bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chylocladia wynnei sp. nov. (Champiaceae, Rhodophyta) from the Mediterranean Sea
Authors: Alongi Giuseppina , Cormaci Mario , Furnari Giovanni 
Published: May 2008

Abstract
A new species, Chylocladia wynnei sp. nov., is described from the Mediterranean Sea. It consists of 2–4 terete, unbranched erect axes, 5–10(–13) mm high, arising from a discoid holdfast. Axes, covered by a thick mucilaginous layer, are hollow throughout. They are divided into segments by monostromatic diaphragms and are constricted at the diaphragms. Axes have a unilayered cortex and longitudinal filaments lining their inner surface; gland cells are cut off from these filaments. Gametophytic plants are dioecious and consist of only two segments. Male thalli have spermatangia in superficial sori located between the two segments. One or two spherical sessile cystocarps are borne on the distal part of the basal segment. Tetrasporic plants comprise 4–5 segments; tetrahedrally divided tetrasporangia are scattered throughout the thallus. These sporangia are transformed from larger cortical cells and, when mature, they protrude into the thallus cavity. Diminutive stature and unbranched erect axes covered with a thick mucilaginous layer clearly distinguish C. wynnei from previously described species of Chylocladia.
RNA-Based 5-Fluorouracil Toxicity Requires the Pseudouridylation Activity of Cbf5p
Authors: Hoskins Jason , Butler J Scott 
Published: May 2008

Abstract
The chemotherapeutic drug 5-fluorouracil (5FU) disrupts DNA synthesis by inhibiting the enzymatic conversion of dUMP to dTMP. However, mounting evidence indicates that 5FU has important effects on RNA metabolism that contribute significantly to the toxicity of the drug. Strains with mutations in nuclear RNA-processing exosome components, including Rrp6p, exhibit strong 5FU hypersensitivity. Studies also suggest that 5FU-containing RNA can inhibit pseudouridylation, the most abundant post-transcriptional modification of noncoding RNA. We examined the effect of modulating the expression and activity of the essential yeast rRNA pseudouridylase Cbf5p on the 5FU hypersensitivity of an rrp6-Δ mutant strain. Depletion of Cbf5p suppressed the 5FU hypersensitivity of an rrp6-Δ strain, while high-copy expression enhanced sensitivity to the drug. A mutation in the catalytic site of Cbf5p also suppressed the 5FU hypersensitivity in the rrp6-Δ mutant, suggesting that RNA-based 5FU toxicity requires the pseudouridylation activity of Cbf5p. High-copy expression of box H/ACA snoRNAs also suppressed the 5FU hypersensitivity of an rrp6-Δ strain, suggesting that sequestration of Cbf5p to a particular guide RNA reduces Cbf5p-dependent 5FU toxicity. On the basis of these results and previous reports that certain pseudouridylases form stable adducts with 5FU-containing RNA, we suggest that Cbf5p binds tightly to substrates containing 5FU, causing their degradation by the TRAMP/exosome-mediated RNA surveillance pathway.
A Thermodynamic Switch for Chromosome Colocalization
Authors: Nicodemi Mario , Panning Barbara , Prisco Antonella 
Published: May 2008

Abstract
A general model for the early recognition and colocalization of homologous DNA sequences is proposed. We show, on thermodynamic grounds, how the distance between two homologous DNA sequences is spontaneously regulated by the concentration and affinity of diffusible mediators binding them, which act as a switch between two phases corresponding to independence or colocalization of pairing regions.
Impact of Amplified Fragment Length Polymorphism Size Homoplasy on the Estimation of Population Genetic Diversity and the Detection of Selective Loci
Authors: Caballero Armando , Quesada Humberto , Rolán-Alvarez Emilio 
Published: May 2008

Abstract
AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15–25%) may occur with ∼50–100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a reduction of up to 15% in the power to detect selective loci.
Management of Subdivided Populations in Conservation Programs: Development of a Novel Dynamic System
Authors: Fernández J , Toro M A , Caballero A 
Published: May 2008

