bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Damage Checkpoints Are Involved in Postreplication Repair
Authors: Barbour Leslie , Ball Lindsay G , Zhang Ke , Xiao Wei 
Published: October 2006

AbstractSaccharomyces cerevisiae MMS2 encodes a ubiquitin-conjugating enzyme variant, belongs to the error-free branch of the RAD6 postreplication repair (PRR) pathway, and is parallel to the REV3-mediated mutagenesis branch. A mutation in genes of either the MMS2 or the REV3 branch does not result in extreme sensitivity to DNA-damaging agents; however, deletion of both subpathways of PRR results in a synergistic phenotype. Nevertheless, the double mutant is not as sensitive to DNA-damaging agents as a rad6 or rad18 mutant defective in the entire PRR pathway, suggesting the presence of an additional subpathway within PRR. A synthetic lethal screen was employed in the presence of a sublethal dose of a DNA-damaging agent to identify novel genes involved in PRR, which resulted in the isolation of RAD9 as a candidate PRR gene. Epistatic analysis showed that rad9 is synergistic to both mms2 and rev3 with respect to killing by methyl methanesulfonate (MMS), and the triple mutant is nearly as sensitive as the rad18 single mutant. In addition, rad9 rad18 is no more sensitive to MMS than the rad18 single mutant, suggesting that rad9 plays a role within the PRR pathway. Moreover, deletion of RAD9 reduces damage-induced mutagenesis and the mms2 spontaneous and induced mutagenesis is partially dependent on the RAD9 gene. We further demonstrated that the observed synergistic interactions apply to any two members between different branches of PRR and G1/S and G2/M checkpoint genes. These results suggest that a damage checkpoint is essential for tolerance mediated by both the error-free and error-prone branches of PRR.
Nuclear Sex-Determining Genes Cause Large Sex-Ratio Variation in the Apple Snail Pomacea canaliculata
Authors: Yusa Yoichi 
Published: October 2006

Abstract
Evolutionary maintenance of genetic sex-ratio variation is enigmatic since genes for biased sex ratios are disadvantageous in finite populations (the “Verner effect”). However, such variation could be maintained if a small number of nuclear sex-determining genes were responsible, although this has not been fully demonstrated experimentally. Brood sex ratios of the freshwater snail Pomacea canaliculata are highly variable among parents, but population sex ratios are near unity. In this study, the effect of each parent on the brood sex ratio was investigated by exchanging partners among mating pairs. There were positive correlations between sex ratios of half-sib broods of the common mother (r = 0.42) or of the common father (r = 0.47). Moreover, the correlation between full-sib broods was very high (r = 0.92). Thus, both parents contributed equally to the sex-ratio variation, which indicates that nuclear genes are involved and their effects are additive. Since the half-sib correlations were much stronger than the parent–offspring regressions previously obtained, the variation was caused by zygotic sex-determining genes rather than by parental sex-ratio genes. The number of relevant genes appears to be small.
A New Strategy for Estimating Recombination Fractions Between Dominant Markers From an F2 Population
Authors: Tan Yuan-De , Fu Yun-Xin 
Published: October 2006

Abstract
Although most high-density linkage maps have been constructed from codominant markers such as single-nucleotide polymorphisms (SNPs) and microsatellites due to their high linkage information, dominant markers can be expected to be even more significant as proteomic technique becomes widely applicable to generate protein polymorphism data from large samples. However, for dominant markers, two possible linkage phases between a pair of markers complicate the estimation of recombination fractions between markers and consequently the construction of linkage maps. The low linkage information of the repulsion phase and high linkage information of coupling phase have led geneticists to construct two separate but related linkage maps. To circumvent this problem, we proposed a new method for estimating the recombination fraction between markers, which greatly improves the accuracy of estimation through distinction between the coupling phase and the repulsion phase of the linked loci. The results obtained from both real and simulated F2 dominant marker data indicate that the recombination fractions estimated by the new method contain a large amount of linkage information for constructing a complete linkage map. In addition, the new method is also applicable to data with mixed types of markers (dominant and codominant) with unknown linkage phase.
SVF1 Regulates Cell Survival by Affecting Sphingolipid Metabolism in Saccharomyces cerevisiae
Authors: Brace Jennifer L , Lester Robert L , Dickson Robert C , Rudin Charles M 
Published: October 2006

