bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Functional Module of Yeast Mediator That Governs the Dynamic Range of Heat-Shock Gene Expression
Authors: Singh Harpreet , Erkine Alexander M , Kremer Selena B , Duttweiler Harry M , Davis Donnie A , Iqbal Jabed , Gross Rachel R , Gross David S 
Published: February 2006

Abstract
We report the results of a genetic screen designed to identify transcriptional coregulators of yeast heat-shock factor (HSF). This sequence-specific activator is required to stimulate both basal and induced transcription; however, the identity of factors that collaborate with HSF in governing noninduced heat-shock gene expression is unknown. In an effort to identify these factors, we isolated spontaneous extragenic suppressors of hsp82-ΔHSE1, an allele of HSP82 that bears a 32-bp deletion of its high-affinity HSF-binding site, yet retains its two low-affinity HSF sites. Nearly 200 suppressors of the null phenotype of hsp82-ΔHSE1 were isolated and characterized, and they sorted into six expression without heat-shock element (EWE) complementation groups. Strikingly, all six groups contain alleles of genes that encode subunits of Mediator. Three of the six subunits, Med7, Med10/Nut2, and Med21/Srb7, map to Mediator's middle domain; two subunits, Med14/Rgr1 and Med16/Sin4, to its tail domain; and one subunit, Med19/Rox3, to its head domain. Mutations in genes encoding these factors enhance not only the basal transcription of hsp82-ΔHSE1, but also that of wild-type heat-shock genes. In contrast to their effect on basal transcription, the more severe ewe mutations strongly reduce activated transcription, drastically diminishing the dynamic range of heat-shock gene expression. Notably, targeted deletion of other Mediator subunits, including the negative regulators Cdk8/Srb10, Med5/Nut1, and Med15/Gal11 fail to derepress hsp82-ΔHSE1. Taken together, our data suggest that the Ewe subunits constitute a distinct functional module within Mediator that modulates both basal and induced heat-shock gene transcription.
Palmitoyl-Protein Thioesterase 1 Deficiency in Drosophila melanogaster Causes Accumulation of Abnormal Storage Material and Reduced Life Span
Authors: Hickey Anthony J , Chotkowski Heather L , Singh Navjot , Ault Jeffrey G , Korey Christopher A , MacDonald Marcy E , Glaser Robert L 
Published: February 2006

Abstract
Human neuronal ceroid lipofuscinoses (NCLs) are a group of genetic neurodegenerative diseases characterized by progressive death of neurons in the central nervous system (CNS) and accumulation of abnormal lysosomal storage material. Infantile NCL (INCL), the most severe form of NCL, is caused by mutations in the Ppt1 gene, which encodes the lysosomal enzyme palmitoyl-protein thioesterase 1 (Ppt1). We generated mutations in the Ppt1 ortholog of Drosophila melanogaster to characterize phenotypes caused by Ppt1 deficiency in flies. Ppt1-deficient flies accumulate abnormal autofluorescent storage material predominantly in the adult CNS and have a life span 30% shorter than wild type, phenotypes that generally recapitulate disease-associated phenotypes common to all forms of NCL. In contrast, some phenotypes of Ppt1-deficient flies differed from those observed in human INCL. Storage material in flies appeared as highly laminar spherical deposits in cells of the brain and as curvilinear profiles in cells of the thoracic ganglion. This contrasts with the granular deposits characteristic of human INCL. In addition, the reduced life span of Ppt1-deficient flies is not caused by progressive death of CNS neurons. No changes in brain morphology or increases in apoptotic cell death of CNS neurons were detected in Ppt1-deficient flies, even at advanced ages. Thus, Ppt1-deficient flies accumulate abnormal storage material and have a shortened life span without evidence of concomitant neurodegeneration.
Mismatch Tolerance by DNA Polymerase Pol4 in the Course of Nonhomologous End Joining in Saccharomyces cerevisiae
Authors: Pardo Benjamin , Ma Emilie , Marcand Stéphane 
Published: February 2006

Abstract
In yeast, the nonhomologous end joining pathway (NHEJ) mobilizes the DNA polymerase Pol4 to repair DNA double-strand breaks when gap filling is required prior to ligation. Using telomere–telomere fusions caused by loss of the telomeric protein Rap1 and double-strand break repair on transformed DNA as assays for NHEJ between fully uncohesive ends, we show that Pol4 is able to extend a 3′-end whose last bases are mismatched, i.e., mispaired or unpaired, to the template strand.
The C Terminus of Collagen SQT-3 Has Complex and Essential Functions in Nematode Collagen Assembly
Authors: Novelli Jacopo , Page Antony P , Hodgkin Jonathan 
Published: February 2006

