bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Control of Temperature Preference in the Nematode Caenorhabditis elegans
Authors: Mohri Akiko , Kodama Eiji , Kimura Koutarou D , Koike Mizuho , Mizuno Takafumi , Mori Ikue 
Published: January 2005

Abstract
Animals modify behavioral outputs in response to environmental changes. C. elegans exhibits thermotaxis, where well-fed animals show attraction to their cultivation temperature on a thermal gradient without food. We show here that feeding-state-dependent modulation of thermotaxis is a powerful behavioral paradigm for elucidating the mechanism underlying neural plasticity, learning, and memory in higher animals. Starved experience alone could induce aversive response to cultivation temperature. Changing both cultivation temperature and feeding state simultaneously evoked transient attraction to or aversion to the previous cultivation temperature: recultivation of starved animals with food immediately induced attraction to the temperature associated with starvation, although the animals eventually exhibited thermotaxis to the new temperature associated with food. These results suggest that the change in feeding state quickly stimulates the switch between attraction and aversion for the temperature in memory and that the acquisition of new temperature memory establishes more slowly. We isolated aho (abnormal hunger orientation) mutants that are defective in starvation-induced cultivation-temperature avoidance. Some aho mutants responded normally to changes in feeding state with respect to locomotory activity, implying that the primary thermosensation followed by temperature memory formation remains normal and the modulatory aspect of thermotaxis is specifically impaired in these mutants.
Systematic, RNA-Interference-Mediated Identification of mus-101 Modifier Genes in Caenorhabditis elegans
Authors: Holway Antonia H , Hung Crystal , Michael W Matthew 
Published: January 2005

Abstract
The Mus101 family of chromosomal proteins, identified initially in Drosophila, is widely conserved and has been shown to function in a variety of DNA metabolic processes. Such functions include DNA replication, DNA damage repair, postreplication repair, damage checkpoint activation, chromosome stability, and chromosome condensation. Despite its conservation and widespread involvement in chromosome biogenesis, very little is known about how Mus101 is regulated and what other proteins are required for Mus101 to exert its functions. To learn more about Mus101, we have initiated an analysis of the protein in C. elegans. Here, we show that C. elegans mus-101 is an essential gene, that it is required for DNA replication, and that it also plays an important role in the DNA damage response. Furthermore, we use RNA interference (RNAi)-mediated reverse genetics to screen for genes that modify a mus-101 partial loss-of-function RNAi phenotype. Using a systematic approach toward modifier gene discovery, we have found five chromosome I genes that modify the mus-101 RNAi phenotype, and we go on to show that one of them encodes an E3 SUMO ligase that promotes SUMO modification of MUS-101 in vitro. These results expand our understanding of MUS-101 regulation and show that genetic interactions can be uncovered using screening strategies that rely solely on RNAi.
Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers
Authors: Excoffier Laurent , Estoup Arnaud , Cornuet Jean-Marie 
Published: January 2005

AbstractWe introduce here a Bayesian analysis of a classical admixture model in which all parameters are simultaneously estimated. Our approach follows the approximate Bayesian computation (ABC) framework, relying on massive simulations and a rejection-regression algorithm. Although computationally intensive, this approach can easily deal with complex mutation models and partially linked loci, and it can be thoroughly validated without much additional computation cost. Compared to a recent maximum-likelihood (ML) method, the ABC approach leads to similarly accurate estimates of admixture proportions in the case of recent admixture events, but it is found superior when the admixture is more ancient. All other parameters of the admixture model such as the divergence time between parental populations, the admixture time, and the population sizes are also well estimated, unlike the ML method. The use of partially linked markers does not introduce any particular bias in the estimation of admixture, but ML confidence intervals are found too narrow if linkage is not specifically accounted for. The application of our method to an artificially admixed domestic bee population from northwest Italy suggests that the admixture occurred in the last 10–40 generations and that the parental Apis mellifera and A. ligustica populations were completely separated since the last glacial maximum.
Infrequent Co-conversion of Markers Flanking a Meiotic Recombination Initiation Site in Saccharomyces cerevisiae
Authors: Jessop Lea , Allers Thorsten , Lichten Michael 
Published: January 2005