Abstract
Sphingolipid signaling plays an important role in the regulation of central cellular processes, including cell growth, survival, and differentiation. Many of the essential pathways responsible for sphingolipid biogenesis, and key cellular responses to changes in sphingolipid balance, are conserved between mammalian and yeast cells. Here we demonstrate a novel function for the survival factor Svf1p in the yeast sphingolipid pathway and provide evidence that Svf1p regulates the generation of a specific subset of phytosphingosine. Genetic analyses suggest that Svf1p acts in concert with Lcb4p and Lcb3p to generate a localized pool of phytosphingosine distinct from phytosphingosine generated by Sur2p. This subset is implicated in cellular responses to stress, as loss of SVF1 is associated with defects in the diauxic shift and the oxidative stress response. A genetic interaction between SVF1 and SUR2 demonstrates that both factors are required for optimal growth and survival, and phenotypic similarities between svf1Δsur2Δ and ypk1Δ suggest that pathways controlled by Svf1p and Sur2p converge on a signaling cascade regulated by Ypk1p. Loss of YPK1 together with disruption of either SVF1 or SUR2 is lethal. Together, these data suggest that compartmentalized generation of distinct intracellular subsets of sphingoid bases may be critical for activation of signaling pathways that control cell growth and survival.
Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies (L.) Karst]
Authors: Heuertz Myriam , De Paoli Emanuele , Källman Thomas , Larsson Hanna , Jurman Irena , Morgante Michele , Lascoux Martin , Gyllenstrand Niclas 
Published: October 2006

Abstract
DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico–Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively.
Homeologous Recombination in Solanum lycopersicoides Introgression Lines of Cultivated Tomato
Authors: Canady Michael A , Ji Yuanfu , Chetelat Roger T 
Published: October 2006

Abstract
A library of “introgression lines” containing Solanum lycopersicoides chromosome segments in the genetic background of cultivated tomato (Lycopersicon esculentum) was used to study factors affecting homeologous recombination. Recombination rates were estimated in progeny of 43 heterozygous introgressions and whole-chromosome substitution lines, together representing 11 of the 12 tomato chromosomes. Recombination within homeologous segments was reduced to as little as 0–10% of expected frequencies. Relative recombination rates were positively correlated with the length of introgressed segments on the tomato map. The highest recombination (up to 40–50% of normal) was observed in long introgressions or substitution lines. Double-introgression lines containing two homeologous segments on opposite chromosome arms were synthesized to increase their combined length. Recombination was higher in the double than in the single segment lines, despite a preference for crossovers in the region of homology between segments. A greater increase in homeologous recombination was obtained by crossing the S. lycopersicoides introgression lines to L. pennellii—a phylogenetically intermediate species—or to L. esculentum lines containing single L. pennellii segments on the same chromosome. Recombination rates were highest in regions of overlap between S. lycopersicoides and L. pennellii segments. The potential application of these results to breeding with introgression lines is discussed.
Low Impact of Germline Transposition on the Rate of Mildly Deleterious Mutation in Caenorhabditis elegans
Authors: Bégin Mattieu , Schoen Daniel J 
Published: October 2006

Abstract
Little is known about the role of transposable element (TE) insertion in the production of mutations with mild effects on fitness, the class of mutations thought to be central to the evolution of many basic features of natural populations. We propagated mutation-accumulation (MA) lines of two RNAi-deficient strains of Caenorhabditis elegans that exhibit germline transposition. We show here that the impact of TE activity was to raise the level of mildly deleterious mutation by 2- to 8.5-fold, as estimated from fecundity, longevity, and body length measurements, compared to that observed in a parallel MA experiment with a control strain characterized by a lack of germline transposition. Despite this increase, the rate of mildly deleterious mutation was between one and two orders of magnitude lower than the rate of TE accumulation, which was approximately two new insertions per genome per generation. This study suggests that high rates of TE activity do not necessarily translate into high rates of detectable nonlethal mutation.
Construction and Uses of New Compound B-A-A Maize Chromosome Translocations
Authors: Sheridan William F , Auger Donald L 
Published: October 2006