Abstract
The nematode exoskeleton is a multilayered structure secreted by the underlying hypodermal cells and mainly composed of small collagens, which are encoded by a large gene family. In previous work, we reported analysis of the C. elegans dpy-31 locus, encoding a hypodermally expressed zinc-metalloprotease of the BMP-1/TOLLOID family essential for viability and cuticle deposition. We have generated a large set of extragenic suppressors of dpy-31 lethality, most of which we show here to be allelic to the cuticle collagen genes sqt-3 and dpy-17. We analyzed the interaction among dpy-31, sqt-3, and dpy-17 using a SQT-3-specific antiserum, which was employed in immunofluorescence experiments. Our results support a role for DPY-31 in SQT-3 extracellular processing and suggest that the SQT-3 C-terminal nontrimeric region serves multiple roles during SQT-3 assembly. Different missense mutations of this region have diverse phenotypic consequences, including cold-sensitive lethality. Furthermore, the biochemical and genetic data indicate that the extracellular assemblies of DPY-17 and SQT-3 are interdependent, most likely because the collagens are incorporated into the same cuticular substructure. We find that absence of DPY-17 causes extensive intracellular retention of SQT-3, indicating that formation of the SQT-3–DPY-17 polymer could begin in the intracellular environment before secretion.
Smc5p Promotes Faithful Chromosome Transmission and DNA Repair in Saccharomyces cerevisiae
Authors: Cost Gregory J , Cozzarelli Nicholas R 
Published: February 2006

Abstract
Heterodimers of structural maintenance of chromosomes (SMC) proteins form the core of several protein complexes involved in the organization of DNA, including condensation and cohesion of the chromosomes at metaphase. The functions of the complexes with a heterodimer of Smc5p and Smc6p are less clear. To better understand them, we created two S. cerevisiae strains bearing temperature-sensitive alleles of SMC5. When shifted to the restrictive temperature, both mutants lose viability gradually, concomitant with the appearance of nuclear abnormalities and phosphorylation of the Rad53p DNA damage checkpoint protein. Removal of Rad52p or overexpression of the SUMO ligase Mms21p partially suppresses the temperature sensitivity of smc5 strains and increases their survival at the restrictive temperature. At the permissive temperature, smc5-31 but not smc5-33 cells exhibit hypersensitivity to several DNA-damaging agents despite induction of the DNA damage checkpoint. Similarly, smc5-31 but not smc5-33 cells are killed by overexpression of the SUMO ligase-defective Mms21-SAp but not by overexpression of wild-type Mms21p. Both smc5 alleles are synthetically lethal with mms21-SA and exhibit Rad52p-independent chromosome fragmentation and loss at semipermissive temperatures. Our data indicate a critical role for the S. cerevisiae Smc5/6-containing complexes in both DNA repair and chromosome segregation.
De Novo Appearance and “Strain” Formation of Yeast Prion [PSI+] Are Regulated by the Heat-Shock Transcription Factor
Authors: Park Kyung-Won , Hahn Ji-Sook , Fan Qing , Thiele Dennis J , Li Liming 
Published: February 2006

Abstract
Yeast prions are non-Mendelian genetic elements that are conferred by altered and self-propagating protein conformations. Such a protein conformation-based transmission is similar to that of PrPSc, the infectious protein responsible for prion diseases. Despite recent progress in understanding the molecular nature and epigenetic transmission of prions, the underlying mechanisms governing prion conformational switch and determining prion “strains” are not understood. We report here that the evolutionarily conserved heat-shock transcription factor (HSF) strongly influences yeast prion formation and strain determination. An hsf1 mutant lacking the amino-terminal activation domain inhibits the yeast prion [PSI+] formation whereas a mutant lacking the carboxyl-terminal activation domain promotes [PSI+] formation. Moreover, specific [PSI+] strains are preferentially formed in these mutants, demonstrating the importance of genetic makeup in determining de novo appearance of prion strains. Although these hsf1 mutants preferentially support the formation of certain [PSI+] strains, they are capable of receiving and faithfully propagating nonpreferable strains, suggesting that prion initiation and propagation are distinct processes requiring different cellular components. Our findings establish the importance of HSF in prion initiation and strain determination and imply a similar regulatory role of mammalian HSFs in the complex etiology of prion disease.
Genomic Organization of gypsy Chromatin Insulators in Drosophila melanogaster
Authors: Ramos Edward , Ghosh Dolanchanpa , Baxter Ellen , Corces Victor G 
Published: February 2006

