractThe initial stage of adsorption and beryllium oxidation by water (clearly a nonadiabatic process) was studied for a wide temperature range, using AES, XPS, DRS, and CPD measurements. The mechanism of room temperature (RT) oxidation by water vapor was found to be by nucleation and growth of 3 monolayer oxide islands, laterally spreading until coalescence takes place. When a full oxide layer is achieved, a further slow oxidation takes place, virtually stopping at ∼6 monolayer depth. Exposure of the surface to water vapor at 150 K yielded dissociation to H and OH, chemisorbed on the surface, as detected by an XPS chemical shift. The lack of such a shift at RT indicates a full dissociation of the water molecule on the surface. A giant effect of Be electron‐stimulated oxidation (ESO) by water vapor, as opposed to Be mild ESO by O2, was observed, reaching the maximal possible oxidation rate for the ratio of ≥150 impinging electrons per water molecule. It is suggested that the mechanism is a Mott—Cabrera‐like one, enabled by a combination of an electric field applied by negative OH and/or oxygen ions formed at the surface, probably by secondary electron attachment, and a very fast diffusion of Be2+ ions enabled by the presence of hydrogen in the oxide bulk. The water vapor ESO exhibits an inverse dependence on the substrate temperature, presumably due to the decrease with temperature of hydroxyl surface concentration, leading to the weakening of the electric field formed across the oxide.
Photophysics and photochemistry of ice films on graphite
Authors: Chakarov Dinko 
Published: June 2005

AbstractWe consider model systems consisting of submonolayer‐ to several monolayers‐thick ice films grown at ultrahigh vacuum (UHV) and low (from ∼15 K) temperatures on an atomically clean graphite (0001) surface. They are characterized experimentally with temperature‐programmed desorption‐isothermal desorption spectroscopy (TPD‐ITD) and high‐resolution electron energy loss spectroscopy (HREELS). We provide examples of how ice structure and chemical properties are altered by incoming photons. The phenomena of “photon annealing” of pure amorphous films and their structure‐selective laser ablation are discussed. In the case of water ice doped with alkali metals and coadsorbed with NO, we report on the observations of photoreactions taking place on the graphite/ice interface. Depending on the composition of the coadsorbed ice layer, irradiation leads to formation of H2, CH4, CO, NH3, and CO2. More specifically, we address the mechanisms of water photo‐dissociation at surfaces and interfaces with emphasis on the role of (i) perturbation of water molecules by coadsorbates and/or substrate; (ii) the light‐initiated electron (charge) transfer reactions leading to water splitting; and (iii) confinement of the precursor system and reaction products. In all examples the attention is on the operating mechanism for the transformations. The role of photo‐excited charge carriers in the graphite substrate is underlined. Increased understanding of photo‐stimulated reactions and processes involving water is needed to allow these processes to be effectively controlled and fully utilized.
Laser‐induced desorption of small molecules from oxide surfaces: A first‐principles study
Authors: Klüner Thorsten 
Published: June 2005

AbstractRecent efforts in the theoretical simulation of laser‐induced desorption of small molecules from surfaces are summarized. As a representative example, photodesorption of CO molecules from a Cr2O3(0001) surface is investigated since detailed quantum state resolved experimental results are available for this system.In particular, vectorial properties such as the alignment of the desorbing species are considered. Furthermore, the influence of surface temperature as a control parameter is investigated, and lateral velocity distributions are calculated and compared with experimental results.All simulations presented in the present study are based on ab initio potential energy surfaces (PESs) for the electronic ground state as well as electronically excited states involved in the desorption process. These PESs provide the prerequisite for extensive high‐dimensional quantum mechanical simulations of the dynamics of nuclear motion based on a stochastic wave packet scheme.These wave packet calculations allow for a detailed microscopic understanding of experimental results and provide a perspective for future experiments.
Time‐dependent density functional theory for nonadiabatic processes
Authors: Baer Roi , Kurzweil Yair , Cederbaum Lorenz S. 
Published: June 2005

AbstractTime‐dependent density functional theory (TDDFT) is a general and robust method allowing the study of electron dynamics whether induced by nuclear motion or by external fields. We give a brief overview of the theory and some numerical methods together with recent applications stressing the generality and wide applicability of the method. We also discuss recent attempts to extend the present TDDFT by incorporating memory terms into the exchange correlation potentials.
Laser‐driven electron dynamics at interfaces
Authors: Saalfrank Peter , Klamroth Tillmann , Huber Christian , Krause Pascal 
Published: June 2005

