bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Features of Surface Layers of Bifunctional Polysiloxane Xerogels Containing 3-Aminopropyl Groups and 3-Mercaptopropyl Groups
Authors: Zub Yuriy L. , Melnyk Inna V. , White Mark G. , Alonso Bruno 
Published: October 2008

Polysiloxane xerogels containing both –SH and –NH2 functions have been prepared using the sol–gel method with alkoxysilane precursors [such as Si(OEt)4, (MeO)3Si(CH2)3SH and (EtO)3Si(CH2)3NH2]. Molar ratios of 3.2:1, 1.1:1 and 0.4:1 for the two functions –SH and –NH2 were employed. Xerogels which contain only one of the two functions were also synthesized for comparative purposes. It was shown that the use of stannic compounds as catalysts for xerogels with 3-mercaptopropyl groups resulted in a product which possessed a non-porous structure, while the use of fluoride ions allowed the synthesis of a sample with a porous structure (Ssp = 216 m2/g, Vs = 0.152 cm3/g, d = 3.5 nm). Xerogels with a bifunctional surface layer possess a bimodal structure. Infrared, Raman and multinuclear solid-state NMR (1H, 13C, 29Si) spectroscopy data showed: (i) the absence of deprotonation for the 3-mercaptopropyl groups in the bifunctional surface layer of the xerogels; and (ii) that 3-aminopropyl groups form hydrogen bonds in these surface layers. The type of hydrogen bond formed depends on the ratio of the amount of water to the amount of 3-aminopropyl groups in the surface layer. When this ratio is about 1:1, the amino group forms a hydrogen bond with the silanol group associated with the water molecule. Re-organization of the surface layer is observed when the amount of water decreases, the amino groups forming hydrogen bonds between themselves. Hence, the system of hydrogen bonds in the surface layer of such xerogels depends primarily on the drying regime employed for the samples.
Elucidation of the Adsorption/Desorption Mechanism of Ions by an Electrical Double Layer Capacitor
Authors: Oda H. , Mizutaki K. , Yamamoto M. , Sano M. 
Published: October 2008

The phenomena associated with the adsorption/desorption of ammonium, nitrate and phosphate ions by an electrical double layer capacitor (EDLC) were examined as a new application of this device for the removal of environmental pollutants from freshwater rivers, lakes and marshes. An electrode modified by introducing acidic functional groups onto its surface was used as the negative electrode of an EDLC, and this resulted in a 1.7-times increase in the amount of ammonium ions removed compared with that of an unmodified electrode. However, when the quantity of functional groups was increased to over 1.5 mmol/g, the amount of ammonium ions removed gradually decreased due to steric hindrance of the functional groups on the surface of the electrode and/or redox reactions with these groups. Similarly, it was found that the EDLC easily adsorbed nitrate ions but did not easily desorb them, whereas the opposite was the case for phosphate ions. The relationship between these phenomena and the pHpzc (pH value at the point of zero charge) of the electrode in nitrate and phosphate solutions is presented.
Mass Transfer and Adsorption Kinetics of Phenolic Compounds onto Activated Carbon Prepared from Rice Husk
Authors: Nassar Mamdouh M. , Magdy Yehia H. , Daifullah Abd El Hakim , Kelany H. 
Published: October 2008

Activated carbon from an agriculture by-product (rice husk) was prepared by carbonization at 500°C (50°C/15 min) followed by activation at 850°C for 1 h. The adsorption of phenolic compounds onto this activated carbon was studied using batch adsorber methods. The experimental results showed that the prepared activated carbon removed phenolic compounds effectively from aqueous solution. Analysis of the contact time data gave an indication of the mechanism. The external mass-transfer constant, kf, involved in the adsorption process was determined using different initial adsorbate concentrations (C0) and adsorbent masses (M). The following relationships were obtained: kf = 0.0023(M)−0.55 and kf = 0.0006(C0)0.17. A macropore rate parameter for intraparticle diffusion, kp, was defined and used to correlate the experimental data via the following expression: kp = 0.183(C0)0.48. A twin-resistance mass-transfer model based on external mass transfer and pore diffusion was applied successfully to the system under investigation. Concentration decay curves were predicted using a single modified mass-transfer coefficient, kf, and a single effective diffusion coefficient, Deff, for studies involving variable adsorbent masses and initial adsorbate concentrations.
Factors Affecting the Adsorption of Zn2+ and Cd2+ Ions from Aqueous Solution onto Vermiculite
Authors: Xiaofu Wu , Fang Zhao , Mingli Chen , Yangli Zhang , Chong Zhao , Hailan Zhou 
Published: October 2008