Abstract
Within the context of a conservation program the management of subdivided populations implies a compromise between the control of the global genetic diversity, the avoidance of high inbreeding levels, and, sometimes, the maintenance of a certain degree of differentiation between subpopulations. We present a dynamic and flexible methodology, based on genealogical information, for the maximization of the genetic diversity (measured through the global population coancestry) in captive subdivided populations while controlling/restricting the levels of inbreeding. The method is able to implement specific restrictions on the desired relative levels of coancestry between and within subpopulations. By accounting for the particular genetic population structure, the method determines the optimal contributions (i.e., number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of individuals. Computer simulations are used to illustrate the procedure and its performance in a range of reasonable scenarios. The method performs well in most situations and is shown to be more efficient than the commonly accepted one-migrant-per-generation strategy.
Barren inflorescence1 Functions in Organogenesis During Vegetative and Inflorescence Development in Maize
Authors: Barazesh Solmaz , McSteen Paula 
Published: May 2008

Abstract
Maize (Zea mays) has a highly branched inflorescence due to the production of different types of axillary meristems. Characterization of the barren inflorescence class of mutants has led to the discovery of genes required for axillary meristem initiation in the inflorescence. Previous studies showed that barren inflorescence2 (bif2) encodes a serine/threonine protein kinase that regulates auxin transport, and barren stalk1 (ba1) encodes a basic helix-loop-helix transcription factor that acts downstream of auxin transport. Here, we characterize Barren inflorescence1 (Bif1), a classical semidominant mutation of maize. Developmental, histological, and genetic analyses show that Bif1 mutants are defective in the initiation of all axillary meristems in the inflorescence. Real time RT–PCR experiments show that both bif2 and ba1 are expressed at lower levels in Bif1 mutants. Double-mutant analyses demonstrate that Bif1 exhibits an epistatic interaction with ba1 and a synergistic interaction with bif2. The dramatic phenotypic enhancement observed in Bif1; bif2 double mutants implies that bif1 plays an overlapping role with bif2 in the initiation of lateral organs during vegetative development. The phenotypic resemblance of Bif1 to bif2 mutants and the reduction of auxin transport in Bif1 mutants suggest that bif1 functions as a regulator of auxin transport in maize.
Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig
Authors: Amaral Andreia J , Megens Hendrik-Jan , Crooijmans Richard P M A , Heuven Henri C M , Groenen Martien A M 
Published: May 2008

Abstract
Linkage disequilibrium (LD) may reveal much about domestication and breed history. An investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total, 371 single-nucleotide-polymorphisms located in three genomic regions were genotyped. The extent of LD differed significantly between European and Chinese breeds, extending up to 2 cM in Europe and up to 0.05 cM in China. In European breeds, LD extended over large haploblocks up to 400 kb, whereas in Chinese breeds the extent of LD was smaller and generally did not exceed 10 kb. The European wild boar showed an intermediate level of LD between Chinese and European breeds. In Europe, the extent of LD also differed according to genomic region. Chinese breeds showed a higher level of haplotype diversity and shared high levels of frequent haplotypes with Large White, Landrace, and Duroc. The extent of LD differs between both centers of pig domestication, being higher in Europe. Two hypotheses can explain these findings. First, the European ancestral stock had a higher level of LD. Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds.
De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae
Authors: Cai Jing , Zhao Ruoping , Jiang Huifeng , Wang Wen 
Published: May 2008

Abstract
Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a new de novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-amino-acid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of S. cerevisiae, when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence.
Estimation of 2Nes From Temporal Allele Frequency Data
Authors: Bollback Jonathan P , York Thomas L , Nielsen Rasmus 
Published: May 2008

Abstract
We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ∼0.43.
Regulators of Cellular Levels of Histone Acetylation in Saccharomyces cerevisiae
Authors: Peng Weimin , Togawa Cynthia , Zhang Kangling , Kurdistani Siavash K 
Published: May 2008