AbstractIn this paper we present time‐dependent, quantum‐dynamical simulations of photoinduced processes at solid surfaces involving nonadiabatic transitions of electrons to and from short‐lived intermediate excited states. In particular, two‐photon photoemission (2PPE) spectra of naked metal surfaces and free‐standing metal films are considered. One major problem in both cases is the presence of electron—electron scattering, which is treated here in various ways. The first way is to adopt an open‐system density matrix approach, in which a single electron is weakly coupled to a “bath” of other electrons. The second approach is based on a many‐electron Schrödinger equation, which is solved with the help of a time‐dependent configuration interactions singles (TD—CIS) method.
Time‐resolved two‐photon photoemission at metal—dielectric interfaces
Authors: Berthold Wolfram , Höfer Ulrich 
Published: June 2005

AbstractWe review the influence of rare‐gas layers on image‐potential states at metal surfaces. Experiments on Xe, Kr, and Ar on Cu(100) and on Xe/Ru(0001) that use the technique of time‐resolved two‐photon photoemission are discussed. The energetic position of the electron affinity, the geometry of the adsorbate layer, and dielectric screening are the factors that influence the dynamical and energetic properties of the states. Theories on various levels are compared, including 1‐ and 3‐dimensional models and the GW approximation of many‐body theory. We also present new results on buried interface states that exist in the band gaps of both the Cu(100) substrate and a thick adsorbed Ar layer.
Theoretical study of halogen‐substituted benzene at a Si(111)7×7 surface
Authors: Petsalakis Ioannis D. , Theodorakopoulos Giannoula 
Published: June 2005

AbstractThe adsorption of halobenzene (for halogens F, Cl, Br, and I) on Si(111)7×7 was investigated using AM1 quantum mechanical calculations. First the 1,4‐cyclohexadiene type of chemisorbed structures with two C—Si bonds at C atoms 1 and 4 have been calculated. Generally, the calculated binding energy increases with the size of the halogen atom, in the series F, Cl, Br, and I. The sp2 carbon positions are the most favorable for the halogen atom, and for bromobenzene and iodobenzene there is significant additional stabilization for the geometry that allows interaction of the halogen atom with a nearby Si adatom. This stabilization hinders the transfer of the heavier halogen atoms, Br and I, to the surface. Other chemisorbed structures, involving formally divalent halogen atoms in a C‐X‐Si type of binding, have also been found to correspond to energy minima in the AM1 calculations. Furthermore, it was possible to calculate physisorbed structures for chlorobenzene and bromobenzene once the Si rest atoms were capped with H atoms. Two types of binding structures are suggested for chemisorption in excess of three molecules per half‐unit cell: one is a radical structure binding by a single C‐Si adatom bond, and the second one is binding by a single C‐X‐Si adatom interaction. Both of these singly‐bonded structures have been calculated to correspond to energy minima with binding energies smaller than the 1,4‐cyclohexadiene type of chemisorbed structure.
Photochemistry of molecules at confined environment: CD3Br/O/Ru(001) and CO2@Ice
Authors: Berger Raphael , Lilach Yigal , Ayoub Yousif , Asscher Micha 
Published: June 2005

AbstractThe photochemistry of molecules constrained within a confining environment on surfaces has been studied. Orientation of methyl bromide could be controlled methyl down or up by varying the pre‐adsorbed oxygen coverage due to electrostatic interactions on Ru(001) under UHV conditions. Irradiation of the coadsorption system at 193 nm has shown that the resulting photochemical activity is sensitive to the molecular orientation. Photodesorption and dissociation cross sections were 1.0·10−19 cm−2 for methyl‐down and 3.0·10−19 cm−2 for the methyl‐up configurations. This observation represents the first report of the steric effect in electron‐molecule interaction due to the dissociative electron attachment mechanism of photochemical processes on surfaces.A second system of CO2 molecules caged within ice has also been studied. Here the trapped carbon dioxide molecules cannot leave the surface at their normal desorption temperature near 100 K, but are explosively desorbing at the onset of ice evaporation near 165 K. Upon UV irradiation, enhanced dissociation to adsorbed CO and oxygen is recorded. In addition, a new reactivity channel is observed to form H2CO, tentatively identified as formaldehyde. The relevance of photochemistry of caged molecules within ice to interstellar hydrocarbon formation as a possible route for the origin of life is discussed.
Electron transfer/transport at metal‐molecule interfaces probed by femtosecond time‐resolved two‐photon photoemission: Heptane and fullerene on Au(111)
Authors: Lindstrom Chad , Dutton Gregory , Quinn Daniel P. , Zhu Xiaoyang 
Published: June 2005