Abstract
Maize B-A translocations result from reciprocal interchanges between a supernumerary B chromosome and an arm of an essential A chromosome. Because of the frequent nondisjunction of the B centromere at the second pollen mitosis, B-A translocations have been used to locate genes to chromosome arms and to study the dosage effects of specific A segments. Compound B-A translocations (B-A-A translocations) are created by bringing together a simple B-A translocation with an A-A translocation in which breakpoints in the A-A and B-A translocations are in the same arm. Recombination in the region of shared homology of these A chromosome segments creates a B-A-A translocation. Success in creating and testing for a new B-A-A translocation requires that the B-A translocation be proximal to the A-A translocation and that the A-A translocation be proximal to the tester locus. The breakpoints of most of the A-A translocations have been cytologically defined by earlier investigators. Previous investigators have produced 16 B-A-A translocations and one B-A-A-A translocation, which collectively define 35 A chromosome breakpoints. We have enlarged this group by creating 64 new B-A-A translocations. We present a summary of the total of 81 B-A-A translocations showing their distribution among the chromosome arms and the 163 cytologically defined chromosome segments delimited by them. We also illustrate the method of construction of these B-A-A stocks and their uses.
Spectrum of the Y=2 pentaquarks
Authors: Buccella Franco , Falcone Domenico , Tramontano Francesco 
Published: October 2006

Abstract
Based on an assumed mass formula for the spectrum of the Y=2 pentaquarks, where the chromo-magnetic interaction plays an important role, and identifying the lightest state with the Θ+(1540), we predict a spectrum in good agreement with the few I=0 and I=1 candidates proposed in the past.
The effect of electron irradiation on the optical properties of the natural armenian zeolite-clinoptilolite
Authors: Yeritsyan Hrant , Harutiunian Vachagan , Gevorkyan Volodia , Grigoryan Norair , Hakhverdyan Eleonora , Nikoghosyan Sergey , Sahakyan Aram , Gevorgyan Rudolf , Sargisyan Hakob , Keheyan Yeghis 
Published: October 2006

Abstract
Infrared (IR) absorption and luminescence in chemically and radiation-modified natural Armenian Zeolite (clinoptilolite) samples have been studied. The luminescence was studied in 390–450 nm and 620–710 nm wavelength bands, and the IR measurements were carried out in the 400–5400 cm−1 range. It is shown that the luminescence intensity depends on the content of pure clinoptilolite in the samples and, probably on the distribution of “passive” luminescence centers over Si and Al sites that became “active” under radiation or chemical treatment. The samples of electron irradiated clinoptilolite have higher luminescence intensity than the chemically and thermally treated ones. A decrease in the intensity of IR absorption bands at 3550 cm−1 and 3650 cm−1 was found after irradiation.
One‐Pot Synthesis of Lactams from Cycloalkanes and tert‐Butyl Nitrite by Using N‐Hydroxyphthalimide as Key Catalyst
Authors: Hashimoto Masaharu , Sakaguchi Satoshi , Ishii Yasutaka 
Published: October 2006

AbstractLactams were successfully synthesized in the one‐pot reaction of cycloalkanes and tBuONO in the presence of N‐hydroxyphthalimide as a key catalyst. Cyclododecane and cyclohexane were treated with tBuONO followed by triethylamine and then cyanuric chloride in a one‐pot manner to give laurolactam and ε‐caprolactam, respectively, in good yields. The Beckmann rearrangement of oximes by cyanuric chloride was found to be accelerated by the use of 1,1,1,3,3,3‐hexafluoro‐2‐propanol as solvent. The method provides the first successful environmentally benign direct synthetic route to lactams from cycloalkanes without the formation of any salt.
Comment on mathematical models which describe transcription and calculate the relationship between mRNA and protein expression ratio
Authors: Kremling A. 
Published: October 2006