Abstract
Histone acetylation levels are regulated through the opposing activities of histone acetyltransferases (HATs) and deacetylases (HDACs). While much is known about gene-specific control of histone acetylation, little is understood about how total or cellular levels of histone acetylation are regulated. To identify regulators of cellular levels of histone acetylation, we developed an immunofluorescence-based approach to screen the single-gene deletion library of Saccharomyces cerevisiae for strains with significant reductions in cellular histone acetylation levels. Of the 4848 mutants screened, we identified 63 strains with considerable cellular hypoacetylation of N-terminal lysines in histones H3 and H4. The cellular hypoacetylation was validated for subsets of the identified strains through secondary screens including mass spectrometric analysis of individual lysines and chromatin immunoprecipitation of specific genomic loci. Among the identified mutants were several members of the Ccr4-Not complex, V-type ATPases, and vacuolar protein-sorting complexes as well as genes with unknown functions. We show that Gcn5, a major HAT in yeast, has diminished histone acetyltransferase activity in particular mutants, providing a plausible explanation for reduction of cellular acetylation levels in vivo. Our findings have revealed unexpected and novel links between histone acetylation, Gcn5 HAT activity, and diverse processes such as transcription, cellular ion homeostasis, and protein transport.
Quantitative Trait Loci for Urinary Albumin in Crosses Between C57BL/6J and A/J Inbred Mice in the Presence and Absence of Apoe
Authors: Doorenbos Carolien , Tsaih Shirng-Wern , Sheehan Susan , Ishimori Naoki , Navis Gerjan , Churchill Gary , DiPetrillo Keith , Korstanje Ron 
Published: May 2008

Abstract
We investigated the effect of apolipoprotein E (Apoe) on albuminuria in the males of two independent F2 intercrosses between C57BL/6J and A/J mice, using wild-type inbred strains in the first cross and B6-Apoe−/− animals in the second cross. In the first cross, we identified three quantitative trait loci (QTL): chromosome (Chr) 2 [LOD 3.5, peak at 70 cM, confidence interval (C.I.) 28–88 cM]; Chr 9 (LOD 2.0, peak 5 cM, C.I. 5–25 cM); and Chr 19 (LOD 1.9, peak 49 cM, C.I. 23–54 cM). The Chr 2 and Chr 19 QTL were concordant with previously found QTL for renal damage in rat and human. The Chr 9 QTL was concordant with a locus found in rat. The second cross, testing only Apoe−/− progeny, did not identify any of these loci, but detected two other loci on Chr 4 (LOD 3.2, peak 54 cM, C.I. 29–73 cM) and Chr 6 (LOD 2.6, peak 33 cM, C.I. 11–61 cM), one of which was concordant with a QTL found in rat. The dependence of QTL detection on the presence of Apoe and the concordance of these QTL with rat and human kidney disease QTL suggest that Apoe plays a role in renal damage.
Coincidence of P-Insertion Sites and Breakpoints of Deletions Induced by Activating P Elements in Drosophila
Authors: Sudi Jyotsna , Zhang Sen , Intrieri Gino , Hao Ximing , Zhang Ping 
Published: May 2008

Abstract
We isolated a set of seven deletions in the 67B region by activating a nearby P-element insertion. The structures of the deletions were characterized by cloning and sequencing. The results showed that the P-induced deletions occurred nonrandomly in the genomic sites. One breakpoint of the deletions was located precisely at the end of the starting element, i.e., at the end of the inverted terminal repeats. The other breakpoint was nearby the retained starting element and coincided with preferential P-element insertion sites that harbor transcription initiation activities. It is known that P elements induce male recombination near the starting elements, giving rise to deletions with one breakpoint precisely located at an inverted terminal repeat of the retained starting element. Database analyses further revealed that deletions generated in P-induced male recombination also contained the other breakpoint in genomic regions that coincided with preferential P-insertion sites. The results suggest that nonrandom distribution of the deletion breakpoints is characteristic of the mechanism by which P elements induce deletions near the starting elements.
Expressed Sequence Tags With cDNA Termini: Previously Overlooked Resources for Gene Annotation and Transcriptome Exploration in Chlamydomonas reinhardtii
Authors: Liang Chun , Liu Yuansheng , Liu Lin , Davis Adam C , Shen Yingjia , Li Qingshun Quinn 
Published: May 2008