Abstract
To study the mechanism of meiotic recombination in Saccharomyces cerevisiae, we examined recombination in an interval where the majority of events are initiated at a single hotspot for DNA double-strand breaks (DSBs), with little or no expected contribution by outside initiation events. This interval contained infrequently corrected palindromic markers 300 bp to the left and 600 bp to the right of the DSB hotspot. Conversion of single markers occurred frequently, while conversion of both markers occurred rarely, and many of the tetrads in which both markers converted were the products of multiple events. These data indicate that most meiotic recombination intermediates are asymmetrically positioned around the initiating DSB, with a short (&lt;300 bp) tract of heteroduplex DNA (hDNA) to one side and hDNA on the other side frequently extending 600 bp or more. One consequence of this asymmetry is the preferential concentration of crossovers in the vicinity of the initiating DSB.
Seizure Suppression by Gain-of-Function escargot Mutations
Authors: Hekmat-Scafe Daria S , Dang Kim N , Tanouye Mark A 
Published: January 2005

Abstract
Suppressor mutations provide potentially powerful tools for examining mechanisms underlying neurological disorders and identifying novel targets for pharmacological intervention. Here we describe mutations that suppress seizures in a Drosophila model of human epilepsy. A screen utilizing the Drosophila easily shocked (eas) “epilepsy” mutant identified dominant suppressors of seizure sensitivity. Among several mutations identified, neuronal escargot (esg) reduced eas seizures almost 90%. The esg gene encodes a member of the snail family of transcription factors. Whereas esg is normally expressed in a limited number of neurons during a defined period of nervous system development, here normal esg was expressed in all neurons and throughout development. This greatly ameliorated both the electrophysiological and the behavioral epilepsy phenotypes of eas. Neuronal esg appears to act as a general seizure suppressor in the Drosophila epilepsy model as it reduces the susceptibility of several seizure-prone mutants. We observed that esg must be ectopically expressed during nervous system development to reduce seizure susceptibility in adults. Furthermore, induction of esg in a small subset of neurons (interneurons) will reduce seizure susceptibility. A combination of microarray and computational analyses revealed 100 genes that represent possible targets of neuronal esg. We anticipate that some of these genes may ultimately serve as targets for novel antiepileptic drugs.
A Genetic Screen for top3 Suppressors in Saccharomyces cerevisiae Identifies SHU1, SHU2, PSY3 and CSM2
Authors: Shor Erika , Weinstein Justin , Rothstein Rodney 
Published: January 2005

Abstract
Helicases of the RecQ family and topoisomerase III are evolutionarily conserved proteins important for maintenance of genome stability. In Saccharomyces cerevisiae, loss of the TOP3 gene, encoding topoisomerase III, results in a phenotype of slow growth, DNA damage sensitivity, meiotic defects, and hyperrecombination. The sole RecQ helicase in budding yeast, Sgs1, interacts with Top3 both physically and genetically, and the two proteins are thought to act in concert in vivo. Much recent genetic and biochemical evidence points to the role of RecQ helicases and topoisomerase III in regulating homologous recombination (HR) during DNA replication. Previously, we found that mutations in HR genes partially suppress top3 slow growth. Here, we describe the analysis of four additional mutational suppressors of top3 defects: shu1, shu2, psy3, and csm2. These genes belong to one epistasis group and their protein products interact with each other, strongly suggesting that they function as a complex in vivo. Their mutant phenotype indicates that they are important for error-free repair of spontaneous and induced DNA lesions, protecting the genome from mutation. These mutants exhibit an epistatic relationship with rad52 and show altered dynamics of Rad52-YFP foci, suggesting a role for these proteins in recombinational repair.
The Heme Activator Protein Hap1 Represses Transcription by a Heme-Independent Mechanism in Saccharomyces cerevisiae
Authors: Hon Thomas , Lee Hee Chul , Hu Zhanzhi , Iyer Vishwanath R , Zhang Li 
Published: January 2005