Experiments were conducted to investigate the influence of different factors on the adsorption of Zn2+ and Cd2+ ions from aqueous solution onto vermiculite. The ratio of the initial concentration of ions, C0, to the adsorbent concentration, W0, was shown to be the key factor determining the equilibrium ion adsorption density, qe. Subject to the magnitude of C0/W0, the value of qe could either attain its maximum level, qm (the maximum adsorption density), when the solid surface was fully saturated, or approach its critical limit, qc (the C0/W0 ratio), when the ions in the bulk solution had been completely removed. The main mechanism for adsorption in the systems studied was ion-exchange. An increase in Zn2+ or Cd2+ ion adsorption from the single metal ion solution resulted in an increase in the concentrations of unadsorbed K+, Na+, Ca2+ and Mg2+ ions remaining in the bulk solution. Competition between adsorbing ions was observed in the mixed K+–Zn2+–Cd2+ ion system. Although temperature had a positive effect upon the adsorption of Zn2+ and Cd2+ ions, its effect was statistically negligible over the range 15–45°C. The negative effect of decreasing pH values on the adsorption process was only significant below a pH value of 4.0, indicating that the adsorption of Zn2+ and Cd2+ ions would be significantly depressed when high amounts of H+ ions are present in the system.
GnRH analogues: applications in assisted reproductive techniques
Authors: Hayden Catherine 
Published: October 2008

The ability to prevent an endogenous LH surge revolutionised the efficacy of assisted reproductive techniques (ART) such that GnRH agonists were rapidly adopted in the 1980s. Prior to this, premature luteinisation occurred in up to 25% of superovulated cycles leading to cycle cancellation and severely compromised outcomes. Analogues have been applied in a variety of drug protocols (long, short flare) but there has been little research to moderate the degree of pituitary suppression. There has also been ongoing and unresolved debate about the role of LH in supporting follicular development.By 2001, the first GnRH antagonists were registered for use in ART. Their ability to cause immediate suppression of gonadotrophin (particularly LH) secretion means that they can be given after exogenous stimulation has begun and thereby dramatically shorten the total duration of a treatment cycle. After initial enthusiasm and then scepticism that pregnancy rates may not be as high as the established agonist regimens, these preparations are now being increasingly adopted with at least comparable outcomes in large trials. They are certainly favoured by patients for their reduced side-effect profile and particularly for the shortening of the total cycle length. This shift in practice is occurring alongside gathering momentum in favour of milder stimulation protocols and a new perception of what constitutes successful treatment. The focus is moving away from surrogate outcomes such as oocyte numbers and conception rates towards long-term outcomes for women and their offspring, namely the achievement of a live singleton birth per treatment started.
Practical Applications of the Bioinformatics Toolbox for Narrowing Quantitative Trait Loci
Authors: Burgess-Herbert Sarah L , Cox Allison , Tsaih Shirng-Wern , Paigen Beverly 
Published: October 2008

AbstractDissecting the genes involved in complex traits can be confounded by multiple factors, including extensive epistatic interactions among genes, the involvement of epigenetic regulators, and the variable expressivity of traits. Although quantitative trait locus (QTL) analysis has been a powerful tool for localizing the chromosomal regions underlying complex traits, systematically identifying the causal genes remains challenging. Here, through its application to plasma levels of high-density lipoprotein cholesterol (HDL) in mice, we demonstrate a strategy for narrowing QTL that utilizes comparative genomics and bioinformatics techniques. We show how QTL detected in multiple crosses are subjected to both combined cross analysis and haplotype block analysis; how QTL from one species are mapped to the concordant regions in another species; and how genomewide scans associating haplotype groups with their phenotypes can be used to prioritize the narrowed regions. Then we illustrate how these individual methods for narrowing QTL can be systematically integrated for mouse chromosomes 12 and 15, resulting in a significantly reduced number of candidate genes, often from hundreds to &lt;10. Finally, we give an example of how additional bioinformatics resources can be combined with experiments to determine the most likely quantitative trait genes.
Complex Genetics Control Natural Variation inArabidopsis thalianaResistance toBotrytis cinerea
Authors: Rowe Heather C , Kliebenstein Daniel J 
Published: October 2008

AbstractThe genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to necrotrophic pathogens have used large plant mapping populations to dissect the genetic structure of resistance. Using a large structured mapping population of Arabidopsis thaliana, we identified quantitative trait loci influencing plant response to B. cinerea, measured as expansion of necrotic lesions on leaves and accumulation of the antimicrobial compound camalexin. Testing multiple B. cinerea isolates, we identified 23 separate QTL in this population, ranging in isolate-specificity from being identified with a single isolate to controlling resistance against all isolates tested. We identified a set of QTL controlling accumulation of camalexin in response to pathogen infection that largely colocalized with lesion QTL. The identified resistance QTL appear to function in epistatic networks involving three or more loci. Detection of multilocus connections suggests that natural variation in specific signaling or response networks may control A. thaliana–B. cinerea interaction in this population.
The Mating-Type-Related Bias of Gene Conversion inSchizosaccharomyces pombe
Authors: Parvanov Emil , Kohli Juerg , Ludin Katja 
Published: October 2008