Abstract
Chromatin insulators have been implicated in the regulation of higher-order chromatin structure and may function to compartmentalize the eukaryotic genome into independent domains of gene expression. To test this possibility, we used biochemical and computational approaches to identify gypsy-like genomic-binding sites for the Suppressor of Hairy-wing [Su(Hw)] protein, a component of the gypsy insulator. EMSA and FISH analyses suggest that these are genuine Su(Hw)-binding sites. In addition, functional tests indicate that genomic Su(Hw)-binding sites can inhibit enhancer–promoter interactions and thus function as bona fide insulators. The insulator strength is dependent on the genomic location of the transgene and the number of Su(Hw)-binding sites, with clusters of two to three sites showing a stronger effect than individual sites. These clusters of Su(Hw)-binding sites are located mostly in intergenic regions or in introns of large genes, an arrangement that fits well with their proposed role in the formation of chromatin domains. Taken together, these data suggest that genomic gypsy-like insulators may provide a means for the compartmentalization of the genome within the nucleus.
A Mutation in Tac1p, a Transcription Factor Regulating CDR1 and CDR2, Is Coupled With Loss of Heterozygosity at Chromosome 5 to Mediate Antifungal Resistance in Candida albicans
Authors: Coste Alix , Turner Vincent , Ischer Françoise , Morschhäuser Joachim , Forche Anja , Selmecki Anna , Berman Judith , Bille Jacques , Sanglard Dominique 
Published: February 2006

Abstract
TAC1, a Candida albicans transcription factor situated near the mating-type locus on chromosome 5, is necessary for the upregulation of the ABC-transporter genes CDR1 and CDR2, which mediate azole resistance. We showed previously the existence of both wild-type and hyperactive TAC1 alleles. Wild-type alleles mediate upregulation of CDR1 and CDR2 upon exposure to inducers such as fluphenazine, while hyperactive alleles result in constitutive high expression of CDR1 and CDR2. Here we recovered TAC1 alleles from two pairs of matched azole-susceptible (DSY294; FH1: heterozygous at mating-type locus) and azole-resistant isolates (DSY296; FH3: homozygous at mating-type locus). Two different TAC1 wild-type alleles were recovered from DSY294 (TAC1-3 and TAC1-4) while a single hyperactive allele (TAC1-5) was isolated from DSY296. A single amino acid (aa) difference between TAC1-4 and TAC1-5 (Asn977 to Asp or N977D) was observed in a region corresponding to the predicted activation domain of Tac1p. Two TAC1 alleles were recovered from FH1 (TAC1-6 and TAC1-7) and a single hyperactive allele (TAC1-7) was recovered from FH3. The N977D change was seen in TAC1-7 in addition to several other aa differences. The importance of N977D in conferring hyperactivity to TAC1 was confirmed by site-directed mutagenesis. Both hyperactive alleles TAC1-5 and TAC1-7 were codominant with wild-type alleles and conferred hyperactive phenotypes only when homozygous. The mechanisms by which hyperactive alleles become homozygous was addressed by comparative genome hybridization and single nucleotide polymorphism arrays and indicated that loss of TAC1 heterozygosity can occur by recombination between portions of chromosome 5 or by chromosome 5 duplication.
Aberrant Nucleo-cytoplasmic Cross-Talk Results in Donor Cell mtDNA Persistence in Cloned Embryos
Authors: Lloyd Rhiannon E , Lee Joon-Hee , Alberio Ramiro , Bowles Emma J , Ramalho-Santos João , Campbell Keith H S , St. John Justin C 
Published: February 2006