Abstract
The yeast heme activator protein Hap1 binds to DNA and activates transcription of genes encoding functions required for respiration and for controlling oxidative damage, in response to heme. Hap1 contains a DNA-binding domain with a C6 zinc cluster motif, a coiled-coil dimerization element, typical of the members of the yeast Gal4 family, and an acidic activation domain. The regulation of Hap1 transcription-activating activity is controlled by two classes of Hap1 elements, repression modules (RPM1–3) and heme-responsive motifs (HRM1–7). Previous indirect evidence indicates that Hap1 may repress transcription directly. Here we show, by promoter analysis, by chromatin immunoprecipitation, and by electrophoretic mobility shift assay, that Hap1 binds directly to DNA and represses transcription of its own gene by at least 20-fold. We found that Hap1 repression of the HAP1 gene occurs independently of heme concentrations. While DNA binding is required for transcriptional repression by Hap1, deletion of Hap1 activation domain and heme-regulatory elements has varying effects on repression. Further, we found that repression by Hap1 requires the function of Hsp70 (Ssa), but not Hsp90. These results show that Hap1 binds to its own promoter and represses transcription in a heme-independent but Hsp70-dependent manner.
A Novel Recombination Pathway Initiated by the Mre11/Rad50/Nbs1 Complex Eliminates Palindromes During Meiosis in Schizosaccharomyces pombe
Authors: Farah Joseph A , Cromie Gareth , Steiner Walter W , Smith Gerald R 
Published: January 2005

Abstract
DNA palindromes are rare in humans but are associated with meiosis-specific translocations. The conserved Mre11/Rad50/Nbs1 (MRN) complex is likely directly involved in processing palindromes through the homologous recombination pathway of DNA repair. Using the fission yeast Schizosaccharomyces pombe as a model system, we show that a 160-bp palindrome (M-pal) is a meiotic recombination hotspot and is preferentially eliminated by gene conversion. Importantly, this hotspot depends on the MRN complex for full activity and reveals a new pathway for generating meiotic DNA double-strand breaks (DSBs), separately from the Rec12 (ortholog of Spo11) pathway. We show that MRN-dependent DSBs are formed at or near the M-pal in vivo, and in contrast to the Rec12-dependent breaks, they appear early, during premeiotic replication. Analysis of mrn mutants indicates that the early DSBs are generated by the MRN nuclease activity, demonstrating the previously hypothesized MRN-dependent breakage of hairpins during replication. Our studies provide a genetic and physical basis for frequent translocations between palindromes in human meiosis and identify a conserved meiotic process that constantly selects against palindromes in eukaryotic genomes.
Insertion/Deletion and Nucleotide Polymorphism Data Reveal Constraints in Drosophila melanogaster Introns and Intergenic Regions
Authors: Ometto Lino , Stephan Wolfgang , De Lorenzo David 
Published: January 2005

Abstract
Our study of nucleotide sequence and insertion/deletion polymorphism in Drosophila melanogaster noncoding DNA provides evidence for selective pressures in both intergenic regions and introns (of the large size class). Intronic and intergenic sequences show a similar polymorphic deletion bias. Insertions have smaller sizes and higher frequencies than deletions, supporting the hypothesis that insertions are selected to compensate for the loss of DNA caused by deletion bias. Analysis of a simple model of selective constraints suggests that the blocks of functional elements located in intergenic sequences are on average larger than those in introns, while the length distribution of relatively unconstrained sequences interspaced between these blocks is similar in intronic and intergenic regions.
Characterization of Mos1-Mediated Mutagenesis in Caenorhabditis elegans
Authors: Williams Daniel C , Boulin Thomas , Ruaud Anne-Françoise , Jorgensen Erik M , Bessereau Jean-Louis 
Published: January 2005