AbstractThe mating-type bias (mat-bias) of gene conversion was previously described as a phenomenon in which the number of prototrophic recombinants in an ura4A heteroallelic two-factor cross relates to the mating types of the parents. We show now that the mat-bias is restricted neither to ura4A nor to recombination hotspots, but occurs at other genomic loci, too. It is specific for gene conversion and absent in azygotic meiosis. Thus, the mat-bias must originate from mating-type-specific “imprinting” events before karyogamy takes place. Structural variations of the mating-type locus, such as h+N, h+S, h−S, h+smtΔ, or h−smtΔ, showed mat-bias manifestation. Mutations in genes coding for histone acetylase (gcn5, ada2) and histone deacetylase (hos2, clr6) activities smooth or abolish the mat-bias. In addition, the mat-bias depends on the presence of Swi5. We propose a new role for Swi5 and the histone acetylation status in mat-bias establishment through directionality of repair from the intact chromatid to the broken chromatid.
Telomere Loss Provokes Multiple Pathways to Apoptosis and Produces Genomic Instability inDrosophila melanogaster
Authors: Titen Simon W A , Golic Kent G 
Published: October 2008

AbstractTelomere loss was produced during development of Drosophila melanogaster by breakage of an induced dicentric chromosome. The most prominent outcome of this event is cell death through Chk2 and Chk1 controlled p53-dependent apoptotic pathways. A third p53-independent apoptotic pathway is additionally utilized when telomere loss is accompanied by the generation of significant aneuploidy. In spite of these three lines of defense against the proliferation of cells with damaged genomes a small fraction of cells that have lost a telomere escape apoptosis and divide repeatedly. Evasion of apoptosis is accompanied by the accumulation of karyotypic abnormalites that often typify cancer cells, including end-to-end chromosome fusions, anaphase bridges, aneuploidy, and polyploidy. There was clear evidence of bridge–breakage–fusion cycles, and surprisingly, chromosome segments without centromeres could persist and accumulate to high-copy number. Cells manifesting these signs of genomic instability were much more frequent when the apoptotic mechanisms were crippled. We conclude that loss of a single telomere is sufficient to generate at least two phenotypes of early cancer cells: genomic instability that involves multiple chromosomes and aneuploidy. This aneuploidy may facilitate the continued escape of such cells from the normal checkpoint mechanisms.
Sexual Back Talk With Evolutionary Implications: Stimulation of the Drosophila Sex-Determination Gene Sex-lethal by Its Target transformer
Authors: Siera Scott G , Cline Thomas W 
Published: October 2008

Abstract
We describe a surprising new regulatory relationship between two key genes of the Drosophila sex-determination gene hierarchy, Sex-lethal (Sxl) and transformer (tra). A positive autoregulatory feedback loop for Sxl was known to maintain somatic cell female identity by producing SXL-F protein to continually instruct the target gene transformer (tra) to make its feminizing product, TRA-F. We discovered the reciprocal regulatory effect by studying genetically sensitized females: TRA-F from either maternal or zygotic tra expression stimulates Sxl-positive autoregulation. We found female-specific tra mRNA in eggs as predicted by this tra maternal effect, but not predicted by the prevailing view that tra has no germline function. TRA-F stimulation of Sxl seems to be direct at some point, since Sxl harbors highly conserved predicted TRA-F binding sites. Nevertheless, TRA-F stimulation of Sxl autoregulation in the gonadal soma also appears to have a cell-nonautonomous aspect, unprecedented for somatic Sxl regulation. This tra–Sxl retrograde regulatory circuit has evolutionary implications. In some Diptera, tra occupies Sxl's position as the gene that epigenetically maintains female identity through direct positive feedback on pre-mRNA splicing. The tra-mediated Sxl feedback in Drosophila may be a vestige of regulatory redundancy that facilitated the evolutionary transition from tra to Sxl as the master sex switch.
A G2-Phase Microtubule-Damage Response in Fission Yeast
Authors: Balestra Fernando R , Jimenez Juan 
Published: October 2008

AbstractMicrotubules assume a variety of structures throughout the different stages of the cell cycle. Ensuring the correct assembly of such structures is essential to guarantee cell division. During mitosis, it is well established that the spindle assembly checkpoint monitors the correct attachment of sister chromatids to the mitotic spindle. However, the role that microtubule cytoskeleton integrity plays for cell-cycle progression during interphase is uncertain. Here we describe the existence of a mechanism, independent of the mitotic checkpoint, that delays entry into mitosis in response to G2-phase microtubule damage. Disassembly of the G2-phase microtubule array leads to the stabilization of the universal mitotic inhibitor Wee1, thus actively delaying entry into mitosis via inhibitory Cdc2 Tyr15 phosphorylation.
Outcrossing as an Explanation of the Apparent Unconventional Genetic Behavior ofArabidopsis thaliana hthMutants
Authors: Mercier Raphael , Jolivet Sylvie , Vignard Julien , Durand Stéphanie , Drouaud Jan , Pelletier Georges , Nogué Fabien 
Published: October 2008