AbstractMathematical models to describe transcription (Arnold et al. (2001); Biotech Bioeng 72:548–561) and translation (Mehra et al. (2003); Biotech Bioeng 84:822–841) in bacteria are modified in order to improve reaction kinetics and to include the number of polymerase molecules that are active on the DNA, as well as to include the number of ribosomes that are active on the nascent and on the completed mRNA, respectively. Biotechnol. Bioeng. 2007;96:815–819. © 2006 Wiley Periodicals, Inc.
The penicillin G acylase production by B. megaterium is amino acid consumption dependent
Authors: Marina Pinotti Laura , Ribeiro de Souza Vanessa , de Campos Giordano Roberto , de Lima Camargo Giordano Raquel 
Published: October 2006

AbstractAiming at to enhance the production of penicillin G acylase (PGA) by Bacillus megaterium, we have performed flasks experiments using different medium composition. Using 51 g/L of casein hydrolyzed with Alcalase® and 2.7 g/L of phenylacetic acid (PhAc), the following carbon substrates were tested, individually and combined: glucose, glycerol, and lactose (present in cheese whey). Glycerol and glucose showed to be effective nutrients for the microorganism growth but delayed the PGA production. Cheese whey always increased enzyme production and cell mass. However, lactose (present in cheese whey) was not a significant carbon source for B. megaterium. PhAc, amino acids, and small peptides present in the hydrolyzed casein were the actual carbon sources for enzyme production. Replacement of hydrolyzed casein by free amino acids, 10.0 g/L, led to a significant increase in enzyme production (app. 150%), with a preferential consumption of alanine, aspartic acid, glycine, serine, arginine, threonine, lysine, and glutamic acid. A decrease of the enzyme production was observed when 20.0 g/L of amino acids were used. Using the single omission technique, it was shown that none of the 18 tested amino acids was essential for enzyme production. The use of a medium containing eight of the preferentially consumed amino acids lead to similar enzyme production level obtained when using 18 amino acids. PhAc, up to 2.7 g/L, did not inhibit enzyme production, even if added at the beginning of the cultivation. Biotechnol. Bioeng. 2007;97: 346–353. © 2006 Wiley Periodicals, Inc.
Theoretical analysis of inter‐observer variability in the determination of luminance thresholds
Authors: Carreño Fernando , Ezquerro José Miguel , Zoido Jesús M. 
Published: October 2006

AbstractWe present an analytical method to analyze, from a theoretical point of view, the influence of color‐matching functions on the perception of luminance thresholds. We show that the thresholds depend on the spectral responsivities of each observer. We also analyze the influence of luminance level on the thresholds: a strong inter‐observer variability is found at low or moderate luminance levels (0.02 < Y < 1 ft−L) whereas at high intensities (1 < Y < 7 ft−L) the thresholds are observer‐independent. © 2006 Wiley Periodicals, Inc. Col Res Appl, 31, 468–474, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.20259
Transfer of bacteria between biomaterials surfaces in the operating room—An experimental study
Authors: Knobben Bas A.S. , van der Mei Henny C. , van Horn Jim R. , Busscher Henk J. 
Published: October 2006

AbstractBacterial adhesion to and transfer between surfaces is a complicated process. With regard to the success of biomaterials implants, studies on bacterial adhesion and transfer should not be confined to biomaterials surfaces in the human body, but also encompass surfaces in the operating room, where the origin of many biomaterials related infections is found. The purpose of this study was to quantify the transfer of Staphylococcus aureus, Staphylococcus epidermidis, and Propionibacterium acnes from one operating room material to another, while accounting for surface hydrophobicity and roughness, moistness and application of friction during transfer. The tested operating room materials were gloves, broaches (orthopaedic drills), theatre gowns, and light handles. As a possible clinical intervention method to prevent transfer, it was investigated whether dipping the gloves in a chlorhexidine splash‐basin affected the viability of the transferred bacteria. Transfer (moist and without friction) was demonstrated to some extent with all bacterial strains and with every material, ranging from 17% to 71%, and was influenced by the bacterial strain, moistness of the inoculum, the application of friction, and the characteristics of both the donating and the receiving surface. Dipping the glove material in 4% or 0.4% chlorhexidine solutions killed all bacteria present, regardless of whether surfaces were dried or moist and thus prevented transfer. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Valence bond theory for chemical dynamics
Authors: Truhlar Donald G. 
Published: October 2006