Abstract
Insertional mutagenesis with a heterologous transposon provides a method to rapidly determine the molecular identity of mutated genes. The Drosophila transposon Mos1 can be mobilized to cause mutations in Caenorhabditis elegans (Bessereau et al. 2001); however, the mutagenic rate was initially too low for use in most forward genetic screens. To increase the effectiveness of Mos1-mediated mutagenesis we examined the conditions influencing Mos1 transposition. First, optimal transposition occurs 24 hr after expression of the transposase and is unlikely to occur in differentiated sperm or oocytes. Second, transposition is limited to germ-cell nuclei that contain donor elements, but the transposase enzyme can diffuse throughout the gonad syncytium. Third, silencing of transposition is caused by changes in the donor array that occur over time. Finally, multiple transposition events occur in individual germ cells. By using screening techniques based on these results, Mos1 mutagenicity was increased to within an order of magnitude of chemical mutagens.
The Integration of Recombination and Physical Maps in a Large-Genome Monocot Using Haploid Genome Analysis in a Trihybrid Allium Population
Authors: Khrustaleva L I , de Melo P E , van Heusden A W , Kik C 
Published: January 2005

Abstract
Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa × (A. roylei × A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.
Quantification of polycyclic aromatic hydrocarbons (PAHs) in human hair by HPLC with fluorescence detection: a biological monitoring method to evaluate the exposure to PAHs
Authors: Toriba Akira , Kuramae Yayoi , Chetiyanukornkul Thaneeya , Kizu Ryoichi , Makino Tsunehisa , Nakazawa Hiroyuki , Hayakawa Kazuichi 
Published: January 2005

AbstractA high‐performance liquid chromatographic (HPLC) method with fluorescence detection was developed for the quantification of polycyclic aromatic hydrocarbons (PAHs) in human hair. Fifteen kinds of PAHs classified as priority pollutants by the US EPA were quantified with four perdeuterated PAHs as internal standards. After 50 mg hair samples were washed with n‐hexane to remove external contamination of PAHs, the samples were digested in 2.5 M sodium hydroxide. The digests were extracted with n‐hexane and then analyzed by HPLC. Eleven kinds of PAHs were identified in hair samples of 20 subjects, and 10 kinds of PAHs were eventually quantified using the internal standards. For anthracene, chrysene and benzo[k]fluoranthene, significant differences were observed between smokers and non‐smokers. Although benzo[b]fluoranthene, dibenz[a,h]anthracene, benzo[ghi]perylene and indeno[1,2,3‐cd]pyrene were observed in the particulates of indoor and outdoor air, they were not detected in all hair samples. The analysis of PAHs in human hair should be useful as a new biomarker to evaluate the exposure to PAHs. Copyright ­© 2003 John Wiley & Sons, Ltd.
Analysis of perchlorate in difficult matrices by LC/MS
Authors: Di Rienzo Robert P. , Lin Kham , McKay Thomas T. , Wade Richard W. 
Published: January 2005

AbstractA method has been developed and validated for the determination of perchlorate in drinking water, soil, biota, groundwater, and saline water using highperformance liquid chromatography/mass spectrometry (LC/MS) without sample pretreatment. Mass spectrometry is used to monitor perchlorate at mass 83. The 83/85 isotopic ratio is used for additional identification of perchlorate, along with an internal standard containing Oxygen‐18 isotopic labeled perchlorate. The method can achieve a method detection limit in aqueous samples of 0.05 μg/L and can easily quantify perchlorate at 0.2 μg/L in any aqueous environmental sample matrix. This method uses simple determinative techniques available to LC/MS technologies and does not require any instrumentation additions or systematic pretreatment of samples. Inadequacies of current EPA Method 314.0 caused by matrix interference, high dissolved solids, and conductivity are eliminated and confirmation of perchlorate is accomplished with this new method. © 2005 Wiley Periodicals, Inc.
Investigation of nickel suppression and cytocompatibility of surface‐treated nickel‐titanium shape memory alloys by using plasma immersion ion implantation
Authors: Yeung K. W. K. , Poon R. W. Y. , Liu X. Y. , Ho J. P. Y. , Chung C. Y. , Chu P. K. , Lu W. W. , Chan D. , Cheung K. M. C. 
Published: January 2005