AbstractThe reappearance of HTH alleles in the offspring of homozygous Arabidopsis hth mutants is not consistent with classical Mendelian genetics. It has been suggested that stored RNA may be used to restore genetic information. However, Peng et al. reported that hth mutants tend to display outcrossing and suggested that outcrossing might provide an alternative explanation for the apparent genetic instability. We have confirmed and extended these results, corroborating that the apparent non-Mendelian behavior of hth mutants can be explained by their susceptibility to outcrossing.
RNA-Dependent RNA Polymerase Is Required for Enhancer-Mediated Transcriptional Silencing Associated With Paramutation at the Maizep1Gene
Authors: Sidorenko Lyudmila , Chandler Vicki 
Published: October 2008

AbstractParamutation is the ability of an endogenous gene or a transgene to heritably silence another closely related allele or gene. At the maize p1 (pericarp color1) gene, paramutation is associated with decreases in transcript levels and reduced pigmentation of the endogenous allele that normally specifies red seed coat (pericarp) and cob pigmentation. Herein we demonstrate that this silencing occurs at the transcriptional level and that a specific enhancer fragment from p1 is sufficient to induce all aspects of paramutation. Further, we demonstrate that a mutation in the mop1 gene (mediator of paramutation1), which encodes a RNA-dependent RNA polymerase, is absolutely required for establishing the silencing associated with p1 paramutation. In contrast to its effects on other paramutation loci, the mop1 mutation does not immediately reactivate a previously silenced allele; several generations in the presence of the mop1 mutation are required. In addition, the mop1 mutation was also able to release tissue-specific silencing of another p1 allele that does not participate in paramutation, but does contain a tandem repeated structure and is likely regulated through epigenetic mechanisms. These results demonstrate that RNA-mediated gene-silencing mechanisms play key roles in p1 paramutation and the spectrum of roles for MOP1 is broadened to include tissue-specific expression patterns.
Loss of the Histone Variant H2A.Z Restores Capping to Checkpoint-Defective Telomeres in Drosophila
Authors: Rong Yikang S 
Published: October 2008

Abstract
The conserved histone variant H2A.Z fulfills many functions by being an integral part of the nucleosomes placed at specific regions of the genome. Telomeres cap natural ends of chromosomes to prevent their recognition as double-strand breaks. At yeast telomeres, H2A.Z prevents the spreading of silent chromatin into proximal euchromatin. A role for H2A.Z in capping, however, has not been reported in any organism. Here, I uncover such a role for Drosophila H2A.Z. Loss of H2A.Z, through mutations in either its gene or the domino gene for the Swr1 chromatin-remodeling protein, suppressed the fusion of telomeres that lacked the protection of checkpoint proteins: ATM, ATR, and the Mre11–Rad50–NBS complex. Loss of H2A.Z partially restores the loading of the HOAP capping protein, possibly accounting for the partial restoration in capping. I propose that, in the absence of H2A.Z, checkpoint-defective telomeres adopt alternative structures, which are permissive for the loading of the capping machinery at Drosophila telomeres.
A and C Genome Distinction and Chromosome Identification inBrassica napusby Sequential Fluorescencein SituHybridization and Genomicin SituHybridization
Authors: Howell Elaine C , Kearsey Michael J , Jones Gareth H , King Graham J , Armstrong Susan J 
Published: October 2008

AbstractThe two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)—with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes—followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.
Informed Consent Revisited: A Doctrine in the Service of Cancer Care
Authors: Schachter Madeleine , Fins Joseph J. 
Published: October 2008

AbstractInformed consent traditionally has been viewed as a safeguard for the protection of patients' decisional autonomy. While informed consent is a critical means for the protection of the patient's dominion over the integrity of his body, exclusive consideration of the doctrine as a safeguard for patients eclipses the doctrine's significant benefits for the therapeutic endeavor. Undertaking a thorough informed consent process helps the physician avoid the unilateral burdens of paternalism; furthers compliance with the doctor's legal obligations, ethical duties, and clinical responsibilities; and, as importantly, enhances the collaborative treatment enterprise.When informed consent is viewed narrowly and solely as a protective device for patients' rights, the physician may be less likely to engage the patient in ongoing discussions. Important opportunities may be missed to elicit additional clinical information, assess psychosocial concerns, and reiterate the commitment to collaboration and patient autonomy.