Abstract
Mitochondrial DNA is an extranuclear genome normally maternally inherited through the oocyte. However, the use of nuclear transfer can result in both donor cell and recipient oocyte mitochondrial DNA persisting through to blastocyst and being transmitted to the offspring. The degree of donor mitochondrial DNA transmission appears to be random and currently no evidence exists to explain this phenomenon. To determine whether this is a dilution factor or directly related to the transcriptional status of the donor cell in respect of mitochondrial DNA transcription factors, we have generated sheep nuclear transfer embryos using donor cells: (1) possessing their full mitochondrial DNA complement, (2) those partially depleted, and (3) those depleted but containing residual levels. For each donor type, donor mitochondrial DNA persisted in some blastocysts. It is evident from the donor cells used that nuclear-encoded mitochondrial DNA transcription and replication factors persist even after mitochondrial DNA depletion, as do transcripts for some of the mitochondrial-encoded genes. These cells are therefore still programmed to drive mitochondrial DNA replication and transcription. In nuclear transfer-derived embryos, we have observed the persistence of these nuclear-encoded mitochondrial DNA transcription and replication factors but not in those embryos generated through in vitro fertilization. Consequently, nucleo-mitochondrial interaction following nuclear transfer is out of sequence as the onset of mitochondrial replication is a postimplantation event.
Endemic Iron Deficiency Associated With Helicobacter pylori Infection Among School-Aged Children in Alaska
Authors: Baggett Henry C. , Parkinson Alan J. , Muth Pam T. , Gold Benjamin D. , Gessner Bradford D. 
Published: February 2006

OBJECTIVES. Rural Alaska Natives have a high prevalence of iron deficiency and Helicobacter pylori infection. The objective of this study was to estimate the prevalence of iron deficiency, iron-deficiency anemia, and active H pylori infection among school-aged children in rural Alaska.
METHODS. We enrolled 68% (688) of the 7- to 11-year-old children from 10 predominantly Alaska Native villages in southwestern Alaska. We collected venous blood samples to assess iron deficiency and anemia. Each child was tested for active H pylori infection by 13C-urea breath test (UBT). Evaluated risk factors included age, gender, village of residence, number of household members, number of household members who were younger than 5 years, recent antibiotic use, and household water source.
RESULTS. Of 688 enrolled children, iron deficiency was present in 38%, iron-deficiency anemia was present in 7.8%, and H pylori infection by UBT was present in 86%. Iron deficiency was independently associated with living in a household with &gt;6 people and village of residence. H pylori infection by UBT was independently associated with child's age ≥10 years and village of residence. Ninety-one percent of children with iron deficiency had H pylori infection by UBT, and children with active H pylori infection were more likely to be iron deficient than uninfected children. Children with H pylori infection by UBT were also more likely to have iron-deficiency anemia than uninfected children.
CONCLUSIONS. In this study of nearly 700 children in 10 different villages in Alaska, we confirmed that the high prevalence of iron deficiency persists among school-aged children. We found that active H pylori infection was independently associated with iron deficiency and iron-deficiency anemia among children in this region. H pylori infection may account for a portion of the iron deficiency and iron-deficiency anemia in rural Alaska and other areas with high prevalences of both conditions. Innovative approaches are critically needed to address the iron deficiency in high prevalence areas such as rural Alaska and most of the developing world.
Influence of Human Serum Albumin on Photodegradation of Folic Acid in Solution
Authors: Vorobey Pavel , Steindal Arnfinn Engeset , Off Morten Kristian , Vorobey Alexander , Moan Johan 
Published: February 2006

ABSTRACTIt has been proposed that photodegradation of folates may be the reason for the pigmentation of races living under high fluence rates of ultraviolet radiation. The photodegradation of folic acid (FA) induced by ultraviolet‐A (UV‐A) radiation, in solution and in the presence of human serum albumin (HSA), was studied with absorption and fluorescence spectroscopy. FA photodegradation, with formation of p‐aminobenzoyl‐L‐glutamic acid, 6‐formylpterin and pterin‐6‐carboxylic acid, was found to follow an exponential trend. A scheme of FA photodegradation, which involves photosensitization of FA degradation by its photoproducts, was proposed. The rate of FA photodegradation decreased drastically in the presence of HSA, whereas the spectral characteristics of the photo‐products remained constant. The reduction of the FA photo‐degradation rate by HSA was accompanied by degradation of tryptophan in HSA. Tryptophan, when added to solutions of FA, had a similar effect as HSA. In solutions of FA and HSA the FA photoproducts cause photodamage mainly to HSA rather than to FA itself. The oxygen dependence of FA photo‐degradation and the inhibition of this process by sodium azide indicate that singlet oxygen may participate in the photosensitizing activity of FA photoproducts.
Variation of Morphology among Juvenile Chinook Salmon of Hatchery, Hybrid, and Wild Origin
Authors: Wessel Maria Lang , Smoker William W. , Joyce John E. 
Published: February 2006