AbstractNickel‐titanium (NiTi) shape memory alloys are increasingly being used in orthopedic applications. However, there is a concern that Ni is harmful to the human body. We have recently investigated the use of nitrogen, or oxygen plasma immersion ion implantation to mitigate this deleterious effect. Our results reveal that the near‐surface Ni concentration in all the treated samples is significantly suppressed. In addition, our in vitro tests show that the plasma‐treated surfaces are cytologically compatible allowing the attachment and proliferation of osteoblasts. Among the two types of samples, the best biological effects are found on the samples with nitrogen implantation. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res 72A: 238–245, 2005
One‐Minute Wear‐Rate Measurement
Authors: Schaake Richard P. , den Toonder Jaap M. J. , Vellinga Willem‐Pier , Meijer Han E. H. 
Published: January 2005

AbstractSummary: Single‐asperity wear measurements were performed on small quantities of polyethylene with different molecular weights. Experiments could be performed on a surface area of 25 × 3000 μm2. A quantitative value of wear rate could be obtained that was proportional to macroscopic results relating the wear rate to the molecular weight. Material transfer limited the maximum sliding velocity to 1 μm · s−1. Possible solutions for this problem have been identified and will be a subject of further investigation.Indentation profile for high‐molecular‐weight polyethylene (PE‐H).imageIndentation profile for high‐molecular‐weight polyethylene (PE‐H).
Comparison of Hyperbranched and Linear Polyglycidol Unimolecular Reverse Micelles as Nanoreactors and Nanocapsules
Authors: Kumar Kainthan Rajesh , Brooks Donald E. 
Published: January 2005

AbstractSummary: Amphiphilic‐hyperbranched polyglycidols and a linear analogue were tested for their ability to act as nanoreactors for the unimolecular elimination (E1) reactions of tert‐alkyl iodides. Their encapsulation properties were also compared. The linear polymer was found to have very good “unimolecular reverse micellar” characteristics as well, even though the results showed the advantages of a hyperbranched nature over a linear one. Our results stress the need for a direct comparison of branched and linear polymers for any application.Amphiphilic polyglycidol unimolecular reverse micelles.imageAmphiphilic polyglycidol unimolecular reverse micelles.
Repellency and toxicity of aromatic plant extracts against the mosquito Culex pipiens molestus (Diptera: Culicidae)
Authors: Traboulsi Abdallah F , El‐Haj Samih , Tueni Marie , Taoubi Khalil , Nader Natalie Abi , Mrad Abir 
Published: January 2005

AbstractThe insecticidal activities of essential oil extracts from leaves, flowers and roots of aromatic plants against fourth‐instar larvae of the mosquito Culex pipiens molestus Forskål were determined. Extracts of Foeniculum vulgare Mill were the most toxic, followed by those of Ferula hermonis Boiss, Citrus sinensis Osbeck, Pinus pinea L, Laurus nobilis L and Eucalyptus spp with LC50 values of 24.5, 44.0, 60.0, 75.0, 117.0 and 120.0 mg litre−1, respectively. Combination tests between the LC50 and the maximum sub‐lethal concentration (MSLC) were determined. Over 20 major components were identified in extracts from each plant species tested. Five essential oils and nine pure components were studied for their repellency against mosquito bites. Terpineol and 1,8‐cineole were the most effective against Culex pipiens molestus bites offering complete protection for 1.6 and 2 h, respectively. Copyright © 2005 Society of Chemical Industry
Unconventional density wave as possible explanation of the Nernst signal in CeCoIn5
Authors: Dóra Balázs , Maki Kazumi , Virosztek Attila , Ványolos András 
Published: January 2005

AbstractRecently large Nernst effect and Seebeck effect were observed above the superconducting transition temperature 2.3 K in a heavy fermion superconductor CeCoIn5. We interpret this large Nernst effect in terms of unconventional density wave (UDW), which appears around T = 18 K. In the presence of magnetic field, Landau levels are formed in UDW, and the transport is dominated by thermally excited quasiparticles across the levels. Our theory describes successfully the available experimental data, and the deduced fitting parameters are in accordance with what is expected in the vicinity of a quantum critical point. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)