AbstractThis essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential energy surfaces (an early example of specific reaction parameters), by multiconfiguration molecular mechanics, by the combined valence bond‐molecular mechanics method, and by the use of valence bond states as coupled diabatic states for describing electronically nonadiabatic processes (photochemistry). The essay includes both ab initio and semiempirical approaches. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007
Between ends and fibers
Authors: Bonnington C. Paul , Richter R. Bruce , Watkins Mark E. 
Published: October 2006

AbstractLet Γ be an infinite, locally finite, connected graph with distance function δ. Given a ray P in Γ and a constant C ≥ 1, a vertex‐sequence $\{{{x}}_{{n}}\}_{{{n}}={{0}}}^\infty\subseteq {{VP}}$ is said to be regulated by C if, for all nϵℕ, ${{x}}_{{{n}}+{{1}}}$ never precedes xn on P, each vertex of P appears at most C times in the sequence, and $\delta_{{P}}({{x}}_{{n}},{{x}}_{{{n}}+{{1}}})\leq {{C}}$. R. Halin (Math. Ann., 157, 1964, 125–137) defined two rays to be end‐equivalent if they are joined by infinitely many pairwise‐disjoint paths; the resulting equivalence classes are called ends. More recently H. A. Jung (Graph Structure Theory, Contemporary Mathematics, 147, 1993, 477–484) defined rays P and Q to be b‐equivalent if there exist sequences $\{{{x}}_{{n}}\}_{{{n}}={{0}}}^\infty\subseteq {{VP}}$ and $\{{{y}}_{{n}}\}_{{{n}}={{0}}}^\infty\subseteq {{VQ}}$ VQ regulated by some constant C ≥ 1 such that $\delta({{x}}_{{n}},{{y}}_{{n}})\leq {{C}}$ for all nϵℕ; he named the resulting equivalence classes b‐fibers. Let $F_0$ denote the set of nondecreasing functions from $N$ into the set of positive real numbers. The relation ${{P}}\sim_{{f}} {{Q}}$ (called f‐equivalence) generalizes Jung's condition to $\delta({{x}}_{{n}},{{y}}_{{n}})\leq {{Cf}}({{n}})$. As f runs through $\cal{F}_{{0}}$, uncountably many equivalence relations are produced on the set of rays that are no finer than b‐equivalence while, under specified conditions, are no coarser than end‐equivalence. Indeed, for every Γ there exists an “end‐defining function” ${{f}}\in F_{{0}}$ that is unbounded and sublinear and such that ${{P}}\sim_{{f}} {{Q}}$ implies that P and Q are end‐equivalent. Say ${{P}}\approx {{Q}}$ if there exists a sublinear function ${{f}}\in F_{{0}}$ such that ${{P}}\sim_{{f}} {{Q}}$. The equivalence classes with respect to $\approx$ are called bundles. We pursue the notion of “initially metric” rays in relation to bundles, and show that in any bundle either all or none of its rays are initially metric. Furthermore, initially metric rays in the same bundle are end‐equivalent. In the case that Γ contains translatable rays we give some sufficient conditions for every f‐equivalence class to contain uncountably many g‐equivalence classes (where ${lim}_{{{n}}\to\infty}{{g}}({{n}})/{{f}}({{n}})={{0}}$). We conclude with a variety of applications to infinite planar graphs. Among these, it is shown that two rays whose union is the boundary of an infinite face of an almost‐transitive planar map are never bundle‐ equivalent. © 2006 Wiley Periodicals, Inc. J Graph Theory 54: 125–153, 2007