AbstractBody morphology differed significantly between juvenile hatchery Chinook salmon Oncorhynchus tshawytscha that have experienced five generations of hatchery culture and juveniles derived from the wild founding stock and cultured in the same environment. All lines tested were raised in a similar hatchery environment. Thin‐plate spline analysis was used to characterize the morphometric variation among these lines of fish. Hatchery fish had a more compressed body, a narrower head, shorter maxillae, and a longer and narrower caudal peduncle than wild fish. Canonical discriminant analysis was able to correctly classify 88% of hatchery fish and 90% of wild fish. Second‐generation hybrids of the two lines were morphologically intermediate to but significantly different from both the hatchery and wild lines, and they appeared to be more similar to the wild line. These results suggest that the differences observed between lines are largely genetic in origin and may be a result of the divergence of the hatchery stock from the founding wild stock. In addition, family of origin had a significant effect on body morphology.
Patterns of Intra‐ and Interspecies Genetic Diversity in Klamath River Basin Suckers
Authors: Tranah Gregory J. , May Bernie 
Published: February 2006

AbstractThe Klamath River basin, Oregon, is home to four catostomid species: The Klamath smallscale suckerCatostomus rimiculus, the Klamath largescale suckerCatostomus snyderi, the shortnose suckerChasmistes brevirostris, and the Lost River suckerDeltistes luxatus. A decline in Lost River and shortnose sucker abundances resulted in these species being listed as endangered under the U.S. Endangered Species Act in 1988. The primary aims of this study were to measure interspecific and intraspecific genetic variation in Klamath River basin suckers by examining 15 microsatellite loci. Over 300 suckers were sampled from four subbasins within the Klamath River basin (Lost River, upper Klamath–Sprague rivers, lower Klamath River, and upper Williamson River) and one region outside of the basin (Rogue River). A hierarchical analysis of population subdivision based on groups generated from microsatellite genetic distance (RST) data was performed by use of analysis of molecular variance. Assignment of individuals to known populations was performed with the program WHICHLOCI. The program STRUCTURE was used to assign individuals probabilistically to homogeneous clusters without population or species identifiers. Klamath smallscale and Lost River suckers were genetically distinct from each other and from shortnose and Klamath largescale suckers. Sympatrically occurring shortnose and Klamath largescale suckers from the Lost and upper Klamath–Sprague River subbasins were genetically indistinguishable from one another, which indicates that interspecific hybridization has occurred between these two species. Managing for the long‐term survival and recovery of endangered Klamath River basin suckers should focus on preserving the genetic diversity of all four sucker species. Continued protection of endangered shortnose suckers requires the protection of Klamath largescale suckers, since each of these species may be a crucial contributor to the evolutionary legacy of the other. Maintenance of healthy and abundant sucker spawning and rearing habitat should minimize the chance of losing genetically unique populations while maintaining genetically diverse populations and facilitating the recovery of all Klamath River basin suckers.
Comparison of an indirect immunofluorescence assay, western blot analysis, and a commercially available ELISA for detection of Ehrlichia canis antibodies in canine sera
Authors: O'Connor Thomas P. , Hanscom Jancy L. , Hegarty Barbara C. , Groat Randall G. , Breitschwerdt Edward B. 
Published: February 2006

Abstract
Objective—To examine the correlation between results for an indirect immunofluorescence assay (IFA) that uses Ehrlichia canis antigen as a substrate (ie, E canis-IFA), 2 western blot (WB) analyses, and a commercially available ELISA in the detection of E canis antibody in dog sera.
Sample Population—54 canine serum samples that were reactive on E canis-IFA and 16 canine serum samples that were E canis-IFA nonreactive.
Procedure—Serum samples were evaluated by use of 2 WB analyses and a commercially available ELISA. Correlation between results of the 3 testing modalities (ie, IFA, WB analyses, and the ELISA) was examined by use of nonreactive (E canis-IFA reciprocal titer, < 20), low-titer (reciprocal titer, 80 to 160), medium-titer (reciprocal titer, 320 to 2,560), and high-titer (reciprocal titer, 5,120 to > 20,480) serum samples.
Results—For all serum samples in the nonreactive (n = 16), medium-titer (17), and high-titer (18) groups, correlation of results among IFA, WB analyses, and the commercially available ELISA was excellent. A poor correlation was found between IFA results and those of WB analyses and the ELISA for serum samples in the low-titer group (19), with only 4 of the 19 serum samples having positive results on both WB analyses and the commercially available ELISA.
Conclusions and Clinical Relevance—The discrepancy between E canis-IFA, WB analyses, and the commercially available ELISA results for the low-titer serum samples may be related to a high IFA sensitivity or, more likely, a lack of specificity associated with cross-reactivity among Ehrlichia spp.