AbstractElectron transfer and transport at metal‐molecule interfaces has been a central problem in a number of disciplines. There is renewed interest in this problem from the rapidly growing field of molecule‐based electronics, where the so‐called “contact problem” is usually probed in transport measurements. Here, we probe interfacial electron transfer/transport using time‐resolved two‐photon photo‐emission spectroscopy. Such an approach allows us to quantitatively measure the energetic alignment of occupied and unoccupied molecular orbitals to the metal Fermi level, the electronic coupling strength (or spectral density) between the molecular orbital and the metal substrate, and electronic‐nuclear coupling leading to dynamic localization. These three types of information are in fact key ingredients in quantitative theories for electron transfer and transport at molecule‐metal surfaces. Recent examples from our laboratory are used to illustrate the point. They include femtosecond dynamics of image potential resonances on heptane‐covered Au(111) and exciton relaxation dynamics in C60 epitaxial films on Au(111). On heptane/Au(111), the lifetime of the n = 1 image potential resonance increases from 52 fs at one monolayer (ML) coverage to 700 fs at 2 ML and 2.8 ps at 3 ML. On C60/Au(111), the Frenkel exciton (involving the LUMO+1 level) couples over long distance to the metal substrate, with lifetime of 350 fs at 30 ML to 80 fs at 2 ML coverage. The film‐thickness‐dependent decay dynamics in both cases can be attributed to interfacial electron transfer. Fitting the distance‐dependent electron transfer rates to a simple exponential function gives the characteristic distance parameter of ß = 0.6 ± 0.1 and 0.023 ± 0.005 Å−1 for heptane‐ and C60‐covered Au(111), respectively. The difference in the ß parameters illustrates the essential role of the electronic structure of molecules in mediating interfacial electron transfer/transport.
Langevin‐schroedinger formulation of electronic tunneling through a molecular bridge with a dissipative acceptor
Authors: Malka Alon , Peskin Uri 
Published: June 2005

AbstractModeling electronic tunneling through molecular bridges is desired in order to understand the mechanism of long‐range electron transfer reactions in nature, as well as for the design of novel molecular electronics devices. Particularly interesting is the effect of the nuclear motion at the molecular bridge on the electron transfer mechanism and rate. In this work we study the effect of electronic nuclear coupling at the molecular bridge on a unidirectional electronic tunneling process from an electron donor into a dissipative acceptor, as may appear in controlled electron transfer reactions at biological membranes, or in heterogeneous electron transfer reactions. The model includes a collection of harmonic bath modes coupled to the dissipative acceptor site and a single mode at the molecular bridge. The parameters of the dissipative bath are tuned such that the electronic population decays from the donor to the acceptor. This process is simulated using a time‐dependent nonlinear Langevin‐Schroedinger equation, based on a mean‐field approximation for the electronic‐nuclear coupling at the acceptor site and a numerically exact treatment of the electronic‐nuclear coupling at the molecular bridge. The simulations at zero temperature and weak electronic‐nuclear coupling demonstrate that electronic tunneling is promoted by coupling to the nuclear mode at the bridge. This result is consistent with our previous studies of electronic tunneling oscillations in a symmetric donor‐bridge‐acceptor complex, and it emphasizes the importance of electronic nuclear coupling in analyzing long‐range electron transfer processes through molecular bridges or wires.
Theoretical study of benzene, toluene, and dibromobenzene at a Si(111)7×7 surface
Authors: Petsalakis Ioannis D. , Polanyi John C. , Theodorakopoulos Giannoula 
Published: June 2005

AbstractTheoretical Austin model 1 (AM1) calculations on the adsorption of benzene and toluene on Si(111)7×7 are presented. Both physisorbed and chemi‐sorbed states have been calculated for up to three adsorbed molecules per half unit cell of the Si(111)7×7 surface. Secondly, theoretical calculations on the induced attachment of benzene as well as rationalization of the dynamics of the halogenation reaction of 1,2‐ and 1,4‐dibromobenzene on Si(111)7×7 are reviewed. The main incentive for this study was the interpretation of recent experimental scanning tunneling microscopy (STM) results from the Toronto laboratory on a new electron‐induced or photo‐induced attachment process for benzene on Si(111), and, particularly, experimental results related to the thermal dissociative reactions of 1,2‐ and 1,4‐dibromobenzene on a Si(111)7×7 surface. The central objective is to relate the reagent geometry in 1,2‐dibromobenzene and 1,4‐dibromobenzene to the Br‐Br pair distance of dibrominated Si(111)7×7. For benzene, we propose a possible path for the conversion from the normal strained di‐sigma‐bound state (S) at Si(111) to a more strongly bound state (B) consisting of a phenyl plus an H‐atom adsorbed species. For 1,2‐ and 1,4‐dibromobenzene dibromination of silicon, evidence has been found for two mechanisms of reaction. One reaction pathway involves intermediate binding of the organic molecule on the Si surface through C‐Si bonds, analogous to the benzene S structure. The second dynamical pathway involves intermediate binding through weak Br. Si attachment followed by formation of pairs of covalently‐bound Br‐Si. The outcomes from the two dynamical pathways are consistent with the observed STM patterns for pairs of Br‐Si at Si(111) 7×7 due to the reaction of 1,2‐ and 1,4‐dibromobenzene.