Abstract
Many of Chlamydomonas reinhardtii expressed sequence tags (ESTs) in GenBank dbEST and community EST assemblies were either over- or undertrimmed in terms of their cDNA termini, which are defined as the diagnostic sequence elements that delineate 3′/5′ ends of mRNA transcripts. Overtrimming represents a loss of directional, positional, and structural information of transcript ends whereas undertrimming causes unclean spurious sequences retained in ESTs that exert deleterious impacts on downstream EST-based applications. We examined 309,278 raw EST sequencing trace files of C. reinhardtii and found that only 57% had cDNA termini that matched the expected structures specified in their cDNA library constructions while satisfying our minimum length requirement for their final clean sequences. Using GMAP, 156,963 individual ESTs were mapped to the genome successfully, with their in silico-verified cDNA termini anchored to the genome. Our data analysis suggested strong macro- and microheterogeneity of 3′/5′ end positions of individual transcripts derived from the same genes in C. reinhardtii. This work annotating differential ends of individual transcripts in the draft genome presents the research community with a new stream of data that will facilitate accurate determination of gene structures, genome annotation, and exploration of the transcriptome and mRNA metabolism in C. reinhardtii.
The Chloroplast Protein Translocation Complexes ofChlamydomonas reinhardtii: A Bioinformatic Comparison of Toc and Tic Components in Plants, Green Algae and Red Algae
Authors: Kalanon Ming , McFadden Geoffrey I 
Published: May 2008

AbstractThe recently completed genome of Chlamydomonas reinhardtii was surveyed for components of the chloroplast protein translocation complexes. Putative components were identified using reciprocal BlastP searches with the protein sequences of Arabidopsis thaliana as queries. As a comparison, we also surveyed the new genomes of the bryophyte Physcomitrella patens, two prasinophyte green algae (Ostreococcus lucimarinus and Ostreococcus tauri), the red alga Cyanidioschizon merolae, and several cyanobacteria. Overall, we found that the components of the import pathway are remarkably well conserved, particularly among the Viridiplantae lineages. Specifically, C. reinhardtii contained almost all the components found in A. thaliana, with two exceptions. Missing from C. reinhardtii are the C-terminal ferredoxin-NADPH-reductase (FNR) binding domain of Tic62 and a full-length, TPR-bearing Toc64. Further, the N-terminal domain of C. reinhardtii Toc34 is highly acidic, whereas the analogous region in C. reinhardtii Toc159 is not. This reversal of the vascular plant model may explain the similarity of C. reinhardtii chloroplast transit peptides to mitochondrial-targeting peptides. Other findings from our genome survey include the absence of Tic22 in both Ostreococcus genomes; the presence of only one Toc75 homolog in C. merolae; and, finally, a distinctive propensity for gene duplication in P. patens.
Contrasting Patterns of Transposable-Element Insertion Polymorphism and Nucleotide Diversity in Autotetraploid and Allotetraploid Arabidopsis Species
Authors: Hazzouri Khaled M , Mohajer Arezou , Dejak Steven I , Otto Sarah P , Wright Stephen I 
Published: May 2008

AbstractIt has been hypothesized that polyploidy permits the proliferation of transposable elements, due to both the masking of deleterious recessive mutations and the breakdown of host silencing mechanisms. We investigated the patterns of insertion polymorphism of an Ac-like transposable element and nucleotide diversity at 18 gene fragments in the allotetraploid Arabidopsis suecica and the autotetraploid A. arenosa. All identified insertions were fixed in A. suecica, and many were clearly inherited from the parental species A. thaliana or A. arenosa. These results are inconsistent with a rapid increase in transposition associated with hybrid breakdown but support the evidence from nucleotide polymorphism patterns of a recent single origin of this species leading to genomewide fixations of transposable elements. In contrast, most insertions were segregating at very low frequencies in A. arenosa samples, showing a significant departure from neutrality in favor of purifying selection, even when we account for population subdivision inferred from sequence variation. Patterns of nucleotide variation at reference genes are consistent with the TE results, showing evidence for higher effective population sizes in A. arenosa than in related diploid taxa but a near complete population bottleneck associated with the origins of A. suecica.
Genetic Characterization of the Drosophila jaguar322 Mutant Reveals That Complete Myosin VI Loss of Function Is Not Lethal
Authors: Morrison Julie K , Miller Kathryn G 
Published: May 2008

Abstract
Myosin VI is an actin-based motor that has been implicated in many cellular processes. Studies in vertebrates have demonstrated that animals lacking this ubiquitously expressed myosin are viable. However in Drosophila, myosin VI loss of function has been thought to be lethal. We show here that complete loss of myosin VI is not lethal in flies and that the previously reported lethality of the null mutation (jar322) is most likely due to deletion of a neighboring gene. Maternally provided myosin VI does not account for the survival of myosin VI null animals. Mutant animals are recovered at a lower than expected Mendelian frequency, suggesting that myosin VI participates in processes which contribute to normal development, but its participation is not essential.